Diff of the two buildlogs: -- --- b1/build.log 2024-11-05 20:59:31.845267045 +0000 +++ b2/build.log 2024-11-05 22:31:23.217188930 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Dec 8 14:57:46 -12 2025 -I: pbuilder-time-stamp: 1765249066 +I: Current time: Wed Nov 6 10:59:36 +14 2024 +I: pbuilder-time-stamp: 1730840376 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -32,52 +32,84 @@ dpkg-source: info: applying doc_no_mdanalysis_sphinx.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/48191/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3299335/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 Nov 5 21:00 /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/3299335/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3299335/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=42 ' - 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]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(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=20 ' + 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='34699d26a47949c9804b7d13c6c11ada' - 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='48191' - PS1='# ' - PS2='> ' + INVOCATION_ID=99eca58cdf4a4b2b8077a83632f9a56a + 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=3299335 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.6HsJuGYO/pbuilderrc_SDlR --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.6HsJuGYO/b1 --logfile b1/build.log mdanalysis_2.7.0-5.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.6HsJuGYO/pbuilderrc_5LiR --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.6HsJuGYO/b2 --logfile b2/build.log mdanalysis_2.7.0-5.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/48191/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3299335/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -440,7 +472,7 @@ Get: 259 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-sitemap all 2.6.0-1 [8508 B] Get: 260 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.bibtex all 2.6.2-1 [32.4 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 python3-tqdm all 4.66.5-1 [90.1 kB] -Fetched 180 MB in 9s (20.2 MB/s) +Fetched 180 MB in 9s (19.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19968 files and directories currently installed.) @@ -1284,8 +1316,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Dec 9 03:00:50 UTC 2025. -Universal Time is now: Tue Dec 9 03:00:50 UTC 2025. +Local time is now: Tue Nov 5 21:05:28 UTC 2024. +Universal Time is now: Tue Nov 5 21:05:28 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... @@ -1528,7 +1560,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/mdanalysis-2.7.0/ && 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_2.7.0-5_source.changes +I: user script /srv/workspace/pbuilder/3299335/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3299335/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/mdanalysis-2.7.0/ && 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_2.7.0-5_source.changes dpkg-buildpackage: info: source package mdanalysis dpkg-buildpackage: info: source version 2.7.0-5 dpkg-buildpackage: info: source distribution unstable @@ -1648,205 +1684,205 @@ running build running build_py creating build/lib.linux-x86_64-cpython-312/MDAnalysis -copying MDAnalysis/version.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis -copying MDAnalysis/authors.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis copying MDAnalysis/units.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis +copying MDAnalysis/exceptions.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis +copying MDAnalysis/version.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis copying MDAnalysis/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis copying MDAnalysis/due.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis -copying MDAnalysis/exceptions.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis -creating build/lib.linux-x86_64-cpython-312/MDAnalysis/tests -copying MDAnalysis/tests/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/tests -copying MDAnalysis/tests/datafiles.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/tests +copying MDAnalysis/authors.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis creating build/lib.linux-x86_64-cpython-312/MDAnalysis/selections +copying MDAnalysis/selections/charmm.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/base.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/selections -copying MDAnalysis/selections/pymol.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/selections -copying MDAnalysis/selections/gromacs.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/selections +copying MDAnalysis/selections/jmol.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/vmd.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/selections +copying MDAnalysis/selections/gromacs.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/selections -copying MDAnalysis/selections/jmol.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/selections -copying MDAnalysis/selections/charmm.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/selections +copying MDAnalysis/selections/pymol.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/selections creating build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/base.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/base.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/memory.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/chain.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/null.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/core.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/TRC.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/memory.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TNG.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/TRC.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates -copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/chain.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/null.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates +copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates creating build/lib.linux-x86_64-cpython-312/MDAnalysis/topology -copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology -copying MDAnalysis/topology/base.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology -copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology -copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology -copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology -copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology -copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology -copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology -copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology -copying MDAnalysis/topology/tables.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology -copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology -copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology +copying MDAnalysis/topology/guessers.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology -copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology +copying MDAnalysis/topology/base.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology +copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology +copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology +copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology +copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/core.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology -copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology -copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology +copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology -copying MDAnalysis/topology/GROParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology -copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology -copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology -copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology -copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology +copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology +copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology +copying MDAnalysis/topology/tables.