0s autopkgtest [01:53:11]: starting date and time: 2025-03-16 01:53:11+0000 0s autopkgtest [01:53:11]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [01:53:11]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7w1ysf2b/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:scikit-learn --apt-upgrade mdtraj --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=scikit-learn/1.4.2+dfsg-8 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-37.secgroup --name adt-plucky-arm64-mdtraj-20250316-012700-juju-7f2275-prod-proposed-migration-environment-20-ab98cc85-a8b9-4abc-9da3-15a25841cc81 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 74s autopkgtest [01:54:25]: testbed dpkg architecture: arm64 74s autopkgtest [01:54:25]: testbed apt version: 2.9.33 74s autopkgtest [01:54:25]: @@@@@@@@@@@@@@@@@@@@ test bed setup 75s autopkgtest [01:54:26]: testbed release detected to be: None 75s autopkgtest [01:54:26]: updating testbed package index (apt update) 76s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 76s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 76s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 76s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 76s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.7 kB] 76s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [42.9 kB] 76s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [382 kB] 76s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [72.2 kB] 76s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1760 B] 76s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 76s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [338 kB] 77s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [13.6 kB] 77s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [16.8 kB] 77s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [436 B] 77s Fetched 1012 kB in 1s (808 kB/s) 78s Reading package lists... 79s Reading package lists... 79s Building dependency tree... 79s Reading state information... 80s Calculating upgrade... 80s Calculating upgrade... 80s The following packages will be upgraded: 80s cron cron-daemon-common 81s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 81s Need to get 101 kB of archives. 81s After this operation, 0 B of additional disk space will be used. 81s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 cron arm64 3.0pl1-194ubuntu1 [86.6 kB] 81s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 cron-daemon-common all 3.0pl1-194ubuntu1 [14.6 kB] 81s Fetched 101 kB in 0s (291 kB/s) 82s (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 ... 81647 files and directories currently installed.) 82s Preparing to unpack .../cron_3.0pl1-194ubuntu1_arm64.deb ... 82s Unpacking cron (3.0pl1-194ubuntu1) over (3.0pl1-192ubuntu1) ... 82s Preparing to unpack .../cron-daemon-common_3.0pl1-194ubuntu1_all.deb ... 82s Unpacking cron-daemon-common (3.0pl1-194ubuntu1) over (3.0pl1-192ubuntu1) ... 82s Setting up cron-daemon-common (3.0pl1-194ubuntu1) ... 82s Setting up cron (3.0pl1-194ubuntu1) ... 82s Processing triggers for man-db (2.13.0-1) ... 84s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s Solving dependencies... 85s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 85s autopkgtest [01:54:36]: upgrading testbed (apt dist-upgrade and autopurge) 85s Reading package lists... 85s Building dependency tree... 85s Reading state information... 86s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 86s Starting 2 pkgProblemResolver with broken count: 0 86s Done 87s Entering ResolveByKeep 87s 87s Calculating upgrade... 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 89s Starting pkgProblemResolver with broken count: 0 89s Starting 2 pkgProblemResolver with broken count: 0 89s Done 89s Solving dependencies... 89s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 90s autopkgtest [01:54:41]: rebooting testbed after setup commands that affected boot 115s autopkgtest [01:55:06]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 117s autopkgtest [01:55:08]: @@@@@@@@@@@@@@@@@@@@ apt-source mdtraj 123s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.3-2build1 (dsc) [2701 B] 123s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.3-2build1 (tar) [22.0 MB] 123s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.3-2build1 (diff) [297 kB] 123s gpgv: Signature made Tue Mar 4 15:08:42 2025 UTC 123s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 123s gpgv: Can't check signature: No public key 123s dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.10.3-2build1.dsc: no acceptable signature found 124s autopkgtest [01:55:15]: testing package mdtraj version 1.10.3-2build1 125s autopkgtest [01:55:16]: build not needed 128s autopkgtest [01:55:19]: test command1: preparing testbed 128s Reading package lists... 129s Building dependency tree... 129s Reading state information... 129s Starting pkgProblemResolver with broken count: 0 129s Starting 2 pkgProblemResolver with broken count: 0 129s Done 130s The following NEW packages will be installed: 130s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx gdb 130s libaec0 libbabeltrace1 libblas3 libblosc1 libblosc2-4 libdeflate0 130s libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 130s libhdf5-310 libhdf5-hl-310 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 130s libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 130s libnetcdf22 libnorm1t64 libopenjp2-7 libpgm-5.3-0t64 libqhull-r8.0 libraqm0 130s libsharpyuv0 libsnappy1v5 libsodium23 libsource-highlight-common 130s libsource-highlight4t64 libsz2 libtcl8.6 libtiff6 libtk8.6 libwebp7 130s libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 libzmq5 130s python-matplotlib-data python-tables-data python3-asttokens python3-brotli 130s python3-cftime python3-comm python3-contourpy python3-coverage 130s python3-cpuinfo python3-cycler python3-dateutil python3-debugpy 130s python3-decorator python3-executing python3-fastjsonschema python3-fonttools 130s python3-fs python3-gsd python3-iniconfig python3-ipykernel python3-ipython 130s python3-jedi python3-joblib python3-jupyter-client python3-jupyter-core 130s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 130s python3-matplotlib-inline python3-mdtraj python3-mpmath python3-nbformat 130s python3-nest-asyncio python3-netcdf4 python3-networkx python3-numexpr 130s python3-numpy python3-numpy-dev python3-packaging python3-pandas 130s python3-pandas-lib python3-parso python3-pexpect python3-pil 130s python3-pil.imagetk python3-platformdirs python3-pluggy 130s python3-prompt-toolkit python3-psutil python3-ptyprocess python3-pure-eval 130s python3-pytest python3-pytz python3-scipy python3-sklearn 130s python3-sklearn-lib python3-stack-data python3-sympy python3-tables 130s python3-tables-lib python3-threadpoolctl python3-tk python3-tornado 130s python3-traitlets python3-typeshed python3-tz python3-ufolib2 130s python3-unicodedata2 python3-wcwidth python3-zmq python3.12-tk python3.13-tk 130s tk8.6-blt2.5 unicode-data x11-common 130s 0 upgraded, 128 newly installed, 0 to remove and 0 not upgraded. 130s Need to get 112 MB of archives. 130s After this operation, 513 MB of additional disk space will be used. 130s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [146 kB] 130s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 130s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 130s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 131s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3981 kB] 131s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 131s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 131s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 131s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 131s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 131s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 131s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 131s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 131s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 131s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 131s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-8 [624 kB] 131s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-8 [4824 B] 131s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.3-1 [171 kB] 131s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libbabeltrace1 arm64 1.5.11-4build2 [159 kB] 131s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libsource-highlight-common all 3.1.9-4.3build1 [64.2 kB] 131s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libsource-highlight4t64 arm64 3.1.9-4.3build1 [243 kB] 131s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 gdb arm64 16.2-2ubuntu2 [4758 kB] 131s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 131s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libsnappy1v5 arm64 1.2.1-1 [30.4 kB] 131s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 libblosc1 arm64 1.21.5+ds-1build1 [25.7 kB] 131s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 libblosc2-4 arm64 2.16.0+ds-1 [158 kB] 131s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 131s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 131s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 131s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 131s Get:31 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 132s Get:32 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-310 arm64 1.14.5+repack-3 [1331 kB] 132s Get:33 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [59.8 kB] 132s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 132s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 132s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 132s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 132s Get:38 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 132s Get:39 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 132s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 132s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 132s Get:42 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnetcdf22 arm64 1:4.9.3-1 [504 kB] 132s Get:43 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnorm1t64 arm64 1.5.9+dfsg-3.1build1 [150 kB] 132s Get:44 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpgm-5.3-0t64 arm64 5.3.128~dfsg-2.1build1 [162 kB] 132s Get:45 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 132s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 132s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 132s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libsodium23 arm64 1.0.18-1build3 [119 kB] 132s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 132s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 132s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 132s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 132s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 132s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu2 [168 kB] 132s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 libzmq5 arm64 4.3.5-1build2 [247 kB] 132s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-7build1 [2934 kB] 132s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-tables-data all 3.10.2-2build1 [49.7 kB] 132s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-asttokens all 3.0.0-1 [20.4 kB] 132s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build4 [342 kB] 132s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cftime arm64 1.6.4-2 [208 kB] 132s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 132s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-comm all 0.2.1-1 [7016 B] 132s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.1-1build1 [182 kB] 132s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-coverage arm64 7.6.0+dfsg1-2build1 [153 kB] 132s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cpuinfo all 9.0.0+git20221119-3 [21.7 kB] 132s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 132s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB] 132s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-debugpy arm64 1.8.8+ds-2ubuntu1 [1054 kB] 132s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 132s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-executing all 2.2.0-0.1 [25.0 kB] 132s Get:71 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fastjsonschema all 2.21.1-1 [20.4 kB] 132s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB] 132s Get:73 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-7 [90.8 kB] 132s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.1-1build1 [1258 kB] 132s Get:75 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.4.0+dfsg-1build1 [27.1 kB] 132s Get:76 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-4ubuntu2 [16.7 MB] 133s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 133s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-5 [4229 kB] 133s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 133s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build3 [360 kB] 133s Get:81 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 133s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.55.3-2build1 [1466 kB] 133s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-gsd arm64 3.4.2-2build1 [209 kB] 133s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 133s Get:85 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-parso all 0.8.4-1 [67.6 kB] 133s Get:86 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-typeshed all 0.0~git20241223.ea91db2-1 [1548 kB] 133s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-jedi all 0.19.1+ds1-1 [693 kB] 133s Get:88 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 133s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 133s Get:90 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-prompt-toolkit all 3.0.50-1 [257 kB] 133s Get:91 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pure-eval all 0.2.3-1 [11.4 kB] 133s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-stack-data all 0.6.3-1 [22.0 kB] 133s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-ptyprocess all 0.7.0-6 [14.8 kB] 133s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pexpect all 4.9-3 [48.1 kB] 133s Get:95 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ipython all 8.30.0-2 [569 kB] 133s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-jupyter-core all 5.7.2-5 [28.1 kB] 133s Get:97 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-psutil arm64 5.9.8-2build3 [196 kB] 133s Get:98 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tornado arm64 6.4.2-1 [299 kB] 133s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-zmq arm64 26.2.1-1build1 [184 kB] 133s Get:100 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-jupyter-client all 8.6.3-2 [78.5 kB] 133s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-nest-asyncio all 1.5.4-1 [6256 B] 133s Get:102 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 134s Get:103 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ipykernel all 6.29.5-2 [82.7 kB] 134s Get:104 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-joblib all 1.4.2-3 [205 kB] 134s Get:105 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-3build1 [50.7 kB] 134s Get:106 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.3-2 [183 kB] 134s Get:107 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 11.1.0-5build1 [463 kB] 134s Get:108 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.9-1 [115 kB] 134s Get:109 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.2-2 [106 kB] 134s Get:110 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.13.1-1 [9770 B] 134s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 11.1.0-5build1 [9892 B] 134s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-7build1 [17.3 MB] 134s Get:113 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-netcdf4 arm64 1.7.2-1build4 [587 kB] 134s Get:114 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 135s Get:115 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pytz all 2025.1-3 [162 kB] 135s Get:116 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2025.1-3 [1866 B] 135s Get:117 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-8build1 [4586 kB] 135s Get:118 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-8build1 [3112 kB] 135s Get:119 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-numexpr arm64 2.10.2-1build2 [120 kB] 135s Get:120 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tables-lib arm64 3.10.2-2build1 [510 kB] 135s Get:121 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tables all 3.10.2-2build1 [354 kB] 135s Get:122 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mdtraj arm64 1.10.3-2build1 [1088 kB] 135s Get:123 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-nbformat all 5.9.1-1 [41.2 kB] 135s Get:124 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 135s Get:125 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.5-1 [252 kB] 135s Get:126 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 135s Get:127 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-8 [4109 kB] 135s Get:128 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-sklearn all 1.4.2+dfsg-8 [2258 kB] 136s Fetched 112 MB in 6s (19.7 MB/s) 136s Selecting previously unselected package python3-numpy-dev:arm64. 