0s autopkgtest [20:16:42]: starting date and time: 2025-10-20 20:16:42+0000 0s autopkgtest [20:16:42]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [20:16:42]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.8fwlrhmy/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest,src:python-pluggy --apt-upgrade mdtraj --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.4.2-1 python-pluggy/1.6.0-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-14.secgroup --name adt-resolute-arm64-mdtraj-20251020-201642-juju-7f2275-prod-proposed-migration-environment-15-77241d4f-a645-4ff8-8da7-8340c0dfd5f4 --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/ 4s Creating nova instance adt-resolute-arm64-mdtraj-20251020-201642-juju-7f2275-prod-proposed-migration-environment-15-77241d4f-a645-4ff8-8da7-8340c0dfd5f4 from image adt/ubuntu-resolute-arm64-server-20251020.img (UUID 53f7e888-0b33-40b7-be7f-09b2db152d64)... 63s autopkgtest [20:17:45]: testbed dpkg architecture: arm64 63s autopkgtest [20:17:45]: testbed apt version: 3.1.8ubuntu1 63s autopkgtest [20:17:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 64s autopkgtest [20:17:46]: testbed release detected to be: None 64s autopkgtest [20:17:46]: updating testbed package index (apt update) 65s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 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 65s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [14.3 kB] 65s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 65s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [646 kB] 65s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [59.3 kB] 65s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [115 kB] 65s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [43.8 kB] 65s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [409 kB] 66s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [5672 B] 66s Fetched 1382 kB in 1s (1435 kB/s) 66s Reading package lists... 67s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 67s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 67s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 67s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 69s Reading package lists... 69s Reading package lists... 69s Building dependency tree... 69s Reading state information... 69s Calculating upgrade... 70s The following packages will be upgraded: 70s libbrotli1 libjson-c5 python3-inflect python3-oauthlib python3-zipp 70s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 70s Need to get 512 kB of archives. 70s After this operation, 31.7 kB of additional disk space will be used. 70s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libjson-c5 arm64 0.18+ds-1.1 [37.5 kB] 70s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libbrotli1 arm64 1.1.0-2build6 [336 kB] 70s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-inflect all 7.5.0-1 [33.9 kB] 70s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-oauthlib all 3.3.1-1 [93.5 kB] 71s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-zipp all 3.23.0-1 [10.4 kB] 71s dpkg-preconfigure: unable to re-open stdin: No such file or directory 71s Fetched 512 kB in 1s (824 kB/s) 71s (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 ... 83364 files and directories currently installed.) 71s Preparing to unpack .../libjson-c5_0.18+ds-1.1_arm64.deb ... 71s Unpacking libjson-c5:arm64 (0.18+ds-1.1) over (0.18+ds-1) ... 71s Preparing to unpack .../libbrotli1_1.1.0-2build6_arm64.deb ... 71s Unpacking libbrotli1:arm64 (1.1.0-2build6) over (1.1.0-2build5) ... 72s Preparing to unpack .../python3-inflect_7.5.0-1_all.deb ... 72s Unpacking python3-inflect (7.5.0-1) over (7.3.1-2) ... 72s Preparing to unpack .../python3-oauthlib_3.3.1-1_all.deb ... 72s Unpacking python3-oauthlib (3.3.1-1) over (3.2.2-3) ... 72s Preparing to unpack .../python3-zipp_3.23.0-1_all.deb ... 72s Unpacking python3-zipp (3.23.0-1) over (3.21.0-1) ... 72s Setting up libbrotli1:arm64 (1.1.0-2build6) ... 72s Setting up python3-zipp (3.23.0-1) ... 73s Setting up python3-inflect (7.5.0-1) ... 73s Setting up python3-oauthlib (3.3.1-1) ... 73s Setting up libjson-c5:arm64 (0.18+ds-1.1) ... 73s Processing triggers for libc-bin (2.42-0ubuntu3) ... 73s autopkgtest [20:17:55]: upgrading testbed (apt dist-upgrade and autopurge) 74s Reading package lists... 74s Building dependency tree... 74s Reading state information... 74s Calculating upgrade... 75s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 75s Reading package lists... 75s Building dependency tree... 75s Reading state information... 75s Solving dependencies... 76s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 78s autopkgtest [20:18:00]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025 79s autopkgtest [20:18:01]: @@@@@@@@@@@@@@@@@@@@ apt-source mdtraj 83s Get:1 http://ftpmaster.internal/ubuntu resolute/universe mdtraj 1.10.3-2build1 (dsc) [2701 B] 83s Get:2 http://ftpmaster.internal/ubuntu resolute/universe mdtraj 1.10.3-2build1 (tar) [22.0 MB] 83s Get:3 http://ftpmaster.internal/ubuntu resolute/universe mdtraj 1.10.3-2build1 (diff) [297 kB] 83s gpgv: Signature made Tue Mar 4 15:08:42 2025 UTC 83s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 83s gpgv: Can't check signature: No public key 83s dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.10.3-2build1.dsc: no acceptable signature found 84s autopkgtest [20:18:06]: testing package mdtraj version 1.10.3-2build1 87s autopkgtest [20:18:09]: build not needed 93s autopkgtest [20:18:15]: test command1: preparing testbed 93s Reading package lists... 93s Building dependency tree... 93s Reading state information... 94s Solving dependencies... 94s The following NEW packages will be installed: 94s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx gdb 94s libaec0 libbabeltrace1 libblas3 libblosc1 libblosc2-4 libdeflate0 94s libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 94s libhdf5-310 libhdf5-hl-310 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 94s libjs-jquery libjs-jquery-ui liblapack3 liblcms2-2 liblerc4 libnetcdf22 94s libnorm1t64 libopenjp2-7 libpgm-5.3-0t64 libqhull-r8.0 libraqm0 libsharpyuv0 94s libsnappy1v5 libsodium23 libsource-highlight-common libsource-highlight4t64 94s libsz2 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 94s libxft2 libxrender1 libxslt1.1 libxss1 libzmq5 libzopfli1 94s python-matplotlib-data python-tables-data python3-asttokens python3-brotli 94s python3-cftime python3-comm python3-contourpy python3-coverage 94s python3-cpuinfo python3-cycler python3-dateutil python3-debugpy 94s python3-decorator python3-executing python3-fastjsonschema python3-fonttools 94s python3-fs python3-gsd python3-iniconfig python3-ipykernel python3-ipython 94s python3-jedi python3-joblib python3-jupyter-client python3-jupyter-core 94s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 94s python3-matplotlib-inline python3-mdtraj python3-mpmath python3-nbformat 94s python3-nest-asyncio python3-netcdf4 python3-networkx python3-numexpr 94s python3-numpy python3-numpy-dev python3-packaging python3-pandas 94s python3-pandas-lib python3-parso python3-pexpect python3-pil 94s python3-pil.imagetk python3-platformdirs python3-pluggy 94s python3-prompt-toolkit python3-psutil python3-ptyprocess python3-pure-eval 94s python3-pytest python3-pytz python3-scipy python3-sklearn 94s python3-sklearn-lib python3-stack-data python3-sympy python3-tables 94s python3-tables-lib python3-threadpoolctl python3-tk python3-tornado 94s python3-traitlets python3-typeshed python3-ufolib2 python3-unicodedata2 94s python3-wcwidth python3-zmq python3-zopfli python3.13-tk tk8.6-blt2.5 94s unicode-data x11-common 94s 0 upgraded, 127 newly installed, 0 to remove and 0 not upgraded. 94s Need to get 113 MB of archives. 94s After this operation, 526 MB of additional disk space will be used. 94s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB] 95s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-6build1 [186 kB] 95s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-5ubuntu1 [450 kB] 95s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-6build1 [2340 kB] 95s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB] 96s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libtcl8.6 arm64 8.6.17+dfsg-1 [1024 kB] 96s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 96s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 96s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.15.0-2.3ubuntu1 [38.1 kB] 96s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.15.0-2.3ubuntu1 [144 kB] 96s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 96s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 96s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 96s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 96s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libtk8.6 arm64 8.6.17-1 [811 kB] 96s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-8 [624 kB] 96s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 blt arm64 2.5.3+dfsg-8 [4824 B] 96s Get:18 http://ftpmaster.internal/ubuntu resolute/universe arm64 fonts-lyx all 2.4.4-1 [171 kB] 96s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libbabeltrace1 arm64 1.5.11-4build2 [159 kB] 96s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libsource-highlight-common all 3.1.9-4.3build1 [64.2 kB] 96s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libsource-highlight4t64 arm64 3.1.9-4.3build1 [243 kB] 96s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 gdb arm64 16.3-1ubuntu2 [4952 kB] 96s Get:23 http://ftpmaster.internal/ubuntu resolute/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 96s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 libsnappy1v5 arm64 1.2.2-1 [30.5 kB] 96s Get:25 http://ftpmaster.internal/ubuntu resolute/universe arm64 libblosc1 arm64 1.21.5+ds-1build1 [25.7 kB] 96s Get:26 http://ftpmaster.internal/ubuntu resolute/universe arm64 libblosc2-4 arm64 2.17.1+ds-2 [154 kB] 96s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 96s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-5ubuntu1 [148 kB] 96s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 96s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.1.0-1 [523 kB] 96s Get:31 http://ftpmaster.internal/ubuntu resolute/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 96s Get:32 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhdf5-310 arm64 1.14.5+repack-3build1 [1331 kB] 97s Get:33 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhdf5-hl-310 arm64 1.14.5+repack-3build1 [59.8 kB] 97s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 97s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu2 [165 kB] 97s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 97s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 97s Get:38 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 97s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 97s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 97s Get:41 http://ftpmaster.internal/ubuntu resolute/universe arm64 libnetcdf22 arm64 1:4.9.3-1build1 [555 kB] 97s Get:42 http://ftpmaster.internal/ubuntu resolute/universe arm64 libnorm1t64 arm64 1.5.9+dfsg-3.1build2 [152 kB] 97s Get:43 http://ftpmaster.internal/ubuntu resolute/universe arm64 libpgm-5.3-0t64 arm64 5.3.128~dfsg-2.1build1 [162 kB] 97s Get:44 http://ftpmaster.internal/ubuntu resolute/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 97s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 libraqm0 arm64 0.10.3-1 [15.0 kB] 97s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 97s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 libsodium23 arm64 1.0.18-1build3 [119 kB] 97s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 97s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 97s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 97s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 97s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 97s Get:53 http://ftpmaster.internal/ubuntu resolute/main arm64 libxslt1.1 arm64 1.1.43-0.1 [171 kB] 97s Get:54 http://ftpmaster.internal/ubuntu resolute/universe arm64 libzmq5 arm64 4.3.5-1build2 [247 kB] 97s Get:55 http://ftpmaster.internal/ubuntu resolute/universe arm64 libzopfli1 arm64 1.0.3-3 [108 kB] 97s Get:56 http://ftpmaster.internal/ubuntu resolute/universe arm64 python-matplotlib-data all 3.10.1+dfsg1-4 [2930 kB] 97s Get:57 http://ftpmaster.internal/ubuntu resolute/universe arm64 python-tables-data all 3.10.2-3build1 [49.7 kB] 97s Get:58 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-asttokens all 3.0.0-2 [20.5 kB] 97s Get:59 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-brotli arm64 1.1.0-2build6 [343 kB] 97s Get:60 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-cftime arm64 1.6.4-2 [208 kB] 97s Get:61 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 97s Get:62 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-comm all 0.2.1-1 [7016 B] 97s Get:63 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-contourpy arm64 1.3.1-1build1 [182 kB] 97s Get:64 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-coverage arm64 7.8.2+dfsg1-1 [157 kB] 97s Get:65 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-cpuinfo all 9.0.0+git20221119-3 [21.7 kB] 97s Get:66 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 97s Get:67 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-dateutil all 2.9.0-4 [80.3 kB] 97s Get:68 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-debugpy arm64 1.8.12+ds-1ubuntu1 [741 kB] 97s Get:69 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-decorator all 5.2.1-2 [28.1 kB] 97s Get:70 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-executing all 2.2.0-0.2 [25.0 kB] 97s Get:71 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-fastjsonschema all 2.21.1-1 [20.4 kB] 97s Get:72 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-platformdirs all 4.3.7-1 [16.9 kB] 97s Get:73 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-fs all 2.4.16-7 [90.8 kB] 97s Get:74 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-lxml arm64 6.0.1-1 [1428 kB] 97s Get:75 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-lz4 arm64 4.4.0+dfsg-2 [27.1 kB] 97s Get:76 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-scipy arm64 1.15.3-1 [15.8 MB] 98s Get:77 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 98s Get:78 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-sympy all 1.13.3-5 [4229 kB] 98s Get:79 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 98s Get:80 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-unicodedata2 arm64 16.0.0+ds-1build1 [398 kB] 98s Get:81 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-zopfli arm64 0.2.3.post1-1 [10.7 kB] 98s Get:82 http://ftpmaster.internal/ubuntu resolute/universe arm64 unicode-data all 16.0.0-1 [9513 kB] 98s Get:83 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-fonttools arm64 4.57.0-1 [1453 kB] 98s Get:84 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-gsd arm64 3.4.2-2build1 [209 kB] 98s Get:85 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 98s Get:86 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-parso all 0.8.4-1 [67.6 kB] 98s Get:87 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-typeshed