Running as unit: rb-build-amd64_37-82773.service; invocation ID: 2303633c4a85417e9868f9b3454ed048 ==================================================================================== Mon Sep 15 02:07:28 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_37) on jenkins, called using "infom01-amd64 infom02-amd64" as arguments. Mon Sep 15 02:07:28 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-zODcC3kP" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Sep 15 02:07:28 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Mon Sep 15 02:07:28 UTC 2025 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-cuRgvW' Mon Sep 15 02:07:28 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Mon Sep 15 02:07:28 UTC 2025 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-LscalB' ok, let's check if mdanalysis is building anywhere yet… ok, mdanalysis is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of mdanalysis in unstable on amd64 on jenkins now. 1st build will be done on infom01-amd64.debian.net. 2nd build will be done on infom02-amd64.debian.net. ============================================================================= Mon Sep 15 02:07:31 UTC 2025 I: starting to build mdanalysis/unstable/amd64 on jenkins on '2025-09-15 02:07' Mon Sep 15 02:07:31 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_37/82773/console.log 1757902051 amd64 unstable mdanalysis Mon Sep 15 02:07:31 UTC 2025 I: Downloading source for unstable/mdanalysis=2.9.0-12 --2025-09-15 02:07:31-- http://deb.debian.org/debian/pool/main/m/mdanalysis/mdanalysis_2.9.0-12.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2945 (2.9K) [text/prs.lines.tag] Saving to: ‘mdanalysis_2.9.0-12.dsc’ 0K .. 100% 321M=0s 2025-09-15 02:07:31 (321 MB/s) - ‘mdanalysis_2.9.0-12.dsc’ saved [2945/2945] --2025-09-15 02:07:31-- http://deb.debian.org/debian/pool/main/m/mdanalysis/mdanalysis_2.9.0-12.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2945 (2.9K) [text/prs.lines.tag] Saving to: ‘mdanalysis_2.9.0-12.dsc’ 0K .. 100% 321M=0s 2025-09-15 02:07:31 (321 MB/s) - ‘mdanalysis_2.9.0-12.dsc’ saved [2945/2945] Mon Sep 15 02:07:31 UTC 2025 I: mdanalysis_2.9.0-12.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: mdanalysis Binary: python3-mdanalysis, python-mdanalysis-doc Architecture: any all Version: 2.9.0-12 Maintainer: Debichem Team Uploaders: Drew Parsons Homepage: https://www.mdanalysis.org/ Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/debichem-team/mdanalysis Vcs-Git: https://salsa.debian.org/debichem-team/mdanalysis.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@, python3-all, python3-hypothesis, python3-pytest, python3-sklearn Build-Depends: debhelper-compat (= 13), cython3, dh-sequence-python3, pybuild-plugin-pyproject, python3-all-dev, python3-setuptools, python3-numpy, python3-biopython (>= 1.80) [amd64 arm64 armel armhf i386 mips64el ppc64el riscv64 s390x], python3-networkx, python3-griddataformats, python3-mmtf, python3-joblib, python3-scipy, python3-matplotlib, python3-mda-xdrlib, python3-tqdm, python3-threadpoolctl, python3-packaging, python3-filelock, python3-fasteners, python3-gsd (>= 3.0.1~) [!s390x !hppa !m68k !powerpc !ppc64 !sparc64], python3-netcdf4, python3-h5py, python3-seaborn, python3-sklearn, python3-duecredit, python3-hypothesis , python3-pytest , python3-sphinx Build-Depends-Indep: python3-msmb-theme, python3-pybtex, python3-sphinx-rtd-theme, python3-sphinx-sitemap, python3-sphinxcontrib.bibtex, libjs-mathjax Package-List: python-mdanalysis-doc deb doc optional arch=all python3-mdanalysis deb python optional arch=any Checksums-Sha1: f2606c497528efce3e62fafbf7dc92d28d90d811 61025537 mdanalysis_2.9.0.orig.tar.gz 240d9e5287c77e6fc6708e2fadfd4b1d9185426a 13888 mdanalysis_2.9.0-12.debian.tar.xz Checksums-Sha256: 216c62feeaa75b810c5f6d539243d90ddea866ac06dbf73e38f8a864bfb4fb7d 61025537 mdanalysis_2.9.0.orig.tar.gz 009904701eef5802492559d4293454a4c32f7b170c91243454409f6aaeffd701 13888 mdanalysis_2.9.0-12.debian.tar.xz Files: 6bccd5d4b45aa8d56ea120c0674179fc 61025537 mdanalysis_2.9.0.orig.tar.gz 028468422ba3555926d89cbcd7e5bcfc 13888 mdanalysis_2.9.0-12.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEI8mpPlhYGekSbQo2Vz7x5L1aAfoFAmhvhc4ACgkQVz7x5L1a AfoWIw//Zl+tDccNrXKyL6OGlP/Ppb24vyaO9YvjGLEefM6XkwpC4AYoLP8ZCvmZ B3HhTuhbROgJoumx5Gr9fNA5EvKC+xSanVEHS1MRb8wwLPrz7/scKZO7QghG0/3C EA9Mj8kJOXl/+oMPHp4FXmtypP8Gaoofbzun1pCgt0icXagiPhlC/Xw1nm1ERHFT YZfs7QOmwXbQuhcuwhxGft5YXDYYdjgx5nPCU2Gr2r0dFUcG+DWi469uI4i4ghvu GRMDcINCq3jKQHCcn9K9DmtR8M2PxUyaIAFy4I84SmW8KKjOvcqPm7zp2WqVPxcs VUXkrttBFxHQ2kBS2tYHnF3Mj3/afGHq5C45uYEWHoe2KHEm2nlXhT85ij2JcMH5 CkXAZitPKudPP5D1kC66cIAJ0wCQg6eT5b6L9OFtepD+kwiEmZZxHkStC0CUZvgv rKAnZjlJHAO94Xg63pAAK0wwoDP+ieCKCWZIfJLMUCQ6ANdEjdK1egvbtk09YAwT Q38xk7I0LWZqVMnWzvbKstygi+Rfnxd24WI1hWlyL0ti+M2a1Btws6JALuCYfIya CewF9QIlV041Lx+VarL4tKVLnXdqwXFld6Jt58R1FzIRN9zdqS+BISLdjj1spnZS 6AMHN1xx/W67prhYoNGmnqwQ3Sujw71mh4I3nW5+6rdOJVn+B4U= =dtf8 -----END PGP SIGNATURE----- Mon Sep 15 02:07:31 UTC 2025 I: Checking whether the package is not for us Mon Sep 15 02:07:31 UTC 2025 I: Starting 1st build on remote node infom01-amd64.debian.net. Mon Sep 15 02:07:31 UTC 2025 I: Preparing to do remote build '1' on infom01-amd64.debian.net. Mon Sep 15 02:07:31 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Mon Sep 15 02:07:31 UTC 2025 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-FGV0Ko' ==================================================================================== Mon Sep 15 02:07:32 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom01-amd64, called using "1 mdanalysis unstable /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN 2.9.0-12" as arguments. Mon Sep 15 02:07:32 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-7oo6DDx0" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Sep 15 02:07:32 UTC 2025 I: Downloading source for unstable/mdanalysis=2.9.0-12 Reading package lists... NOTICE: 'mdanalysis' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/mdanalysis.git Please use: git clone https://salsa.debian.org/debichem-team/mdanalysis.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 61.0 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main mdanalysis 2.9.0-12 (dsc) [2945 B] Get:2 http://deb.debian.org/debian unstable/main mdanalysis 2.9.0-12 (tar) [61.0 MB] Get:3 http://deb.debian.org/debian unstable/main mdanalysis 2.9.0-12 (diff) [13.9 kB] Fetched 61.0 MB in 1s (105 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'mdanalysis' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/mdanalysis.git Please use: git clone https://salsa.debian.org/debichem-team/mdanalysis.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 61.0 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main mdanalysis 2.9.0-12 (dsc) [2945 B] Get:2 http://deb.debian.org/debian unstable/main mdanalysis 2.9.0-12 (tar) [61.0 MB] Get:3 http://deb.debian.org/debian unstable/main mdanalysis 2.9.0-12 (diff) [13.9 kB] Fetched 61.0 MB in 1s (105 MB/s) Download complete and in download only mode ============================================================================= Building mdanalysis in unstable on amd64 on infom01-amd64 now. Date: Mon Sep 15 02:07:34 UTC 2025 Date UTC: Mon Sep 15 02:07:34 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Sun Sep 14 14:07:34 -12 2025 I: pbuilder-time-stamp: 1757902054 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [mdanalysis_2.9.0-12.dsc] I: copying [./mdanalysis_2.9.0.orig.tar.gz] I: copying [./mdanalysis_2.9.0-12.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.9.0-12.dsc: no acceptable signature found dpkg-source: info: extracting mdanalysis in mdanalysis-2.9.0 dpkg-source: info: unpacking mdanalysis_2.9.0.orig.tar.gz dpkg-source: info: unpacking mdanalysis_2.9.0-12.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying docs_use_built_module.patch dpkg-source: info: applying docs_sphinx_warnings_are_not_errors.patch dpkg-source: info: applying docs_local_mathjax.patch dpkg-source: info: applying doc_no_mdanalysis_sphinx.patch dpkg-source: info: applying improve_test_timeout_PR4584.diff dpkg-source: info: applying skip_gsd_tests.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1370099/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='c576bcf55cdf444f9202a0e0a27566f4' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1370099' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/pbuilderrc_zXRO --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/b1 --logfile b1/build.log mdanalysis_2.9.0-12.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom01-amd64 6.12.43+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1370099/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), cython3, dh-sequence-python3, pybuild-plugin-pyproject, python3-all-dev, python3-setuptools, python3-numpy, python3-biopython (>= 1.80), python3-networkx, python3-griddataformats, python3-mmtf, python3-joblib, python3-scipy, python3-matplotlib, python3-mda-xdrlib, python3-tqdm, python3-threadpoolctl, python3-packaging, python3-filelock, python3-fasteners, python3-gsd (>= 3.0.1~), python3-netcdf4, python3-h5py, python3-seaborn, python3-sklearn, python3-duecredit, python3-hypothesis, python3-pytest, python3-sphinx, python3-msmb-theme, python3-pybtex, python3-sphinx-rtd-theme, python3-sphinx-sitemap, python3-sphinxcontrib.bibtex, libjs-mathjax dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on pybuild-plugin-pyproject; however: Package pybuild-plugin-pyproject is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython (>= 1.80); however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-griddataformats; however: Package python3-griddataformats is not installed. pbuilder-satisfydepends-dummy depends on python3-mmtf; however: Package python3-mmtf is not installed. pbuilder-satisfydepends-dummy depends on python3-joblib; however: Package python3-joblib is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-mda-xdrlib; however: Package python3-mda-xdrlib is not installed. pbuilder-satisfydepends-dummy depends on python3-tqdm; however: Package python3-tqdm is not installed. pbuilder-satisfydepends-dummy depends on python3-threadpoolctl; however: Package python3-threadpoolctl is not installed. pbuilder-satisfydepends-dummy depends on python3-packaging; however: Package python3-packaging is not installed. pbuilder-satisfydepends-dummy depends on python3-filelock; however: Package python3-filelock is not installed. pbuilder-satisfydepends-dummy depends on python3-fasteners; however: Package python3-fasteners is not installed. pbuilder-satisfydepends-dummy depends on python3-gsd (>= 3.0.1~); however: Package python3-gsd is not installed. pbuilder-satisfydepends-dummy depends on python3-netcdf4; however: Package python3-netcdf4 is not installed. pbuilder-satisfydepends-dummy depends on python3-h5py; however: Package python3-h5py is not installed. pbuilder-satisfydepends-dummy depends on python3-seaborn; however: Package python3-seaborn is not installed. pbuilder-satisfydepends-dummy depends on python3-sklearn; however: Package python3-sklearn is not installed. pbuilder-satisfydepends-dummy depends on python3-duecredit; however: Package python3-duecredit is not installed. pbuilder-satisfydepends-dummy depends on python3-hypothesis; however: Package python3-hypothesis is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-msmb-theme; however: Package python3-msmb-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-pybtex; however: Package python3-pybtex is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-rtd-theme; however: Package python3-sphinx-rtd-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-sitemap; however: Package python3-sphinx-sitemap is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinxcontrib.bibtex; however: Package python3-sphinxcontrib.bibtex is not installed. pbuilder-satisfydepends-dummy depends on libjs-mathjax; however: Package libjs-mathjax is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} blt{a} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-font-awesome{a} fonts-lato{a} fonts-lyx{a} fonts-mathjax{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libabsl20240722{a} libaec0{a} libaom3{a} libarchive-zip-perl{a} libavif16{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdav1d7{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgcrypt20{a} libgfortran5{a} libglib2.0-0t64{a} libgnutls30t64{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhdf5-310{a} libhdf5-hl-310{a} libidn2-0{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} liblzf1{a} libmagic-mgc{a} libmagic1t64{a} libnetcdf22{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libopenjp2-7{a} libp11-kit0{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libraqm0{a} librav1e0.7{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{a} libsvtav1enc2{a} libsz2{a} libtasn1-6{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2-16{a} libxrender1{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} libyuv0{a} libzopfli1{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} procps{a} pybuild-plugin-pyproject{a} python-babel-localedata{a} python-matplotlib-data{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-attr{a} python3-autocommand{a} python3-babel{a} python3-biopython{a} python3-brotli{a} python3-build{a} python3-cairo{a} python3-certifi{a} python3-cftime{a} python3-chardet{a} python3-charset-normalizer{a} python3-citeproc{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-duecredit{a} python3-fasteners{a} python3-filelock{a} python3-fonttools{a} python3-freetype{a} python3-fs{a} python3-griddataformats{a} python3-gsd{a} python3-h5py{a} python3-h5py-serial{a} python3-hypothesis{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-iniconfig{a} python3-installer{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-joblib{a} python3-kiwisolver{a} python3-latexcodec{a} python3-looseversion{a} python3-lxml{a} python3-lz4{a} python3-markupsafe{a} python3-matplotlib{a} python3-mda-xdrlib{a} python3-minimal{a} python3-mmtf{a} python3-monotonic{a} python3-more-itertools{a} python3-mpmath{a} python3-mrcfile{a} python3-msgpack{a} python3-msmb-theme{a} python3-netcdf4{a} python3-networkx{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pluggy{a} python3-pybtex{a} python3-pybtex-docutils{a} python3-pygments{a} python3-pyparsing{a} python3-pyproject-hooks{a} python3-pytest{a} python3-pytz{a} python3-reportlab{a} python3-requests{a} python3-rlpycairo{a} python3-roman{a} python3-roman-numerals{a} python3-scipy{a} python3-seaborn{a} python3-setuptools{a} python3-sklearn{a} python3-sklearn-lib{a} python3-snowballstemmer{a} python3-sortedcontainers{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-sphinx-sitemap{a} python3-sphinxcontrib.bibtex{a} python3-sphinxcontrib.jquery{a} python3-sympy{a} python3-threadpoolctl{a} python3-tk{a} python3-tqdm{a} python3-typeguard{a} python3-typing-extensions{a} python3-ufolib2{a} python3-urllib3{a} python3-wheel{a} python3-yaml{a} python3-zipp{a} python3-zopfli{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} python3.13-tk{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-rtd-theme-common{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-dejavu-extra isympy-common javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libgpg-error-l10n libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules linux-sysctl-defaults lynx ncbi-blast+ psmisc publicsuffix python-biopython-doc python3-bottleneck python3-bs4 python3-click python3-cssselect python3-gdal python3-html5lib python3-numba python3-numexpr python3-odf python3-olefile python3-openpyxl python3-pooch python3-psutil python3-pydot python3-pygraphviz python3-tables python3-tz shared-mime-info wget xdg-user-dirs 0 packages upgraded, 272 newly installed, 0 to remove and 0 not upgraded. Need to get 203 MB of archives. After unpacking 833 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1.2 [142 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.2.4+ds-1.2 [5224 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.5.2-1 [1493 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20250419 [162 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1041 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.50-1 [282 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+25 [217 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 51 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2.4 [318 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2.4 [401 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.17-1 [794 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [591 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 blt amd64 2.5.3+dfsg-8 [5984 B] Get: 65 http://deb.debian.org/debian unstable/main amd64 cython3 amd64 3.0.11+dfsg-2+b1 [2504 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 72 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250414 [116 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 fonts-lyx all 2.4.4-1 [190 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libabsl20240722 amd64 20240722.0-4 [492 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.4-2 [23.8 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libaom3 amd64 3.12.1-1 [1871 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.1-1 [559 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libgav1-1 amd64 0.19.0-3+b1 [353 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 librav1e0.7 amd64 0.7.1-9+b2 [946 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libsvtav1enc2 amd64 2.3.0+dfsg-1 [2489 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libyuv0 amd64 0.0.1916.20250814-1 [172 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libavif16 amd64 1.3.0-1 [135 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 109 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.15.1-1 [140 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.15.1-1 [20.9 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.16.0-1 [431 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.16.0-1 [437 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.7.1-2 [161 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libgpg-error0 amd64 1.55-2 [88.1 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libgcrypt20 amd64 1.11.2-2 [865 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.84.4-3 [1518 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-7 [76.3 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 11.4.5-1 [505 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.4-2 [8108 B] Get: 132 http://deb.debian.org/debian unstable/main amd64 libhdf5-310 amd64 1.14.5+repack-4 [1448 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-4 [72.6 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 4.4.0-3 [251 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1 [319 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-6 [27.5 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 liblzf1 amd64 3.6-4+b3 [10.1 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libnetcdf22 amd64 1:4.9.3-1+b1 [517 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [204 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.7-1 [2162 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.7-1 [5279 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.7-1 [10.5 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.13.7-1 [1068 B] Get: 150 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-7 [248 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.3-1 [14.0 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.7.0-5 [364 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.43-0.2 [155 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libzopfli1 amd64 1.0.3-3 [106 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 python3-wheel all 0.46.1-2 [21.7 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 python3-build all 1.2.2-4 [36.2 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 pybuild-plugin-pyproject all 6.20250414 [11.8 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.17.0-1 [6050 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 python-matplotlib-data all 3.10.1+dfsg1-5 [2737 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.7-1 [1048 B] Get: 170 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.7-1 [504 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.7-1 [26.1 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.13.7-1 [1068 B] Get: 173 http://deb.debian.org/debian unstable/main amd64 python3-attr all 25.3.0-1 [69.5 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.17.0-1 [117 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.3-1 [131 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 python3.13-tk amd64 3.13.7-1 [108 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 python3-tk amd64 3.13.5-1 [9604 B] Get: 179 http://deb.debian.org/debian unstable/main amd64 python3-pil.imagetk amd64 11.3.0-1 [81.1 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 11.3.0-1 [526 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 python3-cairo amd64 1.27.0-2 [114 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 python3-freetype all 2.5.1-2 [89.4 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 184 http://deb.debian.org/debian unstable/main amd64 python3-reportlab all 4.4.3-1 [1168 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 python3-biopython amd64 1.85+dfsg-5 [1674 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 python3-brotli amd64 1.1.0-2+b7 [320 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 189 http://deb.debian.org/debian unstable/main amd64 python3-cftime amd64 1.6.4-2 [216 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 6.0.1-1 [1434 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 python3-citeproc all 0.8.3-1 [99.8 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 python3-contourpy amd64 1.3.1-2 [215 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 python3-cycler all 0.12.1-2 [9616 B] Get: 195 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-4 [79.4 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.2.1-2 [33.0 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 python3-roman all 5.1-1 [11.0 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 python3-looseversion all 1.3.0-3 [8964 B] Get: 201 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.10-1 [42.0 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.5.0-1 [116 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.5+dfsg-1 [72.4 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 python3-duecredit all 0.10.2-2 [70.6 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 python3-monotonic all 1.6-3 [5340 B] Get: 206 http://deb.debian.org/debian unstable/main amd64 python3-fasteners all 0.18-2 [14.0 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 python3-filelock all 3.19.1-1 [12.6 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 python3-platformdirs all 4.4.0-1 [16.7 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 python3-fs all 2.4.16-8 [95.2 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 python3-lz4 amd64 4.4.4+dfsg-1 [25.4 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.15.3-1.1 [17.0 MB] Get: 212 http://deb.debian.org/debian unstable/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 python3-sympy all 1.14.0-2 [4228 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.0 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 python3-zopfli amd64 0.2.3.post1-1+b1 [10.5 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 unicode-data all 16.0.0-1 [9197 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 python3-fonttools amd64 4.57.0-2 [1457 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1023 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 python3-mrcfile all 1.5.4-2 [118 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 python3-griddataformats all 1.0.2-2 [2048 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 python3-gsd amd64 4.0.0-1 [209 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 python3-h5py-serial amd64 3.14.0-3 [1157 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 python3-h5py all 3.14.0-3 [18.3 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 python3-hypothesis all 6.138.14-1 [364 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 227 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 232 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 238 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b3 [14.0 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.6-1 [107 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 python3-joblib all 1.4.2-5 [216 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 python3-kiwisolver amd64 1.4.7-3+b1 [62.0 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 python3-latexcodec all 3.0.0-1 [17.5 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib amd64 3.10.1+dfsg1-5 [23.8 MB] Get: 245 http://deb.debian.org/debian unstable/main amd64 python3-mda-xdrlib all 0.2.0-3 [11.6 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 python3-msgpack amd64 1.0.3-3+b4 [84.5 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 python3-mmtf all 1.1.3-1 [17.0 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 8.2.3-6 [619 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 python3-roman-numerals all 3.1.0-2 [8740 B] Get: 251 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 3.0.1-1 [63.5 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 8.2.3-6 [477 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.jquery all 4.1-6 [7496 B] Get: 254 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-rtd-theme all 3.0.2+dfsg-3 [29.7 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 python3-msmb-theme all 1.2.0-4 [33.8 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 python3-netcdf4 amd64 1.7.2-1+b4 [622 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 258 http://deb.debian.org/debian unstable/main amd64 python3-pytz all 2025.2-3 [152 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-9 [4595 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 python3-pandas all 2.2.3+dfsg-9 [3097 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.6.0-1 [27.1 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.2-2 [137 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 python3-pybtex all 0.25.1-1 [75.2 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 python3-pybtex-docutils all 1.0.3-1 [8224 B] Get: 265 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.4.2-1 [266 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 python3-seaborn all 0.13.2-5 [215 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 python3-sklearn-lib amd64 1.4.2+dfsg-8 [3980 kB] Get: 269 http://deb.debian.org/debian unstable/main amd64 python3-sklearn all 1.4.2+dfsg-8 [2248 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-sitemap all 2.6.0-1 [8508 B] Get: 271 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.bibtex all 2.6.5-2 [33.2 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 python3-tqdm all 4.67.1-5 [90.8 kB] Fetched 203 MB in 8s (26.0 MB/s) Preconfiguring packages ... Selecting previously unselected package fonts-lato. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.7-1_amd64.deb ... Unpacking python3.13-minimal (3.13.7-1) ... Setting up libpython3.13-minimal:amd64 (3.13.7-1) ... Setting up libexpat1:amd64 (2.7.1-2) ... Setting up python3.13-minimal (3.13.7-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20277 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-5_all.deb ... Unpacking tzdata (2025b-5) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.3-3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21292 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.7-1_amd64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package python3-numpy-dev:amd64. Preparing to unpack .../001-python3-numpy-dev_1%3a2.2.4+ds-1.2_amd64.deb ... Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1.2) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../002-libblas3_3.12.1-7_amd64.deb ... Unpacking libblas3:amd64 (3.12.1-7) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../003-libgfortran5_15.2.0-4_amd64.deb ... Unpacking libgfortran5:amd64 (15.2.0-4) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../004-liblapack3_3.12.1-7_amd64.deb ... Unpacking liblapack3:amd64 (3.12.1-7) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../005-python3-numpy_1%3a2.2.4+ds-1.2_amd64.deb ... Unpacking python3-numpy (1:2.2.4+ds-1.2) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../006-libproc2-0_2%3a4.0.4-9_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-9) ... 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Setting up python3-pybtex-docutils (1.0.3-1) ... Setting up python3-sphinx (8.2.3-6) ... Setting up python3-sphinxcontrib.bibtex (2.6.5-2) ... Setting up python3-sphinx-sitemap (2.6.0-1) ... Setting up python3-sphinxcontrib.jquery (4.1-6) ... Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-3) ... Setting up python3-msmb-theme (1.2.0-4) ... Processing triggers for ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/mdanalysis-2.9.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../mdanalysis_2.9.0-12_source.changes dpkg-buildpackage: info: source package mdanalysis dpkg-buildpackage: info: source version 2.9.0-12 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Drew Parsons dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from mdanalysis-2.9.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --with sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/mdanalysis-2.9.0' rm -f .duecredit.p rm -f package/MDAnalysis/authors.py rm -f package/MDAnalysis/analysis/encore/clustering/affinityprop.c \ package/MDAnalysis/analysis/encore/cutils.c \ package/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c \ package/MDAnalysis/coordinates/timestep.cpp \ package/MDAnalysis/lib/_augment.cpp \ package/MDAnalysis/lib/_cutil.cpp \ package/MDAnalysis/lib/c_distances.c \ package/MDAnalysis/lib/c_distances_openmp.c \ package/MDAnalysis/lib/formats/cython_util.c \ package/MDAnalysis/lib/formats/libdcd.c \ package/MDAnalysis/lib/formats/libmdaxdr.c \ package/MDAnalysis/lib/nsgrid.cpp \ package/MDAnalysis/lib/qcprot.c rm -rf package/MDAnalysis.egg-info rm -f testsuite/MDAnalysisTests/data/.*_offsets.npz testsuite/MDAnalysisTests/data/*/.*_offsets.npz rm -rf testsuite/.pytest_cache make[1]: Leaving directory '/build/reproducible-path/mdanalysis-2.9.0' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild dh_auto_build -O--buildsystem=pybuild I: pybuild plugin_pyproject:129: Building wheel for python3.13 with "build" module I: pybuild base:311: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis * Building wheel... performance hint: MDAnalysis/lib/c_distances.pyx:275:5: Exception check on '_minimum_image_orthogonal' will always require the GIL to be acquired. Possible solutions: 1. Declare '_minimum_image_orthogonal' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '_minimum_image_orthogonal' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:302:5: Exception check on '_minimum_image_triclinic' will always require the GIL to be acquired. Possible solutions: 1. Declare '_minimum_image_triclinic' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '_minimum_image_triclinic' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:390:37: Exception check after calling '__pyx_fuse_0_minimum_image_orthogonal' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_0_minimum_image_orthogonal' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_0_minimum_image_orthogonal' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:390:37: Exception check after calling '__pyx_fuse_1_minimum_image_orthogonal' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_1_minimum_image_orthogonal' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_1_minimum_image_orthogonal' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:414:36: Exception check after calling '__pyx_fuse_0_minimum_image_triclinic' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_0_minimum_image_triclinic' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_0_minimum_image_triclinic' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:414:36: Exception check after calling '__pyx_fuse_1_minimum_image_triclinic' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_1_minimum_image_triclinic' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_1_minimum_image_triclinic' to allow an error code to be returned. performance hint: MDAnalysis/lib/nsgrid.pyx:417:37: Exception check after calling 'coord2cellid' will always require the GIL to be acquired. Declare 'coord2cellid' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: MDAnalysis/lib/nsgrid.pyx:431:26: Exception check after calling 'coord2cellxyz' will always require the GIL to be acquired. Possible solutions: 1. Declare 'coord2cellxyz' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'coord2cellxyz' to allow an error code to be returned. performance hint: MDAnalysis/lib/nsgrid.pyx:559:34: Exception check after calling 'coord2cellxyz' will always require the GIL to be acquired. Possible solutions: 1. Declare 'coord2cellxyz' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'coord2cellxyz' to allow an error code to be returned. performance hint: MDAnalysis/lib/nsgrid.pyx:567:56: Exception check after calling 'cellxyz2cellid' will always require the GIL to be acquired. Declare 'cellxyz2cellid' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: MDAnalysis/lib/nsgrid.pyx:574:53: Exception check after calling 'calc_distsq' will always require the GIL to be acquired. Declare 'calc_distsq' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: MDAnalysis/lib/nsgrid.pyx:578:57: Exception check after calling 'add_neighbors' will always require the GIL to be acquired. Possible solutions: 1. Declare 'add_neighbors' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'add_neighbors' to allow an error code to be returned. Attempting to autodetect OpenMP support... Compiler supports OpenMP Will attempt to use Cython. Compiling MDAnalysis/lib/formats/libdcd.pyx because it changed. Compiling MDAnalysis/lib/c_distances.pyx because it changed. Compiling MDAnalysis/lib/c_distances_openmp.pyx because it changed. Compiling MDAnalysis/lib/qcprot.pyx because it changed. Compiling MDAnalysis/lib/formats/libmdaxdr.pyx because it changed. Compiling MDAnalysis/lib/formats/cython_util.pyx because it changed. Compiling MDAnalysis/analysis/encore/cutils.pyx because it changed. Compiling MDAnalysis/analysis/encore/clustering/affinityprop.pyx because it changed. Compiling MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx because it changed. Compiling MDAnalysis/lib/_cutil.pyx because it changed. Compiling MDAnalysis/lib/_augment.pyx because it changed. Compiling MDAnalysis/lib/nsgrid.pyx because it changed. Compiling MDAnalysis/coordinates/timestep.pyx because it changed. [ 1/13] Cythonizing MDAnalysis/analysis/encore/clustering/affinityprop.pyx [ 2/13] Cythonizing MDAnalysis/analysis/encore/cutils.pyx [ 3/13] Cythonizing MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx [ 4/13] Cythonizing MDAnalysis/coordinates/timestep.pyx [ 5/13] Cythonizing MDAnalysis/lib/_augment.pyx [ 6/13] Cythonizing MDAnalysis/lib/_cutil.pyx [ 7/13] Cythonizing MDAnalysis/lib/c_distances.pyx [ 8/13] Cythonizing MDAnalysis/lib/c_distances_openmp.pyx [ 9/13] Cythonizing MDAnalysis/lib/formats/cython_util.pyx [10/13] Cythonizing MDAnalysis/lib/formats/libdcd.pyx [11/13] Cythonizing MDAnalysis/lib/formats/libmdaxdr.pyx [12/13] Cythonizing MDAnalysis/lib/nsgrid.pyx [13/13] Cythonizing MDAnalysis/lib/qcprot.pyx /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). By 2026-Feb-18, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! corresp(dist, value, root_dir) /usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! dist._finalize_license_expression() /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running bdist_wheel running build running build_py creating build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/exceptions.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/authors.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/version.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/units.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/due.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source copying doc/sphinx/source/conf.py -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/distances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/util.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/log.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/correlations.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/transformations.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_distopia.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/mdamath.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib creating build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/guessers.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/GROParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/tables.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology creating build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/RDKit.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/distances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/psa.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/bat.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/pca.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/backends.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/rdf.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/dielectric.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/msd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/align.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/atomicdistances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/rms.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/density.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/results.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/polymer.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/contacts.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/nucleicacids.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/gnm.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis creating build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser copying MDAnalysis/guesser/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser copying MDAnalysis/guesser/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser copying MDAnalysis/guesser/default_guesser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser copying MDAnalysis/guesser/tables.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser creating build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/groups.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/accessors.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/_get_readers.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/selection.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/topology.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/universe.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core creating build/lib.linux-x86_64-cpython-313/MDAnalysis/tests copying MDAnalysis/tests/datafiles.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/tests copying MDAnalysis/tests/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/tests creating build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization copying MDAnalysis/visualization/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization creating build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TNG.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/chain.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRC.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/null.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/memory.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates creating build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/vmd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/gromacs.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/charmm.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/jmol.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/pymol.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections creating build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/translate.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/wrap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/nojump.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/rotate.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/fit.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations creating build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/EDR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis copying MDAnalysis/lib/libmdanalysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include copying MDAnalysis/lib/include/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include creating build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2 creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp copying MDAnalysis/analysis/dssp/pydssp_numpy.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp copying MDAnalysis/analysis/dssp/dssp.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp copying MDAnalysis/analysis/dssp/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering running egg_info creating MDAnalysis.egg-info writing MDAnalysis.egg-info/PKG-INFO writing dependency_links to MDAnalysis.egg-info/dependency_links.txt writing requirements to MDAnalysis.egg-info/requires.txt writing top-level names to MDAnalysis.egg-info/top_level.txt writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/clustering/include/ap.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative reading manifest file 'MDAnalysis.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching 'doc/html/html' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.pyd' found anywhere in distribution warning: no previously-included files matching '*~' found anywhere in distribution warning: no previously-included files matching '.git' found anywhere in distribution adding license file 'LICENSE' adding license file 'AUTHORS' writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' copying doc/README -> build/lib.linux-x86_64-cpython-313/doc copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data copying doc/sphinx/Makefile -> build/lib.linux-x86_64-cpython-313/doc/sphinx copying doc/sphinx/source/index.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source copying doc/sphinx/source/references.bib -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/AnalysisBase_parallel.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/RSMD_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/janin_demo_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/janin_ref_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/msd_demo_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/parallelization_time.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/rama_demo_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/rama_ref_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/analysis_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/auxiliary_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/converters.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/coordinates_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/core_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/exceptions.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/guesser_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/lib_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/overview.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/references.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/selections.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/selections_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/topology.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/topology_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/trajectory_transformations.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/units.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/version.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/visualization_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/c_distances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/correlations.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/distances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/log.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/mdamath.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/nsgrid.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/picklable_file_io.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/pkdtree.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/qcprot.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/transformations.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/util.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/CRDParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/DMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/GMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/GROParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/GSDParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/ITPParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/MMTFParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/MinimalParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PDBParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PQRParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PSFParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/TOPParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/TPRParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/TXYZParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/XYZParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/core.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/guessers.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/tables.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/tpr_util.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/OpenMM.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/ParmEd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/RDKit.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/default_guesser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/tables.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/align.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/atomicdistances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/backends.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/bat.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/contacts.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/data.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/density.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/dielectric.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/diffusionmap.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/dihedrals.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/distances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/dssp.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/encore.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/gnm.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel_deprecated.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/helix_analysis.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hole2.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hydrogenbonds.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/leaflet.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/legacy_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/lineardensity.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/msd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/nucleicacids.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/nuclinfo.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/parallelization.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/pca.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/polymer.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/psa.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/rdf.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/results.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/rms.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/waterdynamics.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/wbridge_analysis.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/accessors.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/groups.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/selection.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/topology.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/topologyattrs.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/topologyobjects.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/universe.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/streamlines.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/streamlines_3D.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/test_streamplot_3D.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/testing_streamline.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/CRD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/DCD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/DLPoly.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/DMS.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/FHIAIMS.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/GMS.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/GRO.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/GSD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/H5MD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/INPCRD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/LAMMPS.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/MMTF.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/MOL2.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/NAMDBIN.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/PDB.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/PDBQT.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/PQR.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TNG.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRC.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRJ.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRR.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRZ.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TXYZ.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/XDR.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/XTC.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/XYZ.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/chain.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/chemfiles.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/core.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/memory.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/null.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/pickle_readers.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/timestep.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/charmm.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/gromacs.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/jmol.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/pymol.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/vmd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/fit.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/nojump.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/positionaveraging.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/rotate.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/translate.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/wrap.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/EDR.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/XVG.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/core.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats copying doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats copying doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy copying doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/bootstrap.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/clustering.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/confdistmatrix.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/covariance.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/dimensionality_reduction.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/similarity.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/utils.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying MDAnalysis/lib/_augment.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_augment.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_cutil.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/qcprot.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/qcprot.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/coordinates/timestep.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis copying MDAnalysis/lib/formats/cython_util.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/include/calc_distances.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/formats/src/trr_seek.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/include/endianswap.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/fastio.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/readdcd.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/trr_seek.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xtc_seek.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/analysis/encore/cutils.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include running build_ext building 'MDAnalysis.lib.formats.libdcd' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/usr/include/python3.13 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/formats/libdcd.c:1261: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib.c_distances' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include -I/usr/include/python3.13 -c MDAnalysis/lib/c_distances.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/c_distances.c:1263: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.o -L/usr/lib/x86_64-linux-gnu -lm -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib.c_distances_openmp' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPARALLEL -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include -I/usr/include/python3.13 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/c_distances_openmp.c:1272: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.o -L/usr/lib/x86_64-linux-gnu -lm -lgomp -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.cpython-313-x86_64-linux-gnu.so -fopenmp building 'MDAnalysis.lib.qcprot' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/lib/qcprot.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/qcprot.c:1255: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib._transformations' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/transformations.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/src/transformations/transformations.c:73: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/transformations.o -L/usr/lib/x86_64-linux-gnu -lm -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_transformations.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib.formats.libmdaxdr' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/formats/libmdaxdr.c:1282: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/trr_seek.o -std=c11 -O3 -funroll-loops -fsigned-zeros x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile.o -std=c11 -O3 -funroll-loops -fsigned-zeros x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/xdrfile_trr.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_trr.o -std=c11 -O3 -funroll-loops -fsigned-zeros x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/xdrfile_xtc.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_xtc.o -std=c11 -O3 -funroll-loops -fsigned-zeros x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/xtc_seek.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xtc_seek.o -std=c11 -O3 -funroll-loops -fsigned-zeros x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/trr_seek.o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile.o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_trr.o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_xtc.o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xtc_seek.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib.formats.cython_util' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/lib/formats/cython_util.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/formats/cython_util.c:1272: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.analysis.encore.cutils' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/cutils.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.o -std=c11 -funroll-loops -fsigned-zeros -O3 In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/analysis/encore/cutils.c:1255: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering creating build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/clustering/affinityprop.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.o -std=c11 -funroll-loops -fsigned-zeros -O3 In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/analysis/encore/clustering/affinityprop.c:1261: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/clustering/src/ap.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src/ap.o -std=c11 -funroll-loops -fsigned-zeros -O3 x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.o build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src/ap.o -L/usr/lib/x86_64-linux-gnu -lm -o build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -std=c11 -funroll-loops -fsigned-zeros -O3 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -std=c11 -funroll-loops -fsigned-zeros -O3 In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:1261: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -L/usr/lib/x86_64-linux-gnu -lm -o build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib._cutil' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include -I/usr/include/python3.13 -c MDAnalysis/lib/_cutil.cpp -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.o -O3 -funroll-loops -fsigned-zeros -std=c++11 In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/_cutil.cpp:1273: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.o -L/usr/lib/x86_64-linux-gnu -lm -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib._augment' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/lib/_augment.cpp -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.o -O3 -funroll-loops -fsigned-zeros -std=c++11 In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/_augment.cpp:1268: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib.nsgrid' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include -I/usr/include/python3.13 -c MDAnalysis/lib/nsgrid.cpp -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.o -O3 -funroll-loops -fsigned-zeros -std=c++11 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.coordinates.timestep' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/coordinates x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/coordinates/timestep.cpp -o build/temp.