136s (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 ... 81647 files and directories currently installed.) 136s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.3+ds-5_arm64.deb ... 136s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 136s Selecting previously unselected package libblas3:arm64. 137s Preparing to unpack .../001-libblas3_3.12.1-2_arm64.deb ... 137s Unpacking libblas3:arm64 (3.12.1-2) ... 137s Selecting previously unselected package libgfortran5:arm64. 137s Preparing to unpack .../002-libgfortran5_15-20250222-0ubuntu1_arm64.deb ... 137s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ... 137s Selecting previously unselected package liblapack3:arm64. 137s Preparing to unpack .../003-liblapack3_3.12.1-2_arm64.deb ... 137s Unpacking liblapack3:arm64 (3.12.1-2) ... 137s Selecting previously unselected package python3-numpy. 137s Preparing to unpack .../004-python3-numpy_1%3a2.2.3+ds-5_arm64.deb ... 137s Unpacking python3-numpy (1:2.2.3+ds-5) ... 137s Selecting previously unselected package libtcl8.6:arm64. 137s Preparing to unpack .../005-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... 137s Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... 137s Selecting previously unselected package fonts-dejavu-mono. 137s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ... 137s Unpacking fonts-dejavu-mono (2.37-8) ... 137s Selecting previously unselected package fonts-dejavu-core. 137s Preparing to unpack .../007-fonts-dejavu-core_2.37-8_all.deb ... 137s Unpacking fonts-dejavu-core (2.37-8) ... 137s Selecting previously unselected package fontconfig-config. 137s Preparing to unpack .../008-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 137s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 137s Selecting previously unselected package libfontconfig1:arm64. 137s Preparing to unpack .../009-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 137s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 137s Selecting previously unselected package libxrender1:arm64. 137s Preparing to unpack .../010-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 137s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 137s Selecting previously unselected package libxft2:arm64. 137s Preparing to unpack .../011-libxft2_2.3.6-1build1_arm64.deb ... 137s Unpacking libxft2:arm64 (2.3.6-1build1) ... 137s Selecting previously unselected package x11-common. 137s Preparing to unpack .../012-x11-common_1%3a7.7+23ubuntu3_all.deb ... 137s Unpacking x11-common (1:7.7+23ubuntu3) ... 137s Selecting previously unselected package libxss1:arm64. 137s Preparing to unpack .../013-libxss1_1%3a1.2.3-1build3_arm64.deb ... 137s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 138s Selecting previously unselected package libtk8.6:arm64. 138s Preparing to unpack .../014-libtk8.6_8.6.16-1_arm64.deb ... 138s Unpacking libtk8.6:arm64 (8.6.16-1) ... 138s Selecting previously unselected package tk8.6-blt2.5. 138s Preparing to unpack .../015-tk8.6-blt2.5_2.5.3+dfsg-8_arm64.deb ... 138s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 138s Selecting previously unselected package blt. 138s Preparing to unpack .../016-blt_2.5.3+dfsg-8_arm64.deb ... 138s Unpacking blt (2.5.3+dfsg-8) ... 138s Selecting previously unselected package fonts-lyx. 138s Preparing to unpack .../017-fonts-lyx_2.4.3-1_all.deb ... 138s Unpacking fonts-lyx (2.4.3-1) ... 138s Selecting previously unselected package libbabeltrace1:arm64. 138s Preparing to unpack .../018-libbabeltrace1_1.5.11-4build2_arm64.deb ... 138s Unpacking libbabeltrace1:arm64 (1.5.11-4build2) ... 138s Selecting previously unselected package libsource-highlight-common. 138s Preparing to unpack .../019-libsource-highlight-common_3.1.9-4.3build1_all.deb ... 138s Unpacking libsource-highlight-common (3.1.9-4.3build1) ... 138s Selecting previously unselected package libsource-highlight4t64:arm64. 138s Preparing to unpack .../020-libsource-highlight4t64_3.1.9-4.3build1_arm64.deb ... 138s Unpacking libsource-highlight4t64:arm64 (3.1.9-4.3build1) ... 138s Selecting previously unselected package gdb. 138s Preparing to unpack .../021-gdb_16.2-2ubuntu2_arm64.deb ... 138s Unpacking gdb (16.2-2ubuntu2) ... 138s Selecting previously unselected package libaec0:arm64. 138s Preparing to unpack .../022-libaec0_1.1.3-1_arm64.deb ... 138s Unpacking libaec0:arm64 (1.1.3-1) ... 138s Selecting previously unselected package libsnappy1v5:arm64. 138s Preparing to unpack .../023-libsnappy1v5_1.2.1-1_arm64.deb ... 138s Unpacking libsnappy1v5:arm64 (1.2.1-1) ... 138s Selecting previously unselected package libblosc1:arm64. 138s Preparing to unpack .../024-libblosc1_1.21.5+ds-1build1_arm64.deb ... 138s Unpacking libblosc1:arm64 (1.21.5+ds-1build1) ... 138s Selecting previously unselected package libblosc2-4:arm64. 138s Preparing to unpack .../025-libblosc2-4_2.16.0+ds-1_arm64.deb ... 138s Unpacking libblosc2-4:arm64 (2.16.0+ds-1) ... 138s Selecting previously unselected package libdeflate0:arm64. 138s Preparing to unpack .../026-libdeflate0_1.23-1_arm64.deb ... 138s Unpacking libdeflate0:arm64 (1.23-1) ... 138s Selecting previously unselected package libgomp1:arm64. 138s Preparing to unpack .../027-libgomp1_15-20250222-0ubuntu1_arm64.deb ... 138s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 138s Selecting previously unselected package libgraphite2-3:arm64. 138s Preparing to unpack .../028-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 138s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 138s Selecting previously unselected package libharfbuzz0b:arm64. 138s Preparing to unpack .../029-libharfbuzz0b_10.2.0-1_arm64.deb ... 138s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 138s Selecting previously unselected package libsz2:arm64. 138s Preparing to unpack .../030-libsz2_1.1.3-1_arm64.deb ... 138s Unpacking libsz2:arm64 (1.1.3-1) ... 138s Selecting previously unselected package libhdf5-310:arm64. 138s Preparing to unpack .../031-libhdf5-310_1.14.5+repack-3_arm64.deb ... 138s Unpacking libhdf5-310:arm64 (1.14.5+repack-3) ... 138s Selecting previously unselected package libhdf5-hl-310:arm64. 138s Preparing to unpack .../032-libhdf5-hl-310_1.14.5+repack-3_arm64.deb ... 138s Unpacking libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 138s Selecting previously unselected package libimagequant0:arm64. 138s Preparing to unpack .../033-libimagequant0_2.18.0-1build1_arm64.deb ... 138s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 138s Selecting previously unselected package libjpeg-turbo8:arm64. 138s Preparing to unpack .../034-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 138s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 138s Selecting previously unselected package libjpeg8:arm64. 138s Preparing to unpack .../035-libjpeg8_8c-2ubuntu11_arm64.deb ... 138s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 139s Selecting previously unselected package libjs-jquery. 139s Preparing to unpack .../036-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 139s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 139s Selecting previously unselected package libjs-jquery-ui. 139s Preparing to unpack .../037-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 139s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 139s Selecting previously unselected package liblbfgsb0:arm64. 139s Preparing to unpack .../038-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 139s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 139s Selecting previously unselected package liblcms2-2:arm64. 139s Preparing to unpack .../039-liblcms2-2_2.16-2_arm64.deb ... 139s Unpacking liblcms2-2:arm64 (2.16-2) ... 139s Selecting previously unselected package liblerc4:arm64. 139s Preparing to unpack .../040-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 139s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 139s Selecting previously unselected package libnetcdf22:arm64. 139s Preparing to unpack .../041-libnetcdf22_1%3a4.9.3-1_arm64.deb ... 139s Unpacking libnetcdf22:arm64 (1:4.9.3-1) ... 139s Selecting previously unselected package libnorm1t64:arm64. 139s Preparing to unpack .../042-libnorm1t64_1.5.9+dfsg-3.1build1_arm64.deb ... 139s Unpacking libnorm1t64:arm64 (1.5.9+dfsg-3.1build1) ... 139s Selecting previously unselected package libpgm-5.3-0t64:arm64. 139s Preparing to unpack .../043-libpgm-5.3-0t64_5.3.128~dfsg-2.1build1_arm64.deb ... 139s Unpacking libpgm-5.3-0t64:arm64 (5.3.128~dfsg-2.1build1) ... 139s Selecting previously unselected package libqhull-r8.0:arm64. 139s Preparing to unpack .../044-libqhull-r8.0_2020.2-6build1_arm64.deb ... 139s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 139s Selecting previously unselected package libraqm0:arm64. 139s Preparing to unpack .../045-libraqm0_0.10.2-1_arm64.deb ... 139s Unpacking libraqm0:arm64 (0.10.2-1) ... 139s Selecting previously unselected package libsharpyuv0:arm64. 139s Preparing to unpack .../046-libsharpyuv0_1.5.0-0.1_arm64.deb ... 139s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 139s Selecting previously unselected package libsodium23:arm64. 139s Preparing to unpack .../047-libsodium23_1.0.18-1build3_arm64.deb ... 139s Unpacking libsodium23:arm64 (1.0.18-1build3) ... 139s Selecting previously unselected package libjbig0:arm64. 139s Preparing to unpack .../048-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 139s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 139s Selecting previously unselected package libwebp7:arm64. 139s Preparing to unpack .../049-libwebp7_1.5.0-0.1_arm64.deb ... 139s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 139s Selecting previously unselected package libtiff6:arm64. 139s Preparing to unpack .../050-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 139s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 139s Selecting previously unselected package libwebpdemux2:arm64. 139s Preparing to unpack .../051-libwebpdemux2_1.5.0-0.1_arm64.deb ... 139s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 139s Selecting previously unselected package libwebpmux3:arm64. 139s Preparing to unpack .../052-libwebpmux3_1.5.0-0.1_arm64.deb ... 139s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 139s Selecting previously unselected package libxslt1.1:arm64. 139s Preparing to unpack .../053-libxslt1.1_1.1.39-0exp1ubuntu2_arm64.deb ... 139s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ... 139s Selecting previously unselected package libzmq5:arm64. 139s Preparing to unpack .../054-libzmq5_4.3.5-1build2_arm64.deb ... 139s Unpacking libzmq5:arm64 (4.3.5-1build2) ... 139s Selecting previously unselected package python-matplotlib-data. 139s Preparing to unpack .../055-python-matplotlib-data_3.8.3-7build1_all.deb ... 139s Unpacking python-matplotlib-data (3.8.3-7build1) ... 139s Selecting previously unselected package python-tables-data. 139s Preparing to unpack .../056-python-tables-data_3.10.2-2build1_all.deb ... 139s Unpacking python-tables-data (3.10.2-2build1) ... 139s Selecting previously unselected package python3-asttokens. 139s Preparing to unpack .../057-python3-asttokens_3.0.0-1_all.deb ... 139s Unpacking python3-asttokens (3.0.0-1) ... 139s Selecting previously unselected package python3-brotli. 139s Preparing to unpack .../058-python3-brotli_1.1.0-2build4_arm64.deb ... 139s Unpacking python3-brotli (1.1.0-2build4) ... 139s Selecting previously unselected package python3-cftime. 140s Preparing to unpack .../059-python3-cftime_1.6.4-2_arm64.deb ... 140s Unpacking python3-cftime (1.6.4-2) ... 140s Selecting previously unselected package python3-traitlets. 140s Preparing to unpack .../060-python3-traitlets_5.14.3+really5.14.3-1_all.deb ... 140s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ... 140s Selecting previously unselected package python3-comm. 140s Preparing to unpack .../061-python3-comm_0.2.1-1_all.deb ... 140s Unpacking python3-comm (0.2.1-1) ... 140s Selecting previously unselected package python3-contourpy. 140s Preparing to unpack .../062-python3-contourpy_1.3.1-1build1_arm64.deb ... 140s Unpacking python3-contourpy (1.3.1-1build1) ... 140s Selecting previously unselected package python3-coverage. 140s Preparing to unpack .../063-python3-coverage_7.6.0+dfsg1-2build1_arm64.deb ... 140s Unpacking python3-coverage (7.6.0+dfsg1-2build1) ... 140s Selecting previously unselected package python3-cpuinfo. 140s Preparing to unpack .../064-python3-cpuinfo_9.0.0+git20221119-3_all.deb ... 140s Unpacking python3-cpuinfo (9.0.0+git20221119-3) ... 140s Selecting previously unselected package python3-cycler. 140s Preparing to unpack .../065-python3-cycler_0.12.1-1_all.deb ... 140s Unpacking python3-cycler (0.12.1-1) ... 140s Selecting previously unselected package python3-dateutil. 140s Preparing to unpack .../066-python3-dateutil_2.9.0-3_all.deb ... 140s Unpacking python3-dateutil (2.9.0-3) ... 140s Selecting previously unselected package python3-debugpy. 140s Preparing to unpack .../067-python3-debugpy_1.8.8+ds-2ubuntu1_arm64.deb ... 140s Unpacking python3-debugpy (1.8.8+ds-2ubuntu1) ... 140s Selecting previously unselected package python3-decorator. 140s Preparing to unpack .../068-python3-decorator_5.1.1-5_all.deb ... 140s Unpacking python3-decorator (5.1.1-5) ... 140s Selecting previously unselected package python3-executing. 140s Preparing to unpack .../069-python3-executing_2.2.0-0.1_all.deb ... 140s Unpacking python3-executing (2.2.0-0.1) ... 140s Selecting previously unselected package python3-fastjsonschema. 140s Preparing to unpack .../070-python3-fastjsonschema_2.21.1-1_all.deb ... 140s Unpacking python3-fastjsonschema (2.21.1-1) ... 140s Selecting previously unselected package python3-platformdirs. 140s Preparing to unpack .../071-python3-platformdirs_4.3.6-1_all.deb ... 140s Unpacking python3-platformdirs (4.3.6-1) ... 140s Selecting previously unselected package python3-fs. 140s Preparing to unpack .../072-python3-fs_2.4.16-7_all.deb ... 140s Unpacking python3-fs (2.4.16-7) ... 140s Selecting previously unselected package python3-lxml:arm64. 140s Preparing to unpack .../073-python3-lxml_5.3.1-1build1_arm64.deb ... 140s Unpacking python3-lxml:arm64 (5.3.1-1build1) ... 140s Selecting previously unselected package python3-lz4. 140s Preparing to unpack .../074-python3-lz4_4.4.0+dfsg-1build1_arm64.deb ... 140s Unpacking python3-lz4 (4.4.0+dfsg-1build1) ... 140s Selecting previously unselected package python3-scipy. 140s Preparing to unpack .../075-python3-scipy_1.14.1-4ubuntu2_arm64.deb ... 140s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 141s Selecting previously unselected package python3-mpmath. 141s Preparing to unpack .../076-python3-mpmath_1.3.0-1_all.deb ... 141s Unpacking python3-mpmath (1.3.0-1) ... 141s Selecting previously unselected package python3-sympy. 141s Preparing to unpack .../077-python3-sympy_1.13.3-5_all.deb ... 141s Unpacking python3-sympy (1.13.3-5) ... 141s Selecting previously unselected package python3-ufolib2. 141s Preparing to unpack .../078-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 141s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 141s Selecting previously unselected package python3-unicodedata2. 141s Preparing to unpack .../079-python3-unicodedata2_15.1.0+ds-1build3_arm64.deb ... 141s Unpacking python3-unicodedata2 (15.1.0+ds-1build3) ... 141s Selecting previously unselected package unicode-data. 141s Preparing to unpack .../080-unicode-data_15.1.0-1_all.deb ... 141s Unpacking unicode-data (15.1.0-1) ... 141s Selecting previously unselected package python3-fonttools. 141s Preparing to unpack .../081-python3-fonttools_4.55.3-2build1_arm64.deb ... 141s Unpacking python3-fonttools (4.55.3-2build1) ... 141s Selecting previously unselected package python3-gsd. 141s Preparing to unpack .../082-python3-gsd_3.4.2-2build1_arm64.deb ... 141s Unpacking python3-gsd (3.4.2-2build1) ... 141s Selecting previously unselected package python3-iniconfig. 141s Preparing to unpack .../083-python3-iniconfig_1.1.1-2_all.deb ... 141s Unpacking python3-iniconfig (1.1.1-2) ... 141s Selecting previously unselected package python3-parso. 141s Preparing to unpack .../084-python3-parso_0.8.4-1_all.deb ... 