0s autopkgtest [13:09:27]: starting date and time: 2025-02-19 13:09:27+0000 0s autopkgtest [13:09:27]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [13:09:27]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.91zvs61d/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:sphinx --apt-upgrade mdtraj --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/8.1.3-5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@lcy02-4.secgroup --name adt-plucky-amd64-mdtraj-20250219-113248-juju-7f2275-prod-proposed-migration-environment-20-be4e8c96-f92c-4442-9629-4496fc17a245 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 40s autopkgtest [13:10:07]: testbed dpkg architecture: amd64 40s autopkgtest [13:10:07]: testbed apt version: 2.9.29 41s autopkgtest [13:10:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 41s autopkgtest [13:10:08]: testbed release detected to be: None 41s autopkgtest [13:10:08]: updating testbed package index (apt update) 41s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 41s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 41s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 41s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 41s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 41s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 41s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [744 kB] 41s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 41s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [92.7 kB] 41s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 41s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [7984 B] 41s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2412 B] 41s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [711 kB] 41s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [262 kB] 41s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [11.5 kB] 41s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3128 B] 42s Fetched 2150 kB in 0s (7722 kB/s) 42s Reading package lists... 43s Reading package lists... 43s Building dependency tree... 43s Reading state information... 43s Calculating upgrade... 43s The following NEW packages will be installed: 43s libapt-pkg7.0 43s The following packages will be upgraded: 43s apt apt-utils iproute2 libgpgme11t64 liblsof0 libp11-kit0 lsof rsyslog 43s sysvinit-utils 44s 9 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 44s Need to get 5425 kB of archives. 44s After this operation, 4076 kB of additional disk space will be used. 44s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 sysvinit-utils amd64 3.14-1ubuntu1 [35.7 kB] 44s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.30 [1131 kB] 44s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.30 [1434 kB] 44s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.30 [222 kB] 44s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 iproute2 amd64 6.13.0-1ubuntu1 [1277 kB] 44s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libp11-kit0 amd64 0.25.5-2ubuntu3 [311 kB] 44s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu1 [555 kB] 44s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 lsof amd64 4.99.4+dfsg-1 [245 kB] 44s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsof0 amd64 4.99.4+dfsg-1 [59.6 kB] 44s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.2-1ubuntu1 [155 kB] 44s Preconfiguring packages ... 44s Fetched 5425 kB in 0s (35.1 MB/s) 44s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 108925 files and directories currently installed.) 44s Preparing to unpack .../sysvinit-utils_3.14-1ubuntu1_amd64.deb ... 44s Unpacking sysvinit-utils (3.14-1ubuntu1) over (3.08-6ubuntu3) ... 44s Setting up sysvinit-utils (3.14-1ubuntu1) ... 44s Selecting previously unselected package libapt-pkg7.0:amd64. 44s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 108925 files and directories currently installed.) 44s Preparing to unpack .../libapt-pkg7.0_2.9.30_amd64.deb ... 44s Unpacking libapt-pkg7.0:amd64 (2.9.30) ... 45s Setting up libapt-pkg7.0:amd64 (2.9.30) ... 45s (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 ... 108974 files and directories currently installed.) 45s Preparing to unpack .../archives/apt_2.9.30_amd64.deb ... 45s Unpacking apt (2.9.30) over (2.9.29) ... 45s Setting up apt (2.9.30) ... 45s (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 ... 108974 files and directories currently installed.) 45s Preparing to unpack .../0-apt-utils_2.9.30_amd64.deb ... 45s Unpacking apt-utils (2.9.30) over (2.9.29) ... 46s Preparing to unpack .../1-iproute2_6.13.0-1ubuntu1_amd64.deb ... 46s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 46s Preparing to unpack .../2-libp11-kit0_0.25.5-2ubuntu3_amd64.deb ... 46s Unpacking libp11-kit0:amd64 (0.25.5-2ubuntu3) over (0.25.5-2ubuntu2) ... 46s Preparing to unpack .../3-rsyslog_8.2412.0-2ubuntu1_amd64.deb ... 46s Unpacking rsyslog (8.2412.0-2ubuntu1) over (8.2412.0-1ubuntu1) ... 46s Preparing to unpack .../4-lsof_4.99.4+dfsg-1_amd64.deb ... 46s Unpacking lsof (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 46s Preparing to unpack .../5-liblsof0_4.99.4+dfsg-1_amd64.deb ... 46s Unpacking liblsof0 (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 46s Preparing to unpack .../6-libgpgme11t64_1.24.2-1ubuntu1_amd64.deb ... 46s Unpacking libgpgme11t64:amd64 (1.24.2-1ubuntu1) over (1.24.1-4ubuntu1) ... 46s Setting up apt-utils (2.9.30) ... 46s Setting up liblsof0 (4.99.4+dfsg-1) ... 46s Setting up iproute2 (6.13.0-1ubuntu1) ... 46s Setting up rsyslog (8.2412.0-2ubuntu1) ... 46s info: The user `syslog' is already a member of `adm'. 47s Setting up libp11-kit0:amd64 (0.25.5-2ubuntu3) ... 47s Setting up lsof (4.99.4+dfsg-1) ... 47s Setting up libgpgme11t64:amd64 (1.24.2-1ubuntu1) ... 47s Processing triggers for man-db (2.13.0-1) ... 49s Processing triggers for libc-bin (2.40-4ubuntu1) ... 50s Reading package lists... 51s Building dependency tree... 51s Reading state information... 51s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 51s autopkgtest [13:10:18]: upgrading testbed (apt dist-upgrade and autopurge) 51s Reading package lists... 51s Building dependency tree... 51s Reading state information... 52s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 52s Starting 2 pkgProblemResolver with broken count: 0 52s Done 52s Entering ResolveByKeep 53s 53s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 53s Reading package lists... 53s Building dependency tree... 53s Reading state information... 53s Starting pkgProblemResolver with broken count: 0 53s Starting 2 pkgProblemResolver with broken count: 0 53s Done 54s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 54s autopkgtest [13:10:21]: rebooting testbed after setup commands that affected boot 58s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 69s autopkgtest [13:10:36]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 16:02:16 UTC 2025 70s autopkgtest [13:10:37]: @@@@@@@@@@@@@@@@@@@@ apt-source mdtraj 72s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.3-2 (dsc) [2677 B] 72s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.3-2 (tar) [22.0 MB] 72s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.3-2 (diff) [300 kB] 72s gpgv: Signature made Tue Feb 11 15:16:54 2025 UTC 72s gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA 72s gpgv: Can't check signature: No public key 72s dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.10.3-2.dsc: no acceptable signature found 73s autopkgtest [13:10:40]: testing package mdtraj version 1.10.3-2 73s autopkgtest [13:10:40]: build not needed 74s autopkgtest [13:10:41]: test command1: preparing testbed 74s Reading package lists... 75s Building dependency tree... 75s Reading state information... 75s Starting pkgProblemResolver with broken count: 0 75s Starting 2 pkgProblemResolver with broken count: 0 75s Done 75s The following NEW packages will be installed: 75s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx gdb 75s libaec0 libbabeltrace1 libblas3 libblosc1 libblosc2-4 libdebuginfod-common 75s libdebuginfod1t64 libdeflate0 libfontconfig1 libgfortran5 libgomp1 75s libgraphite2-3 libharfbuzz0b libhdf5-310 libhdf5-hl-310 libimagequant0 75s libipt2 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 75s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libnetcdf22 libnorm1t64 75s libopenjp2-7 libpgm-5.3-0t64 libqhull-r8.0 libraqm0 libsharpyuv0 75s libsnappy1v5 libsodium23 libsource-highlight-common libsource-highlight4t64 75s libsz2 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 75s libxft2 libxrender1 libxslt1.1 libxss1 libzmq5 python-matplotlib-data 75s python-tables-data python3-asttokens python3-brotli python3-cftime 75s python3-comm python3-contourpy python3-coverage python3-cpuinfo 75s python3-cycler python3-dateutil python3-debugpy python3-decorator 75s python3-executing python3-fastjsonschema python3-fonttools python3-fs 75s python3-gsd python3-iniconfig python3-ipykernel python3-ipython python3-jedi 75s python3-joblib python3-jupyter-client python3-jupyter-core 75s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 75s python3-matplotlib-inline python3-mdtraj python3-mpmath python3-nbformat 75s python3-nest-asyncio python3-netcdf4 python3-networkx python3-numexpr 75s python3-numpy python3-packaging python3-pandas python3-pandas-lib 75s python3-parso python3-pexpect python3-pil python3-pil.imagetk 75s python3-platformdirs python3-pluggy python3-prompt-toolkit python3-psutil 75s python3-ptyprocess python3-pure-eval python3-pytest python3-pytz 75s python3-scipy python3-sklearn python3-sklearn-lib python3-stack-data 75s python3-sympy python3-tables python3-tables-lib python3-threadpoolctl 75s python3-tk python3-tornado python3-traitlets python3-typeshed python3-tz 75s python3-ufolib2 python3-unicodedata2 python3-wcwidth python3-zmq python3.12 75s python3.12-minimal python3.12-tk python3.13-tk tk8.6-blt2.5 unicode-data 75s x11-common 76s 0 upgraded, 132 newly installed, 0 to remove and 0 not upgraded. 76s Need to get 125 MB of archives. 76s After this operation, 662 MB of additional disk space will be used. 76s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-minimal amd64 3.12.9-1 [2348 kB] 76s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 76s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12 amd64 3.12.9-1 [671 kB] 76s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 76s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 76s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 76s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 76s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 76s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 76s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 76s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 76s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 76s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 76s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 76s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 76s Get:16 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.3-1 [171 kB] 76s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libbabeltrace1 amd64 1.5.11-4build1 [185 kB] 76s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 76s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libipt2 amd64 2.1.2-1 [58.9 kB] 76s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libsource-highlight-common all 3.1.9-4.3build1 [64.2 kB] 76s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libsource-highlight4t64 amd64 3.1.9-4.3build1 [258 kB] 76s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 gdb amd64 16.2-1ubuntu1 [8934 kB] 76s Get:23 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 76s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 76s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libsnappy1v5 amd64 1.2.1-1 [30.4 kB] 76s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 libblosc1 amd64 1.21.5+ds-1build1 [36.2 kB] 76s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 libblosc2-4 amd64 2.16.0+ds-1 [171 kB] 76s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 76s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250213-1ubuntu1 [920 kB] 76s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250213-1ubuntu1 [148 kB] 76s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 76s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 76s Get:33 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 76s Get:34 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-310 amd64 1.14.5+repack-3 [1519 kB] 76s Get:35 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [62.6 kB] 76s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 76s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 76s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 76s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 76s Get:40 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 76s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 76s Get:42 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 76s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 76s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 76s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnetcdf22 amd64 1:4.9.3-1 [574 kB] 76s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnorm1t64 amd64 1.5.9+dfsg-3.1build1 [154 kB] 76s Get:47 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpgm-5.3-0t64 amd64 5.3.128~dfsg-2.1build1 [167 kB] 76s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 76s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 76s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 76s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libsodium23 amd64 1.0.18-1build3 [161 kB] 76s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 76s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 76s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 76s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 76s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 76s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu2 [175 kB] 76s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 libzmq5 amd64 4.3.5-1build2 [260 kB] 76s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3ubuntu2 [2929 kB] 77s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-tables-data all 3.10.2-2 [49.6 kB] 77s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-asttokens all 3.0.0-1 [20.4 kB] 77s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build3 [368 kB] 77s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-13 [5319 kB] 77s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cftime amd64 1.6.4-1build2 [346 kB] 77s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 77s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-comm all 0.2.1-1 [7016 B] 77s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.1-1 [271 kB] 77s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-coverage amd64 7.4.4+dfsg1-0ubuntu3 [150 kB] 77s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cpuinfo all 9.0.0+git20221119-3 [21.7 kB] 77s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 77s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB] 77s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-debugpy amd64 1.8.8+ds-2ubuntu1 [1145 kB] 77s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 77s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-executing all 2.2.0-0.1 [25.0 kB] 77s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fastjsonschema all 2.21.1-1 [20.4 kB] 77s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pytz all 2025.1-3 [162 kB] 77s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2025.1-3 [1866 B] 