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.o -O3 -funroll-loops -fsigned-zeros -std=c++11 In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/coordinates/timestep.cpp:1269: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.cpython-313-x86_64-linux-gnu.so installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/doc copying build/lib.linux-x86_64-cpython-313/doc/README -> build/bdist.linux-x86_64/wheel/./doc creating build/bdist.linux-x86_64/wheel/doc/sphinx creating build/bdist.linux-x86_64/wheel/doc/sphinx/source copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/index.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/rama_ref_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/parallelization_time.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/msd_demo_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/rama_demo_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/AnalysisBase_parallel.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/janin_demo_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/RSMD_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/janin_ref_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/mdamath.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/pkdtree.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/lib/formats copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib/formats copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib/formats copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/correlations.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/nsgrid.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/c_distances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/qcprot.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/distances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/picklable_file_io.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/log.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/util.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/transformations.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/units.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/TXYZParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PDBParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/GROParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/core.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/XYZParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/CRDParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/DMSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/TPRParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PSFParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/MMTFParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/TOPParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/guessers.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/GMSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PQRParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/tpr_util.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/MinimalParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/GSDParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/ITPParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/tables.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/converters copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/OpenMM.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/RDKit.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/ParmEd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/guesser_modules copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/default_guesser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/tables.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/helix_analysis.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/pca.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/density.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/rms.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/results.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/wbridge_analysis.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/msd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/psa.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/analysis/legacy copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/legacy copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/polymer.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/atomicdistances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/clustering.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/dimensionality_reduction.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/utils.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/similarity.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/confdistmatrix.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/covariance.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/bootstrap.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/nucleicacids.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel_deprecated.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/waterdynamics.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/nuclinfo.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/dihedrals.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/bat.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/parallelization.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/lineardensity.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/align.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/dielectric.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/diffusionmap.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/distances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/data.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/gnm.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hole2.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/contacts.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/backends.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/dssp.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/rdf.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hydrogenbonds.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/leaflet.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/accessors.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/universe.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/groups.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/topologyattrs.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/selection.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/topology.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/topologyobjects.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/visualization copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/test_streamplot_3D.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/streamlines_3D.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/streamlines.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/testing_streamline.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/overview.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/exceptions.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/references.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/version.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/chemfiles.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRC.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/null.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/chain.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/CRD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/GMS.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/DMS.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/LAMMPS.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/memory.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/core.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TXYZ.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/NAMDBIN.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/INPCRD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/PDBQT.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/MOL2.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/H5MD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/XYZ.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/MMTF.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRJ.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/GSD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/GRO.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TNG.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/PDB.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/XDR.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRZ.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/DLPoly.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/pickle_readers.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/PQR.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/XTC.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/FHIAIMS.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/timestep.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/DCD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRR.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/selections copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/pymol.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/vmd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/charmm.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/jmol.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/gromacs.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/fit.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/nojump.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/wrap.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/translate.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/positionaveraging.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/rotate.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/trajectory_transformations.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/auxiliary copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/EDR.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/XVG.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/core.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/references.bib -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/conf.py -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source copying build/lib.linux-x86_64-cpython-313/doc/sphinx/Makefile -> build/bdist.linux-x86_64/wheel/./doc/sphinx creating build/bdist.linux-x86_64/wheel/MDAnalysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/distances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/libmdanalysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/libmdanalysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/libmdanalysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/util.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/log.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/src creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/src/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/LICENCE -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/AUTHOR -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/transformations.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/correlations.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/transformations.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xtc_seek.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/trr_seek.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xdrfile.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/fastio.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/endianswap.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/readdcd.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/trr_seek.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xtc_seek.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/picklable_file_io.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_distopia.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_transformations.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/mdamath.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include/calc_distances.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/exceptions.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/ParmEdParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology creating build/bdist.linux-x86_64/wheel/MDAnalysis/topology/tpr copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/setting.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/guessers.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/GROParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/ITPParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/FHIAIMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tables.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/authors.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/version.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/ParmEd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/ParmEdParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/RDKit.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/OpenMMParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/OpenMM.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/RDKitParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/distances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/psa.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hole2 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hole2 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/bat.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dihedrals.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/pca.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/backends.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/rdf.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dielectric.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/legacy copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/legacy copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/legacy creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/msd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/similarity.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/covariance.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src/ap.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include/ap.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering/include creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/data copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/janin_ref_data.npy -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/align.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/atomicdistances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/rms.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/density.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/results.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/polymer.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/helix_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/dssp copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp/pydssp_numpy.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/dssp copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp/dssp.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/dssp copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/dssp copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/contacts.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/nucleicacids.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/gnm.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/guesser copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/default_guesser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/tables.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser creating build/bdist.linux-x86_64/wheel/MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/groups.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/accessors.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/_get_readers.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/selection.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/topology.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/universe.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core creating build/bdist.linux-x86_64/wheel/MDAnalysis/tests copying build/lib.linux-x86_64-cpython-313/MDAnalysis/tests/datafiles.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/tests copying build/lib.linux-x86_64-cpython-313/MDAnalysis/tests/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/tests creating build/bdist.linux-x86_64/wheel/MDAnalysis/visualization copying build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization copying build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization copying build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization copying build/lib.linux-x86_64-cpython-313/MDAnalysis/units.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TXYZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/ParmEd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TNG.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/chain.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/XDR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/H5MD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRC.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/null.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/NAMDBIN.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/memory.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates creating build/bdist.linux-x86_64/wheel/MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/vmd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/gromacs.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/charmm.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/jmol.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/pymol.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/due.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/translate.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/wrap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/boxdimensions.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/nojump.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/rotate.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/fit.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations creating build/bdist.linux-x86_64/wheel/MDAnalysis/auxiliary copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/EDR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary running install_egg_info Copying MDAnalysis.egg-info to build/bdist.linux-x86_64/wheel/./MDAnalysis-2.9.0.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/mdanalysis-2.9.0.dist-info/WHEEL creating '/build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/.tmp-zjdtpibb/mdanalysis-2.9.0-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'MDAnalysis/__init__.py' adding 'MDAnalysis/authors.py' adding 'MDAnalysis/due.py' adding 'MDAnalysis/exceptions.py' adding 'MDAnalysis/units.py' adding 'MDAnalysis/version.py' adding 'MDAnalysis/analysis/__init__.py' adding 'MDAnalysis/analysis/align.py' adding 'MDAnalysis/analysis/atomicdistances.py' adding 'MDAnalysis/analysis/backends.py' adding 'MDAnalysis/analysis/base.py' adding 'MDAnalysis/analysis/bat.py' adding 'MDAnalysis/analysis/contacts.py' adding 'MDAnalysis/analysis/density.py' adding 'MDAnalysis/analysis/dielectric.py' adding 'MDAnalysis/analysis/diffusionmap.py' adding 'MDAnalysis/analysis/dihedrals.py' adding 'MDAnalysis/analysis/distances.py' adding 'MDAnalysis/analysis/gnm.py' adding 'MDAnalysis/analysis/helix_analysis.py' adding 'MDAnalysis/analysis/leaflet.py' adding 'MDAnalysis/analysis/lineardensity.py' adding 'MDAnalysis/analysis/msd.py' adding 'MDAnalysis/analysis/nucleicacids.py' adding 'MDAnalysis/analysis/nuclinfo.py' adding 'MDAnalysis/analysis/pca.py' adding 'MDAnalysis/analysis/polymer.py' adding 'MDAnalysis/analysis/psa.py' adding 'MDAnalysis/analysis/rdf.py' adding 'MDAnalysis/analysis/results.py' adding 'MDAnalysis/analysis/rms.py' adding 'MDAnalysis/analysis/waterdynamics.py' adding 'MDAnalysis/analysis/data/__init__.py' adding 'MDAnalysis/analysis/data/filenames.py' adding 'MDAnalysis/analysis/data/janin_ref_data.npy' adding 'MDAnalysis/analysis/data/rama_ref_data.npy' adding 'MDAnalysis/analysis/dssp/__init__.py' adding 'MDAnalysis/analysis/dssp/dssp.py' adding 'MDAnalysis/analysis/dssp/pydssp_numpy.py' adding 'MDAnalysis/analysis/encore/__init__.py' adding 'MDAnalysis/analysis/encore/bootstrap.py' adding 'MDAnalysis/analysis/encore/confdistmatrix.py' adding 'MDAnalysis/analysis/encore/covariance.py' adding 'MDAnalysis/analysis/encore/cutils.c' adding 'MDAnalysis/analysis/encore/cutils.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/analysis/encore/cutils.pyx' adding 'MDAnalysis/analysis/encore/similarity.py' adding 'MDAnalysis/analysis/encore/utils.py' adding 'MDAnalysis/analysis/encore/clustering/ClusterCollection.py' adding 'MDAnalysis/analysis/encore/clustering/ClusteringMethod.py' adding 'MDAnalysis/analysis/encore/clustering/__init__.py' adding 'MDAnalysis/analysis/encore/clustering/affinityprop.c' adding 'MDAnalysis/analysis/encore/clustering/affinityprop.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/analysis/encore/clustering/affinityprop.pyx' adding 'MDAnalysis/analysis/encore/clustering/cluster.py' adding 'MDAnalysis/analysis/encore/clustering/include/ap.h' adding 'MDAnalysis/analysis/encore/clustering/src/ap.c' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c' adding 'MDAnalysis/analysis/hbonds/__init__.py' adding 'MDAnalysis/analysis/hbonds/hbond_autocorrel.py' adding 'MDAnalysis/analysis/hole2/__init__.py' adding 'MDAnalysis/analysis/hydrogenbonds/__init__.py' adding 'MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py' adding 'MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py' adding 'MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py' adding 'MDAnalysis/analysis/legacy/__init__.py' adding 'MDAnalysis/analysis/legacy/x3dna.py' adding 'MDAnalysis/auxiliary/EDR.py' adding 'MDAnalysis/auxiliary/XVG.py' adding 'MDAnalysis/auxiliary/__init__.py' adding 'MDAnalysis/auxiliary/base.py' adding 'MDAnalysis/auxiliary/core.py' adding 'MDAnalysis/converters/OpenMM.py' adding 'MDAnalysis/converters/OpenMMParser.py' adding 'MDAnalysis/converters/ParmEd.py' adding 'MDAnalysis/converters/ParmEdParser.py' adding 'MDAnalysis/converters/RDKit.py' adding 'MDAnalysis/converters/RDKitParser.py' adding 'MDAnalysis/converters/__init__.py' adding 'MDAnalysis/converters/base.py' adding 'MDAnalysis/coordinates/CRD.py' adding 'MDAnalysis/coordinates/DCD.py' adding 'MDAnalysis/coordinates/DLPoly.py' adding 'MDAnalysis/coordinates/DMS.py' adding 'MDAnalysis/coordinates/FHIAIMS.py' adding 'MDAnalysis/coordinates/GMS.py' adding 'MDAnalysis/coordinates/GRO.py' adding 'MDAnalysis/coordinates/GSD.py' adding 'MDAnalysis/coordinates/H5MD.py' adding 'MDAnalysis/coordinates/INPCRD.py' adding 'MDAnalysis/coordinates/LAMMPS.py' adding 'MDAnalysis/coordinates/MMTF.py' adding 'MDAnalysis/coordinates/MOL2.py' adding 'MDAnalysis/coordinates/NAMDBIN.py' adding 'MDAnalysis/coordinates/PDB.py' adding 'MDAnalysis/coordinates/PDBQT.py' adding 'MDAnalysis/coordinates/PQR.py' adding 'MDAnalysis/coordinates/ParmEd.py' adding 'MDAnalysis/coordinates/TNG.py' adding 'MDAnalysis/coordinates/TRC.py' adding 'MDAnalysis/coordinates/TRJ.py' adding 'MDAnalysis/coordinates/TRR.py' adding 'MDAnalysis/coordinates/TRZ.py' adding 'MDAnalysis/coordinates/TXYZ.py' adding 'MDAnalysis/coordinates/XDR.py' adding 'MDAnalysis/coordinates/XTC.py' adding 'MDAnalysis/coordinates/XYZ.py' adding 'MDAnalysis/coordinates/__init__.py' adding 'MDAnalysis/coordinates/base.py' adding 'MDAnalysis/coordinates/chain.py' adding 'MDAnalysis/coordinates/chemfiles.py' adding 'MDAnalysis/coordinates/core.py' adding 'MDAnalysis/coordinates/memory.py' adding 'MDAnalysis/coordinates/null.py' adding 'MDAnalysis/coordinates/timestep.cpp' adding 'MDAnalysis/coordinates/timestep.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/coordinates/timestep.pxd' adding 'MDAnalysis/coordinates/timestep.pyx' adding 'MDAnalysis/core/__init__.py' adding 'MDAnalysis/core/_get_readers.py' adding 'MDAnalysis/core/accessors.py' adding 'MDAnalysis/core/groups.py' adding 'MDAnalysis/core/selection.py' adding 'MDAnalysis/core/topology.py' adding 'MDAnalysis/core/topologyattrs.py' adding 'MDAnalysis/core/topologyobjects.py' adding 'MDAnalysis/core/universe.py' adding 'MDAnalysis/guesser/__init__.py' adding 'MDAnalysis/guesser/base.py' adding 'MDAnalysis/guesser/default_guesser.py' adding 'MDAnalysis/guesser/tables.py' adding 'MDAnalysis/lib/NeighborSearch.py' adding 'MDAnalysis/lib/__init__.py' adding 'MDAnalysis/lib/_augment.cpp' adding 'MDAnalysis/lib/_augment.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/_augment.pyx' adding 'MDAnalysis/lib/_cutil.cpp' adding 'MDAnalysis/lib/_cutil.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/_cutil.pxd' adding 'MDAnalysis/lib/_cutil.pyx' adding 'MDAnalysis/lib/_distopia.py' adding 'MDAnalysis/lib/_transformations.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/c_distances.c' adding 'MDAnalysis/lib/c_distances.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/c_distances.pxd' adding 'MDAnalysis/lib/c_distances.pyx' adding 'MDAnalysis/lib/c_distances_openmp.c' adding 'MDAnalysis/lib/c_distances_openmp.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/c_distances_openmp.pyx' adding 'MDAnalysis/lib/correlations.py' adding 'MDAnalysis/lib/distances.py' adding 'MDAnalysis/lib/log.py' adding 'MDAnalysis/lib/mdamath.py' adding 'MDAnalysis/lib/nsgrid.cpp' adding 'MDAnalysis/lib/nsgrid.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/nsgrid.pyx' adding 'MDAnalysis/lib/picklable_file_io.py' adding 'MDAnalysis/lib/pkdtree.py' adding 'MDAnalysis/lib/qcprot.c' adding 'MDAnalysis/lib/qcprot.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/qcprot.pyx' adding 'MDAnalysis/lib/transformations.py' adding 'MDAnalysis/lib/util.py' adding 'MDAnalysis/lib/formats/__init__.py' adding 'MDAnalysis/lib/formats/cython_util.c' adding 'MDAnalysis/lib/formats/cython_util.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/formats/cython_util.pxd' adding 'MDAnalysis/lib/formats/cython_util.pyx' adding 'MDAnalysis/lib/formats/libdcd.c' adding 'MDAnalysis/lib/formats/libdcd.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/formats/libdcd.pxd' adding 'MDAnalysis/lib/formats/libdcd.pyx' adding 'MDAnalysis/lib/formats/libmdaxdr.c' adding 'MDAnalysis/lib/formats/libmdaxdr.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/formats/libmdaxdr.pxd' adding 'MDAnalysis/lib/formats/libmdaxdr.pyx' adding 'MDAnalysis/lib/formats/include/__init__.py' adding 'MDAnalysis/lib/formats/include/endianswap.h' adding 'MDAnalysis/lib/formats/include/fastio.h' adding 'MDAnalysis/lib/formats/include/readdcd.h' adding 'MDAnalysis/lib/formats/include/trr_seek.h' adding 'MDAnalysis/lib/formats/include/xdrfile.h' adding 'MDAnalysis/lib/formats/include/xdrfile_trr.h' adding 'MDAnalysis/lib/formats/include/xdrfile_xtc.h' adding 'MDAnalysis/lib/formats/include/xtc_seek.h' adding 'MDAnalysis/lib/formats/src/__init__.py' adding 'MDAnalysis/lib/formats/src/trr_seek.c' adding 'MDAnalysis/lib/formats/src/xdrfile.c' adding 'MDAnalysis/lib/formats/src/xdrfile_trr.c' adding 'MDAnalysis/lib/formats/src/xdrfile_xtc.c' adding 'MDAnalysis/lib/formats/src/xtc_seek.c' adding 'MDAnalysis/lib/include/__init__.py' adding 'MDAnalysis/lib/include/calc_distances.h' adding 'MDAnalysis/lib/libmdanalysis/__init__.pxd' adding 'MDAnalysis/lib/libmdanalysis/__init__.py' adding 'MDAnalysis/lib/src/transformations/AUTHOR' adding 'MDAnalysis/lib/src/transformations/LICENCE' adding 'MDAnalysis/lib/src/transformations/__init__.py' adding 'MDAnalysis/lib/src/transformations/transformations.c' adding 'MDAnalysis/selections/__init__.py' adding 'MDAnalysis/selections/base.py' adding 'MDAnalysis/selections/charmm.py' adding 'MDAnalysis/selections/gromacs.py' adding 'MDAnalysis/selections/jmol.py' adding 'MDAnalysis/selections/pymol.py' adding 'MDAnalysis/selections/vmd.py' adding 'MDAnalysis/tests/__init__.py' adding 'MDAnalysis/tests/datafiles.py' adding 'MDAnalysis/topology/CRDParser.py' adding 'MDAnalysis/topology/DLPolyParser.py' adding 'MDAnalysis/topology/DMSParser.py' adding 'MDAnalysis/topology/ExtendedPDBParser.py' adding 'MDAnalysis/topology/FHIAIMSParser.py' adding 'MDAnalysis/topology/GMSParser.py' adding 'MDAnalysis/topology/GROParser.py' adding 'MDAnalysis/topology/GSDParser.py' adding 'MDAnalysis/topology/HoomdXMLParser.py' adding 'MDAnalysis/topology/ITPParser.py' adding 'MDAnalysis/topology/LAMMPSParser.py' adding 'MDAnalysis/topology/MMTFParser.py' adding 'MDAnalysis/topology/MOL2Parser.py' adding 'MDAnalysis/topology/MinimalParser.py' adding 'MDAnalysis/topology/PDBParser.py' adding 'MDAnalysis/topology/PDBQTParser.py' adding 'MDAnalysis/topology/PQRParser.py' adding 'MDAnalysis/topology/PSFParser.py' adding 'MDAnalysis/topology/ParmEdParser.py' adding 'MDAnalysis/topology/TOPParser.py' adding 'MDAnalysis/topology/TPRParser.py' adding 'MDAnalysis/topology/TXYZParser.py' adding 'MDAnalysis/topology/XYZParser.py' adding 'MDAnalysis/topology/__init__.py' adding 'MDAnalysis/topology/base.py' adding 'MDAnalysis/topology/core.py' adding 'MDAnalysis/topology/guessers.py' adding 'MDAnalysis/topology/tables.py' adding 'MDAnalysis/topology/tpr/__init__.py' adding 'MDAnalysis/topology/tpr/obj.py' adding 'MDAnalysis/topology/tpr/setting.py' adding 'MDAnalysis/topology/tpr/utils.py' adding 'MDAnalysis/transformations/__init__.py' adding 'MDAnalysis/transformations/base.py' adding 'MDAnalysis/transformations/boxdimensions.py' adding 'MDAnalysis/transformations/fit.py' adding 'MDAnalysis/transformations/nojump.py' adding 'MDAnalysis/transformations/positionaveraging.py' adding 'MDAnalysis/transformations/rotate.py' adding 'MDAnalysis/transformations/translate.py' adding 'MDAnalysis/transformations/wrap.py' adding 'MDAnalysis/visualization/__init__.py' adding 'MDAnalysis/visualization/streamlines.py' adding 'MDAnalysis/visualization/streamlines_3D.py' adding 'doc/README' adding 'doc/sphinx/Makefile' adding 'doc/sphinx/source/conf.py' adding 'doc/sphinx/source/index.rst' adding 'doc/sphinx/source/references.bib' adding 'doc/sphinx/source/documentation_pages/analysis_modules.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary_modules.rst' adding 'doc/sphinx/source/documentation_pages/converters.rst' adding 'doc/sphinx/source/documentation_pages/coordinates_modules.rst' adding 'doc/sphinx/source/documentation_pages/core_modules.rst' adding 'doc/sphinx/source/documentation_pages/exceptions.rst' adding 'doc/sphinx/source/documentation_pages/guesser_modules.rst' adding 'doc/sphinx/source/documentation_pages/lib_modules.rst' adding 'doc/sphinx/source/documentation_pages/overview.rst' adding 'doc/sphinx/source/documentation_pages/references.rst' adding 'doc/sphinx/source/documentation_pages/selections.rst' adding 'doc/sphinx/source/documentation_pages/selections_modules.rst' adding 'doc/sphinx/source/documentation_pages/topology.rst' adding 'doc/sphinx/source/documentation_pages/topology_modules.rst' adding 'doc/sphinx/source/documentation_pages/trajectory_transformations.rst' adding 'doc/sphinx/source/documentation_pages/units.rst' adding 'doc/sphinx/source/documentation_pages/version.rst' adding 'doc/sphinx/source/documentation_pages/visualization_modules.rst' adding 'doc/sphinx/source/documentation_pages/analysis/align.rst' adding 'doc/sphinx/source/documentation_pages/analysis/atomicdistances.rst' adding 'doc/sphinx/source/documentation_pages/analysis/backends.rst' adding 'doc/sphinx/source/documentation_pages/analysis/base.rst' adding 'doc/sphinx/source/documentation_pages/analysis/bat.rst' adding 'doc/sphinx/source/documentation_pages/analysis/contacts.rst' adding 'doc/sphinx/source/documentation_pages/analysis/data.rst' adding 'doc/sphinx/source/documentation_pages/analysis/density.rst' adding 'doc/sphinx/source/documentation_pages/analysis/dielectric.rst' adding 'doc/sphinx/source/documentation_pages/analysis/diffusionmap.rst' adding 'doc/sphinx/source/documentation_pages/analysis/dihedrals.rst' adding 'doc/sphinx/source/documentation_pages/analysis/distances.rst' adding 'doc/sphinx/source/documentation_pages/analysis/dssp.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore.rst' adding 'doc/sphinx/source/documentation_pages/analysis/gnm.rst' adding 'doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel.rst' adding 'doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel_deprecated.rst' adding 'doc/sphinx/source/documentation_pages/analysis/helix_analysis.rst' adding 'doc/sphinx/source/documentation_pages/analysis/hole2.rst' adding 'doc/sphinx/source/documentation_pages/analysis/hydrogenbonds.rst' adding 'doc/sphinx/source/documentation_pages/analysis/leaflet.rst' adding 'doc/sphinx/source/documentation_pages/analysis/legacy_modules.rst' adding 'doc/sphinx/source/documentation_pages/analysis/lineardensity.rst' adding 'doc/sphinx/source/documentation_pages/analysis/msd.rst' adding 'doc/sphinx/source/documentation_pages/analysis/nucleicacids.rst' adding 'doc/sphinx/source/documentation_pages/analysis/nuclinfo.rst' adding 'doc/sphinx/source/documentation_pages/analysis/parallelization.rst' adding 'doc/sphinx/source/documentation_pages/analysis/pca.rst' adding 'doc/sphinx/source/documentation_pages/analysis/polymer.rst' adding 'doc/sphinx/source/documentation_pages/analysis/psa.rst' adding 'doc/sphinx/source/documentation_pages/analysis/rdf.rst' adding 'doc/sphinx/source/documentation_pages/analysis/results.rst' adding 'doc/sphinx/source/documentation_pages/analysis/rms.rst' adding 'doc/sphinx/source/documentation_pages/analysis/waterdynamics.rst' adding 'doc/sphinx/source/documentation_pages/analysis/wbridge_analysis.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/bootstrap.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/clustering.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/confdistmatrix.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/covariance.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/dimensionality_reduction.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/similarity.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/utils.rst' adding 'doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary/EDR.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary/XVG.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary/base.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary/core.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary/init.rst' adding 'doc/sphinx/source/documentation_pages/converters/OpenMM.rst' adding 'doc/sphinx/source/documentation_pages/converters/ParmEd.rst' adding 'doc/sphinx/source/documentation_pages/converters/RDKit.rst' adding 'doc/sphinx/source/documentation_pages/converters/base.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/CRD.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/DCD.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/DLPoly.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/DMS.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/FHIAIMS.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/GMS.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/GRO.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/GSD.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/H5MD.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/INPCRD.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/LAMMPS.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/MMTF.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/MOL2.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/NAMDBIN.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/PDB.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/PDBQT.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/PQR.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TNG.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TRC.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TRJ.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TRR.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TRZ.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TXYZ.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/XDR.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/XTC.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/XYZ.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/base.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/chain.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/chemfiles.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/core.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/init.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/memory.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/null.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/pickle_readers.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/timestep.rst' adding 'doc/sphinx/source/documentation_pages/core/accessors.rst' adding 'doc/sphinx/source/documentation_pages/core/groups.rst' adding 'doc/sphinx/source/documentation_pages/core/init.rst' adding 'doc/sphinx/source/documentation_pages/core/selection.rst' adding 'doc/sphinx/source/documentation_pages/core/topology.rst' adding 'doc/sphinx/source/documentation_pages/core/topologyattrs.rst' adding 'doc/sphinx/source/documentation_pages/core/topologyobjects.rst' adding 'doc/sphinx/source/documentation_pages/core/universe.rst' adding 'doc/sphinx/source/documentation_pages/guesser_modules/base.rst' adding 'doc/sphinx/source/documentation_pages/guesser_modules/default_guesser.rst' adding 'doc/sphinx/source/documentation_pages/guesser_modules/init.rst' adding 'doc/sphinx/source/documentation_pages/guesser_modules/tables.rst' adding 'doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst' adding 'doc/sphinx/source/documentation_pages/lib/c_distances.rst' adding 'doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst' adding 'doc/sphinx/source/documentation_pages/lib/correlations.rst' adding 'doc/sphinx/source/documentation_pages/lib/distances.rst' adding 'doc/sphinx/source/documentation_pages/lib/log.rst' adding 'doc/sphinx/source/documentation_pages/lib/mdamath.rst' adding 'doc/sphinx/source/documentation_pages/lib/nsgrid.rst' adding 'doc/sphinx/source/documentation_pages/lib/picklable_file_io.rst' adding 'doc/sphinx/source/documentation_pages/lib/pkdtree.rst' adding 'doc/sphinx/source/documentation_pages/lib/qcprot.rst' adding 'doc/sphinx/source/documentation_pages/lib/transformations.rst' adding 'doc/sphinx/source/documentation_pages/lib/util.rst' adding 'doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst' adding 'doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst' adding 'doc/sphinx/source/documentation_pages/selections/base.rst' adding 'doc/sphinx/source/documentation_pages/selections/charmm.rst' adding 'doc/sphinx/source/documentation_pages/selections/gromacs.rst' adding 'doc/sphinx/source/documentation_pages/selections/jmol.rst' adding 'doc/sphinx/source/documentation_pages/selections/pymol.rst' adding 'doc/sphinx/source/documentation_pages/selections/vmd.rst' adding 'doc/sphinx/source/documentation_pages/topology/CRDParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/DMSParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/GMSParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/GROParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/GSDParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/ITPParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/MMTFParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst' adding 'doc/sphinx/source/documentation_pages/topology/MinimalParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/PDBParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/PQRParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/PSFParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/TOPParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/TPRParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/TXYZParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/XYZParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/base.rst' adding 'doc/sphinx/source/documentation_pages/topology/core.rst' adding 'doc/sphinx/source/documentation_pages/topology/guessers.rst' adding 'doc/sphinx/source/documentation_pages/topology/init.rst' adding 'doc/sphinx/source/documentation_pages/topology/tables.rst' adding 'doc/sphinx/source/documentation_pages/topology/tpr_util.rst' adding 'doc/sphinx/source/documentation_pages/transformations/base.rst' adding 'doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst' adding 'doc/sphinx/source/documentation_pages/transformations/fit.rst' adding 'doc/sphinx/source/documentation_pages/transformations/nojump.rst' adding 'doc/sphinx/source/documentation_pages/transformations/positionaveraging.rst' adding 'doc/sphinx/source/documentation_pages/transformations/rotate.rst' adding 'doc/sphinx/source/documentation_pages/transformations/translate.rst' adding 'doc/sphinx/source/documentation_pages/transformations/wrap.rst' adding 'doc/sphinx/source/documentation_pages/visualization/streamlines.rst' adding 'doc/sphinx/source/documentation_pages/visualization/streamlines_3D.rst' adding 'doc/sphinx/source/documentation_pages/visualization/test_streamplot_3D.png' adding 'doc/sphinx/source/documentation_pages/visualization/testing_streamline.png' adding 'doc/sphinx/source/images/AnalysisBase_parallel.png' adding 'doc/sphinx/source/images/RSMD_plot.png' adding 'doc/sphinx/source/images/janin_demo_plot.png' adding 'doc/sphinx/source/images/janin_ref_plot.png' adding 'doc/sphinx/source/images/msd_demo_plot.png' adding 'doc/sphinx/source/images/parallelization_time.png' adding 'doc/sphinx/source/images/rama_demo_plot.png' adding 'doc/sphinx/source/images/rama_ref_plot.png' adding 'mdanalysis-2.9.0.dist-info/licenses/AUTHORS' adding 'mdanalysis-2.9.0.dist-info/licenses/LICENSE' adding 'mdanalysis-2.9.0.dist-info/METADATA' adding 'mdanalysis-2.9.0.dist-info/WHEEL' adding 'mdanalysis-2.9.0.dist-info/top_level.txt' adding 'mdanalysis-2.9.0.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Successfully built mdanalysis-2.9.0-cp313-cp313-linux_x86_64.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.13 with "installer" module debian/rules execute_after_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/mdanalysis-2.9.0' PYTHONPATH=/build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build make html -C package/doc/sphinx/ BUILDDIR=/build/reproducible-path/mdanalysis-2.9.0/.pybuild # HTML generator make[2]: Entering directory '/build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx' sphinx-build -v -b html source /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html Running Sphinx v8.2.3 loading translations [en]... locale_dir /build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist locale_dir /build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist done Original exception: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/sphinx/registry.py", line 541, in load_extension mod = import_module(extname) File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module return _bootstrap._gcd_import(name[level:], package, level) ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "", line 1387, in _gcd_import File "", line 1360, in _find_and_load File "", line 1324, in _find_and_load_unlocked ModuleNotFoundError: No module named 'sphinxcontrib.applehelp' Original exception: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/sphinx/registry.py", line 541, in load_extension mod = import_module(extname) File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module return _bootstrap._gcd_import(name[level:], package, level) ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "", line 1387, in _gcd_import File "", line 1360, in _find_and_load File "", line 1324, in _find_and_load_unlocked ModuleNotFoundError: No module named 'sphinxcontrib.devhelp' Original exception: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/sphinx/registry.py", line 541, in load_extension mod = import_module(extname) File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module return _bootstrap._gcd_import(name[level:], package, level) ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "", line 1387, in _gcd_import File "", line 1360, in _find_and_load File "", line 1324, in _find_and_load_unlocked ModuleNotFoundError: No module named 'sphinxcontrib.htmlhelp' Original exception: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/sphinx/registry.py", line 541, in load_extension mod = import_module(extname) File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module return _bootstrap._gcd_import(name[level:], package, level) ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "", line 1387, in _gcd_import File "", line 1360, in _find_and_load File "", line 1324, in _find_and_load_unlocked ModuleNotFoundError: No module named 'sphinxcontrib.serializinghtml' Original exception: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/sphinx/registry.py", line 541, in load_extension mod = import_module(extname) File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module return _bootstrap._gcd_import(name[level:], package, level) ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "", line 1387, in _gcd_import File "", line 1360, in _find_and_load File "", line 1324, in _find_and_load_unlocked ModuleNotFoundError: No module named 'sphinxcontrib.qthelp' making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. checking bibtex cache... out of date parsing bibtex file /build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx/source/references.bib... parsed 69 entries locale_dir /build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist loading intersphinx inventory 'h5py' from https://docs.h5py.org/en/stable/objects.inv ... loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv ... loading intersphinx inventory 'scipy' from https://docs.scipy.org/doc/scipy/objects.inv ... loading intersphinx inventory 'gsd' from https://gsd.readthedocs.io/en/stable/objects.inv ... loading intersphinx inventory 'maplotlib' from https://matplotlib.org/stable/objects.inv ... loading intersphinx inventory 'griddataformats' from https://mdanalysis.org/GridDataFormats/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.h5py.org/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.h5py.org', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'networkx' from https://networkx.org/documentation/stable/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://gsd.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='gsd.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.scipy.org/doc/scipy/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.scipy.org', port=443): Max retries exceeded with url: /doc/scipy/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'pmda' from https://mdanalysis.org/pmda/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://mdanalysis.org/pmda/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /pmda/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'waterdynamics' from https://www.mdanalysis.org/waterdynamics/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://mdanalysis.org/GridDataFormats/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /GridDataFormats/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'parmed' from https://parmed.github.io/ParmEd/html/objects.inv ... loading intersphinx inventory 'rdkit' from https://rdkit.org/docs/objects.inv ... loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv ... loading intersphinx inventory 'pathsimanalysis' from https://www.mdanalysis.org/PathSimAnalysis/objects.inv ... loading intersphinx inventory 'dask' from https://docs.dask.org/en/stable/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://www.mdanalysis.org/waterdynamics/objects.inv' not fetchable due to : HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /waterdynamics/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.dask.org/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.dask.org', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'mdahole2' from https://www.mdanalysis.org/mdahole2/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://matplotlib.org/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='matplotlib.org', port=443): Max retries exceeded with url: /stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://www.mdanalysis.org/PathSimAnalysis/objects.inv' not fetchable due to : HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /PathSimAnalysis/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://networkx.org/documentation/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='networkx.org', port=443): Max retries exceeded with url: /documentation/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://rdkit.org/docs/objects.inv' not fetchable due to : HTTPSConnectionPool(host='rdkit.org', port=443): Max retries exceeded with url: /docs/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://numpy.org/doc/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='numpy.org', port=443): Max retries exceeded with url: /doc/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://parmed.github.io/ParmEd/html/objects.inv' not fetchable due to : HTTPSConnectionPool(host='parmed.github.io', port=443): Max retries exceeded with url: /ParmEd/html/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://www.mdanalysis.org/mdahole2/objects.inv' not fetchable due to : HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /mdahole2/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) locale_dir /build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 177 source files that are out of date updating environment: locale_dir /build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist [new config] 177 added, 0 changed, 0 removed reading sources... [ 1%] documentation_pages/analysis/align /usr/lib/python3/dist-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated. Due to the on going maintenance burden of keeping command line application wrappers up to date, we have decided to deprecate and eventually remove these modules. We instead now recommend building your command line and invoking it directly with the subprocess module. warnings.warn( reading sources... [ 1%] documentation_pages/analysis/atomicdistances reading sources... [ 2%] documentation_pages/analysis/backends reading sources... [ 2%] documentation_pages/analysis/base reading sources... [ 3%] documentation_pages/analysis/bat reading sources... [ 3%] documentation_pages/analysis/contacts reading sources... [ 4%] documentation_pages/analysis/data reading sources... [ 5%] documentation_pages/analysis/density reading sources... [ 5%] documentation_pages/analysis/dielectric reading sources... [ 6%] documentation_pages/analysis/diffusionmap reading sources... [ 6%] documentation_pages/analysis/dihedrals mkdir -p failed for path /nonexistent/first-build/.config/matplotlib: [Errno 13] Permission denied: '/nonexistent' Matplotlib created a temporary cache directory at /tmp/matplotlib-a626_uu3 because there was an issue with the default path (/nonexistent/first-build/.config/matplotlib); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. reading sources... [ 7%] documentation_pages/analysis/distances reading sources... [ 7%] documentation_pages/analysis/dssp reading sources... [ 8%] documentation_pages/analysis/encore reading sources... 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[ 13%] documentation_pages/analysis/hbond_autocorrel reading sources... [ 14%] documentation_pages/analysis/hbond_autocorrel_deprecated /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:54: DeprecationWarning: This module was moved to MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel; hbonds.hbond_autocorrel will be removed in 3.0.0. warnings.warn(wmsg, category=DeprecationWarning) reading sources... [ 14%] documentation_pages/analysis/helix_analysis reading sources... [ 15%] documentation_pages/analysis/hole2 /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/analysis/hole2/__init__.py:50: UserWarning: Please install the mdahole2 mdakit to use it in MDAnalysis. More details can be found here: https://www.mdanalysis.org/mdahole2/getting_started.html warnings.warn(wmsg, category=UserWarning) reading sources... 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[100%] index /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/analysis/dssp/dssp.py:docstring of MDAnalysis.analysis.dssp.dssp:25: WARNING: Explicit markup ends without a blank line; unexpected unindent. [docutils] WARNING: autodoc: failed to import module 'utils' from module 'MDAnalysis.analysis.hole2'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'MDAnalysis.analysis.hole2.utils'\n"] [autodoc.import_object] WARNING: autodoc: failed to import module 'templates' from module 'MDAnalysis.analysis.hole2'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'MDAnalysis.analysis.hole2.templates'\n"] [autodoc.import_object] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/core/universe.py:docstring of MDAnalysis.core.universe.Universe:127: WARNING: Definition list ends without a blank line; unexpected unindent. [docutils] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/core/universe.py:docstring of MDAnalysis.core.universe.Universe:127: WARNING: Inline strong start-string without end-string. [docutils] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/guesser/default_guesser.py:docstring of MDAnalysis.guesser.default_guesser.DefaultGuesser:5: ERROR: Unexpected indentation. [docutils] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/topology/ExtendedPDBParser.py:docstring of MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser:29: CRITICAL: Unexpected section title. See Also -------- [docutils] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/topology/TPRParser.py:docstring of MDAnalysis.topology.TPRParser:46: WARNING: Footnote [*] is not referenced. [ref.footnote] docstring of MDAnalysis.topology.tables.atomelements:3: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.atomelements:4: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] docstring of MDAnalysis.topology.tables.atomelements:7: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.atomelements:8: WARNING: Inline strong start-string without end-string. [docutils] docstring of MDAnalysis.topology.tables.masses:3: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.masses:4: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] docstring of MDAnalysis.topology.tables.masses:7: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.masses:8: WARNING: Inline strong start-string without end-string. [docutils] docstring of MDAnalysis.topology.tables.vdwradii:3: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.vdwradii:4: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] docstring of MDAnalysis.topology.tables.vdwradii:7: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.vdwradii:8: WARNING: Inline strong start-string without end-string. [docutils] looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... WARNING: unsupported theme option 'mda_official' given done copying assets... copying static files... Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/basic.css Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/alabaster.css copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [ 1%] documentation_pages/analysis/align writing output... [ 1%] documentation_pages/analysis/atomicdistances writing output... [ 2%] documentation_pages/analysis/backends writing output... [ 2%] documentation_pages/analysis/base writing output... [ 3%] documentation_pages/analysis/bat writing output... [ 3%] documentation_pages/analysis/contacts writing output... 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[100%] index /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.openany:3: WARNING: unknown keyword: 'with' [ref.keyword] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.anyopen:25: WARNING: unknown keyword: 'with' [ref.keyword] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.NamedStream:32: WARNING: unknown keyword: 'with' [ref.keyword] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.NamedStream:67: WARNING: unknown keyword: 'with' [ref.keyword] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.NamedStream:74: WARNING: unknown keyword: 'with' [ref.keyword] generating indices... genindex py-modindex done highlighting module code... 