0s autopkgtest [12:58:08]: starting date and time: 2025-10-23 12:58:08+0000 0s autopkgtest [12:58:08]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [12:58:08]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.m23itw08/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-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-7.secgroup --name adt-resolute-amd64-mdtraj-20251023-125808-juju-7f2275-prod-proposed-migration-environment-20-ebffcc35-cb64-488e-a7ad-37ad32ae77a6 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-mdtraj-20251023-125808-juju-7f2275-prod-proposed-migration-environment-20-ebffcc35-cb64-488e-a7ad-37ad32ae77a6 from image adt/ubuntu-resolute-amd64-server-20251022.img (UUID e0b5cd61-c9ee-4e30-97a7-7c67c05c2ee7)... 110s autopkgtest [12:59:58]: testbed dpkg architecture: amd64 110s autopkgtest [12:59:58]: testbed apt version: 3.1.8ubuntu1 110s autopkgtest [12:59:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup 110s autopkgtest [12:59:58]: testbed release detected to be: None 111s autopkgtest [12:59:59]: updating testbed package index (apt update) 111s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 111s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 111s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 111s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 111s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [535 kB] 112s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [59.9 kB] 112s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 112s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.0 kB] 112s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [89.5 kB] 112s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [140 kB] 112s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3208 B] 113s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [28.0 kB] 113s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [128 kB] 113s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [350 kB] 113s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [6744 B] 113s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [3156 B] 113s Fetched 1447 kB in 2s (761 kB/s) 113s Reading package lists... 114s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 114s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 114s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 114s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 115s Reading package lists... 115s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s Calculating upgrade... 115s The following packages will be upgraded: 115s python3-pyparsing python3-yaml 115s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s Need to get 275 kB of archives. 115s After this operation, 272 kB of additional disk space will be used. 115s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-yaml amd64 6.0.2-2 [188 kB] 115s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pyparsing all 3.1.3-1 [87.0 kB] 115s dpkg-preconfigure: unable to re-open stdin: No such file or directory 115s Fetched 275 kB in 0s (0 B/s) 115s (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 ... 78458 files and directories currently installed.) 115s Preparing to unpack .../python3-yaml_6.0.2-2_amd64.deb ... 115s Unpacking python3-yaml (6.0.2-2) over (6.0.2-1build2) ... 116s Preparing to unpack .../python3-pyparsing_3.1.3-1_all.deb ... 116s Unpacking python3-pyparsing (3.1.3-1) over (3.1.2-1) ... 116s Setting up python3-yaml (6.0.2-2) ... 116s Setting up python3-pyparsing (3.1.3-1) ... 116s autopkgtest [13:00:04]: upgrading testbed (apt dist-upgrade and autopurge) 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s Calculating upgrade... 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s Solving dependencies... 117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s autopkgtest [13:00:07]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025 119s autopkgtest [13:00:07]: @@@@@@@@@@@@@@@@@@@@ apt-source mdtraj 177s Get:1 http://ftpmaster.internal/ubuntu resolute/universe mdtraj 1.10.3-2build1 (dsc) [2701 B] 177s Get:2 http://ftpmaster.internal/ubuntu resolute/universe mdtraj 1.10.3-2build1 (tar) [22.0 MB] 177s Get:3 http://ftpmaster.internal/ubuntu resolute/universe mdtraj 1.10.3-2build1 (diff) [297 kB] 177s gpgv: Signature made Tue Mar 4 15:08:42 2025 UTC 177s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 177s gpgv: Can't check signature: No public key 177s dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.10.3-2build1.dsc: no acceptable signature found 177s autopkgtest [13:01:05]: testing package mdtraj version 1.10.3-2build1 178s autopkgtest [13:01:06]: build not needed 181s autopkgtest [13:01:09]: test command1: preparing testbed 182s Reading package lists... 182s Building dependency tree... 182s Reading state information... 182s Solving dependencies... 182s The following NEW packages will be installed: 182s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx gdb 182s libaec0 libbabeltrace1 libblas3 libblosc1 libblosc2-4 libdeflate0 182s libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 182s libhdf5-310 libhdf5-hl-310 libimagequant0 libipt2 libjbig0 libjpeg-turbo8 182s libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblcms2-2 liblerc4 182s liblzo2-2 libnetcdf22 libnorm1t64 libopenjp2-7 libpgm-5.3-0t64 libqhull-r8.0 182s libraqm0 libsharpyuv0 libsnappy1v5 libsodium23 libsource-highlight-common 182s libsource-highlight4t64 libsz2 libtcl8.6 libtiff6 libtk8.6 libwebp7 182s libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 libzmq5 182s libzopfli1 python-matplotlib-data python-tables-data python3-asttokens 182s python3-brotli python3-cftime python3-comm python3-contourpy 182s python3-coverage python3-cpuinfo python3-cycler python3-dateutil 182s python3-debugpy python3-decorator python3-executing python3-fastjsonschema 182s python3-fonttools python3-fs python3-gsd python3-iniconfig python3-ipykernel 182s python3-ipython python3-jedi python3-joblib python3-jupyter-client 182s python3-jupyter-core python3-kiwisolver python3-lxml python3-lz4 182s python3-matplotlib python3-matplotlib-inline python3-mdtraj python3-mpmath 182s python3-nbformat python3-nest-asyncio python3-netcdf4 python3-networkx 182s python3-numexpr python3-numpy python3-numpy-dev python3-packaging 182s python3-pandas python3-pandas-lib python3-parso python3-pexpect python3-pil 182s python3-pil.imagetk python3-platformdirs python3-pluggy 182s python3-prompt-toolkit python3-psutil python3-ptyprocess python3-pure-eval 182s python3-pytest python3-pytz python3-scipy python3-sklearn 182s python3-sklearn-lib python3-stack-data python3-sympy python3-tables 182s python3-tables-lib python3-threadpoolctl python3-tk python3-tornado 182s python3-traitlets python3-typeshed python3-ufolib2 python3-unicodedata2 182s python3-wcwidth python3-zmq python3-zopfli python3.13-tk tk8.6-blt2.5 182s unicode-data x11-common 182s 0 upgraded, 129 newly installed, 0 to remove and 0 not upgraded. 182s Need to get 122 MB of archives. 182s After this operation, 591 MB of additional disk space will be used. 182s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 182s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-6build1 [263 kB] 182s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-5ubuntu1 [939 kB] 186s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-6build1 [2762 kB] 199s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 223s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1036 kB] 225s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 225s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 227s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB] 227s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB] 227s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 227s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 227s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 227s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 227s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 229s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [694 kB] 232s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 blt amd64 2.5.3+dfsg-8 [4824 B] 232s Get:18 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-lyx all 2.4.4-1 [171 kB] 232s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libbabeltrace1 amd64 1.5.11-4build3 [166 kB] 232s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libipt2 amd64 2.1.2-1 [58.9 kB] 232s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libsource-highlight-common all 3.1.9-4.3build1 [64.2 kB] 232s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libsource-highlight4t64 amd64 3.1.9-4.3build1 [258 kB] 232s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 gdb amd64 16.3-1ubuntu2 [4218 kB] 248s Get:24 http://ftpmaster.internal/ubuntu resolute/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 248s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libsnappy1v5 amd64 1.2.2-1 [30.9 kB] 248s Get:26 http://ftpmaster.internal/ubuntu resolute/universe amd64 libblosc1 amd64 1.21.5+ds-1build1 [36.2 kB] 248s Get:27 http://ftpmaster.internal/ubuntu resolute/universe amd64 libblosc2-4 amd64 2.17.1+ds-2 [173 kB] 248s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 248s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-5ubuntu1 [151 kB] 248s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 248s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.1.0-1 [535 kB] 251s Get:32 http://ftpmaster.internal/ubuntu resolute/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 251s Get:33 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhdf5-310 amd64 1.14.5+repack-3build1 [1411 kB] 254s Get:34 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhdf5-hl-310 amd64 1.14.5+repack-3build1 [59.8 kB] 254s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 254s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 254s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 254s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 254s Get:39 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 254s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 254s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 254s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 liblzo2-2 amd64 2.10-3build1 [57.5 kB] 254s Get:43 http://ftpmaster.internal/ubuntu resolute/universe amd64 libnetcdf22 amd64 1:4.9.3-1build1 [561 kB] 255s Get:44 http://ftpmaster.internal/ubuntu resolute/universe amd64 libnorm1t64 amd64 1.5.9+dfsg-3.1build2 [157 kB] 255s Get:45 http://ftpmaster.internal/ubuntu resolute/universe amd64 libpgm-5.3-0t64 amd64 5.3.128~dfsg-2.1build1 [167 kB] 255s Get:46 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 255s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libraqm0 amd64 0.10.3-1 [15.4 kB] 255s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 255s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libsodium23 amd64 1.0.18-1build3 [161 kB] 255s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 255s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 255s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 255s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 255s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 255s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libxslt1.1 amd64 1.1.43-0.1 [172 kB] 255s Get:56 http://ftpmaster.internal/ubuntu resolute/universe amd64 libzmq5 amd64 4.3.5-1build2 [260 kB] 255s Get:57 http://ftpmaster.internal/ubuntu resolute/universe amd64 libzopfli1 amd64 1.0.3-3 [141 kB] 255s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-matplotlib-data all 3.10.1+dfsg1-4 [2930 kB] 262s Get:59 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-tables-data all 3.10.2-3build1 [49.7 kB] 262s Get:60 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-asttokens all 3.0.0-2 [20.5 kB] 262s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-brotli amd64 1.1.0-2build6 [340 kB] 262s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cftime amd64 1.6.4-2build1 [337 kB] 262s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 262s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-comm all 0.2.1-1 [7016 B] 262s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-contourpy amd64 1.3.1-1build1 [218 kB] 262s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-coverage amd64 7.8.2+dfsg1-1 [157 kB] 262s Get:67 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cpuinfo all 9.0.0+git20221119-3 [21.7 kB] 262s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cycler all 0.12.1-2 [9850 B] 262s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-dateutil all 2.9.0-4 [80.3 kB] 262s Get:70 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-debugpy amd64 1.8.12+ds-1ubuntu1 [778 kB] 264s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-decorator all 5.2.1-2 [28.1 kB] 264s Get:72 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-executing all 2.2.0-0.2 [25.0 kB] 264s Get:73 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fastjsonschema all 2.21.1-1 [20.4 kB] 264s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-platformdirs all 4.3.7-1 [16.9 kB] 264s Get:75 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fs all 2.4.16-7 [90.8 kB] 264s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-lxml amd64 6.0.1-1build1 [2336 kB] 269s Get:77 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-lz4 amd64 4.4.4+dfsg-3 [27.5 kB] 269s Get:78 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-scipy amd64 1.15.3-1ubuntu1 [20.3 MB] 287s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 287s Get:80 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sympy all 1.13.3-5 [4229 kB] 291s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 291s Get:82 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-unicodedata2 amd64 16.0.0+ds-1build1 [400 kB] 291s Get:83 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-zopfli amd64 0.2.3.post1-1 [10.8 kB] 291s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 unicode-data all 16.0.0-1 [9513 kB] 297s Get:85 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fonttools amd64 4.57.0-2build1 [1731 kB] 297s Get:86 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-gsd amd64 4.0.0-1 [244 kB] 297s Get:87 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 297s Get:88 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-parso all 0.8.4-1 [67.6 kB] 297s Get:89 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-typeshed all 0.0~git20241223.ea91db2-3 [1554 kB] 298s Get:90 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-jedi all 0.19.1+ds1-1 [693 kB] 298s Get:91 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-matplotlib-inline all 0.1.7-1 [9186 B] 298s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 298s Get:93 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-prompt-toolkit all 3.0.51-2 [257 kB] 298s Get:94 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pure-eval all 0.2.3-1 [11.4 kB] 298s Get:95 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-stack-data all 0.6.3-1 [22.0 kB] 298s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-ptyprocess all 0.7.0-6 [14.8 kB] 