77s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-platformdirs all 4.3.6-1 [16.8 kB] 77s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-6 [90.7 kB] 77s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.1-1 [1831 kB] 77s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.4.0+dfsg-1 [27.4 kB] 77s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.14.1-4ubuntu1 [22.3 MB] 77s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 77s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 77s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 77s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build2 [360 kB] 77s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 77s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.55.3-2 [1755 kB] 77s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-gsd amd64 3.3.0-1build2 [234 kB] 77s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 77s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-parso all 0.8.4-1 [67.6 kB] 77s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-typeshed all 0.0~git20241223.ea91db2-1 [1548 kB] 77s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-jedi all 0.19.1+ds1-1 [693 kB] 77s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 77s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 77s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-prompt-toolkit all 3.0.50-1 [257 kB] 77s Get:97 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pure-eval all 0.2.3-1 [11.4 kB] 77s Get:98 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-stack-data all 0.6.3-1 [22.0 kB] 77s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-ptyprocess all 0.7.0-6 [14.8 kB] 77s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pexpect all 4.9-3 [48.1 kB] 77s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ipython all 8.30.0-2 [569 kB] 77s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-jupyter-core all 5.7.2-5 [28.1 kB] 77s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-psutil amd64 5.9.8-2build3 [196 kB] 77s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tornado amd64 6.4.2-1 [299 kB] 77s Get:105 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-zmq amd64 26.2.1-1 [226 kB] 77s Get:106 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-jupyter-client all 8.6.3-2 [78.5 kB] 77s Get:107 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-nest-asyncio all 1.5.4-1 [6256 B] 77s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 78s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ipykernel all 6.29.5-2 [82.7 kB] 78s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.4.2-2 [205 kB] 78s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-3 [70.4 kB] 78s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu3 [217 kB] 78s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 11.1.0-5 [589 kB] 78s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.9-1 [116 kB] 78s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.2-1 [107 kB] 78s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.13.1-1 [9770 B] 78s Get:117 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 11.1.0-5 [9936 B] 78s Get:118 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3ubuntu2 [4697 kB] 78s Get:119 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-netcdf4 amd64 1.7.2-1build3 [942 kB] 78s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 78s Get:121 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-8 [8248 kB] 78s Get:122 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-8 [3112 kB] 78s Get:123 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-numexpr amd64 2.10.2-1build1 [133 kB] 78s Get:124 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-tables-lib amd64 3.10.2-2 [859 kB] 78s Get:125 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-tables all 3.10.2-2 [354 kB] 78s Get:126 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mdtraj amd64 1.10.3-2 [1629 kB] 78s Get:127 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-nbformat all 5.9.1-1 [41.2 kB] 78s Get:128 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 78s Get:129 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.4-1 [252 kB] 78s Get:130 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 78s Get:131 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-7build1 [6872 kB] 78s Get:132 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn all 1.4.2+dfsg-7build1 [2258 kB] 79s Preconfiguring packages ... 79s Fetched 125 MB in 3s (42.8 MB/s) 79s Selecting previously unselected package python3.12-minimal. 79s (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 ... 108975 files and directories currently installed.) 79s Preparing to unpack .../000-python3.12-minimal_3.12.9-1_amd64.deb ... 79s Unpacking python3.12-minimal (3.12.9-1) ... 79s Selecting previously unselected package libdebuginfod-common. 79s Preparing to unpack .../001-libdebuginfod-common_0.192-4_all.deb ... 79s Unpacking libdebuginfod-common (0.192-4) ... 79s Selecting previously unselected package python3.12. 79s Preparing to unpack .../002-python3.12_3.12.9-1_amd64.deb ... 79s Unpacking python3.12 (3.12.9-1) ... 79s Selecting previously unselected package libtcl8.6:amd64. 79s Preparing to unpack .../003-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 79s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 79s Selecting previously unselected package fonts-dejavu-mono. 79s Preparing to unpack .../004-fonts-dejavu-mono_2.37-8_all.deb ... 79s Unpacking fonts-dejavu-mono (2.37-8) ... 79s Selecting previously unselected package fonts-dejavu-core. 80s Preparing to unpack .../005-fonts-dejavu-core_2.37-8_all.deb ... 80s Unpacking fonts-dejavu-core (2.37-8) ... 80s Selecting previously unselected package fontconfig-config. 80s Preparing to unpack .../006-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 80s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 80s Selecting previously unselected package libfontconfig1:amd64. 80s Preparing to unpack .../007-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 80s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 80s Selecting previously unselected package libxrender1:amd64. 80s Preparing to unpack .../008-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 80s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 80s Selecting previously unselected package libxft2:amd64. 80s Preparing to unpack .../009-libxft2_2.3.6-1build1_amd64.deb ... 80s Unpacking libxft2:amd64 (2.3.6-1build1) ... 80s Selecting previously unselected package x11-common. 80s Preparing to unpack .../010-x11-common_1%3a7.7+23ubuntu3_all.deb ... 80s Unpacking x11-common (1:7.7+23ubuntu3) ... 80s Selecting previously unselected package libxss1:amd64. 80s Preparing to unpack .../011-libxss1_1%3a1.2.3-1build3_amd64.deb ... 80s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 80s Selecting previously unselected package libtk8.6:amd64. 80s Preparing to unpack .../012-libtk8.6_8.6.16-1_amd64.deb ... 80s Unpacking libtk8.6:amd64 (8.6.16-1) ... 80s Selecting previously unselected package tk8.6-blt2.5. 80s Preparing to unpack .../013-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 80s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 80s Selecting previously unselected package blt. 80s Preparing to unpack .../014-blt_2.5.3+dfsg-7build1_amd64.deb ... 80s Unpacking blt (2.5.3+dfsg-7build1) ... 80s Selecting previously unselected package fonts-lyx. 80s Preparing to unpack .../015-fonts-lyx_2.4.3-1_all.deb ... 80s Unpacking fonts-lyx (2.4.3-1) ... 80s Selecting previously unselected package libbabeltrace1:amd64. 80s Preparing to unpack .../016-libbabeltrace1_1.5.11-4build1_amd64.deb ... 80s Unpacking libbabeltrace1:amd64 (1.5.11-4build1) ... 80s Selecting previously unselected package libdebuginfod1t64:amd64. 80s Preparing to unpack .../017-libdebuginfod1t64_0.192-4_amd64.deb ... 80s Unpacking libdebuginfod1t64:amd64 (0.192-4) ... 80s Selecting previously unselected package libipt2. 80s Preparing to unpack .../018-libipt2_2.1.2-1_amd64.deb ... 80s Unpacking libipt2 (2.1.2-1) ... 80s Selecting previously unselected package libsource-highlight-common. 80s Preparing to unpack .../019-libsource-highlight-common_3.1.9-4.3build1_all.deb ... 80s Unpacking libsource-highlight-common (3.1.9-4.3build1) ... 80s Selecting previously unselected package libsource-highlight4t64:amd64. 80s Preparing to unpack .../020-libsource-highlight4t64_3.1.9-4.3build1_amd64.deb ... 80s Unpacking libsource-highlight4t64:amd64 (3.1.9-4.3build1) ... 80s Selecting previously unselected package gdb. 80s Preparing to unpack .../021-gdb_16.2-1ubuntu1_amd64.deb ... 80s Unpacking gdb (16.2-1ubuntu1) ... 81s Selecting previously unselected package libaec0:amd64. 81s Preparing to unpack .../022-libaec0_1.1.3-1_amd64.deb ... 81s Unpacking libaec0:amd64 (1.1.3-1) ... 81s Selecting previously unselected package libblas3:amd64. 81s Preparing to unpack .../023-libblas3_3.12.1-2_amd64.deb ... 81s Unpacking libblas3:amd64 (3.12.1-2) ... 81s Selecting previously unselected package libsnappy1v5:amd64. 81s Preparing to unpack .../024-libsnappy1v5_1.2.1-1_amd64.deb ... 81s Unpacking libsnappy1v5:amd64 (1.2.1-1) ... 81s Selecting previously unselected package libblosc1:amd64. 81s Preparing to unpack .../025-libblosc1_1.21.5+ds-1build1_amd64.deb ... 81s Unpacking libblosc1:amd64 (1.21.5+ds-1build1) ... 81s Selecting previously unselected package libblosc2-4:amd64. 81s Preparing to unpack .../026-libblosc2-4_2.16.0+ds-1_amd64.deb ... 81s Unpacking libblosc2-4:amd64 (2.16.0+ds-1) ... 81s Selecting previously unselected package libdeflate0:amd64. 81s Preparing to unpack .../027-libdeflate0_1.23-1_amd64.deb ... 81s Unpacking libdeflate0:amd64 (1.23-1) ... 81s Selecting previously unselected package libgfortran5:amd64. 81s Preparing to unpack .../028-libgfortran5_15-20250213-1ubuntu1_amd64.deb ... 81s Unpacking libgfortran5:amd64 (15-20250213-1ubuntu1) ... 81s Selecting previously unselected package libgomp1:amd64. 81s Preparing to unpack .../029-libgomp1_15-20250213-1ubuntu1_amd64.deb ... 81s Unpacking libgomp1:amd64 (15-20250213-1ubuntu1) ... 81s Selecting previously unselected package libgraphite2-3:amd64. 81s Preparing to unpack .../030-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 81s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 81s Selecting previously unselected package libharfbuzz0b:amd64. 81s Preparing to unpack .../031-libharfbuzz0b_10.2.0-1_amd64.deb ... 81s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 81s Selecting previously unselected package libsz2:amd64. 81s Preparing to unpack .../032-libsz2_1.1.3-1_amd64.deb ... 81s Unpacking libsz2:amd64 (1.1.3-1) ... 81s Selecting previously unselected package libhdf5-310:amd64. 81s Preparing to unpack .../033-libhdf5-310_1.14.5+repack-3_amd64.deb ... 81s Unpacking libhdf5-310:amd64 (1.14.5+repack-3) ... 81s Selecting previously unselected package libhdf5-hl-310:amd64. 81s Preparing to unpack .../034-libhdf5-hl-310_1.14.5+repack-3_amd64.deb ... 81s Unpacking libhdf5-hl-310:amd64 (1.14.5+repack-3) ... 81s Selecting previously unselected package libimagequant0:amd64. 81s Preparing to unpack .../035-libimagequant0_2.18.0-1build1_amd64.deb ... 81s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 81s Selecting previously unselected package libjpeg-turbo8:amd64. 81s Preparing to unpack .../036-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 81s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 81s Selecting previously unselected package libjpeg8:amd64. 81s Preparing to unpack .../037-libjpeg8_8c-2ubuntu11_amd64.deb ... 81s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 81s Selecting previously unselected package libjs-jquery. 81s Preparing to unpack .../038-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 81s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 81s Selecting previously unselected package libjs-jquery-ui. 81s Preparing to unpack .../039-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 81s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 81s Selecting previously unselected package liblapack3:amd64. 81s Preparing to unpack .../040-liblapack3_3.12.1-2_amd64.deb ... 81s Unpacking liblapack3:amd64 (3.12.1-2) ... 81s Selecting previously unselected package liblbfgsb0:amd64. 81s Preparing to unpack .../041-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 81s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 82s Selecting previously unselected package liblcms2-2:amd64. 82s Preparing to unpack .../042-liblcms2-2_2.16-2_amd64.deb ... 82s Unpacking liblcms2-2:amd64 (2.16-2) ... 82s Selecting previously unselected package liblerc4:amd64. 82s Preparing to unpack .../043-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 82s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 82s Selecting previously unselected package libnetcdf22:amd64. 82s Preparing to unpack .../044-libnetcdf22_1%3a4.9.3-1_amd64.deb ... 82s Unpacking libnetcdf22:amd64 (1:4.9.3-1) ... 82s Selecting previously unselected package libnorm1t64:amd64. 82s Preparing to unpack .../045-libnorm1t64_1.5.9+dfsg-3.1build1_amd64.deb ... 82s Unpacking libnorm1t64:amd64 (1.5.9+dfsg-3.1build1) ... 82s Selecting previously unselected package libpgm-5.3-0t64:amd64. 82s Preparing to unpack .../046-libpgm-5.3-0t64_5.3.128~dfsg-2.1build1_amd64.deb ... 82s Unpacking libpgm-5.3-0t64:amd64 (5.3.128~dfsg-2.1build1) ... 82s Selecting previously unselected package libqhull-r8.0:amd64. 82s Preparing to unpack .../047-libqhull-r8.0_2020.2-6build1_amd64.deb ... 82s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 82s Selecting previously unselected package libraqm0:amd64. 82s Preparing to unpack .../048-libraqm0_0.10.2-1_amd64.deb ... 82s Unpacking libraqm0:amd64 (0.10.2-1) ... 82s Selecting previously unselected package libsharpyuv0:amd64. 82s Preparing to unpack .../049-libsharpyuv0_1.5.0-0.1_amd64.deb ... 82s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 82s Selecting previously unselected package libsodium23:amd64. 82s Preparing to unpack .../050-libsodium23_1.0.18-1build3_amd64.deb ... 82s Unpacking libsodium23:amd64 (1.0.18-1build3) ... 82s Selecting previously unselected package libjbig0:amd64. 82s Preparing to unpack .../051-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 82s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 82s Selecting previously unselected package libwebp7:amd64. 82s Preparing to unpack .../052-libwebp7_1.5.0-0.1_amd64.deb ... 82s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 82s Selecting previously unselected package libtiff6:amd64. 82s Preparing to unpack .../053-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 82s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 82s Selecting previously unselected package libwebpdemux2:amd64. 82s Preparing to unpack .../054-libwebpdemux2_1.5.0-0.1_amd64.deb ... 82s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 82s Selecting previously unselected package libwebpmux3:amd64. 82s Preparing to unpack .../055-libwebpmux3_1.5.0-0.1_amd64.deb ... 82s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 82s Selecting previously unselected package libxslt1.1:amd64. 82s Preparing to unpack .../056-libxslt1.1_1.1.39-0exp1ubuntu2_amd64.deb ... 82s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu2) ... 82s Selecting previously unselected package libzmq5:amd64. 82s Preparing to unpack .../057-libzmq5_4.3.5-1build2_amd64.deb ... 82s Unpacking libzmq5:amd64 (4.3.5-1build2) ... 82s Selecting previously unselected package python-matplotlib-data. 82s Preparing to unpack .../058-python-matplotlib-data_3.8.3-3ubuntu2_all.deb ... 82s Unpacking python-matplotlib-data (3.8.3-3ubuntu2) ... 