I: pbuilder: network access will be disabled during build I: Current time: Sat May 16 11:07:33 +14 2026 I: pbuilder-time-stamp: 1778879253 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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_2.9.0-1.dsc] I: copying [./mdanalysis_2.9.0.orig.tar.gz] I: copying [./mdanalysis_2.9.0-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.9.0-1.dsc: unsupported subcommand 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_2.9.0-1.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2668625/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-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 May 15 21:07 /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/2668625/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2668625/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]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(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=42 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=cb90a44bfd874a1db26e08c29e4cf534 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=2668625 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.o7Rqknct/pbuilderrc_oZh0 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.o7Rqknct/b2 --logfile b2/build.log mdanalysis_2.9.0-1.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2668625/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 ... 19831 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} libaec0{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{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} 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-jquery-ui{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{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} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{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{a} libxrender1{a} libxslt1.1{a} libxss1{a} libyaml-0-2{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-scipy{a} python3-seaborn{a} python3-setuptools{a} python3-six{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-toml{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-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, 267 newly installed, 0 to remove and 0 not upgraded. Need to get 193 MB of archives. After unpacking 796 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-3 [861 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-3 [2212 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.2-2 [27.1 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025b-1 [259 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-3 [1952 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-3 [746 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.1 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.2-2 [28.1 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1 [139 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:2.2.4+ds-1 [5096 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-7 [878 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.5.0-1 [1491 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-4 [94.6 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-7 [294 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.47-1.1 [282 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 52 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2.2 [318 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2.2 [391 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [591 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 blt amd64 2.5.3+dfsg-8 [5984 B] Get: 66 http://deb.debian.org/debian trixie/main amd64 cython3 amd64 3.0.11+dfsg-2+b1 [2504 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 73 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.4 [698 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20250308 [115 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 fonts-lyx all 2.4.3-1 [190 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1+b1 [24.3 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 100 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-2 [194 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.13.0-1 [374 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.13.0-1 [381 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.7.1-1 [161 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libgpg-error0 amd64 1.51-4 [82.1 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.84.1-1 [1514 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1+b1 [479 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B] Get: 123 http://deb.debian.org/debian trixie/main amd64 libhdf5-310 amd64 1.14.5+repack-3 [1344 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [69.3 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 liblzf1 amd64 3.6-4+b3 [10.1 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libnetcdf22 amd64 1:4.9.3-1 [517 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.3-2 [204 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libpython3.13 amd64 3.13.2-3 [2158 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libpython3.13-dev amd64 3.13.2-3 [5015 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libpython3-dev amd64 3.13.2-2 [10.3 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libpython3-all-dev amd64 3.13.2-2 [1068 B] Get: 144 http://deb.debian.org/debian trixie/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.7.0-3 [346 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libxslt1.1 amd64 1.1.35-1.2 [233 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libzopfli1 amd64 1.0.3-3 [106 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 python3-toml all 0.10.2-1 [16.2 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 python3-wheel all 0.45.1-1 [56.7 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 python3-build all 1.2.2-1 [36.0 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 pybuild-plugin-pyproject all 6.20250308 [11.7 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 python-babel-localedata all 2.17.0-1 [6050 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 python-matplotlib-data all 3.10.1+dfsg1-2 [2736 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.13.2-2 [1044 B] Get: 165 http://deb.debian.org/debian trixie/main amd64 python3.13-dev amd64 3.13.2-3 [506 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.13.2-2 [26.1 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 python3-all-dev amd64 3.13.2-2 [1064 B] Get: 168 http://deb.debian.org/debian trixie/main amd64 python3-attr all 25.3.0-1 [69.5 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 python3-babel all 2.17.0-1 [117 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 python3.13-tk amd64 3.13.2-3 [107 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 python3-tk amd64 3.13.2-1 [9516 B] Get: 174 http://deb.debian.org/debian trixie/main amd64 python3-pil.imagetk amd64 11.1.0-5+b1 [81.6 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 11.1.0-5+b1 [513 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 python3-cairo amd64 1.27.0-2 [114 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 python3-freetype all 2.5.1-1 [89.3 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 179 http://deb.debian.org/debian trixie/main amd64 python3-reportlab all 4.3.1-1 [1158 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 python3-biopython amd64 1.85+dfsg-2+b1 [1672 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 python3-brotli amd64 1.1.0-2+b7 [320 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 184 http://deb.debian.org/debian trixie/main amd64 python3-cftime amd64 1.6.4-2 [216 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.4.1-1+b1 [125 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 python3-lxml amd64 5.3.1-1+b1 [1288 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 python3-citeproc all 0.8.2-1 [99.0 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 python3-contourpy amd64 1.3.1-1+b1 [216 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get: 190 http://deb.debian.org/debian trixie/main amd64 python3-dateutil all 2.9.0-4 [79.4 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 192 http://deb.debian.org/debian trixie/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 python3-roman all 5.0-1 [10.6 kB] Get: 194 http://deb.debian.org/debian trixie/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 python3-looseversion all 1.3.0-3 [8964 B] Get: 196 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.10-1 [42.0 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.3.0-2 [114 kB] Get: 198 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-4 [72.1 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 python3-duecredit all 0.10.2-2 [70.6 kB] Get: 200 http://deb.debian.org/debian trixie/main amd64 python3-monotonic all 1.6-3 [5340 B] Get: 201 http://deb.debian.org/debian trixie/main amd64 python3-fasteners all 0.18-2 [14.0 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 python3-filelock all 3.18.0-1 [12.8 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 python3-platformdirs all 4.3.7-1 [16.6 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 python3-fs all 2.4.16-7 [95.2 kB] Get: 205 http://deb.debian.org/debian trixie/main amd64 python3-lz4 amd64 4.4.0+dfsg-2 [25.3 kB] Get: 206 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.15.2-7 [16.3 MB] Get: 207 http://deb.debian.org/debian trixie/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 python3-sympy all 1.13.3-5 [4148 kB] Get: 209 http://deb.debian.org/debian trixie/main amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.0 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 python3-zopfli amd64 0.2.3.post1-1+b1 [10.5 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 python3-fonttools amd64 4.57.0-1 [1438 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1023 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 python3-mrcfile all 1.5.4-2 [118 kB] Get: 215 http://deb.debian.org/debian trixie/main amd64 python3-griddataformats all 1.0.2-2 [2048 kB] Get: 216 http://deb.debian.org/debian trixie/main amd64 python3-gsd amd64 3.4.2-2+b1 [209 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 python3-h5py-serial amd64 3.13.0-1+b1 [1065 kB] Get: 218 http://deb.debian.org/debian trixie/main amd64 python3-h5py all 3.13.0-1 [15.0 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get: 220 http://deb.debian.org/debian trixie/main amd64 python3-hypothesis all 6.127.4-1 [330 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 222 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 223 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.13.0-1 [90.1 kB] Get: 224 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 225 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 226 http://deb.debian.org/debian trixie/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 227 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 228 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.8.0-1 [222 kB] Get: 229 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 230 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 231 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 75.8.0-1 [724 kB] Get: 232 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 233 http://deb.debian.org/debian trixie/main amd64 python3-markupsafe amd64 2.1.5-1+b3 [14.0 kB] Get: 234 http://deb.debian.org/debian trixie/main amd64 python3-jinja2 all 3.1.6-1 [107 kB] Get: 235 http://deb.debian.org/debian trixie/main amd64 python3-joblib all 1.4.2-3 [216 kB] Get: 236 http://deb.debian.org/debian trixie/main amd64 python3-kiwisolver amd64 1.4.7-3+b1 [62.0 kB] Get: 237 http://deb.debian.org/debian trixie/main amd64 python3-latexcodec all 3.0.0-1 [17.5 kB] Get: 238 http://deb.debian.org/debian trixie/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 239 http://deb.debian.org/debian trixie/main amd64 python3-matplotlib amd64 3.10.1+dfsg1-2 [23.8 MB] Get: 240 http://deb.debian.org/debian trixie/main amd64 python3-mda-xdrlib all 0.2.0-3 [11.6 kB] Get: 241 http://deb.debian.org/debian trixie/main amd64 python3-msgpack amd64 1.0.3-3+b4 [84.5 kB] Get: 242 http://deb.debian.org/debian trixie/main amd64 python3-mmtf all 1.1.3-1 [17.0 kB] Get: 243 http://deb.debian.org/debian trixie/main amd64 sphinx-common all 8.1.3-5 [617 kB] Get: 244 http://deb.debian.org/debian trixie/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 245 http://deb.debian.org/debian trixie/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 246 http://deb.debian.org/debian trixie/main amd64 python3-sphinx all 8.1.3-5 [468 kB] Get: 247 http://deb.debian.org/debian trixie/main amd64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 248 http://deb.debian.org/debian trixie/main amd64 python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [29.7 kB] Get: 249 http://deb.debian.org/debian trixie/main amd64 python3-msmb-theme all 1.2.0-4 [33.8 kB] Get: 250 http://deb.debian.org/debian trixie/main amd64 python3-netcdf4 amd64 1.7.2-1+b4 [622 kB] Get: 251 http://deb.debian.org/debian trixie/main amd64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 252 http://deb.debian.org/debian trixie/main amd64 python3-pytz all 2025.1-3 [150 kB] Get: 253 http://deb.debian.org/debian trixie/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-9 [4595 kB] Get: 254 http://deb.debian.org/debian trixie/main amd64 python3-pandas all 2.2.3+dfsg-9 [3097 kB] Get: 255 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 256 http://deb.debian.org/debian trixie/main amd64 python3-six all 1.17.0-1 [16.5 kB] Get: 257 http://deb.debian.org/debian trixie/main amd64 python3-yaml amd64 6.0.2-1+b2 [136 kB] Get: 258 http://deb.debian.org/debian trixie/main amd64 python3-pybtex all 0.24.0-4 [74.6 kB] Get: 259 http://deb.debian.org/debian trixie/main amd64 python3-pybtex-docutils all 1.0.2-1 [8064 B] Get: 260 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 8.3.5-1 [250 kB] Get: 261 http://deb.debian.org/debian trixie/main amd64 python3-seaborn all 0.13.2-5 [215 kB] Get: 262 http://deb.debian.org/debian trixie/main amd64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 263 http://deb.debian.org/debian trixie/main amd64 python3-sklearn-lib amd64 1.4.2+dfsg-8 [3980 kB] Get: 264 http://deb.debian.org/debian trixie/main amd64 python3-sklearn all 1.4.2+dfsg-8 [2248 kB] Get: 265 http://deb.debian.org/debian trixie/main amd64 python3-sphinx-sitemap all 2.6.0-1 [8508 B] Get: 266 http://deb.debian.org/debian trixie/main amd64 python3-sphinxcontrib.bibtex all 2.6.2-1 [32.4 kB] Get: 267 http://deb.debian.org/debian trixie/main amd64 python3-tqdm all 4.67.1-3 [90.3 kB] Fetched 193 MB in 7s (27.1 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 ... 