0s autopkgtest [20:14:28]: starting date and time: 2025-10-29 20:14:28+0000 0s autopkgtest [20:14:28]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [20:14:28]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.1zr7l3gu/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:netcdf4-python --apt-upgrade mdtraj --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=netcdf4-python/1.7.3-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-3.secgroup --name adt-resolute-arm64-mdtraj-20251029-201428-juju-7f2275-prod-proposed-migration-environment-15-a796928d-0545-4dd7-8e58-7ef11a384da8 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-mdtraj-20251029-201428-juju-7f2275-prod-proposed-migration-environment-15-a796928d-0545-4dd7-8e58-7ef11a384da8 from image adt/ubuntu-resolute-arm64-server-20251029.img (UUID 4abae604-564c-468a-9647-ef513510018c)... 57s autopkgtest [20:15:25]: testbed dpkg architecture: arm64 58s autopkgtest [20:15:26]: testbed apt version: 3.1.11 58s autopkgtest [20:15:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup 58s autopkgtest [20:15:26]: testbed release detected to be: None 59s autopkgtest [20:15:27]: updating testbed package index (apt update) 60s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 60s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 60s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 60s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 60s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [206 kB] 60s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [3669 kB] 61s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5856 B] 61s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [70.5 kB] 61s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [276 kB] 61s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [5720 B] 61s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [44.3 kB] 61s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [324 B] 61s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [2529 kB] 61s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [66.4 kB] 61s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [42.0 kB] 61s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [1616 B] 63s Fetched 7005 kB in 2s (3585 kB/s) 64s Reading package lists... 65s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 65s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 65s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 65s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 67s Reading package lists... 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 67s Calculating upgrade... 68s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 68s autopkgtest [20:15:36]: upgrading testbed (apt dist-upgrade and autopurge) 68s Reading package lists... 69s Building dependency tree... 69s Reading state information... 69s Calculating upgrade... 71s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 71s Reading package lists... 71s Building dependency tree... 71s Reading state information... 71s Solving dependencies... 72s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 76s autopkgtest [20:15:43]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025 76s autopkgtest [20:15:44]: @@@@@@@@@@@@@@@@@@@@ apt-source mdtraj 80s Get:1 http://ftpmaster.internal/ubuntu resolute/universe mdtraj 1.10.3-2build1 (dsc) [2701 B] 80s Get:2 http://ftpmaster.internal/ubuntu resolute/universe mdtraj 1.10.3-2build1 (tar) [22.0 MB] 80s Get:3 http://ftpmaster.internal/ubuntu resolute/universe mdtraj 1.10.3-2build1 (diff) [297 kB] 81s gpgv: Signature made Tue Mar 4 15:08:42 2025 UTC 81s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 81s gpgv: Can't check signature: No public key 81s dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.10.3-2build1.dsc: no acceptable signature found 81s autopkgtest [20:15:49]: testing package mdtraj version 1.10.3-2build1 88s autopkgtest [20:15:56]: build not needed 98s autopkgtest [20:16:06]: test command1: preparing testbed 98s Reading package lists... 98s Building dependency tree... 98s Reading state information... 99s Solving dependencies... 99s The following NEW packages will be installed: 99s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx gdb 99s libaec0 libbabeltrace1 libblas3 libblosc1 libblosc2-4 libdeflate0 99s libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 99s libhdf5-310 libhdf5-hl-310 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 99s liblapack3 liblcms2-2 liblerc4 libnetcdf22 libnorm1t64 libopenjp2-7 99s libpgm-5.3-0t64 libqhull-r8.0 libraqm0 libsharpyuv0 libsnappy1v5 libsodium23 99s libsource-highlight-common libsource-highlight4t64 libsz2 libtcl8.6 libtiff6 99s libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 99s libxss1 libzmq5 libzopfli1 python-matplotlib-data python-tables-data 99s python3-asttokens python3-brotli python3-cftime python3-comm 99s python3-contourpy python3-coverage python3-cpuinfo python3-cycler 99s python3-dateutil python3-debugpy python3-decorator python3-executing 99s python3-fastjsonschema python3-fonttools python3-fs python3-gsd 99s python3-iniconfig python3-ipykernel python3-ipython python3-jedi 99s python3-joblib python3-jupyter-client python3-jupyter-core 99s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 99s python3-matplotlib-inline python3-mdtraj python3-mpmath python3-nbformat 99s python3-nest-asyncio python3-netcdf4 python3-networkx python3-numexpr 99s python3-numpy python3-numpy-dev python3-packaging python3-pandas 99s python3-pandas-lib python3-parso python3-pexpect python3-pil 99s python3-pil.imagetk python3-platformdirs python3-pluggy 99s python3-prompt-toolkit python3-psutil python3-ptyprocess python3-pure-eval 99s python3-pytest python3-pytz python3-scipy python3-sklearn 99s python3-sklearn-lib python3-stack-data python3-sympy python3-tables 99s python3-tables-lib python3-threadpoolctl python3-tk python3-tornado 99s python3-traitlets python3-typeshed python3-ufolib2 python3-unicodedata2 99s python3-wcwidth python3-zmq python3-zopfli python3.13-tk python3.14-tk 99s tk8.6-blt2.5 unicode-data x11-common 100s 0 upgraded, 126 newly installed, 0 to remove and 0 not upgraded. 100s Need to get 118 MB of archives. 100s After this operation, 586 MB of additional disk space will be used. 100s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB] 100s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-6build1 [186 kB] 100s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-5ubuntu1 [450 kB] 100s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-6build1 [2340 kB] 102s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB] 106s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libtcl8.6 arm64 8.6.17+dfsg-1 [1024 kB] 106s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 106s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 107s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.15.0-2.3ubuntu1 [38.1 kB] 107s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.15.0-2.3ubuntu1 [144 kB] 107s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 107s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 107s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 107s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 107s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libtk8.6 arm64 8.6.17-1 [811 kB] 108s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-8 [624 kB] 108s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 blt arm64 2.5.3+dfsg-8 [4824 B] 108s Get:18 http://ftpmaster.internal/ubuntu resolute/universe arm64 fonts-lyx all 2.4.4-1 [171 kB] 108s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libbabeltrace1 arm64 1.5.11-4build3 [157 kB] 108s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libsource-highlight-common all 3.1.9-4.3build1 [64.2 kB] 108s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libsource-highlight4t64 arm64 3.1.9-4.3build1 [243 kB] 108s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 gdb arm64 16.3-1ubuntu2 [4952 kB] 110s Get:23 http://ftpmaster.internal/ubuntu resolute/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 110s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 libsnappy1v5 arm64 1.2.2-1 [30.5 kB] 110s Get:25 http://ftpmaster.internal/ubuntu resolute/universe arm64 libblosc1 arm64 1.21.5+ds-1build1 [25.7 kB] 110s Get:26 http://ftpmaster.internal/ubuntu resolute/universe arm64 libblosc2-4 arm64 2.17.1+ds-2 [154 kB] 110s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 110s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-5ubuntu1 [148 kB] 110s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 110s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.1.0-1 [523 kB] 110s Get:31 http://ftpmaster.internal/ubuntu resolute/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 110s Get:32 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhdf5-310 arm64 1.14.5+repack-3build1 [1331 kB] 111s Get:33 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhdf5-hl-310 arm64 1.14.5+repack-3build1 [59.8 kB] 111s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 111s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu2 [165 kB] 111s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 111s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 111s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 111s Get:39 http://ftpmaster.internal/ubuntu resolute/universe arm64 libnetcdf22 arm64 1:4.9.3-1build1 [555 kB] 111s Get:40 http://ftpmaster.internal/ubuntu resolute/universe arm64 libnorm1t64 arm64 1.5.9+dfsg-3.1build2 [152 kB] 111s Get:41 http://ftpmaster.internal/ubuntu resolute/universe arm64 libpgm-5.3-0t64 arm64 5.3.128~dfsg-2.1build1 [162 kB] 111s Get:42 http://ftpmaster.internal/ubuntu resolute/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 111s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libraqm0 arm64 0.10.3-1 [15.0 kB] 111s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 111s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 libsodium23 arm64 1.0.18-1build3 [119 kB] 111s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 111s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 111s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 111s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 111s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 111s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 libxslt1.1 arm64 1.1.43-0.3 [172 kB] 111s Get:52 http://ftpmaster.internal/ubuntu resolute/universe arm64 libzmq5 arm64 4.3.5-1build2 [247 kB] 111s Get:53 http://ftpmaster.internal/ubuntu resolute/universe arm64 libzopfli1 arm64 1.0.3-3 [108 kB] 111s Get:54 http://ftpmaster.internal/ubuntu resolute/universe arm64 python-matplotlib-data all 3.10.7+dfsg1-1 [2930 kB] 112s Get:55 http://ftpmaster.internal/ubuntu resolute/universe arm64 python-tables-data all 3.10.2-3build1 [49.7 kB] 112s Get:56 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-asttokens all 3.0.0-2 [20.5 kB] 112s Get:57 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-brotli arm64 1.1.0-2build6 [343 kB] 112s Get:58 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-cftime arm64 1.6.4-2build1 [300 kB] 112s Get:59 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 112s Get:60 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-comm all 0.2.1-1 [7016 B] 112s Get:61 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-contourpy arm64 1.3.1-1build2 [253 kB] 112s Get:62 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-coverage arm64 7.8.2+dfsg1-1 [157 kB] 112s Get:63 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-cpuinfo all 9.0.0+git20221119-3 [21.7 kB] 112s Get:64 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-cycler all 0.12.1-2 [9850 B] 112s Get:65 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-dateutil all 2.9.0-4 [80.3 kB] 112s Get:66 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-debugpy arm64 1.8.12+ds-1ubuntu1 [741 kB] 113s Get:67 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-decorator all 5.2.1-2 [28.1 kB] 113s Get:68 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-executing all 2.2.0-0.2 [25.0 kB] 113s Get:69 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-fastjsonschema all 2.21.1-1 [20.4 kB] 113s Get:70 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-platformdirs all 4.3.7-1 [16.9 kB] 113s Get:71 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-fs all 2.4.16-7 [90.8 kB] 113s Get:72 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-lxml arm64 6.0.1-1build1 [2149 kB] 113s Get:73 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-lz4 arm64 4.4.4+dfsg-3 [27.6 kB] 113s Get:74 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-scipy arm64 1.15.3-1ubuntu1 [18.7 MB] 117s Get:75 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 118s Get:76 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-sympy all 1.13.3-5 [4229 kB] 118s Get:77 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 118s Get:78 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-unicodedata2 arm64 16.0.0+ds-1build1 [398 kB] 118s Get:79 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-zopfli arm64 0.2.3.post1-1 [10.7 kB] 118s Get:80 http://ftpmaster.internal/ubuntu resolute/universe arm64 unicode-data all 16.0.0-1 [9513 kB] 120s Get:81 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-fonttools arm64 4.57.0-2build1 [1648 kB] 120s Get:82 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-gsd arm64 4.0.0-1 [235 kB] 120s Get:83 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 120s Get:84 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-parso all 0.8.4-1 [67.6 kB] 120s Get:85 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-typeshed all 0.0~git20241223.ea91db2-3 [1554 kB] 120s Get:86 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-jedi all 0.19.1+ds1-1 [693 kB] 120s Get:87 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-matplotlib-inline all 0.1.7-1 [9186 B] 120s Get:88 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 120s Get:89 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-prompt-toolkit all 3.0.51-2 [257 kB] 121s Get:90 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pure-eval all 0.2.3-1 [11.4 kB] 121s Get:91 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-stack-data all 0.6.3-1 [22.0 kB] 121s Get:92 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-ptyprocess all 0.7.0-6 [14.8 kB] 121s Get:93 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pexpect all 4.9-3 [48.1 kB] 121s Get:94 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-ipython all 8.35.0-1 [575 kB] 121s Get:95 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-jupyter-core all 5.7.2-5 [28.1 kB] 121s Get:96 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-psutil arm64 7.1.0-1ubuntu1 [191 kB] 121s Get:97 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-tornado