0s autopkgtest [03:06:07]: starting date and time: 2025-02-19 03:06:07+0000 0s autopkgtest [03:06:07]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [03:06:07]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.yub5jlsn/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python-gsd --apt-upgrade mdtraj --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python-gsd/3.4.2-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-11.secgroup --name adt-plucky-amd64-mdtraj-20250219-030606-juju-7f2275-prod-proposed-migration-environment-2-1a1ceb4d-f089-4ffe-8fcc-118bd609ccec --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -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/ 104s autopkgtest [03:07:51]: testbed dpkg architecture: amd64 104s autopkgtest [03:07:51]: testbed apt version: 2.9.29 104s autopkgtest [03:07:51]: @@@@@@@@@@@@@@@@@@@@ test bed setup 104s autopkgtest [03:07:51]: testbed release detected to be: None 105s autopkgtest [03:07:52]: updating testbed package index (apt update) 106s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 106s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 106s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 106s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 106s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.6 kB] 106s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [79.1 kB] 106s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 106s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [788 kB] 107s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [106 kB] 107s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [84.0 kB] 107s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [7984 B] 107s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2412 B] 107s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [712 kB] 107s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [271 kB] 107s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [12.4 kB] 107s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3440 B] 108s Fetched 2194 kB in 2s (1159 kB/s) 108s Reading package lists... 109s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s Calculating upgrade... 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s autopkgtest [03:07:57]: upgrading testbed (apt dist-upgrade and autopurge) 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 111s Starting 2 pkgProblemResolver with broken count: 0 111s Done 111s Entering ResolveByKeep 112s 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s Starting pkgProblemResolver with broken count: 0 112s Starting 2 pkgProblemResolver with broken count: 0 112s Done 113s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s autopkgtest [03:08:03]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 16:02:16 UTC 2025 117s autopkgtest [03:08:04]: @@@@@@@@@@@@@@@@@@@@ apt-source mdtraj 123s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.3-2 (dsc) [2677 B] 123s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.3-2 (tar) [22.0 MB] 123s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.3-2 (diff) [300 kB] 123s gpgv: Signature made Tue Feb 11 15:16:54 2025 UTC 123s gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA 123s gpgv: Can't check signature: No public key 123s dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.10.3-2.dsc: no acceptable signature found 124s autopkgtest [03:08:11]: testing package mdtraj version 1.10.3-2 126s autopkgtest [03:08:13]: build not needed 131s autopkgtest [03:08:18]: test command1: preparing testbed 131s Reading package lists... 131s Building dependency tree... 131s Reading state information... 132s Starting pkgProblemResolver with broken count: 0 132s Starting 2 pkgProblemResolver with broken count: 0 132s Done 132s The following NEW packages will be installed: 132s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx gdb 132s libaec0 libbabeltrace1 libblas3 libblosc1 libblosc2-4 libdebuginfod-common 132s libdebuginfod1t64 libdeflate0 libfontconfig1 libgfortran5 libgomp1 132s libgraphite2-3 libharfbuzz0b libhdf5-310 libhdf5-hl-310 libimagequant0 132s libipt2 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 132s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libnetcdf22 libnorm1t64 132s libopenjp2-7 libpgm-5.3-0t64 libqhull-r8.0 libraqm0 libsharpyuv0 132s libsnappy1v5 libsodium23 libsource-highlight-common libsource-highlight4t64 132s libsz2 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 132s libxft2 libxrender1 libxslt1.1 libxss1 libzmq5 python-matplotlib-data 132s python-tables-data python3-asttokens python3-brotli python3-cftime 132s python3-comm python3-contourpy python3-coverage python3-cpuinfo 132s python3-cycler python3-dateutil python3-debugpy python3-decorator 132s python3-executing python3-fastjsonschema python3-fonttools python3-fs 132s python3-gsd python3-iniconfig python3-ipykernel python3-ipython python3-jedi 132s python3-joblib python3-jupyter-client python3-jupyter-core 132s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 132s python3-matplotlib-inline python3-mdtraj python3-mpmath python3-nbformat 132s python3-nest-asyncio python3-netcdf4 python3-networkx python3-numexpr 132s python3-numpy python3-packaging python3-pandas python3-pandas-lib 132s python3-parso python3-pexpect python3-pil python3-pil.imagetk 132s python3-platformdirs python3-pluggy python3-prompt-toolkit python3-psutil 132s python3-ptyprocess python3-pure-eval python3-pytest python3-pytz 132s python3-scipy python3-sklearn python3-sklearn-lib python3-stack-data 132s python3-sympy python3-tables python3-tables-lib python3-threadpoolctl 132s python3-tk python3-tornado python3-traitlets python3-typeshed python3-tz 132s python3-ufolib2 python3-unicodedata2 python3-wcwidth python3-zmq python3.12 132s python3.12-minimal python3.12-tk python3.13-tk tk8.6-blt2.5 unicode-data 132s x11-common 132s 0 upgraded, 132 newly installed, 0 to remove and 0 not upgraded. 132s Need to get 125 MB of archives. 132s After this operation, 663 MB of additional disk space will be used. 132s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-minimal amd64 3.12.9-1 [2348 kB] 133s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 133s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12 amd64 3.12.9-1 [671 kB] 133s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 133s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 133s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 133s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 133s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 133s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 133s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 133s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 133s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 133s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 134s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 134s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 134s Get:16 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.3-1 [171 kB] 134s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libbabeltrace1 amd64 1.5.11-4build1 [185 kB] 134s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 134s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libipt2 amd64 2.1.2-1 [58.9 kB] 134s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libsource-highlight-common all 3.1.9-4.3build1 [64.2 kB] 134s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libsource-highlight4t64 amd64 3.1.9-4.3build1 [258 kB] 134s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 gdb amd64 16.2-1ubuntu1 [8934 kB] 134s Get:23 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 134s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 134s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libsnappy1v5 amd64 1.2.1-1 [30.4 kB] 134s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 libblosc1 amd64 1.21.5+ds-1build1 [36.2 kB] 134s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 libblosc2-4 amd64 2.16.0+ds-1 [171 kB] 134s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 134s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250213-1ubuntu1 [920 kB] 134s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250213-1ubuntu1 [148 kB] 134s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 134s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 134s Get:33 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 134s Get:34 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-310 amd64 1.14.5+repack-3 [1519 kB] 134s Get:35 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [62.6 kB] 134s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 134s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 134s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 134s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 134s Get:40 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 134s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 135s Get:42 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 135s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 135s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 135s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnetcdf22 amd64 1:4.9.3-1 [574 kB] 135s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnorm1t64 amd64 1.5.9+dfsg-3.1build1 [154 kB] 135s Get:47 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpgm-5.3-0t64 amd64 5.3.128~dfsg-2.1build1 [167 kB] 135s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 135s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 135s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 135s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libsodium23 amd64 1.0.18-1build3 [161 kB] 135s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 135s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 135s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 135s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 135s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 135s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu2 [175 kB] 135s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 libzmq5 amd64 4.3.5-1build2 [260 kB] 135s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3ubuntu2 [2929 kB] 135s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-tables-data all 3.10.2-2 [49.6 kB] 135s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-asttokens all 3.0.0-1 [20.4 kB] 135s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build3 [368 kB] 135s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-13 [5319 kB] 135s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cftime amd64 1.6.4-1build2 [346 kB] 135s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 135s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-comm all 0.2.1-1 [7016 B] 135s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.1-1 [271 kB] 135s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-coverage amd64 7.4.4+dfsg1-0ubuntu3 [150 kB] 135s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cpuinfo all 9.0.0+git20221119-3 [21.7 kB] 135s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 135s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB] 135s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-debugpy amd64 1.8.8+ds-2ubuntu1 [1145 kB] 135s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 135s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-executing all 2.2.0-0.1 [25.0 kB] 135s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fastjsonschema all 2.21.1-1 [20.4 kB] 135s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pytz all 2025.1-3 [162 kB] 135s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2025.1-3 [1866 B] 135s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-platformdirs all 4.3.6-1 [16.8 kB] 135s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-6 [90.7 kB] 135s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.1-1 [1831 kB] 135s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.4.0+dfsg-1 [27.4 kB] 135s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.14.1-4ubuntu1 [22.3 MB] 136s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 136s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 136s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 136s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build2 [360 kB] 136s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 136s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.55.3-2 [1755 kB] 136s Get:89 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-gsd amd64 3.4.2-2 [242 kB] 136s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 136s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-parso all 0.8.4-1 [67.6 kB] 136s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-typeshed all 0.0~git20241223.ea91db2-1 [1548 kB] 136s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-jedi all 0.19.1+ds1-1 [693 kB] 136s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 136s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 136s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-prompt-toolkit all 3.0.50-1 [257 kB] 136s Get:97 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pure-eval all 0.2.3-1 [11.4 kB] 136s Get:98 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-stack-data all 0.6.3-1 [22.0 kB] 136s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-ptyprocess all 0.7.0-6 [14.8 kB] 136s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pexpect all 4.9-3 [48.1 kB] 136s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ipython all 8.30.0-2 [569 kB] 137s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-jupyter-core all 5.7.2-5 [28.1 kB] 137s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-psutil amd64 5.9.8-2build3 [196 kB] 137s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tornado amd64 6.4.2-1 [299 kB] 137s Get:105 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-zmq amd64 26.2.1-1 [226 kB] 137s Get:106 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-jupyter-client all 8.6.3-2 [78.5 kB] 137s Get:107 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-nest-asyncio all 1.5.4-1 [6256 B] 137s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 137s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ipykernel all 6.29.5-2 [82.7 kB] 137s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.4.2-2 [205 kB] 137s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-3 [70.4 kB] 137s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu3 [217 kB] 137s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 11.1.0-5 [589 kB] 137s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.9-1 [116 kB] 137s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.2-1 [107 kB] 137s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.13.1-1 [9770 B] 137s Get:117 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 11.1.0-5 [9936 B] 137s Get:118 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3ubuntu2 [4697 kB] 137s Get:119 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-netcdf4 amd64 1.7.2-1build3 [942 kB] 137s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 138s Get:121 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-8 [8248 kB] 138s Get:122 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-8 [3112 kB] 138s Get:123 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-numexpr amd64 2.10.2-1build1 [133 kB] 138s Get:124 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-tables-lib amd64 3.10.2-2 [859 kB] 138s Get:125 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-tables all 3.10.2-2 [354 kB] 138s Get:126 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mdtraj amd64 1.10.3-2 [1629 kB] 138s Get:127 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-nbformat all 5.9.1-1 [41.2 kB] 138s Get:128 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 138s Get:129 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.4-1 [252 kB] 138s Get:130 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 138s Get:131 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-7build1 [6872 kB] 139s Get:132 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn all 1.4.2+dfsg-7build1 [2258 kB] 139s Preconfiguring packages ... 