0s autopkgtest [08:53:57]: starting date and time: 2024-11-13 08:53:57+0000 1s autopkgtest [08:53:58]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 1s autopkgtest [08:53:58]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.kn18tx7n/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-12.secgroup --name adt-plucky-amd64-mdtraj-20241113-085357-juju-7f2275-prod-proposed-migration-environment-20-2582060d-857b-4159-ab7a-828362947049 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -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/ 48s autopkgtest [08:54:45]: testbed dpkg architecture: amd64 49s autopkgtest [08:54:46]: testbed apt version: 2.9.8 49s autopkgtest [08:54:46]: @@@@@@@@@@@@@@@@@@@@ test bed setup 49s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 50s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 50s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 50s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 50s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 50s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 50s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 50s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 50s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [637 kB] 50s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 50s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 50s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 50s Fetched 2173 kB in 1s (2675 kB/s) 50s Reading package lists... 52s Reading package lists... 53s Building dependency tree... 53s Reading state information... 53s Calculating upgrade... 53s The following NEW packages will be installed: 53s python3.13-gdbm 53s The following packages will be upgraded: 53s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 53s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 53s Need to get 253 kB of archives. 53s After this operation, 147 kB of additional disk space will be used. 53s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 53s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 53s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 53s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 53s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 53s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 54s Fetched 253 kB in 0s (560 kB/s) 54s (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 ... 75541 files and directories currently installed.) 54s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 54s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 54s Setting up python3-minimal (3.12.7-1) ... 54s (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 ... 75541 files and directories currently installed.) 54s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 54s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 54s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 54s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 54s Selecting previously unselected package python3.13-gdbm. 54s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 54s Unpacking python3.13-gdbm (3.13.0-2) ... 54s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 54s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 54s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 54s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 54s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 54s Setting up python3.13-gdbm (3.13.0-2) ... 54s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 54s Setting up python3 (3.12.7-1) ... 55s Setting up python3-gdbm:amd64 (3.12.7-1) ... 55s Processing triggers for man-db (2.12.1-3) ... 55s Processing triggers for libc-bin (2.40-1ubuntu3) ... 55s Reading package lists... 55s Building dependency tree... 55s Reading state information... 56s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 56s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 56s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 56s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 57s Reading package lists... 57s Reading package lists... 57s Building dependency tree... 57s Reading state information... 57s Calculating upgrade... 58s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 58s Reading package lists... 58s Building dependency tree... 58s Reading state information... 58s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s autopkgtest [08:54:58]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 61s autopkgtest [08:54:58]: @@@@@@@@@@@@@@@@@@@@ apt-source mdtraj 65s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.1-2 (dsc) [2702 B] 65s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.1-2 (tar) [21.9 MB] 65s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.1-2 (diff) [296 kB] 65s gpgv: Signature made Mon Nov 11 19:58:43 2024 UTC 65s gpgv: using RSA key 13796755BBC72BB8ABE2AEB5FA9DEC5DE11C63F1 65s gpgv: issuer "eamanu@debian.org" 65s gpgv: Can't check signature: No public key 65s dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.10.1-2.dsc: no acceptable signature found 66s autopkgtest [08:55:03]: testing package mdtraj version 1.10.1-2 67s autopkgtest [08:55:04]: build not needed 70s autopkgtest [08:55:07]: test command1: preparing testbed 77s Reading package lists... 77s Building dependency tree... 77s Reading state information... 77s Starting pkgProblemResolver with broken count: 0 77s Starting 2 pkgProblemResolver with broken count: 0 77s Done 77s The following additional packages will be installed: 77s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx gdb 77s libaec0 libbabeltrace1 libblas3 libblosc1 libblosc2-4 libdebuginfod-common 77s libdebuginfod1t64 libdeflate0 libfontconfig1 libgfortran5 libgomp1 77s libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 77s libimagequant0 libipt2 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 77s libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libnetcdf19t64 77s libnorm1t64 libopenjp2-7 libpgm-5.3-0t64 libqhull-r8.0 libraqm0 libsharpyuv0 77s libsnappy1v5 libsodium23 libsource-highlight-common libsource-highlight4t64 77s libsz2 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 77s libxft2 libxrender1 libxslt1.1 libxss1 libzmq5 python-matplotlib-data 77s python-tables-data python3-appdirs python3-asttokens python3-brotli 77s python3-cftime python3-comm python3-contourpy python3-coverage 77s python3-cpuinfo python3-cycler python3-dateutil python3-debugpy 77s python3-decorator python3-executing python3-fastjsonschema python3-fonttools 77s python3-fs python3-gsd python3-iniconfig python3-ipykernel python3-ipython 77s python3-jedi python3-joblib python3-jupyter-client python3-jupyter-core 77s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 