arm64 6.5.2-3 [305 kB] 121s Get:98 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-zmq arm64 27.1.0-1 [231 kB] 121s Get:99 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-jupyter-client all 8.6.3-2 [78.5 kB] 121s Get:100 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-nest-asyncio all 1.5.4-1 [6256 B] 121s Get:101 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-packaging all 25.0-1 [52.8 kB] 121s Get:102 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-ipykernel all 6.29.5-2 [82.7 kB] 121s Get:103 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-joblib all 1.4.2-4 [205 kB] 121s Get:104 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-kiwisolver arm64 1.4.7-3build2 [60.7 kB] 121s Get:105 http://ftpmaster.internal/ubuntu resolute/main arm64 libopenjp2-7 arm64 2.5.3-2.1 [179 kB] 122s Get:106 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pil arm64 11.3.0-1ubuntu2 [492 kB] 122s Get:107 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-tk arm64 3.14.0-4 [107 kB] 122s Get:108 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.13-tk arm64 3.13.9-1 [106 kB] 122s Get:109 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-tk arm64 3.13.9-1 [8946 B] 122s Get:110 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pil.imagetk arm64 11.3.0-1ubuntu2 [9582 B] 122s Get:111 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-matplotlib arm64 3.10.7+dfsg1-1 [17.1 MB] 126s Get:112 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 python3-netcdf4 arm64 1.7.3-1 [823 kB] 126s Get:113 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 128s Get:114 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pytz all 2025.2-4 [32.3 kB] 128s Get:115 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas-lib arm64 2.3.3+dfsg-1ubuntu1 [6979 kB] 133s Get:116 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas all 2.3.3+dfsg-1ubuntu1 [2948 kB] 135s Get:117 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-numexpr arm64 2.13.0-1 [133 kB] 135s Get:118 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-tables-lib arm64 3.10.2-3build1 [737 kB] 136s Get:119 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-tables all 3.10.2-3build1 [354 kB] 136s Get:120 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-mdtraj arm64 1.10.3-2build1 [1088 kB] 137s Get:121 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-nbformat all 5.9.1-1 [41.2 kB] 137s Get:122 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pluggy all 1.6.0-1 [21.0 kB] 137s Get:123 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytest all 8.3.5-2 [252 kB] 137s Get:124 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 137s Get:125 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-8 [4109 kB] 139s Get:126 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-sklearn all 1.4.2+dfsg-8 [2258 kB] 141s Fetched 118 MB in 41s (2899 kB/s) 141s Selecting previously unselected package python3-numpy-dev:arm64. 141s (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 ... 83457 files and directories currently installed.) 141s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 141s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 141s Selecting previously unselected package libblas3:arm64. 141s Preparing to unpack .../001-libblas3_3.12.1-6build1_arm64.deb ... 141s Unpacking libblas3:arm64 (3.12.1-6build1) ... 141s Selecting previously unselected package libgfortran5:arm64. 141s Preparing to unpack .../002-libgfortran5_15.2.0-5ubuntu1_arm64.deb ... 141s Unpacking libgfortran5:arm64 (15.2.0-5ubuntu1) ... 141s Selecting previously unselected package liblapack3:arm64. 141s Preparing to unpack .../003-liblapack3_3.12.1-6build1_arm64.deb ... 141s Unpacking liblapack3:arm64 (3.12.1-6build1) ... 141s Selecting previously unselected package python3-numpy. 141s Preparing to unpack .../004-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 141s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 142s Selecting previously unselected package libtcl8.6:arm64. 142s Preparing to unpack .../005-libtcl8.6_8.6.17+dfsg-1_arm64.deb ... 142s Unpacking libtcl8.6:arm64 (8.6.17+dfsg-1) ... 142s Selecting previously unselected package fonts-dejavu-mono. 142s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ... 142s Unpacking fonts-dejavu-mono (2.37-8) ... 142s Selecting previously unselected package fonts-dejavu-core. 142s Preparing to unpack .../007-fonts-dejavu-core_2.37-8_all.deb ... 142s Unpacking fonts-dejavu-core (2.37-8) ... 142s Selecting previously unselected package fontconfig-config. 142s Preparing to unpack .../008-fontconfig-config_2.15.0-2.3ubuntu1_arm64.deb ... 142s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 142s Selecting previously unselected package libfontconfig1:arm64. 142s Preparing to unpack .../009-libfontconfig1_2.15.0-2.3ubuntu1_arm64.deb ... 142s Unpacking libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 142s Selecting previously unselected package libxrender1:arm64. 142s Preparing to unpack .../010-libxrender1_1%3a0.9.12-1_arm64.deb ... 142s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 142s Selecting previously unselected package libxft2:arm64. 142s Preparing to unpack .../011-libxft2_2.3.6-1build1_arm64.deb ... 142s Unpacking libxft2:arm64 (2.3.6-1build1) ... 142s Selecting previously unselected package x11-common. 142s Preparing to unpack .../012-x11-common_1%3a7.7+24ubuntu1_all.deb ... 142s Unpacking x11-common (1:7.7+24ubuntu1) ... 143s Selecting previously unselected package libxss1:arm64. 143s Preparing to unpack .../013-libxss1_1%3a1.2.3-1build3_arm64.deb ... 143s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 143s Selecting previously unselected package libtk8.6:arm64. 143s Preparing to unpack .../014-libtk8.6_8.6.17-1_arm64.deb ... 143s Unpacking libtk8.6:arm64 (8.6.17-1) ... 143s Selecting previously unselected package tk8.6-blt2.5. 143s Preparing to unpack .../015-tk8.6-blt2.5_2.5.3+dfsg-8_arm64.deb ... 143s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 143s Selecting previously unselected package blt. 143s Preparing to unpack .../016-blt_2.5.3+dfsg-8_arm64.deb ... 143s Unpacking blt (2.5.3+dfsg-8) ... 143s Selecting previously unselected package fonts-lyx. 143s Preparing to unpack .../017-fonts-lyx_2.4.4-1_all.deb ... 143s Unpacking fonts-lyx (2.4.4-1) ... 143s Selecting previously unselected package libbabeltrace1:arm64. 143s Preparing to unpack .../018-libbabeltrace1_1.5.11-4build3_arm64.deb ... 143s Unpacking libbabeltrace1:arm64 (1.5.11-4build3) ... 143s Selecting previously unselected package libsource-highlight-common. 143s Preparing to unpack .../019-libsource-highlight-common_3.1.9-4.3build1_all.deb ... 143s Unpacking libsource-highlight-common (3.1.9-4.3build1) ... 143s Selecting previously unselected package libsource-highlight4t64:arm64. 143s Preparing to unpack .../020-libsource-highlight4t64_3.1.9-4.3build1_arm64.deb ... 143s Unpacking libsource-highlight4t64:arm64 (3.1.9-4.3build1) ... 143s Selecting previously unselected package gdb. 143s Preparing to unpack .../021-gdb_16.3-1ubuntu2_arm64.deb ... 143s Unpacking gdb (16.3-1ubuntu2) ... 143s Selecting previously unselected package libaec0:arm64. 143s Preparing to unpack .../022-libaec0_1.1.3-1_arm64.deb ... 143s Unpacking libaec0:arm64 (1.1.3-1) ... 143s Selecting previously unselected package libsnappy1v5:arm64. 143s Preparing to unpack .../023-libsnappy1v5_1.2.2-1_arm64.deb ... 143s Unpacking libsnappy1v5:arm64 (1.2.2-1) ... 143s Selecting previously unselected package libblosc1:arm64. 143s Preparing to unpack .../024-libblosc1_1.21.5+ds-1build1_arm64.deb ... 143s Unpacking libblosc1:arm64 (1.21.5+ds-1build1) ... 143s Selecting previously unselected package libblosc2-4:arm64. 143s Preparing to unpack .../025-libblosc2-4_2.17.1+ds-2_arm64.deb ... 143s Unpacking libblosc2-4:arm64 (2.17.1+ds-2) ... 143s Selecting previously unselected package libdeflate0:arm64. 143s Preparing to unpack .../026-libdeflate0_1.23-2_arm64.deb ... 143s Unpacking libdeflate0:arm64 (1.23-2) ... 143s Selecting previously unselected package libgomp1:arm64. 143s Preparing to unpack .../027-libgomp1_15.2.0-5ubuntu1_arm64.deb ... 143s Unpacking libgomp1:arm64 (15.2.0-5ubuntu1) ... 143s Selecting previously unselected package libgraphite2-3:arm64. 143s Preparing to unpack .../028-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 143s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 143s Selecting previously unselected package libharfbuzz0b:arm64. 143s Preparing to unpack .../029-libharfbuzz0b_12.1.0-1_arm64.deb ... 143s Unpacking libharfbuzz0b:arm64 (12.1.0-1) ... 143s Selecting previously unselected package libsz2:arm64. 144s Preparing to unpack .../030-libsz2_1.1.3-1_arm64.deb ... 144s Unpacking libsz2:arm64 (1.1.3-1) ... 144s Selecting previously unselected package libhdf5-310:arm64. 144s Preparing to unpack .../031-libhdf5-310_1.14.5+repack-3build1_arm64.deb ... 144s Unpacking libhdf5-310:arm64 (1.14.5+repack-3build1) ... 144s Selecting previously unselected package libhdf5-hl-310:arm64. 144s Preparing to unpack .../032-libhdf5-hl-310_1.14.5+repack-3build1_arm64.deb ... 144s Unpacking libhdf5-hl-310:arm64 (1.14.5+repack-3build1) ... 144s Selecting previously unselected package libimagequant0:arm64. 144s Preparing to unpack .../033-libimagequant0_2.18.0-1build1_arm64.deb ... 144s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 144s Selecting previously unselected package libjpeg-turbo8:arm64. 144s Preparing to unpack .../034-libjpeg-turbo8_2.1.5-4ubuntu2_arm64.deb ... 144s Unpacking libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 144s Selecting previously unselected package libjpeg8:arm64. 144s Preparing to unpack .../035-libjpeg8_8c-2ubuntu11_arm64.deb ... 144s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 144s Selecting previously unselected package liblcms2-2:arm64. 144s Preparing to unpack .../036-liblcms2-2_2.16-2_arm64.deb ... 144s Unpacking liblcms2-2:arm64 (2.16-2) ... 144s Selecting previously unselected package liblerc4:arm64. 144s Preparing to unpack .../037-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 144s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 144s Selecting previously unselected package libnetcdf22:arm64. 144s Preparing to unpack .../038-libnetcdf22_1%3a4.9.3-1build1_arm64.deb ... 144s Unpacking libnetcdf22:arm64 (1:4.9.3-1build1) ... 144s Selecting previously unselected package libnorm1t64:arm64. 144s Preparing to unpack .../039-libnorm1t64_1.5.9+dfsg-3.1build2_arm64.deb ... 144s Unpacking libnorm1t64:arm64 (1.5.9+dfsg-3.1build2) ... 144s Selecting previously unselected package libpgm-5.3-0t64:arm64. 144s Preparing to unpack .../040-libpgm-5.3-0t64_5.3.128~dfsg-2.1build1_arm64.deb ... 144s Unpacking libpgm-5.3-0t64:arm64 (5.3.128~dfsg-2.1build1) ... 144s Selecting previously unselected package libqhull-r8.0:arm64. 144s Preparing to unpack .../041-libqhull-r8.0_2020.2-6build1_arm64.deb ... 144s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 144s Selecting previously unselected package libraqm0:arm64. 144s Preparing to unpack .../042-libraqm0_0.10.3-1_arm64.deb ... 144s Unpacking libraqm0:arm64 (0.10.3-1) ... 144s Selecting previously unselected package libsharpyuv0:arm64. 144s Preparing to unpack .../043-libsharpyuv0_1.5.0-0.1_arm64.deb ... 144s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 144s Selecting previously unselected package libsodium23:arm64. 144s Preparing to unpack .../044-libsodium23_1.0.18-1build3_arm64.deb ... 144s Unpacking libsodium23:arm64 (1.0.18-1build3) ... 144s Selecting previously unselected package libjbig0:arm64. 144s Preparing to unpack .../045-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 144s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 144s Selecting previously unselected package libwebp7:arm64. 144s Preparing to unpack .../046-libwebp7_1.5.0-0.1_arm64.deb ... 144s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 144s Selecting previously unselected package libtiff6:arm64. 144s Preparing to unpack .../047-libtiff6_4.7.0-3ubuntu3_arm64.deb ... 144s Unpacking libtiff6:arm64 (4.7.0-3ubuntu3) ... 144s Selecting previously unselected package libwebpdemux2:arm64. 144s Preparing to unpack .../048-libwebpdemux2_1.5.0-0.1_arm64.deb ... 144s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 144s Selecting previously unselected package libwebpmux3:arm64. 144s Preparing to unpack .../049-libwebpmux3_1.5.0-0.1_arm64.deb ... 144s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 144s Selecting previously unselected package libxslt1.1:arm64. 145s Preparing to unpack .../050-libxslt1.1_1.1.43-0.3_arm64.deb ... 145s Unpacking libxslt1.1:arm64 (1.1.43-0.3) ... 145s Selecting previously unselected package libzmq5:arm64. 145s Preparing to unpack .../051-libzmq5_4.3.5-1build2_arm64.deb ... 145s Unpacking libzmq5:arm64 (4.3.5-1build2) ... 145s Selecting previously unselected package libzopfli1. 145s Preparing to unpack .../052-libzopfli1_1.0.3-3_arm64.deb ... 145s Unpacking libzopfli1 (1.0.3-3) ... 145s Selecting previously unselected package python-matplotlib-data. 145s Preparing to unpack .../053-python-matplotlib-data_3.10.7+dfsg1-1_all.deb ... 145s Unpacking python-matplotlib-data (3.10.7+dfsg1-1) ... 145s Selecting previously unselected package python-tables-data. 145s Preparing to unpack .../054-python-tables-data_3.10.2-3build1_all.deb ... 145s Unpacking python-tables-data (3.10.2-3build1) ... 145s Selecting previously unselected package python3-asttokens. 145s Preparing to unpack .../055-python3-asttokens_3.0.0-2_all.deb ... 145s Unpacking python3-asttokens (3.0.0-2) ... 145s Selecting previously unselected package python3-brotli. 145s Preparing to unpack .../056-python3-brotli_1.1.0-2build6_arm64.deb ... 145s Unpacking python3-brotli (1.1.0-2build6) ... 145s Selecting previously unselected package python3-cftime. 145s Preparing to unpack .../057-python3-cftime_1.6.4-2build1_arm64.deb ... 145s Unpacking python3-cftime (1.6.4-2build1) ... 145s Selecting previously unselected package python3-traitlets. 145s Preparing to unpack .../058-python3-traitlets_5.14.3+really5.14.3-1_all.deb ... 145s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ... 145s Selecting previously unselected package python3-comm. 145s Preparing to unpack .../059-python3-comm_0.2.1-1_all.deb ... 145s Unpacking python3-comm (0.2.1-1) ... 145s Selecting previously unselected package python3-contourpy. 145s Preparing to unpack .../060-python3-contourpy_1.3.1-1build2_arm64.deb ... 145s Unpacking python3-contourpy (1.3.1-1build2) ... 145s Selecting previously unselected package python3-coverage. 145s Preparing to unpack .../061-python3-coverage_7.8.2+dfsg1-1_arm64.deb ... 145s Unpacking python3-coverage (7.8.2+dfsg1-1) ... 145s Selecting previously unselected package python3-cpuinfo. 