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[ 75%] MDAnalysis.selections.jmol highlighting module code... [ 76%] MDAnalysis.selections.pymol highlighting module code... [ 76%] MDAnalysis.selections.vmd highlighting module code... [ 77%] MDAnalysis.topology.CRDParser highlighting module code... [ 78%] MDAnalysis.topology.DLPolyParser highlighting module code... [ 78%] MDAnalysis.topology.DMSParser highlighting module code... [ 79%] MDAnalysis.topology.ExtendedPDBParser highlighting module code... [ 80%] MDAnalysis.topology.FHIAIMSParser highlighting module code... [ 80%] MDAnalysis.topology.GMSParser highlighting module code... [ 81%] MDAnalysis.topology.GROParser highlighting module code... [ 82%] MDAnalysis.topology.GSDParser highlighting module code... [ 82%] MDAnalysis.topology.HoomdXMLParser highlighting module code... [ 83%] MDAnalysis.topology.ITPParser highlighting module code... [ 83%] MDAnalysis.topology.LAMMPSParser highlighting module code... [ 84%] MDAnalysis.topology.MMTFParser highlighting module code... [ 85%] MDAnalysis.topology.MOL2Parser highlighting module code... [ 85%] MDAnalysis.topology.MinimalParser highlighting module code... [ 86%] MDAnalysis.topology.PDBParser highlighting module code... [ 87%] MDAnalysis.topology.PDBQTParser highlighting module code... [ 87%] MDAnalysis.topology.PQRParser highlighting module code... [ 88%] MDAnalysis.topology.PSFParser highlighting module code... [ 89%] MDAnalysis.topology.TOPParser highlighting module code... [ 89%] MDAnalysis.topology.TPRParser highlighting module code... [ 90%] MDAnalysis.topology.TXYZParser highlighting module code... [ 90%] MDAnalysis.topology.XYZParser highlighting module code... [ 91%] MDAnalysis.topology.base highlighting module code... [ 92%] MDAnalysis.topology.tpr.obj highlighting module code... [ 92%] MDAnalysis.topology.tpr.utils highlighting module code... [ 93%] MDAnalysis.transformations.base highlighting module code... [ 94%] MDAnalysis.transformations.boxdimensions highlighting module code... [ 94%] MDAnalysis.transformations.fit highlighting module code... [ 95%] MDAnalysis.transformations.nojump highlighting module code... [ 96%] MDAnalysis.transformations.positionaveraging highlighting module code... [ 96%] MDAnalysis.transformations.rotate highlighting module code... [ 97%] MDAnalysis.transformations.translate highlighting module code... [ 97%] MDAnalysis.transformations.wrap highlighting module code... [ 98%] MDAnalysis.units highlighting module code... [ 99%] MDAnalysis.visualization.streamlines highlighting module code... [ 99%] MDAnalysis.visualization.streamlines_3D highlighting module code... [100%] builtins writing additional pages... search opensearch done copying images... [ 10%] images/rama_ref_plot.png copying images... [ 20%] images/janin_ref_plot.png copying images... [ 30%] images/rama_demo_plot.png copying images... [ 40%] images/janin_demo_plot.png copying images... [ 50%] images/msd_demo_plot.png copying images... [ 60%] images/AnalysisBase_parallel.png copying images... [ 70%] images/parallelization_time.png copying images... [ 80%] images/RSMD_plot.png copying images... [ 90%] documentation_pages/visualization/testing_streamline.png copying images... [100%] documentation_pages/visualization/test_streamplot_3D.png dumping search index in English (code: en)... done dumping object inventory... done sphinx-sitemap: sitemap.xml was generated for URL https://docs.mdanalysis.org/ in /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/sitemap.xml build succeeded, 41 warnings. The HTML pages are in ../../../.pybuild/html. Build finished. The HTML pages are in /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html. make[2]: Leaving directory '/build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx' make[1]: Leaving directory '/build/reproducible-path/mdanalysis-2.9.0' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild plugin_pyproject:178: Copying package built for python3.13 to destdir dh_installdocs -O--buildsystem=pybuild dh_installdocs: warning: Cannot auto-detect main package for python-mdanalysis-doc. If the default is wrong, please use --doc-main-package dh_sphinxdoc -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild debian/rules execute_after_dh_python3 make[1]: Entering directory '/build/reproducible-path/mdanalysis-2.9.0' dh_numpy3 Possible precedence issue with control flow operator (return) at /usr/bin/dh_numpy3 line 57. rm -rf debian/python3-mdanalysis/usr/lib/python3.* make[1]: Leaving directory '/build/reproducible-path/mdanalysis-2.9.0' dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package python-mdanalysis-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-mdanalysis' in '../python3-mdanalysis_2.9.0-12_amd64.deb'. dpkg-deb: building package 'python3-mdanalysis-dbgsym' in '../python3-mdanalysis-dbgsym_2.9.0-12_amd64.deb'. dpkg-deb: building package 'python-mdanalysis-doc' in '../python-mdanalysis-doc_2.9.0-12_all.deb'. dpkg-genbuildinfo --build=binary -O../mdanalysis_2.9.0-12_amd64.buildinfo dpkg-genchanges --build=binary -O../mdanalysis_2.9.0-12_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from mdanalysis-2.9.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1370099 and its subdirectories I: Current time: Sun Sep 14 14:16:37 -12 2025 I: pbuilder-time-stamp: 1757902597 Mon Sep 15 02:16:37 UTC 2025 I: Signing ./b1/mdanalysis_2.9.0-12_amd64.buildinfo as mdanalysis_2.9.0-12_amd64.buildinfo.asc Mon Sep 15 02:16:37 UTC 2025 I: Signed ./b1/mdanalysis_2.9.0-12_amd64.buildinfo as ./b1/mdanalysis_2.9.0-12_amd64.buildinfo.asc Mon Sep 15 02:16:37 UTC 2025 - build #1 for mdanalysis/unstable/amd64 on infom01-amd64 done. Starting cleanup. All cleanup done. Mon Sep 15 02:16:37 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-7oo6DDx0, removing. /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Sep 15 02:16 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 15 02:07 b2 -rw-rw-r-- 1 jenkins jenkins 2945 Jul 10 09:34 mdanalysis_2.9.0-12.dsc -rw------- 1 jenkins jenkins 4073 Sep 15 02:07 rbuildlog.VTaIaaa /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/b1: total 13696 -rw-r--r-- 1 jenkins jenkins 379573 Sep 15 02:16 build.log -rw-r--r-- 1 jenkins jenkins 13888 Sep 15 02:16 mdanalysis_2.9.0-12.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2945 Sep 15 02:16 mdanalysis_2.9.0-12.dsc -rw-r--r-- 1 jenkins jenkins 12936 Sep 15 02:16 mdanalysis_2.9.0-12_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 13818 Sep 15 02:16 mdanalysis_2.9.0-12_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1876 Sep 15 02:16 mdanalysis_2.9.0-12_amd64.changes -rw-r--r-- 1 jenkins jenkins 1237 Sep 15 02:16 mdanalysis_2.9.0-12_source.changes -rw-r--r-- 1 jenkins jenkins 3502376 Sep 15 02:16 python-mdanalysis-doc_2.9.0-12_all.deb -rw-r--r-- 1 jenkins jenkins 5861236 Sep 15 02:16 python3-mdanalysis-dbgsym_2.9.0-12_amd64.deb -rw-r--r-- 1 jenkins jenkins 4214124 Sep 15 02:16 python3-mdanalysis_2.9.0-12_amd64.deb /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/b2: total 0 Mon Sep 15 02:16:38 UTC 2025 I: Deleting $TMPDIR on infom01-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Sep 14 14:07:34 -12 2025 I: pbuilder-time-stamp: 1757902054 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [mdanalysis_2.9.0-12.dsc] I: copying [./mdanalysis_2.9.0.orig.tar.gz] I: copying [./mdanalysis_2.9.0-12.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.9.0-12.dsc: no acceptable signature found dpkg-source: info: extracting mdanalysis in mdanalysis-2.9.0 dpkg-source: info: unpacking mdanalysis_2.9.0.orig.tar.gz dpkg-source: info: unpacking mdanalysis_2.9.0-12.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying docs_use_built_module.patch dpkg-source: info: applying docs_sphinx_warnings_are_not_errors.patch dpkg-source: info: applying docs_local_mathjax.patch dpkg-source: info: applying doc_no_mdanalysis_sphinx.patch dpkg-source: info: applying improve_test_timeout_PR4584.diff dpkg-source: info: applying skip_gsd_tests.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1370099/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='c576bcf55cdf444f9202a0e0a27566f4' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1370099' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/pbuilderrc_zXRO --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/b1 --logfile b1/build.log mdanalysis_2.9.0-12.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom01-amd64 6.12.43+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1370099/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), cython3, dh-sequence-python3, pybuild-plugin-pyproject, python3-all-dev, python3-setuptools, python3-numpy, python3-biopython (>= 1.80), python3-networkx, python3-griddataformats, python3-mmtf, python3-joblib, python3-scipy, python3-matplotlib, python3-mda-xdrlib, python3-tqdm, python3-threadpoolctl, python3-packaging, python3-filelock, python3-fasteners, python3-gsd (>= 3.0.1~), python3-netcdf4, python3-h5py, python3-seaborn, python3-sklearn, python3-duecredit, python3-hypothesis, python3-pytest, python3-sphinx, python3-msmb-theme, python3-pybtex, python3-sphinx-rtd-theme, python3-sphinx-sitemap, python3-sphinxcontrib.bibtex, libjs-mathjax dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on pybuild-plugin-pyproject; however: Package pybuild-plugin-pyproject is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython (>= 1.80); however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-griddataformats; however: Package python3-griddataformats is not installed. pbuilder-satisfydepends-dummy depends on python3-mmtf; however: Package python3-mmtf is not installed. pbuilder-satisfydepends-dummy depends on python3-joblib; however: Package python3-joblib is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-mda-xdrlib; however: Package python3-mda-xdrlib is not installed. pbuilder-satisfydepends-dummy depends on python3-tqdm; however: Package python3-tqdm is not installed. pbuilder-satisfydepends-dummy depends on python3-threadpoolctl; however: Package python3-threadpoolctl is not installed. pbuilder-satisfydepends-dummy depends on python3-packaging; however: Package python3-packaging is not installed. pbuilder-satisfydepends-dummy depends on python3-filelock; however: Package python3-filelock is not installed. pbuilder-satisfydepends-dummy depends on python3-fasteners; however: Package python3-fasteners is not installed. pbuilder-satisfydepends-dummy depends on python3-gsd (>= 3.0.1~); however: Package python3-gsd is not installed. pbuilder-satisfydepends-dummy depends on python3-netcdf4; however: Package python3-netcdf4 is not installed. pbuilder-satisfydepends-dummy depends on python3-h5py; however: Package python3-h5py is not installed. pbuilder-satisfydepends-dummy depends on python3-seaborn; however: Package python3-seaborn is not installed. pbuilder-satisfydepends-dummy depends on python3-sklearn; however: Package python3-sklearn is not installed. pbuilder-satisfydepends-dummy depends on python3-duecredit; however: Package python3-duecredit is not installed. pbuilder-satisfydepends-dummy depends on python3-hypothesis; however: Package python3-hypothesis is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-msmb-theme; however: Package python3-msmb-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-pybtex; however: Package python3-pybtex is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-rtd-theme; however: Package python3-sphinx-rtd-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-sitemap; however: Package python3-sphinx-sitemap is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinxcontrib.bibtex; however: Package python3-sphinxcontrib.bibtex is not installed. pbuilder-satisfydepends-dummy depends on libjs-mathjax; however: Package libjs-mathjax is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} blt{a} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-font-awesome{a} fonts-lato{a} fonts-lyx{a} fonts-mathjax{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libabsl20240722{a} libaec0{a} libaom3{a} libarchive-zip-perl{a} libavif16{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdav1d7{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgcrypt20{a} libgfortran5{a} libglib2.0-0t64{a} libgnutls30t64{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhdf5-310{a} libhdf5-hl-310{a} libidn2-0{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} liblzf1{a} libmagic-mgc{a} libmagic1t64{a} libnetcdf22{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libopenjp2-7{a} libp11-kit0{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libraqm0{a} librav1e0.7{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{a} libsvtav1enc2{a} libsz2{a} libtasn1-6{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2-16{a} libxrender1{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} libyuv0{a} libzopfli1{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} procps{a} pybuild-plugin-pyproject{a} python-babel-localedata{a} python-matplotlib-data{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-attr{a} python3-autocommand{a} python3-babel{a} python3-biopython{a} python3-brotli{a} python3-build{a} python3-cairo{a} python3-certifi{a} python3-cftime{a} python3-chardet{a} python3-charset-normalizer{a} python3-citeproc{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-duecredit{a} python3-fasteners{a} python3-filelock{a} python3-fonttools{a} python3-freetype{a} python3-fs{a} python3-griddataformats{a} python3-gsd{a} python3-h5py{a} python3-h5py-serial{a} python3-hypothesis{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-iniconfig{a} python3-installer{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-joblib{a} python3-kiwisolver{a} python3-latexcodec{a} python3-looseversion{a} python3-lxml{a} python3-lz4{a} python3-markupsafe{a} python3-matplotlib{a} python3-mda-xdrlib{a} python3-minimal{a} python3-mmtf{a} python3-monotonic{a} python3-more-itertools{a} python3-mpmath{a} python3-mrcfile{a} python3-msgpack{a} python3-msmb-theme{a} python3-netcdf4{a} python3-networkx{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pluggy{a} python3-pybtex{a} python3-pybtex-docutils{a} python3-pygments{a} python3-pyparsing{a} python3-pyproject-hooks{a} python3-pytest{a} python3-pytz{a} python3-reportlab{a} python3-requests{a} python3-rlpycairo{a} python3-roman{a} python3-roman-numerals{a} python3-scipy{a} python3-seaborn{a} python3-setuptools{a} python3-sklearn{a} python3-sklearn-lib{a} python3-snowballstemmer{a} python3-sortedcontainers{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-sphinx-sitemap{a} python3-sphinxcontrib.bibtex{a} python3-sphinxcontrib.jquery{a} python3-sympy{a} python3-threadpoolctl{a} python3-tk{a} python3-tqdm{a} python3-typeguard{a} python3-typing-extensions{a} python3-ufolib2{a} python3-urllib3{a} python3-wheel{a} python3-yaml{a} python3-zipp{a} python3-zopfli{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} python3.13-tk{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-rtd-theme-common{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-dejavu-extra isympy-common javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libgpg-error-l10n libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules linux-sysctl-defaults lynx ncbi-blast+ psmisc publicsuffix python-biopython-doc python3-bottleneck python3-bs4 python3-click python3-cssselect python3-gdal python3-html5lib python3-numba python3-numexpr python3-odf python3-olefile python3-openpyxl python3-pooch python3-psutil python3-pydot python3-pygraphviz python3-tables python3-tz shared-mime-info wget xdg-user-dirs 0 packages upgraded, 272 newly installed, 0 to remove and 0 not upgraded. Need to get 203 MB of archives. After unpacking 833 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1.2 [142 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.2.4+ds-1.2 [5224 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.5.2-1 [1493 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20250419 [162 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1041 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.50-1 [282 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+25 [217 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 51 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2.4 [318 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2.4 [401 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.17-1 [794 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [591 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 blt amd64 2.5.3+dfsg-8 [5984 B] Get: 65 http://deb.debian.org/debian unstable/main amd64 cython3 amd64 3.0.11+dfsg-2+b1 [2504 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 72 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250414 [116 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 fonts-lyx all 2.4.4-1 [190 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libabsl20240722 amd64 20240722.0-4 [492 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.4-2 [23.8 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libaom3 amd64 3.12.1-1 [1871 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.1-1 [559 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libgav1-1 amd64 0.19.0-3+b1 [353 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 librav1e0.7 amd64 0.7.1-9+b2 [946 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libsvtav1enc2 amd64 2.3.0+dfsg-1 [2489 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libyuv0 amd64 0.0.1916.20250814-1 [172 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libavif16 amd64 1.3.0-1 [135 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 109 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.15.1-1 [140 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.15.1-1 [20.9 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.16.0-1 [431 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.16.0-1 [437 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.7.1-2 [161 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libgpg-error0 amd64 1.55-2 [88.1 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libgcrypt20 amd64 1.11.2-2 [865 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.84.4-3 [1518 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-7 [76.3 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 11.4.5-1 [505 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.4-2 [8108 B] Get: 132 http://deb.debian.org/debian unstable/main amd64 libhdf5-310 amd64 1.14.5+repack-4 [1448 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-4 [72.6 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 4.4.0-3 [251 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1 [319 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-6 [27.5 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 liblzf1 amd64 3.6-4+b3 [10.1 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libnetcdf22 amd64 1:4.9.3-1+b1 [517 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [204 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.7-1 [2162 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.7-1 [5279 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.7-1 [10.5 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.13.7-1 [1068 B] Get: 150 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-7 [248 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.3-1 [14.0 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.7.0-5 [364 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.43-0.2 [155 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libzopfli1 amd64 1.0.3-3 [106 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 python3-wheel all 0.46.1-2 [21.7 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 python3-build all 1.2.2-4 [36.2 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 pybuild-plugin-pyproject all 6.20250414 [11.8 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.17.0-1 [6050 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 python-matplotlib-data all 3.10.1+dfsg1-5 [2737 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.7-1 [1048 B] Get: 170 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.7-1 [504 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.7-1 [26.1 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.13.7-1 [1068 B] Get: 173 http://deb.debian.org/debian unstable/main amd64 python3-attr all 25.3.0-1 [69.5 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.17.0-1 [117 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.3-1 [131 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 python3.13-tk amd64 3.13.7-1 [108 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 python3-tk amd64 3.13.5-1 [9604 B] Get: 179 http://deb.debian.org/debian unstable/main amd64 python3-pil.imagetk amd64 11.3.0-1 [81.1 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 11.3.0-1 [526 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 python3-cairo amd64 1.27.0-2 [114 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 python3-freetype all 2.5.1-2 [89.4 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 184 http://deb.debian.org/debian unstable/main amd64 python3-reportlab all 4.4.3-1 [1168 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 python3-biopython amd64 1.85+dfsg-5 [1674 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 python3-brotli amd64 1.1.0-2+b7 [320 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 189 http://deb.debian.org/debian unstable/main amd64 python3-cftime amd64 1.6.4-2 [216 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 6.0.1-1 [1434 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 python3-citeproc all 0.8.3-1 [99.8 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 python3-contourpy amd64 1.3.1-2 [215 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 python3-cycler all 0.12.1-2 [9616 B] Get: 195 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-4 [79.4 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.2.1-2 [33.0 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 python3-roman all 5.1-1 [11.0 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 python3-looseversion all 1.3.0-3 [8964 B] Get: 201 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.10-1 [42.0 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.5.0-1 [116 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.5+dfsg-1 [72.4 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 python3-duecredit all 0.10.2-2 [70.6 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 python3-monotonic all 1.6-3 [5340 B] Get: 206 http://deb.debian.org/debian unstable/main amd64 python3-fasteners all 0.18-2 [14.0 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 python3-filelock all 3.19.1-1 [12.6 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 python3-platformdirs all 4.4.0-1 [16.7 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 python3-fs all 2.4.16-8 [95.2 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 python3-lz4 amd64 4.4.4+dfsg-1 [25.4 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.15.3-1.1 [17.0 MB] Get: 212 http://deb.debian.org/debian unstable/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 python3-sympy all 1.14.0-2 [4228 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.0 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 python3-zopfli amd64 0.2.3.post1-1+b1 [10.5 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 unicode-data all 16.0.0-1 [9197 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 python3-fonttools amd64 4.57.0-2 [1457 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1023 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 python3-mrcfile all 1.5.4-2 [118 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 python3-griddataformats all 1.0.2-2 [2048 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 python3-gsd amd64 4.0.0-1 [209 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 python3-h5py-serial amd64 3.14.0-3 [1157 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 python3-h5py all 3.14.0-3 [18.3 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 python3-hypothesis all 6.138.14-1 [364 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 227 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 232 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 238 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b3 [14.0 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.6-1 [107 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 python3-joblib all 1.4.2-5 [216 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 python3-kiwisolver amd64 1.4.7-3+b1 [62.0 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 python3-latexcodec all 3.0.0-1 [17.5 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib amd64 3.10.1+dfsg1-5 [23.8 MB] Get: 245 http://deb.debian.org/debian unstable/main amd64 python3-mda-xdrlib all 0.2.0-3 [11.6 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 python3-msgpack amd64 1.0.3-3+b4 [84.5 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 python3-mmtf all 1.1.3-1 [17.0 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 8.2.3-6 [619 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 python3-roman-numerals all 3.1.0-2 [8740 B] Get: 251 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 3.0.1-1 [63.5 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 8.2.3-6 [477 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.jquery all 4.1-6 [7496 B] Get: 254 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-rtd-theme all 3.0.2+dfsg-3 [29.7 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 python3-msmb-theme all 1.2.0-4 [33.8 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 python3-netcdf4 amd64 1.7.2-1+b4 [622 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 258 http://deb.debian.org/debian unstable/main amd64 python3-pytz all 2025.2-3 [152 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-9 [4595 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 python3-pandas all 2.2.3+dfsg-9 [3097 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.6.0-1 [27.1 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.2-2 [137 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 python3-pybtex all 0.25.1-1 [75.2 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 python3-pybtex-docutils all 1.0.3-1 [8224 B] Get: 265 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.4.2-1 [266 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 python3-seaborn all 0.13.2-5 [215 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 python3-sklearn-lib amd64 1.4.2+dfsg-8 [3980 kB] Get: 269 http://deb.debian.org/debian unstable/main amd64 python3-sklearn all 1.4.2+dfsg-8 [2248 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-sitemap all 2.6.0-1 [8508 B] Get: 271 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.bibtex all 2.6.5-2 [33.2 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 python3-tqdm all 4.67.1-5 [90.8 kB] Fetched 203 MB in 8s (26.0 MB/s) Preconfiguring packages ... Selecting previously unselected package fonts-lato. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.7-1_amd64.deb ... Unpacking python3.13-minimal (3.13.7-1) ... Setting up libpython3.13-minimal:amd64 (3.13.7-1) ... Setting up libexpat1:amd64 (2.7.1-2) ... Setting up python3.13-minimal (3.13.7-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20277 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-5_all.deb ... Unpacking tzdata (2025b-5) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.3-3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21292 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.7-1_amd64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package python3-numpy-dev:amd64. Preparing to unpack .../001-python3-numpy-dev_1%3a2.2.4+ds-1.2_amd64.deb ... Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1.2) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../002-libblas3_3.12.1-7_amd64.deb ... Unpacking libblas3:amd64 (3.12.1-7) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../003-libgfortran5_15.2.0-4_amd64.deb ... Unpacking libgfortran5:amd64 (15.2.0-4) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../004-liblapack3_3.12.1-7_amd64.deb ... Unpacking liblapack3:amd64 (3.12.1-7) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../005-python3-numpy_1%3a2.2.4+ds-1.2_amd64.deb ... Unpacking python3-numpy (1:2.2.4+ds-1.2) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../006-libproc2-0_2%3a4.0.4-9_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-9) ... 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Setting up python3-pybtex-docutils (1.0.3-1) ... Setting up python3-sphinx (8.2.3-6) ... Setting up python3-sphinxcontrib.bibtex (2.6.5-2) ... Setting up python3-sphinx-sitemap (2.6.0-1) ... Setting up python3-sphinxcontrib.jquery (4.1-6) ... Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-3) ... Setting up python3-msmb-theme (1.2.0-4) ... Processing triggers for ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/mdanalysis-2.9.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../mdanalysis_2.9.0-12_source.changes dpkg-buildpackage: info: source package mdanalysis dpkg-buildpackage: info: source version 2.9.0-12 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Drew Parsons dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from mdanalysis-2.9.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --with sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/mdanalysis-2.9.0' rm -f .duecredit.p rm -f package/MDAnalysis/authors.py rm -f package/MDAnalysis/analysis/encore/clustering/affinityprop.c \ package/MDAnalysis/analysis/encore/cutils.c \ package/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c \ package/MDAnalysis/coordinates/timestep.cpp \ package/MDAnalysis/lib/_augment.cpp \ package/MDAnalysis/lib/_cutil.cpp \ package/MDAnalysis/lib/c_distances.c \ package/MDAnalysis/lib/c_distances_openmp.c \ package/MDAnalysis/lib/formats/cython_util.c \ package/MDAnalysis/lib/formats/libdcd.c \ package/MDAnalysis/lib/formats/libmdaxdr.c \ package/MDAnalysis/lib/nsgrid.cpp \ package/MDAnalysis/lib/qcprot.c rm -rf package/MDAnalysis.egg-info rm -f testsuite/MDAnalysisTests/data/.*_offsets.npz testsuite/MDAnalysisTests/data/*/.*_offsets.npz rm -rf testsuite/.pytest_cache make[1]: Leaving directory '/build/reproducible-path/mdanalysis-2.9.0' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild dh_auto_build -O--buildsystem=pybuild I: pybuild plugin_pyproject:129: Building wheel for python3.13 with "build" module I: pybuild base:311: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis * Building wheel... performance hint: MDAnalysis/lib/c_distances.pyx:275:5: Exception check on '_minimum_image_orthogonal' will always require the GIL to be acquired. Possible solutions: 1. Declare '_minimum_image_orthogonal' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '_minimum_image_orthogonal' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:302:5: Exception check on '_minimum_image_triclinic' will always require the GIL to be acquired. Possible solutions: 1. Declare '_minimum_image_triclinic' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '_minimum_image_triclinic' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:390:37: Exception check after calling '__pyx_fuse_0_minimum_image_orthogonal' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_0_minimum_image_orthogonal' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_0_minimum_image_orthogonal' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:390:37: Exception check after calling '__pyx_fuse_1_minimum_image_orthogonal' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_1_minimum_image_orthogonal' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_1_minimum_image_orthogonal' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:414:36: Exception check after calling '__pyx_fuse_0_minimum_image_triclinic' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_0_minimum_image_triclinic' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_0_minimum_image_triclinic' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:414:36: Exception check after calling '__pyx_fuse_1_minimum_image_triclinic' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_1_minimum_image_triclinic' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_1_minimum_image_triclinic' to allow an error code to be returned. performance hint: MDAnalysis/lib/nsgrid.pyx:417:37: Exception check after calling 'coord2cellid' will always require the GIL to be acquired. Declare 'coord2cellid' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: MDAnalysis/lib/nsgrid.pyx:431:26: Exception check after calling 'coord2cellxyz' will always require the GIL to be acquired. Possible solutions: 1. Declare 'coord2cellxyz' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'coord2cellxyz' to allow an error code to be returned. performance hint: MDAnalysis/lib/nsgrid.pyx:559:34: Exception check after calling 'coord2cellxyz' will always require the GIL to be acquired. Possible solutions: 1. Declare 'coord2cellxyz' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'coord2cellxyz' to allow an error code to be returned. performance hint: MDAnalysis/lib/nsgrid.pyx:567:56: Exception check after calling 'cellxyz2cellid' will always require the GIL to be acquired. Declare 'cellxyz2cellid' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: MDAnalysis/lib/nsgrid.pyx:574:53: Exception check after calling 'calc_distsq' will always require the GIL to be acquired. Declare 'calc_distsq' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: MDAnalysis/lib/nsgrid.pyx:578:57: Exception check after calling 'add_neighbors' will always require the GIL to be acquired. Possible solutions: 1. Declare 'add_neighbors' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'add_neighbors' to allow an error code to be returned. Attempting to autodetect OpenMP support... Compiler supports OpenMP Will attempt to use Cython. Compiling MDAnalysis/lib/formats/libdcd.pyx because it changed. Compiling MDAnalysis/lib/c_distances.pyx because it changed. Compiling MDAnalysis/lib/c_distances_openmp.pyx because it changed. Compiling MDAnalysis/lib/qcprot.pyx because it changed. Compiling MDAnalysis/lib/formats/libmdaxdr.pyx because it changed. Compiling MDAnalysis/lib/formats/cython_util.pyx because it changed. Compiling MDAnalysis/analysis/encore/cutils.pyx because it changed. Compiling MDAnalysis/analysis/encore/clustering/affinityprop.pyx because it changed. Compiling MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx because it changed. Compiling MDAnalysis/lib/_cutil.pyx because it changed. Compiling MDAnalysis/lib/_augment.pyx because it changed. Compiling MDAnalysis/lib/nsgrid.pyx because it changed. Compiling MDAnalysis/coordinates/timestep.pyx because it changed. [ 1/13] Cythonizing MDAnalysis/analysis/encore/clustering/affinityprop.pyx [ 2/13] Cythonizing MDAnalysis/analysis/encore/cutils.pyx [ 3/13] Cythonizing MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx [ 4/13] Cythonizing MDAnalysis/coordinates/timestep.pyx [ 5/13] Cythonizing MDAnalysis/lib/_augment.pyx [ 6/13] Cythonizing MDAnalysis/lib/_cutil.pyx [ 7/13] Cythonizing MDAnalysis/lib/c_distances.pyx [ 8/13] Cythonizing MDAnalysis/lib/c_distances_openmp.pyx [ 9/13] Cythonizing MDAnalysis/lib/formats/cython_util.pyx [10/13] Cythonizing MDAnalysis/lib/formats/libdcd.pyx [11/13] Cythonizing MDAnalysis/lib/formats/libmdaxdr.pyx [12/13] Cythonizing MDAnalysis/lib/nsgrid.pyx [13/13] Cythonizing MDAnalysis/lib/qcprot.pyx /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). By 2026-Feb-18, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! corresp(dist, value, root_dir) /usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! dist._finalize_license_expression() /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running bdist_wheel running build running build_py creating build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/exceptions.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/authors.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/version.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/units.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/due.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source copying doc/sphinx/source/conf.py -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/distances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/util.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/log.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/correlations.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/transformations.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_distopia.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/mdamath.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib creating build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/guessers.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/GROParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/tables.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology creating build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/RDKit.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/distances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/psa.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/bat.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/pca.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/backends.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/rdf.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/dielectric.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/msd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/align.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/atomicdistances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/rms.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/density.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/results.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/polymer.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/contacts.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/nucleicacids.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/gnm.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis creating build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser copying MDAnalysis/guesser/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser copying MDAnalysis/guesser/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser copying MDAnalysis/guesser/default_guesser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser copying MDAnalysis/guesser/tables.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser creating build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/groups.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/accessors.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/_get_readers.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/selection.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/topology.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/universe.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core creating build/lib.linux-x86_64-cpython-313/MDAnalysis/tests copying MDAnalysis/tests/datafiles.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/tests copying MDAnalysis/tests/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/tests creating build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization copying MDAnalysis/visualization/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization creating build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TNG.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/chain.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRC.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/null.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/memory.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates creating build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/vmd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/gromacs.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/charmm.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/jmol.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/pymol.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections creating build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/translate.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/wrap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/nojump.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/rotate.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/fit.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations creating build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/EDR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis copying MDAnalysis/lib/libmdanalysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include copying MDAnalysis/lib/include/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include creating build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2 creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp copying MDAnalysis/analysis/dssp/pydssp_numpy.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp copying MDAnalysis/analysis/dssp/dssp.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp copying MDAnalysis/analysis/dssp/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering running egg_info creating MDAnalysis.egg-info writing MDAnalysis.egg-info/PKG-INFO writing dependency_links to MDAnalysis.egg-info/dependency_links.txt writing requirements to MDAnalysis.egg-info/requires.txt writing top-level names to MDAnalysis.egg-info/top_level.txt writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/clustering/include/ap.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative reading manifest file 'MDAnalysis.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching 'doc/html/html' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.pyd' found anywhere in distribution warning: no previously-included files matching '*~' found anywhere in distribution warning: no previously-included files matching '.git' found anywhere in distribution adding license file 'LICENSE' adding license file 'AUTHORS' writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' copying doc/README -> build/lib.linux-x86_64-cpython-313/doc copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data copying doc/sphinx/Makefile -> build/lib.linux-x86_64-cpython-313/doc/sphinx copying doc/sphinx/source/index.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source copying doc/sphinx/source/references.bib -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/AnalysisBase_parallel.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/RSMD_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/janin_demo_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/janin_ref_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/msd_demo_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/parallelization_time.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/rama_demo_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/rama_ref_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/analysis_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/auxiliary_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/converters.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/coordinates_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/core_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/exceptions.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/guesser_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/lib_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/overview.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/references.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/selections.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/selections_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/topology.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/topology_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/trajectory_transformations.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/units.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/version.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/visualization_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/c_distances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/correlations.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/distances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/log.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/mdamath.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/nsgrid.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/picklable_file_io.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/pkdtree.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/qcprot.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/transformations.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/util.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/CRDParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/DMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/GMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/GROParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/GSDParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/ITPParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/MMTFParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/MinimalParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PDBParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PQRParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PSFParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/TOPParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/TPRParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/TXYZParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/XYZParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/core.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/guessers.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/tables.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/tpr_util.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/OpenMM.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/ParmEd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/RDKit.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/default_guesser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/tables.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/align.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/atomicdistances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/backends.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/bat.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/contacts.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/data.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/density.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/dielectric.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/diffusionmap.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/dihedrals.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/distances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/dssp.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/encore.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/gnm.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel_deprecated.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/helix_analysis.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hole2.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hydrogenbonds.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/leaflet.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/legacy_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/lineardensity.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/msd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/nucleicacids.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/nuclinfo.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/parallelization.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/pca.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/polymer.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/psa.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/rdf.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/results.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/rms.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/waterdynamics.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/wbridge_analysis.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/accessors.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/groups.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/selection.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/topology.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/topologyattrs.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/topologyobjects.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/universe.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/streamlines.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/streamlines_3D.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/test_streamplot_3D.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/testing_streamline.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/CRD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/DCD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/DLPoly.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/DMS.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/FHIAIMS.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/GMS.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/GRO.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/GSD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/H5MD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/INPCRD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/LAMMPS.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/MMTF.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/MOL2.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/NAMDBIN.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/PDB.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/PDBQT.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/PQR.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TNG.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRC.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRJ.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRR.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRZ.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TXYZ.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/XDR.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/XTC.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/XYZ.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/chain.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/chemfiles.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/core.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/memory.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/null.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/pickle_readers.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/timestep.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/charmm.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/gromacs.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/jmol.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/pymol.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/vmd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/fit.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/nojump.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/positionaveraging.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/rotate.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/translate.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/wrap.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/EDR.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/XVG.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/core.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats copying doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats copying doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy copying doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/bootstrap.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/clustering.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/confdistmatrix.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/covariance.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/dimensionality_reduction.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/similarity.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/utils.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying MDAnalysis/lib/_augment.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_augment.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_cutil.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/qcprot.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/qcprot.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/coordinates/timestep.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis copying MDAnalysis/lib/formats/cython_util.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/include/calc_distances.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/formats/src/trr_seek.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/include/endianswap.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/fastio.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/readdcd.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/trr_seek.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xtc_seek.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/analysis/encore/cutils.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include running build_ext building 'MDAnalysis.lib.formats.libdcd' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/usr/include/python3.13 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/formats/libdcd.c:1261: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib.c_distances' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include -I/usr/include/python3.13 -c MDAnalysis/lib/c_distances.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/c_distances.c:1263: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.o -L/usr/lib/x86_64-linux-gnu -lm -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib.c_distances_openmp' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPARALLEL -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include -I/usr/include/python3.13 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/c_distances_openmp.c:1272: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.o -L/usr/lib/x86_64-linux-gnu -lm -lgomp -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.cpython-313-x86_64-linux-gnu.so -fopenmp building 'MDAnalysis.lib.qcprot' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/lib/qcprot.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/qcprot.c:1255: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib._transformations' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/transformations.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/src/transformations/transformations.c:73: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/transformations.o -L/usr/lib/x86_64-linux-gnu -lm -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_transformations.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib.formats.libmdaxdr' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/formats/libmdaxdr.c:1282: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/trr_seek.o -std=c11 -O3 -funroll-loops -fsigned-zeros x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile.o -std=c11 -O3 -funroll-loops -fsigned-zeros x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/xdrfile_trr.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_trr.o -std=c11 -O3 -funroll-loops -fsigned-zeros x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/xdrfile_xtc.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_xtc.o -std=c11 -O3 -funroll-loops -fsigned-zeros x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/xtc_seek.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xtc_seek.o -std=c11 -O3 -funroll-loops -fsigned-zeros x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/trr_seek.o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile.o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_trr.o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_xtc.o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xtc_seek.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib.formats.cython_util' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/lib/formats/cython_util.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/formats/cython_util.c:1272: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.analysis.encore.cutils' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/cutils.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.o -std=c11 -funroll-loops -fsigned-zeros -O3 In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/analysis/encore/cutils.c:1255: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering creating build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/clustering/affinityprop.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.o -std=c11 -funroll-loops -fsigned-zeros -O3 In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/analysis/encore/clustering/affinityprop.c:1261: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/clustering/src/ap.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src/ap.o -std=c11 -funroll-loops -fsigned-zeros -O3 x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.o build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src/ap.o -L/usr/lib/x86_64-linux-gnu -lm -o build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -std=c11 -funroll-loops -fsigned-zeros -O3 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -std=c11 -funroll-loops -fsigned-zeros -O3 In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:1261: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -L/usr/lib/x86_64-linux-gnu -lm -o build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib._cutil' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include -I/usr/include/python3.13 -c MDAnalysis/lib/_cutil.cpp -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.o -O3 -funroll-loops -fsigned-zeros -std=c++11 In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/_cutil.cpp:1273: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.o -L/usr/lib/x86_64-linux-gnu -lm -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib._augment' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/lib/_augment.cpp -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.o -O3 -funroll-loops -fsigned-zeros -std=c++11 In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/_augment.cpp:1268: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib.nsgrid' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include -I/usr/include/python3.13 -c MDAnalysis/lib/nsgrid.cpp -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.o -O3 -funroll-loops -fsigned-zeros -std=c++11 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.coordinates.timestep' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/coordinates x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/coordinates/timestep.cpp -o build/temp.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.o -O3 -funroll-loops -fsigned-zeros -std=c++11 In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/coordinates/timestep.cpp:1269: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.cpython-313-x86_64-linux-gnu.so installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/doc copying build/lib.linux-x86_64-cpython-313/doc/README -> build/bdist.linux-x86_64/wheel/./doc creating build/bdist.linux-x86_64/wheel/doc/sphinx creating build/bdist.linux-x86_64/wheel/doc/sphinx/source copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/index.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/rama_ref_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/parallelization_time.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/msd_demo_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/rama_demo_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/AnalysisBase_parallel.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/janin_demo_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/RSMD_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/janin_ref_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/mdamath.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/pkdtree.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/lib/formats copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib/formats copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib/formats copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/correlations.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/nsgrid.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/c_distances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/qcprot.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/distances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/picklable_file_io.