298s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pexpect all 4.9-3 [48.1 kB] 299s Get:98 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ipython all 8.35.0-1 [575 kB] 299s Get:99 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-jupyter-core all 5.7.2-5 [28.1 kB] 299s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-psutil amd64 7.0.0-2ubuntu1 [188 kB] 299s Get:101 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-tornado amd64 6.5.2-3 [304 kB] 299s Get:102 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-zmq amd64 27.1.0-1 [234 kB] 299s Get:103 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-jupyter-client all 8.6.3-2 [78.5 kB] 299s Get:104 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-nest-asyncio all 1.5.4-1 [6256 B] 299s Get:105 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-packaging all 25.0-1 [52.8 kB] 299s Get:106 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ipykernel all 6.29.5-2 [82.7 kB] 299s Get:107 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-joblib all 1.4.2-4 [205 kB] 299s Get:108 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-kiwisolver amd64 1.4.7-3build2 [63.0 kB] 299s Get:109 http://ftpmaster.internal/ubuntu resolute/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [188 kB] 299s Get:110 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pil amd64 11.3.0-1ubuntu2 [504 kB] 299s Get:111 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-tk amd64 3.13.9-1 [108 kB] 299s Get:112 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-tk amd64 3.13.5-1 [9916 B] 299s Get:113 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pil.imagetk amd64 11.3.0-1ubuntu2 [9804 B] 299s Get:114 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-matplotlib amd64 3.10.1+dfsg1-4 [18.0 MB] 303s Get:115 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-netcdf4 amd64 1.7.2-1build4 [667 kB] 303s Get:116 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 305s Get:117 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pytz all 2025.2-4 [32.3 kB] 305s Get:118 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-9 [4949 kB] 305s Get:119 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas all 2.2.3+dfsg-9 [3112 kB] 306s Get:120 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-numexpr amd64 2.13.0-1 [139 kB] 306s Get:121 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-tables-lib amd64 3.10.2-3build1 [805 kB] 306s Get:122 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-tables all 3.10.2-3build1 [354 kB] 306s Get:123 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mdtraj amd64 1.10.3-2build1 [1126 kB] 306s Get:124 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-nbformat all 5.9.1-1 [41.2 kB] 306s Get:125 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pluggy all 1.6.0-1 [21.0 kB] 306s Get:126 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 python3-pytest all 8.4.2-1 [268 kB] 306s Get:127 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 306s Get:128 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-8 [4359 kB] 306s Get:129 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sklearn all 1.4.2+dfsg-8 [2258 kB] 307s Fetched 122 MB in 2min 5s (982 kB/s) 307s Selecting previously unselected package python3-numpy-dev:amd64. 307s (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 ... 78459 files and directories currently installed.) 307s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 307s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 307s Selecting previously unselected package libblas3:amd64. 307s Preparing to unpack .../001-libblas3_3.12.1-6build1_amd64.deb ... 307s Unpacking libblas3:amd64 (3.12.1-6build1) ... 307s Selecting previously unselected package libgfortran5:amd64. 307s Preparing to unpack .../002-libgfortran5_15.2.0-5ubuntu1_amd64.deb ... 307s Unpacking libgfortran5:amd64 (15.2.0-5ubuntu1) ... 307s Selecting previously unselected package liblapack3:amd64. 307s Preparing to unpack .../003-liblapack3_3.12.1-6build1_amd64.deb ... 307s Unpacking liblapack3:amd64 (3.12.1-6build1) ... 307s Selecting previously unselected package python3-numpy. 307s Preparing to unpack .../004-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 307s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 307s Selecting previously unselected package libtcl8.6:amd64. 307s Preparing to unpack .../005-libtcl8.6_8.6.17+dfsg-1_amd64.deb ... 307s Unpacking libtcl8.6:amd64 (8.6.17+dfsg-1) ... 307s Selecting previously unselected package fonts-dejavu-mono. 307s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ... 307s Unpacking fonts-dejavu-mono (2.37-8) ... 307s Selecting previously unselected package fonts-dejavu-core. 307s Preparing to unpack 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307s Unpacking x11-common (1:7.7+24ubuntu1) ... 307s Selecting previously unselected package libxss1:amd64. 307s Preparing to unpack .../013-libxss1_1%3a1.2.3-1build3_amd64.deb ... 307s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 307s Selecting previously unselected package libtk8.6:amd64. 307s Preparing to unpack .../014-libtk8.6_8.6.17-1_amd64.deb ... 307s Unpacking libtk8.6:amd64 (8.6.17-1) ... 307s Selecting previously unselected package tk8.6-blt2.5. 307s Preparing to unpack .../015-tk8.6-blt2.5_2.5.3+dfsg-8_amd64.deb ... 307s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 307s Selecting previously unselected package blt. 307s Preparing to unpack .../016-blt_2.5.3+dfsg-8_amd64.deb ... 307s Unpacking blt (2.5.3+dfsg-8) ... 307s Selecting previously unselected package fonts-lyx. 307s Preparing to unpack .../017-fonts-lyx_2.4.4-1_all.deb ... 307s Unpacking fonts-lyx (2.4.4-1) ... 307s Selecting previously unselected package libbabeltrace1:amd64. 307s Preparing to unpack .../018-libbabeltrace1_1.5.11-4build3_amd64.deb ... 307s Unpacking libbabeltrace1:amd64 (1.5.11-4build3) ... 307s Selecting previously unselected package libipt2. 307s Preparing to unpack .../019-libipt2_2.1.2-1_amd64.deb ... 307s Unpacking libipt2 (2.1.2-1) ... 307s Selecting previously unselected package libsource-highlight-common. 307s Preparing to unpack .../020-libsource-highlight-common_3.1.9-4.3build1_all.deb ... 307s Unpacking libsource-highlight-common (3.1.9-4.3build1) ... 307s Selecting previously unselected package libsource-highlight4t64:amd64. 307s Preparing to unpack .../021-libsource-highlight4t64_3.1.9-4.3build1_amd64.deb ... 307s Unpacking libsource-highlight4t64:amd64 (3.1.9-4.3build1) ... 307s Selecting previously unselected package gdb. 307s Preparing to unpack .../022-gdb_16.3-1ubuntu2_amd64.deb ... 307s Unpacking gdb (16.3-1ubuntu2) ... 307s Selecting previously unselected package libaec0:amd64. 307s Preparing to unpack .../023-libaec0_1.1.3-1_amd64.deb ... 307s Unpacking libaec0:amd64 (1.1.3-1) ... 307s Selecting previously unselected package libsnappy1v5:amd64. 307s Preparing to unpack .../024-libsnappy1v5_1.2.2-1_amd64.deb ... 307s Unpacking libsnappy1v5:amd64 (1.2.2-1) ... 307s Selecting previously unselected package libblosc1:amd64. 307s Preparing to unpack .../025-libblosc1_1.21.5+ds-1build1_amd64.deb ... 307s Unpacking libblosc1:amd64 (1.21.5+ds-1build1) ... 307s Selecting previously unselected package libblosc2-4:amd64. 307s Preparing to unpack .../026-libblosc2-4_2.17.1+ds-2_amd64.deb ... 307s Unpacking libblosc2-4:amd64 (2.17.1+ds-2) ... 307s Selecting previously unselected package libdeflate0:amd64. 307s Preparing to unpack .../027-libdeflate0_1.23-2_amd64.deb ... 307s Unpacking libdeflate0:amd64 (1.23-2) ... 307s Selecting previously unselected package libgomp1:amd64. 307s Preparing to unpack .../028-libgomp1_15.2.0-5ubuntu1_amd64.deb ... 307s Unpacking libgomp1:amd64 (15.2.0-5ubuntu1) ... 307s Selecting previously unselected package libgraphite2-3:amd64. 307s Preparing to unpack .../029-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 307s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 307s Selecting previously unselected package libharfbuzz0b:amd64. 307s Preparing to unpack .../030-libharfbuzz0b_12.1.0-1_amd64.deb ... 307s Unpacking libharfbuzz0b:amd64 (12.1.0-1) ... 307s Selecting previously unselected package libsz2:amd64. 307s Preparing to unpack .../031-libsz2_1.1.3-1_amd64.deb ... 307s Unpacking libsz2:amd64 (1.1.3-1) ... 307s Selecting previously unselected package libhdf5-310:amd64. 307s Preparing to unpack .../032-libhdf5-310_1.14.5+repack-3build1_amd64.deb ... 307s Unpacking libhdf5-310:amd64 (1.14.5+repack-3build1) ... 307s Selecting previously unselected package libhdf5-hl-310:amd64. 307s Preparing to unpack .../033-libhdf5-hl-310_1.14.5+repack-3build1_amd64.deb ... 307s Unpacking libhdf5-hl-310:amd64 (1.14.5+repack-3build1) ... 307s Selecting previously unselected package libimagequant0:amd64. 307s Preparing to unpack .../034-libimagequant0_2.18.0-1build1_amd64.deb ... 307s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 307s Selecting previously unselected package libjpeg-turbo8:amd64. 307s Preparing to unpack .../035-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 307s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 307s Selecting previously unselected package libjpeg8:amd64. 307s Preparing to unpack .../036-libjpeg8_8c-2ubuntu11_amd64.deb ... 307s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 307s Selecting previously unselected package libjs-jquery. 307s Preparing to unpack .../037-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 307s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 307s Selecting previously unselected package libjs-jquery-ui. 308s Preparing to unpack .../038-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 308s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 308s Selecting previously unselected package liblcms2-2:amd64. 308s Preparing to unpack .../039-liblcms2-2_2.16-2_amd64.deb ... 308s Unpacking liblcms2-2:amd64 (2.16-2) ... 308s Selecting previously unselected package liblerc4:amd64. 308s Preparing to unpack .../040-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 308s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 308s Selecting previously unselected package liblzo2-2:amd64. 308s Preparing to unpack .../041-liblzo2-2_2.10-3build1_amd64.deb ... 308s Unpacking liblzo2-2:amd64 (2.10-3build1) ... 308s Selecting previously unselected package libnetcdf22:amd64. 308s Preparing to unpack .../042-libnetcdf22_1%3a4.9.3-1build1_amd64.deb ... 308s Unpacking libnetcdf22:amd64 (1:4.9.3-1build1) ... 308s Selecting previously unselected package libnorm1t64:amd64. 308s Preparing to unpack .../043-libnorm1t64_1.5.9+dfsg-3.1build2_amd64.deb ... 308s Unpacking libnorm1t64:amd64 (1.5.9+dfsg-3.1build2) ... 308s Selecting previously unselected package libpgm-5.3-0t64:amd64. 308s Preparing to unpack .../044-libpgm-5.3-0t64_5.3.128~dfsg-2.1build1_amd64.deb ... 308s Unpacking libpgm-5.3-0t64:amd64 (5.3.128~dfsg-2.1build1) ... 308s Selecting previously unselected package libqhull-r8.0:amd64. 308s Preparing to unpack .../045-libqhull-r8.0_2020.2-6build1_amd64.deb ... 308s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 308s Selecting previously unselected package libraqm0:amd64. 308s Preparing to unpack .../046-libraqm0_0.10.3-1_amd64.deb ... 308s Unpacking libraqm0:amd64 (0.10.3-1) ... 308s Selecting previously unselected package libsharpyuv0:amd64. 308s Preparing to unpack .../047-libsharpyuv0_1.5.0-0.1_amd64.deb ... 308s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 308s Selecting previously unselected package libsodium23:amd64. 308s Preparing to unpack .../048-libsodium23_1.0.18-1build3_amd64.deb ... 308s Unpacking libsodium23:amd64 (1.0.18-1build3) ... 308s Selecting previously unselected package libjbig0:amd64. 308s Preparing to unpack .../049-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 308s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 308s Selecting previously unselected package libwebp7:amd64. 308s Preparing to unpack .../050-libwebp7_1.5.0-0.1_amd64.deb ... 308s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 308s Selecting previously unselected package libtiff6:amd64. 308s Preparing to unpack .../051-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 308s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 308s Selecting previously unselected package libwebpdemux2:amd64. 308s Preparing to unpack .../052-libwebpdemux2_1.5.0-0.1_amd64.deb ... 308s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 308s Selecting previously unselected package libwebpmux3:amd64. 308s Preparing to unpack .../053-libwebpmux3_1.5.0-0.1_amd64.deb ... 308s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 308s Selecting previously unselected package libxslt1.1:amd64. 308s Preparing to unpack .../054-libxslt1.1_1.1.43-0.1_amd64.deb ... 308s Unpacking libxslt1.1:amd64 (1.1.43-0.1) ... 308s Selecting previously unselected package libzmq5:amd64. 308s Preparing to unpack .../055-libzmq5_4.3.5-1build2_amd64.deb ... 308s Unpacking libzmq5:amd64 (4.3.5-1build2) ... 308s Selecting previously unselected package libzopfli1. 308s Preparing to unpack .../056-libzopfli1_1.0.3-3_amd64.deb ... 308s Unpacking libzopfli1 (1.0.3-3) ... 308s Selecting previously unselected package python-matplotlib-data. 308s Preparing to unpack .../057-python-matplotlib-data_3.10.1+dfsg1-4_all.deb ... 308s Unpacking python-matplotlib-data (3.10.1+dfsg1-4) ... 308s Selecting previously unselected package python-tables-data. 308s Preparing to unpack .../058-python-tables-data_3.10.2-3build1_all.deb ... 308s Unpacking python-tables-data (3.10.2-3build1) ... 308s Selecting previously unselected package python3-asttokens. 308s Preparing to unpack .../059-python3-asttokens_3.0.0-2_all.deb ... 308s Unpacking python3-asttokens (3.0.0-2) ... 308s Selecting previously unselected package python3-brotli. 308s Preparing to unpack .../060-python3-brotli_1.1.0-2build6_amd64.deb ... 308s Unpacking python3-brotli (1.1.0-2build6) ... 308s Selecting previously unselected package python3-cftime. 308s Preparing to unpack .../061-python3-cftime_1.6.4-2build1_amd64.deb ... 308s Unpacking python3-cftime (1.6.4-2build1) ... 308s Selecting previously unselected package python3-traitlets. 308s Preparing to unpack .../062-python3-traitlets_5.14.3+really5.14.3-1_all.deb ... 308s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ... 308s Selecting previously unselected package python3-comm. 308s Preparing to unpack .../063-python3-comm_0.2.1-1_all.deb ... 308s Unpacking python3-comm (0.2.1-1) ... 308s Selecting previously unselected package python3-contourpy. 308s Preparing to unpack .../064-python3-contourpy_1.3.1-1build1_amd64.deb ... 308s Unpacking python3-contourpy (1.3.1-1build1) ... 308s Selecting previously unselected package python3-coverage. 308s Preparing to unpack .../065-python3-coverage_7.8.2+dfsg1-1_amd64.deb ... 308s Unpacking python3-coverage (7.8.2+dfsg1-1) ... 308s Selecting previously unselected package python3-cpuinfo. 308s Preparing to unpack .../066-python3-cpuinfo_9.0.0+git20221119-3_all.deb ... 308s Unpacking python3-cpuinfo (9.0.0+git20221119-3) ... 308s Selecting previously unselected package python3-cycler. 