19831 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 libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.2-3_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.2-3) ... 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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 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-3_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.2-3) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-3_amd64.deb ... Unpacking python3.13 (3.13.2-3) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libglib2.0-0t64:amd64 (2.84.1-1) ... No schema files found: doing nothing. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libjs-sphinxdoc (8.1.3-5) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:amd64 (1.1.35-1.2) ... Setting up libharfbuzz0b:amd64 (10.2.0-1+b1) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-2.2) ... Setting up libpython3.13-stdlib:amd64 (3.13.2-3) ... Setting up libpython3-stdlib:amd64 (3.13.2-2) ... Setting up libpython3.13:amd64 (3.13.2-3) ... Setting up libgnutls30t64:amd64 (3.8.9-2) ... Setting up libxft2:amd64 (2.3.6-1+b4) ... 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Setting up python3-biopython (1.85+dfsg-2+b1) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-pybtex-docutils (1.0.2-1) ... Setting up python3-sphinx (8.1.3-5) ... Setting up python3-sphinxcontrib.bibtex (2.6.2-1) ... Setting up python3-sphinx-sitemap (2.6.0-1) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-2) ... Setting up python3-msmb-theme (1.2.0-4) ... Processing triggers for ca-certificates (20241223) ... 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/2668625/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2668625/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_2.9.0-1_source.changes dpkg-buildpackage: info: source package mdanalysis dpkg-buildpackage: info: source version 2.9.0-1 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:270: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) 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/units.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/version.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/due.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/authors.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/__init__.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/util.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/NeighborSearch.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/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/__init__.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/pkdtree.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/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/topology copying MDAnalysis/topology/ParmEdParser.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/ExtendedPDBParser.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/TOPParser.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/TXYZParser.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/CRDParser.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/PSFParser.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/LAMMPSParser.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/tables.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/MinimalParser.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/PDBQTParser.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/core.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/PQRParser.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/FHIAIMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology 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/rotate.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/base.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/__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/nojump.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations 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/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 copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization 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/topology.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/__init__.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/universe.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/accessors.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core creating 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/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/__init__.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/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 creating 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/rdf.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/helix_analysis.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/base.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/nucleicacids.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/atomicdistances.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/lineardensity.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/align.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/msd.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/diffusionmap.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/dielectric.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/rms.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/contacts.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/distances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis 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/__init__.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 creating 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/__init__.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/ParmEd.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 copying MDAnalysis/converters/RDKit.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters creating 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/TRR.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/PDBQT.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/base.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/LAMMPS.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/XTC.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/null.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/PQR.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/memory.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/ParmEd.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/NAMDBIN.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/TXYZ.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/chemfiles.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/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/DMS.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/MMTF.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/H5MD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates 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/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/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/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/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/obj.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/utils.py -> 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 creating 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_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 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/dssp copying MDAnalysis/analysis/dssp/__init__.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/dssp.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp creating 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/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/bootstrap.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 creating 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/analysis/legacy/x3dna.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy creating 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/data/filenames.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data 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/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/encore/dimensionality_reduction/reduce_dimensionality.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/__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 copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.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/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/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/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/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/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/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/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/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/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/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 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/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/libmdanalysis/__init__.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis 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/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/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/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/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/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/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/clustering/src copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src 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 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 creating 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/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/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/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/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/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/parallelization_time.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images 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/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/topology.rst -> 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/util.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/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/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/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/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/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/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/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/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/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/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/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/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/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/lib_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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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 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/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/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/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/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/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 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 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/analysis_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/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/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/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/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/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/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/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/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.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_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/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/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/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/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/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/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/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/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/topologyobjects.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core 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/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/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/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/vmd.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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/psa.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/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/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/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/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/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/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/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/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/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/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/encore.