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/log.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/util.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/transformations.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/units.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/TXYZParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PDBParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/GROParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/core.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/XYZParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/CRDParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/DMSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/TPRParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PSFParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/MMTFParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/TOPParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/guessers.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/GMSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PQRParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/tpr_util.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/MinimalParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/GSDParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/ITPParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/tables.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/converters copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/OpenMM.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/RDKit.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/ParmEd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/guesser_modules copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/default_guesser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/tables.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/helix_analysis.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/pca.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/density.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/rms.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/results.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/wbridge_analysis.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/msd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/psa.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/analysis/legacy copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/legacy copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/polymer.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/atomicdistances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/clustering.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/dimensionality_reduction.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/utils.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/similarity.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/confdistmatrix.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/covariance.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/bootstrap.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/nucleicacids.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel_deprecated.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/waterdynamics.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/nuclinfo.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/dihedrals.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/bat.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/parallelization.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/lineardensity.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/align.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/dielectric.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/diffusionmap.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/distances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/data.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/gnm.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hole2.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/contacts.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/backends.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/dssp.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/rdf.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hydrogenbonds.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/leaflet.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/accessors.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/universe.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/groups.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/topologyattrs.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/selection.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/topology.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/topologyobjects.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/visualization copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/test_streamplot_3D.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/streamlines_3D.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/streamlines.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/testing_streamline.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/overview.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/exceptions.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/references.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/version.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/chemfiles.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRC.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/null.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/chain.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/CRD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/GMS.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/DMS.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/LAMMPS.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/memory.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/core.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TXYZ.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/NAMDBIN.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/INPCRD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/PDBQT.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/MOL2.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/H5MD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/XYZ.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/MMTF.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRJ.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/GSD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/GRO.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TNG.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/PDB.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/XDR.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRZ.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/DLPoly.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/pickle_readers.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/PQR.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/XTC.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/FHIAIMS.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/timestep.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/DCD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRR.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/selections copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/pymol.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/vmd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/charmm.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/jmol.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/gromacs.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/fit.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/nojump.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/wrap.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/translate.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/positionaveraging.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/rotate.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/trajectory_transformations.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/auxiliary copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/EDR.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/XVG.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/core.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/references.bib -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/conf.py -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source copying build/lib.linux-x86_64-cpython-313/doc/sphinx/Makefile -> build/bdist.linux-x86_64/wheel/./doc/sphinx creating build/bdist.linux-x86_64/wheel/MDAnalysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/distances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/libmdanalysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/libmdanalysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/libmdanalysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/util.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/log.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/src creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/src/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/LICENCE -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/AUTHOR -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/transformations.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/correlations.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/transformations.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xtc_seek.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/trr_seek.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xdrfile.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/fastio.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/endianswap.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/readdcd.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/trr_seek.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xtc_seek.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/picklable_file_io.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_distopia.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_transformations.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/mdamath.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include/calc_distances.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/exceptions.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/ParmEdParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology creating build/bdist.linux-x86_64/wheel/MDAnalysis/topology/tpr copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/setting.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/guessers.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/GROParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/ITPParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/FHIAIMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tables.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/authors.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/version.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/ParmEd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/ParmEdParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/RDKit.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/OpenMMParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/OpenMM.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/RDKitParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/distances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/psa.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hole2 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hole2 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/bat.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dihedrals.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/pca.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/backends.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/rdf.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dielectric.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/legacy copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/legacy copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/legacy creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/msd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/similarity.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/covariance.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src/ap.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include/ap.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering/include creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/data copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/janin_ref_data.npy -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/align.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/atomicdistances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/rms.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/density.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/results.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/polymer.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/helix_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/dssp copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp/pydssp_numpy.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/dssp copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp/dssp.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/dssp copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/dssp copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/contacts.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/nucleicacids.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/gnm.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/guesser copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/default_guesser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/tables.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser creating build/bdist.linux-x86_64/wheel/MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/groups.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/accessors.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/_get_readers.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/selection.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/topology.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/universe.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core creating build/bdist.linux-x86_64/wheel/MDAnalysis/tests copying build/lib.linux-x86_64-cpython-313/MDAnalysis/tests/datafiles.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/tests copying build/lib.linux-x86_64-cpython-313/MDAnalysis/tests/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/tests creating build/bdist.linux-x86_64/wheel/MDAnalysis/visualization copying build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization copying build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization copying build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization copying build/lib.linux-x86_64-cpython-313/MDAnalysis/units.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TXYZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/ParmEd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TNG.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/chain.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/XDR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/H5MD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRC.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/null.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/NAMDBIN.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/memory.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates creating build/bdist.linux-x86_64/wheel/MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/vmd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/gromacs.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/charmm.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/jmol.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/pymol.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/due.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/translate.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/wrap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/boxdimensions.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/nojump.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/rotate.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/fit.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations creating build/bdist.linux-x86_64/wheel/MDAnalysis/auxiliary copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/EDR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary running install_egg_info Copying MDAnalysis.egg-info to build/bdist.linux-x86_64/wheel/./MDAnalysis-2.9.0.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/mdanalysis-2.9.0.dist-info/WHEEL creating '/build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/.tmp-zjdtpibb/mdanalysis-2.9.0-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'MDAnalysis/__init__.py' adding 'MDAnalysis/authors.py' adding 'MDAnalysis/due.py' adding 'MDAnalysis/exceptions.py' adding 'MDAnalysis/units.py' adding 'MDAnalysis/version.py' adding 'MDAnalysis/analysis/__init__.py' adding 'MDAnalysis/analysis/align.py' adding 'MDAnalysis/analysis/atomicdistances.py' adding 'MDAnalysis/analysis/backends.py' adding 'MDAnalysis/analysis/base.py' adding 'MDAnalysis/analysis/bat.py' adding 'MDAnalysis/analysis/contacts.py' adding 'MDAnalysis/analysis/density.py' adding 'MDAnalysis/analysis/dielectric.py' adding 'MDAnalysis/analysis/diffusionmap.py' adding 'MDAnalysis/analysis/dihedrals.py' adding 'MDAnalysis/analysis/distances.py' adding 'MDAnalysis/analysis/gnm.py' adding 'MDAnalysis/analysis/helix_analysis.py' adding 'MDAnalysis/analysis/leaflet.py' adding 'MDAnalysis/analysis/lineardensity.py' adding 'MDAnalysis/analysis/msd.py' adding 'MDAnalysis/analysis/nucleicacids.py' adding 'MDAnalysis/analysis/nuclinfo.py' adding 'MDAnalysis/analysis/pca.py' adding 'MDAnalysis/analysis/polymer.py' adding 'MDAnalysis/analysis/psa.py' adding 'MDAnalysis/analysis/rdf.py' adding 'MDAnalysis/analysis/results.py' adding 'MDAnalysis/analysis/rms.py' adding 'MDAnalysis/analysis/waterdynamics.py' adding 'MDAnalysis/analysis/data/__init__.py' adding 'MDAnalysis/analysis/data/filenames.py' adding 'MDAnalysis/analysis/data/janin_ref_data.npy' adding 'MDAnalysis/analysis/data/rama_ref_data.npy' adding 'MDAnalysis/analysis/dssp/__init__.py' adding 'MDAnalysis/analysis/dssp/dssp.py' adding 'MDAnalysis/analysis/dssp/pydssp_numpy.py' adding 'MDAnalysis/analysis/encore/__init__.py' adding 'MDAnalysis/analysis/encore/bootstrap.py' adding 'MDAnalysis/analysis/encore/confdistmatrix.py' adding 'MDAnalysis/analysis/encore/covariance.py' adding 'MDAnalysis/analysis/encore/cutils.c' adding 'MDAnalysis/analysis/encore/cutils.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/analysis/encore/cutils.pyx' adding 'MDAnalysis/analysis/encore/similarity.py' adding 'MDAnalysis/analysis/encore/utils.py' adding 'MDAnalysis/analysis/encore/clustering/ClusterCollection.py' adding 'MDAnalysis/analysis/encore/clustering/ClusteringMethod.py' adding 'MDAnalysis/analysis/encore/clustering/__init__.py' adding 'MDAnalysis/analysis/encore/clustering/affinityprop.c' adding 'MDAnalysis/analysis/encore/clustering/affinityprop.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/analysis/encore/clustering/affinityprop.pyx' adding 'MDAnalysis/analysis/encore/clustering/cluster.py' adding 'MDAnalysis/analysis/encore/clustering/include/ap.h' adding 'MDAnalysis/analysis/encore/clustering/src/ap.c' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c' adding 'MDAnalysis/analysis/hbonds/__init__.py' adding 'MDAnalysis/analysis/hbonds/hbond_autocorrel.py' adding 'MDAnalysis/analysis/hole2/__init__.py' adding 'MDAnalysis/analysis/hydrogenbonds/__init__.py' adding 'MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py' adding 'MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py' adding 'MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py' adding 'MDAnalysis/analysis/legacy/__init__.py' adding 'MDAnalysis/analysis/legacy/x3dna.py' adding 'MDAnalysis/auxiliary/EDR.py' adding 'MDAnalysis/auxiliary/XVG.py' adding 'MDAnalysis/auxiliary/__init__.py' adding 'MDAnalysis/auxiliary/base.py' adding 'MDAnalysis/auxiliary/core.py' adding 'MDAnalysis/converters/OpenMM.py' adding 'MDAnalysis/converters/OpenMMParser.py' adding 'MDAnalysis/converters/ParmEd.py' adding 'MDAnalysis/converters/ParmEdParser.py' adding 'MDAnalysis/converters/RDKit.py' adding 'MDAnalysis/converters/RDKitParser.py' adding 'MDAnalysis/converters/__init__.py' adding 'MDAnalysis/converters/base.py' adding 'MDAnalysis/coordinates/CRD.py' adding 'MDAnalysis/coordinates/DCD.py' adding 'MDAnalysis/coordinates/DLPoly.py' adding 'MDAnalysis/coordinates/DMS.py' adding 'MDAnalysis/coordinates/FHIAIMS.py' adding 'MDAnalysis/coordinates/GMS.py' adding 'MDAnalysis/coordinates/GRO.py' adding 'MDAnalysis/coordinates/GSD.py' adding 'MDAnalysis/coordinates/H5MD.py' adding 'MDAnalysis/coordinates/INPCRD.py' adding 'MDAnalysis/coordinates/LAMMPS.py' adding 'MDAnalysis/coordinates/MMTF.py' adding 'MDAnalysis/coordinates/MOL2.py' adding 'MDAnalysis/coordinates/NAMDBIN.py' adding 'MDAnalysis/coordinates/PDB.py' adding 'MDAnalysis/coordinates/PDBQT.py' adding 'MDAnalysis/coordinates/PQR.py' adding 'MDAnalysis/coordinates/ParmEd.py' adding 'MDAnalysis/coordinates/TNG.py' adding 'MDAnalysis/coordinates/TRC.py' adding 'MDAnalysis/coordinates/TRJ.py' adding 'MDAnalysis/coordinates/TRR.py' adding 'MDAnalysis/coordinates/TRZ.py' adding 'MDAnalysis/coordinates/TXYZ.py' adding 'MDAnalysis/coordinates/XDR.py' adding 'MDAnalysis/coordinates/XTC.py' adding 'MDAnalysis/coordinates/XYZ.py' adding 'MDAnalysis/coordinates/__init__.py' adding 'MDAnalysis/coordinates/base.py' adding 'MDAnalysis/coordinates/chain.py' adding 'MDAnalysis/coordinates/chemfiles.py' adding 'MDAnalysis/coordinates/core.py' adding 'MDAnalysis/coordinates/memory.py' adding 'MDAnalysis/coordinates/null.py' adding 'MDAnalysis/coordinates/timestep.cpp' adding 'MDAnalysis/coordinates/timestep.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/coordinates/timestep.pxd' adding 'MDAnalysis/coordinates/timestep.pyx' adding 'MDAnalysis/core/__init__.py' adding 'MDAnalysis/core/_get_readers.py' adding 'MDAnalysis/core/accessors.py' adding 'MDAnalysis/core/groups.py' adding 'MDAnalysis/core/selection.py' adding 'MDAnalysis/core/topology.py' adding 'MDAnalysis/core/topologyattrs.py' adding 'MDAnalysis/core/topologyobjects.py' adding 'MDAnalysis/core/universe.py' adding 'MDAnalysis/guesser/__init__.py' adding 'MDAnalysis/guesser/base.py' adding 'MDAnalysis/guesser/default_guesser.py' adding 'MDAnalysis/guesser/tables.py' adding 'MDAnalysis/lib/NeighborSearch.py' adding 'MDAnalysis/lib/__init__.py' adding 'MDAnalysis/lib/_augment.cpp' adding 'MDAnalysis/lib/_augment.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/_augment.pyx' adding 'MDAnalysis/lib/_cutil.cpp' adding 'MDAnalysis/lib/_cutil.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/_cutil.pxd' adding 'MDAnalysis/lib/_cutil.pyx' adding 'MDAnalysis/lib/_distopia.py' adding 'MDAnalysis/lib/_transformations.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/c_distances.c' adding 'MDAnalysis/lib/c_distances.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/c_distances.pxd' adding 'MDAnalysis/lib/c_distances.pyx' adding 'MDAnalysis/lib/c_distances_openmp.c' adding 'MDAnalysis/lib/c_distances_openmp.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/c_distances_openmp.pyx' adding 'MDAnalysis/lib/correlations.py' adding 'MDAnalysis/lib/distances.py' adding 'MDAnalysis/lib/log.py' adding 'MDAnalysis/lib/mdamath.py' adding 'MDAnalysis/lib/nsgrid.cpp' adding 'MDAnalysis/lib/nsgrid.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/nsgrid.pyx' adding 'MDAnalysis/lib/picklable_file_io.py' adding 'MDAnalysis/lib/pkdtree.py' adding 'MDAnalysis/lib/qcprot.c' adding 'MDAnalysis/lib/qcprot.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/qcprot.pyx' adding 'MDAnalysis/lib/transformations.py' adding 'MDAnalysis/lib/util.py' adding 'MDAnalysis/lib/formats/__init__.py' adding 'MDAnalysis/lib/formats/cython_util.c' adding 'MDAnalysis/lib/formats/cython_util.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/formats/cython_util.pxd' adding 'MDAnalysis/lib/formats/cython_util.pyx' adding 'MDAnalysis/lib/formats/libdcd.c' adding 'MDAnalysis/lib/formats/libdcd.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/formats/libdcd.pxd' adding 'MDAnalysis/lib/formats/libdcd.pyx' adding 'MDAnalysis/lib/formats/libmdaxdr.c' adding 'MDAnalysis/lib/formats/libmdaxdr.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/formats/libmdaxdr.pxd' adding 'MDAnalysis/lib/formats/libmdaxdr.pyx' adding 'MDAnalysis/lib/formats/include/__init__.py' adding 'MDAnalysis/lib/formats/include/endianswap.h' adding 'MDAnalysis/lib/formats/include/fastio.h' adding 'MDAnalysis/lib/formats/include/readdcd.h' adding 'MDAnalysis/lib/formats/include/trr_seek.h' adding 'MDAnalysis/lib/formats/include/xdrfile.h' adding 'MDAnalysis/lib/formats/include/xdrfile_trr.h' adding 'MDAnalysis/lib/formats/include/xdrfile_xtc.h' adding 'MDAnalysis/lib/formats/include/xtc_seek.h' adding 'MDAnalysis/lib/formats/src/__init__.py' adding 'MDAnalysis/lib/formats/src/trr_seek.c' adding 'MDAnalysis/lib/formats/src/xdrfile.c' adding 'MDAnalysis/lib/formats/src/xdrfile_trr.c' adding 'MDAnalysis/lib/formats/src/xdrfile_xtc.c' adding 'MDAnalysis/lib/formats/src/xtc_seek.c' adding 'MDAnalysis/lib/include/__init__.py' adding 'MDAnalysis/lib/include/calc_distances.h' adding 'MDAnalysis/lib/libmdanalysis/__init__.pxd' adding 'MDAnalysis/lib/libmdanalysis/__init__.py' adding 'MDAnalysis/lib/src/transformations/AUTHOR' adding 'MDAnalysis/lib/src/transformations/LICENCE' adding 'MDAnalysis/lib/src/transformations/__init__.py' adding 'MDAnalysis/lib/src/transformations/transformations.c' adding 'MDAnalysis/selections/__init__.py' adding 'MDAnalysis/selections/base.py' adding 'MDAnalysis/selections/charmm.py' adding 'MDAnalysis/selections/gromacs.py' adding 'MDAnalysis/selections/jmol.py' adding 'MDAnalysis/selections/pymol.py' adding 'MDAnalysis/selections/vmd.py' adding 'MDAnalysis/tests/__init__.py' adding 'MDAnalysis/tests/datafiles.py' adding 'MDAnalysis/topology/CRDParser.py' adding 'MDAnalysis/topology/DLPolyParser.py' adding 'MDAnalysis/topology/DMSParser.py' adding 'MDAnalysis/topology/ExtendedPDBParser.py' adding 'MDAnalysis/topology/FHIAIMSParser.py' adding 'MDAnalysis/topology/GMSParser.py' adding 'MDAnalysis/topology/GROParser.py' adding 'MDAnalysis/topology/GSDParser.py' adding 'MDAnalysis/topology/HoomdXMLParser.py' adding 'MDAnalysis/topology/ITPParser.py' adding 'MDAnalysis/topology/LAMMPSParser.py' adding 'MDAnalysis/topology/MMTFParser.py' adding 'MDAnalysis/topology/MOL2Parser.py' adding 'MDAnalysis/topology/MinimalParser.py' adding 'MDAnalysis/topology/PDBParser.py' adding 'MDAnalysis/topology/PDBQTParser.py' adding 'MDAnalysis/topology/PQRParser.py' adding 'MDAnalysis/topology/PSFParser.py' adding 'MDAnalysis/topology/ParmEdParser.py' adding 'MDAnalysis/topology/TOPParser.py' adding 'MDAnalysis/topology/TPRParser.py' adding 'MDAnalysis/topology/TXYZParser.py' adding 'MDAnalysis/topology/XYZParser.py' adding 'MDAnalysis/topology/__init__.py' adding 'MDAnalysis/topology/base.py' adding 'MDAnalysis/topology/core.py' adding 'MDAnalysis/topology/guessers.py' adding 'MDAnalysis/topology/tables.py' adding 'MDAnalysis/topology/tpr/__init__.py' adding 'MDAnalysis/topology/tpr/obj.py' adding 'MDAnalysis/topology/tpr/setting.py' adding 'MDAnalysis/topology/tpr/utils.py' adding 'MDAnalysis/transformations/__init__.py' adding 'MDAnalysis/transformations/base.py' adding 'MDAnalysis/transformations/boxdimensions.py' adding 'MDAnalysis/transformations/fit.py' adding 'MDAnalysis/transformations/nojump.py' adding 'MDAnalysis/transformations/positionaveraging.py' adding 'MDAnalysis/transformations/rotate.py' adding 'MDAnalysis/transformations/translate.py' adding 'MDAnalysis/transformations/wrap.py' adding 'MDAnalysis/visualization/__init__.py' adding 'MDAnalysis/visualization/streamlines.py' adding 'MDAnalysis/visualization/streamlines_3D.py' adding 'doc/README' adding 'doc/sphinx/Makefile' adding 'doc/sphinx/source/conf.py' adding 'doc/sphinx/source/index.rst' adding 'doc/sphinx/source/references.bib' adding 'doc/sphinx/source/documentation_pages/analysis_modules.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary_modules.rst' adding 'doc/sphinx/source/documentation_pages/converters.rst' adding 'doc/sphinx/source/documentation_pages/coordinates_modules.rst' adding 'doc/sphinx/source/documentation_pages/core_modules.rst' adding 'doc/sphinx/source/documentation_pages/exceptions.rst' adding 'doc/sphinx/source/documentation_pages/guesser_modules.rst' adding 'doc/sphinx/source/documentation_pages/lib_modules.rst' adding 'doc/sphinx/source/documentation_pages/overview.rst' adding 'doc/sphinx/source/documentation_pages/references.rst' adding 'doc/sphinx/source/documentation_pages/selections.rst' adding 'doc/sphinx/source/documentation_pages/selections_modules.rst' adding 'doc/sphinx/source/documentation_pages/topology.rst' adding 'doc/sphinx/source/documentation_pages/topology_modules.rst' adding 'doc/sphinx/source/documentation_pages/trajectory_transformations.rst' adding 'doc/sphinx/source/documentation_pages/units.rst' adding 'doc/sphinx/source/documentation_pages/version.rst' adding 'doc/sphinx/source/documentation_pages/visualization_modules.rst' adding 'doc/sphinx/source/documentation_pages/analysis/align.rst' adding 'doc/sphinx/source/documentation_pages/analysis/atomicdistances.rst' adding 'doc/sphinx/source/documentation_pages/analysis/backends.rst' adding 'doc/sphinx/source/documentation_pages/analysis/base.rst' adding 'doc/sphinx/source/documentation_pages/analysis/bat.rst' adding 'doc/sphinx/source/documentation_pages/analysis/contacts.rst' adding 'doc/sphinx/source/documentation_pages/analysis/data.rst' adding 'doc/sphinx/source/documentation_pages/analysis/density.rst' adding 'doc/sphinx/source/documentation_pages/analysis/dielectric.rst' adding 'doc/sphinx/source/documentation_pages/analysis/diffusionmap.rst' adding 'doc/sphinx/source/documentation_pages/analysis/dihedrals.rst' adding 'doc/sphinx/source/documentation_pages/analysis/distances.rst' adding 'doc/sphinx/source/documentation_pages/analysis/dssp.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore.rst' adding 'doc/sphinx/source/documentation_pages/analysis/gnm.rst' adding 'doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel.rst' adding 'doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel_deprecated.rst' adding 'doc/sphinx/source/documentation_pages/analysis/helix_analysis.rst' adding 'doc/sphinx/source/documentation_pages/analysis/hole2.rst' adding 'doc/sphinx/source/documentation_pages/analysis/hydrogenbonds.rst' adding 'doc/sphinx/source/documentation_pages/analysis/leaflet.rst' adding 'doc/sphinx/source/documentation_pages/analysis/legacy_modules.rst' adding 'doc/sphinx/source/documentation_pages/analysis/lineardensity.rst' adding 'doc/sphinx/source/documentation_pages/analysis/msd.rst' adding 'doc/sphinx/source/documentation_pages/analysis/nucleicacids.rst' adding 'doc/sphinx/source/documentation_pages/analysis/nuclinfo.rst' adding 'doc/sphinx/source/documentation_pages/analysis/parallelization.rst' adding 'doc/sphinx/source/documentation_pages/analysis/pca.rst' adding 'doc/sphinx/source/documentation_pages/analysis/polymer.rst' adding 'doc/sphinx/source/documentation_pages/analysis/psa.rst' adding 'doc/sphinx/source/documentation_pages/analysis/rdf.rst' adding 'doc/sphinx/source/documentation_pages/analysis/results.rst' adding 'doc/sphinx/source/documentation_pages/analysis/rms.rst' adding 'doc/sphinx/source/documentation_pages/analysis/waterdynamics.rst' adding 'doc/sphinx/source/documentation_pages/analysis/wbridge_analysis.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/bootstrap.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/clustering.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/confdistmatrix.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/covariance.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/dimensionality_reduction.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/similarity.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/utils.rst' adding 'doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary/EDR.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary/XVG.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary/base.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary/core.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary/init.rst' adding 'doc/sphinx/source/documentation_pages/converters/OpenMM.rst' adding 'doc/sphinx/source/documentation_pages/converters/ParmEd.rst' adding 'doc/sphinx/source/documentation_pages/converters/RDKit.rst' adding 'doc/sphinx/source/documentation_pages/converters/base.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/CRD.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/DCD.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/DLPoly.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/DMS.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/FHIAIMS.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/GMS.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/GRO.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/GSD.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/H5MD.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/INPCRD.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/LAMMPS.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/MMTF.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/MOL2.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/NAMDBIN.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/PDB.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/PDBQT.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/PQR.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TNG.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TRC.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TRJ.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TRR.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TRZ.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TXYZ.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/XDR.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/XTC.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/XYZ.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/base.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/chain.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/chemfiles.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/core.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/init.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/memory.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/null.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/pickle_readers.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/timestep.rst' adding 'doc/sphinx/source/documentation_pages/core/accessors.rst' adding 'doc/sphinx/source/documentation_pages/core/groups.rst' adding 'doc/sphinx/source/documentation_pages/core/init.rst' adding 'doc/sphinx/source/documentation_pages/core/selection.rst' adding 'doc/sphinx/source/documentation_pages/core/topology.rst' adding 'doc/sphinx/source/documentation_pages/core/topologyattrs.rst' adding 'doc/sphinx/source/documentation_pages/core/topologyobjects.rst' adding 'doc/sphinx/source/documentation_pages/core/universe.rst' adding 'doc/sphinx/source/documentation_pages/guesser_modules/base.rst' adding 'doc/sphinx/source/documentation_pages/guesser_modules/default_guesser.rst' adding 'doc/sphinx/source/documentation_pages/guesser_modules/init.rst' adding 'doc/sphinx/source/documentation_pages/guesser_modules/tables.rst' adding 'doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst' adding 'doc/sphinx/source/documentation_pages/lib/c_distances.rst' adding 'doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst' adding 'doc/sphinx/source/documentation_pages/lib/correlations.rst' adding 'doc/sphinx/source/documentation_pages/lib/distances.rst' adding 'doc/sphinx/source/documentation_pages/lib/log.rst' adding 'doc/sphinx/source/documentation_pages/lib/mdamath.rst' adding 'doc/sphinx/source/documentation_pages/lib/nsgrid.rst' adding 'doc/sphinx/source/documentation_pages/lib/picklable_file_io.rst' adding 'doc/sphinx/source/documentation_pages/lib/pkdtree.rst' adding 'doc/sphinx/source/documentation_pages/lib/qcprot.rst' adding 'doc/sphinx/source/documentation_pages/lib/transformations.rst' adding 'doc/sphinx/source/documentation_pages/lib/util.rst' adding 'doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst' adding 'doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst' adding 'doc/sphinx/source/documentation_pages/selections/base.rst' adding 'doc/sphinx/source/documentation_pages/selections/charmm.rst' adding 'doc/sphinx/source/documentation_pages/selections/gromacs.rst' adding 'doc/sphinx/source/documentation_pages/selections/jmol.rst' adding 'doc/sphinx/source/documentation_pages/selections/pymol.rst' adding 'doc/sphinx/source/documentation_pages/selections/vmd.rst' adding 'doc/sphinx/source/documentation_pages/topology/CRDParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/DMSParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/GMSParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/GROParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/GSDParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/ITPParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/MMTFParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst' adding 'doc/sphinx/source/documentation_pages/topology/MinimalParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/PDBParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/PQRParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/PSFParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/TOPParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/TPRParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/TXYZParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/XYZParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/base.rst' adding 'doc/sphinx/source/documentation_pages/topology/core.rst' adding 'doc/sphinx/source/documentation_pages/topology/guessers.rst' adding 'doc/sphinx/source/documentation_pages/topology/init.rst' adding 'doc/sphinx/source/documentation_pages/topology/tables.rst' adding 'doc/sphinx/source/documentation_pages/topology/tpr_util.rst' adding 'doc/sphinx/source/documentation_pages/transformations/base.rst' adding 'doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst' adding 'doc/sphinx/source/documentation_pages/transformations/fit.rst' adding 'doc/sphinx/source/documentation_pages/transformations/nojump.rst' adding 'doc/sphinx/source/documentation_pages/transformations/positionaveraging.rst' adding 'doc/sphinx/source/documentation_pages/transformations/rotate.rst' adding 'doc/sphinx/source/documentation_pages/transformations/translate.rst' adding 'doc/sphinx/source/documentation_pages/transformations/wrap.rst' adding 'doc/sphinx/source/documentation_pages/visualization/streamlines.rst' adding 'doc/sphinx/source/documentation_pages/visualization/streamlines_3D.rst' adding 'doc/sphinx/source/documentation_pages/visualization/test_streamplot_3D.png' adding 'doc/sphinx/source/documentation_pages/visualization/testing_streamline.png' adding 'doc/sphinx/source/images/AnalysisBase_parallel.png' adding 'doc/sphinx/source/images/RSMD_plot.png' adding 'doc/sphinx/source/images/janin_demo_plot.png' adding 'doc/sphinx/source/images/janin_ref_plot.png' adding 'doc/sphinx/source/images/msd_demo_plot.png' adding 'doc/sphinx/source/images/parallelization_time.png' adding 'doc/sphinx/source/images/rama_demo_plot.png' adding 'doc/sphinx/source/images/rama_ref_plot.png' adding 'mdanalysis-2.9.0.dist-info/licenses/AUTHORS' adding 'mdanalysis-2.9.0.dist-info/licenses/LICENSE' adding 'mdanalysis-2.9.0.dist-info/METADATA' adding 'mdanalysis-2.9.0.dist-info/WHEEL' adding 'mdanalysis-2.9.0.dist-info/top_level.txt' adding 'mdanalysis-2.9.0.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Successfully built mdanalysis-2.9.0-cp313-cp313-linux_x86_64.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.13 with "installer" module debian/rules execute_after_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/mdanalysis-2.9.0' PYTHONPATH=/build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build make html -C package/doc/sphinx/ BUILDDIR=/build/reproducible-path/mdanalysis-2.9.0/.pybuild # HTML generator make[2]: Entering directory '/build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx' sphinx-build -v -b html source /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html Running Sphinx v8.2.3 loading translations [en]... locale_dir /build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist locale_dir /build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist done Original exception: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/sphinx/registry.py", line 541, in load_extension mod = import_module(extname) File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module return _bootstrap._gcd_import(name[level:], package, level) ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "", line 1387, in _gcd_import File "", line 1360, in _find_and_load File "", line 1324, in _find_and_load_unlocked ModuleNotFoundError: No module named 'sphinxcontrib.applehelp' Original exception: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/sphinx/registry.py", line 541, in load_extension mod = import_module(extname) File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module return _bootstrap._gcd_import(name[level:], package, level) ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "", line 1387, in _gcd_import File "", line 1360, in _find_and_load File "", line 1324, in _find_and_load_unlocked ModuleNotFoundError: No module named 'sphinxcontrib.devhelp' Original exception: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/sphinx/registry.py", line 541, in load_extension mod = import_module(extname) File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module return _bootstrap._gcd_import(name[level:], package, level) ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "", line 1387, in _gcd_import File "", line 1360, in _find_and_load File "", line 1324, in _find_and_load_unlocked ModuleNotFoundError: No module named 'sphinxcontrib.htmlhelp' Original exception: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/sphinx/registry.py", line 541, in load_extension mod = import_module(extname) File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module return _bootstrap._gcd_import(name[level:], package, level) ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "", line 1387, in _gcd_import File "", line 1360, in _find_and_load File "", line 1324, in _find_and_load_unlocked ModuleNotFoundError: No module named 'sphinxcontrib.serializinghtml' Original exception: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/sphinx/registry.py", line 541, in load_extension mod = import_module(extname) File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module return _bootstrap._gcd_import(name[level:], package, level) ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "", line 1387, in _gcd_import File "", line 1360, in _find_and_load File "", line 1324, in _find_and_load_unlocked ModuleNotFoundError: No module named 'sphinxcontrib.qthelp' making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. checking bibtex cache... out of date parsing bibtex file /build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx/source/references.bib... parsed 69 entries locale_dir /build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist loading intersphinx inventory 'h5py' from https://docs.h5py.org/en/stable/objects.inv ... loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv ... loading intersphinx inventory 'scipy' from https://docs.scipy.org/doc/scipy/objects.inv ... loading intersphinx inventory 'gsd' from https://gsd.readthedocs.io/en/stable/objects.inv ... loading intersphinx inventory 'maplotlib' from https://matplotlib.org/stable/objects.inv ... loading intersphinx inventory 'griddataformats' from https://mdanalysis.org/GridDataFormats/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.h5py.org/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.h5py.org', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'networkx' from https://networkx.org/documentation/stable/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://gsd.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='gsd.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.scipy.org/doc/scipy/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.scipy.org', port=443): Max retries exceeded with url: /doc/scipy/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'pmda' from https://mdanalysis.org/pmda/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://mdanalysis.org/pmda/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /pmda/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'waterdynamics' from https://www.mdanalysis.org/waterdynamics/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://mdanalysis.org/GridDataFormats/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /GridDataFormats/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'parmed' from https://parmed.github.io/ParmEd/html/objects.inv ... loading intersphinx inventory 'rdkit' from https://rdkit.org/docs/objects.inv ... loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv ... loading intersphinx inventory 'pathsimanalysis' from https://www.mdanalysis.org/PathSimAnalysis/objects.inv ... loading intersphinx inventory 'dask' from https://docs.dask.org/en/stable/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://www.mdanalysis.org/waterdynamics/objects.inv' not fetchable due to : HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /waterdynamics/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.dask.org/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.dask.org', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'mdahole2' from https://www.mdanalysis.org/mdahole2/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://matplotlib.org/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='matplotlib.org', port=443): Max retries exceeded with url: /stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://www.mdanalysis.org/PathSimAnalysis/objects.inv' not fetchable due to : HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /PathSimAnalysis/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://networkx.org/documentation/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='networkx.org', port=443): Max retries exceeded with url: /documentation/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://rdkit.org/docs/objects.inv' not fetchable due to : HTTPSConnectionPool(host='rdkit.org', port=443): Max retries exceeded with url: /docs/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://numpy.org/doc/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='numpy.org', port=443): Max retries exceeded with url: /doc/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://parmed.github.io/ParmEd/html/objects.inv' not fetchable due to : HTTPSConnectionPool(host='parmed.github.io', port=443): Max retries exceeded with url: /ParmEd/html/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://www.mdanalysis.org/mdahole2/objects.inv' not fetchable due to : HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /mdahole2/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) locale_dir /build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 177 source files that are out of date updating environment: locale_dir /build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist [new config] 177 added, 0 changed, 0 removed reading sources... [ 1%] documentation_pages/analysis/align /usr/lib/python3/dist-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated. Due to the on going maintenance burden of keeping command line application wrappers up to date, we have decided to deprecate and eventually remove these modules. We instead now recommend building your command line and invoking it directly with the subprocess module. warnings.warn( reading sources... [ 1%] documentation_pages/analysis/atomicdistances reading sources... [ 2%] documentation_pages/analysis/backends reading sources... [ 2%] documentation_pages/analysis/base reading sources... [ 3%] documentation_pages/analysis/bat reading sources... [ 3%] documentation_pages/analysis/contacts reading sources... [ 4%] documentation_pages/analysis/data reading sources... [ 5%] documentation_pages/analysis/density reading sources... [ 5%] documentation_pages/analysis/dielectric reading sources... [ 6%] documentation_pages/analysis/diffusionmap reading sources... [ 6%] documentation_pages/analysis/dihedrals mkdir -p failed for path /nonexistent/first-build/.config/matplotlib: [Errno 13] Permission denied: '/nonexistent' Matplotlib created a temporary cache directory at /tmp/matplotlib-a626_uu3 because there was an issue with the default path (/nonexistent/first-build/.config/matplotlib); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. reading sources... [ 7%] documentation_pages/analysis/distances reading sources... [ 7%] documentation_pages/analysis/dssp reading sources... [ 8%] documentation_pages/analysis/encore reading sources... 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[ 13%] documentation_pages/analysis/hbond_autocorrel reading sources... [ 14%] documentation_pages/analysis/hbond_autocorrel_deprecated /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:54: DeprecationWarning: This module was moved to MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel; hbonds.hbond_autocorrel will be removed in 3.0.0. warnings.warn(wmsg, category=DeprecationWarning) reading sources... [ 14%] documentation_pages/analysis/helix_analysis reading sources... [ 15%] documentation_pages/analysis/hole2 /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/analysis/hole2/__init__.py:50: UserWarning: Please install the mdahole2 mdakit to use it in MDAnalysis. More details can be found here: https://www.mdanalysis.org/mdahole2/getting_started.html warnings.warn(wmsg, category=UserWarning) reading sources... 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[100%] index /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/analysis/dssp/dssp.py:docstring of MDAnalysis.analysis.dssp.dssp:25: WARNING: Explicit markup ends without a blank line; unexpected unindent. [docutils] WARNING: autodoc: failed to import module 'utils' from module 'MDAnalysis.analysis.hole2'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'MDAnalysis.analysis.hole2.utils'\n"] [autodoc.import_object] WARNING: autodoc: failed to import module 'templates' from module 'MDAnalysis.analysis.hole2'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'MDAnalysis.analysis.hole2.templates'\n"] [autodoc.import_object] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/core/universe.py:docstring of MDAnalysis.core.universe.Universe:127: WARNING: Definition list ends without a blank line; unexpected unindent. [docutils] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/core/universe.py:docstring of MDAnalysis.core.universe.Universe:127: WARNING: Inline strong start-string without end-string. [docutils] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/guesser/default_guesser.py:docstring of MDAnalysis.guesser.default_guesser.DefaultGuesser:5: ERROR: Unexpected indentation. [docutils] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/topology/ExtendedPDBParser.py:docstring of MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser:29: CRITICAL: Unexpected section title. See Also -------- [docutils] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/topology/TPRParser.py:docstring of MDAnalysis.topology.TPRParser:46: WARNING: Footnote [*] is not referenced. [ref.footnote] docstring of MDAnalysis.topology.tables.atomelements:3: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.atomelements:4: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] docstring of MDAnalysis.topology.tables.atomelements:7: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.atomelements:8: WARNING: Inline strong start-string without end-string. [docutils] docstring of MDAnalysis.topology.tables.masses:3: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.masses:4: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] docstring of MDAnalysis.topology.tables.masses:7: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.masses:8: WARNING: Inline strong start-string without end-string. [docutils] docstring of MDAnalysis.topology.tables.vdwradii:3: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.vdwradii:4: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] docstring of MDAnalysis.topology.tables.vdwradii:7: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.vdwradii:8: WARNING: Inline strong start-string without end-string. [docutils] looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... WARNING: unsupported theme option 'mda_official' given done copying assets... copying static files... Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/basic.css Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/alabaster.css copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [ 1%] documentation_pages/analysis/align writing output... [ 1%] documentation_pages/analysis/atomicdistances writing output... [ 2%] documentation_pages/analysis/backends writing output... [ 2%] documentation_pages/analysis/base writing output... [ 3%] documentation_pages/analysis/bat writing output... [ 3%] documentation_pages/analysis/contacts writing output... 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[100%] index /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.openany:3: WARNING: unknown keyword: 'with' [ref.keyword] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.anyopen:25: WARNING: unknown keyword: 'with' [ref.keyword] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.NamedStream:32: WARNING: unknown keyword: 'with' [ref.keyword] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.NamedStream:67: WARNING: unknown keyword: 'with' [ref.keyword] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.NamedStream:74: WARNING: unknown keyword: 'with' [ref.keyword] generating indices... genindex py-modindex done highlighting module code... 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[ 55%] MDAnalysis.coordinates.timestep highlighting module code... [ 55%] MDAnalysis.core._get_readers highlighting module code... [ 56%] MDAnalysis.core.accessors highlighting module code... [ 57%] MDAnalysis.core.groups highlighting module code... [ 57%] MDAnalysis.core.selection highlighting module code... [ 58%] MDAnalysis.core.topology highlighting module code... [ 59%] MDAnalysis.core.topologyattrs highlighting module code... [ 59%] MDAnalysis.core.topologyobjects highlighting module code... [ 60%] MDAnalysis.core.universe highlighting module code... [ 61%] MDAnalysis.exceptions highlighting module code... [ 61%] MDAnalysis.guesser.base highlighting module code... [ 62%] MDAnalysis.guesser.default_guesser highlighting module code... [ 62%] MDAnalysis.guesser.tables highlighting module code... [ 63%] MDAnalysis.lib.NeighborSearch highlighting module code... [ 64%] MDAnalysis.lib._augment highlighting module code... [ 64%] MDAnalysis.lib._cutil highlighting module code... [ 65%] MDAnalysis.lib.correlations highlighting module code... [ 66%] MDAnalysis.lib.distances highlighting module code... [ 66%] MDAnalysis.lib.formats.libdcd highlighting module code... [ 67%] MDAnalysis.lib.formats.libmdaxdr highlighting module code... [ 68%] MDAnalysis.lib.log highlighting module code... [ 68%] MDAnalysis.lib.mdamath highlighting module code... [ 69%] MDAnalysis.lib.nsgrid highlighting module code... [ 69%] MDAnalysis.lib.picklable_file_io highlighting module code... [ 70%] MDAnalysis.lib.pkdtree highlighting module code... [ 71%] MDAnalysis.lib.qcprot highlighting module code... [ 71%] MDAnalysis.lib.transformations highlighting module code... [ 72%] MDAnalysis.lib.util highlighting module code... [ 73%] MDAnalysis.selections highlighting module code... [ 73%] MDAnalysis.selections.base highlighting module code... [ 74%] MDAnalysis.selections.charmm highlighting module code... [ 75%] MDAnalysis.selections.gromacs highlighting module code... [ 75%] MDAnalysis.selections.jmol highlighting module code... [ 76%] MDAnalysis.selections.pymol highlighting module code... [ 76%] MDAnalysis.selections.vmd highlighting module code... [ 77%] MDAnalysis.topology.CRDParser highlighting module code... [ 78%] MDAnalysis.topology.DLPolyParser highlighting module code... [ 78%] MDAnalysis.topology.DMSParser highlighting module code... [ 79%] MDAnalysis.topology.ExtendedPDBParser highlighting module code... [ 80%] MDAnalysis.topology.FHIAIMSParser highlighting module code... [ 80%] MDAnalysis.topology.GMSParser highlighting module code... [ 81%] MDAnalysis.topology.GROParser highlighting module code... [ 82%] MDAnalysis.topology.GSDParser highlighting module code... [ 82%] MDAnalysis.topology.HoomdXMLParser highlighting module code... [ 83%] MDAnalysis.topology.ITPParser highlighting module code... [ 83%] MDAnalysis.topology.LAMMPSParser highlighting module code... [ 84%] MDAnalysis.topology.MMTFParser highlighting module code... [ 85%] MDAnalysis.topology.MOL2Parser highlighting module code... [ 85%] MDAnalysis.topology.MinimalParser highlighting module code... [ 86%] MDAnalysis.topology.PDBParser highlighting module code... [ 87%] MDAnalysis.topology.PDBQTParser highlighting module code... [ 87%] MDAnalysis.topology.PQRParser highlighting module code... [ 88%] MDAnalysis.topology.PSFParser highlighting module code... [ 89%] MDAnalysis.topology.TOPParser highlighting module code... [ 89%] MDAnalysis.topology.TPRParser highlighting module code... [ 90%] MDAnalysis.topology.TXYZParser highlighting module code... [ 90%] MDAnalysis.topology.XYZParser highlighting module code... [ 91%] MDAnalysis.topology.base highlighting module code... [ 92%] MDAnalysis.topology.tpr.obj highlighting module code... [ 92%] MDAnalysis.topology.tpr.utils highlighting module code... [ 93%] MDAnalysis.transformations.base highlighting module code... [ 94%] MDAnalysis.transformations.boxdimensions highlighting module code... [ 94%] MDAnalysis.transformations.fit highlighting module code... [ 95%] MDAnalysis.transformations.nojump highlighting module code... [ 96%] MDAnalysis.transformations.positionaveraging highlighting module code... [ 96%] MDAnalysis.transformations.rotate highlighting module code... [ 97%] MDAnalysis.transformations.translate highlighting module code... [ 97%] MDAnalysis.transformations.wrap highlighting module code... [ 98%] MDAnalysis.units highlighting module code... [ 99%] MDAnalysis.visualization.streamlines highlighting module code... [ 99%] MDAnalysis.visualization.streamlines_3D highlighting module code... [100%] builtins writing additional pages... search opensearch done copying images... [ 10%] images/rama_ref_plot.png copying images... [ 20%] images/janin_ref_plot.png copying images... [ 30%] images/rama_demo_plot.png copying images... [ 40%] images/janin_demo_plot.png copying images... [ 50%] images/msd_demo_plot.png copying images... [ 60%] images/AnalysisBase_parallel.png copying images... [ 70%] images/parallelization_time.png copying images... [ 80%] images/RSMD_plot.png copying images... [ 90%] documentation_pages/visualization/testing_streamline.png copying images... [100%] documentation_pages/visualization/test_streamplot_3D.png dumping search index in English (code: en)... done dumping object inventory... done sphinx-sitemap: sitemap.xml was generated for URL https://docs.mdanalysis.org/ in /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/sitemap.xml build succeeded, 41 warnings. The HTML pages are in ../../../.pybuild/html. Build finished. The HTML pages are in /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html. make[2]: Leaving directory '/build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx' make[1]: Leaving directory '/build/reproducible-path/mdanalysis-2.9.0' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild plugin_pyproject:178: Copying package built for python3.13 to destdir dh_installdocs -O--buildsystem=pybuild dh_installdocs: warning: Cannot auto-detect main package for python-mdanalysis-doc. If the default is wrong, please use --doc-main-package dh_sphinxdoc -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild debian/rules execute_after_dh_python3 make[1]: Entering directory '/build/reproducible-path/mdanalysis-2.9.0' dh_numpy3 Possible precedence issue with control flow operator (return) at /usr/bin/dh_numpy3 line 57. rm -rf debian/python3-mdanalysis/usr/lib/python3.