0s autopkgtest [09:37:08]: starting date and time: 2024-11-13 09:37:08+0000 0s autopkgtest [09:37:08]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [09:37:08]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.o9g57k3_/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade mdtraj --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-27.secgroup --name adt-plucky-arm64-mdtraj-20241113-093707-juju-7f2275-prod-proposed-migration-environment-2-c17bdc01-0664-44a9-8270-ccab5c952585 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 81s autopkgtest [09:38:29]: testbed dpkg architecture: arm64 82s autopkgtest [09:38:30]: testbed apt version: 2.9.8 82s autopkgtest [09:38:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup 83s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 83s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 83s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 83s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 83s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 83s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 83s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 83s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 83s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 84s Fetched 1793 kB in 1s (1890 kB/s) 84s Reading package lists... 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 88s Calculating upgrade... 88s The following NEW packages will be installed: 88s python3.13-gdbm 88s The following packages will be upgraded: 88s libpython3-stdlib python3 python3-gdbm python3-minimal 89s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 89s Need to get 101 kB of archives. 89s After this operation, 141 kB of additional disk space will be used. 89s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 89s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 89s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 89s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 89s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 89s Fetched 101 kB in 0s (252 kB/s) 90s (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 ... 79924 files and directories currently installed.) 90s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 90s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 90s Setting up python3-minimal (3.12.7-1) ... 90s (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 ... 79924 files and directories currently installed.) 90s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 90s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 90s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 90s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 90s Selecting previously unselected package python3.13-gdbm. 90s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 90s Unpacking python3.13-gdbm (3.13.0-2) ... 90s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 90s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 90s Setting up python3.13-gdbm (3.13.0-2) ... 90s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 90s Setting up python3 (3.12.7-1) ... 91s Setting up python3-gdbm:arm64 (3.12.7-1) ... 91s Processing triggers for man-db (2.12.1-3) ... 92s Reading package lists... 92s Building dependency tree... 92s Reading state information... 93s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 93s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 93s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 93s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 93s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 95s Reading package lists... 95s Reading package lists... 95s Building dependency tree... 95s Reading state information... 96s Calculating upgrade... 96s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 96s Reading package lists... 97s Building dependency tree... 97s Reading state information... 97s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s autopkgtest [09:38:48]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 101s autopkgtest [09:38:49]: @@@@@@@@@@@@@@@@@@@@ apt-source mdtraj 105s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.1-2 (dsc) [2702 B] 105s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.1-2 (tar) [21.9 MB] 105s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.1-2 (diff) [296 kB] 105s gpgv: Signature made Mon Nov 11 19:58:43 2024 UTC 105s gpgv: using RSA key 13796755BBC72BB8ABE2AEB5FA9DEC5DE11C63F1 105s gpgv: issuer "eamanu@debian.org" 105s gpgv: Can't check signature: No public key 105s dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.10.1-2.dsc: no acceptable signature found 106s autopkgtest [09:38:54]: testing package mdtraj version 1.10.1-2 108s autopkgtest [09:38:56]: build not needed 113s autopkgtest [09:39:01]: test command1: preparing testbed 114s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s Starting pkgProblemResolver with broken count: 0 115s Starting 2 pkgProblemResolver with broken count: 0 115s Done 116s The following additional packages will be installed: 116s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx gdb 116s libaec0 libbabeltrace1 libblas3 libblosc1 libblosc2-4 libdebuginfod-common 116s libdebuginfod1t64 libdeflate0 libfontconfig1 libgfortran5 libgomp1 116s libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 116s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 116s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libnetcdf19t64 libnorm1t64 116s libopenjp2-7 libpgm-5.3-0t64 libqhull-r8.0 libraqm0 libsharpyuv0 116s libsnappy1v5 libsodium23 libsource-highlight-common libsource-highlight4t64 116s libsz2 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 116s libxft2 libxrender1 libxslt1.1 libxss1 libzmq5 python-matplotlib-data 116s python-tables-data python3-appdirs python3-asttokens python3-brotli 116s python3-cftime python3-comm python3-contourpy python3-coverage 116s python3-cpuinfo python3-cycler python3-dateutil python3-debugpy 116s python3-decorator python3-executing python3-fastjsonschema python3-fonttools 116s python3-fs python3-gsd python3-iniconfig python3-ipykernel python3-ipython 116s python3-jedi python3-joblib python3-jupyter-client python3-jupyter-core 116s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 116s python3-matplotlib-inline python3-mdtraj python3-mpmath python3-nbformat 116s python3-nest-asyncio python3-netcdf4 python3-networkx python3-numexpr 116s python3-numpy python3-packaging python3-pandas python3-pandas-lib 116s python3-parso python3-pexpect python3-pil python3-pil.imagetk 116s python3-platformdirs python3-pluggy python3-prompt-toolkit python3-psutil 116s python3-ptyprocess python3-pure-eval python3-py python3-pytest python3-scipy 116s python3-six python3-sklearn python3-sklearn-lib python3-stack-data 116s python3-sympy python3-tables python3-tables-lib python3-threadpoolctl 116s python3-tk python3-tornado python3-traitlets python3-typeshed python3-tz 116s python3-ufolib2 python3-unicodedata2 python3-wcwidth python3-zmq 116s python3.12-tk python3.13-tk tk8.6-blt2.5 unicode-data x11-common 116s Suggested packages: 116s blt-demo gdb-doc gdbserver libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 116s python-coverage-doc python-cycler-doc python-fastjsonschema-doc 116s python-gsd-doc python-ipython-doc python-joblib-doc 116s python-jupyter-client-doc python3-pip python-lxml-doc cm-super-minimal 116s dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 116s librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi-cairo 116s python3-gobject python3-pyqt5 python3-sip texlive-extra-utils 116s texlive-latex-extra python-mdtraj-doc python-mpmath-doc python3-gmpy2 116s python3-gdal python3-pydot python3-pygraphviz gcc gfortran python-numpy-doc 116s python3-dev python-pandas-doc python3-statsmodels python-pexpect-doc 116s python-pil-doc subversion python-scipy-doc python3-dap python-sklearn-doc 116s texlive-fonts-extra python-sympy-doc python-tables-doc vitables tix 116s python3-tk-dbg python3-pycurl python-tornado-doc python3-twisted 116s python-traitlets-doc 116s Recommended packages: 116s libc-dbg javascript-common python3-simplejson python3-bs4 python3-cssselect 116s python3-html5lib python3-bottleneck python3-odf python3-openpyxl 116s python3-olefile g++ | c++-compiler isympy-common 116s The following NEW packages will be installed: 116s autopkgtest-satdep blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono 116s fonts-lyx gdb libaec0 libbabeltrace1 libblas3 libblosc1 libblosc2-4 116s libdebuginfod-common libdebuginfod1t64 libdeflate0 libfontconfig1 116s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 116s libhdf5-hl-100t64 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 116s libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 116s libnetcdf19t64 libnorm1t64 libopenjp2-7 libpgm-5.3-0t64 libqhull-r8.0 116s libraqm0 libsharpyuv0 libsnappy1v5 libsodium23 libsource-highlight-common 116s libsource-highlight4t64 libsz2 libtcl8.6 libtiff6 libtk8.6 libwebp7 116s libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 libzmq5 116s python-matplotlib-data python-tables-data python3-appdirs python3-asttokens 116s python3-brotli python3-cftime python3-comm python3-contourpy 116s python3-coverage python3-cpuinfo python3-cycler python3-dateutil 116s python3-debugpy python3-decorator python3-executing python3-fastjsonschema 116s python3-fonttools python3-fs python3-gsd python3-iniconfig python3-ipykernel 116s python3-ipython python3-jedi python3-joblib python3-jupyter-client 116s python3-jupyter-core python3-kiwisolver python3-lxml python3-lz4 116s python3-matplotlib python3-matplotlib-inline python3-mdtraj python3-mpmath 116s python3-nbformat python3-nest-asyncio python3-netcdf4 python3-networkx 116s python3-numexpr python3-numpy python3-packaging python3-pandas 116s python3-pandas-lib python3-parso python3-pexpect python3-pil 116s python3-pil.imagetk python3-platformdirs python3-pluggy 116s python3-prompt-toolkit python3-psutil python3-ptyprocess python3-pure-eval 116s python3-py python3-pytest python3-scipy python3-six python3-sklearn 116s python3-sklearn-lib python3-stack-data python3-sympy python3-tables 116s python3-tables-lib python3-threadpoolctl python3-tk python3-tornado 116s python3-traitlets python3-typeshed python3-tz python3-ufolib2 116s python3-unicodedata2 python3-wcwidth python3-zmq python3.12-tk python3.13-tk 116s tk8.6-blt2.5 unicode-data x11-common 116s 0 upgraded, 132 newly installed, 0 to remove and 0 not upgraded. 116s Need to get 97.1 MB/97.1 MB of archives. 116s After this operation, 463 MB of additional disk space will be used. 116s Get:1 /tmp/autopkgtest.PzEck5/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [776 B] 116s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebuginfod-common all 0.192-4 [15.4 kB] 116s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [987 kB] 117s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 117s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 117s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 117s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 117s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 117s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 117s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 117s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 117s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.15-1 [774 kB] 117s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 117s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 117s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.2.1-1 [171 kB] 117s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libbabeltrace1 arm64 1.5.11-4 [159 kB] 117s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebuginfod1t64 arm64 0.192-4 [20.8 kB] 117s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libsource-highlight-common all 3.1.9-4.3build1 [64.2 kB] 117s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libsource-highlight4t64 arm64 3.1.9-4.3build1 [243 kB] 117s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 gdb arm64 15.1-1ubuntu2 [4550 kB] 118s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 118s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 118s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libsnappy1v5 arm64 1.2.1-1 [30.4 kB] 118s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 libblosc1 arm64 1.21.5+ds-1build1 [25.7 kB] 118s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 libblosc2-4 arm64 2.15.1+ds-1 [157 kB] 118s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 118s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 118s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 118s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 118s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB] 118s Get:31 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 118s Get:32 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4ubuntu3 [1207 kB] 118s Get:33 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4ubuntu3 [56.9 kB] 118s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 118s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 118s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 118s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 119s Get:38 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 119s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 119s Get:40 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 119s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 119s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 119s Get:43 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnetcdf19t64 arm64 1:4.9.2-6ubuntu1 [466 kB] 119s Get:44 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnorm1t64 arm64 1.5.9+dfsg-3.1build1 [150 kB] 119s Get:45 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpgm-5.3-0t64 arm64 5.3.128~dfsg-2.1build1 [162 kB] 119s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 119s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 119s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 119s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libsodium23 arm64 1.0.18-1build3 [119 kB] 119s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 119s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 119s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 119s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 119s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 119s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu1 [167 kB] 119s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 libzmq5 arm64 4.3.5-1build2 [247 kB] 119s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3 [2928 kB] 120s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-tables-data all 3.10.1-1 [49.3 kB] 120s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 120s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-asttokens all 2.4.1-2 [20.8 kB] 120s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build2 [340 kB] 120s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 120s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cftime