145s Preparing to unpack .../062-python3-cpuinfo_9.0.0+git20221119-3_all.deb ... 145s Unpacking python3-cpuinfo (9.0.0+git20221119-3) ... 145s Selecting previously unselected package python3-cycler. 145s Preparing to unpack .../063-python3-cycler_0.12.1-2_all.deb ... 145s Unpacking python3-cycler (0.12.1-2) ... 145s Selecting previously unselected package python3-dateutil. 145s Preparing to unpack .../064-python3-dateutil_2.9.0-4_all.deb ... 145s Unpacking python3-dateutil (2.9.0-4) ... 145s Selecting previously unselected package python3-debugpy. 145s Preparing to unpack .../065-python3-debugpy_1.8.12+ds-1ubuntu1_arm64.deb ... 145s Unpacking python3-debugpy (1.8.12+ds-1ubuntu1) ... 145s Selecting previously unselected package python3-decorator. 145s Preparing to unpack .../066-python3-decorator_5.2.1-2_all.deb ... 145s Unpacking python3-decorator (5.2.1-2) ... 145s Selecting previously unselected package python3-executing. 145s Preparing to unpack .../067-python3-executing_2.2.0-0.2_all.deb ... 145s Unpacking python3-executing (2.2.0-0.2) ... 145s Selecting previously unselected package python3-fastjsonschema. 145s Preparing to unpack .../068-python3-fastjsonschema_2.21.1-1_all.deb ... 145s Unpacking python3-fastjsonschema (2.21.1-1) ... 146s Selecting previously unselected package python3-platformdirs. 146s Preparing to unpack .../069-python3-platformdirs_4.3.7-1_all.deb ... 146s Unpacking python3-platformdirs (4.3.7-1) ... 146s Selecting previously unselected package python3-fs. 146s Preparing to unpack .../070-python3-fs_2.4.16-7_all.deb ... 146s Unpacking python3-fs (2.4.16-7) ... 146s Selecting previously unselected package python3-lxml:arm64. 146s Preparing to unpack .../071-python3-lxml_6.0.1-1build1_arm64.deb ... 146s Unpacking python3-lxml:arm64 (6.0.1-1build1) ... 146s Selecting previously unselected package python3-lz4. 146s Preparing to unpack .../072-python3-lz4_4.4.4+dfsg-3_arm64.deb ... 146s Unpacking python3-lz4 (4.4.4+dfsg-3) ... 146s Selecting previously unselected package python3-scipy. 146s Preparing to unpack .../073-python3-scipy_1.15.3-1ubuntu1_arm64.deb ... 146s Unpacking python3-scipy (1.15.3-1ubuntu1) ... 146s Selecting previously unselected package python3-mpmath. 146s Preparing to unpack .../074-python3-mpmath_1.3.0-1_all.deb ... 146s Unpacking python3-mpmath (1.3.0-1) ... 147s Selecting previously unselected package python3-sympy. 147s Preparing to unpack .../075-python3-sympy_1.13.3-5_all.deb ... 147s Unpacking python3-sympy (1.13.3-5) ... 147s Selecting previously unselected package python3-ufolib2. 147s Preparing to unpack .../076-python3-ufolib2_0.17.1+dfsg1-1_all.deb ... 147s Unpacking python3-ufolib2 (0.17.1+dfsg1-1) ... 147s Selecting previously unselected package python3-unicodedata2. 147s Preparing to unpack .../077-python3-unicodedata2_16.0.0+ds-1build1_arm64.deb ... 147s Unpacking python3-unicodedata2 (16.0.0+ds-1build1) ... 147s Selecting previously unselected package python3-zopfli. 147s Preparing to unpack .../078-python3-zopfli_0.2.3.post1-1_arm64.deb ... 147s Unpacking python3-zopfli (0.2.3.post1-1) ... 147s Selecting previously unselected package unicode-data. 147s Preparing to unpack .../079-unicode-data_16.0.0-1_all.deb ... 147s Unpacking unicode-data (16.0.0-1) ... 147s Selecting previously unselected package python3-fonttools. 147s Preparing to unpack .../080-python3-fonttools_4.57.0-2build1_arm64.deb ... 147s Unpacking python3-fonttools (4.57.0-2build1) ... 147s Selecting previously unselected package python3-gsd. 147s Preparing to unpack .../081-python3-gsd_4.0.0-1_arm64.deb ... 147s Unpacking python3-gsd (4.0.0-1) ... 147s Selecting previously unselected package python3-iniconfig. 147s Preparing to unpack .../082-python3-iniconfig_1.1.1-2_all.deb ... 147s Unpacking python3-iniconfig (1.1.1-2) ... 147s Selecting previously unselected package python3-parso. 147s Preparing to unpack .../083-python3-parso_0.8.4-1_all.deb ... 148s Unpacking python3-parso (0.8.4-1) ... 148s Selecting previously unselected package python3-typeshed. 148s Preparing to unpack .../084-python3-typeshed_0.0~git20241223.ea91db2-3_all.deb ... 148s Unpacking python3-typeshed (0.0~git20241223.ea91db2-3) ... 148s Selecting previously unselected package python3-jedi. 148s Preparing to unpack .../085-python3-jedi_0.19.1+ds1-1_all.deb ... 148s Unpacking python3-jedi (0.19.1+ds1-1) ... 148s Selecting previously unselected package python3-matplotlib-inline. 148s Preparing to unpack .../086-python3-matplotlib-inline_0.1.7-1_all.deb ... 148s Unpacking python3-matplotlib-inline (0.1.7-1) ... 148s Selecting previously unselected package python3-wcwidth. 148s Preparing to unpack .../087-python3-wcwidth_0.2.13+dfsg1-1_all.deb ... 148s Unpacking python3-wcwidth (0.2.13+dfsg1-1) ... 148s Selecting previously unselected package python3-prompt-toolkit. 148s Preparing to unpack .../088-python3-prompt-toolkit_3.0.51-2_all.deb ... 148s Unpacking python3-prompt-toolkit (3.0.51-2) ... 148s Selecting previously unselected package python3-pure-eval. 148s Preparing to unpack .../089-python3-pure-eval_0.2.3-1_all.deb ... 148s Unpacking python3-pure-eval (0.2.3-1) ... 148s Selecting previously unselected package python3-stack-data. 149s Preparing to unpack .../090-python3-stack-data_0.6.3-1_all.deb ... 149s Unpacking python3-stack-data (0.6.3-1) ... 149s Selecting previously unselected package python3-ptyprocess. 149s Preparing to unpack .../091-python3-ptyprocess_0.7.0-6_all.deb ... 149s Unpacking python3-ptyprocess (0.7.0-6) ... 149s Selecting previously unselected package python3-pexpect. 149s Preparing to unpack .../092-python3-pexpect_4.9-3_all.deb ... 149s Unpacking python3-pexpect (4.9-3) ... 149s Selecting previously unselected package python3-ipython. 149s Preparing to unpack .../093-python3-ipython_8.35.0-1_all.deb ... 149s Unpacking python3-ipython (8.35.0-1) ... 149s Selecting previously unselected package python3-jupyter-core. 149s Preparing to unpack .../094-python3-jupyter-core_5.7.2-5_all.deb ... 149s Unpacking python3-jupyter-core (5.7.2-5) ... 149s Selecting previously unselected package python3-psutil. 149s Preparing to unpack .../095-python3-psutil_7.1.0-1ubuntu1_arm64.deb ... 149s Unpacking python3-psutil (7.1.0-1ubuntu1) ... 149s Selecting previously unselected package python3-tornado. 149s Preparing to unpack .../096-python3-tornado_6.5.2-3_arm64.deb ... 149s Unpacking python3-tornado (6.5.2-3) ... 149s Selecting previously unselected package python3-zmq. 149s Preparing to unpack .../097-python3-zmq_27.1.0-1_arm64.deb ... 149s Unpacking python3-zmq (27.1.0-1) ... 149s Selecting previously unselected package python3-jupyter-client. 149s Preparing to unpack .../098-python3-jupyter-client_8.6.3-2_all.deb ... 149s Unpacking python3-jupyter-client (8.6.3-2) ... 149s Selecting previously unselected package python3-nest-asyncio. 149s Preparing to unpack .../099-python3-nest-asyncio_1.5.4-1_all.deb ... 149s Unpacking python3-nest-asyncio (1.5.4-1) ... 149s Selecting previously unselected package python3-packaging. 149s Preparing to unpack .../100-python3-packaging_25.0-1_all.deb ... 149s Unpacking python3-packaging (25.0-1) ... 149s Selecting previously unselected package python3-ipykernel. 149s Preparing to unpack .../101-python3-ipykernel_6.29.5-2_all.deb ... 149s Unpacking python3-ipykernel (6.29.5-2) ... 149s Selecting previously unselected package python3-joblib. 149s Preparing to unpack .../102-python3-joblib_1.4.2-4_all.deb ... 149s Unpacking python3-joblib 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python3-tk:arm64. 150s Preparing to unpack .../108-python3-tk_3.13.9-1_arm64.deb ... 150s Unpacking python3-tk:arm64 (3.13.9-1) ... 150s Selecting previously unselected package python3-pil.imagetk:arm64. 150s Preparing to unpack .../109-python3-pil.imagetk_11.3.0-1ubuntu2_arm64.deb ... 150s Unpacking python3-pil.imagetk:arm64 (11.3.0-1ubuntu2) ... 150s Selecting previously unselected package python3-matplotlib. 150s Preparing to unpack .../110-python3-matplotlib_3.10.7+dfsg1-1_arm64.deb ... 150s Unpacking python3-matplotlib (3.10.7+dfsg1-1) ... 150s Selecting previously unselected package python3-netcdf4. 150s Preparing to unpack .../111-python3-netcdf4_1.7.3-1_arm64.deb ... 150s Unpacking python3-netcdf4 (1.7.3-1) ... 150s Selecting previously unselected package python3-networkx. 150s Preparing to unpack .../112-python3-networkx_3.2.1-4ubuntu1_all.deb ... 150s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 151s Selecting previously unselected package python3-pytz. 151s Preparing to unpack .../113-python3-pytz_2025.2-4_all.deb ... 151s Unpacking python3-pytz (2025.2-4) ... 151s Selecting previously unselected package python3-pandas-lib:arm64. 151s Preparing to unpack .../114-python3-pandas-lib_2.3.3+dfsg-1ubuntu1_arm64.deb ... 151s Unpacking python3-pandas-lib:arm64 (2.3.3+dfsg-1ubuntu1) ... 151s Selecting previously unselected package python3-pandas. 151s Preparing to unpack .../115-python3-pandas_2.3.3+dfsg-1ubuntu1_all.deb ... 151s Unpacking python3-pandas (2.3.3+dfsg-1ubuntu1) ... 152s Selecting previously unselected package python3-numexpr. 152s Preparing to unpack .../116-python3-numexpr_2.13.0-1_arm64.deb ... 152s Unpacking python3-numexpr (2.13.0-1) ... 152s Selecting previously unselected package python3-tables-lib. 152s Preparing to unpack .../117-python3-tables-lib_3.10.2-3build1_arm64.deb ... 152s Unpacking python3-tables-lib (3.10.2-3build1) ... 152s Selecting previously unselected package python3-tables. 152s Preparing to unpack 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python3-parso (0.8.4-1) ... 154s Setting up python3-lz4 (4.4.4+dfsg-3) ... 154s Setting up python3-asttokens (3.0.0-2) ... 154s Setting up python3-unicodedata2 (16.0.0+ds-1build1) ... 154s Setting up fonts-lyx (2.4.4-1) ... 154s Setting up python3-threadpoolctl (3.1.0-1) ... 154s Setting up x11-common (1:7.7+24ubuntu1) ... 155s Setting up libdeflate0:arm64 (1.23-2) ... 155s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 155s Setting up python3-coverage (7.8.2+dfsg1-1) ... 155s Setting up python3-pytz (2025.2-4) ... 155s Setting up libgomp1:arm64 (15.2.0-5ubuntu1) ... 155s Setting up python3-networkx (3.2.1-4ubuntu1) ... 156s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 156s Setting up libaec0:arm64 (1.1.3-1) ... 156s Setting up python3-platformdirs (4.3.7-1) ... 157s Setting up python3-psutil (7.1.0-1ubuntu1) ... 157s Setting up libsource-highlight-common (3.1.9-4.3build1) ... 157s Setting up libsnappy1v5:arm64 (1.2.2-1) ... 157s Setting up python3-fs (2.4.16-7) ... 157s Setting up unicode-data (16.0.0-1) ... 157s Setting up libpgm-5.3-0t64:arm64 (5.3.128~dfsg-2.1build1) ... 157s Setting up python3-decorator (5.2.1-2) ... 157s Setting up libblosc2-4:arm64 (2.17.1+ds-2) ... 157s Setting up libblas3:arm64 (3.12.1-6build1) ... 157s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 157s Setting up python3-packaging (25.0-1) ... 157s Setting up python3-wcwidth (0.2.13+dfsg1-1) ... 158s Setting up libzopfli1 (1.0.3-3) ... 158s Setting up python3-typeshed (0.0~git20241223.ea91db2-3) ... 158s Setting up python3-executing (2.2.0-0.2) ... 158s Setting up python3-nest-asyncio (1.5.4-1) ... 158s Setting up python3-brotli (1.1.0-2build6) ... 158s Setting up python3-cycler (0.12.1-2) ... 158s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 158s Setting up fonts-dejavu-mono (2.37-8) ... 158s Setting up python3-kiwisolver (1.4.7-3build2) ... 158s Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 158s Setting up libtcl8.6:arm64 (8.6.17+dfsg-1) ... 158s Setting up fonts-dejavu-core (2.37-8) ... 158s Setting up libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 159s Setting up python3-cpuinfo (9.0.0+git20221119-3) ... 159s Setting up libbabeltrace1:arm64 (1.5.11-4build3) ... 159s Setting up libgfortran5:arm64 (15.2.0-5ubuntu1) ... 159s Setting up python3-pluggy (1.6.0-1) ... 159s Setting up libwebp7:arm64 (1.5.0-0.1) ... 159s Setting up python3-fastjsonschema (2.21.1-1) ... 159s Setting up python3-traitlets (5.14.3+really5.14.3-1) ... 159s Setting up libxslt1.1:arm64 (1.1.43-0.3) ... 159s Setting up libblosc1:arm64 (1.21.5+ds-1build1) ... 159s Setting up libopenjp2-7:arm64 (2.5.3-2.1) ... 159s Setting up libharfbuzz0b:arm64 (12.1.0-1) ... 159s Setting up python3-dateutil (2.9.0-4) ... 159s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 159s Setting up python3-mpmath (1.3.0-1) ... 160s Setting up python-matplotlib-data (3.10.7+dfsg1-1) 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(3.10.2-3build1) ... 177s Setting up libtk8.6:arm64 (8.6.17-1) ... 177s Setting up python3-pandas-lib:arm64 (2.3.3+dfsg-1ubuntu1) ... 177s Setting up libnetcdf22:arm64 (1:4.9.3-1build1) ... 177s Setting up python3-sklearn-lib:arm64 (1.4.2+dfsg-8) ... 177s Setting up python3-gsd (4.0.0-1) ... 177s Setting up python3-debugpy (1.8.12+ds-1ubuntu1) ... 178s Setting up python3.13-tk (3.13.9-1) ... 178s Setting up python3-pil:arm64 (11.3.0-1ubuntu2) ... 179s Setting up python3-pandas (2.3.3+dfsg-1ubuntu1) ... 184s Setting up python3-ipython (8.35.0-1) ... 185s Setting up python3-ipykernel (6.29.5-2) ... 185s Setting up python3-sklearn (1.4.2+dfsg-8) ... 187s Setting up python3-cftime (1.6.4-2build1) ... 187s Setting up python3-numexpr (2.13.0-1) ... 187s Setting up python3-netcdf4 (1.7.3-1) ... 187s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 187s Setting up python3.14-tk (3.14.0-4) ... 187s Setting up blt (2.5.3+dfsg-8) ... 187s Setting up python3-tk:arm64 (3.13.9-1) ... 187s Setting up python3-tables (3.10.2-3build1) ... 188s Setting up python3-mdtraj (1.10.3-2build1) ... 188s Setting up python3-pil.imagetk:arm64 (11.3.0-1ubuntu2) ... 189s Setting up python3-fonttools (4.57.0-2build1) ... 189s Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... 190s Setting up python3-matplotlib (3.10.7+dfsg1-1) ... 191s Processing triggers for libc-bin (2.42-0ubuntu3) ... 191s Processing triggers for man-db (2.13.1-1) ... 