139s Fetched 125 MB in 7s (19.1 MB/s) 139s Selecting previously unselected package python3.12-minimal. 139s (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 ... 108925 files and directories currently installed.) 139s Preparing to unpack .../000-python3.12-minimal_3.12.9-1_amd64.deb ... 139s Unpacking python3.12-minimal (3.12.9-1) ... 140s Selecting previously unselected package libdebuginfod-common. 140s Preparing to unpack .../001-libdebuginfod-common_0.192-4_all.deb ... 140s Unpacking libdebuginfod-common (0.192-4) ... 140s Selecting previously unselected package python3.12. 140s Preparing to unpack .../002-python3.12_3.12.9-1_amd64.deb ... 140s Unpacking python3.12 (3.12.9-1) ... 140s Selecting previously unselected package libtcl8.6:amd64. 140s Preparing to unpack .../003-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 140s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 140s Selecting previously unselected package fonts-dejavu-mono. 140s Preparing to unpack .../004-fonts-dejavu-mono_2.37-8_all.deb ... 140s Unpacking fonts-dejavu-mono (2.37-8) ... 140s Selecting previously unselected package fonts-dejavu-core. 140s Preparing to unpack .../005-fonts-dejavu-core_2.37-8_all.deb ... 140s Unpacking fonts-dejavu-core (2.37-8) ... 140s Selecting previously unselected package fontconfig-config. 140s Preparing to unpack .../006-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 140s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 140s Selecting previously unselected package libfontconfig1:amd64. 140s Preparing to unpack .../007-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 140s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 140s Selecting previously unselected package libxrender1:amd64. 140s Preparing to unpack .../008-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 140s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 140s Selecting previously unselected package libxft2:amd64. 140s Preparing to unpack .../009-libxft2_2.3.6-1build1_amd64.deb ... 140s Unpacking libxft2:amd64 (2.3.6-1build1) ... 140s Selecting previously unselected package x11-common. 140s Preparing to unpack .../010-x11-common_1%3a7.7+23ubuntu3_all.deb ... 140s Unpacking x11-common (1:7.7+23ubuntu3) ... 140s Selecting previously unselected package libxss1:amd64. 140s Preparing to unpack .../011-libxss1_1%3a1.2.3-1build3_amd64.deb ... 140s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 140s Selecting previously unselected package libtk8.6:amd64. 140s Preparing to unpack .../012-libtk8.6_8.6.16-1_amd64.deb ... 140s Unpacking libtk8.6:amd64 (8.6.16-1) ... 140s Selecting previously unselected package tk8.6-blt2.5. 140s Preparing to unpack .../013-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 140s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 140s Selecting previously unselected package blt. 140s Preparing to unpack .../014-blt_2.5.3+dfsg-7build1_amd64.deb ... 140s Unpacking blt (2.5.3+dfsg-7build1) ... 140s Selecting previously unselected package fonts-lyx. 140s Preparing to unpack .../015-fonts-lyx_2.4.3-1_all.deb ... 140s Unpacking fonts-lyx (2.4.3-1) ... 140s Selecting previously unselected package libbabeltrace1:amd64. 140s Preparing to unpack .../016-libbabeltrace1_1.5.11-4build1_amd64.deb ... 140s Unpacking libbabeltrace1:amd64 (1.5.11-4build1) ... 140s Selecting previously unselected package libdebuginfod1t64:amd64. 140s Preparing to unpack .../017-libdebuginfod1t64_0.192-4_amd64.deb ... 140s Unpacking libdebuginfod1t64:amd64 (0.192-4) ... 141s Selecting previously unselected package libipt2. 141s Preparing to unpack .../018-libipt2_2.1.2-1_amd64.deb ... 141s Unpacking libipt2 (2.1.2-1) ... 141s Selecting previously unselected package libsource-highlight-common. 141s Preparing to unpack .../019-libsource-highlight-common_3.1.9-4.3build1_all.deb ... 141s Unpacking libsource-highlight-common (3.1.9-4.3build1) ... 141s Selecting previously unselected package libsource-highlight4t64:amd64. 141s Preparing to unpack .../020-libsource-highlight4t64_3.1.9-4.3build1_amd64.deb ... 141s Unpacking libsource-highlight4t64:amd64 (3.1.9-4.3build1) ... 141s Selecting previously unselected package gdb. 141s Preparing to unpack .../021-gdb_16.2-1ubuntu1_amd64.deb ... 141s Unpacking gdb (16.2-1ubuntu1) ... 141s Selecting previously unselected package libaec0:amd64. 141s Preparing to unpack .../022-libaec0_1.1.3-1_amd64.deb ... 141s Unpacking libaec0:amd64 (1.1.3-1) ... 141s Selecting previously unselected package libblas3:amd64. 141s Preparing to unpack .../023-libblas3_3.12.1-2_amd64.deb ... 141s Unpacking libblas3:amd64 (3.12.1-2) ... 141s Selecting previously unselected package libsnappy1v5:amd64. 141s Preparing to unpack .../024-libsnappy1v5_1.2.1-1_amd64.deb ... 141s Unpacking libsnappy1v5:amd64 (1.2.1-1) ... 141s Selecting previously unselected package libblosc1:amd64. 141s Preparing to unpack .../025-libblosc1_1.21.5+ds-1build1_amd64.deb ... 141s Unpacking libblosc1:amd64 (1.21.5+ds-1build1) ... 141s Selecting previously unselected package libblosc2-4:amd64. 141s Preparing to unpack .../026-libblosc2-4_2.16.0+ds-1_amd64.deb ... 141s Unpacking libblosc2-4:amd64 (2.16.0+ds-1) ... 141s Selecting previously unselected package libdeflate0:amd64. 141s Preparing to unpack .../027-libdeflate0_1.23-1_amd64.deb ... 141s Unpacking libdeflate0:amd64 (1.23-1) ... 141s Selecting previously unselected package libgfortran5:amd64. 141s Preparing to unpack .../028-libgfortran5_15-20250213-1ubuntu1_amd64.deb ... 141s Unpacking libgfortran5:amd64 (15-20250213-1ubuntu1) ... 141s Selecting previously unselected package libgomp1:amd64. 141s Preparing to unpack .../029-libgomp1_15-20250213-1ubuntu1_amd64.deb ... 141s Unpacking libgomp1:amd64 (15-20250213-1ubuntu1) ... 141s Selecting previously unselected package libgraphite2-3:amd64. 141s Preparing to unpack .../030-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 141s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 141s Selecting previously unselected package libharfbuzz0b:amd64. 141s Preparing to unpack .../031-libharfbuzz0b_10.2.0-1_amd64.deb ... 141s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 141s Selecting previously unselected package libsz2:amd64. 141s Preparing to unpack .../032-libsz2_1.1.3-1_amd64.deb ... 141s Unpacking libsz2:amd64 (1.1.3-1) ... 141s Selecting previously unselected package libhdf5-310:amd64. 141s Preparing to unpack .../033-libhdf5-310_1.14.5+repack-3_amd64.deb ... 141s Unpacking libhdf5-310:amd64 (1.14.5+repack-3) ... 141s Selecting previously unselected package libhdf5-hl-310:amd64. 141s Preparing to unpack .../034-libhdf5-hl-310_1.14.5+repack-3_amd64.deb ... 141s Unpacking libhdf5-hl-310:amd64 (1.14.5+repack-3) ... 141s Selecting previously unselected package libimagequant0:amd64. 141s Preparing to unpack .../035-libimagequant0_2.18.0-1build1_amd64.deb ... 141s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 141s Selecting previously unselected package libjpeg-turbo8:amd64. 141s Preparing to unpack .../036-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 141s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 141s Selecting previously unselected package libjpeg8:amd64. 141s Preparing to unpack .../037-libjpeg8_8c-2ubuntu11_amd64.deb ... 141s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 141s Selecting previously unselected package libjs-jquery. 141s Preparing to unpack .../038-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 141s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 142s Selecting previously unselected package libjs-jquery-ui. 142s Preparing to unpack .../039-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 142s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 142s Selecting previously unselected package liblapack3:amd64. 142s Preparing to unpack .../040-liblapack3_3.12.1-2_amd64.deb ... 142s Unpacking liblapack3:amd64 (3.12.1-2) ... 142s Selecting previously unselected package liblbfgsb0:amd64. 142s Preparing to unpack .../041-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 142s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 142s Selecting previously unselected package liblcms2-2:amd64. 142s Preparing to unpack .../042-liblcms2-2_2.16-2_amd64.deb ... 142s Unpacking liblcms2-2:amd64 (2.16-2) ... 142s Selecting previously unselected package liblerc4:amd64. 142s Preparing to unpack .../043-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 142s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 142s Selecting previously unselected package libnetcdf22:amd64. 142s Preparing to unpack .../044-libnetcdf22_1%3a4.9.3-1_amd64.deb ... 142s Unpacking libnetcdf22:amd64 (1:4.9.3-1) ... 142s Selecting previously unselected package libnorm1t64:amd64. 142s Preparing to unpack .../045-libnorm1t64_1.5.9+dfsg-3.1build1_amd64.deb ... 142s Unpacking libnorm1t64:amd64 (1.5.9+dfsg-3.1build1) ... 142s Selecting previously unselected package libpgm-5.3-0t64:amd64. 142s Preparing to unpack .../046-libpgm-5.3-0t64_5.3.128~dfsg-2.1build1_amd64.deb ... 142s Unpacking libpgm-5.3-0t64:amd64 (5.3.128~dfsg-2.1build1) ... 142s Selecting previously unselected package libqhull-r8.0:amd64. 142s Preparing to unpack .../047-libqhull-r8.0_2020.2-6build1_amd64.deb ... 142s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 142s Selecting previously unselected package libraqm0:amd64. 142s Preparing to unpack .../048-libraqm0_0.10.2-1_amd64.deb ... 142s Unpacking libraqm0:amd64 (0.10.2-1) ... 142s Selecting previously unselected package libsharpyuv0:amd64. 142s Preparing to unpack .../049-libsharpyuv0_1.5.0-0.1_amd64.deb ... 142s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 142s Selecting previously unselected package libsodium23:amd64. 142s Preparing to unpack .../050-libsodium23_1.0.18-1build3_amd64.deb ... 142s Unpacking libsodium23:amd64 (1.0.18-1build3) ... 142s Selecting previously unselected package libjbig0:amd64. 142s Preparing to unpack .../051-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 142s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 142s Selecting previously unselected package libwebp7:amd64. 142s Preparing to unpack .../052-libwebp7_1.5.0-0.1_amd64.deb ... 142s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 142s Selecting previously unselected package libtiff6:amd64. 142s Preparing to unpack .../053-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 142s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 142s Selecting previously unselected package libwebpdemux2:amd64. 142s Preparing to unpack .../054-libwebpdemux2_1.5.0-0.1_amd64.deb ... 142s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 142s Selecting previously unselected package libwebpmux3:amd64. 142s Preparing to unpack .../055-libwebpmux3_1.5.0-0.1_amd64.deb ... 142s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 142s Selecting previously unselected package libxslt1.1:amd64. 142s Preparing to unpack .../056-libxslt1.1_1.1.39-0exp1ubuntu2_amd64.deb ... 142s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu2) ... 142s Selecting previously unselected package libzmq5:amd64. 142s Preparing to unpack .../057-libzmq5_4.3.5-1build2_amd64.deb ... 142s Unpacking libzmq5:amd64 (4.3.5-1build2) ... 142s Selecting previously unselected package python-matplotlib-data. 142s Preparing to unpack .../058-python-matplotlib-data_3.8.3-3ubuntu2_all.deb ... 142s Unpacking python-matplotlib-data (3.8.3-3ubuntu2) ... 142s Selecting previously unselected package python-tables-data. 142s Preparing to unpack .../059-python-tables-data_3.10.2-2_all.deb ... 142s Unpacking python-tables-data (3.10.2-2) ... 142s Selecting previously unselected package python3-asttokens. 142s Preparing to unpack .../060-python3-asttokens_3.0.0-1_all.deb ... 142s Unpacking python3-asttokens (3.0.0-1) ... 142s Selecting previously unselected package python3-brotli. 142s Preparing to unpack .../061-python3-brotli_1.1.0-2build3_amd64.deb ... 142s Unpacking python3-brotli (1.1.0-2build3) ... 143s Selecting previously unselected package python3-numpy. 143s Preparing to unpack .../062-python3-numpy_1%3a1.26.4+ds-13_amd64.deb ... 143s Unpacking python3-numpy (1:1.26.4+ds-13) ... 143s Selecting previously unselected package python3-cftime. 143s Preparing to unpack .../063-python3-cftime_1.6.4-1build2_amd64.deb ... 143s Unpacking python3-cftime (1.6.4-1build2) ... 143s Selecting previously unselected package python3-traitlets. 143s Preparing to unpack .../064-python3-traitlets_5.14.3+really5.14.3-1_all.deb ... 143s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ... 143s Selecting previously unselected package python3-comm. 143s Preparing to unpack .../065-python3-comm_0.2.1-1_all.deb ... 143s Unpacking python3-comm (0.2.1-1) ... 143s Selecting previously unselected package python3-contourpy. 143s Preparing to unpack .../066-python3-contourpy_1.3.1-1_amd64.deb ... 143s Unpacking python3-contourpy (1.3.1-1) ... 143s Selecting previously unselected package python3-coverage. 143s Preparing to unpack .../067-python3-coverage_7.4.4+dfsg1-0ubuntu3_amd64.deb ... 143s Unpacking python3-coverage (7.4.4+dfsg1-0ubuntu3) ... 143s Selecting previously unselected package python3-cpuinfo. 143s Preparing to unpack .../068-python3-cpuinfo_9.0.0+git20221119-3_all.deb ... 143s Unpacking python3-cpuinfo (9.0.0+git20221119-3) ... 143s Selecting previously unselected package python3-cycler. 143s Preparing to unpack .../069-python3-cycler_0.12.1-1_all.deb ... 143s Unpacking python3-cycler (0.12.1-1) ... 143s Selecting previously unselected package python3-dateutil. 143s Preparing to unpack .../070-python3-dateutil_2.9.0-3_all.deb ... 143s Unpacking python3-dateutil (2.9.0-3) ... 143s Selecting previously unselected package python3-debugpy. 143s Preparing to unpack .../071-python3-debugpy_1.8.8+ds-2ubuntu1_amd64.deb ... 143s Unpacking python3-debugpy (1.8.8+ds-2ubuntu1) ... 143s Selecting previously unselected package python3-decorator. 143s Preparing to unpack .../072-python3-decorator_5.1.1-5_all.deb ... 143s Unpacking python3-decorator (5.1.1-5) ... 143s Selecting previously unselected package python3-executing. 143s Preparing to unpack .../073-python3-executing_2.2.0-0.1_all.deb ... 143s Unpacking python3-executing (2.2.0-0.1) ... 143s Selecting previously unselected package python3-fastjsonschema. 143s Preparing to unpack .../074-python3-fastjsonschema_2.21.1-1_all.deb ... 143s Unpacking python3-fastjsonschema (2.21.1-1) ... 143s Selecting previously unselected package python3-pytz. 143s Preparing to unpack .../075-python3-pytz_2025.1-3_all.deb ... 143s Unpacking python3-pytz (2025.1-3) ... 143s Selecting previously unselected package python3-tz. 143s Preparing to unpack .../076-python3-tz_2025.1-3_all.deb ... 143s Unpacking python3-tz (2025.1-3) ... 143s Selecting previously unselected package python3-platformdirs. 143s Preparing to unpack .../077-python3-platformdirs_4.3.6-1_all.deb ... 143s Unpacking python3-platformdirs (4.3.6-1) ... 143s Selecting previously unselected package python3-fs. 143s Preparing to unpack .../078-python3-fs_2.4.16-6_all.deb ... 143s Unpacking python3-fs (2.4.16-6) ... 143s Selecting previously unselected package python3-lxml:amd64. 143s Preparing to unpack .../079-python3-lxml_5.3.1-1_amd64.deb ... 143s Unpacking python3-lxml:amd64 (5.3.1-1) ... 143s Selecting previously unselected package python3-lz4. 143s Preparing to unpack .../080-python3-lz4_4.4.0+dfsg-1_amd64.deb ... 143s Unpacking python3-lz4 (4.4.0+dfsg-1) ... 