arm64 1.6.4-1 [195 kB] 120s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 120s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-comm all 0.2.1-1 [7016 B] 120s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.0-2 [179 kB] 120s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-coverage arm64 7.4.4+dfsg1-0ubuntu2 [148 kB] 120s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cpuinfo all 9.0.0+git20221119-2 [21.6 kB] 120s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 120s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB] 120s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 120s Get:72 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-debugpy arm64 1.8.8+ds-1ubuntu1 [887 kB] 120s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 120s Get:74 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-executing all 2.1.0-0.1 [24.4 kB] 120s Get:75 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fastjsonschema all 2.20.0-1 [20.1 kB] 120s Get:76 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB] 121s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 121s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 121s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 121s Get:80 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 121s Get:81 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-4 [91.3 kB] 121s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.0-1 [1205 kB] 121s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build4 [26.7 kB] 121s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build1 [362 kB] 121s Get:85 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 121s Get:86 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.46.0-1build2 [1398 kB] 121s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-gsd arm64 3.3.0-1 [200 kB] 121s Get:88 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 121s Get:89 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-parso all 0.8.3-1 [67.2 kB] 121s Get:90 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-typeshed all 0.0~git20231111.6764465-3 [1274 kB] 121s Get:91 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-jedi all 0.19.1+ds1-1 [693 kB] 121s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 121s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-ptyprocess all 0.7.0-6 [14.8 kB] 121s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pexpect all 4.9-2 [48.1 kB] 121s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 121s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-prompt-toolkit all 3.0.48-1 [256 kB] 121s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pure-eval all 0.2.3-1 [11.4 kB] 121s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-stack-data all 0.6.3-1 [22.0 kB] 121s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ipython all 8.20.0-1ubuntu1 [561 kB] 121s Get:100 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB] 121s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-jupyter-core all 5.7.2-4 [28.0 kB] 121s Get:102 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-psutil arm64 5.9.8-2build2 [196 kB] 121s Get:103 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tornado arm64 6.4.1-3 [299 kB] 122s Get:104 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-py all 1.11.0-2 [72.7 kB] 122s Get:105 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-zmq arm64 24.0.1-5build1 [280 kB] 122s Get:106 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-jupyter-client all 8.6.2-3 [78.1 kB] 122s Get:107 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-nest-asyncio all 1.5.4-1 [6256 B] 122s Get:108 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 122s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ipykernel all 6.29.5-1 [82.5 kB] 122s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-joblib all 1.3.2-5 [206 kB] 122s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-2 [50.4 kB] 122s Get:112 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 122s Get:113 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 122s Get:114 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.7-3 [115 kB] 122s Get:115 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.0-2 [105 kB] 122s Get:116 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-tk arm64 3.12.7-1 [9752 B] 122s Get:117 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 10.4.0-1ubuntu1 [9504 B] 122s Get:118 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3 [4515 kB] 122s Get:119 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 123s Get:120 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5 [4422 kB] 123s Get:121 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 123s Get:122 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-numexpr arm64 2.10.1-2 [114 kB] 123s Get:123 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tables-lib arm64 3.10.1-1 [516 kB] 123s Get:124 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tables all 3.10.1-1 [354 kB] 123s Get:125 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mdtraj arm64 1.10.1-2 [1078 kB] 123s Get:126 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-nbformat all 5.9.1-1 [41.2 kB] 123s Get:127 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-netcdf4 arm64 1.7.2-1 [567 kB] 123s Get:128 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 123s Get:129 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB] 123s Get:130 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 123s Get:131 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-6 [3806 kB] 123s Get:132 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn all 1.4.2+dfsg-6 [2257 kB] 124s Preconfiguring packages ... 124s Fetched 97.1 MB in 7s (13.5 MB/s) 124s Selecting previously unselected package libdebuginfod-common. 124s (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 ... 79931 files and directories currently installed.) 124s Preparing to unpack .../000-libdebuginfod-common_0.192-4_all.deb ... 124s Unpacking libdebuginfod-common (0.192-4) ... 124s Selecting previously unselected package libtcl8.6:arm64. 124s Preparing to unpack .../001-libtcl8.6_8.6.15+dfsg-2_arm64.deb ... 124s Unpacking libtcl8.6:arm64 (8.6.15+dfsg-2) ... 124s Selecting previously unselected package fonts-dejavu-mono. 124s Preparing to unpack .../002-fonts-dejavu-mono_2.37-8_all.deb ... 124s Unpacking fonts-dejavu-mono (2.37-8) ... 124s Selecting previously unselected package fonts-dejavu-core. 124s Preparing to unpack .../003-fonts-dejavu-core_2.37-8_all.deb ... 124s Unpacking fonts-dejavu-core (2.37-8) ... 124s Selecting previously unselected package fontconfig-config. 124s Preparing to unpack .../004-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 125s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 125s Selecting previously unselected package libfontconfig1:arm64. 125s Preparing to unpack .../005-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 125s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 125s Selecting previously unselected package libxrender1:arm64. 125s Preparing to unpack .../006-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 125s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 125s Selecting previously unselected package libxft2:arm64. 125s Preparing to unpack .../007-libxft2_2.3.6-1build1_arm64.deb ... 125s Unpacking libxft2:arm64 (2.3.6-1build1) ... 125s Selecting previously unselected package x11-common. 125s Preparing to unpack .../008-x11-common_1%3a7.7+23ubuntu3_all.deb ... 125s Unpacking x11-common (1:7.7+23ubuntu3) ... 125s Selecting previously unselected package libxss1:arm64. 125s Preparing to unpack .../009-libxss1_1%3a1.2.3-1build3_arm64.deb ... 125s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 125s Selecting previously unselected package libtk8.6:arm64. 125s Preparing to unpack .../010-libtk8.6_8.6.15-1_arm64.deb ... 125s Unpacking libtk8.6:arm64 (8.6.15-1) ... 125s Selecting previously unselected package tk8.6-blt2.5. 125s Preparing to unpack .../011-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ... 125s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 125s Selecting previously unselected package blt. 125s Preparing to unpack .../012-blt_2.5.3+dfsg-7build1_arm64.deb ... 125s Unpacking blt (2.5.3+dfsg-7build1) ... 126s Selecting previously unselected package fonts-lyx. 126s Preparing to unpack .../013-fonts-lyx_2.4.2.1-1_all.deb ... 126s Unpacking fonts-lyx (2.4.2.1-1) ... 126s Selecting previously unselected package libbabeltrace1:arm64. 126s Preparing to unpack .../014-libbabeltrace1_1.5.11-4_arm64.deb ... 126s Unpacking libbabeltrace1:arm64 (1.5.11-4) ... 126s Selecting previously unselected package libdebuginfod1t64:arm64. 126s Preparing to unpack .../015-libdebuginfod1t64_0.192-4_arm64.deb ... 126s Unpacking libdebuginfod1t64:arm64 (0.192-4) ... 126s Selecting previously unselected package libsource-highlight-common. 126s Preparing to unpack .../016-libsource-highlight-common_3.1.9-4.3build1_all.deb ... 126s Unpacking libsource-highlight-common (3.1.9-4.3build1) ... 126s Selecting previously unselected package libsource-highlight4t64:arm64. 126s Preparing to unpack .../017-libsource-highlight4t64_3.1.9-4.3build1_arm64.deb ... 126s Unpacking libsource-highlight4t64:arm64 (3.1.9-4.3build1) ... 126s Selecting previously unselected package gdb. 126s Preparing to unpack .../018-gdb_15.1-1ubuntu2_arm64.deb ... 126s Unpacking gdb (15.1-1ubuntu2) ... 126s Selecting previously unselected package libaec0:arm64. 126s Preparing to unpack .../019-libaec0_1.1.3-1_arm64.deb ... 126s Unpacking libaec0:arm64 (1.1.3-1) ... 126s Selecting previously unselected package libblas3:arm64. 126s Preparing to unpack .../020-libblas3_3.12.0-3build2_arm64.deb ... 126s Unpacking libblas3:arm64 (3.12.0-3build2) ... 126s Selecting previously unselected package libsnappy1v5:arm64. 126s Preparing to unpack .../021-libsnappy1v5_1.2.1-1_arm64.deb ... 126s Unpacking libsnappy1v5:arm64 (1.2.1-1) ... 126s Selecting previously unselected package libblosc1:arm64. 126s Preparing to unpack .../022-libblosc1_1.21.5+ds-1build1_arm64.deb ... 126s Unpacking libblosc1:arm64 (1.21.5+ds-1build1) ... 126s Selecting previously unselected package libblosc2-4:arm64. 126s Preparing to unpack .../023-libblosc2-4_2.15.1+ds-1_arm64.deb ... 126s Unpacking libblosc2-4:arm64 (2.15.1+ds-1) ... 126s Selecting previously unselected package libdeflate0:arm64. 126s Preparing to unpack .../024-libdeflate0_1.22-1_arm64.deb ... 126s Unpacking libdeflate0:arm64 (1.22-1) ... 126s Selecting previously unselected package libgfortran5:arm64. 126s Preparing to unpack .../025-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 126s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 126s Selecting previously unselected package libgomp1:arm64. 126s Preparing to unpack .../026-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 126s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 126s Selecting previously unselected package libgraphite2-3:arm64. 127s Preparing to unpack .../027-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 127s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 127s Selecting previously unselected package libharfbuzz0b:arm64. 127s Preparing to unpack .../028-libharfbuzz0b_10.0.1-1_arm64.deb ... 127s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... 127s Selecting previously unselected package libsz2:arm64. 127s Preparing to unpack .../029-libsz2_1.1.3-1_arm64.deb ... 127s Unpacking libsz2:arm64 (1.1.3-1) ... 127s Selecting previously unselected package libhdf5-103-1t64:arm64. 127s Preparing to unpack .../030-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_arm64.deb ... 127s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 127s Selecting previously unselected package libhdf5-hl-100t64:arm64. 127s Preparing to unpack .../031-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_arm64.deb ... 127s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 127s Selecting previously unselected package libimagequant0:arm64. 127s Preparing to unpack .../032-libimagequant0_2.18.0-1build1_arm64.deb ... 127s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 127s Selecting previously unselected package libjpeg-turbo8:arm64. 127s Preparing to unpack .../033-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ... 127s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 127s Selecting previously unselected package libjpeg8:arm64. 127s Preparing to unpack .../034-libjpeg8_8c-2ubuntu11_arm64.deb ... 127s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 127s Selecting previously unselected package libjs-jquery. 127s Preparing to unpack .../035-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 127s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 127s Selecting previously unselected package libjs-jquery-ui. 127s Preparing to unpack .../036-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 127s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 127s Selecting previously unselected package liblapack3:arm64. 127s Preparing to unpack .../037-liblapack3_3.12.0-3build2_arm64.deb ... 127s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 127s Selecting previously unselected package liblbfgsb0:arm64. 127s Preparing to unpack .../038-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 127s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 127s Selecting previously unselected package liblcms2-2:arm64. 127s Preparing to unpack .../039-liblcms2-2_2.16-2_arm64.deb ... 127s Unpacking liblcms2-2:arm64 (2.16-2) ... 127s Selecting previously unselected package liblerc4:arm64. 127s Preparing to unpack .../040-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ... 127s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 127s Selecting previously unselected package libnetcdf19t64:arm64. 128s Preparing to unpack .../041-libnetcdf19t64_1%3a4.9.2-6ubuntu1_arm64.deb ... 128s Unpacking libnetcdf19t64:arm64 (1:4.9.2-6ubuntu1) ... 128s Selecting previously unselected package libnorm1t64:arm64. 128s Preparing to unpack .../042-libnorm1t64_1.5.9+dfsg-3.1build1_arm64.deb ... 128s Unpacking libnorm1t64:arm64 (1.5.9+dfsg-3.1build1) ... 128s Selecting previously unselected package libpgm-5.3-0t64:arm64. 128s Preparing to unpack .../043-libpgm-5.3-0t64_5.3.128~dfsg-2.1build1_arm64.deb ... 128s Unpacking libpgm-5.3-0t64:arm64 (5.3.128~dfsg-2.1build1) ... 128s Selecting previously unselected package libqhull-r8.0:arm64. 128s Preparing to unpack .../044-libqhull-r8.0_2020.2-6build1_arm64.deb ... 128s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 128s Selecting previously unselected package libraqm0:arm64. 128s Preparing to unpack .../045-libraqm0_0.10.1-1build1_arm64.deb ... 128s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 128s Selecting previously unselected package libsharpyuv0:arm64. 128s Preparing to unpack .../046-libsharpyuv0_1.4.0-0.1_arm64.deb ... 128s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... 128s Selecting previously unselected package libsodium23:arm64. 