Diff of the two buildlogs:

--
--- b1/build.log	2025-07-31 01:49:46.875336307 +0000
+++ b2/build.log	2025-07-31 01:55:43.775787980 +0000
@@ -1,6 +1,6 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Tue Sep  1 20:03:55 -12 2026
-I: pbuilder-time-stamp: 1788336235
+I: Current time: Thu Jul 31 15:49:49 +14 2025
+I: pbuilder-time-stamp: 1753926589
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
 I: copying local configuration
@@ -29,51 +29,83 @@
 dpkg-source: info: applying skip_gsd_tests.patch
 I: Not using root during the build.
 I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/3239140/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/3214920/tmp/hooks/D01_modify_environment starting
+debug: Running on infom01-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 Jul 31 01:50 /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/3214920/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/3214920/tmp/hooks/D02_print_environment starting
 I: set
-  BUILDDIR='/build/reproducible-path'
-  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
-  BUILDUSERNAME='pbuilder1'
-  BUILD_ARCH='amd64'
-  DEBIAN_FRONTEND='noninteractive'
-  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 '
-  DISTRIBUTION='unstable'
-  HOME='/root'
-  HOST_ARCH='amd64'
+  BASH=/bin/sh
+  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
+  BASH_ALIASES=()
+  BASH_ARGC=()
+  BASH_ARGV=()
+  BASH_CMDS=()
+  BASH_LINENO=([0]="12" [1]="0")
+  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
+  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+  BASH_VERSINFO=([0]="5" [1]="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=12 '
+  DIRSTACK=()
+  DISTRIBUTION=unstable
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=x86_64
+  HOST_ARCH=amd64
   IFS=' 	
   '
-  INVOCATION_ID='562b8f4eea9f4bc39a2d7a6124f19044'
-  LANG='C'
-  LANGUAGE='en_US:en'
-  LC_ALL='C'
-  MAIL='/var/mail/root'
-  OPTIND='1'
-  PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
-  PBCURRENTCOMMANDLINEOPERATION='build'
-  PBUILDER_OPERATION='build'
-  PBUILDER_PKGDATADIR='/usr/share/pbuilder'
-  PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
-  PBUILDER_SYSCONFDIR='/etc'
-  PPID='3239140'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=13fe00a8604945fcad82d89691e48206
+  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=3214920
   PS4='+ '
-  PWD='/'
-  SHELL='/bin/bash'
-  SHLVL='2'
-  SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.RHQo3wvc/pbuilderrc_Ncp4 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.RHQo3wvc/b1 --logfile b1/build.log mdanalysis_2.9.0-12.dsc'
-  SUDO_GID='109'
-  SUDO_UID='104'
-  SUDO_USER='jenkins'
-  TERM='unknown'
-  TZ='/usr/share/zoneinfo/Etc/GMT+12'
-  USER='root'
-  _='/usr/bin/systemd-run'
+  PWD=/
+  SHELL=/bin/bash
+  SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
+  SHLVL=3
+  SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.RHQo3wvc/pbuilderrc_3esY --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.RHQo3wvc/b2 --logfile b2/build.log mdanalysis_2.9.0-12.dsc'
+  SUDO_GID=109
+  SUDO_UID=104
+  SUDO_USER=jenkins
+  TERM=unknown
+  TZ=/usr/share/zoneinfo/Etc/GMT-14
+  UID=0
+  USER=root
+  _='I: set'
 I: uname -a
-  Linux infom02-amd64 6.12.33+deb12-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.33-1~bpo12+1 (2025-07-09) x86_64 GNU/Linux
+  Linux i-capture-the-hostname 6.1.0-37-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux
 I: ls -l /bin
-  lrwxrwxrwx 1 root root 7 May 12  2025 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/3239140/tmp/hooks/D02_print_environment finished
+  lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/3214920/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -443,7 +475,7 @@
 Get: 264 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-sitemap all 2.6.0-1 [8508 B]
 Get: 265 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.bibtex all 2.6.2-1 [32.4 kB]
 Get: 266 http://deb.debian.org/debian unstable/main amd64 python3-tqdm all 4.67.1-5 [90.8 kB]
-Fetched 193 MB in 3s (68.1 MB/s)
+Fetched 193 MB in 2s (106 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 ... 19850 files and directories currently installed.)
@@ -1299,8 +1331,8 @@
 Setting up tzdata (2025b-4) ...
 
 Current default time zone: 'Etc/UTC'
-Local time is now:      Wed Sep  2 08:07:16 UTC 2026.
-Universal Time is now:  Wed Sep  2 08:07:16 UTC 2026.
+Local time is now:      Thu Jul 31 01:51:34 UTC 2025.
+Universal Time is now:  Thu Jul 31 01:51:34 UTC 2025.
 Run 'dpkg-reconfigure tzdata' if you wish to change it.
 
 Setting up unicode-data (15.1.0-1) ...
@@ -1549,7 +1581,11 @@
 Building tag database...
  -> Finished parsing the build-deps
 I: Building the package
-I: Running cd /build/reproducible-path/mdanalysis-2.9.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S  > ../mdanalysis_2.9.0-12_source.changes
+I: user script /srv/workspace/pbuilder/3214920/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for unstable
+I: user script /srv/workspace/pbuilder/3214920/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/mdanalysis-2.9.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S  > ../mdanalysis_2.9.0-12_source.changes
 dpkg-buildpackage: info: source package mdanalysis
 dpkg-buildpackage: info: source version 2.9.0-12
 dpkg-buildpackage: info: source distribution unstable
@@ -1669,8 +1705,8 @@
         ********************************************************************************
         Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).
 
-        This deprecation is overdue, please update your project and remove deprecated
-        calls to avoid build errors in the future.
+        By 2026-Feb-18, you need to update your project and remove deprecated calls
+        or your builds will no longer be supported.