77s python3-matplotlib-inline python3-mdtraj python3-mpmath python3-nbformat 77s python3-nest-asyncio python3-netcdf4 python3-networkx python3-numexpr 77s python3-numpy python3-packaging python3-pandas python3-pandas-lib 77s python3-parso python3-pexpect python3-pil python3-pil.imagetk 77s python3-platformdirs python3-pluggy python3-prompt-toolkit python3-psutil 77s python3-ptyprocess python3-pure-eval python3-py python3-pytest python3-scipy 77s python3-six python3-sklearn python3-sklearn-lib python3-stack-data 77s python3-sympy python3-tables python3-tables-lib python3-threadpoolctl 77s python3-tk python3-tornado python3-traitlets python3-typeshed python3-tz 77s python3-ufolib2 python3-unicodedata2 python3-wcwidth python3-zmq 77s python3.12-tk python3.13-tk tk8.6-blt2.5 unicode-data x11-common 77s Suggested packages: 77s blt-demo gdb-doc gdbserver libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 77s python-coverage-doc python-cycler-doc python-fastjsonschema-doc 77s python-gsd-doc python-ipython-doc python-joblib-doc 77s python-jupyter-client-doc python3-pip python-lxml-doc cm-super-minimal 77s dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 77s librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi-cairo 77s python3-gobject python3-pyqt5 python3-sip texlive-extra-utils 77s texlive-latex-extra python-mdtraj-doc python-mpmath-doc python3-gmpy2 77s python3-gdal python3-pydot python3-pygraphviz gcc gfortran python-numpy-doc 77s python3-dev python-pandas-doc python3-statsmodels python-pexpect-doc 77s python-pil-doc subversion python-scipy-doc python3-dap python-sklearn-doc 77s texlive-fonts-extra python-sympy-doc python-tables-doc vitables tix 77s python3-tk-dbg python3-pycurl python-tornado-doc python3-twisted 77s python-traitlets-doc 77s Recommended packages: 77s libc-dbg javascript-common python3-simplejson python3-bs4 python3-cssselect 77s python3-html5lib python3-bottleneck python3-odf python3-openpyxl 77s python3-numba python3-olefile g++ | c++-compiler isympy-common 77s The following NEW packages will be installed: 77s autopkgtest-satdep blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono 77s fonts-lyx gdb libaec0 libbabeltrace1 libblas3 libblosc1 libblosc2-4 77s libdebuginfod-common libdebuginfod1t64 libdeflate0 libfontconfig1 77s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 77s libhdf5-hl-100t64 libimagequant0 libipt2 libjbig0 libjpeg-turbo8 libjpeg8 77s libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 77s libnetcdf19t64 libnorm1t64 libopenjp2-7 libpgm-5.3-0t64 libqhull-r8.0 77s libraqm0 libsharpyuv0 libsnappy1v5 libsodium23 libsource-highlight-common 77s libsource-highlight4t64 libsz2 libtcl8.6 libtiff6 libtk8.6 libwebp7 77s libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 libzmq5 77s python-matplotlib-data python-tables-data python3-appdirs python3-asttokens 77s python3-brotli python3-cftime python3-comm python3-contourpy 77s python3-coverage python3-cpuinfo python3-cycler python3-dateutil 77s python3-debugpy python3-decorator python3-executing python3-fastjsonschema 77s python3-fonttools python3-fs python3-gsd python3-iniconfig python3-ipykernel 77s python3-ipython python3-jedi python3-joblib python3-jupyter-client 77s python3-jupyter-core python3-kiwisolver python3-lxml python3-lz4 77s python3-matplotlib python3-matplotlib-inline python3-mdtraj python3-mpmath 77s python3-nbformat python3-nest-asyncio python3-netcdf4 python3-networkx 77s python3-numexpr python3-numpy python3-packaging python3-pandas 77s python3-pandas-lib python3-parso python3-pexpect python3-pil 77s python3-pil.imagetk python3-platformdirs python3-pluggy 77s python3-prompt-toolkit python3-psutil python3-ptyprocess python3-pure-eval 77s python3-py python3-pytest python3-scipy python3-six python3-sklearn 77s python3-sklearn-lib python3-stack-data python3-sympy python3-tables 77s python3-tables-lib python3-threadpoolctl python3-tk python3-tornado 77s python3-traitlets python3-typeshed python3-tz python3-ufolib2 77s python3-unicodedata2 python3-wcwidth python3-zmq python3.12-tk python3.13-tk 77s tk8.6-blt2.5 unicode-data x11-common 77s 0 upgraded, 133 newly installed, 0 to remove and 0 not upgraded. 77s Need to get 102 MB/102 MB of archives. 77s After this operation, 481 MB of additional disk space will be used. 77s Get:1 /tmp/autopkgtest.rpGlbR/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [776 B] 77s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 78s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB] 78s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 78s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 78s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 78s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 78s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 78s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 78s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 78s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 78s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB] 78s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 78s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 78s Get:15 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB] 78s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libbabeltrace1 amd64 1.5.11-4 [164 kB] 78s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 78s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libipt2 amd64 2.1.1-1 [58.9 kB] 78s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libsource-highlight-common all 3.1.9-4.3build1 [64.2 kB] 78s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libsource-highlight4t64 amd64 3.1.9-4.3build1 [258 kB] 78s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 gdb amd64 15.1-1ubuntu2 [4119 kB] 79s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 79s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 79s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libsnappy1v5 amd64 1.2.1-1 [30.4 kB] 79s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 libblosc1 amd64 1.21.5+ds-1build1 [36.2 kB] 79s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 libblosc2-4 amd64 2.15.1+ds-1 [171 kB] 79s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 79s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 79s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 79s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 79s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 79s Get:32 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 79s Get:33 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4ubuntu3 [1280 kB] 79s Get:34 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-4ubuntu3 [56.6 kB] 