141s Unpacking python3-parso (0.8.4-1) ... 141s Selecting previously unselected package python3-typeshed. 142s Preparing to unpack .../085-python3-typeshed_0.0~git20241223.ea91db2-1_all.deb ... 142s Unpacking python3-typeshed (0.0~git20241223.ea91db2-1) ... 142s Selecting previously unselected package python3-jedi. 142s Preparing to unpack .../086-python3-jedi_0.19.1+ds1-1_all.deb ... 142s Unpacking python3-jedi (0.19.1+ds1-1) ... 142s Selecting previously unselected package python3-matplotlib-inline. 142s Preparing to unpack .../087-python3-matplotlib-inline_0.1.6-2_all.deb ... 142s Unpacking python3-matplotlib-inline (0.1.6-2) ... 142s Selecting previously unselected package python3-wcwidth. 142s Preparing to unpack .../088-python3-wcwidth_0.2.13+dfsg1-1_all.deb ... 142s Unpacking python3-wcwidth (0.2.13+dfsg1-1) ... 142s Selecting previously unselected package python3-prompt-toolkit. 142s Preparing to unpack .../089-python3-prompt-toolkit_3.0.50-1_all.deb ... 142s Unpacking python3-prompt-toolkit (3.0.50-1) ... 142s Selecting previously unselected package python3-pure-eval. 142s Preparing to unpack .../090-python3-pure-eval_0.2.3-1_all.deb ... 142s Unpacking python3-pure-eval (0.2.3-1) ... 142s Selecting previously unselected package python3-stack-data. 142s Preparing to unpack .../091-python3-stack-data_0.6.3-1_all.deb ... 142s Unpacking python3-stack-data (0.6.3-1) ... 142s Selecting previously unselected package python3-ptyprocess. 142s Preparing to unpack .../092-python3-ptyprocess_0.7.0-6_all.deb ... 142s Unpacking python3-ptyprocess (0.7.0-6) ... 142s Selecting previously unselected package python3-pexpect. 142s Preparing to unpack .../093-python3-pexpect_4.9-3_all.deb ... 142s Unpacking python3-pexpect (4.9-3) ... 142s Selecting previously unselected package python3-ipython. 143s Preparing to unpack .../094-python3-ipython_8.30.0-2_all.deb ... 143s Unpacking python3-ipython (8.30.0-2) ... 143s Selecting previously unselected package python3-jupyter-core. 143s Preparing to unpack .../095-python3-jupyter-core_5.7.2-5_all.deb ... 143s Unpacking python3-jupyter-core (5.7.2-5) ... 143s Selecting previously unselected package python3-psutil. 143s Preparing to unpack .../096-python3-psutil_5.9.8-2build3_arm64.deb ... 143s Unpacking python3-psutil (5.9.8-2build3) ... 143s Selecting previously unselected package python3-tornado. 143s Preparing to unpack .../097-python3-tornado_6.4.2-1_arm64.deb ... 143s Unpacking python3-tornado (6.4.2-1) ... 143s Selecting previously unselected package python3-zmq. 143s Preparing to unpack .../098-python3-zmq_26.2.1-1build1_arm64.deb ... 143s Unpacking python3-zmq (26.2.1-1build1) ... 143s Selecting previously unselected package python3-jupyter-client. 143s Preparing to unpack .../099-python3-jupyter-client_8.6.3-2_all.deb ... 143s Unpacking python3-jupyter-client (8.6.3-2) ... 143s Selecting previously unselected package python3-nest-asyncio. 143s Preparing to unpack .../100-python3-nest-asyncio_1.5.4-1_all.deb ... 143s Unpacking python3-nest-asyncio (1.5.4-1) ... 143s Selecting previously unselected package python3-packaging. 143s Preparing to unpack .../101-python3-packaging_24.2-1_all.deb ... 143s Unpacking python3-packaging (24.2-1) ... 143s Selecting previously unselected package python3-ipykernel. 143s Preparing to unpack .../102-python3-ipykernel_6.29.5-2_all.deb ... 143s Unpacking python3-ipykernel (6.29.5-2) ... 143s Selecting previously unselected package python3-joblib. 143s Preparing to unpack .../103-python3-joblib_1.4.2-3_all.deb ... 143s Unpacking python3-joblib (1.4.2-3) ... 143s Selecting previously unselected package python3-kiwisolver. 143s Preparing to unpack .../104-python3-kiwisolver_1.4.7-3build1_arm64.deb ... 143s Unpacking python3-kiwisolver (1.4.7-3build1) ... 143s Selecting previously unselected package libopenjp2-7:arm64. 143s Preparing to unpack .../105-libopenjp2-7_2.5.3-2_arm64.deb ... 143s Unpacking libopenjp2-7:arm64 (2.5.3-2) ... 143s Selecting previously unselected package python3-pil:arm64. 143s Preparing to unpack .../106-python3-pil_11.1.0-5build1_arm64.deb ... 143s Unpacking python3-pil:arm64 (11.1.0-5build1) ... 143s Selecting previously unselected package python3.12-tk. 143s Preparing to unpack .../107-python3.12-tk_3.12.9-1_arm64.deb ... 143s Unpacking python3.12-tk (3.12.9-1) ... 143s Selecting previously unselected package python3.13-tk. 143s Preparing to unpack .../108-python3.13-tk_3.13.2-2_arm64.deb ... 143s Unpacking python3.13-tk (3.13.2-2) ... 143s Selecting previously unselected package python3-tk:arm64. 143s Preparing to unpack .../109-python3-tk_3.13.1-1_arm64.deb ... 143s Unpacking python3-tk:arm64 (3.13.1-1) ... 143s Selecting previously unselected package python3-pil.imagetk:arm64. 143s Preparing to unpack .../110-python3-pil.imagetk_11.1.0-5build1_arm64.deb ... 143s Unpacking python3-pil.imagetk:arm64 (11.1.0-5build1) ... 143s Selecting previously unselected package python3-matplotlib. 143s Preparing to unpack .../111-python3-matplotlib_3.8.3-7build1_arm64.deb ... 143s Unpacking python3-matplotlib (3.8.3-7build1) ... 144s Selecting previously unselected package python3-netcdf4. 144s Preparing to unpack .../112-python3-netcdf4_1.7.2-1build4_arm64.deb ... 144s Unpacking python3-netcdf4 (1.7.2-1build4) ... 144s Selecting previously unselected package python3-networkx. 144s Preparing to unpack .../113-python3-networkx_3.2.1-4ubuntu1_all.deb ... 144s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 144s Selecting previously unselected package python3-pytz. 144s Preparing to unpack .../114-python3-pytz_2025.1-3_all.deb ... 144s Unpacking python3-pytz (2025.1-3) ... 144s Selecting previously unselected package python3-tz. 145s Preparing to unpack .../115-python3-tz_2025.1-3_all.deb ... 145s Unpacking python3-tz (2025.1-3) ... 145s Selecting previously unselected package python3-pandas-lib:arm64. 145s Preparing to unpack .../116-python3-pandas-lib_2.2.3+dfsg-8build1_arm64.deb ... 145s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-8build1) ... 145s Selecting previously unselected package python3-pandas. 145s Preparing to unpack .../117-python3-pandas_2.2.3+dfsg-8build1_all.deb ... 145s Unpacking python3-pandas (2.2.3+dfsg-8build1) ... 145s Selecting previously unselected package python3-numexpr. 145s Preparing to unpack .../118-python3-numexpr_2.10.2-1build2_arm64.deb ... 145s Unpacking python3-numexpr (2.10.2-1build2) ... 145s Selecting previously unselected package python3-tables-lib. 145s Preparing to unpack .../119-python3-tables-lib_3.10.2-2build1_arm64.deb ... 145s Unpacking python3-tables-lib (3.10.2-2build1) ... 145s Selecting previously unselected package python3-tables. 145s Preparing to unpack .../120-python3-tables_3.10.2-2build1_all.deb ... 145s Unpacking python3-tables (3.10.2-2build1) ... 145s Selecting previously unselected package python3-mdtraj. 145s Preparing to unpack .../121-python3-mdtraj_1.10.3-2build1_arm64.deb ... 145s Unpacking python3-mdtraj (1.10.3-2build1) ... 145s Selecting previously unselected package python3-nbformat. 145s Preparing to unpack .../122-python3-nbformat_5.9.1-1_all.deb ... 145s Unpacking python3-nbformat (5.9.1-1) ... 145s Selecting previously unselected package python3-pluggy. 145s Preparing to unpack .../123-python3-pluggy_1.5.0-1_all.deb ... 145s Unpacking python3-pluggy (1.5.0-1) ... 145s Selecting previously unselected package python3-pytest. 145s Preparing to unpack .../124-python3-pytest_8.3.5-1_all.deb ... 145s Unpacking python3-pytest (8.3.5-1) ... 145s Selecting previously unselected package python3-threadpoolctl. 145s Preparing to unpack .../125-python3-threadpoolctl_3.1.0-1_all.deb ... 145s Unpacking python3-threadpoolctl (3.1.0-1) ... 145s Selecting previously unselected package python3-sklearn-lib:arm64. 145s Preparing to unpack .../126-python3-sklearn-lib_1.4.2+dfsg-8_arm64.deb ... 145s Unpacking python3-sklearn-lib:arm64 (1.4.2+dfsg-8) ... 146s Selecting previously unselected package python3-sklearn. 146s Preparing to unpack .../127-python3-sklearn_1.4.2+dfsg-8_all.deb ... 146s Unpacking python3-sklearn (1.4.2+dfsg-8) ... 146s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 146s Setting up liblcms2-2:arm64 (2.16-2) ... 146s Setting up python3-iniconfig (1.1.1-2) ... 146s Setting up python3-tornado (6.4.2-1) ... 146s Setting up libnorm1t64:arm64 (1.5.9+dfsg-3.1build1) ... 146s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 146s Setting up python3-pure-eval (0.2.3-1) ... 147s Setting up libsodium23:arm64 (1.0.18-1build3) ... 147s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 147s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 147s Setting up python3-joblib (1.4.2-3) ... 147s Setting up python3-parso (0.8.4-1) ... 147s Setting up python3-lz4 (4.4.0+dfsg-1build1) ... 147s Setting up python3-asttokens (3.0.0-1) ... 147s Setting up python3-unicodedata2 (15.1.0+ds-1build3) ... 147s Setting up fonts-lyx (2.4.3-1) ... 147s Setting up python3-threadpoolctl (3.1.0-1) ... 147s Setting up x11-common (1:7.7+23ubuntu3) ... 148s Setting up libdeflate0:arm64 (1.23-1) ... 148s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 148s Setting up python3-coverage (7.6.0+dfsg1-2build1) ... 148s Setting up python3-pytz (2025.1-3) ... 148s Setting up libgomp1:arm64 (15-20250222-0ubuntu1) ... 148s Setting up python3-networkx (3.2.1-4ubuntu1) ... 150s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 150s Setting up libaec0:arm64 (1.1.3-1) ... 150s Setting up python3-platformdirs (4.3.6-1) ... 150s Setting up python3-psutil (5.9.8-2build3) ... 150s Setting up libsource-highlight-common (3.1.9-4.3build1) ... 150s Setting up python3-tz (2025.1-3) ... 150s Setting up libsnappy1v5:arm64 (1.2.1-1) ... 150s Setting up python3-fs (2.4.16-7) ... 150s Setting up unicode-data (15.1.0-1) ... 150s Setting up libpgm-5.3-0t64:arm64 (5.3.128~dfsg-2.1build1) ... 150s Setting up python3-decorator (5.1.1-5) ... 151s Setting up libblosc2-4:arm64 (2.16.0+ds-1) ... 151s Setting up libblas3:arm64 (3.12.1-2) ... 151s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 151s Setting up python3-packaging (24.2-1) ... 151s Setting up python3-wcwidth (0.2.13+dfsg1-1) ... 151s Setting up python3-typeshed 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Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ... 152s Setting up libblosc1:arm64 (1.21.5+ds-1build1) ... 152s Setting up libopenjp2-7:arm64 (2.5.3-2) ... 152s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 152s Setting up python3-dateutil (2.9.0-3) ... 153s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 153s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 153s Setting up python3-mpmath (1.3.0-1) ... 153s Setting up python-matplotlib-data (3.8.3-7build1) ... 153s Setting up libwebpmux3:arm64 (1.5.0-0.1) ... 153s Setting up python3-stack-data (0.6.3-1) ... 153s Setting up python-tables-data (3.10.2-2build1) ... 153s Setting up python3-jupyter-core (5.7.2-5) ... 153s Setting up libsz2:arm64 (1.1.3-1) ... 153s Setting up python3-ptyprocess (0.7.0-6) ... 154s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 154s Setting up python3-prompt-toolkit (3.0.50-1) ... 154s Setting up python3-sympy (1.13.3-5) ... 160s Setting up liblapack3:arm64 (3.12.1-2) ... 160s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 160s Setting up libzmq5:arm64 (4.3.5-1build2) ... 160s Setting up python3-jedi (0.19.1+ds1-1) ... 161s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 161s Setting up python3-pytest (8.3.5-1) ... 161s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 161s Setting up libsource-highlight4t64:arm64 (3.1.9-4.3build1) ... 161s Setting up python3-nbformat (5.9.1-1) ... 161s Setting up python3-matplotlib-inline (0.1.6-2) ... 161s Setting up python3-comm (0.2.1-1) ... 162s Setting up gdb (16.2-2ubuntu2) ... 162s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 162s Setting up python3-pexpect (4.9-3) ... 162s Setting up python3-zmq (26.2.1-1build1) ... 162s Setting up libraqm0:arm64 (0.10.2-1) ... 162s Setting up python3-numpy (1:2.2.3+ds-5) ... 164s Setting up libhdf5-310:arm64 (1.14.5+repack-3) ... 164s Setting up python3-lxml:arm64 (5.3.1-1build1) ... 164s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 164s Setting up python3-jupyter-client (8.6.3-2) ... 164s Setting up python3-contourpy (1.3.1-1build1) ... 164s Setting up libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 164s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 164s Setting up libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 164s Setting up libxft2:arm64 (2.3.6-1build1) ... 164s Setting up python3-scipy (1.14.1-4ubuntu2) ... 168s Setting up python3-tables-lib (3.10.2-2build1) ... 168s Setting up libtk8.6:arm64 (8.6.16-1) ... 168s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-8build1) ... 168s Setting up python3.12-tk (3.12.9-1) ... 168s Setting up libnetcdf22:arm64 (1:4.9.3-1) ... 168s Setting up python3-sklearn-lib:arm64 (1.4.2+dfsg-8) ... 168s Setting up python3-gsd (3.4.2-2build1) ... 168s Setting up python3-debugpy (1.8.8+ds-2ubuntu1) ... 169s Setting up python3.13-tk (3.13.2-2) ... 169s Setting up python3-pil:arm64 (11.1.0-5build1) ... 169s Setting up python3-pandas (2.2.3+dfsg-8build1) ... 174s Setting up python3-ipython (8.30.0-2) ... 175s Setting up python3-ipykernel (6.29.5-2) ... 175s Setting up python3-sklearn (1.4.2+dfsg-8) ... 177s Setting up python3-cftime (1.6.4-2) ... 177s Setting up python3-numexpr (2.10.2-1build2) ... 177s Setting up python3-netcdf4 (1.7.2-1build4) ... 177s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 177s Setting up blt (2.5.3+dfsg-8) ... 177s Setting up python3-tk:arm64 (3.13.1-1) ... 177s Setting up python3-tables (3.10.2-2build1) ... 178s Setting up python3-mdtraj (1.10.3-2build1) ... 178s Setting up python3-pil.imagetk:arm64 (11.1.0-5build1) ... 178s Setting up python3-fonttools (4.55.3-2build1) ... 179s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 179s Setting up python3-matplotlib (3.8.3-7build1) ... 181s Processing triggers for libc-bin (2.41-1ubuntu1) ... 181s Processing triggers for man-db (2.13.0-1) ... 183s autopkgtest [01:56:14]: test command1: pytest-3 -k 'not (nmr.ipynb or test_image_molecules) and not (test_3 or test_pdb_from_url or test_1vii_url_and_gz)' 183s autopkgtest [01:56:14]: test command1: [----------------------- 184s ============================= test session starts ============================== 184s platform linux -- Python 3.13.2, pytest-8.3.5, pluggy-1.5.0 -- /usr/bin/python3 184s cachedir: .pytest_cache 184s rootdir: /tmp/autopkgtest.wJz48l/build.8P3/src 184s configfile: pyproject.toml 184s testpaths: tests, examples 184s plugins: typeguard-4.4.2 185s collecting ... collected 1145 items / 12 deselected / 1133 selected 185s 185s tests/test_alignment.py::test_rmsd_zero PASSED [ 0%] 185s tests/test_alignment.py::test_rmsd_nonzero PASSED [ 0%] 185s tests/test_alignment.py::test_transform PASSED [ 0%] 185s tests/test_alignment.py::test_transform2 PASSED [ 0%] 185s tests/test_angles.py::test_angle_pbc_0 PASSED [ 0%] 185s tests/test_angles.py::test_generator PASSED [ 0%] 185s tests/test_angles.py::test_angle_180[True] PASSED [ 0%] 185s 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[ 6%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.core.element] PASSED [ 6%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.core.residue_names] PASSED [ 6%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.core.selection] PASSED [ 6%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.core.topology] PASSED [ 6%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.core.trajectory] PASSED [ 6%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.amberrst] PASSED [ 6%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.arc] PASSED [ 6%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.dcd] PASSED [ 6%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.dtr] PASSED [ 6%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.gro] PASSED [ 7%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.gsd] PASSED [ 7%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.hdf5] SKIPPED [ 7%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.hoomdxml] PASSED [ 7%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.lammpstrj] PASSED [ 7%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.lh5] SKIPPED [ 7%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.mdcrd] PASSED [ 7%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.mol2] PASSED [ 7%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.netcdf] PASSED [ 7%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.openmmxml] PASSED [ 7%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdb.pdbfile] PASSED [ 