308s Preparing to unpack .../067-python3-cycler_0.12.1-2_all.deb ... 308s Unpacking python3-cycler (0.12.1-2) ... 308s Selecting previously unselected package python3-dateutil. 308s Preparing to unpack .../068-python3-dateutil_2.9.0-4_all.deb ... 308s Unpacking python3-dateutil (2.9.0-4) ... 308s Selecting previously unselected package python3-debugpy. 308s Preparing to unpack .../069-python3-debugpy_1.8.12+ds-1ubuntu1_amd64.deb ... 308s Unpacking python3-debugpy (1.8.12+ds-1ubuntu1) ... 308s Selecting previously unselected package python3-decorator. 308s Preparing to unpack .../070-python3-decorator_5.2.1-2_all.deb ... 308s Unpacking python3-decorator (5.2.1-2) ... 308s Selecting previously unselected package python3-executing. 308s Preparing to unpack .../071-python3-executing_2.2.0-0.2_all.deb ... 308s Unpacking python3-executing (2.2.0-0.2) ... 308s Selecting previously unselected package python3-fastjsonschema. 308s Preparing to unpack .../072-python3-fastjsonschema_2.21.1-1_all.deb ... 308s Unpacking python3-fastjsonschema (2.21.1-1) ... 308s Selecting previously unselected package python3-platformdirs. 308s Preparing to unpack .../073-python3-platformdirs_4.3.7-1_all.deb ... 308s Unpacking python3-platformdirs (4.3.7-1) ... 308s Selecting previously unselected package python3-fs. 308s Preparing to unpack .../074-python3-fs_2.4.16-7_all.deb ... 308s Unpacking python3-fs (2.4.16-7) ... 308s Selecting previously unselected package python3-lxml:amd64. 308s Preparing to unpack .../075-python3-lxml_6.0.1-1build1_amd64.deb ... 308s Unpacking python3-lxml:amd64 (6.0.1-1build1) ... 308s Selecting previously unselected package python3-lz4. 308s Preparing to unpack .../076-python3-lz4_4.4.4+dfsg-3_amd64.deb ... 308s Unpacking python3-lz4 (4.4.4+dfsg-3) ... 308s Selecting previously unselected package python3-scipy. 308s Preparing to unpack .../077-python3-scipy_1.15.3-1ubuntu1_amd64.deb ... 308s Unpacking python3-scipy (1.15.3-1ubuntu1) ... 308s Selecting previously unselected package python3-mpmath. 308s Preparing to unpack .../078-python3-mpmath_1.3.0-1_all.deb ... 308s Unpacking python3-mpmath (1.3.0-1) ... 308s Selecting previously unselected package python3-sympy. 308s Preparing to unpack .../079-python3-sympy_1.13.3-5_all.deb ... 308s Unpacking python3-sympy (1.13.3-5) ... 308s Selecting previously unselected package python3-ufolib2. 308s Preparing to unpack .../080-python3-ufolib2_0.17.1+dfsg1-1_all.deb ... 308s Unpacking python3-ufolib2 (0.17.1+dfsg1-1) ... 308s Selecting previously unselected package python3-unicodedata2. 308s Preparing to unpack .../081-python3-unicodedata2_16.0.0+ds-1build1_amd64.deb ... 308s Unpacking python3-unicodedata2 (16.0.0+ds-1build1) ... 309s Selecting previously unselected package python3-zopfli. 309s Preparing to unpack .../082-python3-zopfli_0.2.3.post1-1_amd64.deb ... 309s Unpacking python3-zopfli (0.2.3.post1-1) ... 309s Selecting previously unselected package unicode-data. 309s Preparing to unpack .../083-unicode-data_16.0.0-1_all.deb ... 309s Unpacking unicode-data (16.0.0-1) ... 309s Selecting previously unselected package python3-fonttools. 309s Preparing to unpack .../084-python3-fonttools_4.57.0-2build1_amd64.deb ... 309s Unpacking python3-fonttools (4.57.0-2build1) ... 309s Selecting previously unselected package python3-gsd. 309s Preparing to unpack .../085-python3-gsd_4.0.0-1_amd64.deb ... 309s Unpacking python3-gsd (4.0.0-1) ... 309s Selecting previously unselected package python3-iniconfig. 309s Preparing to unpack .../086-python3-iniconfig_1.1.1-2_all.deb ... 309s Unpacking python3-iniconfig (1.1.1-2) ... 309s Selecting previously unselected package python3-parso. 309s Preparing to unpack .../087-python3-parso_0.8.4-1_all.deb ... 309s Unpacking python3-parso (0.8.4-1) ... 309s Selecting previously unselected package python3-typeshed. 309s Preparing to unpack .../088-python3-typeshed_0.0~git20241223.ea91db2-3_all.deb ... 309s Unpacking python3-typeshed (0.0~git20241223.ea91db2-3) ... 309s Selecting previously unselected package python3-jedi. 309s Preparing to unpack .../089-python3-jedi_0.19.1+ds1-1_all.deb ... 309s Unpacking python3-jedi (0.19.1+ds1-1) ... 309s Selecting previously unselected package python3-matplotlib-inline. 309s Preparing to unpack .../090-python3-matplotlib-inline_0.1.7-1_all.deb ... 309s Unpacking python3-matplotlib-inline (0.1.7-1) ... 309s Selecting previously unselected package python3-wcwidth. 309s Preparing to unpack .../091-python3-wcwidth_0.2.13+dfsg1-1_all.deb ... 309s Unpacking python3-wcwidth (0.2.13+dfsg1-1) ... 309s Selecting previously unselected package python3-prompt-toolkit. 309s Preparing to unpack .../092-python3-prompt-toolkit_3.0.51-2_all.deb ... 309s Unpacking python3-prompt-toolkit (3.0.51-2) ... 309s Selecting previously unselected package python3-pure-eval. 309s Preparing to unpack .../093-python3-pure-eval_0.2.3-1_all.deb ... 309s Unpacking python3-pure-eval (0.2.3-1) ... 309s Selecting previously unselected package python3-stack-data. 309s Preparing to unpack .../094-python3-stack-data_0.6.3-1_all.deb ... 309s Unpacking python3-stack-data (0.6.3-1) ... 309s Selecting previously unselected package python3-ptyprocess. 309s Preparing to unpack .../095-python3-ptyprocess_0.7.0-6_all.deb ... 309s Unpacking python3-ptyprocess (0.7.0-6) ... 309s Selecting previously unselected package python3-pexpect. 309s Preparing to unpack .../096-python3-pexpect_4.9-3_all.deb ... 309s Unpacking python3-pexpect (4.9-3) ... 309s Selecting previously unselected package python3-ipython. 309s Preparing to unpack .../097-python3-ipython_8.35.0-1_all.deb ... 309s Unpacking python3-ipython 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python3-iniconfig (1.1.1-2) ... 310s Setting up python3-tornado (6.5.2-3) ... 311s Setting up libnorm1t64:amd64 (1.5.9+dfsg-3.1build2) ... 311s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 311s Setting up python3-pure-eval (0.2.3-1) ... 311s Setting up libsodium23:amd64 (1.0.18-1build3) ... 311s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 311s Setting up libxrender1:amd64 (1:0.9.12-1) ... 311s Setting up python3-joblib (1.4.2-4) ... 311s Setting up python3-parso (0.8.4-1) ... 311s Setting up python3-lz4 (4.4.4+dfsg-3) ... 311s Setting up python3-asttokens (3.0.0-2) ... 311s Setting up python3-unicodedata2 (16.0.0+ds-1build1) ... 311s Setting up fonts-lyx (2.4.4-1) ... 311s Setting up python3-threadpoolctl (3.1.0-1) ... 311s Setting up x11-common (1:7.7+24ubuntu1) ... 311s Setting up libdeflate0:amd64 (1.23-2) ... 311s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 311s Setting up python3-coverage (7.8.2+dfsg1-1) ... 311s Setting up liblzo2-2:amd64 (2.10-3build1) ... 311s Setting up python3-pytz (2025.2-4) ... 312s Setting up libgomp1:amd64 (15.2.0-5ubuntu1) ... 312s Setting up python3-networkx (3.2.1-4ubuntu1) ... 312s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 312s Setting up libaec0:amd64 (1.1.3-1) ... 312s Setting up python3-platformdirs (4.3.7-1) ... 312s Setting up python3-psutil (7.0.0-2ubuntu1) ... 312s Setting up libsource-highlight-common (3.1.9-4.3build1) ... 312s Setting up libsnappy1v5:amd64 (1.2.2-1) ... 312s Setting up python3-fs (2.4.16-7) ... 313s Setting up unicode-data (16.0.0-1) ... 313s Setting up libpgm-5.3-0t64:amd64 (5.3.128~dfsg-2.1build1) ... 313s Setting up python3-decorator (5.2.1-2) ... 313s Setting up libblosc2-4:amd64 (2.17.1+ds-2) ... 313s Setting up libblas3:amd64 (3.12.1-6build1) ... 313s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 313s Setting up python3-packaging (25.0-1) ... 313s Setting up python3-wcwidth (0.2.13+dfsg1-1) ... 313s Setting up libzopfli1 (1.0.3-3) ... 313s Setting up python3-typeshed (0.0~git20241223.ea91db2-3) ... 313s Setting up python3-executing (2.2.0-0.2) ... 313s Setting up python3-nest-asyncio (1.5.4-1) ... 313s Setting up python3-brotli (1.1.0-2build6) ... 313s Setting up python3-cycler (0.12.1-2) ... 313s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 313s Setting up fonts-dejavu-mono (2.37-8) ... 313s Setting up python3-kiwisolver (1.4.7-3build2) ... 313s Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 313s Setting up libtcl8.6:amd64 (8.6.17+dfsg-1) ... 313s Setting up libipt2 (2.1.2-1) ... 313s Setting up fonts-dejavu-core (2.37-8) ... 313s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 313s Setting up python3-cpuinfo (9.0.0+git20221119-3) ... 313s Setting up libbabeltrace1:amd64 (1.5.11-4build3) ... 313s Setting up libgfortran5:amd64 (15.2.0-5ubuntu1) ... 313s Setting up python3-pluggy (1.6.0-1) ... 313s Setting up libwebp7:amd64 (1.5.0-0.1) ... 313s Setting up python3-fastjsonschema (2.21.1-1) ... 313s Setting up python3-traitlets (5.14.3+really5.14.3-1) ... 313s Setting up libxslt1.1:amd64 (1.1.43-0.1) ... 313s Setting up libblosc1:amd64 (1.21.5+ds-1build1) ... 313s Setting up libopenjp2-7:amd64 (2.5.3-2.1) ... 313s Setting up libharfbuzz0b:amd64 (12.1.0-1) ... 313s Setting up python3-dateutil (2.9.0-4) ... 314s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 314s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 314s Setting up python3-mpmath (1.3.0-1) ... 314s Setting up python-matplotlib-data (3.10.1+dfsg1-4) ... 314s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 314s Setting up python3-stack-data (0.6.3-1) ... 314s Setting up python-tables-data (3.10.2-3build1) ... 314s Setting up python3-jupyter-core (5.7.2-5) ... 314s Setting up libsz2:amd64 (1.1.3-1) ... 314s Setting up python3-ptyprocess (0.7.0-6) ... 314s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 314s Setting up python3-prompt-toolkit (3.0.51-2) ... 314s Setting up python3-sympy (1.13.3-5) ... 318s Setting up liblapack3:amd64 (3.12.1-6build1) ... 318s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 318s Setting up libzmq5:amd64 (4.3.5-1build2) ... 318s Setting up python3-jedi (0.19.1+ds1-1) ... 318s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 318s Setting up python3-pytest (8.4.2-1) ... 318s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 318s Setting up libsource-highlight4t64:amd64 (3.1.9-4.3build1) ... 318s Setting up python3-nbformat (5.9.1-1) ... 318s Setting up python3-zopfli (0.2.3.post1-1) ... 318s Setting up python3-matplotlib-inline (0.1.7-1) ... 318s Setting up python3-comm (0.2.1-1) ... 318s Setting up gdb (16.3-1ubuntu2) ... 318s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 318s Setting up python3-pexpect (4.9-3) ... 318s Setting up python3-zmq (27.1.0-1) ... 319s Setting up libraqm0:amd64 (0.10.3-1) ... 319s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 320s Setting up libhdf5-310:amd64 (1.14.5+repack-3build1) ... 320s Setting up python3-lxml:amd64 (6.0.1-1build1) ... 320s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 320s Setting up python3-jupyter-client (8.6.3-2) ... 320s Setting up python3-contourpy (1.3.1-1build1) ... 320s Setting up libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 320s Setting up libhdf5-hl-310:amd64 (1.14.5+repack-3build1) ... 320s Setting up libxft2:amd64 (2.3.6-1build1) ... 320s Setting up python3-scipy (1.15.3-1ubuntu1) ... 322s Setting up python3-tables-lib (3.10.2-3build1) ... 322s Setting up libtk8.6:amd64 (8.6.17-1) ... 322s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-9) ... 322s Setting up libnetcdf22:amd64 (1:4.9.3-1build1) ... 322s Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-8) ... 322s Setting up python3-gsd (4.0.0-1) ... 322s Setting up python3-debugpy (1.8.12+ds-1ubuntu1) ... 322s Setting up python3.13-tk (3.13.9-1) ... 322s Setting up python3-pil:amd64 (11.3.0-1ubuntu2) ... 323s Setting up python3-pandas (2.2.3+dfsg-9) ... 325s Setting up python3-ipython (8.35.0-1) ... 325s Setting up python3-ipykernel (6.29.5-2) ... 326s Setting up python3-sklearn (1.4.2+dfsg-8) ... 327s Setting up python3-cftime (1.6.4-2build1) ... 327s Setting up python3-numexpr (2.13.0-1) ... 327s Setting up python3-netcdf4 (1.7.2-1build4) ... 327s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 327s Setting up blt (2.5.3+dfsg-8) ... 327s Setting up python3-tk:amd64 (3.13.5-1) ... 327s Setting up python3-tables (3.10.2-3build1) ... 327s Setting up python3-mdtraj (1.10.3-2build1) ... 327s Setting up python3-pil.imagetk:amd64 (11.3.0-1ubuntu2) ... 327s Setting up python3-fonttools (4.57.0-2build1) ... 328s Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... 328s Setting up python3-matplotlib (3.10.1+dfsg1-4) ... 329s Processing triggers for libc-bin (2.42-0ubuntu3) ... 329s Processing triggers for man-db (2.13.1-1) ... 330s autopkgtest [13:03:38]: 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)' 330s autopkgtest [13:03:38]: test command1: [----------------------- 331s ============================= test session starts ============================== 331s platform linux -- Python 3.13.9, pytest-8.4.2, pluggy-1.6.0 -- /usr/bin/python3 331s cachedir: .pytest_cache 331s rootdir: /tmp/autopkgtest.2cbSxH/build.ErL/src 331s configfile: pyproject.toml 331s testpaths: tests, examples 331s plugins: typeguard-4.4.2 332s collecting ... collected 1145 items / 12 deselected / 1133 selected 332s 332s tests/test_alignment.py::test_rmsd_zero PASSED [ 0%] 332s tests/test_alignment.py::test_rmsd_nonzero PASSED [ 0%] 332s tests/test_alignment.py::test_transform PASSED [ 0%] 332s tests/test_alignment.py::test_transform2 PASSED [ 0%] 332s tests/test_angles.py::test_angle_pbc_0 PASSED [ 0%] 332s 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tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.standard_dimensions] PASSED [ 12%] 336s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit] SKIPPED [ 12%] 336s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_definitions] SKIPPED [ 12%] 336s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_math] SKIPPED [ 12%] 336s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_operators] SKIPPED [ 12%] 336s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unitcell] PASSED [ 12%] 336s tests/test_docstrings.py::test_docstrings[mdtraj.utils.validation] PASSED [ 12%] 336s tests/test_docstrings.py::test_docstrings[mdtraj.utils.zipped] PASSED [ 12%] 336s tests/test_drid.py::test_drid_1 PASSED [ 13%] 336s tests/test_drid.py::test_drid_2 PASSED [ 13%] 336s tests/test_dssp.py::test_1[1bpi.pdb] PASSED [ 13%] 336s tests/test_dssp.py::test_1[1vii.pdb] PASSED [ 13%] 336s tests/test_dssp.py::test_1[4ZUO.pdb] PASSED [ 13%] 336s 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tests/test_hoomdxml.py::test_correct_ordering PASSED [ 21%] 344s tests/test_io.py::test_overwrite_1 PASSED [ 21%] 344s tests/test_io.py::test_overwrite_2 PASSED [ 21%] 344s tests/test_io.py::test_io::test_load_1 PASSED [ 21%] 344s tests/test_io.py::test_io::test_load_2 PASSED [ 22%] 344s tests/test_io.py::test_io::test_load_3 PASSED [ 22%] 344s tests/test_io.py::test_io::test_save PASSED [ 22%] 344s tests/test_io.py::test_io_int::test_load_1 PASSED [ 22%] 344s tests/test_io.py::test_io_int::test_load_2 PASSED [ 22%] 344s tests/test_io.py::test_io_int::test_load_3 PASSED [ 22%] 344s tests/test_io.py::test_io_int::test_save PASSED [ 22%] 344s tests/test_io.py::test_groups PASSED [ 22%] 345s tests/test_lammpstrj.py::test_read_0 PASSED [ 22%] 