143s Selecting previously unselected package python3-scipy. 144s Preparing to unpack .../081-python3-scipy_1.14.1-4ubuntu1_amd64.deb ... 144s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 144s Selecting previously unselected package python3-mpmath. 144s Preparing to unpack .../082-python3-mpmath_1.3.0-1_all.deb ... 144s Unpacking python3-mpmath (1.3.0-1) ... 144s Selecting previously unselected package python3-sympy. 144s Preparing to unpack .../083-python3-sympy_1.13.3-1_all.deb ... 144s Unpacking python3-sympy (1.13.3-1) ... 144s Selecting previously unselected package python3-ufolib2. 144s Preparing to unpack .../084-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 144s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 145s Selecting previously unselected package python3-unicodedata2. 145s Preparing to unpack .../085-python3-unicodedata2_15.1.0+ds-1build2_amd64.deb ... 145s Unpacking python3-unicodedata2 (15.1.0+ds-1build2) ... 145s Selecting previously unselected package unicode-data. 145s Preparing to unpack .../086-unicode-data_15.1.0-1_all.deb ... 145s Unpacking unicode-data (15.1.0-1) ... 145s Selecting previously unselected package python3-fonttools. 145s Preparing to unpack .../087-python3-fonttools_4.55.3-2_amd64.deb ... 145s Unpacking python3-fonttools (4.55.3-2) ... 145s Selecting previously unselected package python3-gsd. 145s Preparing to unpack .../088-python3-gsd_3.4.2-2_amd64.deb ... 145s Unpacking python3-gsd (3.4.2-2) ... 145s Selecting previously unselected package python3-iniconfig. 145s Preparing to unpack .../089-python3-iniconfig_1.1.1-2_all.deb ... 145s Unpacking python3-iniconfig (1.1.1-2) ... 145s Selecting previously unselected package python3-parso. 145s Preparing to unpack .../090-python3-parso_0.8.4-1_all.deb ... 145s Unpacking python3-parso (0.8.4-1) ... 145s Selecting previously unselected package python3-typeshed. 145s Preparing to unpack .../091-python3-typeshed_0.0~git20241223.ea91db2-1_all.deb ... 145s Unpacking python3-typeshed (0.0~git20241223.ea91db2-1) ... 146s Selecting previously unselected package python3-jedi. 146s Preparing to unpack .../092-python3-jedi_0.19.1+ds1-1_all.deb ... 146s Unpacking python3-jedi (0.19.1+ds1-1) ... 146s Selecting previously unselected package python3-matplotlib-inline. 146s Preparing to unpack .../093-python3-matplotlib-inline_0.1.6-2_all.deb ... 146s Unpacking python3-matplotlib-inline (0.1.6-2) ... 146s Selecting previously unselected package python3-wcwidth. 146s Preparing to unpack .../094-python3-wcwidth_0.2.13+dfsg1-1_all.deb ... 146s Unpacking python3-wcwidth (0.2.13+dfsg1-1) ... 146s Selecting previously unselected package python3-prompt-toolkit. 146s Preparing to unpack .../095-python3-prompt-toolkit_3.0.50-1_all.deb ... 146s Unpacking python3-prompt-toolkit (3.0.50-1) ... 146s Selecting previously unselected package python3-pure-eval. 146s Preparing to unpack .../096-python3-pure-eval_0.2.3-1_all.deb ... 146s Unpacking python3-pure-eval (0.2.3-1) ... 146s Selecting previously unselected package python3-stack-data. 146s Preparing to unpack .../097-python3-stack-data_0.6.3-1_all.deb ... 146s Unpacking python3-stack-data (0.6.3-1) ... 146s Selecting previously unselected package python3-ptyprocess. 146s Preparing to unpack .../098-python3-ptyprocess_0.7.0-6_all.deb ... 146s Unpacking python3-ptyprocess (0.7.0-6) ... 146s Selecting previously unselected package python3-pexpect. 146s Preparing to unpack .../099-python3-pexpect_4.9-3_all.deb ... 146s Unpacking python3-pexpect (4.9-3) ... 146s Selecting previously unselected package python3-ipython. 146s Preparing to unpack .../100-python3-ipython_8.30.0-2_all.deb ... 146s Unpacking python3-ipython (8.30.0-2) ... 146s Selecting previously unselected package python3-jupyter-core. 146s Preparing to unpack .../101-python3-jupyter-core_5.7.2-5_all.deb ... 146s Unpacking python3-jupyter-core (5.7.2-5) ... 146s Selecting previously unselected package python3-psutil. 146s Preparing to unpack .../102-python3-psutil_5.9.8-2build3_amd64.deb ... 146s Unpacking python3-psutil (5.9.8-2build3) ... 146s Selecting previously unselected package python3-tornado. 146s Preparing to unpack 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(6.29.5-2) ... 147s Selecting previously unselected package python3-joblib. 147s Preparing to unpack .../109-python3-joblib_1.4.2-2_all.deb ... 147s Unpacking python3-joblib (1.4.2-2) ... 147s Selecting previously unselected package python3-kiwisolver. 147s Preparing to unpack .../110-python3-kiwisolver_1.4.7-3_amd64.deb ... 147s Unpacking python3-kiwisolver (1.4.7-3) ... 147s Selecting previously unselected package libopenjp2-7:amd64. 147s Preparing to unpack .../111-libopenjp2-7_2.5.0-2ubuntu3_amd64.deb ... 147s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu3) ... 147s Selecting previously unselected package python3-pil:amd64. 147s Preparing to unpack .../112-python3-pil_11.1.0-5_amd64.deb ... 147s Unpacking python3-pil:amd64 (11.1.0-5) ... 147s Selecting previously unselected package python3.12-tk. 147s Preparing to unpack .../113-python3.12-tk_3.12.9-1_amd64.deb ... 147s Unpacking python3.12-tk (3.12.9-1) ... 147s Selecting previously unselected package python3.13-tk. 147s Preparing to unpack .../114-python3.13-tk_3.13.2-1_amd64.deb ... 147s Unpacking python3.13-tk (3.13.2-1) ... 147s Selecting previously unselected package python3-tk:amd64. 147s Preparing to unpack .../115-python3-tk_3.13.1-1_amd64.deb ... 147s Unpacking python3-tk:amd64 (3.13.1-1) ... 147s Selecting previously unselected package python3-pil.imagetk:amd64. 147s Preparing to unpack .../116-python3-pil.imagetk_11.1.0-5_amd64.deb ... 147s Unpacking python3-pil.imagetk:amd64 (11.1.0-5) ... 147s Selecting previously unselected package python3-matplotlib. 147s Preparing to unpack .../117-python3-matplotlib_3.8.3-3ubuntu2_amd64.deb ... 147s Unpacking python3-matplotlib (3.8.3-3ubuntu2) ... 147s Selecting previously unselected package python3-netcdf4. 147s Preparing to unpack .../118-python3-netcdf4_1.7.2-1build3_amd64.deb ... 147s Unpacking python3-netcdf4 (1.7.2-1build3) ... 147s Selecting previously unselected package python3-networkx. 147s Preparing to unpack .../119-python3-networkx_3.2.1-4ubuntu1_all.deb ... 147s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 148s Selecting previously unselected package python3-pandas-lib:amd64. 148s Preparing to unpack .../120-python3-pandas-lib_2.2.3+dfsg-8_amd64.deb ... 148s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-8) ... 148s Selecting previously unselected package python3-pandas. 148s Preparing to unpack .../121-python3-pandas_2.2.3+dfsg-8_all.deb ... 148s Unpacking python3-pandas (2.2.3+dfsg-8) ... 148s Selecting previously unselected package python3-numexpr. 148s Preparing to unpack .../122-python3-numexpr_2.10.2-1build1_amd64.deb ... 148s Unpacking python3-numexpr (2.10.2-1build1) ... 148s Selecting previously unselected package python3-tables-lib. 148s Preparing to unpack .../123-python3-tables-lib_3.10.2-2_amd64.deb ... 148s Unpacking python3-tables-lib (3.10.2-2) ... 148s Selecting previously unselected package python3-tables. 148s Preparing to unpack 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previously unselected package python3-sklearn-lib:amd64. 148s Preparing to unpack .../130-python3-sklearn-lib_1.4.2+dfsg-7build1_amd64.deb ... 148s Unpacking python3-sklearn-lib:amd64 (1.4.2+dfsg-7build1) ... 149s Selecting previously unselected package python3-sklearn. 149s Preparing to unpack .../131-python3-sklearn_1.4.2+dfsg-7build1_all.deb ... 149s Unpacking python3-sklearn (1.4.2+dfsg-7build1) ... 149s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 149s Setting up liblcms2-2:amd64 (2.16-2) ... 149s Setting up python3-iniconfig (1.1.1-2) ... 149s Setting up python3.12-minimal (3.12.9-1) ... 150s Setting up python3-tornado (6.4.2-1) ... 150s Setting up libnorm1t64:amd64 (1.5.9+dfsg-3.1build1) ... 150s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 150s Setting up python3-pure-eval (0.2.3-1) ... 150s Setting up libsodium23:amd64 (1.0.18-1build3) ... 150s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 150s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 150s Setting up libdebuginfod-common (0.192-4) ... 151s Setting up python3-joblib (1.4.2-2) ... 151s Setting up python3-parso (0.8.4-1) ... 151s Setting up python3-lz4 (4.4.0+dfsg-1) ... 151s Setting up python3-asttokens (3.0.0-1) ... 151s Setting up python3-unicodedata2 (15.1.0+ds-1build2) ... 151s Setting up fonts-lyx (2.4.3-1) ... 151s Setting up python3.12 (3.12.9-1) ... 152s Setting up python3-threadpoolctl (3.1.0-1) ... 153s Setting up x11-common (1:7.7+23ubuntu3) ... 153s Setting up libdeflate0:amd64 (1.23-1) ... 153s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 153s Setting up python3-coverage (7.4.4+dfsg1-0ubuntu3) ... 153s Setting up python3-pytz (2025.1-3) ... 153s Setting up libgomp1:amd64 (15-20250213-1ubuntu1) ... 153s Setting up python3-networkx (3.2.1-4ubuntu1) ... 155s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 155s Setting up libaec0:amd64 (1.1.3-1) ... 155s Setting up python3-platformdirs (4.3.6-1) ... 156s Setting up python3-psutil (5.9.8-2build3) ... 156s Setting up libsource-highlight-common (3.1.9-4.3build1) ... 156s Setting up python3-tz (2025.1-3) ... 156s Setting up libsnappy1v5:amd64 (1.2.1-1) ... 156s Setting up python3-fs (2.4.16-6) ... 156s Setting up unicode-data (15.1.0-1) ... 156s Setting up libpgm-5.3-0t64:amd64 (5.3.128~dfsg-2.1build1) ... 156s Setting up python3-decorator (5.1.1-5) ... 156s Setting up libblosc2-4:amd64 (2.16.0+ds-1) ... 156s Setting up libblas3:amd64 (3.12.1-2) ... 156s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 156s Setting up python3-packaging (24.2-1) ... 157s Setting up python3-wcwidth (0.2.13+dfsg1-1) ... 157s Setting up python3-typeshed (0.0~git20241223.ea91db2-1) ... 157s Setting up python3-executing (2.2.0-0.1) ... 157s Setting up python3-nest-asyncio (1.5.4-1) ... 157s Setting up python3-brotli (1.1.0-2build3) ... 157s Setting up python3-cycler (0.12.1-1) ... 158s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 158s Setting up fonts-dejavu-mono (2.37-8) ... 158s Setting up python3-kiwisolver (1.4.7-3) ... 158s Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... 158s Setting up libipt2 (2.1.2-1) ... 158s Setting up fonts-dejavu-core (2.37-8) ... 158s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 158s Setting up python3-cpuinfo (9.0.0+git20221119-3) ... 158s Setting up libbabeltrace1:amd64 (1.5.11-4build1) ... 158s Setting up libgfortran5:amd64 (15-20250213-1ubuntu1) ... 158s Setting up python3-pluggy (1.5.0-1) ... 158s Setting up libwebp7:amd64 (1.5.0-0.1) ... 158s Setting up python3-fastjsonschema (2.21.1-1) ... 158s Setting up python3-traitlets (5.14.3+really5.14.3-1) ... 159s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu2) ... 159s Setting up libblosc1:amd64 (1.21.5+ds-1build1) ... 159s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu3) ... 159s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 159s Setting up python3-dateutil (2.9.0-3) ... 159s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 159s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 159s Setting up python3-mpmath (1.3.0-1) ... 160s Setting up python-matplotlib-data (3.8.3-3ubuntu2) ... 160s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 160s Setting up python3-stack-data (0.6.3-1) ... 160s Setting up python-tables-data (3.10.2-2) ... 160s Setting up python3-jupyter-core (5.7.2-5) ... 160s Setting up libsz2:amd64 (1.1.3-1) ... 160s Setting up python3-ptyprocess (0.7.0-6) ... 160s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 160s Setting up python3-prompt-toolkit (3.0.50-1) ... 161s Setting up python3-sympy (1.13.3-1) ... 171s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 171s Setting up liblapack3:amd64 (3.12.1-2) ... 171s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 171s Setting up libzmq5:amd64 (4.3.5-1build2) ... 171s Setting up python3-jedi 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Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 177s Setting up libhdf5-hl-310:amd64 (1.14.5+repack-3) ... 177s Setting up libxft2:amd64 (2.3.6-1build1) ... 177s Setting up python3-scipy (1.14.1-4ubuntu1) ... 183s Setting up python3-tables-lib (3.10.2-2) ... 183s Setting up libtk8.6:amd64 (8.6.16-1) ... 183s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-8) ... 183s Setting up python3.12-tk (3.12.9-1) ... 183s Setting up libnetcdf22:amd64 (1:4.9.3-1) ... 183s Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-7build1) ... 183s Setting up python3-gsd (3.4.2-2) ... 183s Setting up python3-debugpy (1.8.8+ds-2ubuntu1) ... 184s Setting up python3.13-tk (3.13.2-1) ... 184s Setting up python3-pil:amd64 (11.1.0-5) ... 185s Setting up python3-pandas (2.2.3+dfsg-8) ... 192s Setting up python3-ipython (8.30.0-2) ... 193s Setting up python3-ipykernel (6.29.5-2) ... 193s Setting up python3-sklearn (1.4.2+dfsg-7build1) ... 197s Setting up python3-cftime (1.6.4-1build2) ... 197s Setting up python3-numexpr (2.10.2-1build1) ... 197s Setting up python3-netcdf4 (1.7.2-1build3) ... 197s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 197s Setting up blt (2.5.3+dfsg-7build1) ... 197s Setting up python3-tk:amd64 (3.13.1-1) ... 197s Setting up python3-tables (3.10.2-2) ... 198s Setting up python3-mdtraj (1.10.3-2) ... 198s Setting up python3-pil.imagetk:amd64 (11.1.0-5) ... 199s Setting up python3-fonttools (4.55.3-2) ... 200s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 200s Setting up python3-matplotlib (3.8.3-3ubuntu2) ... 203s Processing triggers for libc-bin (2.40-4ubuntu1) ... 203s Processing triggers for systemd (257.2-3ubuntu1) ... 203s Processing triggers for man-db (2.13.0-1) ... 