all 0.0~git20241223.ea91db2-3 [1554 kB] 98s Get:88 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-jedi all 0.19.1+ds1-1 [693 kB] 98s Get:89 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-matplotlib-inline all 0.1.7-1 [9186 B] 98s Get:90 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 98s Get:91 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-prompt-toolkit all 3.0.51-2 [257 kB] 98s Get:92 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pure-eval all 0.2.3-1 [11.4 kB] 98s Get:93 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-stack-data all 0.6.3-1 [22.0 kB] 98s Get:94 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-ptyprocess all 0.7.0-6 [14.8 kB] 98s Get:95 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pexpect all 4.9-3 [48.1 kB] 98s Get:96 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-ipython all 8.35.0-1 [575 kB] 98s Get:97 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-jupyter-core all 5.7.2-5 [28.1 kB] 98s Get:98 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-psutil arm64 7.0.0-2ubuntu1 [188 kB] 98s Get:99 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-tornado arm64 6.4.2-3 [299 kB] 98s Get:100 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-zmq arm64 26.4.0-1 [179 kB] 98s Get:101 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-jupyter-client all 8.6.3-2 [78.5 kB] 99s Get:102 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-nest-asyncio all 1.5.4-1 [6256 B] 99s Get:103 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-packaging all 25.0-1 [52.8 kB] 99s Get:104 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-ipykernel all 6.29.5-2 [82.7 kB] 99s Get:105 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-joblib all 1.4.2-4 [205 kB] 99s Get:106 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-kiwisolver arm64 1.4.7-3build2 [60.7 kB] 99s Get:107 http://ftpmaster.internal/ubuntu resolute/main arm64 libopenjp2-7 arm64 2.5.3-2.1 [179 kB] 99s Get:108 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pil arm64 11.3.0-1ubuntu1 [483 kB] 99s Get:109 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.13-tk arm64 3.13.7-1 [108 kB] 99s Get:110 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-tk arm64 3.13.5-1 [9916 B] 99s Get:111 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pil.imagetk arm64 11.3.0-1ubuntu1 [9878 B] 99s Get:112 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-matplotlib arm64 3.10.1+dfsg1-4 [18.0 MB] 102s Get:113 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-netcdf4 arm64 1.7.2-1build4 [587 kB] 102s Get:114 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 103s Get:115 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pytz all 2025.2-3 [163 kB] 103s Get:116 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-9 [4579 kB] 103s Get:117 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas all 2.2.3+dfsg-9 [3112 kB] 103s Get:118 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-numexpr arm64 2.10.2-1build2 [120 kB] 103s Get:119 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-tables-lib arm64 3.10.2-3build1 [737 kB] 103s Get:120 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-tables all 3.10.2-3build1 [354 kB] 103s Get:121 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-mdtraj arm64 1.10.3-2build1 [1088 kB] 103s Get:122 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-nbformat all 5.9.1-1 [41.2 kB] 103s Get:123 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 python3-pluggy all 1.6.0-1 [21.0 kB] 103s Get:124 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 python3-pytest all 8.4.2-1 [268 kB] 103s Get:125 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 103s Get:126 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-8 [4109 kB] 103s Get:127 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-sklearn all 1.4.2+dfsg-8 [2258 kB] 104s Fetched 113 MB in 9s (12.2 MB/s) 104s Selecting previously unselected package python3-numpy-dev:arm64. 104s (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 ... 83374 files and directories currently installed.) 104s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 104s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 104s Selecting previously unselected package libblas3:arm64. 104s Preparing to unpack .../001-libblas3_3.12.1-6build1_arm64.deb ... 104s Unpacking libblas3:arm64 (3.12.1-6build1) ... 104s Selecting previously unselected package libgfortran5:arm64. 104s Preparing to unpack .../002-libgfortran5_15.2.0-5ubuntu1_arm64.deb ... 104s Unpacking libgfortran5:arm64 (15.2.0-5ubuntu1) ... 104s Selecting previously unselected package liblapack3:arm64. 104s Preparing to unpack .../003-liblapack3_3.12.1-6build1_arm64.deb ... 104s Unpacking liblapack3:arm64 (3.12.1-6build1) ... 104s Selecting previously unselected package python3-numpy. 104s Preparing to unpack .../004-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 104s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 105s Selecting previously unselected package libtcl8.6:arm64. 105s Preparing to unpack .../005-libtcl8.6_8.6.17+dfsg-1_arm64.deb ... 105s Unpacking libtcl8.6:arm64 (8.6.17+dfsg-1) ... 105s Selecting previously unselected package fonts-dejavu-mono. 105s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ... 105s Unpacking fonts-dejavu-mono (2.37-8) ... 105s Selecting previously unselected package fonts-dejavu-core. 105s Preparing to unpack .../007-fonts-dejavu-core_2.37-8_all.deb ... 105s Unpacking fonts-dejavu-core (2.37-8) ... 105s Selecting previously unselected package fontconfig-config. 105s Preparing to unpack .../008-fontconfig-config_2.15.0-2.3ubuntu1_arm64.deb ... 105s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 105s Selecting previously unselected package libfontconfig1:arm64. 105s Preparing to unpack .../009-libfontconfig1_2.15.0-2.3ubuntu1_arm64.deb ... 105s Unpacking libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 105s Selecting previously unselected package libxrender1:arm64. 105s Preparing to unpack .../010-libxrender1_1%3a0.9.12-1_arm64.deb ... 105s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 105s Selecting previously unselected package libxft2:arm64. 105s Preparing to unpack .../011-libxft2_2.3.6-1build1_arm64.deb ... 105s Unpacking libxft2:arm64 (2.3.6-1build1) ... 105s Selecting previously unselected package x11-common. 105s Preparing to unpack .../012-x11-common_1%3a7.7+24ubuntu1_all.deb ... 105s Unpacking x11-common (1:7.7+24ubuntu1) ... 105s Selecting previously unselected package libxss1:arm64. 105s Preparing to unpack .../013-libxss1_1%3a1.2.3-1build3_arm64.deb ... 105s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 105s Selecting previously unselected package libtk8.6:arm64. 105s Preparing to unpack .../014-libtk8.6_8.6.17-1_arm64.deb ... 105s Unpacking libtk8.6:arm64 (8.6.17-1) ... 105s Selecting previously unselected package tk8.6-blt2.5. 105s Preparing to unpack .../015-tk8.6-blt2.5_2.5.3+dfsg-8_arm64.deb ... 105s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 106s Selecting previously unselected package blt. 106s Preparing to unpack .../016-blt_2.5.3+dfsg-8_arm64.deb ... 106s Unpacking blt (2.5.3+dfsg-8) ... 106s Selecting previously unselected package fonts-lyx. 106s Preparing to unpack .../017-fonts-lyx_2.4.4-1_all.deb ... 106s Unpacking fonts-lyx (2.4.4-1) ... 106s Selecting previously unselected package libbabeltrace1:arm64. 106s Preparing to unpack .../018-libbabeltrace1_1.5.11-4build2_arm64.deb ... 106s Unpacking libbabeltrace1:arm64 (1.5.11-4build2) ... 106s Selecting previously unselected package libsource-highlight-common. 106s Preparing to unpack .../019-libsource-highlight-common_3.1.9-4.3build1_all.deb ... 106s Unpacking libsource-highlight-common (3.1.9-4.3build1) ... 106s Selecting previously unselected package libsource-highlight4t64:arm64. 106s Preparing to unpack .../020-libsource-highlight4t64_3.1.9-4.3build1_arm64.deb ... 106s Unpacking libsource-highlight4t64:arm64 (3.1.9-4.3build1) ... 106s Selecting previously unselected package gdb. 106s Preparing to unpack .../021-gdb_16.3-1ubuntu2_arm64.deb ... 106s Unpacking gdb (16.3-1ubuntu2) ... 106s Selecting previously unselected package libaec0:arm64. 106s Preparing to unpack .../022-libaec0_1.1.3-1_arm64.deb ... 106s Unpacking libaec0:arm64 (1.1.3-1) ... 106s Selecting previously unselected package libsnappy1v5:arm64. 106s Preparing to unpack .../023-libsnappy1v5_1.2.2-1_arm64.deb ... 106s Unpacking libsnappy1v5:arm64 (1.2.2-1) ... 106s Selecting previously unselected package libblosc1:arm64. 106s Preparing to unpack .../024-libblosc1_1.21.5+ds-1build1_arm64.deb ... 106s Unpacking libblosc1:arm64 (1.21.5+ds-1build1) ... 106s Selecting previously unselected package libblosc2-4:arm64. 106s Preparing to unpack .../025-libblosc2-4_2.17.1+ds-2_arm64.deb ... 106s Unpacking libblosc2-4:arm64 (2.17.1+ds-2) ... 106s Selecting previously unselected package libdeflate0:arm64. 106s Preparing to unpack .../026-libdeflate0_1.23-2_arm64.deb ... 106s Unpacking libdeflate0:arm64 (1.23-2) ... 106s Selecting previously unselected package libgomp1:arm64. 106s Preparing to unpack .../027-libgomp1_15.2.0-5ubuntu1_arm64.deb ... 106s Unpacking libgomp1:arm64 (15.2.0-5ubuntu1) ... 106s Selecting previously unselected package libgraphite2-3:arm64. 106s Preparing to unpack .../028-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 106s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 106s Selecting previously unselected package libharfbuzz0b:arm64. 106s Preparing to unpack .../029-libharfbuzz0b_12.1.0-1_arm64.deb ... 106s Unpacking libharfbuzz0b:arm64 (12.1.0-1) ... 106s Selecting previously unselected package libsz2:arm64. 106s Preparing to unpack .../030-libsz2_1.1.3-1_arm64.deb ... 106s Unpacking libsz2:arm64 (1.1.3-1) ... 106s Selecting previously unselected package libhdf5-310:arm64. 106s Preparing to unpack .../031-libhdf5-310_1.14.5+repack-3build1_arm64.deb ... 106s Unpacking libhdf5-310:arm64 (1.14.5+repack-3build1) ... 106s Selecting previously unselected package libhdf5-hl-310:arm64. 106s Preparing to unpack .../032-libhdf5-hl-310_1.14.5+repack-3build1_arm64.deb ... 106s Unpacking libhdf5-hl-310:arm64 (1.14.5+repack-3build1) ... 106s Selecting previously unselected package libimagequant0:arm64. 106s Preparing to unpack .../033-libimagequant0_2.18.0-1build1_arm64.deb ... 106s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 106s Selecting previously unselected package libjpeg-turbo8:arm64. 106s Preparing to unpack .../034-libjpeg-turbo8_2.1.5-4ubuntu2_arm64.deb ... 106s Unpacking libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 107s Selecting previously unselected package libjpeg8:arm64. 107s Preparing to unpack .../035-libjpeg8_8c-2ubuntu11_arm64.deb ... 107s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 107s Selecting previously unselected package libjs-jquery. 107s Preparing to unpack .../036-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 107s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 107s Selecting previously unselected package libjs-jquery-ui. 107s Preparing to unpack .../037-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 107s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 107s Selecting previously unselected package liblcms2-2:arm64. 107s Preparing to unpack .../038-liblcms2-2_2.16-2_arm64.deb ... 107s Unpacking liblcms2-2:arm64 (2.16-2) ... 107s Selecting previously unselected package liblerc4:arm64. 107s Preparing to unpack .../039-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 107s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 107s Selecting previously unselected package libnetcdf22:arm64. 107s Preparing to unpack .../040-libnetcdf22_1%3a4.9.3-1build1_arm64.deb ... 107s Unpacking libnetcdf22:arm64 (1:4.9.3-1build1) ... 107s Selecting previously unselected package libnorm1t64:arm64. 107s Preparing to unpack .../041-libnorm1t64_1.5.9+dfsg-3.1build2_arm64.deb ... 107s Unpacking libnorm1t64:arm64 (1.5.9+dfsg-3.1build2) ... 107s Selecting previously unselected package libpgm-5.3-0t64:arm64. 107s Preparing to unpack .../042-libpgm-5.3-0t64_5.3.128~dfsg-2.1build1_arm64.deb ... 107s Unpacking libpgm-5.3-0t64:arm64 (5.3.128~dfsg-2.1build1) ... 107s Selecting previously unselected package libqhull-r8.0:arm64. 107s Preparing to unpack .../043-libqhull-r8.0_2020.2-6build1_arm64.deb ... 107s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 107s Selecting previously unselected package libraqm0:arm64. 107s Preparing to unpack .../044-libraqm0_0.10.3-1_arm64.deb ... 107s Unpacking libraqm0:arm64 (0.10.3-1) ... 107s Selecting previously unselected package libsharpyuv0:arm64. 107s Preparing to unpack .../045-libsharpyuv0_1.5.0-0.1_arm64.deb ... 107s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 107s Selecting previously unselected package libsodium23:arm64. 107s Preparing to unpack .../046-libsodium23_1.0.18-1build3_arm64.deb ... 107s Unpacking libsodium23:arm64 (1.0.18-1build3) ... 107s Selecting previously unselected package libjbig0:arm64. 107s Preparing to unpack .../047-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 107s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 107s Selecting previously unselected package libwebp7:arm64. 107s Preparing to unpack .../048-libwebp7_1.5.0-0.1_arm64.deb ... 107s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 107s Selecting previously unselected package libtiff6:arm64. 107s Preparing to unpack .../049-libtiff6_4.7.0-3ubuntu3_arm64.deb ... 107s Unpacking libtiff6:arm64 (4.7.0-3ubuntu3) ... 107s Selecting previously unselected package libwebpdemux2:arm64. 107s Preparing to unpack .../050-libwebpdemux2_1.5.0-0.1_arm64.deb ... 107s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 107s Selecting previously unselected package libwebpmux3:arm64. 107s Preparing to unpack .../051-libwebpmux3_1.5.0-0.1_arm64.deb ... 107s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 107s Selecting previously unselected package libxslt1.1:arm64. 107s Preparing to unpack .../052-libxslt1.1_1.1.43-0.1_arm64.deb ... 107s Unpacking libxslt1.1:arm64 (1.1.43-0.1) ... 107s Selecting previously unselected package libzmq5:arm64. 107s Preparing to unpack .../053-libzmq5_4.3.5-1build2_arm64.deb ... 107s Unpacking libzmq5:arm64 (4.3.5-1build2) ... 107s Selecting previously unselected package libzopfli1. 107s Preparing to unpack .../054-libzopfli1_1.0.3-3_arm64.deb ... 107s Unpacking libzopfli1 (1.0.3-3) ... 107s Selecting previously unselected package python-matplotlib-data. 107s Preparing to unpack .../055-python-matplotlib-data_3.10.1+dfsg1-4_all.deb ... 107s Unpacking python-matplotlib-data (3.10.1+dfsg1-4) ... 108s Selecting previously unselected package python-tables-data. 108s Preparing to unpack .../056-python-tables-data_3.10.2-3build1_all.deb ... 108s Unpacking python-tables-data (3.10.2-3build1) ... 108s Selecting previously unselected package python3-asttokens. 108s Preparing to unpack .../057-python3-asttokens_3.0.0-2_all.deb ... 108s Unpacking python3-asttokens (3.0.0-2) ... 108s Selecting previously unselected package python3-brotli. 108s Preparing to unpack .../058-python3-brotli_1.1.0-2build6_arm64.deb ... 108s Unpacking python3-brotli (1.1.0-2build6) ... 