345s tests/test_lammpstrj.py::test_read_1 PASSED [ 22%] 345s tests/test_lammpstrj.py::test_read_write_0 PASSED [ 22%] 345s tests/test_lammpstrj.py::test_mdwrite PASSED [ 23%] 345s tests/test_lammpstrj.py::test_multiread PASSED [ 23%] 345s tests/test_lammpstrj.py::test_seek PASSED [ 23%] 345s tests/test_lammpstrj.py::test_custom PASSED [ 23%] 345s tests/test_lh5.py::test_write_coordinates PASSED [ 23%] 345s tests/test_lh5.py::test_write_coordinates_reshape PASSED [ 23%] 345s tests/test_lh5.py::test_write_multiple PASSED [ 23%] 345s tests/test_lh5.py::test_topology PASSED [ 23%] 345s tests/test_lh5.py::test_read_slice_0 PASSED [ 23%] 345s tests/test_lh5.py::test_vsite_elements PASSED [ 23%] 345s tests/test_lh5.py::test_do_overwrite_0 PASSED [ 23%] 345s tests/test_lh5.py::test_do_overwrite_1 PASSED [ 24%] 345s tests/test_load.py::test_load_single PASSED [ 24%] 345s tests/test_load.py::test_load_single_top_none PASSED [ 24%] 345s tests/test_load.py::test_load_single_list PASSED [ 24%] 346s tests/test_load.py::test_load_many_list PASSED [ 24%] 346s tests/test_load.py::test_load_atom_indices_multiple_files PASSED [ 24%] 346s tests/test_lprmsd.py::test_munkres_0 PASSED [ 24%] 346s tests/test_lprmsd.py::test_lprmsd_null PASSED [ 24%] 346s tests/test_lprmsd.py::test_lprmsd_0 PASSED [ 24%] 346s tests/test_lprmsd.py::test_lprmsd_1 PASSED [ 24%] 346s tests/test_lprmsd.py::test_lprmsd_2 PASSED [ 24%] 346s tests/test_lprmsd.py::test_lprmsd_3 PASSED [ 24%] 346s tests/test_lprmsd.py::test_lprmsd_4 PASSED [ 25%] 346s tests/test_lprmsd.py::test_lprmsd_5 PASSED [ 25%] 346s tests/test_mdconvert.py::test_index PASSED [ 25%] 346s tests/test_mdconvert.py::test_slice PASSED [ 25%] 352s tests/test_mdconvert.py::test_pairwise[from-xtc] PASSED [ 25%] 359s tests/test_mdconvert.py::test_pairwise[from-dcd] PASSED [ 25%] 365s tests/test_mdconvert.py::test_pairwise[from-trr] PASSED [ 25%] 377s tests/test_mdconvert.py::test_pairwise[from-nc] PASSED [ 25%] 384s tests/test_mdconvert.py::test_pairwise[from-pdb] PASSED [ 25%] 390s tests/test_mdconvert.py::test_pairwise[from-h5] PASSED [ 25%] 397s tests/test_mdconvert.py::test_pairwise[from-lh5] PASSED [ 25%] 403s tests/test_mdconvert.py::test_pairwise[from-netcdf] PASSED [ 26%] 403s tests/test_mdcrd.py::test_read_0 PASSED [ 26%] 403s tests/test_mdcrd.py::test_read_1 PASSED [ 26%] 403s tests/test_mdcrd.py::test_read_write_0 PASSED [ 26%] 403s tests/test_mdcrd.py::test_read_write_1 PASSED [ 26%] 403s tests/test_mdcrd.py::test_read_write_2 PASSED [ 26%] 403s tests/test_mdcrd.py::test_multiread PASSED [ 26%] 403s tests/test_mdcrd.py::test_seek PASSED [ 26%] 403s tests/test_mdcrd.py::test_atom_indices_0 PASSED [ 26%] 403s tests/test_mdcrd.py::test_atom_indices_1 PASSED [ 26%] 403s tests/test_mol2.py::test_load_mol2 PASSED [ 26%] 403s tests/test_mol2.py::test_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb SKIPPED [ 27%] 403s tests/test_mol2.py::test_mol2_dataframe PASSED [ 27%] 403s tests/test_mol2.py::test_mol2_dataframe_status PASSED [ 27%] 403s tests/test_mol2.py::test_mol2_warnings PASSED [ 27%] 403s tests/test_mol2.py::test_mol2_status_bits PASSED [ 27%] 403s tests/test_mol2.py::test_mol2_without_bonds PASSED [ 27%] 403s tests/test_mol2.py::test_mol2_element_name PASSED [ 27%] 403s tests/test_mol2.py::test_load_all_mol2[li.mol2] PASSED [ 27%] 403s tests/test_mol2.py::test_load_all_mol2[lysozyme-ligand-tripos.mol2] PASSED [ 27%] 403s tests/test_mol2.py::test_load_all_mol2[imatinib.mol2] PASSED [ 27%] 403s tests/test_mol2.py::test_load_all_mol2[status-bits.mol2] PASSED [ 27%] 403s tests/test_mol2.py::test_load_all_mol2[adp.mol2] PASSED [ 27%] 403s tests/test_mol2.py::test_load_all_mol2[water_acn.mol2] PASSED [ 28%] 403s tests/test_mol2.py::test_mol2_n_residues PASSED [ 28%] 403s tests/test_neighborlist.py::test_nonperiodic PASSED [ 28%] 403s tests/test_neighborlist.py::test_periodic PASSED [ 28%] 404s tests/test_neighborlist.py::test_triclinic PASSED [ 28%] 404s tests/test_neighbors.py::test_compute_neighbors_1 PASSED [ 28%] 404s tests/test_neighbors.py::test_compute_neighbors_2 PASSED [ 28%] 405s tests/test_neighbors.py::test_compute_neighbors_3 PASSED [ 28%] 405s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_after_close PASSED [ 28%] 405s tests/test_netcdf.py::TestNetCDFNetCDF4::test_shape PASSED [ 28%] 405s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_1 PASSED [ 28%] 405s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_2 PASSED [ 29%] 405s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_3 PASSED [ 29%] 405s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_1 PASSED [ 29%] 405s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_2 PASSED [ 29%] 405s tests/test_netcdf.py::TestNetCDFNetCDF4::test_ragged_1 PASSED [ 29%] 405s tests/test_netcdf.py::TestNetCDFNetCDF4::test_ragged_2 PASSED [ 29%] 405s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_25 PASSED [ 29%] 405s tests/test_netcdf.py::TestNetCDFNetCDF4::test_write_3 PASSED [ 29%] 405s tests/test_netcdf.py::TestNetCDFNetCDF4::test_n_atoms PASSED [ 29%] 405s tests/test_netcdf.py::TestNetCDFNetCDF4::test_do_overwrite PASSED [ 29%] 405s tests/test_netcdf.py::TestNetCDFNetCDF4::test_do_not_overwrite PASSED [ 29%] 405s tests/test_netcdf.py::TestNetCDFNetCDF4::test_trajectory_save_load PASSED [ 30%] 405s tests/test_netcdf.py::TestNetCDFScipy::test_read_after_close PASSED [ 30%] 405s tests/test_netcdf.py::TestNetCDFScipy::test_shape PASSED [ 30%] 405s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_1 PASSED [ 30%] 405s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_2 PASSED [ 30%] 405s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_3 PASSED [ 30%] 405s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_1 PASSED [ 30%] 405s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_2 PASSED [ 30%] 405s tests/test_netcdf.py::TestNetCDFScipy::test_ragged_1 PASSED [ 30%] 405s tests/test_netcdf.py::TestNetCDFScipy::test_ragged_2 PASSED [ 30%] 405s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_25 PASSED [ 30%] 405s tests/test_netcdf.py::TestNetCDFScipy::test_write_3 PASSED [ 30%] 405s tests/test_netcdf.py::TestNetCDFScipy::test_n_atoms PASSED [ 31%] 405s tests/test_netcdf.py::TestNetCDFScipy::test_do_overwrite PASSED [ 31%] 405s tests/test_netcdf.py::TestNetCDFScipy::test_do_not_overwrite PASSED [ 31%] 405s tests/test_netcdf.py::TestNetCDFScipy::test_trajectory_save_load PASSED [ 31%] 405s tests/test_netcdf.py::test_cpptraj SKIPPED (This test requires cpptr...) [ 31%] 405s tests/test_nmr.py::test_spartaplus SKIPPED (SPARTA+ binary not found) [ 31%] 405s tests/test_nmr.py::test_ppm SKIPPED (PPM binary not found) [ 31%] 405s tests/test_nmr.py::test_shiftx2 SKIPPED (SHIFTX2 binary not found or...) [ 31%] 405s tests/test_nmr.py::test_2_scalar_couplings PASSED [ 31%] 405s tests/test_order.py::test_nematic_order PASSED [ 31%] 405s tests/test_order.py::test_director PASSED [ 31%] 405s tests/test_order.py::test_inertia PASSED [ 32%] 405s tests/test_order.py::test_nematic_order_args PASSED [ 32%] 405s tests/test_order.py::test_order_from_traj PASSED [ 32%] 405s tests/test_order.py::test_directors_angle_from_traj PASSED [ 32%] 405s tests/test_pdb.py::test_pdbread PASSED [ 32%] 405s tests/test_pdb.py::test_pdbread_with_input_top PASSED [ 32%] 405s tests/test_pdb.py::test_pdbwrite PASSED [ 32%] 405s tests/test_pdb.py::test_load_multiframe PASSED [ 32%] 405s tests/test_pdb.py::test_4ZUO PASSED [ 32%] 405s tests/test_pdb.py::test_2EQQ_0 PASSED [ 32%] 406s tests/test_pdb.py::test_1vii_solvated_with_ligand PASSED [ 32%] 406s tests/test_pdb.py::test_write_large PASSED [ 33%] 406s tests/test_pdb.py::test_write_large_2 PASSED [ 33%] 406s tests/test_pdb.py::test_pdbstructure_0 PASSED [ 33%] 406s tests/test_pdb.py::test_pdbstructure_1 PASSED [ 33%] 406s tests/test_pdb.py::test_pdbstructure_2 PASSED [ 33%] 406s tests/test_pdb.py::test_pdbstructure_3 PASSED [ 33%] 406s tests/test_pdb.py::test_1ncw PASSED [ 33%] 406s tests/test_pdb.py::test_segment_id PASSED [ 33%] 406s tests/test_pdb.py::test_bfactors PASSED [ 33%] 407s tests/test_pdb.py::test_hex PASSED [ 33%] 407s tests/test_pdb.py::test_dummy_pdb_box_detection PASSED [ 33%] 407s tests/test_pdb.py::test_multichain_load_cycle PASSED [ 33%] 407s tests/test_pdb.py::test_multichain_load_cycle_noter PASSED [ 34%] 407s tests/test_pdb.py::test_load_pdb_input_top PASSED [ 34%] 407s tests/test_pdb.py::test_chimera_indexing PASSED [ 34%] 407s tests/test_pdb.py::test_chimera_indexing_skip PASSED [ 34%] 407s tests/test_pdb.py::test_vmd_indexing PASSED [ 34%] 407s tests/test_pdb.py::test_overflow_indexing PASSED [ 34%] 407s tests/test_pdb.py::test_blank_indexing PASSED [ 34%] 407s tests/test_pdb.py::test_pdb_charge_read PASSED [ 34%] 407s tests/test_pdb.py::test_pdb_charge_write PASSED [ 34%] 407s tests/test_pdbx.py::test_convert SKIPPED (test_pdbx.py needs OpenMM.) [ 34%] 407s tests/test_prmtop.py::test_load_prmtop PASSED [ 34%] 407s tests/test_prmtop.py::test_load_chamber_prmtop PASSED [ 35%] 407s tests/test_psf.py::test_load_psf PASSED [ 35%] 410s tests/test_psf.py::test_multichain_psf PASSED [ 35%] 410s tests/test_psf.py::test_load_mdcrd_with_psf PASSED [ 35%] 410s tests/test_psf.py::test_against_vmd[1vii.pdb] SKIPPED (This test req...) [ 35%] 410s tests/test_psf.py::test_against_vmd[2EQQ.pdb] SKIPPED (This test req...) [ 35%] 410s tests/test_quaternion.py::test_quaternion_0 PASSED [ 35%] 410s tests/test_quaternion.py::test_quaternion_1 PASSED [ 35%] 410s tests/test_quaternion.py::test_quaternion_2 PASSED [ 35%] 412s tests/test_rdf.py::test_rdf_norm PASSED [ 35%] 412s tests/test_rdf.py::test_compare_rdf_to_gromacs SKIPPED (Binning does...) [ 35%] 412s tests/test_rdf.py::test_rdf_t[True-True] PASSED [ 36%] 414s tests/test_rdf.py::test_rdf_t[True-False] PASSED [ 36%] 414s tests/test_rdf.py::test_rdf_t[False-True] PASSED [ 36%] 414s tests/test_rdf.py::test_rdf_t[False-False] PASSED [ 36%] 415s tests/test_rdf.py::test_rdf_t_norm[0] PASSED [ 36%] 415s tests/test_rdf.py::test_rdf_t_norm[2] PASSED [ 36%] 415s tests/test_rdf.py::test_rdf_t_norm[4] PASSED [ 36%] 415s tests/test_rdf.py::test_compare_rdf_t_at_0[True-True] PASSED [ 36%] 416s tests/test_rdf.py::test_compare_rdf_t_at_0[True-False] PASSED [ 36%] 416s tests/test_rdf.py::test_compare_rdf_t_at_0[False-True] PASSED [ 36%] 416s tests/test_rdf.py::test_compare_rdf_t_at_0[False-False] PASSED [ 36%] 416s tests/test_rdf.py::test_amber_rdf_t[True-True] PASSED [ 36%] 416s tests/test_rdf.py::test_amber_rdf_t[True-False] PASSED [ 37%] 417s tests/test_rdf.py::test_amber_rdf_t[False-True] PASSED [ 37%] 417s tests/test_rdf.py::test_amber_rdf_t[False-False] PASSED [ 37%] 417s tests/test_rdf.py::test_compare_gromacs_rdf_t SKIPPED (Binning does ...) [ 37%] 417s tests/test_rdf.py::test_compare_rdf_t_master PASSED [ 37%] 417s tests/test_rdf.py::test_compare_n_concurrent_pairs PASSED [ 37%] 417s tests/test_reporter.py::test_reporter SKIPPED (test_reporter.py need...) [ 37%] 417s tests/test_reporter.py::test_reporter_subset SKIPPED (test_reporter....) [ 37%] 417s tests/test_reporter.py::test_xtc_reporter_append SKIPPED (test_repor...) [ 37%] 417s tests/test_restart.py::test_read_after_close PASSED [ 37%] 417s tests/test_restart.py::test_shape PASSED [ 37%] 417s tests/test_restart.py::test_shape_2 PASSED [ 38%] 417s tests/test_restart.py::test_read_write_1 PASSED [ 38%] 417s tests/test_restart.py::test_read_write_2 PASSED [ 38%] 417s tests/test_restart.py::test_read_write_3 PASSED [ 38%] 417s tests/test_restart.py::test_read_write_4 PASSED [ 38%] 417s tests/test_rmsd.py::test_trajectory_rmsd PASSED [ 38%] 417s tests/test_rmsd.py::test_precentered_1 PASSED [ 38%] 417s tests/test_rmsd.py::test_precentered_2 PASSED [ 38%] 417s tests/test_rmsd.py::test_superpose_0 PASSED [ 38%] 417s tests/test_rmsd.py::test_superpose_1 PASSED [ 38%] 417s tests/test_rmsd.py::test_superpose_2 PASSED [ 38%] 417s tests/test_rmsd.py::test_superpose_refinds PASSED [ 39%] 417s tests/test_rmsd.py::test_rmsd_atom_indices PASSED [ 39%] 417s tests/test_rmsd.py::test_rmsd_ref_ainds PASSED [ 39%] 417s tests/test_rmsd.py::test_average_structure PASSED [ 39%] 417s tests/test_rmsd.py::test_trajectory_rmsf PASSED [ 39%] 417s tests/test_rmsd.py::test_trajectory_rmsf_aligned PASSED [ 39%] 417s tests/test_rmsd.py::test_rmsd_atom_indices_vs_ref_indices PASSED [ 39%] 417s tests/test_rmsd_memmap.py::test_1 PASSED [ 39%] 417s tests/test_rmsd_memmap.py::test_2 PASSED [ 39%] 417s tests/test_sasa.py::test_sasa_0 PASSED [ 39%] 417s tests/test_sasa.py::test_sasa_1 PASSED [ 39%] 418s tests/test_sasa.py::test_sasa_2 PASSED [ 39%] 418s tests/test_sasa.py::test_sasa_3 PASSED [ 40%] 418s tests/test_sasa.py::test_sasa_4 PASSED [ 40%] 418s tests/test_sasa.py::test_sasa_5 PASSED [ 40%] 419s tests/test_sasa.py::test_sasa_6 PASSED [ 40%] 419s tests/test_sasa.py::test_sasa_7 PASSED [ 40%] 419s tests/test_selection.py::test_range PASSED [ 40%] 419s tests/test_selection.py::test_unary_2 PASSED [ 40%] 419s tests/test_selection.py::test_unary_3 PASSED [ 40%] 419s tests/test_selection.py::test_binary_1 PASSED [ 40%] 419s tests/test_selection.py::test_binary_2 PASSED [ 40%] 419s tests/test_selection.py::test_simple PASSED [ 40%] 419s tests/test_selection.py::test_alias PASSED [ 41%] 419s tests/test_selection.py::test_unary_1 PASSED [ 41%] 419s tests/test_selection.py::test_binary_selection_operator PASSED [ 41%] 419s tests/test_selection.py::test_raises PASSED [ 41%] 419s tests/test_selection.py::test_raises2 PASSED [ 41%] 419s tests/test_selection.py::test_bool PASSED [ 41%] 419s tests/test_selection.py::test_nested_bool PASSED [ 41%] 419s tests/test_selection.py::test_values PASSED [ 41%] 419s tests/test_selection.py::test_element PASSED [ 41%] 419s tests/test_selection.py::test_not PASSED [ 41%] 419s tests/test_selection.py::test_re PASSED [ 41%] 419s tests/test_selection.py::test_within SKIPPED (failed to parse selection) [ 42%] 419s tests/test_selection.py::test_quotes PASSED [ 42%] 419s tests/test_selection.py::test_top PASSED [ 42%] 419s tests/test_selection.py::test_top_2 PASSED [ 42%] 419s tests/test_selection.py::test_backbone PASSED [ 42%] 419s tests/test_selection.py::test_sidechain PASSED [ 42%] 420s tests/test_selection.py::test_literal PASSED [ 42%] 420s tests/test_selection.py::test_in PASSED [ 42%] 420s tests/test_shape.py::test_gyration PASSED [ 42%] 420s tests/test_shape.py::test_principal_moments PASSED [ 42%] 420s tests/test_shape.py::test_asphericity PASSED [ 42%] 420s tests/test_shape.py::test_shape_metrics PASSED [ 42%] 420s tests/test_thermodynamic_properties.py::test_volume PASSED [ 43%] 420s tests/test_thermodynamic_properties.py::test_density PASSED [ 43%] 420s tests/test_thermodynamic_properties.py::test_dipole_moments PASSED [ 43%] 420s tests/test_thermodynamic_properties.py::test_static_dielectric PASSED [ 43%] 420s tests/test_thermodynamic_properties.py::test_kappa PASSED [ 43%] 420s tests/test_thermodynamic_properties.py::test_alpha SKIPPED (Thermal ...) [ 43%] 420s tests/test_topology.py::test_topology_openmm SKIPPED (needs OpenMM) [ 43%] 420s tests/test_topology.py::test_topology_openmm_preserve_chain_id_when_specified SKIPPED [ 43%] 420s tests/test_topology.py::test_topology_openmm_roundtrip_chain_id