7%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdb.pdbstructure] SKIPPED [ 8%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdbx] PASSED [ 8%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.prmtop] PASSED [ 8%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.psf] PASSED [ 8%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.registry] PASSED [ 8%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.trr] PASSED [ 8%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.xtc] PASSED [ 8%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.formats.xyzfile] PASSED [ 8%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.geometry._geometry] PASSED [ 8%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.alignment] PASSED [ 8%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.angle] PASSED [ 8%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.contact] PASSED [ 9%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.dihedral] PASSED [ 9%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.distance] PASSED [ 9%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.drid] PASSED [ 9%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.dssp] PASSED [ 9%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.hbond] PASSED [ 9%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.internal] PASSED [ 9%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.neighborlist] PASSED [ 9%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.neighbors] PASSED [ 9%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.order] PASSED [ 9%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.rdf] PASSED [ 9%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.rg] PASSED [ 9%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.sasa] PASSED [ 10%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.shape] PASSED [ 10%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.thermodynamic_properties] PASSED [ 10%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.io] SKIPPED (Skip c...) [ 10%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.nmr.scalar_couplings] PASSED [ 10%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.nmr.shift_wrappers] PASSED [ 10%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.basereporter] PASSED [ 10%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.dcdreporter] PASSED [ 10%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.hdf5reporter] PASSED [ 10%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.netcdfreporter] PASSED [ 10%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.xtcreporter] PASSED [ 10%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.scripts.mdconvert] SKIPPED [ 11%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.scripts.mdinspect] SKIPPED [ 11%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.testing.docscrape] SKIPPED [ 11%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.testing.docstrings] PASSED [ 11%] 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tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.standard_dimensions] PASSED [ 12%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit] SKIPPED [ 12%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_definitions] SKIPPED [ 12%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_math] SKIPPED [ 12%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_operators] SKIPPED [ 12%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unitcell] PASSED [ 12%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.utils.validation] PASSED [ 12%] 194s tests/test_docstrings.py::test_docstrings[mdtraj.utils.zipped] PASSED [ 12%] 194s tests/test_drid.py::test_drid_1 PASSED [ 13%] 194s tests/test_drid.py::test_drid_2 PASSED [ 13%] 194s tests/test_dssp.py::test_1[1bpi.pdb] PASSED [ 13%] 194s tests/test_dssp.py::test_1[1vii.pdb] PASSED [ 13%] 194s tests/test_dssp.py::test_1[4ZUO.pdb] PASSED [ 13%] 194s tests/test_dssp.py::test_1[1am7_protein.pdb] PASSED [ 13%] 195s tests/test_dssp.py::test_2[2EQQ.pdb] PASSED [ 13%] 195s tests/test_dssp.py::test_4 PASSED [ 13%] 195s tests/test_dssp.py::test_5 PASSED [ 13%] 195s tests/test_dssp.py::test_7 PASSED [ 13%] 195s tests/test_dtr.py::test_read PASSED [ 13%] 195s tests/test_dtr.py::test_read_1 PASSED [ 14%] 195s tests/test_dtr.py::test_read_2 PASSED [ 14%] 195s tests/test_dtr.py::test_read_3 PASSED [ 14%] 195s tests/test_dtr.py::test_read_stride PASSED [ 14%] 195s tests/test_dtr.py::test_read_4 PASSED [ 14%] 195s tests/test_dtr.py::test_read_5 PASSED [ 14%] 195s tests/test_dtr.py::test_read_6 PASSED [ 14%] 195s tests/test_dtr.py::test_read_7 PASSED [ 14%] 195s tests/test_dtr.py::test_read_8 PASSED [ 14%] 197s tests/test_dtr.py::test_write_1 PASSED [ 14%] 199s tests/test_dtr.py::test_write_2 PASSED [ 14%] 199s tests/test_dtr.py::test_write_3 PASSED [ 15%] 199s tests/test_dtr.py::test_write_4 PASSED [ 15%] 199s tests/test_dtr.py::test_seek PASSED 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tests/test_hoomdxml.py::test_correct_ordering PASSED [ 21%] 211s tests/test_io.py::test_overwrite_1 PASSED [ 21%] 211s tests/test_io.py::test_overwrite_2 PASSED [ 21%] 211s tests/test_io.py::test_io::test_load_1 PASSED [ 21%] 211s tests/test_io.py::test_io::test_load_2 PASSED [ 22%] 211s tests/test_io.py::test_io::test_load_3 PASSED [ 22%] 211s tests/test_io.py::test_io::test_save PASSED [ 22%] 211s tests/test_io.py::test_io_int::test_load_1 PASSED [ 22%] 211s tests/test_io.py::test_io_int::test_load_2 PASSED [ 22%] 211s tests/test_io.py::test_io_int::test_load_3 PASSED [ 22%] 211s tests/test_io.py::test_io_int::test_save PASSED [ 22%] 211s tests/test_io.py::test_groups PASSED [ 22%] 211s tests/test_lammpstrj.py::test_read_0 PASSED [ 22%] 211s tests/test_lammpstrj.py::test_read_1 PASSED [ 22%] 211s tests/test_lammpstrj.py::test_read_write_0 PASSED [ 22%] 211s tests/test_lammpstrj.py::test_mdwrite PASSED [ 23%] 211s tests/test_lammpstrj.py::test_multiread PASSED [ 23%] 211s tests/test_lammpstrj.py::test_seek PASSED [ 23%] 211s tests/test_lammpstrj.py::test_custom PASSED [ 23%] 211s tests/test_lh5.py::test_write_coordinates PASSED [ 23%] 211s tests/test_lh5.py::test_write_coordinates_reshape PASSED [ 23%] 211s tests/test_lh5.py::test_write_multiple PASSED [ 23%] 211s tests/test_lh5.py::test_topology PASSED [ 23%] 211s tests/test_lh5.py::test_read_slice_0 PASSED [ 23%] 212s tests/test_lh5.py::test_vsite_elements PASSED [ 23%] 212s tests/test_lh5.py::test_do_overwrite_0 PASSED [ 23%] 212s tests/test_lh5.py::test_do_overwrite_1 PASSED [ 24%] 212s tests/test_load.py::test_load_single PASSED [ 24%] 212s tests/test_load.py::test_load_single_top_none PASSED [ 24%] 212s tests/test_load.py::test_load_single_list PASSED [ 24%] 213s tests/test_load.py::test_load_many_list PASSED [ 24%] 213s tests/test_load.py::test_load_atom_indices_multiple_files PASSED [ 24%] 213s tests/test_lprmsd.py::test_munkres_0 PASSED [ 24%] 213s tests/test_lprmsd.py::test_lprmsd_null PASSED 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tests/test_mdcrd.py::test_read_0 PASSED [ 26%] 335s tests/test_mdcrd.py::test_read_1 PASSED [ 26%] 335s tests/test_mdcrd.py::test_read_write_0 PASSED [ 26%] 335s tests/test_mdcrd.py::test_read_write_1 PASSED [ 26%] 335s tests/test_mdcrd.py::test_read_write_2 PASSED [ 26%] 335s tests/test_mdcrd.py::test_multiread PASSED [ 26%] 335s tests/test_mdcrd.py::test_seek PASSED [ 26%] 335s tests/test_mdcrd.py::test_atom_indices_0 PASSED [ 26%] 335s tests/test_mdcrd.py::test_atom_indices_1 PASSED [ 26%] 335s tests/test_mol2.py::test_load_mol2 PASSED [ 26%] 335s tests/test_mol2.py::test_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb SKIPPED [ 27%] 335s tests/test_mol2.py::test_mol2_dataframe PASSED [ 27%] 335s tests/test_mol2.py::test_mol2_dataframe_status PASSED [ 27%] 335s tests/test_mol2.py::test_mol2_warnings PASSED [ 27%] 335s tests/test_mol2.py::test_mol2_status_bits PASSED [ 27%] 335s tests/test_mol2.py::test_mol2_without_bonds PASSED [ 27%] 335s tests/test_mol2.py::test_mol2_element_name PASSED [ 27%] 335s tests/test_mol2.py::test_load_all_mol2[li.mol2] PASSED [ 27%] 335s tests/test_mol2.py::test_load_all_mol2[lysozyme-ligand-tripos.mol2] PASSED [ 27%] 335s tests/test_mol2.py::test_load_all_mol2[imatinib.mol2] PASSED [ 27%] 335s tests/test_mol2.py::test_load_all_mol2[status-bits.mol2] PASSED [ 27%] 335s tests/test_mol2.py::test_load_all_mol2[adp.mol2] PASSED [ 27%] 335s tests/test_mol2.py::test_load_all_mol2[water_acn.mol2] PASSED [ 28%] 335s tests/test_mol2.py::test_mol2_n_residues PASSED [ 28%] 335s tests/test_neighborlist.py::test_nonperiodic PASSED [ 28%] 336s tests/test_neighborlist.py::test_periodic PASSED [ 28%] 337s tests/test_neighborlist.py::test_triclinic PASSED [ 28%] 337s tests/test_neighbors.py::test_compute_neighbors_1 PASSED [ 28%] 337s tests/test_neighbors.py::test_compute_neighbors_2 PASSED [ 28%] 338s tests/test_neighbors.py::test_compute_neighbors_3 PASSED [ 28%] 338s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_after_close PASSED [ 28%] 338s tests/test_netcdf.py::TestNetCDFNetCDF4::test_shape PASSED [ 28%] 338s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_1 PASSED [ 28%] 338s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_2 PASSED [ 29%] 338s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_3 PASSED [ 29%] 338s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_1 PASSED [ 29%] 338s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_2 PASSED [ 29%] 338s tests/test_netcdf.py::TestNetCDFNetCDF4::test_ragged_1 PASSED [ 29%] 338s tests/test_netcdf.py::TestNetCDFNetCDF4::test_ragged_2 PASSED [ 29%] 338s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_25 PASSED [ 29%] 338s tests/test_netcdf.py::TestNetCDFNetCDF4::test_write_3 PASSED [ 29%] 338s tests/test_netcdf.py::TestNetCDFNetCDF4::test_n_atoms PASSED [ 29%] 338s tests/test_netcdf.py::TestNetCDFNetCDF4::test_do_overwrite PASSED [ 29%] 338s tests/test_netcdf.py::TestNetCDFNetCDF4::test_do_not_overwrite PASSED [ 29%] 338s tests/test_netcdf.py::TestNetCDFNetCDF4::test_trajectory_save_load PASSED [ 30%] 338s tests/test_netcdf.py::TestNetCDFScipy::test_read_after_close PASSED [ 30%] 338s tests/test_netcdf.py::TestNetCDFScipy::test_shape PASSED [ 30%] 338s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_1 PASSED [ 30%] 338s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_2 PASSED [ 30%] 338s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_3 PASSED [ 30%] 338s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_1 PASSED [ 30%] 338s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_2 PASSED [ 30%] 338s tests/test_netcdf.py::TestNetCDFScipy::test_ragged_1 PASSED [ 30%] 338s tests/test_netcdf.py::TestNetCDFScipy::test_ragged_2 PASSED [ 30%] 338s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_25 PASSED [ 30%] 338s tests/test_netcdf.py::TestNetCDFScipy::test_write_3 PASSED [ 30%] 338s tests/test_netcdf.py::TestNetCDFScipy::test_n_atoms PASSED [ 31%] 338s tests/test_netcdf.py::TestNetCDFScipy::test_do_overwrite PASSED [ 31%] 338s tests/test_netcdf.py::TestNetCDFScipy::test_do_not_overwrite PASSED [ 31%] 338s tests/test_netcdf.py::TestNetCDFScipy::test_trajectory_save_load PASSED [ 31%] 338s tests/test_netcdf.py::test_cpptraj SKIPPED (This test requires cpptr...) [ 31%] 338s tests/test_nmr.py::test_spartaplus SKIPPED (SPARTA+ binary not found) [ 31%] 338s tests/test_nmr.py::test_ppm SKIPPED (PPM binary not found) [ 31%] 338s tests/test_nmr.py::test_shiftx2 SKIPPED (SHIFTX2 binary not found or...) [ 31%] 338s tests/test_nmr.py::test_2_scalar_couplings PASSED [ 31%] 338s tests/test_order.py::test_nematic_order PASSED [ 31%] 338s tests/test_order.py::test_director PASSED [ 31%] 338s tests/test_order.py::test_inertia PASSED [ 32%] 338s tests/test_order.py::test_nematic_order_args PASSED [ 32%] 338s tests/test_order.py::test_order_from_traj PASSED [ 32%] 338s tests/test_order.py::test_directors_angle_from_traj PASSED [ 32%] 338s tests/test_pdb.py::test_pdbread PASSED [ 32%] 338s tests/test_pdb.py::test_pdbread_with_input_top PASSED [ 32%] 338s tests/test_pdb.py::test_pdbwrite PASSED [ 32%] 338s tests/test_pdb.py::test_load_multiframe PASSED [ 32%] 339s tests/test_pdb.py::test_4ZUO PASSED [ 32%] 339s tests/test_pdb.py::test_2EQQ_0 PASSED [ 32%] 340s tests/test_pdb.py::test_1vii_solvated_with_ligand PASSED [ 32%] 340s tests/test_pdb.py::test_write_large PASSED [ 33%] 340s tests/test_pdb.py::test_write_large_2 PASSED [ 33%] 340s tests/test_pdb.py::test_pdbstructure_0 PASSED [ 33%] 340s tests/test_pdb.py::test_pdbstructure_1 PASSED [ 33%] 340s tests/test_pdb.py::test_pdbstructure_2 PASSED [ 33%] 340s tests/test_pdb.py::test_pdbstructure_3 PASSED [ 33%] 340s tests/test_pdb.py::test_1ncw PASSED [ 33%] 340s tests/test_pdb.py::test_segment_id PASSED [ 33%] 340s tests/test_pdb.py::test_bfactors PASSED [ 33%] 342s tests/test_pdb.py::test_hex PASSED [ 33%] 343s tests/test_pdb.py::test_dummy_pdb_box_detection PASSED [ 33%] 343s tests/test_pdb.py::test_multichain_load_cycle PASSED [ 33%] 343s tests/test_pdb.py::test_multichain_load_cycle_noter PASSED [ 34%] 343s tests/test_pdb.py::test_load_pdb_input_top PASSED [ 34%] 343s tests/test_pdb.py::test_chimera_indexing PASSED [ 34%] 343s tests/test_pdb.py::test_chimera_indexing_skip PASSED [ 34%] 343s tests/test_pdb.py::test_vmd_indexing PASSED [ 34%] 343s tests/test_pdb.py::test_overflow_indexing PASSED [ 34%] 343s tests/test_pdb.py::test_blank_indexing PASSED [ 34%] 343s tests/test_pdb.py::test_pdb_charge_read PASSED [ 34%] 343s tests/test_pdb.py::test_pdb_charge_write PASSED [ 34%] 343s tests/test_pdbx.py::test_convert SKIPPED (test_pdbx.py needs OpenMM.) [ 34%] 343s tests/test_prmtop.py::test_load_prmtop PASSED [ 34%] 343s tests/test_prmtop.py::test_load_chamber_prmtop PASSED [ 35%] 343s tests/test_psf.py::test_load_psf PASSED [ 35%] 346s tests/test_psf.py::test_multichain_psf PASSED [ 35%] 346s tests/test_psf.py::test_load_mdcrd_with_psf PASSED [ 35%] 346s tests/test_psf.py::test_against_vmd[1vii.pdb] SKIPPED (This test req...) [ 35%] 346s tests/test_psf.py::test_against_vmd[2EQQ.pdb] SKIPPED (This test req...) [ 35%] 346s tests/test_quaternion.py::test_quaternion_0 PASSED [ 35%] 346s tests/test_quaternion.py::test_quaternion_1 PASSED [ 35%] 346s tests/test_quaternion.py::test_quaternion_2 PASSED [ 35%] 350s tests/test_rdf.py::test_rdf_norm PASSED [ 35%] 350s tests/test_rdf.py::test_compare_rdf_to_gromacs SKIPPED (Binning does...) [ 35%] 350s tests/test_rdf.py::test_rdf_t[True-True] PASSED [ 36%] 355s tests/test_rdf.py::test_rdf_t[True-False] PASSED [ 36%] 355s tests/test_rdf.py::test_rdf_t[False-True] PASSED [ 36%] 356s tests/test_rdf.py::test_rdf_t[False-False] PASSED [ 36%] 356s tests/test_rdf.py::test_rdf_t_norm[0] PASSED [ 36%] 357s tests/test_rdf.py::test_rdf_t_norm[2] PASSED [ 36%] 357s tests/test_rdf.py::test_rdf_t_norm[4] PASSED [ 36%] 357s tests/test_rdf.py::test_compare_rdf_t_at_0[True-True] PASSED [ 36%] 358s tests/test_rdf.py::test_compare_rdf_t_at_0[True-False] PASSED [ 36%] 358s tests/test_rdf.py::test_compare_rdf_t_at_0[False-True] PASSED [ 36%] 359s tests/test_rdf.py::test_compare_rdf_t_at_0[False-False] PASSED [ 36%] 359s tests/test_rdf.py::test_amber_rdf_t[True-True] PASSED [ 36%] 359s tests/test_rdf.py::test_amber_rdf_t[True-False] PASSED [ 37%] 359s tests/test_rdf.py::test_amber_rdf_t[False-True] PASSED [ 37%] 360s tests/test_rdf.py::test_amber_rdf_t[False-False] PASSED [ 37%] 360s tests/test_rdf.py::test_compare_gromacs_rdf_t SKIPPED (Binning does ...) [ 37%] 360s tests/test_rdf.py::test_compare_rdf_t_master PASSED [ 37%] 360s tests/test_rdf.py::test_compare_n_concurrent_pairs PASSED [ 37%] 360s tests/test_reporter.py::test_reporter SKIPPED (test_reporter.py need...) [ 37%] 360s tests/test_reporter.py::test_reporter_subset SKIPPED (test_reporter....) [ 37%] 360s tests/test_reporter.py::test_xtc_reporter_append SKIPPED (test_repor...) [ 37%] 360s tests/test_restart.py::test_read_after_close PASSED [ 37%] 360s tests/test_restart.py::test_shape PASSED [ 37%] 360s tests/test_restart.py::test_shape_2 PASSED [ 38%] 360s tests/test_restart.py::test_read_write_1 PASSED [ 38%] 360s tests/test_restart.py::test_read_write_2 PASSED [ 38%] 360s tests/test_restart.py::test_read_write_3 PASSED [ 38%] 361s tests/test_restart.py::test_read_write_4 PASSED [ 38%] 361s tests/test_rmsd.py::test_trajectory_rmsd PASSED [ 38%] 361s tests/test_rmsd.py::test_precentered_1 PASSED [ 38%] 361s tests/test_rmsd.py::test_precentered_2 PASSED [ 38%] 361s tests/test_rmsd.py::test_superpose_0 PASSED [ 38%] 361s tests/test_rmsd.py::test_superpose_1 PASSED [ 38%] 361s tests/test_rmsd.py::test_superpose_2 PASSED [ 38%] 361s tests/test_rmsd.py::test_superpose_refinds PASSED [ 39%] 361s tests/test_rmsd.py::test_rmsd_atom_indices PASSED [ 39%] 361s tests/test_rmsd.py::test_rmsd_ref_ainds