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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/nuclinfo.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/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/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/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 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/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/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/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/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/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/visualization_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/units.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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/selections.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages 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/source/index.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source copying build/lib.linux-x86_64-cpython-313/doc/README -> build/bdist.linux-x86_64/wheel/./doc creating build/bdist.linux-x86_64/wheel/MDAnalysis 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/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/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/_augment.cpp -> 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 creating 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.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/cython_util.c -> 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/readdcd.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/fastio.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/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/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/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/libmdaxdr.pxd -> 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 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/__init__.py -> 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/cython_util.pyx -> 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 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/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_trr.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/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/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src 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/_cutil.pxd -> 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/_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/_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.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/NeighborSearch.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 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/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/picklable_file_io.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 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/_distopia.py -> 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/__init__.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/_cutil.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 creating 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/libmdanalysis/__init__.pxd -> 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/c_distances.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/nsgrid.cpp -> 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.pxd -> 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/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/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/pkdtree.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/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/distances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib 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 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 creating 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/__init__.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/setting.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr 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/DLPolyParser.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/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 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/GSDParser.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/GMSParser.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/__init__.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/guessers.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/DMSParser.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/MMTFParser.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/PDBParser.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/HoomdXMLParser.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/XYZParser.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/MOL2Parser.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/TPRParser.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 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/rotate.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/base.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/__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/nojump.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/authors.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/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/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 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization 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/topology.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/__init__.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/universe.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/accessors.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core creating 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/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/__init__.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/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 creating 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 creating 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_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/rdf.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 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/bat.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/density.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/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 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/atomicdistances.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/pca.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/__init__.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/dssp.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/dssp copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore 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/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 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/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/__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/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/cutils.pyx -> 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.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 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/__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 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/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/ClusteringMethod.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering 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/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/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/bootstrap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore 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/polymer.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/__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/__init__.py -> 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/msd.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/diffusionmap.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/dielectric.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/rms.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/rama_ref_data.npy -> 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/data/__init__.py -> 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/leaflet.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 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/distances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis 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/__init__.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 creating 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/__init__.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/ParmEd.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 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/RDKit.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/XDR.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/GSD.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/PDBQT.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/base.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/LAMMPS.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/XTC.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/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/TRZ.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/TRC.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/__init__.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.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/NAMDBIN.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/TXYZ.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/timestep.cpp -> 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/chain.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/DMS.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/MMTF.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/H5MD.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 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-f912jsy1/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 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'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/AUTHORS' adding 'MDAnalysis-2.9.0.dist-info/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 v8.1.3 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 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 ... 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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://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'))) loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/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 'parmed' from https://parmed.github.io/ParmEd/html/objects.inv ... loading intersphinx inventory 'rdkit' from https://rdkit.org/docs/objects.inv ... loading intersphinx inventory 'waterdynamics' from https://www.mdanalysis.org/waterdynamics/objects.inv ... 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://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://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 'dask' from https://docs.dask.org/en/stable/objects.inv ... 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://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://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'))) 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://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/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'))) 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'))) 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( Didn't find AlignTraj.reference_atoms in MDAnalysis.analysis.align Didn't find AlignTraj.mobile_atoms in MDAnalysis.analysis.align Didn't find AlignTraj.results.rmsd in MDAnalysis.analysis.align Didn't find AlignTraj.filename in MDAnalysis.analysis.align Didn't find AverageStructure.reference_atoms in MDAnalysis.analysis.align Didn't find AverageStructure.mobile_atoms in MDAnalysis.analysis.align Didn't find AverageStructure.results.universe in MDAnalysis.analysis.align Didn't find AverageStructure.results.positions in MDAnalysis.analysis.align Didn't find AverageStructure.results.rmsd in MDAnalysis.analysis.align Didn't find AverageStructure.filename in MDAnalysis.analysis.align reading sources... [ 1%] documentation_pages/analysis/atomicdistances Didn't find AtomicDistances.results in MDAnalysis.analysis.atomicdistances Didn't find AtomicDistances.n_frames in MDAnalysis.analysis.atomicdistances Didn't find AtomicDistances.n_atoms in MDAnalysis.analysis.atomicdistances reading sources... [ 2%] documentation_pages/analysis/backends reading sources... [ 2%] documentation_pages/analysis/base Didn't find AnalysisBase.times in MDAnalysis.analysis.base Didn't find AnalysisBase.frames in MDAnalysis.analysis.base Didn't find AnalysisBase.results in MDAnalysis.analysis.base Didn't find AnalysisFromFunction.results.frames in MDAnalysis.analysis.base Didn't find AnalysisFromFunction.results.times in MDAnalysis.analysis.base Didn't find AnalysisFromFunction.results.timeseries in MDAnalysis.analysis.base Didn't find results.frames in MDAnalysis.analysis.base Didn't find results.times in MDAnalysis.analysis.base Didn't find results.timeseries in MDAnalysis.analysis.base reading sources... [ 3%] documentation_pages/analysis/bat Didn't find BAT.results.bat in MDAnalysis.analysis.bat reading sources... [ 3%] documentation_pages/analysis/contacts Didn't find Contacts.results.timeseries in MDAnalysis.analysis.contacts Didn't find Contacts.n_initial_contacts in MDAnalysis.analysis.contacts Didn't find Contacts.r0 in MDAnalysis.analysis.contacts reading sources... [ 4%] documentation_pages/analysis/data reading sources... [ 5%] documentation_pages/analysis/density Didn't find DensityAnalysis.results.density in MDAnalysis.analysis.density Didn't find Density.grid in MDAnalysis.analysis.density Didn't find Density.edges in MDAnalysis.analysis.density Didn't find Density.delta in MDAnalysis.analysis.density Didn't find Density.origin in MDAnalysis.analysis.density Didn't find Density.units in MDAnalysis.analysis.density reading sources... [ 5%] documentation_pages/analysis/dielectric Didn't find DielectricConstant.results.M in MDAnalysis.analysis.dielectric Didn't find DielectricConstant.results.M2 in MDAnalysis.analysis.dielectric Didn't find DielectricConstant.results.fluct in MDAnalysis.analysis.dielectric Didn't find DielectricConstant.results.eps in MDAnalysis.analysis.dielectric Didn't find DielectricConstant.results.eps_mean in MDAnalysis.analysis.dielectric reading sources... [ 6%] documentation_pages/analysis/diffusionmap Didn't find DiffusionMap.eigenvalues in MDAnalysis.analysis.diffusionmap Didn't find DistanceMatrix.atoms in MDAnalysis.analysis.diffusionmap Didn't find DistanceMatrix.results.dist_matrix in MDAnalysis.