82s Selecting previously unselected package python-tables-data. 82s Preparing to unpack .../059-python-tables-data_3.10.2-2_all.deb ... 82s Unpacking python-tables-data (3.10.2-2) ... 82s Selecting previously unselected package python3-asttokens. 82s Preparing to unpack .../060-python3-asttokens_3.0.0-1_all.deb ... 82s Unpacking python3-asttokens (3.0.0-1) ... 82s Selecting previously unselected package python3-brotli. 82s Preparing to unpack .../061-python3-brotli_1.1.0-2build3_amd64.deb ... 82s Unpacking python3-brotli (1.1.0-2build3) ... 82s Selecting previously unselected package python3-numpy. 82s Preparing to unpack .../062-python3-numpy_1%3a1.26.4+ds-13_amd64.deb ... 82s Unpacking python3-numpy (1:1.26.4+ds-13) ... 83s Selecting previously unselected package python3-cftime. 83s Preparing to unpack .../063-python3-cftime_1.6.4-1build2_amd64.deb ... 83s Unpacking python3-cftime (1.6.4-1build2) ... 83s Selecting previously unselected package python3-traitlets. 83s Preparing to unpack .../064-python3-traitlets_5.14.3+really5.14.3-1_all.deb ... 83s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ... 83s Selecting previously unselected package python3-comm. 83s Preparing to unpack .../065-python3-comm_0.2.1-1_all.deb ... 83s Unpacking python3-comm (0.2.1-1) ... 83s Selecting previously unselected package python3-contourpy. 83s Preparing to unpack .../066-python3-contourpy_1.3.1-1_amd64.deb ... 83s Unpacking python3-contourpy (1.3.1-1) ... 83s Selecting previously unselected package python3-coverage. 83s Preparing to unpack .../067-python3-coverage_7.4.4+dfsg1-0ubuntu3_amd64.deb ... 83s Unpacking python3-coverage (7.4.4+dfsg1-0ubuntu3) ... 83s Selecting previously unselected package python3-cpuinfo. 83s Preparing to unpack .../068-python3-cpuinfo_9.0.0+git20221119-3_all.deb ... 83s Unpacking python3-cpuinfo (9.0.0+git20221119-3) ... 83s Selecting previously unselected package python3-cycler. 83s Preparing to unpack .../069-python3-cycler_0.12.1-1_all.deb ... 83s Unpacking python3-cycler (0.12.1-1) ... 83s Selecting previously unselected package python3-dateutil. 83s Preparing to unpack .../070-python3-dateutil_2.9.0-3_all.deb ... 83s Unpacking python3-dateutil (2.9.0-3) ... 83s Selecting previously unselected package python3-debugpy. 83s Preparing to unpack .../071-python3-debugpy_1.8.8+ds-2ubuntu1_amd64.deb ... 83s Unpacking python3-debugpy (1.8.8+ds-2ubuntu1) ... 83s Selecting previously unselected package python3-decorator. 83s Preparing to unpack .../072-python3-decorator_5.1.1-5_all.deb ... 83s Unpacking python3-decorator (5.1.1-5) ... 83s Selecting previously unselected package python3-executing. 83s Preparing to unpack .../073-python3-executing_2.2.0-0.1_all.deb ... 83s Unpacking python3-executing (2.2.0-0.1) ... 83s Selecting previously unselected package python3-fastjsonschema. 83s Preparing to unpack .../074-python3-fastjsonschema_2.21.1-1_all.deb ... 83s Unpacking python3-fastjsonschema (2.21.1-1) ... 83s Selecting previously unselected package python3-pytz. 83s Preparing to unpack .../075-python3-pytz_2025.1-3_all.deb ... 83s Unpacking python3-pytz (2025.1-3) ... 83s Selecting previously unselected package python3-tz. 83s Preparing to unpack .../076-python3-tz_2025.1-3_all.deb ... 83s Unpacking python3-tz (2025.1-3) ... 83s Selecting previously unselected package python3-platformdirs. 83s Preparing to unpack .../077-python3-platformdirs_4.3.6-1_all.deb ... 83s Unpacking python3-platformdirs (4.3.6-1) ... 83s Selecting previously unselected package python3-fs. 83s Preparing to unpack .../078-python3-fs_2.4.16-6_all.deb ... 83s Unpacking python3-fs (2.4.16-6) ... 83s Selecting previously unselected package python3-lxml:amd64. 83s Preparing to unpack .../079-python3-lxml_5.3.1-1_amd64.deb ... 83s Unpacking python3-lxml:amd64 (5.3.1-1) ... 83s Selecting previously unselected package python3-lz4. 83s Preparing to unpack .../080-python3-lz4_4.4.0+dfsg-1_amd64.deb ... 83s Unpacking python3-lz4 (4.4.0+dfsg-1) ... 84s Selecting previously unselected package python3-scipy. 84s Preparing to unpack .../081-python3-scipy_1.14.1-4ubuntu1_amd64.deb ... 84s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 84s Selecting previously unselected package python3-mpmath. 84s Preparing to unpack .../082-python3-mpmath_1.3.0-1_all.deb ... 84s Unpacking python3-mpmath (1.3.0-1) ... 84s Selecting previously unselected package python3-sympy. 84s Preparing to unpack .../083-python3-sympy_1.13.3-1_all.deb ... 84s Unpacking python3-sympy (1.13.3-1) ... 85s Selecting previously unselected package python3-ufolib2. 85s Preparing to unpack .../084-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 85s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 85s Selecting previously unselected package python3-unicodedata2. 85s Preparing to unpack .../085-python3-unicodedata2_15.1.0+ds-1build2_amd64.deb ... 85s Unpacking python3-unicodedata2 (15.1.0+ds-1build2) ... 85s Selecting previously unselected package unicode-data. 85s Preparing to unpack .../086-unicode-data_15.1.0-1_all.deb ... 85s Unpacking unicode-data (15.1.0-1) ... 85s Selecting previously unselected package python3-fonttools. 85s Preparing to unpack .../087-python3-fonttools_4.55.3-2_amd64.deb ... 85s Unpacking python3-fonttools (4.55.3-2) ... 85s Selecting previously unselected package python3-gsd. 85s Preparing to unpack .../088-python3-gsd_3.3.0-1build2_amd64.deb ... 85s Unpacking python3-gsd (3.3.0-1build2) ... 85s Selecting previously unselected package python3-iniconfig. 85s Preparing to unpack .../089-python3-iniconfig_1.1.1-2_all.deb ... 85s Unpacking python3-iniconfig (1.1.1-2) ... 85s Selecting previously unselected package python3-parso. 85s Preparing to unpack .../090-python3-parso_0.8.4-1_all.deb ... 85s Unpacking python3-parso (0.8.4-1) ... 85s Selecting previously unselected package python3-typeshed. 85s Preparing to unpack .../091-python3-typeshed_0.0~git20241223.ea91db2-1_all.deb ... 85s Unpacking python3-typeshed (0.0~git20241223.ea91db2-1) ... 86s Selecting previously unselected package python3-jedi. 86s Preparing to unpack .../092-python3-jedi_0.19.1+ds1-1_all.deb ... 86s Unpacking python3-jedi (0.19.1+ds1-1) ... 86s Selecting previously unselected package python3-matplotlib-inline. 86s Preparing to unpack .../093-python3-matplotlib-inline_0.1.6-2_all.deb ... 86s Unpacking python3-matplotlib-inline (0.1.6-2) ... 86s Selecting previously unselected package python3-wcwidth. 86s Preparing to unpack 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90s Setting up liblcms2-2:amd64 (2.16-2) ... 90s Setting up python3-iniconfig (1.1.1-2) ... 90s Setting up python3.12-minimal (3.12.9-1) ... 91s Setting up python3-tornado (6.4.2-1) ... 92s Setting up libnorm1t64:amd64 (1.5.9+dfsg-3.1build1) ... 92s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 92s Setting up python3-pure-eval (0.2.3-1) ... 92s Setting up libsodium23:amd64 (1.0.18-1build3) ... 92s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 92s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 92s Setting up libdebuginfod-common (0.192-4) ... 92s Setting up python3-joblib (1.4.2-2) ... 92s Setting up python3-parso (0.8.4-1) ... 93s Setting up python3-lz4 (4.4.0+dfsg-1) ... 93s Setting up python3-asttokens (3.0.0-1) ... 93s Setting up python3-unicodedata2 (15.1.0+ds-1build2) ... 93s Setting up fonts-lyx (2.4.3-1) ... 93s Setting up python3.12 (3.12.9-1) ... 94s Setting up python3-threadpoolctl (3.1.0-1) ... 94s Setting up x11-common (1:7.7+23ubuntu3) ... 95s Setting up libdeflate0:amd64 (1.23-1) ... 95s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 95s Setting up python3-coverage (7.4.4+dfsg1-0ubuntu3) ... 95s Setting up python3-pytz (2025.1-3) ... 95s Setting up libgomp1:amd64 (15-20250213-1ubuntu1) ... 95s Setting up python3-networkx (3.2.1-4ubuntu1) ... 98s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 98s Setting up libaec0:amd64 (1.1.3-1) ... 98s Setting up python3-platformdirs (4.3.6-1) ... 98s Setting up python3-psutil (5.9.8-2build3) ... 98s Setting up libsource-highlight-common (3.1.9-4.3build1) ... 98s Setting up python3-tz (2025.1-3) ... 98s Setting up libsnappy1v5:amd64 (1.2.1-1) ... 98s Setting up python3-fs (2.4.16-6) ... 99s Setting up unicode-data (15.1.0-1) ... 99s Setting up libpgm-5.3-0t64:amd64 (5.3.128~dfsg-2.1build1) ... 99s Setting up python3-decorator (5.1.1-5) ... 99s Setting up libblosc2-4:amd64 (2.16.0+ds-1) ... 99s Setting up libblas3:amd64 (3.12.1-2) ... 99s 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 99s Setting up python3-packaging (24.2-1) ... 99s Setting up python3-wcwidth (0.2.13+dfsg1-1) ... 99s Setting up python3-typeshed (0.0~git20241223.ea91db2-1) ... 99s Setting up python3-executing (2.2.0-0.1) ... 100s Setting up python3-nest-asyncio (1.5.4-1) ... 100s Setting up python3-brotli (1.1.0-2build3) ... 100s Setting up python3-cycler (0.12.1-1) ... 100s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 100s Setting up fonts-dejavu-mono (2.37-8) ... 100s Setting up python3-kiwisolver (1.4.7-3) ... 100s Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... 100s Setting up libipt2 (2.1.2-1) ... 100s Setting up fonts-dejavu-core (2.37-8) ... 100s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 100s Setting up python3-cpuinfo (9.0.0+git20221119-3) ... 100s Setting up libbabeltrace1:amd64 (1.5.11-4build1) ... 100s Setting up libgfortran5:amd64 (15-20250213-1ubuntu1) ... 100s Setting up python3-pluggy (1.5.0-1) ... 101s Setting up libwebp7:amd64 (1.5.0-0.1) ... 101s Setting up python3-fastjsonschema (2.21.1-1) ... 101s Setting up python3-traitlets (5.14.3+really5.14.3-1) ... 101s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu2) ... 101s Setting up libblosc1:amd64 (1.21.5+ds-1build1) ... 101s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu3) ... 101s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 101s Setting up python3-dateutil (2.9.0-3) ... 101s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 101s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 101s Setting up python3-mpmath (1.3.0-1) ... 102s Setting up python-matplotlib-data (3.8.3-3ubuntu2) ... 102s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 102s Setting up python3-stack-data (0.6.3-1) ... 102s Setting up python-tables-data (3.10.2-2) ... 102s Setting up python3-jupyter-core (5.7.2-5) ... 103s Setting up libsz2:amd64 (1.1.3-1) ... 103s Setting up python3-ptyprocess (0.7.0-6) ... 103s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 103s Setting up python3-prompt-toolkit (3.0.50-1) ... 103s Setting up python3-sympy (1.13.3-1) ... 115s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 115s Setting up liblapack3:amd64 (3.12.1-2) ... 115s 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 115s Setting up libzmq5:amd64 (4.3.5-1build2) ... 115s Setting up python3-jedi (0.19.1+ds1-1) ... 115s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 115s Setting up python3-pytest (8.3.4-1) ... 116s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 116s Setting up libsource-highlight4t64:amd64 (3.1.9-4.3build1) ... 116s Setting up python3-nbformat (5.9.1-1) ... 116s Setting up python3-matplotlib-inline (0.1.6-2) ... 116s Setting up python3-comm (0.2.1-1) ... 116s Setting up gdb (16.2-1ubuntu1) ... 116s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 116s Setting up python3-pexpect (4.9-3) ... 117s Setting up python3-zmq (26.2.1-1) ... 117s Setting up libraqm0:amd64 (0.10.2-1) ... 117s Setting up python3-numpy (1:1.26.4+ds-13) ... 120s Setting up libhdf5-310:amd64 (1.14.5+repack-3) ... 120s Setting up python3-lxml:amd64 (5.3.1-1) ... 121s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 121s Setting up python3-jupyter-client (8.6.3-2) ... 121s Setting up python3-contourpy (1.3.1-1) ... 121s Setting up libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 121s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 121s Setting up libhdf5-hl-310:amd64 (1.14.5+repack-3) ... 121s Setting up libxft2:amd64 (2.3.6-1build1) ... 121s Setting up python3-scipy (1.14.1-4ubuntu1) ... 127s Setting up python3-tables-lib (3.10.2-2) ... 127s Setting up libtk8.6:amd64 (8.6.16-1) ... 127s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-8) ... 127s Setting up python3.12-tk (3.12.9-1) ... 127s Setting up libnetcdf22:amd64 (1:4.9.3-1) ... 127s Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-7build1) ... 127s Setting up python3-gsd (3.3.0-1build2) ... 128s Setting up python3-debugpy (1.8.8+ds-2ubuntu1) ... 129s Setting up python3.13-tk (3.13.2-1) ... 129s Setting up python3-pil:amd64 (11.1.0-5) ... 129s Setting up python3-pandas (2.2.3+dfsg-8) ... 138s Setting up python3-ipython (8.30.0-2) ... 139s Setting up python3-ipykernel (6.29.5-2) ... 139s Setting up python3-sklearn (1.4.2+dfsg-7build1) ... 142s Setting up python3-cftime (1.6.4-1build2) ... 142s Setting up python3-numexpr (2.10.2-1build1) ... 143s Setting up python3-netcdf4 (1.7.2-1build3) ... 143s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 143s Setting up blt (2.5.3+dfsg-7build1) ... 143s Setting up python3-tk:amd64 (3.13.1-1) ... 143s Setting up python3-tables (3.10.2-2) ... 144s Setting up python3-mdtraj (1.10.3-2) ... 145s Setting up python3-pil.imagetk:amd64 (11.1.0-5) ... 145s Setting up python3-fonttools (4.55.3-2) ... 146s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 147s Setting up python3-matplotlib (3.8.3-3ubuntu2) ... 149s Processing triggers for libc-bin (2.40-4ubuntu1) ... 149s Processing triggers for systemd (257.2-3ubuntu1) ... 149s Processing triggers for man-db (2.13.0-1) ... 