193s autopkgtest [20:17:41]: 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)' 193s autopkgtest [20:17:41]: test command1: [----------------------- 194s ============================= test session starts ============================== 194s platform linux -- Python 3.13.9, pytest-8.3.5, pluggy-1.6.0 -- /usr/bin/python3 194s cachedir: .pytest_cache 194s rootdir: /tmp/autopkgtest.hirK8O/build.pPu/src 194s configfile: pyproject.toml 194s testpaths: tests, examples 194s plugins: typeguard-4.4.2 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tests/test_mdcrd.py::test_read_0 PASSED [ 26%] 359s tests/test_mdcrd.py::test_read_1 PASSED [ 26%] 359s tests/test_mdcrd.py::test_read_write_0 PASSED [ 26%] 359s tests/test_mdcrd.py::test_read_write_1 PASSED [ 26%] 359s tests/test_mdcrd.py::test_read_write_2 PASSED [ 26%] 359s tests/test_mdcrd.py::test_multiread PASSED [ 26%] 359s tests/test_mdcrd.py::test_seek PASSED [ 26%] 359s tests/test_mdcrd.py::test_atom_indices_0 PASSED [ 26%] 359s tests/test_mdcrd.py::test_atom_indices_1 PASSED [ 26%] 359s tests/test_mol2.py::test_load_mol2 PASSED [ 26%] 359s tests/test_mol2.py::test_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb SKIPPED [ 27%] 359s tests/test_mol2.py::test_mol2_dataframe PASSED [ 27%] 359s tests/test_mol2.py::test_mol2_dataframe_status PASSED [ 27%] 359s tests/test_mol2.py::test_mol2_warnings PASSED [ 27%] 359s tests/test_mol2.py::test_mol2_status_bits PASSED [ 27%] 359s tests/test_mol2.py::test_mol2_without_bonds PASSED [ 27%] 359s tests/test_mol2.py::test_mol2_element_name PASSED [ 27%] 359s tests/test_mol2.py::test_load_all_mol2[li.mol2] PASSED [ 27%] 359s tests/test_mol2.py::test_load_all_mol2[lysozyme-ligand-tripos.mol2] PASSED [ 27%] 359s tests/test_mol2.py::test_load_all_mol2[imatinib.mol2] PASSED [ 27%] 359s tests/test_mol2.py::test_load_all_mol2[status-bits.mol2] PASSED [ 27%] 359s tests/test_mol2.py::test_load_all_mol2[adp.mol2] PASSED [ 27%] 359s tests/test_mol2.py::test_load_all_mol2[water_acn.mol2] PASSED [ 28%] 359s tests/test_mol2.py::test_mol2_n_residues PASSED [ 28%] 359s tests/test_neighborlist.py::test_nonperiodic PASSED [ 28%] 359s tests/test_neighborlist.py::test_periodic PASSED [ 28%] 360s tests/test_neighborlist.py::test_triclinic PASSED [ 28%] 360s tests/test_neighbors.py::test_compute_neighbors_1 PASSED [ 28%] 361s tests/test_neighbors.py::test_compute_neighbors_2 PASSED [ 28%] 362s tests/test_neighbors.py::test_compute_neighbors_3 PASSED [ 28%] 362s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_after_close PASSED [ 28%] 362s tests/test_netcdf.py::TestNetCDFNetCDF4::test_shape PASSED [ 28%] 362s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_1 PASSED [ 28%] 362s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_2 PASSED [ 29%] 362s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_3 PASSED [ 29%] 362s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_1 PASSED [ 29%] 362s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_2 PASSED [ 29%] 362s tests/test_netcdf.py::TestNetCDFNetCDF4::test_ragged_1 PASSED [ 29%] 362s tests/test_netcdf.py::TestNetCDFNetCDF4::test_ragged_2 PASSED [ 29%] 362s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_25 PASSED [ 29%] 362s tests/test_netcdf.py::TestNetCDFNetCDF4::test_write_3 PASSED [ 29%] 362s tests/test_netcdf.py::TestNetCDFNetCDF4::test_n_atoms PASSED [ 29%] 362s tests/test_netcdf.py::TestNetCDFNetCDF4::test_do_overwrite PASSED [ 29%] 362s tests/test_netcdf.py::TestNetCDFNetCDF4::test_do_not_overwrite PASSED [ 29%] 362s tests/test_netcdf.py::TestNetCDFNetCDF4::test_trajectory_save_load PASSED [ 30%] 362s tests/test_netcdf.py::TestNetCDFScipy::test_read_after_close PASSED [ 30%] 362s tests/test_netcdf.py::TestNetCDFScipy::test_shape PASSED [ 30%] 362s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_1 PASSED [ 30%] 362s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_2 PASSED [ 30%] 362s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_3 PASSED [ 30%] 362s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_1 PASSED [ 30%] 362s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_2 PASSED [ 30%] 362s tests/test_netcdf.py::TestNetCDFScipy::test_ragged_1 PASSED [ 30%] 362s tests/test_netcdf.py::TestNetCDFScipy::test_ragged_2 PASSED [ 30%] 362s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_25 PASSED [ 30%] 362s tests/test_netcdf.py::TestNetCDFScipy::test_write_3 PASSED [ 30%] 362s tests/test_netcdf.py::TestNetCDFScipy::test_n_atoms PASSED [ 31%] 362s tests/test_netcdf.py::TestNetCDFScipy::test_do_overwrite PASSED [ 31%] 362s tests/test_netcdf.py::TestNetCDFScipy::test_do_not_overwrite PASSED [ 31%] 362s tests/test_netcdf.py::TestNetCDFScipy::test_trajectory_save_load PASSED [ 31%] 362s tests/test_netcdf.py::test_cpptraj SKIPPED (This test requires cpptr...) [ 31%] 362s tests/test_nmr.py::test_spartaplus SKIPPED (SPARTA+ binary not found) [ 31%] 362s tests/test_nmr.py::test_ppm SKIPPED (PPM binary not found) [ 31%] 362s tests/test_nmr.py::test_shiftx2 SKIPPED (SHIFTX2 binary not found or...) [ 31%] 362s tests/test_nmr.py::test_2_scalar_couplings PASSED [ 31%] 362s tests/test_order.py::test_nematic_order PASSED [ 31%] 362s tests/test_order.py::test_director PASSED [ 31%] 362s tests/test_order.py::test_inertia PASSED [ 32%] 362s tests/test_order.py::test_nematic_order_args PASSED [ 32%] 362s tests/test_order.py::test_order_from_traj PASSED [ 32%] 362s tests/test_order.py::test_directors_angle_from_traj PASSED [ 32%] 362s tests/test_pdb.py::test_pdbread PASSED [ 32%] 362s tests/test_pdb.py::test_pdbread_with_input_top PASSED [ 32%] 362s tests/test_pdb.py::test_pdbwrite PASSED [ 32%] 362s tests/test_pdb.py::test_load_multiframe PASSED [ 32%] 362s tests/test_pdb.py::test_4ZUO PASSED [ 32%] 363s tests/test_pdb.py::test_2EQQ_0 PASSED [ 32%] 364s tests/test_pdb.py::test_1vii_solvated_with_ligand PASSED [ 32%] 364s tests/test_pdb.py::test_write_large PASSED [ 33%] 364s tests/test_pdb.py::test_write_large_2 PASSED [ 33%] 364s tests/test_pdb.py::test_pdbstructure_0 PASSED [ 33%] 364s tests/test_pdb.py::test_pdbstructure_1 PASSED [ 33%] 364s tests/test_pdb.py::test_pdbstructure_2 PASSED [ 33%] 364s tests/test_pdb.py::test_pdbstructure_3 PASSED [ 33%] 364s tests/test_pdb.py::test_1ncw PASSED [ 33%] 364s tests/test_pdb.py::test_segment_id PASSED [ 33%] 364s tests/test_pdb.py::test_bfactors PASSED [ 33%] 367s tests/test_pdb.py::test_hex PASSED [ 33%] 367s tests/test_pdb.py::test_dummy_pdb_box_detection PASSED [ 33%] 367s tests/test_pdb.py::test_multichain_load_cycle PASSED [ 33%] 367s tests/test_pdb.py::test_multichain_load_cycle_noter PASSED [ 34%] 367s tests/test_pdb.py::test_load_pdb_input_top PASSED [ 34%] 367s tests/test_pdb.py::test_chimera_indexing PASSED [ 34%] 367s tests/test_pdb.py::test_chimera_indexing_skip PASSED [ 34%] 367s tests/test_pdb.py::test_vmd_indexing PASSED [ 34%] 367s tests/test_pdb.py::test_overflow_indexing PASSED [ 34%] 367s tests/test_pdb.py::test_blank_indexing PASSED [ 34%] 367s tests/test_pdb.py::test_pdb_charge_read PASSED [ 34%] 367s tests/test_pdb.py::test_pdb_charge_write PASSED [ 34%] 367s tests/test_pdbx.py::test_convert SKIPPED (test_pdbx.py needs OpenMM.) [ 34%] 367s tests/test_prmtop.py::test_load_prmtop PASSED [ 34%] 367s tests/test_prmtop.py::test_load_chamber_prmtop PASSED [ 35%] 367s tests/test_psf.py::test_load_psf PASSED [ 35%] 371s tests/test_psf.py::test_multichain_psf PASSED [ 35%] 371s tests/test_psf.py::test_load_mdcrd_with_psf PASSED [ 35%] 371s tests/test_psf.py::test_against_vmd[1vii.pdb] SKIPPED (This test req...) [ 35%] 371s tests/test_psf.py::test_against_vmd[2EQQ.pdb] SKIPPED (This test req...) [ 35%] 371s tests/test_quaternion.py::test_quaternion_0 PASSED [ 35%] 371s tests/test_quaternion.py::test_quaternion_1 PASSED [ 35%] 371s tests/test_quaternion.py::test_quaternion_2 PASSED [ 35%] 375s tests/test_rdf.py::test_rdf_norm PASSED [ 35%] 375s tests/test_rdf.py::test_compare_rdf_to_gromacs SKIPPED (Binning does...) [ 35%] 375s tests/test_rdf.py::test_rdf_t[True-True] PASSED [ 36%] 380s tests/test_rdf.py::test_rdf_t[True-False] PASSED [ 36%] 380s tests/test_rdf.py::test_rdf_t[False-True] PASSED [ 36%] 381s tests/test_rdf.py::test_rdf_t[False-False] PASSED [ 36%] 381s tests/test_rdf.py::test_rdf_t_norm[0] PASSED [ 36%] 383s tests/test_rdf.py::test_rdf_t_norm[2] PASSED [ 36%] 383s tests/test_rdf.py::test_rdf_t_norm[4] PASSED [ 36%] 383s tests/test_rdf.py::test_compare_rdf_t_at_0[True-True] PASSED [ 36%] 383s tests/test_rdf.py::test_compare_rdf_t_at_0[True-False] PASSED [ 36%] 383s tests/test_rdf.py::test_compare_rdf_t_at_0[False-True] PASSED [ 36%] 384s tests/test_rdf.py::test_compare_rdf_t_at_0[False-False] PASSED [ 36%] 384s tests/test_rdf.py::test_amber_rdf_t[True-True] PASSED [ 36%] 384s tests/test_rdf.py::test_amber_rdf_t[True-False] PASSED [ 37%] 385s tests/test_rdf.py::test_amber_rdf_t[False-True] PASSED [ 37%] 385s tests/test_rdf.py::test_amber_rdf_t[False-False] PASSED [ 37%] 385s tests/test_rdf.py::test_compare_gromacs_rdf_t SKIPPED (Binning does ...) [ 37%] 385s tests/test_rdf.py::test_compare_rdf_t_master PASSED [ 37%] 385s tests/test_rdf.py::test_compare_n_concurrent_pairs PASSED [ 37%] 385s tests/test_reporter.py::test_reporter SKIPPED (test_reporter.py need...) [ 37%] 385s tests/test_reporter.py::test_reporter_subset SKIPPED (test_reporter....) [ 37%] 385s tests/test_reporter.py::test_xtc_reporter_append SKIPPED (test_repor...) [ 37%] 385s tests/test_restart.py::test_read_after_close PASSED [ 37%] 385s tests/test_restart.py::test_shape PASSED [ 37%] 385s tests/test_restart.py::test_shape_2 PASSED [ 38%] 385s tests/test_restart.py::test_read_write_1 PASSED [ 38%] 385s tests/test_restart.py::test_read_write_2 PASSED [ 38%] 385s tests/test_restart.py::test_read_write_3 PASSED [ 38%] 386s tests/test_restart.py::test_read_write_4 PASSED [ 38%] 386s tests/test_rmsd.py::test_trajectory_rmsd PASSED [ 38%] 386s tests/test_rmsd.py::test_precentered_1 PASSED [ 38%] 386s tests/test_rmsd.py::test_precentered_2 PASSED [ 38%] 386s tests/test_rmsd.py::test_superpose_0 PASSED [ 38%] 386s tests/test_rmsd.py::test_superpose_1 PASSED [ 38%] 386s tests/test_rmsd.py::test_superpose_2 PASSED [ 38%] 386s tests/test_rmsd.py::test_superpose_refinds PASSED [ 39%] 386s tests/test_rmsd.py::test_rmsd_atom_indices PASSED [ 39%] 386s tests/test_rmsd.py::test_rmsd_ref_ainds PASSED [ 39%] 387s tests/test_rmsd.py::test_average_structure PASSED [ 39%] 387s tests/test_rmsd.py::test_trajectory_rmsf PASSED [ 39%] 387s tests/test_rmsd.py::test_trajectory_rmsf_aligned PASSED [ 39%] 387s tests/test_rmsd.py::test_rmsd_atom_indices_vs_ref_indices PASSED [ 39%] 387s tests/test_rmsd_memmap.py::test_1 PASSED [ 39%] 387s tests/test_rmsd_memmap.py::test_2 PASSED [ 39%] 387s tests/test_sasa.py::test_sasa_0 PASSED [ 39%] 387s tests/test_sasa.py::test_sasa_1 PASSED [ 39%] 387s tests/test_sasa.py::test_sasa_2 PASSED [ 39%] 387s tests/test_sasa.py::test_sasa_3 PASSED [ 40%] 388s tests/test_sasa.py::test_sasa_4 PASSED [ 40%] 388s tests/test_sasa.py::test_sasa_5 PASSED [ 40%] 388s tests/test_sasa.py::test_sasa_6 PASSED [ 40%] 389s tests/test_sasa.py::test_sasa_7 PASSED [ 40%] 389s tests/test_selection.py::test_range PASSED [ 40%] 389s tests/test_selection.py::test_unary_2 PASSED [ 40%] 389s tests/test_selection.py::test_unary_3 PASSED [ 40%] 389s tests/test_selection.py::test_binary_1 PASSED [ 40%] 389s tests/test_selection.py::test_binary_2 PASSED [ 40%] 389s tests/test_selection.py::test_simple PASSED [ 40%] 389s tests/test_selection.py::test_alias PASSED [ 41%] 389s tests/test_selection.py::test_unary_1 PASSED [ 41%] 389s tests/test_selection.py::test_binary_selection_operator PASSED [ 41%] 389s tests/test_selection.py::test_raises PASSED [ 41%] 389s tests/test_selection.py::test_raises2 PASSED [ 41%] 389s tests/test_selection.py::test_bool PASSED [ 41%] 389s tests/test_selection.py::test_nested_bool PASSED [ 41%] 389s tests/test_selection.py::test_values PASSED [ 41%] 389s tests/test_selection.py::test_element PASSED [ 41%] 389s tests/test_selection.py::test_not PASSED [ 41%] 389s tests/test_selection.py::test_re PASSED [ 41%] 389s tests/test_selection.py::test_within SKIPPED (failed to parse selection) [ 42%] 389s tests/test_selection.py::test_quotes PASSED [ 42%] 389s tests/test_selection.py::test_top PASSED [ 42%] 389s tests/test_selection.py::test_top_2 PASSED [ 42%] 390s tests/test_selection.py::test_backbone PASSED [ 42%] 390s tests/test_selection.py::test_sidechain PASSED [ 42%] 390s tests/test_selection.py::test_literal PASSED [ 42%] 390s tests/test_selection.py::test_in PASSED [ 42%] 390s tests/test_shape.py::test_gyration PASSED [ 42%] 390s tests/test_shape.py::test_principal_moments PASSED [ 42%] 391s tests/test_shape.py::test_asphericity PASSED [ 42%] 391s tests/test_shape.py::test_shape_metrics PASSED [ 42%] 391s tests/test_thermodynamic_properties.py::test_volume PASSED [ 43%] 391s tests/test_thermodynamic_properties.py::test_density PASSED [ 43%] 391s tests/test_thermodynamic_properties.py::test_dipole_moments PASSED [ 43%] 391s tests/test_thermodynamic_properties.py::test_static_dielectric PASSED [ 43%] 391s tests/test_thermodynamic_properties.py::test_kappa PASSED [ 43%] 391s tests/test_thermodynamic_properties.py::test_alpha SKIPPED (Thermal ...) [ 43%] 391s tests/test_topology.py::test_topology_openmm SKIPPED (needs OpenMM) [ 43%] 391s tests/test_topology.py::test_topology_openmm_preserve_chain_id_when_specified SKIPPED [ 43%] 391s tests/test_topology.py::test_topology_openmm_roundtrip_chain_id SKIPPED [ 43%] 391s tests/test_topology.py::test_topology_openmm_preserve_chain_id_even_when_empty SKIPPED [ 43%] 391s tests/test_topology.py::test_topology_openmm_boxes SKIPPED (needs Op...) [ 43%] 391s tests/test_topology.py::test_topology_openmm_formal_charges SKIPPED [ 44%] 391s tests/test_topology.py::test_topology_pandas PASSED [ 44%] 391s tests/test_topology.py::test_topology_pandas_TIP4PEW PASSED [ 44%] 391s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq PASSED [ 44%] 391s tests/test_topology.py::test_topology_numbers PASSED [ 44%] 391s tests/test_topology.py::test_topology_unique_elements_bpti PASSED [ 44%] 391s tests/test_topology.py::test_chain PASSED [ 44%] 391s tests/test_topology.py::test_residue PASSED [ 44%] 391s tests/test_topology.py::test_segment_id PASSED [ 44%] 391s tests/test_topology.py::test_nonconsective_resSeq PASSED [ 44%] 391s tests/test_topology.py::test_pickle PASSED [ 44%] 391s tests/test_topology.py::test_atoms_by_name PASSED [ 45%] 391s tests/test_topology.py::test_select_atom_indices PASSED [ 45%] 391s tests/test_topology.py::test_top_dataframe_openmm_roundtrip SKIPPED [ 45%] 392s tests/test_topology.py::test_n_bonds PASSED [ 45%] 392s tests/test_topology.py::test_load_unknown_topology PASSED [ 45%] 392s tests/test_topology.py::test_unique_pairs PASSED [ 45%] 393s tests/test_topology.py::test_select_pairs PASSED [ 45%] 393s tests/test_topology.py::test_to_fasta PASSED [ 45%] 393s tests/test_topology.py::test_subset PASSED [ 45%] 393s tests/test_topology.py::test_subset_re_index_residues PASSED [ 45%] 393s tests/test_topology.py::test_molecules PASSED [ 45%] 393s tests/test_topology.py::test_copy_and_hash PASSED [ 45%] 393s tests/test_topology.py::test_topology_sliced_residue_indices PASSED [ 46%] 393s tests/test_topology.py::test_topology_join PASSED [ 46%] 394s tests/test_topology.py::test_topology_join_keep_resSeq PASSED [ 46%] 394s tests/test_trajectory.py::test_mismatch PASSED [ 46%] 394s tests/test_trajectory.py::test_box PASSED [ 46%] 394s tests/test_trajectory.py::test_load_pdb_box PASSED [ 46%] 394s tests/test_trajectory.py::test_load_pdb_gz PASSED [ 46%] 394s tests/test_trajectory.py::test_box_load_save[nc] PASSED [ 46%] 394s