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-dnxq2lnf 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. Didn't find Dihedral.results.angles in MDAnalysis.analysis.dihedrals Didn't find Ramachandran.results.angles in MDAnalysis.analysis.dihedrals Didn't find Janin.results.angles in MDAnalysis.analysis.dihedrals reading sources... [ 7%] documentation_pages/analysis/distances reading sources... [ 7%] documentation_pages/analysis/dssp Didn't find DSSP.results.dssp in MDAnalysis.analysis.dssp.dssp Didn't find DSSP.results.dssp_ndarray in MDAnalysis.analysis.dssp.dssp Didn't find DSSP.results.resids in MDAnalysis.analysis.dssp.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 Didn't find Cluster.id in MDAnalysis.analysis.encore.clustering.ClusterCollection Didn't find Cluster.metadata in MDAnalysis.analysis.encore.clustering.ClusterCollection Didn't find Cluster.size in MDAnalysis.analysis.encore.clustering.ClusterCollection Didn't find Cluster.centroid in MDAnalysis.analysis.encore.clustering.ClusterCollection Didn't find Cluster.elements in MDAnalysis.analysis.encore.clustering.ClusterCollection Didn't find ClusterCollection.clusters in MDAnalysis.analysis.encore.clustering.ClusterCollection 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 Didn't find ParallelCalculation.n_jobs in MDAnalysis.analysis.encore.utils Didn't find ParallelCalculation.function in MDAnalysis.analysis.encore.utils Didn't find ParallelCalculation.args in MDAnalysis.analysis.encore.utils Didn't find ParallelCalculation.kwargs in MDAnalysis.analysis.encore.utils Didn't find ParallelCalculation.nruns in MDAnalysis.analysis.encore.utils reading sources... [ 12%] documentation_pages/analysis/gnm Didn't find GNMAnalysis.results.times in MDAnalysis.analysis.gnm Didn't find GNMAnalysis.results.eigenvalues in MDAnalysis.analysis.gnm Didn't find GNMAnalysis.results.eigenvectors in MDAnalysis.analysis.gnm Didn't find closeContactGNMAnalysis.results.times in MDAnalysis.analysis.gnm Didn't find closeContactGNMAnalysis.results.eigenvalues in MDAnalysis.analysis.gnm Didn't find closeContactGNMAnalysis.results.eigenvectors in MDAnalysis.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 Didn't find HELANAL.results.local_twists in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.local_nres_per_turn in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.local_axes in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.local_heights in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.local_helix_directions in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.local_origins in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.local_screw_angles in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.local_bends in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.all_bends in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.global_axis in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.global_tilts in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.summary in MDAnalysis.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... [ 15%] documentation_pages/analysis/hydrogenbonds Didn't find HydrogenBondAnalysis.results.hbonds in MDAnalysis.analysis.hydrogenbonds.hbond_analysis reading sources... [ 16%] documentation_pages/analysis/leaflet reading sources... [ 16%] documentation_pages/analysis/legacy/x3dna Didn't find X3DNA.profiles in MDAnalysis.analysis.legacy.x3dna Didn't find X3DNAtraj.profiles in MDAnalysis.analysis.legacy.x3dna reading sources... [ 17%] documentation_pages/analysis/legacy_modules reading sources... [ 18%] documentation_pages/analysis/lineardensity Didn't find LinearDensity.results.x.dim in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.mass_density in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.mass_density_stddev in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.charge_density in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.charge_density_stddev in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.pos in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.pos_std in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.char in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.char_std in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.slice_volume in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.hist_bin_edges in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.Note in MDAnalysis.analysis.lineardensity reading sources... [ 18%] documentation_pages/analysis/msd Didn't find EinsteinMSD.dim_fac in MDAnalysis.analysis.msd Didn't find EinsteinMSD.results.timeseries in MDAnalysis.analysis.msd Didn't find EinsteinMSD.results.msds_by_particle in MDAnalysis.analysis.msd Didn't find EinsteinMSD.ag in MDAnalysis.analysis.msd Didn't find EinsteinMSD.n_frames in MDAnalysis.analysis.msd Didn't find EinsteinMSD.n_particles in MDAnalysis.analysis.msd reading sources... [ 19%] documentation_pages/analysis/nucleicacids Didn't find NucPairDist.results.pair_distances in MDAnalysis.analysis.nucleicacids Didn't find NucPairDist.results.distances in MDAnalysis.analysis.nucleicacids Didn't find NucPairDist.times in MDAnalysis.analysis.nucleicacids Didn't find WatsonCrickDist.results.distances in MDAnalysis.analysis.nucleicacids Didn't find WatsonCrickDist.results.pair_distances in MDAnalysis.analysis.nucleicacids Didn't find WatsonCrickDist.times in MDAnalysis.analysis.nucleicacids Didn't find MinorPairDist.results.distances in MDAnalysis.analysis.nucleicacids Didn't find MinorPairDist.times in MDAnalysis.analysis.nucleicacids Didn't find MajorPairDist.results.distances in MDAnalysis.analysis.nucleicacids Didn't find MajorPairDist.times in MDAnalysis.analysis.nucleicacids reading sources... [ 19%] documentation_pages/analysis/nuclinfo reading sources... [ 20%] documentation_pages/analysis/parallelization reading sources... [ 20%] documentation_pages/analysis/pca Didn't find PCA.results.p_components in MDAnalysis.analysis.pca Didn't find PCA.results.variance in MDAnalysis.analysis.pca Didn't find PCA.results.cumulated_variance in MDAnalysis.analysis.pca reading sources... [ 21%] documentation_pages/analysis/polymer Didn't find PersistenceLength.results.bond_autocorrelation in MDAnalysis.analysis.polymer Didn't find PersistenceLength.results.lb in MDAnalysis.analysis.polymer Didn't find PersistenceLength.results.x in MDAnalysis.analysis.polymer Didn't find PersistenceLength.results.lp in MDAnalysis.analysis.polymer Didn't find PersistenceLength.results.fit in MDAnalysis.analysis.polymer reading sources... [ 21%] documentation_pages/analysis/psa /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/analysis/psa.py:72: UserWarning: Please install the PathSimAnalysis mdakit to use it in MDAnalysis. More details can be found here: https://www.mdanalysis.org/PathSimAnalysis/getting_started.html warnings.warn(wmsg, category=UserWarning) reading sources... [ 22%] documentation_pages/analysis/rdf Didn't find InterRDF.results.bins in MDAnalysis.analysis.rdf Didn't find InterRDF.results.edges in MDAnalysis.analysis.rdf Didn't find InterRDF.results.rdf in MDAnalysis.analysis.rdf Didn't find InterRDF.results.count in MDAnalysis.analysis.rdf Didn't find InterRDF_s.results.bins in MDAnalysis.analysis.rdf Didn't find InterRDF_s.results.edges in MDAnalysis.analysis.rdf Didn't find InterRDF_s.results.rdf in MDAnalysis.analysis.rdf Didn't find InterRDF_s.results.count in MDAnalysis.analysis.rdf Didn't find InterRDF_s.results.cdf in MDAnalysis.analysis.rdf reading sources... [ 23%] documentation_pages/analysis/results reading sources... [ 23%] documentation_pages/analysis/rms Didn't find RMSD.results.rmsd in MDAnalysis.analysis.rms Didn't find RMSF.results.rmsf in MDAnalysis.analysis.rms reading sources... [ 24%] documentation_pages/analysis/waterdynamics /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/analysis/waterdynamics.py:57: UserWarning: Please install the waterdynamics mdakit to use it in MDAnalysis. More details can be found here: https://www.mdanalysis.org/waterdynamics/getting_started.html warnings.warn(wmsg, category=UserWarning) reading sources... [ 24%] documentation_pages/analysis/wbridge_analysis Didn't find WaterBridgeAnalysis.timesteps in MDAnalysis.analysis.hydrogenbonds.wbridge_analysis Didn't find WaterBridgeAnalysis.results.network in MDAnalysis.analysis.hydrogenbonds.wbridge_analysis Didn't find WaterBridgeAnalysis.table in MDAnalysis.analysis.hydrogenbonds.wbridge_analysis Didn't find WaterBridgeAnalysis.results.timeseries in MDAnalysis.analysis.hydrogenbonds.wbridge_analysis reading sources... [ 25%] documentation_pages/analysis_modules reading sources... [ 25%] documentation_pages/auxiliary/EDR Didn't find EDRReader._auxdata in MDAnalysis.auxiliary.EDR Didn't find EDRReader.data_dict in MDAnalysis.auxiliary.EDR Didn't find EDRReader.unit_dict in MDAnalysis.auxiliary.EDR Didn't find EDRReader._n_steps in MDAnalysis.auxiliary.EDR Didn't find EDRReader.terms in MDAnalysis.auxiliary.EDR reading sources... [ 26%] documentation_pages/auxiliary/XVG reading sources... [ 27%] documentation_pages/auxiliary/base Didn't find AuxStep.step in MDAnalysis.auxiliary.base Didn't find AuxReader.auxstep in MDAnalysis.auxiliary.base Didn't find AuxReader.frame_data in MDAnalysis.auxiliary.base Didn't find AuxReader.frame_rep in MDAnalysis.auxiliary.base Didn't find AuxFileReader.auxfile in MDAnalysis.auxiliary.base reading sources... [ 27%] documentation_pages/auxiliary/core reading sources... [ 28%] documentation_pages/auxiliary/init reading sources... [ 28%] documentation_pages/auxiliary_modules reading sources... [ 29%] documentation_pages/converters reading sources... [ 29%] documentation_pages/converters/OpenMM reading sources... [ 30%] documentation_pages/converters/ParmEd reading sources... [ 31%] documentation_pages/converters/RDKit reading sources... [ 31%] documentation_pages/converters/base reading sources... [ 32%] documentation_pages/coordinates/CRD reading sources... [ 32%] documentation_pages/coordinates/DCD reading sources... [ 33%] documentation_pages/coordinates/DLPoly reading sources... [ 33%] documentation_pages/coordinates/DMS reading sources... [ 34%] documentation_pages/coordinates/FHIAIMS reading sources... [ 34%] documentation_pages/coordinates/GMS reading sources... [ 35%] documentation_pages/coordinates/GRO reading sources... [ 36%] documentation_pages/coordinates/GSD reading sources... [ 36%] documentation_pages/coordinates/H5MD reading sources... [ 37%] documentation_pages/coordinates/INPCRD reading sources... [ 37%] documentation_pages/coordinates/LAMMPS reading sources... [ 38%] documentation_pages/coordinates/MMTF reading sources... [ 38%] documentation_pages/coordinates/MOL2 reading sources... [ 39%] documentation_pages/coordinates/NAMDBIN reading sources... [ 40%] documentation_pages/coordinates/PDB reading sources... [ 40%] documentation_pages/coordinates/PDBQT reading sources... [ 41%] documentation_pages/coordinates/PQR reading sources... [ 41%] documentation_pages/coordinates/TNG reading sources... [ 42%] documentation_pages/coordinates/TRC reading sources... [ 42%] documentation_pages/coordinates/TRJ reading sources... [ 43%] documentation_pages/coordinates/TRR reading sources... [ 44%] documentation_pages/coordinates/TRZ Didn't find TRZReader.ts in MDAnalysis.coordinates.TRZ reading sources... [ 44%] documentation_pages/coordinates/TXYZ reading sources... [ 45%] documentation_pages/coordinates/XDR reading sources... [ 45%] documentation_pages/coordinates/XTC reading sources... [ 46%] documentation_pages/coordinates/XYZ reading sources... [ 46%] documentation_pages/coordinates/base reading sources... [ 47%] documentation_pages/coordinates/chain reading sources... [ 47%] documentation_pages/coordinates/chemfiles reading sources... [ 48%] documentation_pages/coordinates/core reading sources... [ 49%] documentation_pages/coordinates/init reading sources... [ 49%] documentation_pages/coordinates/memory reading sources... [ 50%] documentation_pages/coordinates/null reading sources... [ 50%] documentation_pages/coordinates/pickle_readers reading sources... [ 51%] documentation_pages/coordinates/timestep reading sources... [ 51%] documentation_pages/coordinates_modules reading sources... [ 52%] documentation_pages/core/accessors reading sources... [ 53%] documentation_pages/core/groups reading sources... [ 53%] documentation_pages/core/init reading sources... [ 54%] documentation_pages/core/selection reading sources... [ 54%] documentation_pages/core/topology Didn't find TransTable.n_atoms in MDAnalysis.core.topology Didn't find TransTable.n_residues in MDAnalysis.core.topology Didn't find TransTable.n_segments in MDAnalysis.core.topology reading sources... [ 55%] documentation_pages/core/topologyattrs reading sources... [ 55%] documentation_pages/core/topologyobjects reading sources... [ 56%] documentation_pages/core/universe Didn't find Universe.atoms in MDAnalysis.core.universe Didn't find Universe.residues in