 
         See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
         ********************************************************************************
@@ -1707,225 +1743,225 @@
 running build
 running build_py
 creating build/lib.linux-x86_64-cpython-313/MDAnalysis
-copying MDAnalysis/due.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis
-copying MDAnalysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis
-copying MDAnalysis/authors.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis
 copying MDAnalysis/exceptions.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis
-copying MDAnalysis/units.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis
+copying MDAnalysis/authors.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis
 copying MDAnalysis/version.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis
+copying MDAnalysis/units.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis
+copying MDAnalysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis
+copying MDAnalysis/due.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis
+creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source
+copying doc/sphinx/source/conf.py -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/distances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/util.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/log.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/correlations.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/transformations.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/_distopia.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/mdamath.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/guessers.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/GROParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/tables.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/converters
+copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters
+copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters
+copying MDAnalysis/converters/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters
+copying MDAnalysis/converters/RDKit.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters
+copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters
+copying MDAnalysis/converters/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters
+copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters
+copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters
 creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
-copying MDAnalysis/analysis/results.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
-copying MDAnalysis/analysis/density.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
-copying MDAnalysis/analysis/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
-copying MDAnalysis/analysis/contacts.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
+copying MDAnalysis/analysis/distances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
+copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
+copying MDAnalysis/analysis/psa.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
+copying MDAnalysis/analysis/bat.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
 copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
+copying MDAnalysis/analysis/pca.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
+copying MDAnalysis/analysis/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
 copying MDAnalysis/analysis/backends.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
-copying MDAnalysis/analysis/dielectric.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
 copying MDAnalysis/analysis/rdf.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
+copying MDAnalysis/analysis/dielectric.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
 copying MDAnalysis/analysis/msd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
-copying MDAnalysis/analysis/nucleicacids.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
-copying MDAnalysis/analysis/atomicdistances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
 copying MDAnalysis/analysis/align.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
+copying MDAnalysis/analysis/atomicdistances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
+copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
 copying MDAnalysis/analysis/rms.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
-copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
-copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
-copying MDAnalysis/analysis/bat.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
 copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
-copying MDAnalysis/analysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
-copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
-copying MDAnalysis/analysis/gnm.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
-copying MDAnalysis/analysis/pca.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
-copying MDAnalysis/analysis/psa.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
+copying MDAnalysis/analysis/density.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
 copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
+copying MDAnalysis/analysis/results.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
 copying MDAnalysis/analysis/polymer.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
-copying MDAnalysis/analysis/distances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
-copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/converters
-copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters
-copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters
-copying MDAnalysis/converters/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters
-copying MDAnalysis/converters/RDKit.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters
-copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters
-copying MDAnalysis/converters/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters
-copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters
-copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters
+copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
+copying MDAnalysis/analysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
+copying MDAnalysis/analysis/contacts.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
+copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
+copying MDAnalysis/analysis/nucleicacids.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
+copying MDAnalysis/analysis/gnm.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser
+copying MDAnalysis/guesser/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser
+copying MDAnalysis/guesser/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser
+copying MDAnalysis/guesser/default_guesser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser
+copying MDAnalysis/guesser/tables.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/core
+copying MDAnalysis/core/groups.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core
+copying MDAnalysis/core/accessors.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core
+copying MDAnalysis/core/_get_readers.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core
+copying MDAnalysis/core/selection.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core
+copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core
+copying MDAnalysis/core/topology.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core
+copying MDAnalysis/core/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core
+copying MDAnalysis/core/universe.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core
+copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/tests
+copying MDAnalysis/tests/datafiles.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/tests
+copying MDAnalysis/tests/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/tests
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization
+copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization
+copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization
+copying MDAnalysis/visualization/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization
 creating build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
 copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
 copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/TNG.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
 copying MDAnalysis/coordinates/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
 copying MDAnalysis/coordinates/chain.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
 copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
 copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
 copying MDAnalysis/coordinates/TRC.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
 copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/null.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
 copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
 copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/null.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/TNG.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
 copying MDAnalysis/coordinates/memory.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser
-copying MDAnalysis/guesser/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser
-copying MDAnalysis/guesser/tables.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser
-copying MDAnalysis/guesser/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser
-copying MDAnalysis/guesser/default_guesser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser
+copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
 creating build/lib.linux-x86_64-cpython-313/MDAnalysis/selections
-copying MDAnalysis/selections/vmd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections
 copying MDAnalysis/selections/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections
-copying MDAnalysis/selections/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections
-copying MDAnalysis/selections/pymol.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections
+copying MDAnalysis/selections/vmd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections
 copying MDAnalysis/selections/gromacs.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections
 copying MDAnalysis/selections/charmm.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections
 copying MDAnalysis/selections/jmol.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary
-copying MDAnalysis/auxiliary/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary
-copying MDAnalysis/auxiliary/EDR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary
-copying MDAnalysis/auxiliary/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary
-copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary
-copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/transformations.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/util.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/correlations.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/mdamath.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/log.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/_distopia.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/distances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/selections/pymol.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections
+copying MDAnalysis/selections/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections
 creating build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations
 copying MDAnalysis/transformations/translate.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations
 copying MDAnalysis/transformations/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations
-copying MDAnalysis/transformations/nojump.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations
-copying MDAnalysis/transformations/fit.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations
+copying MDAnalysis/transformations/wrap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations
 copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations
-copying MDAnalysis/transformations/rotate.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations
-copying MDAnalysis/transformations/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations
 copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations
-copying MDAnalysis/transformations/wrap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/core
-copying MDAnalysis/core/selection.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core
-copying MDAnalysis/core/topology.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core
-copying MDAnalysis/core/accessors.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core
-copying MDAnalysis/core/groups.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core
-copying MDAnalysis/core/_get_readers.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core
-copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core
-copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core
-copying MDAnalysis/core/universe.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core