PASSED [ 39%] 361s tests/test_rmsd.py::test_average_structure PASSED [ 39%] 361s tests/test_rmsd.py::test_trajectory_rmsf PASSED [ 39%] 361s tests/test_rmsd.py::test_trajectory_rmsf_aligned PASSED [ 39%] 361s tests/test_rmsd.py::test_rmsd_atom_indices_vs_ref_indices PASSED [ 39%] 361s tests/test_rmsd_memmap.py::test_1 PASSED [ 39%] 361s tests/test_rmsd_memmap.py::test_2 PASSED [ 39%] 361s tests/test_sasa.py::test_sasa_0 PASSED [ 39%] 361s tests/test_sasa.py::test_sasa_1 PASSED [ 39%] 361s tests/test_sasa.py::test_sasa_2 PASSED [ 39%] 362s tests/test_sasa.py::test_sasa_3 PASSED [ 40%] 362s tests/test_sasa.py::test_sasa_4 PASSED [ 40%] 362s tests/test_sasa.py::test_sasa_5 PASSED [ 40%] 363s tests/test_sasa.py::test_sasa_6 PASSED [ 40%] 363s tests/test_sasa.py::test_sasa_7 PASSED [ 40%] 363s tests/test_selection.py::test_range PASSED [ 40%] 363s tests/test_selection.py::test_unary_2 PASSED [ 40%] 363s tests/test_selection.py::test_unary_3 PASSED [ 40%] 363s tests/test_selection.py::test_binary_1 PASSED [ 40%] 363s tests/test_selection.py::test_binary_2 PASSED [ 40%] 363s tests/test_selection.py::test_simple PASSED [ 40%] 363s tests/test_selection.py::test_alias PASSED [ 41%] 363s tests/test_selection.py::test_unary_1 PASSED [ 41%] 363s tests/test_selection.py::test_binary_selection_operator PASSED [ 41%] 363s tests/test_selection.py::test_raises PASSED [ 41%] 363s tests/test_selection.py::test_raises2 PASSED [ 41%] 363s tests/test_selection.py::test_bool PASSED [ 41%] 364s tests/test_selection.py::test_nested_bool PASSED [ 41%] 364s tests/test_selection.py::test_values PASSED [ 41%] 364s tests/test_selection.py::test_element PASSED [ 41%] 364s tests/test_selection.py::test_not PASSED [ 41%] 364s tests/test_selection.py::test_re PASSED [ 41%] 364s tests/test_selection.py::test_within SKIPPED (failed to parse selection) [ 42%] 364s tests/test_selection.py::test_quotes PASSED [ 42%] 364s tests/test_selection.py::test_top PASSED [ 42%] 364s tests/test_selection.py::test_top_2 PASSED [ 42%] 364s tests/test_selection.py::test_backbone PASSED [ 42%] 364s tests/test_selection.py::test_sidechain PASSED [ 42%] 364s tests/test_selection.py::test_literal PASSED [ 42%] 364s tests/test_selection.py::test_in PASSED [ 42%] 364s tests/test_shape.py::test_gyration PASSED [ 42%] 365s tests/test_shape.py::test_principal_moments PASSED [ 42%] 365s tests/test_shape.py::test_asphericity PASSED [ 42%] 365s tests/test_shape.py::test_shape_metrics PASSED [ 42%] 365s tests/test_thermodynamic_properties.py::test_volume PASSED [ 43%] 365s tests/test_thermodynamic_properties.py::test_density PASSED [ 43%] 365s tests/test_thermodynamic_properties.py::test_dipole_moments PASSED [ 43%] 365s tests/test_thermodynamic_properties.py::test_static_dielectric PASSED [ 43%] 365s tests/test_thermodynamic_properties.py::test_kappa PASSED [ 43%] 365s tests/test_thermodynamic_properties.py::test_alpha SKIPPED (Thermal ...) [ 43%] 365s tests/test_topology.py::test_topology_openmm SKIPPED (needs OpenMM) [ 43%] 365s tests/test_topology.py::test_topology_openmm_preserve_chain_id_when_specified SKIPPED [ 43%] 365s tests/test_topology.py::test_topology_openmm_roundtrip_chain_id SKIPPED [ 43%] 365s tests/test_topology.py::test_topology_openmm_preserve_chain_id_even_when_empty SKIPPED [ 43%] 365s tests/test_topology.py::test_topology_openmm_boxes SKIPPED (needs Op...) [ 43%] 365s tests/test_topology.py::test_topology_openmm_formal_charges SKIPPED [ 44%] 365s tests/test_topology.py::test_topology_pandas PASSED [ 44%] 365s tests/test_topology.py::test_topology_pandas_TIP4PEW PASSED [ 44%] 365s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq PASSED [ 44%] 365s tests/test_topology.py::test_topology_numbers PASSED [ 44%] 365s tests/test_topology.py::test_topology_unique_elements_bpti PASSED [ 44%] 366s tests/test_topology.py::test_chain PASSED [ 44%] 366s tests/test_topology.py::test_residue PASSED [ 44%] 366s tests/test_topology.py::test_segment_id PASSED [ 44%] 366s tests/test_topology.py::test_nonconsective_resSeq PASSED [ 44%] 366s tests/test_topology.py::test_pickle PASSED [ 44%] 366s tests/test_topology.py::test_atoms_by_name PASSED [ 45%] 366s tests/test_topology.py::test_select_atom_indices PASSED [ 45%] 366s tests/test_topology.py::test_top_dataframe_openmm_roundtrip SKIPPED [ 45%] 366s tests/test_topology.py::test_n_bonds PASSED [ 45%] 366s tests/test_topology.py::test_load_unknown_topology PASSED [ 45%] 366s tests/test_topology.py::test_unique_pairs PASSED [ 45%] 367s tests/test_topology.py::test_select_pairs PASSED [ 45%] 367s tests/test_topology.py::test_to_fasta PASSED [ 45%] 367s tests/test_topology.py::test_subset PASSED [ 45%] 367s tests/test_topology.py::test_subset_re_index_residues PASSED [ 45%] 367s tests/test_topology.py::test_molecules PASSED [ 45%] 367s tests/test_topology.py::test_copy_and_hash PASSED [ 45%] 367s tests/test_topology.py::test_topology_sliced_residue_indices PASSED [ 46%] 369s tests/test_topology.py::test_topology_join PASSED [ 46%] 369s tests/test_topology.py::test_topology_join_keep_resSeq PASSED [ 46%] 369s tests/test_trajectory.py::test_mismatch PASSED [ 46%] 369s tests/test_trajectory.py::test_box PASSED [ 46%] 369s tests/test_trajectory.py::test_load_pdb_box PASSED [ 46%] 369s tests/test_trajectory.py::test_load_pdb_gz PASSED [ 46%] 369s tests/test_trajectory.py::test_box_load_save[nc] PASSED [ 46%] 369s tests/test_trajectory.py::test_box_load_save[h5] PASSED [ 46%] 369s tests/test_trajectory.py::test_box_load_save[xtc] PASSED [ 46%] 369s tests/test_trajectory.py::test_box_load_save[trr] PASSED [ 46%] 369s tests/test_trajectory.py::test_box_load_save[dcd] PASSED [ 47%] 369s tests/test_trajectory.py::test_box_load_save[mdcrd] PASSED [ 47%] 369s tests/test_trajectory.py::test_box_load_save[dtr] PASSED [ 47%] 369s tests/test_trajectory.py::test_box_load_save[xyz] SKIPPED (xyz does ...) [ 47%] 369s tests/test_trajectory.py::test_box_load_save[xyz.gz] SKIPPED (xyz.gz...) [ 47%] 369s tests/test_trajectory.py::test_box_load_save[lammpstrj] PASSED [ 47%] 369s tests/test_trajectory.py::test_box_load_save[lh5] SKIPPED (lh5 does ...) [ 47%] 369s tests/test_trajectory.py::test_box_load_save[pdb] SKIPPED (pdb does ...) [ 47%] 369s tests/test_trajectory.py::test_box_load_save[pdb.gz] SKIPPED (pdb.gz...) [ 47%] 369s tests/test_trajectory.py::test_box_load_save[ncrst] PASSED [ 47%] 369s tests/test_trajectory.py::test_box_load_save[rst7] PASSED [ 47%] 369s tests/test_trajectory.py::test_box_load_save[gro] PASSED [ 48%] 369s tests/test_trajectory.py::test_slice PASSED [ 48%] 369s tests/test_trajectory.py::test_slice2 PASSED [ 48%] 369s tests/test_trajectory.py::test_read_path[nc] PASSED [ 48%] 369s tests/test_trajectory.py::test_read_path[h5] PASSED [ 48%] 369s tests/test_trajectory.py::test_read_path[xtc] PASSED [ 48%] 369s tests/test_trajectory.py::test_read_path[trr] PASSED [ 48%] 369s tests/test_trajectory.py::test_read_path[dcd] PASSED [ 48%] 369s tests/test_trajectory.py::test_read_path[mdcrd] PASSED [ 48%] 369s tests/test_trajectory.py::test_read_path[dtr] PASSED [ 48%] 369s tests/test_trajectory.py::test_read_path[xyz] PASSED [ 48%] 369s tests/test_trajectory.py::test_read_path[xyz.gz] PASSED [ 48%] 369s tests/test_trajectory.py::test_read_path[lammpstrj] PASSED [ 49%] 369s tests/test_trajectory.py::test_read_path[lh5] PASSED [ 49%] 369s tests/test_trajectory.py::test_read_path[pdb] PASSED [ 49%] 369s tests/test_trajectory.py::test_read_path[pdb.gz] PASSED [ 49%] 369s tests/test_trajectory.py::test_read_path[ncrst] XFAIL (These referen...) [ 49%] 369s tests/test_trajectory.py::test_read_path[rst7] XFAIL (These referenc...) [ 49%] 369s tests/test_trajectory.py::test_read_path[gro] PASSED [ 49%] 369s tests/test_trajectory.py::test_write_path[nc] PASSED [ 49%] 369s tests/test_trajectory.py::test_write_path[h5] PASSED [ 49%] 369s tests/test_trajectory.py::test_write_path[xtc] PASSED [ 49%] 369s tests/test_trajectory.py::test_write_path[trr] PASSED [ 49%] 369s tests/test_trajectory.py::test_write_path[dcd] PASSED [ 50%] 369s tests/test_trajectory.py::test_write_path[mdcrd] SKIPPED (mdcrd can ...) [ 50%] 369s tests/test_trajectory.py::test_write_path[dtr] PASSED [ 50%] 369s tests/test_trajectory.py::test_write_path[xyz] PASSED [ 50%] 369s tests/test_trajectory.py::test_write_path[xyz.gz] PASSED [ 50%] 369s tests/test_trajectory.py::test_write_path[lammpstrj] PASSED [ 50%] 369s tests/test_trajectory.py::test_write_path[lh5] PASSED [ 50%] 369s tests/test_trajectory.py::test_write_path[pdb] PASSED [ 50%] 369s tests/test_trajectory.py::test_write_path[pdb.gz] PASSED [ 50%] 369s tests/test_trajectory.py::test_write_path[ncrst] SKIPPED (ncrst can ...) [ 50%] 369s tests/test_trajectory.py::test_write_path[rst7] SKIPPED (rst7 can on...) [ 50%] 369s tests/test_trajectory.py::test_write_path[gro] PASSED [ 51%] 369s tests/test_trajectory.py::test_read_write[nc-nc] PASSED [ 51%] 369s tests/test_trajectory.py::test_read_write[nc-h5] PASSED [ 51%] 369s tests/test_trajectory.py::test_read_write[nc-xtc] PASSED [ 51%] 369s tests/test_trajectory.py::test_read_write[nc-trr] PASSED [ 51%] 369s tests/test_trajectory.py::test_read_write[nc-dcd] PASSED [ 51%] 369s tests/test_trajectory.py::test_read_write[nc-mdcrd] SKIPPED (mdcrd c...) [ 51%] 371s tests/test_trajectory.py::test_read_write[nc-dtr] PASSED [ 51%] 371s tests/test_trajectory.py::test_read_write[nc-xyz] PASSED [ 51%] 371s tests/test_trajectory.py::test_read_write[nc-xyz.gz] PASSED [ 51%] 372s tests/test_trajectory.py::test_read_write[nc-lammpstrj] PASSED [ 51%] 372s tests/test_trajectory.py::test_read_write[nc-lh5] PASSED [ 51%] 372s tests/test_trajectory.py::test_read_write[nc-pdb] PASSED [ 52%] 373s tests/test_trajectory.py::test_read_write[nc-pdb.gz] PASSED [ 52%] 373s tests/test_trajectory.py::test_read_write[nc-ncrst] SKIPPED (ncrst c...) [ 52%] 373s tests/test_trajectory.py::test_read_write[nc-rst7] SKIPPED (rst7 can...) [ 52%] 373s tests/test_trajectory.py::test_read_write[nc-gro] PASSED [ 52%] 373s tests/test_trajectory.py::test_read_write[h5-nc] PASSED [ 52%] 373s tests/test_trajectory.py::test_read_write[h5-h5] PASSED [ 52%] 373s tests/test_trajectory.py::test_read_write[h5-xtc] PASSED [ 52%] 373s tests/test_trajectory.py::test_read_write[h5-trr] PASSED [ 52%] 373s tests/test_trajectory.py::test_read_write[h5-dcd] PASSED [ 52%] 373s tests/test_trajectory.py::test_read_write[h5-mdcrd] SKIPPED (mdcrd c...) [ 52%] 374s tests/test_trajectory.py::test_read_write[h5-dtr] PASSED [ 53%] 374s tests/test_trajectory.py::test_read_write[h5-xyz] PASSED [ 53%] 374s tests/test_trajectory.py::test_read_write[h5-xyz.gz] PASSED [ 53%] 374s tests/test_trajectory.py::test_read_write[h5-lammpstrj] PASSED [ 53%] 375s tests/test_trajectory.py::test_read_write[h5-lh5] PASSED [ 53%] 375s tests/test_trajectory.py::test_read_write[h5-pdb] PASSED [ 53%] 375s tests/test_trajectory.py::test_read_write[h5-pdb.gz] PASSED [ 53%] 375s tests/test_trajectory.py::test_read_write[h5-ncrst] SKIPPED (ncrst c...) [ 53%] 375s tests/test_trajectory.py::test_read_write[h5-rst7] SKIPPED (rst7 can...) [ 53%] 375s tests/test_trajectory.py::test_read_write[h5-gro] PASSED [ 53%] 375s tests/test_trajectory.py::test_read_write[xtc-nc] PASSED [ 53%] 375s tests/test_trajectory.py::test_read_write[xtc-h5] PASSED [ 54%] 375s tests/test_trajectory.py::test_read_write[xtc-xtc] PASSED [ 54%] 375s tests/test_trajectory.py::test_read_write[xtc-trr] PASSED [ 54%] 375s tests/test_trajectory.py::test_read_write[xtc-dcd] PASSED [ 54%] 375s tests/test_trajectory.py::test_read_write[xtc-mdcrd] SKIPPED (mdcrd ...) [ 54%] 376s tests/test_trajectory.py::test_read_write[xtc-dtr] PASSED [ 54%] 376s tests/test_trajectory.py::test_read_write[xtc-xyz] PASSED [ 54%] 377s tests/test_trajectory.py::test_read_write[xtc-xyz.gz] PASSED [ 54%] 377s tests/test_trajectory.py::test_read_write[xtc-lammpstrj] PASSED [ 54%] 377s tests/test_trajectory.py::test_read_write[xtc-lh5] PASSED [ 54%] 377s tests/test_trajectory.py::test_read_write[xtc-pdb] PASSED [ 54%] 377s tests/test_trajectory.py::test_read_write[xtc-pdb.gz] PASSED [ 54%] 377s tests/test_trajectory.py::test_read_write[xtc-ncrst] SKIPPED (ncrst ...) [ 55%] 377s tests/test_trajectory.py::test_read_write[xtc-rst7] SKIPPED (rst7 ca...) [ 55%] 378s tests/test_trajectory.py::test_read_write[xtc-gro] PASSED [ 55%] 378s tests/test_trajectory.py::test_read_write[trr-nc] PASSED [ 55%] 378s tests/test_trajectory.py::test_read_write[trr-h5] PASSED [ 55%] 378s tests/test_trajectory.py::test_read_write[trr-xtc] PASSED [ 55%] 378s tests/test_trajectory.py::test_read_write[trr-trr] PASSED [ 55%] 378s tests/test_trajectory.py::test_read_write[trr-dcd] PASSED [ 55%] 378s tests/test_trajectory.py::test_read_write[trr-mdcrd] SKIPPED (mdcrd ...) [ 55%] 379s tests/test_trajectory.py::test_read_write[trr-dtr] PASSED [ 55%] 379s tests/test_trajectory.py::test_read_write[trr-xyz] PASSED [ 55%] 379s tests/test_trajectory.py::test_read_write[trr-xyz.gz] PASSED [ 56%] 379s tests/test_trajectory.py::test_read_write[trr-lammpstrj] PASSED [ 56%] 379s tests/test_trajectory.py::test_read_write[trr-lh5] PASSED [ 56%] 379s tests/test_trajectory.py::test_read_write[trr-pdb] PASSED [ 56%] 380s tests/test_trajectory.py::test_read_write[trr-pdb.gz] PASSED [ 56%] 380s tests/test_trajectory.py::test_read_write[trr-ncrst] SKIPPED (ncrst ...) [ 56%] 380s tests/test_trajectory.py::test_read_write[trr-rst7] SKIPPED (rst7 ca...) [ 56%] 380s tests/test_trajectory.py::test_read_write[trr-gro] PASSED [ 56%] 380s tests/test_trajectory.py::test_read_write[dcd-nc] PASSED [ 56%] 380s tests/test_trajectory.py::test_read_write[dcd-h5] PASSED [ 56%] 380s tests/test_trajectory.py::test_read_write[dcd-xtc] PASSED [ 56%] 380s tests/test_trajectory.py::test_read_write[dcd-trr] PASSED [ 57%] 380s tests/test_trajectory.py::test_read_write[dcd-dcd] PASSED [ 57%] 380s tests/test_trajectory.py::test_read_write[dcd-mdcrd] SKIPPED (mdcrd ...) [ 57%] 381s tests/test_trajectory.py::test_read_write[dcd-dtr] PASSED [ 57%] 381s tests/test_trajectory.py::test_read_write[dcd-xyz] PASSED [ 57%] 381s tests/test_trajectory.py::test_read_write[dcd-xyz.gz] PASSED [ 57%] 381s tests/test_trajectory.py::test_read_write[dcd-lammpstrj] PASSED [ 57%] 381s tests/test_trajectory.py::test_read_write[dcd-lh5] PASSED [ 57%] 381s tests/test_trajectory.py::test_read_write[dcd-pdb] PASSED [ 57%] 382s tests/test_trajectory.py::test_read_write[dcd-pdb.gz] PASSED [ 57%] 382s tests/test_trajectory.py::test_read_write[dcd-ncrst] SKIPPED (ncrst ...) [ 57%] 382s tests/test_trajectory.py::test_read_write[dcd-rst7] SKIPPED (rst7 ca...) [ 57%] 382s tests/test_trajectory.py::test_read_write[dcd-gro] PASSED [ 58%] 382s tests/test_trajectory.py::test_read_write[mdcrd-nc] PASSED [ 58%] 382s tests/test_trajectory.py::test_read_write[mdcrd-h5] PASSED [ 58%] 382s tests/test_trajectory.py::test_read_write[mdcrd-xtc] PASSED [ 58%] 382s tests/test_trajectory.py::test_read_write[mdcrd-trr] PASSED [ 58%] 382s tests/test_trajectory.py::test_read_write[mdcrd-dcd] PASSED [ 58%] 382s tests/test_trajectory.py::test_read_write[mdcrd-mdcrd] SKIPPED (mdcr...) [ 58%] 382s tests/test_trajectory.py::test_read_write[mdcrd-dtr] SKIPPED (dtr ne...) [ 58%] 382s tests/test_trajectory.py::test_read_write[mdcrd-xyz] PASSED [ 58%] 383s tests/test_trajectory.py::test_read_write[mdcrd-xyz.gz] PASSED [ 58%] 383s tests/test_trajectory.py::test_read_write[mdcrd-lammpstrj] SKIPPED (...) [ 58%] 383s tests/test_trajectory.py::test_read_write[mdcrd-lh5] PASSED [ 59%] 383s tests/test_trajectory.py::test_read_write[mdcrd-pdb] PASSED [ 59%] 384s tests/test_trajectory.py::test_read_write[mdcrd-pdb.gz] PASSED [ 59%] 384s tests/test_trajectory.py::test_read_write[mdcrd-ncrst] SKIPPED (ncrs...) [ 59%] 384s tests/test_trajectory.py::test_read_write[mdcrd-rst7] SKIPPED (rst7 ...) [ 59%] 384s tests/test_trajectory.py::test_read_write[mdcrd-gro] PASSED [ 59%] 384s tests/test_trajectory.py::test_read_write[dtr-nc] PASSED [ 59%] 384s tests/test_trajectory.py::test_read_write[dtr-h5] PASSED [ 59%] 384s tests/test_trajectory.py::test_read_write[dtr-xtc] PASSED [ 59%] 384s tests/test_trajectory.py::test_read_write[dtr-trr] PASSED [ 59%] 384s tests/test_trajectory.py::test_read_write[dtr-dcd] PASSED [ 59%] 384s tests/test_trajectory.py::test_read_write[dtr-mdcrd] SKIPPED (mdcrd ...) [ 60%] 385s tests/test_trajectory.py::test_read_write[dtr-dtr] PASSED [ 60%] 385s tests/test_trajectory.py::test_read_write[dtr-xyz] PASSED [ 60%] 385s tests/test_trajectory.py::test_read_write[dtr-xyz.gz] PASSED [ 60%] 386s tests/test_trajectory.py::test_read_write[dtr-lammpstrj] PASSED [ 60%] 386s tests/test_trajectory.py::test_read_write[dtr-lh5] PASSED [ 60%] 386s tests/test_trajectory.py::test_read_write[dtr-pdb] PASSED [ 60%] 