MDAnalysis.core.universe Didn't find Universe.segments in MDAnalysis.core.universe reading sources... [ 56%] documentation_pages/core_modules reading sources... [ 57%] documentation_pages/exceptions reading sources... [ 58%] documentation_pages/guesser_modules reading sources... [ 58%] documentation_pages/guesser_modules/base reading sources... [ 59%] documentation_pages/guesser_modules/default_guesser reading sources... [ 59%] documentation_pages/guesser_modules/init reading sources... [ 60%] documentation_pages/guesser_modules/tables reading sources... [ 60%] documentation_pages/lib/NeighborSearch reading sources... [ 61%] documentation_pages/lib/c_distances reading sources... [ 62%] documentation_pages/lib/c_distances_openmp reading sources... [ 62%] documentation_pages/lib/correlations reading sources... [ 63%] documentation_pages/lib/distances reading sources... [ 63%] documentation_pages/lib/formats/libdcd reading sources... [ 64%] documentation_pages/lib/formats/libmdaxdr reading sources... [ 64%] documentation_pages/lib/log reading sources... [ 65%] documentation_pages/lib/mdamath reading sources... [ 66%] documentation_pages/lib/nsgrid reading sources... [ 66%] documentation_pages/lib/picklable_file_io reading sources... [ 67%] documentation_pages/lib/pkdtree reading sources... [ 67%] documentation_pages/lib/qcprot reading sources... [ 68%] documentation_pages/lib/transformations reading sources... [ 68%] documentation_pages/lib/util reading sources... [ 69%] documentation_pages/lib_modules reading sources... [ 69%] documentation_pages/overview reading sources... [ 70%] documentation_pages/references reading sources... [ 71%] documentation_pages/selections reading sources... [ 71%] documentation_pages/selections/base reading sources... [ 72%] documentation_pages/selections/charmm reading sources... [ 72%] documentation_pages/selections/gromacs reading sources... [ 73%] documentation_pages/selections/jmol reading sources... [ 73%] documentation_pages/selections/pymol reading sources... [ 74%] documentation_pages/selections/vmd reading sources... [ 75%] documentation_pages/selections_modules reading sources... [ 75%] documentation_pages/topology reading sources... [ 76%] documentation_pages/topology/CRDParser reading sources... [ 76%] documentation_pages/topology/DLPolyParser reading sources... [ 77%] documentation_pages/topology/DMSParser reading sources... [ 77%] documentation_pages/topology/ExtendedPDBParser reading sources... [ 78%] documentation_pages/topology/FHIAIMSParser reading sources... [ 79%] documentation_pages/topology/GMSParser reading sources... [ 79%] documentation_pages/topology/GROParser reading sources... [ 80%] documentation_pages/topology/GSDParser reading sources... [ 80%] documentation_pages/topology/HoomdXMLParser reading sources... [ 81%] documentation_pages/topology/ITPParser reading sources... [ 81%] documentation_pages/topology/LAMMPSParser reading sources... [ 82%] documentation_pages/topology/MMTFParser reading sources... [ 82%] documentation_pages/topology/MOL2Parser reading sources... [ 83%] documentation_pages/topology/MinimalParser reading sources... [ 84%] documentation_pages/topology/PDBParser reading sources... [ 84%] documentation_pages/topology/PDBQTParser reading sources... [ 85%] documentation_pages/topology/PQRParser reading sources... [ 85%] documentation_pages/topology/PSFParser reading sources... [ 86%] documentation_pages/topology/TOPParser reading sources... [ 86%] documentation_pages/topology/TPRParser reading sources... [ 87%] documentation_pages/topology/TXYZParser reading sources... [ 88%] documentation_pages/topology/XYZParser reading sources... [ 88%] documentation_pages/topology/base reading sources... [ 89%] documentation_pages/topology/core reading sources... [ 89%] documentation_pages/topology/guessers reading sources... [ 90%] documentation_pages/topology/init reading sources... [ 90%] documentation_pages/topology/tables /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/topology/tables.py:52: DeprecationWarning: Deprecated in version 2.8.0 MDAnalysis.topology.tables has been moved to MDAnalysis.guesser.tables. This import point will be removed in MDAnalysis version 3.0.0 warnings.warn(wmsg, category=DeprecationWarning) reading sources... [ 91%] documentation_pages/topology/tpr_util reading sources... [ 92%] documentation_pages/topology_modules reading sources... [ 92%] documentation_pages/trajectory_transformations reading sources... [ 93%] documentation_pages/transformations/base reading sources... [ 93%] documentation_pages/transformations/boxdimensions reading sources... [ 94%] documentation_pages/transformations/fit reading sources... [ 94%] documentation_pages/transformations/nojump reading sources... [ 95%] documentation_pages/transformations/positionaveraging reading sources... [ 95%] documentation_pages/transformations/rotate reading sources... [ 96%] documentation_pages/transformations/translate reading sources... [ 97%] documentation_pages/transformations/wrap reading sources... [ 97%] documentation_pages/units reading sources... [ 98%] documentation_pages/version reading sources... [ 98%] documentation_pages/visualization/streamlines reading sources... [ 99%] documentation_pages/visualization/streamlines_3D reading sources... [ 99%] documentation_pages/visualization_modules reading sources... [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: No module named 'MDAnalysis.analysis.hole2.utils' [autodoc.import_object] WARNING: autodoc: failed to import module 'templates' from module 'MDAnalysis.analysis.hole2'; the following exception was raised: No module named 'MDAnalysis.analysis.hole2.templates' [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. 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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' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/mdanalysis-2.9.0' py3versions: no X-Python3-Version in control file, using supported versions set -e; \ for py in 3.13; do \ echo "=== testing with python$py ==="; \ pydir=`pybuild -p $py --system=distutils --print {build_dir}`; \ MPLBACKEND=agg PYTHONPATH=$pydir python$py -mpytest -v -k "not ( test_all_import[.analysis.hole2] or journal.pcbi.1004568 )" --disable-pytest-warnings testsuite; \ rm -rf $pydir/MDAnalysis/.hypothesis; \ rm -rf $pydir/MDAnalysis/.duecredit.p; \ done === testing with python3.13 === ============================= test session starts ============================== platform linux -- Python 3.13.2, pytest-8.3.5, pluggy-1.5.0 -- /usr/bin/python3.13 cachedir: .pytest_cache hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase(PosixPath('/build/reproducible-path/mdanalysis-2.9.0/.hypothesis/examples')) rootdir: /build/reproducible-path/mdanalysis-2.9.0/testsuite configfile: pyproject.toml plugins: typeguard-4.4.2, hypothesis-6.127.4 collecting ... collected 19886 items / 1 deselected / 6 skipped / 19885 selected testsuite/MDAnalysisTests/analysis/test_align.py::TestRotationMatrix::test_rotation_matrix_input[a0-b0-None-0.15785647734415692] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestRotationMatrix::test_rotation_matrix_input[a1-b1-weights1-0.13424643502242328] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestRotationMatrix::test_list_args PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestRotationMatrix::test_exception PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestGetMatchingAtoms::test_match[True] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestGetMatchingAtoms::test_match[False] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestGetMatchingAtoms::test_nomatch_atoms_raise[True] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestGetMatchingAtoms::test_nomatch_atoms_raise[False] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestGetMatchingAtoms::test_nomatch_residues_raise_empty[True] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestGetMatchingAtoms::test_nomatch_residues_raise_empty[False] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestGetMatchingAtoms::test_toggle_atom_mismatch_default_error PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestGetMatchingAtoms::test_toggle_atom_mismatch_kwarg_error PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestGetMatchingAtoms::test_toggle_atom_nomatch PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestGetMatchingAtoms::test_toggle_atom_nomatch_mismatch_atoms PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestGetMatchingAtoms::test_subselection_alignto[resname ALA and name CA-expectation0] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestGetMatchingAtoms::test_subselection_alignto[subselection1-expectation1] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestGetMatchingAtoms::test_subselection_alignto[1234-expectation2] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestGetMatchingAtoms::test_no_atom_masses PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestGetMatchingAtoms::test_one_universe_has_masses PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAlign::test_rmsd PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAlign::test_rmsd_custom_mass_weights PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAlign::test_rmsd_custom_weights PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAlign::test_AlignTraj_outfile_default PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAlign::test_AlignTraj_outfile_default_exists PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAlign::test_AlignTraj_step_works PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAlign::test_AlignTraj_deprecated_attribute PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAlign::test_AlignTraj PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAlign::test_AlignTraj_weighted PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAlign::test_AlignTraj_custom_weights PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAlign::test_AlignTraj_custom_mass_weights PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAlign::test_AlignTraj_partial_fit PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAlign::test_AlignTraj_in_memory PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAlign::test_AlignTraj_writer_kwargs PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAlign::test_alignto_checks_selections PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAlign::test_alignto_partial_universe PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAverageStructure::test_average_structure_deprecated_attrs PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAverageStructure::test_average_structure PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAverageStructure::test_average_structure_mass_weighted PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAverageStructure::test_average_structure_select PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAverageStructure::test_average_structure_no_ref PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAverageStructure::test_average_structure_no_msf PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAverageStructure::test_mismatch_atoms PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAverageStructure::test_average_structure_ref_frame PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAverageStructure::test_average_structure_in_memory PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAlignmentProcessing::test_importerror_biopython SKIPPED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAlignmentProcessing::test_fasta2select_aligned PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAlignmentProcessing::test_fasta2select_file SKIPPED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAlignmentProcessing::test_fasta2select_ClustalW SKIPPED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestAlignmentProcessing::test_fasta2select_resids PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestSequenceAlignmentFunction::test_biopython_import_error SKIPPED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestSequenceAlignmentFunction::test_sequence_alignment PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestSequenceAlignmentFunction::test_sequence_alignment_deprecation PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestIterativeAverage::test_iterative_average_default PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestIterativeAverage::test_iterative_average_eps_high PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestIterativeAverage::test_iterative_average_weights_mass PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestIterativeAverage::test_iterative_average_convergence_failure PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::TestIterativeAverage::test_iterative_average_convergence_verbose PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_align.py::test_alignto_reorder_atomgroups PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_atomicdistances.py::TestAtomicDistances::test_ad_exceptions PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_atomicdistances.py::TestAtomicDistances::test_ad_pairwise_dist PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_atomicdistances.py::TestAtomicDistances::test_ad_pairwise_dist_pbc PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_backends.py::Test_Backends::test_fails_incorrect_n_workers[BackendBase--1] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_backends.py::Test_Backends::test_fails_incorrect_n_workers[BackendSerial-None] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_backends.py::Test_Backends::test_fails_incorrect_n_workers[BackendMultiprocessing-string] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_backends.py::Test_Backends::test_fails_incorrect_n_workers[BackendDask-n_workers3] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_backends.py::Test_Backends::test_all_backends_give_correct_results[square-iterable0-answer0] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_backends.py::Test_Backends::test_all_backends_give_correct_results[square-iterable1-answer1] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_backends.py::Test_Backends::test_all_backends_give_correct_results[noop-iterable2-answer2] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_backends.py::Test_Backends::test_all_backends_give_correct_results[upper-asdf-answer3] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_backends.py::Test_Backends::test_get_warnings[BackendSerial-params0-n_workers