79s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 79s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 79s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 79s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 79s Get:39 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 79s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 79s Get:41 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 79s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 79s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 79s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnetcdf19t64 amd64 1:4.9.2-6ubuntu1 [472 kB] 79s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnorm1t64 amd64 1.5.9+dfsg-3.1build1 [154 kB] 79s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpgm-5.3-0t64 amd64 5.3.128~dfsg-2.1build1 [167 kB] 79s Get:47 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 79s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 79s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 79s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libsodium23 amd64 1.0.18-1build3 [161 kB] 79s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 79s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 79s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 79s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 79s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 79s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 79s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 libzmq5 amd64 4.3.5-1build2 [260 kB] 79s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3 [2928 kB] 79s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-tables-data all 3.10.1-1 [49.3 kB] 79s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 79s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-asttokens all 2.4.1-2 [20.8 kB] 79s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 79s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 79s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cftime amd64 1.6.4-1 [214 kB] 79s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 79s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-comm all 0.2.1-1 [7016 B] 79s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2 [217 kB] 80s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-coverage amd64 7.4.4+dfsg1-0ubuntu2 [147 kB] 80s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cpuinfo all 9.0.0+git20221119-2 [21.6 kB] 80s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 80s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 80s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 80s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-debugpy amd64 1.8.8+ds-1ubuntu1 [936 kB] 80s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 80s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-executing all 2.1.0-0.1 [24.4 kB] 80s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fastjsonschema all 2.20.0-1 [20.1 kB] 80s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 80s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 80s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 80s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 80s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 80s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 80s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB] 80s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 80s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build1 [362 kB] 80s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 80s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 80s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-gsd amd64 3.3.0-1 [203 kB] 80s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 80s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-parso all 0.8.3-1 [67.2 kB] 80s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-typeshed all 0.0~git20231111.6764465-3 [1274 kB] 80s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-jedi all 0.19.1+ds1-1 [693 kB] 80s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 81s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-ptyprocess all 0.7.0-6 [14.8 kB] 81s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pexpect all 4.9-2 [48.1 kB] 81s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 81s Get:97 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-prompt-toolkit all 3.0.48-1 [256 kB] 81s Get:98 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pure-eval all 0.2.3-1 [11.4 kB] 81s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-stack-data all 0.6.3-1 [22.0 kB] 81s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ipython all 8.20.0-1ubuntu1 [561 kB] 81s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-platformdirs all 4.3.6-1 [16.8 kB] 81s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-jupyter-core all 5.7.2-4 [28.0 kB] 81s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-psutil amd64 5.9.8-2build2 [195 kB] 81s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tornado amd64 6.4.1-3 [299 kB] 81s Get:105 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-py all 1.11.0-2 [72.7 kB] 81s Get:106 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-zmq amd64 24.0.1-5build1 [286 kB] 81s Get:107 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-jupyter-client all 8.6.2-3 [78.1 kB] 81s Get:108 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-nest-asyncio all 1.5.4-1 [6256 B] 81s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 81s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ipykernel all 6.29.5-1 [82.5 kB] 81s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.3.2-5 [206 kB] 81s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2 [55.1 kB] 81s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 81s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 81s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB] 81s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.0-2 [106 kB] 81s Get:117 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-tk amd64 3.12.7-1 [9752 B] 81s Get:118 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu1 [9394 B] 81s Get:119 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3 [4545 kB] 81s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 82s Get:121 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB] 82s Get:122 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 82s Get:123 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-numexpr amd64 2.10.1-2 [117 kB] 82s Get:124 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-tables-lib amd64 3.10.1-1 [592 kB] 82s Get:125 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-tables all 3.10.1-1 [354 kB] 82s Get:126 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mdtraj amd64 1.10.1-2 [1117 kB] 82s Get:127 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-nbformat all 5.9.1-1 [41.2 kB] 82s Get:128 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-netcdf4 amd64 1.7.2-1 [645 kB] 82s Get:129 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 82s Get:130 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB] 82s Get:131 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 82s Get:132 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-6 [3920 kB] 83s Get:133 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn all 1.4.2+dfsg-6 [2257 kB] 83s Preconfiguring packages ... 