SKIPPED [ 43%] 420s tests/test_topology.py::test_topology_openmm_preserve_chain_id_even_when_empty SKIPPED [ 43%] 420s tests/test_topology.py::test_topology_openmm_boxes SKIPPED (needs Op...) [ 43%] 420s tests/test_topology.py::test_topology_openmm_formal_charges SKIPPED [ 44%] 420s tests/test_topology.py::test_topology_pandas PASSED [ 44%] 420s tests/test_topology.py::test_topology_pandas_TIP4PEW PASSED [ 44%] 420s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq PASSED [ 44%] 420s tests/test_topology.py::test_topology_numbers PASSED [ 44%] 420s tests/test_topology.py::test_topology_unique_elements_bpti PASSED [ 44%] 420s tests/test_topology.py::test_chain PASSED [ 44%] 420s tests/test_topology.py::test_residue PASSED [ 44%] 420s tests/test_topology.py::test_segment_id PASSED [ 44%] 420s tests/test_topology.py::test_nonconsective_resSeq PASSED [ 44%] 420s tests/test_topology.py::test_pickle PASSED [ 44%] 420s tests/test_topology.py::test_atoms_by_name PASSED [ 45%] 420s tests/test_topology.py::test_select_atom_indices PASSED [ 45%] 420s tests/test_topology.py::test_top_dataframe_openmm_roundtrip SKIPPED [ 45%] 420s tests/test_topology.py::test_n_bonds PASSED [ 45%] 420s tests/test_topology.py::test_load_unknown_topology PASSED [ 45%] 420s tests/test_topology.py::test_unique_pairs PASSED [ 45%] 421s tests/test_topology.py::test_select_pairs PASSED [ 45%] 421s tests/test_topology.py::test_to_fasta PASSED [ 45%] 421s tests/test_topology.py::test_subset PASSED [ 45%] 421s tests/test_topology.py::test_subset_re_index_residues PASSED [ 45%] 421s tests/test_topology.py::test_molecules PASSED [ 45%] 421s tests/test_topology.py::test_copy_and_hash PASSED [ 45%] 421s tests/test_topology.py::test_topology_sliced_residue_indices PASSED [ 46%] 421s tests/test_topology.py::test_topology_join PASSED [ 46%] 421s tests/test_topology.py::test_topology_join_keep_resSeq PASSED [ 46%] 421s tests/test_trajectory.py::test_mismatch PASSED [ 46%] 421s tests/test_trajectory.py::test_box PASSED [ 46%] 421s tests/test_trajectory.py::test_load_pdb_box PASSED [ 46%] 421s tests/test_trajectory.py::test_load_pdb_gz PASSED [ 46%] 421s tests/test_trajectory.py::test_box_load_save[nc] PASSED [ 46%] 421s tests/test_trajectory.py::test_box_load_save[h5] PASSED [ 46%] 421s tests/test_trajectory.py::test_box_load_save[xtc] PASSED [ 46%] 421s tests/test_trajectory.py::test_box_load_save[trr] PASSED [ 46%] 421s tests/test_trajectory.py::test_box_load_save[dcd] PASSED [ 47%] 421s tests/test_trajectory.py::test_box_load_save[mdcrd] PASSED [ 47%] 421s tests/test_trajectory.py::test_box_load_save[dtr] PASSED [ 47%] 421s tests/test_trajectory.py::test_box_load_save[xyz] SKIPPED (xyz does ...) [ 47%] 421s tests/test_trajectory.py::test_box_load_save[xyz.gz] SKIPPED (xyz.gz...) [ 47%] 421s tests/test_trajectory.py::test_box_load_save[lammpstrj] PASSED [ 47%] 421s tests/test_trajectory.py::test_box_load_save[lh5] SKIPPED (lh5 does ...) [ 47%] 421s tests/test_trajectory.py::test_box_load_save[pdb] SKIPPED (pdb does ...) [ 47%] 421s tests/test_trajectory.py::test_box_load_save[pdb.gz] SKIPPED (pdb.gz...) [ 47%] 421s tests/test_trajectory.py::test_box_load_save[ncrst] PASSED [ 47%] 423s tests/test_trajectory.py::test_box_load_save[rst7] PASSED [ 47%] 423s tests/test_trajectory.py::test_box_load_save[gro] PASSED [ 48%] 423s tests/test_trajectory.py::test_slice PASSED [ 48%] 423s tests/test_trajectory.py::test_slice2 PASSED [ 48%] 423s tests/test_trajectory.py::test_read_path[nc] PASSED [ 48%] 423s tests/test_trajectory.py::test_read_path[h5] PASSED [ 48%] 423s tests/test_trajectory.py::test_read_path[xtc] PASSED [ 48%] 423s tests/test_trajectory.py::test_read_path[trr] PASSED [ 48%] 423s tests/test_trajectory.py::test_read_path[dcd] PASSED [ 48%] 423s tests/test_trajectory.py::test_read_path[mdcrd] PASSED [ 48%] 423s tests/test_trajectory.py::test_read_path[dtr] PASSED [ 48%] 423s tests/test_trajectory.py::test_read_path[xyz] PASSED [ 48%] 423s tests/test_trajectory.py::test_read_path[xyz.gz] PASSED [ 48%] 423s tests/test_trajectory.py::test_read_path[lammpstrj] PASSED [ 49%] 423s tests/test_trajectory.py::test_read_path[lh5] PASSED [ 49%] 423s tests/test_trajectory.py::test_read_path[pdb] PASSED [ 49%] 423s tests/test_trajectory.py::test_read_path[pdb.gz] PASSED [ 49%] 423s tests/test_trajectory.py::test_read_path[ncrst] XFAIL (These referen...) [ 49%] 423s tests/test_trajectory.py::test_read_path[rst7] XFAIL (These referenc...) [ 49%] 423s tests/test_trajectory.py::test_read_path[gro] PASSED [ 49%] 423s tests/test_trajectory.py::test_write_path[nc] PASSED [ 49%] 423s tests/test_trajectory.py::test_write_path[h5] PASSED [ 49%] 423s tests/test_trajectory.py::test_write_path[xtc] PASSED [ 49%] 423s tests/test_trajectory.py::test_write_path[trr] PASSED [ 49%] 423s tests/test_trajectory.py::test_write_path[dcd] PASSED [ 50%] 423s tests/test_trajectory.py::test_write_path[mdcrd] SKIPPED (mdcrd can ...) [ 50%] 423s tests/test_trajectory.py::test_write_path[dtr] PASSED [ 50%] 423s tests/test_trajectory.py::test_write_path[xyz] PASSED [ 50%] 423s tests/test_trajectory.py::test_write_path[xyz.gz] PASSED [ 50%] 423s tests/test_trajectory.py::test_write_path[lammpstrj] PASSED [ 50%] 423s tests/test_trajectory.py::test_write_path[lh5] PASSED [ 50%] 423s tests/test_trajectory.py::test_write_path[pdb] PASSED [ 50%] 423s tests/test_trajectory.py::test_write_path[pdb.gz] PASSED [ 50%] 423s tests/test_trajectory.py::test_write_path[ncrst] SKIPPED (ncrst can ...) [ 50%] 423s tests/test_trajectory.py::test_write_path[rst7] SKIPPED (rst7 can on...) [ 50%] 423s tests/test_trajectory.py::test_write_path[gro] PASSED [ 51%] 423s tests/test_trajectory.py::test_read_write[nc-nc] PASSED [ 51%] 423s tests/test_trajectory.py::test_read_write[nc-h5] PASSED [ 51%] 423s tests/test_trajectory.py::test_read_write[nc-xtc] PASSED [ 51%] 423s tests/test_trajectory.py::test_read_write[nc-trr] PASSED [ 51%] 423s tests/test_trajectory.py::test_read_write[nc-dcd] PASSED [ 51%] 423s tests/test_trajectory.py::test_read_write[nc-mdcrd] SKIPPED (mdcrd c...) [ 51%] 423s tests/test_trajectory.py::test_read_write[nc-dtr] PASSED [ 51%] 423s tests/test_trajectory.py::test_read_write[nc-xyz] PASSED [ 51%] 423s tests/test_trajectory.py::test_read_write[nc-xyz.gz] PASSED [ 51%] 423s tests/test_trajectory.py::test_read_write[nc-lammpstrj] PASSED [ 51%] 423s tests/test_trajectory.py::test_read_write[nc-lh5] PASSED [ 51%] 424s tests/test_trajectory.py::test_read_write[nc-pdb] PASSED [ 52%] 424s tests/test_trajectory.py::test_read_write[nc-pdb.gz] PASSED [ 52%] 424s tests/test_trajectory.py::test_read_write[nc-ncrst] SKIPPED (ncrst c...) [ 52%] 424s tests/test_trajectory.py::test_read_write[nc-rst7] SKIPPED (rst7 can...) [ 52%] 424s tests/test_trajectory.py::test_read_write[nc-gro] PASSED [ 52%] 424s tests/test_trajectory.py::test_read_write[h5-nc] PASSED [ 52%] 424s tests/test_trajectory.py::test_read_write[h5-h5] PASSED [ 52%] 424s tests/test_trajectory.py::test_read_write[h5-xtc] PASSED [ 52%] 424s tests/test_trajectory.py::test_read_write[h5-trr] PASSED [ 52%] 424s tests/test_trajectory.py::test_read_write[h5-dcd] PASSED [ 52%] 424s tests/test_trajectory.py::test_read_write[h5-mdcrd] SKIPPED (mdcrd c...) [ 52%] 425s tests/test_trajectory.py::test_read_write[h5-dtr] PASSED [ 53%] 425s tests/test_trajectory.py::test_read_write[h5-xyz] PASSED [ 53%] 425s tests/test_trajectory.py::test_read_write[h5-xyz.gz] PASSED [ 53%] 425s tests/test_trajectory.py::test_read_write[h5-lammpstrj] PASSED [ 53%] 425s tests/test_trajectory.py::test_read_write[h5-lh5] PASSED [ 53%] 425s tests/test_trajectory.py::test_read_write[h5-pdb] PASSED [ 53%] 425s tests/test_trajectory.py::test_read_write[h5-pdb.gz] PASSED [ 53%] 425s tests/test_trajectory.py::test_read_write[h5-ncrst] SKIPPED (ncrst c...) [ 53%] 425s tests/test_trajectory.py::test_read_write[h5-rst7] SKIPPED (rst7 can...) [ 53%] 425s tests/test_trajectory.py::test_read_write[h5-gro] PASSED [ 53%] 425s tests/test_trajectory.py::test_read_write[xtc-nc] PASSED [ 53%] 425s tests/test_trajectory.py::test_read_write[xtc-h5] PASSED [ 54%] 425s tests/test_trajectory.py::test_read_write[xtc-xtc] PASSED [ 54%] 425s tests/test_trajectory.py::test_read_write[xtc-trr] PASSED [ 54%] 425s tests/test_trajectory.py::test_read_write[xtc-dcd] PASSED [ 54%] 425s tests/test_trajectory.py::test_read_write[xtc-mdcrd] SKIPPED (mdcrd ...) [ 54%] 426s tests/test_trajectory.py::test_read_write[xtc-dtr] PASSED [ 54%] 426s tests/test_trajectory.py::test_read_write[xtc-xyz] PASSED [ 54%] 426s tests/test_trajectory.py::test_read_write[xtc-xyz.gz] PASSED [ 54%] 426s tests/test_trajectory.py::test_read_write[xtc-lammpstrj] PASSED [ 54%] 426s tests/test_trajectory.py::test_read_write[xtc-lh5] PASSED [ 54%] 426s tests/test_trajectory.py::test_read_write[xtc-pdb] PASSED [ 54%] 426s tests/test_trajectory.py::test_read_write[xtc-pdb.gz] PASSED [ 54%] 426s tests/test_trajectory.py::test_read_write[xtc-ncrst] SKIPPED (ncrst ...) [ 55%] 426s tests/test_trajectory.py::test_read_write[xtc-rst7] SKIPPED (rst7 ca...) [ 55%] 426s tests/test_trajectory.py::test_read_write[xtc-gro] PASSED [ 55%] 427s tests/test_trajectory.py::test_read_write[trr-nc] PASSED [ 55%] 427s tests/test_trajectory.py::test_read_write[trr-h5] PASSED [ 55%] 427s tests/test_trajectory.py::test_read_write[trr-xtc] PASSED [ 55%] 427s tests/test_trajectory.py::test_read_write[trr-trr] PASSED [ 55%] 427s tests/test_trajectory.py::test_read_write[trr-dcd] PASSED [ 55%] 427s tests/test_trajectory.py::test_read_write[trr-mdcrd] SKIPPED (mdcrd ...) [ 55%] 427s tests/test_trajectory.py::test_read_write[trr-dtr] PASSED [ 55%] 427s tests/test_trajectory.py::test_read_write[trr-xyz] PASSED [ 55%] 427s tests/test_trajectory.py::test_read_write[trr-xyz.gz] PASSED [ 56%] 427s tests/test_trajectory.py::test_read_write[trr-lammpstrj] PASSED [ 56%] 427s tests/test_trajectory.py::test_read_write[trr-lh5] PASSED [ 56%] 427s tests/test_trajectory.py::test_read_write[trr-pdb] PASSED [ 56%] 428s tests/test_trajectory.py::test_read_write[trr-pdb.gz] PASSED [ 56%] 428s tests/test_trajectory.py::test_read_write[trr-ncrst] SKIPPED (ncrst ...) [ 56%] 428s tests/test_trajectory.py::test_read_write[trr-rst7] SKIPPED (rst7 ca...) [ 56%] 428s tests/test_trajectory.py::test_read_write[trr-gro] PASSED [ 56%] 428s tests/test_trajectory.py::test_read_write[dcd-nc] PASSED [ 56%] 428s tests/test_trajectory.py::test_read_write[dcd-h5] PASSED [ 56%] 428s tests/test_trajectory.py::test_read_write[dcd-xtc] PASSED [ 56%] 428s tests/test_trajectory.py::test_read_write[dcd-trr] PASSED [ 57%] 428s tests/test_trajectory.py::test_read_write[dcd-dcd] PASSED [ 57%] 428s tests/test_trajectory.py::test_read_write[dcd-mdcrd] SKIPPED (mdcrd ...) [ 57%] 428s tests/test_trajectory.py::test_read_write[dcd-dtr] PASSED [ 57%] 428s tests/test_trajectory.py::test_read_write[dcd-xyz] PASSED [ 57%] 428s tests/test_trajectory.py::test_read_write[dcd-xyz.gz] PASSED [ 57%] 428s tests/test_trajectory.py::test_read_write[dcd-lammpstrj] PASSED [ 57%] 428s tests/test_trajectory.py::test_read_write[dcd-lh5] PASSED [ 57%] 429s tests/test_trajectory.py::test_read_write[dcd-pdb] PASSED [ 57%] 429s tests/test_trajectory.py::test_read_write[dcd-pdb.gz] PASSED [ 57%] 429s tests/test_trajectory.py::test_read_write[dcd-ncrst] SKIPPED (ncrst ...) [ 57%] 429s tests/test_trajectory.py::test_read_write[dcd-rst7] SKIPPED (rst7 ca...) [ 57%] 429s tests/test_trajectory.py::test_read_write[dcd-gro] PASSED [ 58%] 429s tests/test_trajectory.py::test_read_write[mdcrd-nc] PASSED [ 58%] 429s tests/test_trajectory.py::test_read_write[mdcrd-h5] PASSED [ 58%] 429s tests/test_trajectory.py::test_read_write[mdcrd-xtc] PASSED [ 58%] 429s tests/test_trajectory.py::test_read_write[mdcrd-trr] PASSED [ 58%] 429s tests/test_trajectory.py::test_read_write[mdcrd-dcd] PASSED [ 58%] 429s tests/test_trajectory.py::test_read_write[mdcrd-mdcrd] SKIPPED (mdcr...) [ 58%] 429s tests/test_trajectory.py::test_read_write[mdcrd-dtr] SKIPPED (dtr ne...) [ 58%] 429s tests/test_trajectory.py::test_read_write[mdcrd-xyz] PASSED [ 58%] 429s tests/test_trajectory.py::test_read_write[mdcrd-xyz.gz] PASSED [ 58%] 429s tests/test_trajectory.py::test_read_write[mdcrd-lammpstrj] SKIPPED (...) [ 58%] 429s tests/test_trajectory.py::test_read_write[mdcrd-lh5] PASSED [ 59%] 430s tests/test_trajectory.py::test_read_write[mdcrd-pdb] PASSED [ 59%] 430s tests/test_trajectory.py::test_read_write[mdcrd-pdb.gz] PASSED [ 59%] 430s tests/test_trajectory.py::test_read_write[mdcrd-ncrst] SKIPPED (ncrs...) [ 59%] 430s tests/test_trajectory.py::test_read_write[mdcrd-rst7] SKIPPED (rst7 ...) [ 59%] 430s tests/test_trajectory.py::test_read_write[mdcrd-gro] PASSED [ 59%] 430s tests/test_trajectory.py::test_read_write[dtr-nc] PASSED [ 59%] 430s tests/test_trajectory.py::test_read_write[dtr-h5] PASSED [ 59%] 430s tests/test_trajectory.py::test_read_write[dtr-xtc] PASSED [ 59%] 430s tests/test_trajectory.py::test_read_write[dtr-trr] PASSED [ 59%] 430s tests/test_trajectory.py::test_read_write[dtr-dcd] PASSED [ 59%] 430s tests/test_trajectory.py::test_read_write[dtr-mdcrd] SKIPPED (mdcrd ...) [ 60%] 431s tests/test_trajectory.py::test_read_write[dtr-dtr] PASSED [ 60%] 431s tests/test_trajectory.py::test_read_write[dtr-xyz] PASSED [ 60%] 431s tests/test_trajectory.py::test_read_write[dtr-xyz.gz] PASSED [ 60%] 431s tests/test_trajectory.py::test_read_write[dtr-lammpstrj] PASSED [ 60%] 431s tests/test_trajectory.py::test_read_write[dtr-lh5] PASSED [ 60%] 431s tests/test_trajectory.py::test_read_write[dtr-pdb] PASSED [ 60%] 431s tests/test_trajectory.py::test_read_write[dtr-pdb.gz] PASSED [ 60%] 431s tests/test_trajectory.py::test_read_write[dtr-ncrst] SKIPPED (ncrst ...) [ 60%] 431s tests/test_trajectory.py::test_read_write[dtr-rst7] SKIPPED (rst7 ca...) [ 60%] 431s tests/test_trajectory.py::test_read_write[dtr-gro] PASSED [ 60%] 431s tests/test_trajectory.py::test_read_write[xyz-nc] PASSED [ 60%] 431s tests/test_trajectory.py::test_read_write[xyz-h5] PASSED [ 61%] 431s tests/test_trajectory.py::test_read_write[xyz-xtc] PASSED [ 61%] 431s tests/test_trajectory.py::test_read_write[xyz-trr] PASSED [ 61%] 431s tests/test_trajectory.py::test_read_write[xyz-dcd] PASSED [ 61%] 431s tests/test_trajectory.py::test_read_write[xyz-mdcrd] SKIPPED (mdcrd ...) [ 61%] 431s tests/test_trajectory.py::test_read_write[xyz-dtr] SKIPPED (dtr need...) [ 61%] 432s tests/test_trajectory.py::test_read_write[xyz-xyz] PASSED [ 61%] 432s tests/test_trajectory.py::test_read_write[xyz-xyz.gz] PASSED [ 61%] 432s tests/test_trajectory.py::test_read_write[xyz-lammpstrj] SKIPPED (la...) [ 61%] 432s tests/test_trajectory.py::test_read_write[xyz-lh5] PASSED [ 61%] 432s tests/test_trajectory.py::test_read_write[xyz-pdb] PASSED [ 61%] 432s tests/test_trajectory.py::test_read_write[xyz-pdb.gz] PASSED [ 62%] 432s tests/test_trajectory.py::test_read_write[xyz-ncrst] SKIPPED (ncrst ...) [ 62%] 432s tests/test_trajectory.py::test_read_write[xyz-rst7] SKIPPED (rst7 ca...) [ 62%] 432s tests/test_trajectory.py::test_read_write[xyz-gro] PASSED [ 62%] 432s tests/test_trajectory.py::test_read_write[xyz.gz-nc] PASSED [ 62%] 432s