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology +copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology +copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology +copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology +copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology +copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology +copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology +copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology +copying MDAnalysis/topology/GROParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology +copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology +copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology -copying MDAnalysis/topology/guessers.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology -creating build/lib.linux-x86_64-cpython-312/MDAnalysis/visualization -copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/visualization -copying MDAnalysis/visualization/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/visualization -copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/visualization -creating build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary -copying MDAnalysis/auxiliary/base.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary -copying MDAnalysis/auxiliary/core.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary -copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary -copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary -copying MDAnalysis/auxiliary/EDR.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary +copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology creating build/lib.linux-x86_64-cpython-312/MDAnalysis/core -copying MDAnalysis/core/_get_readers.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core -copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core -copying MDAnalysis/core/topology.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core -copying MDAnalysis/core/groups.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core -copying MDAnalysis/core/universe.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core -copying MDAnalysis/core/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core copying MDAnalysis/core/selection.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core copying MDAnalysis/core/accessors.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core +copying MDAnalysis/core/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core +copying MDAnalysis/core/topology.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core +copying MDAnalysis/core/universe.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core +copying MDAnalysis/core/_get_readers.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core +copying MDAnalysis/core/groups.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core +copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core +creating build/lib.linux-x86_64-cpython-312/MDAnalysis/tests +copying MDAnalysis/tests/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/tests +copying MDAnalysis/tests/datafiles.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/tests creating build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations +copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations +copying MDAnalysis/transformations/rotate.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations +copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/base.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/wrap.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/fit.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations -copying MDAnalysis/transformations/nojump.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations -copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations -copying MDAnalysis/transformations/rotate.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations -copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations +copying MDAnalysis/transformations/nojump.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/translate.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations +creating build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary +copying MDAnalysis/auxiliary/base.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary +copying MDAnalysis/auxiliary/core.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary +copying MDAnalysis/auxiliary/EDR.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary +copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary +copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary +creating build/lib.linux-x86_64-cpython-312/MDAnalysis/lib +copying MDAnalysis/lib/transformations.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib +copying MDAnalysis/lib/log.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib +copying MDAnalysis/lib/distances.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib +copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib +copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib +copying MDAnalysis/lib/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib +copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib +copying MDAnalysis/lib/correlations.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib +copying MDAnalysis/lib/mdamath.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib +copying MDAnalysis/lib/_distopia.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib +copying MDAnalysis/lib/util.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis +copying MDAnalysis/analysis/bat.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis +copying MDAnalysis/analysis/msd.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis +copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis +copying MDAnalysis/analysis/nucleicacids.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/base.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis +copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis +copying MDAnalysis/analysis/distances.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis +copying MDAnalysis/analysis/align.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis +copying MDAnalysis/analysis/contacts.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis +copying MDAnalysis/analysis/rdf.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/polymer.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis +copying MDAnalysis/analysis/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis +copying MDAnalysis/analysis/gnm.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/psa.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis -copying MDAnalysis/analysis/rdf.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis +copying MDAnalysis/analysis/rms.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis +copying MDAnalysis/analysis/pca.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis +copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis +copying MDAnalysis/analysis/atomicdistances.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/dielectric.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/density.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis -copying MDAnalysis/analysis/contacts.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis -copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis -copying MDAnalysis/analysis/rms.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis -copying MDAnalysis/analysis/msd.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis -copying MDAnalysis/analysis/align.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis -copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis -copying MDAnalysis/analysis/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis -copying MDAnalysis/analysis/pca.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis -copying MDAnalysis/analysis/gnm.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis -copying MDAnalysis/analysis/atomicdistances.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis -copying MDAnalysis/analysis/distances.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis -copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis -copying MDAnalysis/analysis/nucleicacids.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis -copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis -copying MDAnalysis/analysis/bat.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis -creating build/lib.linux-x86_64-cpython-312/MDAnalysis/lib -copying MDAnalysis/lib/correlations.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib -copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib -copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib -copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib -copying MDAnalysis/lib/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib -copying MDAnalysis/lib/mdamath.