128s Preparing to unpack .../047-libsodium23_1.0.18-1build3_arm64.deb ... 128s Unpacking libsodium23:arm64 (1.0.18-1build3) ... 128s Selecting previously unselected package libjbig0:arm64. 128s Preparing to unpack .../048-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 128s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 128s Selecting previously unselected package libwebp7:arm64. 128s Preparing to unpack .../049-libwebp7_1.4.0-0.1_arm64.deb ... 128s Unpacking libwebp7:arm64 (1.4.0-0.1) ... 128s Selecting previously unselected package libtiff6:arm64. 128s Preparing to unpack .../050-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 128s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 128s Selecting previously unselected package libwebpdemux2:arm64. 128s Preparing to unpack .../051-libwebpdemux2_1.4.0-0.1_arm64.deb ... 128s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 128s Selecting previously unselected package libwebpmux3:arm64. 128s Preparing to unpack .../052-libwebpmux3_1.4.0-0.1_arm64.deb ... 128s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 128s Selecting previously unselected package libxslt1.1:arm64. 128s Preparing to unpack .../053-libxslt1.1_1.1.39-0exp1ubuntu1_arm64.deb ... 128s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 128s Selecting previously unselected package libzmq5:arm64. 128s Preparing to unpack .../054-libzmq5_4.3.5-1build2_arm64.deb ... 128s Unpacking libzmq5:arm64 (4.3.5-1build2) ... 128s Selecting previously unselected package python-matplotlib-data. 128s Preparing to unpack .../055-python-matplotlib-data_3.8.3-3_all.deb ... 128s Unpacking python-matplotlib-data (3.8.3-3) ... 129s Selecting previously unselected package python-tables-data. 129s Preparing to unpack .../056-python-tables-data_3.10.1-1_all.deb ... 129s Unpacking python-tables-data (3.10.1-1) ... 129s Selecting previously unselected package python3-appdirs. 129s Preparing to unpack .../057-python3-appdirs_1.4.4-4_all.deb ... 129s Unpacking python3-appdirs (1.4.4-4) ... 129s Selecting previously unselected package python3-asttokens. 129s Preparing to unpack .../058-python3-asttokens_2.4.1-2_all.deb ... 129s Unpacking python3-asttokens (2.4.1-2) ... 129s Selecting previously unselected package python3-brotli. 129s Preparing to unpack .../059-python3-brotli_1.1.0-2build2_arm64.deb ... 129s Unpacking python3-brotli (1.1.0-2build2) ... 129s Selecting previously unselected package python3-numpy. 129s Preparing to unpack .../060-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 129s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 129s Selecting previously unselected package python3-cftime. 129s Preparing to unpack .../061-python3-cftime_1.6.4-1_arm64.deb ... 129s Unpacking python3-cftime (1.6.4-1) ... 129s Selecting previously unselected package python3-traitlets. 129s Preparing to unpack .../062-python3-traitlets_5.14.3+really5.14.3-1_all.deb ... 129s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ... 129s Selecting previously unselected package python3-comm. 129s Preparing to unpack .../063-python3-comm_0.2.1-1_all.deb ... 129s Unpacking python3-comm (0.2.1-1) ... 129s Selecting previously unselected package python3-contourpy. 129s Preparing to unpack .../064-python3-contourpy_1.3.0-2_arm64.deb ... 129s Unpacking python3-contourpy (1.3.0-2) ... 129s Selecting previously unselected package python3-coverage. 129s Preparing to unpack .../065-python3-coverage_7.4.4+dfsg1-0ubuntu2_arm64.deb ... 129s Unpacking python3-coverage (7.4.4+dfsg1-0ubuntu2) ... 129s Selecting previously unselected package python3-cpuinfo. 129s Preparing to unpack .../066-python3-cpuinfo_9.0.0+git20221119-2_all.deb ... 129s Unpacking python3-cpuinfo (9.0.0+git20221119-2) ... 129s Selecting previously unselected package python3-cycler. 129s Preparing to unpack .../067-python3-cycler_0.12.1-1_all.deb ... 129s Unpacking python3-cycler (0.12.1-1) ... 129s Selecting previously unselected package python3-six. 129s Preparing to unpack .../068-python3-six_1.16.0-7_all.deb ... 129s Unpacking python3-six (1.16.0-7) ... 129s Selecting previously unselected package python3-dateutil. 129s Preparing to unpack .../069-python3-dateutil_2.9.0-2_all.deb ... 129s Unpacking python3-dateutil (2.9.0-2) ... 129s Selecting previously unselected package python3-debugpy. 129s Preparing to unpack .../070-python3-debugpy_1.8.8+ds-1ubuntu1_arm64.deb ... 129s Unpacking python3-debugpy (1.8.8+ds-1ubuntu1) ... 130s Selecting previously unselected package python3-decorator. 130s Preparing to unpack .../071-python3-decorator_5.1.1-5_all.deb ... 130s Unpacking python3-decorator (5.1.1-5) ... 130s Selecting previously unselected package python3-executing. 130s Preparing to unpack .../072-python3-executing_2.1.0-0.1_all.deb ... 130s Unpacking python3-executing (2.1.0-0.1) ... 130s Selecting previously unselected package python3-fastjsonschema. 130s Preparing to unpack .../073-python3-fastjsonschema_2.20.0-1_all.deb ... 130s Unpacking python3-fastjsonschema (2.20.0-1) ... 130s Selecting previously unselected package python3-scipy. 130s Preparing to unpack .../074-python3-scipy_1.13.1-5_arm64.deb ... 130s Unpacking python3-scipy (1.13.1-5) ... 130s Selecting previously unselected package python3-ufolib2. 130s Preparing to unpack .../075-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 130s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 130s Selecting previously unselected package python3-mpmath. 130s Preparing to unpack .../076-python3-mpmath_1.3.0-1_all.deb ... 130s Unpacking python3-mpmath (1.3.0-1) ... 130s Selecting previously unselected package python3-sympy. 130s Preparing to unpack .../077-python3-sympy_1.13.3-1_all.deb ... 130s Unpacking python3-sympy (1.13.3-1) ... 131s Selecting previously unselected package python3-tz. 131s Preparing to unpack .../078-python3-tz_2024.1-2_all.deb ... 131s Unpacking python3-tz (2024.1-2) ... 131s Selecting previously unselected package python3-fs. 131s Preparing to unpack .../079-python3-fs_2.4.16-4_all.deb ... 131s Unpacking python3-fs (2.4.16-4) ... 131s Selecting previously unselected package python3-lxml:arm64. 131s Preparing to unpack .../080-python3-lxml_5.3.0-1_arm64.deb ... 131s Unpacking python3-lxml:arm64 (5.3.0-1) ... 131s Selecting previously unselected package python3-lz4. 131s Preparing to unpack .../081-python3-lz4_4.0.2+dfsg-1build4_arm64.deb ... 131s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 131s Selecting previously unselected package python3-unicodedata2. 131s Preparing to unpack .../082-python3-unicodedata2_15.1.0+ds-1build1_arm64.deb ... 131s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 131s Selecting previously unselected package unicode-data. 131s Preparing to unpack .../083-unicode-data_15.1.0-1_all.deb ... 131s Unpacking unicode-data (15.1.0-1) ... 131s Selecting previously unselected package python3-fonttools. 131s Preparing to unpack .../084-python3-fonttools_4.46.0-1build2_arm64.deb ... 131s Unpacking python3-fonttools (4.46.0-1build2) ... 131s Selecting previously unselected package python3-gsd. 131s Preparing to unpack .../085-python3-gsd_3.3.0-1_arm64.deb ... 131s Unpacking python3-gsd (3.3.0-1) ... 131s Selecting previously unselected package python3-iniconfig. 131s Preparing to unpack .../086-python3-iniconfig_1.1.1-2_all.deb ... 131s Unpacking python3-iniconfig (1.1.1-2) ... 132s Selecting previously unselected package python3-parso. 132s Preparing to unpack .../087-python3-parso_0.8.3-1_all.deb ... 132s Unpacking python3-parso (0.8.3-1) ... 132s Selecting previously unselected package python3-typeshed. 132s Preparing to unpack .../088-python3-typeshed_0.0~git20231111.6764465-3_all.deb ... 132s Unpacking python3-typeshed (0.0~git20231111.6764465-3) ... 132s Selecting previously unselected package python3-jedi. 132s Preparing to unpack .../089-python3-jedi_0.19.1+ds1-1_all.deb ... 132s Unpacking python3-jedi (0.19.1+ds1-1) ... 132s Selecting previously unselected package python3-matplotlib-inline. 132s Preparing to unpack .../090-python3-matplotlib-inline_0.1.6-2_all.deb ... 132s Unpacking python3-matplotlib-inline (0.1.6-2) ... 132s Selecting previously unselected package python3-ptyprocess. 132s Preparing to unpack .../091-python3-ptyprocess_0.7.0-6_all.deb ... 132s Unpacking python3-ptyprocess (0.7.0-6) ... 133s Selecting previously unselected package python3-pexpect. 133s Preparing to unpack .../092-python3-pexpect_4.9-2_all.deb ... 133s Unpacking python3-pexpect (4.9-2) ... 133s Selecting previously unselected package python3-wcwidth. 133s Preparing to unpack .../093-python3-wcwidth_0.2.13+dfsg1-1_all.deb ... 133s Unpacking python3-wcwidth (0.2.13+dfsg1-1) ... 133s Selecting previously unselected package python3-prompt-toolkit. 133s Preparing to unpack .../094-python3-prompt-toolkit_3.0.48-1_all.deb ... 133s Unpacking python3-prompt-toolkit (3.0.48-1) ... 133s Selecting previously unselected package python3-pure-eval. 133s Preparing to unpack .../095-python3-pure-eval_0.2.3-1_all.deb ... 133s Unpacking python3-pure-eval (0.2.3-1) ... 133s Selecting previously unselected package python3-stack-data. 133s Preparing to unpack .../096-python3-stack-data_0.6.3-1_all.deb ... 133s Unpacking python3-stack-data (0.6.3-1) ... 133s Selecting previously unselected package python3-ipython. 133s Preparing to unpack .../097-python3-ipython_8.20.0-1ubuntu1_all.deb ... 133s Unpacking python3-ipython (8.20.0-1ubuntu1) ... 133s Selecting previously unselected package python3-platformdirs. 133s Preparing to unpack .../098-python3-platformdirs_4.3.6-1_all.deb ... 133s Unpacking python3-platformdirs (4.3.6-1) ... 133s Selecting previously unselected package python3-jupyter-core. 133s Preparing to unpack .../099-python3-jupyter-core_5.7.2-4_all.deb ... 133s Unpacking python3-jupyter-core (5.7.2-4) ... 133s Selecting previously unselected package python3-psutil. 133s Preparing to unpack .../100-python3-psutil_5.9.8-2build2_arm64.deb ... 133s Unpacking python3-psutil (5.9.8-2build2) ... 133s Selecting previously unselected package python3-tornado. 133s Preparing to unpack .../101-python3-tornado_6.4.1-3_arm64.deb ... 133s Unpacking python3-tornado (6.4.1-3) ... 133s Selecting previously unselected package python3-py. 133s Preparing to unpack .../102-python3-py_1.11.0-2_all.deb ... 133s Unpacking python3-py (1.11.0-2) ... 133s Selecting previously unselected package python3-zmq. 133s Preparing to unpack .../103-python3-zmq_24.0.1-5build1_arm64.deb ... 133s Unpacking python3-zmq (24.0.1-5build1) ... 133s Selecting previously unselected package python3-jupyter-client. 133s Preparing to unpack .../104-python3-jupyter-client_8.6.2-3_all.deb ... 133s Unpacking python3-jupyter-client (8.6.2-3) ... 133s Selecting previously unselected package python3-nest-asyncio. 133s Preparing to unpack .../105-python3-nest-asyncio_1.5.4-1_all.deb ... 133s Unpacking python3-nest-asyncio (1.5.4-1) ... 133s Selecting previously unselected package python3-packaging. 133s Preparing to unpack .../106-python3-packaging_24.1-1_all.deb ... 133s Unpacking python3-packaging (24.1-1) ... 133s Selecting previously unselected package python3-ipykernel. 133s Preparing to unpack .../107-python3-ipykernel_6.29.5-1_all.deb ... 133s Unpacking python3-ipykernel (6.29.5-1) ... 133s Selecting previously unselected package python3-joblib. 134s Preparing to unpack .../108-python3-joblib_1.3.2-5_all.deb ... 134s Unpacking python3-joblib (1.3.2-5) ... 134s Selecting previously unselected package python3-kiwisolver. 134s Preparing to unpack .../109-python3-kiwisolver_1.4.7-2_arm64.deb ... 134s Unpacking python3-kiwisolver (1.4.7-2) ... 134s Selecting previously unselected package libopenjp2-7:arm64. 134s Preparing to unpack .../110-libopenjp2-7_2.5.0-2ubuntu1_arm64.deb ... 134s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 134s Selecting previously unselected package python3-pil:arm64. 134s Preparing to unpack .../111-python3-pil_10.4.0-1ubuntu1_arm64.deb ... 134s Unpacking python3-pil:arm64 (10.4.0-1ubuntu1) ... 134s Selecting previously unselected package python3.12-tk. 134s Preparing to unpack .../112-python3.12-tk_3.12.7-3_arm64.deb ... 134s Unpacking python3.12-tk (3.12.7-3) ... 134s Selecting previously unselected package python3.13-tk. 134s Preparing to unpack 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python3-mdtraj (1.10.1-2) ... 136s Selecting previously unselected package python3-nbformat. 136s Preparing to unpack .../124-python3-nbformat_5.9.1-1_all.deb ... 136s Unpacking python3-nbformat (5.9.1-1) ... 136s Selecting previously unselected package python3-netcdf4. 136s Preparing to unpack .../125-python3-netcdf4_1.7.2-1_arm64.deb ... 136s Unpacking python3-netcdf4 (1.7.2-1) ... 136s Selecting previously unselected package python3-pluggy. 136s Preparing to unpack .../126-python3-pluggy_1.5.0-1_all.deb ... 136s Unpacking python3-pluggy (1.5.0-1) ... 136s Selecting previously unselected package python3-pytest. 136s Preparing to unpack .../127-python3-pytest_8.3.3-1_all.deb ... 136s Unpacking python3-pytest (8.3.3-1) ... 136s Selecting previously unselected package python3-threadpoolctl. 136s Preparing to unpack .../128-python3-threadpoolctl_3.1.0-1_all.deb ... 136s Unpacking python3-threadpoolctl (3.1.0-1) ... 136s Selecting previously unselected package python3-sklearn-lib:arm64. 136s Preparing to unpack .../129-python3-sklearn-lib_1.4.2+dfsg-6_arm64.deb ... 136s Unpacking python3-sklearn-lib:arm64 (1.4.2+dfsg-6) ... 136s Selecting previously unselected package python3-sklearn. 136s Preparing to unpack .../130-python3-sklearn_1.4.2+dfsg-6_all.deb ... 136s Unpacking python3-sklearn (1.4.2+dfsg-6) ... 136s Selecting previously unselected package autopkgtest-satdep. 136s Preparing to unpack .../131-1-autopkgtest-satdep.deb ... 136s Unpacking autopkgtest-satdep (0) ... 136s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 136s Setting up liblcms2-2:arm64 (2.16-2) ... 136s Setting up python3-iniconfig (1.1.1-2) ... 136s Setting up python3-tornado (6.4.1-3) ... 137s Setting up libnorm1t64:arm64 (1.5.9+dfsg-3.1build1) ... 137s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ... 137s Setting up python3-pure-eval (0.2.3-1) ... 137s Setting up libsodium23:arm64 (1.0.18-1build3) ... 137s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 137s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 137s Setting up python3-py (1.11.0-2) ... 137s Setting up libdebuginfod-common (0.192-4) ... 137s Setting up python3-joblib (1.3.2-5) ... 138s Setting up python3-parso (0.8.3-1) ... 138s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 138s Setting up python3-asttokens (2.4.1-2) ... 138s Setting up python3-unicodedata2 (15.1.0+ds-1build1) ... 138s Setting up fonts-lyx (2.4.2.1-1) ... 138s Setting up python3-threadpoolctl (3.1.0-1) ... 138s Setting up x11-common (1:7.7+23ubuntu3) ... 139s Setting up libdeflate0:arm64 (1.22-1) ... 139s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 139s Setting up python3-coverage (7.4.4+dfsg1-0ubuntu2) ... 139s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ... 