151s autopkgtest [13:11:58]: 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)' 151s autopkgtest [13:11:58]: test command1: [----------------------- 152s ============================= test session starts ============================== 152s platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 -- /usr/bin/python3 152s cachedir: .pytest_cache 152s rootdir: /tmp/autopkgtest.OuqIYg/build.quR/src 152s configfile: pyproject.toml 152s testpaths: tests, examples 152s plugins: typeguard-4.4.1 153s collecting ... collected 1145 items / 12 deselected / 1133 selected 153s 153s tests/test_alignment.py::test_rmsd_zero PASSED [ 0%] 153s 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[ 6%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.core.element] PASSED [ 6%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.core.residue_names] PASSED [ 6%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.core.selection] PASSED [ 6%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.core.topology] PASSED [ 6%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.core.trajectory] PASSED [ 6%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.amberrst] PASSED [ 6%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.arc] PASSED [ 6%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.dcd] PASSED [ 6%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.dtr] PASSED [ 6%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.gro] PASSED [ 7%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.gsd] PASSED [ 7%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.hdf5] SKIPPED [ 7%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.hoomdxml] PASSED [ 7%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.lammpstrj] PASSED [ 7%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.lh5] SKIPPED [ 7%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.mdcrd] PASSED [ 7%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.mol2] PASSED [ 7%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.netcdf] PASSED [ 7%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.openmmxml] PASSED [ 7%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdb.pdbfile] PASSED [ 7%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdb.pdbstructure] SKIPPED [ 8%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdbx] PASSED [ 8%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.prmtop] PASSED [ 8%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.psf] PASSED [ 8%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.registry] PASSED [ 8%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.trr] PASSED [ 8%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.xtc] PASSED [ 8%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.formats.xyzfile] PASSED [ 8%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.geometry._geometry] PASSED [ 8%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.alignment] PASSED [ 8%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.angle] PASSED [ 8%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.contact] PASSED [ 9%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.dihedral] PASSED [ 9%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.distance] PASSED [ 9%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.drid] PASSED [ 9%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.dssp] PASSED [ 9%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.hbond] PASSED [ 9%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.internal] PASSED [ 9%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.neighborlist] PASSED [ 9%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.neighbors] PASSED [ 9%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.order] PASSED [ 9%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.rdf] PASSED [ 9%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.rg] PASSED [ 9%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.sasa] PASSED [ 10%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.shape] PASSED [ 10%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.thermodynamic_properties] PASSED [ 10%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.io] SKIPPED (Skip c...) [ 10%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.nmr.scalar_couplings] PASSED [ 10%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.nmr.shift_wrappers] PASSED [ 10%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.basereporter] PASSED [ 10%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.dcdreporter] PASSED [ 10%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.hdf5reporter] PASSED [ 10%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.netcdfreporter] PASSED [ 10%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.xtcreporter] PASSED [ 10%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.scripts.mdconvert] SKIPPED [ 11%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.scripts.mdinspect] SKIPPED [ 11%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.testing.docscrape] SKIPPED [ 11%] 163s tests/test_docstrings.py::test_docstrings[mdtraj.testing.docstrings] PASSED [ 11%] 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tests/test_hoomdxml.py::test_correct_ordering PASSED [ 21%] 178s tests/test_io.py::test_overwrite_1 PASSED [ 21%] 178s tests/test_io.py::test_overwrite_2 PASSED [ 21%] 178s tests/test_io.py::test_io::test_load_1 PASSED [ 21%] 178s tests/test_io.py::test_io::test_load_2 PASSED [ 22%] 178s tests/test_io.py::test_io::test_load_3 PASSED [ 22%] 178s tests/test_io.py::test_io::test_save PASSED [ 22%] 178s tests/test_io.py::test_io_int::test_load_1 PASSED [ 22%] 178s tests/test_io.py::test_io_int::test_load_2 PASSED [ 22%] 178s tests/test_io.py::test_io_int::test_load_3 PASSED [ 22%] 178s tests/test_io.py::test_io_int::test_save PASSED [ 22%] 178s tests/test_io.py::test_groups PASSED [ 22%] 178s tests/test_lammpstrj.py::test_read_0 PASSED [ 22%] 178s tests/test_lammpstrj.py::test_read_1 PASSED [ 22%] 178s tests/test_lammpstrj.py::test_read_write_0 PASSED [ 22%] 178s tests/test_lammpstrj.py::test_mdwrite PASSED [ 23%] 178s tests/test_lammpstrj.py::test_multiread PASSED [ 23%] 178s 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tests/test_mdcrd.py::test_read_0 PASSED [ 26%] 277s tests/test_mdcrd.py::test_read_1 PASSED [ 26%] 277s tests/test_mdcrd.py::test_read_write_0 PASSED [ 26%] 277s tests/test_mdcrd.py::test_read_write_1 PASSED [ 26%] 277s tests/test_mdcrd.py::test_read_write_2 PASSED [ 26%] 277s tests/test_mdcrd.py::test_multiread PASSED [ 26%] 277s tests/test_mdcrd.py::test_seek PASSED [ 26%] 277s tests/test_mdcrd.py::test_atom_indices_0 PASSED [ 26%] 277s tests/test_mdcrd.py::test_atom_indices_1 PASSED [ 26%] 277s tests/test_mol2.py::test_load_mol2 PASSED [ 26%] 277s tests/test_mol2.py::test_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb SKIPPED [ 27%] 277s tests/test_mol2.py::test_mol2_dataframe PASSED [ 27%] 277s tests/test_mol2.py::test_mol2_dataframe_status PASSED [ 27%] 277s tests/test_mol2.py::test_mol2_warnings PASSED [ 27%] 277s tests/test_mol2.py::test_mol2_status_bits PASSED [ 27%] 277s tests/test_mol2.py::test_mol2_without_bonds PASSED [ 27%] 277s tests/test_mol2.py::test_mol2_element_name 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tests/test_netcdf.py::TestNetCDFNetCDF4::test_shape PASSED [ 28%] 280s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_1 PASSED [ 28%] 280s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_2 PASSED [ 29%] 280s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_3 PASSED [ 29%] 280s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_1 PASSED [ 29%] 280s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_2 PASSED [ 29%] 280s tests/test_netcdf.py::TestNetCDFNetCDF4::test_ragged_1 PASSED [ 29%] 280s tests/test_netcdf.py::TestNetCDFNetCDF4::test_ragged_2 PASSED [ 29%] 280s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_25 PASSED [ 29%] 280s tests/test_netcdf.py::TestNetCDFNetCDF4::test_write_3 PASSED [ 29%] 280s tests/test_netcdf.py::TestNetCDFNetCDF4::test_n_atoms PASSED [ 29%] 280s tests/test_netcdf.py::TestNetCDFNetCDF4::test_do_overwrite PASSED [ 29%] 280s tests/test_netcdf.py::TestNetCDFNetCDF4::test_do_not_overwrite PASSED [ 29%] 280s tests/test_netcdf.py::TestNetCDFNetCDF4::test_trajectory_save_load PASSED [ 30%] 280s tests/test_netcdf.py::TestNetCDFScipy::test_read_after_close PASSED [ 30%] 280s tests/test_netcdf.py::TestNetCDFScipy::test_shape PASSED [ 30%] 280s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_1 PASSED [ 30%] 280s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_2 PASSED [ 30%] 280s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_3 PASSED [ 30%] 280s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_1 PASSED [ 30%] 280s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_2 PASSED [ 30%] 280s tests/test_netcdf.py::TestNetCDFScipy::test_ragged_1 PASSED [ 30%] 280s tests/test_netcdf.py::TestNetCDFScipy::test_ragged_2 PASSED [ 30%] 280s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_25 PASSED [ 30%] 280s tests/test_netcdf.py::TestNetCDFScipy::test_write_3 PASSED [ 30%] 280s tests/test_netcdf.py::TestNetCDFScipy::test_n_atoms PASSED [ 31%] 280s tests/test_netcdf.py::TestNetCDFScipy::test_do_overwrite PASSED [ 31%] 280s tests/test_netcdf.py::TestNetCDFScipy::test_do_not_overwrite PASSED [ 31%] 280s tests/test_netcdf.py::TestNetCDFScipy::test_trajectory_save_load PASSED [ 31%] 280s tests/test_netcdf.py::test_cpptraj SKIPPED (This test requires cpptr...) [ 31%] 280s tests/test_nmr.py::test_spartaplus SKIPPED (SPARTA+ binary not found) [ 31%] 280s tests/test_nmr.py::test_ppm SKIPPED (PPM binary not found) [ 31%] 280s tests/test_nmr.py::test_shiftx2 SKIPPED (SHIFTX2 binary not found or...) [ 31%] 280s tests/test_nmr.py::test_2_scalar_couplings PASSED [ 31%] 280s tests/test_order.py::test_nematic_order PASSED [ 31%] 280s tests/test_order.py::test_director PASSED [ 31%] 280s tests/test_order.py::test_inertia PASSED [ 32%] 280s tests/test_order.py::test_nematic_order_args PASSED [ 32%] 280s tests/test_order.py::test_order_from_traj PASSED [ 32%] 280s tests/test_order.py::test_directors_angle_from_traj PASSED [ 32%] 280s tests/test_pdb.py::test_pdbread PASSED [ 32%] 280s tests/test_pdb.py::test_pdbread_with_input_top PASSED [ 32%] 280s tests/test_pdb.py::test_pdbwrite PASSED [ 32%] 280s tests/test_pdb.py::test_load_multiframe PASSED [ 32%] 280s tests/test_pdb.py::test_4ZUO PASSED [ 32%] 280s tests/test_pdb.py::test_2EQQ_0 PASSED [ 32%] 282s tests/test_pdb.py::test_1vii_solvated_with_ligand PASSED [ 32%] 282s tests/test_pdb.py::test_write_large PASSED [ 33%] 282s tests/test_pdb.py::test_write_large_2 PASSED [ 33%] 282s tests/test_pdb.py::test_pdbstructure_0 PASSED [ 33%] 282s tests/test_pdb.py::test_pdbstructure_1 PASSED [ 33%] 282s tests/test_pdb.py::test_pdbstructure_2 PASSED [ 33%] 282s tests/test_pdb.py::test_pdbstructure_3 PASSED [ 33%] 282s tests/test_pdb.py::test_1ncw PASSED [ 33%] 282s tests/test_pdb.py::test_segment_id PASSED [ 33%] 282s tests/test_pdb.py::test_bfactors PASSED [ 33%] 286s tests/test_pdb.py::test_hex PASSED [ 33%] 286s tests/test_pdb.py::test_dummy_pdb_box_detection PASSED [ 33%] 286s tests/test_pdb.py::test_multichain_load_cycle PASSED [ 33%] 286s tests/test_pdb.py::test_multichain_load_cycle_noter PASSED [ 34%] 286s tests/test_pdb.py::test_load_pdb_input_top PASSED [ 34%] 286s tests/test_pdb.py::test_chimera_indexing PASSED [ 34%] 286s tests/test_pdb.py::test_chimera_indexing_skip PASSED [ 34%] 286s tests/test_pdb.py::test_vmd_indexing PASSED [ 34%] 286s tests/test_pdb.py::test_overflow_indexing PASSED [ 34%] 286s tests/test_pdb.py::test_blank_indexing PASSED [ 34%] 286s tests/test_pdb.py::test_pdb_charge_read PASSED [ 34%] 286s tests/test_pdb.py::test_pdb_charge_write PASSED [ 34%] 286s tests/test_pdbx.py::test_convert SKIPPED (test_pdbx.py needs OpenMM.) [ 34%] 286s tests/test_prmtop.py::test_load_prmtop PASSED [ 34%] 286s tests/test_prmtop.py::test_load_chamber_prmtop PASSED [ 35%] 286s tests/test_psf.py::test_load_psf PASSED [ 35%] 290s tests/test_psf.py::test_multichain_psf PASSED [ 35%] 290s tests/test_psf.py::test_load_mdcrd_with_psf PASSED [ 35%] 290s tests/test_psf.py::test_against_vmd[1vii.pdb] SKIPPED (This test req...) [ 35%] 290s tests/test_psf.py::test_against_vmd[2EQQ.pdb] SKIPPED (This test req...) [ 35%] 290s tests/test_quaternion.py::test_quaternion_0 PASSED [ 35%] 290s tests/test_quaternion.py::test_quaternion_1 PASSED [ 35%] 290s tests/test_quaternion.py::test_quaternion_2 PASSED [ 35%] 294s tests/test_rdf.py::test_rdf_norm PASSED [ 35%] 294s tests/test_rdf.py::test_compare_rdf_to_gromacs SKIPPED (Binning does...) [ 35%] 294s tests/test_rdf.py::test_rdf_t[True-True] PASSED [ 36%] 299s tests/test_rdf.py::test_rdf_t[True-False] PASSED [ 36%] 299s tests/test_rdf.py::test_rdf_t[False-True] PASSED [ 36%] 300s tests/test_rdf.py::test_rdf_t[False-False] PASSED [ 36%] 300s tests/test_rdf.py::test_rdf_t_norm[0] PASSED [ 36%] 301s tests/test_rdf.py::test_rdf_t_norm[2] PASSED [ 36%] 301s tests/test_rdf.py::test_rdf_t_norm[4] PASSED [ 36%] 301s tests/test_rdf.py::test_compare_rdf_t_at_0[True-True] PASSED [ 36%] 303s tests/test_rdf.py::test_compare_rdf_t_at_0[True-False] PASSED [ 36%] 303s tests/test_rdf.py::test_compare_rdf_t_at_0[False-True] PASSED [ 36%] 303s tests/test_rdf.py::test_compare_rdf_t_at_0[False-False] PASSED [ 36%] 303s tests/test_rdf.py::test_amber_rdf_t[True-True] PASSED [ 36%] 303s tests/test_rdf.py::test_amber_rdf_t[True-False] PASSED [ 37%] 304s tests/test_rdf.py::test_amber_rdf_t[False-True] PASSED [ 37%] 304s tests/test_rdf.py::test_amber_rdf_t[False-False] PASSED [ 37%] 304s tests/test_rdf.py::test_compare_gromacs_rdf_t SKIPPED (Binning does ...) [ 37%] 304s tests/test_rdf.py::test_compare_rdf_t_master SKIPPED (Expected failu...) [ 37%] 304s tests/test_rdf.py::test_compare_n_concurrent_pairs PASSED [ 37%] 304s tests/test_reporter.py::test_reporter SKIPPED (test_reporter.py need...) [ 37%] 304s tests/test_reporter.py::test_reporter_subset SKIPPED (test_reporter....) [ 37%] 304s tests/test_reporter.py::test_xtc_reporter_append SKIPPED (test_repor...) [ 37%] 304s tests/test_restart.py::test_read_after_close PASSED [ 37%] 304s tests/test_restart.py::test_shape PASSED [ 37%] 304s tests/test_restart.py::test_shape_2 PASSED [ 38%] 304s tests/test_restart.py::test_read_write_1 PASSED [ 38%] 304s tests/test_restart.py::test_read_write_2 PASSED [ 38%] 304s tests/test_restart.py::test_read_write_3 PASSED [ 38%] 305s tests/test_restart.py::test_read_write_4 PASSED [ 38%] 305s tests/test_rmsd.py::test_trajectory_rmsd PASSED [ 38%] 305s tests/test_rmsd.py::test_precentered_1 PASSED [ 38%] 305s tests/test_rmsd.py::test_precentered_2 PASSED [ 38%] 305s tests/test_rmsd.py::test_superpose_0 PASSED [ 38%] 305s tests/test_rmsd.py::test_superpose_1 PASSED [ 38%] 305s tests/test_rmsd.py::test_superpose_2 PASSED [ 38%] 305s tests/test_rmsd.py::test_superpose_refinds PASSED [ 39%] 305s tests/test_rmsd.py::test_rmsd_atom_indices PASSED [ 39%] 305s tests/test_rmsd.py::test_rmsd_ref_ainds PASSED [ 39%] 305s tests/test_rmsd.py::test_average_structure PASSED [ 39%] 305s tests/test_rmsd.py::test_trajectory_rmsf PASSED [ 39%] 305s tests/test_rmsd.py::test_trajectory_rmsf_aligned PASSED [ 39%] 305s tests/test_rmsd.py::test_rmsd_atom_indices_vs_ref_indices PASSED [ 39%] 305s tests/test_rmsd_memmap.py::test_1 PASSED [ 39%] 305s tests/test_rmsd_memmap.py::test_2 PASSED [ 39%] 305s tests/test_sasa.py::test_sasa_0 PASSED [ 39%] 305s tests/test_sasa.py::test_sasa_1 PASSED [ 39%] 306s tests/test_sasa.py::test_sasa_2 PASSED [ 39%] 306s tests/test_sasa.py::test_sasa_3 PASSED [ 40%] 307s tests/test_sasa.py::test_sasa_4 PASSED [ 40%] 307s tests/test_sasa.py::test_sasa_5 PASSED [ 40%] 308s tests/test_sasa.py::test_sasa_6 PASSED [ 40%] 308s tests/test_sasa.py::test_sasa_7 PASSED [ 40%] 308s tests/test_selection.py::test_range PASSED [ 40%] 308s tests/test_selection.py::test_unary_2 PASSED [ 40%] 308s tests/test_selection.py::test_unary_3 PASSED [ 40%] 308s tests/test_selection.py::test_binary_1 PASSED [ 40%] 308s tests/test_selection.py::test_binary_2 PASSED [ 40%] 308s tests/test_selection.py::test_simple PASSED [ 40%] 308s tests/test_selection.py::test_alias PASSED [ 41%] 308s tests/test_selection.py::test_unary_1 PASSED [ 41%] 308s tests/test_selection.py::test_binary_selection_operator PASSED [ 41%] 308s tests/test_selection.py::test_raises PASSED [ 41%] 308s tests/test_selection.py::test_raises2 PASSED [ 41%] 308s tests/test_selection.py::test_bool PASSED [ 41%] 308s tests/test_selection.py::test_nested_bool PASSED [ 41%] 308s tests/test_selection.py::test_values PASSED [ 41%] 308s tests/test_selection.py::test_element PASSED [ 41%] 308s tests/test_selection.py::test_not PASSED [ 41%] 308s tests/test_selection.py::test_re PASSED [ 41%] 308s tests/test_selection.py::test_within SKIPPED (failed to parse selection) [ 42%] 309s tests/test_selection.py::test_quotes PASSED [ 42%] 309s tests/test_selection.py::test_top PASSED [ 42%] 309s tests/test_selection.py::test_top_2 PASSED [ 42%] 309s tests/test_selection.py::test_backbone PASSED [ 42%] 309s tests/test_selection.py::test_sidechain PASSED [ 42%] 309s tests/test_selection.py::test_literal PASSED [ 42%] 309s tests/test_selection.py::test_in PASSED [ 42%] 309s tests/test_shape.py::test_gyration PASSED [ 42%] 309s tests/test_shape.py::test_principal_moments PASSED [ 42%] 310s tests/test_shape.py::test_asphericity PASSED [ 42%] 310s tests/test_shape.py::test_shape_metrics PASSED [ 42%] 310s tests/test_thermodynamic_properties.py::test_volume PASSED [ 43%] 310s tests/test_thermodynamic_properties.py::test_density PASSED [ 43%] 310s tests/test_thermodynamic_properties.py::test_dipole_moments PASSED [ 43%] 310s tests/test_thermodynamic_properties.py::test_static_dielectric PASSED [ 43%] 310s