83s Fetched 102 MB in 5s (18.8 MB/s) 83s Selecting previously unselected package libdebuginfod-common. 83s (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 ... 75548 files and directories currently installed.) 83s Preparing to unpack .../000-libdebuginfod-common_0.192-4_all.deb ... 83s Unpacking libdebuginfod-common (0.192-4) ... 83s Selecting previously unselected package libtcl8.6:amd64. 83s Preparing to unpack .../001-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... 83s Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... 83s Selecting previously unselected package fonts-dejavu-mono. 83s Preparing to unpack .../002-fonts-dejavu-mono_2.37-8_all.deb ... 83s Unpacking fonts-dejavu-mono (2.37-8) ... 83s Selecting previously unselected package fonts-dejavu-core. 83s Preparing to unpack .../003-fonts-dejavu-core_2.37-8_all.deb ... 83s Unpacking fonts-dejavu-core (2.37-8) ... 83s Selecting previously unselected package fontconfig-config. 83s Preparing to unpack .../004-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 84s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 84s Selecting previously unselected package libfontconfig1:amd64. 84s Preparing to unpack .../005-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 84s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 84s Selecting previously unselected package libxrender1:amd64. 84s Preparing to unpack .../006-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 84s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 84s Selecting previously unselected package libxft2:amd64. 84s Preparing to unpack .../007-libxft2_2.3.6-1build1_amd64.deb ... 84s Unpacking libxft2:amd64 (2.3.6-1build1) ... 84s Selecting previously unselected package x11-common. 84s Preparing to unpack .../008-x11-common_1%3a7.7+23ubuntu3_all.deb ... 84s Unpacking x11-common (1:7.7+23ubuntu3) ... 84s Selecting previously unselected package libxss1:amd64. 84s Preparing to unpack .../009-libxss1_1%3a1.2.3-1build3_amd64.deb ... 84s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 84s Selecting previously unselected package libtk8.6:amd64. 84s Preparing to unpack .../010-libtk8.6_8.6.15-1_amd64.deb ... 84s Unpacking libtk8.6:amd64 (8.6.15-1) ... 84s Selecting previously unselected package tk8.6-blt2.5. 84s Preparing to unpack .../011-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 84s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 84s Selecting previously unselected package blt. 84s Preparing to unpack .../012-blt_2.5.3+dfsg-7build1_amd64.deb ... 84s Unpacking blt (2.5.3+dfsg-7build1) ... 84s Selecting previously unselected package fonts-lyx. 84s Preparing to unpack .../013-fonts-lyx_2.4.2.1-1_all.deb ... 84s Unpacking fonts-lyx (2.4.2.1-1) ... 84s Selecting previously unselected package libbabeltrace1:amd64. 84s Preparing to unpack .../014-libbabeltrace1_1.5.11-4_amd64.deb ... 84s Unpacking libbabeltrace1:amd64 (1.5.11-4) ... 84s Selecting previously unselected package libdebuginfod1t64:amd64. 84s Preparing to unpack .../015-libdebuginfod1t64_0.192-4_amd64.deb ... 84s Unpacking libdebuginfod1t64:amd64 (0.192-4) ... 84s Selecting previously unselected package libipt2. 84s Preparing to unpack .../016-libipt2_2.1.1-1_amd64.deb ... 84s Unpacking libipt2 (2.1.1-1) ... 84s Selecting previously unselected package libsource-highlight-common. 84s Preparing to unpack .../017-libsource-highlight-common_3.1.9-4.3build1_all.deb ... 84s Unpacking libsource-highlight-common (3.1.9-4.3build1) ... 84s Selecting previously unselected package libsource-highlight4t64:amd64. 84s Preparing to unpack .../018-libsource-highlight4t64_3.1.9-4.3build1_amd64.deb ... 84s Unpacking libsource-highlight4t64:amd64 (3.1.9-4.3build1) ... 84s Selecting previously unselected package gdb. 84s Preparing to unpack .../019-gdb_15.1-1ubuntu2_amd64.deb ... 84s Unpacking gdb (15.1-1ubuntu2) ... 84s Selecting previously unselected package libaec0:amd64. 84s Preparing to unpack .../020-libaec0_1.1.3-1_amd64.deb ... 84s Unpacking libaec0:amd64 (1.1.3-1) ... 84s Selecting previously unselected package libblas3:amd64. 84s Preparing to unpack .../021-libblas3_3.12.0-3build2_amd64.deb ... 84s Unpacking libblas3:amd64 (3.12.0-3build2) ... 84s Selecting previously unselected package libsnappy1v5:amd64. 84s Preparing to unpack .../022-libsnappy1v5_1.2.1-1_amd64.deb ... 84s Unpacking libsnappy1v5:amd64 (1.2.1-1) ... 84s Selecting previously unselected package libblosc1:amd64. 84s Preparing to unpack .../023-libblosc1_1.21.5+ds-1build1_amd64.deb ... 84s Unpacking libblosc1:amd64 (1.21.5+ds-1build1) ... 84s Selecting previously unselected package libblosc2-4:amd64. 84s Preparing to unpack .../024-libblosc2-4_2.15.1+ds-1_amd64.deb ... 84s Unpacking libblosc2-4:amd64 (2.15.1+ds-1) ... 84s Selecting previously unselected package libdeflate0:amd64. 84s Preparing to unpack .../025-libdeflate0_1.22-1_amd64.deb ... 84s Unpacking libdeflate0:amd64 (1.22-1) ... 84s Selecting previously unselected package libgfortran5:amd64. 84s Preparing to unpack .../026-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 84s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 84s Selecting previously unselected package libgomp1:amd64. 84s Preparing to unpack .../027-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 84s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 84s Selecting previously unselected package libgraphite2-3:amd64. 84s Preparing to unpack .../028-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 84s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 84s Selecting previously unselected package libharfbuzz0b:amd64. 84s Preparing to unpack .../029-libharfbuzz0b_10.0.1-1_amd64.deb ... 84s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 84s Selecting previously unselected package libsz2:amd64. 84s Preparing to unpack .../030-libsz2_1.1.3-1_amd64.deb ... 84s Unpacking libsz2:amd64 (1.1.3-1) ... 84s Selecting previously unselected package libhdf5-103-1t64:amd64. 