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib -copying MDAnalysis/lib/_distopia.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib -copying MDAnalysis/lib/transformations.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib -copying MDAnalysis/lib/distances.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib -copying MDAnalysis/lib/util.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib -copying MDAnalysis/lib/log.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib +copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis creating build/lib.linux-x86_64-cpython-312/MDAnalysis/converters -copying MDAnalysis/converters/base.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/converters -copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/converters -copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/converters -copying MDAnalysis/converters/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/RDKit.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/converters +copying MDAnalysis/converters/base.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/converters +copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/converters +copying MDAnalysis/converters/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/converters +copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/converters +creating build/lib.linux-x86_64-cpython-312/MDAnalysis/visualization +copying MDAnalysis/visualization/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/visualization +copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/visualization +copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/visualization creating build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/tpr +copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/tpr +copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/tpr -copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/tpr -copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/tpr +creating build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats +copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats +creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/legacy +copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/legacy +copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/legacy creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore -copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore -copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore +copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore +copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore -creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/data -copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/data -copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/data -creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/legacy -copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/legacy -copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/legacy -creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hbonds -copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hbonds -copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hbonds creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hydrogenbonds -copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hydrogenbonds -copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hydrogenbonds +copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hydrogenbonds +copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hydrogenbonds creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hole2 -copying MDAnalysis/analysis/hole2/hole.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hole2 -copying MDAnalysis/analysis/hole2/utils.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hole2 +copying MDAnalysis/analysis/hole2/utils.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/templates.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hole2 -creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction -copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction -copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction -copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction +copying MDAnalysis/analysis/hole2/hole.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hole2 +creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/data +copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/data +copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/data +creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hbonds +copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hbonds +copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hbonds creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering -copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering -creating build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats -copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats +copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering +creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction +copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction +copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction +copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction running egg_info creating MDAnalysis.egg-info writing MDAnalysis.egg-info/PKG-INFO @@ -2327,20 +2363,6 @@ copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/src/transformations -copying MDAnalysis/analysis/encore/cutils.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore -copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore -copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction -copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction -creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/include -copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/include -creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/src -copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/src -copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering -copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering -creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering/include -copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering/include -creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering/src -copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering/src copying MDAnalysis/lib/formats/cython_util.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats @@ -2365,6 +2387,20 @@ copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/src +copying MDAnalysis/analysis/encore/cutils.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore +copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore +copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering +copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering +creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering/include +copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering/include +creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering/src +copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering/src +copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction +copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction +creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/include +copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/include +creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/src +copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/src running build_ext building 'MDAnalysis.lib.formats.libdcd' extension creating build/temp.linux-x86_64-cpython-312/MDAnalysis/lib/formats @@ -2761,290 +2797,290 @@ running install_lib creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/MDAnalysis -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/version.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/authors.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis -creating build/bdist.linux-x86_64/wheel/MDAnalysis/tests -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/tests/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/tests -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/tests/datafiles.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/tests creating build/bdist.linux-x86_64/wheel/MDAnalysis/selections +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/selections/charmm.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-312/MDAnalysis/selections/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/selections/pymol.