tests/test_trajectory.py::test_read_write[xyz.gz-h5] PASSED [ 62%] 432s tests/test_trajectory.py::test_read_write[xyz.gz-xtc] PASSED [ 62%] 432s tests/test_trajectory.py::test_read_write[xyz.gz-trr] PASSED [ 62%] 432s tests/test_trajectory.py::test_read_write[xyz.gz-dcd] PASSED [ 62%] 432s tests/test_trajectory.py::test_read_write[xyz.gz-mdcrd] SKIPPED (mdc...) [ 62%] 432s tests/test_trajectory.py::test_read_write[xyz.gz-dtr] SKIPPED (dtr n...) [ 62%] 432s tests/test_trajectory.py::test_read_write[xyz.gz-xyz] PASSED [ 63%] 432s tests/test_trajectory.py::test_read_write[xyz.gz-xyz.gz] PASSED [ 63%] 432s tests/test_trajectory.py::test_read_write[xyz.gz-lammpstrj] SKIPPED [ 63%] 432s tests/test_trajectory.py::test_read_write[xyz.gz-lh5] PASSED [ 63%] 433s tests/test_trajectory.py::test_read_write[xyz.gz-pdb] PASSED [ 63%] 433s tests/test_trajectory.py::test_read_write[xyz.gz-pdb.gz] PASSED [ 63%] 433s tests/test_trajectory.py::test_read_write[xyz.gz-ncrst] SKIPPED (ncr...) [ 63%] 433s tests/test_trajectory.py::test_read_write[xyz.gz-rst7] SKIPPED (rst7...) [ 63%] 433s tests/test_trajectory.py::test_read_write[xyz.gz-gro] PASSED [ 63%] 433s tests/test_trajectory.py::test_read_write[lammpstrj-nc] PASSED [ 63%] 433s tests/test_trajectory.py::test_read_write[lammpstrj-h5] PASSED [ 63%] 433s tests/test_trajectory.py::test_read_write[lammpstrj-xtc] PASSED [ 63%] 433s tests/test_trajectory.py::test_read_write[lammpstrj-trr] PASSED [ 64%] 433s tests/test_trajectory.py::test_read_write[lammpstrj-dcd] PASSED [ 64%] 433s tests/test_trajectory.py::test_read_write[lammpstrj-mdcrd] SKIPPED (...) [ 64%] 433s tests/test_trajectory.py::test_read_write[lammpstrj-dtr] PASSED [ 64%] 433s tests/test_trajectory.py::test_read_write[lammpstrj-xyz] PASSED [ 64%] 434s tests/test_trajectory.py::test_read_write[lammpstrj-xyz.gz] PASSED [ 64%] 434s tests/test_trajectory.py::test_read_write[lammpstrj-lammpstrj] PASSED [ 64%] 434s tests/test_trajectory.py::test_read_write[lammpstrj-lh5] PASSED [ 64%] 434s tests/test_trajectory.py::test_read_write[lammpstrj-pdb] PASSED [ 64%] 434s tests/test_trajectory.py::test_read_write[lammpstrj-pdb.gz] PASSED [ 64%] 434s tests/test_trajectory.py::test_read_write[lammpstrj-ncrst] SKIPPED (...) [ 64%] 434s tests/test_trajectory.py::test_read_write[lammpstrj-rst7] SKIPPED (r...) [ 65%] 434s tests/test_trajectory.py::test_read_write[lammpstrj-gro] PASSED [ 65%] 434s tests/test_trajectory.py::test_read_write[lh5-nc] PASSED [ 65%] 434s tests/test_trajectory.py::test_read_write[lh5-h5] PASSED [ 65%] 434s tests/test_trajectory.py::test_read_write[lh5-xtc] PASSED [ 65%] 434s tests/test_trajectory.py::test_read_write[lh5-trr] PASSED [ 65%] 434s tests/test_trajectory.py::test_read_write[lh5-dcd] PASSED [ 65%] 434s tests/test_trajectory.py::test_read_write[lh5-mdcrd] SKIPPED (mdcrd ...) [ 65%] 434s tests/test_trajectory.py::test_read_write[lh5-dtr] SKIPPED (dtr need...) [ 65%] 434s tests/test_trajectory.py::test_read_write[lh5-xyz] PASSED [ 65%] 434s tests/test_trajectory.py::test_read_write[lh5-xyz.gz] PASSED [ 65%] 434s tests/test_trajectory.py::test_read_write[lh5-lammpstrj] SKIPPED (la...) [ 66%] 434s tests/test_trajectory.py::test_read_write[lh5-lh5] PASSED [ 66%] 435s tests/test_trajectory.py::test_read_write[lh5-pdb] PASSED [ 66%] 435s tests/test_trajectory.py::test_read_write[lh5-pdb.gz] PASSED [ 66%] 435s tests/test_trajectory.py::test_read_write[lh5-ncrst] SKIPPED (ncrst ...) [ 66%] 435s tests/test_trajectory.py::test_read_write[lh5-rst7] SKIPPED (rst7 ca...) [ 66%] 435s tests/test_trajectory.py::test_read_write[lh5-gro] PASSED [ 66%] 435s tests/test_trajectory.py::test_read_write[pdb-nc] PASSED [ 66%] 435s tests/test_trajectory.py::test_read_write[pdb-h5] PASSED [ 66%] 435s tests/test_trajectory.py::test_read_write[pdb-xtc] PASSED [ 66%] 435s tests/test_trajectory.py::test_read_write[pdb-trr] PASSED [ 66%] 435s tests/test_trajectory.py::test_read_write[pdb-dcd] PASSED [ 66%] 435s tests/test_trajectory.py::test_read_write[pdb-mdcrd] SKIPPED (mdcrd ...) [ 67%] 436s tests/test_trajectory.py::test_read_write[pdb-dtr] PASSED [ 67%] 436s tests/test_trajectory.py::test_read_write[pdb-xyz] PASSED [ 67%] 436s tests/test_trajectory.py::test_read_write[pdb-xyz.gz] PASSED [ 67%] 436s tests/test_trajectory.py::test_read_write[pdb-lammpstrj] PASSED [ 67%] 436s tests/test_trajectory.py::test_read_write[pdb-lh5] PASSED [ 67%] 436s tests/test_trajectory.py::test_read_write[pdb-pdb] PASSED [ 67%] 437s tests/test_trajectory.py::test_read_write[pdb-pdb.gz] PASSED [ 67%] 437s tests/test_trajectory.py::test_read_write[pdb-ncrst] SKIPPED (ncrst ...) [ 67%] 437s tests/test_trajectory.py::test_read_write[pdb-rst7] SKIPPED (rst7 ca...) [ 67%] 437s tests/test_trajectory.py::test_read_write[pdb-gro] PASSED [ 67%] 437s tests/test_trajectory.py::test_read_write[pdb.gz-nc] PASSED [ 68%] 437s tests/test_trajectory.py::test_read_write[pdb.gz-h5] PASSED [ 68%] 437s tests/test_trajectory.py::test_read_write[pdb.gz-xtc] PASSED [ 68%] 437s tests/test_trajectory.py::test_read_write[pdb.gz-trr] PASSED [ 68%] 437s tests/test_trajectory.py::test_read_write[pdb.gz-dcd] PASSED [ 68%] 437s tests/test_trajectory.py::test_read_write[pdb.gz-mdcrd] SKIPPED (mdc...) [ 68%] 438s tests/test_trajectory.py::test_read_write[pdb.gz-dtr] PASSED [ 68%] 438s tests/test_trajectory.py::test_read_write[pdb.gz-xyz] PASSED [ 68%] 438s tests/test_trajectory.py::test_read_write[pdb.gz-xyz.gz] PASSED [ 68%] 438s tests/test_trajectory.py::test_read_write[pdb.gz-lammpstrj] PASSED [ 68%] 438s tests/test_trajectory.py::test_read_write[pdb.gz-lh5] PASSED [ 68%] 439s tests/test_trajectory.py::test_read_write[pdb.gz-pdb] PASSED [ 69%] 439s tests/test_trajectory.py::test_read_write[pdb.gz-pdb.gz] PASSED [ 69%] 439s tests/test_trajectory.py::test_read_write[pdb.gz-ncrst] SKIPPED (ncr...) [ 69%] 439s tests/test_trajectory.py::test_read_write[pdb.gz-rst7] SKIPPED (rst7...) [ 69%] 439s tests/test_trajectory.py::test_read_write[pdb.gz-gro] PASSED [ 69%] 439s tests/test_trajectory.py::test_read_write[ncrst-nc] XFAIL (These ref...) [ 69%] 439s tests/test_trajectory.py::test_read_write[ncrst-h5] XFAIL (These ref...) [ 69%] 439s tests/test_trajectory.py::test_read_write[ncrst-xtc] XFAIL (These re...) [ 69%] 439s tests/test_trajectory.py::test_read_write[ncrst-trr] XFAIL (These re...) [ 69%] 439s tests/test_trajectory.py::test_read_write[ncrst-dcd] XFAIL (These re...) [ 69%] 439s tests/test_trajectory.py::test_read_write[ncrst-mdcrd] XFAIL (These ...) [ 69%] 439s tests/test_trajectory.py::test_read_write[ncrst-dtr] XFAIL (These re...) [ 69%] 439s tests/test_trajectory.py::test_read_write[ncrst-xyz] XFAIL (These re...) [ 70%] 439s tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] XFAIL (These...) [ 70%] 439s tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] XFAIL (Th...) [ 70%] 439s tests/test_trajectory.py::test_read_write[ncrst-lh5] XFAIL (These re...) [ 70%] 439s tests/test_trajectory.py::test_read_write[ncrst-pdb] XFAIL (These re...) [ 70%] 439s tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] XFAIL (These...) [ 70%] 439s tests/test_trajectory.py::test_read_write[ncrst-ncrst] XFAIL (These ...) [ 70%] 439s tests/test_trajectory.py::test_read_write[ncrst-rst7] XFAIL (These r...) [ 70%] 439s tests/test_trajectory.py::test_read_write[ncrst-gro] XFAIL (These re...) [ 70%] 439s tests/test_trajectory.py::test_read_write[rst7-nc] XFAIL (These refe...) [ 70%] 439s tests/test_trajectory.py::test_read_write[rst7-h5] XFAIL (These refe...) [ 70%] 439s tests/test_trajectory.py::test_read_write[rst7-xtc] XFAIL (These ref...) [ 71%] 439s tests/test_trajectory.py::test_read_write[rst7-trr] XFAIL (These ref...) [ 71%] 439s tests/test_trajectory.py::test_read_write[rst7-dcd] XFAIL (These ref...) [ 71%] 439s tests/test_trajectory.py::test_read_write[rst7-mdcrd] XFAIL (These r...) [ 71%] 439s tests/test_trajectory.py::test_read_write[rst7-dtr] XFAIL (These ref...) [ 71%] 439s tests/test_trajectory.py::test_read_write[rst7-xyz] XFAIL (These ref...) [ 71%] 439s tests/test_trajectory.py::test_read_write[rst7-xyz.gz] XFAIL (These ...) [ 71%] 439s tests/test_trajectory.py::test_read_write[rst7-lammpstrj] XFAIL (The...) [ 71%] 439s tests/test_trajectory.py::test_read_write[rst7-lh5] XFAIL (These ref...) [ 71%] 439s tests/test_trajectory.py::test_read_write[rst7-pdb] XFAIL (These ref...) [ 71%] 439s tests/test_trajectory.py::test_read_write[rst7-pdb.gz] XFAIL (These ...) [ 71%] 439s tests/test_trajectory.py::test_read_write[rst7-ncrst] XFAIL (These r...) [ 72%] 439s tests/test_trajectory.py::test_read_write[rst7-rst7] XFAIL (These re...) [ 72%] 439s tests/test_trajectory.py::test_read_write[rst7-gro] XFAIL (These ref...) [ 72%] 439s tests/test_trajectory.py::test_read_write[gro-nc] PASSED [ 72%] 439s tests/test_trajectory.py::test_read_write[gro-h5] PASSED [ 72%] 439s tests/test_trajectory.py::test_read_write[gro-xtc] PASSED [ 72%] 439s tests/test_trajectory.py::test_read_write[gro-trr] PASSED [ 72%] 439s tests/test_trajectory.py::test_read_write[gro-dcd] PASSED [ 72%] 440s tests/test_trajectory.py::test_read_write[gro-mdcrd] SKIPPED (mdcrd ...) [ 72%] 440s tests/test_trajectory.py::test_read_write[gro-dtr] PASSED [ 72%] 440s tests/test_trajectory.py::test_read_write[gro-xyz] PASSED [ 72%] 440s tests/test_trajectory.py::test_read_write[gro-xyz.gz] PASSED [ 72%] 440s tests/test_trajectory.py::test_read_write[gro-lammpstrj] PASSED [ 73%] 440s tests/test_trajectory.py::test_read_write[gro-lh5] PASSED [ 73%] 440s tests/test_trajectory.py::test_read_write[gro-pdb] PASSED [ 73%] 441s tests/test_trajectory.py::test_read_write[gro-pdb.gz] PASSED [ 73%] 441s tests/test_trajectory.py::test_read_write[gro-ncrst] SKIPPED (ncrst ...) [ 73%] 441s tests/test_trajectory.py::test_read_write[gro-rst7] SKIPPED (rst7 ca...) [ 73%] 441s tests/test_trajectory.py::test_read_write[gro-gro] PASSED [ 73%] 441s tests/test_trajectory.py::test_load[nc] PASSED [ 73%] 441s tests/test_trajectory.py::test_load[h5] PASSED [ 73%] 441s tests/test_trajectory.py::test_load[xtc] PASSED [ 73%] 441s tests/test_trajectory.py::test_load[trr] PASSED [ 73%] 441s tests/test_trajectory.py::test_load[dcd] PASSED [ 74%] 441s tests/test_trajectory.py::test_load[mdcrd] PASSED [ 74%] 441s tests/test_trajectory.py::test_load[dtr] PASSED [ 74%] 441s tests/test_trajectory.py::test_load[xyz] PASSED [ 74%] 441s tests/test_trajectory.py::test_load[xyz.gz] PASSED [ 74%] 441s tests/test_trajectory.py::test_load[lammpstrj] PASSED [ 74%] 441s tests/test_trajectory.py::test_load[lh5] PASSED [ 74%] 442s tests/test_trajectory.py::test_load[pdb] PASSED [ 74%] 442s tests/test_trajectory.py::test_load[pdb.gz] PASSED [ 74%] 442s tests/test_trajectory.py::test_load[ncrst] XFAIL (These reference fi...) [ 74%] 442s tests/test_trajectory.py::test_load[rst7] XFAIL (These reference fil...) [ 74%] 443s tests/test_trajectory.py::test_load[gro] PASSED [ 75%] 443s tests/test_trajectory.py::test_hdf5 PASSED [ 75%] 443s tests/test_trajectory.py::test_center PASSED [ 75%] 443s tests/test_trajectory.py::test_center_aind PASSED [ 75%] 443s tests/test_trajectory.py::test_float_atom_indices_exception[nc] PASSED [ 75%] 443s tests/test_trajectory.py::test_float_atom_indices_exception[h5] PASSED [ 75%] 443s tests/test_trajectory.py::test_float_atom_indices_exception[xtc] PASSED [ 75%] 443s tests/test_trajectory.py::test_float_atom_indices_exception[trr] PASSED [ 75%] 443s tests/test_trajectory.py::test_float_atom_indices_exception[dcd] PASSED [ 75%] 443s tests/test_trajectory.py::test_float_atom_indices_exception[mdcrd] PASSED [ 75%] 443s tests/test_trajectory.py::test_float_atom_indices_exception[dtr] PASSED [ 75%] 443s tests/test_trajectory.py::test_float_atom_indices_exception[xyz] PASSED [ 75%] 443s tests/test_trajectory.py::test_float_atom_indices_exception[xyz.gz] PASSED [ 76%] 443s tests/test_trajectory.py::test_float_atom_indices_exception[lammpstrj] PASSED [ 76%] 443s tests/test_trajectory.py::test_float_atom_indices_exception[lh5] PASSED [ 76%] 443s tests/test_trajectory.py::test_float_atom_indices_exception[pdb] PASSED [ 76%] 443s tests/test_trajectory.py::test_float_atom_indices_exception[pdb.gz] PASSED [ 76%] 443s tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] XFAIL [ 76%] 443s tests/test_trajectory.py::test_float_atom_indices_exception[rst7] XFAIL [ 76%] 443s tests/test_trajectory.py::test_float_atom_indices_exception[gro] PASSED [ 76%] 443s tests/test_trajectory.py::test_restrict_atoms PASSED [ 76%] 443s tests/test_trajectory.py::test_restrict_atoms_not_inplace PASSED [ 76%] 443s tests/test_trajectory.py::test_array_vs_matrix PASSED [ 76%] 443s tests/test_trajectory.py::test_pdb_unitcell_loadsave PASSED [ 77%] 443s tests/test_trajectory.py::test_load_combination[nc] PASSED [ 77%] 443s tests/test_trajectory.py::test_load_combination[h5] PASSED [ 77%] 443s tests/test_trajectory.py::test_load_combination[xtc] PASSED [ 77%] 443s tests/test_trajectory.py::test_load_combination[trr] PASSED [ 77%] 443s tests/test_trajectory.py::test_load_combination[dcd] PASSED [ 77%] 443s tests/test_trajectory.py::test_load_combination[mdcrd] PASSED [ 77%] 443s tests/test_trajectory.py::test_load_combination[dtr] PASSED [ 77%] 443s tests/test_trajectory.py::test_load_combination[xyz] PASSED [ 77%] 443s tests/test_trajectory.py::test_load_combination[xyz.gz] PASSED [ 77%] 443s tests/test_trajectory.py::test_load_combination[lammpstrj] PASSED [ 77%] 443s tests/test_trajectory.py::test_load_combination[lh5] PASSED [ 78%] 443s tests/test_trajectory.py::test_load_combination[pdb] PASSED [ 78%] 443s tests/test_trajectory.py::test_load_combination[pdb.gz] PASSED [ 78%] 443s tests/test_trajectory.py::test_load_combination[ncrst] XFAIL (These ...) [ 78%] 443s tests/test_trajectory.py::test_load_combination[rst7] XFAIL (These r...) [ 78%] 443s tests/test_trajectory.py::test_load_combination[gro] PASSED [ 78%] 443s tests/test_trajectory.py::test_no_topology PASSED [ 78%] 443s tests/test_trajectory.py::test_join PASSED [ 78%] 443s tests/test_trajectory.py::test_md_join PASSED [ 78%] 443s tests/test_trajectory.py::test_stack_1 PASSED [ 78%] 443s tests/test_trajectory.py::test_stack_2 PASSED [ 78%] 444s tests/test_trajectory.py::test_seek_read_mode[nc] PASSED [ 78%] 444s tests/test_trajectory.py::test_seek_read_mode[h5] PASSED [ 79%] 444s tests/test_trajectory.py::test_seek_read_mode[xtc] PASSED [ 79%] 444s tests/test_trajectory.py::test_seek_read_mode[trr] PASSED [ 79%] 444s tests/test_trajectory.py::test_seek_read_mode[dcd] PASSED [ 79%] 444s tests/test_trajectory.py::test_seek_read_mode[mdcrd] PASSED [ 79%] 444s tests/test_trajectory.py::test_seek_read_mode[dtr] PASSED [ 79%] 444s tests/test_trajectory.py::test_seek_read_mode[xyz] PASSED [ 79%] 444s tests/test_trajectory.py::test_seek_read_mode[xyz.gz] XFAIL (This is...) [ 79%] 444s tests/test_trajectory.py::test_seek_read_mode[lammpstrj] PASSED [ 79%] 444s tests/test_trajectory.py::test_seek_read_mode[lh5] PASSED [ 79%] 444s tests/test_trajectory.py::test_seek_read_mode[pdb] XFAIL (PDB Files ...) [ 79%] 444s tests/test_trajectory.py::test_seek_read_mode[pdb.gz] XFAIL (PDB Fil...) [ 80%] 444s tests/test_trajectory.py::test_seek_read_mode[ncrst] XFAIL (These re...) [ 