205s autopkgtest [03:09:32]: 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)' 205s autopkgtest [03:09:32]: test command1: [----------------------- 206s ============================= test session starts ============================== 206s platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 -- /usr/bin/python3 206s cachedir: .pytest_cache 206s rootdir: /tmp/autopkgtest.Wg29hx/build.gDu/src 206s configfile: pyproject.toml 206s testpaths: tests, examples 206s plugins: typeguard-4.4.1 207s collecting ... collected 1145 items / 12 deselected / 1133 selected 207s 207s tests/test_alignment.py::test_rmsd_zero PASSED [ 0%] 207s tests/test_alignment.py::test_rmsd_nonzero PASSED [ 0%] 207s tests/test_alignment.py::test_transform PASSED [ 0%] 207s tests/test_alignment.py::test_transform2 PASSED [ 0%] 207s tests/test_angles.py::test_angle_pbc_0 PASSED [ 0%] 207s tests/test_angles.py::test_generator PASSED [ 0%] 207s tests/test_angles.py::test_angle_180[True] PASSED [ 0%] 207s tests/test_angles.py::test_angle_180[False] PASSED [ 0%] 207s tests/test_arc.py::test_read_0 PASSED [ 0%] 207s tests/test_arc.py::test_read_arctraj PASSED [ 0%] 207s tests/test_arc.py::test_read_pbc PASSED [ 0%] 207s 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tests/test_mdcrd.py::test_read_0 PASSED [ 26%] 315s tests/test_mdcrd.py::test_read_1 PASSED [ 26%] 315s tests/test_mdcrd.py::test_read_write_0 PASSED [ 26%] 315s tests/test_mdcrd.py::test_read_write_1 PASSED [ 26%] 315s tests/test_mdcrd.py::test_read_write_2 PASSED [ 26%] 315s tests/test_mdcrd.py::test_multiread PASSED [ 26%] 315s tests/test_mdcrd.py::test_seek PASSED [ 26%] 315s tests/test_mdcrd.py::test_atom_indices_0 PASSED [ 26%] 315s tests/test_mdcrd.py::test_atom_indices_1 PASSED [ 26%] 315s tests/test_mol2.py::test_load_mol2 PASSED [ 26%] 315s tests/test_mol2.py::test_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb SKIPPED [ 27%] 315s tests/test_mol2.py::test_mol2_dataframe PASSED [ 27%] 315s tests/test_mol2.py::test_mol2_dataframe_status PASSED [ 27%] 315s tests/test_mol2.py::test_mol2_warnings PASSED [ 27%] 315s tests/test_mol2.py::test_mol2_status_bits PASSED [ 27%] 315s tests/test_mol2.py::test_mol2_without_bonds PASSED [ 27%] 315s tests/test_mol2.py::test_mol2_element_name PASSED [ 27%] 315s tests/test_mol2.py::test_load_all_mol2[li.mol2] PASSED [ 27%] 315s tests/test_mol2.py::test_load_all_mol2[lysozyme-ligand-tripos.mol2] PASSED [ 27%] 315s tests/test_mol2.py::test_load_all_mol2[imatinib.mol2] PASSED [ 27%] 315s tests/test_mol2.py::test_load_all_mol2[status-bits.mol2] PASSED [ 27%] 315s tests/test_mol2.py::test_load_all_mol2[adp.mol2] PASSED [ 27%] 315s tests/test_mol2.py::test_load_all_mol2[water_acn.mol2] PASSED [ 28%] 315s tests/test_mol2.py::test_mol2_n_residues PASSED [ 28%] 315s tests/test_neighborlist.py::test_nonperiodic PASSED [ 28%] 315s tests/test_neighborlist.py::test_periodic PASSED [ 28%] 316s tests/test_neighborlist.py::test_triclinic PASSED [ 28%] 316s tests/test_neighbors.py::test_compute_neighbors_1 PASSED [ 28%] 316s tests/test_neighbors.py::test_compute_neighbors_2 PASSED [ 28%] 317s tests/test_neighbors.py::test_compute_neighbors_3 PASSED [ 28%] 317s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_after_close PASSED [ 28%] 317s tests/test_netcdf.py::TestNetCDFNetCDF4::test_shape PASSED [ 28%] 317s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_1 PASSED [ 28%] 317s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_2 PASSED [ 29%] 317s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_3 PASSED [ 29%] 317s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_1 PASSED [ 29%] 317s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_2 PASSED [ 29%] 317s tests/test_netcdf.py::TestNetCDFNetCDF4::test_ragged_1 PASSED [ 29%] 317s tests/test_netcdf.py::TestNetCDFNetCDF4::test_ragged_2 PASSED [ 29%] 317s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_25 PASSED [ 29%] 317s tests/test_netcdf.py::TestNetCDFNetCDF4::test_write_3 PASSED [ 29%] 317s tests/test_netcdf.py::TestNetCDFNetCDF4::test_n_atoms PASSED [ 29%] 317s tests/test_netcdf.py::TestNetCDFNetCDF4::test_do_overwrite PASSED [ 29%] 317s tests/test_netcdf.py::TestNetCDFNetCDF4::test_do_not_overwrite PASSED [ 29%] 317s tests/test_netcdf.py::TestNetCDFNetCDF4::test_trajectory_save_load PASSED [ 30%] 317s tests/test_netcdf.py::TestNetCDFScipy::test_read_after_close PASSED [ 30%] 317s tests/test_netcdf.py::TestNetCDFScipy::test_shape PASSED [ 30%] 317s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_1 PASSED [ 30%] 317s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_2 PASSED [ 30%] 317s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_3 PASSED [ 30%] 317s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_1 PASSED [ 30%] 317s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_2 PASSED [ 30%] 317s tests/test_netcdf.py::TestNetCDFScipy::test_ragged_1 PASSED [ 30%] 317s tests/test_netcdf.py::TestNetCDFScipy::test_ragged_2 PASSED [ 30%] 317s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_25 PASSED [ 30%] 317s tests/test_netcdf.py::TestNetCDFScipy::test_write_3 PASSED [ 30%] 317s tests/test_netcdf.py::TestNetCDFScipy::test_n_atoms PASSED [ 31%] 317s tests/test_netcdf.py::TestNetCDFScipy::test_do_overwrite PASSED [ 31%] 317s tests/test_netcdf.py::TestNetCDFScipy::test_do_not_overwrite PASSED [ 31%] 317s tests/test_netcdf.py::TestNetCDFScipy::test_trajectory_save_load PASSED [ 31%] 317s tests/test_netcdf.py::test_cpptraj SKIPPED (This test requires cpptr...) [ 31%] 317s tests/test_nmr.py::test_spartaplus SKIPPED (SPARTA+ binary not found) [ 31%] 317s tests/test_nmr.py::test_ppm SKIPPED (PPM binary not found) [ 31%] 317s tests/test_nmr.py::test_shiftx2 SKIPPED (SHIFTX2 binary not found or...) [ 31%] 317s tests/test_nmr.py::test_2_scalar_couplings PASSED [ 31%] 317s tests/test_order.py::test_nematic_order PASSED [ 31%] 317s tests/test_order.py::test_director PASSED [ 31%] 317s tests/test_order.py::test_inertia PASSED [ 32%] 317s tests/test_order.py::test_nematic_order_args PASSED [ 32%] 317s tests/test_order.py::test_order_from_traj PASSED [ 32%] 317s tests/test_order.py::test_directors_angle_from_traj PASSED [ 32%] 317s tests/test_pdb.py::test_pdbread PASSED [ 32%] 317s tests/test_pdb.py::test_pdbread_with_input_top PASSED [ 32%] 317s tests/test_pdb.py::test_pdbwrite PASSED [ 32%] 317s tests/test_pdb.py::test_load_multiframe PASSED [ 32%] 317s tests/test_pdb.py::test_4ZUO PASSED [ 32%] 318s tests/test_pdb.py::test_2EQQ_0 PASSED [ 32%] 319s tests/test_pdb.py::test_1vii_solvated_with_ligand PASSED [ 32%] 319s tests/test_pdb.py::test_write_large PASSED [ 33%] 319s tests/test_pdb.py::test_write_large_2 PASSED [ 33%] 319s tests/test_pdb.py::test_pdbstructure_0 PASSED [ 33%] 319s tests/test_pdb.py::test_pdbstructure_1 PASSED [ 33%] 319s tests/test_pdb.py::test_pdbstructure_2 PASSED [ 33%] 319s tests/test_pdb.py::test_pdbstructure_3 PASSED [ 33%] 319s tests/test_pdb.py::test_1ncw PASSED [ 33%] 319s tests/test_pdb.py::test_segment_id PASSED [ 33%] 319s tests/test_pdb.py::test_bfactors PASSED [ 33%] 322s tests/test_pdb.py::test_hex PASSED [ 33%] 322s tests/test_pdb.py::test_dummy_pdb_box_detection PASSED [ 33%] 322s tests/test_pdb.py::test_multichain_load_cycle PASSED [ 33%] 322s tests/test_pdb.py::test_multichain_load_cycle_noter PASSED [ 34%] 322s tests/test_pdb.py::test_load_pdb_input_top PASSED [ 34%] 322s tests/test_pdb.py::test_chimera_indexing PASSED [ 34%] 322s tests/test_pdb.py::test_chimera_indexing_skip PASSED [ 34%] 322s tests/test_pdb.py::test_vmd_indexing PASSED [ 34%] 322s tests/test_pdb.py::test_overflow_indexing PASSED [ 34%] 322s tests/test_pdb.py::test_blank_indexing PASSED [ 34%] 322s tests/test_pdb.py::test_pdb_charge_read PASSED [ 34%] 322s tests/test_pdb.py::test_pdb_charge_write PASSED [ 34%] 322s tests/test_pdbx.py::test_convert SKIPPED (test_pdbx.py needs OpenMM.) [ 34%] 322s tests/test_prmtop.py::test_load_prmtop PASSED [ 34%] 322s tests/test_prmtop.py::test_load_chamber_prmtop PASSED [ 35%] 322s tests/test_psf.py::test_load_psf PASSED [ 35%] 326s tests/test_psf.py::test_multichain_psf PASSED [ 35%] 326s tests/test_psf.py::test_load_mdcrd_with_psf PASSED [ 35%] 326s tests/test_psf.py::test_against_vmd[1vii.pdb] SKIPPED (This test req...) [ 35%] 326s tests/test_psf.py::test_against_vmd[2EQQ.pdb] SKIPPED (This test req...) [ 35%] 326s tests/test_quaternion.py::test_quaternion_0 PASSED [ 35%] 326s tests/test_quaternion.py::test_quaternion_1 PASSED [ 35%] 326s tests/test_quaternion.py::test_quaternion_2 PASSED [ 35%] 328s tests/test_rdf.py::test_rdf_norm PASSED [ 35%] 328s tests/test_rdf.py::test_compare_rdf_to_gromacs SKIPPED (Binning does...) [ 35%] 329s tests/test_rdf.py::test_rdf_t[True-True] PASSED [ 36%] 333s tests/test_rdf.py::test_rdf_t[True-False] PASSED [ 36%] 333s tests/test_rdf.py::test_rdf_t[False-True] PASSED [ 36%] 333s tests/test_rdf.py::test_rdf_t[False-False] PASSED [ 36%] 333s tests/test_rdf.py::test_rdf_t_norm[0] PASSED [ 36%] 334s tests/test_rdf.py::test_rdf_t_norm[2] PASSED [ 36%] 334s tests/test_rdf.py::test_rdf_t_norm[4] PASSED [ 36%] 334s tests/test_rdf.py::test_compare_rdf_t_at_0[True-True] PASSED [ 36%] 336s tests/test_rdf.py::test_compare_rdf_t_at_0[True-False] PASSED [ 36%] 336s tests/test_rdf.py::test_compare_rdf_t_at_0[False-True] PASSED [ 36%] 336s tests/test_rdf.py::test_compare_rdf_t_at_0[False-False] PASSED [ 36%] 336s tests/test_rdf.py::test_amber_rdf_t[True-True] PASSED [ 36%] 336s tests/test_rdf.py::test_amber_rdf_t[True-False] PASSED [ 37%] 337s tests/test_rdf.py::test_amber_rdf_t[False-True] PASSED [ 37%] 337s tests/test_rdf.py::test_amber_rdf_t[False-False] PASSED [ 37%] 337s tests/test_rdf.py::test_compare_gromacs_rdf_t SKIPPED (Binning does ...) [ 37%] 337s tests/test_rdf.py::test_compare_rdf_t_master SKIPPED (Expected failu...) [ 37%] 337s tests/test_rdf.py::test_compare_n_concurrent_pairs PASSED [ 37%] 337s tests/test_reporter.py::test_reporter SKIPPED (test_reporter.py need...) [ 37%] 337s tests/test_reporter.py::test_reporter_subset SKIPPED (test_reporter....) [ 37%] 337s tests/test_reporter.py::test_xtc_reporter_append SKIPPED (test_repor...) [ 37%] 337s tests/test_restart.py::test_read_after_close PASSED [ 37%] 337s tests/test_restart.py::test_shape PASSED [ 37%] 337s tests/test_restart.py::test_shape_2 PASSED [ 38%] 337s tests/test_restart.py::test_read_write_1 PASSED [ 38%] 337s tests/test_restart.py::test_read_write_2 PASSED [ 38%] 337s tests/test_restart.py::test_read_write_3 PASSED [ 38%] 337s tests/test_restart.py::test_read_write_4 PASSED [ 38%] 337s tests/test_rmsd.py::test_trajectory_rmsd PASSED [ 38%] 338s tests/test_rmsd.py::test_precentered_1 PASSED [ 38%] 338s tests/test_rmsd.py::test_precentered_2 PASSED [ 38%] 338s tests/test_rmsd.py::test_superpose_0 PASSED [ 38%] 338s tests/test_rmsd.py::test_superpose_1 PASSED [ 38%] 338s tests/test_rmsd.py::test_superpose_2 PASSED [ 38%] 338s tests/test_rmsd.py::test_superpose_refinds PASSED [ 39%] 338s tests/test_rmsd.py::test_rmsd_atom_indices PASSED [ 39%] 338s tests/test_rmsd.py::test_rmsd_ref_ainds PASSED [ 39%] 338s tests/test_rmsd.py::test_average_structure PASSED [ 39%] 338s tests/test_rmsd.py::test_trajectory_rmsf PASSED [ 39%] 338s tests/test_rmsd.py::test_trajectory_rmsf_aligned PASSED [ 39%] 338s tests/test_rmsd.py::test_rmsd_atom_indices_vs_ref_indices PASSED [ 39%] 338s tests/test_rmsd_memmap.py::test_1 PASSED [ 39%] 338s tests/test_rmsd_memmap.py::test_2 PASSED [ 39%] 338s tests/test_sasa.py::test_sasa_0 PASSED [ 39%] 338s tests/test_sasa.py::test_sasa_1 PASSED [ 39%] 338s tests/test_sasa.py::test_sasa_2 PASSED [ 39%] 338s tests/test_sasa.py::test_sasa_3 PASSED [ 40%] 339s tests/test_sasa.py::test_sasa_4 PASSED [ 40%] 339s tests/test_sasa.py::test_sasa_5 PASSED [ 40%] 340s tests/test_sasa.py::test_sasa_6 PASSED [ 40%] 340s tests/test_sasa.py::test_sasa_7 PASSED [ 40%] 340s tests/test_selection.py::test_range PASSED [ 40%] 340s tests/test_selection.py::test_unary_2 PASSED [ 40%] 340s tests/test_selection.py::test_unary_3 PASSED [ 40%] 340s tests/test_selection.py::test_binary_1 PASSED [ 40%] 340s tests/test_selection.py::test_binary_2 PASSED [ 40%] 340s tests/test_selection.py::test_simple PASSED [ 40%] 340s tests/test_selection.py::test_alias PASSED [ 41%] 340s tests/test_selection.py::test_unary_1 PASSED [ 41%] 340s tests/test_selection.py::test_binary_selection_operator PASSED [ 41%] 340s tests/test_selection.py::test_raises PASSED [ 41%] 340s tests/test_selection.py::test_raises2 PASSED [ 41%] 340s tests/test_selection.py::test_bool PASSED [ 41%] 340s tests/test_selection.py::test_nested_bool PASSED [ 41%] 340s tests/test_selection.py::test_values PASSED [ 41%] 340s tests/test_selection.py::test_element PASSED [ 41%] 340s tests/test_selection.py::test_not PASSED [ 41%] 340s tests/test_selection.py::test_re PASSED [ 41%] 340s tests/test_selection.py::test_within SKIPPED (failed to parse selection) [ 42%] 340s tests/test_selection.py::test_quotes PASSED [ 42%] 340s tests/test_selection.py::test_top PASSED [ 42%] 340s tests/test_selection.py::test_top_2 PASSED [ 42%] 341s tests/test_selection.py::test_backbone PASSED [ 42%] 341s tests/test_selection.py::test_sidechain PASSED [ 42%] 341s tests/test_selection.py::test_literal PASSED [ 42%] 341s tests/test_selection.py::test_in PASSED [ 42%] 341s tests/test_shape.py::test_gyration PASSED [ 42%] 341s tests/test_shape.py::test_principal_moments PASSED [ 42%] 341s tests/test_shape.py::test_asphericity PASSED [ 42%] 341s tests/test_shape.py::test_shape_metrics PASSED [ 42%] 341s tests/test_thermodynamic_properties.py::test_volume PASSED [ 43%] 341s tests/test_thermodynamic_properties.py::test_density PASSED [ 43%] 342s tests/test_thermodynamic_properties.py::test_dipole_moments PASSED [ 43%] 342s tests/test_thermodynamic_properties.py::test_static_dielectric PASSED [ 43%] 342s tests/test_thermodynamic_properties.py::test_kappa PASSED [ 43%] 342s tests/test_thermodynamic_properties.py::test_alpha SKIPPED (Thermal ...) [ 43%] 342s tests/test_topology.py::test_topology_openmm SKIPPED (needs OpenMM) [ 43%] 342s tests/test_topology.py::test_topology_openmm_preserve_chain_id_when_specified SKIPPED [ 43%] 342s tests/test_topology.py::test_topology_openmm_roundtrip_chain_id SKIPPED [ 43%] 342s tests/test_topology.py::test_topology_openmm_preserve_chain_id_even_when_empty SKIPPED [ 43%] 342s tests/test_topology.py::test_topology_openmm_boxes SKIPPED (needs Op...) [ 43%] 342s tests/test_topology.py::test_topology_openmm_formal_charges SKIPPED [ 44%] 342s tests/test_topology.py::test_topology_pandas PASSED [ 44%] 342s tests/test_topology.py::test_topology_pandas_TIP4PEW PASSED [ 44%] 342s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq PASSED [ 44%] 342s tests/test_topology.py::test_topology_numbers PASSED [ 44%] 342s tests/test_topology.py::test_topology_unique_elements_bpti PASSED [ 44%] 342s tests/test_topology.py::test_chain PASSED [ 44%] 342s tests/test_topology.py::test_residue PASSED [ 44%] 342s tests/test_topology.py::test_segment_id PASSED [ 44%] 342s tests/test_topology.py::test_nonconsective_resSeq PASSED [ 44%] 342s tests/test_topology.py::test_pickle PASSED [ 44%] 342s tests/test_topology.py::test_atoms_by_name PASSED [ 45%] 342s tests/test_topology.py::test_select_atom_indices PASSED [ 45%] 342s tests/test_topology.py::test_top_dataframe_openmm_roundtrip SKIPPED [ 45%] 342s tests/test_topology.py::test_n_bonds PASSED [ 45%] 342s tests/test_topology.py::test_load_unknown_topology PASSED [ 45%] 342s tests/test_topology.py::test_unique_pairs PASSED [ 45%] 343s tests/test_topology.py::test_select_pairs PASSED [ 45%] 343s tests/test_topology.py::test_to_fasta PASSED [ 45%] 343s tests/test_topology.py::test_subset PASSED [ 45%] 343s tests/test_topology.py::test_subset_re_index_residues PASSED [ 45%] 343s tests/test_topology.py::test_molecules PASSED [ 45%] 343s tests/test_topology.py::test_copy_and_hash PASSED [ 45%] 343s tests/test_topology.py::test_topology_sliced_residue_indices PASSED [ 46%] 343s tests/test_topology.py::test_topology_join PASSED [ 46%] 343s tests/test_topology.py::test_topology_join_keep_resSeq PASSED [ 46%] 344s tests/test_trajectory.py::test_mismatch PASSED [ 46%] 344s tests/test_trajectory.py::test_box PASSED [ 46%] 344s tests/test_trajectory.py::test_load_pdb_box PASSED [ 46%] 344s tests/test_trajectory.py::test_load_pdb_gz PASSED [ 46%] 344s tests/test_trajectory.py::test_box_load_save[nc] PASSED [ 46%] 344s tests/test_trajectory.py::test_box_load_save[h5] PASSED [ 46%] 344s tests/test_trajectory.py::test_box_load_save[xtc] PASSED [ 46%] 344s tests/test_trajectory.py::test_box_load_save[trr] PASSED [ 46%] 344s tests/test_trajectory.py::test_box_load_save[dcd] PASSED [ 47%] 344s tests/test_trajectory.py::test_box_load_save[mdcrd] PASSED [ 47%] 344s tests/test_trajectory.py::test_box_load_save[dtr] PASSED [ 47%] 344s tests/test_trajectory.py::test_box_load_save[xyz] SKIPPED (xyz does ...) [ 47%] 344s tests/test_trajectory.py::test_box_load_save[xyz.gz] SKIPPED (xyz.gz...) [ 47%] 344s tests/test_trajectory.py::test_box_load_save[lammpstrj] PASSED [ 47%] 344s tests/test_trajectory.py::test_box_load_save[lh5] SKIPPED (lh5 does ...) [ 47%] 344s tests/test_trajectory.py::test_box_load_save[pdb] SKIPPED (pdb does ...) [ 47%] 344s tests/test_trajectory.py::test_box_load_save[pdb.gz] SKIPPED (pdb.gz...) [ 47%] 344s tests/test_trajectory.py::test_box_load_save[ncrst] PASSED [ 47%] 344s tests/test_trajectory.py::test_box_load_save[rst7] PASSED [ 47%] 344s tests/test_trajectory.py::test_box_load_save[gro] PASSED [ 48%] 344s tests/test_trajectory.py::test_slice PASSED [ 48%] 344s tests/test_trajectory.py::test_slice2 PASSED [ 48%] 344s tests/test_trajectory.py::test_read_path[nc] PASSED [ 48%] 344s tests/test_trajectory.py::test_read_path[h5] PASSED [ 48%] 344s tests/test_trajectory.py::test_read_path[xtc] PASSED [ 48%] 344s tests/test_trajectory.py::test_read_path[trr] PASSED [ 48%] 344s tests/test_trajectory.py::test_read_path[dcd] PASSED [ 48%] 344s tests/test_trajectory.py::test_read_path[mdcrd] PASSED [ 48%] 344s tests/test_trajectory.py::test_read_path[dtr] PASSED [ 48%] 344s tests/test_trajectory.py::test_read_path[xyz] PASSED [ 48%] 344s tests/test_trajectory.py::test_read_path[xyz.gz] PASSED [ 48%] 344s tests/test_trajectory.py::test_read_path[lammpstrj] PASSED [ 49%] 344s tests/test_trajectory.py::test_read_path[lh5] PASSED [ 49%] 344s tests/test_trajectory.py::test_read_path[pdb] PASSED [ 49%] 344s tests/test_trajectory.py::test_read_path[pdb.gz] PASSED [ 49%] 344s tests/test_trajectory.py::test_read_path[ncrst] XFAIL (These referen...) [ 49%] 344s tests/test_trajectory.py::test_read_path[rst7] XFAIL (These referenc...) [ 49%] 344s tests/test_trajectory.py::test_read_path[gro] PASSED [ 49%] 344s tests/test_trajectory.py::test_write_path[nc] PASSED [ 49%] 344s tests/test_trajectory.py::test_write_path[h5] PASSED [ 49%] 344s tests/test_trajectory.py::test_write_path[xtc] PASSED [ 49%] 344s tests/test_trajectory.py::test_write_path[trr] PASSED [ 49%] 344s tests/test_trajectory.py::test_write_path[dcd] PASSED [ 50%] 344s tests/test_trajectory.py::test_write_path[mdcrd] SKIPPED (mdcrd can ...) [ 50%] 344s tests/test_trajectory.py::test_write_path[dtr] PASSED [ 50%] 344s tests/test_trajectory.py::test_write_path[xyz] PASSED [ 50%] 344s tests/test_trajectory.py::test_write_path[xyz.gz] PASSED [ 50%] 344s tests/test_trajectory.py::test_write_path[lammpstrj] PASSED [ 50%] 344s tests/test_trajectory.py::test_write_path[lh5] PASSED [ 50%] 345s tests/test_trajectory.py::test_write_path[pdb] PASSED [ 50%] 345s tests/test_trajectory.py::test_write_path[pdb.gz] PASSED [ 50%] 345s tests/test_trajectory.py::test_write_path[ncrst] SKIPPED (ncrst can ...) [ 50%] 345s tests/test_trajectory.py::test_write_path[rst7] SKIPPED (rst7 can on...) [ 50%] 345s tests/test_trajectory.py::test_write_path[gro] PASSED [ 51%] 345s tests/test_trajectory.py::test_read_write[nc-nc] PASSED [ 51%] 345s tests/test_trajectory.py::test_read_write[nc-h5] PASSED [ 51%] 345s tests/test_trajectory.py::test_read_write[nc-xtc] PASSED [ 51%] 345s tests/test_trajectory.py::test_read_write[nc-trr] PASSED [ 51%] 345s tests/test_trajectory.py::test_read_write[nc-dcd] PASSED [ 51%] 345s tests/test_trajectory.py::test_read_write[nc-mdcrd] SKIPPED (mdcrd c...) [ 51%] 346s tests/test_trajectory.py::test_read_write[nc-dtr] PASSED [ 51%] 346s tests/test_trajectory.py::test_read_write[nc-xyz] PASSED [ 51%] 347s tests/test_trajectory.py::test_read_write[nc-xyz.gz] PASSED [ 51%] 347s tests/test_trajectory.py::test_read_write[nc-lammpstrj] PASSED [ 51%] 347s tests/test_trajectory.py::test_read_write[nc-lh5] PASSED [ 51%] 348s tests/test_trajectory.py::test_read_write[nc-pdb] PASSED [ 52%] 348s tests/test_trajectory.py::test_read_write[nc-pdb.gz] PASSED [ 52%] 348s tests/test_trajectory.py::test_read_write[nc-ncrst] SKIPPED (ncrst c...) [ 52%] 348s tests/test_trajectory.py::test_read_write[nc-rst7] SKIPPED (rst7 can...) [ 52%] 349s tests/test_trajectory.py::test_read_write[nc-gro] PASSED [ 52%] 349s tests/test_trajectory.py::test_read_write[h5-nc] PASSED [ 52%] 349s tests/test_trajectory.py::test_read_write[h5-h5] PASSED [ 52%] 349s tests/test_trajectory.py::test_read_write[h5-xtc] PASSED [ 52%] 349s tests/test_trajectory.py::test_read_write[h5-trr] PASSED [ 52%] 349s tests/test_trajectory.py::test_read_write[h5-dcd] PASSED [ 52%] 349s tests/test_trajectory.py::test_read_write[h5-mdcrd] SKIPPED (mdcrd c...) [ 52%] 349s tests/test_trajectory.py::test_read_write[h5-dtr] PASSED [ 53%] 349s tests/test_trajectory.py::test_read_write[h5-xyz] PASSED [ 53%] 350s tests/test_trajectory.py::test_read_write[h5-xyz.gz] PASSED [ 53%] 350s tests/test_trajectory.py::test_read_write[h5-lammpstrj] PASSED [ 53%] 350s tests/test_trajectory.py::test_read_write[h5-lh5] PASSED [ 53%] 350s tests/test_trajectory.py::test_read_write[h5-pdb] PASSED [ 53%] 350s tests/test_trajectory.py::test_read_write[h5-pdb.gz] PASSED [ 53%] 350s tests/test_trajectory.py::test_read_write[h5-ncrst] SKIPPED (ncrst c...) [ 53%] 350s tests/test_trajectory.py::test_read_write[h5-rst7] SKIPPED (rst7 can...) [ 53%] 350s tests/test_trajectory.py::test_read_write[h5-gro] PASSED [ 53%] 350s tests/test_trajectory.py::test_read_write[xtc-nc] PASSED [ 53%] 350s tests/test_trajectory.py::test_read_write[xtc-h5] PASSED [ 54%] 351s tests/test_trajectory.py::test_read_write[xtc-xtc] PASSED [ 54%] 351s tests/test_trajectory.py::test_read_write[xtc-trr] PASSED [ 54%] 351s tests/test_trajectory.py::test_read_write[xtc-dcd] PASSED [ 54%] 351s tests/test_trajectory.py::test_read_write[xtc-mdcrd] SKIPPED (mdcrd ...) [ 54%] 351s tests/test_trajectory.py::test_read_write[xtc-dtr] PASSED [ 54%] 351s tests/test_trajectory.py::test_read_write[xtc-xyz] PASSED [ 54%] 352s tests/test_trajectory.py::test_read_write[xtc-xyz.gz] PASSED [ 54%] 352s tests/test_trajectory.py::test_read_write[xtc-lammpstrj] PASSED [ 54%] 352s tests/test_trajectory.py::test_read_write[xtc-lh5] PASSED [ 54%] 352s tests/test_trajectory.py::test_read_write[xtc-pdb] PASSED [ 54%] 352s tests/test_trajectory.py::test_read_write[xtc-pdb.gz] PASSED [ 54%] 352s tests/test_trajectory.py::test_read_write[xtc-ncrst] SKIPPED (ncrst ...) [ 55%] 352s tests/test_trajectory.py::test_read_write[xtc-rst7] SKIPPED (rst7 ca...) [ 55%] 352s tests/test_trajectory.py::test_read_write[xtc-gro] PASSED [ 55%] 352s tests/test_trajectory.py::test_read_write[trr-nc] PASSED [ 55%] 353s tests/test_trajectory.py::test_read_write[trr-h5] PASSED [ 55%] 353s tests/test_trajectory.py::test_read_write[trr-xtc] PASSED [ 55%] 353s tests/test_trajectory.py::test_read_write[trr-trr] PASSED [ 55%] 353s tests/test_trajectory.py::test_read_write[trr-dcd] PASSED [ 55%] 353s tests/test_trajectory.py::test_read_write[trr-mdcrd] SKIPPED (mdcrd ...) [ 55%] 353s tests/test_trajectory.py::test_read_write[trr-dtr] PASSED [ 55%] 353s tests/test_trajectory.py::test_read_write[trr-xyz] PASSED [ 55%] 354s tests/test_trajectory.py::test_read_write[trr-xyz.gz] PASSED [ 56%] 354s tests/test_trajectory.py::test_read_write[trr-lammpstrj] PASSED [ 56%] 354s tests/test_trajectory.py::test_read_write[trr-lh5] PASSED [ 56%] 354s tests/test_trajectory.py::test_read_write[trr-pdb] PASSED [ 56%] 354s tests/test_trajectory.py::test_read_write[trr-pdb.gz] PASSED [ 56%] 354s tests/test_trajectory.py::test_read_write[trr-ncrst] SKIPPED (ncrst ...) [ 56%] 354s tests/test_trajectory.py::test_read_write[trr-rst7] SKIPPED (rst7 ca...) [ 56%] 354s tests/test_trajectory.py::test_read_write[trr-gro] PASSED [ 56%] 354s tests/test_trajectory.py::test_read_write[dcd-nc] PASSED [ 56%] 354s tests/test_trajectory.py::test_read_write[dcd-h5] PASSED [ 56%] 354s tests/test_trajectory.py::test_read_write[dcd-xtc] PASSED [ 56%] 355s tests/test_trajectory.py::test_read_write[dcd-trr] PASSED [ 57%] 355s tests/test_trajectory.py::test_read_write[dcd-dcd] PASSED [ 57%] 355s tests/test_trajectory.py::test_read_write[dcd-mdcrd] SKIPPED (mdcrd ...) [ 57%] 355s tests/test_trajectory.py::test_read_write[dcd-dtr] PASSED [ 57%] 355s tests/test_trajectory.py::test_read_write[dcd-xyz] PASSED [ 57%] 356s tests/test_trajectory.py::test_read_write[dcd-xyz.gz] PASSED [ 57%] 356s tests/test_trajectory.py::test_read_write[dcd-lammpstrj] PASSED [ 57%] 356s tests/test_trajectory.py::test_read_write[dcd-lh5] PASSED [ 57%] 356s tests/test_trajectory.py::test_read_write[dcd-pdb] PASSED [ 57%] 357s tests/test_trajectory.py::test_read_write[dcd-pdb.gz] PASSED [ 57%] 357s tests/test_trajectory.py::test_read_write[dcd-ncrst] SKIPPED (ncrst ...) [ 57%] 357s tests/test_trajectory.py::test_read_write[dcd-rst7] SKIPPED (rst7 ca...) [ 57%] 357s tests/test_trajectory.py::test_read_write[dcd-gro] PASSED [ 58%] 357s tests/test_trajectory.py::test_read_write[mdcrd-nc] PASSED [ 58%] 357s tests/test_trajectory.py::test_read_write[mdcrd-h5] PASSED [ 58%] 357s tests/test_trajectory.py::test_read_write[mdcrd-xtc] PASSED [ 58%] 357s tests/test_trajectory.py::test_read_write[mdcrd-trr] PASSED [ 58%] 357s tests/test_trajectory.py::test_read_write[mdcrd-dcd] PASSED [ 58%] 357s tests/test_trajectory.py::test_read_write[mdcrd-mdcrd] SKIPPED (mdcr...) [ 58%] 357s tests/test_trajectory.py::test_read_write[mdcrd-dtr] SKIPPED (dtr ne...) [ 58%] 357s tests/test_trajectory.py::test_read_write[mdcrd-xyz] PASSED [ 58%] 357s tests/test_trajectory.py::test_read_write[mdcrd-xyz.gz] PASSED [ 58%] 357s tests/test_trajectory.py::test_read_write[mdcrd-lammpstrj] SKIPPED (...) [ 58%] 357s tests/test_trajectory.py::test_read_write[mdcrd-lh5] PASSED [ 59%] 358s tests/test_trajectory.py::test_read_write[mdcrd-pdb] PASSED [ 59%] 359s tests/test_trajectory.py::test_read_write[mdcrd-pdb.gz] PASSED [ 59%] 359s tests/test_trajectory.py::test_read_write[mdcrd-ncrst] SKIPPED (ncrs...) [ 59%] 359s tests/test_trajectory.py::test_read_write[mdcrd-rst7] SKIPPED (rst7 ...) [ 59%] 359s tests/test_trajectory.py::test_read_write[mdcrd-gro] PASSED [ 59%] 359s tests/test_trajectory.py::test_read_write[dtr-nc] PASSED [ 59%] 359s tests/test_trajectory.py::test_read_write[dtr-h5] PASSED [ 59%] 359s tests/test_trajectory.py::test_read_write[dtr-xtc] PASSED [ 59%] 359s tests/test_trajectory.py::test_read_write[dtr-trr] PASSED [ 59%] 359s tests/test_trajectory.py::test_read_write[dtr-dcd] PASSED [ 59%] 359s tests/test_trajectory.py::test_read_write[dtr-mdcrd] SKIPPED (mdcrd ...) [ 60%] 360s tests/test_trajectory.py::test_read_write[dtr-dtr] PASSED [ 60%] 360s tests/test_trajectory.py::test_read_write[dtr-xyz] PASSED [ 60%] 360s tests/test_trajectory.py::test_read_write[dtr-xyz.gz] PASSED [ 60%] 360s tests/test_trajectory.py::test_read_write[dtr-lammpstrj] PASSED [ 60%] 360s tests/test_trajectory.py::test_read_write[dtr-lh5] PASSED [ 60%] 361s tests/test_trajectory.py::test_read_write[dtr-pdb] PASSED [ 60%] 361s tests/test_trajectory.py::test_read_write[dtr-pdb.gz] PASSED [ 60%] 361s tests/test_trajectory.py::test_read_write[dtr-ncrst] SKIPPED (ncrst ...) [ 60%] 361s tests/test_trajectory.py::test_read_write[dtr-rst7] SKIPPED (rst7 ca...) [ 60%] 361s tests/test_trajectory.py::test_read_write[dtr-gro] PASSED [ 60%] 361s tests/test_trajectory.py::test_read_write[xyz-nc] PASSED [ 60%] 361s tests/test_trajectory.py::test_read_write[xyz-h5] PASSED [ 61%] 361s tests/test_trajectory.py::test_read_write[xyz-xtc] PASSED [ 61%] 362s tests/test_trajectory.py::test_read_write[xyz-trr] PASSED [ 61%] 362s tests/test_trajectory.py::test_read_write[xyz-dcd] PASSED [ 61%] 362s tests/test_trajectory.py::test_read_write[xyz-mdcrd] SKIPPED (mdcrd ...) [ 61%] 362s tests/test_trajectory.py::test_read_write[xyz-dtr] SKIPPED (dtr need...) [ 61%] 362s tests/test_trajectory.py::test_read_write[xyz-xyz] PASSED [ 61%] 362s tests/test_trajectory.py::test_read_write[xyz-xyz.gz] PASSED [ 61%] 362s tests/test_trajectory.py::test_read_write[xyz-lammpstrj] SKIPPED (la...) [ 61%] 362s tests/test_trajectory.py::test_read_write[xyz-lh5] PASSED [ 61%] 362s tests/test_trajectory.py::test_read_write[xyz-pdb] PASSED [ 61%] 363s tests/test_trajectory.py::test_read_write[xyz-pdb.gz] PASSED [ 62%] 363s tests/test_trajectory.py::test_read_write[xyz-ncrst] SKIPPED (ncrst ...) [ 62%] 363s tests/test_trajectory.py::test_read_write[xyz-rst7] SKIPPED (rst7 ca...) [ 62%] 363s tests/test_trajectory.py::test_read_write[xyz-gro] PASSED [ 62%] 363s tests/test_trajectory.py::test_read_write[xyz.gz-nc] PASSED [ 62%] 363s tests/test_trajectory.py::test_read_write[xyz.gz-h5] PASSED [ 62%] 363s tests/test_trajectory.py::test_read_write[xyz.gz-xtc] PASSED [ 62%] 363s tests/test_trajectory.py::test_read_write[xyz.gz-trr] PASSED [ 62%] 363s tests/test_trajectory.py::test_read_write[xyz.gz-dcd] PASSED [ 62%] 363s tests/test_trajectory.py::test_read_write[xyz.gz-mdcrd] SKIPPED (mdc...) [ 62%] 363s tests/test_trajectory.py::test_read_write[xyz.gz-dtr] SKIPPED (dtr n...) [ 62%] 363s tests/test_trajectory.py::test_read_write[xyz.gz-xyz] PASSED [ 63%] 363s tests/test_trajectory.py::test_read_write[xyz.gz-xyz.gz] PASSED [ 63%] 363s tests/test_trajectory.py::test_read_write[xyz.gz-lammpstrj] SKIPPED [ 63%] 363s tests/test_trajectory.py::test_read_write[xyz.gz-lh5] PASSED [ 63%] 363s tests/test_trajectory.py::test_read_write[xyz.gz-pdb] PASSED [ 63%] 364s tests/test_trajectory.py::test_read_write[xyz.gz-pdb.gz] PASSED [ 63%] 364s tests/test_trajectory.py::test_read_write[xyz.gz-ncrst] SKIPPED (ncr...) [ 63%] 364s tests/test_trajectory.py::test_read_write[xyz.gz-rst7] SKIPPED (rst7...) [ 63%] 364s tests/test_trajectory.py::test_read_write[xyz.gz-gro] PASSED [ 63%] 364s tests/test_trajectory.py::test_read_write[lammpstrj-nc] PASSED [ 63%] 364s tests/test_trajectory.py::test_read_write[lammpstrj-h5] PASSED [ 63%] 364s tests/test_trajectory.py::test_read_write[lammpstrj-xtc] PASSED [ 63%] 364s tests/test_trajectory.py::test_read_write[lammpstrj-trr] PASSED [ 64%] 364s tests/test_trajectory.py::test_read_write[lammpstrj-dcd] PASSED [ 64%] 364s tests/test_trajectory.py::test_read_write[lammpstrj-mdcrd] SKIPPED (...) [ 64%] 365s tests/test_trajectory.py::test_read_write[lammpstrj-dtr] PASSED [ 64%] 365s tests/test_trajectory.py::test_read_write[lammpstrj-xyz] PASSED [ 64%] 365s tests/test_trajectory.py::test_read_write[lammpstrj-xyz.gz] PASSED [ 64%] 365s tests/test_trajectory.py::test_read_write[lammpstrj-lammpstrj] PASSED [ 64%] 365s tests/test_trajectory.py::test_read_write[lammpstrj-lh5] PASSED [ 64%] 366s tests/test_trajectory.py::test_read_write[lammpstrj-pdb] PASSED [ 64%] 366s tests/test_trajectory.py::test_read_write[lammpstrj-pdb.gz] PASSED [ 64%] 366s tests/test_trajectory.py::test_read_write[lammpstrj-ncrst] SKIPPED (...) [ 64%] 366s tests/test_trajectory.py::test_read_write[lammpstrj-rst7] SKIPPED (r...) [ 65%] 366s tests/test_trajectory.py::test_read_write[lammpstrj-gro] PASSED [ 65%] 366s tests/test_trajectory.py::test_read_write[lh5-nc] PASSED [ 65%] 366s tests/test_trajectory.py::test_read_write[lh5-h5] PASSED [ 65%] 366s tests/test_trajectory.py::test_read_write[lh5-xtc] PASSED [ 65%] 366s tests/test_trajectory.py::test_read_write[lh5-trr] PASSED [ 65%] 366s tests/test_trajectory.py::test_read_write[lh5-dcd] PASSED [ 65%] 366s tests/test_trajectory.py::test_read_write[lh5-mdcrd] SKIPPED (mdcrd ...) [ 65%] 366s tests/test_trajectory.py::test_read_write[lh5-dtr] SKIPPED (dtr need...) [ 65%] 366s tests/test_trajectory.py::test_read_write[lh5-xyz] PASSED [ 65%] 367s tests/test_trajectory.py::test_read_write[lh5-xyz.gz] PASSED [ 65%] 367s tests/test_trajectory.py::test_read_write[lh5-lammpstrj] SKIPPED (la...) [ 66%] 367s tests/test_trajectory.py::test_read_write[lh5-lh5] PASSED [ 66%] 367s tests/test_trajectory.py::test_read_write[lh5-pdb] PASSED [ 66%] 367s tests/test_trajectory.py::test_read_write[lh5-pdb.gz] PASSED [ 66%] 367s tests/test_trajectory.py::test_read_write[lh5-ncrst] SKIPPED (ncrst ...) [ 66%] 367s tests/test_trajectory.py::test_read_write[lh5-rst7] SKIPPED (rst7 ca...) [ 66%] 367s tests/test_trajectory.py::test_read_write[lh5-gro] PASSED [ 66%] 368s tests/test_trajectory.py::test_read_write[pdb-nc] PASSED [ 66%] 368s tests/test_trajectory.py::test_read_write[pdb-h5] PASSED [ 66%] 368s tests/test_trajectory.py::test_read_write[pdb-xtc] PASSED [ 66%] 368s tests/test_trajectory.py::test_read_write[pdb-trr] PASSED [ 66%] 368s tests/test_trajectory.py::test_read_write[pdb-dcd] PASSED [ 66%] 368s tests/test_trajectory.py::test_read_write[pdb-mdcrd] SKIPPED (mdcrd ...) [ 67%] 369s tests/test_trajectory.py::test_read_write[pdb-dtr] PASSED [ 67%] 369s tests/test_trajectory.py::test_read_write[pdb-xyz] PASSED [ 67%] 370s tests/test_trajectory.py::test_read_write[pdb-xyz.gz] PASSED [ 67%] 370s tests/test_trajectory.py::test_read_write[pdb-lammpstrj] PASSED [ 67%] 370s tests/test_trajectory.py::test_read_write[pdb-lh5] PASSED [ 67%] 370s