386s tests/test_trajectory.py::test_read_write[dtr-pdb.gz] PASSED [ 60%] 386s tests/test_trajectory.py::test_read_write[dtr-ncrst] SKIPPED (ncrst ...) [ 60%] 386s tests/test_trajectory.py::test_read_write[dtr-rst7] SKIPPED (rst7 ca...) [ 60%] 386s tests/test_trajectory.py::test_read_write[dtr-gro] PASSED [ 60%] 386s tests/test_trajectory.py::test_read_write[xyz-nc] PASSED [ 60%] 386s tests/test_trajectory.py::test_read_write[xyz-h5] PASSED [ 61%] 387s tests/test_trajectory.py::test_read_write[xyz-xtc] PASSED [ 61%] 387s tests/test_trajectory.py::test_read_write[xyz-trr] PASSED [ 61%] 387s tests/test_trajectory.py::test_read_write[xyz-dcd] PASSED [ 61%] 387s tests/test_trajectory.py::test_read_write[xyz-mdcrd] SKIPPED (mdcrd ...) [ 61%] 387s tests/test_trajectory.py::test_read_write[xyz-dtr] SKIPPED (dtr need...) [ 61%] 387s tests/test_trajectory.py::test_read_write[xyz-xyz] PASSED [ 61%] 387s tests/test_trajectory.py::test_read_write[xyz-xyz.gz] PASSED [ 61%] 387s tests/test_trajectory.py::test_read_write[xyz-lammpstrj] SKIPPED (la...) [ 61%] 387s tests/test_trajectory.py::test_read_write[xyz-lh5] PASSED [ 61%] 387s tests/test_trajectory.py::test_read_write[xyz-pdb] PASSED [ 61%] 388s tests/test_trajectory.py::test_read_write[xyz-pdb.gz] PASSED [ 62%] 388s tests/test_trajectory.py::test_read_write[xyz-ncrst] SKIPPED (ncrst ...) [ 62%] 388s tests/test_trajectory.py::test_read_write[xyz-rst7] SKIPPED (rst7 ca...) [ 62%] 388s tests/test_trajectory.py::test_read_write[xyz-gro] PASSED [ 62%] 388s tests/test_trajectory.py::test_read_write[xyz.gz-nc] PASSED [ 62%] 388s tests/test_trajectory.py::test_read_write[xyz.gz-h5] PASSED [ 62%] 388s tests/test_trajectory.py::test_read_write[xyz.gz-xtc] PASSED [ 62%] 388s tests/test_trajectory.py::test_read_write[xyz.gz-trr] PASSED [ 62%] 388s tests/test_trajectory.py::test_read_write[xyz.gz-dcd] PASSED [ 62%] 388s tests/test_trajectory.py::test_read_write[xyz.gz-mdcrd] SKIPPED (mdc...) [ 62%] 388s tests/test_trajectory.py::test_read_write[xyz.gz-dtr] SKIPPED (dtr n...) [ 62%] 388s tests/test_trajectory.py::test_read_write[xyz.gz-xyz] PASSED [ 63%] 388s tests/test_trajectory.py::test_read_write[xyz.gz-xyz.gz] PASSED [ 63%] 388s tests/test_trajectory.py::test_read_write[xyz.gz-lammpstrj] SKIPPED [ 63%] 388s tests/test_trajectory.py::test_read_write[xyz.gz-lh5] PASSED [ 63%] 388s tests/test_trajectory.py::test_read_write[xyz.gz-pdb] PASSED [ 63%] 389s tests/test_trajectory.py::test_read_write[xyz.gz-pdb.gz] PASSED [ 63%] 389s tests/test_trajectory.py::test_read_write[xyz.gz-ncrst] SKIPPED (ncr...) [ 63%] 389s tests/test_trajectory.py::test_read_write[xyz.gz-rst7] SKIPPED (rst7...) [ 63%] 389s tests/test_trajectory.py::test_read_write[xyz.gz-gro] PASSED [ 63%] 389s tests/test_trajectory.py::test_read_write[lammpstrj-nc] PASSED [ 63%] 389s tests/test_trajectory.py::test_read_write[lammpstrj-h5] PASSED [ 63%] 389s tests/test_trajectory.py::test_read_write[lammpstrj-xtc] PASSED [ 63%] 389s tests/test_trajectory.py::test_read_write[lammpstrj-trr] PASSED [ 64%] 389s tests/test_trajectory.py::test_read_write[lammpstrj-dcd] PASSED [ 64%] 389s tests/test_trajectory.py::test_read_write[lammpstrj-mdcrd] SKIPPED (...) [ 64%] 390s tests/test_trajectory.py::test_read_write[lammpstrj-dtr] PASSED [ 64%] 391s tests/test_trajectory.py::test_read_write[lammpstrj-xyz] PASSED [ 64%] 391s tests/test_trajectory.py::test_read_write[lammpstrj-xyz.gz] PASSED [ 64%] 391s tests/test_trajectory.py::test_read_write[lammpstrj-lammpstrj] PASSED [ 64%] 391s tests/test_trajectory.py::test_read_write[lammpstrj-lh5] PASSED [ 64%] 391s tests/test_trajectory.py::test_read_write[lammpstrj-pdb] PASSED [ 64%] 391s tests/test_trajectory.py::test_read_write[lammpstrj-pdb.gz] PASSED [ 64%] 391s tests/test_trajectory.py::test_read_write[lammpstrj-ncrst] SKIPPED (...) [ 64%] 391s tests/test_trajectory.py::test_read_write[lammpstrj-rst7] SKIPPED (r...) [ 65%] 391s tests/test_trajectory.py::test_read_write[lammpstrj-gro] PASSED [ 65%] 391s tests/test_trajectory.py::test_read_write[lh5-nc] PASSED [ 65%] 391s tests/test_trajectory.py::test_read_write[lh5-h5] PASSED [ 65%] 391s tests/test_trajectory.py::test_read_write[lh5-xtc] PASSED [ 65%] 391s tests/test_trajectory.py::test_read_write[lh5-trr] PASSED [ 65%] 391s tests/test_trajectory.py::test_read_write[lh5-dcd] PASSED [ 65%] 391s tests/test_trajectory.py::test_read_write[lh5-mdcrd] SKIPPED (mdcrd ...) [ 65%] 391s tests/test_trajectory.py::test_read_write[lh5-dtr] SKIPPED (dtr need...) [ 65%] 392s tests/test_trajectory.py::test_read_write[lh5-xyz] PASSED [ 65%] 392s tests/test_trajectory.py::test_read_write[lh5-xyz.gz] PASSED [ 65%] 392s tests/test_trajectory.py::test_read_write[lh5-lammpstrj] SKIPPED (la...) [ 66%] 392s tests/test_trajectory.py::test_read_write[lh5-lh5] PASSED [ 66%] 392s tests/test_trajectory.py::test_read_write[lh5-pdb] PASSED [ 66%] 392s tests/test_trajectory.py::test_read_write[lh5-pdb.gz] PASSED [ 66%] 392s tests/test_trajectory.py::test_read_write[lh5-ncrst] SKIPPED (ncrst ...) [ 66%] 392s tests/test_trajectory.py::test_read_write[lh5-rst7] SKIPPED (rst7 ca...) [ 66%] 392s tests/test_trajectory.py::test_read_write[lh5-gro] PASSED [ 66%] 393s tests/test_trajectory.py::test_read_write[pdb-nc] PASSED [ 66%] 393s tests/test_trajectory.py::test_read_write[pdb-h5] PASSED [ 66%] 393s tests/test_trajectory.py::test_read_write[pdb-xtc] PASSED [ 66%] 393s tests/test_trajectory.py::test_read_write[pdb-trr] PASSED [ 66%] 393s tests/test_trajectory.py::test_read_write[pdb-dcd] PASSED [ 66%] 393s tests/test_trajectory.py::test_read_write[pdb-mdcrd] SKIPPED (mdcrd ...) [ 67%] 394s tests/test_trajectory.py::test_read_write[pdb-dtr] PASSED [ 67%] 394s tests/test_trajectory.py::test_read_write[pdb-xyz] PASSED [ 67%] 395s tests/test_trajectory.py::test_read_write[pdb-xyz.gz] PASSED [ 67%] 396s tests/test_trajectory.py::test_read_write[pdb-lammpstrj] PASSED [ 67%] 396s tests/test_trajectory.py::test_read_write[pdb-lh5] PASSED [ 67%] 396s tests/test_trajectory.py::test_read_write[pdb-pdb] PASSED [ 67%] 396s tests/test_trajectory.py::test_read_write[pdb-pdb.gz] PASSED [ 67%] 396s tests/test_trajectory.py::test_read_write[pdb-ncrst] SKIPPED (ncrst ...) [ 67%] 396s tests/test_trajectory.py::test_read_write[pdb-rst7] SKIPPED (rst7 ca...) [ 67%] 396s tests/test_trajectory.py::test_read_write[pdb-gro] PASSED [ 67%] 397s tests/test_trajectory.py::test_read_write[pdb.gz-nc] PASSED [ 68%] 397s tests/test_trajectory.py::test_read_write[pdb.gz-h5] PASSED [ 68%] 397s tests/test_trajectory.py::test_read_write[pdb.gz-xtc] PASSED [ 68%] 397s tests/test_trajectory.py::test_read_write[pdb.gz-trr] PASSED [ 68%] 397s tests/test_trajectory.py::test_read_write[pdb.gz-dcd] PASSED [ 68%] 397s tests/test_trajectory.py::test_read_write[pdb.gz-mdcrd] SKIPPED (mdc...) [ 68%] 398s tests/test_trajectory.py::test_read_write[pdb.gz-dtr] PASSED [ 68%] 398s tests/test_trajectory.py::test_read_write[pdb.gz-xyz] PASSED [ 68%] 399s tests/test_trajectory.py::test_read_write[pdb.gz-xyz.gz] PASSED [ 68%] 399s tests/test_trajectory.py::test_read_write[pdb.gz-lammpstrj] PASSED [ 68%] 399s tests/test_trajectory.py::test_read_write[pdb.gz-lh5] PASSED [ 68%] 400s tests/test_trajectory.py::test_read_write[pdb.gz-pdb] PASSED [ 69%] 400s tests/test_trajectory.py::test_read_write[pdb.gz-pdb.gz] PASSED [ 69%] 400s tests/test_trajectory.py::test_read_write[pdb.gz-ncrst] SKIPPED (ncr...) [ 69%] 400s tests/test_trajectory.py::test_read_write[pdb.gz-rst7] SKIPPED (rst7...) [ 69%] 400s tests/test_trajectory.py::test_read_write[pdb.gz-gro] PASSED [ 69%] 400s tests/test_trajectory.py::test_read_write[ncrst-nc] XFAIL (These ref...) [ 69%] 400s tests/test_trajectory.py::test_read_write[ncrst-h5] XFAIL (These ref...) [ 69%] 400s tests/test_trajectory.py::test_read_write[ncrst-xtc] XFAIL (These re...) [ 69%] 400s tests/test_trajectory.py::test_read_write[ncrst-trr] XFAIL (These re...) [ 69%] 400s tests/test_trajectory.py::test_read_write[ncrst-dcd] XFAIL (These re...) [ 69%] 400s tests/test_trajectory.py::test_read_write[ncrst-mdcrd] XFAIL (These ...) [ 69%] 400s tests/test_trajectory.py::test_read_write[ncrst-dtr] XFAIL (These re...) [ 69%] 401s tests/test_trajectory.py::test_read_write[ncrst-xyz] XFAIL (These re...) [ 70%] 401s tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] XFAIL (These...) [ 70%] 401s tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] XFAIL (Th...) [ 70%] 401s tests/test_trajectory.py::test_read_write[ncrst-lh5] XFAIL (These re...) [ 70%] 401s tests/test_trajectory.py::test_read_write[ncrst-pdb] XFAIL (These re...) [ 70%] 401s tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] XFAIL (These...) [ 70%] 401s tests/test_trajectory.py::test_read_write[ncrst-ncrst] XFAIL (These ...) [ 70%] 401s tests/test_trajectory.py::test_read_write[ncrst-rst7] XFAIL (These r...) [ 70%] 401s tests/test_trajectory.py::test_read_write[ncrst-gro] XFAIL (These re...) [ 70%] 401s tests/test_trajectory.py::test_read_write[rst7-nc] XFAIL (These refe...) [ 70%] 401s tests/test_trajectory.py::test_read_write[rst7-h5] XFAIL (These refe...) [ 70%] 401s tests/test_trajectory.py::test_read_write[rst7-xtc] XFAIL (These ref...) [ 71%] 401s tests/test_trajectory.py::test_read_write[rst7-trr] XFAIL (These ref...) [ 71%] 401s tests/test_trajectory.py::test_read_write[rst7-dcd] XFAIL (These ref...) [ 71%] 401s tests/test_trajectory.py::test_read_write[rst7-mdcrd] XFAIL (These r...) [ 71%] 401s tests/test_trajectory.py::test_read_write[rst7-dtr] XFAIL (These ref...) [ 71%] 401s tests/test_trajectory.py::test_read_write[rst7-xyz] XFAIL (These ref...) [ 71%] 401s tests/test_trajectory.py::test_read_write[rst7-xyz.gz] XFAIL (These ...) [ 71%] 401s tests/test_trajectory.py::test_read_write[rst7-lammpstrj] XFAIL (The...) [ 71%] 401s tests/test_trajectory.py::test_read_write[rst7-lh5] XFAIL (These ref...) [ 71%] 401s tests/test_trajectory.py::test_read_write[rst7-pdb] XFAIL (These ref...) [ 71%] 401s tests/test_trajectory.py::test_read_write[rst7-pdb.gz] XFAIL (These ...) [ 71%] 401s tests/test_trajectory.py::test_read_write[rst7-ncrst] XFAIL (These r...) [ 72%] 401s tests/test_trajectory.py::test_read_write[rst7-rst7] XFAIL (These re...) [ 72%] 401s tests/test_trajectory.py::test_read_write[rst7-gro] XFAIL (These ref...) [ 72%] 401s tests/test_trajectory.py::test_read_write[gro-nc] PASSED [ 72%] 401s tests/test_trajectory.py::test_read_write[gro-h5] PASSED [ 72%] 401s tests/test_trajectory.py::test_read_write[gro-xtc] PASSED [ 72%] 401s tests/test_trajectory.py::test_read_write[gro-trr] PASSED [ 72%] 401s tests/test_trajectory.py::test_read_write[gro-dcd] PASSED [ 72%] 401s tests/test_trajectory.py::test_read_write[gro-mdcrd] SKIPPED (mdcrd ...) [ 72%] 402s tests/test_trajectory.py::test_read_write[gro-dtr] PASSED [ 72%] 402s tests/test_trajectory.py::test_read_write[gro-xyz] PASSED [ 72%] 403s tests/test_trajectory.py::test_read_write[gro-xyz.gz] PASSED [ 72%] 403s tests/test_trajectory.py::test_read_write[gro-lammpstrj] PASSED [ 73%] 403s tests/test_trajectory.py::test_read_write[gro-lh5] PASSED [ 73%] 403s tests/test_trajectory.py::test_read_write[gro-pdb] PASSED [ 73%] 403s tests/test_trajectory.py::test_read_write[gro-pdb.gz] PASSED [ 73%] 403s tests/test_trajectory.py::test_read_write[gro-ncrst] SKIPPED (ncrst ...) [ 73%] 403s tests/test_trajectory.py::test_read_write[gro-rst7] SKIPPED (rst7 ca...) [ 73%] 403s tests/test_trajectory.py::test_read_write[gro-gro] PASSED [ 73%] 404s tests/test_trajectory.py::test_load[nc] PASSED [ 73%] 404s tests/test_trajectory.py::test_load[h5] PASSED [ 73%] 404s tests/test_trajectory.py::test_load[xtc] PASSED [ 73%] 404s tests/test_trajectory.py::test_load[trr] PASSED [ 73%] 404s tests/test_trajectory.py::test_load[dcd] PASSED [ 74%] 404s tests/test_trajectory.py::test_load[mdcrd] PASSED [ 74%] 404s tests/test_trajectory.py::test_load[dtr] PASSED [ 74%] 404s tests/test_trajectory.py::test_load[xyz] PASSED [ 74%] 404s tests/test_trajectory.py::test_load[xyz.gz] PASSED [ 74%] 404s tests/test_trajectory.py::test_load[lammpstrj] PASSED [ 74%] 404s tests/test_trajectory.py::test_load[lh5] PASSED [ 74%] 405s tests/test_trajectory.py::test_load[pdb] PASSED [ 74%] 407s tests/test_trajectory.py::test_load[pdb.gz] PASSED [ 74%] 407s tests/test_trajectory.py::test_load[ncrst] XFAIL (These reference fi...) [ 74%] 407s tests/test_trajectory.py::test_load[rst7] XFAIL (These reference fil...) [ 74%] 407s tests/test_trajectory.py::test_load[gro] PASSED [ 75%] 407s tests/test_trajectory.py::test_hdf5 PASSED [ 75%] 407s tests/test_trajectory.py::test_center PASSED [ 75%] 407s tests/test_trajectory.py::test_center_aind PASSED [ 75%] 407s tests/test_trajectory.py::test_float_atom_indices_exception[nc] PASSED [ 75%] 407s tests/test_trajectory.py::test_float_atom_indices_exception[h5] PASSED [ 75%] 407s tests/test_trajectory.py::test_float_atom_indices_exception[xtc] PASSED [ 75%] 407s tests/test_trajectory.py::test_float_atom_indices_exception[trr] PASSED [ 75%] 407s tests/test_trajectory.py::test_float_atom_indices_exception[dcd] PASSED [ 75%] 407s tests/test_trajectory.py::test_float_atom_indices_exception[mdcrd] PASSED [ 75%] 407s tests/test_trajectory.py::test_float_atom_indices_exception[dtr] PASSED [ 75%] 407s tests/test_trajectory.py::test_float_atom_indices_exception[xyz] PASSED [ 75%] 407s tests/test_trajectory.py::test_float_atom_indices_exception[xyz.gz] PASSED [ 76%] 407s tests/test_trajectory.py::test_float_atom_indices_exception[lammpstrj] PASSED [ 76%] 407s tests/test_trajectory.py::test_float_atom_indices_exception[lh5] PASSED [ 76%] 407s tests/test_trajectory.py::test_float_atom_indices_exception[pdb] PASSED [ 76%] 407s tests/test_trajectory.py::test_float_atom_indices_exception[pdb.gz] PASSED [ 76%] 407s tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] XFAIL [ 76%] 407s tests/test_trajectory.py::test_float_atom_indices_exception[rst7] XFAIL [ 76%] 407s tests/test_trajectory.py::test_float_atom_indices_exception[gro] PASSED [ 76%] 407s tests/test_trajectory.py::test_restrict_atoms PASSED [ 76%] 407s tests/test_trajectory.py::test_restrict_atoms_not_inplace PASSED [ 76%] 407s tests/test_trajectory.py::test_array_vs_matrix PASSED [ 76%] 407s tests/test_trajectory.py::test_pdb_unitcell_loadsave PASSED [ 77%] 407s tests/test_trajectory.py::test_load_combination[nc] PASSED [ 77%] 407s tests/test_trajectory.py::test_load_combination[h5] PASSED [ 77%] 407s tests/test_trajectory.py::test_load_combination[xtc] PASSED [ 77%] 407s tests/test_trajectory.py::test_load_combination[trr] PASSED [ 77%] 407s tests/test_trajectory.py::test_load_combination[dcd] PASSED [ 77%] 407s tests/test_trajectory.py::test_load_combination[mdcrd] PASSED [ 77%] 407s tests/test_trajectory.py::test_load_combination[dtr] PASSED [ 77%] 407s tests/test_trajectory.py::test_load_combination[xyz] PASSED [ 77%] 407s tests/test_trajectory.py::test_load_combination[xyz.gz] PASSED [ 77%] 407s tests/test_trajectory.py::test_load_combination[lammpstrj] PASSED [ 77%] 407s tests/test_trajectory.py::test_load_combination[lh5] PASSED [ 78%] 408s tests/test_trajectory.py::test_load_combination[pdb] PASSED [ 78%] 408s tests/test_trajectory.py::test_load_combination[pdb.gz] PASSED [ 78%] 408s tests/test_trajectory.py::test_load_combination[ncrst] XFAIL (These ...) [ 78%] 408s tests/test_trajectory.py::test_load_combination[rst7] XFAIL (These r...) [ 78%] 408s tests/test_trajectory.py::test_load_combination[gro] PASSED [ 78%] 408s tests/test_trajectory.py::test_no_topology PASSED [ 78%] 408s tests/test_trajectory.py::test_join PASSED [ 78%] 408s tests/test_trajectory.py::test_md_join PASSED [ 78%] 408s tests/test_trajectory.py::test_stack_1 PASSED [ 78%] 408s tests/test_trajectory.py::test_stack_2 PASSED [ 78%] 409s tests/test_trajectory.py::test_seek_read_mode[nc] PASSED [ 78%] 409s tests/test_trajectory.py::test_seek_read_mode[h5] PASSED [ 79%] 409s tests/test_trajectory.py::test_seek_read_mode[xtc] PASSED [ 79%] 409s tests/test_trajectory.py::test_seek_read_mode[trr] PASSED [ 79%] 409s tests/test_trajectory.py::test_seek_read_mode[dcd] PASSED [ 79%] 409s tests/test_trajectory.py::test_seek_read_mode[mdcrd] PASSED [ 79%] 409s tests/test_trajectory.py::test_seek_read_mode[dtr] PASSED [ 79%] 409s tests/test_trajectory.py::test_seek_read_mode[xyz] PASSED [ 79%] 409s tests/test_trajectory.py::test_seek_read_mode[xyz.gz] XFAIL (This is...) [ 79%] 409s tests/test_trajectory.py::test_seek_read_mode[lammpstrj] PASSED [ 79%] 409s tests/test_trajectory.py::test_seek_read_mode[lh5] PASSED [ 79%] 409s tests/test_trajectory.py::test_seek_read_mode[pdb] XFAIL (PDB Files ...) [ 79%] 409s tests/test_trajectory.py::test_seek_read_mode[pdb.gz] XFAIL (PDB Fil...) [ 80%] 409s tests/test_trajectory.py::test_seek_read_mode[ncrst] XFAIL (These re...) [ 80%] 409s tests/test_trajectory.py::test_seek_read_mode[rst7] XFAIL (These ref...) [ 80%] 409s tests/test_trajectory.py::test_seek_read_mode[gro] XFAIL (This is br...) [ 80%] 409s tests/test_trajectory.py::test_load_frame[nc] PASSED [ 80%] 409s tests/test_trajectory.py::test_load_frame[h5] PASSED [ 80%] 409s tests/test_trajectory.py::test_load_frame[xtc] PASSED [ 80%] 409s tests/test_trajectory.py::test_load_frame[trr] PASSED [ 80%] 409s tests/test_trajectory.py::test_load_frame[dcd] PASSED [ 80%] 409s tests/test_trajectory.py::test_load_frame[mdcrd] PASSED [ 80%] 409s tests/test_trajectory.py::test_load_frame[dtr] XFAIL (DTR doesn't lo...) [ 80%] 409s tests/test_trajectory.py::test_load_frame[xyz] PASSED [ 81%] 409s tests/test_trajectory.py::test_load_frame[xyz.gz] PASSED [ 81%] 409s tests/test_trajectory.py::test_load_frame[lammpstrj] PASSED [ 81%] 409s tests/test_trajectory.py::test_load_frame[lh5] PASSED [ 81%] 410s tests/test_trajectory.py::test_load_frame[pdb] PASSED [ 81%] 410s tests/test_trajectory.py::test_load_frame[pdb.gz] PASSED [ 81%] 410s tests/test_trajectory.py::test_load_frame[ncrst] XFAIL (These refere...) [ 81%] 410s tests/test_trajectory.py::test_load_frame[rst7] XFAIL (These referen...) [ 81%] 410s tests/test_trajectory.py::test_load_frame[gro] XFAIL (Gro doesn't im...) [ 81%] 410s tests/test_trajectory.py::test_load_frame_2eqq PASSED [ 81%] 410s tests/test_trajectory.py::test_iterload[nc] PASSED [ 81%] 410s tests/test_trajectory.py::test_iterload[h5] PASSED [ 81%] 410s tests/test_trajectory.py::test_iterload[xtc] PASSED [ 82%] 410s tests/test_trajectory.py::test_iterload[trr] PASSED [ 82%] 410s tests/test_trajectory.py::test_iterload[dcd] PASSED [ 82%] 410s tests/test_trajectory.py::test_iterload[mdcrd] PASSED [ 82%] 410s tests/test_trajectory.py::test_iterload[dtr] XFAIL (This is broken w...) [ 82%] 410s tests/test_trajectory.py::test_iterload[xyz] PASSED [ 82%] 410s tests/test_trajectory.py::test_iterload[xyz.gz] PASSED [ 82%] 411s tests/test_trajectory.py::test_iterload[lammpstrj] PASSED [ 82%] 411s tests/test_trajectory.py::test_iterload[lh5] PASSED [ 82%] 411s tests/test_trajectory.py::test_iterload[pdb] PASSED [ 82%] 411s tests/test_trajectory.py::test_iterload[pdb.gz] PASSED [ 82%] 411s tests/test_trajectory.py::test_iterload[ncrst] SKIPPED (Only 1 frame...) [ 83%] 411s tests/test_trajectory.py::test_iterload[rst7] SKIPPED (Only 1 frame ...) [ 83%] 411s tests/test_trajectory.py::test_iterload[gro] PASSED [ 83%] 414s tests/test_trajectory.py::test_iterload_skip[nc] PASSED [ 83%] 416s tests/test_trajectory.py::test_iterload_skip[h5] PASSED [ 83%] 417s tests/test_trajectory.py::test_iterload_skip[xtc] PASSED [ 83%] 418s tests/test_trajectory.py::test_iterload_skip[trr] PASSED [ 83%] 419s tests/test_trajectory.py::test_iterload_skip[dcd] PASSED [ 83%] 421s tests/test_trajectory.py::test_iterload_skip[mdcrd] PASSED [ 83%] 421s tests/test_trajectory.py::test_iterload_skip[dtr] PASSED [ 83%] 422s tests/test_trajectory.py::test_iterload_skip[xyz] PASSED [ 83%] 423s tests/test_trajectory.py::test_iterload_skip[xyz.gz] PASSED [ 84%] 424s tests/test_trajectory.py::test_iterload_skip[lammpstrj] PASSED [ 84%] 426s tests/test_trajectory.py::test_iterload_skip[lh5] PASSED [ 84%] 426s tests/test_trajectory.py::test_iterload_skip[pdb] XFAIL (PDB Iterloa...) [ 84%] 426s tests/test_trajectory.py::test_iterload_skip[pdb.gz] XFAIL (PDB Iter...) [ 84%] 426s tests/test_trajectory.py::test_iterload_skip[ncrst] XFAIL (These ref...) [ 84%] 426s tests/test_trajectory.py::test_iterload_skip[rst7] XFAIL (These refe...) [ 84%] 426s tests/test_trajectory.py::test_iterload_skip[gro] XFAIL (Not impleme...) [ 84%] 426s tests/test_trajectory.py::test_iterload_chunk_dcd PASSED [ 84%] 426s tests/test_trajectory.py::test_save_load[nc] PASSED [ 84%] 426s tests/test_trajectory.py::test_save_load[h5] PASSED [ 84%] 426s tests/test_trajectory.py::test_save_load[xtc] PASSED [ 84%] 426s tests/test_trajectory.py::test_save_load[trr] PASSED [ 85%] 426s tests/test_trajectory.py::test_save_load[dcd] PASSED [ 85%] 426s tests/test_trajectory.py::test_save_load[mdcrd] PASSED [ 85%] 426s tests/test_trajectory.py::test_save_load[dtr] PASSED [ 85%] 426s tests/test_trajectory.py::test_save_load[xyz] PASSED [ 85%] 426s tests/test_trajectory.py::test_save_load[xyz.gz] PASSED [ 85%] 426s tests/test_trajectory.py::test_save_load[lammpstrj] PASSED [ 85%] 426s tests/test_trajectory.py::test_save_load[lh5] PASSED [ 85%] 426s tests/test_trajectory.py::test_save_load[pdb] PASSED [ 85%] 426s tests/test_trajectory.py::test_save_load[pdb.gz] PASSED [ 85%] 426s tests/test_trajectory.py::test_save_load[ncrst] PASSED [ 85%] 426s tests/test_trajectory.py::test_save_load[rst7] PASSED [ 86%] 426s tests/test_trajectory.py::test_save_load[gro] PASSED [ 86%] 426s tests/test_trajectory.py::test_force_overwrite[nc] PASSED [ 86%] 426s tests/test_trajectory.py::test_force_overwrite[h5] PASSED [ 86%] 426s tests/test_trajectory.py::test_force_overwrite[xtc] PASSED [ 86%] 426s tests/test_trajectory.py::test_force_overwrite[trr] PASSED [ 86%] 426s tests/test_trajectory.py::test_force_overwrite[dcd] PASSED [ 86%] 426s tests/test_trajectory.py::test_force_overwrite[mdcrd] PASSED [ 86%] 426s tests/test_trajectory.py::test_force_overwrite[dtr] XFAIL (This is b...) [ 86%] 426s tests/test_trajectory.py::test_force_overwrite[xyz] PASSED [ 86%] 426s tests/test_trajectory.py::test_force_overwrite[xyz.gz] PASSED [ 86%] 426s tests/test_trajectory.py::test_force_overwrite[lammpstrj] PASSED [ 87%] 426s tests/test_trajectory.py::test_force_overwrite[lh5] PASSED [ 87%] 426s tests/test_trajectory.py::test_force_overwrite[pdb] PASSED [ 87%] 426s tests/test_trajectory.py::test_force_overwrite[pdb.gz] PASSED [ 87%] 426s tests/test_trajectory.py::test_force_overwrite[ncrst] PASSED [ 87%] 426s tests/test_trajectory.py::test_force_overwrite[rst7] PASSED [ 87%] 426s tests/test_trajectory.py::test_force_overwrite[gro] PASSED [ 87%] 426s tests/test_trajectory.py::test_force_noverwrite[nc] PASSED [ 87%] 426s tests/test_trajectory.py::test_force_noverwrite[h5] PASSED [ 87%] 426s tests/test_trajectory.py::test_force_noverwrite[xtc] PASSED [ 87%] 426s tests/test_trajectory.py::test_force_noverwrite[trr] PASSED [ 87%] 426s tests/test_trajectory.py::test_force_noverwrite[dcd] PASSED [ 87%] 426s tests/test_trajectory.py::test_force_noverwrite[mdcrd] PASSED [ 88%] 426s tests/test_trajectory.py::test_force_noverwrite[dtr] PASSED [ 88%] 426s tests/test_trajectory.py::test_force_noverwrite[xyz] PASSED [ 88%] 426s tests/test_trajectory.py::test_force_noverwrite[xyz.gz] PASSED [ 88%] 426s tests/test_trajectory.py::test_force_noverwrite[lammpstrj] PASSED [ 88%] 426s tests/test_trajectory.py::test_force_noverwrite[lh5] PASSED [ 88%] 426s tests/test_trajectory.py::test_force_noverwrite[pdb] PASSED [ 88%] 426s tests/test_trajectory.py::test_force_noverwrite[pdb.gz] PASSED [ 88%] 426s tests/test_trajectory.py::test_force_noverwrite[ncrst] PASSED [ 88%] 426s tests/test_trajectory.py::test_force_noverwrite[rst7] PASSED [ 88%] 426s tests/test_trajectory.py::test_force_noverwrite[gro] PASSED [ 88%] 426s tests/test_trajectory.py::test_open_and_load PASSED [ 89%] 426s tests/test_trajectory.py::test_length PASSED [ 89%] 426s tests/test_trajectory.py::test_unitcell[nc] PASSED [ 89%] 426s tests/test_trajectory.py::test_unitcell[h5] PASSED [ 89%] 426s tests/test_trajectory.py::test_unitcell[xtc] PASSED [ 89%] 426s tests/test_trajectory.py::test_unitcell[trr] PASSED [ 89%] 426s tests/test_trajectory.py::test_unitcell[dcd] PASSED [ 89%] 426s tests/test_trajectory.py::test_unitcell[mdcrd] PASSED [ 89%] 427s tests/test_trajectory.py::test_unitcell[dtr] XFAIL (dtr seems to nee...) [ 89%] 427s tests/test_trajectory.py::test_unitcell[xyz] PASSED [ 89%] 427s tests/test_trajectory.py::test_unitcell[xyz.gz] PASSED [ 89%] 427s tests/test_trajectory.py::test_unitcell[lammpstrj] XFAIL (lammpstrj ...) [ 90%] 427s tests/test_trajectory.py::test_unitcell[lh5] PASSED [ 90%] 427s tests/test_trajectory.py::test_unitcell[pdb] PASSED [ 90%] 427s tests/test_trajectory.py::test_unitcell[pdb.gz] PASSED [ 90%] 427s tests/test_trajectory.py::test_unitcell[ncrst] XFAIL (ncrst seems to...) [ 90%] 427s tests/test_trajectory.py::test_unitcell[rst7] XFAIL (rst7 seems to n...) [ 90%] 427s tests/test_trajectory.py::test_unitcell[gro] PASSED [ 90%] 427s tests/test_trajectory.py::test_chunk0_iterload PASSED [ 90%] 427s tests/test_trajectory.py::test_hashing PASSED [ 90%] 427s tests/test_trajectory.py::test_smooth PASSED [ 90%] 427s tests/test_trajectory.py::test_load_pdb_no_standard_names PASSED [ 90%] 427s tests/test_trajectory.py::test_load_with_atom_indices PASSED [ 90%] 427s tests/test_trajectory.py::test_atom_slicing PASSED [ 91%] 427s tests/test_trajectory.py::test_load_with_frame PASSED [ 91%] 427s tests/test_trajectory.py::test_add_remove_atoms PASSED [ 91%] 427s tests/test_trr.py::test_1 PASSED [ 91%] 427s tests/test_trr.py::test_read_stride PASSED [ 91%] 427s tests/test_trr.py::test_read_stride_n_frames PASSED [ 91%] 427s tests/test_trr.py::test_read_stride_offsets PASSED [ 91%] 427s tests/test_trr.py::test_read_stride_n_frames_offsets PASSED [ 91%] 427s tests/test_trr.py::test_read_stride_switching PASSED [ 91%] 427s tests/test_trr.py::test_write_read PASSED [ 91%] 427s tests/test_trr.py::test_read_atomindices_1 PASSED [ 91%] 427s tests/test_trr.py::test_read_atomindices_2 PASSED [ 92%] 427s tests/test_trr.py::test_deficient_shape PASSED [ 92%] 427s tests/test_trr.py::test_ragged_1 PASSED [ 92%] 427s tests/test_trr.py::test_ragged_2 PASSED [ 92%] 427s tests/test_trr.py::test_malformed PASSED [ 92%] 427s tests/test_trr.py::test_tell PASSED [ 92%] 427s tests/test_trr.py::test_seek PASSED [ 92%] 427s tests/test_trr.py::test_get_velocities PASSED [ 92%] 427s tests/test_trr.py::test_get_forces PASSED [ 92%] 427s tests/test_trr.py::test_get_velocities_and_forces PASSED [ 92%] 427s tests/test_trr.py::test_get_velocities_forces_atom_indices_1 PASSED [ 92%] 428s tests/test_trr.py::test_get_velocities_forces_atom_indices_2 PASSED [ 93%] 428s tests/test_trr.py::test_read_velocities_do_not_exist PASSED [ 93%] 428s tests/test_trr.py::test_read_forces_do_not_exist PASSED [ 93%] 428s tests/test_utils.py::test_unitcell_0 PASSED [ 93%] 428s tests/test_utils.py::test_unitcell_1 PASSED [ 93%] 428s tests/test_utils.py::test_ensure_type_1 PASSED [ 93%] 428s tests/test_utils.py::test_ensure_type_2 PASSED [ 93%] 428s tests/test_utils.py::test_ensure_type_25 PASSED [ 93%] 428s tests/test_utils.py::test_ensure_type_3 PASSED [ 93%] 428s tests/test_utils.py::test_ensure_type_4 PASSED [ 93%] 428s tests/test_utils.py::test_ensure_type_5 PASSED [ 93%] 428s tests/test_utils.py::test_ensure_type_6 PASSED [ 93%] 428s tests/test_utils.py::test_ensure_type_7 PASSED [ 94%] 428s tests/test_utils.py::test_ensure_type_8 PASSED [ 94%] 428s tests/test_utils.py::test_ensure_type_9 PASSED [ 94%] 428s tests/test_utils.py::test_ensure_type_10 PASSED [ 94%] 428s tests/test_utils.py::test_ensure_type_11 PASSED [ 94%] 428s tests/test_utils.py::test_ensure_type_12 PASSED [ 94%] 428s tests/test_utils.py::test_ensure_type_13 PASSED [ 94%] 428s tests/test_utils.py::test_ensure_type_14 PASSED [ 94%] 428s tests/test_utils.py::test_ensure_type_15 PASSED [ 94%] 428s tests/test_utils.py::test_delay_import_fail_1 PASSED [ 94%] 428s tests/test_utils.py::test_delay_import PASSED [ 94%] 428s tests/test_utils.py::test_unit_0 PASSED [ 95%] 428s tests/test_utils.py::test_unit_1 PASSED [ 95%] 428s tests/test_utils.py::test_unit_2 PASSED [ 95%] 428s tests/test_utils.py::test_unit_3 PASSED [ 95%] 428s tests/test_xml.py::test_xml PASSED [ 95%] 428s tests/test_xtc.py::test_read_chunk1 PASSED [ 95%] 428s tests/test_xtc.py::test_read_stride PASSED [ 95%] 428s tests/test_xtc.py::test_read_stride_n_frames PASSED [ 95%] 428s tests/test_xtc.py::test_read_stride_offsets PASSED [ 95%] 428s tests/test_xtc.py::test_read_stride_n_frames_offsets PASSED [ 95%] 428s tests/test_xtc.py::test_read_stride_switching_offsets PASSED [ 95%] 428s tests/test_xtc.py::test_read_atomindices_1 PASSED [ 96%] 428s tests/test_xtc.py::test_read_atomindices_w_stride PASSED [ 96%] 428s tests/test_xtc.py::test_read_atomindices_2 PASSED [ 96%] 428s tests/test_xtc.py::test_read_chunk2 PASSED [ 96%] 428s tests/test_xtc.py::test_read_chunk3 PASSED [ 96%] 428s tests/test_xtc.py::test_write_0 PASSED [ 96%] 428s tests/test_xtc.py::test_write_1 PASSED [ 96%] 428s tests/test_xtc.py::test_write_2 PASSED [ 96%] 428s tests/test_xtc.py::test_read_error_0 PASSED [ 96%] 428s tests/test_xtc.py::test_write_error_0 PASSED [ 96%] 428s tests/test_xtc.py::test_read_error_1 PASSED [ 96%] 428s tests/test_xtc.py::test_read_error_2 PASSED [ 96%] 428s tests/test_xtc.py::test_xtc_write_wierd_0 PASSED [ 97%] 428s tests/test_xtc.py::test_tell PASSED [ 97%] 428s tests/test_xtc.py::test_seek PASSED [ 97%] 428s tests/test_xtc.py::test_seek_natoms9 PASSED [ 97%] 428s tests/test_xtc.py::test_seek_out_of_bounds PASSED [ 97%] 428s tests/test_xtc.py::test_ragged_1 PASSED [ 97%] 428s tests/test_xtc.py::test_ragged_2 PASSED [ 97%] 428s tests/test_xtc.py::test_short_traj PASSED [ 97%] 428s tests/test_xtc.py::test_flush PASSED [ 97%] 428s tests/test_xyz.py::test_read_0 PASSED [ 97%] 428s tests/test_xyz.py::test_read_1 PASSED [ 97%] 428s tests/test_xyz.py::test_read_gz PASSED [ 98%] 428s tests/test_xyz.py::test_read_write PASSED [ 98%] 428s tests/test_xyz.py::test_mdwrite PASSED [ 98%] 428s tests/test_xyz.py::test_multiread PASSED [ 98%] 428s tests/test_xyz.py::test_seek PASSED [ 98%] 428s tests/test_xyz.py::test_len PASSED [ 98%] 428s tests/test_zipped.py::test_read_gz PASSED [ 98%] 428s tests/test_zipped.py::test_write_gz PASSED [ 98%] 428s tests/test_zipped.py::test_read_bz2 PASSED [ 98%] 428s tests/test_zipped.py::test_write_bz2 PASSED [ 98%] 430s examples/test_examples.py::test_example_notebook[iterload.ipynb] PASSED [ 98%] 433s examples/test_examples.py::test_example_notebook[principal-components.ipynb] PASSED [ 99%] 435s examples/test_examples.py::test_example_notebook[rmsd-drift.ipynb] PASSED [ 99%] 436s examples/test_examples.py::test_example_notebook[atom-selection.ipynb] PASSED [ 99%] 436s examples/test_examples.py::test_example_notebook[hbonds.ipynb] SKIPPED [ 99%] 438s examples/test_examples.py::test_example_notebook[solvent-accessible-surface-area.ipynb] PASSED [ 99%] 440s examples/test_examples.py::test_example_notebook[ramachandran-plot.ipynb] PASSED [ 99%] 442s examples/test_examples.py::test_example_notebook[clustering.ipynb] PASSED [ 99%] 444s examples/test_examples.py::test_example_notebook[two-pass-clustering.ipynb] PASSED [ 99%] 445s examples/test_examples.py::test_example_notebook[rmsd-benchmark.ipynb] PASSED [ 99%] 445s examples/test_examples.py::test_example_notebook[native-contact.ipynb] SKIPPED [ 99%] 447s examples/test_examples.py::test_example_notebook[centroids.ipynb] PASSED [ 99%] 447s examples/test_examples.py::test_example_notebook[simulation-with-openmm.ipynb] SKIPPED [100%] 447s 447s =============================== warnings summary =============================== 447s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:56 447s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:56: DeprecationWarning: Name.__init__ got an unexpected keyword argument 'SINGLETON'. Support for arbitrary keyword arguments is deprecated and will be removed in Python 3.15. 447s THIS_ATOM = ast.Name(id="atom", ctx=ast.Load(), SINGLETON=True) 447s 447s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:57 447s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:57: DeprecationWarning: Name.__init__ got an unexpected keyword argument 'SINGLETON'. Support for arbitrary keyword arguments is deprecated and will be removed in Python 3.15. 447s RE_MODULE = ast.Name(id="re", ctx=ast.Load(), SINGLETON=True) 447s 447s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 447s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 447s given by the platformdirs library. To remove this warning and 447s see the appropriate new directories, set the environment variable 447s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 447s The use of platformdirs will be the default in `jupyter_core` v6 447s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 447s 447s examples/test_examples.py:26 447s /tmp/autopkgtest.wJz48l/build.8P3/src/examples/test_examples.py:26: PytestUnknownMarkWarning: Unknown pytest.mark.flaky - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 447s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 447s 447s tests/test_contact.py::test_contact_0 447s tests/test_contact.py::test_contact_4 447s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:220: UserWarning: selected topology includes at least one glycine residue, which has no heavy atoms in its sidechain. The distances involving glycine residues will be computed using the sidechain hydrogen instead. 