139s Setting up python3-networkx (3.2.1-4ubuntu1) ... 141s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 141s Setting up libaec0:arm64 (1.1.3-1) ... 141s Setting up python3-platformdirs (4.3.6-1) ... 141s Setting up python3-psutil (5.9.8-2build2) ... 141s Setting up libsource-highlight-common (3.1.9-4.3build1) ... 141s Setting up python3-tz (2024.1-2) ... 141s Setting up libsnappy1v5:arm64 (1.2.1-1) ... 141s Setting up unicode-data (15.1.0-1) ... 141s Setting up python3-six (1.16.0-7) ... 141s Setting up libpgm-5.3-0t64:arm64 (5.3.128~dfsg-2.1build1) ... 141s Setting up python3-decorator (5.1.1-5) ... 142s Setting up libblosc2-4:arm64 (2.15.1+ds-1) ... 142s Setting up libblas3:arm64 (3.12.0-3build2) ... 142s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 142s Setting up python3-packaging (24.1-1) ... 142s Setting up python3-wcwidth (0.2.13+dfsg1-1) ... 142s Setting up python3-typeshed (0.0~git20231111.6764465-3) ... 142s Setting up python3-executing (2.1.0-0.1) ... 142s Setting up python3-nest-asyncio (1.5.4-1) ... 142s Setting up python3-brotli (1.1.0-2build2) ... 142s Setting up python3-cycler (0.12.1-1) ... 143s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 143s Setting up fonts-dejavu-mono (2.37-8) ... 143s Setting up python3-kiwisolver (1.4.7-2) ... 143s Setting up libtcl8.6:arm64 (8.6.15+dfsg-2) ... 143s Setting up fonts-dejavu-core (2.37-8) ... 143s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 143s Setting up python3-cpuinfo (9.0.0+git20221119-2) ... 143s Setting up libbabeltrace1:arm64 (1.5.11-4) ... 143s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 143s Setting up python3-pluggy (1.5.0-1) ... 143s Setting up libwebp7:arm64 (1.4.0-0.1) ... 143s Setting up python3-fastjsonschema (2.20.0-1) ... 143s Setting up python3-traitlets (5.14.3+really5.14.3-1) ... 144s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 144s Setting up libblosc1:arm64 (1.21.5+ds-1build1) ... 144s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 144s Setting up libharfbuzz0b:arm64 (10.0.1-1) ... 144s Setting up python3-dateutil (2.9.0-2) ... 144s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 144s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 144s Setting up python3-mpmath (1.3.0-1) ... 144s Setting up python-matplotlib-data (3.8.3-3) ... 144s Setting up libwebpmux3:arm64 (1.4.0-0.1) ... 144s Setting up python3-appdirs (1.4.4-4) ... 145s Setting up python3-stack-data (0.6.3-1) ... 145s Setting up python-tables-data (3.10.1-1) ... 145s Setting up python3-jupyter-core (5.7.2-4) ... 145s Setting up libsz2:arm64 (1.1.3-1) ... 145s Setting up python3-ptyprocess (0.7.0-6) ... 145s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 145s Setting up python3-prompt-toolkit (3.0.48-1) ... 146s Setting up python3-sympy (1.13.3-1) ... 153s Setting up libdebuginfod1t64:arm64 (0.192-4) ... 153s Setting up liblapack3:arm64 (3.12.0-3build2) ... 153s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 153s Setting up libzmq5:arm64 (4.3.5-1build2) ... 153s Setting up python3-jedi (0.19.1+ds1-1) ... 154s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 154s Setting up python3-pytest (8.3.3-1) ... 154s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... 154s Setting up libsource-highlight4t64:arm64 (3.1.9-4.3build1) ... 154s Setting up python3-nbformat (5.9.1-1) ... 154s Setting up python3-matplotlib-inline (0.1.6-2) ... 155s Setting up python3-comm (0.2.1-1) ... 155s Setting up python3-fs (2.4.16-4) ... 155s Setting up gdb (15.1-1ubuntu2) ... 155s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 155s Setting up python3-pexpect (4.9-2) ... 155s Setting up python3-zmq (24.0.1-5build1) ... 156s Setting up libraqm0:arm64 (0.10.1-1build1) ... 156s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 158s Setting up python3-lxml:arm64 (5.3.0-1) ... 158s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 158s Setting up python3-jupyter-client (8.6.2-3) ... 158s Setting up python3-contourpy (1.3.0-2) ... 158s Setting up libfontconfig1:arm64 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Setting up python3-sklearn (1.4.2+dfsg-6) ... 173s Setting up python3-cftime (1.6.4-1) ... 173s Setting up python3-numexpr (2.10.1-2) ... 173s Setting up python3-netcdf4 (1.7.2-1) ... 173s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 173s Setting up blt (2.5.3+dfsg-7build1) ... 173s Setting up python3-tk:arm64 (3.12.7-1) ... 173s Setting up python3-tables (3.10.1-1) ... 174s Setting up python3-mdtraj (1.10.1-2) ... 174s Setting up python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 174s Setting up python3-fonttools (4.46.0-1build2) ... 175s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 175s Setting up python3-matplotlib (3.8.3-3) ... 177s Setting up autopkgtest-satdep (0) ... 177s Processing triggers for libc-bin (2.40-1ubuntu3) ... 177s Processing triggers for man-db (2.12.1-3) ... 186s (Reading database ... 102500 files and directories currently installed.) 186s Removing autopkgtest-satdep (0) ... 187s autopkgtest [09:40:15]: test command1: pytest-3 -k 'not nmr.ipynb and not test_image_molecules' 187s autopkgtest [09:40:15]: test command1: [----------------------- 188s ============================= test session starts ============================== 188s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3 188s cachedir: .pytest_cache 188s rootdir: /tmp/autopkgtest.PzEck5/build.ROp/src 188s configfile: pytest.ini 188s testpaths: tests, examples 188s plugins: typeguard-4.4.1 190s collecting ... collected 1129 items / 2 deselected / 1127 selected 190s 190s tests/test_alignment.py::test_rmsd_zero PASSED [ 0%] 190s tests/test_alignment.py::test_rmsd_nonzero PASSED [ 0%] 190s tests/test_alignment.py::test_transform PASSED [ 0%] 190s tests/test_alignment.py::test_transform2 PASSED [ 0%] 190s tests/test_angles.py::test_angle_pbc_0 PASSED [ 0%] 190s tests/test_angles.py::test_generator PASSED [ 0%] 190s tests/test_angles.py::test_angle_180[True] PASSED [ 0%] 190s tests/test_angles.py::test_angle_180[False] PASSED [ 0%] 190s 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tests/test_mol2.py::test_load_all_mol2[li.mol2] PASSED [ 27%] 343s tests/test_mol2.py::test_load_all_mol2[lysozyme-ligand-tripos.mol2] PASSED [ 27%] 343s tests/test_mol2.py::test_load_all_mol2[imatinib.mol2] PASSED [ 27%] 343s tests/test_mol2.py::test_load_all_mol2[status-bits.mol2] PASSED [ 27%] 343s tests/test_mol2.py::test_load_all_mol2[adp.mol2] PASSED [ 28%] 343s tests/test_mol2.py::test_load_all_mol2[water_acn.mol2] PASSED [ 28%] 343s tests/test_mol2.py::test_mol2_n_residues PASSED [ 28%] 343s tests/test_neighborlist.py::test_nonperiodic PASSED [ 28%] 343s tests/test_neighborlist.py::test_periodic PASSED [ 28%] 344s tests/test_neighborlist.py::test_triclinic PASSED [ 28%] 344s tests/test_neighbors.py::test_compute_neighbors_1 PASSED [ 28%] 345s tests/test_neighbors.py::test_compute_neighbors_2 PASSED [ 28%] 346s tests/test_neighbors.py::test_compute_neighbors_3 PASSED [ 28%] 346s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_after_close PASSED [ 28%] 346s tests/test_netcdf.py::TestNetCDFNetCDF4::test_shape PASSED [ 28%] 346s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_1 PASSED [ 29%] 346s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_2 PASSED [ 29%] 346s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_3 PASSED [ 29%] 346s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_1 PASSED [ 29%] 346s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_2 PASSED [ 29%] 346s tests/test_netcdf.py::TestNetCDFNetCDF4::test_ragged_1 PASSED [ 29%] 346s tests/test_netcdf.py::TestNetCDFNetCDF4::test_ragged_2 PASSED [ 29%] 346s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_25 PASSED [ 29%] 346s tests/test_netcdf.py::TestNetCDFNetCDF4::test_write_3 PASSED [ 29%] 346s tests/test_netcdf.py::TestNetCDFNetCDF4::test_n_atoms PASSED [ 29%] 346s tests/test_netcdf.py::TestNetCDFNetCDF4::test_do_overwrite PASSED [ 29%] 346s tests/test_netcdf.py::TestNetCDFNetCDF4::test_do_not_overwrite PASSED [ 29%] 346s tests/test_netcdf.py::TestNetCDFNetCDF4::test_trajectory_save_load PASSED [ 30%] 346s tests/test_netcdf.py::TestNetCDFScipy::test_read_after_close PASSED [ 30%] 346s tests/test_netcdf.py::TestNetCDFScipy::test_shape PASSED [ 30%] 346s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_1 PASSED [ 30%] 346s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_2 PASSED [ 30%] 346s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_3 PASSED [ 30%] 346s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_1 PASSED [ 30%] 346s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_2 PASSED [ 30%] 346s tests/test_netcdf.py::TestNetCDFScipy::test_ragged_1 PASSED [ 30%] 346s tests/test_netcdf.py::TestNetCDFScipy::test_ragged_2 PASSED [ 30%] 346s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_25 PASSED [ 30%] 346s tests/test_netcdf.py::TestNetCDFScipy::test_write_3 PASSED [ 31%] 346s tests/test_netcdf.py::TestNetCDFScipy::test_n_atoms PASSED [ 31%] 346s tests/test_netcdf.py::TestNetCDFScipy::test_do_overwrite PASSED [ 31%] 346s tests/test_netcdf.py::TestNetCDFScipy::test_do_not_overwrite PASSED [ 31%] 346s tests/test_netcdf.py::TestNetCDFScipy::test_trajectory_save_load PASSED [ 31%] 346s tests/test_netcdf.py::test_cpptraj SKIPPED (This test requires cpptr...) [ 31%] 346s tests/test_nmr.py::test_spartaplus SKIPPED (SPARTA+ binary not found) [ 31%] 346s tests/test_nmr.py::test_ppm SKIPPED (PPM binary not found) [ 31%] 346s tests/test_nmr.py::test_shiftx2 SKIPPED (SHIFTX2 binary not found or...) [ 31%] 346s tests/test_nmr.py::test_2_scalar_couplings PASSED [ 31%] 346s tests/test_nmr.py::test_3_scalar_couplings PASSED [ 31%] 346s tests/test_order.py::test_nematic_order PASSED [ 32%] 346s tests/test_order.py::test_director PASSED [ 32%] 346s tests/test_order.py::test_inertia PASSED [ 32%] 346s tests/test_order.py::test_nematic_order_args PASSED [ 32%] 346s tests/test_order.py::test_order_from_traj PASSED [ 32%] 347s tests/test_order.py::test_directors_angle_from_traj PASSED [ 32%] 347s tests/test_pdb.py::test_pdbread PASSED [ 32%] 347s tests/test_pdb.py::test_pdbread_with_input_top PASSED [ 32%] 347s tests/test_pdb.py::test_pdbwrite PASSED [ 32%] 347s tests/test_pdb.py::test_load_multiframe PASSED [ 32%] 347s tests/test_pdb.py::test_4ZUO PASSED [ 32%] 347s tests/test_pdb.py::test_2EQQ_0 PASSED [ 33%] 350s tests/test_pdb.py::test_1vii_solvated_with_ligand PASSED [ 33%] 350s tests/test_pdb.py::test_write_large PASSED [ 33%] 350s tests/test_pdb.py::test_write_large_2 PASSED [ 33%] 350s tests/test_pdb.py::test_pdbstructure_0 PASSED [ 33%] 350s tests/test_pdb.py::test_pdbstructure_1 PASSED [ 33%] 350s tests/test_pdb.py::test_pdbstructure_2 PASSED [ 33%] 350s tests/test_pdb.py::test_pdbstructure_3 PASSED [ 33%] 354s tests/test_pdb.py::test_pdb_from_url PASSED [ 33%] 355s tests/test_pdb.py::test_3nch_conect PASSED [ 33%] 357s tests/test_pdb.py::test_3nch_serial_resSeq PASSED [ 33%] 358s tests/test_pdb.py::test_1ncw PASSED [ 33%] 361s tests/test_pdb.py::test_1vii_url_and_gz PASSED [ 34%] 361s tests/test_pdb.py::test_segment_id PASSED [ 34%] 361s tests/test_pdb.py::test_bfactors PASSED [ 34%] 366s tests/test_pdb.py::test_hex PASSED [ 34%] 366s tests/test_pdb.py::test_dummy_pdb_box_detection PASSED [ 34%] 366s tests/test_pdb.py::test_multichain_load_cycle PASSED [ 34%] 366s tests/test_pdb.py::test_multichain_load_cycle_noter PASSED [ 34%] 366s tests/test_pdb.py::test_load_pdb_input_top PASSED [ 34%] 366s tests/test_pdb.py::test_chimera_indexing PASSED [ 34%] 366s tests/test_pdb.py::test_vmd_indexing PASSED [ 34%] 366s tests/test_pdbx.py::test_convert SKIPPED (test_pdbx.py needs OpenMM.) [ 34%] 366s tests/test_prmtop.py::test_load_prmtop PASSED [ 35%] 366s tests/test_prmtop.py::test_load_chamber_prmtop PASSED [ 35%] 366s tests/test_psf.py::test_load_psf PASSED [ 35%] 371s tests/test_psf.py::test_multichain_psf PASSED [ 35%] 371s tests/test_psf.py::test_load_mdcrd_with_psf PASSED [ 35%] 371s tests/test_psf.py::test_against_vmd[1vii.pdb] SKIPPED (This test req...) [ 35%] 371s tests/test_psf.py::test_against_vmd[2EQQ.pdb] SKIPPED (This test req...) [ 35%] 371s tests/test_quaternion.py::test_quaternion_0 PASSED [ 35%] 371s tests/test_quaternion.py::test_quaternion_1 PASSED [ 35%] 371s tests/test_quaternion.py::test_quaternion_2 PASSED [ 35%] 375s tests/test_rdf.py::test_rdf_norm PASSED [ 35%] 375s tests/test_rdf.py::test_compare_rdf_to_gromacs SKIPPED (Binning does...) [ 36%] 375s tests/test_rdf.py::test_rdf_t[True-True] PASSED [ 36%] 380s tests/test_rdf.py::test_rdf_t[True-False] PASSED [ 36%] 381s tests/test_rdf.py::test_rdf_t[False-True] PASSED [ 36%] 381s tests/test_rdf.py::test_rdf_t[False-False] PASSED [ 36%] 382s tests/test_rdf.py::test_rdf_t_norm[0] PASSED [ 36%] 382s tests/test_rdf.py::test_rdf_t_norm[2] PASSED [ 36%] 383s tests/test_rdf.py::test_rdf_t_norm[4] PASSED [ 36%] 383s tests/test_rdf.py::test_compare_rdf_t_at_0[True-True] PASSED [ 36%] 384s tests/test_rdf.py::test_compare_rdf_t_at_0[True-False] PASSED [ 36%] 384s tests/test_rdf.py::test_compare_rdf_t_at_0[False-True] PASSED [ 36%] 385s tests/test_rdf.py::test_compare_rdf_t_at_0[False-False] PASSED [ 37%] 385s tests/test_rdf.py::test_amber_rdf_t[True-True] PASSED [ 37%] 386s tests/test_rdf.py::test_amber_rdf_t[True-False] PASSED [ 37%] 386s tests/test_rdf.py::test_amber_rdf_t[False-True] PASSED [ 37%] 386s tests/test_rdf.py::test_amber_rdf_t[False-False] PASSED [ 37%] 386s tests/test_rdf.py::test_compare_gromacs_rdf_t SKIPPED (Binning does ...) [ 37%] 386s tests/test_rdf.py::test_compare_rdf_t_master PASSED [ 37%] 387s tests/test_rdf.py::test_compare_n_concurrent_pairs PASSED [ 37%] 387s tests/test_reporter.py::test_reporter SKIPPED (test_reporter.py need...) [ 37%] 387s tests/test_reporter.py::test_reporter_subset SKIPPED (test_reporter....) [ 37%] 387s tests/test_reporter.py::test_xtc_reporter_append SKIPPED (test_repor...) [ 37%] 387s tests/test_restart.py::test_read_after_close PASSED [ 37%] 387s tests/test_restart.py::test_shape PASSED [ 38%] 387s tests/test_restart.py::test_shape_2 PASSED [ 38%] 387s tests/test_restart.py::test_read_write_1 PASSED [ 38%] 387s tests/test_restart.py::test_read_write_2 PASSED [ 38%] 387s tests/test_restart.py::test_read_write_3 PASSED [ 38%] 387s tests/test_restart.py::test_read_write_4 PASSED [ 38%] 388s tests/test_rmsd.py::test_trajectory_rmsd PASSED [ 38%] 388s tests/test_rmsd.py::test_precentered_1 PASSED [ 38%] 388s tests/test_rmsd.py::test_precentered_2 PASSED [ 38%] 388s tests/test_rmsd.py::test_superpose_0 PASSED [ 38%] 388s tests/test_rmsd.py::test_superpose_1 PASSED [ 38%] 388s tests/test_rmsd.py::test_superpose_2 PASSED [ 39%] 388s tests/test_rmsd.py::test_superpose_refinds PASSED [ 39%] 388s tests/test_rmsd.py::test_rmsd_atom_indices PASSED [ 39%] 388s tests/test_rmsd.py::test_rmsd_ref_ainds PASSED [ 39%] 388s tests/test_rmsd.py::test_average_structure PASSED [ 39%] 388s tests/test_rmsd.py::test_trajectory_rmsf PASSED [ 39%] 388s tests/test_rmsd.py::test_trajectory_rmsf_aligned PASSED [ 39%] 388s tests/test_rmsd.py::test_rmsd_atom_indices_vs_ref_indices