108s Selecting previously unselected package python3-cftime. 108s Preparing to unpack .../059-python3-cftime_1.6.4-2_arm64.deb ... 108s Unpacking python3-cftime (1.6.4-2) ... 108s Selecting previously unselected package python3-traitlets. 108s Preparing to unpack .../060-python3-traitlets_5.14.3+really5.14.3-1_all.deb ... 108s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ... 108s Selecting previously unselected package python3-comm. 108s Preparing to unpack .../061-python3-comm_0.2.1-1_all.deb ... 108s Unpacking python3-comm (0.2.1-1) ... 108s Selecting previously unselected package python3-contourpy. 108s Preparing to unpack .../062-python3-contourpy_1.3.1-1build1_arm64.deb ... 108s Unpacking python3-contourpy (1.3.1-1build1) ... 108s Selecting previously unselected package python3-coverage. 108s Preparing to unpack .../063-python3-coverage_7.8.2+dfsg1-1_arm64.deb ... 108s Unpacking python3-coverage (7.8.2+dfsg1-1) ... 108s Selecting previously unselected package python3-cpuinfo. 108s Preparing to unpack .../064-python3-cpuinfo_9.0.0+git20221119-3_all.deb ... 108s Unpacking python3-cpuinfo (9.0.0+git20221119-3) ... 108s Selecting previously unselected package python3-cycler. 108s Preparing to unpack .../065-python3-cycler_0.12.1-1_all.deb ... 108s Unpacking python3-cycler (0.12.1-1) ... 108s Selecting previously unselected package python3-dateutil. 108s Preparing to unpack .../066-python3-dateutil_2.9.0-4_all.deb ... 108s Unpacking python3-dateutil (2.9.0-4) ... 108s Selecting previously unselected package python3-debugpy. 108s Preparing to unpack .../067-python3-debugpy_1.8.12+ds-1ubuntu1_arm64.deb ... 108s Unpacking python3-debugpy (1.8.12+ds-1ubuntu1) ... 108s Selecting previously unselected package python3-decorator. 108s Preparing to unpack .../068-python3-decorator_5.2.1-2_all.deb ... 108s Unpacking python3-decorator (5.2.1-2) ... 108s Selecting previously unselected package python3-executing. 108s Preparing to unpack .../069-python3-executing_2.2.0-0.2_all.deb ... 108s Unpacking python3-executing (2.2.0-0.2) ... 108s Selecting previously unselected package python3-fastjsonschema. 108s Preparing to unpack .../070-python3-fastjsonschema_2.21.1-1_all.deb ... 108s Unpacking python3-fastjsonschema (2.21.1-1) ... 108s Selecting previously unselected package python3-platformdirs. 108s Preparing to unpack .../071-python3-platformdirs_4.3.7-1_all.deb ... 108s Unpacking python3-platformdirs (4.3.7-1) ... 108s Selecting previously unselected package python3-fs. 108s Preparing to unpack .../072-python3-fs_2.4.16-7_all.deb ... 108s Unpacking python3-fs (2.4.16-7) ... 108s Selecting previously unselected package python3-lxml:arm64. 108s Preparing to unpack .../073-python3-lxml_6.0.1-1_arm64.deb ... 108s Unpacking python3-lxml:arm64 (6.0.1-1) ... 108s Selecting previously unselected package python3-lz4. 109s Preparing to unpack .../074-python3-lz4_4.4.0+dfsg-2_arm64.deb ... 109s Unpacking python3-lz4 (4.4.0+dfsg-2) ... 109s Selecting previously unselected package python3-scipy. 109s Preparing to unpack .../075-python3-scipy_1.15.3-1_arm64.deb ... 109s Unpacking python3-scipy (1.15.3-1) ... 109s Selecting previously unselected package python3-mpmath. 109s Preparing to unpack .../076-python3-mpmath_1.3.0-1_all.deb ... 109s Unpacking python3-mpmath (1.3.0-1) ... 109s Selecting previously unselected package python3-sympy. 109s Preparing to unpack .../077-python3-sympy_1.13.3-5_all.deb ... 109s Unpacking python3-sympy (1.13.3-5) ... 109s Selecting previously unselected package python3-ufolib2. 109s Preparing to unpack .../078-python3-ufolib2_0.17.1+dfsg1-1_all.deb ... 109s Unpacking python3-ufolib2 (0.17.1+dfsg1-1) ... 109s Selecting previously unselected package python3-unicodedata2. 109s Preparing to unpack .../079-python3-unicodedata2_16.0.0+ds-1build1_arm64.deb ... 109s Unpacking python3-unicodedata2 (16.0.0+ds-1build1) ... 109s Selecting previously unselected package python3-zopfli. 109s Preparing to unpack .../080-python3-zopfli_0.2.3.post1-1_arm64.deb ... 109s Unpacking python3-zopfli (0.2.3.post1-1) ... 110s Selecting previously unselected package unicode-data. 110s Preparing to unpack .../081-unicode-data_16.0.0-1_all.deb ... 110s Unpacking unicode-data (16.0.0-1) ... 110s Selecting previously unselected package python3-fonttools. 110s Preparing to unpack .../082-python3-fonttools_4.57.0-1_arm64.deb ... 110s Unpacking python3-fonttools (4.57.0-1) ... 110s Selecting previously unselected package python3-gsd. 110s Preparing to unpack .../083-python3-gsd_3.4.2-2build1_arm64.deb ... 110s Unpacking python3-gsd (3.4.2-2build1) ... 110s Selecting previously unselected package python3-iniconfig. 110s Preparing to unpack .../084-python3-iniconfig_1.1.1-2_all.deb ... 110s Unpacking python3-iniconfig (1.1.1-2) ... 110s Selecting previously unselected package python3-parso. 110s Preparing to unpack .../085-python3-parso_0.8.4-1_all.deb ... 110s Unpacking python3-parso (0.8.4-1) ... 110s Selecting previously unselected package python3-typeshed. 110s Preparing to unpack .../086-python3-typeshed_0.0~git20241223.ea91db2-3_all.deb ... 110s Unpacking python3-typeshed (0.0~git20241223.ea91db2-3) ... 110s Selecting previously unselected package python3-jedi. 111s Preparing to unpack .../087-python3-jedi_0.19.1+ds1-1_all.deb ... 111s Unpacking python3-jedi (0.19.1+ds1-1) ... 111s Selecting previously unselected package python3-matplotlib-inline. 111s Preparing to unpack .../088-python3-matplotlib-inline_0.1.7-1_all.deb ... 111s Unpacking python3-matplotlib-inline (0.1.7-1) ... 111s Selecting previously unselected package python3-wcwidth. 111s Preparing to unpack .../089-python3-wcwidth_0.2.13+dfsg1-1_all.deb ... 111s Unpacking python3-wcwidth (0.2.13+dfsg1-1) ... 111s Selecting previously unselected package python3-prompt-toolkit. 111s Preparing to unpack .../090-python3-prompt-toolkit_3.0.51-2_all.deb ... 111s Unpacking python3-prompt-toolkit (3.0.51-2) ... 111s Selecting previously unselected package python3-pure-eval. 111s Preparing to unpack .../091-python3-pure-eval_0.2.3-1_all.deb ... 111s Unpacking python3-pure-eval (0.2.3-1) ... 111s Selecting previously unselected package python3-stack-data. 111s Preparing to unpack .../092-python3-stack-data_0.6.3-1_all.deb ... 111s Unpacking python3-stack-data (0.6.3-1) ... 111s Selecting previously unselected package python3-ptyprocess. 111s Preparing to unpack .../093-python3-ptyprocess_0.7.0-6_all.deb ... 111s Unpacking python3-ptyprocess (0.7.0-6) ... 111s Selecting previously unselected package python3-pexpect. 111s Preparing to unpack .../094-python3-pexpect_4.9-3_all.deb ... 111s Unpacking python3-pexpect (4.9-3) ... 111s Selecting previously unselected package python3-ipython. 111s Preparing to unpack .../095-python3-ipython_8.35.0-1_all.deb ... 111s Unpacking python3-ipython (8.35.0-1) ... 111s Selecting previously unselected package python3-jupyter-core. 111s Preparing to unpack .../096-python3-jupyter-core_5.7.2-5_all.deb ... 111s Unpacking python3-jupyter-core (5.7.2-5) ... 111s Selecting previously unselected package python3-psutil. 111s Preparing to unpack .../097-python3-psutil_7.0.0-2ubuntu1_arm64.deb ... 111s Unpacking python3-psutil 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112s Unpacking python3.13-tk (3.13.7-1) ... 112s Selecting previously unselected package python3-tk:arm64. 112s Preparing to unpack .../109-python3-tk_3.13.5-1_arm64.deb ... 112s Unpacking python3-tk:arm64 (3.13.5-1) ... 112s Selecting previously unselected package python3-pil.imagetk:arm64. 112s Preparing to unpack .../110-python3-pil.imagetk_11.3.0-1ubuntu1_arm64.deb ... 112s Unpacking python3-pil.imagetk:arm64 (11.3.0-1ubuntu1) ... 112s Selecting previously unselected package python3-matplotlib. 112s Preparing to unpack .../111-python3-matplotlib_3.10.1+dfsg1-4_arm64.deb ... 112s Unpacking python3-matplotlib (3.10.1+dfsg1-4) ... 112s Selecting previously unselected package python3-netcdf4. 113s Preparing to unpack .../112-python3-netcdf4_1.7.2-1build4_arm64.deb ... 113s Unpacking python3-netcdf4 (1.7.2-1build4) ... 113s Selecting previously unselected package python3-networkx. 113s Preparing to unpack .../113-python3-networkx_3.2.1-4ubuntu1_all.deb ... 113s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 113s Selecting previously unselected package python3-pytz. 113s Preparing to unpack .../114-python3-pytz_2025.2-3_all.deb ... 113s Unpacking python3-pytz (2025.2-3) ... 113s Selecting previously unselected package python3-pandas-lib:arm64. 113s Preparing to unpack .../115-python3-pandas-lib_2.2.3+dfsg-9_arm64.deb ... 113s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-9) ... 113s Selecting previously unselected package python3-pandas. 113s Preparing to unpack .../116-python3-pandas_2.2.3+dfsg-9_all.deb ... 113s Unpacking python3-pandas (2.2.3+dfsg-9) ... 114s Selecting previously unselected package python3-numexpr. 114s Preparing to unpack .../117-python3-numexpr_2.10.2-1build2_arm64.deb ... 114s Unpacking python3-numexpr (2.10.2-1build2) ... 114s Selecting previously unselected package python3-tables-lib. 114s Preparing to unpack .../118-python3-tables-lib_3.10.2-3build1_arm64.deb ... 114s Unpacking python3-tables-lib (3.10.2-3build1) ... 114s 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libxrender1:arm64 (1:0.9.12-1) ... 115s Setting up python3-joblib (1.4.2-4) ... 116s Setting up python3-parso (0.8.4-1) ... 116s Setting up python3-lz4 (4.4.0+dfsg-2) ... 116s Setting up python3-asttokens (3.0.0-2) ... 116s Setting up python3-unicodedata2 (16.0.0+ds-1build1) ... 116s Setting up fonts-lyx (2.4.4-1) ... 116s Setting up python3-threadpoolctl (3.1.0-1) ... 116s Setting up x11-common (1:7.7+24ubuntu1) ... 117s Setting up libdeflate0:arm64 (1.23-2) ... 117s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 117s Setting up python3-coverage (7.8.2+dfsg1-1) ... 117s Setting up python3-pytz (2025.2-3) ... 117s Setting up libgomp1:arm64 (15.2.0-5ubuntu1) ... 117s Setting up python3-networkx (3.2.1-4ubuntu1) ... 119s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 119s Setting up libaec0:arm64 (1.1.3-1) ... 119s Setting up python3-platformdirs (4.3.7-1) ... 119s Setting up python3-psutil (7.0.0-2ubuntu1) ... 120s Setting up libsource-highlight-common (3.1.9-4.3build1) ... 120s Setting up libsnappy1v5:arm64 (1.2.2-1) ... 120s Setting up python3-fs (2.4.16-7) ... 120s Setting up unicode-data (16.0.0-1) ... 120s Setting up libpgm-5.3-0t64:arm64 (5.3.128~dfsg-2.1build1) ... 120s Setting up python3-decorator (5.2.1-2) ... 120s Setting up libblosc2-4:arm64 (2.17.1+ds-2) ... 120s Setting up libblas3:arm64 (3.12.1-6build1) ... 120s 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 120s Setting up python3-packaging (25.0-1) ... 120s Setting up python3-wcwidth (0.2.13+dfsg1-1) ... 121s Setting up libzopfli1 (1.0.3-3) ... 121s Setting up python3-typeshed (0.0~git20241223.ea91db2-3) ... 121s Setting up python3-executing (2.2.0-0.2) ... 121s Setting up python3-nest-asyncio (1.5.4-1) ... 121s Setting up python3-brotli (1.1.0-2build6) ... 121s Setting up python3-cycler (0.12.1-1) ... 122s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 122s Setting up fonts-dejavu-mono (2.37-8) ... 122s Setting up python3-kiwisolver (1.4.7-3build2) ... 122s Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 122s Setting up libtcl8.6:arm64 (8.6.17+dfsg-1) ... 122s Setting up fonts-dejavu-core (2.37-8) ... 122s Setting up libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 122s Setting up python3-cpuinfo (9.0.0+git20221119-3) ... 122s Setting up libbabeltrace1:arm64 (1.5.11-4build2) ... 122s Setting up libgfortran5:arm64 (15.2.0-5ubuntu1) ... 122s Setting up python3-pluggy (1.6.0-1) ... 122s Setting up libwebp7:arm64 (1.5.0-0.1) ... 122s Setting up python3-fastjsonschema (2.21.1-1) ... 123s Setting up python3-traitlets (5.14.3+really5.14.3-1) ... 123s Setting up libxslt1.1:arm64 (1.1.43-0.1) ... 123s Setting up libblosc1:arm64 (1.21.5+ds-1build1) ... 123s Setting up libopenjp2-7:arm64 (2.5.3-2.1) ... 123s Setting up libharfbuzz0b:arm64 (12.1.0-1) ... 123s Setting up python3-dateutil (2.9.0-4) ... 123s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 123s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 123s Setting up python3-mpmath (1.3.0-1) ... 124s Setting up python-matplotlib-data (3.10.1+dfsg1-4) ... 124s Setting up libwebpmux3:arm64 (1.5.0-0.1) ... 124s Setting up python3-stack-data (0.6.3-1) ... 124s Setting up python-tables-data (3.10.2-3build1) ... 124s Setting up python3-jupyter-core (5.7.2-5) ... 124s Setting up libsz2:arm64 (1.1.3-1) ... 124s Setting up python3-ptyprocess (0.7.0-6) ... 124s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 124s Setting up python3-prompt-toolkit (3.0.51-2) ... 125s Setting up python3-sympy (1.13.3-5) ... 132s Setting up liblapack3:arm64 (3.12.1-6build1) ... 132s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 132s Setting up libzmq5:arm64 (4.3.5-1build2) ... 132s Setting up python3-jedi (0.19.1+ds1-1) ... 132s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 132s Setting up python3-pytest (8.4.2-1) ... 133s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 133s Setting up libsource-highlight4t64:arm64 (3.1.9-4.3build1) ... 133s Setting up python3-nbformat (5.9.1-1) ... 133s Setting up python3-zopfli (0.2.3.post1-1) ... 133s Setting up python3-matplotlib-inline (0.1.7-1) ... 133s Setting up python3-comm (0.2.1-1) ... 133s Setting up gdb (16.3-1ubuntu2) ... 133s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 133s Setting up python3-pexpect (4.9-3) ... 134s Setting up python3-zmq (26.4.0-1) ... 134s Setting up libraqm0:arm64 (0.10.3-1) ... 134s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 136s Setting up libhdf5-310:arm64 (1.14.5+repack-3build1) ... 136s Setting up python3-lxml:arm64 (6.0.1-1) ... 136s Setting up libtiff6:arm64 (4.7.0-3ubuntu3) ... 136s Setting up python3-jupyter-client (8.6.3-2) ... 136s Setting up python3-contourpy (1.3.1-1build1) ... 137s Setting up libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 137s Setting up libhdf5-hl-310:arm64 (1.14.5+repack-3build1) ... 137s Setting up libxft2:arm64 (2.3.6-1build1) ... 137s Setting up python3-scipy (1.15.3-1) ... 141s Setting up python3-tables-lib (3.10.2-3build1) ... 141s Setting up libtk8.6:arm64 (8.6.17-1) ... 141s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-9) ... 141s Setting up libnetcdf22:arm64 (1:4.9.3-1build1) ... 141s Setting up python3-sklearn-lib:arm64 (1.4.2+dfsg-8) ... 141s Setting up python3-gsd (3.4.2-2build1) ... 141s Setting up python3-debugpy (1.8.12+ds-1ubuntu1) ... 142s Setting up python3.13-tk (3.13.7-1) ... 142s Setting up python3-pil:arm64 (11.3.0-1ubuntu1) ... 142s Setting up python3-pandas (2.2.3+dfsg-9) ... 148s Setting up python3-ipython (8.35.0-1) ... 148s Setting up python3-ipykernel (6.29.5-2) ... 149s Setting up python3-sklearn (1.4.2+dfsg-8) ... 151s Setting up python3-cftime (1.6.4-2) ... 151s Setting up python3-numexpr (2.10.2-1build2) ... 151s Setting up python3-netcdf4 (1.7.2-1build4) ... 151s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 151s Setting up blt (2.5.3+dfsg-8) ... 151s Setting up python3-tk:arm64 (3.13.5-1) ... 151s Setting up python3-tables (3.10.2-3build1) ... 