84s Preparing to unpack .../031-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_amd64.deb ... 84s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 84s Selecting previously unselected package libhdf5-hl-100t64:amd64. 84s Preparing to unpack .../032-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_amd64.deb ... 84s Unpacking libhdf5-hl-100t64:amd64 (1.10.10+repack-4ubuntu3) ... 84s Selecting previously unselected package libimagequant0:amd64. 84s Preparing to unpack .../033-libimagequant0_2.18.0-1build1_amd64.deb ... 84s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 84s Selecting previously unselected package libjpeg-turbo8:amd64. 84s Preparing to unpack .../034-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 84s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 84s Selecting previously unselected package libjpeg8:amd64. 84s Preparing to unpack .../035-libjpeg8_8c-2ubuntu11_amd64.deb ... 84s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 84s Selecting previously unselected package libjs-jquery. 84s Preparing to unpack .../036-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 84s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 84s Selecting previously unselected package libjs-jquery-ui. 84s Preparing to unpack .../037-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 84s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 84s Selecting previously unselected package liblapack3:amd64. 84s Preparing to unpack .../038-liblapack3_3.12.0-3build2_amd64.deb ... 84s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 84s Selecting previously unselected package liblbfgsb0:amd64. 84s Preparing to unpack .../039-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 84s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 84s Selecting previously unselected package liblcms2-2:amd64. 84s Preparing to unpack .../040-liblcms2-2_2.16-2_amd64.deb ... 84s Unpacking liblcms2-2:amd64 (2.16-2) ... 84s Selecting previously unselected package liblerc4:amd64. 85s Preparing to unpack .../041-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 85s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 85s Selecting previously unselected package libnetcdf19t64:amd64. 85s Preparing to unpack .../042-libnetcdf19t64_1%3a4.9.2-6ubuntu1_amd64.deb ... 85s Unpacking libnetcdf19t64:amd64 (1:4.9.2-6ubuntu1) ... 85s Selecting previously unselected package libnorm1t64:amd64. 85s Preparing to unpack .../043-libnorm1t64_1.5.9+dfsg-3.1build1_amd64.deb ... 85s Unpacking libnorm1t64:amd64 (1.5.9+dfsg-3.1build1) ... 85s Selecting previously unselected package libpgm-5.3-0t64:amd64. 85s Preparing to unpack .../044-libpgm-5.3-0t64_5.3.128~dfsg-2.1build1_amd64.deb ... 85s Unpacking libpgm-5.3-0t64:amd64 (5.3.128~dfsg-2.1build1) ... 85s Selecting previously unselected package libqhull-r8.0:amd64. 85s Preparing to unpack .../045-libqhull-r8.0_2020.2-6build1_amd64.deb ... 85s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 85s Selecting previously unselected package libraqm0:amd64. 85s Preparing to unpack .../046-libraqm0_0.10.1-1build1_amd64.deb ... 85s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 85s Selecting previously unselected package libsharpyuv0:amd64. 85s Preparing to unpack .../047-libsharpyuv0_1.4.0-0.1_amd64.deb ... 85s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 85s Selecting previously unselected package libsodium23:amd64. 85s Preparing to unpack .../048-libsodium23_1.0.18-1build3_amd64.deb ... 85s Unpacking libsodium23:amd64 (1.0.18-1build3) ... 85s Selecting previously unselected package libjbig0:amd64. 85s Preparing to unpack .../049-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 85s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 85s Selecting previously unselected package libwebp7:amd64. 85s Preparing to unpack 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(4.3.5-1build2) ... 85s Selecting previously unselected package python-matplotlib-data. 85s Preparing to unpack .../056-python-matplotlib-data_3.8.3-3_all.deb ... 85s Unpacking python-matplotlib-data (3.8.3-3) ... 85s Selecting previously unselected package python-tables-data. 85s Preparing to unpack .../057-python-tables-data_3.10.1-1_all.deb ... 85s Unpacking python-tables-data (3.10.1-1) ... 85s Selecting previously unselected package python3-appdirs. 85s Preparing to unpack .../058-python3-appdirs_1.4.4-4_all.deb ... 85s Unpacking python3-appdirs (1.4.4-4) ... 85s Selecting previously unselected package python3-asttokens. 85s Preparing to unpack .../059-python3-asttokens_2.4.1-2_all.deb ... 85s Unpacking python3-asttokens (2.4.1-2) ... 85s Selecting previously unselected package python3-brotli. 85s Preparing to unpack .../060-python3-brotli_1.1.0-2build2_amd64.deb ... 85s Unpacking python3-brotli (1.1.0-2build2) ... 85s Selecting previously unselected package python3-numpy. 85s 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package python3-decorator. 85s Preparing to unpack .../072-python3-decorator_5.1.1-5_all.deb ... 85s Unpacking python3-decorator (5.1.1-5) ... 85s Selecting previously unselected package python3-executing. 85s Preparing to unpack .../073-python3-executing_2.1.0-0.1_all.deb ... 85s Unpacking python3-executing (2.1.0-0.1) ... 85s Selecting previously unselected package python3-fastjsonschema. 85s Preparing to unpack .../074-python3-fastjsonschema_2.20.0-1_all.deb ... 85s Unpacking python3-fastjsonschema (2.20.0-1) ... 85s Selecting previously unselected package python3-scipy. 85s Preparing to unpack .../075-python3-scipy_1.13.1-5_amd64.deb ... 85s Unpacking python3-scipy (1.13.1-5) ... 86s Selecting previously unselected package python3-ufolib2. 86s Preparing to unpack .../076-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 86s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 86s Selecting previously unselected package python3-mpmath. 86s Preparing to unpack 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python3-unicodedata2. 86s Preparing to unpack .../083-python3-unicodedata2_15.1.0+ds-1build1_amd64.deb ... 86s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 86s Selecting previously unselected package unicode-data. 86s Preparing to unpack .../084-unicode-data_15.1.0-1_all.deb ... 86s Unpacking unicode-data (15.1.0-1) ... 86s Selecting previously unselected package python3-fonttools. 86s Preparing to unpack .../085-python3-fonttools_4.46.0-1build2_amd64.deb ... 86s Unpacking python3-fonttools (4.46.0-1build2) ... 87s Selecting previously unselected package python3-gsd. 87s Preparing to unpack .../086-python3-gsd_3.3.0-1_amd64.deb ... 87s Unpacking python3-gsd (3.3.0-1) ... 87s Selecting previously unselected package python3-iniconfig. 