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/selections/gromacs.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/selections/jmol.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-312/MDAnalysis/selections/vmd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/selections/gromacs.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections copying build/lib.linux-x86_64-cpython-312/MDAnalysis/selections/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/selections/jmol.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/selections/charmm.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/selections/pymol.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/selections +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/units.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/TXYZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/ParmEd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/NAMDBIN.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/timestep.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/memory.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/XDR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/chain.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/TXYZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/timestep.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/null.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/timestep.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/ParmEd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/TNG.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/TRC.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/H5MD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/memory.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/TNG.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/NAMDBIN.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/chain.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/null.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/timestep.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/units.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates/timestep.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/coordinates +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/exceptions.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/version.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/ITPParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/ParmEdParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/FHIAIMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/tables.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology creating build/bdist.linux-x86_64/wheel/MDAnalysis/topology/tpr +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/tpr/setting.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology/tpr +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/guessers.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/ParmEdParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/GROParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/tables.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/FHIAIMSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/GROParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/ITPParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/guessers.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology -creating build/bdist.linux-x86_64/wheel/MDAnalysis/visualization -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/visualization/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization -creating build/bdist.linux-x86_64/wheel/MDAnalysis/auxiliary -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary/EDR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/topology creating build/bdist.linux-x86_64/wheel/MDAnalysis/core -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/core/_get_readers.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/core/topology.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/core/groups.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/core/universe.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/core/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-312/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-312/MDAnalysis/core/selection.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core copying build/lib.linux-x86_64-cpython-312/MDAnalysis/core/accessors.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/due.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/core/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/core/topology.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/core/universe.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/core/_get_readers.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/core/groups.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/core +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/core/topologyattrs.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-312/MDAnalysis/tests/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/tests +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/tests/datafiles.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/tests creating build/bdist.linux-x86_64/wheel/MDAnalysis/transformations +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations/rotate.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations/boxdimensions.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations/wrap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations/fit.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations/nojump.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations/rotate.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations/boxdimensions.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations/nojump.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations/translate.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/transformations -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/exceptions.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/due.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis +creating build/bdist.linux-x86_64/wheel/MDAnalysis/auxiliary +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary/core.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary/EDR.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/auxiliary +creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/qcprot.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/c_distances_openmp.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-312/MDAnalysis/lib/include/calc_distances.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/include +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/qcprot.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/transformations.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/log.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/c_distances_openmp.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/c_distances_openmp.cpython-312-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-312/MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/libmdanalysis +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/qcprot.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/distances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/_augment.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/nsgrid.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/_augment.cpp -> 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-312/MDAnalysis/lib/formats/libmdaxdr.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/libdcd.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/include +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include/fastio.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include/xdrfile.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include/readdcd.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include/xtc_seek.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include/trr_seek.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include/endianswap.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/libdcd.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/cython_util.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/libmdaxdr.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/libmdaxdr.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/cython_util.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/cython_util.