152s Setting up python3-mdtraj (1.10.3-2build1) ... 152s Setting up python3-pil.imagetk:arm64 (11.3.0-1ubuntu1) ... 152s Setting up python3-fonttools (4.57.0-1) ... 153s Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... 154s Setting up python3-matplotlib (3.10.1+dfsg1-4) ... 155s Processing triggers for libc-bin (2.42-0ubuntu3) ... 156s Processing triggers for man-db (2.13.1-1) ... 157s autopkgtest [20:19:19]: 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)' 157s autopkgtest [20:19:19]: test command1: [----------------------- 159s ============================= test session starts ============================== 159s platform linux -- Python 3.13.7, pytest-8.4.2, pluggy-1.6.0 -- /usr/bin/python3 159s cachedir: .pytest_cache 159s rootdir: /tmp/autopkgtest.1wtJrD/build.vF3/src 159s configfile: pyproject.toml 159s testpaths: tests, examples 159s plugins: typeguard-4.4.2 161s collecting ... collected 1145 items / 12 deselected / 1133 selected 161s 161s tests/test_alignment.py::test_rmsd_zero PASSED [ 0%] 161s tests/test_alignment.py::test_rmsd_nonzero PASSED [ 0%] 161s tests/test_alignment.py::test_transform PASSED [ 0%] 161s tests/test_alignment.py::test_transform2 PASSED [ 0%] 161s tests/test_angles.py::test_angle_pbc_0 PASSED [ 0%] 161s tests/test_angles.py::test_generator PASSED [ 0%] 161s tests/test_angles.py::test_angle_180[True] PASSED [ 0%] 161s tests/test_angles.py::test_angle_180[False] PASSED [ 0%] 161s tests/test_arc.py::test_read_0 PASSED [ 0%] 161s tests/test_arc.py::test_read_arctraj PASSED [ 0%] 161s tests/test_arc.py::test_read_pbc PASSED [ 0%] 161s tests/test_capi.py::test_1 PASSED [ 1%] 161s tests/test_contact.py::test_contact_0 PASSED [ 1%] 161s tests/test_contact.py::test_contact_1 PASSED [ 1%] 162s 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tests/test_mdcrd.py::test_read_0 PASSED [ 26%] 337s tests/test_mdcrd.py::test_read_1 PASSED [ 26%] 337s tests/test_mdcrd.py::test_read_write_0 PASSED [ 26%] 337s tests/test_mdcrd.py::test_read_write_1 PASSED [ 26%] 337s tests/test_mdcrd.py::test_read_write_2 PASSED [ 26%] 337s tests/test_mdcrd.py::test_multiread PASSED [ 26%] 337s tests/test_mdcrd.py::test_seek PASSED [ 26%] 337s tests/test_mdcrd.py::test_atom_indices_0 PASSED [ 26%] 337s tests/test_mdcrd.py::test_atom_indices_1 PASSED [ 26%] 337s tests/test_mol2.py::test_load_mol2 PASSED [ 26%] 337s tests/test_mol2.py::test_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb SKIPPED [ 27%] 337s tests/test_mol2.py::test_mol2_dataframe PASSED [ 27%] 337s tests/test_mol2.py::test_mol2_dataframe_status PASSED [ 27%] 337s tests/test_mol2.py::test_mol2_warnings PASSED [ 27%] 337s tests/test_mol2.py::test_mol2_status_bits PASSED [ 27%] 337s tests/test_mol2.py::test_mol2_without_bonds PASSED [ 27%] 337s tests/test_mol2.py::test_mol2_element_name PASSED [ 27%] 337s tests/test_mol2.py::test_load_all_mol2[li.mol2] PASSED [ 27%] 337s tests/test_mol2.py::test_load_all_mol2[lysozyme-ligand-tripos.mol2] PASSED [ 27%] 337s tests/test_mol2.py::test_load_all_mol2[imatinib.mol2] PASSED [ 27%] 337s tests/test_mol2.py::test_load_all_mol2[status-bits.mol2] PASSED [ 27%] 337s tests/test_mol2.py::test_load_all_mol2[adp.mol2] PASSED [ 27%] 337s tests/test_mol2.py::test_load_all_mol2[water_acn.mol2] PASSED [ 28%] 337s tests/test_mol2.py::test_mol2_n_residues PASSED [ 28%] 337s tests/test_neighborlist.py::test_nonperiodic PASSED [ 28%] 337s tests/test_neighborlist.py::test_periodic PASSED [ 28%] 338s tests/test_neighborlist.py::test_triclinic PASSED [ 28%] 338s tests/test_neighbors.py::test_compute_neighbors_1 PASSED [ 28%] 339s tests/test_neighbors.py::test_compute_neighbors_2 PASSED [ 28%] 340s tests/test_neighbors.py::test_compute_neighbors_3 PASSED [ 28%] 340s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_after_close PASSED [ 28%] 340s tests/test_netcdf.py::TestNetCDFNetCDF4::test_shape PASSED [ 28%] 340s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_1 PASSED [ 28%] 340s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_2 PASSED [ 29%] 340s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_3 PASSED [ 29%] 340s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_1 PASSED [ 29%] 340s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_2 PASSED [ 29%] 340s tests/test_netcdf.py::TestNetCDFNetCDF4::test_ragged_1 PASSED [ 29%] 340s tests/test_netcdf.py::TestNetCDFNetCDF4::test_ragged_2 PASSED [ 29%] 340s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_25 PASSED [ 29%] 340s tests/test_netcdf.py::TestNetCDFNetCDF4::test_write_3 PASSED [ 29%] 340s tests/test_netcdf.py::TestNetCDFNetCDF4::test_n_atoms PASSED [ 29%] 340s tests/test_netcdf.py::TestNetCDFNetCDF4::test_do_overwrite PASSED [ 29%] 340s tests/test_netcdf.py::TestNetCDFNetCDF4::test_do_not_overwrite PASSED [ 29%] 340s tests/test_netcdf.py::TestNetCDFNetCDF4::test_trajectory_save_load PASSED [ 30%] 340s tests/test_netcdf.py::TestNetCDFScipy::test_read_after_close PASSED [ 30%] 340s tests/test_netcdf.py::TestNetCDFScipy::test_shape PASSED [ 30%] 340s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_1 PASSED [ 30%] 340s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_2 PASSED [ 30%] 340s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_3 PASSED [ 30%] 340s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_1 PASSED [ 30%] 340s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_2 PASSED [ 30%] 340s tests/test_netcdf.py::TestNetCDFScipy::test_ragged_1 PASSED [ 30%] 340s tests/test_netcdf.py::TestNetCDFScipy::test_ragged_2 PASSED [ 30%] 340s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_25 PASSED [ 30%] 340s tests/test_netcdf.py::TestNetCDFScipy::test_write_3 PASSED [ 30%] 340s tests/test_netcdf.py::TestNetCDFScipy::test_n_atoms PASSED [ 31%] 340s tests/test_netcdf.py::TestNetCDFScipy::test_do_overwrite PASSED [ 31%] 340s tests/test_netcdf.py::TestNetCDFScipy::test_do_not_overwrite PASSED [ 31%] 340s tests/test_netcdf.py::TestNetCDFScipy::test_trajectory_save_load PASSED [ 31%] 340s tests/test_netcdf.py::test_cpptraj SKIPPED (This test requires cpptr...) [ 31%] 340s tests/test_nmr.py::test_spartaplus SKIPPED (SPARTA+ binary not found) [ 31%] 340s tests/test_nmr.py::test_ppm SKIPPED (PPM binary not found) [ 31%] 340s tests/test_nmr.py::test_shiftx2 SKIPPED (SHIFTX2 binary not found or...) [ 31%] 340s tests/test_nmr.py::test_2_scalar_couplings PASSED [ 31%] 340s tests/test_order.py::test_nematic_order PASSED [ 31%] 340s tests/test_order.py::test_director PASSED [ 31%] 340s tests/test_order.py::test_inertia PASSED [ 32%] 340s tests/test_order.py::test_nematic_order_args PASSED [ 32%] 340s tests/test_order.py::test_order_from_traj PASSED [ 32%] 340s tests/test_order.py::test_directors_angle_from_traj PASSED [ 32%] 340s tests/test_pdb.py::test_pdbread PASSED [ 32%] 340s tests/test_pdb.py::test_pdbread_with_input_top PASSED [ 32%] 340s tests/test_pdb.py::test_pdbwrite PASSED [ 32%] 340s tests/test_pdb.py::test_load_multiframe PASSED [ 32%] 341s tests/test_pdb.py::test_4ZUO PASSED [ 32%] 341s tests/test_pdb.py::test_2EQQ_0 PASSED [ 32%] 343s tests/test_pdb.py::test_1vii_solvated_with_ligand PASSED [ 32%] 343s tests/test_pdb.py::test_write_large PASSED [ 33%] 343s tests/test_pdb.py::test_write_large_2 PASSED [ 33%] 343s tests/test_pdb.py::test_pdbstructure_0 PASSED [ 33%] 343s tests/test_pdb.py::test_pdbstructure_1 PASSED [ 33%] 343s tests/test_pdb.py::test_pdbstructure_2 PASSED [ 33%] 343s tests/test_pdb.py::test_pdbstructure_3 PASSED [ 33%] 343s tests/test_pdb.py::test_1ncw PASSED [ 33%] 343s tests/test_pdb.py::test_segment_id PASSED [ 33%] 343s tests/test_pdb.py::test_bfactors PASSED [ 33%] 345s tests/test_pdb.py::test_hex PASSED [ 33%] 345s tests/test_pdb.py::test_dummy_pdb_box_detection PASSED [ 33%] 345s tests/test_pdb.py::test_multichain_load_cycle PASSED [ 33%] 345s tests/test_pdb.py::test_multichain_load_cycle_noter PASSED [ 34%] 345s tests/test_pdb.py::test_load_pdb_input_top PASSED [ 34%] 345s tests/test_pdb.py::test_chimera_indexing PASSED [ 34%] 345s tests/test_pdb.py::test_chimera_indexing_skip PASSED [ 34%] 345s tests/test_pdb.py::test_vmd_indexing PASSED [ 34%] 345s tests/test_pdb.py::test_overflow_indexing PASSED [ 34%] 345s tests/test_pdb.py::test_blank_indexing PASSED [ 34%] 345s tests/test_pdb.py::test_pdb_charge_read PASSED [ 34%] 345s tests/test_pdb.py::test_pdb_charge_write PASSED [ 34%] 345s tests/test_pdbx.py::test_convert SKIPPED (test_pdbx.py needs OpenMM.) [ 34%] 345s tests/test_prmtop.py::test_load_prmtop PASSED [ 34%] 345s tests/test_prmtop.py::test_load_chamber_prmtop PASSED [ 35%] 345s tests/test_psf.py::test_load_psf PASSED [ 35%] 349s tests/test_psf.py::test_multichain_psf PASSED [ 35%] 349s tests/test_psf.py::test_load_mdcrd_with_psf PASSED [ 35%] 349s tests/test_psf.py::test_against_vmd[1vii.pdb] SKIPPED (This test req...) [ 35%] 349s tests/test_psf.py::test_against_vmd[2EQQ.pdb] SKIPPED (This test req...) [ 35%] 349s tests/test_quaternion.py::test_quaternion_0 PASSED [ 35%] 349s tests/test_quaternion.py::test_quaternion_1 PASSED [ 35%] 349s tests/test_quaternion.py::test_quaternion_2 PASSED [ 35%] 353s tests/test_rdf.py::test_rdf_norm PASSED [ 35%] 353s tests/test_rdf.py::test_compare_rdf_to_gromacs SKIPPED (Binning does...) [ 35%] 353s tests/test_rdf.py::test_rdf_t[True-True] PASSED [ 36%] 358s tests/test_rdf.py::test_rdf_t[True-False] PASSED [ 36%] 358s tests/test_rdf.py::test_rdf_t[False-True] PASSED [ 36%] 359s tests/test_rdf.py::test_rdf_t[False-False] PASSED [ 36%] 360s tests/test_rdf.py::test_rdf_t_norm[0] PASSED [ 36%] 360s tests/test_rdf.py::test_rdf_t_norm[2] PASSED [ 36%] 361s tests/test_rdf.py::test_rdf_t_norm[4] PASSED [ 36%] 361s tests/test_rdf.py::test_compare_rdf_t_at_0[True-True] PASSED [ 36%] 362s tests/test_rdf.py::test_compare_rdf_t_at_0[True-False] PASSED [ 36%] 362s tests/test_rdf.py::test_compare_rdf_t_at_0[False-True] PASSED [ 36%] 363s tests/test_rdf.py::test_compare_rdf_t_at_0[False-False] PASSED [ 36%] 363s tests/test_rdf.py::test_amber_rdf_t[True-True] PASSED [ 36%] 363s tests/test_rdf.py::test_amber_rdf_t[True-False] PASSED [ 37%] 364s tests/test_rdf.py::test_amber_rdf_t[False-True] PASSED [ 37%] 364s tests/test_rdf.py::test_amber_rdf_t[False-False] PASSED [ 37%] 364s tests/test_rdf.py::test_compare_gromacs_rdf_t SKIPPED (Binning does ...) [ 37%] 364s tests/test_rdf.py::test_compare_rdf_t_master PASSED [ 37%] 364s tests/test_rdf.py::test_compare_n_concurrent_pairs PASSED [ 37%] 364s tests/test_reporter.py::test_reporter SKIPPED (test_reporter.py need...) [ 37%] 364s tests/test_reporter.py::test_reporter_subset SKIPPED (test_reporter....) [ 37%] 364s tests/test_reporter.py::test_xtc_reporter_append SKIPPED (test_repor...) [ 37%] 364s tests/test_restart.py::test_read_after_close PASSED [ 37%] 364s tests/test_restart.py::test_shape PASSED [ 37%] 364s tests/test_restart.py::test_shape_2 PASSED [ 38%] 364s tests/test_restart.py::test_read_write_1 PASSED [ 38%] 364s tests/test_restart.py::test_read_write_2 PASSED [ 38%] 364s tests/test_restart.py::test_read_write_3 PASSED [ 38%] 365s tests/test_restart.py::test_read_write_4 PASSED [ 38%] 365s tests/test_rmsd.py::test_trajectory_rmsd PASSED [ 38%] 365s tests/test_rmsd.py::test_precentered_1 PASSED [ 38%] 365s tests/test_rmsd.py::test_precentered_2 PASSED [ 38%] 365s tests/test_rmsd.py::test_superpose_0 PASSED [ 38%] 365s tests/test_rmsd.py::test_superpose_1 PASSED [ 38%] 365s tests/test_rmsd.py::test_superpose_2 PASSED [ 38%] 365s tests/test_rmsd.py::test_superpose_refinds PASSED [ 39%] 365s tests/test_rmsd.py::test_rmsd_atom_indices PASSED [ 39%] 365s tests/test_rmsd.py::test_rmsd_ref_ainds PASSED [ 39%] 366s tests/test_rmsd.py::test_average_structure PASSED [ 39%] 366s tests/test_rmsd.py::test_trajectory_rmsf PASSED [ 39%] 366s tests/test_rmsd.py::test_trajectory_rmsf_aligned PASSED [ 39%] 366s tests/test_rmsd.py::test_rmsd_atom_indices_vs_ref_indices PASSED [ 39%] 366s tests/test_rmsd_memmap.py::test_1 PASSED [ 39%] 366s tests/test_rmsd_memmap.py::test_2 PASSED [ 39%] 366s tests/test_sasa.py::test_sasa_0 PASSED [ 39%] 366s tests/test_sasa.py::test_sasa_1 PASSED [ 39%] 366s tests/test_sasa.py::test_sasa_2 PASSED [ 39%] 366s tests/test_sasa.py::test_sasa_3 PASSED [ 40%] 367s tests/test_sasa.py::test_sasa_4 PASSED [ 40%] 367s tests/test_sasa.py::test_sasa_5 PASSED [ 40%] 367s tests/test_sasa.py::test_sasa_6 PASSED [ 40%] 368s tests/test_sasa.py::test_sasa_7 PASSED [ 40%] 368s tests/test_selection.py::test_range PASSED [ 40%] 368s tests/test_selection.py::test_unary_2 PASSED [ 40%] 368s tests/test_selection.py::test_unary_3 PASSED [ 40%] 368s tests/test_selection.py::test_binary_1 PASSED [ 40%] 368s tests/test_selection.py::test_binary_2 PASSED [ 40%] 368s tests/test_selection.py::test_simple PASSED [ 40%] 368s tests/test_selection.py::test_alias PASSED [ 41%] 368s tests/test_selection.py::test_unary_1 PASSED [ 41%] 368s tests/test_selection.py::test_binary_selection_operator PASSED [ 41%] 368s tests/test_selection.py::test_raises PASSED [ 41%] 368s tests/test_selection.py::test_raises2 PASSED [ 41%] 368s tests/test_selection.py::test_bool PASSED [ 41%] 368s tests/test_selection.py::test_nested_bool PASSED [ 41%] 368s tests/test_selection.py::test_values PASSED [ 41%] 368s tests/test_selection.py::test_element PASSED [ 41%] 368s tests/test_selection.py::test_not PASSED [ 41%] 368s tests/test_selection.py::test_re PASSED [ 41%] 368s tests/test_selection.py::test_within SKIPPED (failed to parse selection) [ 42%] 368s tests/test_selection.py::test_quotes PASSED [ 42%] 368s tests/test_selection.py::test_top PASSED [ 42%] 369s tests/test_selection.py::test_top_2 PASSED [ 42%] 369s tests/test_selection.py::test_backbone PASSED [ 42%] 369s tests/test_selection.py::test_sidechain PASSED [ 42%] 369s tests/test_selection.py::test_literal PASSED [ 42%] 369s tests/test_selection.py::test_in PASSED [ 42%] 369s tests/test_shape.py::test_gyration PASSED [ 42%] 369s tests/test_shape.py::test_principal_moments PASSED [ 42%] 370s tests/test_shape.py::test_asphericity PASSED [ 42%] 370s tests/test_shape.py::test_shape_metrics PASSED [ 42%] 370s tests/test_thermodynamic_properties.py::test_volume PASSED [ 43%] 370s tests/test_thermodynamic_properties.py::test_density PASSED [ 43%] 370s tests/test_thermodynamic_properties.py::test_dipole_moments PASSED [ 43%] 370s tests/test_thermodynamic_properties.py::test_static_dielectric PASSED [ 43%] 370s tests/test_thermodynamic_properties.py::test_kappa PASSED [ 43%] 370s tests/test_thermodynamic_properties.py::test_alpha SKIPPED (Thermal ...) [ 43%] 370s tests/test_topology.py::test_topology_openmm SKIPPED (needs OpenMM) [ 43%] 370s tests/test_topology.py::test_topology_openmm_preserve_chain_id_when_specified SKIPPED [ 43%] 370s tests/test_topology.py::test_topology_openmm_roundtrip_chain_id SKIPPED [ 43%] 370s tests/test_topology.py::test_topology_openmm_preserve_chain_id_even_when_empty SKIPPED [ 43%] 370s tests/test_topology.py::test_topology_openmm_boxes SKIPPED (needs Op...) [ 43%] 370s tests/test_topology.py::test_topology_openmm_formal_charges SKIPPED [ 44%] 370s tests/test_topology.py::test_topology_pandas PASSED [ 44%] 371s tests/test_topology.py::test_topology_pandas_TIP4PEW PASSED [ 44%] 371s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq PASSED [ 44%] 371s tests/test_topology.py::test_topology_numbers PASSED [ 44%] 371s tests/test_topology.py::test_topology_unique_elements_bpti PASSED [ 44%] 371s tests/test_topology.py::test_chain PASSED [ 44%] 371s tests/test_topology.py::test_residue PASSED [ 44%] 371s tests/test_topology.py::test_segment_id PASSED [ 44%] 371s tests/test_topology.py::test_nonconsective_resSeq PASSED [ 44%] 371s tests/test_topology.py::test_pickle PASSED [ 44%] 371s tests/test_topology.py::test_atoms_by_name PASSED [ 45%] 371s tests/test_topology.py::test_select_atom_indices PASSED [ 45%] 371s tests/test_topology.py::test_top_dataframe_openmm_roundtrip SKIPPED [ 45%] 371s tests/test_topology.py::test_n_bonds PASSED [ 45%] 371s tests/test_topology.py::test_load_unknown_topology PASSED [ 45%] 371s tests/test_topology.py::test_unique_pairs PASSED [ 45%] 372s tests/test_topology.py::test_select_pairs PASSED [ 45%] 372s tests/test_topology.py::test_to_fasta PASSED [ 45%] 372s tests/test_topology.py::test_subset PASSED [ 45%] 373s tests/test_topology.py::test_subset_re_index_residues PASSED [ 45%] 373s tests/test_topology.py::test_molecules PASSED [ 45%] 373s tests/test_topology.py::test_copy_and_hash PASSED [ 45%] 373s tests/test_topology.py::test_topology_sliced_residue_indices PASSED [ 46%] 373s tests/test_topology.py::test_topology_join PASSED [ 46%] 373s tests/test_topology.py::test_topology_join_keep_resSeq PASSED [ 46%] 373s tests/test_trajectory.py::test_mismatch PASSED [ 46%] 373s tests/test_trajectory.py::test_box PASSED [ 46%] 373s tests/test_trajectory.py::test_load_pdb_box PASSED [ 46%] 373s tests/test_trajectory.py::test_load_pdb_gz PASSED [ 46%] 374s tests/test_trajectory.py::test_box_load_save[nc] PASSED [ 46%] 374s tests/test_trajectory.py::test_box_load_save[h5] PASSED [ 46%] 374s tests/test_trajectory.py::test_box_load_save[xtc] PASSED [ 46%] 374s tests/test_trajectory.py::test_box_load_save[trr] PASSED [ 46%] 374s tests/test_trajectory.py::test_box_load_save[dcd] PASSED [ 47%] 374s tests/test_trajectory.py::test_box_load_save[mdcrd] PASSED [ 47%] 374s tests/test_trajectory.py::test_box_load_save[dtr] PASSED [ 47%] 374s tests/test_trajectory.py::test_box_load_save[xyz] SKIPPED (xyz does ...) [ 47%] 374s tests/test_trajectory.py::test_box_load_save[xyz.gz] SKIPPED (xyz.gz...) [ 47%] 374s tests/test_trajectory.py::test_box_load_save[lammpstrj] PASSED [ 47%] 374s tests/test_trajectory.py::test_box_load_save[lh5] SKIPPED (lh5 does ...) [ 47%] 374s tests/test_trajectory.py::test_box_load_save[pdb] SKIPPED (pdb does ...) [ 47%] 374s tests/test_trajectory.py::test_box_load_save[pdb.gz] SKIPPED (pdb.gz...) [ 47%] 374s tests/test_trajectory.py::test_box_load_save[ncrst] PASSED [ 47%] 374s tests/test_trajectory.py::test_box_load_save[rst7] PASSED [ 47%] 374s tests/test_trajectory.py::test_box_load_save[gro] PASSED [ 48%] 374s tests/test_trajectory.py::test_slice PASSED [ 48%] 374s tests/test_trajectory.py::test_slice2 PASSED [ 48%] 374s tests/test_trajectory.py::test_read_path[nc] PASSED [ 48%] 374s tests/test_trajectory.py::test_read_path[h5] PASSED [ 48%] 374s tests/test_trajectory.py::test_read_path[xtc] PASSED [ 48%] 374s tests/test_trajectory.py::test_read_path[trr] PASSED [ 48%] 374s tests/test_trajectory.py::test_read_path[dcd] PASSED [ 48%] 374s tests/test_trajectory.py::test_read_path[mdcrd] PASSED [ 48%] 374s tests/test_trajectory.py::test_read_path[dtr] PASSED [ 48%] 374s tests/test_trajectory.py::test_read_path[xyz] PASSED [ 48%] 374s tests/test_trajectory.py::test_read_path[xyz.gz] PASSED [ 48%] 374s tests/test_trajectory.py::test_read_path[lammpstrj] PASSED [ 49%] 374s tests/test_trajectory.py::test_read_path[lh5] PASSED [ 49%] 374s tests/test_trajectory.py::test_read_path[pdb] PASSED [ 49%] 374s tests/test_trajectory.py::test_read_path[pdb.gz] PASSED [ 49%] 374s tests/test_trajectory.py::test_read_path[ncrst] XFAIL (These referen...) [ 49%] 374s tests/test_trajectory.py::test_read_path[rst7] XFAIL (These referenc...) [ 49%] 374s tests/test_trajectory.py::test_read_path[gro] PASSED [ 49%] 374s tests/test_trajectory.py::test_write_path[nc] PASSED [ 49%] 374s tests/test_trajectory.py::test_write_path[h5] PASSED [ 49%] 374s tests/test_trajectory.py::test_write_path[xtc] PASSED [ 49%] 374s tests/test_trajectory.py::test_write_path[trr] PASSED [ 49%] 374s tests/test_trajectory.py::test_write_path[dcd] PASSED [ 50%] 374s tests/test_trajectory.py::test_write_path[mdcrd] SKIPPED (mdcrd can ...) [ 50%] 375s tests/test_trajectory.py::test_write_path[dtr] PASSED [ 50%] 375s tests/test_trajectory.py::test_write_path[xyz] PASSED [ 50%] 375s tests/test_trajectory.py::test_write_path[xyz.gz] PASSED [ 50%] 375s tests/test_trajectory.py::test_write_path[lammpstrj] PASSED [ 50%] 375s tests/test_trajectory.py::test_write_path[lh5] PASSED [ 50%] 375s tests/test_trajectory.py::test_write_path[pdb] PASSED [ 50%] 375s tests/test_trajectory.py::test_write_path[pdb.gz] PASSED [ 50%] 375s tests/test_trajectory.py::test_write_path[ncrst] SKIPPED (ncrst can ...) [ 50%] 375s tests/test_trajectory.py::test_write_path[rst7] SKIPPED (rst7 can on...) [ 50%] 375s tests/test_trajectory.py::test_write_path[gro] PASSED [ 51%] 375s tests/test_trajectory.py::test_read_write[nc-nc] PASSED [ 51%] 375s tests/test_trajectory.py::test_read_write[nc-h5] PASSED [ 51%] 375s tests/test_trajectory.py::test_read_write[nc-xtc] PASSED [ 51%] 375s tests/test_trajectory.py::test_read_write[nc-trr] PASSED [ 51%] 375s tests/test_trajectory.py::test_read_write[nc-dcd] PASSED [ 51%] 375s tests/test_trajectory.py::test_read_write[nc-mdcrd] SKIPPED (mdcrd c...) [ 51%] 379s tests/test_trajectory.py::test_read_write[nc-dtr] PASSED [ 51%] 379s tests/test_trajectory.py::test_read_write[nc-xyz] PASSED [ 51%] 379s tests/test_trajectory.py::test_read_write[nc-xyz.gz] PASSED [ 51%] 380s tests/test_trajectory.py::test_read_write[nc-lammpstrj] PASSED [ 51%] 380s tests/test_trajectory.py::test_read_write[nc-lh5] PASSED [ 51%] 380s tests/test_trajectory.py::test_read_write[nc-pdb] PASSED [ 52%] 381s tests/test_trajectory.py::test_read_write[nc-pdb.gz] PASSED [ 52%] 381s tests/test_trajectory.py::test_read_write[nc-ncrst] SKIPPED (ncrst c...) [ 52%] 381s tests/test_trajectory.py::test_read_write[nc-rst7] SKIPPED (rst7 can...) [ 52%] 381s tests/test_trajectory.py::test_read_write[nc-gro] PASSED [ 52%] 381s tests/test_trajectory.py::test_read_write[h5-nc] PASSED [ 52%] 381s tests/test_trajectory.py::test_read_write[h5-h5] PASSED [ 52%] 381s tests/test_trajectory.py::test_read_write[h5-xtc] PASSED [ 52%] 381s tests/test_trajectory.py::test_read_write[h5-trr] PASSED [ 52%] 381s tests/test_trajectory.py::test_read_write[h5-dcd] PASSED [ 52%] 381s tests/test_trajectory.py::test_read_write[h5-mdcrd] SKIPPED (mdcrd c...) [ 52%] 383s tests/test_trajectory.py::test_read_write[h5-dtr] PASSED [ 53%] 383s tests/test_trajectory.py::test_read_write[h5-xyz] PASSED [ 53%] 384s tests/test_trajectory.py::test_read_write[h5-xyz.gz] PASSED [ 53%] 384s tests/test_trajectory.py::test_read_write[h5-lammpstrj] PASSED [ 53%] 384s tests/test_trajectory.py::test_read_write[h5-lh5] PASSED [ 53%] 384s tests/test_trajectory.py::test_read_write[h5-pdb] PASSED [ 53%] 384s tests/test_trajectory.py::test_read_write[h5-pdb.gz] PASSED [ 53%] 384s tests/test_trajectory.py::test_read_write[h5-ncrst] SKIPPED (ncrst c...) [ 53%] 384s tests/test_trajectory.py::test_read_write[h5-rst7] SKIPPED (rst7 can...) [ 53%] 385s tests/test_trajectory.py::test_read_write[h5-gro] PASSED [ 53%] 385s tests/test_trajectory.py::test_read_write[xtc-nc] PASSED [ 53%] 385s tests/test_trajectory.py::test_read_write[xtc-h5] PASSED [ 54%] 385s tests/test_trajectory.py::test_read_write[xtc-xtc] PASSED [ 54%] 385s tests/test_trajectory.py::test_read_write[xtc-trr] PASSED [ 54%] 385s tests/test_trajectory.py::test_read_write[xtc-dcd] PASSED [ 54%] 385s tests/test_trajectory.py::test_read_write[xtc-mdcrd] SKIPPED (mdcrd ...) [ 54%] 387s tests/test_trajectory.py::test_read_write[xtc-dtr] PASSED [ 54%] 387s tests/test_trajectory.py::test_read_write[xtc-xyz] PASSED [ 54%] 387s tests/test_trajectory.py::test_read_write[xtc-xyz.gz] PASSED [ 54%] 387s tests/test_trajectory.py::test_read_write[xtc-lammpstrj] PASSED [ 54%] 387s tests/test_trajectory.py::test_read_write[xtc-lh5] PASSED [ 54%] 388s tests/test_trajectory.py::test_read_write[xtc-pdb] PASSED [ 54%] 388s tests/test_trajectory.py::test_read_write[xtc-pdb.gz] PASSED [ 54%] 388s tests/test_trajectory.py::test_read_write[xtc-ncrst] SKIPPED (ncrst ...) [ 55%] 388s tests/test_trajectory.py::test_read_write[xtc-rst7] SKIPPED (rst7 ca...) [ 55%] 388s tests/test_trajectory.py::test_read_write[xtc-gro] PASSED [ 55%] 388s tests/test_trajectory.py::test_read_write[trr-nc] PASSED [ 55%] 388s tests/test_trajectory.py::test_read_write[trr-h5] PASSED [ 55%] 388s tests/test_trajectory.py::test_read_write[trr-xtc] PASSED [ 55%] 388s tests/test_trajectory.py::test_read_write[trr-trr] PASSED [ 55%] 388s tests/test_trajectory.py::test_read_write[trr-dcd] PASSED [ 55%] 388s tests/test_trajectory.py::test_read_write[trr-mdcrd] SKIPPED (mdcrd ...) [ 55%] 390s tests/test_trajectory.py::test_read_write[trr-dtr] PASSED [ 55%] 390s tests/test_trajectory.py::test_read_write[trr-xyz] PASSED [ 55%] 391s tests/test_trajectory.py::test_read_write[trr-xyz.gz] PASSED [ 56%] 391s tests/test_trajectory.py::test_read_write[trr-lammpstrj] PASSED [ 56%] 391s tests/test_trajectory.py::test_read_write[trr-lh5] PASSED [ 56%] 391s tests/test_trajectory.py::test_read_write[trr-pdb] PASSED [ 56%] 391s tests/test_trajectory.py::test_read_write[trr-pdb.gz] PASSED [ 56%] 391s tests/test_trajectory.py::test_read_write[trr-ncrst] SKIPPED (ncrst ...) [ 56%] 391s tests/test_trajectory.py::test_read_write[trr-rst7] SKIPPED (rst7 ca...) [ 56%] 392s tests/test_trajectory.py::test_read_write[trr-gro] PASSED [ 56%] 392s tests/test_trajectory.py::test_read_write[dcd-nc] PASSED [ 56%] 392s tests/test_trajectory.py::test_read_write[dcd-h5] PASSED [ 56%] 392s tests/test_trajectory.py::test_read_write[dcd-xtc] PASSED [ 56%] 392s tests/test_trajectory.py::test_read_write[dcd-trr] PASSED [ 57%] 392s tests/test_trajectory.py::test_read_write[dcd-dcd] PASSED [ 57%] 392s tests/test_trajectory.py::test_read_write[dcd-mdcrd] SKIPPED (mdcrd ...) [ 57%] 393s tests/test_trajectory.py::test_read_write[dcd-dtr] PASSED [ 57%] 394s tests/test_trajectory.py::test_read_write[dcd-xyz] PASSED [ 57%] 394s tests/test_trajectory.py::test_read_write[dcd-xyz.gz] PASSED [ 57%] 394s tests/test_trajectory.py::test_read_write[dcd-lammpstrj] PASSED [ 57%] 394s tests/test_trajectory.py::test_read_write[dcd-lh5] PASSED [ 57%] 394s tests/test_trajectory.py::test_read_write[dcd-pdb] PASSED [ 57%] 395s tests/test_trajectory.py::test_read_write[dcd-pdb.gz] PASSED [ 57%] 395s tests/test_trajectory.py::test_read_write[dcd-ncrst] SKIPPED (ncrst ...) [ 57%] 395s tests/test_trajectory.py::test_read_write[dcd-rst7] SKIPPED (rst7 ca...) [ 57%] 395s tests/test_trajectory.py::test_read_write[dcd-gro] PASSED [ 58%] 395s tests/test_trajectory.py::test_read_write[mdcrd-nc] PASSED [ 58%] 395s tests/test_trajectory.py::test_read_write[mdcrd-h5] PASSED [ 58%] 395s tests/test_trajectory.py::test_read_write[mdcrd-xtc] PASSED [ 58%] 395s tests/test_trajectory.py::test_read_write[mdcrd-trr] PASSED [ 58%] 395s tests/test_trajectory.py::test_read_write[mdcrd-dcd] PASSED [ 58%] 395s tests/test_trajectory.py::test_read_write[mdcrd-mdcrd] SKIPPED (mdcr...) [ 58%] 395s tests/test_trajectory.py::test_read_write[mdcrd-dtr] SKIPPED (dtr ne...) [ 58%] 395s tests/test_trajectory.py::test_read_write[mdcrd-xyz] PASSED [ 58%] 396s tests/test_trajectory.py::test_read_write[mdcrd-xyz.gz] PASSED [ 58%] 396s tests/test_trajectory.py::test_read_write[mdcrd-lammpstrj] SKIPPED (...) [ 58%] 396s tests/test_trajectory.py::test_read_write[mdcrd-lh5] PASSED [ 59%] 396s tests/test_trajectory.py::test_read_write[mdcrd-pdb] PASSED [ 59%] 397s tests/test_trajectory.py::test_read_write[mdcrd-pdb.gz] PASSED [ 59%] 397s tests/test_trajectory.py::test_read_write[mdcrd-ncrst] SKIPPED (ncrs...) [ 59%] 397s tests/test_trajectory.py::test_read_write[mdcrd-rst7] SKIPPED (rst7 ...) [ 59%] 397s tests/test_trajectory.py::test_read_write[mdcrd-gro] PASSED [ 59%] 397s tests/test_trajectory.py::test_read_write[dtr-nc] PASSED [ 59%] 397s tests/test_trajectory.py::test_read_write[dtr-h5] PASSED [ 59%] 397s tests/test_trajectory.py::test_read_write[dtr-xtc] PASSED [ 59%] 397s tests/test_trajectory.py::test_read_write[dtr-trr] PASSED [ 59%] 397s tests/test_trajectory.py::test_read_write[dtr-dcd] PASSED [ 59%] 397s tests/test_trajectory.py::test_read_write[dtr-mdcrd] SKIPPED (mdcrd ...) [ 60%] 399s tests/test_trajectory.py::test_read_write[dtr-dtr] PASSED [ 60%] 399s tests/test_trajectory.py::test_read_write[dtr-xyz] PASSED [ 60%] 399s tests/test_trajectory.py::test_read_write[dtr-xyz.gz] PASSED [ 60%] 399s tests/test_trajectory.py::test_read_write[dtr-lammpstrj] PASSED [ 60%] 399s tests/test_trajectory.py::test_read_write[dtr-lh5] PASSED [ 60%] 400s tests/test_trajectory.py::test_read_write[dtr-pdb] PASSED [ 60%] 400s tests/test_trajectory.py::test_read_write[dtr-pdb.gz] PASSED [ 60%] 400s tests/test_trajectory.py::test_read_write[dtr-ncrst] SKIPPED (ncrst ...) [ 60%] 400s tests/test_trajectory.py::test_read_write[dtr-rst7] SKIPPED (rst7 ca...) [ 60%] 400s tests/test_trajectory.py::test_read_write[dtr-gro] PASSED [ 60%] 400s tests/test_trajectory.py::test_read_write[xyz-nc] PASSED [ 60%] 400s tests/test_trajectory.py::test_read_write[xyz-h5] PASSED [ 61%] 400s tests/test_trajectory.py::test_read_write[xyz-xtc] PASSED [ 61%] 401s tests/test_trajectory.py::test_read_write[xyz-trr] PASSED [ 61%] 401s tests/test_trajectory.py::test_read_write[xyz-dcd] PASSED [ 61%] 401s tests/test_trajectory.py::test_read_write[xyz-mdcrd] SKIPPED (mdcrd ...) [ 61%] 401s tests/test_trajectory.py::test_read_write[xyz-dtr] SKIPPED (dtr need...) [ 61%] 401s tests/test_trajectory.py::test_read_write[xyz-xyz] PASSED [ 61%] 401s tests/test_trajectory.py::test_read_write[xyz-xyz.gz] PASSED [ 61%] 401s tests/test_trajectory.py::test_read_write[xyz-lammpstrj] SKIPPED (la...) [ 61%] 401s tests/test_trajectory.py::test_read_write[xyz-lh5] PASSED [ 61%] 401s tests/test_trajectory.py::test_read_write[xyz-pdb] PASSED [ 61%] 402s tests/test_trajectory.py::test_read_write[xyz-pdb.gz] PASSED [ 62%] 402s tests/test_trajectory.py::test_read_write[xyz-ncrst] SKIPPED (ncrst ...) [ 62%] 402s tests/test_trajectory.py::test_read_write[xyz-rst7] SKIPPED (rst7 ca...) [ 62%] 402s tests/test_trajectory.py::test_read_write[xyz-gro] PASSED [ 62%] 402s tests/test_trajectory.py::test_read_write[xyz.gz-nc] PASSED [ 62%] 402s tests/test_trajectory.py::test_read_write[xyz.gz-h5] PASSED [ 62%] 402s tests/test_trajectory.py::test_read_write[xyz.gz-xtc] PASSED [ 62%] 402s tests/test_trajectory.py::test_read_write[xyz.gz-trr] PASSED [ 62%] 402s tests/test_trajectory.py::test_read_write[xyz.gz-dcd] PASSED [ 62%] 402s tests/test_trajectory.py::test_read_write[xyz.gz-mdcrd] SKIPPED (mdc...) [ 62%] 402s tests/test_trajectory.py::test_read_write[xyz.gz-dtr] SKIPPED (dtr n...) [ 62%] 402s tests/test_trajectory.py::test_read_write[xyz.gz-xyz] PASSED [ 63%] 402s tests/test_trajectory.py::test_read_write[xyz.gz-xyz.gz] PASSED [ 63%] 402s tests/test_trajectory.py::test_read_write[xyz.gz-lammpstrj] SKIPPED [ 63%] 402s tests/test_trajectory.py::test_read_write[xyz.gz-lh5] PASSED [ 63%] 403s tests/test_trajectory.py::test_read_write[xyz.gz-pdb] PASSED [ 63%] 403s tests/test_trajectory.py::test_read_write[xyz.gz-pdb.gz] PASSED [ 63%] 403s tests/test_trajectory.py::test_read_write[xyz.gz-ncrst] SKIPPED (ncr...) [ 63%] 403s tests/test_trajectory.py::test_read_write[xyz.gz-rst7] SKIPPED (rst7...) [ 63%] 403s tests/test_trajectory.py::test_read_write[xyz.gz-gro] PASSED [ 63%] 403s tests/test_trajectory.py::test_read_write[lammpstrj-nc] PASSED [ 63%] 403s tests/test_trajectory.py::test_read_write[lammpstrj-h5] PASSED [ 63%] 403s tests/test_trajectory.py::test_read_write[lammpstrj-xtc] PASSED [ 63%] 403s tests/test_trajectory.py::test_read_write[lammpstrj-trr] PASSED [ 64%] 403s tests/test_trajectory.py::test_read_write[lammpstrj-dcd] PASSED [ 64%] 403s tests/test_trajectory.py::test_read_write[lammpstrj-mdcrd] SKIPPED (...) [ 64%] 406s tests/test_trajectory.py::test_read_write[lammpstrj-dtr] PASSED [ 64%] 406s tests/test_trajectory.py::test_read_write[lammpstrj-xyz] PASSED [ 64%] 406s tests/test_trajectory.py::test_read_write[lammpstrj-xyz.gz] PASSED [ 64%] 406s tests/test_trajectory.py::test_read_write[lammpstrj-lammpstrj] PASSED [ 64%] 406s tests/test_trajectory.py::test_read_write[lammpstrj-lh5] PASSED [ 64%] 407s tests/test_trajectory.py::test_read_write[lammpstrj-pdb] PASSED [ 64%] 407s tests/test_trajectory.py::test_read_write[lammpstrj-pdb.gz] PASSED [ 64%] 407s tests/test_trajectory.py::test_read_write[lammpstrj-ncrst] SKIPPED (...) [ 64%] 407s tests/test_trajectory.py::test_read_write[lammpstrj-rst7] SKIPPED (r...) [ 65%] 407s tests/test_trajectory.py::test_read_write[lammpstrj-gro] PASSED [ 65%] 407s tests/test_trajectory.py::test_read_write[lh5-nc] PASSED [ 65%] 407s tests/test_trajectory.py::test_read_write[lh5-h5] PASSED [ 65%] 407s tests/test_trajectory.py::test_read_write[lh5-xtc] PASSED [ 65%] 407s tests/test_trajectory.py::test_read_write[lh5-trr] PASSED [ 65%] 407s tests/test_trajectory.py::test_read_write[lh5-dcd] PASSED [ 65%] 407s tests/test_trajectory.py::test_read_write[lh5-mdcrd] SKIPPED (mdcrd ...) [ 65%] 407s tests/test_trajectory.py::test_read_write[lh5-dtr] SKIPPED (dtr need...) [ 65%] 407s tests/test_trajectory.py::test_read_write[lh5-xyz] PASSED [ 65%] 408s tests/test_trajectory.py::test_read_write[lh5-xyz.gz] PASSED [ 65%] 408s tests/test_trajectory.py::test_read_write[lh5-lammpstrj] SKIPPED (la...) [ 66%] 408s tests/test_trajectory.py::test_read_write[lh5-lh5] PASSED [ 66%] 408s tests/test_trajectory.py::test_read_write[lh5-pdb] PASSED [ 66%] 408s tests/test_trajectory.py::test_read_write[lh5-pdb.gz] PASSED [ 66%] 408s tests/test_trajectory.py::test_read_write[lh5-ncrst] SKIPPED (ncrst ...) [ 66%] 408s tests/test_trajectory.py::test_read_write[lh5-rst7] SKIPPED (rst7 ca...) [ 66%] 408s tests/test_trajectory.py::test_read_write[lh5-gro] PASSED [ 66%] 409s tests/test_trajectory.py::test_read_write[pdb-nc] PASSED [ 66%] 409s tests/test_trajectory.py::test_read_write[pdb-h5] PASSED [ 66%] 409s tests/test_trajectory.py::test_read_write[pdb-xtc] PASSED [ 66%] 409s tests/test_trajectory.py::test_read_write[pdb-trr] PASSED [ 66%] 409s tests/test_trajectory.py::test_read_write[pdb-dcd] PASSED [ 66%] 409s tests/test_trajectory.py::test_read_write[pdb-mdcrd] SKIPPED (mdcrd ...) [ 67%] 412s tests/test_trajectory.py::test_read_write[pdb-dtr] PASSED [ 67%] 412s tests/test_trajectory.py::test_read_write[pdb-xyz] PASSED [ 67%] 413s tests/test_trajectory.py::test_read_write[pdb-xyz.gz] PASSED [ 67%] 413s tests/test_trajectory.py::test_read_write[pdb-lammpstrj] PASSED [ 67%] 413s tests/test_trajectory.py::test_read_write[pdb-lh5] PASSED [ 67%] 414s tests/test_trajectory.py::test_read_write[pdb-pdb] PASSED [ 67%] 414s tests/test_trajectory.py::test_read_write[pdb-pdb.gz] PASSED [ 67%] 414s tests/test_trajectory.py::test_read_write[pdb-ncrst] SKIPPED (ncrst ...) [ 67%] 414s tests/test_trajectory.py::test_read_write[pdb-rst7] SKIPPED (rst7 ca...) [ 67%] 414s tests/test_trajectory.py::test_read_write[pdb-gro] PASSED [ 67%] 415s tests/test_trajectory.py::test_read_write[pdb.gz-nc] PASSED [ 68%] 415s tests/test_trajectory.py::test_read_write[pdb.gz-h5] PASSED [ 68%] 415s tests/test_trajectory.py::test_read_write[pdb.gz-xtc] PASSED [ 68%] 415s tests/test_trajectory.py::test_read_write[pdb.gz-trr] PASSED [ 68%] 415s tests/test_trajectory.py::test_read_write[pdb.gz-dcd] PASSED [ 68%] 415s tests/test_trajectory.py::test_read_write[pdb.gz-mdcrd] SKIPPED (mdc...) [ 68%] 417s tests/test_trajectory.py::test_read_write[pdb.gz-dtr] PASSED [ 68%] 418s tests/test_trajectory.py::test_read_write[pdb.gz-xyz] PASSED [ 68%] 418s tests/test_trajectory.py::test_read_write[pdb.gz-xyz.gz] PASSED [ 68%] 418s tests/test_trajectory.py::test_read_write[pdb.gz-lammpstrj] PASSED [ 68%] 418s tests/test_trajectory.py::test_read_write[pdb.gz-lh5] PASSED [ 68%] 419s tests/test_trajectory.py::test_read_write[pdb.gz-pdb] PASSED [ 69%] 419s tests/test_trajectory.py::test_read_write[pdb.gz-pdb.gz] PASSED [ 69%] 419s tests/test_trajectory.py::test_read_write[pdb.gz-ncrst] SKIPPED (ncr...) [ 69%] 419s tests/test_trajectory.py::test_read_write[pdb.gz-rst7] SKIPPED (rst7...) [ 69%] 420s tests/test_trajectory.py::test_read_write[pdb.gz-gro] PASSED [ 69%] 420s tests/test_trajectory.py::test_read_write[ncrst-nc] XFAIL (These ref...) [ 69%] 420s tests/test_trajectory.py::test_read_write[ncrst-h5] XFAIL (These ref...) [ 69%] 420s tests/test_trajectory.py::test_read_write[ncrst-xtc] XFAIL (These re...) [ 69%] 420s tests/test_trajectory.py::test_read_write[ncrst-trr] XFAIL (These re...) [ 69%] 420s tests/test_trajectory.py::test_read_write[ncrst-dcd] XFAIL (These re...) [ 69%] 420s tests/test_trajectory.py::test_read_write[ncrst-mdcrd] XFAIL (These ...) [ 69%] 420s tests/test_trajectory.py::test_read_write[ncrst-dtr] XFAIL (These re...) [ 69%] 420s tests/test_trajectory.py::test_read_write[ncrst-xyz] XFAIL (These re...) [ 70%] 420s tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] XFAIL (These...) [ 70%] 420s tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] XFAIL (Th...) [ 70%] 420s tests/test_trajectory.py::test_read_write[ncrst-lh5] XFAIL (These re...) [ 70%] 420s tests/test_trajectory.py::test_read_write[ncrst-pdb] XFAIL (These re...) [ 70%] 420s tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] XFAIL (These...) [ 70%] 420s tests/test_trajectory.py::test_read_write[ncrst-ncrst] XFAIL (These ...) [ 70%] 420s tests/test_trajectory.py::test_read_write[ncrst-rst7] XFAIL (These r...) [ 70%] 420s tests/test_trajectory.py::test_read_write[ncrst-gro] XFAIL (These re...) [ 70%] 420s tests/test_trajectory.py::test_read_write[rst7-nc] XFAIL (These refe...) [ 70%] 420s tests/test_trajectory.py::test_read_write[rst7-h5] XFAIL (These refe...) [ 70%] 420s tests/test_trajectory.py::test_read_write[rst7-xtc] XFAIL (These ref...) [ 71%] 420s tests/test_trajectory.py::test_read_write[rst7-trr] XFAIL (These ref...) [ 71%] 420s tests/test_trajectory.py::test_read_write[rst7-dcd] XFAIL (These ref...) [ 71%] 420s tests/test_trajectory.py::test_read_write[rst7-mdcrd] XFAIL (These r...) [ 71%] 420s tests/test_trajectory.py::test_read_write[rst7-dtr] XFAIL (These ref...) [ 71%] 420s tests/test_trajectory.py::test_read_write[rst7-xyz] XFAIL (These ref...) [ 71%] 420s tests/test_trajectory.py::test_read_write[rst7-xyz.gz] XFAIL (These ...) [ 71%] 420s tests/test_trajectory.py::test_read_write[rst7-lammpstrj] XFAIL (The...) [ 71%] 420s tests/test_trajectory.py::test_read_write[rst7-lh5] XFAIL (These ref...) [ 71%] 420s tests/test_trajectory.py::test_read_write[rst7-pdb] XFAIL (These ref...) [ 71%] 421s tests/test_trajectory.py::test_read_write[rst7-pdb.gz] XFAIL (These ...) [ 71%] 421s tests/test_trajectory.py::test_read_write[rst7-ncrst] XFAIL (These r...) [ 72%] 421s tests/test_trajectory.py::test_read_write[rst7-rst7] XFAIL (These re...) [ 72%] 421s tests/test_trajectory.py::test_read_write[rst7-gro] XFAIL (These ref...) [ 72%] 421s tests/test_trajectory.py::test_read_write[gro-nc] PASSED [ 72%] 421s tests/test_trajectory.py::test_read_write[gro-h5] PASSED [ 72%] 421s tests/test_trajectory.py::test_read_write[gro-xtc] PASSED [ 72%] 421s tests/test_trajectory.py::test_read_write[gro-trr] PASSED [ 72%] 421s tests/test_trajectory.py::test_read_write[gro-dcd] PASSED [ 72%] 421s tests/test_trajectory.py::test_read_write[gro-mdcrd] SKIPPED (mdcrd ...) [ 72%] 423s tests/test_trajectory.py::test_read_write[gro-dtr] PASSED [ 72%] 423s tests/test_trajectory.py::test_read_write[gro-xyz] PASSED [ 72%] 423s tests/test_trajectory.py::test_read_write[gro-xyz.gz] PASSED [ 72%] 423s tests/test_trajectory.py::test_read_write[gro-lammpstrj] PASSED [ 73%] 423s tests/test_trajectory.py::test_read_write[gro-lh5] PASSED [ 73%] 424s tests/test_trajectory.py::test_read_write[gro-pdb] PASSED [ 73%] 424s tests/test_trajectory.py::test_read_write[gro-pdb.gz] PASSED [ 73%] 424s tests/test_trajectory.py::test_read_write[gro-ncrst] SKIPPED (ncrst ...) [ 73%] 424s tests/test_trajectory.py::test_read_write[gro-rst7] SKIPPED (rst7 ca...) [ 73%] 424s tests/test_trajectory.py::test_read_write[gro-gro] PASSED [ 73%] 424s tests/test_trajectory.py::test_load[nc] PASSED [ 73%] 424s tests/test_trajectory.py::test_load[h5] PASSED [ 73%] 424s tests/test_trajectory.py::test_load[xtc] PASSED [ 73%] 424s tests/test_trajectory.py::test_load[trr] PASSED [ 73%] 424s tests/test_trajectory.py::test_load[dcd] PASSED [ 74%] 425s tests/test_trajectory.py::test_load[mdcrd] PASSED [ 74%] 425s tests/test_trajectory.py::test_load[dtr] PASSED [ 74%] 425s tests/test_trajectory.py::test_load[xyz] PASSED [ 74%] 425s tests/test_trajectory.py::test_load[xyz.gz] PASSED [ 74%] 425s tests/test_trajectory.py::test_load[lammpstrj] PASSED [ 74%] 425s tests/test_trajectory.py::test_load[lh5] PASSED [ 74%] 426s tests/test_trajectory.py::test_load[pdb] PASSED [ 74%] 428s tests/test_trajectory.py::test_load[pdb.gz] PASSED [ 74%] 428s tests/test_trajectory.py::test_load[ncrst] XFAIL (These reference fi...) [ 74%] 428s tests/test_trajectory.py::test_load[rst7] XFAIL (These reference fil...) [ 74%] 428s tests/test_trajectory.py::test_load[gro] PASSED [ 75%] 428s tests/test_trajectory.py::test_hdf5 PASSED [ 75%] 428s tests/test_trajectory.py::test_center PASSED [ 75%] 428s tests/test_trajectory.py::test_center_aind PASSED [ 75%] 428s tests/test_trajectory.py::test_float_atom_indices_exception[nc] PASSED [ 75%] 428s tests/test_trajectory.py::test_float_atom_indices_exception[h5] PASSED [ 75%] 428s tests/test_trajectory.py::test_float_atom_indices_exception[xtc] PASSED [ 75%] 428s tests/test_trajectory.py::test_float_atom_indices_exception[trr] PASSED [ 75%] 428s tests/test_trajectory.py::test_float_atom_indices_exception[dcd] PASSED [ 75%] 428s tests/test_trajectory.py::test_float_atom_indices_exception[mdcrd] PASSED [ 75%] 428s tests/test_trajectory.py::test_float_atom_indices_exception[dtr] PASSED [ 75%] 428s tests/test_trajectory.py::test_float_atom_indices_exception[xyz] PASSED [ 75%] 428s tests/test_trajectory.py::test_float_atom_indices_exception[xyz.gz] PASSED [ 76%] 428s tests/test_trajectory.py::test_float_atom_indices_exception[lammpstrj] PASSED [ 76%] 428s tests/test_trajectory.py::test_float_atom_indices_exception[lh5] PASSED [ 76%] 428s tests/test_trajectory.py::test_float_atom_indices_exception[pdb] PASSED [ 76%] 428s tests/test_trajectory.py::test_float_atom_indices_exception[pdb.gz] PASSED [ 76%] 428s tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] XFAIL [ 76%] 428s tests/test_trajectory.py::test_float_atom_indices_exception[rst7] XFAIL [ 76%] 428s tests/test_trajectory.py::test_float_atom_indices_exception[gro] PASSED [ 76%] 428s tests/test_trajectory.py::test_restrict_atoms PASSED [ 76%] 428s tests/test_trajectory.py::test_restrict_atoms_not_inplace PASSED [ 76%] 428s tests/test_trajectory.py::test_array_vs_matrix PASSED [ 76%] 428s tests/test_trajectory.py::test_pdb_unitcell_loadsave PASSED [ 77%] 428s tests/test_trajectory.py::test_load_combination[nc] PASSED [ 77%] 428s tests/test_trajectory.py::test_load_combination[h5] PASSED [ 77%] 428s tests/test_trajectory.py::test_load_combination[xtc] PASSED [ 77%] 428s tests/test_trajectory.py::test_load_combination[trr] PASSED [ 77%] 428s tests/test_trajectory.py::test_load_combination[dcd] PASSED [ 77%] 429s tests/test_trajectory.py::test_load_combination[mdcrd] PASSED [ 77%] 429s tests/test_trajectory.py::test_load_combination[dtr] PASSED [ 77%] 429s tests/test_trajectory.py::test_load_combination[xyz] PASSED [ 77%] 429s tests/test_trajectory.py::test_load_combination[xyz.gz] PASSED [ 77%] 429s tests/test_trajectory.py::test_load_combination[lammpstrj] PASSED [ 77%] 429s tests/test_trajectory.py::test_load_combination[lh5] PASSED [ 78%] 429s tests/test_trajectory.py::test_load_combination[pdb] PASSED [ 78%] 430s tests/test_trajectory.py::test_load_combination[pdb.gz] PASSED [ 78%] 430s tests/test_trajectory.py::test_load_combination[ncrst] XFAIL (These ...) [ 78%] 430s tests/test_trajectory.py::test_load_combination[rst7] XFAIL (These r...) [ 78%] 430s tests/test_trajectory.py::test_load_combination[gro] PASSED [ 78%] 430s tests/test_trajectory.py::test_no_topology PASSED [ 78%] 430s tests/test_trajectory.py::test_join PASSED [ 78%] 430s tests/test_trajectory.py::test_md_join PASSED [ 78%] 430s tests/test_trajectory.py::test_stack_1 PASSED [ 78%] 430s tests/test_trajectory.py::test_stack_2 PASSED [ 78%] 430s tests/test_trajectory.py::test_seek_read_mode[nc] PASSED [ 78%] 430s tests/test_trajectory.py::test_seek_read_mode[h5] PASSED [ 79%] 430s tests/test_trajectory.py::test_seek_read_mode[xtc] PASSED [ 79%] 430s tests/test_trajectory.py::test_seek_read_mode[trr] PASSED [ 79%] 430s tests/test_trajectory.py::test_seek_read_mode[dcd] PASSED [ 79%] 430s tests/test_trajectory.py::test_seek_read_mode[mdcrd] PASSED [ 79%] 430s tests/test_trajectory.py::test_seek_read_mode[dtr] PASSED [ 79%] 430s tests/test_trajectory.py::test_seek_read_mode[xyz] PASSED [ 79%] 430s tests/test_trajectory.py::test_seek_read_mode[xyz.gz] XFAIL (This is...) [ 79%] 431s tests/test_trajectory.py::test_seek_read_mode[lammpstrj] PASSED [ 79%] 431s tests/test_trajectory.py::test_seek_read_mode[lh5] PASSED [ 79%] 431s tests/test_trajectory.py::test_seek_read_mode[pdb] XFAIL (PDB Files ...) [ 79%] 431s tests/test_trajectory.py::test_seek_read_mode[pdb.gz] XFAIL (PDB Fil...) [ 80%] 431s tests/test_trajectory.py::test_seek_read_mode[ncrst] XFAIL (These re...) [ 80%] 431s tests/test_trajectory.py::test_seek_read_mode[rst7] XFAIL (These ref...) [ 80%] 431s tests/test_trajectory.py::test_seek_read_mode[gro] XFAIL (This is br...) [ 80%] 431s tests/test_trajectory.py::test_load_frame[nc] PASSED [ 80%] 431s tests/test_trajectory.py::test_load_frame[h5] PASSED [ 80%] 431s tests/test_trajectory.py::test_load_frame[xtc] PASSED [ 80%] 431s tests/test_trajectory.py::test_load_frame[trr] PASSED [ 80%] 431s tests/test_trajectory.py::test_load_frame[dcd] PASSED [ 80%] 431s tests/test_trajectory.py::test_load_frame[mdcrd] PASSED [ 80%] 431s tests/test_trajectory.py::test_load_frame[dtr] XFAIL (DTR doesn't lo...) [ 