tests/test_trajectory.py::test_box_load_save[h5] PASSED [ 46%] 394s tests/test_trajectory.py::test_box_load_save[xtc] PASSED [ 46%] 394s tests/test_trajectory.py::test_box_load_save[trr] PASSED [ 46%] 394s tests/test_trajectory.py::test_box_load_save[dcd] PASSED [ 47%] 394s tests/test_trajectory.py::test_box_load_save[mdcrd] PASSED [ 47%] 394s tests/test_trajectory.py::test_box_load_save[dtr] PASSED [ 47%] 394s tests/test_trajectory.py::test_box_load_save[xyz] SKIPPED (xyz does ...) [ 47%] 394s tests/test_trajectory.py::test_box_load_save[xyz.gz] SKIPPED (xyz.gz...) [ 47%] 394s tests/test_trajectory.py::test_box_load_save[lammpstrj] PASSED [ 47%] 394s tests/test_trajectory.py::test_box_load_save[lh5] SKIPPED (lh5 does ...) [ 47%] 394s tests/test_trajectory.py::test_box_load_save[pdb] SKIPPED (pdb does ...) [ 47%] 394s tests/test_trajectory.py::test_box_load_save[pdb.gz] SKIPPED (pdb.gz...) [ 47%] 394s tests/test_trajectory.py::test_box_load_save[ncrst] PASSED [ 47%] 394s tests/test_trajectory.py::test_box_load_save[rst7] PASSED [ 47%] 394s tests/test_trajectory.py::test_box_load_save[gro] PASSED [ 48%] 394s tests/test_trajectory.py::test_slice PASSED [ 48%] 394s tests/test_trajectory.py::test_slice2 PASSED [ 48%] 394s tests/test_trajectory.py::test_read_path[nc] PASSED [ 48%] 394s tests/test_trajectory.py::test_read_path[h5] PASSED [ 48%] 394s tests/test_trajectory.py::test_read_path[xtc] PASSED [ 48%] 394s tests/test_trajectory.py::test_read_path[trr] PASSED [ 48%] 394s tests/test_trajectory.py::test_read_path[dcd] PASSED [ 48%] 394s tests/test_trajectory.py::test_read_path[mdcrd] PASSED [ 48%] 394s tests/test_trajectory.py::test_read_path[dtr] PASSED [ 48%] 394s tests/test_trajectory.py::test_read_path[xyz] PASSED [ 48%] 394s tests/test_trajectory.py::test_read_path[xyz.gz] PASSED [ 48%] 394s tests/test_trajectory.py::test_read_path[lammpstrj] PASSED [ 49%] 394s tests/test_trajectory.py::test_read_path[lh5] PASSED [ 49%] 394s tests/test_trajectory.py::test_read_path[pdb] PASSED [ 49%] 394s tests/test_trajectory.py::test_read_path[pdb.gz] PASSED [ 49%] 395s tests/test_trajectory.py::test_read_path[ncrst] XFAIL (These referen...) [ 49%] 395s tests/test_trajectory.py::test_read_path[rst7] XFAIL (These referenc...) [ 49%] 395s tests/test_trajectory.py::test_read_path[gro] PASSED [ 49%] 395s tests/test_trajectory.py::test_write_path[nc] PASSED [ 49%] 395s tests/test_trajectory.py::test_write_path[h5] PASSED [ 49%] 395s tests/test_trajectory.py::test_write_path[xtc] PASSED [ 49%] 395s tests/test_trajectory.py::test_write_path[trr] PASSED [ 49%] 395s tests/test_trajectory.py::test_write_path[dcd] PASSED [ 50%] 395s tests/test_trajectory.py::test_write_path[mdcrd] SKIPPED (mdcrd can ...) [ 50%] 395s tests/test_trajectory.py::test_write_path[dtr] PASSED [ 50%] 395s tests/test_trajectory.py::test_write_path[xyz] PASSED [ 50%] 395s tests/test_trajectory.py::test_write_path[xyz.gz] PASSED [ 50%] 395s tests/test_trajectory.py::test_write_path[lammpstrj] PASSED [ 50%] 395s tests/test_trajectory.py::test_write_path[lh5] PASSED [ 50%] 395s tests/test_trajectory.py::test_write_path[pdb] PASSED [ 50%] 395s tests/test_trajectory.py::test_write_path[pdb.gz] PASSED [ 50%] 395s tests/test_trajectory.py::test_write_path[ncrst] SKIPPED (ncrst can ...) [ 50%] 395s tests/test_trajectory.py::test_write_path[rst7] SKIPPED (rst7 can on...) [ 50%] 395s tests/test_trajectory.py::test_write_path[gro] PASSED [ 51%] 395s tests/test_trajectory.py::test_read_write[nc-nc] PASSED [ 51%] 395s tests/test_trajectory.py::test_read_write[nc-h5] PASSED [ 51%] 395s tests/test_trajectory.py::test_read_write[nc-xtc] PASSED [ 51%] 395s tests/test_trajectory.py::test_read_write[nc-trr] PASSED [ 51%] 395s tests/test_trajectory.py::test_read_write[nc-dcd] PASSED [ 51%] 395s tests/test_trajectory.py::test_read_write[nc-mdcrd] SKIPPED (mdcrd c...) [ 51%] 398s tests/test_trajectory.py::test_read_write[nc-dtr] PASSED [ 51%] 398s tests/test_trajectory.py::test_read_write[nc-xyz] PASSED [ 51%] 398s tests/test_trajectory.py::test_read_write[nc-xyz.gz] PASSED [ 51%] 399s tests/test_trajectory.py::test_read_write[nc-lammpstrj] PASSED [ 51%] 399s tests/test_trajectory.py::test_read_write[nc-lh5] PASSED [ 51%] 399s tests/test_trajectory.py::test_read_write[nc-pdb] PASSED [ 52%] 400s tests/test_trajectory.py::test_read_write[nc-pdb.gz] PASSED [ 52%] 400s tests/test_trajectory.py::test_read_write[nc-ncrst] SKIPPED (ncrst c...) [ 52%] 400s tests/test_trajectory.py::test_read_write[nc-rst7] SKIPPED (rst7 can...) [ 52%] 400s tests/test_trajectory.py::test_read_write[nc-gro] PASSED [ 52%] 400s tests/test_trajectory.py::test_read_write[h5-nc] PASSED [ 52%] 400s tests/test_trajectory.py::test_read_write[h5-h5] PASSED [ 52%] 400s tests/test_trajectory.py::test_read_write[h5-xtc] PASSED [ 52%] 400s tests/test_trajectory.py::test_read_write[h5-trr] PASSED [ 52%] 400s tests/test_trajectory.py::test_read_write[h5-dcd] PASSED [ 52%] 400s tests/test_trajectory.py::test_read_write[h5-mdcrd] SKIPPED (mdcrd c...) [ 52%] 402s tests/test_trajectory.py::test_read_write[h5-dtr] PASSED [ 53%] 402s tests/test_trajectory.py::test_read_write[h5-xyz] PASSED [ 53%] 402s tests/test_trajectory.py::test_read_write[h5-xyz.gz] PASSED [ 53%] 402s tests/test_trajectory.py::test_read_write[h5-lammpstrj] PASSED [ 53%] 402s tests/test_trajectory.py::test_read_write[h5-lh5] PASSED [ 53%] 402s tests/test_trajectory.py::test_read_write[h5-pdb] PASSED [ 53%] 403s tests/test_trajectory.py::test_read_write[h5-pdb.gz] PASSED [ 53%] 403s tests/test_trajectory.py::test_read_write[h5-ncrst] SKIPPED (ncrst c...) [ 53%] 403s tests/test_trajectory.py::test_read_write[h5-rst7] SKIPPED (rst7 can...) [ 53%] 403s tests/test_trajectory.py::test_read_write[h5-gro] PASSED [ 53%] 403s tests/test_trajectory.py::test_read_write[xtc-nc] PASSED [ 53%] 403s tests/test_trajectory.py::test_read_write[xtc-h5] PASSED [ 54%] 403s tests/test_trajectory.py::test_read_write[xtc-xtc] PASSED [ 54%] 403s tests/test_trajectory.py::test_read_write[xtc-trr] PASSED [ 54%] 403s tests/test_trajectory.py::test_read_write[xtc-dcd] PASSED [ 54%] 403s tests/test_trajectory.py::test_read_write[xtc-mdcrd] SKIPPED (mdcrd ...) [ 54%] 404s tests/test_trajectory.py::test_read_write[xtc-dtr] PASSED [ 54%] 404s tests/test_trajectory.py::test_read_write[xtc-xyz] PASSED [ 54%] 404s tests/test_trajectory.py::test_read_write[xtc-xyz.gz] PASSED [ 54%] 405s tests/test_trajectory.py::test_read_write[xtc-lammpstrj] PASSED [ 54%] 405s tests/test_trajectory.py::test_read_write[xtc-lh5] PASSED [ 54%] 405s tests/test_trajectory.py::test_read_write[xtc-pdb] PASSED [ 54%] 405s tests/test_trajectory.py::test_read_write[xtc-pdb.gz] PASSED [ 54%] 405s tests/test_trajectory.py::test_read_write[xtc-ncrst] SKIPPED (ncrst ...) [ 55%] 405s tests/test_trajectory.py::test_read_write[xtc-rst7] SKIPPED (rst7 ca...) [ 55%] 405s tests/test_trajectory.py::test_read_write[xtc-gro] PASSED [ 55%] 405s tests/test_trajectory.py::test_read_write[trr-nc] PASSED [ 55%] 405s tests/test_trajectory.py::test_read_write[trr-h5] PASSED [ 55%] 405s tests/test_trajectory.py::test_read_write[trr-xtc] PASSED [ 55%] 405s tests/test_trajectory.py::test_read_write[trr-trr] PASSED [ 55%] 405s tests/test_trajectory.py::test_read_write[trr-dcd] PASSED [ 55%] 405s tests/test_trajectory.py::test_read_write[trr-mdcrd] SKIPPED (mdcrd ...) [ 55%] 407s tests/test_trajectory.py::test_read_write[trr-dtr] PASSED [ 55%] 407s tests/test_trajectory.py::test_read_write[trr-xyz] PASSED [ 55%] 407s tests/test_trajectory.py::test_read_write[trr-xyz.gz] PASSED [ 56%] 407s tests/test_trajectory.py::test_read_write[trr-lammpstrj] PASSED [ 56%] 407s tests/test_trajectory.py::test_read_write[trr-lh5] PASSED [ 56%] 408s tests/test_trajectory.py::test_read_write[trr-pdb] PASSED [ 56%] 409s tests/test_trajectory.py::test_read_write[trr-pdb.gz] PASSED [ 56%] 409s tests/test_trajectory.py::test_read_write[trr-ncrst] SKIPPED (ncrst ...) [ 56%] 409s tests/test_trajectory.py::test_read_write[trr-rst7] SKIPPED (rst7 ca...) [ 56%] 409s tests/test_trajectory.py::test_read_write[trr-gro] PASSED [ 56%] 409s tests/test_trajectory.py::test_read_write[dcd-nc] PASSED [ 56%] 409s tests/test_trajectory.py::test_read_write[dcd-h5] PASSED [ 56%] 409s tests/test_trajectory.py::test_read_write[dcd-xtc] PASSED [ 56%] 409s tests/test_trajectory.py::test_read_write[dcd-trr] PASSED [ 57%] 409s tests/test_trajectory.py::test_read_write[dcd-dcd] PASSED [ 57%] 409s tests/test_trajectory.py::test_read_write[dcd-mdcrd] SKIPPED (mdcrd ...) [ 57%] 410s tests/test_trajectory.py::test_read_write[dcd-dtr] PASSED [ 57%] 410s tests/test_trajectory.py::test_read_write[dcd-xyz] PASSED [ 57%] 411s tests/test_trajectory.py::test_read_write[dcd-xyz.gz] PASSED [ 57%] 411s tests/test_trajectory.py::test_read_write[dcd-lammpstrj] PASSED [ 57%] 411s tests/test_trajectory.py::test_read_write[dcd-lh5] PASSED [ 57%] 411s tests/test_trajectory.py::test_read_write[dcd-pdb] PASSED [ 57%] 412s tests/test_trajectory.py::test_read_write[dcd-pdb.gz] PASSED [ 57%] 412s tests/test_trajectory.py::test_read_write[dcd-ncrst] SKIPPED (ncrst ...) [ 57%] 412s tests/test_trajectory.py::test_read_write[dcd-rst7] SKIPPED (rst7 ca...) [ 57%] 412s tests/test_trajectory.py::test_read_write[dcd-gro] PASSED [ 58%] 412s tests/test_trajectory.py::test_read_write[mdcrd-nc] PASSED [ 58%] 412s tests/test_trajectory.py::test_read_write[mdcrd-h5] PASSED [ 58%] 412s tests/test_trajectory.py::test_read_write[mdcrd-xtc] PASSED [ 58%] 412s tests/test_trajectory.py::test_read_write[mdcrd-trr] PASSED [ 58%] 412s tests/test_trajectory.py::test_read_write[mdcrd-dcd] PASSED [ 58%] 412s tests/test_trajectory.py::test_read_write[mdcrd-mdcrd] SKIPPED (mdcr...) [ 58%] 412s tests/test_trajectory.py::test_read_write[mdcrd-dtr] SKIPPED (dtr ne...) [ 58%] 412s tests/test_trajectory.py::test_read_write[mdcrd-xyz] PASSED [ 58%] 413s tests/test_trajectory.py::test_read_write[mdcrd-xyz.gz] PASSED [ 58%] 413s tests/test_trajectory.py::test_read_write[mdcrd-lammpstrj] SKIPPED (...) [ 58%] 413s tests/test_trajectory.py::test_read_write[mdcrd-lh5] PASSED [ 59%] 413s tests/test_trajectory.py::test_read_write[mdcrd-pdb] PASSED [ 59%] 414s tests/test_trajectory.py::test_read_write[mdcrd-pdb.gz] PASSED [ 59%] 414s tests/test_trajectory.py::test_read_write[mdcrd-ncrst] SKIPPED (ncrs...) [ 59%] 414s tests/test_trajectory.py::test_read_write[mdcrd-rst7] SKIPPED (rst7 ...) [ 59%] 414s tests/test_trajectory.py::test_read_write[mdcrd-gro] PASSED [ 59%] 414s tests/test_trajectory.py::test_read_write[dtr-nc] PASSED [ 59%] 414s tests/test_trajectory.py::test_read_write[dtr-h5] PASSED [ 59%] 414s tests/test_trajectory.py::test_read_write[dtr-xtc] PASSED [ 59%] 414s tests/test_trajectory.py::test_read_write[dtr-trr] PASSED [ 59%] 414s tests/test_trajectory.py::test_read_write[dtr-dcd] PASSED [ 59%] 414s tests/test_trajectory.py::test_read_write[dtr-mdcrd] SKIPPED (mdcrd ...) [ 60%] 415s tests/test_trajectory.py::test_read_write[dtr-dtr] PASSED [ 60%] 416s tests/test_trajectory.py::test_read_write[dtr-xyz] PASSED [ 60%] 416s tests/test_trajectory.py::test_read_write[dtr-xyz.gz] PASSED [ 60%] 416s tests/test_trajectory.py::test_read_write[dtr-lammpstrj] PASSED [ 60%] 416s tests/test_trajectory.py::test_read_write[dtr-lh5] PASSED [ 60%] 416s tests/test_trajectory.py::test_read_write[dtr-pdb] PASSED [ 60%] 417s tests/test_trajectory.py::test_read_write[dtr-pdb.gz] PASSED [ 60%] 417s tests/test_trajectory.py::test_read_write[dtr-ncrst] SKIPPED (ncrst ...) [ 60%] 417s tests/test_trajectory.py::test_read_write[dtr-rst7] SKIPPED (rst7 ca...) [ 60%] 417s tests/test_trajectory.py::test_read_write[dtr-gro] PASSED [ 60%] 417s tests/test_trajectory.py::test_read_write[xyz-nc] PASSED [ 60%] 417s tests/test_trajectory.py::test_read_write[xyz-h5] PASSED [ 61%] 417s tests/test_trajectory.py::test_read_write[xyz-xtc] PASSED [ 61%] 417s tests/test_trajectory.py::test_read_write[xyz-trr] PASSED [ 61%] 417s tests/test_trajectory.py::test_read_write[xyz-dcd] PASSED [ 61%] 417s tests/test_trajectory.py::test_read_write[xyz-mdcrd] SKIPPED (mdcrd ...) [ 61%] 417s tests/test_trajectory.py::test_read_write[xyz-dtr] SKIPPED (dtr need...) [ 61%] 417s tests/test_trajectory.py::test_read_write[xyz-xyz] PASSED [ 61%] 417s tests/test_trajectory.py::test_read_write[xyz-xyz.gz] PASSED [ 61%] 417s tests/test_trajectory.py::test_read_write[xyz-lammpstrj] SKIPPED (la...) [ 61%] 417s tests/test_trajectory.py::test_read_write[xyz-lh5] PASSED [ 61%] 418s tests/test_trajectory.py::test_read_write[xyz-pdb] PASSED [ 61%] 418s tests/test_trajectory.py::test_read_write[xyz-pdb.gz] PASSED [ 62%] 418s tests/test_trajectory.py::test_read_write[xyz-ncrst] SKIPPED (ncrst ...) [ 62%] 418s tests/test_trajectory.py::test_read_write[xyz-rst7] SKIPPED (rst7 ca...) [ 62%] 418s tests/test_trajectory.py::test_read_write[xyz-gro] PASSED [ 62%] 418s tests/test_trajectory.py::test_read_write[xyz.gz-nc] PASSED [ 62%] 418s tests/test_trajectory.py::test_read_write[xyz.gz-h5] PASSED [ 62%] 418s tests/test_trajectory.py::test_read_write[xyz.gz-xtc] PASSED [ 62%] 418s tests/test_trajectory.py::test_read_write[xyz.gz-trr] PASSED [ 62%] 418s tests/test_trajectory.py::test_read_write[xyz.gz-dcd] PASSED [ 62%] 418s tests/test_trajectory.py::test_read_write[xyz.gz-mdcrd] SKIPPED (mdc...) [ 62%] 418s tests/test_trajectory.py::test_read_write[xyz.gz-dtr] SKIPPED (dtr n...) [ 62%] 418s tests/test_trajectory.py::test_read_write[xyz.gz-xyz] PASSED [ 63%] 419s tests/test_trajectory.py::test_read_write[xyz.gz-xyz.gz] PASSED [ 63%] 419s tests/test_trajectory.py::test_read_write[xyz.gz-lammpstrj] SKIPPED [ 63%] 419s tests/test_trajectory.py::test_read_write[xyz.gz-lh5] PASSED [ 63%] 419s tests/test_trajectory.py::test_read_write[xyz.gz-pdb] PASSED [ 63%] 419s tests/test_trajectory.py::test_read_write[xyz.gz-pdb.gz] PASSED [ 63%] 419s tests/test_trajectory.py::test_read_write[xyz.gz-ncrst] SKIPPED (ncr...) [ 63%] 419s tests/test_trajectory.py::test_read_write[xyz.gz-rst7] SKIPPED (rst7...) [ 63%] 419s tests/test_trajectory.py::test_read_write[xyz.gz-gro] PASSED [ 63%] 419s tests/test_trajectory.py::test_read_write[lammpstrj-nc] PASSED [ 63%] 419s tests/test_trajectory.py::test_read_write[lammpstrj-h5] PASSED [ 63%] 419s tests/test_trajectory.py::test_read_write[lammpstrj-xtc] PASSED [ 63%] 420s tests/test_trajectory.py::test_read_write[lammpstrj-trr] PASSED [ 64%] 420s tests/test_trajectory.py::test_read_write[lammpstrj-dcd] PASSED [ 64%] 420s tests/test_trajectory.py::test_read_write[lammpstrj-mdcrd] SKIPPED (...) [ 64%] 421s tests/test_trajectory.py::test_read_write[lammpstrj-dtr] PASSED [ 64%] 421s tests/test_trajectory.py::test_read_write[lammpstrj-xyz] PASSED [ 64%] 421s tests/test_trajectory.py::test_read_write[lammpstrj-xyz.gz] PASSED [ 64%] 421s tests/test_trajectory.py::test_read_write[lammpstrj-lammpstrj] PASSED [ 64%] 422s