80%] 444s tests/test_trajectory.py::test_seek_read_mode[rst7] XFAIL (These ref...) [ 80%] 444s tests/test_trajectory.py::test_seek_read_mode[gro] XFAIL (This is br...) [ 80%] 444s tests/test_trajectory.py::test_load_frame[nc] PASSED [ 80%] 444s tests/test_trajectory.py::test_load_frame[h5] PASSED [ 80%] 444s tests/test_trajectory.py::test_load_frame[xtc] PASSED [ 80%] 444s tests/test_trajectory.py::test_load_frame[trr] PASSED [ 80%] 444s tests/test_trajectory.py::test_load_frame[dcd] PASSED [ 80%] 444s tests/test_trajectory.py::test_load_frame[mdcrd] PASSED [ 80%] 444s tests/test_trajectory.py::test_load_frame[dtr] XFAIL (DTR doesn't lo...) [ 80%] 444s tests/test_trajectory.py::test_load_frame[xyz] PASSED [ 81%] 444s tests/test_trajectory.py::test_load_frame[xyz.gz] PASSED [ 81%] 444s tests/test_trajectory.py::test_load_frame[lammpstrj] PASSED [ 81%] 444s tests/test_trajectory.py::test_load_frame[lh5] PASSED [ 81%] 444s tests/test_trajectory.py::test_load_frame[pdb] PASSED [ 81%] 444s tests/test_trajectory.py::test_load_frame[pdb.gz] PASSED [ 81%] 444s tests/test_trajectory.py::test_load_frame[ncrst] XFAIL (These refere...) [ 81%] 444s tests/test_trajectory.py::test_load_frame[rst7] XFAIL (These referen...) [ 81%] 444s tests/test_trajectory.py::test_load_frame[gro] XFAIL (Gro doesn't im...) [ 81%] 444s tests/test_trajectory.py::test_load_frame_2eqq PASSED [ 81%] 444s tests/test_trajectory.py::test_iterload[nc] PASSED [ 81%] 445s tests/test_trajectory.py::test_iterload[h5] PASSED [ 81%] 445s tests/test_trajectory.py::test_iterload[xtc] PASSED [ 82%] 445s tests/test_trajectory.py::test_iterload[trr] PASSED [ 82%] 445s tests/test_trajectory.py::test_iterload[dcd] PASSED [ 82%] 445s tests/test_trajectory.py::test_iterload[mdcrd] PASSED [ 82%] 445s tests/test_trajectory.py::test_iterload[dtr] XFAIL (This is broken w...) [ 82%] 445s tests/test_trajectory.py::test_iterload[xyz] PASSED [ 82%] 445s tests/test_trajectory.py::test_iterload[xyz.gz] PASSED [ 82%] 445s tests/test_trajectory.py::test_iterload[lammpstrj] PASSED [ 82%] 445s tests/test_trajectory.py::test_iterload[lh5] PASSED [ 82%] 445s tests/test_trajectory.py::test_iterload[pdb] PASSED [ 82%] 445s tests/test_trajectory.py::test_iterload[pdb.gz] PASSED [ 82%] 445s tests/test_trajectory.py::test_iterload[ncrst] SKIPPED (Only 1 frame...) [ 83%] 445s tests/test_trajectory.py::test_iterload[rst7] SKIPPED (Only 1 frame ...) [ 83%] 445s tests/test_trajectory.py::test_iterload[gro] PASSED [ 83%] 446s tests/test_trajectory.py::test_iterload_skip[nc] PASSED [ 83%] 447s tests/test_trajectory.py::test_iterload_skip[h5] PASSED [ 83%] 448s tests/test_trajectory.py::test_iterload_skip[xtc] PASSED [ 83%] 448s tests/test_trajectory.py::test_iterload_skip[trr] PASSED [ 83%] 449s tests/test_trajectory.py::test_iterload_skip[dcd] PASSED [ 83%] 450s tests/test_trajectory.py::test_iterload_skip[mdcrd] PASSED [ 83%] 450s tests/test_trajectory.py::test_iterload_skip[dtr] PASSED [ 83%] 450s tests/test_trajectory.py::test_iterload_skip[xyz] PASSED [ 83%] 451s tests/test_trajectory.py::test_iterload_skip[xyz.gz] PASSED [ 84%] 451s tests/test_trajectory.py::test_iterload_skip[lammpstrj] PASSED [ 84%] 452s tests/test_trajectory.py::test_iterload_skip[lh5] PASSED [ 84%] 452s tests/test_trajectory.py::test_iterload_skip[pdb] XFAIL (PDB Iterloa...) [ 84%] 452s tests/test_trajectory.py::test_iterload_skip[pdb.gz] XFAIL (PDB Iter...) [ 84%] 452s tests/test_trajectory.py::test_iterload_skip[ncrst] XFAIL (These ref...) [ 84%] 452s tests/test_trajectory.py::test_iterload_skip[rst7] XFAIL (These refe...) [ 84%] 452s tests/test_trajectory.py::test_iterload_skip[gro] XFAIL (Not impleme...) [ 84%] 452s tests/test_trajectory.py::test_iterload_chunk_dcd PASSED [ 84%] 452s tests/test_trajectory.py::test_save_load[nc] PASSED [ 84%] 452s tests/test_trajectory.py::test_save_load[h5] PASSED [ 84%] 452s tests/test_trajectory.py::test_save_load[xtc] PASSED [ 84%] 452s tests/test_trajectory.py::test_save_load[trr] PASSED [ 85%] 452s tests/test_trajectory.py::test_save_load[dcd] PASSED [ 85%] 452s tests/test_trajectory.py::test_save_load[mdcrd] PASSED [ 85%] 452s tests/test_trajectory.py::test_save_load[dtr] PASSED [ 85%] 452s tests/test_trajectory.py::test_save_load[xyz] PASSED [ 85%] 452s tests/test_trajectory.py::test_save_load[xyz.gz] PASSED [ 85%] 452s tests/test_trajectory.py::test_save_load[lammpstrj] PASSED [ 85%] 452s tests/test_trajectory.py::test_save_load[lh5] PASSED [ 85%] 452s tests/test_trajectory.py::test_save_load[pdb] PASSED [ 85%] 452s tests/test_trajectory.py::test_save_load[pdb.gz] PASSED [ 85%] 452s tests/test_trajectory.py::test_save_load[ncrst] PASSED [ 85%] 452s tests/test_trajectory.py::test_save_load[rst7] PASSED [ 86%] 452s tests/test_trajectory.py::test_save_load[gro] PASSED [ 86%] 452s tests/test_trajectory.py::test_force_overwrite[nc] PASSED [ 86%] 452s tests/test_trajectory.py::test_force_overwrite[h5] PASSED [ 86%] 452s tests/test_trajectory.py::test_force_overwrite[xtc] PASSED [ 86%] 452s tests/test_trajectory.py::test_force_overwrite[trr] PASSED [ 86%] 452s tests/test_trajectory.py::test_force_overwrite[dcd] PASSED [ 86%] 452s tests/test_trajectory.py::test_force_overwrite[mdcrd] PASSED [ 86%] 452s tests/test_trajectory.py::test_force_overwrite[dtr] XFAIL (This is b...) [ 86%] 452s tests/test_trajectory.py::test_force_overwrite[xyz] PASSED [ 86%] 452s tests/test_trajectory.py::test_force_overwrite[xyz.gz] PASSED [ 86%] 452s tests/test_trajectory.py::test_force_overwrite[lammpstrj] PASSED [ 87%] 452s tests/test_trajectory.py::test_force_overwrite[lh5] PASSED [ 87%] 452s tests/test_trajectory.py::test_force_overwrite[pdb] PASSED [ 87%] 452s tests/test_trajectory.py::test_force_overwrite[pdb.gz] PASSED [ 87%] 452s tests/test_trajectory.py::test_force_overwrite[ncrst] PASSED [ 87%] 452s tests/test_trajectory.py::test_force_overwrite[rst7] PASSED [ 87%] 452s tests/test_trajectory.py::test_force_overwrite[gro] PASSED [ 87%] 452s tests/test_trajectory.py::test_force_noverwrite[nc] PASSED [ 87%] 452s tests/test_trajectory.py::test_force_noverwrite[h5] PASSED [ 87%] 452s tests/test_trajectory.py::test_force_noverwrite[xtc] PASSED [ 87%] 452s tests/test_trajectory.py::test_force_noverwrite[trr] PASSED [ 87%] 452s tests/test_trajectory.py::test_force_noverwrite[dcd] PASSED [ 87%] 452s tests/test_trajectory.py::test_force_noverwrite[mdcrd] PASSED [ 88%] 452s tests/test_trajectory.py::test_force_noverwrite[dtr] PASSED [ 88%] 452s tests/test_trajectory.py::test_force_noverwrite[xyz] PASSED [ 88%] 452s tests/test_trajectory.py::test_force_noverwrite[xyz.gz] PASSED [ 88%] 452s tests/test_trajectory.py::test_force_noverwrite[lammpstrj] PASSED [ 88%] 452s tests/test_trajectory.py::test_force_noverwrite[lh5] PASSED [ 88%] 452s tests/test_trajectory.py::test_force_noverwrite[pdb] PASSED [ 88%] 452s tests/test_trajectory.py::test_force_noverwrite[pdb.gz] PASSED [ 88%] 452s tests/test_trajectory.py::test_force_noverwrite[ncrst] PASSED [ 88%] 452s tests/test_trajectory.py::test_force_noverwrite[rst7] PASSED [ 88%] 452s tests/test_trajectory.py::test_force_noverwrite[gro] PASSED [ 88%] 452s tests/test_trajectory.py::test_open_and_load PASSED [ 89%] 453s tests/test_trajectory.py::test_length PASSED [ 89%] 453s tests/test_trajectory.py::test_unitcell[nc] PASSED [ 89%] 453s tests/test_trajectory.py::test_unitcell[h5] PASSED [ 89%] 453s tests/test_trajectory.py::test_unitcell[xtc] PASSED [ 89%] 453s tests/test_trajectory.py::test_unitcell[trr] PASSED [ 89%] 453s tests/test_trajectory.py::test_unitcell[dcd] PASSED [ 89%] 453s tests/test_trajectory.py::test_unitcell[mdcrd] PASSED [ 89%] 453s tests/test_trajectory.py::test_unitcell[dtr] XFAIL (dtr seems to nee...) [ 89%] 453s tests/test_trajectory.py::test_unitcell[xyz] PASSED [ 89%] 453s tests/test_trajectory.py::test_unitcell[xyz.gz] PASSED [ 89%] 453s tests/test_trajectory.py::test_unitcell[lammpstrj] XFAIL (lammpstrj ...) [ 90%] 453s tests/test_trajectory.py::test_unitcell[lh5] PASSED [ 90%] 453s tests/test_trajectory.py::test_unitcell[pdb] PASSED [ 90%] 453s tests/test_trajectory.py::test_unitcell[pdb.gz] PASSED [ 90%] 453s tests/test_trajectory.py::test_unitcell[ncrst] XFAIL (ncrst seems to...) [ 90%] 453s tests/test_trajectory.py::test_unitcell[rst7] XFAIL (rst7 seems to n...) [ 90%] 453s tests/test_trajectory.py::test_unitcell[gro] PASSED [ 90%] 453s tests/test_trajectory.py::test_chunk0_iterload PASSED [ 90%] 453s tests/test_trajectory.py::test_hashing PASSED [ 90%] 453s tests/test_trajectory.py::test_smooth PASSED [ 90%] 453s tests/test_trajectory.py::test_load_pdb_no_standard_names PASSED [ 90%] 453s tests/test_trajectory.py::test_load_with_atom_indices PASSED [ 90%] 453s tests/test_trajectory.py::test_atom_slicing PASSED [ 91%] 453s tests/test_trajectory.py::test_load_with_frame PASSED [ 91%] 453s tests/test_trajectory.py::test_add_remove_atoms PASSED [ 91%] 453s tests/test_trr.py::test_1 PASSED [ 91%] 453s tests/test_trr.py::test_read_stride PASSED [ 91%] 453s tests/test_trr.py::test_read_stride_n_frames PASSED [ 91%] 453s tests/test_trr.py::test_read_stride_offsets PASSED [ 91%] 453s tests/test_trr.py::test_read_stride_n_frames_offsets PASSED [ 91%] 453s tests/test_trr.py::test_read_stride_switching PASSED [ 91%] 453s tests/test_trr.py::test_write_read PASSED [ 91%] 453s tests/test_trr.py::test_read_atomindices_1 PASSED [ 91%] 453s tests/test_trr.py::test_read_atomindices_2 PASSED [ 92%] 453s tests/test_trr.py::test_deficient_shape PASSED [ 92%] 453s tests/test_trr.py::test_ragged_1 PASSED [ 92%] 453s tests/test_trr.py::test_ragged_2 PASSED [ 92%] 453s tests/test_trr.py::test_malformed PASSED [ 92%] 453s tests/test_trr.py::test_tell PASSED [ 92%] 453s tests/test_trr.py::test_seek PASSED [ 92%] 453s tests/test_trr.py::test_get_velocities PASSED [ 92%] 453s tests/test_trr.py::test_get_forces PASSED [ 92%] 453s tests/test_trr.py::test_get_velocities_and_forces PASSED [ 92%] 453s tests/test_trr.py::test_get_velocities_forces_atom_indices_1 PASSED [ 92%] 453s tests/test_trr.py::test_get_velocities_forces_atom_indices_2 PASSED [ 93%] 453s tests/test_trr.py::test_read_velocities_do_not_exist PASSED [ 93%] 453s tests/test_trr.py::test_read_forces_do_not_exist PASSED [ 93%] 453s tests/test_utils.py::test_unitcell_0 PASSED [ 93%] 453s tests/test_utils.py::test_unitcell_1 PASSED [ 93%] 453s tests/test_utils.py::test_ensure_type_1 PASSED [ 93%] 453s tests/test_utils.py::test_ensure_type_2 PASSED [ 93%] 453s tests/test_utils.py::test_ensure_type_25 PASSED [ 93%] 453s tests/test_utils.py::test_ensure_type_3 PASSED [ 93%] 453s tests/test_utils.py::test_ensure_type_4 PASSED [ 93%] 453s tests/test_utils.py::test_ensure_type_5 PASSED [ 93%] 453s tests/test_utils.py::test_ensure_type_6 PASSED [ 93%] 453s tests/test_utils.py::test_ensure_type_7 PASSED [ 94%] 453s tests/test_utils.py::test_ensure_type_8 PASSED [ 94%] 453s tests/test_utils.py::test_ensure_type_9 PASSED [ 94%] 453s tests/test_utils.py::test_ensure_type_10 PASSED [ 94%] 453s tests/test_utils.py::test_ensure_type_11 PASSED [ 94%] 453s tests/test_utils.py::test_ensure_type_12 PASSED [ 94%] 453s tests/test_utils.py::test_ensure_type_13 PASSED [ 94%] 453s tests/test_utils.py::test_ensure_type_14 PASSED [ 94%] 453s tests/test_utils.py::test_ensure_type_15 PASSED [ 94%] 453s tests/test_utils.py::test_delay_import_fail_1 PASSED [ 94%] 453s tests/test_utils.py::test_delay_import PASSED [ 94%] 453s tests/test_utils.py::test_unit_0 PASSED [ 95%] 453s tests/test_utils.py::test_unit_1 PASSED [ 95%] 453s tests/test_utils.py::test_unit_2 PASSED [ 95%] 453s tests/test_utils.py::test_unit_3 PASSED [ 95%] 453s tests/test_xml.py::test_xml PASSED [ 95%] 453s tests/test_xtc.py::test_read_chunk1 PASSED [ 95%] 453s tests/test_xtc.py::test_read_stride PASSED [ 95%] 453s tests/test_xtc.py::test_read_stride_n_frames PASSED [ 95%] 453s tests/test_xtc.py::test_read_stride_offsets PASSED [ 95%] 453s tests/test_xtc.py::test_read_stride_n_frames_offsets PASSED [ 95%] 453s tests/test_xtc.py::test_read_stride_switching_offsets PASSED [ 95%] 453s tests/test_xtc.py::test_read_atomindices_1 PASSED [ 96%] 453s tests/test_xtc.py::test_read_atomindices_w_stride PASSED [ 96%] 453s tests/test_xtc.py::test_read_atomindices_2 PASSED [ 96%] 453s tests/test_xtc.py::test_read_chunk2 PASSED [ 96%] 453s 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%] 454s tests/test_xyz.py::test_mdwrite PASSED [ 98%] 454s tests/test_xyz.py::test_multiread PASSED [ 98%] 454s tests/test_xyz.py::test_seek PASSED [ 98%] 454s tests/test_xyz.py::test_len PASSED [ 98%] 454s tests/test_zipped.py::test_read_gz PASSED [ 98%] 454s tests/test_zipped.py::test_write_gz PASSED [ 98%] 454s tests/test_zipped.py::test_read_bz2 PASSED [ 98%] 454s tests/test_zipped.py::test_write_bz2 PASSED [ 98%] 590s examples/test_examples.py::test_example_notebook[iterload.ipynb] PASSED [ 98%] 590s examples/test_examples.py::test_example_notebook[simulation-with-openmm.ipynb] SKIPPED [ 99%] 725s examples/test_examples.py::test_example_notebook[atom-selection.ipynb] PASSED [ 99%] 861s examples/test_examples.py::test_example_notebook[rmsd-benchmark.ipynb] PASSED [ 99%] 996s examples/test_examples.py::test_example_notebook[rmsd-drift.ipynb] PASSED [ 99%] 1130s examples/test_examples.py::test_example_notebook[native-contact.ipynb] SKIPPED [ 99%] 1266s examples/test_examples.py::test_example_notebook[centroids.ipynb] PASSED [ 99%] 1401s examples/test_examples.py::test_example_notebook[two-pass-clustering.ipynb] PASSED [ 99%] 1537s examples/test_examples.py::test_example_notebook[principal-components.ipynb] PASSED [ 99%] 1672s examples/test_examples.py::test_example_notebook[solvent-accessible-surface-area.ipynb] PASSED [ 99%] 1806s examples/test_examples.py::test_example_notebook[hbonds.ipynb] SKIPPED [ 99%] 1942s examples/test_examples.py::test_example_notebook[ramachandran-plot.ipynb] PASSED [ 99%] 2077s examples/test_examples.py::test_example_notebook[clustering.ipynb] PASSED [100%] 2077s 2077s =============================== warnings summary =============================== 2077s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:56 2077s /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. 2077s THIS_ATOM = ast.Name(id="atom", ctx=ast.Load(), SINGLETON=True) 2077s 2077s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:57 2077s /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. 2077s RE_MODULE = ast.Name(id="re", ctx=ast.Load(), SINGLETON=True) 2077s 2077s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 2077s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 2077s given by the platformdirs library. To remove this warning and 2077s see the appropriate new directories, set the environment variable 2077s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 2077s The use of platformdirs will be the default in `jupyter_core` v6 2077s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 2077s 2077s examples/test_examples.py:26 2077s /tmp/autopkgtest.2cbSxH/build.ErL/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 2077s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 2077s 2077s tests/test_contact.py::test_contact_0 2077s tests/test_contact.py::test_contact_4 2077s /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. 