80%] 431s tests/test_trajectory.py::test_load_frame[xyz] PASSED [ 81%] 431s tests/test_trajectory.py::test_load_frame[xyz.gz] PASSED [ 81%] 431s tests/test_trajectory.py::test_load_frame[lammpstrj] PASSED [ 81%] 431s tests/test_trajectory.py::test_load_frame[lh5] PASSED [ 81%] 431s tests/test_trajectory.py::test_load_frame[pdb] PASSED [ 81%] 432s tests/test_trajectory.py::test_load_frame[pdb.gz] PASSED [ 81%] 432s tests/test_trajectory.py::test_load_frame[ncrst] XFAIL (These refere...) [ 81%] 432s tests/test_trajectory.py::test_load_frame[rst7] XFAIL (These referen...) [ 81%] 432s tests/test_trajectory.py::test_load_frame[gro] XFAIL (Gro doesn't im...) [ 81%] 432s tests/test_trajectory.py::test_load_frame_2eqq PASSED [ 81%] 432s tests/test_trajectory.py::test_iterload[nc] PASSED [ 81%] 432s tests/test_trajectory.py::test_iterload[h5] PASSED [ 81%] 432s tests/test_trajectory.py::test_iterload[xtc] PASSED [ 82%] 432s tests/test_trajectory.py::test_iterload[trr] PASSED [ 82%] 432s tests/test_trajectory.py::test_iterload[dcd] PASSED [ 82%] 432s tests/test_trajectory.py::test_iterload[mdcrd] PASSED [ 82%] 432s tests/test_trajectory.py::test_iterload[dtr] XFAIL (This is broken w...) [ 82%] 432s tests/test_trajectory.py::test_iterload[xyz] PASSED [ 82%] 432s tests/test_trajectory.py::test_iterload[xyz.gz] PASSED [ 82%] 432s tests/test_trajectory.py::test_iterload[lammpstrj] PASSED [ 82%] 433s tests/test_trajectory.py::test_iterload[lh5] PASSED [ 82%] 433s tests/test_trajectory.py::test_iterload[pdb] PASSED [ 82%] 433s tests/test_trajectory.py::test_iterload[pdb.gz] PASSED [ 82%] 433s tests/test_trajectory.py::test_iterload[ncrst] SKIPPED (Only 1 frame...) [ 83%] 433s tests/test_trajectory.py::test_iterload[rst7] SKIPPED (Only 1 frame ...) [ 83%] 433s tests/test_trajectory.py::test_iterload[gro] PASSED [ 83%] 436s tests/test_trajectory.py::test_iterload_skip[nc] PASSED [ 83%] 439s tests/test_trajectory.py::test_iterload_skip[h5] PASSED [ 83%] 440s tests/test_trajectory.py::test_iterload_skip[xtc] PASSED [ 83%] 441s tests/test_trajectory.py::test_iterload_skip[trr] PASSED [ 83%] 442s tests/test_trajectory.py::test_iterload_skip[dcd] PASSED [ 83%] 444s tests/test_trajectory.py::test_iterload_skip[mdcrd] PASSED [ 83%] 444s tests/test_trajectory.py::test_iterload_skip[dtr] PASSED [ 83%] 445s tests/test_trajectory.py::test_iterload_skip[xyz] PASSED [ 83%] 447s tests/test_trajectory.py::test_iterload_skip[xyz.gz] PASSED [ 84%] 448s tests/test_trajectory.py::test_iterload_skip[lammpstrj] PASSED [ 84%] 450s tests/test_trajectory.py::test_iterload_skip[lh5] PASSED [ 84%] 450s tests/test_trajectory.py::test_iterload_skip[pdb] XFAIL (PDB Iterloa...) [ 84%] 450s tests/test_trajectory.py::test_iterload_skip[pdb.gz] XFAIL (PDB Iter...) [ 84%] 450s tests/test_trajectory.py::test_iterload_skip[ncrst] XFAIL (These ref...) [ 84%] 450s tests/test_trajectory.py::test_iterload_skip[rst7] XFAIL (These refe...) [ 84%] 450s tests/test_trajectory.py::test_iterload_skip[gro] XFAIL (Not impleme...) [ 84%] 450s tests/test_trajectory.py::test_iterload_chunk_dcd PASSED [ 84%] 450s tests/test_trajectory.py::test_save_load[nc] PASSED [ 84%] 450s tests/test_trajectory.py::test_save_load[h5] PASSED [ 84%] 450s tests/test_trajectory.py::test_save_load[xtc] PASSED [ 84%] 450s tests/test_trajectory.py::test_save_load[trr] PASSED [ 85%] 450s tests/test_trajectory.py::test_save_load[dcd] PASSED [ 85%] 450s tests/test_trajectory.py::test_save_load[mdcrd] PASSED [ 85%] 450s tests/test_trajectory.py::test_save_load[dtr] PASSED [ 85%] 450s tests/test_trajectory.py::test_save_load[xyz] PASSED [ 85%] 450s tests/test_trajectory.py::test_save_load[xyz.gz] PASSED [ 85%] 450s tests/test_trajectory.py::test_save_load[lammpstrj] PASSED [ 85%] 450s tests/test_trajectory.py::test_save_load[lh5] PASSED [ 85%] 450s tests/test_trajectory.py::test_save_load[pdb] PASSED [ 85%] 450s tests/test_trajectory.py::test_save_load[pdb.gz] PASSED [ 85%] 450s tests/test_trajectory.py::test_save_load[ncrst] PASSED [ 85%] 450s tests/test_trajectory.py::test_save_load[rst7] PASSED [ 86%] 450s tests/test_trajectory.py::test_save_load[gro] PASSED [ 86%] 450s tests/test_trajectory.py::test_force_overwrite[nc] PASSED [ 86%] 450s tests/test_trajectory.py::test_force_overwrite[h5] PASSED [ 86%] 450s tests/test_trajectory.py::test_force_overwrite[xtc] PASSED [ 86%] 450s tests/test_trajectory.py::test_force_overwrite[trr] PASSED [ 86%] 450s tests/test_trajectory.py::test_force_overwrite[dcd] PASSED [ 86%] 450s tests/test_trajectory.py::test_force_overwrite[mdcrd] PASSED [ 86%] 450s tests/test_trajectory.py::test_force_overwrite[dtr] XFAIL (This is b...) [ 86%] 450s tests/test_trajectory.py::test_force_overwrite[xyz] PASSED [ 86%] 450s tests/test_trajectory.py::test_force_overwrite[xyz.gz] PASSED [ 86%] 450s tests/test_trajectory.py::test_force_overwrite[lammpstrj] PASSED [ 87%] 450s tests/test_trajectory.py::test_force_overwrite[lh5] PASSED [ 87%] 450s tests/test_trajectory.py::test_force_overwrite[pdb] PASSED [ 87%] 450s tests/test_trajectory.py::test_force_overwrite[pdb.gz] PASSED [ 87%] 450s tests/test_trajectory.py::test_force_overwrite[ncrst] PASSED [ 87%] 450s tests/test_trajectory.py::test_force_overwrite[rst7] PASSED [ 87%] 450s tests/test_trajectory.py::test_force_overwrite[gro] PASSED [ 87%] 450s tests/test_trajectory.py::test_force_noverwrite[nc] PASSED [ 87%] 450s tests/test_trajectory.py::test_force_noverwrite[h5] PASSED [ 87%] 450s tests/test_trajectory.py::test_force_noverwrite[xtc] PASSED [ 87%] 450s tests/test_trajectory.py::test_force_noverwrite[trr] PASSED [ 87%] 450s tests/test_trajectory.py::test_force_noverwrite[dcd] PASSED [ 87%] 450s tests/test_trajectory.py::test_force_noverwrite[mdcrd] PASSED [ 88%] 450s tests/test_trajectory.py::test_force_noverwrite[dtr] PASSED [ 88%] 450s tests/test_trajectory.py::test_force_noverwrite[xyz] PASSED [ 88%] 450s tests/test_trajectory.py::test_force_noverwrite[xyz.gz] PASSED [ 88%] 450s tests/test_trajectory.py::test_force_noverwrite[lammpstrj] PASSED [ 88%] 450s tests/test_trajectory.py::test_force_noverwrite[lh5] PASSED [ 88%] 450s tests/test_trajectory.py::test_force_noverwrite[pdb] PASSED [ 88%] 450s tests/test_trajectory.py::test_force_noverwrite[pdb.gz] PASSED [ 88%] 450s tests/test_trajectory.py::test_force_noverwrite[ncrst] PASSED [ 88%] 450s tests/test_trajectory.py::test_force_noverwrite[rst7] PASSED [ 88%] 451s tests/test_trajectory.py::test_force_noverwrite[gro] PASSED [ 88%] 451s tests/test_trajectory.py::test_open_and_load PASSED [ 89%] 451s tests/test_trajectory.py::test_length PASSED [ 89%] 451s tests/test_trajectory.py::test_unitcell[nc] PASSED [ 89%] 451s tests/test_trajectory.py::test_unitcell[h5] PASSED [ 89%] 451s tests/test_trajectory.py::test_unitcell[xtc] PASSED [ 89%] 451s tests/test_trajectory.py::test_unitcell[trr] PASSED [ 89%] 451s tests/test_trajectory.py::test_unitcell[dcd] PASSED [ 89%] 451s tests/test_trajectory.py::test_unitcell[mdcrd] PASSED [ 89%] 451s tests/test_trajectory.py::test_unitcell[dtr] XFAIL (dtr seems to nee...) [ 89%] 451s tests/test_trajectory.py::test_unitcell[xyz] PASSED [ 89%] 451s tests/test_trajectory.py::test_unitcell[xyz.gz] PASSED [ 89%] 451s tests/test_trajectory.py::test_unitcell[lammpstrj] XFAIL (lammpstrj ...) [ 90%] 451s tests/test_trajectory.py::test_unitcell[lh5] PASSED [ 90%] 451s tests/test_trajectory.py::test_unitcell[pdb] PASSED [ 90%] 451s tests/test_trajectory.py::test_unitcell[pdb.gz] PASSED [ 90%] 451s tests/test_trajectory.py::test_unitcell[ncrst] XFAIL (ncrst seems to...) [ 90%] 451s tests/test_trajectory.py::test_unitcell[rst7] XFAIL (rst7 seems to n...) [ 90%] 451s tests/test_trajectory.py::test_unitcell[gro] PASSED [ 90%] 451s tests/test_trajectory.py::test_chunk0_iterload PASSED [ 90%] 451s tests/test_trajectory.py::test_hashing PASSED [ 90%] 452s tests/test_trajectory.py::test_smooth PASSED [ 90%] 452s tests/test_trajectory.py::test_load_pdb_no_standard_names PASSED [ 90%] 452s tests/test_trajectory.py::test_load_with_atom_indices PASSED [ 90%] 452s tests/test_trajectory.py::test_atom_slicing PASSED [ 91%] 452s tests/test_trajectory.py::test_load_with_frame PASSED [ 91%] 452s tests/test_trajectory.py::test_add_remove_atoms PASSED [ 91%] 452s tests/test_trr.py::test_1 PASSED [ 91%] 452s tests/test_trr.py::test_read_stride PASSED [ 91%] 452s tests/test_trr.py::test_read_stride_n_frames PASSED [ 91%] 452s tests/test_trr.py::test_read_stride_offsets PASSED [ 91%] 452s tests/test_trr.py::test_read_stride_n_frames_offsets PASSED [ 91%] 452s tests/test_trr.py::test_read_stride_switching PASSED [ 91%] 452s tests/test_trr.py::test_write_read PASSED [ 91%] 452s tests/test_trr.py::test_read_atomindices_1 PASSED [ 91%] 452s tests/test_trr.py::test_read_atomindices_2 PASSED [ 92%] 452s tests/test_trr.py::test_deficient_shape PASSED [ 92%] 452s tests/test_trr.py::test_ragged_1 PASSED [ 92%] 452s tests/test_trr.py::test_ragged_2 PASSED [ 92%] 452s tests/test_trr.py::test_malformed PASSED [ 92%] 452s tests/test_trr.py::test_tell PASSED [ 92%] 452s tests/test_trr.py::test_seek PASSED [ 92%] 452s tests/test_trr.py::test_get_velocities PASSED [ 92%] 452s tests/test_trr.py::test_get_forces PASSED [ 92%] 452s tests/test_trr.py::test_get_velocities_and_forces PASSED [ 92%] 452s tests/test_trr.py::test_get_velocities_forces_atom_indices_1 PASSED [ 92%] 452s tests/test_trr.py::test_get_velocities_forces_atom_indices_2 PASSED [ 93%] 452s tests/test_trr.py::test_read_velocities_do_not_exist PASSED [ 93%] 452s tests/test_trr.py::test_read_forces_do_not_exist PASSED [ 93%] 452s tests/test_utils.py::test_unitcell_0 PASSED [ 93%] 452s tests/test_utils.py::test_unitcell_1 PASSED [ 93%] 452s tests/test_utils.py::test_ensure_type_1 PASSED [ 93%] 452s tests/test_utils.py::test_ensure_type_2 PASSED [ 93%] 452s tests/test_utils.py::test_ensure_type_25 PASSED [ 93%] 452s tests/test_utils.py::test_ensure_type_3 PASSED [ 93%] 452s tests/test_utils.py::test_ensure_type_4 PASSED [ 93%] 452s tests/test_utils.py::test_ensure_type_5 PASSED [ 93%] 452s tests/test_utils.py::test_ensure_type_6 PASSED [ 93%] 452s tests/test_utils.py::test_ensure_type_7 PASSED [ 94%] 452s tests/test_utils.py::test_ensure_type_8 PASSED [ 94%] 452s tests/test_utils.py::test_ensure_type_9 PASSED [ 94%] 452s tests/test_utils.py::test_ensure_type_10 PASSED [ 94%] 452s tests/test_utils.py::test_ensure_type_11 PASSED [ 94%] 452s tests/test_utils.py::test_ensure_type_12 PASSED [ 94%] 452s tests/test_utils.py::test_ensure_type_13 PASSED [ 94%] 452s tests/test_utils.py::test_ensure_type_14 PASSED [ 94%] 452s tests/test_utils.py::test_ensure_type_15 PASSED [ 94%] 452s tests/test_utils.py::test_delay_import_fail_1 PASSED [ 94%] 452s tests/test_utils.py::test_delay_import PASSED [ 94%] 452s tests/test_utils.py::test_unit_0 PASSED [ 95%] 452s tests/test_utils.py::test_unit_1 PASSED [ 95%] 452s tests/test_utils.py::test_unit_2 PASSED [ 95%] 452s tests/test_utils.py::test_unit_3 PASSED [ 95%] 452s tests/test_xml.py::test_xml PASSED [ 95%] 452s tests/test_xtc.py::test_read_chunk1 PASSED [ 95%] 452s tests/test_xtc.py::test_read_stride PASSED [ 95%] 452s tests/test_xtc.py::test_read_stride_n_frames PASSED [ 95%] 452s tests/test_xtc.py::test_read_stride_offsets PASSED [ 95%] 452s tests/test_xtc.py::test_read_stride_n_frames_offsets PASSED [ 95%] 452s tests/test_xtc.py::test_read_stride_switching_offsets PASSED [ 95%] 452s tests/test_xtc.py::test_read_atomindices_1 PASSED [ 96%] 452s tests/test_xtc.py::test_read_atomindices_w_stride PASSED [ 96%] 452s tests/test_xtc.py::test_read_atomindices_2 PASSED [ 96%] 452s tests/test_xtc.py::test_read_chunk2 PASSED [ 96%] 452s tests/test_xtc.py::test_read_chunk3 PASSED [ 96%] 453s tests/test_xtc.py::test_write_0 PASSED [ 96%] 453s tests/test_xtc.py::test_write_1 PASSED [ 96%] 453s tests/test_xtc.py::test_write_2 PASSED [ 96%] 453s tests/test_xtc.py::test_read_error_0 PASSED [ 96%] 453s tests/test_xtc.py::test_write_error_0 PASSED [ 96%] 453s tests/test_xtc.py::test_read_error_1 PASSED [ 96%] 453s tests/test_xtc.py::test_read_error_2 PASSED [ 96%] 453s tests/test_xtc.py::test_xtc_write_wierd_0 PASSED [ 97%] 453s tests/test_xtc.py::test_tell PASSED [ 97%] 453s tests/test_xtc.py::test_seek PASSED [ 97%] 453s tests/test_xtc.py::test_seek_natoms9 PASSED [ 97%] 453s tests/test_xtc.py::test_seek_out_of_bounds PASSED [ 97%] 453s tests/test_xtc.py::test_ragged_1 PASSED [ 97%] 453s tests/test_xtc.py::test_ragged_2 PASSED [ 97%] 453s tests/test_xtc.py::test_short_traj PASSED [ 97%] 453s tests/test_xtc.py::test_flush PASSED [ 97%] 453s tests/test_xyz.py::test_read_0 PASSED [ 97%] 453s tests/test_xyz.py::test_read_1 PASSED [ 97%] 453s tests/test_xyz.py::test_read_gz PASSED [ 98%] 453s tests/test_xyz.py::test_read_write PASSED [ 98%] 453s tests/test_xyz.py::test_mdwrite PASSED [ 98%] 453s tests/test_xyz.py::test_multiread PASSED [ 98%] 453s tests/test_xyz.py::test_seek PASSED [ 98%] 453s tests/test_xyz.py::test_len PASSED [ 98%] 453s tests/test_zipped.py::test_read_gz PASSED [ 98%] 453s tests/test_zipped.py::test_write_gz PASSED [ 98%] 453s tests/test_zipped.py::test_read_bz2 PASSED [ 98%] 453s tests/test_zipped.py::test_write_bz2 PASSED [ 98%] 456s examples/test_examples.py::test_example_notebook[solvent-accessible-surface-area.ipynb] PASSED [ 98%] 458s examples/test_examples.py::test_example_notebook[two-pass-clustering.ipynb] PASSED [ 99%] 458s examples/test_examples.py::test_example_notebook[native-contact.ipynb] SKIPPED [ 99%] 461s examples/test_examples.py::test_example_notebook[principal-components.ipynb] PASSED [ 99%] 461s examples/test_examples.py::test_example_notebook[simulation-with-openmm.ipynb] SKIPPED [ 99%] 463s examples/test_examples.py::test_example_notebook[atom-selection.ipynb] PASSED [ 99%] 466s examples/test_examples.py::test_example_notebook[ramachandran-plot.ipynb] PASSED [ 99%] 468s examples/test_examples.py::test_example_notebook[rmsd-benchmark.ipynb] PASSED [ 99%] 470s examples/test_examples.py::test_example_notebook[iterload.ipynb] PASSED [ 99%] 472s examples/test_examples.py::test_example_notebook[clustering.ipynb] PASSED [ 99%] 474s examples/test_examples.py::test_example_notebook[centroids.ipynb] PASSED [ 99%] 474s examples/test_examples.py::test_example_notebook[hbonds.ipynb] SKIPPED [ 99%] 476s examples/test_examples.py::test_example_notebook[rmsd-drift.ipynb] PASSED [100%] 476s 476s =============================== warnings summary =============================== 476s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:56 476s /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. 476s THIS_ATOM = ast.Name(id="atom", ctx=ast.Load(), SINGLETON=True) 476s 476s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:57 476s /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. 476s RE_MODULE = ast.Name(id="re", ctx=ast.Load(), SINGLETON=True) 476s 476s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 476s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 476s given by the platformdirs library. To remove this warning and 476s see the appropriate new directories, set the environment variable 476s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 476s The use of platformdirs will be the default in `jupyter_core` v6 476s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 476s 476s examples/test_examples.py:26 476s /tmp/autopkgtest.1wtJrD/build.vF3/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 476s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 476s 476s tests/test_contact.py::test_contact_0 476s tests/test_contact.py::test_contact_4 476s /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. 