-copying MDAnalysis/core/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/GROParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/tables.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/guessers.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/tests
-copying MDAnalysis/tests/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/tests
-copying MDAnalysis/tests/datafiles.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/tests
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization
-copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization
-copying MDAnalysis/visualization/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization
-copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data
-copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data
-copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp
-copying MDAnalysis/analysis/dssp/dssp.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp
-copying MDAnalysis/analysis/dssp/pydssp_numpy.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp
-copying MDAnalysis/analysis/dssp/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp
+copying MDAnalysis/transformations/nojump.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations
+copying MDAnalysis/transformations/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations
+copying MDAnalysis/transformations/rotate.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations
+copying MDAnalysis/transformations/fit.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary
+copying MDAnalysis/auxiliary/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary
+copying MDAnalysis/auxiliary/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary
+copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary
+copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary
+copying MDAnalysis/auxiliary/EDR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis
+copying MDAnalysis/lib/libmdanalysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats
+copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include
+copying MDAnalysis/lib/include/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations
+copying MDAnalysis/lib/src/transformations/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src
+copying MDAnalysis/lib/formats/src/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include
+copying MDAnalysis/lib/formats/include/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr
+copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr
+copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr
+copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr
+copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2
+copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy
+copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy
+copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy
 creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds
-copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds
 copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds
+copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds
 creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore
-copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore
-copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore
 copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore
+copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore
 copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore
+copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore
+copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore
 copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore
-copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy
-copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy
-copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2
-copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data
+copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data
+copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data
 creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds
 copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds
-copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds
-copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds
 copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds
+copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds
+copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp
+copying MDAnalysis/analysis/dssp/pydssp_numpy.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp
+copying MDAnalysis/analysis/dssp/dssp.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp
+copying MDAnalysis/analysis/dssp/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction
+copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction
+copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction
+copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction
 creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering
+copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering
 copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering
 copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering
-copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering
 copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction
-copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction
-copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction
-copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats
-copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis
-copying MDAnalysis/lib/libmdanalysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include
-copying MDAnalysis/lib/include/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src
-copying MDAnalysis/lib/formats/src/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include
-copying MDAnalysis/lib/formats/include/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations
-copying MDAnalysis/lib/src/transformations/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr
-copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr
-copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr
-copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr
-copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr
-creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source
-copying doc/sphinx/source/conf.py -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source
 running egg_info
 creating MDAnalysis.egg-info
 writing MDAnalysis.egg-info/PKG-INFO
@@ -2010,67 +2046,9 @@
 adding license file 'LICENSE'
 adding license file 'AUTHORS'
 writing manifest file 'MDAnalysis.egg-info/SOURCES.txt'
+copying doc/README -> build/lib.linux-x86_64-cpython-313/doc
 copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data
 copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data
-copying doc/README -> build/lib.linux-x86_64-cpython-313/doc
-copying MDAnalysis/coordinates/timestep.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/timestep.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/coordinates/timestep.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
-copying MDAnalysis/lib/_augment.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/_augment.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/_cutil.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/_cutil.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/_cutil.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/c_distances.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/c_distances.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/c_distances.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/c_distances_openmp.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/c_distances_openmp.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/nsgrid.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/nsgrid.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/qcprot.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/lib/qcprot.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
-copying MDAnalysis/analysis/encore/cutils.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore
-copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore
-copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering
-copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering
-copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction
-copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src
-copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include
-copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src
-copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src
-creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include
-copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include
-copying MDAnalysis/lib/formats/cython_util.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats
-copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats
-copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats
-copying MDAnalysis/lib/formats/libdcd.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats
-copying MDAnalysis/lib/formats/libdcd.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats
-copying MDAnalysis/lib/formats/libdcd.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats
-copying MDAnalysis/lib/formats/libmdaxdr.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats
-copying MDAnalysis/lib/formats/libmdaxdr.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats
-copying MDAnalysis/lib/formats/libmdaxdr.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats
-copying MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis
-copying MDAnalysis/lib/include/calc_distances.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include
-copying MDAnalysis/lib/formats/src/trr_seek.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src
-copying MDAnalysis/lib/formats/src/xdrfile.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src
-copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src
-copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src
-copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src
-copying MDAnalysis/lib/formats/include/endianswap.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include
-copying MDAnalysis/lib/formats/include/fastio.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include
-copying MDAnalysis/lib/formats/include/readdcd.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include
-copying MDAnalysis/lib/formats/include/trr_seek.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include
-copying MDAnalysis/lib/formats/include/xdrfile.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include
-copying MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include
-copying MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include
-copying MDAnalysis/lib/formats/include/xtc_seek.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include
-copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations
-copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations
-copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations
 copying doc/sphinx/Makefile -> build/lib.linux-x86_64-cpython-313/doc/sphinx
 copying doc/sphinx/source/index.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source
 copying doc/sphinx/source/references.bib -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source
@@ -2102,6 +2080,59 @@
 copying doc/sphinx/source/documentation_pages/units.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages
 copying doc/sphinx/source/documentation_pages/version.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages
 copying doc/sphinx/source/documentation_pages/visualization_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages
+creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
+copying doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
+copying doc/sphinx/source/documentation_pages/lib/c_distances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
+copying doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
+copying doc/sphinx/source/documentation_pages/lib/correlations.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
+copying doc/sphinx/source/documentation_pages/lib/distances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
+copying doc/sphinx/source/documentation_pages/lib/log.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
+copying doc/sphinx/source/documentation_pages/lib/mdamath.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
+copying doc/sphinx/source/documentation_pages/lib/nsgrid.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
+copying doc/sphinx/source/documentation_pages/lib/picklable_file_io.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
+copying doc/sphinx/source/documentation_pages/lib/pkdtree.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
+copying doc/sphinx/source/documentation_pages/lib/qcprot.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
+copying doc/sphinx/source/documentation_pages/lib/transformations.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
+copying doc/sphinx/source/documentation_pages/lib/util.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
+creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/CRDParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/DMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/GMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/GROParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/GSDParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/ITPParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/MMTFParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/MinimalParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/PDBParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/PQRParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/PSFParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/TOPParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/TPRParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/TXYZParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/XYZParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/core.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/guessers.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/tables.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+copying doc/sphinx/source/documentation_pages/topology/tpr_util.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
+creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters
+copying doc/sphinx/source/documentation_pages/converters/OpenMM.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters
+copying doc/sphinx/source/documentation_pages/converters/ParmEd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters
+copying doc/sphinx/source/documentation_pages/converters/RDKit.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters
+copying doc/sphinx/source/documentation_pages/converters/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters
+creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules
+copying doc/sphinx/source/documentation_pages/guesser_modules/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules
+copying doc/sphinx/source/documentation_pages/guesser_modules/default_guesser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules
+copying doc/sphinx/source/documentation_pages/guesser_modules/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules
+copying doc/sphinx/source/documentation_pages/guesser_modules/tables.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules
 creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis
 copying doc/sphinx/source/documentation_pages/analysis/align.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis
 copying doc/sphinx/source/documentation_pages/analysis/atomicdistances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis
@@ -2138,11 +2169,20 @@
 copying doc/sphinx/source/documentation_pages/analysis/rms.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis
 copying doc/sphinx/source/documentation_pages/analysis/waterdynamics.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis
 copying doc/sphinx/source/documentation_pages/analysis/wbridge_analysis.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis
-creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters
-copying doc/sphinx/source/documentation_pages/converters/OpenMM.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters
-copying doc/sphinx/source/documentation_pages/converters/ParmEd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters
-copying doc/sphinx/source/documentation_pages/converters/RDKit.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters
-copying doc/sphinx/source/documentation_pages/converters/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters
+creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core
+copying doc/sphinx/source/documentation_pages/core/accessors.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core
+copying doc/sphinx/source/documentation_pages/core/groups.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core
+copying doc/sphinx/source/documentation_pages/core/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core
+copying doc/sphinx/source/documentation_pages/core/selection.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core
+copying doc/sphinx/source/documentation_pages/core/topology.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core
+copying doc/sphinx/source/documentation_pages/core/topologyattrs.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core
+copying doc/sphinx/source/documentation_pages/core/topologyobjects.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core
+copying doc/sphinx/source/documentation_pages/core/universe.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core
+creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization
+copying doc/sphinx/source/documentation_pages/visualization/streamlines.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization
+copying doc/sphinx/source/documentation_pages/visualization/streamlines_3D.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization
+copying doc/sphinx/source/documentation_pages/visualization/test_streamplot_3D.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization
+copying doc/sphinx/source/documentation_pages/visualization/testing_streamline.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization
 creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates
 copying doc/sphinx/source/documentation_pages/coordinates/CRD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates
 copying doc/sphinx/source/documentation_pages/coordinates/DCD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates
@@ -2186,26 +2226,6 @@
 copying doc/sphinx/source/documentation_pages/selections/jmol.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections
 copying doc/sphinx/source/documentation_pages/selections/pymol.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections
 copying doc/sphinx/source/documentation_pages/selections/vmd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections
-creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary
-copying doc/sphinx/source/documentation_pages/auxiliary/EDR.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary
-copying doc/sphinx/source/documentation_pages/auxiliary/XVG.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary
-copying doc/sphinx/source/documentation_pages/auxiliary/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary
-copying doc/sphinx/source/documentation_pages/auxiliary/core.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary
-copying doc/sphinx/source/documentation_pages/auxiliary/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary
-creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
-copying doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
-copying doc/sphinx/source/documentation_pages/lib/c_distances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
-copying doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
-copying doc/sphinx/source/documentation_pages/lib/correlations.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
-copying doc/sphinx/source/documentation_pages/lib/distances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
-copying doc/sphinx/source/documentation_pages/lib/log.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
-copying doc/sphinx/source/documentation_pages/lib/mdamath.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
-copying doc/sphinx/source/documentation_pages/lib/nsgrid.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
-copying doc/sphinx/source/documentation_pages/lib/picklable_file_io.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
-copying doc/sphinx/source/documentation_pages/lib/pkdtree.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
-copying doc/sphinx/source/documentation_pages/lib/qcprot.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
-copying doc/sphinx/source/documentation_pages/lib/transformations.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
-copying doc/sphinx/source/documentation_pages/lib/util.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib
 creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations
 copying doc/sphinx/source/documentation_pages/transformations/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations
 copying doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations
@@ -2215,54 +2235,17 @@
 copying doc/sphinx/source/documentation_pages/transformations/rotate.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations
 copying doc/sphinx/source/documentation_pages/transformations/translate.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations
 copying doc/sphinx/source/documentation_pages/transformations/wrap.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations
-creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules
-copying doc/sphinx/source/documentation_pages/guesser_modules/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules
-copying doc/sphinx/source/documentation_pages/guesser_modules/default_guesser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules
-copying doc/sphinx/source/documentation_pages/guesser_modules/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules
-copying doc/sphinx/source/documentation_pages/guesser_modules/tables.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules
-creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core
-copying doc/sphinx/source/documentation_pages/core/accessors.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core
-copying doc/sphinx/source/documentation_pages/core/groups.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core
-copying doc/sphinx/source/documentation_pages/core/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core
-copying doc/sphinx/source/documentation_pages/core/selection.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core
-copying doc/sphinx/source/documentation_pages/core/topology.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core
-copying doc/sphinx/source/documentation_pages/core/topologyattrs.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core
-copying doc/sphinx/source/documentation_pages/core/topologyobjects.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core
-copying doc/sphinx/source/documentation_pages/core/universe.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core
-creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/CRDParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/DMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/GMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/GROParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/GSDParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/ITPParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/MMTFParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/MinimalParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/PDBParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/PQRParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/PSFParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/TOPParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/TPRParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/TXYZParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/XYZParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/core.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/guessers.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/tables.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-copying doc/sphinx/source/documentation_pages/topology/tpr_util.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology
-creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization
-copying doc/sphinx/source/documentation_pages/visualization/streamlines.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization
-copying doc/sphinx/source/documentation_pages/visualization/streamlines_3D.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization
-copying doc/sphinx/source/documentation_pages/visualization/test_streamplot_3D.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization
-copying doc/sphinx/source/documentation_pages/visualization/testing_streamline.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization
+creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary
+copying doc/sphinx/source/documentation_pages/auxiliary/EDR.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary
+copying doc/sphinx/source/documentation_pages/auxiliary/XVG.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary
+copying doc/sphinx/source/documentation_pages/auxiliary/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary
+copying doc/sphinx/source/documentation_pages/auxiliary/core.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary
+copying doc/sphinx/source/documentation_pages/auxiliary/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary
+creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats
+copying doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats
+copying doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats
+creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy
+copying doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy
 creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore
 copying doc/sphinx/source/documentation_pages/analysis/encore/bootstrap.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore
 copying doc/sphinx/source/documentation_pages/analysis/encore/clustering.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore
@@ -2271,11 +2254,64 @@
 copying doc/sphinx/source/documentation_pages/analysis/encore/dimensionality_reduction.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore
 copying doc/sphinx/source/documentation_pages/analysis/encore/similarity.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore
 copying doc/sphinx/source/documentation_pages/analysis/encore/utils.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore
-creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy
-copying doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy
-creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats
-copying doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats
-copying doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats
+copying MDAnalysis/lib/_augment.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/_augment.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/_cutil.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/_cutil.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/_cutil.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/c_distances.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/c_distances.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/c_distances.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/c_distances_openmp.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/c_distances_openmp.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/nsgrid.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/nsgrid.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/qcprot.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/lib/qcprot.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib
+copying MDAnalysis/coordinates/timestep.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/timestep.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/coordinates/timestep.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates
+copying MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis
+copying MDAnalysis/lib/formats/cython_util.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats
+copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats
+copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats
+copying MDAnalysis/lib/formats/libdcd.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats
+copying MDAnalysis/lib/formats/libdcd.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats
+copying MDAnalysis/lib/formats/libdcd.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats
+copying MDAnalysis/lib/formats/libmdaxdr.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats
+copying MDAnalysis/lib/formats/libmdaxdr.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats
+copying MDAnalysis/lib/formats/libmdaxdr.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats
+copying MDAnalysis/lib/include/calc_distances.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include
+copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations
+copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations
+copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations
+copying MDAnalysis/lib/formats/src/trr_seek.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src
+copying MDAnalysis/lib/formats/src/xdrfile.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src
+copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src
+copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src
+copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src
+copying MDAnalysis/lib/formats/include/endianswap.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include
+copying MDAnalysis/lib/formats/include/fastio.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include
+copying MDAnalysis/lib/formats/include/readdcd.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include
+copying MDAnalysis/lib/formats/include/trr_seek.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include
+copying MDAnalysis/lib/formats/include/xdrfile.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include
+copying MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include
+copying MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include
+copying MDAnalysis/lib/formats/include/xtc_seek.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include
+copying MDAnalysis/analysis/encore/cutils.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore
+copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore
+copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction
+copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction
+copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering
+copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src
+copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include
+copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src
+copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src
+creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include
+copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include
 running build_ext
 building 'MDAnalysis.lib.formats.libdcd' extension
 creating build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats
@@ -2429,514 +2465,514 @@
 running install
 running install_lib
 creating build/bdist.linux-x86_64/wheel
+creating build/bdist.linux-x86_64/wheel/doc
+copying build/lib.linux-x86_64-cpython-313/doc/README -> build/bdist.linux-x86_64/wheel/./doc
+creating build/bdist.linux-x86_64/wheel/doc/sphinx
+creating build/bdist.linux-x86_64/wheel/doc/sphinx/source
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/index.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source
+creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/images
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/rama_ref_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/parallelization_time.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/msd_demo_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/rama_demo_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/AnalysisBase_parallel.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/janin_demo_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/RSMD_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images/janin_ref_plot.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/images
+creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages
+creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/lib
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/mdamath.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/pkdtree.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
+creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/lib/formats
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib/formats
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib/formats
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/correlations.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/nsgrid.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/c_distances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/qcprot.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/distances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/picklable_file_io.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/log.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/util.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/transformations.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/units.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages
+creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/TXYZParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PDBParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/GROParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/core.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/XYZParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/CRDParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/DMSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/TPRParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PSFParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/MMTFParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/TOPParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/guessers.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/GMSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PQRParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/tpr_util.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/MinimalParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/GSDParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/ITPParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/tables.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages
+creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/converters
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/OpenMM.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/RDKit.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters/ParmEd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/converters
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages
+creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/guesser_modules
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/default_guesser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/tables.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules
+creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/analysis
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/helix_analysis.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/pca.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/density.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/rms.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/results.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/wbridge_analysis.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/msd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/psa.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis
+creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/analysis/legacy
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/legacy
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/polymer.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/atomicdistances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis
+creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/analysis/encore
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/clustering.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/dimensionality_reduction.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/utils.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/similarity.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/confdistmatrix.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/covariance.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/bootstrap.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/nucleicacids.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel_deprecated.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/waterdynamics.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/nuclinfo.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/dihedrals.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/bat.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/parallelization.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/lineardensity.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis
+copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/align.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/analysis
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+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
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 creating build/bdist.linux-x86_64/wheel/MDAnalysis
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+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/trr_seek.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
+creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/include
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xdrfile.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/fastio.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/endianswap.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/readdcd.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/trr_seek.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xtc_seek.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
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+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/picklable_file_io.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_distopia.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_transformations.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/mdamath.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
+creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/include
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/include
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include/calc_distances.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/include
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/exceptions.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis
+creating build/bdist.linux-x86_64/wheel/MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/ParmEdParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+creating build/bdist.linux-x86_64/wheel/MDAnalysis/topology/tpr
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+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/guessers.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/GROParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/ITPParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/FHIAIMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tables.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/authors.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/version.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis
+creating build/bdist.linux-x86_64/wheel/MDAnalysis/converters
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/ParmEd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/ParmEdParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/RDKit.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/OpenMMParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/OpenMM.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/RDKitParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters
 creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/results.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/density.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/contacts.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/distances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/psa.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
+creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hole2
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hole2
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/bat.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dihedrals.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/pca.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/backends.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dielectric.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/rdf.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
-creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/data
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data
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-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data
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-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/msd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
-creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/dssp
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-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp/pydssp_numpy.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/dssp
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/dssp
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dielectric.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
+creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/legacy
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/legacy
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/legacy
 creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hbonds
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 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hbonds
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hbonds
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/msd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
 creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore
-creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering
-creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering/src
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src/ap.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering/src
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering
-creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering/include
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include/ap.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering/include
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore
 creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction
 creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/src
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction/src
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction
 creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/include
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction/include
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/similarity.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/covariance.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/cutils.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/nucleicacids.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/atomicdistances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
+creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering
+creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering/src
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src/ap.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering/src
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering
+creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering/include
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include/ap.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering/include
+creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/data
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data/janin_ref_data.npy -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/align.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/atomicdistances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/rms.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/bat.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
-creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/legacy
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/legacy
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/legacy
-creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hole2
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hole2
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/helix_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/density.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/results.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/polymer.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
 creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hydrogenbonds
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/helix_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
+creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/dssp
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp/pydssp_numpy.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/dssp
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp/dssp.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/dssp
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/dssp
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/contacts.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/nucleicacids.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/gnm.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/pca.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/psa.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/polymer.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/distances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis
-creating build/bdist.linux-x86_64/wheel/MDAnalysis/converters
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/ParmEd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/RDKitParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/RDKit.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/ParmEdParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/OpenMMParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/converters/OpenMM.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters
+creating build/bdist.linux-x86_64/wheel/MDAnalysis/guesser
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/default_guesser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/tables.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser
+creating build/bdist.linux-x86_64/wheel/MDAnalysis/core
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/groups.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/accessors.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/_get_readers.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/selection.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/topology.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/universe.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core
+creating build/bdist.linux-x86_64/wheel/MDAnalysis/tests
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/tests/datafiles.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/tests
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/tests/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/tests
+creating build/bdist.linux-x86_64/wheel/MDAnalysis/visualization
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/units.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis
 creating build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TXYZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/ParmEd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/GSD.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/TRR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TNG.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/H5MD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/chain.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/XDR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/H5MD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRC.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/NAMDBIN.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/null.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/timestep.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/null.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/TNG.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/NAMDBIN.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/memory.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
-creating build/bdist.linux-x86_64/wheel/MDAnalysis/guesser
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/tables.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser/default_guesser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/guesser
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates
 creating build/bdist.linux-x86_64/wheel/MDAnalysis/selections
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/vmd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/pymol.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/vmd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/gromacs.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/charmm.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/jmol.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections
-creating build/bdist.linux-x86_64/wheel/MDAnalysis/auxiliary
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/EDR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/pymol.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/selections/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/due.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis
-creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib
-creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
-creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/src
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xtc_seek.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/trr_seek.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
-creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/include
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/readdcd.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/endianswap.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/trr_seek.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/fastio.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xtc_seek.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xdrfile.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/cython_util.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats
-creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/src
-creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/src/transformations
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/LICENCE -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/AUTHOR -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/transformations.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/transformations.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_transformations.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/util.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/correlations.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/mdamath.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/picklable_file_io.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/libmdanalysis
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/libmdanalysis
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/libmdanalysis