tests/test_thermodynamic_properties.py::test_kappa PASSED [ 43%] 310s tests/test_thermodynamic_properties.py::test_alpha SKIPPED (Thermal ...) [ 43%] 310s tests/test_topology.py::test_topology_openmm SKIPPED (needs OpenMM) [ 43%] 310s tests/test_topology.py::test_topology_openmm_preserve_chain_id_when_specified SKIPPED [ 43%] 310s tests/test_topology.py::test_topology_openmm_roundtrip_chain_id SKIPPED [ 43%] 310s tests/test_topology.py::test_topology_openmm_preserve_chain_id_even_when_empty SKIPPED [ 43%] 310s tests/test_topology.py::test_topology_openmm_boxes SKIPPED (needs Op...) [ 43%] 310s tests/test_topology.py::test_topology_openmm_formal_charges SKIPPED [ 44%] 310s tests/test_topology.py::test_topology_pandas PASSED [ 44%] 310s tests/test_topology.py::test_topology_pandas_TIP4PEW PASSED [ 44%] 310s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq PASSED [ 44%] 310s tests/test_topology.py::test_topology_numbers PASSED [ 44%] 310s tests/test_topology.py::test_topology_unique_elements_bpti PASSED [ 44%] 310s tests/test_topology.py::test_chain PASSED [ 44%] 310s tests/test_topology.py::test_residue PASSED [ 44%] 310s tests/test_topology.py::test_segment_id PASSED [ 44%] 310s tests/test_topology.py::test_nonconsective_resSeq PASSED [ 44%] 310s tests/test_topology.py::test_pickle PASSED [ 44%] 310s tests/test_topology.py::test_atoms_by_name PASSED [ 45%] 310s tests/test_topology.py::test_select_atom_indices PASSED [ 45%] 310s tests/test_topology.py::test_top_dataframe_openmm_roundtrip SKIPPED [ 45%] 311s tests/test_topology.py::test_n_bonds PASSED [ 45%] 311s tests/test_topology.py::test_load_unknown_topology PASSED [ 45%] 311s tests/test_topology.py::test_unique_pairs PASSED [ 45%] 311s tests/test_topology.py::test_select_pairs PASSED [ 45%] 312s tests/test_topology.py::test_to_fasta PASSED [ 45%] 312s tests/test_topology.py::test_subset PASSED [ 45%] 312s tests/test_topology.py::test_subset_re_index_residues PASSED [ 45%] 312s tests/test_topology.py::test_molecules PASSED [ 45%] 312s tests/test_topology.py::test_copy_and_hash PASSED [ 45%] 312s tests/test_topology.py::test_topology_sliced_residue_indices PASSED [ 46%] 312s tests/test_topology.py::test_topology_join PASSED [ 46%] 312s tests/test_topology.py::test_topology_join_keep_resSeq PASSED [ 46%] 312s tests/test_trajectory.py::test_mismatch PASSED [ 46%] 313s tests/test_trajectory.py::test_box PASSED [ 46%] 313s tests/test_trajectory.py::test_load_pdb_box PASSED [ 46%] 313s tests/test_trajectory.py::test_load_pdb_gz PASSED [ 46%] 313s tests/test_trajectory.py::test_box_load_save[nc] PASSED [ 46%] 313s tests/test_trajectory.py::test_box_load_save[h5] PASSED [ 46%] 313s tests/test_trajectory.py::test_box_load_save[xtc] PASSED [ 46%] 313s tests/test_trajectory.py::test_box_load_save[trr] PASSED [ 46%] 313s tests/test_trajectory.py::test_box_load_save[dcd] PASSED [ 47%] 313s tests/test_trajectory.py::test_box_load_save[mdcrd] PASSED [ 47%] 313s tests/test_trajectory.py::test_box_load_save[dtr] PASSED [ 47%] 313s tests/test_trajectory.py::test_box_load_save[xyz] SKIPPED (xyz does ...) [ 47%] 313s tests/test_trajectory.py::test_box_load_save[xyz.gz] SKIPPED (xyz.gz...) [ 47%] 313s tests/test_trajectory.py::test_box_load_save[lammpstrj] PASSED [ 47%] 313s tests/test_trajectory.py::test_box_load_save[lh5] SKIPPED (lh5 does ...) [ 47%] 313s tests/test_trajectory.py::test_box_load_save[pdb] SKIPPED (pdb does ...) [ 47%] 313s tests/test_trajectory.py::test_box_load_save[pdb.gz] SKIPPED (pdb.gz...) [ 47%] 313s tests/test_trajectory.py::test_box_load_save[ncrst] PASSED [ 47%] 313s tests/test_trajectory.py::test_box_load_save[rst7] PASSED [ 47%] 313s tests/test_trajectory.py::test_box_load_save[gro] PASSED [ 48%] 313s tests/test_trajectory.py::test_slice PASSED [ 48%] 313s tests/test_trajectory.py::test_slice2 PASSED [ 48%] 313s tests/test_trajectory.py::test_read_path[nc] PASSED [ 48%] 313s tests/test_trajectory.py::test_read_path[h5] PASSED [ 48%] 313s tests/test_trajectory.py::test_read_path[xtc] PASSED [ 48%] 313s tests/test_trajectory.py::test_read_path[trr] PASSED [ 48%] 313s tests/test_trajectory.py::test_read_path[dcd] PASSED [ 48%] 313s tests/test_trajectory.py::test_read_path[mdcrd] PASSED [ 48%] 313s tests/test_trajectory.py::test_read_path[dtr] PASSED [ 48%] 313s tests/test_trajectory.py::test_read_path[xyz] PASSED [ 48%] 313s tests/test_trajectory.py::test_read_path[xyz.gz] PASSED [ 48%] 313s tests/test_trajectory.py::test_read_path[lammpstrj] PASSED [ 49%] 313s tests/test_trajectory.py::test_read_path[lh5] PASSED [ 49%] 313s tests/test_trajectory.py::test_read_path[pdb] PASSED [ 49%] 313s tests/test_trajectory.py::test_read_path[pdb.gz] PASSED [ 49%] 313s tests/test_trajectory.py::test_read_path[ncrst] XFAIL (These referen...) [ 49%] 313s tests/test_trajectory.py::test_read_path[rst7] XFAIL (These referenc...) [ 49%] 313s tests/test_trajectory.py::test_read_path[gro] PASSED [ 49%] 313s tests/test_trajectory.py::test_write_path[nc] PASSED [ 49%] 313s tests/test_trajectory.py::test_write_path[h5] PASSED [ 49%] 313s tests/test_trajectory.py::test_write_path[xtc] PASSED [ 49%] 313s tests/test_trajectory.py::test_write_path[trr] PASSED [ 49%] 313s tests/test_trajectory.py::test_write_path[dcd] PASSED [ 50%] 313s tests/test_trajectory.py::test_write_path[mdcrd] SKIPPED (mdcrd can ...) [ 50%] 313s tests/test_trajectory.py::test_write_path[dtr] PASSED [ 50%] 314s tests/test_trajectory.py::test_write_path[xyz] PASSED [ 50%] 314s tests/test_trajectory.py::test_write_path[xyz.gz] PASSED [ 50%] 314s tests/test_trajectory.py::test_write_path[lammpstrj] PASSED [ 50%] 314s tests/test_trajectory.py::test_write_path[lh5] PASSED [ 50%] 314s tests/test_trajectory.py::test_write_path[pdb] PASSED [ 50%] 314s tests/test_trajectory.py::test_write_path[pdb.gz] PASSED [ 50%] 314s tests/test_trajectory.py::test_write_path[ncrst] SKIPPED (ncrst can ...) [ 50%] 314s tests/test_trajectory.py::test_write_path[rst7] SKIPPED (rst7 can on...) [ 50%] 314s tests/test_trajectory.py::test_write_path[gro] PASSED [ 51%] 314s tests/test_trajectory.py::test_read_write[nc-nc] PASSED [ 51%] 314s tests/test_trajectory.py::test_read_write[nc-h5] PASSED [ 51%] 314s tests/test_trajectory.py::test_read_write[nc-xtc] PASSED [ 51%] 314s tests/test_trajectory.py::test_read_write[nc-trr] PASSED [ 51%] 314s tests/test_trajectory.py::test_read_write[nc-dcd] PASSED [ 51%] 314s tests/test_trajectory.py::test_read_write[nc-mdcrd] SKIPPED (mdcrd c...) [ 51%] 315s tests/test_trajectory.py::test_read_write[nc-dtr] PASSED [ 51%] 315s tests/test_trajectory.py::test_read_write[nc-xyz] PASSED [ 51%] 316s tests/test_trajectory.py::test_read_write[nc-xyz.gz] PASSED [ 51%] 316s tests/test_trajectory.py::test_read_write[nc-lammpstrj] PASSED [ 51%] 316s tests/test_trajectory.py::test_read_write[nc-lh5] PASSED [ 51%] 317s tests/test_trajectory.py::test_read_write[nc-pdb] PASSED [ 52%] 318s tests/test_trajectory.py::test_read_write[nc-pdb.gz] PASSED [ 52%] 318s tests/test_trajectory.py::test_read_write[nc-ncrst] SKIPPED (ncrst c...) [ 52%] 318s tests/test_trajectory.py::test_read_write[nc-rst7] SKIPPED (rst7 can...) [ 52%] 318s tests/test_trajectory.py::test_read_write[nc-gro] PASSED [ 52%] 318s tests/test_trajectory.py::test_read_write[h5-nc] PASSED [ 52%] 318s tests/test_trajectory.py::test_read_write[h5-h5] PASSED [ 52%] 318s tests/test_trajectory.py::test_read_write[h5-xtc] PASSED [ 52%] 318s tests/test_trajectory.py::test_read_write[h5-trr] PASSED [ 52%] 318s tests/test_trajectory.py::test_read_write[h5-dcd] PASSED [ 52%] 318s tests/test_trajectory.py::test_read_write[h5-mdcrd] SKIPPED (mdcrd c...) [ 52%] 318s tests/test_trajectory.py::test_read_write[h5-dtr] PASSED [ 53%] 318s tests/test_trajectory.py::test_read_write[h5-xyz] PASSED [ 53%] 319s tests/test_trajectory.py::test_read_write[h5-xyz.gz] PASSED [ 53%] 319s tests/test_trajectory.py::test_read_write[h5-lammpstrj] PASSED [ 53%] 319s tests/test_trajectory.py::test_read_write[h5-lh5] PASSED [ 53%] 319s tests/test_trajectory.py::test_read_write[h5-pdb] PASSED [ 53%] 320s tests/test_trajectory.py::test_read_write[h5-pdb.gz] PASSED [ 53%] 320s tests/test_trajectory.py::test_read_write[h5-ncrst] SKIPPED (ncrst c...) [ 53%] 320s tests/test_trajectory.py::test_read_write[h5-rst7] SKIPPED (rst7 can...) [ 53%] 320s tests/test_trajectory.py::test_read_write[h5-gro] PASSED [ 53%] 320s tests/test_trajectory.py::test_read_write[xtc-nc] PASSED [ 53%] 320s tests/test_trajectory.py::test_read_write[xtc-h5] PASSED [ 54%] 320s tests/test_trajectory.py::test_read_write[xtc-xtc] PASSED [ 54%] 320s tests/test_trajectory.py::test_read_write[xtc-trr] PASSED [ 54%] 320s tests/test_trajectory.py::test_read_write[xtc-dcd] PASSED [ 54%] 320s tests/test_trajectory.py::test_read_write[xtc-mdcrd] SKIPPED (mdcrd ...) [ 54%] 321s tests/test_trajectory.py::test_read_write[xtc-dtr] PASSED [ 54%] 321s tests/test_trajectory.py::test_read_write[xtc-xyz] PASSED [ 54%] 321s tests/test_trajectory.py::test_read_write[xtc-xyz.gz] PASSED [ 54%] 321s tests/test_trajectory.py::test_read_write[xtc-lammpstrj] PASSED [ 54%] 321s tests/test_trajectory.py::test_read_write[xtc-lh5] PASSED [ 54%] 322s tests/test_trajectory.py::test_read_write[xtc-pdb] PASSED [ 54%] 322s tests/test_trajectory.py::test_read_write[xtc-pdb.gz] PASSED [ 54%] 322s tests/test_trajectory.py::test_read_write[xtc-ncrst] SKIPPED (ncrst ...) [ 55%] 322s tests/test_trajectory.py::test_read_write[xtc-rst7] SKIPPED (rst7 ca...) [ 55%] 322s tests/test_trajectory.py::test_read_write[xtc-gro] PASSED [ 55%] 322s tests/test_trajectory.py::test_read_write[trr-nc] PASSED [ 55%] 322s tests/test_trajectory.py::test_read_write[trr-h5] PASSED [ 55%] 322s tests/test_trajectory.py::test_read_write[trr-xtc] PASSED [ 55%] 322s tests/test_trajectory.py::test_read_write[trr-trr] PASSED [ 55%] 322s tests/test_trajectory.py::test_read_write[trr-dcd] PASSED [ 55%] 322s tests/test_trajectory.py::test_read_write[trr-mdcrd] SKIPPED (mdcrd ...) [ 55%] 323s tests/test_trajectory.py::test_read_write[trr-dtr] PASSED [ 55%] 323s tests/test_trajectory.py::test_read_write[trr-xyz] PASSED [ 55%] 323s tests/test_trajectory.py::test_read_write[trr-xyz.gz] PASSED [ 56%] 323s tests/test_trajectory.py::test_read_write[trr-lammpstrj] PASSED [ 56%] 323s tests/test_trajectory.py::test_read_write[trr-lh5] PASSED [ 56%] 324s tests/test_trajectory.py::test_read_write[trr-pdb] PASSED [ 56%] 324s tests/test_trajectory.py::test_read_write[trr-pdb.gz] PASSED [ 56%] 324s tests/test_trajectory.py::test_read_write[trr-ncrst] SKIPPED (ncrst ...) [ 56%] 324s tests/test_trajectory.py::test_read_write[trr-rst7] SKIPPED (rst7 ca...) [ 56%] 324s tests/test_trajectory.py::test_read_write[trr-gro] PASSED [ 56%] 324s tests/test_trajectory.py::test_read_write[dcd-nc] PASSED [ 56%] 324s tests/test_trajectory.py::test_read_write[dcd-h5] PASSED [ 56%] 324s tests/test_trajectory.py::test_read_write[dcd-xtc] PASSED [ 56%] 324s tests/test_trajectory.py::test_read_write[dcd-trr] PASSED [ 57%] 324s tests/test_trajectory.py::test_read_write[dcd-dcd] PASSED [ 57%] 324s tests/test_trajectory.py::test_read_write[dcd-mdcrd] SKIPPED (mdcrd ...) [ 57%] 325s tests/test_trajectory.py::test_read_write[dcd-dtr] PASSED [ 57%] 325s tests/test_trajectory.py::test_read_write[dcd-xyz] PASSED [ 57%] 325s tests/test_trajectory.py::test_read_write[dcd-xyz.gz] PASSED [ 57%] 325s tests/test_trajectory.py::test_read_write[dcd-lammpstrj] PASSED [ 57%] 325s tests/test_trajectory.py::test_read_write[dcd-lh5] PASSED [ 57%] 326s tests/test_trajectory.py::test_read_write[dcd-pdb] PASSED [ 57%] 326s tests/test_trajectory.py::test_read_write[dcd-pdb.gz] PASSED [ 57%] 326s tests/test_trajectory.py::test_read_write[dcd-ncrst] SKIPPED (ncrst ...) [ 57%] 326s tests/test_trajectory.py::test_read_write[dcd-rst7] SKIPPED (rst7 ca...) [ 57%] 326s tests/test_trajectory.py::test_read_write[dcd-gro] PASSED [ 58%] 327s tests/test_trajectory.py::test_read_write[mdcrd-nc] PASSED [ 58%] 327s tests/test_trajectory.py::test_read_write[mdcrd-h5] PASSED [ 58%] 327s tests/test_trajectory.py::test_read_write[mdcrd-xtc] PASSED [ 58%] 327s tests/test_trajectory.py::test_read_write[mdcrd-trr] PASSED [ 58%] 327s tests/test_trajectory.py::test_read_write[mdcrd-dcd] PASSED [ 58%] 327s tests/test_trajectory.py::test_read_write[mdcrd-mdcrd] SKIPPED (mdcr...) [ 58%] 327s tests/test_trajectory.py::test_read_write[mdcrd-dtr] SKIPPED (dtr ne...) [ 58%] 327s tests/test_trajectory.py::test_read_write[mdcrd-xyz] PASSED [ 58%] 327s tests/test_trajectory.py::test_read_write[mdcrd-xyz.gz] PASSED [ 58%] 327s tests/test_trajectory.py::test_read_write[mdcrd-lammpstrj] SKIPPED (...) [ 58%] 327s tests/test_trajectory.py::test_read_write[mdcrd-lh5] PASSED [ 59%] 328s tests/test_trajectory.py::test_read_write[mdcrd-pdb] PASSED [ 59%] 329s tests/test_trajectory.py::test_read_write[mdcrd-pdb.gz] PASSED [ 59%] 329s tests/test_trajectory.py::test_read_write[mdcrd-ncrst] SKIPPED (ncrs...) [ 59%] 329s tests/test_trajectory.py::test_read_write[mdcrd-rst7] SKIPPED (rst7 ...) [ 59%] 329s tests/test_trajectory.py::test_read_write[mdcrd-gro] PASSED [ 59%] 329s tests/test_trajectory.py::test_read_write[dtr-nc] PASSED [ 59%] 329s tests/test_trajectory.py::test_read_write[dtr-h5] PASSED [ 59%] 329s tests/test_trajectory.py::test_read_write[dtr-xtc] PASSED [ 59%] 329s tests/test_trajectory.py::test_read_write[dtr-trr] PASSED [ 59%] 329s tests/test_trajectory.py::test_read_write[dtr-dcd] PASSED [ 59%] 329s tests/test_trajectory.py::test_read_write[dtr-mdcrd] SKIPPED (mdcrd ...) [ 60%] 330s tests/test_trajectory.py::test_read_write[dtr-dtr] PASSED [ 60%] 330s tests/test_trajectory.py::test_read_write[dtr-xyz] PASSED [ 60%] 330s tests/test_trajectory.py::test_read_write[dtr-xyz.gz] PASSED [ 60%] 331s tests/test_trajectory.py::test_read_write[dtr-lammpstrj] PASSED [ 60%] 331s tests/test_trajectory.py::test_read_write[dtr-lh5] PASSED [ 60%] 331s tests/test_trajectory.py::test_read_write[dtr-pdb] PASSED [ 60%] 332s tests/test_trajectory.py::test_read_write[dtr-pdb.gz] PASSED [ 60%] 332s tests/test_trajectory.py::test_read_write[dtr-ncrst] SKIPPED (ncrst ...) [ 60%] 332s tests/test_trajectory.py::test_read_write[dtr-rst7] SKIPPED (rst7 ca...) [ 60%] 332s tests/test_trajectory.py::test_read_write[dtr-gro] PASSED [ 60%] 332s tests/test_trajectory.py::test_read_write[xyz-nc] PASSED [ 60%] 332s tests/test_trajectory.py::test_read_write[xyz-h5] PASSED [ 61%] 332s tests/test_trajectory.py::test_read_write[xyz-xtc] PASSED [ 61%] 332s tests/test_trajectory.py::test_read_write[xyz-trr] PASSED [ 61%] 332s tests/test_trajectory.py::test_read_write[xyz-dcd] PASSED [ 61%] 332s tests/test_trajectory.py::test_read_write[xyz-mdcrd] SKIPPED (mdcrd ...) [ 61%] 332s tests/test_trajectory.py::test_read_write[xyz-dtr] SKIPPED (dtr need...) [ 61%] 332s tests/test_trajectory.py::test_read_write[xyz-xyz] PASSED [ 61%] 332s tests/test_trajectory.py::test_read_write[xyz-xyz.gz] PASSED [ 61%] 332s tests/test_trajectory.py::test_read_write[xyz-lammpstrj] SKIPPED (la...) [ 61%] 332s tests/test_trajectory.py::test_read_write[xyz-lh5] PASSED [ 61%] 333s tests/test_trajectory.py::test_read_write[xyz-pdb] PASSED [ 61%] 333s tests/test_trajectory.py::test_read_write[xyz-pdb.gz] PASSED [ 62%] 333s tests/test_trajectory.py::test_read_write[xyz-ncrst] SKIPPED (ncrst ...) [ 62%] 333s tests/test_trajectory.py::test_read_write[xyz-rst7] SKIPPED (rst7 ca...) [ 62%] 333s tests/test_trajectory.py::test_read_write[xyz-gro] PASSED [ 62%] 333s tests/test_trajectory.py::test_read_write[xyz.gz-nc] PASSED [ 62%] 333s tests/test_trajectory.py::test_read_write[xyz.gz-h5] PASSED [ 62%] 333s tests/test_trajectory.py::test_read_write[xyz.gz-xtc] PASSED [ 62%] 333s tests/test_trajectory.py::test_read_write[xyz.gz-trr] PASSED [ 62%] 333s tests/test_trajectory.py::test_read_write[xyz.gz-dcd] PASSED [ 62%] 333s tests/test_trajectory.py::test_read_write[xyz.gz-mdcrd] SKIPPED (mdc...) [ 62%] 333s tests/test_trajectory.py::test_read_write[xyz.gz-dtr] SKIPPED (dtr n...) [ 62%] 334s tests/test_trajectory.py::test_read_write[xyz.gz-xyz] PASSED [ 63%] 334s tests/test_trajectory.py::test_read_write[xyz.gz-xyz.gz] PASSED [ 63%] 334s tests/test_trajectory.py::test_read_write[xyz.gz-lammpstrj] SKIPPED [ 63%] 334s tests/test_trajectory.py::test_read_write[xyz.gz-lh5] PASSED [ 63%] 334s tests/test_trajectory.py::test_read_write[xyz.gz-pdb] PASSED [ 63%] 335s tests/test_trajectory.py::test_read_write[xyz.gz-pdb.gz] PASSED [ 63%] 335s tests/test_trajectory.py::test_read_write[xyz.gz-ncrst] SKIPPED (ncr...) [ 63%] 335s tests/test_trajectory.py::test_read_write[xyz.gz-rst7] SKIPPED (rst7...) [ 63%] 335s tests/test_trajectory.py::test_read_write[xyz.gz-gro] PASSED [ 63%] 335s tests/test_trajectory.py::test_read_write[lammpstrj-nc] PASSED [ 63%] 335s tests/test_trajectory.py::test_read_write[lammpstrj-h5] PASSED [ 63%] 335s tests/test_trajectory.py::test_read_write[lammpstrj-xtc] PASSED [ 63%] 335s tests/test_trajectory.py::test_read_write[lammpstrj-trr] PASSED [ 64%] 335s tests/test_trajectory.py::test_read_write[lammpstrj-dcd] PASSED [ 64%] 335s tests/test_trajectory.py::test_read_write[lammpstrj-mdcrd] SKIPPED (...) [ 64%] 336s tests/test_trajectory.py::test_read_write[lammpstrj-dtr] PASSED [ 64%] 336s tests/test_trajectory.py::test_read_write[lammpstrj-xyz] PASSED [ 64%] 336s tests/test_trajectory.py::test_read_write[lammpstrj-xyz.gz] PASSED [ 64%] 336s tests/test_trajectory.py::test_read_write[lammpstrj-lammpstrj] PASSED [ 64%] 336s tests/test_trajectory.py::test_read_write[lammpstrj-lh5] PASSED [ 64%] 337s tests/test_trajectory.py::test_read_write[lammpstrj-pdb] PASSED [ 64%] 337s tests/test_trajectory.py::test_read_write[lammpstrj-pdb.gz] PASSED [ 64%] 337s tests/test_trajectory.py::test_read_write[lammpstrj-ncrst] SKIPPED (...) [ 64%] 337s tests/test_trajectory.py::test_read_write[lammpstrj-rst7] SKIPPED (r...) [ 65%] 337s tests/test_trajectory.py::test_read_write[lammpstrj-gro] PASSED [ 65%] 337s tests/test_trajectory.py::test_read_write[lh5-nc] PASSED [ 65%] 337s tests/test_trajectory.py::test_read_write[lh5-h5] PASSED [ 65%] 337s tests/test_trajectory.py::test_read_write[lh5-xtc] PASSED [ 65%] 337s tests/test_trajectory.py::test_read_write[lh5-trr] PASSED [ 65%] 337s tests/test_trajectory.py::test_read_write[lh5-dcd] PASSED [ 65%] 337s tests/test_trajectory.py::test_read_write[lh5-mdcrd] SKIPPED (mdcrd ...) [ 65%] 337s tests/test_trajectory.py::test_read_write[lh5-dtr] SKIPPED (dtr need...) [ 65%] 338s tests/test_trajectory.py::test_read_write[lh5-xyz] PASSED [ 65%] 338s tests/test_trajectory.py::test_read_write[lh5-xyz.gz] PASSED [ 65%] 338s tests/test_trajectory.py::test_read_write[lh5-lammpstrj] SKIPPED (la...) [ 66%] 338s tests/test_trajectory.py::test_read_write[lh5-lh5] PASSED [ 66%] 338s tests/test_trajectory.py::test_read_write[lh5-pdb] PASSED [ 66%] 338s tests/test_trajectory.py::test_read_write[lh5-pdb.gz] PASSED [ 66%] 338s tests/test_trajectory.py::test_read_write[lh5-ncrst] SKIPPED (ncrst ...) [ 66%] 338s tests/test_trajectory.py::test_read_write[lh5-rst7] SKIPPED (rst7 ca...) [ 66%] 339s tests/test_trajectory.py::test_read_write[lh5-gro] PASSED [ 66%] 339s tests/test_trajectory.py::test_read_write[pdb-nc] PASSED [ 66%] 339s tests/test_trajectory.py::test_read_write[pdb-h5] PASSED [ 66%] 339s tests/test_trajectory.py::test_read_write[pdb-xtc] PASSED [ 66%] 339s tests/test_trajectory.py::test_read_write[pdb-trr] PASSED [ 66%] 339s tests/test_trajectory.py::test_read_write[pdb-dcd] PASSED [ 66%] 339s tests/test_trajectory.py::test_read_write[pdb-mdcrd] SKIPPED (mdcrd ...) [ 67%] 340s tests/test_trajectory.py::test_read_write[pdb-dtr] PASSED [ 67%] 341s tests/test_trajectory.py::test_read_write[pdb-xyz] PASSED [ 67%] 341s tests/test_trajectory.py::test_read_write[pdb-xyz.gz] PASSED [ 67%] 341s tests/test_trajectory.py::test_read_write[pdb-lammpstrj] PASSED [ 67%] 341s tests/test_trajectory.py::test_read_write[pdb-lh5] PASSED [ 67%] 342s tests/test_trajectory.py::test_read_write[pdb-pdb] PASSED [ 67%] 343s tests/test_trajectory.py::test_read_write[pdb-pdb.gz] PASSED [ 67%] 343s tests/test_trajectory.py::test_read_write[pdb-ncrst] SKIPPED (ncrst ...) [ 67%] 343s tests/test_trajectory.py::test_read_write[pdb-rst7] SKIPPED (rst7 ca...) [ 67%] 343s tests/test_trajectory.py::test_read_write[pdb-gro] PASSED [ 67%] 343s tests/test_trajectory.py::test_read_write[pdb.gz-nc] PASSED [ 68%] 343s tests/test_trajectory.py::test_read_write[pdb.gz-h5] PASSED [ 68%] 343s tests/test_trajectory.py::test_read_write[pdb.gz-xtc] PASSED [ 68%] 344s tests/test_trajectory.py::test_read_write[pdb.gz-trr] PASSED [ 68%] 344s tests/test_trajectory.py::test_read_write[pdb.gz-dcd] PASSED [ 68%] 344s tests/test_trajectory.py::test_read_write[pdb.gz-mdcrd] SKIPPED (mdc...) [ 68%] 345s tests/test_trajectory.py::test_read_write[pdb.gz-dtr] PASSED [ 68%] 345s tests/test_trajectory.py::test_read_write[pdb.gz-xyz] PASSED [ 68%] 345s tests/test_trajectory.py::test_read_write[pdb.gz-xyz.gz] PASSED [ 68%] 345s tests/test_trajectory.py::test_read_write[pdb.gz-lammpstrj] PASSED [ 68%] 345s tests/test_trajectory.py::test_read_write[pdb.gz-lh5] PASSED [ 68%] 346s tests/test_trajectory.py::test_read_write[pdb.gz-pdb] PASSED [ 69%] 347s tests/test_trajectory.py::test_read_write[pdb.gz-pdb.gz] PASSED [ 69%] 347s tests/test_trajectory.py::test_read_write[pdb.gz-ncrst] SKIPPED (ncr...) [ 69%] 347s tests/test_trajectory.py::test_read_write[pdb.gz-rst7] SKIPPED (rst7...) [ 69%] 347s tests/test_trajectory.py::test_read_write[pdb.gz-gro] PASSED [ 69%] 347s tests/test_trajectory.py::test_read_write[ncrst-nc] XFAIL (These ref...) [ 69%] 347s tests/test_trajectory.py::test_read_write[ncrst-h5] XFAIL (These ref...) [ 69%] 347s tests/test_trajectory.py::test_read_write[ncrst-xtc] XFAIL (These re...) [ 69%] 347s tests/test_trajectory.py::test_read_write[ncrst-trr] XFAIL (These re...) [ 69%] 347s tests/test_trajectory.py::test_read_write[ncrst-dcd] XFAIL (These re...) [ 69%] 347s tests/test_trajectory.py::test_read_write[ncrst-mdcrd] XFAIL (These ...) [ 69%] 347s tests/test_trajectory.py::test_read_write[ncrst-dtr] XFAIL (These re...) [ 69%] 347s tests/test_trajectory.py::test_read_write[ncrst-xyz] XFAIL (These re...) [ 70%] 347s tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] XFAIL (These...) [ 70%] 347s tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] XFAIL (Th...) [ 70%] 347s tests/test_trajectory.py::test_read_write[ncrst-lh5] XFAIL (These re...) [ 70%] 347s tests/test_trajectory.py::test_read_write[ncrst-pdb] XFAIL (These re...) [ 70%] 347s tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] XFAIL (These...) [ 70%] 347s tests/test_trajectory.py::test_read_write[ncrst-ncrst] XFAIL (These ...) [ 70%] 347s tests/test_trajectory.py::test_read_write[ncrst-rst7] XFAIL (These r...) [ 70%] 347s tests/test_trajectory.py::test_read_write[ncrst-gro] XFAIL (These re...) [ 70%] 347s tests/test_trajectory.py::test_read_write[rst7-nc] XFAIL (These refe...) [ 70%] 347s tests/test_trajectory.py::test_read_write[rst7-h5] XFAIL (These refe...) [ 70%] 347s tests/test_trajectory.py::test_read_write[rst7-xtc] XFAIL (These ref...) [ 71%] 347s tests/test_trajectory.py::test_read_write[rst7-trr] XFAIL (These ref...) [ 71%] 347s tests/test_trajectory.py::test_read_write[rst7-dcd] XFAIL (These ref...) [ 71%] 347s tests/test_trajectory.py::test_read_write[rst7-mdcrd] XFAIL (These r...) [ 71%] 347s tests/test_trajectory.py::test_read_write[rst7-dtr] XFAIL (These ref...) [ 71%] 347s tests/test_trajectory.py::test_read_write[rst7-xyz] XFAIL (These ref...) [ 71%] 347s tests/test_trajectory.py::test_read_write[rst7-xyz.gz] XFAIL (These ...) [ 71%] 347s tests/test_trajectory.py::test_read_write[rst7-lammpstrj] XFAIL (The...) [ 71%] 347s tests/test_trajectory.py::test_read_write[rst7-lh5] XFAIL (These ref...) [ 71%] 347s tests/test_trajectory.py::test_read_write[rst7-pdb] XFAIL (These ref...) [ 71%] 347s tests/test_trajectory.py::test_read_write[rst7-pdb.gz] XFAIL (These ...) [ 71%] 347s tests/test_trajectory.py::test_read_write[rst7-ncrst] XFAIL (These r...) [ 72%] 347s tests/test_trajectory.py::test_read_write[rst7-rst7] XFAIL (These re...) [ 72%] 348s tests/test_trajectory.py::test_read_write[rst7-gro] XFAIL (These ref...) [ 72%] 348s tests/test_trajectory.py::test_read_write[gro-nc] PASSED [ 72%] 348s tests/test_trajectory.py::test_read_write[gro-h5] PASSED [ 72%] 348s tests/test_trajectory.py::test_read_write[gro-xtc] PASSED [ 72%] 348s tests/test_trajectory.py::test_read_write[gro-trr] PASSED [ 72%] 348s tests/test_trajectory.py::test_read_write[gro-dcd] PASSED [ 72%] 348s tests/test_trajectory.py::test_read_write[gro-mdcrd] SKIPPED (mdcrd ...) [ 72%] 349s tests/test_trajectory.py::test_read_write[gro-dtr] PASSED [ 72%] 349s tests/test_trajectory.py::test_read_write[gro-xyz] PASSED [ 72%] 349s tests/test_trajectory.py::test_read_write[gro-xyz.gz] PASSED [ 72%] 349s tests/test_trajectory.py::test_read_write[gro-lammpstrj] PASSED [ 73%] 349s tests/test_trajectory.py::test_read_write[gro-lh5] PASSED [ 73%] 350s tests/test_trajectory.py::test_read_write[gro-pdb] PASSED [ 73%] 350s tests/test_trajectory.py::test_read_write[gro-pdb.gz] PASSED [ 73%] 350s tests/test_trajectory.py::test_read_write[gro-ncrst] SKIPPED (ncrst ...) [ 73%] 350s tests/test_trajectory.py::test_read_write[gro-rst7] SKIPPED (rst7 ca...) [ 73%] 350s tests/test_trajectory.py::test_read_write[gro-gro] PASSED [ 73%] 350s tests/test_trajectory.py::test_load[nc] PASSED [ 73%] 350s tests/test_trajectory.py::test_load[h5] PASSED [ 73%] 350s tests/test_trajectory.py::test_load[xtc] PASSED [ 73%] 350s tests/test_trajectory.py::test_load[trr] PASSED [ 73%] 350s tests/test_trajectory.py::test_load[dcd] PASSED [ 74%] 351s tests/test_trajectory.py::test_load[mdcrd] PASSED [ 74%] 351s tests/test_trajectory.py::test_load[dtr] PASSED [ 74%] 351s tests/test_trajectory.py::test_load[xyz] PASSED [ 74%] 351s tests/test_trajectory.py::test_load[xyz.gz] PASSED [ 74%] 351s tests/test_trajectory.py::test_load[lammpstrj] PASSED [ 74%] 351s tests/test_trajectory.py::test_load[lh5] PASSED [ 74%] 352s tests/test_trajectory.py::test_load[pdb] PASSED [ 74%] 353s tests/test_trajectory.py::test_load[pdb.gz] PASSED [ 74%] 353s tests/test_trajectory.py::test_load[ncrst] XFAIL (These reference fi...) [ 74%] 353s tests/test_trajectory.py::test_load[rst7] XFAIL (These reference fil...) [ 74%] 354s tests/test_trajectory.py::test_load[gro] PASSED [ 75%] 354s tests/test_trajectory.py::test_hdf5 PASSED [ 75%] 354s tests/test_trajectory.py::test_center PASSED [ 75%] 354s tests/test_trajectory.py::test_center_aind PASSED [ 75%] 354s tests/test_trajectory.py::test_float_atom_indices_exception[nc] PASSED [ 75%] 354s tests/test_trajectory.py::test_float_atom_indices_exception[h5] PASSED [ 75%] 354s tests/test_trajectory.py::test_float_atom_indices_exception[xtc] PASSED [ 75%] 354s tests/test_trajectory.py::test_float_atom_indices_exception[trr] PASSED [ 75%] 354s tests/test_trajectory.py::test_float_atom_indices_exception[dcd] PASSED [ 75%] 354s tests/test_trajectory.py::test_float_atom_indices_exception[mdcrd] PASSED [ 75%] 354s tests/test_trajectory.py::test_float_atom_indices_exception[dtr] PASSED [ 75%] 354s tests/test_trajectory.py::test_float_atom_indices_exception[xyz] PASSED [ 75%] 354s tests/test_trajectory.py::test_float_atom_indices_exception[xyz.gz] PASSED [ 76%] 354s tests/test_trajectory.py::test_float_atom_indices_exception[lammpstrj] PASSED [ 76%] 354s tests/test_trajectory.py::test_float_atom_indices_exception[lh5] PASSED [ 76%] 354s tests/test_trajectory.py::test_float_atom_indices_exception[pdb] PASSED [ 76%] 354s tests/test_trajectory.py::test_float_atom_indices_exception[pdb.gz] PASSED [ 76%] 354s tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] XFAIL [ 76%] 354s tests/test_trajectory.py::test_float_atom_indices_exception[rst7] XFAIL [ 76%] 354s tests/test_trajectory.py::test_float_atom_indices_exception[gro] PASSED [ 76%] 354s tests/test_trajectory.py::test_restrict_atoms PASSED [ 76%] 354s tests/test_trajectory.py::test_restrict_atoms_not_inplace PASSED [ 76%] 354s tests/test_trajectory.py::test_array_vs_matrix PASSED [ 76%] 354s tests/test_trajectory.py::test_pdb_unitcell_loadsave PASSED [ 77%] 354s tests/test_trajectory.py::test_load_combination[nc] PASSED [ 77%] 354s tests/test_trajectory.py::test_load_combination[h5] PASSED [ 77%] 354s tests/test_trajectory.py::test_load_combination[xtc] PASSED [ 77%] 354s tests/test_trajectory.py::test_load_combination[trr] PASSED [ 77%] 354s tests/test_trajectory.py::test_load_combination[dcd] PASSED [ 77%] 354s tests/test_trajectory.py::test_load_combination[mdcrd] PASSED [ 77%] 354s tests/test_trajectory.py::test_load_combination[dtr] PASSED [ 77%] 354s tests/test_trajectory.py::test_load_combination[xyz] PASSED [ 77%] 354s tests/test_trajectory.py::test_load_combination[xyz.gz] PASSED [ 77%] 354s tests/test_trajectory.py::test_load_combination[lammpstrj] PASSED [ 77%] 354s tests/test_trajectory.py::test_load_combination[lh5] PASSED [ 78%] 354s tests/test_trajectory.py::test_load_combination[pdb] PASSED [ 78%] 355s tests/test_trajectory.py::test_load_combination[pdb.gz] PASSED [ 78%] 355s tests/test_trajectory.py::test_load_combination[ncrst] XFAIL (These ...) [ 78%] 355s tests/test_trajectory.py::test_load_combination[rst7] XFAIL (These r...) [ 78%] 355s tests/test_trajectory.py::test_load_combination[gro] PASSED [ 78%] 355s tests/test_trajectory.py::test_no_topology PASSED [ 78%] 355s tests/test_trajectory.py::test_join PASSED [ 78%] 355s tests/test_trajectory.py::test_md_join PASSED [ 78%] 355s tests/test_trajectory.py::test_stack_1 PASSED [ 78%] 355s tests/test_trajectory.py::test_stack_2 PASSED [ 78%] 355s tests/test_trajectory.py::test_seek_read_mode[nc] PASSED [ 78%] 355s tests/test_trajectory.py::test_seek_read_mode[h5] PASSED [ 79%] 355s tests/test_trajectory.py::test_seek_read_mode[xtc] PASSED [ 79%] 355s tests/test_trajectory.py::test_seek_read_mode[trr] PASSED [ 79%] 355s tests/test_trajectory.py::test_seek_read_mode[dcd] PASSED [ 79%] 355s tests/test_trajectory.py::test_seek_read_mode[mdcrd] PASSED [ 79%] 355s tests/test_trajectory.py::test_seek_read_mode[dtr] PASSED [ 79%] 355s tests/test_trajectory.py::test_seek_read_mode[xyz] PASSED [ 79%] 355s tests/test_trajectory.py::test_seek_read_mode[xyz.gz] XFAIL (This is...) [ 79%] 356s tests/test_trajectory.py::test_seek_read_mode[lammpstrj] PASSED [ 79%] 356s tests/test_trajectory.py::test_seek_read_mode[lh5] PASSED [ 79%] 356s tests/test_trajectory.py::test_seek_read_mode[pdb] XFAIL (PDB Files ...) [ 79%] 356s tests/test_trajectory.py::test_seek_read_mode[pdb.gz] XFAIL (PDB Fil...) [ 80%] 356s tests/test_trajectory.py::test_seek_read_mode[ncrst] XFAIL (These re...) [ 80%] 356s tests/test_trajectory.py::test_seek_read_mode[rst7] XFAIL (These ref...) [ 80%] 356s tests/test_trajectory.py::test_seek_read_mode[gro] XFAIL (This is br...) [ 80%] 356s tests/test_trajectory.py::test_load_frame[nc] PASSED [ 80%] 356s tests/test_trajectory.py::test_load_frame[h5] PASSED [ 80%] 356s tests/test_trajectory.py::test_load_frame[xtc] PASSED [ 80%] 356s tests/test_trajectory.py::test_load_frame[trr] PASSED [ 80%] 356s tests/test_trajectory.py::test_load_frame[dcd] PASSED [ 80%] 356s tests/test_trajectory.py::test_load_frame[mdcrd] PASSED [ 80%] 356s tests/test_trajectory.py::test_load_frame[dtr] XFAIL (DTR doesn't lo...) [ 80%] 356s tests/test_trajectory.py::test_load_frame[xyz] PASSED [ 81%] 356s tests/test_trajectory.py::test_load_frame[xyz.gz] PASSED [ 81%] 356s tests/test_trajectory.py::test_load_frame[lammpstrj] PASSED [ 81%] 356s tests/test_trajectory.py::test_load_frame[lh5] PASSED [ 81%] 356s tests/test_trajectory.py::test_load_frame[pdb] PASSED [ 81%] 357s tests/test_trajectory.py::test_load_frame[pdb.gz] PASSED [ 81%] 357s tests/test_trajectory.py::test_load_frame[ncrst] XFAIL (These refere...) [ 81%] 357s tests/test_trajectory.py::test_load_frame[rst7] XFAIL (These referen...) [ 81%] 357s tests/test_trajectory.py::test_load_frame[gro] XFAIL (Gro doesn't im...) [ 81%] 357s tests/test_trajectory.py::test_load_frame_2eqq PASSED [ 81%] 357s tests/test_trajectory.py::test_iterload[nc] PASSED [ 81%] 357s tests/test_trajectory.py::test_iterload[h5] PASSED [ 81%] 357s tests/test_trajectory.py::test_iterload[xtc] PASSED [ 82%] 357s tests/test_trajectory.py::test_iterload[trr] PASSED [ 82%] 357s tests/test_trajectory.py::test_iterload[dcd] PASSED [ 82%] 357s tests/test_trajectory.py::test_iterload[mdcrd] PASSED [ 82%] 357s tests/test_trajectory.py::test_iterload[dtr] XFAIL (This is broken w...) [ 82%] 357s tests/test_trajectory.py::test_iterload[xyz] PASSED [ 82%] 357s tests/test_trajectory.py::test_iterload[xyz.gz] PASSED [ 82%] 357s tests/test_trajectory.py::test_iterload[lammpstrj] PASSED [ 82%] 357s tests/test_trajectory.py::test_iterload[lh5] PASSED [ 82%] 357s tests/test_trajectory.py::test_iterload[pdb] PASSED [ 82%] 357s tests/test_trajectory.py::test_iterload[pdb.gz] PASSED [ 82%] 357s tests/test_trajectory.py::test_iterload[ncrst] SKIPPED (Only 1 frame...) [ 83%] 357s tests/test_trajectory.py::test_iterload[rst7] SKIPPED (Only 1 frame ...) [ 83%] 357s tests/test_trajectory.py::test_iterload[gro] PASSED [ 83%] 360s tests/test_trajectory.py::test_iterload_skip[nc] PASSED [ 83%] 362s tests/test_trajectory.py::test_iterload_skip[h5] PASSED [ 83%] 364s tests/test_trajectory.py::test_iterload_skip[xtc] PASSED [ 83%] 365s tests/test_trajectory.py::test_iterload_skip[trr] PASSED [ 83%] 366s tests/test_trajectory.py::test_iterload_skip[dcd] PASSED [ 83%] 367s tests/test_trajectory.py::test_iterload_skip[mdcrd] PASSED [ 83%] 368s tests/test_trajectory.py::test_iterload_skip[dtr] PASSED [ 83%] 369s tests/test_trajectory.py::test_iterload_skip[xyz] PASSED [ 83%] 370s tests/test_trajectory.py::test_iterload_skip[xyz.gz] PASSED [ 84%] 371s tests/test_trajectory.py::test_iterload_skip[lammpstrj] PASSED [ 84%] 372s tests/test_trajectory.py::test_iterload_skip[lh5] PASSED [ 84%] 373s tests/test_trajectory.py::test_iterload_skip[pdb] XFAIL (PDB Iterloa...) [ 84%] 373s tests/test_trajectory.py::test_iterload_skip[pdb.gz] XFAIL (PDB Iter...) [ 84%] 373s tests/test_trajectory.py::test_iterload_skip[ncrst] XFAIL (These ref...) [ 84%] 373s tests/test_trajectory.py::test_iterload_skip[rst7] XFAIL (These refe...) [ 84%] 373s tests/test_trajectory.py::test_iterload_skip[gro] XFAIL (Not impleme...) [ 84%] 373s tests/test_trajectory.py::test_iterload_chunk_dcd PASSED [ 84%] 373s tests/test_trajectory.py::test_save_load[nc] PASSED [ 84%] 373s tests/test_trajectory.py::test_save_load[h5] PASSED [ 84%] 373s tests/test_trajectory.py::test_save_load[xtc] PASSED [ 84%] 373s tests/test_trajectory.py::test_save_load[trr] PASSED [ 85%] 373s tests/test_trajectory.py::test_save_load[dcd] PASSED [ 85%] 373s tests/test_trajectory.py::test_save_load[mdcrd] PASSED [ 85%] 373s tests/test_trajectory.py::test_save_load[dtr] PASSED [ 85%] 373s tests/test_trajectory.py::test_save_load[xyz] PASSED [ 85%] 373s tests/test_trajectory.py::test_save_load[xyz.gz] PASSED [ 85%] 373s tests/test_trajectory.py::test_save_load[lammpstrj] PASSED [ 85%] 373s tests/test_trajectory.py::test_save_load[lh5] PASSED [ 85%] 373s tests/test_trajectory.py::test_save_load[pdb] PASSED [ 85%] 373s tests/test_trajectory.py::test_save_load[pdb.gz] PASSED [ 85%] 373s tests/test_trajectory.py::test_save_load[ncrst] PASSED [ 85%] 373s tests/test_trajectory.py::test_save_load[rst7] PASSED [ 86%] 373s tests/test_trajectory.py::test_save_load[gro] PASSED [ 86%] 373s tests/test_trajectory.py::test_force_overwrite[nc] PASSED [ 86%] 373s tests/test_trajectory.py::test_force_overwrite[h5] PASSED [ 86%] 373s tests/test_trajectory.py::test_force_overwrite[xtc] PASSED [ 86%] 373s tests/test_trajectory.py::test_force_overwrite[trr] PASSED [ 86%] 373s tests/test_trajectory.py::test_force_overwrite[dcd] PASSED [ 86%] 373s tests/test_trajectory.py::test_force_overwrite[mdcrd] PASSED [ 86%] 373s tests/test_trajectory.py::test_force_overwrite[dtr] XFAIL (This is b...) [ 86%] 373s tests/test_trajectory.py::test_force_overwrite[xyz] PASSED [ 86%] 373s tests/test_trajectory.py::test_force_overwrite[xyz.gz] PASSED [ 86%] 373s tests/test_trajectory.py::test_force_overwrite[lammpstrj] PASSED [ 87%] 373s tests/test_trajectory.py::test_force_overwrite[lh5] PASSED [ 87%] 373s tests/test_trajectory.py::test_force_overwrite[pdb] PASSED [ 87%] 373s tests/test_trajectory.py::test_force_overwrite[pdb.gz] PASSED [ 87%] 373s tests/test_trajectory.py::test_force_overwrite[ncrst] PASSED [ 87%] 373s tests/test_trajectory.py::test_force_overwrite[rst7] PASSED [ 87%] 373s tests/test_trajectory.py::test_force_overwrite[gro] PASSED [ 87%] 373s tests/test_trajectory.py::test_force_noverwrite[nc] PASSED [ 87%] 373s tests/test_trajectory.py::test_force_noverwrite[h5] PASSED [ 87%] 373s tests/test_trajectory.py::test_force_noverwrite[xtc] PASSED [ 87%] 373s tests/test_trajectory.py::test_force_noverwrite[trr] PASSED [ 87%] 373s tests/test_trajectory.py::test_force_noverwrite[dcd] PASSED [ 87%] 373s tests/test_trajectory.py::test_force_noverwrite[mdcrd] PASSED [ 88%] 373s tests/test_trajectory.py::test_force_noverwrite[dtr] PASSED [ 88%] 373s tests/test_trajectory.py::test_force_noverwrite[xyz] PASSED [ 88%] 373s tests/test_trajectory.py::test_force_noverwrite[xyz.gz] PASSED [ 88%] 373s tests/test_trajectory.py::test_force_noverwrite[lammpstrj] PASSED [ 88%] 373s tests/test_trajectory.py::test_force_noverwrite[lh5] PASSED [ 88%] 373s tests/test_trajectory.py::test_force_noverwrite[pdb] PASSED [ 88%] 373s tests/test_trajectory.py::test_force_noverwrite[pdb.gz] PASSED [ 88%] 373s tests/test_trajectory.py::test_force_noverwrite[ncrst] PASSED [ 88%] 373s tests/test_trajectory.py::test_force_noverwrite[rst7] PASSED [ 88%] 373s tests/test_trajectory.py::test_force_noverwrite[gro] PASSED [ 88%] 373s tests/test_trajectory.py::test_open_and_load PASSED [ 89%] 373s tests/test_trajectory.py::test_length PASSED [ 89%] 373s tests/test_trajectory.py::test_unitcell[nc] PASSED [ 89%] 373s tests/test_trajectory.py::test_unitcell[h5] PASSED [ 89%] 373s tests/test_trajectory.py::test_unitcell[xtc] PASSED [ 89%] 373s tests/test_trajectory.py::test_unitcell[trr] PASSED [ 89%] 373s tests/test_trajectory.py::test_unitcell[dcd] PASSED [ 89%] 373s tests/test_trajectory.py::test_unitcell[mdcrd] PASSED [ 89%] 373s tests/test_trajectory.py::test_unitcell[dtr] XFAIL (dtr seems to nee...) [ 89%] 373s tests/test_trajectory.py::test_unitcell[xyz] PASSED [ 89%] 373s tests/test_trajectory.py::test_unitcell[xyz.gz] PASSED [ 89%] 373s tests/test_trajectory.py::test_unitcell[lammpstrj] XFAIL (lammpstrj ...) [ 90%] 373s tests/test_trajectory.py::test_unitcell[lh5] PASSED [ 90%] 373s tests/test_trajectory.py::test_unitcell[pdb] PASSED [ 90%] 373s tests/test_trajectory.py::test_unitcell[pdb.gz] PASSED [ 90%] 374s tests/test_trajectory.py::test_unitcell[ncrst] XFAIL (ncrst seems to...) [ 90%] 374s tests/test_trajectory.py::test_unitcell[rst7] XFAIL (rst7 seems to n...) [ 90%] 374s tests/test_trajectory.py::test_unitcell[gro] PASSED [ 90%] 374s tests/test_trajectory.py::test_chunk0_iterload PASSED [ 90%] 374s tests/test_trajectory.py::test_hashing PASSED [ 90%] 374s tests/test_trajectory.py::test_smooth PASSED [ 90%] 374s tests/test_trajectory.py::test_load_pdb_no_standard_names PASSED [ 90%] 374s tests/test_trajectory.py::test_load_with_atom_indices PASSED [ 90%] 374s tests/test_trajectory.py::test_atom_slicing PASSED [ 91%] 374s tests/test_trajectory.py::test_load_with_frame PASSED [ 91%] 374s tests/test_trajectory.py::test_add_remove_atoms PASSED [ 91%] 374s tests/test_trr.py::test_1 PASSED [ 91%] 374s tests/test_trr.py::test_read_stride PASSED [ 91%] 374s tests/test_trr.py::test_read_stride_n_frames PASSED [ 91%] 374s tests/test_trr.py::test_read_stride_offsets PASSED [ 91%] 374s tests/test_trr.py::test_read_stride_n_frames_offsets PASSED [ 91%] 374s tests/test_trr.py::test_read_stride_switching PASSED [ 91%] 374s tests/test_trr.py::test_write_read PASSED [ 91%] 374s tests/test_trr.py::test_read_atomindices_1 PASSED [ 91%] 374s tests/test_trr.py::test_read_atomindices_2 PASSED [ 92%] 374s tests/test_trr.py::test_deficient_shape PASSED [ 92%] 374s tests/test_trr.py::test_ragged_1 PASSED [ 92%] 374s tests/test_trr.py::test_ragged_2 PASSED [ 92%] 374s tests/test_trr.py::test_malformed PASSED [ 92%] 374s tests/test_trr.py::test_tell PASSED [ 92%] 374s tests/test_trr.py::test_seek PASSED [ 92%] 374s tests/test_trr.py::test_get_velocities PASSED [ 92%] 374s tests/test_trr.py::test_get_forces PASSED [ 92%] 374s tests/test_trr.py::test_get_velocities_and_forces PASSED [ 92%] 374s tests/test_trr.py::test_get_velocities_forces_atom_indices_1 PASSED [ 92%] 374s tests/test_trr.py::test_get_velocities_forces_atom_indices_2 PASSED [ 93%] 374s tests/test_trr.py::test_read_velocities_do_not_exist PASSED [ 93%] 374s tests/test_trr.py::test_read_forces_do_not_exist PASSED [ 93%] 374s tests/test_utils.py::test_unitcell_0 PASSED [ 93%] 374s tests/test_utils.py::test_unitcell_1 PASSED [ 93%] 374s tests/test_utils.py::test_ensure_type_1 PASSED [ 93%] 374s tests/test_utils.py::test_ensure_type_2 PASSED [ 93%] 374s tests/test_utils.py::test_ensure_type_25 PASSED [ 93%] 374s tests/test_utils.py::test_ensure_type_3 PASSED [ 93%] 374s tests/test_utils.py::test_ensure_type_4 PASSED [ 93%] 374s tests/test_utils.py::test_ensure_type_5 PASSED [ 93%] 374s tests/test_utils.py::test_ensure_type_6 PASSED [ 93%] 374s tests/test_utils.py::test_ensure_type_7 PASSED [ 94%] 374s tests/test_utils.py::test_ensure_type_8 PASSED [ 94%] 374s tests/test_utils.py::test_ensure_type_9 PASSED [ 94%] 374s tests/test_utils.py::test_ensure_type_10 PASSED [ 94%] 374s tests/test_utils.py::test_ensure_type_11 PASSED [ 94%] 374s tests/test_utils.py::test_ensure_type_12 PASSED [ 94%] 374s tests/test_utils.py::test_ensure_type_13 PASSED [ 94%] 374s tests/test_utils.py::test_ensure_type_14 PASSED [ 94%] 374s tests/test_utils.py::test_ensure_type_15 PASSED [ 94%] 374s tests/test_utils.py::test_delay_import_fail_1 PASSED [ 94%] 374s tests/test_utils.py::test_delay_import PASSED [ 94%] 374s tests/test_utils.py::test_unit_0 PASSED [ 95%] 374s tests/test_utils.py::test_unit_1 PASSED [ 95%] 374s tests/test_utils.py::test_unit_2 PASSED [ 95%] 374s tests/test_utils.py::test_unit_3 PASSED [ 95%] 374s tests/test_xml.py::test_xml PASSED [ 95%] 374s tests/test_xtc.py::test_read_chunk1 PASSED [ 95%] 374s tests/test_xtc.py::test_read_stride PASSED [ 95%] 374s tests/test_xtc.py::test_read_stride_n_frames PASSED [ 95%] 374s tests/test_xtc.py::test_read_stride_offsets PASSED [ 95%] 374s tests/test_xtc.py::test_read_stride_n_frames_offsets PASSED [ 95%] 374s tests/test_xtc.py::test_read_stride_switching_offsets PASSED [ 95%] 374s tests/test_xtc.py::test_read_atomindices_1 PASSED [ 96%] 374s tests/test_xtc.py::test_read_atomindices_w_stride PASSED [ 96%] 374s tests/test_xtc.py::test_read_atomindices_2 PASSED [ 96%] 374s tests/test_xtc.py::test_read_chunk2 PASSED [ 96%] 374s tests/test_xtc.py::test_read_chunk3 PASSED [ 96%] 375s tests/test_xtc.py::test_write_0 PASSED [ 96%] 375s tests/test_xtc.py::test_write_1 PASSED [ 96%] 375s tests/test_xtc.py::test_write_2 PASSED [ 96%] 375s tests/test_xtc.py::test_read_error_0 PASSED [ 96%] 375s tests/test_xtc.py::test_write_error_0 PASSED [ 96%] 375s tests/test_xtc.py::test_read_error_1 PASSED [ 96%] 375s tests/test_xtc.py::test_read_error_2 PASSED [ 96%] 375s tests/test_xtc.py::test_xtc_write_wierd_0 PASSED [ 97%] 375s tests/test_xtc.py::test_tell PASSED [ 97%] 375s tests/test_xtc.py::test_seek PASSED [ 97%] 375s tests/test_xtc.py::test_seek_natoms9 PASSED [ 97%] 375s tests/test_xtc.py::test_seek_out_of_bounds PASSED [ 97%] 375s tests/test_xtc.py::test_ragged_1 PASSED [ 97%] 375s tests/test_xtc.py::test_ragged_2 PASSED [ 97%] 375s tests/test_xtc.py::test_short_traj PASSED [ 97%] 375s tests/test_xtc.py::test_flush PASSED [ 97%] 375s tests/test_xyz.py::test_read_0 PASSED [ 97%] 375s tests/test_xyz.py::test_read_1 PASSED [ 97%] 375s tests/test_xyz.py::test_read_gz PASSED [ 98%] 375s tests/test_xyz.py::test_read_write PASSED [ 98%] 375s tests/test_xyz.py::test_mdwrite PASSED [ 98%] 375s tests/test_xyz.py::test_multiread PASSED [ 98%] 375s tests/test_xyz.py::test_seek PASSED [ 98%] 375s tests/test_xyz.py::test_len PASSED [ 98%] 375s tests/test_zipped.py::test_read_gz PASSED [ 98%] 375s tests/test_zipped.py::test_write_gz PASSED [ 98%] 375s tests/test_zipped.py::test_read_bz2 PASSED [ 98%] 375s tests/test_zipped.py::test_write_bz2 PASSED [ 98%] 510s examples/test_examples.py::test_example_notebook[rmsd-drift.ipynb] PASSED [ 98%] 645s examples/test_examples.py::test_example_notebook[solvent-accessible-surface-area.ipynb] PASSED [ 99%] 778s examples/test_examples.py::test_example_notebook[native-contact.ipynb] SKIPPED [ 99%] 915s examples/test_examples.py::test_example_notebook[centroids.ipynb] PASSED [ 99%] 915s examples/test_examples.py::test_example_notebook[simulation-with-openmm.ipynb] SKIPPED [ 99%] 1051s examples/test_examples.py::test_example_notebook[ramachandran-plot.ipynb] PASSED [ 99%] 1186s examples/test_examples.py::test_example_notebook[principal-components.ipynb] PASSED [ 99%] 1319s examples/test_examples.py::test_example_notebook[hbonds.ipynb] SKIPPED [ 99%] 1455s examples/test_examples.py::test_example_notebook[iterload.ipynb] PASSED [ 99%] 1590s examples/test_examples.py::test_example_notebook[atom-selection.ipynb] PASSED [ 99%] 1726s examples/test_examples.py::test_example_notebook[clustering.ipynb] PASSED [ 99%] 1861s examples/test_examples.py::test_example_notebook[two-pass-clustering.ipynb] PASSED [ 99%] 1996s examples/test_examples.py::test_example_notebook[rmsd-benchmark.ipynb] PASSED [100%] 1996s 1996s =============================== warnings summary =============================== 1996s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:56 1996s /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. 1996s THIS_ATOM = ast.Name(id="atom", ctx=ast.Load(), SINGLETON=True) 1996s 1996s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:57 1996s /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. 1996s RE_MODULE = ast.Name(id="re", ctx=ast.Load(), SINGLETON=True) 1996s 1996s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 1996s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 1996s given by the platformdirs library. To remove this warning and 1996s see the appropriate new directories, set the environment variable 1996s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 1996s The use of platformdirs will be the default in `jupyter_core` v6 1996s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 1996s 1996s examples/test_examples.py:26 1996s /tmp/autopkgtest.OuqIYg/build.quR/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 1996s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 1996s 1996s tests/test_contact.py::test_contact_0 1996s tests/test_contact.py::test_contact_4 1996s /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. 