476s warnings.warn( 476s 476s tests/test_contact.py::test_contact_3 476s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:271: RuntimeWarning: overflow encountered in exp 476s np.exp( 476s 476s tests/test_contact.py::test_contact_3 476s /tmp/autopkgtest.1wtJrD/build.vF3/src/tests/test_contact.py:115: RuntimeWarning: divide by zero encountered in scalar divide 476s beta / np.log(np.sum(np.exp(beta / maps[t, r0, r1]))), 476s 476s tests/test_dcd.py::test_do_overwrite 476s tests/test_dcd.py::test_ragged_1 476s tests/test_dcd.py::test_ragged_2 476s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting xyz dtype=float64 to 476s warnings.warn( 476s 476s tests/test_distance.py::test_6 476s :488: RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject 476s 476s tests/test_drid.py::test_drid_2 476s /tmp/autopkgtest.1wtJrD/build.vF3/src/tests/test_drid.py:62: RuntimeWarning: divide by zero encountered in divide 476s recip = 1 / squareform(pdist(t.xyz[i])) 476s 476s tests/test_dssp.py::test_1[1vii.pdb] 476s tests/test_gro.py::test_read_write 476s tests/test_gro.py::test_read_write_precision 476s tests/test_gro.py::test_load 476s tests/test_shape.py::test_principal_moments 476s tests/test_shape.py::test_asphericity 476s tests/test_shape.py::test_shape_metrics 476s /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. 476s warnings.warn( 476s 476s tests/test_geometry.py::test_dihedral_indices 476s tests/test_geometry.py::test_dihedral_indices 476s /usr/lib/python3/dist-packages/mdtraj/geometry/dihedral.py:237: DeprecationWarning: Passing a Trajectory object to _atom_sequence isdeprecated. Please pass a Topology object 476s warnings.warn( 476s 476s tests/test_gro.py::test_load 476s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq 476s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:364: UserWarning: WARNING: two consecutive residues with same number (GST, HST) 476s warnings.warn( 476s 476s tests/test_pdb.py::test_blank_indexing 476s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:204: UserWarning: Need to guess atom number starting from atom 100000. 476s warnings.warn(f'Need to guess atom number {num_str} starting from atom {pdbstructure._next_atom_number}.') 476s 476s tests/test_pdb.py::test_blank_indexing 476s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:271: UserWarning: Need to guess residue number string starting from residue10000, atom 100000. 476s warnings.warn(f'Need to guess residue number string {num_str} starting from residue{pdbstructure._next_residue_number}, atom {pdbstructure._next_atom_number}.') 476s 476s tests/test_rdf.py::test_rdf_norm 476s tests/test_rdf.py::test_rdf_t_norm[0] 476s tests/test_rdf.py::test_rdf_t_norm[2] 476s tests/test_rdf.py::test_rdf_t_norm[4] 476s tests/test_selection.py::test_re 476s tests/test_selection.py::test_re 476s tests/test_topology.py::test_select_pairs 476s tests/test_topology.py::test_select_pairs 476s /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. 476s left=ast.Call( 476s 476s tests/test_rdf.py::test_rdf_norm 476s tests/test_rdf.py::test_rdf_t_norm[0] 476s tests/test_rdf.py::test_rdf_t_norm[2] 476s tests/test_rdf.py::test_rdf_t_norm[4] 476s tests/test_selection.py::test_re 476s tests/test_selection.py::test_re 476s tests/test_topology.py::test_select_pairs 476s tests/test_topology.py::test_select_pairs 476s /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. 476s left=ast.Call( 476s 476s tests/test_trajectory.py::test_float_atom_indices_exception[gro] 476s tests/test_trajectory.py::test_atom_slicing 476s /usr/lib/python3/dist-packages/mdtraj/core/topology.py:84: UserWarning: atom_indices are not monotonically increasing 476s warnings.warn("atom_indices are not monotonically increasing") 476s 476s tests/test_utils.py::test_ensure_type_8 476s tests/test_utils.py::test_ensure_type_9 476s tests/test_utils.py::test_ensure_type_13 476s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=float64 to 476s warnings.warn( 476s 476s tests/test_utils.py::test_ensure_type_11 476s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=int64 to 476s warnings.warn( 476s 476s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 476s =========================== short test summary info ============================ 476s SKIPPED [1] tests/test_dihedral.py:56: pymol executable not found 476s SKIPPED [1] tests/test_dihedral.py:181: pymol executable not found 476s SKIPPED [16] tests/test_docstrings.py:38: Skip checking certain modules' docstrings 476s SKIPPED [1] tests/test_geometry.py:300: Not doing performance testing 476s SKIPPED [1] tests/test_geometry.py:322: Not doing performance testing 476s SKIPPED [1] tests/test_hdf5.py:104: requires openmm.units 476s SKIPPED [1] tests/test_hdf5.py:156: requires openmm.units 476s SKIPPED [1] tests/test_hdf5.py:223: requires openmm.units 476s SKIPPED [1] tests/test_mol2.py:59: Requires obabel 476s SKIPPED [1] tests/test_netcdf.py:271: This test requires cpptraj from AmberTools to be installed (http://ambermd.org) 476s SKIPPED [1] tests/test_nmr.py:11: SPARTA+ binary not found 476s SKIPPED [1] tests/test_nmr.py:26: PPM binary not found 476s SKIPPED [1] tests/test_nmr.py:42: SHIFTX2 binary not found or running on travis. 476s SKIPPED [1] tests/test_pdbx.py:43: test_pdbx.py needs OpenMM. 476s SKIPPED [2] tests/test_psf.py:93: This test requires the VMD executable: http://www.ks.uiuc.edu/Research/vmd/ 476s SKIPPED [1] tests/test_rdf.py:64: Binning does not match up with gromacs currently. 476s SKIPPED [1] tests/test_rdf.py:200: Binning does not match up with gromacs currently. 477s SKIPPED [1] tests/test_reporter.py:58: test_reporter.py needs OpenMM. 477s SKIPPED [1] tests/test_reporter.py:145: test_reporter.py needs OpenMM. 477s SKIPPED [1] tests/test_reporter.py:245: test_reporter.py needs OpenMM. 477s SKIPPED [1] tests/test_selection.py:267: failed to parse selection 477s SKIPPED [1] tests/test_thermodynamic_properties.py:161: Thermal expansion test doesn't work. 477s SKIPPED [1] tests/test_topology.py:45: needs OpenMM 477s SKIPPED [1] tests/test_topology.py:62: needs OpenMM 477s SKIPPED [1] tests/test_topology.py:72: needs OpenMM 477s SKIPPED [1] tests/test_topology.py:81: needs OpenMM 477s SKIPPED [1] tests/test_topology.py:91: needs OpenMM 477s SKIPPED [1] tests/test_topology.py:97: needs OpenMM 477s SKIPPED [1] tests/test_topology.py:247: needs OpenMM 477s SKIPPED [1] tests/test_trajectory.py:129: xyz does not store box information 477s SKIPPED [1] tests/test_trajectory.py:129: xyz.gz does not store box information 477s SKIPPED [1] tests/test_trajectory.py:129: lh5 does not store box information 477s SKIPPED [1] tests/test_trajectory.py:129: pdb does not store box information 477s SKIPPED [1] tests/test_trajectory.py:129: pdb.gz does not store box information 477s SKIPPED [1] tests/test_trajectory.py:226: mdcrd can only store rectilinear boxes 477s SKIPPED [1] tests/test_trajectory.py:224: ncrst can only store 1 frame per file 477s SKIPPED [1] tests/test_trajectory.py:224: rst7 can only store 1 frame per file 477s SKIPPED [14] tests/test_trajectory.py:248: mdcrd can only store rectilinear boxes 477s SKIPPED [14] tests/test_trajectory.py:246: ncrst can only store 1 frame per file 477s SKIPPED [14] tests/test_trajectory.py:246: rst7 can only store 1 frame per file 477s SKIPPED [4] tests/test_trajectory.py:256: dtr needs to write unitcells 477s SKIPPED [4] tests/test_trajectory.py:256: lammpstrj needs to write unitcells 477s SKIPPED [2] tests/test_trajectory.py:640: Only 1 frame per file format 477s SKIPPED [2] examples/test_examples.py:77: Network access required 477s SKIPPED [1] examples/test_examples.py:77: Openmm required for example notebook `simulation-with-openmm.ipynb` 477s XFAIL tests/test_trajectory.py::test_read_path[ncrst] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_path[rst7] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[ncrst-nc] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[ncrst-h5] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xtc] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[ncrst-trr] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dcd] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[ncrst-mdcrd] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dtr] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lh5] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[ncrst-ncrst] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[ncrst-rst7] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[ncrst-gro] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[rst7-nc] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[rst7-h5] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[rst7-xtc] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[rst7-trr] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[rst7-dcd] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[rst7-mdcrd] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[rst7-dtr] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz.gz] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[rst7-lammpstrj] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[rst7-lh5] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb.gz] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[rst7-ncrst] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[rst7-rst7] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_read_write[rst7-gro] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_load[ncrst] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_load[rst7] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[rst7] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_load_combination[ncrst] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_load_combination[rst7] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_seek_read_mode[xyz.gz] - This is broken 477s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb] - PDB Files don't support seeking 477s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb.gz] - PDB Files don't support seeking 477s XFAIL tests/test_trajectory.py::test_seek_read_mode[ncrst] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_seek_read_mode[rst7] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_seek_read_mode[gro] - This is broken 477s XFAIL tests/test_trajectory.py::test_load_frame[dtr] - DTR doesn't load a single frame properly 477s XFAIL tests/test_trajectory.py::test_load_frame[ncrst] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_load_frame[rst7] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_load_frame[gro] - Gro doesn't implement seek 477s XFAIL tests/test_trajectory.py::test_iterload[dtr] - This is broken with dtr 477s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb] - PDB Iterloads an extra frame!! 477s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb.gz] - PDB Iterloads an extra frame!! 477s XFAIL tests/test_trajectory.py::test_iterload_skip[ncrst] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_iterload_skip[rst7] - These reference files don't exist yet 477s XFAIL tests/test_trajectory.py::test_iterload_skip[gro] - Not implemented for some reason 477s XFAIL tests/test_trajectory.py::test_force_overwrite[dtr] - This is broken with dtr 477s XFAIL tests/test_trajectory.py::test_unitcell[dtr] - dtr seems to need unit vectors 477s XFAIL tests/test_trajectory.py::test_unitcell[lammpstrj] - lammpstrj seems to need unit vectors 477s XFAIL tests/test_trajectory.py::test_unitcell[ncrst] - ncrst seems to need unit vectors 477s XFAIL tests/test_trajectory.py::test_unitcell[rst7] - rst7 seems to need unit vectors 477s = 964 passed, 108 skipped, 12 deselected, 61 xfailed, 48 warnings in 317.78s (0:05:17) = 478s autopkgtest [20:24:40]: test command1: -----------------------] 479s autopkgtest [20:24:41]: test command1: - - - - - - - - - - results - - - - - - - - - - 479s command1 PASS 479s autopkgtest [20:24:41]: test command2: preparing testbed 480s Reading package lists... 480s Building dependency tree... 480s Reading state information... 480s Solving dependencies... 480s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 481s autopkgtest [20:24:43]: test command2: pytest-3 -k 'test_3 or test_pdb_from_url or test_1vii_url_and_gz' 481s autopkgtest [20:24:43]: test command2: [----------------------- 482s ============================= test session starts ============================== 482s platform linux -- Python 3.13.7, pytest-8.4.2, pluggy-1.6.0 -- /usr/bin/python3 482s cachedir: .pytest_cache 482s rootdir: /tmp/autopkgtest.1wtJrD/build.vF3/src 482s configfile: pyproject.toml 482s testpaths: tests, examples 482s plugins: typeguard-4.4.2 483s collecting ... collected 1145 items / 1135 deselected / 10 selected 483s 483s tests/test_distance.py::test_3 PASSED [ 10%] 483s tests/test_distance.py::test_3p PASSED [ 20%] 486s tests/test_dssp.py::test_3[1GAI] PASSED [ 30%] 488s tests/test_dssp.py::test_3[6gsv] PASSED [ 40%] 490s tests/test_dssp.py::test_3[2AAC] PASSED [ 50%] 490s tests/test_nmr.py::test_3_scalar_couplings PASSED [ 60%] 494s tests/test_pdb.py::test_pdb_from_url PASSED [ 70%] 494s tests/test_pdb.py::test_3nch_conect PASSED [ 80%] 496s tests/test_pdb.py::test_3nch_serial_resSeq PASSED [ 90%] 500s tests/test_pdb.py::test_1vii_url_and_gz PASSED [100%] 500s 500s =============================== warnings summary =============================== 500s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:56 500s /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. 500s THIS_ATOM = ast.Name(id="atom", ctx=ast.Load(), SINGLETON=True) 500s 500s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:57 500s /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. 500s RE_MODULE = ast.Name(id="re", ctx=ast.Load(), SINGLETON=True) 500s 500s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 500s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 500s given by the platformdirs library. To remove this warning and 500s see the appropriate new directories, set the environment variable 500s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 500s The use of platformdirs will be the default in `jupyter_core` v6 500s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 500s 500s examples/test_examples.py:26 500s /tmp/autopkgtest.1wtJrD/build.vF3/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 500s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 500s 500s tests/test_pdb.py::test_1vii_url_and_gz 500s /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. 500s warnings.warn( 500s 500s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 500s =============== 10 passed, 1135 deselected, 5 warnings in 17.64s =============== 501s autopkgtest [20:25:03]: test command2: -----------------------] 502s command2 PASS 502s autopkgtest [20:25:04]: test command2: - - - - - - - - - - results - - - - - - - - - - 502s autopkgtest [20:25:04]: @@@@@@@@@@@@@@@@@@@@ summary 502s command1 PASS 502s command2 PASS