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/libmdaxdr.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/cython_util.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +copying build/lib.linux-x86_64-cpython-312/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-312/MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/src/trr_seek.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/src/xdrfile.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/src/xtc_seek.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/libdcd.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/c_distances.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/_cutil.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/picklable_file_io.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/nsgrid.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/correlations.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/_cutil.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/nsgrid.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/mdamath.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/_distopia.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/_cutil.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/_augment.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/util.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/c_distances.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/c_distances.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/_transformations.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/c_distances.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/src +creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/src/transformations +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/src/transformations/AUTHOR -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/src/transformations/transformations.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/src/transformations/LICENCE -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/_cutil.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/bat.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-312/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/legacy +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/legacy +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/msd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/nucleicacids.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/polymer.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/psa.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/distances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/align.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/contacts.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/rdf.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/dielectric.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/polymer.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-312/MDAnalysis/analysis/encore/similarity.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore -creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction -creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/src -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction/src -creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/include -copying build/lib.linux-x86_64-cpython-312/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-312/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-312/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction -copying build/lib.linux-x86_64-cpython-312/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-312/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-312/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-312/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-312/MDAnalysis/analysis/encore/cutils.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/cutils.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore +copying build/lib.linux-x86_64-cpython-312/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-312/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-312/MDAnalysis/analysis/encore/clustering/ClusteringMethod.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-312/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-312/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/clustering +creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering/src +copying build/lib.linux-x86_64-cpython-312/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-312/MDAnalysis/analysis/encore/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/covariance.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/cutils.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/density.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/contacts.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/diffusionmap.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-312/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/data/janin_ref_data.npy -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/rms.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/msd.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-312/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/legacy -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/legacy -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/align.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hbonds -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hbonds -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hbonds -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/dihedrals.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/similarity.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore +creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction +creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/include +copying build/lib.linux-x86_64-cpython-312/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-312/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-312/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-312/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-312/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction +copying build/lib.linux-x86_64-cpython-312/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-312/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-312/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-312/MDAnalysis/analysis/encore/covariance.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/encore +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/gnm.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/psa.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-312/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/helix_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hydrogenbonds +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/rms.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-312/MDAnalysis/analysis/hole2/hole.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hole2 -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hole2/utils.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hole2 copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hole2/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hole2 +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hole2/utils.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hole2 copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hole2/templates.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hole2 +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hole2/hole.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hole2 copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/pca.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/gnm.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/atomicdistances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/distances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/nucleicacids.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/bat.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/atomicdistances.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-312/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/data/janin_ref_data.npy -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/data +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/dielectric.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/density.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis +creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hbonds +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hbonds +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis/hbonds +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/helix_analysis.