is ignored when executing with backend='serial'] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_backends.py::Test_Backends::test_get_errors[BackendDask-params0-module 'dask' is missing. Please install 'dask': https://docs.dask.org/en/stable/install.html] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_incompatible_n_workers PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_frame_values_incompatability PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_n_workers_conflict_raises_value_error PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_backend_configuration_fails[Parallelizable-not-existing-backend-2] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_backend_configuration_fails[Parallelizable-not-existing-backend-None] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_backend_configuration_fails[SerialOnly-not-existing-backend-2] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_backend_configuration_fails[SerialOnly-not-existing-backend-None] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_backend_configuration_fails[SerialOnly-multiprocessing-2] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_backend_configuration_fails[SerialOnly-dask-None] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_backend_configuration_fails[ParallelizableWithDaskOnly-multiprocessing-None] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_backend_configuration_fails[ParallelizableWithDaskOnly-multiprocessing-2] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_backend_configuration_works_when_unsupported_backend[Parallelizable-CustomSerialBackend-2] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_backend_configuration_works_when_unsupported_backend[ParallelizableWithDaskOnly-CustomSerialBackend-2] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_custom_backend_works[Parallelizable-CustomSerialBackend-1] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_custom_backend_works[ParallelizableWithDaskOnly-CustomSerialBackend-1] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_fails_incorrect_custom_backend[Parallelizable-map-1] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_fails_incorrect_custom_backend[SerialOnly-list-1] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_fails_incorrect_custom_backend[ParallelizableWithDaskOnly-object-1] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_fails_for_unparallelizable[SerialOnly-CustomSerialBackend-1] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_fails_for_unparallelizable[SerialOnly-multiprocessing-1] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_fails_for_unparallelizable[SerialOnly-dask-1] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_start_stop_step_parallel[client_FrameAnalysis0-run_kwargs0-frames0] 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testsuite/MDAnalysisTests/analysis/test_base.py::test_frame_bool_fail[client_FrameAnalysis0] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_rewind[client_FrameAnalysis0] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_frames_times[client_FrameAnalysis0] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_start_stop_step_parallel[client_FrameAnalysis1-run_kwargs0-frames0] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_start_stop_step_parallel[client_FrameAnalysis1-run_kwargs1-frames1] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_start_stop_step_parallel[client_FrameAnalysis1-run_kwargs2-frames2] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_start_stop_step_parallel[client_FrameAnalysis1-run_kwargs3-frames3] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_base.py::test_frame_slice_parallel[client_FrameAnalysis1-run_kwargs0-frames0] PASSED [ 0%] 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testsuite/MDAnalysisTests/analysis/test_bat.py::TestBAT::test_bat_coordinates_single_frame[client_BAT1] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_bat.py::TestBAT::test_bat_reconstruction[client_BAT1] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_bat.py::TestBAT::test_bat_IO[client_BAT1] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_bat.py::TestBAT::test_bat_incorrect_dims[client_BAT1] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_bat.py::TestBAT::test_Cartesian_does_not_modify_input[client_BAT1] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_bat.py::TestBAT::test_bat_nobonds PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_bat.py::TestBAT::test_bat_bad_initial_atom PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_bat.py::TestBAT::test_bat_disconnected_atom_group PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_bat.py::TestBAT::test_bat_multifragments_atomgroup PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_contacts.py::test_soft_cut_q PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_contacts.py::test_soft_cut_q_folded PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_contacts.py::test_soft_cut_q_unfolded PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_contacts.py::test_hard_cut_q[r0-2-1] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_contacts.py::test_hard_cut_q[r1-1-0] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_contacts.py::test_hard_cut_q[r2-1-0.5] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_contacts.py::test_hard_cut_q[r3-cutoff3-1] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_contacts.py::test_hard_cut_q[r4-cutoff4-0] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_contacts.py::test_radius_cut_q[r0-None-2-1] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_contacts.py::test_radius_cut_q[r1-None-1-0] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_contacts.py::test_radius_cut_q[r2-None-1-0.5] PASSED [ 0%] testsuite/MDAnalysisTests/analysis/test_contacts.py::test_contact_matrix PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::test_new_selection PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_select_valid_types[(resname ASP GLU) and (name OE* OD*)] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_select_valid_types[(resname ARG LYS) and (name NH* NZ)] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_contacts_selections[client_Contacts0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_startframe[client_Contacts0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_end_zero[client_Contacts0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_slicing[client_Contacts0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_folded[client_Contacts0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_unfolded[client_Contacts0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_hard_cut_method[client_Contacts0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_radius_cut_method[client_Contacts0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_own_method[client_Contacts0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_own_method_no_array_cast[client_Contacts0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_non_callable_method[client_Contacts0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_distance_box[client_Contacts0-True-expected0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_distance_box[client_Contacts0-False-expected1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_warn_deprecated_attr[client_Contacts0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::test_q1q2[client_Contacts0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_contacts_selections[client_Contacts1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_startframe[client_Contacts1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_end_zero[client_Contacts1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_slicing[client_Contacts1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_folded[client_Contacts1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_unfolded[client_Contacts1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_hard_cut_method[client_Contacts1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_radius_cut_method[client_Contacts1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_own_method[client_Contacts1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_own_method_no_array_cast[client_Contacts1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_non_callable_method[client_Contacts1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_distance_box[client_Contacts1-True-expected0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_distance_box[client_Contacts1-False-expected1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_warn_deprecated_attr[client_Contacts1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::test_q1q2[client_Contacts1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_select_wrong_types[1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_select_wrong_types[ag1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_select_wrong_types[Universe] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_select_wrong_types[USE UPDATING AG] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_n_initial_contacts[datafiles0-0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_n_initial_contacts[datafiles1-41814] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_data.py::test_all_exports PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_shape PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_edges PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_midpoints PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_delta PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_grid PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_origin PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_check_set_unit_keyerror PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_check_set_unit_attributeError PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_check_set_unit_nolength PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_check_set_density_none PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_check_set_density_not_in_units PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_parameters_isdensity PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_check_convert_density_grid_not_density PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_check_convert_density_value_error PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_check_convert_density_units_same_density_units PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_check_convert_density_units_density PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_convert_length_same_length_units PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_convert_length_other_length_units PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_repr PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_check_convert_length_edges PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_check_convert_density_edges PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_export_types[float] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_export_types[double] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_export_types[int] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensity::test_export_types[byte] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_run[client_DensityAnalysis0-static] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_run[client_DensityAnalysis0-dynamic] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_sliced[client_DensityAnalysis0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_eqbox[client_DensityAnalysis0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox[client_DensityAnalysis0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape[client_DensityAnalysis0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_userdefn_padding[client_DensityAnalysis0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_userdefn_smallgrid[client_DensityAnalysis0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_shape[client_DensityAnalysis0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_type[client_DensityAnalysis0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_missing[client_DensityAnalysis0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_type[client_DensityAnalysis0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_nanvalue[client_DensityAnalysis0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_noatomgroup[client_DensityAnalysis0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_noatomgroup[client_DensityAnalysis0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_results_deprecated[client_DensityAnalysis0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_run[client_DensityAnalysis1-static] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_run[client_DensityAnalysis1-dynamic] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_sliced[client_DensityAnalysis1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_eqbox[client_DensityAnalysis1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox[client_DensityAnalysis1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape[client_DensityAnalysis1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_userdefn_padding[client_DensityAnalysis1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_userdefn_smallgrid[client_DensityAnalysis1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_shape[client_DensityAnalysis1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_type[client_DensityAnalysis1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_missing[client_DensityAnalysis1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_type[client_DensityAnalysis1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_nanvalue[client_DensityAnalysis1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_noatomgroup[client_DensityAnalysis1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_noatomgroup[client_DensityAnalysis1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_results_deprecated[client_DensityAnalysis1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_density_analysis_conversion_default_unit PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestGridImport::test_absence_griddata PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_density.py::TestGridImport::test_presence_griddata PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dielectric.py::TestDielectric::test_broken_molecules PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dielectric.py::TestDielectric::test_broken_repaired_molecules PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dielectric.py::TestDielectric::test_temperature PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dielectric.py::TestDielectric::test_non_charges PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dielectric.py::TestDielectric::test_non_neutral PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dielectric.py::TestDielectric::test_free_charges PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_eg PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_dist_weights PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_dist_weights_frames PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_distvalues_ag_universe PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_distvalues_ag_select PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_different_steps PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_transform PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_long_traj PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_updating_atomgroup PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_not_universe_atomgroup_error PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_DistanceMatrix_attr_warning PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_dihedral[client_Dihedral0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_dihedral_single_frame[client_Dihedral0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_atomgroup_list[client_Dihedral0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_enough_atoms[client_Dihedral0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_dihedral_attr_warning[client_Dihedral0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_dihedral[client_Dihedral1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_dihedral_single_frame[client_Dihedral1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_atomgroup_list[client_Dihedral1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_enough_atoms[client_Dihedral1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_dihedral_attr_warning[client_Dihedral1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran[client_Ramachandran0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_single_frame[client_Ramachandran0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_residue_selections[client_Ramachandran0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_outside_protein_length[client_Ramachandran0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_outside_protein_unchecked[client_Ramachandran0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran[client_Ramachandran1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_single_frame[client_Ramachandran1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_residue_selections[client_Ramachandran1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_outside_protein_length[client_Ramachandran1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_outside_protein_unchecked[client_Ramachandran1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_protein_ends PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_None_removal PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_plot PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_attr_warning PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin[client_Janin0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_tpr[client_Janin0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_residue_selections[client_Janin0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin[client_Janin1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_tpr[client_Janin1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_residue_selections[client_Janin1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_single_frame PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_outside_protein_length PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_remove_residues PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_atom_selection PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_plot PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_attr_warning PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::test_class_is_parallelizable[Dihedral-True] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::test_class_is_parallelizable[Ramachandran-True] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::test_class_is_parallelizable[Janin-True] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::test_supported_backends[Dihedral-backends0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::test_supported_backends[Ramachandran-backends1] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::test_supported_backends[Janin-backends2] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_distances.py::TestContactMatrix::test_np PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_distances.py::TestContactMatrix::test_sparse PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_distances.py::TestContactMatrix::test_box_numpy PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_distances.py::TestContactMatrix::test_box_sparse PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_distances.py::TestDist::test_pairwise_dist PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_distances.py::TestDist::test_pairwise_dist_box PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_distances.py::TestDist::test_pairwise_dist_offset_effect PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_distances.py::TestDist::test_offset_calculation PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_distances.py::TestDist::test_mismatch_exception PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_distances.py::TestBetween::test_between_simple_case_indices_only PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_distances.py::TestBetween::test_between_return_type[5.9] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_distances.py::TestBetween::test_between_return_type[0.0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2va0A.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1lpbA.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1eteA.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3nzmA.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1v7mV.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3lqcA.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2a2lA.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1or4A.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3fhkA.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3gwiA.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/4gcnA.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3nngA.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1dx5I.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1y1lA.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1ahsA.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3ii2A.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3on9A.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2gu3A.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1mr1D.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3gknA.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3ny7A.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2i39A.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1i8nA.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3ejfA.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2xr6A.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3so6A.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3q4oA.pdb.gz] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3aqgA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2fvvA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2xdgA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3t5gB.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3hklA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3e8mA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3l4rA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3pivA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3a4rA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3nbkA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2cayA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1pdoA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1bvyF.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/4dkcA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2qdlA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1h4aX.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2xcjA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3ieyB.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3vjzA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2cviA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3gfsA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3k7pA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2j49A.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_trajectory[client_DSSP0] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_atomgroup[client_DSSP0] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_trajectory_with_hydrogens[client_DSSP0] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_trajectory_without_hydrogen_fails[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2xdgA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_trajectory_with_uneven_number_of_atoms_fails[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1mr1D_failing.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_exception_raises_with_atom_index[client_DSSP0-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/wrong_hydrogens.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2va0A.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1lpbA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1eteA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3nzmA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1v7mV.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3lqcA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2a2lA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1or4A.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3fhkA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3gwiA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/4gcnA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3nngA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1dx5I.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1y1lA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1ahsA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3ii2A.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3on9A.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2gu3A.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1mr1D.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3gknA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3ny7A.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2i39A.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1i8nA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3ejfA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2xr6A.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3so6A.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3q4oA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3aqgA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2fvvA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2xdgA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3t5gB.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3hklA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3e8mA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3l4rA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3pivA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3a4rA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3nbkA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2cayA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1pdoA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1bvyF.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/4dkcA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2qdlA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1h4aX.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2xcjA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3ieyB.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3vjzA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2cviA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3gfsA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/3k7pA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2j49A.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_trajectory[client_DSSP1] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_atomgroup[client_DSSP1] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_trajectory_with_hydrogens[client_DSSP1] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_trajectory_without_hydrogen_fails[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/2xdgA.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_trajectory_with_uneven_number_of_atoms_fails[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/1mr1D_failing.