* make[1]: Leaving directory '/build/reproducible-path/mdanalysis-2.9.0' dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package python-mdanalysis-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-mdanalysis' in '../python3-mdanalysis_2.9.0-12_amd64.deb'. dpkg-deb: building package 'python3-mdanalysis-dbgsym' in '../python3-mdanalysis-dbgsym_2.9.0-12_amd64.deb'. dpkg-deb: building package 'python-mdanalysis-doc' in '../python-mdanalysis-doc_2.9.0-12_all.deb'. dpkg-genbuildinfo --build=binary -O../mdanalysis_2.9.0-12_amd64.buildinfo dpkg-genchanges --build=binary -O../mdanalysis_2.9.0-12_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from mdanalysis-2.9.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1370099 and its subdirectories I: Current time: Sun Sep 14 14:16:37 -12 2025 I: pbuilder-time-stamp: 1757902597 Mon Sep 15 02:16:38 UTC 2025 I: 1st build successful. Starting 2nd build on remote node infom02-amd64.debian.net. Mon Sep 15 02:16:38 UTC 2025 I: Preparing to do remote build '2' on infom02-amd64.debian.net. Mon Sep 15 02:16:38 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Mon Sep 15 02:16:38 UTC 2025 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-5UFG7f' ==================================================================================== Sun Oct 18 08:39:39 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom02-amd64, called using "2 mdanalysis unstable /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN 2.9.0-12" as arguments. Sun Oct 18 08:39:39 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-zARnYr3t" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sun Oct 18 08:39:39 UTC 2026 I: Downloading source for unstable/mdanalysis=2.9.0-12 Reading package lists... NOTICE: 'mdanalysis' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/mdanalysis.git Please use: git clone https://salsa.debian.org/debichem-team/mdanalysis.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 61.0 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main mdanalysis 2.9.0-12 (dsc) [2945 B] Get:2 http://deb.debian.org/debian unstable/main mdanalysis 2.9.0-12 (tar) [61.0 MB] Get:3 http://deb.debian.org/debian unstable/main mdanalysis 2.9.0-12 (diff) [13.9 kB] Fetched 61.0 MB in 1s (98.9 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'mdanalysis' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/mdanalysis.git Please use: git clone https://salsa.debian.org/debichem-team/mdanalysis.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 61.0 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main mdanalysis 2.9.0-12 (dsc) [2945 B] Get:2 http://deb.debian.org/debian unstable/main mdanalysis 2.9.0-12 (tar) [61.0 MB] Get:3 http://deb.debian.org/debian unstable/main mdanalysis 2.9.0-12 (diff) [13.9 kB] Fetched 61.0 MB in 1s (98.9 MB/s) Download complete and in download only mode ============================================================================= Re-Building mdanalysis in unstable on amd64 on infom02-amd64 now. Date: Sun Oct 18 08:39:40 UTC 2026 Date UTC: Sun Oct 18 08:39:40 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/pbuilderrc_jLfq + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' mdanalysis = debian-installer -o mdanalysis = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' mdanalysis = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/pbuilderrc_jLfq --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/b2 --logfile b2/build.log mdanalysis_2.9.0-12.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Sun Oct 18 22:39:40 +14 2026 I: pbuilder-time-stamp: 1792312780 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [mdanalysis_2.9.0-12.dsc] I: copying [./mdanalysis_2.9.0.orig.tar.gz] I: copying [./mdanalysis_2.9.0-12.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.9.0-12.dsc: no acceptable signature found dpkg-source: info: extracting mdanalysis in mdanalysis-2.9.0 dpkg-source: info: unpacking mdanalysis_2.9.0.orig.tar.gz dpkg-source: info: unpacking mdanalysis_2.9.0-12.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying docs_use_built_module.patch dpkg-source: info: applying docs_sphinx_warnings_are_not_errors.patch dpkg-source: info: applying docs_local_mathjax.patch dpkg-source: info: applying doc_no_mdanalysis_sphinx.patch dpkg-source: info: applying improve_test_timeout_PR4584.diff dpkg-source: info: applying skip_gsd_tests.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2381421/tmp/hooks/D01_modify_environment starting debug: Running on infom02-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Oct 18 08:40 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2381421/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2381421/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.3.3(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=311c054c0c1d494ea11a28975f9f2bf3 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2381421 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/pbuilderrc_jLfq --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/b2 --logfile b2/build.log mdanalysis_2.9.0-12.dsc' SUDO_GID=109 SUDO_HOME=/var/lib/jenkins SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' I: uname -a Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2381421/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), cython3, dh-sequence-python3, pybuild-plugin-pyproject, python3-all-dev, python3-setuptools, python3-numpy, python3-biopython (>= 1.80), python3-networkx, python3-griddataformats, python3-mmtf, python3-joblib, python3-scipy, python3-matplotlib, python3-mda-xdrlib, python3-tqdm, python3-threadpoolctl, python3-packaging, python3-filelock, python3-fasteners, python3-gsd (>= 3.0.1~), python3-netcdf4, python3-h5py, python3-seaborn, python3-sklearn, python3-duecredit, python3-hypothesis, python3-pytest, python3-sphinx, python3-msmb-theme, python3-pybtex, python3-sphinx-rtd-theme, python3-sphinx-sitemap, python3-sphinxcontrib.bibtex, libjs-mathjax dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on pybuild-plugin-pyproject; however: Package pybuild-plugin-pyproject is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython (>= 1.80); however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-griddataformats; however: Package python3-griddataformats is not installed. pbuilder-satisfydepends-dummy depends on python3-mmtf; however: Package python3-mmtf is not installed. pbuilder-satisfydepends-dummy depends on python3-joblib; however: Package python3-joblib is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-mda-xdrlib; however: Package python3-mda-xdrlib is not installed. pbuilder-satisfydepends-dummy depends on python3-tqdm; however: Package python3-tqdm is not installed. pbuilder-satisfydepends-dummy depends on python3-threadpoolctl; however: Package python3-threadpoolctl is not installed. pbuilder-satisfydepends-dummy depends on python3-packaging; however: Package python3-packaging is not installed. pbuilder-satisfydepends-dummy depends on python3-filelock; however: Package python3-filelock is not installed. pbuilder-satisfydepends-dummy depends on python3-fasteners; however: Package python3-fasteners is not installed. pbuilder-satisfydepends-dummy depends on python3-gsd (>= 3.0.1~); however: Package python3-gsd is not installed. pbuilder-satisfydepends-dummy depends on python3-netcdf4; however: Package python3-netcdf4 is not installed. pbuilder-satisfydepends-dummy depends on python3-h5py; however: Package python3-h5py is not installed. pbuilder-satisfydepends-dummy depends on python3-seaborn; however: Package python3-seaborn is not installed. pbuilder-satisfydepends-dummy depends on python3-sklearn; however: Package python3-sklearn is not installed. pbuilder-satisfydepends-dummy depends on python3-duecredit; however: Package python3-duecredit is not installed. pbuilder-satisfydepends-dummy depends on python3-hypothesis; however: Package python3-hypothesis is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-msmb-theme; however: Package python3-msmb-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-pybtex; however: Package python3-pybtex is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-rtd-theme; however: Package python3-sphinx-rtd-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-sitemap; however: Package python3-sphinx-sitemap is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinxcontrib.bibtex; however: Package python3-sphinxcontrib.bibtex is not installed. pbuilder-satisfydepends-dummy depends on libjs-mathjax; however: Package libjs-mathjax is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} blt{a} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-font-awesome{a} fonts-lato{a} fonts-lyx{a} fonts-mathjax{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libabsl20240722{a} libaec0{a} libaom3{a} libarchive-zip-perl{a} libavif16{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdav1d7{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgcrypt20{a} libgfortran5{a} libglib2.0-0t64{a} libgnutls30t64{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhdf5-310{a} libhdf5-hl-310{a} libidn2-0{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} liblzf1{a} libmagic-mgc{a} libmagic1t64{a} libnetcdf22{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libopenjp2-7{a} libp11-kit0{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libraqm0{a} librav1e0.7{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{a} libsvtav1enc2{a} libsz2{a} libtasn1-6{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2-16{a} libxrender1{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} libyuv0{a} libzopfli1{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} procps{a} pybuild-plugin-pyproject{a} python-babel-localedata{a} python-matplotlib-data{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-attr{a} python3-autocommand{a} python3-babel{a} python3-biopython{a} python3-brotli{a} python3-build{a} python3-cairo{a} python3-certifi{a} python3-cftime{a} python3-chardet{a} python3-charset-normalizer{a} python3-citeproc{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-duecredit{a} python3-fasteners{a} python3-filelock{a} python3-fonttools{a} python3-freetype{a} python3-fs{a} python3-griddataformats{a} python3-gsd{a} python3-h5py{a} python3-h5py-serial{a} python3-hypothesis{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-iniconfig{a} python3-installer{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-joblib{a} python3-kiwisolver{a} python3-latexcodec{a} python3-looseversion{a} python3-lxml{a} python3-lz4{a} python3-markupsafe{a} python3-matplotlib{a} python3-mda-xdrlib{a} python3-minimal{a} python3-mmtf{a} python3-monotonic{a} python3-more-itertools{a} python3-mpmath{a} python3-mrcfile{a} python3-msgpack{a} python3-msmb-theme{a} python3-netcdf4{a} python3-networkx{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pluggy{a} python3-pybtex{a} python3-pybtex-docutils{a} python3-pygments{a} python3-pyparsing{a} python3-pyproject-hooks{a} python3-pytest{a} python3-pytz{a} python3-reportlab{a} python3-requests{a} python3-rlpycairo{a} python3-roman{a} python3-roman-numerals{a} python3-scipy{a} python3-seaborn{a} python3-setuptools{a} python3-sklearn{a} python3-sklearn-lib{a} python3-snowballstemmer{a} python3-sortedcontainers{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-sphinx-sitemap{a} python3-sphinxcontrib.bibtex{a} python3-sphinxcontrib.jquery{a} python3-sympy{a} python3-threadpoolctl{a} python3-tk{a} python3-tqdm{a} python3-typeguard{a} python3-typing-extensions{a} python3-ufolib2{a} python3-urllib3{a} python3-wheel{a} python3-yaml{a} python3-zipp{a} python3-zopfli{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} python3.13-tk{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-rtd-theme-common{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-dejavu-extra isympy-common javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libgpg-error-l10n libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules linux-sysctl-defaults lynx ncbi-blast+ psmisc publicsuffix python-biopython-doc python3-bottleneck python3-bs4 python3-click python3-cssselect python3-gdal python3-html5lib python3-numba python3-numexpr python3-odf python3-olefile python3-openpyxl python3-pooch python3-psutil python3-pydot python3-pygraphviz python3-tables python3-tz shared-mime-info wget xdg-user-dirs 0 packages upgraded, 272 newly installed, 0 to remove and 0 not upgraded. Need to get 203 MB of archives. After unpacking 833 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1.2 [142 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.2.4+ds-1.2 [5224 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.5.2-1 [1493 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20250419 [162 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1041 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.50-1 [282 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+25 [217 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 51 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2.4 [318 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2.4 [401 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.17-1 [794 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [591 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 blt amd64 2.5.3+dfsg-8 [5984 B] Get: 65 http://deb.debian.org/debian unstable/main amd64 cython3 amd64 3.0.11+dfsg-2+b1 [2504 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 72 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250414 [116 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 fonts-lyx all 2.4.4-1 [190 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libabsl20240722 amd64 20240722.0-4 [492 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.4-2 [23.8 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libaom3 amd64 3.12.1-1 [1871 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.1-1 [559 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libgav1-1 amd64 0.19.0-3+b1 [353 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 librav1e0.7 amd64 0.7.1-9+b2 [946 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libsvtav1enc2 amd64 2.3.0+dfsg-1 [2489 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libyuv0 amd64 0.0.1916.20250814-1 [172 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libavif16 amd64 1.3.0-1 [135 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 109 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.15.1-1 [140 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.15.1-1 [20.9 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.16.0-1 [431 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.16.0-1 [437 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.7.1-2 [161 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libgpg-error0 amd64 1.55-2 [88.1 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libgcrypt20 amd64 1.11.2-2 [865 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.84.4-3 [1518 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-7 [76.3 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 11.4.5-1 [505 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.4-2 [8108 B] Get: 132 http://deb.debian.org/debian unstable/main amd64 libhdf5-310 amd64 1.14.5+repack-4 [1448 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-4 [72.6 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 4.4.0-3 [251 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1 [319 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-6 [27.5 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 liblzf1 amd64 3.6-4+b3 [10.1 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libnetcdf22 amd64 1:4.9.3-1+b1 [517 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [204 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.7-1 [2162 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.7-1 [5279 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.7-1 [10.5 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.13.7-1 [1068 B] Get: 150 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-7 [248 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.3-1 [14.0 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.7.0-5 [364 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.43-0.2 [155 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libzopfli1 amd64 1.0.3-3 [106 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 python3-wheel all 0.46.1-2 [21.7 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 python3-build all 1.2.2-4 [36.2 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 pybuild-plugin-pyproject all 6.20250414 [11.8 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.17.0-1 [6050 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 python-matplotlib-data all 3.10.1+dfsg1-5 [2737 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.7-1 [1048 B] Get: 170 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.7-1 [504 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.7-1 [26.1 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.13.7-1 [1068 B] Get: 173 http://deb.debian.org/debian unstable/main amd64 python3-attr all 25.3.0-1 [69.5 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.17.0-1 [117 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.3-1 [131 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 python3.13-tk amd64 3.13.7-1 [108 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 python3-tk amd64 3.13.5-1 [9604 B] Get: 179 http://deb.debian.org/debian unstable/main amd64 python3-pil.imagetk amd64 11.3.0-1 [81.1 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 11.3.0-1 [526 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 python3-cairo amd64 1.27.0-2 [114 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 python3-freetype all 2.5.1-2 [89.4 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 184 http://deb.debian.org/debian unstable/main amd64 python3-reportlab all 4.4.3-1 [1168 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 python3-biopython amd64 1.85+dfsg-5 [1674 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 python3-brotli amd64 1.1.0-2+b7 [320 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 189 http://deb.debian.org/debian unstable/main amd64 python3-cftime amd64 1.6.4-2 [216 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 6.0.1-1 [1434 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 python3-citeproc all 0.8.3-1 [99.8 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 python3-contourpy amd64 1.3.1-2 [215 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 python3-cycler all 0.12.1-2 [9616 B] Get: 195 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-4 [79.4 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.2.1-2 [33.0 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 python3-roman all 5.1-1 [11.0 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 python3-looseversion all 1.3.0-3 [8964 B] Get: 201 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.10-1 [42.0 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.5.0-1 [116 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.5+dfsg-1 [72.4 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 python3-duecredit all 0.10.2-2 [70.6 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 python3-monotonic all 1.6-3 [5340 B] Get: 206 http://deb.debian.org/debian unstable/main amd64 python3-fasteners all 0.18-2 [14.0 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 python3-filelock all 3.19.1-1 [12.6 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 python3-platformdirs all 4.4.0-1 [16.7 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 python3-fs all 2.4.16-8 [95.2 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 python3-lz4 amd64 4.4.4+dfsg-1 [25.4 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.15.3-1.1 [17.0 MB] Get: 212 http://deb.debian.org/debian unstable/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 python3-sympy all 1.14.0-2 [4228 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.0 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 python3-zopfli amd64 0.2.3.post1-1+b1 [10.5 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 unicode-data all 16.0.0-1 [9197 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 python3-fonttools amd64 4.57.0-2 [1457 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1023 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 python3-mrcfile all 1.5.4-2 [118 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 python3-griddataformats all 1.0.2-2 [2048 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 python3-gsd amd64 4.0.0-1 [209 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 python3-h5py-serial amd64 3.14.0-3 [1157 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 python3-h5py all 3.14.0-3 [18.3 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 python3-hypothesis all 6.138.14-1 [364 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 227 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 232 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 238 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b3 [14.0 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.6-1 [107 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 python3-joblib all 1.4.2-5 [216 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 python3-kiwisolver amd64 1.4.7-3+b1 [62.0 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 python3-latexcodec all 3.0.0-1 [17.5 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib amd64 3.10.1+dfsg1-5 [23.8 MB] Get: 245 http://deb.debian.org/debian unstable/main amd64 python3-mda-xdrlib all 0.2.0-3 [11.6 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 python3-msgpack amd64 1.0.3-3+b4 [84.5 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 python3-mmtf all 1.1.3-1 [17.0 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 8.2.3-6 [619 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 python3-roman-numerals all 3.1.0-2 [8740 B] Get: 251 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 3.0.1-1 [63.5 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 8.2.3-6 [477 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.jquery all 4.1-6 [7496 B] Get: 254 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-rtd-theme all 3.0.2+dfsg-3 [29.7 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 python3-msmb-theme all 1.2.0-4 [33.8 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 python3-netcdf4 amd64 1.7.2-1+b4 [622 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 258 http://deb.debian.org/debian unstable/main amd64 python3-pytz all 2025.2-3 [152 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-9 [4595 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 python3-pandas all 2.2.3+dfsg-9 [3097 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.6.0-1 [27.1 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.2-2 [137 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 python3-pybtex all 0.25.1-1 [75.2 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 python3-pybtex-docutils all 1.0.3-1 [8224 B] Get: 265 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.4.2-1 [266 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 python3-seaborn all 0.13.2-5 [215 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 python3-sklearn-lib amd64 1.4.2+dfsg-8 [3980 kB] Get: 269 http://deb.debian.org/debian unstable/main amd64 python3-sklearn all 1.4.2+dfsg-8 [2248 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-sitemap all 2.6.0-1 [8508 B] Get: 271 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.bibtex all 2.6.5-2 [33.2 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 python3-tqdm all 4.67.1-5 [90.8 kB] Fetched 203 MB in 8s (27.0 MB/s) Preconfiguring packages ... Selecting previously unselected package fonts-lato. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.7-1_amd64.deb ... Unpacking python3.13-minimal (3.13.7-1) ... Setting up libpython3.13-minimal:amd64 (3.13.7-1) ... Setting up libexpat1:amd64 (2.7.1-2) ... Setting up python3.13-minimal (3.13.7-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20277 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-5_all.deb ... Unpacking tzdata (2025b-5) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.3-3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Oct 18 08:43:15 UTC 2026. Universal Time is now: Sun Oct 18 08:43:15 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (16.0.0-1) ... Setting up libfontenc1:amd64 (1:1.1.8-1+b2) ... Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libexpat1-dev:amd64 (2.7.1-2) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-4) ... Setting up libzopfli1 (1.0.3-3) ... Setting up libx11-data (2:1.8.12-1) ... Setting up libsvtav1enc2:amd64 (2.3.0+dfsg-1) ... Setting up liblzf1:amd64 (3.6-4+b3) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.16-1) ... 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Setting up libsz2:amd64 (1.1.4-2) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up libavif16:amd64 (1.3.0-1) ... Setting up liblapack3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-2+b1) ... Setting up libxrender1:amd64 (1:0.9.12-1) ... Setting up libtool (2.5.4-5) ... Setting up fontconfig-config (2.15.0-2.4) ... Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libidn2-0:amd64 (2.3.8-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up libglib2.0-0t64:amd64 (2.84.4-3) ... No schema files found: doing nothing. Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up sphinx-common (8.2.3-6) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libreadline8t64:amd64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up xml-core (0.19) ... Setting up libharfbuzz0b:amd64 (11.4.5-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-2.4) ... Setting up libpython3.13-stdlib:amd64 (3.13.7-1) ... Setting up libpython3-stdlib:amd64 (3.13.7-1) ... Setting up libpython3.13:amd64 (3.13.7-1) ... Setting up libgnutls30t64:amd64 (3.8.10-2) ... Setting up libxft2:amd64 (2.3.6-1+b4) ... Setting up python3.13 (3.13.7-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:amd64 (8.6.17-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.7-1) ... Setting up python3-sortedcontainers (2.4.0-2) ... Setting up python3-zipp (3.23.0-1) ... Setting up python3-freetype (2.5.1-2) ... Setting up xfonts-utils (1:7.7+7) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-markupsafe (2.1.5-1+b3) ... Setting up libcairo2:amd64 (1.18.4-1+b1) ... Setting up python3.13-tk (3.13.7-1) ... Setting up python3-mda-xdrlib (0.2.0-3) ... Setting up python3-platformdirs (4.4.0-1) ... Setting up python3-zopfli (0.2.3.post1-1+b1) ... Setting up python3-monotonic (1.6-3) ... Setting up python3-fs (2.4.16-8) ... Setting up python3-roman (5.1-1) ... Setting up python3-decorator (5.2.1-2) ... Setting up python3-jinja2 (3.1.6-1) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up python3-packaging (25.0-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-pyproject-hooks (1.2.0-1) ... 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Setting up python3-babel (2.17.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-lz4 (4.4.4+dfsg-1) ... Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-citeproc (0.8.3-1) ... Setting up python3-charset-normalizer (3.4.3-1) ... Setting up python3.13-dev (3.13.7-1) ... Setting up python3-pytest (8.4.2-1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up blt (2.5.3+dfsg-8) ... Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-9) ... Setting up python3-hypothesis (6.138.14-1) ... Setting up python3-tqdm (4.67.1-5) ... Setting up python3-typeguard (4.4.4-1) ... Setting up python3-threadpoolctl (3.1.0-1) ... Setting up libcurl3t64-gnutls:amd64 (8.16.0-1) ... Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-8) ... Setting up python3-latexcodec (3.0.0-1) ... Setting up python3-all (3.13.7-1) ... Setting up python3-yaml (6.0.2-2) ... Setting up python3-tk:amd64 (3.13.5-1) ... Setting up debhelper (13.26) ... Setting up python3-gsd (4.0.0-1) ... Setting up python3-pytz (2025.2-3) ... Setting up python3-mmtf (1.1.3-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-wheel (0.46.1-2) ... Setting up python3-pil:amd64 (11.3.0-1) ... Setting up python3-inflect (7.5.0-1) ... Setting up python3-griddataformats (1.0.2-2) ... Setting up python3-pandas (2.2.3+dfsg-9) ... Setting up python3-pil.imagetk:amd64 (11.3.0-1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up libpython3-all-dev:amd64 (3.13.7-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.7-1) ... Setting up python3-requests (2.32.5+dfsg-1) ... Setting up python3-sklearn (1.4.2+dfsg-8) ... Setting up python3-cftime (1.6.4-2) ... Setting up python3-reportlab (4.4.3-1) ... Setting up python3-pybtex (0.25.1-1) ... Setting up libhdf5-310:amd64 (1.14.5+repack-4) ... Setting up python3-build (1.2.2-4) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-all-dev (3.13.7-1) ... Setting up libhdf5-hl-310:amd64 (1.14.5+repack-4) ... Setting up python3-setuptools (78.1.1-0.1) ... Setting up python3-duecredit (0.10.2-2) ... Setting up pybuild-plugin-pyproject (6.20250414) ... Setting up libnetcdf22:amd64 (1:4.9.3-1+b1) ... Setting up python3-h5py-serial (3.14.0-3) ... Setting up python3-networkx (3.2.1-5) ... Setting up python3-h5py (3.14.0-3) ... Setting up python3-netcdf4 (1.7.2-1+b4) ... Setting up python3-fonttools (4.57.0-2) ... Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... Setting up python3-matplotlib (3.10.1+dfsg1-5) ... Setting up python3-seaborn (0.13.2-5) ... Processing triggers for libc-bin (2.41-12) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up docutils-common (0.21.2+dfsg-2) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.85+dfsg-5) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-pybtex-docutils (1.0.3-1) ... Setting up python3-sphinx (8.2.3-6) ... Setting up python3-sphinxcontrib.bibtex (2.6.5-2) ... Setting up python3-sphinx-sitemap (2.6.0-1) ... Setting up python3-sphinxcontrib.jquery (4.1-6) ... Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-3) ... Setting up python3-msmb-theme (1.2.0-4) ... Processing triggers for ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2381421/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/2381421/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/mdanalysis-2.9.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../mdanalysis_2.9.0-12_source.changes dpkg-buildpackage: info: source package mdanalysis dpkg-buildpackage: info: source version 2.9.0-12 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Drew Parsons dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from mdanalysis-2.9.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --with sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/mdanalysis-2.9.0' rm -f .duecredit.p rm -f package/MDAnalysis/authors.py rm -f package/MDAnalysis/analysis/encore/clustering/affinityprop.c \ package/MDAnalysis/analysis/encore/cutils.c \ package/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c \ package/MDAnalysis/coordinates/timestep.cpp \ package/MDAnalysis/lib/_augment.cpp \ package/MDAnalysis/lib/_cutil.cpp \ package/MDAnalysis/lib/c_distances.c \ package/MDAnalysis/lib/c_distances_openmp.c \ package/MDAnalysis/lib/formats/cython_util.c \ package/MDAnalysis/lib/formats/libdcd.c \ package/MDAnalysis/lib/formats/libmdaxdr.c \ package/MDAnalysis/lib/nsgrid.cpp \ package/MDAnalysis/lib/qcprot.c rm -rf package/MDAnalysis.egg-info rm -f testsuite/MDAnalysisTests/data/.*_offsets.npz testsuite/MDAnalysisTests/data/*/.*_offsets.npz rm -rf testsuite/.pytest_cache make[1]: Leaving directory '/build/reproducible-path/mdanalysis-2.9.0' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild dh_auto_build -O--buildsystem=pybuild I: pybuild plugin_pyproject:129: Building wheel for python3.13 with "build" module I: pybuild base:311: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis * Building wheel... performance hint: MDAnalysis/lib/c_distances.pyx:275:5: Exception check on '_minimum_image_orthogonal' will always require the GIL to be acquired. Possible solutions: 1. Declare '_minimum_image_orthogonal' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '_minimum_image_orthogonal' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:302:5: Exception check on '_minimum_image_triclinic' will always require the GIL to be acquired. Possible solutions: 1. Declare '_minimum_image_triclinic' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '_minimum_image_triclinic' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:390:37: Exception check after calling '__pyx_fuse_0_minimum_image_orthogonal' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_0_minimum_image_orthogonal' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_0_minimum_image_orthogonal' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:390:37: Exception check after calling '__pyx_fuse_1_minimum_image_orthogonal' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_1_minimum_image_orthogonal' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_1_minimum_image_orthogonal' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:414:36: Exception check after calling '__pyx_fuse_0_minimum_image_triclinic' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_0_minimum_image_triclinic' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_0_minimum_image_triclinic' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:414:36: Exception check after calling '__pyx_fuse_1_minimum_image_triclinic' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_1_minimum_image_triclinic' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_1_minimum_image_triclinic' to allow an error code to be returned. performance hint: MDAnalysis/lib/nsgrid.pyx:417:37: Exception check after calling 'coord2cellid' will always require the GIL to be acquired. Declare 'coord2cellid' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: MDAnalysis/lib/nsgrid.pyx:431:26: Exception check after calling 'coord2cellxyz' will always require the GIL to be acquired. Possible solutions: 1. Declare 'coord2cellxyz' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'coord2cellxyz' to allow an error code to be returned. performance hint: MDAnalysis/lib/nsgrid.pyx:559:34: Exception check after calling 'coord2cellxyz' will always require the GIL to be acquired. Possible solutions: 1. Declare 'coord2cellxyz' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'coord2cellxyz' to allow an error code to be returned. performance hint: MDAnalysis/lib/nsgrid.pyx:567:56: Exception check after calling 'cellxyz2cellid' will always require the GIL to be acquired. Declare 'cellxyz2cellid' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: MDAnalysis/lib/nsgrid.pyx:574:53: Exception check after calling 'calc_distsq' will always require the GIL to be acquired. Declare 'calc_distsq' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: MDAnalysis/lib/nsgrid.pyx:578:57: Exception check after calling 'add_neighbors' will always require the GIL to be acquired. Possible solutions: 1. Declare 'add_neighbors' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'add_neighbors' to allow an error code to be returned. Attempting to autodetect OpenMP support... Compiler supports OpenMP Will attempt to use Cython. Compiling MDAnalysis/lib/formats/libdcd.pyx because it changed. Compiling MDAnalysis/lib/c_distances.pyx because it changed. Compiling MDAnalysis/lib/c_distances_openmp.pyx because it changed. Compiling MDAnalysis/lib/qcprot.pyx because it changed. Compiling MDAnalysis/lib/formats/libmdaxdr.pyx because it changed. Compiling MDAnalysis/lib/formats/cython_util.pyx because it changed. Compiling MDAnalysis/analysis/encore/cutils.pyx because it changed. Compiling MDAnalysis/analysis/encore/clustering/affinityprop.pyx because it changed. Compiling MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx because it changed. Compiling MDAnalysis/lib/_cutil.pyx because it changed. Compiling MDAnalysis/lib/_augment.pyx because it changed. Compiling MDAnalysis/lib/nsgrid.pyx because it changed. Compiling MDAnalysis/coordinates/timestep.pyx because it changed. [ 1/13] Cythonizing MDAnalysis/analysis/encore/clustering/affinityprop.pyx [ 2/13] Cythonizing MDAnalysis/analysis/encore/cutils.pyx [ 3/13] Cythonizing MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx [ 4/13] Cythonizing MDAnalysis/coordinates/timestep.pyx [ 5/13] Cythonizing MDAnalysis/lib/_augment.pyx [ 6/13] Cythonizing MDAnalysis/lib/_cutil.pyx [ 7/13] Cythonizing MDAnalysis/lib/c_distances.pyx [ 8/13] Cythonizing MDAnalysis/lib/c_distances_openmp.pyx [ 9/13] Cythonizing MDAnalysis/lib/formats/cython_util.pyx [10/13] Cythonizing MDAnalysis/lib/formats/libdcd.pyx [11/13] Cythonizing MDAnalysis/lib/formats/libmdaxdr.pyx [12/13] Cythonizing MDAnalysis/lib/nsgrid.pyx [13/13] Cythonizing MDAnalysis/lib/qcprot.pyx /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! corresp(dist, value, root_dir) /usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! dist._finalize_license_expression() /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running bdist_wheel running build running build_py creating build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/due.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/authors.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/exceptions.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/units.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/version.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/results.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/density.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/contacts.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/backends.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/dielectric.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/rdf.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/msd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/nucleicacids.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/atomicdistances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/align.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/rms.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/bat.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/gnm.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/pca.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/psa.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/polymer.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/distances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis creating build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/RDKit.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters creating build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/chain.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRC.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/null.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TNG.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/memory.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates creating build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser copying MDAnalysis/guesser/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser copying MDAnalysis/guesser/tables.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser copying MDAnalysis/guesser/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser copying MDAnalysis/guesser/default_guesser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser creating build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/vmd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/pymol.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/gromacs.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/charmm.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/jmol.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections creating build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/EDR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/transformations.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/util.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/correlations.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/mdamath.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/log.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_distopia.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/distances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib creating build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/translate.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/nojump.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/fit.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/rotate.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/wrap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations creating build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/selection.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/topology.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/accessors.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/groups.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/_get_readers.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/universe.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core creating build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/GROParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/tables.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/guessers.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology creating build/lib.linux-x86_64-cpython-313/MDAnalysis/tests copying MDAnalysis/tests/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/tests copying MDAnalysis/tests/datafiles.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/tests creating build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization copying MDAnalysis/visualization/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp copying MDAnalysis/analysis/dssp/dssp.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp copying MDAnalysis/analysis/dssp/pydssp_numpy.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp copying MDAnalysis/analysis/dssp/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2 creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis copying MDAnalysis/lib/libmdanalysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include copying MDAnalysis/lib/include/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations creating build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source copying doc/sphinx/source/conf.py -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source running egg_info creating MDAnalysis.egg-info writing MDAnalysis.egg-info/PKG-INFO writing dependency_links to MDAnalysis.egg-info/dependency_links.txt writing requirements to MDAnalysis.egg-info/requires.txt writing top-level names to MDAnalysis.egg-info/top_level.txt writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/clustering/include/ap.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative reading manifest file 'MDAnalysis.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching 'doc/html/html' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.pyd' found anywhere in distribution warning: no previously-included files matching '*~' found anywhere in distribution warning: no previously-included files matching '.git' found anywhere in distribution adding license file 'LICENSE' adding license file 'AUTHORS' writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data copying doc/README -> build/lib.linux-x86_64-cpython-313/doc copying MDAnalysis/coordinates/timestep.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/lib/_augment.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_augment.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_cutil.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/qcprot.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/qcprot.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/analysis/encore/cutils.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include copying MDAnalysis/lib/formats/cython_util.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis copying MDAnalysis/lib/include/calc_distances.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include copying MDAnalysis/lib/formats/src/trr_seek.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/include/endianswap.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/fastio.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/readdcd.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/trr_seek.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xtc_seek.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations copying doc/sphinx/Makefile -> build/lib.linux-x86_64-cpython-313/doc/sphinx copying doc/sphinx/source/index.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source copying doc/sphinx/source/references.bib -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/AnalysisBase_parallel.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/RSMD_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/janin_demo_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/janin_ref_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/msd_demo_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/parallelization_time.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/rama_demo_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/rama_ref_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/analysis_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/auxiliary_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/converters.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/coordinates_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/core_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/exceptions.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/guesser_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/lib_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/overview.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/references.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/selections.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/selections_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/topology.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/topology_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/trajectory_transformations.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/units.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/version.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/visualization_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/align.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/atomicdistances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/backends.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/bat.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/contacts.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/data.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/density.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/dielectric.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/diffusionmap.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/dihedrals.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/distances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/dssp.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/encore.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/gnm.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel_deprecated.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/helix_analysis.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hole2.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hydrogenbonds.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/leaflet.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/legacy_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/lineardensity.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/msd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/nucleicacids.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/nuclinfo.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/parallelization.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/pca.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/polymer.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/psa.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/rdf.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/results.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/rms.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/waterdynamics.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/wbridge_analysis.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/OpenMM.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/ParmEd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/RDKit.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/CRD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/DCD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/DLPoly.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/DMS.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/FHIAIMS.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/GMS.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/GRO.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/GSD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/H5MD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/INPCRD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/LAMMPS.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/MMTF.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/MOL2.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/NAMDBIN.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/PDB.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/PDBQT.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/PQR.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TNG.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRC.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRJ.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRR.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRZ.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TXYZ.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/XDR.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/XTC.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/XYZ.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/chain.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/chemfiles.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/core.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/memory.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/null.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/pickle_readers.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/timestep.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/charmm.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/gromacs.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/jmol.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/pymol.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/vmd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/EDR.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/XVG.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/core.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/c_distances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/correlations.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/distances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/log.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/mdamath.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/nsgrid.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/picklable_file_io.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/pkdtree.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/qcprot.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/transformations.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/util.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/fit.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/nojump.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/positionaveraging.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/rotate.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/translate.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/wrap.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/default_guesser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/tables.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/accessors.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/groups.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/selection.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/topology.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/topologyattrs.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/topologyobjects.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/universe.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/CRDParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/DMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/GMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/GROParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/GSDParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/ITPParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/MMTFParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/MinimalParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PDBParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PQRParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PSFParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/TOPParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/TPRParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/TXYZParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/XYZParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/core.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/guessers.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/tables.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/tpr_util.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/streamlines.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/streamlines_3D.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/test_streamplot_3D.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/testing_streamline.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/bootstrap.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/clustering.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/confdistmatrix.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/covariance.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/dimensionality_reduction.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/similarity.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/utils.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy copying doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats copying doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats copying doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats running build_ext building 'MDAnalysis.lib.formats.libdcd' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/usr/include/python3.13 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/formats/libdcd.c:1261: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib.c_distances' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include -I/usr/include/python3.13 -c MDAnalysis/lib/c_distances.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/c_distances.c:1263: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.o -L/usr/lib/x86_64-linux-gnu -lm -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib.c_distances_openmp' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPARALLEL -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include -I/usr/include/python3.13 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/c_distances_openmp.c:1272: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.o -L/usr/lib/x86_64-linux-gnu -lm -lgomp -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.cpython-313-x86_64-linux-gnu.so -fopenmp building 'MDAnalysis.lib.qcprot' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/lib/qcprot.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/qcprot.c:1255: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib._transformations' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/transformations.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/src/transformations/transformations.c:73: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/transformations.o -L/usr/lib/x86_64-linux-gnu -lm -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_transformations.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib.formats.libmdaxdr' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/formats/libmdaxdr.c:1282: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/trr_seek.o -std=c11 -O3 -funroll-loops -fsigned-zeros x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile.o -std=c11 -O3 -funroll-loops -fsigned-zeros x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/xdrfile_trr.