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/analysis -creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib -creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/src -creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/src/transformations -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/src/transformations/transformations.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/src/transformations/AUTHOR -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/src/transformations/LICENCE -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/src/transformations -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/c_distances.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -creating 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-312/MDAnalysis/lib/formats/src/trr_seek.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/src/xdrfile.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/src/xtc_seek.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/src -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/libdcd.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/libdcd.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/libmdaxdr.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/cython_util.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-312/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-312/MDAnalysis/lib/formats/include/readdcd.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include/xdrfile.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include/trr_seek.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include/xtc_seek.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include/endianswap.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include/fastio.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats/include -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/cython_util.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/libmdaxdr.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/cython_util.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/libdcd.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/libmdaxdr.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/libdcd.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/cython_util.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/formats -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/correlations.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/qcprot.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/_transformations.cpython-312-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-312/MDAnalysis/lib/include/calc_distances.h -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/include -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/qcprot.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/picklable_file_io.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/c_distances_openmp.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/_cutil.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/c_distances.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/nsgrid.cpp -> 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-312/MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib/libmdanalysis -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/_cutil.pxd -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/c_distances.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/_augment.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/mdamath.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/_cutil.cpp -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/_distopia.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/transformations.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/c_distances_openmp.c -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/distances.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/qcprot.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/nsgrid.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/c_distances.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/nsgrid.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/util.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/c_distances_openmp.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/_augment.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/_cutil.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/log.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/_augment.pyx -> build/bdist.linux-x86_64/wheel/./MDAnalysis/lib +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/dihedrals.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-312/MDAnalysis/converters/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/converters/ParmEdParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/converters/OpenMMParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-312/MDAnalysis/converters/ParmEd.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters -copying build/lib.linux-x86_64-cpython-312/MDAnalysis/converters/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-312/MDAnalysis/converters/RDKit.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/converters/base.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-312/MDAnalysis/converters/OpenMM.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/converters/ParmEdParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/converters/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters copying build/lib.linux-x86_64-cpython-312/MDAnalysis/converters/RDKitParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/converters/OpenMMParser.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/converters +creating build/bdist.linux-x86_64/wheel/MDAnalysis/visualization +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/visualization/__init__.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis/visualization +copying build/lib.linux-x86_64-cpython-312/MDAnalysis/authors.py -> build/bdist.linux-x86_64/wheel/./MDAnalysis running install_egg_info Copying MDAnalysis.egg-info to build/bdist.linux-x86_64/wheel/./MDAnalysis-2.7.0.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/MDAnalysis-2.7.0.dist-info/WHEEL -creating '/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/.tmp-pbvw7eq3/MDAnalysis-2.7.0-cp312-cp312-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it +creating '/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/.tmp-bt_hsey5/MDAnalysis-2.7.0-cp312-cp312-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' @@ -3317,38 +3353,38 @@ parsing bibtex file /build/reproducible-path/mdanalysis-2.7.0/package/doc/sphinx/source/references.bib... parsed 66 entries locale_dir /build/reproducible-path/mdanalysis-2.7.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist loading intersphinx inventory 'h5py' from https://docs.h5py.org/en/stable/objects.inv... +WARNING: failed to reach any of the inventories with the following issues: +intersphinx inventory 'https://docs.h5py.org/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.h5py.org', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv... +WARNING: failed to reach any of the inventories with the following issues: +intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'scipy' from https://docs.scipy.org/doc/scipy/objects.inv... -loading intersphinx inventory 'gsd' from https://gsd.readthedocs.io/en/stable/objects.inv... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://docs.scipy.org/doc/scipy/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.scipy.org', port=443): Max retries exceeded with url: /doc/scipy/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +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://docs.h5py.org/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.h5py.org', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://matplotlib.org/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='matplotlib.org', port=443): Max retries exceeded with url: /stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://gsd.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='gsd.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://gsd.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='gsd.