PASSED [ 39%] 388s tests/test_rmsd_memmap.py::test_1 PASSED [ 39%] 388s tests/test_rmsd_memmap.py::test_2 PASSED [ 39%] 388s tests/test_sasa.py::test_sasa_0 PASSED [ 39%] 388s tests/test_sasa.py::test_sasa_1 PASSED [ 40%] 389s tests/test_sasa.py::test_sasa_2 PASSED [ 40%] 389s tests/test_sasa.py::test_sasa_3 PASSED [ 40%] 389s tests/test_sasa.py::test_sasa_4 PASSED [ 40%] 389s tests/test_sasa.py::test_sasa_5 PASSED [ 40%] 390s tests/test_sasa.py::test_sasa_6 PASSED [ 40%] 390s tests/test_sasa.py::test_sasa_7 PASSED [ 40%] 390s tests/test_selection.py::test_range PASSED [ 40%] 390s tests/test_selection.py::test_unary_2 PASSED [ 40%] 390s tests/test_selection.py::test_unary_3 PASSED [ 40%] 390s tests/test_selection.py::test_binary_1 PASSED [ 40%] 390s tests/test_selection.py::test_binary_2 PASSED [ 40%] 390s tests/test_selection.py::test_simple PASSED [ 41%] 390s tests/test_selection.py::test_alias PASSED [ 41%] 390s tests/test_selection.py::test_unary_1 PASSED [ 41%] 391s tests/test_selection.py::test_binary_selection_operator PASSED [ 41%] 391s tests/test_selection.py::test_raises PASSED [ 41%] 391s tests/test_selection.py::test_raises2 PASSED [ 41%] 391s tests/test_selection.py::test_bool PASSED [ 41%] 391s tests/test_selection.py::test_nested_bool PASSED [ 41%] 391s tests/test_selection.py::test_values PASSED [ 41%] 391s tests/test_selection.py::test_element PASSED [ 41%] 391s tests/test_selection.py::test_not PASSED [ 41%] 391s tests/test_selection.py::test_re PASSED [ 42%] 391s tests/test_selection.py::test_within SKIPPED (failed to parse selection) [ 42%] 391s tests/test_selection.py::test_quotes PASSED [ 42%] 391s tests/test_selection.py::test_top PASSED [ 42%] 391s tests/test_selection.py::test_top_2 PASSED [ 42%] 392s tests/test_selection.py::test_backbone PASSED [ 42%] 392s tests/test_selection.py::test_sidechain PASSED [ 42%] 393s tests/test_selection.py::test_literal PASSED [ 42%] 393s tests/test_selection.py::test_in PASSED [ 42%] 393s tests/test_shape.py::test_gyration PASSED [ 42%] 393s tests/test_shape.py::test_principal_moments PASSED [ 42%] 393s tests/test_shape.py::test_asphericity PASSED [ 43%] 394s tests/test_shape.py::test_shape_metrics PASSED [ 43%] 394s tests/test_thermodynamic_properties.py::test_volume PASSED [ 43%] 394s tests/test_thermodynamic_properties.py::test_density PASSED [ 43%] 394s tests/test_thermodynamic_properties.py::test_dipole_moments PASSED [ 43%] 394s tests/test_thermodynamic_properties.py::test_static_dielectric PASSED [ 43%] 394s tests/test_thermodynamic_properties.py::test_kappa PASSED [ 43%] 394s tests/test_thermodynamic_properties.py::test_alpha SKIPPED (Thermal ...) [ 43%] 394s tests/test_topology.py::test_topology_openmm SKIPPED (needs OpenMM) [ 43%] 394s tests/test_topology.py::test_topology_openmm_boxes SKIPPED (needs Op...) [ 43%] 394s tests/test_topology.py::test_topology_pandas PASSED [ 43%] 394s tests/test_topology.py::test_topology_pandas_TIP4PEW PASSED [ 44%] 394s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq PASSED [ 44%] 394s tests/test_topology.py::test_topology_numbers PASSED [ 44%] 394s tests/test_topology.py::test_topology_unique_elements_bpti PASSED [ 44%] 395s tests/test_topology.py::test_chain PASSED [ 44%] 395s tests/test_topology.py::test_residue PASSED [ 44%] 395s tests/test_topology.py::test_segment_id PASSED [ 44%] 395s tests/test_topology.py::test_nonconsective_resSeq PASSED [ 44%] 395s tests/test_topology.py::test_pickle PASSED [ 44%] 395s tests/test_topology.py::test_atoms_by_name PASSED [ 44%] 395s tests/test_topology.py::test_select_atom_indices PASSED [ 44%] 395s tests/test_topology.py::test_top_dataframe_openmm_roundtrip SKIPPED [ 44%] 395s tests/test_topology.py::test_n_bonds PASSED [ 45%] 395s tests/test_topology.py::test_load_unknown_topology PASSED [ 45%] 395s tests/test_topology.py::test_unique_pairs PASSED [ 45%] 396s tests/test_topology.py::test_select_pairs PASSED [ 45%] 396s tests/test_topology.py::test_to_fasta PASSED [ 45%] 397s tests/test_topology.py::test_subset PASSED [ 45%] 397s tests/test_topology.py::test_subset_re_index_residues PASSED [ 45%] 397s tests/test_topology.py::test_molecules PASSED [ 45%] 397s tests/test_topology.py::test_copy_and_hash PASSED [ 45%] 397s tests/test_topology.py::test_topology_sliced_residue_indices PASSED [ 45%] 397s tests/test_topology.py::test_topology_join PASSED [ 45%] 398s tests/test_topology.py::test_topology_join_keep_resSeq PASSED [ 46%] 398s tests/test_trajectory.py::test_mismatch PASSED [ 46%] 398s tests/test_trajectory.py::test_box PASSED [ 46%] 398s tests/test_trajectory.py::test_load_pdb_box PASSED [ 46%] 398s tests/test_trajectory.py::test_load_pdb_gz PASSED [ 46%] 398s tests/test_trajectory.py::test_box_load_save[nc] PASSED [ 46%] 398s tests/test_trajectory.py::test_box_load_save[h5] PASSED [ 46%] 398s tests/test_trajectory.py::test_box_load_save[xtc] PASSED [ 46%] 398s tests/test_trajectory.py::test_box_load_save[trr] PASSED [ 46%] 398s tests/test_trajectory.py::test_box_load_save[dcd] PASSED [ 46%] 398s tests/test_trajectory.py::test_box_load_save[mdcrd] PASSED [ 46%] 398s tests/test_trajectory.py::test_box_load_save[dtr] PASSED [ 47%] 398s tests/test_trajectory.py::test_box_load_save[xyz] SKIPPED (xyz does ...) [ 47%] 398s tests/test_trajectory.py::test_box_load_save[xyz.gz] SKIPPED (xyz.gz...) [ 47%] 398s tests/test_trajectory.py::test_box_load_save[lammpstrj] PASSED [ 47%] 398s tests/test_trajectory.py::test_box_load_save[lh5] SKIPPED (lh5 does ...) [ 47%] 398s tests/test_trajectory.py::test_box_load_save[pdb] SKIPPED (pdb does ...) [ 47%] 398s tests/test_trajectory.py::test_box_load_save[pdb.gz] SKIPPED (pdb.gz...) [ 47%] 398s tests/test_trajectory.py::test_box_load_save[ncrst] PASSED [ 47%] 398s tests/test_trajectory.py::test_box_load_save[rst7] PASSED [ 47%] 398s tests/test_trajectory.py::test_box_load_save[gro] PASSED [ 47%] 398s tests/test_trajectory.py::test_slice PASSED [ 47%] 398s tests/test_trajectory.py::test_slice2 PASSED [ 48%] 398s tests/test_trajectory.py::test_read_path[nc] PASSED [ 48%] 398s tests/test_trajectory.py::test_read_path[h5] PASSED [ 48%] 398s tests/test_trajectory.py::test_read_path[xtc] PASSED [ 48%] 399s tests/test_trajectory.py::test_read_path[trr] PASSED [ 48%] 399s tests/test_trajectory.py::test_read_path[dcd] PASSED [ 48%] 399s tests/test_trajectory.py::test_read_path[mdcrd] PASSED [ 48%] 399s tests/test_trajectory.py::test_read_path[dtr] PASSED [ 48%] 399s tests/test_trajectory.py::test_read_path[xyz] PASSED [ 48%] 399s tests/test_trajectory.py::test_read_path[xyz.gz] PASSED [ 48%] 399s tests/test_trajectory.py::test_read_path[lammpstrj] PASSED [ 48%] 399s tests/test_trajectory.py::test_read_path[lh5] PASSED [ 48%] 399s tests/test_trajectory.py::test_read_path[pdb] PASSED [ 49%] 399s tests/test_trajectory.py::test_read_path[pdb.gz] PASSED [ 49%] 399s tests/test_trajectory.py::test_read_path[ncrst] XFAIL (These referen...) [ 49%] 399s tests/test_trajectory.py::test_read_path[rst7] XFAIL (These referenc...) [ 49%] 399s tests/test_trajectory.py::test_read_path[gro] PASSED [ 49%] 399s tests/test_trajectory.py::test_write_path[nc] PASSED [ 49%] 399s tests/test_trajectory.py::test_write_path[h5] PASSED [ 49%] 399s tests/test_trajectory.py::test_write_path[xtc] PASSED [ 49%] 399s tests/test_trajectory.py::test_write_path[trr] PASSED [ 49%] 399s tests/test_trajectory.py::test_write_path[dcd] PASSED [ 49%] 399s tests/test_trajectory.py::test_write_path[mdcrd] SKIPPED (mdcrd can ...) [ 49%] 400s tests/test_trajectory.py::test_write_path[dtr] PASSED [ 50%] 400s tests/test_trajectory.py::test_write_path[xyz] PASSED [ 50%] 400s tests/test_trajectory.py::test_write_path[xyz.gz] PASSED [ 50%] 400s tests/test_trajectory.py::test_write_path[lammpstrj] PASSED [ 50%] 400s tests/test_trajectory.py::test_write_path[lh5] PASSED [ 50%] 400s tests/test_trajectory.py::test_write_path[pdb] PASSED [ 50%] 400s tests/test_trajectory.py::test_write_path[pdb.gz] PASSED [ 50%] 400s tests/test_trajectory.py::test_write_path[ncrst] SKIPPED (ncrst can ...) [ 50%] 400s tests/test_trajectory.py::test_write_path[rst7] SKIPPED (rst7 can on...) [ 50%] 400s tests/test_trajectory.py::test_write_path[gro] PASSED [ 50%] 400s tests/test_trajectory.py::test_read_write[nc-nc] PASSED [ 50%] 400s tests/test_trajectory.py::test_read_write[nc-h5] PASSED [ 51%] 400s tests/test_trajectory.py::test_read_write[nc-xtc] PASSED [ 51%] 400s tests/test_trajectory.py::test_read_write[nc-trr] PASSED [ 51%] 400s tests/test_trajectory.py::test_read_write[nc-dcd] PASSED [ 51%] 400s tests/test_trajectory.py::test_read_write[nc-mdcrd] SKIPPED (mdcrd c...) [ 51%] 402s tests/test_trajectory.py::test_read_write[nc-dtr] PASSED [ 51%] 402s tests/test_trajectory.py::test_read_write[nc-xyz] PASSED [ 51%] 403s tests/test_trajectory.py::test_read_write[nc-xyz.gz] PASSED [ 51%] 403s tests/test_trajectory.py::test_read_write[nc-lammpstrj] PASSED [ 51%] 403s tests/test_trajectory.py::test_read_write[nc-lh5] PASSED [ 51%] 404s tests/test_trajectory.py::test_read_write[nc-pdb] PASSED [ 51%] 406s tests/test_trajectory.py::test_read_write[nc-pdb.gz] PASSED [ 51%] 406s tests/test_trajectory.py::test_read_write[nc-ncrst] SKIPPED (ncrst c...) [ 52%] 406s tests/test_trajectory.py::test_read_write[nc-rst7] SKIPPED (rst7 can...) [ 52%] 406s tests/test_trajectory.py::test_read_write[nc-gro] PASSED [ 52%] 406s tests/test_trajectory.py::test_read_write[h5-nc] PASSED [ 52%] 406s tests/test_trajectory.py::test_read_write[h5-h5] PASSED [ 52%] 406s tests/test_trajectory.py::test_read_write[h5-xtc] PASSED [ 52%] 406s tests/test_trajectory.py::test_read_write[h5-trr] PASSED [ 52%] 406s tests/test_trajectory.py::test_read_write[h5-dcd] PASSED [ 52%] 406s tests/test_trajectory.py::test_read_write[h5-mdcrd] SKIPPED (mdcrd c...) [ 52%] 407s tests/test_trajectory.py::test_read_write[h5-dtr] PASSED [ 52%] 407s tests/test_trajectory.py::test_read_write[h5-xyz] PASSED [ 52%] 408s tests/test_trajectory.py::test_read_write[h5-xyz.gz] PASSED [ 53%] 408s tests/test_trajectory.py::test_read_write[h5-lammpstrj] PASSED [ 53%] 408s tests/test_trajectory.py::test_read_write[h5-lh5] PASSED [ 53%] 408s tests/test_trajectory.py::test_read_write[h5-pdb] PASSED [ 53%] 409s tests/test_trajectory.py::test_read_write[h5-pdb.gz] PASSED [ 53%] 409s tests/test_trajectory.py::test_read_write[h5-ncrst] SKIPPED (ncrst c...) [ 53%] 409s tests/test_trajectory.py::test_read_write[h5-rst7] SKIPPED (rst7 can...) [ 53%] 409s tests/test_trajectory.py::test_read_write[h5-gro] PASSED [ 53%] 409s tests/test_trajectory.py::test_read_write[xtc-nc] PASSED [ 53%] 409s tests/test_trajectory.py::test_read_write[xtc-h5] PASSED [ 53%] 409s tests/test_trajectory.py::test_read_write[xtc-xtc] PASSED [ 53%] 409s tests/test_trajectory.py::test_read_write[xtc-trr] PASSED [ 54%] 409s tests/test_trajectory.py::test_read_write[xtc-dcd] PASSED [ 54%] 409s tests/test_trajectory.py::test_read_write[xtc-mdcrd] SKIPPED (mdcrd ...) [ 54%] 410s tests/test_trajectory.py::test_read_write[xtc-dtr] PASSED [ 54%] 411s tests/test_trajectory.py::test_read_write[xtc-xyz] PASSED [ 54%] 411s tests/test_trajectory.py::test_read_write[xtc-xyz.gz] PASSED [ 54%] 411s tests/test_trajectory.py::test_read_write[xtc-lammpstrj] PASSED [ 54%] 411s tests/test_trajectory.py::test_read_write[xtc-lh5] PASSED [ 54%] 411s tests/test_trajectory.py::test_read_write[xtc-pdb] PASSED [ 54%] 412s tests/test_trajectory.py::test_read_write[xtc-pdb.gz] PASSED [ 54%] 412s tests/test_trajectory.py::test_read_write[xtc-ncrst] SKIPPED (ncrst ...) [ 54%] 412s tests/test_trajectory.py::test_read_write[xtc-rst7] SKIPPED (rst7 ca...) [ 55%] 412s tests/test_trajectory.py::test_read_write[xtc-gro] PASSED [ 55%] 412s tests/test_trajectory.py::test_read_write[trr-nc] PASSED [ 55%] 412s tests/test_trajectory.py::test_read_write[trr-h5] PASSED [ 55%] 412s tests/test_trajectory.py::test_read_write[trr-xtc] PASSED [ 55%] 412s tests/test_trajectory.py::test_read_write[trr-trr] PASSED [ 55%] 412s tests/test_trajectory.py::test_read_write[trr-dcd] PASSED [ 55%] 412s tests/test_trajectory.py::test_read_write[trr-mdcrd] SKIPPED (mdcrd ...) [ 55%] 414s tests/test_trajectory.py::test_read_write[trr-dtr] PASSED [ 55%] 414s tests/test_trajectory.py::test_read_write[trr-xyz] PASSED [ 55%] 414s tests/test_trajectory.py::test_read_write[trr-xyz.gz] PASSED [ 55%] 414s tests/test_trajectory.py::test_read_write[trr-lammpstrj] PASSED [ 55%] 414s tests/test_trajectory.py::test_read_write[trr-lh5] PASSED [ 56%] 415s tests/test_trajectory.py::test_read_write[trr-pdb] PASSED [ 56%] 415s tests/test_trajectory.py::test_read_write[trr-pdb.gz] PASSED [ 56%] 415s tests/test_trajectory.py::test_read_write[trr-ncrst] SKIPPED (ncrst ...) [ 56%] 415s tests/test_trajectory.py::test_read_write[trr-rst7] SKIPPED (rst7 ca...) [ 56%] 416s tests/test_trajectory.py::test_read_write[trr-gro] PASSED [ 56%] 416s tests/test_trajectory.py::test_read_write[dcd-nc] PASSED [ 56%] 416s tests/test_trajectory.py::test_read_write[dcd-h5] PASSED [ 56%] 416s tests/test_trajectory.py::test_read_write[dcd-xtc] PASSED [ 56%] 416s tests/test_trajectory.py::test_read_write[dcd-trr] PASSED [ 56%] 416s tests/test_trajectory.py::test_read_write[dcd-dcd] PASSED [ 56%] 416s tests/test_trajectory.py::test_read_write[dcd-mdcrd] SKIPPED (mdcrd ...) [ 57%] 417s tests/test_trajectory.py::test_read_write[dcd-dtr] PASSED [ 57%] 417s tests/test_trajectory.py::test_read_write[dcd-xyz] PASSED [ 57%] 417s tests/test_trajectory.py::test_read_write[dcd-xyz.gz] PASSED [ 57%] 418s tests/test_trajectory.py::test_read_write[dcd-lammpstrj] PASSED [ 57%] 418s tests/test_trajectory.py::test_read_write[dcd-lh5] PASSED [ 57%] 418s tests/test_trajectory.py::test_read_write[dcd-pdb] PASSED [ 57%] 419s tests/test_trajectory.py::test_read_write[dcd-pdb.gz] PASSED [ 57%] 419s tests/test_trajectory.py::test_read_write[dcd-ncrst] SKIPPED (ncrst ...) [ 57%] 419s tests/test_trajectory.py::test_read_write[dcd-rst7] SKIPPED (rst7 ca...) [ 57%] 419s tests/test_trajectory.py::test_read_write[dcd-gro] PASSED [ 57%] 419s tests/test_trajectory.py::test_read_write[mdcrd-nc] PASSED [ 58%] 419s tests/test_trajectory.py::test_read_write[mdcrd-h5] PASSED [ 58%] 419s tests/test_trajectory.py::test_read_write[mdcrd-xtc] PASSED [ 58%] 419s tests/test_trajectory.py::test_read_write[mdcrd-trr] PASSED [ 58%] 419s tests/test_trajectory.py::test_read_write[mdcrd-dcd] PASSED [ 58%] 419s tests/test_trajectory.py::test_read_write[mdcrd-mdcrd] SKIPPED (mdcr...) [ 58%] 419s tests/test_trajectory.py::test_read_write[mdcrd-dtr] SKIPPED (dtr ne...) [ 58%] 419s tests/test_trajectory.py::test_read_write[mdcrd-xyz] PASSED [ 58%] 420s tests/test_trajectory.py::test_read_write[mdcrd-xyz.gz] PASSED [ 58%] 420s tests/test_trajectory.py::test_read_write[mdcrd-lammpstrj] SKIPPED (...) [ 58%] 420s tests/test_trajectory.py::test_read_write[mdcrd-lh5] PASSED [ 58%] 421s tests/test_trajectory.py::test_read_write[mdcrd-pdb] PASSED [ 59%] 422s tests/test_trajectory.py::test_read_write[mdcrd-pdb.gz] PASSED [ 59%] 422s tests/test_trajectory.py::test_read_write[mdcrd-ncrst] SKIPPED (ncrs...) [ 59%] 422s tests/test_trajectory.py::test_read_write[mdcrd-rst7] SKIPPED (rst7 ...) [ 59%] 422s tests/test_trajectory.py::test_read_write[mdcrd-gro] PASSED [ 59%] 422s tests/test_trajectory.py::test_read_write[dtr-nc] PASSED [ 59%] 422s tests/test_trajectory.py::test_read_write[dtr-h5] PASSED [ 59%] 422s tests/test_trajectory.py::test_read_write[dtr-xtc] PASSED [ 59%] 422s tests/test_trajectory.py::test_read_write[dtr-trr] PASSED [ 59%] 422s tests/test_trajectory.py::test_read_write[dtr-dcd] PASSED [ 59%] 422s tests/test_trajectory.py::test_read_write[dtr-mdcrd] SKIPPED (mdcrd ...) [ 59%] 424s tests/test_trajectory.py::test_read_write[dtr-dtr] PASSED [ 59%] 424s tests/test_trajectory.py::test_read_write[dtr-xyz] PASSED [ 60%] 425s tests/test_trajectory.py::test_read_write[dtr-xyz.gz] PASSED [ 60%] 425s tests/test_trajectory.py::test_read_write[dtr-lammpstrj] PASSED [ 60%] 425s tests/test_trajectory.py::test_read_write[dtr-lh5] PASSED [ 60%] 426s tests/test_trajectory.py::test_read_write[dtr-pdb] PASSED [ 60%] 426s tests/test_trajectory.py::test_read_write[dtr-pdb.gz] PASSED [ 60%] 426s tests/test_trajectory.py::test_read_write[dtr-ncrst] SKIPPED (ncrst ...) [ 60%] 426s tests/test_trajectory.py::test_read_write[dtr-rst7] SKIPPED (rst7 ca...) [ 60%] 426s tests/test_trajectory.py::test_read_write[dtr-gro] PASSED [ 60%] 426s tests/test_trajectory.py::test_read_write[xyz-nc] PASSED [ 60%] 426s tests/test_trajectory.py::test_read_write[xyz-h5] PASSED [ 60%] 426s tests/test_trajectory.py::test_read_write[xyz-xtc] PASSED [ 61%] 426s tests/test_trajectory.py::test_read_write[xyz-trr] PASSED [ 61%] 426s tests/test_trajectory.py::test_read_write[xyz-dcd] PASSED [ 61%] 426s tests/test_trajectory.py::test_read_write[xyz-mdcrd] SKIPPED (mdcrd ...) [ 61%] 426s tests/test_trajectory.py::test_read_write[xyz-dtr] SKIPPED (dtr need...) [ 61%] 426s tests/test_trajectory.py::test_read_write[xyz-xyz] PASSED [ 61%] 427s tests/test_trajectory.py::test_read_write[xyz-xyz.gz] PASSED [ 61%] 427s tests/test_trajectory.py::test_read_write[xyz-lammpstrj] SKIPPED (la...) [ 61%] 427s tests/test_trajectory.py::test_read_write[xyz-lh5] PASSED [ 61%] 428s tests/test_trajectory.py::test_read_write[xyz-pdb] PASSED [ 61%] 428s tests/test_trajectory.py::test_read_write[xyz-pdb.gz] PASSED [ 61%] 428s tests/test_trajectory.py::test_read_write[xyz-ncrst] SKIPPED (ncrst ...) [ 62%] 428s tests/test_trajectory.py::test_read_write[xyz-rst7] SKIPPED (rst7 ca...) [ 62%] 428s tests/test_trajectory.py::test_read_write[xyz-gro] PASSED [ 62%] 428s tests/test_trajectory.py::test_read_write[xyz.gz-nc] PASSED [ 62%] 428s tests/test_trajectory.py::test_read_write[xyz.gz-h5] PASSED [ 62%] 428s tests/test_trajectory.py::test_read_write[xyz.gz-xtc] PASSED [ 62%] 428s tests/test_trajectory.py::test_read_write[xyz.gz-trr] PASSED [ 62%] 428s tests/test_trajectory.py::test_read_write[xyz.gz-dcd] PASSED [ 62%] 428s tests/test_trajectory.py::test_read_write[xyz.gz-mdcrd] SKIPPED (mdc...) [ 62%] 428s tests/test_trajectory.py::test_read_write[xyz.gz-dtr] SKIPPED (dtr n...) [ 62%] 428s tests/test_trajectory.py::test_read_write[xyz.gz-xyz] PASSED [ 62%] 429s tests/test_trajectory.py::test_read_write[xyz.gz-xyz.gz] PASSED [ 62%] 429s tests/test_trajectory.py::test_read_write[xyz.gz-lammpstrj] SKIPPED [ 63%] 429s tests/test_trajectory.py::test_read_write[xyz.gz-lh5] PASSED [ 63%] 429s tests/test_trajectory.py::test_read_write[xyz.gz-pdb] PASSED [ 63%] 430s tests/test_trajectory.py::test_read_write[xyz.gz-pdb.gz] PASSED [ 63%] 430s tests/test_trajectory.py::test_read_write[xyz.gz-ncrst] SKIPPED (ncr...) [ 63%] 430s tests/test_trajectory.py::test_read_write[xyz.gz-rst7] SKIPPED (rst7...) [ 63%] 430s tests/test_trajectory.py::test_read_write[xyz.gz-gro] PASSED [ 63%] 430s tests/test_trajectory.py::test_read_write[lammpstrj-nc] PASSED [ 63%] 430s tests/test_trajectory.py::test_read_write[lammpstrj-h5] PASSED [ 63%] 431s tests/test_trajectory.py::test_read_write[lammpstrj-xtc] PASSED [ 63%] 431s tests/test_trajectory.py::test_read_write[lammpstrj-trr] PASSED [ 63%] 431s tests/test_trajectory.py::test_read_write[lammpstrj-dcd] PASSED [ 64%] 431s tests/test_trajectory.py::test_read_write[lammpstrj-mdcrd] SKIPPED (...) [ 64%] 432s tests/test_trajectory.py::test_read_write[lammpstrj-dtr] PASSED [ 64%] 432s tests/test_trajectory.py::test_read_write[lammpstrj-xyz] PASSED [ 64%] 433s tests/test_trajectory.py::test_read_write[lammpstrj-xyz.gz] PASSED [ 64%] 433s tests/test_trajectory.py::test_read_write[lammpstrj-lammpstrj] PASSED [ 64%] 433s tests/test_trajectory.py::test_read_write[lammpstrj-lh5] PASSED [ 64%] 433s tests/test_trajectory.py::test_read_write[lammpstrj-pdb] PASSED [ 64%] 434s tests/test_trajectory.py::test_read_write[lammpstrj-pdb.gz] PASSED [ 64%] 434s tests/test_trajectory.py::test_read_write[lammpstrj-ncrst] SKIPPED (...) [ 64%] 434s tests/test_trajectory.py::test_read_write[lammpstrj-rst7] SKIPPED (r...) [ 64%] 434s tests/test_trajectory.py::test_read_write[lammpstrj-gro] PASSED [ 65%] 434s tests/test_trajectory.py::test_read_write[lh5-nc] PASSED [ 65%] 434s tests/test_trajectory.py::test_read_write[lh5-h5] PASSED [ 65%] 434s tests/test_trajectory.py::test_read_write[lh5-xtc] PASSED [ 65%] 434s tests/test_trajectory.py::test_read_write[lh5-trr] PASSED [ 65%] 434s tests/test_trajectory.py::test_read_write[lh5-dcd] PASSED [ 65%] 434s tests/test_trajectory.py::test_read_write[lh5-mdcrd] SKIPPED (mdcrd ...) [ 65%] 434s tests/test_trajectory.py::test_read_write[lh5-dtr] SKIPPED (dtr need...) [ 65%] 434s tests/test_trajectory.py::test_read_write[lh5-xyz] PASSED [ 65%] 435s tests/test_trajectory.py::test_read_write[lh5-xyz.gz] PASSED [ 65%] 435s tests/test_trajectory.py::test_read_write[lh5-lammpstrj] SKIPPED (la...) [ 65%] 435s tests/test_trajectory.py::test_read_write[lh5-lh5] PASSED [ 66%] 435s tests/test_trajectory.py::test_read_write[lh5-pdb] PASSED [ 66%] 436s tests/test_trajectory.py::test_read_write[lh5-pdb.gz] PASSED [ 66%] 436s tests/test_trajectory.py::test_read_write[lh5-ncrst] SKIPPED (ncrst ...) [ 66%] 436s tests/test_trajectory.py::test_read_write[lh5-rst7] SKIPPED (rst7 ca...) [ 66%] 436s tests/test_trajectory.py::test_read_write[lh5-gro] PASSED [ 66%] 436s tests/test_trajectory.py::test_read_write[pdb-nc] PASSED [ 66%] 437s tests/test_trajectory.py::test_read_write[pdb-h5] PASSED [ 66%] 437s tests/test_trajectory.py::test_read_write[pdb-xtc] PASSED [ 66%] 437s tests/test_trajectory.py::test_read_write[pdb-trr] PASSED [ 66%] 437s tests/test_trajectory.py::test_read_write[pdb-dcd] PASSED [ 66%] 437s tests/test_trajectory.py::test_read_write[pdb-mdcrd] SKIPPED (mdcrd ...) [ 66%] 439s tests/test_trajectory.py::test_read_write[pdb-dtr] PASSED [ 67%] 440s tests/test_trajectory.py::test_read_write[pdb-xyz] PASSED [ 67%] 440s tests/test_trajectory.py::test_read_write[pdb-xyz.gz] PASSED [ 67%] 440s tests/test_trajectory.py::test_read_write[pdb-lammpstrj] PASSED [ 67%] 441s tests/test_trajectory.py::test_read_write[pdb-lh5] PASSED [ 67%] 441s tests/test_trajectory.py::test_read_write[pdb-pdb] PASSED [ 67%] 442s tests/test_trajectory.py::test_read_write[pdb-pdb.gz] PASSED [ 67%] 442s tests/test_trajectory.py::test_read_write[pdb-ncrst] SKIPPED (ncrst ...) [ 67%] 442s tests/test_trajectory.py::test_read_write[pdb-rst7] SKIPPED (rst7 ca...) [ 67%] 443s tests/test_trajectory.py::test_read_write[pdb-gro] PASSED [ 67%] 443s tests/test_trajectory.py::test_read_write[pdb.gz-nc] PASSED [ 67%] 444s tests/test_trajectory.py::test_read_write[pdb.gz-h5] PASSED [ 68%] 444s tests/test_trajectory.py::test_read_write[pdb.gz-xtc] PASSED [ 68%] 444s tests/test_trajectory.py::test_read_write[pdb.gz-trr] PASSED [ 68%] 445s tests/test_trajectory.py::test_read_write[pdb.gz-dcd] PASSED [ 68%] 445s tests/test_trajectory.py::test_read_write[pdb.gz-mdcrd] SKIPPED (mdc...) [ 68%] 446s tests/test_trajectory.py::test_read_write[pdb.gz-dtr] PASSED [ 68%] 447s tests/test_trajectory.py::test_read_write[pdb.gz-xyz] PASSED [ 68%] 447s tests/test_trajectory.py::test_read_write[pdb.gz-xyz.gz] PASSED [ 68%] 448s tests/test_trajectory.py::test_read_write[pdb.gz-lammpstrj] PASSED [ 68%] 448s tests/test_trajectory.py::test_read_write[pdb.gz-lh5] PASSED [ 68%] 449s tests/test_trajectory.py::test_read_write[pdb.gz-pdb] PASSED [ 68%] 450s tests/test_trajectory.py::test_read_write[pdb.gz-pdb.gz] PASSED [ 69%] 450s tests/test_trajectory.py::test_read_write[pdb.gz-ncrst] SKIPPED (ncr...) [ 69%] 450s tests/test_trajectory.py::test_read_write[pdb.gz-rst7] SKIPPED (rst7...) [ 69%] 450s tests/test_trajectory.py::test_read_write[pdb.gz-gro] PASSED [ 69%] 450s tests/test_trajectory.py::test_read_write[ncrst-nc] XFAIL (These ref...) [ 69%] 450s tests/test_trajectory.py::test_read_write[ncrst-h5] XFAIL (These ref...) [ 69%] 450s tests/test_trajectory.py::test_read_write[ncrst-xtc] XFAIL (These re...) [ 69%] 450s tests/test_trajectory.py::test_read_write[ncrst-trr] XFAIL (These re...) [ 69%] 450s tests/test_trajectory.py::test_read_write[ncrst-dcd] XFAIL (These re...) [ 69%] 450s tests/test_trajectory.py::test_read_write[ncrst-mdcrd] XFAIL (These ...) [ 69%] 450s tests/test_trajectory.py::test_read_write[ncrst-dtr] XFAIL (These re...) [ 69%] 450s tests/test_trajectory.py::test_read_write[ncrst-xyz] XFAIL (These re...) [ 70%] 450s tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] XFAIL (These...) [ 70%] 451s tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] XFAIL (Th...) [ 70%] 451s tests/test_trajectory.py::test_read_write[ncrst-lh5] XFAIL (These re...) [ 70%] 451s tests/test_trajectory.py::test_read_write[ncrst-pdb] XFAIL (These re...) [ 70%] 451s tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] XFAIL (These...) [ 70%] 451s tests/test_trajectory.py::test_read_write[ncrst-ncrst] XFAIL (These ...) [ 70%] 451s tests/test_trajectory.py::test_read_write[ncrst-rst7] XFAIL (These r...) [ 70%] 451s tests/test_trajectory.py::test_read_write[ncrst-gro] XFAIL (These re...) [ 70%] 451s tests/test_trajectory.py::test_read_write[rst7-nc] XFAIL (These refe...) [ 70%] 451s tests/test_trajectory.py::test_read_write[rst7-h5] XFAIL (These refe...) [ 70%] 451s tests/test_trajectory.py::test_read_write[rst7-xtc] XFAIL (These ref...) [ 70%] 451s tests/test_trajectory.py::test_read_write[rst7-trr] XFAIL (These ref...) [ 71%] 451s tests/test_trajectory.py::test_read_write[rst7-dcd] XFAIL (These ref...) [ 71%] 451s tests/test_trajectory.py::test_read_write[rst7-mdcrd] XFAIL (These r...) [ 71%] 451s tests/test_trajectory.py::test_read_write[rst7-dtr] XFAIL (These ref...) [ 71%] 451s tests/test_trajectory.py::test_read_write[rst7-xyz] XFAIL (These ref...) [ 71%] 451s tests/test_trajectory.py::test_read_write[rst7-xyz.gz] XFAIL (These ...) [ 71%] 451s tests/test_trajectory.py::test_read_write[rst7-lammpstrj] XFAIL (The...) [ 71%] 451s tests/test_trajectory.py::test_read_write[rst7-lh5] XFAIL (These ref...) [ 71%] 451s tests/test_trajectory.py::test_read_write[rst7-pdb] XFAIL (These ref...) [ 71%] 451s tests/test_trajectory.py::test_read_write[rst7-pdb.gz] XFAIL (These ...) [ 71%] 451s tests/test_trajectory.py::test_read_write[rst7-ncrst] XFAIL (These r...) [ 71%] 451s tests/test_trajectory.py::test_read_write[rst7-rst7] XFAIL (These re...) [ 72%] 451s tests/test_trajectory.py::test_read_write[rst7-gro] XFAIL (These ref...) [ 72%] 451s tests/test_trajectory.py::test_read_write[gro-nc] PASSED [ 72%] 451s tests/test_trajectory.py::test_read_write[gro-h5] PASSED [ 72%] 451s tests/test_trajectory.py::test_read_write[gro-xtc] PASSED [ 72%] 451s tests/test_trajectory.py::test_read_write[gro-trr] PASSED [ 72%] 451s tests/test_trajectory.py::test_read_write[gro-dcd] PASSED [ 72%] 451s tests/test_trajectory.py::test_read_write[gro-mdcrd] SKIPPED (mdcrd ...) [ 72%] 453s tests/test_trajectory.py::test_read_write[gro-dtr] PASSED [ 72%] 453s tests/test_trajectory.py::test_read_write[gro-xyz] PASSED [ 72%] 453s tests/test_trajectory.py::test_read_write[gro-xyz.gz] PASSED [ 72%] 453s tests/test_trajectory.py::test_read_write[gro-lammpstrj] PASSED [ 73%] 453s tests/test_trajectory.py::test_read_write[gro-lh5] PASSED [ 73%] 454s tests/test_trajectory.py::test_read_write[gro-pdb] PASSED [ 73%] 455s tests/test_trajectory.py::test_read_write[gro-pdb.gz] PASSED [ 73%] 455s tests/test_trajectory.py::test_read_write[gro-ncrst] SKIPPED (ncrst ...) [ 73%] 455s tests/test_trajectory.py::test_read_write[gro-rst7] SKIPPED (rst7 ca...) [ 73%] 455s tests/test_trajectory.py::test_read_write[gro-gro] PASSED [ 73%] 455s tests/test_trajectory.py::test_load[nc] PASSED [ 73%] 455s tests/test_trajectory.py::test_load[h5] PASSED [ 73%] 455s tests/test_trajectory.py::test_load[xtc] PASSED [ 73%] 455s tests/test_trajectory.py::test_load[trr] PASSED [ 73%] 455s tests/test_trajectory.py::test_load[dcd] PASSED [ 74%] 455s tests/test_trajectory.py::test_load[mdcrd] PASSED [ 74%] 455s tests/test_trajectory.py::test_load[dtr] PASSED [ 74%] 455s tests/test_trajectory.py::test_load[xyz] PASSED [ 74%] 456s tests/test_trajectory.py::test_load[xyz.gz] PASSED [ 74%] 456s tests/test_trajectory.py::test_load[lammpstrj] PASSED [ 74%] 456s tests/test_trajectory.py::test_load[lh5] PASSED [ 74%] 458s tests/test_trajectory.py::test_load[pdb] PASSED [ 74%] 460s tests/test_trajectory.py::test_load[pdb.gz] PASSED [ 74%] 460s tests/test_trajectory.py::test_load[ncrst] XFAIL (These reference fi...) [ 74%] 460s tests/test_trajectory.py::test_load[rst7] XFAIL (These reference fil...) [ 74%] 461s tests/test_trajectory.py::test_load[gro] PASSED [ 74%] 461s tests/test_trajectory.py::test_hdf5 PASSED [ 75%] 461s tests/test_trajectory.py::test_center PASSED [ 75%] 461s tests/test_trajectory.py::test_center_aind PASSED [ 75%] 461s tests/test_trajectory.py::test_float_atom_indices_exception[nc] PASSED [ 75%] 461s tests/test_trajectory.py::test_float_atom_indices_exception[h5] PASSED [ 75%] 461s tests/test_trajectory.py::test_float_atom_indices_exception[xtc] PASSED [ 75%] 461s tests/test_trajectory.py::test_float_atom_indices_exception[trr] PASSED [ 75%] 461s tests/test_trajectory.py::test_float_atom_indices_exception[dcd] PASSED [ 75%] 461s tests/test_trajectory.py::test_float_atom_indices_exception[mdcrd] PASSED [ 75%] 461s tests/test_trajectory.py::test_float_atom_indices_exception[dtr] PASSED [ 75%] 461s tests/test_trajectory.py::test_float_atom_indices_exception[xyz] PASSED [ 75%] 461s tests/test_trajectory.py::test_float_atom_indices_exception[xyz.gz] PASSED [ 76%] 461s tests/test_trajectory.py::test_float_atom_indices_exception[lammpstrj] PASSED [ 76%] 461s tests/test_trajectory.py::test_float_atom_indices_exception[lh5] PASSED [ 76%] 461s tests/test_trajectory.py::test_float_atom_indices_exception[pdb] PASSED [ 76%] 461s tests/test_trajectory.py::test_float_atom_indices_exception[pdb.gz] PASSED [ 76%] 461s tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] XFAIL [ 76%] 461s tests/test_trajectory.py::test_float_atom_indices_exception[rst7] XFAIL [ 76%] 461s tests/test_trajectory.py::test_float_atom_indices_exception[gro] PASSED [ 76%] 461s tests/test_trajectory.py::test_restrict_atoms PASSED [ 