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_dssp.py::test_exception_raises_with_atom_index[client_DSSP1-/build/reproducible-path/mdanalysis-2.9.0/testsuite/MDAnalysisTests/data/dssp/wrong_hydrogens.pdb.gz] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::test_moved_to_mdakit_warning PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_triangular_matrix PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_parallel_calculation PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_rmsd_matrix_with_superimposition PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_rmsd_matrix_with_superimposition_custom_weights PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_rmsd_matrix_without_superimposition PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_ensemble_superimposition PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_ensemble_superimposition_to_reference_non_weighted PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_covariance_matrix PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_covariance_matrix_with_reference PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_hes_to_self PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_hes PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_hes_custom_weights PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_hes_align PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_ces_to_self PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_ces PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_dres_to_self PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_dres PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_dres_without_superimposition XPASS [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_ces_convergence PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_dres_convergence PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_hes_error_estimation XPASS [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_ces_error_estimation PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_ces_error_estimation_ensemble_bootstrap PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_dres_error_estimation PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_clustering_one_ensemble PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_clustering_two_ensembles PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_clustering_three_ensembles_two_identical PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_clustering_two_methods PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_clustering_AffinityPropagationNative_direct PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_clustering_AffinityPropagation_direct PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_clustering_KMeans_direct PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_clustering_DBSCAN_direct PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_clustering_two_different_methods PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_clustering_method_w_no_distance_matrix PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_clustering_two_methods_one_w_no_distance_matrix PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_sklearn_affinity_propagation PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_ClusterCollection_init PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_Cluster_init PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_ClusterCollection_get_ids PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_ClusterCollection_get_centroids PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_cluster_add_metadata PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_empty_cluster PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_centroid_not_in_elements PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_metadata_size_error PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_cluster_iteration PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_cluster_len PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClustering::test_cluster_repr PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreClusteringSklearn::test_one PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreDimensionalityReduction::test_dimensionality_reduction_one_ensemble PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreDimensionalityReduction::test_dimensionality_reduction_two_ensembles PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreDimensionalityReduction::test_dimensionality_reduction_three_ensembles_two_identical PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreDimensionalityReduction::test_dimensionality_reduction_specified_dimension PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreDimensionalityReduction::test_dimensionality_reduction_SPENative_direct PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreDimensionalityReduction::test_dimensionality_reduction_PCA_direct PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreDimensionalityReduction::test_dimensionality_reduction_different_method PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreDimensionalityReduction::test_dimensionality_reduction_two_methods PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreDimensionalityReduction::test_dimensionality_reduction_two_different_methods PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreConfDistMatrix::test_get_distance_matrix PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncoreImportWarnings::test_import_warnings PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_gnm.py::test_gnm[client_GNMAnalysis0] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_gnm.py::test_gnm_run_step[client_GNMAnalysis0] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_gnm.py::test_closeContactGNMAnalysis[client_GNMAnalysis0] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_gnm.py::test_closeContactGNMAnalysis_weights_None[client_GNMAnalysis0] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_gnm.py::test_gnm[client_GNMAnalysis1] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_gnm.py::test_gnm_run_step[client_GNMAnalysis1] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_gnm.py::test_closeContactGNMAnalysis[client_GNMAnalysis1] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_gnm.py::test_closeContactGNMAnalysis_weights_None[client_GNMAnalysis1] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_gnm.py::test_generate_kirchoff PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_gnm.py::test_gnm_SVD_fail PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_plane_circle PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_ortho_circle PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_around_circle PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_around_circle_rising PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_parallel_axes PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_helix_analysis_zigzag[ref_axis0-screw_angles0] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_helix_analysis_zigzag[ref_axis1-screw_angles1] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_helix_analysis_zigzag[ref_axis2-screw_angles2] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_helix_analysis_zigzag[ref_axis3-screw_angles3] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_helix_analysis_zigzag[ref_axis4-screw_angles4] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_helix_analysis_zigzag[ref_axis5-screw_angles5] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_helix_analysis_zigzag[ref_axis6-screw_angles6] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_helix_analysis_zigzag[ref_axis7-screw_angles7] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_helix_analysis_zigzag[ref_axis8-screw_angles8] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_helix_analysis_zigzag[ref_axis9-screw_angles9] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_helix_analysis_zigzag[ref_axis10-screw_angles10] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_helix_analysis_zigzag[ref_axis11-screw_angles11] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_helix_analysis_zigzag[ref_axis12-screw_angles12] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_helix_analysis_zigzag[ref_axis13-screw_angles13] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_helix_analysis_zigzag[ref_axis14-screw_angles14] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_helix_analysis_square_oct PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_regression_summary PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_regression_values PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_multiple_selections PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_universe_from_origins PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_universe_from_origins_except PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_multiple_atoms_per_residues PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_residue_gaps_split PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_residue_gaps_no_split PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_len_groups_short PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_helanal_zigzag[ref_axis0-screw_angles0] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_helanal_zigzag[ref_axis1-screw_angles1] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_helanal_zigzag[ref_axis2-screw_angles2] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_helanal_zigzag[ref_axis3-screw_angles3] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_helanal_zigzag[ref_axis4-screw_angles4] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_helanal_zigzag[ref_axis5-screw_angles5] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_helanal_zigzag[ref_axis6-screw_angles6] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_helanal_zigzag[ref_axis7-screw_angles7] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_helanal_zigzag[ref_axis8-screw_angles8] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_helanal_zigzag[ref_axis9-screw_angles9] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_helanal_zigzag[ref_axis10-screw_angles10] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_helanal_zigzag[ref_axis11-screw_angles11] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_helanal_zigzag[ref_axis12-screw_angles12] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_helanal_zigzag[ref_axis13-screw_angles13] PASSED [ 2%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::TestHELANAL::test_helanal_zigzag[ref_axis14-screw_angles14] PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_vector_of_best_fit PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hole2.py::test_moved_to_mdakit_warning SKIPPED [ 3%] testsuite/MDAnalysisTests/analysis/test_hole2.py::test_install_mdakit_warning PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py::TestHydrogenBondAutocorrel::test_continuous PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py::TestHydrogenBondAutocorrel::test_continuous_excl PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py::TestHydrogenBondAutocorrel::test_intermittent PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py::TestHydrogenBondAutocorrel::test_intermittent_timecut PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py::TestHydrogenBondAutocorrel::test_intermittent_excl PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py::TestHydrogenBondAutocorrel::test_solve_continuous PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py::TestHydrogenBondAutocorrel::test_solve_intermittent PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py::TestHydrogenBondAutocorrel::test_wronglength_DA PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py::TestHydrogenBondAutocorrel::test_exclusions PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py::TestHydrogenBondAutocorrel::test_bond_type_VE PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py::TestHydrogenBondAutocorrel::test_solve_before_run_VE PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py::TestHydrogenBondAutocorrel::test_unslicable_traj_VE PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py::TestHydrogenBondAutocorrel::test_repr PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py::test_find_donors PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py::test_donors_nobonds PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous_excl PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_timecut PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_excl PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_continuous PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_intermittent PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_wronglength_DA PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_exclusions PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_bond_type_VE PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_before_run_VE PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_unslicable_traj_VE PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_repr PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_deprecation_warning PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_find_donors PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_donors_nobonds PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_find_hydrogen_donors_deprecation_warning PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_moved_module_warning PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P::test_hbond_analysis[client_HydrogenBondAnalysis0] PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P::test_count_by_time[client_HydrogenBondAnalysis0] PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P::test_count_by_type[client_HydrogenBondAnalysis0] PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P::test_count_by_ids[client_HydrogenBondAnalysis0] PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P::test_hbonds_deprecated_attr[client_HydrogenBondAnalysis0] PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type[client_HydrogenBondAnalysis0] PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_first_hbond[client_HydrogenBondAnalysis0] PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_time[client_HydrogenBondAnalysis0] PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_hydrogen_bond_lifetime[client_HydrogenBondAnalysis0] PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_hydrogen_bond_lifetime_intermittency[client_HydrogenBondAnalysis0] PASSED [ 3%] testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1[client_HydrogenBondAnalysis0] Sat May 16 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