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'griddataformats' from https://mdanalysis.org/GridDataFormats/objects.inv... -loading intersphinx inventory 'pmda' from https://mdanalysis.org/pmda/objects.inv... -loading intersphinx inventory 'networkx' from https://networkx.org/documentation/stable/objects.inv... -loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv... -loading intersphinx inventory 'parmed' from https://parmed.github.io/ParmEd/html/objects.inv... -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://docs.scipy.org/doc/scipy/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.scipy.org', port=443): Max retries exceeded with url: /doc/scipy/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://matplotlib.org/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='matplotlib.org', port=443): Max retries exceeded with url: /stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) -WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://mdanalysis.org/pmda/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /pmda/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://mdanalysis.org/GridDataFormats/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /GridDataFormats/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://parmed.github.io/ParmEd/html/objects.inv' not fetchable due to : HTTPSConnectionPool(host='parmed.github.io', port=443): Max retries exceeded with url: /ParmEd/html/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://numpy.org/doc/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='numpy.org', port=443): Max retries exceeded with url: /doc/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +loading intersphinx inventory 'parmed' from https://parmed.github.io/ParmEd/html/objects.inv... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://numpy.org/doc/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='numpy.org', port=443): Max retries exceeded with url: /doc/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://parmed.github.io/ParmEd/html/objects.inv' not fetchable due to : HTTPSConnectionPool(host='parmed.github.io', port=443): Max retries exceeded with url: /ParmEd/html/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +loading intersphinx inventory 'pmda' from https://mdanalysis.org/pmda/objects.inv... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://mdanalysis.org/GridDataFormats/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /GridDataFormats/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://mdanalysis.org/pmda/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /pmda/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +loading intersphinx inventory 'networkx' from https://networkx.org/documentation/stable/objects.inv... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://networkx.org/documentation/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='networkx.org', port=443): Max retries exceeded with url: /documentation/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://networkx.org/documentation/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='networkx.org', port=443): Max retries exceeded with url: /documentation/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +loading intersphinx inventory 'rdkit' from https://rdkit.org/docs/objects.inv... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://rdkit.org/docs/objects.inv' not fetchable due to : HTTPSConnectionPool(host='rdkit.org', port=443): Max retries exceeded with url: /docs/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://rdkit.org/docs/objects.inv' not fetchable due to : HTTPSConnectionPool(host='rdkit.org', port=443): Max retries exceeded with url: /docs/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) locale_dir /build/reproducible-path/mdanalysis-2.7.0/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... @@ -3412,7 +3448,7 @@ 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 -Matplotlib created a temporary cache directory at /tmp/matplotlib-olll0954 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; 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. +Matplotlib created a temporary cache directory at /tmp/matplotlib-cbasczeg because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; 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 @@ -4621,7 +4657,7 @@ MDAnalysisTests/analysis/test_bat.py: 9 warnings MDAnalysisTests/coordinates/test_mol2.py: 3 warnings - /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/topology/MOL2Parser.py:234: UserWarning: Unknown elements found for some atoms: {'oh', 'hc', 'h1', 'ho', 'c3'}. These have been given an empty element record. + /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/topology/MOL2Parser.py:234: UserWarning: Unknown elements found for some atoms: {'oh', 'ho', 'hc', 'c3', 'h1'}. These have been given an empty element record. warnings.warn("Unknown elements found for some " MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox @@ -4658,7 +4694,7 @@ MDAnalysisTests/analysis/test_encore.py: 5 warnings MDAnalysisTests/parallelism/test_multiprocessing.py: 34 warnings MDAnalysisTests/visualization/test_streamlines.py: 3 warnings - /usr/lib/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=118308) is multi-threaded, use of fork() may lead to deadlocks in the child. + /usr/lib/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=3859987) is multi-threaded, use of fork() may lead to deadlocks in the child. self.pid = os.fork() MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_plane_circle @@ -4952,8 +4988,9 @@ warnings.warn("{} does not support data selection. Reverting to " MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderFormats::test_set_all_formats -MDAnalysisTests/coordinates/test_copying.py::test_reader_filename[ref_reader11] - /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: +MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_unsupported_filetypes +MDAnalysisTests/coordinates/test_h5md.py::TestH5MDWriterWithRealTrajectory::test_step_from_frame + /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1532, in __del__ @@ -5001,7 +5038,7 @@ warnings.warn( MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_empty_dcd - /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: + /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1532, in __del__ @@ -5017,7 +5054,7 @@ MDAnalysisTests/coordinates/test_dcd.py::test_write_no_natoms MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_time_unit MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_unit - /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: + /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/DCD.py", line 482, in __del__ @@ -5085,7 +5122,7 @@ warnings.warn( MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderWithRealTrajectory::test_wrong_driver - /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: + /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1532, in __del__ @@ -5153,7 +5190,7 @@ warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/coordinates/test_h5md.py::TestH5PYNotInstalled::test_reader_no_h5py - /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: + /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1530, in __del__ @@ -5174,7 +5211,7 @@ MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_time_unit MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_unit - /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: + /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1530, in __del__ @@ -5239,7 +5276,7 @@ warnings.warn("Found missing chainIDs." MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterErrorsWarnings::test_zero_atoms_VE - /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: + /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1612, in __del__ @@ -5318,7 +5355,7 @@ warnings.warn( MDAnalysisTests/coordinates/test_tng.py::test_pytng_not_present_raises - /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: + /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1530, in __del__ @@ -5339,7 +5376,7 @@ warnings.warn( MDAnalysisTests/coordinates/test_trj.py::test_trj_no_natoms - /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: + /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1532, in __del__ @@ -5378,7 +5415,7 @@ warnings.warn("Timestep didn't have dimensions information, " MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_long_title - /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: + /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1612, in __del__ @@ -5422,7 +5459,7 @@ warnings.warn(wmsg) MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriter_2::test_no_container - /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: + /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py", line 324, in __del__ @@ -5435,7 +5472,7 @@ warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriter_2::test_no_container - /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: + /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py", line 324, in __del__ @@ -5449,22 +5486,22 @@ MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_io_fails MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_value_fails - /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py:222: UserWarning: Reading offsets from /tmp/pytest-of-pbuilder1/pytest-0/xtc0/.adk_oplsaa.xtc_offsets.npz failed, reading offsets from trajectory instead. + /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py:222: UserWarning: Reading offsets from /tmp/pytest-of-pbuilder2/pytest-0/xtc0/.adk_oplsaa.xtc_offsets.npz failed, reading offsets from trajectory instead. Consider setting 'refresh_offsets=True' when loading your Universe. warnings.warn(f"Reading offsets from {fname} failed, " MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_persistent_offsets_readonly - /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py:202: UserWarning: Cannot write lock/offset file in same location as /tmp/pytest-of-pbuilder1/pytest-0/test_persistent_offsets_readon0/adk_oplsaa.xtc. Using slow offset calculation. + /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py:202: UserWarning: Cannot write lock/offset file in same location as /tmp/pytest-of-pbuilder2/pytest-0/test_persistent_offsets_readon0/adk_oplsaa.xtc. Using slow offset calculation. warnings.warn(f"Cannot write lock/offset file in same location as " MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_io_fails MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_value_fails - /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py:222: UserWarning: Reading offsets from /tmp/pytest-of-pbuilder1/pytest-0/xtc1/.adk_oplsaa.trr_offsets.npz failed, reading offsets from trajectory instead. + /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py:222: UserWarning: Reading offsets from /tmp/pytest-of-pbuilder2/pytest-0/xtc1/.adk_oplsaa.trr_offsets.npz failed, reading offsets from trajectory instead. Consider setting 'refresh_offsets=True' when loading your Universe. warnings.warn(f"Reading offsets from {fname} failed, " MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_persistent_offsets_readonly - /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py:202: UserWarning: Cannot write lock/offset file in same location as /tmp/pytest-of-pbuilder1/pytest-0/test_persistent_offsets_readon0/adk_oplsaa.trr. Using slow offset calculation. + /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py:202: UserWarning: Cannot write lock/offset file in same location as /tmp/pytest-of-pbuilder2/pytest-0/test_persistent_offsets_readon0/adk_oplsaa.trr. Using slow offset calculation. warnings.warn(f"Cannot write lock/offset file in same location as " MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[atoms] @@ -5636,19 +5673,19 @@ See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. MDAnalysisTests/utils/test_pickleio.py::test_pickle_with_write_mode[unpicklable_f0] - /usr/lib/python3/dist-packages/_pytest/python.py:159: ResourceWarning: unclosed file <_io.FileIO name=local('/tmp/pytest-of-pbuilder1/pytest-0/test_pickle_with_write_mode_un0/pickle/test.pdb') mode='wb' closefd=True> + /usr/lib/python3/dist-packages/_pytest/python.py:159: ResourceWarning: unclosed file <_io.FileIO name=local('/tmp/pytest-of-pbuilder2/pytest-0/test_pickle_with_write_mode_un0/pickle/test.pdb') mode='wb' closefd=True> result = testfunction(**testargs) Enable tracemalloc to get traceback where the object was allocated. See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. MDAnalysisTests/utils/test_pickleio.py::test_pickle_with_write_mode[unpicklable_f1] - /usr/lib/python3/dist-packages/_pytest/python.py:159: ResourceWarning: unclosed file <_io.FileIO name=local('/tmp/pytest-of-pbuilder1/pytest-0/test_pickle_with_write_mode_un1/pickle/test.pdb') mode='xb' closefd=True> + /usr/lib/python3/dist-packages/_pytest/python.py:159: ResourceWarning: unclosed file <_io.FileIO name=local('/tmp/pytest-of-pbuilder2/pytest-0/test_pickle_with_write_mode_un1/pickle/test.pdb') mode='xb' closefd=True> result = testfunction(**testargs) Enable tracemalloc to get traceback where the object was allocated. See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. MDAnalysisTests/utils/test_pickleio.py::test_pickle_with_write_mode[unpicklable_f2] - /usr/lib/python3/dist-packages/_pytest/python.py:159: ResourceWarning: unclosed file <_io.FileIO name=local('/tmp/pytest-of-pbuilder1/pytest-0/test_pickle_with_write_mode_un2/pickle/test.pdb') mode='ab' closefd=True> + /usr/lib/python3/dist-packages/_pytest/python.py:159: ResourceWarning: unclosed file <_io.FileIO name=local('/tmp/pytest-of-pbuilder2/pytest-0/test_pickle_with_write_mode_un2/pickle/test.pdb') mode='ab' closefd=True> result = testfunction(**testargs) Enable tracemalloc to get traceback where the object was allocated. See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. @@ -5658,7 +5695,7 @@ warnings.warn(wmsg, DeprecationWarning) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -= 18632 passed, 594 skipped, 7 xfailed, 2 xpassed, 27465 warnings in 885.83s (0:14:45) = += 18632 passed, 594 skipped, 7 xfailed, 2 xpassed, 27466 warnings in 3652.09s (1:00:52) = --- Logging error --- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/duecredit/utils.py", line 209, in wrapped_func @@ -5698,7 +5735,7 @@ Call stack: File "/usr/lib/python3/dist-packages/duecredit/utils.py", line 211, in wrapped_func lgr.warning( -Message: "DueCredit internal failure while running : PermissionError(13, 'Permission denied'). Please report to developers at https://github.com/duecredit/duecredit/issues" +Message: "DueCredit internal failure while running : PermissionError(13, 'Permission denied'). Please report to developers at https://github.com/duecredit/duecredit/issues" Arguments: () DueCredit Report: @@ -5706,14 +5743,14 @@ - Bond-Angle-Torsions Coordinate Transformation / MDAnalysis.analysis.bat.BAT (v 2.7.0) [3] - Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.7.0) [4] - ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.7.0) [5] - - HOLE trajectory analysis with orderparameters, HOLE program / MDAnalysis.analysis.hole2 (v 2.7.0) [6, 7, 8] + - HOLE program, HOLE trajectory analysis with orderparameters / MDAnalysis.analysis.hole2 (v 2.7.0) [6, 7, 8] - Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.7.0) [9] - Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.7.0) [10] - LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.7.0) [2] - Mean Squared Displacements with tidynamics, FCA fast correlation algorithm / MDAnalysis.analysis.msd (v 2.7.0) [11, 12] - Cumulative overlap / MDAnalysis.analysis.pca (v 2.7.0) [13] - Path Similarity Analysis algorithm and implementation / MDAnalysis.analysis.psa (v 2.7.0) [14] - - Specifications of the H5MD standard, MDAnalysis trajectory reader/writer of the H5MDformat / MDAnalysis.coordinates.H5MD (v 2.7.0, 1.1) [15, 16] + - Specifications of the H5MD standard, MDAnalysis trajectory reader/writer of the H5MDformat / MDAnalysis.coordinates.H5MD (v 1.1, 2.7.0) [15, 16] - MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.7.0) [17] - The TNG paper / MDAnalysis.coordinates.TNG (v 2.7.0) [18] - QCProt implementation / MDAnalysis.lib.qcprot (v 2.7.0) [19, 20] @@ -5760,9 +5797,9 @@ dpkg-gencontrol: warning: package python-mdanalysis-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild -dpkg-deb: building package 'python3-mdanalysis' in '../python3-mdanalysis_2.7.0-5_amd64.deb'. dpkg-deb: building package 'python3-mdanalysis-dbgsym' in '../python3-mdanalysis-dbgsym_2.7.0-5_amd64.deb'. dpkg-deb: building package 'python-mdanalysis-doc' in '../python-mdanalysis-doc_2.7.0-5_all.deb'. +dpkg-deb: building package 'python3-mdanalysis' in '../python3-mdanalysis_2.7.0-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../mdanalysis_2.7.0-5_amd64.buildinfo dpkg-genchanges --build=binary -O../mdanalysis_2.7.0-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -5771,12 +5808,14 @@ 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/3299335/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3299335/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/48191 and its subdirectories -I: Current time: Mon Dec 8 15:22:28 -12 2025 -I: pbuilder-time-stamp: 1765250548 +I: removing directory /srv/workspace/pbuilder/3299335 and its subdirectories +I: Current time: Wed Nov 6 12:31:22 +14 2024 +I: pbuilder-time-stamp: 1730845882