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_trr.o -std=c11 -O3 -funroll-loops -fsigned-zeros x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/xdrfile_xtc.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_xtc.o -std=c11 -O3 -funroll-loops -fsigned-zeros x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/xtc_seek.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xtc_seek.o -std=c11 -O3 -funroll-loops -fsigned-zeros x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/trr_seek.o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile.o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_trr.o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_xtc.o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xtc_seek.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib.formats.cython_util' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/lib/formats/cython_util.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/formats/cython_util.c:1272: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.analysis.encore.cutils' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/cutils.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.o -std=c11 -funroll-loops -fsigned-zeros -O3 In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/analysis/encore/cutils.c:1255: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering creating build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/clustering/affinityprop.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.o -std=c11 -funroll-loops -fsigned-zeros -O3 In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/analysis/encore/clustering/affinityprop.c:1261: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/clustering/src/ap.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src/ap.o -std=c11 -funroll-loops -fsigned-zeros -O3 x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.o build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src/ap.o -L/usr/lib/x86_64-linux-gnu -lm -o build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -std=c11 -funroll-loops -fsigned-zeros -O3 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -std=c11 -funroll-loops -fsigned-zeros -O3 In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:1261: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o build/temp.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -L/usr/lib/x86_64-linux-gnu -lm -o build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib._cutil' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include -I/usr/include/python3.13 -c MDAnalysis/lib/_cutil.cpp -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.o -O3 -funroll-loops -fsigned-zeros -std=c++11 In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/_cutil.cpp:1273: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.o -L/usr/lib/x86_64-linux-gnu -lm -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib._augment' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/lib/_augment.cpp -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.o -O3 -funroll-loops -fsigned-zeros -std=c++11 In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/_augment.cpp:1268: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib.nsgrid' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include -I/usr/include/python3.13 -c MDAnalysis/lib/nsgrid.cpp -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.o -O3 -funroll-loops -fsigned-zeros -std=c++11 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.coordinates.timestep' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/coordinates x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/coordinates/timestep.cpp -o build/temp.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.o -O3 -funroll-loops -fsigned-zeros -std=c++11 In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/coordinates/timestep.cpp:1269: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.cpython-313-x86_64-linux-gnu.so installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/MDAnalysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/results.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/density.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/contacts.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dihedrals.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/backends.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dielectric.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/rdf.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/data copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/janin_ref_data.npy -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/msd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/dssp copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp/dssp.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/dssp copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp/pydssp_numpy.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/dssp copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/dssp creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hbonds creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src/ap.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include/ap.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/similarity.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/covariance.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/nucleicacids.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/atomicdistances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/align.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/rms.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/bat.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/legacy copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/legacy copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/legacy creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hole2 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hole2 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/helix_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/gnm.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/pca.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/psa.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/polymer.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/distances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/ParmEd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/RDKitParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/RDKit.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/ParmEdParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/OpenMMParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/OpenMM.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters creating build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TXYZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/ParmEd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/H5MD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/chain.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/XDR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRC.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/NAMDBIN.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/null.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TNG.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/memory.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates creating build/bdist.linux-x86_64/wheel/MDAnalysis/guesser copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/tables.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/default_guesser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser creating build/bdist.linux-x86_64/wheel/MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/vmd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/pymol.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/gromacs.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/charmm.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/jmol.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections creating build/bdist.linux-x86_64/wheel/MDAnalysis/auxiliary copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/EDR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary copying build/lib.linux-x86_64-cpython-313/MDAnalysis/due.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xtc_seek.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/trr_seek.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/readdcd.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/endianswap.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/trr_seek.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/fastio.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xtc_seek.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xdrfile.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/src creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/src/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/LICENCE -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/AUTHOR -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/transformations.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/transformations.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_transformations.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/util.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/correlations.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/mdamath.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/picklable_file_io.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/libmdanalysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/libmdanalysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/libmdanalysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/log.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include/calc_distances.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_distopia.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/distances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib copying build/lib.linux-x86_64-cpython-313/MDAnalysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/authors.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/translate.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/nojump.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/fit.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/boxdimensions.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/rotate.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/wrap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/exceptions.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/selection.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/topology.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/accessors.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/groups.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/_get_readers.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/universe.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-313/MDAnalysis/units.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/GROParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/ITPParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology creating build/bdist.linux-x86_64/wheel/MDAnalysis/topology/tpr copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/setting.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/ParmEdParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tables.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/FHIAIMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/guessers.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-313/MDAnalysis/version.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/tests copying build/lib.linux-x86_64-cpython-313/MDAnalysis/tests/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/tests copying build/lib.linux-x86_64-cpython-313/MDAnalysis/tests/datafiles.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/tests creating build/bdist.linux-x86_64/wheel/MDAnalysis/visualization copying build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization copying build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization copying build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization creating build/bdist.linux-x86_64/wheel/doc creating build/bdist.linux-x86_64/wheel/doc/sphinx copying build/lib.linux-x86_64-cpython-313/doc/sphinx/Makefile -> build/bdist.linux-x86_64/wheel/./doc/sphinx creating build/bdist.linux-x86_64/wheel/doc/sphinx/source copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/conf.py -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/index.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/AnalysisBase_parallel.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/rama_ref_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/msd_demo_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/janin_demo_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/RSMD_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/janin_ref_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/rama_demo_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/parallelization_time.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/references.bib -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/data.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/lineardensity.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/align.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/backends.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/nucleicacids.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/msd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/dihedrals.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/dssp.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/density.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/rdf.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/waterdynamics.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/helix_analysis.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/bat.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/results.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/bootstrap.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/dimensionality_reduction.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/utils.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/similarity.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/confdistmatrix.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/covariance.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/clustering.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/pca.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/parallelization.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hole2.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/distances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/nuclinfo.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/atomicdistances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel_deprecated.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/diffusionmap.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/wbridge_analysis.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/leaflet.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/analysis/legacy copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/legacy copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/rms.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/polymer.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/dielectric.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/gnm.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/psa.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hydrogenbonds.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/contacts.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/converters copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/RDKit.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/ParmEd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/OpenMM.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRR.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/FHIAIMS.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/MMTF.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/LAMMPS.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRJ.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/CRD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/PQR.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/NAMDBIN.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/PDBQT.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/timestep.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/H5MD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/DMS.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/DCD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/GRO.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/PDB.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/XTC.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/GSD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/null.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/memory.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/XDR.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRZ.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/pickle_readers.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRC.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/chemfiles.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/MOL2.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TXYZ.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/chain.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TNG.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/GMS.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/DLPoly.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/core.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/INPCRD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/XYZ.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/exceptions.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/references.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/selections copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/jmol.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/gromacs.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/pymol.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/vmd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/charmm.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/auxiliary copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/XVG.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/EDR.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/core.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/lib creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/lib/formats copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib/formats copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib/formats copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/c_distances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/log.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/correlations.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/transformations.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/nsgrid.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/picklable_file_io.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/distances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/util.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/pkdtree.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/qcprot.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/mdamath.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/units.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/nojump.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/wrap.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/translate.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/rotate.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/positionaveraging.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/fit.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/trajectory_transformations.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/guesser_modules copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/default_guesser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/tables.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/topologyobjects.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/groups.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/selection.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/accessors.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/universe.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/topology.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/topologyattrs.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/overview.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/MMTFParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/GMSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/CRDParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/TOPParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/TXYZParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/TPRParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/MinimalParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/DMSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/tpr_util.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PQRParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PSFParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/ITPParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/tables.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/guessers.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/XYZParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/core.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/GROParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/GSDParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PDBParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/version.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/visualization copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/streamlines_3D.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/test_streamplot_3D.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/testing_streamline.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/streamlines.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization copying build/lib.linux-x86_64-cpython-313/doc/README -> build/bdist.linux-x86_64/wheel/./doc running install_egg_info Copying MDAnalysis.egg-info to build/bdist.linux-x86_64/wheel/./MDAnalysis-2.9.0.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/mdanalysis-2.9.0.dist-info/WHEEL creating '/build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/.tmp-hek2oo9o/mdanalysis-2.9.0-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'MDAnalysis/__init__.py' adding 'MDAnalysis/authors.py' adding 'MDAnalysis/due.py' adding 'MDAnalysis/exceptions.py' adding 'MDAnalysis/units.py' adding 'MDAnalysis/version.py' adding 'MDAnalysis/analysis/__init__.py' adding 'MDAnalysis/analysis/align.py' adding 'MDAnalysis/analysis/atomicdistances.py' adding 'MDAnalysis/analysis/backends.py' adding 'MDAnalysis/analysis/base.py' adding 'MDAnalysis/analysis/bat.py' adding 'MDAnalysis/analysis/contacts.py' adding 'MDAnalysis/analysis/density.py' adding 'MDAnalysis/analysis/dielectric.py' adding 'MDAnalysis/analysis/diffusionmap.py' adding 'MDAnalysis/analysis/dihedrals.py' adding 'MDAnalysis/analysis/distances.py' adding 'MDAnalysis/analysis/gnm.py' adding 'MDAnalysis/analysis/helix_analysis.py' adding 'MDAnalysis/analysis/leaflet.py' adding 'MDAnalysis/analysis/lineardensity.py' adding 'MDAnalysis/analysis/msd.py' adding 'MDAnalysis/analysis/nucleicacids.py' adding 'MDAnalysis/analysis/nuclinfo.py' adding 'MDAnalysis/analysis/pca.py' adding 'MDAnalysis/analysis/polymer.py' adding 'MDAnalysis/analysis/psa.py' adding 'MDAnalysis/analysis/rdf.py' adding 'MDAnalysis/analysis/results.py' adding 'MDAnalysis/analysis/rms.py' adding 'MDAnalysis/analysis/waterdynamics.py' adding 'MDAnalysis/analysis/data/__init__.py' adding 'MDAnalysis/analysis/data/filenames.py' adding 'MDAnalysis/analysis/data/janin_ref_data.npy' adding 'MDAnalysis/analysis/data/rama_ref_data.npy' adding 'MDAnalysis/analysis/dssp/__init__.py' adding 'MDAnalysis/analysis/dssp/dssp.py' adding 'MDAnalysis/analysis/dssp/pydssp_numpy.py' adding 'MDAnalysis/analysis/encore/__init__.py' adding 'MDAnalysis/analysis/encore/bootstrap.py' adding 'MDAnalysis/analysis/encore/confdistmatrix.py' adding 'MDAnalysis/analysis/encore/covariance.py' adding 'MDAnalysis/analysis/encore/cutils.c' adding 'MDAnalysis/analysis/encore/cutils.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/analysis/encore/cutils.pyx' adding 'MDAnalysis/analysis/encore/similarity.py' adding 'MDAnalysis/analysis/encore/utils.py' adding 'MDAnalysis/analysis/encore/clustering/ClusterCollection.py' adding 'MDAnalysis/analysis/encore/clustering/ClusteringMethod.py' adding 'MDAnalysis/analysis/encore/clustering/__init__.py' adding 'MDAnalysis/analysis/encore/clustering/affinityprop.c' adding 'MDAnalysis/analysis/encore/clustering/affinityprop.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/analysis/encore/clustering/affinityprop.pyx' adding 'MDAnalysis/analysis/encore/clustering/cluster.py' adding 'MDAnalysis/analysis/encore/clustering/include/ap.h' adding 'MDAnalysis/analysis/encore/clustering/src/ap.c' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c' adding 'MDAnalysis/analysis/hbonds/__init__.py' adding 'MDAnalysis/analysis/hbonds/hbond_autocorrel.py' adding 'MDAnalysis/analysis/hole2/__init__.py' adding 'MDAnalysis/analysis/hydrogenbonds/__init__.py' adding 'MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py' adding 'MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py' adding 'MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py' adding 'MDAnalysis/analysis/legacy/__init__.py' adding 'MDAnalysis/analysis/legacy/x3dna.py' adding 'MDAnalysis/auxiliary/EDR.py' adding 'MDAnalysis/auxiliary/XVG.py' adding 'MDAnalysis/auxiliary/__init__.py' adding 'MDAnalysis/auxiliary/base.py' adding 'MDAnalysis/auxiliary/core.py' adding 'MDAnalysis/converters/OpenMM.py' adding 'MDAnalysis/converters/OpenMMParser.py' adding 'MDAnalysis/converters/ParmEd.py' adding 'MDAnalysis/converters/ParmEdParser.py' adding 'MDAnalysis/converters/RDKit.py' adding 'MDAnalysis/converters/RDKitParser.py' adding 'MDAnalysis/converters/__init__.py' adding 'MDAnalysis/converters/base.py' adding 'MDAnalysis/coordinates/CRD.py' adding 'MDAnalysis/coordinates/DCD.py' adding 'MDAnalysis/coordinates/DLPoly.py' adding 'MDAnalysis/coordinates/DMS.py' adding 'MDAnalysis/coordinates/FHIAIMS.py' adding 'MDAnalysis/coordinates/GMS.py' adding 'MDAnalysis/coordinates/GRO.py' adding 'MDAnalysis/coordinates/GSD.py' adding 'MDAnalysis/coordinates/H5MD.py' adding 'MDAnalysis/coordinates/INPCRD.py' adding 'MDAnalysis/coordinates/LAMMPS.py' adding 'MDAnalysis/coordinates/MMTF.py' adding 'MDAnalysis/coordinates/MOL2.py' adding 'MDAnalysis/coordinates/NAMDBIN.py' adding 'MDAnalysis/coordinates/PDB.py' adding 'MDAnalysis/coordinates/PDBQT.py' adding 'MDAnalysis/coordinates/PQR.py' adding 'MDAnalysis/coordinates/ParmEd.py' adding 'MDAnalysis/coordinates/TNG.py' adding 'MDAnalysis/coordinates/TRC.py' adding 'MDAnalysis/coordinates/TRJ.py' adding 'MDAnalysis/coordinates/TRR.py' adding 'MDAnalysis/coordinates/TRZ.py' adding 'MDAnalysis/coordinates/TXYZ.py' adding 'MDAnalysis/coordinates/XDR.py' adding 'MDAnalysis/coordinates/XTC.py' adding 'MDAnalysis/coordinates/XYZ.py' adding 'MDAnalysis/coordinates/__init__.py' adding 'MDAnalysis/coordinates/base.py' adding 'MDAnalysis/coordinates/chain.py' adding 'MDAnalysis/coordinates/chemfiles.py' adding 'MDAnalysis/coordinates/core.py' adding 'MDAnalysis/coordinates/memory.py' adding 'MDAnalysis/coordinates/null.py' adding 'MDAnalysis/coordinates/timestep.cpp' adding 'MDAnalysis/coordinates/timestep.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/coordinates/timestep.pxd' adding 'MDAnalysis/coordinates/timestep.pyx' adding 'MDAnalysis/core/__init__.py' adding 'MDAnalysis/core/_get_readers.py' adding 'MDAnalysis/core/accessors.py' adding 'MDAnalysis/core/groups.py' adding 'MDAnalysis/core/selection.py' adding 'MDAnalysis/core/topology.py' adding 'MDAnalysis/core/topologyattrs.py' adding 'MDAnalysis/core/topologyobjects.py' adding 'MDAnalysis/core/universe.py' adding 'MDAnalysis/guesser/__init__.py' adding 'MDAnalysis/guesser/base.py' adding 'MDAnalysis/guesser/default_guesser.py' adding 'MDAnalysis/guesser/tables.py' adding 'MDAnalysis/lib/NeighborSearch.py' adding 'MDAnalysis/lib/__init__.py' adding 'MDAnalysis/lib/_augment.cpp' adding 'MDAnalysis/lib/_augment.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/_augment.pyx' adding 'MDAnalysis/lib/_cutil.cpp' adding 'MDAnalysis/lib/_cutil.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/_cutil.pxd' adding 'MDAnalysis/lib/_cutil.pyx' adding 'MDAnalysis/lib/_distopia.py' adding 'MDAnalysis/lib/_transformations.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/c_distances.c' adding 'MDAnalysis/lib/c_distances.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/c_distances.pxd' adding 'MDAnalysis/lib/c_distances.pyx' adding 'MDAnalysis/lib/c_distances_openmp.c' adding 'MDAnalysis/lib/c_distances_openmp.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/c_distances_openmp.pyx' adding 'MDAnalysis/lib/correlations.py' adding 'MDAnalysis/lib/distances.py' adding 'MDAnalysis/lib/log.py' adding 'MDAnalysis/lib/mdamath.py' adding 'MDAnalysis/lib/nsgrid.cpp' adding 'MDAnalysis/lib/nsgrid.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/nsgrid.pyx' adding 'MDAnalysis/lib/picklable_file_io.py' adding 'MDAnalysis/lib/pkdtree.py' adding 'MDAnalysis/lib/qcprot.c' adding 'MDAnalysis/lib/qcprot.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/qcprot.pyx' adding 'MDAnalysis/lib/transformations.py' adding 'MDAnalysis/lib/util.py' adding 'MDAnalysis/lib/formats/__init__.py' adding 'MDAnalysis/lib/formats/cython_util.c' adding 'MDAnalysis/lib/formats/cython_util.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/formats/cython_util.pxd' adding 'MDAnalysis/lib/formats/cython_util.pyx' adding 'MDAnalysis/lib/formats/libdcd.c' adding 'MDAnalysis/lib/formats/libdcd.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/formats/libdcd.pxd' adding 'MDAnalysis/lib/formats/libdcd.pyx' adding 'MDAnalysis/lib/formats/libmdaxdr.c' adding 'MDAnalysis/lib/formats/libmdaxdr.cpython-313-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/formats/libmdaxdr.pxd' adding 'MDAnalysis/lib/formats/libmdaxdr.pyx' adding 'MDAnalysis/lib/formats/include/__init__.py' adding 'MDAnalysis/lib/formats/include/endianswap.h' adding 'MDAnalysis/lib/formats/include/fastio.h' adding 'MDAnalysis/lib/formats/include/readdcd.h' adding 'MDAnalysis/lib/formats/include/trr_seek.h' adding 'MDAnalysis/lib/formats/include/xdrfile.h' adding 'MDAnalysis/lib/formats/include/xdrfile_trr.h' adding 'MDAnalysis/lib/formats/include/xdrfile_xtc.h' adding 'MDAnalysis/lib/formats/include/xtc_seek.h' adding 'MDAnalysis/lib/formats/src/__init__.py' adding 'MDAnalysis/lib/formats/src/trr_seek.c' adding 'MDAnalysis/lib/formats/src/xdrfile.c' adding 'MDAnalysis/lib/formats/src/xdrfile_trr.c' adding 'MDAnalysis/lib/formats/src/xdrfile_xtc.c' adding 'MDAnalysis/lib/formats/src/xtc_seek.c' adding 'MDAnalysis/lib/include/__init__.py' adding 'MDAnalysis/lib/include/calc_distances.h' adding 'MDAnalysis/lib/libmdanalysis/__init__.pxd' adding 'MDAnalysis/lib/libmdanalysis/__init__.py' adding 'MDAnalysis/lib/src/transformations/AUTHOR' adding 'MDAnalysis/lib/src/transformations/LICENCE' adding 'MDAnalysis/lib/src/transformations/__init__.py' adding 'MDAnalysis/lib/src/transformations/transformations.c' adding 'MDAnalysis/selections/__init__.py' adding 'MDAnalysis/selections/base.py' adding 'MDAnalysis/selections/charmm.py' adding 'MDAnalysis/selections/gromacs.py' adding 'MDAnalysis/selections/jmol.py' adding 'MDAnalysis/selections/pymol.py' adding 'MDAnalysis/selections/vmd.py' adding 'MDAnalysis/tests/__init__.py' adding 'MDAnalysis/tests/datafiles.py' adding 'MDAnalysis/topology/CRDParser.py' adding 'MDAnalysis/topology/DLPolyParser.py' adding 'MDAnalysis/topology/DMSParser.py' adding 'MDAnalysis/topology/ExtendedPDBParser.py' adding 'MDAnalysis/topology/FHIAIMSParser.py' adding 'MDAnalysis/topology/GMSParser.py' adding 'MDAnalysis/topology/GROParser.py' adding 'MDAnalysis/topology/GSDParser.py' adding 'MDAnalysis/topology/HoomdXMLParser.py' adding 'MDAnalysis/topology/ITPParser.py' adding 'MDAnalysis/topology/LAMMPSParser.py' adding 'MDAnalysis/topology/MMTFParser.py' adding 'MDAnalysis/topology/MOL2Parser.py' adding 'MDAnalysis/topology/MinimalParser.py' adding 'MDAnalysis/topology/PDBParser.py' adding 'MDAnalysis/topology/PDBQTParser.py' adding 'MDAnalysis/topology/PQRParser.py' adding 'MDAnalysis/topology/PSFParser.py' adding 'MDAnalysis/topology/ParmEdParser.py' adding 'MDAnalysis/topology/TOPParser.py' adding 'MDAnalysis/topology/TPRParser.py' adding 'MDAnalysis/topology/TXYZParser.py' adding 'MDAnalysis/topology/XYZParser.py' adding 'MDAnalysis/topology/__init__.py' adding 'MDAnalysis/topology/base.py' adding 'MDAnalysis/topology/core.py' adding 'MDAnalysis/topology/guessers.py' adding 'MDAnalysis/topology/tables.py' adding 'MDAnalysis/topology/tpr/__init__.py' adding 'MDAnalysis/topology/tpr/obj.py' adding 'MDAnalysis/topology/tpr/setting.py' adding 'MDAnalysis/topology/tpr/utils.py' adding 'MDAnalysis/transformations/__init__.py' adding 'MDAnalysis/transformations/base.py' adding 'MDAnalysis/transformations/boxdimensions.py' adding 'MDAnalysis/transformations/fit.py' adding 'MDAnalysis/transformations/nojump.py' adding 'MDAnalysis/transformations/positionaveraging.py' adding 'MDAnalysis/transformations/rotate.py' adding 'MDAnalysis/transformations/translate.py' adding 'MDAnalysis/transformations/wrap.py' adding 'MDAnalysis/visualization/__init__.py' adding 'MDAnalysis/visualization/streamlines.py' adding 'MDAnalysis/visualization/streamlines_3D.py' adding 'doc/README' adding 'doc/sphinx/Makefile' adding 'doc/sphinx/source/conf.py' adding 'doc/sphinx/source/index.rst' adding 'doc/sphinx/source/references.bib' adding 'doc/sphinx/source/documentation_pages/analysis_modules.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary_modules.rst' adding 'doc/sphinx/source/documentation_pages/converters.rst' adding 'doc/sphinx/source/documentation_pages/coordinates_modules.rst' adding 'doc/sphinx/source/documentation_pages/core_modules.rst' adding 'doc/sphinx/source/documentation_pages/exceptions.rst' adding 'doc/sphinx/source/documentation_pages/guesser_modules.rst' adding 'doc/sphinx/source/documentation_pages/lib_modules.rst' adding 'doc/sphinx/source/documentation_pages/overview.rst' adding 'doc/sphinx/source/documentation_pages/references.rst' adding 'doc/sphinx/source/documentation_pages/selections.rst' adding 'doc/sphinx/source/documentation_pages/selections_modules.rst' adding 'doc/sphinx/source/documentation_pages/topology.rst' adding 'doc/sphinx/source/documentation_pages/topology_modules.rst' adding 'doc/sphinx/source/documentation_pages/trajectory_transformations.rst' adding 'doc/sphinx/source/documentation_pages/units.rst' adding 'doc/sphinx/source/documentation_pages/version.rst' adding 'doc/sphinx/source/documentation_pages/visualization_modules.rst' adding 'doc/sphinx/source/documentation_pages/analysis/align.rst' adding 'doc/sphinx/source/documentation_pages/analysis/atomicdistances.rst' adding 'doc/sphinx/source/documentation_pages/analysis/backends.rst' adding 'doc/sphinx/source/documentation_pages/analysis/base.rst' adding 'doc/sphinx/source/documentation_pages/analysis/bat.rst' adding 'doc/sphinx/source/documentation_pages/analysis/contacts.rst' adding 'doc/sphinx/source/documentation_pages/analysis/data.rst' adding 'doc/sphinx/source/documentation_pages/analysis/density.rst' adding 'doc/sphinx/source/documentation_pages/analysis/dielectric.rst' adding 'doc/sphinx/source/documentation_pages/analysis/diffusionmap.rst' adding 'doc/sphinx/source/documentation_pages/analysis/dihedrals.rst' adding 'doc/sphinx/source/documentation_pages/analysis/distances.rst' adding 'doc/sphinx/source/documentation_pages/analysis/dssp.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore.rst' adding 'doc/sphinx/source/documentation_pages/analysis/gnm.rst' adding 'doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel.rst' adding 'doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel_deprecated.rst' adding 'doc/sphinx/source/documentation_pages/analysis/helix_analysis.rst' adding 'doc/sphinx/source/documentation_pages/analysis/hole2.rst' adding 'doc/sphinx/source/documentation_pages/analysis/hydrogenbonds.rst' adding 'doc/sphinx/source/documentation_pages/analysis/leaflet.rst' adding 'doc/sphinx/source/documentation_pages/analysis/legacy_modules.rst' adding 'doc/sphinx/source/documentation_pages/analysis/lineardensity.rst' adding 'doc/sphinx/source/documentation_pages/analysis/msd.rst' adding 'doc/sphinx/source/documentation_pages/analysis/nucleicacids.rst' adding 'doc/sphinx/source/documentation_pages/analysis/nuclinfo.rst' adding 'doc/sphinx/source/documentation_pages/analysis/parallelization.rst' adding 'doc/sphinx/source/documentation_pages/analysis/pca.rst' adding 'doc/sphinx/source/documentation_pages/analysis/polymer.rst' adding 'doc/sphinx/source/documentation_pages/analysis/psa.rst' adding 'doc/sphinx/source/documentation_pages/analysis/rdf.rst' adding 'doc/sphinx/source/documentation_pages/analysis/results.rst' adding 'doc/sphinx/source/documentation_pages/analysis/rms.rst' adding 'doc/sphinx/source/documentation_pages/analysis/waterdynamics.rst' adding 'doc/sphinx/source/documentation_pages/analysis/wbridge_analysis.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/bootstrap.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/clustering.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/confdistmatrix.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/covariance.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/dimensionality_reduction.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/similarity.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/utils.rst' adding 'doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary/EDR.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary/XVG.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary/base.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary/core.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary/init.rst' adding 'doc/sphinx/source/documentation_pages/converters/OpenMM.rst' adding 'doc/sphinx/source/documentation_pages/converters/ParmEd.rst' adding 'doc/sphinx/source/documentation_pages/converters/RDKit.rst' adding 'doc/sphinx/source/documentation_pages/converters/base.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/CRD.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/DCD.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/DLPoly.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/DMS.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/FHIAIMS.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/GMS.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/GRO.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/GSD.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/H5MD.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/INPCRD.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/LAMMPS.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/MMTF.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/MOL2.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/NAMDBIN.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/PDB.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/PDBQT.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/PQR.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TNG.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TRC.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TRJ.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TRR.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TRZ.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TXYZ.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/XDR.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/XTC.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/XYZ.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/base.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/chain.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/chemfiles.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/core.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/init.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/memory.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/null.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/pickle_readers.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/timestep.rst' adding 'doc/sphinx/source/documentation_pages/core/accessors.rst' adding 'doc/sphinx/source/documentation_pages/core/groups.rst' adding 'doc/sphinx/source/documentation_pages/core/init.rst' adding 'doc/sphinx/source/documentation_pages/core/selection.rst' adding 'doc/sphinx/source/documentation_pages/core/topology.rst' adding 'doc/sphinx/source/documentation_pages/core/topologyattrs.rst' adding 'doc/sphinx/source/documentation_pages/core/topologyobjects.rst' adding 'doc/sphinx/source/documentation_pages/core/universe.rst' adding 'doc/sphinx/source/documentation_pages/guesser_modules/base.rst' adding 'doc/sphinx/source/documentation_pages/guesser_modules/default_guesser.rst' adding 'doc/sphinx/source/documentation_pages/guesser_modules/init.rst' adding 'doc/sphinx/source/documentation_pages/guesser_modules/tables.rst' adding 'doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst' adding 'doc/sphinx/source/documentation_pages/lib/c_distances.rst' adding 'doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst' adding 'doc/sphinx/source/documentation_pages/lib/correlations.rst' adding 'doc/sphinx/source/documentation_pages/lib/distances.rst' adding 'doc/sphinx/source/documentation_pages/lib/log.rst' adding 'doc/sphinx/source/documentation_pages/lib/mdamath.rst' adding 'doc/sphinx/source/documentation_pages/lib/nsgrid.rst' adding 'doc/sphinx/source/documentation_pages/lib/picklable_file_io.rst' adding 'doc/sphinx/source/documentation_pages/lib/pkdtree.rst' adding 'doc/sphinx/source/documentation_pages/lib/qcprot.rst' adding 'doc/sphinx/source/documentation_pages/lib/transformations.rst' adding 'doc/sphinx/source/documentation_pages/lib/util.rst' adding 'doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst' adding 'doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst' adding 'doc/sphinx/source/documentation_pages/selections/base.rst' adding 'doc/sphinx/source/documentation_pages/selections/charmm.rst' adding 'doc/sphinx/source/documentation_pages/selections/gromacs.rst' adding 'doc/sphinx/source/documentation_pages/selections/jmol.rst' adding 'doc/sphinx/source/documentation_pages/selections/pymol.rst' adding 'doc/sphinx/source/documentation_pages/selections/vmd.rst' adding 'doc/sphinx/source/documentation_pages/topology/CRDParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/DMSParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/GMSParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/GROParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/GSDParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/ITPParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/MMTFParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst' adding 'doc/sphinx/source/documentation_pages/topology/MinimalParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/PDBParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/PQRParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/PSFParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/TOPParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/TPRParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/TXYZParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/XYZParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/base.rst' adding 'doc/sphinx/source/documentation_pages/topology/core.rst' adding 'doc/sphinx/source/documentation_pages/topology/guessers.rst' adding 'doc/sphinx/source/documentation_pages/topology/init.rst' adding 'doc/sphinx/source/documentation_pages/topology/tables.rst' adding 'doc/sphinx/source/documentation_pages/topology/tpr_util.rst' adding 'doc/sphinx/source/documentation_pages/transformations/base.rst' adding 'doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst' adding 'doc/sphinx/source/documentation_pages/transformations/fit.rst' adding 'doc/sphinx/source/documentation_pages/transformations/nojump.rst' adding 'doc/sphinx/source/documentation_pages/transformations/positionaveraging.rst' adding 'doc/sphinx/source/documentation_pages/transformations/rotate.rst' adding 'doc/sphinx/source/documentation_pages/transformations/translate.rst' adding 'doc/sphinx/source/documentation_pages/transformations/wrap.rst' adding 'doc/sphinx/source/documentation_pages/visualization/streamlines.rst' adding 'doc/sphinx/source/documentation_pages/visualization/streamlines_3D.rst' adding 'doc/sphinx/source/documentation_pages/visualization/test_streamplot_3D.png' adding 'doc/sphinx/source/documentation_pages/visualization/testing_streamline.png' adding 'doc/sphinx/source/images/AnalysisBase_parallel.png' adding 'doc/sphinx/source/images/RSMD_plot.png' adding 'doc/sphinx/source/images/janin_demo_plot.png' adding 'doc/sphinx/source/images/janin_ref_plot.png' adding 'doc/sphinx/source/images/msd_demo_plot.png' adding 'doc/sphinx/source/images/parallelization_time.png' adding 'doc/sphinx/source/images/rama_demo_plot.png' adding 'doc/sphinx/source/images/rama_ref_plot.png' adding 'mdanalysis-2.9.0.dist-info/licenses/AUTHORS' adding 'mdanalysis-2.9.0.dist-info/licenses/LICENSE' adding 'mdanalysis-2.9.0.dist-info/METADATA' adding 'mdanalysis-2.9.0.dist-info/WHEEL' adding 'mdanalysis-2.9.0.dist-info/top_level.txt' adding 'mdanalysis-2.9.0.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Successfully built mdanalysis-2.9.0-cp313-cp313-linux_x86_64.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.13 with "installer" module debian/rules execute_after_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/mdanalysis-2.9.0' PYTHONPATH=/build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build make html -C package/doc/sphinx/ BUILDDIR=/build/reproducible-path/mdanalysis-2.9.0/.pybuild # HTML generator make[2]: Entering directory '/build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx' sphinx-build -v -b html source /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html Running Sphinx v8.2.3 loading translations [en]... locale_dir /build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist locale_dir /build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist done Original exception: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/sphinx/registry.py", line 541, in load_extension mod = import_module(extname) File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module return _bootstrap._gcd_import(name[level:], package, level) ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "", line 1387, in _gcd_import File "", line 1360, in _find_and_load File "", line 1324, in _find_and_load_unlocked ModuleNotFoundError: No module named 'sphinxcontrib.applehelp' Original exception: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/sphinx/registry.py", line 541, in load_extension mod = import_module(extname) File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module return _bootstrap._gcd_import(name[level:], package, level) ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "", line 1387, in _gcd_import File "", line 1360, in _find_and_load File "", line 1324, in _find_and_load_unlocked ModuleNotFoundError: No module named 'sphinxcontrib.devhelp' Original exception: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/sphinx/registry.py", line 541, in load_extension mod = import_module(extname) File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module return _bootstrap._gcd_import(name[level:], package, level) ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "", line 1387, in _gcd_import File "", line 1360, in _find_and_load File "", line 1324, in _find_and_load_unlocked ModuleNotFoundError: No module named 'sphinxcontrib.htmlhelp' Original exception: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/sphinx/registry.py", line 541, in load_extension mod = import_module(extname) File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module return _bootstrap._gcd_import(name[level:], package, level) ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "", line 1387, in _gcd_import File "", line 1360, in _find_and_load File "", line 1324, in _find_and_load_unlocked ModuleNotFoundError: No module named 'sphinxcontrib.serializinghtml' Original exception: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/sphinx/registry.py", line 541, in load_extension mod = import_module(extname) File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module return _bootstrap._gcd_import(name[level:], package, level) ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "", line 1387, in _gcd_import File "", line 1360, in _find_and_load File "", line 1324, in _find_and_load_unlocked ModuleNotFoundError: No module named 'sphinxcontrib.qthelp' making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. checking bibtex cache... out of date parsing bibtex file /build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx/source/references.bib... parsed 69 entries locale_dir /build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist loading intersphinx inventory 'h5py' from https://docs.h5py.org/en/stable/objects.inv ... loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv ... loading intersphinx inventory 'scipy' from https://docs.scipy.org/doc/scipy/objects.inv ... loading intersphinx inventory 'gsd' from https://gsd.readthedocs.io/en/stable/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.h5py.org/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.h5py.org', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.scipy.org/doc/scipy/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.scipy.org', port=443): Max retries exceeded with url: /doc/scipy/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'griddataformats' from https://mdanalysis.org/GridDataFormats/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://gsd.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='gsd.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'networkx' from https://networkx.org/documentation/stable/objects.inv ... loading intersphinx inventory 'pmda' from https://mdanalysis.org/pmda/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://networkx.org/documentation/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='networkx.org', port=443): Max retries exceeded with url: /documentation/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://mdanalysis.org/GridDataFormats/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /GridDataFormats/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'maplotlib' from https://matplotlib.org/stable/objects.inv ... loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv ... loading intersphinx inventory 'rdkit' from https://rdkit.org/docs/objects.inv ... loading intersphinx inventory 'parmed' from https://parmed.github.io/ParmEd/html/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://mdanalysis.org/pmda/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /pmda/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://numpy.org/doc/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='numpy.org', port=443): Max retries exceeded with url: /doc/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'pathsimanalysis' from https://www.mdanalysis.org/PathSimAnalysis/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://rdkit.org/docs/objects.inv' not fetchable due to : HTTPSConnectionPool(host='rdkit.org', port=443): Max retries exceeded with url: /docs/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'waterdynamics' from https://www.mdanalysis.org/waterdynamics/objects.inv ... loading intersphinx inventory 'dask' from https://docs.dask.org/en/stable/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://matplotlib.org/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='matplotlib.org', port=443): Max retries exceeded with url: /stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://parmed.github.io/ParmEd/html/objects.inv' not fetchable due to : HTTPSConnectionPool(host='parmed.github.io', port=443): Max retries exceeded with url: /ParmEd/html/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'mdahole2' from https://www.mdanalysis.org/mdahole2/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://www.mdanalysis.org/waterdynamics/objects.inv' not fetchable due to : HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /waterdynamics/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://www.mdanalysis.org/PathSimAnalysis/objects.inv' not fetchable due to : HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /PathSimAnalysis/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://www.mdanalysis.org/mdahole2/objects.inv' not fetchable due to : HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /mdahole2/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.dask.org/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.dask.org', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) locale_dir /build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 177 source files that are out of date updating environment: locale_dir /build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist [new config] 177 added, 0 changed, 0 removed reading sources... [ 1%] documentation_pages/analysis/align /usr/lib/python3/dist-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated. Due to the on going maintenance burden of keeping command line application wrappers up to date, we have decided to deprecate and eventually remove these modules. We instead now recommend building your command line and invoking it directly with the subprocess module. warnings.warn( reading sources... [ 1%] documentation_pages/analysis/atomicdistances reading sources... [ 2%] documentation_pages/analysis/backends reading sources... [ 2%] documentation_pages/analysis/base reading sources... [ 3%] documentation_pages/analysis/bat reading sources... [ 3%] documentation_pages/analysis/contacts reading sources... [ 4%] documentation_pages/analysis/data reading sources... [ 5%] documentation_pages/analysis/density reading sources... [ 5%] documentation_pages/analysis/dielectric reading sources... [ 6%] documentation_pages/analysis/diffusionmap reading sources... [ 6%] documentation_pages/analysis/dihedrals mkdir -p failed for path /nonexistent/second-build/.config/matplotlib: [Errno 13] Permission denied: '/nonexistent' Matplotlib created a temporary cache directory at /tmp/matplotlib-oinpuc9u because there was an issue with the default path (/nonexistent/second-build/.config/matplotlib); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. reading sources... [ 7%] documentation_pages/analysis/distances reading sources... [ 7%] documentation_pages/analysis/dssp reading sources... [ 8%] documentation_pages/analysis/encore reading sources... [ 8%] documentation_pages/analysis/encore/bootstrap /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/analysis/encore/__init__.py:45: DeprecationWarning: Deprecation in version 2.8.0 MDAnalysis.analysis.encore is deprecated in favour of the MDAKit mdaencore (https://www.mdanalysis.org/mdaencore/) and will be removed in MDAnalysis version 3.0.0. warnings.warn(wmsg, category=DeprecationWarning) reading sources... [ 9%] documentation_pages/analysis/encore/clustering reading sources... [ 10%] documentation_pages/analysis/encore/confdistmatrix reading sources... [ 10%] documentation_pages/analysis/encore/covariance reading sources... [ 11%] documentation_pages/analysis/encore/dimensionality_reduction reading sources... [ 11%] documentation_pages/analysis/encore/similarity reading sources... [ 12%] documentation_pages/analysis/encore/utils reading sources... [ 12%] documentation_pages/analysis/gnm reading sources... [ 13%] documentation_pages/analysis/hbond_autocorrel reading sources... [ 14%] documentation_pages/analysis/hbond_autocorrel_deprecated /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:54: DeprecationWarning: This module was moved to MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel; hbonds.hbond_autocorrel will be removed in 3.0.0. warnings.warn(wmsg, category=DeprecationWarning) reading sources... [ 14%] documentation_pages/analysis/helix_analysis reading sources... [ 15%] documentation_pages/analysis/hole2 /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/analysis/hole2/__init__.py:50: UserWarning: Please install the mdahole2 mdakit to use it in MDAnalysis. More details can be found here: https://www.mdanalysis.org/mdahole2/getting_started.html warnings.warn(wmsg, category=UserWarning) reading sources... 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[100%] index /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/analysis/dssp/dssp.py:docstring of MDAnalysis.analysis.dssp.dssp:25: WARNING: Explicit markup ends without a blank line; unexpected unindent. [docutils] WARNING: autodoc: failed to import module 'utils' from module 'MDAnalysis.analysis.hole2'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'MDAnalysis.analysis.hole2.utils'\n"] [autodoc.import_object] WARNING: autodoc: failed to import module 'templates' from module 'MDAnalysis.analysis.hole2'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'MDAnalysis.analysis.hole2.templates'\n"] [autodoc.import_object] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/core/universe.py:docstring of MDAnalysis.core.universe.Universe:127: WARNING: Definition list ends without a blank line; unexpected unindent. [docutils] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/core/universe.py:docstring of MDAnalysis.core.universe.Universe:127: WARNING: Inline strong start-string without end-string. [docutils] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/guesser/default_guesser.py:docstring of MDAnalysis.guesser.default_guesser.DefaultGuesser:5: ERROR: Unexpected indentation. [docutils] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/topology/ExtendedPDBParser.py:docstring of MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser:29: CRITICAL: Unexpected section title. See Also -------- [docutils] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/topology/TPRParser.py:docstring of MDAnalysis.topology.TPRParser:46: WARNING: Footnote [*] is not referenced. [ref.footnote] docstring of MDAnalysis.topology.tables.atomelements:3: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.atomelements:4: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] docstring of MDAnalysis.topology.tables.atomelements:7: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.atomelements:8: WARNING: Inline strong start-string without end-string. [docutils] docstring of MDAnalysis.topology.tables.masses:3: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.masses:4: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] docstring of MDAnalysis.topology.tables.masses:7: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.masses:8: WARNING: Inline strong start-string without end-string. [docutils] docstring of MDAnalysis.topology.tables.vdwradii:3: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.vdwradii:4: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] docstring of MDAnalysis.topology.tables.vdwradii:7: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.vdwradii:8: WARNING: Inline strong start-string without end-string. [docutils] looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... WARNING: unsupported theme option 'mda_official' given done copying assets... copying static files... Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/basic.css Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/alabaster.css copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [ 1%] documentation_pages/analysis/align writing output... [ 1%] documentation_pages/analysis/atomicdistances writing output... [ 2%] documentation_pages/analysis/backends writing output... [ 2%] documentation_pages/analysis/base writing output... [ 3%] documentation_pages/analysis/bat writing output... [ 3%] documentation_pages/analysis/contacts writing output... 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[100%] index /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.openany:3: WARNING: unknown keyword: 'with' [ref.keyword] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.anyopen:25: WARNING: unknown keyword: 'with' [ref.keyword] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.NamedStream:32: WARNING: unknown keyword: 'with' [ref.keyword] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.NamedStream:67: WARNING: unknown keyword: 'with' [ref.keyword] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.NamedStream:74: WARNING: unknown keyword: 'with' [ref.keyword] generating indices... genindex py-modindex done highlighting module code... 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[ 36%] MDAnalysis.coordinates.DLPoly highlighting module code... [ 36%] MDAnalysis.coordinates.DMS highlighting module code... [ 37%] MDAnalysis.coordinates.FHIAIMS highlighting module code... [ 38%] MDAnalysis.coordinates.GMS highlighting module code... [ 38%] MDAnalysis.coordinates.GRO highlighting module code... [ 39%] MDAnalysis.coordinates.GSD highlighting module code... [ 39%] MDAnalysis.coordinates.H5MD highlighting module code... [ 40%] MDAnalysis.coordinates.INPCRD highlighting module code... [ 41%] MDAnalysis.coordinates.LAMMPS highlighting module code... [ 41%] MDAnalysis.coordinates.MMTF highlighting module code... [ 42%] MDAnalysis.coordinates.MOL2 highlighting module code... [ 43%] MDAnalysis.coordinates.NAMDBIN highlighting module code... [ 43%] MDAnalysis.coordinates.PDB highlighting module code... [ 44%] MDAnalysis.coordinates.PDBQT highlighting module code... [ 45%] MDAnalysis.coordinates.PQR highlighting module code... [ 45%] MDAnalysis.coordinates.TNG highlighting module code... [ 46%] MDAnalysis.coordinates.TRC highlighting module code... [ 46%] MDAnalysis.coordinates.TRJ highlighting module code... [ 47%] MDAnalysis.coordinates.TRR highlighting module code... [ 48%] MDAnalysis.coordinates.TRZ highlighting module code... [ 48%] MDAnalysis.coordinates.TXYZ highlighting module code... [ 49%] MDAnalysis.coordinates.XDR highlighting module code... [ 50%] MDAnalysis.coordinates.XTC highlighting module code... [ 50%] MDAnalysis.coordinates.XYZ highlighting module code... [ 51%] MDAnalysis.coordinates.base highlighting module code... [ 52%] MDAnalysis.coordinates.chain highlighting module code... [ 52%] MDAnalysis.coordinates.chemfiles highlighting module code... [ 53%] MDAnalysis.coordinates.core highlighting module code... [ 54%] MDAnalysis.coordinates.memory highlighting module code... [ 54%] MDAnalysis.coordinates.null highlighting module code... [ 55%] MDAnalysis.coordinates.timestep highlighting module code... [ 55%] MDAnalysis.core._get_readers highlighting module code... [ 56%] MDAnalysis.core.accessors highlighting module code... [ 57%] MDAnalysis.core.groups highlighting module code... [ 57%] MDAnalysis.core.selection highlighting module code... [ 58%] MDAnalysis.core.topology highlighting module code... [ 59%] MDAnalysis.core.topologyattrs highlighting module code... [ 59%] MDAnalysis.core.topologyobjects highlighting module code... [ 60%] MDAnalysis.core.universe highlighting module code... [ 61%] MDAnalysis.exceptions highlighting module code... [ 61%] MDAnalysis.guesser.base highlighting module code... [ 62%] MDAnalysis.guesser.default_guesser highlighting module code... [ 62%] MDAnalysis.guesser.tables highlighting module code... [ 63%] MDAnalysis.lib.NeighborSearch highlighting module code... [ 64%] MDAnalysis.lib._augment highlighting module code... [ 64%] MDAnalysis.lib._cutil highlighting module code... [ 65%] MDAnalysis.lib.correlations highlighting module code... [ 66%] MDAnalysis.lib.distances highlighting module code... [ 66%] MDAnalysis.lib.formats.libdcd highlighting module code... [ 67%] MDAnalysis.lib.formats.libmdaxdr highlighting module code... [ 68%] MDAnalysis.lib.log highlighting module code... [ 68%] MDAnalysis.lib.mdamath highlighting module code... [ 69%] MDAnalysis.lib.nsgrid highlighting module code... [ 69%] MDAnalysis.lib.picklable_file_io highlighting module code... [ 70%] MDAnalysis.lib.pkdtree highlighting module code... [ 71%] MDAnalysis.lib.qcprot highlighting module code... [ 71%] MDAnalysis.lib.transformations highlighting module code... [ 72%] MDAnalysis.lib.util highlighting module code... [ 73%] MDAnalysis.selections highlighting module code... [ 73%] MDAnalysis.selections.base highlighting module code... [ 74%] MDAnalysis.selections.charmm highlighting module code... [ 75%] MDAnalysis.selections.gromacs highlighting module code... [ 75%] MDAnalysis.selections.jmol highlighting module code... [ 76%] MDAnalysis.selections.pymol highlighting module code... [ 76%] MDAnalysis.selections.vmd highlighting module code... [ 77%] MDAnalysis.topology.CRDParser highlighting module code... [ 78%] MDAnalysis.topology.DLPolyParser highlighting module code... [ 78%] MDAnalysis.topology.DMSParser highlighting module code... [ 79%] MDAnalysis.topology.ExtendedPDBParser highlighting module code... [ 80%] MDAnalysis.topology.FHIAIMSParser highlighting module code... [ 80%] MDAnalysis.topology.GMSParser highlighting module code... [ 81%] MDAnalysis.topology.GROParser highlighting module code... [ 82%] MDAnalysis.topology.GSDParser highlighting module code... [ 82%] MDAnalysis.topology.HoomdXMLParser highlighting module code... [ 83%] MDAnalysis.topology.ITPParser highlighting module code... [ 83%] MDAnalysis.topology.LAMMPSParser highlighting module code... [ 84%] MDAnalysis.topology.MMTFParser highlighting module code... [ 85%] MDAnalysis.topology.MOL2Parser highlighting module code... [ 85%] MDAnalysis.topology.MinimalParser highlighting module code... [ 86%] MDAnalysis.topology.PDBParser highlighting module code... [ 87%] MDAnalysis.topology.PDBQTParser highlighting module code... [ 87%] MDAnalysis.topology.PQRParser highlighting module code... [ 88%] MDAnalysis.topology.PSFParser highlighting module code... [ 89%] MDAnalysis.topology.TOPParser highlighting module code... [ 89%] MDAnalysis.topology.TPRParser highlighting module code... [ 90%] MDAnalysis.topology.TXYZParser highlighting module code... [ 90%] MDAnalysis.topology.XYZParser highlighting module code... [ 91%] MDAnalysis.topology.base highlighting module code... [ 92%] MDAnalysis.topology.tpr.obj highlighting module code... [ 92%] MDAnalysis.topology.tpr.utils highlighting module code... [ 93%] MDAnalysis.transformations.base highlighting module code... [ 94%] MDAnalysis.transformations.boxdimensions highlighting module code... [ 94%] MDAnalysis.transformations.fit highlighting module code... [ 95%] MDAnalysis.transformations.nojump highlighting module code... [ 96%] MDAnalysis.transformations.positionaveraging highlighting module code... [ 96%] MDAnalysis.transformations.rotate highlighting module code... [ 97%] MDAnalysis.transformations.translate highlighting module code... [ 97%] MDAnalysis.transformations.wrap highlighting module code... [ 98%] MDAnalysis.units highlighting module code... [ 99%] MDAnalysis.visualization.streamlines highlighting module code... [ 99%] MDAnalysis.visualization.streamlines_3D highlighting module code... [100%] builtins writing additional pages... search opensearch done copying images... [ 10%] images/rama_ref_plot.png copying images... [ 20%] images/janin_ref_plot.png copying images... [ 30%] images/rama_demo_plot.png copying images... [ 40%] images/janin_demo_plot.png copying images... [ 50%] images/msd_demo_plot.png copying images... [ 60%] images/AnalysisBase_parallel.png copying images... [ 70%] images/parallelization_time.png copying images... [ 80%] images/RSMD_plot.png copying images... [ 90%] documentation_pages/visualization/testing_streamline.png copying images... [100%] documentation_pages/visualization/test_streamplot_3D.png dumping search index in English (code: en)... done dumping object inventory... done sphinx-sitemap: sitemap.xml was generated for URL https://docs.mdanalysis.org/ in /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/sitemap.xml build succeeded, 41 warnings. The HTML pages are in ../../../.pybuild/html. Build finished. The HTML pages are in /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html. make[2]: Leaving directory '/build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx' make[1]: Leaving directory '/build/reproducible-path/mdanalysis-2.9.0' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild plugin_pyproject:178: Copying package built for python3.13 to destdir dh_installdocs -O--buildsystem=pybuild dh_installdocs: warning: Cannot auto-detect main package for python-mdanalysis-doc. If the default is wrong, please use --doc-main-package dh_sphinxdoc -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild debian/rules execute_after_dh_python3 make[1]: Entering directory '/build/reproducible-path/mdanalysis-2.9.0' dh_numpy3 Possible precedence issue with control flow operator (return) at /usr/bin/dh_numpy3 line 57. rm -rf debian/python3-mdanalysis/usr/lib/python3.* make[1]: Leaving directory '/build/reproducible-path/mdanalysis-2.9.0' dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package python-mdanalysis-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-mdanalysis' in '../python3-mdanalysis_2.9.0-12_amd64.deb'. dpkg-deb: building package 'python-mdanalysis-doc' in '../python-mdanalysis-doc_2.9.0-12_all.deb'. dpkg-deb: building package 'python3-mdanalysis-dbgsym' in '../python3-mdanalysis-dbgsym_2.9.0-12_amd64.deb'. dpkg-genbuildinfo --build=binary -O../mdanalysis_2.9.0-12_amd64.buildinfo dpkg-genchanges --build=binary -O../mdanalysis_2.9.0-12_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from mdanalysis-2.9.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2381421/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2381421/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2381421 and its subdirectories I: Current time: Sun Oct 18 22:48:19 +14 2026 I: pbuilder-time-stamp: 1792313299 + false + set +x Sun Oct 18 08:48:19 UTC 2026 I: Signing ./b2/mdanalysis_2.9.0-12_amd64.buildinfo as mdanalysis_2.9.0-12_amd64.buildinfo.asc Sun Oct 18 08:48:19 UTC 2026 I: Signed ./b2/mdanalysis_2.9.0-12_amd64.buildinfo as ./b2/mdanalysis_2.9.0-12_amd64.buildinfo.asc Sun Oct 18 08:48:19 UTC 2026 - build #2 for mdanalysis/unstable/amd64 on infom02-amd64 done. Starting cleanup. All cleanup done. Sun Oct 18 08:48:19 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-zARnYr3t, removing. /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN: total 392 drwxrwxr-x 2 jenkins jenkins 4096 Sep 15 02:16 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 15 02:25 b2 -rw-rw-r-- 1 jenkins jenkins 2945 Jul 10 09:34 mdanalysis_2.9.0-12.dsc -rw------- 1 jenkins jenkins 383935 Sep 15 02:16 rbuildlog.VTaIaaa /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/b1: total 13720 -rw-r--r-- 1 jenkins jenkins 379573 Sep 15 02:16 build.log -rw-r--r-- 1 jenkins jenkins 13888 Sep 15 02:16 mdanalysis_2.9.0-12.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2945 Sep 15 02:16 mdanalysis_2.9.0-12.dsc -rw-r--r-- 1 jenkins jenkins 12936 Sep 15 02:16 mdanalysis_2.9.0-12_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 13818 Sep 15 02:16 mdanalysis_2.9.0-12_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1876 Sep 15 02:16 mdanalysis_2.9.0-12_amd64.changes -rw-r--r-- 1 jenkins jenkins 1237 Sep 15 02:16 mdanalysis_2.9.0-12_source.changes -rw-r--r-- 1 jenkins jenkins 3502376 Sep 15 02:16 python-mdanalysis-doc_2.9.0-12_all.deb -rw-r--r-- 1 jenkins jenkins 5861236 Sep 15 02:16 python3-mdanalysis-dbgsym_2.9.0-12_amd64.deb -rw-r--r-- 1 jenkins jenkins 4214124 Sep 15 02:16 python3-mdanalysis_2.9.0-12_amd64.deb /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/b2: total 13700 -rw-rw-r-- 1 jenkins jenkins 381500 Sep 15 02:25 build.log -rw-r--r-- 1 jenkins jenkins 13888 Sep 15 02:25 mdanalysis_2.9.0-12.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2945 Sep 15 02:25 mdanalysis_2.9.0-12.dsc -rw-rw-r-- 1 jenkins jenkins 12930 Sep 15 02:25 mdanalysis_2.9.0-12_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 13812 Sep 15 02:25 mdanalysis_2.9.0-12_amd64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 1876 Sep 15 02:25 mdanalysis_2.9.0-12_amd64.changes -rw-rw-r-- 1 jenkins jenkins 1237 Sep 15 02:25 mdanalysis_2.9.0-12_source.changes -rw-r--r-- 1 jenkins jenkins 3502328 Sep 15 02:25 python-mdanalysis-doc_2.9.0-12_all.deb -rw-r--r-- 1 jenkins jenkins 5861236 Sep 15 02:25 python3-mdanalysis-dbgsym_2.9.0-12_amd64.deb -rw-r--r-- 1 jenkins jenkins 4214124 Sep 15 02:25 python3-mdanalysis_2.9.0-12_amd64.deb Mon Sep 15 02:25:20 UTC 2025 I: Deleting $TMPDIR on infom02-amd64.debian.net. Mon Sep 15 02:25:20 UTC 2025 I: mdanalysis_2.9.0-12_amd64.changes: Format: 1.8 Date: Thu, 10 Jul 2025 11:07:57 +0200 Source: mdanalysis Binary: python-mdanalysis-doc python3-mdanalysis python3-mdanalysis-dbgsym Architecture: all amd64 Version: 2.9.0-12 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Drew Parsons Description: python-mdanalysis-doc - analyse molecular dynamics files and trajectories ( documentation python3-mdanalysis - analyse molecular dynamics files and trajectories Changes: mdanalysis (2.9.0-12) unstable; urgency=medium . * skip all tests, both build-time and run-time. See Bug#1108309. Checksums-Sha1: 0046b5ce7a1f9629a45783f0f5dab06aee17e9c9 12936 mdanalysis_2.9.0-12_amd64.buildinfo 082139baf4910a036f0a7bb5855c82e93e222f0a 3502376 python-mdanalysis-doc_2.9.0-12_all.deb 7248cb5a7d6ae594a369265cf7953eee08d86760 5861236 python3-mdanalysis-dbgsym_2.9.0-12_amd64.deb f521a5a51640958d4ea0b929098fc43051804653 4214124 python3-mdanalysis_2.9.0-12_amd64.deb Checksums-Sha256: b5ee7798c86eaf7012532250b3dbf90b16311e1ef1d7f37237a2edaef8d0357c 12936 mdanalysis_2.9.0-12_amd64.buildinfo 61898c71ae089b7eccde078ecfdee558444497ad3df9ac18348d74ffd82fe94f 3502376 python-mdanalysis-doc_2.9.0-12_all.deb e2c6a65649ef75adf4b464a4537185f1dcb843a428e33e6205de883b6c97041a 5861236 python3-mdanalysis-dbgsym_2.9.0-12_amd64.deb 672a0437e6024e4cc353b41de9dca2a9f79c6029dbcef02c0cec6be321e8ba8e 4214124 python3-mdanalysis_2.9.0-12_amd64.deb Files: 56572b2091e2931b1b65ab87e2d2c714 12936 python optional mdanalysis_2.9.0-12_amd64.buildinfo f0e05b556db3c330e60a5c0d797dfb41 3502376 doc optional python-mdanalysis-doc_2.9.0-12_all.deb c20994d8b52a2c273f3da61d1a0c5c54 5861236 debug optional python3-mdanalysis-dbgsym_2.9.0-12_amd64.deb e3be46eedccb540622de0950895bb1ec 4214124 python optional python3-mdanalysis_2.9.0-12_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/mdanalysis_2.9.0-12.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/mdanalysis_2.9.0-12.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/mdanalysis_2.9.0-12.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/mdanalysis_2.9.0-12.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/dbd/unstable/amd64/mdanalysis_2.9.0-12.diffoscope.html' removed '/var/lib/jenkins/userContent/reproducible/debian/dbdtxt/unstable/amd64/mdanalysis_2.9.0-12.diffoscope.txt.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/dbdjson/unstable/amd64/mdanalysis_2.9.0-12.diffoscope.json.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/mdanalysis_2.9.0-12_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/mdanalysis_2.9.0-12.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-09-15 02:16:38.431419794 +0000 +++ b2/build.log 2025-09-15 02:25:20.132085473 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Sep 14 14:07:34 -12 2025 -I: pbuilder-time-stamp: 1757902054 +I: Current time: Sun Oct 18 22:39:40 +14 2026 +I: pbuilder-time-stamp: 1792312780 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -29,52 +29,84 @@ dpkg-source: info: applying skip_gsd_tests.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1370099/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2381421/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 18 08:40 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2381421/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2381421/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='c576bcf55cdf444f9202a0e0a27566f4' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1370099' - PS1='# ' - PS2='> ' + INVOCATION_ID=311c054c0c1d494ea11a28975f9f2bf3 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2381421 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/pbuilderrc_zXRO --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/b1 --logfile b1/build.log mdanalysis_2.9.0-12.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/pbuilderrc_jLfq --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/b2 --logfile b2/build.log mdanalysis_2.9.0-12.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom01-amd64 6.12.43+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1370099/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2381421/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -450,7 +482,7 @@ Get: 270 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-sitemap all 2.6.0-1 [8508 B] Get: 271 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.bibtex all 2.6.5-2 [33.2 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 python3-tqdm all 4.67.1-5 [90.8 kB] -Fetched 203 MB in 8s (26.0 MB/s) +Fetched 203 MB in 8s (27.0 MB/s) Preconfiguring packages ... Selecting previously unselected package fonts-lato. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) @@ -1327,8 +1359,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Sep 15 02:10:16 UTC 2025. -Universal Time is now: Mon Sep 15 02:10:16 UTC 2025. +Local time is now: Sun Oct 18 08:43:15 UTC 2026. +Universal Time is now: Sun Oct 18 08:43:15 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (16.0.0-1) ... @@ -1580,7 +1612,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/mdanalysis-2.9.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../mdanalysis_2.9.0-12_source.changes +I: user script /srv/workspace/pbuilder/2381421/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2381421/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/mdanalysis-2.9.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../mdanalysis_2.9.0-12_source.changes dpkg-buildpackage: info: source package mdanalysis dpkg-buildpackage: info: source version 2.9.0-12 dpkg-buildpackage: info: source distribution unstable @@ -1700,8 +1736,8 @@ ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). - By 2026-Feb-18, you need to update your project and remove deprecated calls - or your builds will no longer be supported. + This deprecation is overdue, please update your project and remove deprecated + calls to avoid build errors in the future. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** @@ -1738,225 +1774,225 @@ running build running build_py creating build/lib.linux-x86_64-cpython-313/MDAnalysis -copying MDAnalysis/exceptions.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis +copying MDAnalysis/due.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis +copying MDAnalysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/authors.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis -copying MDAnalysis/version.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis +copying MDAnalysis/exceptions.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/units.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis -copying MDAnalysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis -copying MDAnalysis/due.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis -creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source -copying doc/sphinx/source/conf.py -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/distances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/util.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/log.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/correlations.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/transformations.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/_distopia.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/mdamath.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/guessers.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/GROParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/tables.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/converters -copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters -copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters -copying MDAnalysis/converters/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters -copying MDAnalysis/converters/RDKit.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters -copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters -copying MDAnalysis/converters/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters -copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters -copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters +copying MDAnalysis/version.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis -copying MDAnalysis/analysis/distances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis -copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis -copying MDAnalysis/analysis/psa.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis -copying MDAnalysis/analysis/bat.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis -copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis -copying MDAnalysis/analysis/pca.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis +copying MDAnalysis/analysis/results.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis +copying MDAnalysis/analysis/density.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis +copying MDAnalysis/analysis/contacts.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis +copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/backends.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis -copying MDAnalysis/analysis/rdf.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/dielectric.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis +copying MDAnalysis/analysis/rdf.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/msd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis -copying MDAnalysis/analysis/align.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis +copying MDAnalysis/analysis/nucleicacids.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/atomicdistances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis -copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis +copying MDAnalysis/analysis/align.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/rms.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis +copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis +copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis +copying MDAnalysis/analysis/bat.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis -copying MDAnalysis/analysis/density.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis -copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis -copying MDAnalysis/analysis/results.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis -copying MDAnalysis/analysis/polymer.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis -copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis -copying MDAnalysis/analysis/contacts.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis -copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis -copying MDAnalysis/analysis/nucleicacids.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis +copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/gnm.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser -copying MDAnalysis/guesser/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser -copying MDAnalysis/guesser/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser -copying MDAnalysis/guesser/default_guesser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser -copying MDAnalysis/guesser/tables.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/core -copying MDAnalysis/core/groups.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core -copying MDAnalysis/core/accessors.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core -copying MDAnalysis/core/_get_readers.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core -copying MDAnalysis/core/selection.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core -copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core -copying MDAnalysis/core/topology.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core -copying MDAnalysis/core/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core -copying MDAnalysis/core/universe.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core -copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/tests -copying MDAnalysis/tests/datafiles.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/tests -copying MDAnalysis/tests/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/tests -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization -copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization -copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization -copying MDAnalysis/visualization/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization +copying MDAnalysis/analysis/pca.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis +copying MDAnalysis/analysis/psa.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis +copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis +copying MDAnalysis/analysis/polymer.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis +copying MDAnalysis/analysis/distances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis +copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/converters +copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters +copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters +copying MDAnalysis/converters/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters +copying MDAnalysis/converters/RDKit.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters +copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters +copying MDAnalysis/converters/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters +copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters +copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters creating build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/TNG.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/chain.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/chain.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRC.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/null.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/memory.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/null.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/TNG.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/memory.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser +copying MDAnalysis/guesser/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser +copying MDAnalysis/guesser/tables.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser +copying MDAnalysis/guesser/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser +copying MDAnalysis/guesser/default_guesser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser creating build/lib.linux-x86_64-cpython-313/MDAnalysis/selections -copying MDAnalysis/selections/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/vmd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections +copying MDAnalysis/selections/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections +copying MDAnalysis/selections/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections +copying MDAnalysis/selections/pymol.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/gromacs.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/charmm.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/jmol.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections -copying MDAnalysis/selections/pymol.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections -copying MDAnalysis/selections/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary +copying MDAnalysis/auxiliary/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary +copying MDAnalysis/auxiliary/EDR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary +copying MDAnalysis/auxiliary/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary +copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary +copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/transformations.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/util.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/correlations.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/mdamath.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/log.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/_distopia.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/distances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib creating build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/translate.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations -copying MDAnalysis/transformations/wrap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations -copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations -copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/nojump.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations -copying MDAnalysis/transformations/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations -copying MDAnalysis/transformations/rotate.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/fit.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary -copying MDAnalysis/auxiliary/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary -copying MDAnalysis/auxiliary/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary -copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary -copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary -copying MDAnalysis/auxiliary/EDR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis -copying MDAnalysis/lib/libmdanalysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats -copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include -copying MDAnalysis/lib/include/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations -copying MDAnalysis/lib/src/transformations/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src -copying MDAnalysis/lib/formats/src/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include -copying MDAnalysis/lib/formats/include/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr -copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr -copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr -copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr -copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2 -copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2 -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy -copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy -copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy +copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations +copying MDAnalysis/transformations/rotate.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations +copying MDAnalysis/transformations/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations +copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations +copying MDAnalysis/transformations/wrap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/core +copying MDAnalysis/core/selection.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core +copying MDAnalysis/core/topology.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core +copying MDAnalysis/core/accessors.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core +copying MDAnalysis/core/groups.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core +copying MDAnalysis/core/_get_readers.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core +copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core +copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core +copying MDAnalysis/core/universe.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core +copying MDAnalysis/core/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/GROParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/tables.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/guessers.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/tests +copying MDAnalysis/tests/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/tests +copying MDAnalysis/tests/datafiles.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/tests +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization +copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization +copying MDAnalysis/visualization/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization +copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data +copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data +copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp +copying MDAnalysis/analysis/dssp/dssp.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp +copying MDAnalysis/analysis/dssp/pydssp_numpy.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp +copying MDAnalysis/analysis/dssp/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds -copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds +copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore +copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore +copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore -copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore -copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore -copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data -copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data -copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data +copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy +copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy +copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2 +copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2 creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds -copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds -copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp -copying MDAnalysis/analysis/dssp/pydssp_numpy.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp -copying MDAnalysis/analysis/dssp/dssp.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp -copying MDAnalysis/analysis/dssp/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction -copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction -copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction -copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction +copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds +copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering -copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering +copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction +copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction +copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction +copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats +copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis +copying MDAnalysis/lib/libmdanalysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include +copying MDAnalysis/lib/include/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src +copying MDAnalysis/lib/formats/src/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include +copying MDAnalysis/lib/formats/include/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations +copying MDAnalysis/lib/src/transformations/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr +copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr +copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr +copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr +copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr +creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source +copying doc/sphinx/source/conf.py -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source running egg_info creating MDAnalysis.egg-info writing MDAnalysis.egg-info/PKG-INFO @@ -2041,9 +2077,67 @@ adding license file 'LICENSE' adding license file 'AUTHORS' writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' -copying doc/README -> build/lib.linux-x86_64-cpython-313/doc copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data +copying doc/README -> build/lib.linux-x86_64-cpython-313/doc +copying MDAnalysis/coordinates/timestep.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/timestep.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/coordinates/timestep.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates +copying MDAnalysis/lib/_augment.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/_augment.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/_cutil.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/_cutil.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/_cutil.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/c_distances.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/c_distances.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/c_distances.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/c_distances_openmp.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/c_distances_openmp.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/nsgrid.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/nsgrid.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/qcprot.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/lib/qcprot.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib +copying MDAnalysis/analysis/encore/cutils.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore +copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore +copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering +copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering +copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction +copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src +copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include +copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src +copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src +creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include +copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include +copying MDAnalysis/lib/formats/cython_util.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats +copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats +copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats +copying MDAnalysis/lib/formats/libdcd.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats +copying MDAnalysis/lib/formats/libdcd.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats +copying MDAnalysis/lib/formats/libdcd.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats +copying MDAnalysis/lib/formats/libmdaxdr.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats +copying MDAnalysis/lib/formats/libmdaxdr.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats +copying MDAnalysis/lib/formats/libmdaxdr.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats +copying MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis +copying MDAnalysis/lib/include/calc_distances.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include +copying MDAnalysis/lib/formats/src/trr_seek.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src +copying MDAnalysis/lib/formats/src/xdrfile.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src +copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src +copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src +copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src +copying MDAnalysis/lib/formats/include/endianswap.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include +copying MDAnalysis/lib/formats/include/fastio.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include +copying MDAnalysis/lib/formats/include/readdcd.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include +copying MDAnalysis/lib/formats/include/trr_seek.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include +copying MDAnalysis/lib/formats/include/xdrfile.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include +copying MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include +copying MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include +copying MDAnalysis/lib/formats/include/xtc_seek.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include +copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations +copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations +copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations copying doc/sphinx/Makefile -> build/lib.linux-x86_64-cpython-313/doc/sphinx copying doc/sphinx/source/index.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source copying doc/sphinx/source/references.bib -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source @@ -2075,59 +2169,6 @@ copying doc/sphinx/source/documentation_pages/units.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/version.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/visualization_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages -creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib -copying doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib -copying doc/sphinx/source/documentation_pages/lib/c_distances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib -copying doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib -copying doc/sphinx/source/documentation_pages/lib/correlations.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib -copying doc/sphinx/source/documentation_pages/lib/distances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib -copying doc/sphinx/source/documentation_pages/lib/log.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib -copying doc/sphinx/source/documentation_pages/lib/mdamath.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib -copying doc/sphinx/source/documentation_pages/lib/nsgrid.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib -copying doc/sphinx/source/documentation_pages/lib/picklable_file_io.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib -copying doc/sphinx/source/documentation_pages/lib/pkdtree.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib -copying doc/sphinx/source/documentation_pages/lib/qcprot.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib -copying doc/sphinx/source/documentation_pages/lib/transformations.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib -copying doc/sphinx/source/documentation_pages/lib/util.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib -creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/CRDParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/DMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/GMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/GROParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/GSDParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/ITPParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/MMTFParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/MinimalParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/PDBParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/PQRParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/PSFParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/TOPParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/TPRParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/TXYZParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/XYZParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/core.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/guessers.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/tables.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -copying doc/sphinx/source/documentation_pages/topology/tpr_util.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology -creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters -copying doc/sphinx/source/documentation_pages/converters/OpenMM.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters -copying doc/sphinx/source/documentation_pages/converters/ParmEd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters -copying doc/sphinx/source/documentation_pages/converters/RDKit.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters -copying doc/sphinx/source/documentation_pages/converters/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters -creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules -copying doc/sphinx/source/documentation_pages/guesser_modules/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules -copying doc/sphinx/source/documentation_pages/guesser_modules/default_guesser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules -copying doc/sphinx/source/documentation_pages/guesser_modules/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules -copying doc/sphinx/source/documentation_pages/guesser_modules/tables.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/align.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/atomicdistances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis @@ -2164,20 +2205,11 @@ copying doc/sphinx/source/documentation_pages/analysis/rms.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/waterdynamics.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/wbridge_analysis.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis -creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core -copying doc/sphinx/source/documentation_pages/core/accessors.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core -copying doc/sphinx/source/documentation_pages/core/groups.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core -copying doc/sphinx/source/documentation_pages/core/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core -copying doc/sphinx/source/documentation_pages/core/selection.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core -copying doc/sphinx/source/documentation_pages/core/topology.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core -copying doc/sphinx/source/documentation_pages/core/topologyattrs.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core -copying doc/sphinx/source/documentation_pages/core/topologyobjects.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core -copying doc/sphinx/source/documentation_pages/core/universe.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core -creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization -copying doc/sphinx/source/documentation_pages/visualization/streamlines.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization -copying doc/sphinx/source/documentation_pages/visualization/streamlines_3D.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization -copying doc/sphinx/source/documentation_pages/visualization/test_streamplot_3D.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization -copying doc/sphinx/source/documentation_pages/visualization/testing_streamline.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization +creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters +copying doc/sphinx/source/documentation_pages/converters/OpenMM.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters +copying doc/sphinx/source/documentation_pages/converters/ParmEd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters +copying doc/sphinx/source/documentation_pages/converters/RDKit.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters +copying doc/sphinx/source/documentation_pages/converters/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/CRD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/DCD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates @@ -2221,6 +2253,26 @@ copying doc/sphinx/source/documentation_pages/selections/jmol.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/pymol.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/vmd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections +creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary +copying doc/sphinx/source/documentation_pages/auxiliary/EDR.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary +copying doc/sphinx/source/documentation_pages/auxiliary/XVG.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary +copying doc/sphinx/source/documentation_pages/auxiliary/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary +copying doc/sphinx/source/documentation_pages/auxiliary/core.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary +copying doc/sphinx/source/documentation_pages/auxiliary/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary +creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib +copying doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib +copying doc/sphinx/source/documentation_pages/lib/c_distances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib +copying doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib +copying doc/sphinx/source/documentation_pages/lib/correlations.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib +copying doc/sphinx/source/documentation_pages/lib/distances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib +copying doc/sphinx/source/documentation_pages/lib/log.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib +copying doc/sphinx/source/documentation_pages/lib/mdamath.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib +copying doc/sphinx/source/documentation_pages/lib/nsgrid.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib +copying doc/sphinx/source/documentation_pages/lib/picklable_file_io.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib +copying doc/sphinx/source/documentation_pages/lib/pkdtree.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib +copying doc/sphinx/source/documentation_pages/lib/qcprot.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib +copying doc/sphinx/source/documentation_pages/lib/transformations.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib +copying doc/sphinx/source/documentation_pages/lib/util.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations @@ -2230,17 +2282,54 @@ copying doc/sphinx/source/documentation_pages/transformations/rotate.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/translate.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/wrap.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations -creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary -copying doc/sphinx/source/documentation_pages/auxiliary/EDR.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary -copying doc/sphinx/source/documentation_pages/auxiliary/XVG.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary -copying doc/sphinx/source/documentation_pages/auxiliary/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary -copying doc/sphinx/source/documentation_pages/auxiliary/core.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary -copying doc/sphinx/source/documentation_pages/auxiliary/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary -creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats -copying doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats -copying doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats -creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy -copying doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy +creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules +copying doc/sphinx/source/documentation_pages/guesser_modules/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules +copying doc/sphinx/source/documentation_pages/guesser_modules/default_guesser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules +copying doc/sphinx/source/documentation_pages/guesser_modules/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules +copying doc/sphinx/source/documentation_pages/guesser_modules/tables.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules +creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core +copying doc/sphinx/source/documentation_pages/core/accessors.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core +copying doc/sphinx/source/documentation_pages/core/groups.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core +copying doc/sphinx/source/documentation_pages/core/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core +copying doc/sphinx/source/documentation_pages/core/selection.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core +copying doc/sphinx/source/documentation_pages/core/topology.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core +copying doc/sphinx/source/documentation_pages/core/topologyattrs.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core +copying doc/sphinx/source/documentation_pages/core/topologyobjects.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core +copying doc/sphinx/source/documentation_pages/core/universe.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core +creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/CRDParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/DMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/GMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/GROParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/GSDParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/ITPParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/MMTFParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/MinimalParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/PDBParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/PQRParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/PSFParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/TOPParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/TPRParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/TXYZParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/XYZParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/core.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/guessers.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/tables.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +copying doc/sphinx/source/documentation_pages/topology/tpr_util.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology +creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization +copying doc/sphinx/source/documentation_pages/visualization/streamlines.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization +copying doc/sphinx/source/documentation_pages/visualization/streamlines_3D.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization +copying doc/sphinx/source/documentation_pages/visualization/test_streamplot_3D.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization +copying doc/sphinx/source/documentation_pages/visualization/testing_streamline.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/bootstrap.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/clustering.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore @@ -2249,64 +2338,11 @@ copying doc/sphinx/source/documentation_pages/analysis/encore/dimensionality_reduction.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/similarity.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/utils.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore -copying MDAnalysis/lib/_augment.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/_augment.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/_cutil.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/_cutil.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/_cutil.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/c_distances.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/c_distances.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/c_distances.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/c_distances_openmp.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/c_distances_openmp.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/nsgrid.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/nsgrid.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/qcprot.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/lib/qcprot.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib -copying MDAnalysis/coordinates/timestep.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/timestep.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/coordinates/timestep.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates -copying MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis -copying MDAnalysis/lib/formats/cython_util.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats -copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats -copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats -copying MDAnalysis/lib/formats/libdcd.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats -copying MDAnalysis/lib/formats/libdcd.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats -copying MDAnalysis/lib/formats/libdcd.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats -copying MDAnalysis/lib/formats/libmdaxdr.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats -copying MDAnalysis/lib/formats/libmdaxdr.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats -copying MDAnalysis/lib/formats/libmdaxdr.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats -copying MDAnalysis/lib/include/calc_distances.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include -copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations -copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations -copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations -copying MDAnalysis/lib/formats/src/trr_seek.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src -copying MDAnalysis/lib/formats/src/xdrfile.