1996s warnings.warn( 1996s 1996s tests/test_contact.py::test_contact_3 1996s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:271: RuntimeWarning: overflow encountered in exp 1996s np.exp( 1996s 1996s tests/test_contact.py::test_contact_3 1996s /tmp/autopkgtest.OuqIYg/build.quR/src/tests/test_contact.py:115: RuntimeWarning: divide by zero encountered in divide 1996s beta / np.log(np.sum(np.exp(beta / maps[t, r0, r1]))), 1996s 1996s tests/test_dcd.py::test_do_overwrite 1996s tests/test_dcd.py::test_ragged_1 1996s tests/test_dcd.py::test_ragged_2 1996s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting xyz dtype=float64 to 1996s warnings.warn( 1996s 1996s tests/test_distance.py::test_6 1996s :488: RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject 1996s 1996s tests/test_drid.py::test_drid_2 1996s /tmp/autopkgtest.OuqIYg/build.quR/src/tests/test_drid.py:62: RuntimeWarning: divide by zero encountered in divide 1996s recip = 1 / squareform(pdist(t.xyz[i])) 1996s 1996s tests/test_dssp.py::test_1[1vii.pdb] 1996s tests/test_gro.py::test_read_write 1996s tests/test_gro.py::test_read_write_precision 1996s tests/test_gro.py::test_load 1996s tests/test_shape.py::test_principal_moments 1996s tests/test_shape.py::test_asphericity 1996s tests/test_shape.py::test_shape_metrics 1996s /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. 1996s warnings.warn( 1996s 1996s tests/test_geometry.py::test_dihedral_indices 1996s tests/test_geometry.py::test_dihedral_indices 1996s /usr/lib/python3/dist-packages/mdtraj/geometry/dihedral.py:237: DeprecationWarning: Passing a Trajectory object to _atom_sequence isdeprecated. Please pass a Topology object 1996s warnings.warn( 1996s 1996s tests/test_gro.py::test_load 1996s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq 1996s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:364: UserWarning: WARNING: two consecutive residues with same number (GST, HST) 1996s warnings.warn( 1996s 1996s tests/test_pdb.py::test_blank_indexing 1996s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:204: UserWarning: Need to guess atom number starting from atom 100000. 1996s warnings.warn(f'Need to guess atom number {num_str} starting from atom {pdbstructure._next_atom_number}.') 1996s 1996s tests/test_pdb.py::test_blank_indexing 1996s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:271: UserWarning: Need to guess residue number string starting from residue10000, atom 100000. 1996s warnings.warn(f'Need to guess residue number string {num_str} starting from residue{pdbstructure._next_residue_number}, atom {pdbstructure._next_atom_number}.') 1996s 1996s tests/test_rdf.py::test_rdf_norm 1996s tests/test_rdf.py::test_rdf_t_norm[0] 1996s tests/test_rdf.py::test_rdf_t_norm[2] 1996s tests/test_rdf.py::test_rdf_t_norm[4] 1996s tests/test_selection.py::test_re 1996s tests/test_selection.py::test_re 1996s tests/test_topology.py::test_select_pairs 1996s tests/test_topology.py::test_select_pairs 1996s /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. 1996s left=ast.Call( 1996s 1996s tests/test_rdf.py::test_rdf_norm 1996s tests/test_rdf.py::test_rdf_t_norm[0] 1996s tests/test_rdf.py::test_rdf_t_norm[2] 1996s tests/test_rdf.py::test_rdf_t_norm[4] 1996s tests/test_selection.py::test_re 1996s tests/test_selection.py::test_re 1996s tests/test_topology.py::test_select_pairs 1996s tests/test_topology.py::test_select_pairs 1996s /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. 1996s left=ast.Call( 1996s 1996s tests/test_trajectory.py::test_float_atom_indices_exception[gro] 1996s tests/test_trajectory.py::test_atom_slicing 1996s /usr/lib/python3/dist-packages/mdtraj/core/topology.py:84: UserWarning: atom_indices are not monotonically increasing 1996s warnings.warn("atom_indices are not monotonically increasing") 1996s 1996s tests/test_utils.py::test_ensure_type_8 1996s tests/test_utils.py::test_ensure_type_9 1996s tests/test_utils.py::test_ensure_type_13 1996s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=float64 to 1996s warnings.warn( 1996s 1996s tests/test_utils.py::test_ensure_type_11 1996s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=int64 to 1996s warnings.warn( 1996s 1996s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1996s =========================== short test summary info ============================ 1996s SKIPPED [1] tests/test_dihedral.py:56: pymol executable not found 1996s SKIPPED [1] tests/test_dihedral.py:181: pymol executable not found 1996s SKIPPED [16] tests/test_docstrings.py:38: Skip checking certain modules' docstrings 1996s SKIPPED [1] tests/test_geometry.py:300: Not doing performance testing 1996s SKIPPED [1] tests/test_geometry.py:322: Not doing performance testing 1996s SKIPPED [1] tests/test_hdf5.py:104: requires openmm.units 1996s SKIPPED [1] tests/test_hdf5.py:156: requires openmm.units 1996s SKIPPED [1] tests/test_hdf5.py:223: requires openmm.units 1996s SKIPPED [1] tests/test_mol2.py:59: Requires obabel 1996s SKIPPED [1] tests/test_netcdf.py:271: This test requires cpptraj from AmberTools to be installed (http://ambermd.org) 1996s SKIPPED [1] tests/test_nmr.py:11: SPARTA+ binary not found 1996s SKIPPED [1] tests/test_nmr.py:26: PPM binary not found 1996s SKIPPED [1] tests/test_nmr.py:42: SHIFTX2 binary not found or running on travis. 1996s SKIPPED [1] tests/test_pdbx.py:43: test_pdbx.py needs OpenMM. 1996s SKIPPED [2] tests/test_psf.py:93: This test requires the VMD executable: http://www.ks.uiuc.edu/Research/vmd/ 1996s SKIPPED [1] tests/test_rdf.py:64: Binning does not match up with gromacs currently. 1996s SKIPPED [1] tests/test_rdf.py:200: Binning does not match up with gromacs currently. 1997s SKIPPED [1] tests/test_rdf.py:219: Expected failure for NumPy < 2.0 due to histogram output differences 1997s SKIPPED [1] tests/test_reporter.py:58: test_reporter.py needs OpenMM. 1997s SKIPPED [1] tests/test_reporter.py:145: test_reporter.py needs OpenMM. 1997s SKIPPED [1] tests/test_reporter.py:245: test_reporter.py needs OpenMM. 1997s SKIPPED [1] tests/test_selection.py:267: failed to parse selection 1997s SKIPPED [1] tests/test_thermodynamic_properties.py:161: Thermal expansion test doesn't work. 1997s SKIPPED [1] tests/test_topology.py:45: needs OpenMM 1997s SKIPPED [1] tests/test_topology.py:62: needs OpenMM 1997s SKIPPED [1] tests/test_topology.py:72: needs OpenMM 1997s SKIPPED [1] tests/test_topology.py:81: needs OpenMM 1997s SKIPPED [1] tests/test_topology.py:91: needs OpenMM 1997s SKIPPED [1] tests/test_topology.py:97: needs OpenMM 1997s SKIPPED [1] tests/test_topology.py:247: needs OpenMM 1997s SKIPPED [1] tests/test_trajectory.py:129: xyz does not store box information 1997s SKIPPED [1] tests/test_trajectory.py:129: xyz.gz does not store box information 1997s SKIPPED [1] tests/test_trajectory.py:129: lh5 does not store box information 1997s SKIPPED [1] tests/test_trajectory.py:129: pdb does not store box information 1997s SKIPPED [1] tests/test_trajectory.py:129: pdb.gz does not store box information 1997s SKIPPED [1] tests/test_trajectory.py:226: mdcrd can only store rectilinear boxes 1997s SKIPPED [1] tests/test_trajectory.py:224: ncrst can only store 1 frame per file 1997s SKIPPED [1] tests/test_trajectory.py:224: rst7 can only store 1 frame per file 1997s SKIPPED [14] tests/test_trajectory.py:248: mdcrd can only store rectilinear boxes 1997s SKIPPED [14] tests/test_trajectory.py:246: ncrst can only store 1 frame per file 1997s SKIPPED [14] tests/test_trajectory.py:246: rst7 can only store 1 frame per file 1997s SKIPPED [4] tests/test_trajectory.py:256: dtr needs to write unitcells 1997s SKIPPED [4] tests/test_trajectory.py:256: lammpstrj needs to write unitcells 1997s SKIPPED [2] tests/test_trajectory.py:640: Only 1 frame per file format 1997s SKIPPED [2] examples/test_examples.py:77: Network access required 1997s SKIPPED [1] examples/test_examples.py:77: Openmm required for example notebook `simulation-with-openmm.ipynb` 1997s XFAIL tests/test_trajectory.py::test_read_path[ncrst] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_path[rst7] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[ncrst-nc] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[ncrst-h5] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xtc] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[ncrst-trr] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dcd] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[ncrst-mdcrd] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dtr] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lh5] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[ncrst-ncrst] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[ncrst-rst7] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[ncrst-gro] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[rst7-nc] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[rst7-h5] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[rst7-xtc] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[rst7-trr] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[rst7-dcd] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[rst7-mdcrd] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[rst7-dtr] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz.gz] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[rst7-lammpstrj] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[rst7-lh5] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb.gz] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[rst7-ncrst] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[rst7-rst7] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_read_write[rst7-gro] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_load[ncrst] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_load[rst7] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[rst7] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_load_combination[ncrst] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_load_combination[rst7] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_seek_read_mode[xyz.gz] - reason: This is broken 1997s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb] - reason: PDB Files don't support seeking 1997s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb.gz] - reason: PDB Files don't support seeking 1997s XFAIL tests/test_trajectory.py::test_seek_read_mode[ncrst] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_seek_read_mode[rst7] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_seek_read_mode[gro] - reason: This is broken 1997s XFAIL tests/test_trajectory.py::test_load_frame[dtr] - reason: DTR doesn't load a single frame properly 1997s XFAIL tests/test_trajectory.py::test_load_frame[ncrst] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_load_frame[rst7] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_load_frame[gro] - reason: Gro doesn't implement seek 1997s XFAIL tests/test_trajectory.py::test_iterload[dtr] - reason: This is broken with dtr 1997s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb] - reason: PDB Iterloads an extra frame!! 1997s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb.gz] - reason: PDB Iterloads an extra frame!! 1997s XFAIL tests/test_trajectory.py::test_iterload_skip[ncrst] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_iterload_skip[rst7] - reason: These reference files don't exist yet 1997s XFAIL tests/test_trajectory.py::test_iterload_skip[gro] - reason: Not implemented for some reason 1997s XFAIL tests/test_trajectory.py::test_force_overwrite[dtr] - reason: This is broken with dtr 1997s XFAIL tests/test_trajectory.py::test_unitcell[dtr] - reason: dtr seems to need unit vectors 1997s XFAIL tests/test_trajectory.py::test_unitcell[lammpstrj] - reason: lammpstrj seems to need unit vectors 1997s XFAIL tests/test_trajectory.py::test_unitcell[ncrst] - reason: ncrst seems to need unit vectors 1997s XFAIL tests/test_trajectory.py::test_unitcell[rst7] - reason: rst7 seems to need unit vectors 1997s = 963 passed, 109 skipped, 12 deselected, 61 xfailed, 48 warnings in 1844.98s (0:30:44) = 1997s autopkgtest [13:42:44]: test command1: -----------------------] 1998s autopkgtest [13:42:45]: test command1: - - - - - - - - - - results - - - - - - - - - - 1998s command1 PASS 1998s autopkgtest [13:42:45]: test command2: preparing testbed 1998s Reading package lists... 1998s Building dependency tree... 1998s Reading state information... 1998s Starting pkgProblemResolver with broken count: 0 1998s Starting 2 pkgProblemResolver with broken count: 0 1998s Done 1999s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1999s autopkgtest [13:42:46]: test command2: pytest-3 -k 'test_3 or test_pdb_from_url or test_1vii_url_and_gz' 1999s autopkgtest [13:42:46]: test command2: [----------------------- 2000s ============================= test session starts ============================== 2000s platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 -- /usr/bin/python3 2000s cachedir: .pytest_cache 2000s rootdir: /tmp/autopkgtest.OuqIYg/build.quR/src 2000s configfile: pyproject.toml 2000s testpaths: tests, examples 2000s plugins: typeguard-4.4.1 2001s collecting ... collected 1145 items / 1135 deselected / 10 selected 2001s 2001s tests/test_distance.py::test_3 PASSED [ 10%] 2001s tests/test_distance.py::test_3p PASSED [ 20%] 2004s tests/test_dssp.py::test_3[1GAI] PASSED [ 30%] 2006s tests/test_dssp.py::test_3[6gsv] PASSED [ 40%] 2010s tests/test_dssp.py::test_3[2AAC] PASSED [ 50%] 2010s tests/test_nmr.py::test_3_scalar_couplings PASSED [ 60%] 2017s tests/test_pdb.py::test_pdb_from_url PASSED [ 70%] 2017s tests/test_pdb.py::test_3nch_conect PASSED [ 80%] 2020s tests/test_pdb.py::test_3nch_serial_resSeq PASSED [ 90%] 2023s tests/test_pdb.py::test_1vii_url_and_gz PASSED [100%] 2023s 2023s =============================== warnings summary =============================== 2023s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:56 2023s /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. 2023s THIS_ATOM = ast.Name(id="atom", ctx=ast.Load(), SINGLETON=True) 2023s 2023s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:57 2023s /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. 2023s RE_MODULE = ast.Name(id="re", ctx=ast.Load(), SINGLETON=True) 2023s 2023s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 2023s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 2023s given by the platformdirs library. To remove this warning and 2023s see the appropriate new directories, set the environment variable 2023s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 2023s The use of platformdirs will be the default in `jupyter_core` v6 2023s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 2023s 2023s examples/test_examples.py:26 2023s /tmp/autopkgtest.OuqIYg/build.quR/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 2023s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 2023s 2023s tests/test_pdb.py::test_1vii_url_and_gz 2023s /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. 2023s warnings.warn( 2023s 2023s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 2023s =============== 10 passed, 1135 deselected, 5 warnings in 23.50s =============== 2024s autopkgtest [13:43:11]: test command2: -----------------------] 2024s command2 PASS 2024s autopkgtest [13:43:11]: test command2: - - - - - - - - - - results - - - - - - - - - - 2024s autopkgtest [13:43:11]: @@@@@@@@@@@@@@@@@@@@ summary 2024s command1 PASS 2024s command2 PASS 2029s nova [W] Skipping flock for amd64 2029s Creating nova instance adt-plucky-amd64-mdtraj-20250219-113248-juju-7f2275-prod-proposed-migration-environment-20-be4e8c96-f92c-4442-9629-4496fc17a245 from image adt/ubuntu-plucky-amd64-server-20250218.img (UUID 0c5f6311-785d-4524-a0d8-db541aaf5c09)... 2029s nova [W] Timed out waiting for 39549227-3cbf-4e38-9266-43d6f23ccad6 to get deleted.