76%] 461s tests/test_trajectory.py::test_restrict_atoms_not_inplace PASSED [ 76%] 461s tests/test_trajectory.py::test_array_vs_matrix PASSED [ 76%] 461s tests/test_trajectory.py::test_pdb_unitcell_loadsave PASSED [ 77%] 461s tests/test_trajectory.py::test_load_combination[nc] PASSED [ 77%] 461s tests/test_trajectory.py::test_load_combination[h5] PASSED [ 77%] 461s tests/test_trajectory.py::test_load_combination[xtc] PASSED [ 77%] 461s tests/test_trajectory.py::test_load_combination[trr] PASSED [ 77%] 461s tests/test_trajectory.py::test_load_combination[dcd] PASSED [ 77%] 461s tests/test_trajectory.py::test_load_combination[mdcrd] PASSED [ 77%] 461s tests/test_trajectory.py::test_load_combination[dtr] PASSED [ 77%] 461s tests/test_trajectory.py::test_load_combination[xyz] PASSED [ 77%] 461s tests/test_trajectory.py::test_load_combination[xyz.gz] PASSED [ 77%] 461s tests/test_trajectory.py::test_load_combination[lammpstrj] PASSED [ 77%] 461s tests/test_trajectory.py::test_load_combination[lh5] PASSED [ 77%] 462s tests/test_trajectory.py::test_load_combination[pdb] PASSED [ 78%] 463s tests/test_trajectory.py::test_load_combination[pdb.gz] PASSED [ 78%] 463s tests/test_trajectory.py::test_load_combination[ncrst] XFAIL (These ...) [ 78%] 463s tests/test_trajectory.py::test_load_combination[rst7] XFAIL (These r...) [ 78%] 463s tests/test_trajectory.py::test_load_combination[gro] PASSED [ 78%] 463s tests/test_trajectory.py::test_no_topology PASSED [ 78%] 463s tests/test_trajectory.py::test_join PASSED [ 78%] 463s tests/test_trajectory.py::test_md_join PASSED [ 78%] 463s tests/test_trajectory.py::test_stack_1 PASSED [ 78%] 463s tests/test_trajectory.py::test_stack_2 PASSED [ 78%] 463s tests/test_trajectory.py::test_seek_read_mode[nc] PASSED [ 78%] 463s tests/test_trajectory.py::test_seek_read_mode[h5] PASSED [ 79%] 463s tests/test_trajectory.py::test_seek_read_mode[xtc] PASSED [ 79%] 463s tests/test_trajectory.py::test_seek_read_mode[trr] PASSED [ 79%] 463s tests/test_trajectory.py::test_seek_read_mode[dcd] PASSED [ 79%] 463s tests/test_trajectory.py::test_seek_read_mode[mdcrd] PASSED [ 79%] 463s tests/test_trajectory.py::test_seek_read_mode[dtr] PASSED [ 79%] 464s tests/test_trajectory.py::test_seek_read_mode[xyz] PASSED [ 79%] 464s tests/test_trajectory.py::test_seek_read_mode[xyz.gz] XFAIL (This is...) [ 79%] 464s tests/test_trajectory.py::test_seek_read_mode[lammpstrj] PASSED [ 79%] 464s tests/test_trajectory.py::test_seek_read_mode[lh5] PASSED [ 79%] 464s tests/test_trajectory.py::test_seek_read_mode[pdb] XFAIL (PDB Files ...) [ 79%] 464s tests/test_trajectory.py::test_seek_read_mode[pdb.gz] XFAIL (PDB Fil...) [ 80%] 464s tests/test_trajectory.py::test_seek_read_mode[ncrst] XFAIL (These re...) [ 80%] 464s tests/test_trajectory.py::test_seek_read_mode[rst7] XFAIL (These ref...) [ 80%] 464s tests/test_trajectory.py::test_seek_read_mode[gro] XFAIL (This is br...) [ 80%] 464s tests/test_trajectory.py::test_load_frame[nc] PASSED [ 80%] 464s tests/test_trajectory.py::test_load_frame[h5] PASSED [ 80%] 464s tests/test_trajectory.py::test_load_frame[xtc] PASSED [ 80%] 464s tests/test_trajectory.py::test_load_frame[trr] PASSED [ 80%] 464s tests/test_trajectory.py::test_load_frame[dcd] PASSED [ 80%] 464s tests/test_trajectory.py::test_load_frame[mdcrd] PASSED [ 80%] 464s tests/test_trajectory.py::test_load_frame[dtr] XFAIL (DTR doesn't lo...) [ 80%] 464s tests/test_trajectory.py::test_load_frame[xyz] PASSED [ 81%] 464s tests/test_trajectory.py::test_load_frame[xyz.gz] PASSED [ 81%] 464s tests/test_trajectory.py::test_load_frame[lammpstrj] PASSED [ 81%] 464s tests/test_trajectory.py::test_load_frame[lh5] PASSED [ 81%] 465s tests/test_trajectory.py::test_load_frame[pdb] PASSED [ 81%] 465s tests/test_trajectory.py::test_load_frame[pdb.gz] PASSED [ 81%] 465s tests/test_trajectory.py::test_load_frame[ncrst] XFAIL (These refere...) [ 81%] 465s tests/test_trajectory.py::test_load_frame[rst7] XFAIL (These referen...) [ 81%] 465s tests/test_trajectory.py::test_load_frame[gro] XFAIL (Gro doesn't im...) [ 81%] 466s tests/test_trajectory.py::test_load_frame_2eqq PASSED [ 81%] 466s tests/test_trajectory.py::test_iterload[nc] PASSED [ 81%] 466s tests/test_trajectory.py::test_iterload[h5] PASSED [ 81%] 466s tests/test_trajectory.py::test_iterload[xtc] PASSED [ 82%] 466s tests/test_trajectory.py::test_iterload[trr] PASSED [ 82%] 466s tests/test_trajectory.py::test_iterload[dcd] PASSED [ 82%] 466s tests/test_trajectory.py::test_iterload[mdcrd] PASSED [ 82%] 466s tests/test_trajectory.py::test_iterload[dtr] XFAIL (This is broken w...) [ 82%] 466s tests/test_trajectory.py::test_iterload[xyz] PASSED [ 82%] 466s tests/test_trajectory.py::test_iterload[xyz.gz] PASSED [ 82%] 466s tests/test_trajectory.py::test_iterload[lammpstrj] PASSED [ 82%] 466s tests/test_trajectory.py::test_iterload[lh5] PASSED [ 82%] 466s tests/test_trajectory.py::test_iterload[pdb] PASSED [ 82%] 466s tests/test_trajectory.py::test_iterload[pdb.gz] PASSED [ 82%] 466s tests/test_trajectory.py::test_iterload[ncrst] SKIPPED (Only 1 frame...) [ 83%] 466s tests/test_trajectory.py::test_iterload[rst7] SKIPPED (Only 1 frame ...) [ 83%] 466s tests/test_trajectory.py::test_iterload[gro] PASSED [ 83%] 470s tests/test_trajectory.py::test_iterload_skip[nc] PASSED [ 83%] 473s tests/test_trajectory.py::test_iterload_skip[h5] PASSED [ 83%] 474s tests/test_trajectory.py::test_iterload_skip[xtc] PASSED [ 83%] 475s tests/test_trajectory.py::test_iterload_skip[trr] PASSED [ 83%] 476s tests/test_trajectory.py::test_iterload_skip[dcd] PASSED [ 83%] 478s tests/test_trajectory.py::test_iterload_skip[mdcrd] PASSED [ 83%] 478s tests/test_trajectory.py::test_iterload_skip[dtr] PASSED [ 83%] 479s tests/test_trajectory.py::test_iterload_skip[xyz] PASSED [ 83%] 481s tests/test_trajectory.py::test_iterload_skip[xyz.gz] PASSED [ 84%] 482s tests/test_trajectory.py::test_iterload_skip[lammpstrj] PASSED [ 84%] 484s tests/test_trajectory.py::test_iterload_skip[lh5] PASSED [ 84%] 484s tests/test_trajectory.py::test_iterload_skip[pdb] XFAIL (PDB Iterloa...) [ 84%] 484s tests/test_trajectory.py::test_iterload_skip[pdb.gz] XFAIL (PDB Iter...) [ 84%] 484s tests/test_trajectory.py::test_iterload_skip[ncrst] XFAIL (These ref...) [ 84%] 484s tests/test_trajectory.py::test_iterload_skip[rst7] XFAIL (These refe...) [ 84%] 484s tests/test_trajectory.py::test_iterload_skip[gro] XFAIL (Not impleme...) [ 84%] 484s tests/test_trajectory.py::test_iterload_chunk_dcd PASSED [ 84%] 484s tests/test_trajectory.py::test_save_load[nc] PASSED [ 84%] 484s tests/test_trajectory.py::test_save_load[h5] PASSED [ 84%] 484s tests/test_trajectory.py::test_save_load[xtc] PASSED [ 85%] 484s tests/test_trajectory.py::test_save_load[trr] PASSED [ 85%] 484s tests/test_trajectory.py::test_save_load[dcd] PASSED [ 85%] 484s tests/test_trajectory.py::test_save_load[mdcrd] PASSED [ 85%] 484s tests/test_trajectory.py::test_save_load[dtr] PASSED [ 85%] 484s tests/test_trajectory.py::test_save_load[xyz] PASSED [ 85%] 484s tests/test_trajectory.py::test_save_load[xyz.gz] PASSED [ 85%] 484s tests/test_trajectory.py::test_save_load[lammpstrj] PASSED [ 85%] 484s tests/test_trajectory.py::test_save_load[lh5] PASSED [ 85%] 484s tests/test_trajectory.py::test_save_load[pdb] PASSED [ 85%] 484s tests/test_trajectory.py::test_save_load[pdb.gz] PASSED [ 85%] 484s tests/test_trajectory.py::test_save_load[ncrst] PASSED [ 85%] 484s tests/test_trajectory.py::test_save_load[rst7] PASSED [ 86%] 484s tests/test_trajectory.py::test_save_load[gro] PASSED [ 86%] 484s tests/test_trajectory.py::test_force_overwrite[nc] PASSED [ 86%] 484s tests/test_trajectory.py::test_force_overwrite[h5] PASSED [ 86%] 484s tests/test_trajectory.py::test_force_overwrite[xtc] PASSED [ 86%] 484s tests/test_trajectory.py::test_force_overwrite[trr] PASSED [ 86%] 484s tests/test_trajectory.py::test_force_overwrite[dcd] PASSED [ 86%] 484s tests/test_trajectory.py::test_force_overwrite[mdcrd] PASSED [ 86%] 484s tests/test_trajectory.py::test_force_overwrite[dtr] XFAIL (This is b...) [ 86%] 484s tests/test_trajectory.py::test_force_overwrite[xyz] PASSED [ 86%] 484s tests/test_trajectory.py::test_force_overwrite[xyz.gz] PASSED [ 86%] 484s tests/test_trajectory.py::test_force_overwrite[lammpstrj] PASSED [ 87%] 484s tests/test_trajectory.py::test_force_overwrite[lh5] PASSED [ 87%] 484s tests/test_trajectory.py::test_force_overwrite[pdb] PASSED [ 87%] 484s tests/test_trajectory.py::test_force_overwrite[pdb.gz] PASSED [ 87%] 484s tests/test_trajectory.py::test_force_overwrite[ncrst] PASSED [ 87%] 484s tests/test_trajectory.py::test_force_overwrite[rst7] PASSED [ 87%] 484s tests/test_trajectory.py::test_force_overwrite[gro] PASSED [ 87%] 484s tests/test_trajectory.py::test_force_noverwrite[nc] PASSED [ 87%] 484s tests/test_trajectory.py::test_force_noverwrite[h5] PASSED [ 87%] 484s tests/test_trajectory.py::test_force_noverwrite[xtc] PASSED [ 87%] 484s tests/test_trajectory.py::test_force_noverwrite[trr] PASSED [ 87%] 484s tests/test_trajectory.py::test_force_noverwrite[dcd] PASSED [ 88%] 484s tests/test_trajectory.py::test_force_noverwrite[mdcrd] PASSED [ 88%] 484s tests/test_trajectory.py::test_force_noverwrite[dtr] PASSED [ 88%] 484s tests/test_trajectory.py::test_force_noverwrite[xyz] PASSED [ 88%] 484s tests/test_trajectory.py::test_force_noverwrite[xyz.gz] PASSED [ 88%] 484s tests/test_trajectory.py::test_force_noverwrite[lammpstrj] PASSED [ 88%] 484s tests/test_trajectory.py::test_force_noverwrite[lh5] PASSED [ 88%] 484s tests/test_trajectory.py::test_force_noverwrite[pdb] PASSED [ 88%] 484s tests/test_trajectory.py::test_force_noverwrite[pdb.gz] PASSED [ 88%] 485s tests/test_trajectory.py::test_force_noverwrite[ncrst] PASSED [ 88%] 485s tests/test_trajectory.py::test_force_noverwrite[rst7] PASSED [ 88%] 485s tests/test_trajectory.py::test_force_noverwrite[gro] PASSED [ 88%] 485s tests/test_trajectory.py::test_open_and_load PASSED [ 89%] 485s tests/test_trajectory.py::test_length PASSED [ 89%] 485s tests/test_trajectory.py::test_unitcell[nc] PASSED [ 89%] 485s tests/test_trajectory.py::test_unitcell[h5] PASSED [ 89%] 485s tests/test_trajectory.py::test_unitcell[xtc] PASSED [ 89%] 485s tests/test_trajectory.py::test_unitcell[trr] PASSED [ 89%] 485s tests/test_trajectory.py::test_unitcell[dcd] PASSED [ 89%] 485s tests/test_trajectory.py::test_unitcell[mdcrd] PASSED [ 89%] 485s tests/test_trajectory.py::test_unitcell[dtr] XFAIL (dtr seems to nee...) [ 89%] 485s tests/test_trajectory.py::test_unitcell[xyz] PASSED [ 89%] 485s tests/test_trajectory.py::test_unitcell[xyz.gz] PASSED [ 89%] 485s tests/test_trajectory.py::test_unitcell[lammpstrj] XFAIL (lammpstrj ...) [ 90%] 485s tests/test_trajectory.py::test_unitcell[lh5] PASSED [ 90%] 485s tests/test_trajectory.py::test_unitcell[pdb] PASSED [ 90%] 485s tests/test_trajectory.py::test_unitcell[pdb.gz] PASSED [ 90%] 485s tests/test_trajectory.py::test_unitcell[ncrst] XFAIL (ncrst seems to...) [ 90%] 485s tests/test_trajectory.py::test_unitcell[rst7] XFAIL (rst7 seems to n...) [ 90%] 485s tests/test_trajectory.py::test_unitcell[gro] PASSED [ 90%] 485s tests/test_trajectory.py::test_chunk0_iterload PASSED [ 90%] 486s tests/test_trajectory.py::test_hashing PASSED [ 90%] 486s tests/test_trajectory.py::test_smooth PASSED [ 90%] 486s tests/test_trajectory.py::test_load_pdb_no_standard_names PASSED [ 90%] 486s tests/test_trajectory.py::test_load_with_atom_indices PASSED [ 91%] 486s tests/test_trajectory.py::test_load_with_frame PASSED [ 91%] 486s tests/test_trajectory.py::test_add_remove_atoms PASSED [ 91%] 486s tests/test_trr.py::test_1 PASSED [ 91%] 486s tests/test_trr.py::test_read_stride PASSED [ 91%] 486s tests/test_trr.py::test_read_stride_n_frames PASSED [ 91%] 487s tests/test_trr.py::test_read_stride_offsets PASSED [ 91%] 487s tests/test_trr.py::test_read_stride_n_frames_offsets PASSED [ 91%] 487s tests/test_trr.py::test_read_stride_switching PASSED [ 91%] 487s tests/test_trr.py::test_write_read PASSED [ 91%] 487s tests/test_trr.py::test_read_atomindices_1 PASSED [ 91%] 487s tests/test_trr.py::test_read_atomindices_2 PASSED [ 92%] 487s tests/test_trr.py::test_deficient_shape PASSED [ 92%] 487s tests/test_trr.py::test_ragged_1 PASSED [ 92%] 487s tests/test_trr.py::test_ragged_2 PASSED [ 92%] 487s tests/test_trr.py::test_malformed PASSED [ 92%] 487s tests/test_trr.py::test_tell PASSED [ 92%] 487s tests/test_trr.py::test_seek PASSED [ 92%] 487s tests/test_trr.py::test_get_velocities PASSED [ 92%] 487s tests/test_trr.py::test_get_forces PASSED [ 92%] 487s tests/test_trr.py::test_get_velocities_and_forces PASSED [ 92%] 487s tests/test_trr.py::test_get_velocities_forces_atom_indices_1 PASSED [ 92%] 487s tests/test_trr.py::test_get_velocities_forces_atom_indices_2 PASSED [ 92%] 487s tests/test_trr.py::test_read_velocities_do_not_exist PASSED [ 93%] 487s tests/test_trr.py::test_read_forces_do_not_exist PASSED [ 93%] 487s tests/test_utils.py::test_unitcell_0 PASSED [ 93%] 487s tests/test_utils.py::test_unitcell_1 PASSED [ 93%] 487s tests/test_utils.py::test_ensure_type_1 PASSED [ 93%] 487s tests/test_utils.py::test_ensure_type_2 PASSED [ 93%] 487s tests/test_utils.py::test_ensure_type_25 PASSED [ 93%] 487s tests/test_utils.py::test_ensure_type_3 PASSED [ 93%] 487s tests/test_utils.py::test_ensure_type_4 PASSED [ 93%] 487s tests/test_utils.py::test_ensure_type_5 PASSED [ 93%] 487s tests/test_utils.py::test_ensure_type_6 PASSED [ 93%] 487s tests/test_utils.py::test_ensure_type_7 PASSED [ 94%] 487s tests/test_utils.py::test_ensure_type_8 PASSED [ 94%] 487s tests/test_utils.py::test_ensure_type_9 PASSED [ 94%] 487s tests/test_utils.py::test_ensure_type_10 PASSED [ 94%] 487s tests/test_utils.py::test_ensure_type_11 PASSED [ 94%] 487s tests/test_utils.py::test_ensure_type_12 PASSED [ 94%] 487s tests/test_utils.py::test_ensure_type_13 PASSED [ 94%] 487s tests/test_utils.py::test_ensure_type_14 PASSED [ 94%] 487s tests/test_utils.py::test_ensure_type_15 PASSED [ 94%] 487s tests/test_utils.py::test_delay_import_fail_1 PASSED [ 94%] 487s tests/test_utils.py::test_delay_import PASSED [ 94%] 487s tests/test_utils.py::test_unit_0 PASSED [ 95%] 487s tests/test_utils.py::test_unit_1 PASSED [ 95%] 487s tests/test_utils.py::test_unit_2 PASSED [ 95%] 487s tests/test_utils.py::test_unit_3 PASSED [ 95%] 487s tests/test_xml.py::test_xml PASSED [ 95%] 487s tests/test_xtc.py::test_read_chunk1 PASSED [ 95%] 487s tests/test_xtc.py::test_read_stride PASSED [ 95%] 487s tests/test_xtc.py::test_read_stride_n_frames PASSED [ 95%] 487s tests/test_xtc.py::test_read_stride_offsets PASSED [ 95%] 487s tests/test_xtc.py::test_read_stride_n_frames_offsets PASSED [ 95%] 487s tests/test_xtc.py::test_read_stride_switching_offsets PASSED [ 95%] 487s tests/test_xtc.py::test_read_atomindices_1 PASSED [ 96%] 487s tests/test_xtc.py::test_read_atomindices_w_stride PASSED [ 96%] 487s tests/test_xtc.py::test_read_atomindices_2 PASSED [ 96%] 487s tests/test_xtc.py::test_read_chunk2 PASSED [ 96%] 487s tests/test_xtc.py::test_read_chunk3 PASSED [ 96%] 487s tests/test_xtc.py::test_write_0 PASSED [ 96%] 487s tests/test_xtc.py::test_write_1 