87s Preparing to unpack .../087-python3-iniconfig_1.1.1-2_all.deb ... 87s Unpacking python3-iniconfig (1.1.1-2) ... 87s Selecting previously unselected package python3-parso. 87s Preparing to unpack .../088-python3-parso_0.8.3-1_all.deb ... 87s 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previously unselected package python3-wcwidth. 87s Preparing to unpack .../094-python3-wcwidth_0.2.13+dfsg1-1_all.deb ... 87s Unpacking python3-wcwidth (0.2.13+dfsg1-1) ... 87s Selecting previously unselected package python3-prompt-toolkit. 87s Preparing to unpack .../095-python3-prompt-toolkit_3.0.48-1_all.deb ... 87s Unpacking python3-prompt-toolkit (3.0.48-1) ... 88s Selecting previously unselected package python3-pure-eval. 88s Preparing to unpack .../096-python3-pure-eval_0.2.3-1_all.deb ... 88s Unpacking python3-pure-eval (0.2.3-1) ... 88s Selecting previously unselected package python3-stack-data. 88s Preparing to unpack .../097-python3-stack-data_0.6.3-1_all.deb ... 88s Unpacking python3-stack-data (0.6.3-1) ... 88s Selecting previously unselected package python3-ipython. 88s Preparing to unpack .../098-python3-ipython_8.20.0-1ubuntu1_all.deb ... 88s Unpacking python3-ipython (8.20.0-1ubuntu1) ... 88s Selecting previously unselected package python3-platformdirs. 88s Preparing to unpack .../099-python3-platformdirs_4.3.6-1_all.deb ... 88s Unpacking python3-platformdirs (4.3.6-1) ... 88s Selecting previously unselected package python3-jupyter-core. 88s Preparing to unpack .../100-python3-jupyter-core_5.7.2-4_all.deb ... 88s Unpacking python3-jupyter-core (5.7.2-4) ... 88s Selecting previously unselected package python3-psutil. 88s Preparing to unpack .../101-python3-psutil_5.9.8-2build2_amd64.deb ... 88s Unpacking python3-psutil (5.9.8-2build2) ... 88s Selecting previously unselected package python3-tornado. 88s Preparing to unpack .../102-python3-tornado_6.4.1-3_amd64.deb ... 88s Unpacking python3-tornado (6.4.1-3) ... 88s Selecting previously unselected package python3-py. 88s Preparing to unpack .../103-python3-py_1.11.0-2_all.deb ... 88s Unpacking python3-py (1.11.0-2) ... 88s Selecting previously unselected package python3-zmq. 88s Preparing to unpack .../104-python3-zmq_24.0.1-5build1_amd64.deb ... 88s Unpacking python3-zmq (24.0.1-5build1) ... 88s 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package autopkgtest-satdep. 90s Preparing to unpack .../132-1-autopkgtest-satdep.deb ... 90s Unpacking autopkgtest-satdep (0) ... 90s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 90s Setting up liblcms2-2:amd64 (2.16-2) ... 90s Setting up python3-iniconfig (1.1.1-2) ... 90s Setting up python3-tornado (6.4.1-3) ... 90s Setting up libnorm1t64:amd64 (1.5.9+dfsg-3.1build1) ... 90s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... 90s Setting up python3-pure-eval (0.2.3-1) ... 91s Setting up libsodium23:amd64 (1.0.18-1build3) ... 91s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 91s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 91s Setting up python3-py (1.11.0-2) ... 91s Setting up libdebuginfod-common (0.192-4) ... 91s Setting up python3-joblib (1.3.2-5) ... 91s Setting up python3-parso (0.8.3-1) ... 91s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 91s Setting up python3-asttokens (2.4.1-2) ... 91s Setting up python3-unicodedata2 (15.1.0+ds-1build1) ... 91s Setting up fonts-lyx (2.4.2.1-1) ... 91s Setting up python3-threadpoolctl (3.1.0-1) ... 91s Setting up x11-common (1:7.7+23ubuntu3) ... 92s Setting up libdeflate0:amd64 (1.22-1) ... 92s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 92s Setting up python3-coverage (7.4.4+dfsg1-0ubuntu2) ... 92s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 92s Setting up python3-networkx (3.2.1-4ubuntu1) ... 93s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 93s Setting up libaec0:amd64 (1.1.3-1) ... 93s Setting up python3-platformdirs (4.3.6-1) ... 93s Setting up python3-psutil (5.9.8-2build2) ... 93s Setting up libsource-highlight-common (3.1.9-4.3build1) ... 93s Setting up python3-tz (2024.1-2) ... 93s Setting up libsnappy1v5:amd64 (1.2.1-1) ... 93s Setting up unicode-data (15.1.0-1) ... 93s Setting up python3-six (1.16.0-7) ... 93s Setting up libpgm-5.3-0t64:amd64 (5.3.128~dfsg-2.1build1) ... 93s Setting up python3-decorator (5.1.1-5) ... 94s Setting up libblosc2-4:amd64 (2.15.1+ds-1) ... 94s Setting up libblas3:amd64 (3.12.0-3build2) ... 94s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 94s Setting up python3-packaging (24.1-1) ... 94s Setting up python3-wcwidth (0.2.13+dfsg1-1) ... 94s Setting up python3-typeshed (0.0~git20231111.6764465-3) ... 94s Setting up python3-executing (2.1.0-0.1) ... 94s Setting up python3-nest-asyncio (1.5.4-1) ... 94s Setting up python3-brotli (1.1.0-2build2) ... 94s Setting up python3-cycler (0.12.1-1) ... 94s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 94s Setting up fonts-dejavu-mono (2.37-8) ... 94s Setting up python3-kiwisolver (1.4.7-2) ... 94s Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ... 94s Setting up libipt2 (2.1.1-1) ... 94s Setting up fonts-dejavu-core (2.37-8) ... 94s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 94s Setting up python3-cpuinfo (9.0.0+git20221119-2) ... 94s Setting up libbabeltrace1:amd64 (1.5.11-4) ... 94s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 94s Setting up python3-pluggy (1.5.0-1) ... 95s Setting up libwebp7:amd64 (1.4.0-0.1) ... 95s Setting up python3-fastjsonschema (2.20.0-1) ... 95s Setting up python3-traitlets (5.14.3+really5.14.3-1) ... 95s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 95s Setting up libblosc1:amd64 (1.21.5+ds-1build1) ... 95s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 95s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 95s Setting up python3-dateutil (2.9.0-2) ... 95s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 95s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 95s Setting up python3-mpmath (1.3.0-1) ... 95s Setting up python-matplotlib-data (3.8.3-3) ... 95s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 95s Setting up python3-appdirs (1.4.4-4) ... 95s Setting up python3-stack-data (0.6.3-1) ... 96s Setting up python-tables-data (3.10.1-1) ... 96s Setting up python3-jupyter-core (5.7.2-4) ... 96s Setting up libsz2:amd64 (1.1.3-1) ... 96s Setting up python3-ptyprocess (0.7.0-6) ... 96s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 96s Setting up python3-prompt-toolkit (3.0.48-1) ... 96s Setting up python3-sympy (1.13.3-1) ... 101s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 101s Setting up liblapack3:amd64 (3.12.0-3build2) ... 101s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 101s Setting up libzmq5:amd64 (4.3.5-1build2) ... 