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_cutil.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/log.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/include
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include/calc_distances.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/include
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/include
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_distopia.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/_augment.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/nsgrid.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/distances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/authors.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis
 creating build/bdist.linux-x86_64/wheel/MDAnalysis/transformations
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/translate.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/nojump.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/fit.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/wrap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/boxdimensions.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/rotate.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations
 copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/wrap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/exceptions.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis
-creating build/bdist.linux-x86_64/wheel/MDAnalysis/core
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/selection.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/topology.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/accessors.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/groups.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/_get_readers.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/universe.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/core/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/units.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis
-creating build/bdist.linux-x86_64/wheel/MDAnalysis/topology
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
-copying build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology
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-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TNG.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/GMS.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/DLPoly.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/core.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/INPCRD.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/XYZ.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/coordinates
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/exceptions.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/references.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages
-creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/selections
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/jmol.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/gromacs.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/pymol.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/vmd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/charmm.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/selections
-creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/auxiliary
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/XVG.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/EDR.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/core.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/auxiliary
-creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/lib
-creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/lib/formats
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib/formats
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib/formats
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/c_distances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/log.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/correlations.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/transformations.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/nsgrid.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/picklable_file_io.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/distances.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/util.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/pkdtree.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/qcprot.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/mdamath.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/lib
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/units.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages
-creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/transformations
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/nojump.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/wrap.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/translate.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/rotate.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/positionaveraging.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/fit.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/transformations
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/trajectory_transformations.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages
-creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/guesser_modules
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/default_guesser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/tables.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages
-creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/core
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/topologyobjects.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/groups.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/selection.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/accessors.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/universe.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/topology.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core/topologyattrs.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/core
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/overview.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages
-creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/MMTFParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/GMSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/init.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/CRDParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/TOPParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/TXYZParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/TPRParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/MinimalParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/DMSParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/tpr_util.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PQRParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PSFParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/ITPParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/tables.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/guessers.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/XYZParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/core.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/GROParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/GSDParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/PDBParser.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology/base.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/topology
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core_modules.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/version.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages
-creating build/bdist.linux-x86_64/wheel/doc/sphinx/source/documentation_pages/visualization
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/streamlines_3D.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/test_streamplot_3D.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/testing_streamline.png -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization
-copying build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization/streamlines.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinx/source/documentation_pages/visualization
-copying build/lib.linux-x86_64-cpython-313/doc/README -> build/bdist.linux-x86_64/wheel/./doc
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/nojump.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/rotate.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations/fit.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations
+creating build/bdist.linux-x86_64/wheel/MDAnalysis/auxiliary
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary
+copying build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary/EDR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary
 running install_egg_info
 Copying MDAnalysis.egg-info to build/bdist.linux-x86_64/wheel/./MDAnalysis-2.9.0.egg-info
 running install_scripts
 creating build/bdist.linux-x86_64/wheel/mdanalysis-2.9.0.dist-info/WHEEL
-creating '/build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/.tmp-o5nqbnx4/mdanalysis-2.9.0-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
+creating '/build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/.tmp-ja_w30v2/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'
@@ -3416,45 +3452,45 @@
 loading intersphinx inventory 'gsd' from https://gsd.readthedocs.io/en/stable/objects.inv ...
 loading intersphinx inventory 'maplotlib' from https://matplotlib.org/stable/objects.inv ...
 WARNING: failed to reach any of the inventories with the following issues:
-intersphinx inventory 'https://gsd.readthedocs.io/en/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='gsd.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f29691b1f90>: Failed to establish a new connection: [Errno 111] Connection refused')))
+intersphinx inventory 'https://docs.scipy.org/doc/scipy/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: 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('<urllib3.connection.HTTPSConnection object at 0x7f63592b5950>: Failed to establish a new connection: [Errno 111] Connection refused')))
+loading intersphinx inventory 'griddataformats' from https://mdanalysis.org/GridDataFormats/objects.inv ...
 WARNING: failed to reach any of the inventories with the following issues:
-intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f29691c0590>: Failed to establish a new connection: [Errno 111] Connection refused')))
+intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f63592b5f90>: Failed to establish a new connection: [Errno 111] Connection refused')))
 WARNING: failed to reach any of the inventories with the following issues:
-intersphinx inventory 'https://docs.scipy.org/doc/scipy/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: 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('<urllib3.connection.HTTPSConnection object at 0x7f29691b1e50>: Failed to establish a new connection: [Errno 111] Connection refused')))
+intersphinx inventory 'https://gsd.readthedocs.io/en/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='gsd.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f63592b60d0>: 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.h5py.org/en/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: 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('<urllib3.connection.HTTPSConnection object at 0x7f29691b1590>: Failed to establish a new connection: [Errno 111] Connection refused')))
-loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv ...
-loading intersphinx inventory 'networkx' from https://networkx.org/documentation/stable/objects.inv ...
+intersphinx inventory 'https://mdanalysis.org/GridDataFormats/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /GridDataFormats/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f63593ede50>: 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 'waterdynamics' from https://www.mdanalysis.org/waterdynamics/objects.inv ...
 loading intersphinx inventory 'pmda' from https://mdanalysis.org/pmda/objects.inv ...
-loading intersphinx inventory 'griddataformats' from https://mdanalysis.org/GridDataFormats/objects.inv ...
 WARNING: failed to reach any of the inventories with the following issues:
-intersphinx inventory 'https://matplotlib.org/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='matplotlib.org', port=443): Max retries exceeded with url: /stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f29691b20d0>: Failed to establish a new connection: [Errno 111] Connection refused')))
+intersphinx inventory 'https://mdanalysis.org/pmda/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /pmda/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f63592b5450>: Failed to establish a new connection: [Errno 111] Connection refused')))
+loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv ...
+loading intersphinx inventory 'networkx' from https://networkx.org/documentation/stable/objects.inv ...