tests/test_trajectory.py::test_read_write[pdb-pdb] PASSED [ 67%] 371s tests/test_trajectory.py::test_read_write[pdb-pdb.gz] PASSED [ 67%] 371s tests/test_trajectory.py::test_read_write[pdb-ncrst] SKIPPED (ncrst ...) [ 67%] 371s tests/test_trajectory.py::test_read_write[pdb-rst7] SKIPPED (rst7 ca...) [ 67%] 371s tests/test_trajectory.py::test_read_write[pdb-gro] PASSED [ 67%] 371s tests/test_trajectory.py::test_read_write[pdb.gz-nc] PASSED [ 68%] 371s tests/test_trajectory.py::test_read_write[pdb.gz-h5] PASSED [ 68%] 372s tests/test_trajectory.py::test_read_write[pdb.gz-xtc] PASSED [ 68%] 372s tests/test_trajectory.py::test_read_write[pdb.gz-trr] PASSED [ 68%] 372s tests/test_trajectory.py::test_read_write[pdb.gz-dcd] PASSED [ 68%] 372s tests/test_trajectory.py::test_read_write[pdb.gz-mdcrd] SKIPPED (mdc...) [ 68%] 373s tests/test_trajectory.py::test_read_write[pdb.gz-dtr] PASSED [ 68%] 373s tests/test_trajectory.py::test_read_write[pdb.gz-xyz] PASSED [ 68%] 373s tests/test_trajectory.py::test_read_write[pdb.gz-xyz.gz] PASSED [ 68%] 373s tests/test_trajectory.py::test_read_write[pdb.gz-lammpstrj] PASSED [ 68%] 373s tests/test_trajectory.py::test_read_write[pdb.gz-lh5] PASSED [ 68%] 374s tests/test_trajectory.py::test_read_write[pdb.gz-pdb] PASSED [ 69%] 374s tests/test_trajectory.py::test_read_write[pdb.gz-pdb.gz] PASSED [ 69%] 374s tests/test_trajectory.py::test_read_write[pdb.gz-ncrst] SKIPPED (ncr...) [ 69%] 374s tests/test_trajectory.py::test_read_write[pdb.gz-rst7] SKIPPED (rst7...) [ 69%] 375s tests/test_trajectory.py::test_read_write[pdb.gz-gro] PASSED [ 69%] 375s tests/test_trajectory.py::test_read_write[ncrst-nc] XFAIL (These ref...) [ 69%] 375s tests/test_trajectory.py::test_read_write[ncrst-h5] XFAIL (These ref...) [ 69%] 375s tests/test_trajectory.py::test_read_write[ncrst-xtc] XFAIL (These re...) [ 69%] 375s tests/test_trajectory.py::test_read_write[ncrst-trr] XFAIL (These re...) [ 69%] 375s tests/test_trajectory.py::test_read_write[ncrst-dcd] XFAIL (These re...) [ 69%] 375s tests/test_trajectory.py::test_read_write[ncrst-mdcrd] XFAIL (These ...) [ 69%] 375s tests/test_trajectory.py::test_read_write[ncrst-dtr] XFAIL (These re...) [ 69%] 375s tests/test_trajectory.py::test_read_write[ncrst-xyz] XFAIL (These re...) [ 70%] 375s tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] XFAIL (These...) [ 70%] 375s tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] XFAIL (Th...) [ 70%] 375s tests/test_trajectory.py::test_read_write[ncrst-lh5] XFAIL (These re...) [ 70%] 375s tests/test_trajectory.py::test_read_write[ncrst-pdb] XFAIL (These re...) [ 70%] 375s tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] XFAIL (These...) [ 70%] 375s tests/test_trajectory.py::test_read_write[ncrst-ncrst] XFAIL (These ...) [ 70%] 375s tests/test_trajectory.py::test_read_write[ncrst-rst7] XFAIL (These r...) [ 70%] 375s tests/test_trajectory.py::test_read_write[ncrst-gro] XFAIL (These re...) [ 70%] 375s tests/test_trajectory.py::test_read_write[rst7-nc] XFAIL (These refe...) [ 70%] 375s tests/test_trajectory.py::test_read_write[rst7-h5] XFAIL (These refe...) [ 70%] 375s tests/test_trajectory.py::test_read_write[rst7-xtc] XFAIL (These ref...) [ 71%] 375s tests/test_trajectory.py::test_read_write[rst7-trr] XFAIL (These ref...) [ 71%] 375s tests/test_trajectory.py::test_read_write[rst7-dcd] XFAIL (These ref...) [ 71%] 375s tests/test_trajectory.py::test_read_write[rst7-mdcrd] XFAIL (These r...) [ 71%] 375s tests/test_trajectory.py::test_read_write[rst7-dtr] XFAIL (These ref...) [ 71%] 375s tests/test_trajectory.py::test_read_write[rst7-xyz] XFAIL (These ref...) [ 71%] 375s tests/test_trajectory.py::test_read_write[rst7-xyz.gz] XFAIL (These ...) [ 71%] 375s tests/test_trajectory.py::test_read_write[rst7-lammpstrj] XFAIL (The...) [ 71%] 375s tests/test_trajectory.py::test_read_write[rst7-lh5] XFAIL (These ref...) [ 71%] 375s tests/test_trajectory.py::test_read_write[rst7-pdb] XFAIL (These ref...) [ 71%] 375s tests/test_trajectory.py::test_read_write[rst7-pdb.gz] XFAIL (These ...) [ 71%] 375s tests/test_trajectory.py::test_read_write[rst7-ncrst] XFAIL (These r...) [ 72%] 375s tests/test_trajectory.py::test_read_write[rst7-rst7] XFAIL (These re...) [ 72%] 375s tests/test_trajectory.py::test_read_write[rst7-gro] XFAIL (These ref...) [ 72%] 375s tests/test_trajectory.py::test_read_write[gro-nc] PASSED [ 72%] 375s tests/test_trajectory.py::test_read_write[gro-h5] PASSED [ 72%] 375s tests/test_trajectory.py::test_read_write[gro-xtc] PASSED [ 72%] 375s tests/test_trajectory.py::test_read_write[gro-trr] PASSED [ 72%] 375s tests/test_trajectory.py::test_read_write[gro-dcd] PASSED [ 72%] 375s tests/test_trajectory.py::test_read_write[gro-mdcrd] SKIPPED (mdcrd ...) [ 72%] 376s tests/test_trajectory.py::test_read_write[gro-dtr] PASSED [ 72%] 376s tests/test_trajectory.py::test_read_write[gro-xyz] PASSED [ 72%] 376s tests/test_trajectory.py::test_read_write[gro-xyz.gz] PASSED [ 72%] 377s tests/test_trajectory.py::test_read_write[gro-lammpstrj] PASSED [ 73%] 377s tests/test_trajectory.py::test_read_write[gro-lh5] PASSED [ 73%] 377s tests/test_trajectory.py::test_read_write[gro-pdb] PASSED [ 73%] 377s tests/test_trajectory.py::test_read_write[gro-pdb.gz] PASSED [ 73%] 377s tests/test_trajectory.py::test_read_write[gro-ncrst] SKIPPED (ncrst ...) [ 73%] 377s tests/test_trajectory.py::test_read_write[gro-rst7] SKIPPED (rst7 ca...) [ 73%] 377s tests/test_trajectory.py::test_read_write[gro-gro] PASSED [ 73%] 377s tests/test_trajectory.py::test_load[nc] PASSED [ 73%] 378s tests/test_trajectory.py::test_load[h5] PASSED [ 73%] 378s tests/test_trajectory.py::test_load[xtc] PASSED [ 73%] 378s tests/test_trajectory.py::test_load[trr] PASSED [ 73%] 378s tests/test_trajectory.py::test_load[dcd] PASSED [ 74%] 378s tests/test_trajectory.py::test_load[mdcrd] PASSED [ 74%] 378s tests/test_trajectory.py::test_load[dtr] PASSED [ 74%] 378s tests/test_trajectory.py::test_load[xyz] PASSED [ 74%] 378s tests/test_trajectory.py::test_load[xyz.gz] PASSED [ 74%] 378s tests/test_trajectory.py::test_load[lammpstrj] PASSED [ 74%] 378s tests/test_trajectory.py::test_load[lh5] PASSED [ 74%] 379s tests/test_trajectory.py::test_load[pdb] PASSED [ 74%] 380s tests/test_trajectory.py::test_load[pdb.gz] PASSED [ 74%] 380s tests/test_trajectory.py::test_load[ncrst] XFAIL (These reference fi...) [ 74%] 380s tests/test_trajectory.py::test_load[rst7] XFAIL (These reference fil...) [ 74%] 380s tests/test_trajectory.py::test_load[gro] PASSED [ 75%] 380s tests/test_trajectory.py::test_hdf5 PASSED [ 75%] 380s tests/test_trajectory.py::test_center PASSED [ 75%] 380s tests/test_trajectory.py::test_center_aind PASSED [ 75%] 380s tests/test_trajectory.py::test_float_atom_indices_exception[nc] PASSED [ 75%] 380s tests/test_trajectory.py::test_float_atom_indices_exception[h5] PASSED [ 75%] 380s tests/test_trajectory.py::test_float_atom_indices_exception[xtc] PASSED [ 75%] 380s tests/test_trajectory.py::test_float_atom_indices_exception[trr] PASSED [ 75%] 380s tests/test_trajectory.py::test_float_atom_indices_exception[dcd] PASSED [ 75%] 380s tests/test_trajectory.py::test_float_atom_indices_exception[mdcrd] PASSED [ 75%] 380s tests/test_trajectory.py::test_float_atom_indices_exception[dtr] PASSED [ 75%] 380s tests/test_trajectory.py::test_float_atom_indices_exception[xyz] PASSED [ 75%] 380s tests/test_trajectory.py::test_float_atom_indices_exception[xyz.gz] PASSED [ 76%] 380s tests/test_trajectory.py::test_float_atom_indices_exception[lammpstrj] PASSED [ 76%] 380s tests/test_trajectory.py::test_float_atom_indices_exception[lh5] PASSED [ 76%] 380s tests/test_trajectory.py::test_float_atom_indices_exception[pdb] PASSED [ 76%] 380s tests/test_trajectory.py::test_float_atom_indices_exception[pdb.gz] PASSED [ 76%] 380s tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] XFAIL [ 76%] 380s tests/test_trajectory.py::test_float_atom_indices_exception[rst7] XFAIL [ 76%] 380s tests/test_trajectory.py::test_float_atom_indices_exception[gro] PASSED [ 76%] 380s tests/test_trajectory.py::test_restrict_atoms PASSED [ 76%] 380s tests/test_trajectory.py::test_restrict_atoms_not_inplace PASSED [ 76%] 380s tests/test_trajectory.py::test_array_vs_matrix PASSED [ 76%] 380s tests/test_trajectory.py::test_pdb_unitcell_loadsave PASSED [ 77%] 380s tests/test_trajectory.py::test_load_combination[nc] PASSED [ 77%] 380s tests/test_trajectory.py::test_load_combination[h5] PASSED [ 77%] 380s tests/test_trajectory.py::test_load_combination[xtc] PASSED [ 77%] 380s tests/test_trajectory.py::test_load_combination[trr] PASSED [ 77%] 380s tests/test_trajectory.py::test_load_combination[dcd] PASSED [ 77%] 380s tests/test_trajectory.py::test_load_combination[mdcrd] PASSED [ 77%] 380s tests/test_trajectory.py::test_load_combination[dtr] PASSED [ 77%] 381s tests/test_trajectory.py::test_load_combination[xyz] PASSED [ 77%] 381s tests/test_trajectory.py::test_load_combination[xyz.gz] PASSED [ 77%] 381s tests/test_trajectory.py::test_load_combination[lammpstrj] PASSED [ 77%] 381s tests/test_trajectory.py::test_load_combination[lh5] PASSED [ 78%] 381s tests/test_trajectory.py::test_load_combination[pdb] PASSED [ 78%] 381s tests/test_trajectory.py::test_load_combination[pdb.gz] PASSED [ 78%] 381s tests/test_trajectory.py::test_load_combination[ncrst] XFAIL (These ...) [ 78%] 381s tests/test_trajectory.py::test_load_combination[rst7] XFAIL (These r...) [ 78%] 381s tests/test_trajectory.py::test_load_combination[gro] PASSED [ 78%] 381s tests/test_trajectory.py::test_no_topology PASSED [ 78%] 381s tests/test_trajectory.py::test_join PASSED [ 78%] 382s tests/test_trajectory.py::test_md_join PASSED [ 78%] 382s tests/test_trajectory.py::test_stack_1 PASSED [ 78%] 382s tests/test_trajectory.py::test_stack_2 PASSED [ 78%] 382s tests/test_trajectory.py::test_seek_read_mode[nc] PASSED [ 78%] 382s tests/test_trajectory.py::test_seek_read_mode[h5] PASSED [ 79%] 382s tests/test_trajectory.py::test_seek_read_mode[xtc] PASSED [ 79%] 382s tests/test_trajectory.py::test_seek_read_mode[trr] PASSED [ 79%] 382s tests/test_trajectory.py::test_seek_read_mode[dcd] PASSED [ 79%] 382s tests/test_trajectory.py::test_seek_read_mode[mdcrd] PASSED [ 79%] 382s tests/test_trajectory.py::test_seek_read_mode[dtr] PASSED [ 79%] 382s tests/test_trajectory.py::test_seek_read_mode[xyz] PASSED [ 79%] 382s tests/test_trajectory.py::test_seek_read_mode[xyz.gz] XFAIL (This is...) [ 79%] 382s tests/test_trajectory.py::test_seek_read_mode[lammpstrj] PASSED [ 79%] 382s tests/test_trajectory.py::test_seek_read_mode[lh5] PASSED [ 79%] 382s tests/test_trajectory.py::test_seek_read_mode[pdb] XFAIL (PDB Files ...) [ 79%] 382s tests/test_trajectory.py::test_seek_read_mode[pdb.gz] XFAIL (PDB Fil...) [ 80%] 382s tests/test_trajectory.py::test_seek_read_mode[ncrst] XFAIL (These re...) [ 80%] 382s tests/test_trajectory.py::test_seek_read_mode[rst7] XFAIL (These ref...) [ 80%] 382s tests/test_trajectory.py::test_seek_read_mode[gro] XFAIL (This is br...) [ 80%] 382s tests/test_trajectory.py::test_load_frame[nc] PASSED [ 80%] 382s tests/test_trajectory.py::test_load_frame[h5] PASSED [ 80%] 382s tests/test_trajectory.py::test_load_frame[xtc] PASSED [ 80%] 382s tests/test_trajectory.py::test_load_frame[trr] PASSED [ 80%] 382s tests/test_trajectory.py::test_load_frame[dcd] PASSED [ 80%] 382s tests/test_trajectory.py::test_load_frame[mdcrd] PASSED [ 80%] 382s tests/test_trajectory.py::test_load_frame[dtr] XFAIL (DTR doesn't lo...) [ 80%] 382s tests/test_trajectory.py::test_load_frame[xyz] PASSED [ 81%] 382s tests/test_trajectory.py::test_load_frame[xyz.gz] PASSED [ 81%] 382s tests/test_trajectory.py::test_load_frame[lammpstrj] PASSED [ 81%] 382s tests/test_trajectory.py::test_load_frame[lh5] PASSED [ 81%] 382s tests/test_trajectory.py::test_load_frame[pdb] PASSED [ 81%] 383s tests/test_trajectory.py::test_load_frame[pdb.gz] PASSED [ 81%] 383s tests/test_trajectory.py::test_load_frame[ncrst] XFAIL (These refere...) [ 81%] 383s tests/test_trajectory.py::test_load_frame[rst7] XFAIL (These referen...) [ 81%] 383s tests/test_trajectory.py::test_load_frame[gro] XFAIL (Gro doesn't im...) [ 81%] 383s tests/test_trajectory.py::test_load_frame_2eqq PASSED [ 81%] 383s tests/test_trajectory.py::test_iterload[nc] PASSED [ 81%] 383s tests/test_trajectory.py::test_iterload[h5] PASSED [ 81%] 383s tests/test_trajectory.py::test_iterload[xtc] PASSED [ 82%] 383s tests/test_trajectory.py::test_iterload[trr] PASSED [ 82%] 383s tests/test_trajectory.py::test_iterload[dcd] PASSED [ 82%] 383s tests/test_trajectory.py::test_iterload[mdcrd] PASSED [ 82%] 383s tests/test_trajectory.py::test_iterload[dtr] XFAIL (This is broken w...) [ 82%] 383s tests/test_trajectory.py::test_iterload[xyz] PASSED [ 82%] 383s tests/test_trajectory.py::test_iterload[xyz.gz] PASSED [ 82%] 383s tests/test_trajectory.py::test_iterload[lammpstrj] PASSED [ 82%] 383s tests/test_trajectory.py::test_iterload[lh5] PASSED [ 82%] 383s tests/test_trajectory.py::test_iterload[pdb] PASSED [ 82%] 383s tests/test_trajectory.py::test_iterload[pdb.gz] PASSED [ 82%] 383s tests/test_trajectory.py::test_iterload[ncrst] SKIPPED (Only 1 frame...) [ 83%] 383s tests/test_trajectory.py::test_iterload[rst7] SKIPPED (Only 1 frame ...) [ 83%] 383s tests/test_trajectory.py::test_iterload[gro] PASSED [ 83%] 386s tests/test_trajectory.py::test_iterload_skip[nc] PASSED [ 83%] 388s tests/test_trajectory.py::test_iterload_skip[h5] PASSED [ 83%] 389s tests/test_trajectory.py::test_iterload_skip[xtc] PASSED [ 83%] 390s tests/test_trajectory.py::test_iterload_skip[trr] PASSED [ 83%] 391s tests/test_trajectory.py::test_iterload_skip[dcd] PASSED [ 83%] 393s tests/test_trajectory.py::test_iterload_skip[mdcrd] PASSED [ 83%] 393s tests/test_trajectory.py::test_iterload_skip[dtr] PASSED [ 83%] 393s tests/test_trajectory.py::test_iterload_skip[xyz] PASSED [ 83%] 394s tests/test_trajectory.py::test_iterload_skip[xyz.gz] PASSED [ 84%] 396s tests/test_trajectory.py::test_iterload_skip[lammpstrj] PASSED [ 84%] 397s tests/test_trajectory.py::test_iterload_skip[lh5] PASSED [ 84%] 397s tests/test_trajectory.py::test_iterload_skip[pdb] XFAIL (PDB Iterloa...) [ 84%] 397s tests/test_trajectory.py::test_iterload_skip[pdb.gz] XFAIL (PDB Iter...) [ 84%] 397s tests/test_trajectory.py::test_iterload_skip[ncrst] XFAIL (These ref...) [ 84%] 397s tests/test_trajectory.py::test_iterload_skip[rst7] XFAIL (These refe...) [ 84%] 397s tests/test_trajectory.py::test_iterload_skip[gro] XFAIL (Not impleme...) [ 84%] 397s tests/test_trajectory.py::test_iterload_chunk_dcd PASSED [ 84%] 397s tests/test_trajectory.py::test_save_load[nc] PASSED [ 84%] 397s tests/test_trajectory.py::test_save_load[h5] PASSED [ 84%] 397s tests/test_trajectory.py::test_save_load[xtc] PASSED [ 84%] 397s tests/test_trajectory.py::test_save_load[trr] PASSED [ 85%] 397s tests/test_trajectory.py::test_save_load[dcd] PASSED [ 85%] 397s tests/test_trajectory.py::test_save_load[mdcrd] PASSED [ 85%] 397s tests/test_trajectory.py::test_save_load[dtr] PASSED [ 85%] 397s tests/test_trajectory.py::test_save_load[xyz] PASSED [ 85%] 397s tests/test_trajectory.py::test_save_load[xyz.gz] PASSED [ 85%] 397s tests/test_trajectory.py::test_save_load[lammpstrj] PASSED [ 85%] 397s tests/test_trajectory.py::test_save_load[lh5] PASSED [ 85%] 397s tests/test_trajectory.py::test_save_load[pdb] PASSED [ 85%] 397s tests/test_trajectory.py::test_save_load[pdb.gz] PASSED [ 85%] 397s tests/test_trajectory.py::test_save_load[ncrst] PASSED [ 85%] 397s tests/test_trajectory.py::test_save_load[rst7] PASSED [ 86%] 397s tests/test_trajectory.py::test_save_load[gro] PASSED [ 86%] 397s tests/test_trajectory.py::test_force_overwrite[nc] PASSED [ 86%] 397s tests/test_trajectory.py::test_force_overwrite[h5] PASSED [ 86%] 397s tests/test_trajectory.py::test_force_overwrite[xtc] PASSED [ 86%] 397s tests/test_trajectory.py::test_force_overwrite[trr] PASSED [ 86%] 397s tests/test_trajectory.py::test_force_overwrite[dcd] PASSED [ 86%] 397s tests/test_trajectory.py::test_force_overwrite[mdcrd] PASSED [ 86%] 397s tests/test_trajectory.py::test_force_overwrite[dtr] XFAIL (This is b...) [ 86%] 397s tests/test_trajectory.py::test_force_overwrite[xyz] PASSED [ 86%] 397s tests/test_trajectory.py::test_force_overwrite[xyz.gz] PASSED [ 86%] 397s tests/test_trajectory.py::test_force_overwrite[lammpstrj] PASSED [ 87%] 397s tests/test_trajectory.py::test_force_overwrite[lh5] PASSED [ 87%] 397s tests/test_trajectory.py::test_force_overwrite[pdb] PASSED [ 87%] 397s tests/test_trajectory.py::test_force_overwrite[pdb.gz] PASSED [ 87%] 397s tests/test_trajectory.py::test_force_overwrite[ncrst] PASSED [ 87%] 397s tests/test_trajectory.py::test_force_overwrite[rst7] PASSED [ 87%] 397s tests/test_trajectory.py::test_force_overwrite[gro] PASSED [ 87%] 397s tests/test_trajectory.py::test_force_noverwrite[nc] PASSED [ 87%] 397s tests/test_trajectory.py::test_force_noverwrite[h5] PASSED [ 87%] 397s tests/test_trajectory.py::test_force_noverwrite[xtc] PASSED [ 87%] 397s tests/test_trajectory.py::test_force_noverwrite[trr] PASSED [ 87%] 397s tests/test_trajectory.py::test_force_noverwrite[dcd] PASSED [ 87%] 397s tests/test_trajectory.py::test_force_noverwrite[mdcrd] PASSED [ 88%] 397s tests/test_trajectory.py::test_force_noverwrite[dtr] PASSED [ 88%] 397s tests/test_trajectory.py::test_force_noverwrite[xyz] PASSED [ 88%] 397s tests/test_trajectory.py::test_force_noverwrite[xyz.gz] PASSED [ 88%] 397s tests/test_trajectory.py::test_force_noverwrite[lammpstrj] PASSED [ 88%] 397s tests/test_trajectory.py::test_force_noverwrite[lh5] PASSED [ 88%] 397s tests/test_trajectory.py::test_force_noverwrite[pdb] PASSED [ 88%] 397s tests/test_trajectory.py::test_force_noverwrite[pdb.gz] PASSED [ 88%] 397s tests/test_trajectory.py::test_force_noverwrite[ncrst] PASSED [ 88%] 397s tests/test_trajectory.py::test_force_noverwrite[rst7] PASSED [ 88%] 397s tests/test_trajectory.py::test_force_noverwrite[gro] PASSED [ 88%] 397s tests/test_trajectory.py::test_open_and_load PASSED [ 89%] 398s tests/test_trajectory.py::test_length PASSED [ 89%] 398s tests/test_trajectory.py::test_unitcell[nc] PASSED [ 89%] 398s tests/test_trajectory.py::test_unitcell[h5] PASSED [ 89%] 398s tests/test_trajectory.py::test_unitcell[xtc] PASSED [ 89%] 398s tests/test_trajectory.py::test_unitcell[trr] PASSED [ 89%] 398s tests/test_trajectory.py::test_unitcell[dcd] PASSED [ 89%] 398s tests/test_trajectory.py::test_unitcell[mdcrd] PASSED [ 89%] 398s tests/test_trajectory.py::test_unitcell[dtr] XFAIL (dtr seems to nee...) [ 89%] 398s tests/test_trajectory.py::test_unitcell[xyz] PASSED [ 89%] 398s tests/test_trajectory.py::test_unitcell[xyz.gz] PASSED [ 89%] 398s tests/test_trajectory.py::test_unitcell[lammpstrj] XFAIL (lammpstrj ...) [ 90%] 398s tests/test_trajectory.py::test_unitcell[lh5] PASSED [ 90%] 398s tests/test_trajectory.py::test_unitcell[pdb] PASSED [ 90%] 398s tests/test_trajectory.py::test_unitcell[pdb.gz] PASSED [ 90%] 398s tests/test_trajectory.py::test_unitcell[ncrst] XFAIL (ncrst seems to...) [ 90%] 398s tests/test_trajectory.py::test_unitcell[rst7] XFAIL (rst7 seems to n...) [ 90%] 398s tests/test_trajectory.py::test_unitcell[gro] PASSED [ 90%] 398s tests/test_trajectory.py::test_chunk0_iterload PASSED [ 90%] 398s tests/test_trajectory.py::test_hashing PASSED [ 90%] 398s tests/test_trajectory.py::test_smooth PASSED [ 90%] 398s tests/test_trajectory.py::test_load_pdb_no_standard_names PASSED [ 90%] 398s tests/test_trajectory.py::test_load_with_atom_indices PASSED [ 90%] 398s tests/test_trajectory.py::test_atom_slicing PASSED [ 91%] 398s tests/test_trajectory.py::test_load_with_frame PASSED [ 91%] 398s tests/test_trajectory.py::test_add_remove_atoms PASSED [ 91%] 398s tests/test_trr.py::test_1 PASSED [ 91%] 398s tests/test_trr.py::test_read_stride PASSED [ 91%] 398s tests/test_trr.py::test_read_stride_n_frames PASSED [ 91%] 398s tests/test_trr.py::test_read_stride_offsets PASSED [ 91%] 398s tests/test_trr.py::test_read_stride_n_frames_offsets PASSED [ 91%] 398s tests/test_trr.py::test_read_stride_switching PASSED [ 91%] 398s tests/test_trr.py::test_write_read PASSED [ 91%] 398s tests/test_trr.py::test_read_atomindices_1 PASSED [ 91%] 398s tests/test_trr.py::test_read_atomindices_2 PASSED [ 92%] 398s tests/test_trr.py::test_deficient_shape PASSED [ 92%] 398s tests/test_trr.py::test_ragged_1 PASSED [ 92%] 398s tests/test_trr.py::test_ragged_2 PASSED [ 92%] 398s tests/test_trr.py::test_malformed PASSED [ 92%] 398s tests/test_trr.py::test_tell PASSED [ 92%] 398s tests/test_trr.py::test_seek PASSED [ 92%] 398s tests/test_trr.py::test_get_velocities PASSED [ 92%] 398s tests/test_trr.py::test_get_forces PASSED [ 92%] 398s tests/test_trr.py::test_get_velocities_and_forces PASSED [ 92%] 398s tests/test_trr.py::test_get_velocities_forces_atom_indices_1 PASSED [ 92%] 399s tests/test_trr.py::test_get_velocities_forces_atom_indices_2 PASSED [ 93%] 399s tests/test_trr.py::test_read_velocities_do_not_exist PASSED [ 93%] 399s tests/test_trr.py::test_read_forces_do_not_exist PASSED [ 93%] 399s tests/test_utils.py::test_unitcell_0 PASSED [ 93%] 399s tests/test_utils.py::test_unitcell_1 PASSED [ 93%] 399s tests/test_utils.py::test_ensure_type_1 PASSED [ 93%] 399s tests/test_utils.py::test_ensure_type_2 PASSED [ 93%] 399s tests/test_utils.py::test_ensure_type_25 PASSED [ 93%] 399s tests/test_utils.py::test_ensure_type_3 PASSED [ 93%] 399s tests/test_utils.py::test_ensure_type_4 PASSED [ 93%] 399s tests/test_utils.py::test_ensure_type_5 PASSED [ 93%] 399s tests/test_utils.py::test_ensure_type_6 PASSED [ 93%] 399s tests/test_utils.py::test_ensure_type_7 PASSED [ 94%] 399s tests/test_utils.py::test_ensure_type_8 PASSED [ 94%] 399s tests/test_utils.py::test_ensure_type_9 PASSED [ 94%] 399s tests/test_utils.py::test_ensure_type_10 PASSED [ 94%] 399s tests/test_utils.py::test_ensure_type_11 PASSED [ 94%] 399s tests/test_utils.py::test_ensure_type_12 PASSED [ 94%] 399s tests/test_utils.py::test_ensure_type_13 PASSED [ 94%] 399s tests/test_utils.py::test_ensure_type_14 PASSED [ 94%] 399s tests/test_utils.py::test_ensure_type_15 PASSED [ 94%] 399s tests/test_utils.py::test_delay_import_fail_1 PASSED [ 94%] 399s tests/test_utils.py::test_delay_import PASSED [ 94%] 399s tests/test_utils.py::test_unit_0 PASSED [ 95%] 399s tests/test_utils.py::test_unit_1 PASSED [ 95%] 399s tests/test_utils.py::test_unit_2 PASSED [ 95%] 399s tests/test_utils.py::test_unit_3 PASSED [ 95%] 399s tests/test_xml.py::test_xml PASSED [ 95%] 399s tests/test_xtc.py::test_read_chunk1 PASSED [ 95%] 399s tests/test_xtc.py::test_read_stride PASSED [ 95%] 399s tests/test_xtc.py::test_read_stride_n_frames PASSED [ 95%] 399s tests/test_xtc.py::test_read_stride_offsets PASSED [ 95%] 399s tests/test_xtc.py::test_read_stride_n_frames_offsets PASSED [ 95%] 399s tests/test_xtc.py::test_read_stride_switching_offsets PASSED [ 95%] 399s tests/test_xtc.py::test_read_atomindices_1 PASSED [ 96%] 399s tests/test_xtc.py::test_read_atomindices_w_stride PASSED [ 96%] 399s tests/test_xtc.py::test_read_atomindices_2 PASSED [ 96%] 399s tests/test_xtc.py::test_read_chunk2 PASSED [ 96%] 399s tests/test_xtc.py::test_read_chunk3 PASSED [ 96%] 399s tests/test_xtc.py::test_write_0 PASSED [ 96%] 399s tests/test_xtc.py::test_write_1 PASSED [ 96%] 399s tests/test_xtc.py::test_write_2 PASSED [ 96%] 399s tests/test_xtc.py::test_read_error_0 PASSED [ 96%] 399s tests/test_xtc.py::test_write_error_0 PASSED [ 96%] 399s tests/test_xtc.py::test_read_error_1 PASSED [ 96%] 399s tests/test_xtc.py::test_read_error_2 PASSED [ 96%] 399s tests/test_xtc.py::test_xtc_write_wierd_0 PASSED [ 97%] 399s tests/test_xtc.py::test_tell PASSED [ 97%] 399s tests/test_xtc.py::test_seek PASSED [ 97%] 399s tests/test_xtc.py::test_seek_natoms9 PASSED [ 97%] 399s tests/test_xtc.py::test_seek_out_of_bounds PASSED [ 97%] 399s tests/test_xtc.py::test_ragged_1 PASSED [ 97%] 399s tests/test_xtc.py::test_ragged_2 PASSED [ 97%] 399s tests/test_xtc.py::test_short_traj PASSED [ 97%] 399s tests/test_xtc.py::test_flush PASSED [ 97%] 399s tests/test_xyz.py::test_read_0 PASSED [ 97%] 399s tests/test_xyz.py::test_read_1 PASSED [ 97%] 399s tests/test_xyz.py::test_read_gz PASSED [ 98%] 399s tests/test_xyz.py::test_read_write PASSED [ 98%] 399s tests/test_xyz.py::test_mdwrite PASSED [ 98%] 399s tests/test_xyz.py::test_multiread PASSED [ 98%] 399s tests/test_xyz.py::test_seek PASSED [ 98%] 399s tests/test_xyz.py::test_len PASSED [ 98%] 399s tests/test_zipped.py::test_read_gz PASSED [ 98%] 399s tests/test_zipped.py::test_write_gz PASSED [ 98%] 399s tests/test_zipped.py::test_read_bz2 PASSED [ 98%] 399s tests/test_zipped.py::test_write_bz2 PASSED [ 98%] 401s examples/test_examples.py::test_example_notebook[rmsd-drift.ipynb] PASSED [ 98%] 403s examples/test_examples.py::test_example_notebook[solvent-accessible-surface-area.ipynb] PASSED [ 99%] 403s examples/test_examples.py::test_example_notebook[native-contact.ipynb] SKIPPED [ 99%] 405s examples/test_examples.py::test_example_notebook[centroids.ipynb] PASSED [ 99%] 405s examples/test_examples.py::test_example_notebook[simulation-with-openmm.ipynb] SKIPPED [ 99%] 407s examples/test_examples.py::test_example_notebook[ramachandran-plot.ipynb] PASSED [ 99%] 409s examples/test_examples.py::test_example_notebook[principal-components.ipynb] PASSED [ 99%] 409s examples/test_examples.py::test_example_notebook[hbonds.ipynb] SKIPPED [ 99%] 410s examples/test_examples.py::test_example_notebook[iterload.ipynb] PASSED [ 99%] 411s examples/test_examples.py::test_example_notebook[atom-selection.ipynb] PASSED [ 99%] 412s examples/test_examples.py::test_example_notebook[clustering.ipynb] PASSED [ 99%] 413s examples/test_examples.py::test_example_notebook[two-pass-clustering.ipynb] PASSED [ 99%] 415s examples/test_examples.py::test_example_notebook[rmsd-benchmark.ipynb] PASSED [100%] 415s 415s =============================== warnings summary =============================== 415s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:56 415s /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. 415s THIS_ATOM = ast.Name(id="atom", ctx=ast.Load(), SINGLETON=True) 415s 415s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:57 415s /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. 415s RE_MODULE = ast.Name(id="re", ctx=ast.Load(), SINGLETON=True) 415s 415s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 415s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 415s given by the platformdirs library. To remove this warning and 415s see the appropriate new directories, set the environment variable 415s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 415s The use of platformdirs will be the default in `jupyter_core` v6 415s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 415s 415s examples/test_examples.py:26 415s /tmp/autopkgtest.Wg29hx/build.gDu/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 415s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 415s 415s tests/test_contact.py::test_contact_0 415s tests/test_contact.py::test_contact_4 415s /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. 415s warnings.warn( 415s 415s tests/test_contact.py::test_contact_3 415s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:271: RuntimeWarning: overflow encountered in exp 415s np.exp( 415s 415s tests/test_contact.py::test_contact_3 415s /tmp/autopkgtest.Wg29hx/build.gDu/src/tests/test_contact.py:115: RuntimeWarning: divide by zero encountered in divide 415s beta / np.log(np.sum(np.exp(beta / maps[t, r0, r1]))), 415s 415s tests/test_dcd.py::test_do_overwrite 415s tests/test_dcd.py::test_ragged_1 415s tests/test_dcd.py::test_ragged_2 415s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting xyz dtype=float64 to 415s warnings.warn( 415s 415s tests/test_distance.py::test_6 415s :488: RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject 415s 415s tests/test_drid.py::test_drid_2 415s /tmp/autopkgtest.Wg29hx/build.gDu/src/tests/test_drid.py:62: RuntimeWarning: divide by zero encountered in divide 415s recip = 1 / squareform(pdist(t.xyz[i])) 415s 415s tests/test_dssp.py::test_1[1vii.pdb] 415s tests/test_gro.py::test_read_write 415s tests/test_gro.py::test_read_write_precision 415s tests/test_gro.py::test_load 415s tests/test_shape.py::test_principal_moments 415s tests/test_shape.py::test_asphericity 415s tests/test_shape.py::test_shape_metrics 415s /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. 415s warnings.warn( 415s 415s tests/test_geometry.py::test_dihedral_indices 415s tests/test_geometry.py::test_dihedral_indices 415s /usr/lib/python3/dist-packages/mdtraj/geometry/dihedral.py:237: DeprecationWarning: Passing a Trajectory object to _atom_sequence isdeprecated. Please pass a Topology object 415s warnings.warn( 415s 415s tests/test_gro.py::test_load 415s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq 415s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:364: UserWarning: WARNING: two consecutive residues with same number (GST, HST) 415s warnings.warn( 415s 415s tests/test_pdb.py::test_blank_indexing 415s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:204: UserWarning: Need to guess atom number starting from atom 100000. 415s warnings.warn(f'Need to guess atom number {num_str} starting from atom {pdbstructure._next_atom_number}.') 415s 415s tests/test_pdb.py::test_blank_indexing 415s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:271: UserWarning: Need to guess residue number string starting from residue10000, atom 100000. 415s warnings.warn(f'Need to guess residue number string {num_str} starting from residue{pdbstructure._next_residue_number}, atom {pdbstructure._next_atom_number}.') 415s 415s tests/test_rdf.py::test_rdf_norm 415s tests/test_rdf.py::test_rdf_t_norm[0] 415s tests/test_rdf.py::test_rdf_t_norm[2] 415s tests/test_rdf.py::test_rdf_t_norm[4] 415s tests/test_selection.py::test_re 415s tests/test_selection.py::test_re 415s tests/test_topology.py::test_select_pairs 415s tests/test_topology.py::test_select_pairs 415s /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. 415s left=ast.Call( 415s 415s tests/test_rdf.py::test_rdf_norm 415s tests/test_rdf.py::test_rdf_t_norm[0] 415s tests/test_rdf.py::test_rdf_t_norm[2] 415s tests/test_rdf.py::test_rdf_t_norm[4] 415s tests/test_selection.py::test_re 415s tests/test_selection.py::test_re 415s tests/test_topology.py::test_select_pairs 415s tests/test_topology.py::test_select_pairs 415s /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. 415s left=ast.Call( 415s 415s tests/test_trajectory.py::test_float_atom_indices_exception[gro] 415s tests/test_trajectory.py::test_atom_slicing 415s /usr/lib/python3/dist-packages/mdtraj/core/topology.py:84: UserWarning: atom_indices are not monotonically increasing 415s warnings.warn("atom_indices are not monotonically increasing") 415s 415s tests/test_utils.py::test_ensure_type_8 415s tests/test_utils.py::test_ensure_type_9 415s tests/test_utils.py::test_ensure_type_13 415s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=float64 to 415s warnings.warn( 415s 415s tests/test_utils.py::test_ensure_type_11 415s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=int64 to 415s warnings.warn( 415s 415s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 415s =========================== short test summary info ============================ 415s SKIPPED [1] tests/test_dihedral.py:56: pymol executable not found 415s SKIPPED [1] tests/test_dihedral.py:181: pymol executable not found 415s SKIPPED [16] tests/test_docstrings.py:38: Skip checking certain modules' docstrings 415s SKIPPED [1] tests/test_geometry.py:300: Not doing performance testing 415s SKIPPED [1] tests/test_geometry.py:322: Not doing performance testing 415s SKIPPED [1] tests/test_hdf5.py:104: requires openmm.units 415s SKIPPED [1] tests/test_hdf5.py:156: requires openmm.units 415s SKIPPED [1] tests/test_hdf5.py:223: requires openmm.units 415s SKIPPED [1] tests/test_mol2.py:59: Requires obabel 415s SKIPPED [1] tests/test_netcdf.py:271: This test requires cpptraj from AmberTools to be installed (http://ambermd.org) 415s SKIPPED [1] tests/test_nmr.py:11: SPARTA+ binary not found 415s SKIPPED [1] tests/test_nmr.py:26: PPM binary not found 415s SKIPPED [1] tests/test_nmr.py:42: SHIFTX2 binary not found or running on travis. 