PASSED [ 96%] 487s tests/test_xtc.py::test_write_2 PASSED [ 96%] 487s tests/test_xtc.py::test_read_error_0 PASSED [ 96%] 487s tests/test_xtc.py::test_write_error_0 PASSED [ 96%] 487s tests/test_xtc.py::test_read_error_1 PASSED [ 96%] 487s tests/test_xtc.py::test_read_error_2 PASSED [ 96%] 487s tests/test_xtc.py::test_xtc_write_wierd_0 PASSED [ 97%] 487s tests/test_xtc.py::test_tell PASSED [ 97%] 487s tests/test_xtc.py::test_seek PASSED [ 97%] 487s tests/test_xtc.py::test_seek_natoms9 PASSED [ 97%] 487s tests/test_xtc.py::test_seek_out_of_bounds PASSED [ 97%] 487s tests/test_xtc.py::test_ragged_1 PASSED [ 97%] 487s tests/test_xtc.py::test_ragged_2 PASSED [ 97%] 487s tests/test_xtc.py::test_short_traj PASSED [ 97%] 487s tests/test_xtc.py::test_flush PASSED [ 97%] 487s tests/test_xyz.py::test_read_0 PASSED [ 97%] 487s tests/test_xyz.py::test_read_1 PASSED [ 97%] 487s tests/test_xyz.py::test_read_gz PASSED [ 98%] 487s tests/test_xyz.py::test_read_write PASSED [ 98%] 487s tests/test_xyz.py::test_mdwrite PASSED [ 98%] 487s tests/test_xyz.py::test_multiread PASSED [ 98%] 487s tests/test_xyz.py::test_seek PASSED [ 98%] 488s tests/test_xyz.py::test_len PASSED [ 98%] 488s tests/test_zipped.py::test_read_gz PASSED [ 98%] 488s tests/test_zipped.py::test_write_gz PASSED [ 98%] 488s tests/test_zipped.py::test_read_bz2 PASSED [ 98%] 488s tests/test_zipped.py::test_write_bz2 PASSED [ 98%] 488s examples/test_examples.py::test_example_notebook[native-contact.ipynb] SKIPPED [ 98%] 488s examples/test_examples.py::test_example_notebook[simulation-with-openmm.ipynb] SKIPPED [ 99%] 490s examples/test_examples.py::test_example_notebook[solvent-accessible-surface-area.ipynb] PASSED [ 99%] 493s examples/test_examples.py::test_example_notebook[ramachandran-plot.ipynb] PASSED [ 99%] 495s examples/test_examples.py::test_example_notebook[two-pass-clustering.ipynb] PASSED [ 99%] 497s examples/test_examples.py::test_example_notebook[rmsd-drift.ipynb] PASSED [ 99%] 498s examples/test_examples.py::test_example_notebook[atom-selection.ipynb] PASSED [ 99%] 499s examples/test_examples.py::test_example_notebook[iterload.ipynb] PASSED [ 99%] 502s examples/test_examples.py::test_example_notebook[rmsd-benchmark.ipynb] PASSED [ 99%] 505s examples/test_examples.py::test_example_notebook[principal-components.ipynb] PASSED [ 99%] 507s examples/test_examples.py::test_example_notebook[clustering.ipynb] PASSED [ 99%] 508s examples/test_examples.py::test_example_notebook[centroids.ipynb] PASSED [ 99%] 508s examples/test_examples.py::test_example_notebook[hbonds.ipynb] SKIPPED [100%] 508s 508s =============================== warnings summary =============================== 508s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 508s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 508s given by the platformdirs library. To remove this warning and 508s see the appropriate new directories, set the environment variable 508s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 508s The use of platformdirs will be the default in `jupyter_core` v6 508s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 508s 508s examples/test_examples.py:26 508s /tmp/autopkgtest.PzEck5/build.ROp/src/examples/test_examples.py:26: PytestUnknownMarkWarning: Unknown pytest.mark.flaky - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 508s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 508s 508s tests/test_arc.py::test_read_arctraj 508s tests/test_order.py::test_nematic_order 508s tests/test_order.py::test_director 508s tests/test_order.py::test_inertia 508s tests/test_order.py::test_nematic_order_args 508s tests/test_shape.py::test_gyration 508s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:204: RuntimeWarning: divide by zero encountered in divide 508s particle_density = traj.top.n_atoms / traj.unitcell_volumes[0] 508s 508s tests/test_arc.py: 1 warning 508s tests/test_gro.py: 3 warnings 508s tests/test_order.py: 4 warnings 508s tests/test_pdb.py: 1 warning 508s tests/test_shape.py: 4 warnings 508s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:206: UserWarning: Unlikely unit cell vectors detected in PDB file likely resulting from a dummy CRYST1 record. Discarding unit cell vectors. 508s warnings.warn( 508s 508s tests/test_contact.py::test_contact_0 508s tests/test_contact.py::test_contact_4 508s /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. 508s warnings.warn( 508s 508s tests/test_contact.py::test_contact_3 508s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:271: RuntimeWarning: overflow encountered in exp 508s np.exp( 508s 508s tests/test_contact.py::test_contact_3 508s /tmp/autopkgtest.PzEck5/build.ROp/src/tests/test_contact.py:114: RuntimeWarning: divide by zero encountered in divide 508s assert np.allclose( 508s 508s tests/test_dcd.py::test_do_overwrite 508s tests/test_dcd.py::test_ragged_1 508s tests/test_dcd.py::test_ragged_2 508s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting xyz dtype=float64 to 508s warnings.warn( 508s 508s tests/test_distance.py::test_6 508s :488: RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject 508s 508s tests/test_drid.py::test_drid_2 508s /tmp/autopkgtest.PzEck5/build.ROp/src/tests/test_drid.py:62: RuntimeWarning: divide by zero encountered in divide 508s recip = 1 / squareform(pdist(t.xyz[i])) 508s 508s tests/test_geometry.py::test_dihedral_indices 508s tests/test_geometry.py::test_dihedral_indices 508s /usr/lib/python3/dist-packages/mdtraj/geometry/dihedral.py:237: DeprecationWarning: Passing a Trajectory object to _atom_sequence isdeprecated. Please pass a Topology object 508s warnings.warn( 508s 508s tests/test_gro.py::test_load 508s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq 508s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:364: UserWarning: WARNING: two consecutive residues with same number (GST, HST) 508s warnings.warn( 508s 508s tests/test_trajectory.py::test_float_atom_indices_exception[gro] 508s /usr/lib/python3/dist-packages/mdtraj/core/topology.py:84: UserWarning: atom_indices are not monotonically increasing 508s warnings.warn("atom_indices are not monotonically increasing") 508s 508s tests/test_trajectory.py::test_array_vs_matrix 508s /tmp/autopkgtest.PzEck5/build.ROp/src/tests/test_trajectory.py:419: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 508s xyz_mat = np.matrix(xyz) 508s 508s tests/test_utils.py::test_ensure_type_8 508s tests/test_utils.py::test_ensure_type_9 508s tests/test_utils.py::test_ensure_type_13 508s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=float64 to 508s warnings.warn( 508s 508s tests/test_utils.py::test_ensure_type_11 508s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=int64 to 508s warnings.warn( 508s 508s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 508s =========================== short test summary info ============================ 508s SKIPPED [1] tests/test_dihedral.py:56: pymol executable not found 508s SKIPPED [1] tests/test_dihedral.py:181: pymol executable not found 508s SKIPPED [15] tests/test_docstrings.py:37: Skip checking certain modules' docstrings 508s SKIPPED [1] tests/test_dssp.py:48: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 508s SKIPPED [1] tests/test_dssp.py:56: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 508s SKIPPED [1] tests/test_dssp.py:63: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 508s SKIPPED [1] tests/test_geometry.py:300: Not doing performance testing 508s SKIPPED [1] tests/test_geometry.py:322: Not doing performance testing 508s SKIPPED [1] tests/test_hbonds.py:44: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 508s SKIPPED [1] tests/test_hdf5.py:103: requires openmm.units 508s SKIPPED [1] tests/test_hdf5.py:154: requires openmm.units 508s SKIPPED [1] tests/test_hdf5.py:221: requires openmm.units 508s SKIPPED [1] tests/test_mol2.py:59: Requires obabel 508s SKIPPED [1] tests/test_netcdf.py:271: This test requires cpptraj from AmberTools to be installed (http://ambermd.org) 508s SKIPPED [1] tests/test_nmr.py:11: SPARTA+ binary not found 508s SKIPPED [1] tests/test_nmr.py:26: PPM binary not found 508s SKIPPED [1] tests/test_nmr.py:42: SHIFTX2 binary not found or running on travis. 508s SKIPPED [1] tests/test_pdbx.py:43: test_pdbx.py needs OpenMM. 508s SKIPPED [2] tests/test_psf.py:93: This test requires the VMD executable: http://www.ks.uiuc.edu/Research/vmd/ 508s SKIPPED [1] tests/test_rdf.py:64: Binning does not match up with gromacs currently. 508s SKIPPED [1] tests/test_rdf.py:200: Binning does not match up with gromacs currently. 508s SKIPPED [1] tests/test_reporter.py:58: test_reporter.py needs OpenMM. 508s SKIPPED [1] tests/test_reporter.py:145: test_reporter.py needs OpenMM. 508s SKIPPED [1] tests/test_reporter.py:245: test_reporter.py needs OpenMM. 508s SKIPPED [1] tests/test_selection.py:267: failed to parse selection 508s SKIPPED [1] tests/test_thermodynamic_properties.py:161: Thermal expansion test doesn't work. 508s SKIPPED [1] tests/test_topology.py:44: needs OpenMM 508s SKIPPED [1] tests/test_topology.py:61: needs OpenMM 508s SKIPPED [1] tests/test_topology.py:192: needs OpenMM 508s SKIPPED [1] tests/test_trajectory.py:129: xyz does not store box information 508s SKIPPED [1] tests/test_trajectory.py:129: xyz.gz does not store box information 508s SKIPPED [1] tests/test_trajectory.py:129: lh5 does not store box information 508s SKIPPED [1] tests/test_trajectory.py:129: pdb does not store box information 508s SKIPPED [1] tests/test_trajectory.py:129: pdb.gz does not store box information 508s SKIPPED [1] tests/test_trajectory.py:226: mdcrd can only store rectilinear boxes 508s SKIPPED [1] tests/test_trajectory.py:224: ncrst can only store 1 frame per file 508s SKIPPED [1] tests/test_trajectory.py:224: rst7 can only store 1 frame per file 508s SKIPPED [14] tests/test_trajectory.py:248: mdcrd can only store rectilinear boxes 508s SKIPPED [14] tests/test_trajectory.py:246: ncrst can only store 1 frame per file 508s SKIPPED [14] tests/test_trajectory.py:246: rst7 can only store 1 frame per file 508s SKIPPED [4] tests/test_trajectory.py:256: dtr needs to write unitcells 508s SKIPPED [4] tests/test_trajectory.py:256: lammpstrj needs to write unitcells 508s SKIPPED [2] tests/test_trajectory.py:640: Only 1 frame per file format 508s SKIPPED [2] examples/test_examples.py:77: Network access required 508s SKIPPED [1] examples/test_examples.py:77: Openmm required for example notebook `simulation-with-openmm.ipynb` 508s XFAIL tests/test_trajectory.py::test_read_path[ncrst] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_path[rst7] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[ncrst-nc] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[ncrst-h5] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xtc] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[ncrst-trr] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dcd] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[ncrst-mdcrd] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dtr] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lh5] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[ncrst-ncrst] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[ncrst-rst7] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[ncrst-gro] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[rst7-nc] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[rst7-h5] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[rst7-xtc] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[rst7-trr] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[rst7-dcd] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[rst7-mdcrd] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[rst7-dtr] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz.gz] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[rst7-lammpstrj] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[rst7-lh5] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb.gz] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[rst7-ncrst] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[rst7-rst7] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_read_write[rst7-gro] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_load[ncrst] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_load[rst7] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[rst7] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_load_combination[ncrst] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_load_combination[rst7] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_seek_read_mode[xyz.gz] - reason: This is broken 508s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb] - reason: PDB Files don't support seeking 508s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb.gz] - reason: PDB Files don't support seeking 508s XFAIL tests/test_trajectory.py::test_seek_read_mode[ncrst] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_seek_read_mode[rst7] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_seek_read_mode[gro] - reason: This is broken 508s XFAIL tests/test_trajectory.py::test_load_frame[dtr] - reason: DTR doesn't load a single frame properly 508s XFAIL tests/test_trajectory.py::test_load_frame[ncrst] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_load_frame[rst7] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_load_frame[gro] - reason: Gro doesn't implement seek 508s XFAIL tests/test_trajectory.py::test_iterload[dtr] - reason: This is broken with dtr 508s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb] - reason: PDB Iterloads an extra frame!! 508s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb.gz] - reason: PDB Iterloads an extra frame!! 508s XFAIL tests/test_trajectory.py::test_iterload_skip[ncrst] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_iterload_skip[rst7] - reason: These reference files don't exist yet 508s XFAIL tests/test_trajectory.py::test_iterload_skip[gro] - reason: Not implemented for some reason 508s XFAIL tests/test_trajectory.py::test_force_overwrite[dtr] - reason: This is broken with dtr 508s XFAIL tests/test_trajectory.py::test_unitcell[dtr] - reason: dtr seems to need unit vectors 508s XFAIL tests/test_trajectory.py::test_unitcell[lammpstrj] - reason: lammpstrj seems to need unit vectors 508s XFAIL tests/test_trajectory.py::test_unitcell[ncrst] - reason: ncrst seems to need unit vectors 508s XFAIL tests/test_trajectory.py::test_unitcell[rst7] - reason: rst7 seems to need unit vectors 508s = 959 passed, 107 skipped, 2 deselected, 61 xfailed, 40 warnings in 320.63s (0:05:20) = 509s autopkgtest [09:45:37]: test command1: -----------------------] 510s autopkgtest [09:45:38]: test command1: - - - - - - - - - - results - - - - - - - - - - 510s command1 PASS 510s autopkgtest [09:45:38]: @@@@@@@@@@@@@@@@@@@@ summary 510s command1 PASS 524s virt: nova [W] Skipping flock in bos03-arm64 524s virt: Creating nova instance adt-plucky-arm64-mdtraj-20241113-093707-juju-7f2275-prod-proposed-migration-environment-2-c17bdc01-0664-44a9-8270-ccab5c952585 from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...