101s Setting up python3-jedi (0.19.1+ds1-1) ... 101s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 101s Setting up python3-pytest (8.3.3-1) ... 102s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 102s Setting up libsource-highlight4t64:amd64 (3.1.9-4.3build1) ... 102s Setting up python3-nbformat (5.9.1-1) ... 102s Setting up python3-matplotlib-inline (0.1.6-2) ... 102s Setting up python3-comm (0.2.1-1) ... 102s Setting up 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Setting up libtk8.6:amd64 (8.6.15-1) ... 107s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... 107s Setting up python3.12-tk (3.12.7-3) ... 107s Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-6) ... 107s Setting up python3-gsd (3.3.0-1) ... 107s Setting up python3-debugpy (1.8.8+ds-1ubuntu1) ... 107s Setting up python3.13-tk (3.13.0-2) ... 107s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 108s Setting up python3-pandas (2.2.3+dfsg-5) ... 111s Setting up python3-ipython (8.20.0-1ubuntu1) ... 112s Setting up python3-ipykernel (6.29.5-1) ... 112s Setting up python3-sklearn (1.4.2+dfsg-6) ... 113s Setting up python3-cftime (1.6.4-1) ... 113s Setting up python3-numexpr (2.10.1-2) ... 113s Setting up python3-netcdf4 (1.7.2-1) ... 114s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 114s Setting up blt (2.5.3+dfsg-7build1) ... 114s Setting up python3-tk:amd64 (3.12.7-1) ... 114s Setting up python3-tables (3.10.1-1) ... 114s Setting up python3-mdtraj (1.10.1-2) ... 114s Setting up python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 114s Setting up python3-fonttools (4.46.0-1build2) ... 115s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 115s Setting up python3-matplotlib (3.8.3-3) ... 116s Setting up autopkgtest-satdep (0) ... 116s Processing triggers for libc-bin (2.40-1ubuntu3) ... 117s Processing triggers for man-db (2.12.1-3) ... 121s (Reading database ... 98123 files and directories currently installed.) 121s Removing autopkgtest-satdep (0) ... 122s autopkgtest [08:55:59]: test command1: pytest-3 -k 'not nmr.ipynb and not test_image_molecules' 122s autopkgtest [08:55:59]: test command1: [----------------------- 123s ============================= test session starts ============================== 123s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3 123s cachedir: .pytest_cache 123s rootdir: /tmp/autopkgtest.rpGlbR/build.G5Q/src 123s configfile: pytest.ini 123s testpaths: tests, examples 123s plugins: typeguard-4.4.1 124s collecting ... collected 1129 items / 2 deselected / 1127 selected 124s 124s tests/test_alignment.py::test_rmsd_zero PASSED [ 0%] 124s tests/test_alignment.py::test_rmsd_nonzero PASSED [ 0%] 124s tests/test_alignment.py::test_transform PASSED [ 0%] 124s tests/test_alignment.py::test_transform2 PASSED [ 0%] 124s tests/test_angles.py::test_angle_pbc_0 PASSED [ 0%] 124s tests/test_angles.py::test_generator PASSED [ 0%] 124s tests/test_angles.py::test_angle_180[True] PASSED [ 0%] 124s tests/test_angles.py::test_angle_180[False] PASSED [ 0%] 124s tests/test_arc.py::test_read_0 PASSED [ 0%] 124s tests/test_arc.py::test_read_arctraj PASSED [ 0%] 124s tests/test_arc.py::test_read_pbc PASSED [ 0%] 124s tests/test_capi.py::test_1 PASSED [ 1%] 124s tests/test_contact.py::test_contact_0 PASSED [ 1%] 124s tests/test_contact.py::test_contact_1 PASSED [ 1%] 125s tests/test_contact.py::test_contact_2 PASSED [ 1%] 125s tests/test_contact.py::test_contact_3 PASSED [ 1%] 125s 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tests/test_dcd.py::test_tell PASSED [ 3%] 126s tests/test_dcd.py::test_seek PASSED [ 3%] 126s tests/test_dcd.py::test_ragged_1 PASSED [ 3%] 126s tests/test_dcd.py::test_ragged_2 PASSED [ 3%] 126s tests/test_dihedral.py::test_compute_phi PASSED [ 3%] 126s tests/test_dihedral.py::test_compute_psi PASSED [ 3%] 126s tests/test_dihedral.py::test_compute_chi SKIPPED (pymol executable n...) [ 3%] 126s tests/test_dihedral.py::test_compute_omega PASSED [ 3%] 126s tests/test_dihedral.py::test_shape_when_none PASSED [ 3%] 126s tests/test_dihedral.py::test_dihedral_1 SKIPPED (pymol executable no...) [ 3%] 126s tests/test_dihedral.py::test_dihedral_2chains PASSED [ 4%] 126s tests/test_dihedral.py::test_generator PASSED [ 4%] 126s tests/test_distance.py::test_generator PASSED [ 4%] 126s tests/test_distance.py::test_0 PASSED [ 4%] 126s tests/test_distance.py::test_compute_distances_core_nonperiodic PASSED [ 4%] 127s tests/test_distance.py::test_compute_distances_core_periodic PASSED [ 4%] 128s tests/test_distance.py::test_1 PASSED [ 4%] 128s tests/test_distance.py::test_2 PASSED [ 4%] 128s tests/test_distance.py::test_3 PASSED [ 4%] 128s tests/test_distance.py::test_0p PASSED [ 4%] 129s tests/test_distance.py::test_1p PASSED [ 4%] 130s tests/test_distance.py::test_2p PASSED [ 5%] 130s tests/test_distance.py::test_3p PASSED [ 5%] 130s tests/test_distance.py::test_4 PASSED [ 5%] 130s tests/test_distance.py::test_5 PASSED [ 5%] 131s tests/test_distance.py::test_6 PASSED [ 5%] 131s tests/test_distance.py::test_7 PASSED [ 5%] 131s tests/test_distance.py::test_closest_contact PASSED [ 5%] 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tests/test_docstrings.py::test_docstrings[mdtraj.core.trajectory] PASSED [ 6%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.amberrst] PASSED [ 6%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.arc] PASSED [ 7%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.dcd] PASSED [ 7%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.dtr] PASSED [ 7%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.gro] PASSED [ 7%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.gsd] PASSED [ 7%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.hdf5] SKIPPED [ 7%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.hoomdxml] PASSED [ 7%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.lammpstrj] PASSED [ 7%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.lh5] SKIPPED [ 7%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.mdcrd] PASSED [ 7%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.mol2] PASSED [ 7%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.netcdf] PASSED [ 7%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.openmmxml] PASSED [ 8%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdb.pdbfile] PASSED [ 8%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdb.pdbstructure] SKIPPED [ 8%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdbx] PASSED [ 8%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.prmtop] PASSED [ 8%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.psf] PASSED [ 8%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.registry] PASSED [ 