2077s warnings.warn( 2077s 2077s tests/test_contact.py::test_contact_3 2077s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:271: RuntimeWarning: overflow encountered in exp 2077s np.exp( 2077s 2077s tests/test_contact.py::test_contact_3 2077s /tmp/autopkgtest.2cbSxH/build.ErL/src/tests/test_contact.py:115: RuntimeWarning: divide by zero encountered in scalar divide 2077s beta / np.log(np.sum(np.exp(beta / maps[t, r0, r1]))), 2077s 2077s tests/test_dcd.py::test_do_overwrite 2077s tests/test_dcd.py::test_ragged_1 2077s tests/test_dcd.py::test_ragged_2 2077s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting xyz dtype=float64 to 2077s warnings.warn( 2077s 2077s tests/test_distance.py::test_6 2077s :488: RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject 2077s 2077s tests/test_drid.py::test_drid_2 2077s /tmp/autopkgtest.2cbSxH/build.ErL/src/tests/test_drid.py:62: RuntimeWarning: divide by zero encountered in divide 2077s recip = 1 / squareform(pdist(t.xyz[i])) 2077s 2077s tests/test_dssp.py::test_1[1vii.pdb] 2077s tests/test_gro.py::test_read_write 2077s tests/test_gro.py::test_read_write_precision 2077s tests/test_gro.py::test_load 2077s tests/test_shape.py::test_principal_moments 2077s tests/test_shape.py::test_asphericity 2077s tests/test_shape.py::test_shape_metrics 2077s /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. 2077s warnings.warn( 2077s 2077s tests/test_geometry.py::test_dihedral_indices 2077s tests/test_geometry.py::test_dihedral_indices 2077s /usr/lib/python3/dist-packages/mdtraj/geometry/dihedral.py:237: DeprecationWarning: Passing a Trajectory object to _atom_sequence isdeprecated. Please pass a Topology object 2077s warnings.warn( 2077s 2077s tests/test_gro.py::test_load 2077s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq 2077s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:364: UserWarning: WARNING: two consecutive residues with same number (GST, HST) 2077s warnings.warn( 2077s 2077s tests/test_pdb.py::test_blank_indexing 2077s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:204: UserWarning: Need to guess atom number starting from atom 100000. 2077s warnings.warn(f'Need to guess atom number {num_str} starting from atom {pdbstructure._next_atom_number}.') 2077s 2077s tests/test_pdb.py::test_blank_indexing 2077s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:271: UserWarning: Need to guess residue number string starting from residue10000, atom 100000. 2077s warnings.warn(f'Need to guess residue number string {num_str} starting from residue{pdbstructure._next_residue_number}, atom {pdbstructure._next_atom_number}.') 2077s 2077s tests/test_rdf.py::test_rdf_norm 2077s tests/test_rdf.py::test_rdf_t_norm[0] 2077s tests/test_rdf.py::test_rdf_t_norm[2] 2077s tests/test_rdf.py::test_rdf_t_norm[4] 2077s tests/test_selection.py::test_re 2077s tests/test_selection.py::test_re 2077s tests/test_topology.py::test_select_pairs 2077s tests/test_topology.py::test_select_pairs 2077s /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. 2077s left=ast.Call( 2077s 2077s tests/test_rdf.py::test_rdf_norm 2077s tests/test_rdf.py::test_rdf_t_norm[0] 2077s tests/test_rdf.py::test_rdf_t_norm[2] 2077s tests/test_rdf.py::test_rdf_t_norm[4] 2077s tests/test_selection.py::test_re 2077s tests/test_selection.py::test_re 2077s tests/test_topology.py::test_select_pairs 2077s tests/test_topology.py::test_select_pairs 2077s /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. 2077s left=ast.Call( 2077s 2077s tests/test_trajectory.py::test_float_atom_indices_exception[gro] 2077s tests/test_trajectory.py::test_atom_slicing 2077s /usr/lib/python3/dist-packages/mdtraj/core/topology.py:84: UserWarning: atom_indices are not monotonically increasing 2077s warnings.warn("atom_indices are not monotonically increasing") 2077s 2077s tests/test_utils.py::test_ensure_type_8 2077s tests/test_utils.py::test_ensure_type_9 2077s tests/test_utils.py::test_ensure_type_13 2077s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=float64 to 2077s warnings.warn( 2077s 2077s tests/test_utils.py::test_ensure_type_11 2077s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=int64 to 2077s warnings.warn( 2077s 2077s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 2077s =========================== short test summary info ============================ 2077s SKIPPED [1] tests/test_dihedral.py:56: pymol executable not found 2077s SKIPPED [1] tests/test_dihedral.py:181: pymol executable not found 2077s SKIPPED [16] tests/test_docstrings.py:38: Skip checking certain modules' docstrings 2077s SKIPPED [1] tests/test_geometry.py:300: Not doing performance testing 2077s SKIPPED [1] tests/test_geometry.py:322: Not doing performance testing 2077s SKIPPED [1] tests/test_hdf5.py:104: requires openmm.units 2077s SKIPPED [1] tests/test_hdf5.py:156: requires openmm.units 2077s SKIPPED [1] tests/test_hdf5.py:223: requires openmm.units 2077s SKIPPED [1] tests/test_mol2.py:59: Requires obabel 2077s SKIPPED [1] tests/test_netcdf.py:271: This test requires cpptraj from AmberTools to be installed (http://ambermd.org) 2077s SKIPPED [1] tests/test_nmr.py:11: SPARTA+ binary not found 2077s SKIPPED [1] tests/test_nmr.py:26: PPM binary not found 2077s SKIPPED [1] tests/test_nmr.py:42: SHIFTX2 binary not found or running on travis. 2077s SKIPPED [1] tests/test_pdbx.py:43: test_pdbx.py needs OpenMM. 2077s SKIPPED [2] tests/test_psf.py:93: This test requires the VMD executable: http://www.ks.uiuc.edu/Research/vmd/ 2077s SKIPPED [1] tests/test_rdf.py:64: Binning does not match up with gromacs currently. 2077s SKIPPED [1] tests/test_rdf.py:200: Binning does not match up with gromacs currently. 2078s SKIPPED [1] tests/test_reporter.py:58: test_reporter.py needs OpenMM. 2078s SKIPPED [1] tests/test_reporter.py:145: test_reporter.py needs OpenMM. 2078s SKIPPED [1] tests/test_reporter.py:245: test_reporter.py needs OpenMM. 2078s SKIPPED [1] tests/test_selection.py:267: failed to parse selection 2078s SKIPPED [1] tests/test_thermodynamic_properties.py:161: Thermal expansion test doesn't work. 2078s SKIPPED [1] tests/test_topology.py:45: needs OpenMM 2078s SKIPPED [1] tests/test_topology.py:62: needs OpenMM 2078s SKIPPED [1] tests/test_topology.py:72: needs OpenMM 2078s SKIPPED [1] tests/test_topology.py:81: needs OpenMM 2078s SKIPPED [1] tests/test_topology.py:91: needs OpenMM 2078s SKIPPED [1] tests/test_topology.py:97: needs OpenMM 2078s SKIPPED [1] tests/test_topology.py:247: needs OpenMM 2078s SKIPPED [1] tests/test_trajectory.py:129: xyz does not store box information 2078s SKIPPED [1] tests/test_trajectory.py:129: xyz.gz does not store box information 2078s SKIPPED [1] tests/test_trajectory.py:129: lh5 does not store box information 2078s SKIPPED [1] tests/test_trajectory.py:129: pdb does not store box information 2078s SKIPPED [1] tests/test_trajectory.py:129: pdb.gz does not store box information 2078s SKIPPED [1] tests/test_trajectory.py:226: mdcrd can only store rectilinear boxes 2078s SKIPPED [1] tests/test_trajectory.py:224: ncrst can only store 1 frame per file 2078s SKIPPED [1] tests/test_trajectory.py:224: rst7 can only store 1 frame per file 2078s SKIPPED [14] tests/test_trajectory.py:248: mdcrd can only store rectilinear boxes 2078s SKIPPED [14] tests/test_trajectory.py:246: ncrst can only store 1 frame per file 2078s SKIPPED [14] tests/test_trajectory.py:246: rst7 can only store 1 frame per file 2078s SKIPPED [4] tests/test_trajectory.py:256: dtr needs to write unitcells 2078s SKIPPED [4] tests/test_trajectory.py:256: lammpstrj needs to write unitcells 2078s SKIPPED [2] tests/test_trajectory.py:640: Only 1 frame per file format 2078s SKIPPED [1] examples/test_examples.py:77: Openmm required for example notebook `simulation-with-openmm.ipynb` 2078s SKIPPED [2] examples/test_examples.py:77: Network access required 2078s XFAIL tests/test_trajectory.py::test_read_path[ncrst] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_path[rst7] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[ncrst-nc] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[ncrst-h5] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xtc] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[ncrst-trr] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dcd] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[ncrst-mdcrd] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dtr] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lh5] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[ncrst-ncrst] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[ncrst-rst7] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[ncrst-gro] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[rst7-nc] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[rst7-h5] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[rst7-xtc] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[rst7-trr] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[rst7-dcd] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[rst7-mdcrd] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[rst7-dtr] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz.gz] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[rst7-lammpstrj] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[rst7-lh5] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb.gz] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[rst7-ncrst] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[rst7-rst7] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_read_write[rst7-gro] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_load[ncrst] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_load[rst7] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[rst7] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_load_combination[ncrst] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_load_combination[rst7] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_seek_read_mode[xyz.gz] - This is broken 2078s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb] - PDB Files don't support seeking 2078s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb.gz] - PDB Files don't support seeking 2078s XFAIL tests/test_trajectory.py::test_seek_read_mode[ncrst] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_seek_read_mode[rst7] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_seek_read_mode[gro] - This is broken 2078s XFAIL tests/test_trajectory.py::test_load_frame[dtr] - DTR doesn't load a single frame properly 2078s XFAIL tests/test_trajectory.py::test_load_frame[ncrst] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_load_frame[rst7] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_load_frame[gro] - Gro doesn't implement seek 2078s XFAIL tests/test_trajectory.py::test_iterload[dtr] - This is broken with dtr 2078s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb] - PDB Iterloads an extra frame!! 2078s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb.gz] - PDB Iterloads an extra frame!! 2078s XFAIL tests/test_trajectory.py::test_iterload_skip[ncrst] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_iterload_skip[rst7] - These reference files don't exist yet 2078s XFAIL tests/test_trajectory.py::test_iterload_skip[gro] - Not implemented for some reason 2078s XFAIL tests/test_trajectory.py::test_force_overwrite[dtr] - This is broken with dtr 2078s XFAIL tests/test_trajectory.py::test_unitcell[dtr] - dtr seems to need unit vectors 2078s XFAIL tests/test_trajectory.py::test_unitcell[lammpstrj] - lammpstrj seems to need unit vectors 2078s XFAIL tests/test_trajectory.py::test_unitcell[ncrst] - ncrst seems to need unit vectors 2078s XFAIL tests/test_trajectory.py::test_unitcell[rst7] - rst7 seems to need unit vectors 2078s = 964 passed, 108 skipped, 12 deselected, 61 xfailed, 48 warnings in 1746.64s (0:29:06) = 2079s autopkgtest [13:32:47]: test command1: -----------------------] 2079s command1 PASS 2079s autopkgtest [13:32:47]: test command1: - - - - - - - - - - results - - - - - - - - - - 2079s autopkgtest [13:32:47]: test command2: preparing testbed 2080s Reading package lists... 2080s Building dependency tree... 2080s Reading state information... 2080s Solving dependencies... 2080s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2081s autopkgtest [13:32:49]: test command2: pytest-3 -k 'test_3 or test_pdb_from_url or test_1vii_url_and_gz' 2081s autopkgtest [13:32:49]: test command2: [----------------------- 2081s ============================= test session starts ============================== 2081s platform linux -- Python 3.13.9, pytest-8.4.2, pluggy-1.6.0 -- /usr/bin/python3 2081s cachedir: .pytest_cache 2081s rootdir: /tmp/autopkgtest.2cbSxH/build.ErL/src 2081s configfile: pyproject.toml 2081s testpaths: tests, examples 2081s plugins: typeguard-4.4.2 2082s collecting ... collected 1145 items / 1135 deselected / 10 selected 2082s 2082s tests/test_distance.py::test_3 PASSED [ 10%] 2082s tests/test_distance.py::test_3p PASSED [ 20%] 2086s tests/test_dssp.py::test_3[1GAI] PASSED [ 30%] 2089s tests/test_dssp.py::test_3[6gsv] PASSED [ 40%] 2093s tests/test_dssp.py::test_3[2AAC] PASSED [ 50%] 2093s tests/test_nmr.py::test_3_scalar_couplings PASSED [ 60%] 2101s tests/test_pdb.py::test_pdb_from_url PASSED [ 70%] 2101s tests/test_pdb.py::test_3nch_conect PASSED [ 80%] 2102s tests/test_pdb.py::test_3nch_serial_resSeq PASSED [ 90%] 2107s tests/test_pdb.py::test_1vii_url_and_gz PASSED [100%] 2107s 2107s =============================== warnings summary =============================== 2107s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:56 2107s /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. 2107s THIS_ATOM = ast.Name(id="atom", ctx=ast.Load(), SINGLETON=True) 2107s 2107s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:57 2107s /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. 2107s RE_MODULE = ast.Name(id="re", ctx=ast.Load(), SINGLETON=True) 2107s 2107s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 2107s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 2107s given by the platformdirs library. To remove this warning and 2107s see the appropriate new directories, set the environment variable 2107s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 2107s The use of platformdirs will be the default in `jupyter_core` v6 2107s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 2107s 2107s examples/test_examples.py:26 2107s /tmp/autopkgtest.2cbSxH/build.ErL/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 2107s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 2107s 2107s tests/test_pdb.py::test_1vii_url_and_gz 2107s /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. 2107s warnings.warn( 2107s 2107s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 2107s =============== 10 passed, 1135 deselected, 5 warnings in 25.79s =============== 2108s autopkgtest [13:33:16]: test command2: -----------------------] 2108s command2 PASS 2108s autopkgtest [13:33:16]: test command2: - - - - - - - - - - results - - - - - - - - - - 2108s autopkgtest [13:33:16]: @@@@@@@@@@@@@@@@@@@@ summary 2108s command1 PASS 2108s command2 PASS