tests/test_trajectory.py::test_read_write[lammpstrj-lh5] PASSED [ 64%] 422s tests/test_trajectory.py::test_read_write[lammpstrj-pdb] PASSED [ 64%] 422s tests/test_trajectory.py::test_read_write[lammpstrj-pdb.gz] PASSED [ 64%] 422s tests/test_trajectory.py::test_read_write[lammpstrj-ncrst] SKIPPED (...) [ 64%] 422s tests/test_trajectory.py::test_read_write[lammpstrj-rst7] SKIPPED (r...) [ 65%] 422s tests/test_trajectory.py::test_read_write[lammpstrj-gro] PASSED [ 65%] 422s tests/test_trajectory.py::test_read_write[lh5-nc] PASSED [ 65%] 423s tests/test_trajectory.py::test_read_write[lh5-h5] PASSED [ 65%] 423s tests/test_trajectory.py::test_read_write[lh5-xtc] PASSED [ 65%] 423s tests/test_trajectory.py::test_read_write[lh5-trr] PASSED [ 65%] 423s tests/test_trajectory.py::test_read_write[lh5-dcd] PASSED [ 65%] 423s tests/test_trajectory.py::test_read_write[lh5-mdcrd] SKIPPED (mdcrd ...) [ 65%] 423s tests/test_trajectory.py::test_read_write[lh5-dtr] SKIPPED (dtr need...) [ 65%] 423s tests/test_trajectory.py::test_read_write[lh5-xyz] PASSED [ 65%] 423s tests/test_trajectory.py::test_read_write[lh5-xyz.gz] PASSED [ 65%] 423s tests/test_trajectory.py::test_read_write[lh5-lammpstrj] SKIPPED (la...) [ 66%] 423s tests/test_trajectory.py::test_read_write[lh5-lh5] PASSED [ 66%] 423s tests/test_trajectory.py::test_read_write[lh5-pdb] PASSED [ 66%] 424s tests/test_trajectory.py::test_read_write[lh5-pdb.gz] PASSED [ 66%] 424s tests/test_trajectory.py::test_read_write[lh5-ncrst] SKIPPED (ncrst ...) [ 66%] 424s tests/test_trajectory.py::test_read_write[lh5-rst7] SKIPPED (rst7 ca...) [ 66%] 424s tests/test_trajectory.py::test_read_write[lh5-gro] PASSED [ 66%] 424s tests/test_trajectory.py::test_read_write[pdb-nc] PASSED [ 66%] 424s tests/test_trajectory.py::test_read_write[pdb-h5] PASSED [ 66%] 424s tests/test_trajectory.py::test_read_write[pdb-xtc] PASSED [ 66%] 424s tests/test_trajectory.py::test_read_write[pdb-trr] PASSED [ 66%] 425s tests/test_trajectory.py::test_read_write[pdb-dcd] PASSED [ 66%] 425s tests/test_trajectory.py::test_read_write[pdb-mdcrd] SKIPPED (mdcrd ...) [ 67%] 426s tests/test_trajectory.py::test_read_write[pdb-dtr] PASSED [ 67%] 426s tests/test_trajectory.py::test_read_write[pdb-xyz] PASSED [ 67%] 427s tests/test_trajectory.py::test_read_write[pdb-xyz.gz] PASSED [ 67%] 427s tests/test_trajectory.py::test_read_write[pdb-lammpstrj] PASSED [ 67%] 427s tests/test_trajectory.py::test_read_write[pdb-lh5] PASSED [ 67%] 427s tests/test_trajectory.py::test_read_write[pdb-pdb] PASSED [ 67%] 428s tests/test_trajectory.py::test_read_write[pdb-pdb.gz] PASSED [ 67%] 428s tests/test_trajectory.py::test_read_write[pdb-ncrst] SKIPPED (ncrst ...) [ 67%] 428s tests/test_trajectory.py::test_read_write[pdb-rst7] SKIPPED (rst7 ca...) [ 67%] 428s tests/test_trajectory.py::test_read_write[pdb-gro] PASSED [ 67%] 428s tests/test_trajectory.py::test_read_write[pdb.gz-nc] PASSED [ 68%] 429s tests/test_trajectory.py::test_read_write[pdb.gz-h5] PASSED [ 68%] 429s tests/test_trajectory.py::test_read_write[pdb.gz-xtc] PASSED [ 68%] 429s tests/test_trajectory.py::test_read_write[pdb.gz-trr] PASSED [ 68%] 429s tests/test_trajectory.py::test_read_write[pdb.gz-dcd] PASSED [ 68%] 429s tests/test_trajectory.py::test_read_write[pdb.gz-mdcrd] SKIPPED (mdc...) [ 68%] 430s tests/test_trajectory.py::test_read_write[pdb.gz-dtr] PASSED [ 68%] 431s tests/test_trajectory.py::test_read_write[pdb.gz-xyz] PASSED [ 68%] 431s tests/test_trajectory.py::test_read_write[pdb.gz-xyz.gz] PASSED [ 68%] 431s tests/test_trajectory.py::test_read_write[pdb.gz-lammpstrj] PASSED [ 68%] 432s tests/test_trajectory.py::test_read_write[pdb.gz-lh5] PASSED [ 68%] 432s tests/test_trajectory.py::test_read_write[pdb.gz-pdb] PASSED [ 69%] 433s tests/test_trajectory.py::test_read_write[pdb.gz-pdb.gz] PASSED [ 69%] 433s tests/test_trajectory.py::test_read_write[pdb.gz-ncrst] SKIPPED (ncr...) [ 69%] 433s tests/test_trajectory.py::test_read_write[pdb.gz-rst7] SKIPPED (rst7...) [ 69%] 433s tests/test_trajectory.py::test_read_write[pdb.gz-gro] PASSED [ 69%] 433s tests/test_trajectory.py::test_read_write[ncrst-nc] XFAIL (These ref...) [ 69%] 433s tests/test_trajectory.py::test_read_write[ncrst-h5] XFAIL (These ref...) [ 69%] 433s tests/test_trajectory.py::test_read_write[ncrst-xtc] XFAIL (These re...) [ 69%] 433s tests/test_trajectory.py::test_read_write[ncrst-trr] XFAIL (These re...) [ 69%] 433s tests/test_trajectory.py::test_read_write[ncrst-dcd] XFAIL (These re...) [ 69%] 433s tests/test_trajectory.py::test_read_write[ncrst-mdcrd] XFAIL (These ...) [ 69%] 433s tests/test_trajectory.py::test_read_write[ncrst-dtr] XFAIL (These re...) [ 69%] 433s tests/test_trajectory.py::test_read_write[ncrst-xyz] XFAIL (These re...) [ 70%] 433s tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] XFAIL (These...) [ 70%] 433s tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] XFAIL (Th...) [ 70%] 433s tests/test_trajectory.py::test_read_write[ncrst-lh5] XFAIL (These re...) [ 70%] 433s tests/test_trajectory.py::test_read_write[ncrst-pdb] XFAIL (These re...) [ 70%] 433s tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] XFAIL (These...) [ 70%] 433s tests/test_trajectory.py::test_read_write[ncrst-ncrst] XFAIL (These ...) [ 70%] 433s tests/test_trajectory.py::test_read_write[ncrst-rst7] XFAIL (These r...) [ 70%] 433s tests/test_trajectory.py::test_read_write[ncrst-gro] XFAIL (These re...) [ 70%] 433s tests/test_trajectory.py::test_read_write[rst7-nc] XFAIL (These refe...) [ 70%] 434s tests/test_trajectory.py::test_read_write[rst7-h5] XFAIL (These refe...) [ 70%] 434s tests/test_trajectory.py::test_read_write[rst7-xtc] XFAIL (These ref...) [ 71%] 434s tests/test_trajectory.py::test_read_write[rst7-trr] XFAIL (These ref...) [ 71%] 434s tests/test_trajectory.py::test_read_write[rst7-dcd] XFAIL (These ref...) [ 71%] 434s tests/test_trajectory.py::test_read_write[rst7-mdcrd] XFAIL (These r...) [ 71%] 434s tests/test_trajectory.py::test_read_write[rst7-dtr] XFAIL (These ref...) [ 71%] 434s tests/test_trajectory.py::test_read_write[rst7-xyz] XFAIL (These ref...) [ 71%] 434s tests/test_trajectory.py::test_read_write[rst7-xyz.gz] XFAIL (These ...) [ 71%] 434s tests/test_trajectory.py::test_read_write[rst7-lammpstrj] XFAIL (The...) [ 71%] 434s tests/test_trajectory.py::test_read_write[rst7-lh5] XFAIL (These ref...) [ 71%] 434s tests/test_trajectory.py::test_read_write[rst7-pdb] XFAIL (These ref...) [ 71%] 434s tests/test_trajectory.py::test_read_write[rst7-pdb.gz] XFAIL (These ...) [ 71%] 434s tests/test_trajectory.py::test_read_write[rst7-ncrst] XFAIL (These r...) [ 72%] 434s tests/test_trajectory.py::test_read_write[rst7-rst7] XFAIL (These re...) [ 72%] 434s tests/test_trajectory.py::test_read_write[rst7-gro] XFAIL (These ref...) [ 72%] 434s tests/test_trajectory.py::test_read_write[gro-nc] PASSED [ 72%] 434s tests/test_trajectory.py::test_read_write[gro-h5] PASSED [ 72%] 434s tests/test_trajectory.py::test_read_write[gro-xtc] PASSED [ 72%] 434s tests/test_trajectory.py::test_read_write[gro-trr] PASSED [ 72%] 434s tests/test_trajectory.py::test_read_write[gro-dcd] PASSED [ 72%] 434s tests/test_trajectory.py::test_read_write[gro-mdcrd] SKIPPED (mdcrd ...) [ 72%] 436s tests/test_trajectory.py::test_read_write[gro-dtr] PASSED [ 72%] 436s tests/test_trajectory.py::test_read_write[gro-xyz] PASSED [ 72%] 437s tests/test_trajectory.py::test_read_write[gro-xyz.gz] PASSED [ 72%] 437s tests/test_trajectory.py::test_read_write[gro-lammpstrj] PASSED [ 73%] 437s tests/test_trajectory.py::test_read_write[gro-lh5] PASSED [ 73%] 437s tests/test_trajectory.py::test_read_write[gro-pdb] PASSED [ 73%] 437s tests/test_trajectory.py::test_read_write[gro-pdb.gz] PASSED [ 73%] 437s tests/test_trajectory.py::test_read_write[gro-ncrst] SKIPPED (ncrst ...) [ 73%] 437s tests/test_trajectory.py::test_read_write[gro-rst7] SKIPPED (rst7 ca...) [ 73%] 438s tests/test_trajectory.py::test_read_write[gro-gro] PASSED [ 73%] 438s tests/test_trajectory.py::test_load[nc] PASSED [ 73%] 438s tests/test_trajectory.py::test_load[h5] PASSED [ 73%] 438s tests/test_trajectory.py::test_load[xtc] PASSED [ 73%] 438s tests/test_trajectory.py::test_load[trr] PASSED [ 73%] 438s tests/test_trajectory.py::test_load[dcd] PASSED [ 74%] 438s tests/test_trajectory.py::test_load[mdcrd] PASSED [ 74%] 438s tests/test_trajectory.py::test_load[dtr] PASSED [ 74%] 438s tests/test_trajectory.py::test_load[xyz] PASSED [ 74%] 438s tests/test_trajectory.py::test_load[xyz.gz] PASSED [ 74%] 438s tests/test_trajectory.py::test_load[lammpstrj] PASSED [ 74%] 439s tests/test_trajectory.py::test_load[lh5] PASSED [ 74%] 440s tests/test_trajectory.py::test_load[pdb] PASSED [ 74%] 441s tests/test_trajectory.py::test_load[pdb.gz] PASSED [ 74%] 441s tests/test_trajectory.py::test_load[ncrst] XFAIL (These reference fi...) [ 74%] 441s tests/test_trajectory.py::test_load[rst7] XFAIL (These reference fil...) [ 74%] 442s tests/test_trajectory.py::test_load[gro] PASSED [ 75%] 442s tests/test_trajectory.py::test_hdf5 PASSED [ 75%] 442s tests/test_trajectory.py::test_center PASSED [ 75%] 442s tests/test_trajectory.py::test_center_aind PASSED [ 75%] 442s tests/test_trajectory.py::test_float_atom_indices_exception[nc] PASSED [ 75%] 442s tests/test_trajectory.py::test_float_atom_indices_exception[h5] PASSED [ 75%] 442s tests/test_trajectory.py::test_float_atom_indices_exception[xtc] PASSED [ 75%] 442s tests/test_trajectory.py::test_float_atom_indices_exception[trr] PASSED [ 75%] 442s tests/test_trajectory.py::test_float_atom_indices_exception[dcd] PASSED [ 75%] 442s tests/test_trajectory.py::test_float_atom_indices_exception[mdcrd] PASSED [ 75%] 442s tests/test_trajectory.py::test_float_atom_indices_exception[dtr] PASSED [ 75%] 442s tests/test_trajectory.py::test_float_atom_indices_exception[xyz] PASSED [ 75%] 442s tests/test_trajectory.py::test_float_atom_indices_exception[xyz.gz] PASSED [ 76%] 442s tests/test_trajectory.py::test_float_atom_indices_exception[lammpstrj] PASSED [ 76%] 442s tests/test_trajectory.py::test_float_atom_indices_exception[lh5] PASSED [ 76%] 442s tests/test_trajectory.py::test_float_atom_indices_exception[pdb] PASSED [ 76%] 442s tests/test_trajectory.py::test_float_atom_indices_exception[pdb.gz] PASSED [ 76%] 442s tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] XFAIL [ 76%] 442s tests/test_trajectory.py::test_float_atom_indices_exception[rst7] XFAIL [ 76%] 442s tests/test_trajectory.py::test_float_atom_indices_exception[gro] PASSED [ 76%] 442s tests/test_trajectory.py::test_restrict_atoms PASSED [ 76%] 442s tests/test_trajectory.py::test_restrict_atoms_not_inplace PASSED [ 76%] 442s tests/test_trajectory.py::test_array_vs_matrix PASSED [ 76%] 442s tests/test_trajectory.py::test_pdb_unitcell_loadsave PASSED [ 77%] 442s tests/test_trajectory.py::test_load_combination[nc] PASSED [ 77%] 442s tests/test_trajectory.py::test_load_combination[h5] PASSED [ 77%] 442s tests/test_trajectory.py::test_load_combination[xtc] PASSED [ 77%] 442s tests/test_trajectory.py::test_load_combination[trr] PASSED [ 77%] 442s tests/test_trajectory.py::test_load_combination[dcd] PASSED [ 77%] 442s tests/test_trajectory.py::test_load_combination[mdcrd] PASSED [ 77%] 442s tests/test_trajectory.py::test_load_combination[dtr] PASSED [ 77%] 442s tests/test_trajectory.py::test_load_combination[xyz] PASSED [ 77%] 442s tests/test_trajectory.py::test_load_combination[xyz.gz] PASSED [ 77%] 442s tests/test_trajectory.py::test_load_combination[lammpstrj] PASSED [ 77%] 442s tests/test_trajectory.py::test_load_combination[lh5] PASSED [ 78%] 443s tests/test_trajectory.py::test_load_combination[pdb] PASSED [ 78%] 443s tests/test_trajectory.py::test_load_combination[pdb.gz] PASSED [ 78%] 443s tests/test_trajectory.py::test_load_combination[ncrst] XFAIL (These ...) [ 78%] 443s tests/test_trajectory.py::test_load_combination[rst7] XFAIL (These r...) [ 78%] 443s tests/test_trajectory.py::test_load_combination[gro] PASSED [ 78%] 443s tests/test_trajectory.py::test_no_topology PASSED [ 78%] 443s tests/test_trajectory.py::test_join PASSED [ 78%] 443s tests/test_trajectory.py::test_md_join PASSED [ 78%] 443s tests/test_trajectory.py::test_stack_1 PASSED [ 78%] 443s tests/test_trajectory.py::test_stack_2 PASSED [ 78%] 443s tests/test_trajectory.py::test_seek_read_mode[nc] PASSED [ 78%] 443s tests/test_trajectory.py::test_seek_read_mode[h5] PASSED [ 79%] 443s tests/test_trajectory.py::test_seek_read_mode[xtc] PASSED [ 79%] 444s tests/test_trajectory.py::test_seek_read_mode[trr] PASSED [ 79%] 444s tests/test_trajectory.py::test_seek_read_mode[dcd] PASSED [ 79%] 444s tests/test_trajectory.py::test_seek_read_mode[mdcrd] PASSED [ 79%] 444s tests/test_trajectory.py::test_seek_read_mode[dtr] PASSED [ 79%] 444s tests/test_trajectory.py::test_seek_read_mode[xyz] PASSED [ 79%] 444s tests/test_trajectory.py::test_seek_read_mode[xyz.gz] XFAIL (This is...) [ 79%] 444s tests/test_trajectory.py::test_seek_read_mode[lammpstrj] PASSED [ 79%] 444s tests/test_trajectory.py::test_seek_read_mode[lh5] PASSED [ 79%] 444s tests/test_trajectory.py::test_seek_read_mode[pdb] XFAIL (PDB Files ...) [ 79%] 444s tests/test_trajectory.py::test_seek_read_mode[pdb.gz] XFAIL (PDB Fil...) [ 80%] 444s tests/test_trajectory.py::test_seek_read_mode[ncrst] XFAIL (These re...) [ 80%] 444s tests/test_trajectory.py::test_seek_read_mode[rst7] XFAIL (These ref...) [ 80%] 444s tests/test_trajectory.py::test_seek_read_mode[gro] XFAIL (This is br...) [ 80%] 444s tests/test_trajectory.py::test_load_frame[nc] PASSED [ 80%] 444s tests/test_trajectory.py::test_load_frame[h5] PASSED [ 80%] 444s tests/test_trajectory.py::test_load_frame[xtc] PASSED [ 80%] 444s tests/test_trajectory.py::test_load_frame[trr] PASSED [ 80%] 444s tests/test_trajectory.py::test_load_frame[dcd] PASSED [ 80%] 444s tests/test_trajectory.py::test_load_frame[mdcrd] PASSED [ 80%] 444s tests/test_trajectory.py::test_load_frame[dtr] XFAIL (DTR doesn't lo...) [ 80%] 444s tests/test_trajectory.py::test_load_frame[xyz] PASSED [ 81%] 444s tests/test_trajectory.py::test_load_frame[xyz.gz] PASSED [ 81%] 444s tests/test_trajectory.py::test_load_frame[lammpstrj] PASSED [ 81%] 444s tests/test_trajectory.py::test_load_frame[lh5] PASSED [ 81%] 445s tests/test_trajectory.py::test_load_frame[pdb] PASSED [ 81%] 445s tests/test_trajectory.py::test_load_frame[pdb.gz] PASSED [ 81%] 445s tests/test_trajectory.py::test_load_frame[ncrst] XFAIL (These refere...) [ 81%] 445s tests/test_trajectory.py::test_load_frame[rst7] XFAIL (These referen...) [ 81%] 445s tests/test_trajectory.py::test_load_frame[gro] XFAIL (Gro doesn't im...) [ 81%] 445s tests/test_trajectory.py::test_load_frame_2eqq PASSED [ 81%] 445s tests/test_trajectory.py::test_iterload[nc] PASSED [ 81%] 445s tests/test_trajectory.py::test_iterload[h5] PASSED [ 81%] 445s tests/test_trajectory.py::test_iterload[xtc] PASSED [ 82%] 445s