+loading intersphinx inventory 'pathsimanalysis' from https://www.mdanalysis.org/PathSimAnalysis/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 <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='numpy.org', port=443): Max retries exceeded with url: /doc/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f29692e9e50>: Failed to establish a new connection: [Errno 111] Connection refused')))
+intersphinx inventory 'https://docs.h5py.org/en/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: 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('<urllib3.connection.HTTPSConnection object at 0x7f63592cc590>: Failed to establish a new connection: [Errno 111] Connection refused')))
+loading intersphinx inventory 'rdkit' from https://rdkit.org/docs/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 <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /pmda/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f29691b2490>: Failed to establish a new connection: [Errno 111] Connection refused')))
+intersphinx inventory 'https://matplotlib.org/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='matplotlib.org', port=443): Max retries exceeded with url: /stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f63592b6210>: Failed to establish a new connection: [Errno 111] Connection refused')))
+loading intersphinx inventory 'dask' from https://docs.dask.org/en/stable/objects.inv ...
 WARNING: failed to reach any of the inventories with the following issues:
-intersphinx inventory 'https://mdanalysis.org/GridDataFormats/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /GridDataFormats/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f29692ea0d0>: Failed to establish a new connection: [Errno 111] Connection refused')))
+intersphinx inventory 'https://www.mdanalysis.org/PathSimAnalysis/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /PathSimAnalysis/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f63592b5950>: 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 <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='networkx.org', port=443): Max retries exceeded with url: /documentation/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f29692e9f90>: 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 'mdahole2' from https://www.mdanalysis.org/mdahole2/objects.inv ...
-loading intersphinx inventory 'rdkit' from https://rdkit.org/docs/objects.inv ...
+intersphinx inventory 'https://docs.dask.org/en/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: 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('<urllib3.connection.HTTPSConnection object at 0x7f63592b6850>: 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 <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /mdahole2/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f29691b2350>: Failed to establish a new connection: [Errno 111] Connection refused')))
-loading intersphinx inventory 'waterdynamics' from https://www.mdanalysis.org/waterdynamics/objects.inv ...
-loading intersphinx inventory 'dask' from https://docs.dask.org/en/stable/objects.inv ...
+intersphinx inventory 'https://networkx.org/documentation/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='networkx.org', port=443): Max retries exceeded with url: /documentation/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f63592b6490>: 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 <class 'requests.exceptions.ProxyError'>: 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('<urllib3.connection.HTTPSConnection object at 0x7f29691b1e50>: Failed to establish a new connection: [Errno 111] Connection refused')))
-loading intersphinx inventory 'pathsimanalysis' from https://www.mdanalysis.org/PathSimAnalysis/objects.inv ...
+intersphinx inventory 'https://www.mdanalysis.org/mdahole2/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /mdahole2/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f63592b5810>: 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 <class 'requests.exceptions.ProxyError'>: 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('<urllib3.connection.HTTPSConnection object at 0x7f29691b0910>: Failed to establish a new connection: [Errno 111] Connection refused')))
+intersphinx inventory 'https://www.mdanalysis.org/waterdynamics/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /waterdynamics/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f63592b4cd0>: 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 <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /waterdynamics/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f29691b0a50>: Failed to establish a new connection: [Errno 111] Connection refused')))
+intersphinx inventory 'https://rdkit.org/docs/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='rdkit.org', port=443): Max retries exceeded with url: /docs/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f63592b4e10>: 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 <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='rdkit.org', port=443): Max retries exceeded with url: /docs/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f29691b0050>: Failed to establish a new connection: [Errno 111] Connection refused')))
+intersphinx inventory 'https://parmed.github.io/ParmEd/html/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: 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('<urllib3.connection.HTTPSConnection object at 0x7f63592b4a50>: 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 <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /PathSimAnalysis/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f29691b0cd0>: Failed to establish a new connection: [Errno 111] Connection refused')))
+intersphinx inventory 'https://numpy.org/doc/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='numpy.org', port=443): Max retries exceeded with url: /doc/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f63592b56d0>: 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... 
@@ -3521,8 +3557,8 @@
 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/first-build/.config/matplotlib: [Errno 13] Permission denied: '/nonexistent'
-Matplotlib created a temporary cache directory at /tmp/matplotlib-b6bwxsxe because there was an issue with the default path (/nonexistent/first-build/.config/matplotlib); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
+mkdir -p failed for path /nonexistent/second-build/.config/matplotlib: [Errno 13] Permission denied: '/nonexistent'
+Matplotlib created a temporary cache directory at /tmp/matplotlib-j0fkdxfq 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
@@ -3845,8 +3881,8 @@
 done
 copying assets... 
 copying static files... 
-Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/documentation_options.js
 Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/language_data.js
+Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/documentation_options.js
 Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/basic.css
 Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/alabaster.css
 copying static files: done
@@ -4260,12 +4296,14 @@
 dpkg-buildpackage: info: binary-only upload (no source included)
 dpkg-genchanges: info: not including original source code in upload
 I: copying local configuration
+I: user script /srv/workspace/pbuilder/3214920/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/3214920/tmp/hooks/B01_cleanup finished
 I: unmounting dev/ptmx filesystem
 I: unmounting dev/pts filesystem
 I: unmounting dev/shm filesystem
 I: unmounting proc filesystem
 I: unmounting sys filesystem
 I: cleaning the build env 
-I: removing directory /srv/workspace/pbuilder/3239140 and its subdirectories
-I: Current time: Tue Sep  1 20:12:46 -12 2026
-I: pbuilder-time-stamp: 1788336766
+I: removing directory /srv/workspace/pbuilder/3214920 and its subdirectories
+I: Current time: Thu Jul 31 15:55:43 +14 2025
+I: pbuilder-time-stamp: 1753926943