447s warnings.warn( 447s 447s tests/test_contact.py::test_contact_3 447s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:271: RuntimeWarning: overflow encountered in exp 447s np.exp( 447s 447s tests/test_contact.py::test_contact_3 447s /tmp/autopkgtest.wJz48l/build.8P3/src/tests/test_contact.py:115: RuntimeWarning: divide by zero encountered in scalar divide 447s beta / np.log(np.sum(np.exp(beta / maps[t, r0, r1]))), 447s 447s tests/test_dcd.py::test_do_overwrite 447s tests/test_dcd.py::test_ragged_1 447s tests/test_dcd.py::test_ragged_2 447s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting xyz dtype=float64 to 447s warnings.warn( 447s 447s tests/test_distance.py::test_6 447s :488: RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject 447s 447s tests/test_drid.py::test_drid_2 447s /tmp/autopkgtest.wJz48l/build.8P3/src/tests/test_drid.py:62: RuntimeWarning: divide by zero encountered in divide 447s recip = 1 / squareform(pdist(t.xyz[i])) 447s 447s tests/test_dssp.py::test_1[1vii.pdb] 447s tests/test_gro.py::test_read_write 447s tests/test_gro.py::test_read_write_precision 447s tests/test_gro.py::test_load 447s tests/test_shape.py::test_principal_moments 447s tests/test_shape.py::test_asphericity 447s tests/test_shape.py::test_shape_metrics 447s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:208: UserWarning: Unlikely unit cell vectors detected in PDB file likely resulting from a dummy CRYST1 record. Discarding unit cell vectors. 447s warnings.warn( 447s 447s tests/test_geometry.py::test_dihedral_indices 447s tests/test_geometry.py::test_dihedral_indices 447s /usr/lib/python3/dist-packages/mdtraj/geometry/dihedral.py:237: DeprecationWarning: Passing a Trajectory object to _atom_sequence isdeprecated. Please pass a Topology object 447s warnings.warn( 447s 447s tests/test_gro.py::test_load 447s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq 447s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:364: UserWarning: WARNING: two consecutive residues with same number (GST, HST) 447s warnings.warn( 447s 447s tests/test_pdb.py::test_blank_indexing 447s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:204: UserWarning: Need to guess atom number starting from atom 100000. 447s warnings.warn(f'Need to guess atom number {num_str} starting from atom {pdbstructure._next_atom_number}.') 447s 447s tests/test_pdb.py::test_blank_indexing 447s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:271: UserWarning: Need to guess residue number string starting from residue10000, atom 100000. 447s warnings.warn(f'Need to guess residue number string {num_str} starting from residue{pdbstructure._next_residue_number}, atom {pdbstructure._next_atom_number}.') 447s 447s tests/test_rdf.py::test_rdf_norm 447s tests/test_rdf.py::test_rdf_t_norm[0] 447s tests/test_rdf.py::test_rdf_t_norm[2] 447s tests/test_rdf.py::test_rdf_t_norm[4] 447s tests/test_selection.py::test_re 447s tests/test_selection.py::test_re 447s tests/test_topology.py::test_select_pairs 447s tests/test_topology.py::test_select_pairs 447s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:199: DeprecationWarning: Call.__init__ got an unexpected keyword argument 'starargs'. Support for arbitrary keyword arguments is deprecated and will be removed in Python 3.15. 447s left=ast.Call( 447s 447s tests/test_rdf.py::test_rdf_norm 447s tests/test_rdf.py::test_rdf_t_norm[0] 447s tests/test_rdf.py::test_rdf_t_norm[2] 447s tests/test_rdf.py::test_rdf_t_norm[4] 447s tests/test_selection.py::test_re 447s tests/test_selection.py::test_re 447s tests/test_topology.py::test_select_pairs 447s tests/test_topology.py::test_select_pairs 447s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:199: DeprecationWarning: Call.__init__ got an unexpected keyword argument 'kwargs'. Support for arbitrary keyword arguments is deprecated and will be removed in Python 3.15. 447s left=ast.Call( 447s 447s tests/test_trajectory.py::test_float_atom_indices_exception[gro] 447s tests/test_trajectory.py::test_atom_slicing 447s /usr/lib/python3/dist-packages/mdtraj/core/topology.py:84: UserWarning: atom_indices are not monotonically increasing 447s warnings.warn("atom_indices are not monotonically increasing") 447s 447s tests/test_utils.py::test_ensure_type_8 447s tests/test_utils.py::test_ensure_type_9 447s tests/test_utils.py::test_ensure_type_13 447s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=float64 to 447s warnings.warn( 447s 447s tests/test_utils.py::test_ensure_type_11 447s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=int64 to 447s warnings.warn( 447s 447s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 447s =========================== short test summary info ============================ 447s SKIPPED [1] tests/test_dihedral.py:56: pymol executable not found 447s SKIPPED [1] tests/test_dihedral.py:181: pymol executable not found 447s SKIPPED [16] tests/test_docstrings.py:38: Skip checking certain modules' docstrings 447s SKIPPED [1] tests/test_geometry.py:300: Not doing performance testing 447s SKIPPED [1] tests/test_geometry.py:322: Not doing performance testing 447s SKIPPED [1] tests/test_hdf5.py:104: requires openmm.units 447s SKIPPED [1] tests/test_hdf5.py:156: requires openmm.units 447s SKIPPED [1] tests/test_hdf5.py:223: requires openmm.units 447s SKIPPED [1] tests/test_mol2.py:59: Requires obabel 447s SKIPPED [1] tests/test_netcdf.py:271: This test requires cpptraj from AmberTools to be installed (http://ambermd.org) 447s SKIPPED [1] tests/test_nmr.py:11: SPARTA+ binary not found 447s SKIPPED [1] tests/test_nmr.py:26: PPM binary not found 447s SKIPPED [1] tests/test_nmr.py:42: SHIFTX2 binary not found or running on travis. 447s SKIPPED [1] tests/test_pdbx.py:43: test_pdbx.py needs OpenMM. 447s SKIPPED [2] tests/test_psf.py:93: This test requires the VMD executable: http://www.ks.uiuc.edu/Research/vmd/ 447s SKIPPED [1] tests/test_rdf.py:64: Binning does not match up with gromacs currently. 447s SKIPPED [1] tests/test_rdf.py:200: Binning does not match up with gromacs currently. 447s SKIPPED [1] tests/test_reporter.py:58: test_reporter.py needs OpenMM. 447s SKIPPED [1] tests/test_reporter.py:145: test_reporter.py needs OpenMM. 447s SKIPPED [1] tests/test_reporter.py:245: test_reporter.py needs OpenMM. 447s SKIPPED [1] tests/test_selection.py:267: failed to parse selection 447s SKIPPED [1] tests/test_thermodynamic_properties.py:161: Thermal expansion test doesn't work. 447s SKIPPED [1] tests/test_topology.py:45: needs OpenMM 447s SKIPPED [1] tests/test_topology.py:62: needs OpenMM 447s SKIPPED [1] tests/test_topology.py:72: needs OpenMM 447s SKIPPED [1] tests/test_topology.py:81: needs OpenMM 447s SKIPPED [1] tests/test_topology.py:91: needs OpenMM 447s SKIPPED [1] tests/test_topology.py:97: needs OpenMM 447s SKIPPED [1] tests/test_topology.py:247: needs OpenMM 447s SKIPPED [1] tests/test_trajectory.py:129: xyz does not store box information 447s SKIPPED [1] tests/test_trajectory.py:129: xyz.gz does not store box information 447s SKIPPED [1] tests/test_trajectory.py:129: lh5 does not store box information 447s SKIPPED [1] tests/test_trajectory.py:129: pdb does not store box information 447s SKIPPED [1] tests/test_trajectory.py:129: pdb.gz does not store box information 447s SKIPPED [1] tests/test_trajectory.py:226: mdcrd can only store rectilinear boxes 447s SKIPPED [1] tests/test_trajectory.py:224: ncrst can only store 1 frame per file 447s SKIPPED [1] tests/test_trajectory.py:224: rst7 can only store 1 frame per file 447s SKIPPED [14] tests/test_trajectory.py:248: mdcrd can only store rectilinear boxes 447s SKIPPED [14] tests/test_trajectory.py:246: ncrst can only store 1 frame per file 447s SKIPPED [14] tests/test_trajectory.py:246: rst7 can only store 1 frame per file 447s SKIPPED [4] tests/test_trajectory.py:256: dtr needs to write unitcells 447s SKIPPED [4] tests/test_trajectory.py:256: lammpstrj needs to write unitcells 447s SKIPPED [2] tests/test_trajectory.py:640: Only 1 frame per file format 447s SKIPPED [2] examples/test_examples.py:77: Network access required 447s SKIPPED [1] examples/test_examples.py:77: Openmm required for example notebook `simulation-with-openmm.ipynb` 447s XFAIL tests/test_trajectory.py::test_read_path[ncrst] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_path[rst7] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[ncrst-nc] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[ncrst-h5] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xtc] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[ncrst-trr] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dcd] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[ncrst-mdcrd] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dtr] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lh5] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[ncrst-ncrst] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[ncrst-rst7] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[ncrst-gro] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[rst7-nc] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[rst7-h5] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[rst7-xtc] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[rst7-trr] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[rst7-dcd] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[rst7-mdcrd] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[rst7-dtr] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz.gz] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[rst7-lammpstrj] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[rst7-lh5] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb.gz] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[rst7-ncrst] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[rst7-rst7] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_read_write[rst7-gro] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_load[ncrst] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_load[rst7] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[rst7] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_load_combination[ncrst] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_load_combination[rst7] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_seek_read_mode[xyz.gz] - reason: This is broken 447s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb] - reason: PDB Files don't support seeking 447s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb.gz] - reason: PDB Files don't support seeking 447s XFAIL tests/test_trajectory.py::test_seek_read_mode[ncrst] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_seek_read_mode[rst7] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_seek_read_mode[gro] - reason: This is broken 447s XFAIL tests/test_trajectory.py::test_load_frame[dtr] - reason: DTR doesn't load a single frame properly 447s XFAIL tests/test_trajectory.py::test_load_frame[ncrst] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_load_frame[rst7] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_load_frame[gro] - reason: Gro doesn't implement seek 447s XFAIL tests/test_trajectory.py::test_iterload[dtr] - reason: This is broken with dtr 447s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb] - reason: PDB Iterloads an extra frame!! 447s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb.gz] - reason: PDB Iterloads an extra frame!! 447s XFAIL tests/test_trajectory.py::test_iterload_skip[ncrst] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_iterload_skip[rst7] - reason: These reference files don't exist yet 447s XFAIL tests/test_trajectory.py::test_iterload_skip[gro] - reason: Not implemented for some reason 447s XFAIL tests/test_trajectory.py::test_force_overwrite[dtr] - reason: This is broken with dtr 447s XFAIL tests/test_trajectory.py::test_unitcell[dtr] - reason: dtr seems to need unit vectors 447s XFAIL tests/test_trajectory.py::test_unitcell[lammpstrj] - reason: lammpstrj seems to need unit vectors 447s XFAIL tests/test_trajectory.py::test_unitcell[ncrst] - reason: ncrst seems to need unit vectors 447s XFAIL tests/test_trajectory.py::test_unitcell[rst7] - reason: rst7 seems to need unit vectors 447s = 964 passed, 108 skipped, 12 deselected, 61 xfailed, 48 warnings in 263.21s (0:04:23) = 448s autopkgtest [02:00:39]: test command1: -----------------------] 448s command1 PASS 448s autopkgtest [02:00:39]: test command1: - - - - - - - - - - results - - - - - - - - - - 449s autopkgtest [02:00:40]: test command2: preparing testbed 449s Reading package lists... 449s Building dependency tree... 449s Reading state information... 449s Starting pkgProblemResolver with broken count: 0 450s Starting 2 pkgProblemResolver with broken count: 0 450s Done 450s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 451s autopkgtest [02:00:42]: test command2: pytest-3 -k 'test_3 or test_pdb_from_url or test_1vii_url_and_gz' 451s autopkgtest [02:00:42]: test command2: [----------------------- 452s ============================= test session starts ============================== 452s platform linux -- Python 3.13.2, pytest-8.3.5, pluggy-1.5.0 -- /usr/bin/python3 452s cachedir: .pytest_cache 452s rootdir: /tmp/autopkgtest.wJz48l/build.8P3/src 452s configfile: pyproject.toml 452s testpaths: tests, examples 452s plugins: typeguard-4.4.2 453s collecting ... collected 1145 items / 1135 deselected / 10 selected 453s 453s tests/test_distance.py::test_3 PASSED [ 10%] 453s tests/test_distance.py::test_3p PASSED [ 20%] 455s tests/test_dssp.py::test_3[1GAI] PASSED [ 30%] 457s tests/test_dssp.py::test_3[6gsv] PASSED [ 40%] 458s tests/test_dssp.py::test_3[2AAC] PASSED [ 50%] 458s tests/test_nmr.py::test_3_scalar_couplings PASSED [ 60%] 464s tests/test_pdb.py::test_pdb_from_url PASSED [ 70%] 465s tests/test_pdb.py::test_3nch_conect PASSED [ 80%] 466s tests/test_pdb.py::test_3nch_serial_resSeq PASSED [ 90%] 470s tests/test_pdb.py::test_1vii_url_and_gz PASSED [100%] 470s 470s =============================== warnings summary =============================== 470s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:56 470s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:56: DeprecationWarning: Name.__init__ got an unexpected keyword argument 'SINGLETON'. Support for arbitrary keyword arguments is deprecated and will be removed in Python 3.15. 470s THIS_ATOM = ast.Name(id="atom", ctx=ast.Load(), SINGLETON=True) 470s 470s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:57 470s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:57: DeprecationWarning: Name.__init__ got an unexpected keyword argument 'SINGLETON'. Support for arbitrary keyword arguments is deprecated and will be removed in Python 3.15. 470s RE_MODULE = ast.Name(id="re", ctx=ast.Load(), SINGLETON=True) 470s 470s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 470s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 470s given by the platformdirs library. To remove this warning and 470s see the appropriate new directories, set the environment variable 470s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 470s The use of platformdirs will be the default in `jupyter_core` v6 470s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 470s 470s examples/test_examples.py:26 470s /tmp/autopkgtest.wJz48l/build.8P3/src/examples/test_examples.py:26: PytestUnknownMarkWarning: Unknown pytest.mark.flaky - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 470s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 470s 470s tests/test_pdb.py::test_1vii_url_and_gz 470s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:208: UserWarning: Unlikely unit cell vectors detected in PDB file likely resulting from a dummy CRYST1 record. Discarding unit cell vectors. 470s warnings.warn( 470s 470s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 470s =============== 10 passed, 1135 deselected, 5 warnings in 17.73s =============== 470s autopkgtest [02:01:01]: test command2: -----------------------] 471s autopkgtest [02:01:02]: test command2: - - - - - - - - - - results - - - - - - - - - - 471s command2 PASS 471s autopkgtest [02:01:02]: @@@@@@@@@@@@@@@@@@@@ summary 471s command1 PASS 471s command2 PASS 476s nova [W] Using flock in prodstack6-arm64 476s Creating nova instance adt-plucky-arm64-mdtraj-20250316-012700-juju-7f2275-prod-proposed-migration-environment-20-ab98cc85-a8b9-4abc-9da3-15a25841cc81 from image adt/ubuntu-plucky-arm64-server-20250316.img (UUID 08b37ce2-d71b-4e08-a72e-06f281931f28)... 476s nova [W] Timed out waiting for 646b7002-9e64-47bb-9898-778e412d0595 to get deleted.