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src -copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src -copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src -copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src -copying MDAnalysis/lib/formats/include/endianswap.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include -copying MDAnalysis/lib/formats/include/fastio.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include -copying MDAnalysis/lib/formats/include/readdcd.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include -copying MDAnalysis/lib/formats/include/trr_seek.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include -copying MDAnalysis/lib/formats/include/xdrfile.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include -copying MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include -copying MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include -copying MDAnalysis/lib/formats/include/xtc_seek.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include -copying MDAnalysis/analysis/encore/cutils.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore -copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore -copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction -copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction -copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering -copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src -copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include -copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src -copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src -creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include -copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include +creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy +copying doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy +creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats +copying doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats +copying doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats running build_ext building 'MDAnalysis.lib.formats.libdcd' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats @@ -2460,514 +2496,514 @@ running install running install_lib creating build/bdist.linux-x86_64/wheel -creating build/bdist.linux-x86_64/wheel/doc -copying build/lib.linux-x86_64-cpython-313/doc/README -> build/bdist.linux-x86_64/wheel/./doc -creating build/bdist.linux-x86_64/wheel/doc/sphinx -creating build/bdist.linux-x86_64/wheel/doc/sphinx/source -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/index.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source -creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/images -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/rama_ref_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/parallelization_time.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/msd_demo_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/rama_demo_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/AnalysisBase_parallel.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/janin_demo_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/RSMD_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/janin_ref_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images -creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages -creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/lib -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/mdamath.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/pkdtree.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib -creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/lib/formats -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib/formats -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib/formats -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/correlations.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/nsgrid.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/c_distances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/qcprot.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/distances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/picklable_file_io.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/log.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/util.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/transformations.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/units.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages -creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/TXYZParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PDBParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/GROParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/core.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/XYZParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/CRDParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/DMSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/TPRParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PSFParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/MMTFParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/TOPParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/guessers.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/GMSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PQRParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/tpr_util.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/MinimalParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/GSDParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/ITPParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/tables.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages -creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/converters -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/OpenMM.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/RDKit.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/ParmEd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages -creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/guesser_modules -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/default_guesser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/tables.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules -creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/helix_analysis.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/pca.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/density.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/rms.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/results.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/wbridge_analysis.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/msd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/psa.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/analysis/legacy -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/legacy -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/polymer.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/atomicdistances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/analysis/encore -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/clustering.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/dimensionality_reduction.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/utils.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/similarity.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/confdistmatrix.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/covariance.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/bootstrap.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/nucleicacids.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel_deprecated.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/waterdynamics.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/nuclinfo.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/dihedrals.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/bat.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/parallelization.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/lineardensity.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/align.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/dielectric.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/diffusionmap.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/distances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/data.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/gnm.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hole2.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/contacts.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/backends.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/dssp.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/rdf.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hydrogenbonds.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/leaflet.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages -creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/core -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/accessors.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/universe.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/groups.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/topologyattrs.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/selection.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/topology.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/topologyobjects.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages -creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/visualization -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/test_streamplot_3D.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/streamlines_3D.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/streamlines.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/testing_streamline.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/overview.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/exceptions.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/references.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/version.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages -creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/chemfiles.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRC.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/null.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/chain.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/CRD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/GMS.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/DMS.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/LAMMPS.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/memory.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/core.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TXYZ.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/NAMDBIN.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/INPCRD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/PDBQT.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/MOL2.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/H5MD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/XYZ.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/MMTF.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRJ.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/GSD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/GRO.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TNG.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/PDB.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/XDR.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRZ.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/DLPoly.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/pickle_readers.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/PQR.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/XTC.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/FHIAIMS.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/timestep.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/DCD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRR.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates -creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/selections -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/pymol.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/vmd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/charmm.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/jmol.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/gromacs.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections -creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/transformations -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/fit.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/nojump.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/wrap.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/translate.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/positionaveraging.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/rotate.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/trajectory_transformations.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages -creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/auxiliary -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/EDR.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/XVG.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/core.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/references.bib -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/conf.py -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source -copying build/lib.linux-x86_64-cpython-313/doc/sphinx/Makefile -> build/bdist.linux-x86_64/wheel/./doc/sphinx creating build/bdist.linux-x86_64/wheel/MDAnalysis -creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/distances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/libmdanalysis -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/libmdanalysis -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/libmdanalysis -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/util.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/log.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/src -creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/src/transformations -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/LICENCE -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/AUTHOR -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/transformations.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/correlations.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/transformations.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/src -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xtc_seek.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/trr_seek.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/include -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xdrfile.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/fastio.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/endianswap.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/readdcd.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/trr_seek.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xtc_seek.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/picklable_file_io.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_distopia.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_transformations.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/mdamath.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/include -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/include -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include/calc_distances.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/include -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/exceptions.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis -creating build/bdist.linux-x86_64/wheel/MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/ParmEdParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -creating build/bdist.linux-x86_64/wheel/MDAnalysis/topology/tpr -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/setting.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/guessers.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/GROParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/ITPParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/FHIAIMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tables.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/authors.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/version.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis -creating build/bdist.linux-x86_64/wheel/MDAnalysis/converters -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/ParmEd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/ParmEdParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/RDKit.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/OpenMMParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/OpenMM.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/RDKitParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/distances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/psa.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hole2 -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hole2 -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/bat.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dihedrals.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/pca.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/results.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/density.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/contacts.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dihedrals.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/backends.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/rdf.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dielectric.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/legacy -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/legacy -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/legacy +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/rdf.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/data +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/janin_ref_data.npy -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/msd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/dssp +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp/dssp.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/dssp +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp/pydssp_numpy.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/dssp +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/dssp creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hbonds -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hbonds -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/msd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hbonds creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore +creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering +creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering/src +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src/ap.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering/src +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering +creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering/include +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include/ap.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering/include +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/src copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction/src +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction/include copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/similarity.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/covariance.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore -creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering -creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering/src -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src/ap.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering/src -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering -creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering/include -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include/ap.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering/include -creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/data -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/janin_ref_data.npy -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/align.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/nucleicacids.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/atomicdistances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/align.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/rms.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/bat.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/density.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/results.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/polymer.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/legacy +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/legacy +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/legacy +creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hole2 +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hole2 +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/helix_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/helix_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/dssp -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp/pydssp_numpy.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/dssp -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp/dssp.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/dssp -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/dssp -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/contacts.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/nucleicacids.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/gnm.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -creating build/bdist.linux-x86_64/wheel/MDAnalysis/guesser -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/default_guesser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/tables.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser -creating build/bdist.linux-x86_64/wheel/MDAnalysis/core -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/groups.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/accessors.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/_get_readers.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/selection.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/topology.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/universe.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core -creating build/bdist.linux-x86_64/wheel/MDAnalysis/tests -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/tests/datafiles.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/tests -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/tests/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/tests -creating build/bdist.linux-x86_64/wheel/MDAnalysis/visualization -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/units.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/pca.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/psa.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/polymer.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/distances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +creating build/bdist.linux-x86_64/wheel/MDAnalysis/converters +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/ParmEd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/RDKitParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/RDKit.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/ParmEdParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/OpenMMParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/OpenMM.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters creating build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TXYZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/ParmEd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TNG.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/chain.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/XDR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/H5MD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/chain.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/XDR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRC.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/null.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/NAMDBIN.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/memory.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/null.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TNG.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/memory.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +creating build/bdist.linux-x86_64/wheel/MDAnalysis/guesser +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/tables.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/default_guesser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser creating build/bdist.linux-x86_64/wheel/MDAnalysis/selections -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/vmd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/pymol.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/gromacs.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/charmm.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/jmol.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/pymol.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections +creating build/bdist.linux-x86_64/wheel/MDAnalysis/auxiliary +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/EDR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary copying build/lib.linux-x86_64-cpython-313/MDAnalysis/due.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis +creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib +creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/src +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xtc_seek.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/trr_seek.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/include +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/readdcd.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/endianswap.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/trr_seek.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/fastio.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xtc_seek.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xdrfile.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/src +creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/src/transformations +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/LICENCE -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/AUTHOR -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/transformations.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/transformations.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_transformations.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/util.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/correlations.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/mdamath.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/picklable_file_io.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/libmdanalysis +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/libmdanalysis +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/libmdanalysis +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/log.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/include +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include/calc_distances.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/include +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/include +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_distopia.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/distances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/authors.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/translate.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/wrap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/boxdimensions.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/nojump.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/rotate.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/fit.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations -creating build/bdist.linux-x86_64/wheel/MDAnalysis/auxiliary -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary -copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/EDR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/boxdimensions.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/rotate.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/wrap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/exceptions.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis +creating build/bdist.linux-x86_64/wheel/MDAnalysis/core +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/selection.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/topology.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/accessors.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/groups.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/_get_readers.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/universe.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/units.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis +creating build/bdist.linux-x86_64/wheel/MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/GROParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/ITPParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +creating build/bdist.linux-x86_64/wheel/MDAnalysis/topology/tpr +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/setting.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/ParmEdParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tables.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/FHIAIMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/guessers.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/version.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis +creating build/bdist.linux-x86_64/wheel/MDAnalysis/tests +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/tests/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/tests +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/tests/datafiles.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/tests +creating build/bdist.linux-x86_64/wheel/MDAnalysis/visualization +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization +copying build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization +creating build/bdist.linux-x86_64/wheel/doc +creating build/bdist.linux-x86_64/wheel/doc/sphinx +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/Makefile -> build/bdist.linux-x86_64/wheel/./doc/sphinx +creating build/bdist.linux-x86_64/wheel/doc/sphinx/source +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/conf.py -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/index.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source +creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/images +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/AnalysisBase_parallel.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/rama_ref_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/msd_demo_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/janin_demo_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/RSMD_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/janin_ref_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/rama_demo_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/parallelization_time.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/references.bib -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source +creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages +creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/data.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/lineardensity.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/align.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/backends.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/nucleicacids.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/msd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/dihedrals.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/dssp.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/density.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/rdf.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/waterdynamics.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/helix_analysis.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/bat.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/results.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/analysis/encore +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/bootstrap.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/dimensionality_reduction.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/utils.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/similarity.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/confdistmatrix.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/covariance.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/clustering.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/pca.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/parallelization.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hole2.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/distances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/nuclinfo.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/atomicdistances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel_deprecated.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/diffusionmap.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/wbridge_analysis.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/leaflet.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/analysis/legacy +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/legacy +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/rms.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/polymer.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/dielectric.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/gnm.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/psa.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hydrogenbonds.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/contacts.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis +creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/converters +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/RDKit.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/ParmEd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/OpenMM.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters +creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRR.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/FHIAIMS.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/MMTF.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/LAMMPS.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRJ.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/CRD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/PQR.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/NAMDBIN.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/PDBQT.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/timestep.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/H5MD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/DMS.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/DCD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/GRO.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/PDB.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/XTC.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/GSD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/null.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/memory.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/XDR.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRZ.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/pickle_readers.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRC.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/chemfiles.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/MOL2.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TXYZ.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/chain.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TNG.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/GMS.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/DLPoly.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/core.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/INPCRD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/XYZ.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/exceptions.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/references.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages +creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/selections +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/jmol.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/gromacs.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/pymol.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/vmd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/charmm.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections +creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/auxiliary +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/XVG.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/EDR.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/core.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary +creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/lib +creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/lib/formats +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib/formats +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib/formats +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/c_distances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/log.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/correlations.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/transformations.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/nsgrid.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/picklable_file_io.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/distances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/util.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/pkdtree.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/qcprot.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/mdamath.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/units.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages +creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/transformations +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/nojump.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/wrap.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/translate.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/rotate.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/positionaveraging.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/fit.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/trajectory_transformations.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages +creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/guesser_modules +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/default_guesser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/tables.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages +creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/core +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/topologyobjects.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/groups.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/selection.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/accessors.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/universe.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/topology.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/topologyattrs.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/overview.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages +creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/MMTFParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/GMSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/CRDParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/TOPParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/TXYZParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/TPRParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/MinimalParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/DMSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/tpr_util.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PQRParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PSFParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/ITPParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/tables.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/guessers.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/XYZParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/core.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/GROParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/GSDParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PDBParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/version.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages +creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/visualization +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/streamlines_3D.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/test_streamplot_3D.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/testing_streamline.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization +copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/streamlines.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization +copying build/lib.linux-x86_64-cpython-313/doc/README -> build/bdist.linux-x86_64/wheel/./doc running install_egg_info Copying MDAnalysis.egg-info to build/bdist.linux-x86_64/wheel/./MDAnalysis-2.9.0.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/mdanalysis-2.9.0.dist-info/WHEEL -creating '/build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/.tmp-zjdtpibb/mdanalysis-2.9.0-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it +creating '/build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/.tmp-hek2oo9o/mdanalysis-2.9.0-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'MDAnalysis/__init__.py' adding 'MDAnalysis/authors.py' adding 'MDAnalysis/due.py' @@ -3505,47 +3541,47 @@ loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv ... loading intersphinx inventory 'scipy' from https://docs.scipy.org/doc/scipy/objects.inv ... loading intersphinx inventory 'gsd' from https://gsd.readthedocs.io/en/stable/objects.inv ... -loading intersphinx inventory 'maplotlib' from https://matplotlib.org/stable/objects.inv ... -loading intersphinx inventory 'griddataformats' from https://mdanalysis.org/GridDataFormats/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://docs.h5py.org/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.h5py.org', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) -loading intersphinx inventory 'networkx' from https://networkx.org/documentation/stable/objects.inv ... +intersphinx inventory 'https://docs.h5py.org/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.h5py.org', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://docs.scipy.org/doc/scipy/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.scipy.org', port=443): Max retries exceeded with url: /doc/scipy/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://gsd.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='gsd.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +loading intersphinx inventory 'griddataformats' from https://mdanalysis.org/GridDataFormats/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://docs.scipy.org/doc/scipy/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.scipy.org', port=443): Max retries exceeded with url: /doc/scipy/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://gsd.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='gsd.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +loading intersphinx inventory 'networkx' from https://networkx.org/documentation/stable/objects.inv ... loading intersphinx inventory 'pmda' from https://mdanalysis.org/pmda/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://mdanalysis.org/pmda/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /pmda/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) -loading intersphinx inventory 'waterdynamics' from https://www.mdanalysis.org/waterdynamics/objects.inv ... +intersphinx inventory 'https://networkx.org/documentation/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='networkx.org', port=443): Max retries exceeded with url: /documentation/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://mdanalysis.org/GridDataFormats/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /GridDataFormats/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) -loading intersphinx inventory 'parmed' from https://parmed.github.io/ParmEd/html/objects.inv ... -loading intersphinx inventory 'rdkit' from https://rdkit.org/docs/objects.inv ... +intersphinx inventory 'https://mdanalysis.org/GridDataFormats/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /GridDataFormats/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +loading intersphinx inventory 'maplotlib' from https://matplotlib.org/stable/objects.inv ... loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv ... -loading intersphinx inventory 'pathsimanalysis' from https://www.mdanalysis.org/PathSimAnalysis/objects.inv ... -loading intersphinx inventory 'dask' from https://docs.dask.org/en/stable/objects.inv ... +loading intersphinx inventory 'rdkit' from https://rdkit.org/docs/objects.inv ... +loading intersphinx inventory 'parmed' from https://parmed.github.io/ParmEd/html/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://www.mdanalysis.org/waterdynamics/objects.inv' not fetchable due to : HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /waterdynamics/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://mdanalysis.org/pmda/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /pmda/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://docs.dask.org/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.dask.org', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) -loading intersphinx inventory 'mdahole2' from https://www.mdanalysis.org/mdahole2/objects.inv ... +intersphinx inventory 'https://numpy.org/doc/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='numpy.org', port=443): Max retries exceeded with url: /doc/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +loading intersphinx inventory 'pathsimanalysis' from https://www.mdanalysis.org/PathSimAnalysis/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://matplotlib.org/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='matplotlib.org', port=443): Max retries exceeded with url: /stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://rdkit.org/docs/objects.inv' not fetchable due to : HTTPSConnectionPool(host='rdkit.org', port=443): Max retries exceeded with url: /docs/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +loading intersphinx inventory 'waterdynamics' from https://www.mdanalysis.org/waterdynamics/objects.inv ... +loading intersphinx inventory 'dask' from https://docs.dask.org/en/stable/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://www.mdanalysis.org/PathSimAnalysis/objects.inv' not fetchable due to : HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /PathSimAnalysis/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://matplotlib.org/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='matplotlib.org', port=443): Max retries exceeded with url: /stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://networkx.org/documentation/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='networkx.org', port=443): Max retries exceeded with url: /documentation/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://parmed.github.io/ParmEd/html/objects.inv' not fetchable due to : HTTPSConnectionPool(host='parmed.github.io', port=443): Max retries exceeded with url: /ParmEd/html/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +loading intersphinx inventory 'mdahole2' from https://www.mdanalysis.org/mdahole2/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://rdkit.org/docs/objects.inv' not fetchable due to : HTTPSConnectionPool(host='rdkit.org', port=443): Max retries exceeded with url: /docs/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://www.mdanalysis.org/waterdynamics/objects.inv' not fetchable due to : HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /waterdynamics/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://numpy.org/doc/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='numpy.org', port=443): Max retries exceeded with url: /doc/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://www.mdanalysis.org/PathSimAnalysis/objects.inv' not fetchable due to : HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /PathSimAnalysis/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://parmed.github.io/ParmEd/html/objects.inv' not fetchable due to : HTTPSConnectionPool(host='parmed.github.io', port=443): Max retries exceeded with url: /ParmEd/html/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://www.mdanalysis.org/mdahole2/objects.inv' not fetchable due to : HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /mdahole2/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://www.mdanalysis.org/mdahole2/objects.inv' not fetchable due to : HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /mdahole2/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://docs.dask.org/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.dask.org', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) locale_dir /build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist building [mo]: targets for 0 po files that are out of date writing output... @@ -3572,8 +3608,8 @@ reading sources... [ 5%] documentation_pages/analysis/dielectric reading sources... [ 6%] documentation_pages/analysis/diffusionmap reading sources... [ 6%] documentation_pages/analysis/dihedrals -mkdir -p failed for path /nonexistent/first-build/.config/matplotlib: [Errno 13] Permission denied: '/nonexistent' -Matplotlib created a temporary cache directory at /tmp/matplotlib-a626_uu3 because there was an issue with the default path (/nonexistent/first-build/.config/matplotlib); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +mkdir -p failed for path /nonexistent/second-build/.config/matplotlib: [Errno 13] Permission denied: '/nonexistent' +Matplotlib created a temporary cache directory at /tmp/matplotlib-oinpuc9u because there was an issue with the default path (/nonexistent/second-build/.config/matplotlib); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. reading sources... [ 7%] documentation_pages/analysis/distances reading sources... [ 7%] documentation_pages/analysis/dssp reading sources... [ 8%] documentation_pages/analysis/encore @@ -3790,8 +3826,8 @@ done copying assets... copying static files... -Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/documentation_options.js +Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/basic.css Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/alabaster.css copying static files: done @@ -4195,8 +4231,8 @@ dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-mdanalysis' in '../python3-mdanalysis_2.9.0-12_amd64.deb'. -dpkg-deb: building package 'python3-mdanalysis-dbgsym' in '../python3-mdanalysis-dbgsym_2.9.0-12_amd64.deb'. dpkg-deb: building package 'python-mdanalysis-doc' in '../python-mdanalysis-doc_2.9.0-12_all.deb'. +dpkg-deb: building package 'python3-mdanalysis-dbgsym' in '../python3-mdanalysis-dbgsym_2.9.0-12_amd64.deb'. dpkg-genbuildinfo --build=binary -O../mdanalysis_2.9.0-12_amd64.buildinfo dpkg-genchanges --build=binary -O../mdanalysis_2.9.0-12_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -4205,12 +4241,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2381421/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2381421/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1370099 and its subdirectories -I: Current time: Sun Sep 14 14:16:37 -12 2025 -I: pbuilder-time-stamp: 1757902597 +I: removing directory /srv/workspace/pbuilder/2381421 and its subdirectories +I: Current time: Sun Oct 18 22:48:19 +14 2026 +I: pbuilder-time-stamp: 1792313299 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/mdanalysis_2.9.0-12.diff: 93.5% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/mdanalysis_2.9.0-12.diff.gz b2/build.log: 89.3% -- replaced with stdout Compressing the 1st log... b1/build.log: 89.5% -- replaced with stdout Mon Sep 15 02:25:21 UTC 2025 I: diffoscope 306 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_mdanalysis_unstable_amd64_1757903121 + touch /var/log/reproducible-builds/diffoscope_stamp_mdanalysis_unstable_amd64_1757903121 + RESULT=0 + systemd-run '--description=diffoscope on mdanalysis/2.9.0-12 in unstable/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_37-82773 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN --run-session -c jenkins-reproducible-unstable-diffoscope-034caeea-1ab5-4649-9b3b-d7401fb36506 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/dbd-tmp-LoixVDM ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/mdanalysis_2.9.0-12.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/mdanalysis_2.9.0-12.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/mdanalysis_2.9.0-12.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/b1/mdanalysis_2.9.0-12_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/b2/mdanalysis_2.9.0-12_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_37-82773.service; invocation ID: f0f61972cedf44989567cc905f82dbc2 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/mdanalysis_2.9.0-12.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/mdanalysis_2.9.0-12.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/mdanalysis_2.9.0-12.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/b1/mdanalysis_2.9.0-12_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.olZAMKQN/b2/mdanalysis_2.9.0-12_amd64.changes ## close_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer ## command (total time: 0.488s) 0.248s 6 calls xz 0.168s 7 calls diff 0.024s 4 calls cmp 0.024s 4 calls cmp (external) 0.023s 11 calls html2text 0.001s 16 calls cmp (internal) ## compare_files (cumulative) (total time: 3.504s) 0.958s 1 call abc.DotChangesFile 0.924s 1 call abc.DebFile 0.902s 2 calls abc.XzFile 0.610s 1 call abc.DebDataTarFile 0.073s 1 call abc.HtmlFile 0.028s 1 call abc.TarFile 0.011s 1 call abc.Md5sumsFile ## container_extract (total time: 0.457s) 0.248s 6 calls diffoscope.comparators.xz.XzContainer 0.198s 1062 calls diffoscope.comparators.deb.DebTarContainer 0.009s 8 calls diffoscope.comparators.deb.DebContainer 0.002s 6 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 0.330s) 0.330s 9 calls linediff ## has_same_content_as (total time: 0.026s) 0.013s 1 call abc.DebDataTarFile 0.009s 3 calls abc.DebFile 0.002s 1 call abc.HtmlFile 0.000s 4 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 2 calls abc.Md5sumsFile 0.000s 2 calls abc.TextFile 0.000s 1 call diffoscope.comparators.binary.FilesystemFile 0.000s 2 calls abc.XzFile 0.000s 1 call abc.TarFile 0.000s 1 call abc.DotChangesFile ## main (total time: 1.657s) 1.656s 2 calls outputs 0.001s 1 call cleanup ## open_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer ## output (total time: 0.390s) 0.389s 1 call html 0.000s 1 call text 0.000s 1 call json ## recognizes (total time: 0.152s) 0.091s 12 calls diffoscope.comparators.binary.FilesystemFile 0.029s 550 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.018s 162 calls diffoscope.comparators.debian.DebControlMember 0.013s 264 calls diffoscope.comparators.utils.archive.ArchiveMember ## specialize (total time: 0.355s) 0.355s 17 calls specialize Finished with result: success Main processes terminated with: code=exited, status=1/FAILURE Service runtime: 1.897s CPU time consumed: 2.002s Memory peak: 163.5M (swap: 0B) Mon Sep 15 02:25:23 UTC 2025 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Mon Sep 15 02:25:23 UTC 2025 E: mdanalysis failed to build reproducibly in unstable on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-09-15 02:25:24] INFO: Starting at 2025-09-15 02:25:24.160516 [2025-09-15 02:25:24] INFO: Generating the pages of 1 package(s) [2025-09-15 02:25:24] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/mdanalysis didn't produce a buildlog, even though it has been built. [2025-09-15 02:25:24] CRITICAL: buildinfo not detected at /var/lib/jenkins/userContent/reproducible/debian/buildinfo/experimental/amd64/mdanalysis_2.9.0-13~exp2_amd64.buildinfo [2025-09-15 02:25:24] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/experimental/amd64/mdanalysis_2.9.0-13~exp2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/experimental/amd64/mdanalysis_2.9.0-13~exp2.diff.gz is missing [2025-09-15 02:25:24] INFO: Finished at 2025-09-15 02:25:24.462065, took: 0:00:00.301551 Mon Sep 15 02:25:24 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/mdanalysis.html Mon Sep 15 02:25:24 UTC 2025 I: Removing signed mdanalysis_2.9.0-12_amd64.buildinfo.asc files: removed './b1/mdanalysis_2.9.0-12_amd64.buildinfo.asc' removed './b2/mdanalysis_2.9.0-12_amd64.buildinfo.asc' 1757903124 amd64 unstable mdanalysis Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/mdanalysis_2.9.0-12.rbuild.log: 88.8% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/mdanalysis_2.9.0-12.rbuild.log.gz [2025-09-15 02:25:24] INFO: Starting at 2025-09-15 02:25:24.793830 [2025-09-15 02:25:24] INFO: Generating the pages of 1 package(s) [2025-09-15 02:25:25] CRITICAL: buildinfo not detected at /var/lib/jenkins/userContent/reproducible/debian/buildinfo/experimental/amd64/mdanalysis_2.9.0-13~exp2_amd64.buildinfo [2025-09-15 02:25:25] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/experimental/amd64/mdanalysis_2.9.0-13~exp2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/experimental/amd64/mdanalysis_2.9.0-13~exp2.diff.gz is missing [2025-09-15 02:25:25] INFO: Finished at 2025-09-15 02:25:25.085001, took: 0:00:00.291175 All cleanup done. Mon Sep 15 02:25:25 UTC 2025 - total duration: 0h 17m 55s. Mon Sep 15 02:25:25 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-zODcC3kP, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 17min 56.932s CPU time consumed: 3.844s Memory peak: 68.9M (swap: 0B)