tests/test_trajectory.py::test_iterload[trr] PASSED [ 82%] 445s tests/test_trajectory.py::test_iterload[dcd] PASSED [ 82%] 445s tests/test_trajectory.py::test_iterload[mdcrd] PASSED [ 82%] 446s tests/test_trajectory.py::test_iterload[dtr] XFAIL (This is broken w...) [ 82%] 446s tests/test_trajectory.py::test_iterload[xyz] PASSED [ 82%] 446s tests/test_trajectory.py::test_iterload[xyz.gz] PASSED [ 82%] 446s tests/test_trajectory.py::test_iterload[lammpstrj] PASSED [ 82%] 446s tests/test_trajectory.py::test_iterload[lh5] PASSED [ 82%] 446s tests/test_trajectory.py::test_iterload[pdb] PASSED [ 82%] 446s tests/test_trajectory.py::test_iterload[pdb.gz] PASSED [ 82%] 446s tests/test_trajectory.py::test_iterload[ncrst] SKIPPED (Only 1 frame...) [ 83%] 446s tests/test_trajectory.py::test_iterload[rst7] SKIPPED (Only 1 frame ...) [ 83%] 446s tests/test_trajectory.py::test_iterload[gro] PASSED [ 83%] 449s tests/test_trajectory.py::test_iterload_skip[nc] PASSED [ 83%] 452s tests/test_trajectory.py::test_iterload_skip[h5] PASSED [ 83%] 453s tests/test_trajectory.py::test_iterload_skip[xtc] PASSED [ 83%] 454s tests/test_trajectory.py::test_iterload_skip[trr] PASSED [ 83%] 455s tests/test_trajectory.py::test_iterload_skip[dcd] PASSED [ 83%] 457s tests/test_trajectory.py::test_iterload_skip[mdcrd] PASSED [ 83%] 457s tests/test_trajectory.py::test_iterload_skip[dtr] PASSED [ 83%] 458s tests/test_trajectory.py::test_iterload_skip[xyz] PASSED [ 83%] 459s tests/test_trajectory.py::test_iterload_skip[xyz.gz] PASSED [ 84%] 460s tests/test_trajectory.py::test_iterload_skip[lammpstrj] PASSED [ 84%] 462s tests/test_trajectory.py::test_iterload_skip[lh5] PASSED [ 84%] 462s tests/test_trajectory.py::test_iterload_skip[pdb] XFAIL (PDB Iterloa...) [ 84%] 462s tests/test_trajectory.py::test_iterload_skip[pdb.gz] XFAIL (PDB Iter...) [ 84%] 462s tests/test_trajectory.py::test_iterload_skip[ncrst] XFAIL (These ref...) [ 84%] 462s tests/test_trajectory.py::test_iterload_skip[rst7] XFAIL (These refe...) [ 84%] 462s tests/test_trajectory.py::test_iterload_skip[gro] XFAIL (Not impleme...) [ 84%] 462s tests/test_trajectory.py::test_iterload_chunk_dcd PASSED [ 84%] 462s tests/test_trajectory.py::test_save_load[nc] PASSED [ 84%] 462s tests/test_trajectory.py::test_save_load[h5] PASSED [ 84%] 462s tests/test_trajectory.py::test_save_load[xtc] PASSED [ 84%] 462s tests/test_trajectory.py::test_save_load[trr] PASSED [ 85%] 462s tests/test_trajectory.py::test_save_load[dcd] PASSED [ 85%] 462s tests/test_trajectory.py::test_save_load[mdcrd] PASSED [ 85%] 462s tests/test_trajectory.py::test_save_load[dtr] PASSED [ 85%] 462s tests/test_trajectory.py::test_save_load[xyz] PASSED [ 85%] 462s tests/test_trajectory.py::test_save_load[xyz.gz] PASSED [ 85%] 462s tests/test_trajectory.py::test_save_load[lammpstrj] PASSED [ 85%] 462s tests/test_trajectory.py::test_save_load[lh5] PASSED [ 85%] 462s tests/test_trajectory.py::test_save_load[pdb] PASSED [ 85%] 462s tests/test_trajectory.py::test_save_load[pdb.gz] PASSED [ 85%] 462s tests/test_trajectory.py::test_save_load[ncrst] PASSED [ 85%] 462s tests/test_trajectory.py::test_save_load[rst7] PASSED [ 86%] 462s tests/test_trajectory.py::test_save_load[gro] PASSED [ 86%] 462s tests/test_trajectory.py::test_force_overwrite[nc] PASSED [ 86%] 462s tests/test_trajectory.py::test_force_overwrite[h5] PASSED [ 86%] 462s tests/test_trajectory.py::test_force_overwrite[xtc] PASSED [ 86%] 462s tests/test_trajectory.py::test_force_overwrite[trr] PASSED [ 86%] 462s tests/test_trajectory.py::test_force_overwrite[dcd] PASSED [ 86%] 462s tests/test_trajectory.py::test_force_overwrite[mdcrd] PASSED [ 86%] 462s tests/test_trajectory.py::test_force_overwrite[dtr] XFAIL (This is b...) [ 86%] 462s tests/test_trajectory.py::test_force_overwrite[xyz] PASSED [ 86%] 462s tests/test_trajectory.py::test_force_overwrite[xyz.gz] PASSED [ 86%] 462s tests/test_trajectory.py::test_force_overwrite[lammpstrj] PASSED [ 87%] 462s tests/test_trajectory.py::test_force_overwrite[lh5] PASSED [ 87%] 462s tests/test_trajectory.py::test_force_overwrite[pdb] PASSED [ 87%] 462s tests/test_trajectory.py::test_force_overwrite[pdb.gz] PASSED [ 87%] 462s tests/test_trajectory.py::test_force_overwrite[ncrst] PASSED [ 87%] 462s tests/test_trajectory.py::test_force_overwrite[rst7] PASSED [ 87%] 462s tests/test_trajectory.py::test_force_overwrite[gro] PASSED [ 87%] 462s tests/test_trajectory.py::test_force_noverwrite[nc] PASSED [ 87%] 462s tests/test_trajectory.py::test_force_noverwrite[h5] PASSED [ 87%] 462s tests/test_trajectory.py::test_force_noverwrite[xtc] PASSED [ 87%] 462s tests/test_trajectory.py::test_force_noverwrite[trr] PASSED [ 87%] 462s tests/test_trajectory.py::test_force_noverwrite[dcd] PASSED [ 87%] 462s tests/test_trajectory.py::test_force_noverwrite[mdcrd] PASSED [ 88%] 462s tests/test_trajectory.py::test_force_noverwrite[dtr] PASSED [ 88%] 462s tests/test_trajectory.py::test_force_noverwrite[xyz] PASSED [ 88%] 462s tests/test_trajectory.py::test_force_noverwrite[xyz.gz] PASSED [ 88%] 462s tests/test_trajectory.py::test_force_noverwrite[lammpstrj] PASSED [ 88%] 462s tests/test_trajectory.py::test_force_noverwrite[lh5] PASSED [ 88%] 462s tests/test_trajectory.py::test_force_noverwrite[pdb] PASSED [ 88%] 462s tests/test_trajectory.py::test_force_noverwrite[pdb.gz] PASSED [ 88%] 462s tests/test_trajectory.py::test_force_noverwrite[ncrst] PASSED [ 88%] 462s tests/test_trajectory.py::test_force_noverwrite[rst7] PASSED [ 88%] 462s tests/test_trajectory.py::test_force_noverwrite[gro] PASSED [ 88%] 462s tests/test_trajectory.py::test_open_and_load PASSED [ 89%] 462s tests/test_trajectory.py::test_length PASSED [ 89%] 462s tests/test_trajectory.py::test_unitcell[nc] PASSED [ 89%] 462s tests/test_trajectory.py::test_unitcell[h5] PASSED [ 89%] 463s tests/test_trajectory.py::test_unitcell[xtc] PASSED [ 89%] 463s tests/test_trajectory.py::test_unitcell[trr] PASSED [ 89%] 463s tests/test_trajectory.py::test_unitcell[dcd] PASSED [ 89%] 463s tests/test_trajectory.py::test_unitcell[mdcrd] PASSED [ 89%] 463s tests/test_trajectory.py::test_unitcell[dtr] XFAIL (dtr seems to nee...) [ 89%] 463s tests/test_trajectory.py::test_unitcell[xyz] PASSED [ 89%] 463s tests/test_trajectory.py::test_unitcell[xyz.gz] PASSED [ 89%] 463s tests/test_trajectory.py::test_unitcell[lammpstrj] XFAIL (lammpstrj ...) [ 90%] 463s tests/test_trajectory.py::test_unitcell[lh5] PASSED [ 90%] 463s tests/test_trajectory.py::test_unitcell[pdb] PASSED [ 90%] 463s tests/test_trajectory.py::test_unitcell[pdb.gz] PASSED [ 90%] 463s tests/test_trajectory.py::test_unitcell[ncrst] XFAIL (ncrst seems to...) [ 90%] 463s tests/test_trajectory.py::test_unitcell[rst7] XFAIL (rst7 seems to n...) [ 90%] 463s tests/test_trajectory.py::test_unitcell[gro] PASSED [ 90%] 463s tests/test_trajectory.py::test_chunk0_iterload PASSED [ 90%] 463s tests/test_trajectory.py::test_hashing PASSED [ 90%] 463s tests/test_trajectory.py::test_smooth PASSED [ 90%] 463s tests/test_trajectory.py::test_load_pdb_no_standard_names PASSED [ 90%] 463s tests/test_trajectory.py::test_load_with_atom_indices PASSED [ 90%] 463s tests/test_trajectory.py::test_atom_slicing PASSED [ 91%] 463s tests/test_trajectory.py::test_load_with_frame PASSED [ 91%] 463s tests/test_trajectory.py::test_add_remove_atoms PASSED [ 91%] 463s tests/test_trr.py::test_1 PASSED [ 91%] 463s tests/test_trr.py::test_read_stride PASSED [ 91%] 463s tests/test_trr.py::test_read_stride_n_frames PASSED [ 91%] 463s tests/test_trr.py::test_read_stride_offsets PASSED [ 91%] 463s tests/test_trr.py::test_read_stride_n_frames_offsets PASSED [ 91%] 463s tests/test_trr.py::test_read_stride_switching PASSED [ 91%] 463s tests/test_trr.py::test_write_read PASSED [ 91%] 463s tests/test_trr.py::test_read_atomindices_1 PASSED [ 91%] 463s tests/test_trr.py::test_read_atomindices_2 PASSED [ 92%] 463s tests/test_trr.py::test_deficient_shape PASSED [ 92%] 463s tests/test_trr.py::test_ragged_1 PASSED [ 92%] 463s tests/test_trr.py::test_ragged_2 PASSED [ 92%] 464s tests/test_trr.py::test_malformed PASSED [ 92%] 464s tests/test_trr.py::test_tell PASSED [ 92%] 464s tests/test_trr.py::test_seek PASSED [ 92%] 464s tests/test_trr.py::test_get_velocities PASSED [ 92%] 464s tests/test_trr.py::test_get_forces PASSED [ 92%] 464s tests/test_trr.py::test_get_velocities_and_forces PASSED [ 92%] 464s tests/test_trr.py::test_get_velocities_forces_atom_indices_1 PASSED [ 92%] 464s tests/test_trr.py::test_get_velocities_forces_atom_indices_2 PASSED [ 93%] 464s tests/test_trr.py::test_read_velocities_do_not_exist PASSED [ 93%] 464s tests/test_trr.py::test_read_forces_do_not_exist PASSED [ 93%] 464s tests/test_utils.py::test_unitcell_0 PASSED [ 93%] 464s tests/test_utils.py::test_unitcell_1 PASSED [ 93%] 464s tests/test_utils.py::test_ensure_type_1 PASSED [ 93%] 464s tests/test_utils.py::test_ensure_type_2 PASSED [ 93%] 464s tests/test_utils.py::test_ensure_type_25 PASSED [ 93%] 464s tests/test_utils.py::test_ensure_type_3 PASSED [ 93%] 464s tests/test_utils.py::test_ensure_type_4 PASSED [ 93%] 464s tests/test_utils.py::test_ensure_type_5 PASSED [ 93%] 464s tests/test_utils.py::test_ensure_type_6 PASSED [ 93%] 464s tests/test_utils.py::test_ensure_type_7 PASSED [ 94%] 464s tests/test_utils.py::test_ensure_type_8 PASSED [ 94%] 464s tests/test_utils.py::test_ensure_type_9 PASSED [ 94%] 464s tests/test_utils.py::test_ensure_type_10 PASSED [ 94%] 464s tests/test_utils.py::test_ensure_type_11 PASSED [ 94%] 464s tests/test_utils.py::test_ensure_type_12 PASSED [ 94%] 464s tests/test_utils.py::test_ensure_type_13 PASSED [ 94%] 464s tests/test_utils.py::test_ensure_type_14 PASSED [ 94%] 464s tests/test_utils.py::test_ensure_type_15 PASSED [ 94%] 464s tests/test_utils.py::test_delay_import_fail_1 PASSED [ 94%] 464s tests/test_utils.py::test_delay_import PASSED [ 94%] 464s tests/test_utils.py::test_unit_0 PASSED [ 95%] 464s tests/test_utils.py::test_unit_1 PASSED [ 95%] 464s tests/test_utils.py::test_unit_2 PASSED [ 95%] 464s tests/test_utils.py::test_unit_3 PASSED [ 95%] 464s tests/test_xml.py::test_xml PASSED [ 95%] 464s tests/test_xtc.py::test_read_chunk1 PASSED [ 95%] 464s tests/test_xtc.py::test_read_stride PASSED [ 95%] 464s tests/test_xtc.py::test_read_stride_n_frames PASSED [ 95%] 464s tests/test_xtc.py::test_read_stride_offsets PASSED [ 95%] 464s tests/test_xtc.py::test_read_stride_n_frames_offsets PASSED [ 95%] 464s tests/test_xtc.py::test_read_stride_switching_offsets PASSED [ 95%] 464s tests/test_xtc.py::test_read_atomindices_1 PASSED [ 96%] 464s tests/test_xtc.py::test_read_atomindices_w_stride PASSED [ 96%] 464s tests/test_xtc.py::test_read_atomindices_2 PASSED [ 96%] 464s tests/test_xtc.py::test_read_chunk2 PASSED [ 96%] 464s tests/test_xtc.py::test_read_chunk3 PASSED [ 96%] 464s tests/test_xtc.py::test_write_0 PASSED [ 96%] 464s tests/test_xtc.py::test_write_1 PASSED [ 96%] 464s tests/test_xtc.py::test_write_2 PASSED [ 96%] 464s tests/test_xtc.py::test_read_error_0 PASSED [ 96%] 464s tests/test_xtc.py::test_write_error_0 PASSED [ 96%] 464s tests/test_xtc.py::test_read_error_1 PASSED [ 96%] 464s tests/test_xtc.py::test_read_error_2 PASSED [ 96%] 464s tests/test_xtc.py::test_xtc_write_wierd_0 PASSED [ 97%] 464s tests/test_xtc.py::test_tell PASSED [ 97%] 464s tests/test_xtc.py::test_seek PASSED [ 97%] 464s tests/test_xtc.py::test_seek_natoms9 PASSED [ 97%] 464s tests/test_xtc.py::test_seek_out_of_bounds PASSED [ 97%] 464s tests/test_xtc.py::test_ragged_1 PASSED [ 97%] 464s tests/test_xtc.py::test_ragged_2 PASSED [ 97%] 464s tests/test_xtc.py::test_short_traj PASSED [ 97%] 464s tests/test_xtc.py::test_flush PASSED [ 97%] 464s tests/test_xyz.py::test_read_0 PASSED [ 97%] 464s tests/test_xyz.py::test_read_1 PASSED [ 97%] 464s tests/test_xyz.py::test_read_gz PASSED [ 98%] 464s tests/test_xyz.py::test_read_write PASSED [ 98%] 464s tests/test_xyz.py::test_mdwrite PASSED [ 98%] 464s tests/test_xyz.py::test_multiread PASSED [ 98%] 464s tests/test_xyz.py::test_seek PASSED [ 98%] 464s tests/test_xyz.py::test_len PASSED [ 98%] 464s tests/test_zipped.py::test_read_gz PASSED [ 98%] 464s tests/test_zipped.py::test_write_gz PASSED [ 98%] 464s tests/test_zipped.py::test_read_bz2 PASSED [ 98%] 464s tests/test_zipped.py::test_write_bz2 PASSED [ 98%] 467s examples/test_examples.py::test_example_notebook[solvent-accessible-surface-area.ipynb] PASSED [ 98%] 469s examples/test_examples.py::test_example_notebook[two-pass-clustering.ipynb] PASSED [ 99%] 469s examples/test_examples.py::test_example_notebook[native-contact.ipynb] SKIPPED [ 99%] 472s examples/test_examples.py::test_example_notebook[principal-components.ipynb] PASSED [ 99%] 472s examples/test_examples.py::test_example_notebook[simulation-with-openmm.ipynb] SKIPPED [ 99%] 473s examples/test_examples.py::test_example_notebook[atom-selection.ipynb] PASSED [ 99%] 476s examples/test_examples.py::test_example_notebook[ramachandran-plot.ipynb] PASSED [ 99%] 478s examples/test_examples.py::test_example_notebook[rmsd-benchmark.ipynb] PASSED [ 99%] 479s examples/test_examples.py::test_example_notebook[iterload.ipynb] PASSED [ 99%] 481s examples/test_examples.py::test_example_notebook[clustering.ipynb] PASSED [ 99%] 483s examples/test_examples.py::test_example_notebook[centroids.ipynb] PASSED [ 99%] 483s examples/test_examples.py::test_example_notebook[hbonds.ipynb] SKIPPED [ 99%] 485s examples/test_examples.py::test_example_notebook[rmsd-drift.ipynb] PASSED [100%] 485s 485s =============================== warnings summary =============================== 485s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:56 485s /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. 485s THIS_ATOM = ast.Name(id="atom", ctx=ast.Load(), SINGLETON=True) 485s 485s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:57 485s /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. 485s RE_MODULE = ast.Name(id="re", ctx=ast.Load(), SINGLETON=True) 485s 485s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 485s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 485s given by the platformdirs library. To remove this warning and 485s see the appropriate new directories, set the environment variable 485s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 485s The use of platformdirs will be the default in `jupyter_core` v6 485s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 485s 485s examples/test_examples.py:26 485s /tmp/autopkgtest.hirK8O/build.pPu/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 485s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 485s 485s tests/test_contact.py::test_contact_0 485s tests/test_contact.py::test_contact_4 485s /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. 