415s SKIPPED [1] tests/test_pdbx.py:43: test_pdbx.py needs OpenMM. 415s SKIPPED [2] tests/test_psf.py:93: This test requires the VMD executable: http://www.ks.uiuc.edu/Research/vmd/ 415s SKIPPED [1] tests/test_rdf.py:64: Binning does not match up with gromacs currently. 415s SKIPPED [1] tests/test_rdf.py:200: Binning does not match up with gromacs currently. 415s SKIPPED [1] tests/test_rdf.py:219: Expected failure for NumPy < 2.0 due to histogram output differences 415s SKIPPED [1] tests/test_reporter.py:58: test_reporter.py needs OpenMM. 415s SKIPPED [1] tests/test_reporter.py:145: test_reporter.py needs OpenMM. 415s SKIPPED [1] tests/test_reporter.py:245: test_reporter.py needs OpenMM. 415s SKIPPED [1] tests/test_selection.py:267: failed to parse selection 415s SKIPPED [1] tests/test_thermodynamic_properties.py:161: Thermal expansion test doesn't work. 415s SKIPPED [1] tests/test_topology.py:45: needs OpenMM 415s SKIPPED [1] tests/test_topology.py:62: needs OpenMM 415s SKIPPED [1] tests/test_topology.py:72: needs OpenMM 415s SKIPPED [1] tests/test_topology.py:81: needs OpenMM 415s SKIPPED [1] tests/test_topology.py:91: needs OpenMM 415s SKIPPED [1] tests/test_topology.py:97: needs OpenMM 415s SKIPPED [1] tests/test_topology.py:247: needs OpenMM 415s SKIPPED [1] tests/test_trajectory.py:129: xyz does not store box information 415s SKIPPED [1] tests/test_trajectory.py:129: xyz.gz does not store box information 415s SKIPPED [1] tests/test_trajectory.py:129: lh5 does not store box information 415s SKIPPED [1] tests/test_trajectory.py:129: pdb does not store box information 415s SKIPPED [1] tests/test_trajectory.py:129: pdb.gz does not store box information 415s SKIPPED [1] tests/test_trajectory.py:226: mdcrd can only store rectilinear boxes 415s SKIPPED [1] tests/test_trajectory.py:224: ncrst can only store 1 frame per file 415s SKIPPED [1] tests/test_trajectory.py:224: rst7 can only store 1 frame per file 415s SKIPPED [14] tests/test_trajectory.py:248: mdcrd can only store rectilinear boxes 415s SKIPPED [14] tests/test_trajectory.py:246: ncrst can only store 1 frame per file 415s SKIPPED [14] tests/test_trajectory.py:246: rst7 can only store 1 frame per file 415s SKIPPED [4] tests/test_trajectory.py:256: dtr needs to write unitcells 415s SKIPPED [4] tests/test_trajectory.py:256: lammpstrj needs to write unitcells 415s SKIPPED [2] tests/test_trajectory.py:640: Only 1 frame per file format 415s SKIPPED [2] examples/test_examples.py:77: Network access required 415s SKIPPED [1] examples/test_examples.py:77: Openmm required for example notebook `simulation-with-openmm.ipynb` 415s XFAIL tests/test_trajectory.py::test_read_path[ncrst] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_path[rst7] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[ncrst-nc] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[ncrst-h5] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xtc] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[ncrst-trr] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dcd] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[ncrst-mdcrd] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dtr] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lh5] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[ncrst-ncrst] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[ncrst-rst7] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[ncrst-gro] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[rst7-nc] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[rst7-h5] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[rst7-xtc] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[rst7-trr] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[rst7-dcd] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[rst7-mdcrd] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[rst7-dtr] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz.gz] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[rst7-lammpstrj] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[rst7-lh5] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb.gz] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[rst7-ncrst] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[rst7-rst7] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_read_write[rst7-gro] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_load[ncrst] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_load[rst7] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[rst7] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_load_combination[ncrst] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_load_combination[rst7] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_seek_read_mode[xyz.gz] - reason: This is broken 415s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb] - reason: PDB Files don't support seeking 415s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb.gz] - reason: PDB Files don't support seeking 415s XFAIL tests/test_trajectory.py::test_seek_read_mode[ncrst] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_seek_read_mode[rst7] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_seek_read_mode[gro] - reason: This is broken 415s XFAIL tests/test_trajectory.py::test_load_frame[dtr] - reason: DTR doesn't load a single frame properly 415s XFAIL tests/test_trajectory.py::test_load_frame[ncrst] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_load_frame[rst7] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_load_frame[gro] - reason: Gro doesn't implement seek 415s XFAIL tests/test_trajectory.py::test_iterload[dtr] - reason: This is broken with dtr 415s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb] - reason: PDB Iterloads an extra frame!! 415s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb.gz] - reason: PDB Iterloads an extra frame!! 415s XFAIL tests/test_trajectory.py::test_iterload_skip[ncrst] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_iterload_skip[rst7] - reason: These reference files don't exist yet 415s XFAIL tests/test_trajectory.py::test_iterload_skip[gro] - reason: Not implemented for some reason 415s XFAIL tests/test_trajectory.py::test_force_overwrite[dtr] - reason: This is broken with dtr 415s XFAIL tests/test_trajectory.py::test_unitcell[dtr] - reason: dtr seems to need unit vectors 415s XFAIL tests/test_trajectory.py::test_unitcell[lammpstrj] - reason: lammpstrj seems to need unit vectors 415s XFAIL tests/test_trajectory.py::test_unitcell[ncrst] - reason: ncrst seems to need unit vectors 415s XFAIL tests/test_trajectory.py::test_unitcell[rst7] - reason: rst7 seems to need unit vectors 415s = 963 passed, 109 skipped, 12 deselected, 61 xfailed, 48 warnings in 209.01s (0:03:29) = 416s autopkgtest [03:13:03]: test command1: -----------------------] 416s autopkgtest [03:13:03]: test command1: - - - - - - - - - - results - - - - - - - - - - 416s command1 PASS 417s autopkgtest [03:13:04]: test command2: preparing testbed 417s Reading package lists... 417s Building dependency tree... 417s Reading state information... 418s Starting pkgProblemResolver with broken count: 0 418s Starting 2 pkgProblemResolver with broken count: 0 418s Done 418s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 419s autopkgtest [03:13:06]: test command2: pytest-3 -k 'test_3 or test_pdb_from_url or test_1vii_url_and_gz' 419s autopkgtest [03:13:06]: test command2: [----------------------- 420s ============================= test session starts ============================== 420s platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 -- /usr/bin/python3 420s cachedir: .pytest_cache 420s rootdir: /tmp/autopkgtest.Wg29hx/build.gDu/src 420s configfile: pyproject.toml 420s testpaths: tests, examples 420s plugins: typeguard-4.4.1 420s collecting ... collected 1145 items / 1135 deselected / 10 selected 420s 420s tests/test_distance.py::test_3 PASSED [ 10%] 420s tests/test_distance.py::test_3p PASSED [ 20%] 424s tests/test_dssp.py::test_3[1GAI] PASSED [ 30%] 427s tests/test_dssp.py::test_3[6gsv] FAILED [ 40%] 429s tests/test_dssp.py::test_3[2AAC] PASSED [ 50%] 429s tests/test_nmr.py::test_3_scalar_couplings PASSED [ 60%] 434s tests/test_pdb.py::test_pdb_from_url PASSED [ 70%] 434s tests/test_pdb.py::test_3nch_conect PASSED [ 80%] 436s tests/test_pdb.py::test_3nch_serial_resSeq PASSED [ 90%] 440s tests/test_pdb.py::test_1vii_url_and_gz PASSED [100%] 440s 440s =================================== FAILURES =================================== 440s _________________________________ test_3[6gsv] _________________________________ 440s 440s get_fn = ._get_fn at 0x7eac48134860> 440s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_3_6gsv_0'), pdbid = '6gsv' 440s 440s @pytest.mark.parametrize('pdbid', ["1GAI", "6gsv", "2AAC"]) 440s def test_3(get_fn, tmpdir, pdbid): 440s """This test checks dssp assignments on pdb files downloaded from rcsb""" 440s # 1COY gives a small error, due to a broken chain. 440s > t = md.load_pdb("http://www.rcsb.org/pdb/files/%s.pdb" % pdbid) 440s 440s tests/test_dssp.py:70: 440s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 440s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:151: in load_pdb 440s with PDBTrajectoryFile(filename, standard_names=standard_names, top=top) as f: 440s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:291: in __init__ 440s self._read_models() 440s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:629: in _read_models 440s pdb = PdbStructure(self._file, load_all_models=True) 440s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:376: in __init__ 440s self._load(input_stream) 440s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:392: in _load 440s self._add_atom(Atom(pdb_line, self)) 440s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 440s 440s self = 440s pdb_line = 'ATOM 20A 22 92 6164 5555 -342 -2115 2125 N \n' 440s pdbstructure = 440s 440s def __init__(self, pdb_line, pdbstructure=None): 440s """Create a new pdb.Atom from an ATOM or HETATM line. 440s 440s Example line: 440s ATOM 2209 CB TYR A 299 6.167 22.607 20.046 1.00 8.12 C 440s 00000000011111111112222222222333333333344444444445555555555666666666677777777778 440s 12345678901234567890123456789012345678901234567890123456789012345678901234567890 440s 440s ATOM line format description from 440s http://deposit.rcsb.org/adit/docs/pdb_atom_format.html: 440s 440s COLUMNS DATA TYPE CONTENTS 440s -------------------------------------------------------------------------------- 440s 1 - 6 Record name "ATOM " 440s 7 - 11 Integer Atom serial number. 440s 13 - 16 Atom Atom name. 440s 17 Character Alternate location indicator. 440s 18 - 20 Residue name Residue name. 440s 22 Character Chain identifier. 440s 23 - 26 Integer Residue sequence number. 440s 27 AChar Code for insertion of residues. 440s 31 - 38 Real(8.3) Orthogonal coordinates for X in Angstroms. 440s 39 - 46 Real(8.3) Orthogonal coordinates for Y in Angstroms. 440s 47 - 54 Real(8.3) Orthogonal coordinates for Z in Angstroms. 440s 55 - 60 Real(6.2) Occupancy (Default = 1.0). 440s 61 - 66 Real(6.2) Temperature factor (Default = 0.0). 440s 73 - 76 LString(4) Segment identifier, left-justified. 440s 77 - 78 LString(2) Element symbol, right-justified. 440s 79 - 80 LString(2) Charge on the atom. 440s 440s """ 440s # We might modify first/final status during _finalize() methods 440s self.is_first_atom_in_chain = False 440s self.is_final_atom_in_chain = False 440s self.is_first_residue_in_chain = False 440s self.is_final_residue_in_chain = False 440s # Start parsing fields from pdb line 440s self.record_name = pdb_line[0:6].strip() 440s 440s self.serial_number = _read_atom_number(pdb_line[6:11], pdbstructure=pdbstructure) 440s 440s self.name_with_spaces = pdb_line[12:16] 440s alternate_location_indicator = pdb_line[16] 440s 440s self.residue_name_with_spaces = pdb_line[17:20] 440s # In some MD codes, notably ffamber in gromacs, residue name has a fourth character in 440s # column 21 440s possible_fourth_character = pdb_line[20:21] 440s if possible_fourth_character != " ": 440s # Fourth character should only be there if official 3 are already full 440s if len(self.residue_name_with_spaces.strip()) != 3: 440s raise ValueError("Misaligned residue name: %s" % pdb_line) 440s self.residue_name_with_spaces += possible_fourth_character 440s self.residue_name = self.residue_name_with_spaces.strip() 440s 440s self.chain_id = pdb_line[21] 440s self.residue_number = _read_residue_number(pdb_line[22:26], pdbstructure, self) 440s 440s self.insertion_code = pdb_line[26] 440s # coordinates, occupancy, and temperature factor belong in Atom.Location object 440s > x = float(pdb_line[30:38]) 440s E ValueError: could not convert string to float: '555 -3' 440s 440s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:973: ValueError 440s =============================== warnings summary =============================== 440s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:56 440s /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. 440s THIS_ATOM = ast.Name(id="atom", ctx=ast.Load(), SINGLETON=True) 440s 440s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:57 440s /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. 440s RE_MODULE = ast.Name(id="re", ctx=ast.Load(), SINGLETON=True) 440s 440s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 440s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 440s given by the platformdirs library. To remove this warning and 440s see the appropriate new directories, set the environment variable 440s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 440s The use of platformdirs will be the default in `jupyter_core` v6 440s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 440s 440s examples/test_examples.py:26 440s /tmp/autopkgtest.Wg29hx/build.gDu/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 440s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 440s 440s tests/test_dssp.py::test_3[6gsv] 440s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:204: UserWarning: Need to guess atom number 20A starting from atom 209. 440s warnings.warn(f'Need to guess atom number {num_str} starting from atom {pdbstructure._next_atom_number}.') 440s 440s tests/test_pdb.py::test_1vii_url_and_gz 440s /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. 440s warnings.warn( 440s 440s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 440s =========================== short test summary info ============================ 440s FAILED tests/test_dssp.py::test_3[6gsv] - ValueError: could not convert strin... 440s ========== 1 failed, 9 passed, 1135 deselected, 6 warnings in 20.47s =========== 441s autopkgtest [03:13:28]: test command2: -----------------------] 441s command2 FAIL non-zero exit status 1 441s autopkgtest [03:13:28]: test command2: - - - - - - - - - - results - - - - - - - - - - 442s autopkgtest [03:13:29]: @@@@@@@@@@@@@@@@@@@@ summary 442s command1 PASS 442s command2 FAIL non-zero exit status 1 503s nova [W] Skipping flock for amd64 503s Creating nova instance adt-plucky-amd64-mdtraj-20250219-030606-juju-7f2275-prod-proposed-migration-environment-2-1a1ceb4d-f089-4ffe-8fcc-118bd609ccec from image adt/ubuntu-plucky-amd64-server-20250219.img (UUID 90711abf-916f-4a80-845a-825250a78697)... 503s nova [W] Timed out waiting for 1af8e43a-0f0e-448b-ae8d-23084290271f to get deleted.