485s warnings.warn( 485s 485s tests/test_contact.py::test_contact_3 485s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:271: RuntimeWarning: overflow encountered in exp 485s np.exp( 485s 485s tests/test_contact.py::test_contact_3 485s /tmp/autopkgtest.hirK8O/build.pPu/src/tests/test_contact.py:115: RuntimeWarning: divide by zero encountered in scalar divide 485s beta / np.log(np.sum(np.exp(beta / maps[t, r0, r1]))), 485s 485s tests/test_dcd.py::test_do_overwrite 485s tests/test_dcd.py::test_ragged_1 485s tests/test_dcd.py::test_ragged_2 485s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting xyz dtype=float64 to 485s warnings.warn( 485s 485s tests/test_distance.py::test_6 485s :488: RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject 485s 485s tests/test_drid.py::test_drid_2 485s /tmp/autopkgtest.hirK8O/build.pPu/src/tests/test_drid.py:62: RuntimeWarning: divide by zero encountered in divide 485s recip = 1 / squareform(pdist(t.xyz[i])) 485s 485s tests/test_dssp.py::test_1[1vii.pdb] 485s tests/test_gro.py::test_read_write 485s tests/test_gro.py::test_read_write_precision 485s tests/test_gro.py::test_load 485s tests/test_shape.py::test_principal_moments 485s tests/test_shape.py::test_asphericity 485s tests/test_shape.py::test_shape_metrics 485s /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. 485s warnings.warn( 485s 485s tests/test_geometry.py::test_dihedral_indices 485s tests/test_geometry.py::test_dihedral_indices 485s /usr/lib/python3/dist-packages/mdtraj/geometry/dihedral.py:237: DeprecationWarning: Passing a Trajectory object to _atom_sequence isdeprecated. Please pass a Topology object 485s warnings.warn( 485s 485s tests/test_gro.py::test_load 485s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq 485s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:364: UserWarning: WARNING: two consecutive residues with same number (GST, HST) 485s warnings.warn( 485s 485s tests/test_pdb.py::test_blank_indexing 485s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:204: UserWarning: Need to guess atom number starting from atom 100000. 485s warnings.warn(f'Need to guess atom number {num_str} starting from atom {pdbstructure._next_atom_number}.') 485s 485s tests/test_pdb.py::test_blank_indexing 485s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:271: UserWarning: Need to guess residue number string starting from residue10000, atom 100000. 485s warnings.warn(f'Need to guess residue number string {num_str} starting from residue{pdbstructure._next_residue_number}, atom {pdbstructure._next_atom_number}.') 485s 485s tests/test_rdf.py::test_rdf_norm 485s tests/test_rdf.py::test_rdf_t_norm[0] 485s tests/test_rdf.py::test_rdf_t_norm[2] 485s tests/test_rdf.py::test_rdf_t_norm[4] 485s tests/test_selection.py::test_re 485s tests/test_selection.py::test_re 485s tests/test_topology.py::test_select_pairs 485s tests/test_topology.py::test_select_pairs 485s /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. 485s left=ast.Call( 485s 485s tests/test_rdf.py::test_rdf_norm 485s tests/test_rdf.py::test_rdf_t_norm[0] 485s tests/test_rdf.py::test_rdf_t_norm[2] 485s tests/test_rdf.py::test_rdf_t_norm[4] 485s tests/test_selection.py::test_re 485s tests/test_selection.py::test_re 485s tests/test_topology.py::test_select_pairs 485s tests/test_topology.py::test_select_pairs 485s /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. 485s left=ast.Call( 485s 485s tests/test_trajectory.py::test_float_atom_indices_exception[gro] 485s tests/test_trajectory.py::test_atom_slicing 485s /usr/lib/python3/dist-packages/mdtraj/core/topology.py:84: UserWarning: atom_indices are not monotonically increasing 485s warnings.warn("atom_indices are not monotonically increasing") 485s 485s tests/test_utils.py::test_ensure_type_8 485s tests/test_utils.py::test_ensure_type_9 485s tests/test_utils.py::test_ensure_type_13 485s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=float64 to 485s warnings.warn( 485s 485s tests/test_utils.py::test_ensure_type_11 485s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=int64 to 485s warnings.warn( 485s 485s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 485s =========================== short test summary info ============================ 485s SKIPPED [1] tests/test_dihedral.py:56: pymol executable not found 485s SKIPPED [1] tests/test_dihedral.py:181: pymol executable not found 485s SKIPPED [16] tests/test_docstrings.py:38: Skip checking certain modules' docstrings 485s SKIPPED [1] tests/test_geometry.py:300: Not doing performance testing 485s SKIPPED [1] tests/test_geometry.py:322: Not doing performance testing 485s SKIPPED [1] tests/test_hdf5.py:104: requires openmm.units 485s SKIPPED [1] tests/test_hdf5.py:156: requires openmm.units 485s SKIPPED [1] tests/test_hdf5.py:223: requires openmm.units 485s SKIPPED [1] tests/test_mol2.py:59: Requires obabel 485s SKIPPED [1] tests/test_netcdf.py:271: This test requires cpptraj from AmberTools to be installed (http://ambermd.org) 485s SKIPPED [1] tests/test_nmr.py:11: SPARTA+ binary not found 485s SKIPPED [1] tests/test_nmr.py:26: PPM binary not found 485s SKIPPED [1] tests/test_nmr.py:42: SHIFTX2 binary not found or running on travis. 485s SKIPPED [1] tests/test_pdbx.py:43: test_pdbx.py needs OpenMM. 485s SKIPPED [2] tests/test_psf.py:93: This test requires the VMD executable: http://www.ks.uiuc.edu/Research/vmd/ 485s SKIPPED [1] tests/test_rdf.py:64: Binning does not match up with gromacs currently. 485s SKIPPED [1] tests/test_rdf.py:200: Binning does not match up with gromacs currently. 485s SKIPPED [1] tests/test_reporter.py:58: test_reporter.py needs OpenMM. 485s SKIPPED [1] tests/test_reporter.py:145: test_reporter.py needs OpenMM. 485s SKIPPED [1] tests/test_reporter.py:245: test_reporter.py needs OpenMM. 485s SKIPPED [1] tests/test_selection.py:267: failed to parse selection 485s SKIPPED [1] tests/test_thermodynamic_properties.py:161: Thermal expansion test doesn't work. 485s SKIPPED [1] tests/test_topology.py:45: needs OpenMM 485s SKIPPED [1] tests/test_topology.py:62: needs OpenMM 485s SKIPPED [1] tests/test_topology.py:72: needs OpenMM 485s SKIPPED [1] tests/test_topology.py:81: needs OpenMM 485s SKIPPED [1] tests/test_topology.py:91: needs OpenMM 485s SKIPPED [1] tests/test_topology.py:97: needs OpenMM 485s SKIPPED [1] tests/test_topology.py:247: needs OpenMM 485s SKIPPED [1] tests/test_trajectory.py:129: xyz does not store box information 485s SKIPPED [1] tests/test_trajectory.py:129: xyz.gz does not store box information 485s SKIPPED [1] tests/test_trajectory.py:129: lh5 does not store box information 485s SKIPPED [1] tests/test_trajectory.py:129: pdb does not store box information 485s SKIPPED [1] tests/test_trajectory.py:129: pdb.gz does not store box information 485s SKIPPED [1] tests/test_trajectory.py:226: mdcrd can only store rectilinear boxes 485s SKIPPED [1] tests/test_trajectory.py:224: ncrst can only store 1 frame per file 485s SKIPPED [1] tests/test_trajectory.py:224: rst7 can only store 1 frame per file 485s SKIPPED [14] tests/test_trajectory.py:248: mdcrd can only store rectilinear boxes 485s SKIPPED [14] tests/test_trajectory.py:246: ncrst can only store 1 frame per file 485s SKIPPED [14] tests/test_trajectory.py:246: rst7 can only store 1 frame per file 485s SKIPPED [4] tests/test_trajectory.py:256: dtr needs to write unitcells 485s SKIPPED [4] tests/test_trajectory.py:256: lammpstrj needs to write unitcells 485s SKIPPED [2] tests/test_trajectory.py:640: Only 1 frame per file format 485s SKIPPED [2] examples/test_examples.py:77: Network access required 485s SKIPPED [1] examples/test_examples.py:77: Openmm required for example notebook `simulation-with-openmm.ipynb` 485s XFAIL tests/test_trajectory.py::test_read_path[ncrst] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_path[rst7] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[ncrst-nc] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[ncrst-h5] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xtc] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[ncrst-trr] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dcd] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[ncrst-mdcrd] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dtr] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lh5] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[ncrst-ncrst] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[ncrst-rst7] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[ncrst-gro] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[rst7-nc] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[rst7-h5] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[rst7-xtc] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[rst7-trr] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[rst7-dcd] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[rst7-mdcrd] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[rst7-dtr] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz.gz] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[rst7-lammpstrj] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[rst7-lh5] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb.gz] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[rst7-ncrst] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[rst7-rst7] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_read_write[rst7-gro] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_load[ncrst] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_load[rst7] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[rst7] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_load_combination[ncrst] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_load_combination[rst7] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_seek_read_mode[xyz.gz] - reason: This is broken 485s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb] - reason: PDB Files don't support seeking 485s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb.gz] - reason: PDB Files don't support seeking 485s XFAIL tests/test_trajectory.py::test_seek_read_mode[ncrst] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_seek_read_mode[rst7] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_seek_read_mode[gro] - reason: This is broken 485s XFAIL tests/test_trajectory.py::test_load_frame[dtr] - reason: DTR doesn't load a single frame properly 485s XFAIL tests/test_trajectory.py::test_load_frame[ncrst] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_load_frame[rst7] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_load_frame[gro] - reason: Gro doesn't implement seek 485s XFAIL tests/test_trajectory.py::test_iterload[dtr] - reason: This is broken with dtr 485s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb] - reason: PDB Iterloads an extra frame!! 485s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb.gz] - reason: PDB Iterloads an extra frame!! 485s XFAIL tests/test_trajectory.py::test_iterload_skip[ncrst] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_iterload_skip[rst7] - reason: These reference files don't exist yet 485s XFAIL tests/test_trajectory.py::test_iterload_skip[gro] - reason: Not implemented for some reason 485s XFAIL tests/test_trajectory.py::test_force_overwrite[dtr] - reason: This is broken with dtr 485s XFAIL tests/test_trajectory.py::test_unitcell[dtr] - reason: dtr seems to need unit vectors 485s XFAIL tests/test_trajectory.py::test_unitcell[lammpstrj] - reason: lammpstrj seems to need unit vectors 485s XFAIL tests/test_trajectory.py::test_unitcell[ncrst] - reason: ncrst seems to need unit vectors 485s XFAIL tests/test_trajectory.py::test_unitcell[rst7] - reason: rst7 seems to need unit vectors 485s = 964 passed, 108 skipped, 12 deselected, 61 xfailed, 48 warnings in 290.26s (0:04:50) = 486s autopkgtest [20:22:34]: test command1: -----------------------] 486s command1 PASS 486s autopkgtest [20:22:34]: test command1: - - - - - - - - - - results - - - - - - - - - - 487s autopkgtest [20:22:35]: test command2: preparing testbed 487s Reading package lists... 487s Building dependency tree... 487s Reading state information... 487s Solving dependencies... 488s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 489s autopkgtest [20:22:37]: test command2: pytest-3 -k 'test_3 or test_pdb_from_url or test_1vii_url_and_gz' 489s autopkgtest [20:22:37]: test command2: [----------------------- 490s ============================= test session starts ============================== 490s platform linux -- Python 3.13.9, pytest-8.3.5, pluggy-1.6.0 -- /usr/bin/python3 490s cachedir: .pytest_cache 490s rootdir: /tmp/autopkgtest.hirK8O/build.pPu/src 490s configfile: pyproject.toml 490s testpaths: tests, examples 490s plugins: typeguard-4.4.2 491s collecting ... collected 1145 items / 1135 deselected / 10 selected 491s 491s tests/test_distance.py::test_3 PASSED [ 10%] 491s tests/test_distance.py::test_3p PASSED [ 20%] 493s tests/test_dssp.py::test_3[1GAI] PASSED [ 30%] 496s tests/test_dssp.py::test_3[6gsv] PASSED [ 40%] 498s tests/test_dssp.py::test_3[2AAC] PASSED [ 50%] 498s tests/test_nmr.py::test_3_scalar_couplings PASSED [ 60%] 502s tests/test_pdb.py::test_pdb_from_url PASSED [ 70%] 502s tests/test_pdb.py::test_3nch_conect PASSED [ 80%] 504s tests/test_pdb.py::test_3nch_serial_resSeq PASSED [ 90%] 508s tests/test_pdb.py::test_1vii_url_and_gz PASSED [100%] 508s 508s =============================== warnings summary =============================== 508s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:56 508s /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. 508s THIS_ATOM = ast.Name(id="atom", ctx=ast.Load(), SINGLETON=True) 508s 508s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:57 508s /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. 508s RE_MODULE = ast.Name(id="re", ctx=ast.Load(), SINGLETON=True) 508s 508s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 508s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 508s given by the platformdirs library. To remove this warning and 508s see the appropriate new directories, set the environment variable 508s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 508s The use of platformdirs will be the default in `jupyter_core` v6 508s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 508s 508s examples/test_examples.py:26 508s /tmp/autopkgtest.hirK8O/build.pPu/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 508s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 508s 508s tests/test_pdb.py::test_1vii_url_and_gz 508s /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. 508s warnings.warn( 508s 508s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 508s =============== 10 passed, 1135 deselected, 5 warnings in 17.92s =============== 509s autopkgtest [20:22:57]: test command2: -----------------------] 509s command2 PASS 509s autopkgtest [20:22:57]: test command2: - - - - - - - - - - results - - - - - - - - - - 509s autopkgtest [20:22:57]: @@@@@@@@@@@@@@@@@@@@ summary 509s command1 PASS 509s command2 PASS