8%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.trr] PASSED [ 8%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.xtc] PASSED [ 8%] 131s tests/test_docstrings.py::test_docstrings[mdtraj.formats.xyzfile] PASSED [ 8%] 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[ 13%] 131s tests/test_dssp.py::test_4 PASSED [ 13%] 131s tests/test_dssp.py::test_5 PASSED [ 13%] 132s tests/test_dssp.py::test_7 PASSED [ 13%] 132s tests/test_dtr.py::test_read PASSED [ 14%] 132s tests/test_dtr.py::test_read_1 PASSED [ 14%] 132s tests/test_dtr.py::test_read_2 PASSED [ 14%] 132s tests/test_dtr.py::test_read_3 PASSED [ 14%] 132s tests/test_dtr.py::test_read_stride PASSED [ 14%] 132s tests/test_dtr.py::test_read_4 PASSED [ 14%] 132s tests/test_dtr.py::test_read_5 PASSED [ 14%] 132s tests/test_dtr.py::test_read_6 PASSED [ 14%] 132s tests/test_dtr.py::test_read_7 PASSED [ 14%] 132s tests/test_dtr.py::test_read_8 PASSED [ 14%] 133s tests/test_dtr.py::test_write_1 PASSED [ 14%] 134s tests/test_dtr.py::test_write_2 PASSED [ 14%] 134s tests/test_dtr.py::test_write_3 PASSED [ 15%] 134s tests/test_dtr.py::test_write_4 PASSED [ 15%] 134s tests/test_dtr.py::test_seek PASSED [ 15%] 134s tests/test_dtr.py::test_read_closed PASSED [ 15%] 134s tests/test_dtr.py::test_tell PASSED [ 15%] 134s tests/test_element.py::test_immutable PASSED [ 15%] 134s tests/test_element.py::test_element_0 PASSED [ 15%] 134s tests/test_element.py::test_element_pickle PASSED [ 15%] 134s tests/test_geometry.py::test_rg PASSED [ 15%] 134s tests/test_geometry.py::test_distances PASSED [ 15%] 134s tests/test_geometry.py::test_center_of_mass PASSED [ 15%] 134s tests/test_geometry.py::test_center_of_geometry PASSED [ 16%] 134s tests/test_geometry.py::test_dihedral_indices PASSED [ 16%] 134s tests/test_geometry.py::test_dihedral_index_offset_generation PASSED [ 16%] 134s tests/test_geometry.py::test_dihedral_0 PASSED [ 16%] 134s tests/test_geometry.py::test_dihedral_1 PASSED [ 16%] 134s tests/test_geometry.py::test_dihedral_triclinic PASSED [ 16%] 134s tests/test_geometry.py::test_angle_0 PASSED [ 16%] 134s tests/test_geometry.py::test_angle_periodic_0 PASSED [ 16%] 134s tests/test_geometry.py::test_angle_triclinic_0 PASSED [ 16%] 134s tests/test_geometry.py::test_angle_1 PASSED [ 16%] 134s tests/test_geometry.py::test_dihedral_performance SKIPPED (Not doing...) 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[ 18%] 141s tests/test_hbonds.py::test_baker_hubbard_0 PASSED [ 19%] 141s tests/test_hbonds.py::test_baker_hubbard_1 PASSED [ 19%] 141s tests/test_hbonds.py::test_baker_hubbard_2 PASSED [ 19%] 141s tests/test_hbonds.py::test_baker_hubbard_3 PASSED [ 19%] 141s tests/test_hbonds.py::test_wernet_nilsson_0 PASSED [ 19%] 142s tests/test_hbonds.py::test_wernet_nilsson_1 PASSED [ 19%] 142s tests/test_hdf5.py::test_write_coordinates PASSED [ 19%] 142s tests/test_hdf5.py::test_write_coordinates_reshape PASSED [ 19%] 142s tests/test_hdf5.py::test_write_multiple PASSED [ 19%] 142s tests/test_hdf5.py::test_write_inconsistent PASSED [ 19%] 142s tests/test_hdf5.py::test_write_inconsistent_2 PASSED [ 19%] 142s tests/test_hdf5.py::test_write_units SKIPPED (requires openmm.units) [ 20%] 142s tests/test_hdf5.py::test_write_units2 PASSED [ 20%] 142s tests/test_hdf5.py::test_write_units_mismatch SKIPPED (requires open...) [ 20%] 142s tests/test_hdf5.py::test_topology PASSED [ 20%] 142s tests/test_hdf5.py::test_constraints PASSED [ 20%] 142s tests/test_hdf5.py::test_constraints2 PASSED [ 20%] 142s tests/test_hdf5.py::test_read_0 PASSED [ 20%] 142s tests/test_hdf5.py::test_read_1 SKIPPED (requires openmm.units) [ 20%] 142s tests/test_hdf5.py::test_read_slice_0 PASSED [ 20%] 142s tests/test_hdf5.py::test_read_slice_1 PASSED [ 20%] 142s tests/test_hdf5.py::test_read_slice_2 PASSED [ 20%] 142s tests/test_hdf5.py::test_read_slice_3 PASSED [ 21%] 142s tests/test_hdf5.py::test_do_overwrite PASSED [ 21%] 142s tests/test_hdf5.py::test_vsite_elements PASSED [ 21%] 142s tests/test_hdf5.py::test_dont_overwrite PASSED [ 21%] 142s tests/test_hdf5.py::test_attributes PASSED [ 21%] 142s tests/test_hdf5.py::test_append PASSED [ 21%] 144s tests/test_hoomdxml.py::test_load PASSED [ 21%] 144s tests/test_hoomdxml.py::test_load_no_chains PASSED [ 21%] 144s tests/test_hoomdxml.py::test_load_no_ions PASSED [ 21%] 144s tests/test_hoomdxml.py::test_correct_ordering PASSED [ 21%] 144s tests/test_io.py::test_overwrite_1 PASSED [ 21%] 144s tests/test_io.py::test_overwrite_2 PASSED [ 22%] 144s tests/test_io.py::test_io::test_load_1 PASSED [ 22%] 144s tests/test_io.py::test_io::test_load_2 PASSED [ 22%] 144s tests/test_io.py::test_io::test_load_3 PASSED [ 22%] 144s tests/test_io.py::test_io::test_save PASSED [ 22%] 144s tests/test_io.py::test_io_int::test_load_1 PASSED [ 22%] 144s tests/test_io.py::test_io_int::test_load_2 PASSED [ 22%] 144s tests/test_io.py::test_io_int::test_load_3 PASSED [ 22%] 144s tests/test_io.py::test_io_int::test_save PASSED [ 22%] 144s tests/test_io.py::test_groups PASSED [ 22%] 144s tests/test_lammpstrj.py::test_read_0 PASSED [ 22%] 144s tests/test_lammpstrj.py::test_read_1 PASSED [ 22%] 144s tests/test_lammpstrj.py::test_read_write_0 PASSED [ 23%] 144s tests/test_lammpstrj.py::test_mdwrite PASSED [ 23%] 144s tests/test_lammpstrj.py::test_multiread PASSED [ 23%] 144s tests/test_lammpstrj.py::test_seek PASSED [ 23%] 144s tests/test_lammpstrj.py::test_custom PASSED [ 23%] 144s tests/test_lh5.py::test_write_coordinates PASSED [ 23%] 144s tests/test_lh5.py::test_write_coordinates_reshape PASSED [ 23%] 144s tests/test_lh5.py::test_write_multiple PASSED [ 23%] 144s tests/test_lh5.py::test_topology PASSED [ 23%] 144s tests/test_lh5.py::test_read_slice_0 PASSED [ 23%] 144s tests/test_lh5.py::test_vsite_elements PASSED [ 23%] 144s tests/test_lh5.py::test_do_overwrite_0 PASSED [ 24%] 144s tests/test_lh5.py::test_do_overwrite_1 PASSED [ 24%] 144s tests/test_load.py::test_load_single PASSED [ 24%] 145s tests/test_load.py::test_load_single_list PASSED [ 24%] 146s tests/test_load.py::test_load_many_list PASSED [ 24%] 146s tests/test_load.py::test_load_atom_indices_multiple_files PASSED [ 24%] 146s tests/test_lprmsd.py::test_munkres_0 PASSED [ 24%] 146s tests/test_lprmsd.py::test_lprmsd_null PASSED [ 24%] 146s tests/test_lprmsd.py::test_lprmsd_0 PASSED [ 24%] 146s tests/test_lprmsd.py::test_lprmsd_1 PASSED [ 24%] 146s tests/test_lprmsd.py::test_lprmsd_2 PASSED [ 24%] 146s tests/test_lprmsd.py::test_lprmsd_3 PASSED [ 25%] 146s tests/test_lprmsd.py::test_lprmsd_4 PASSED [ 25%] 146s tests/test_lprmsd.py::test_lprmsd_5 PASSED [ 25%] 146s tests/test_mdconvert.py::test_index PASSED [ 25%] 146s tests/test_mdconvert.py::test_slice PASSED [ 25%] 154s tests/test_mdconvert.py::test_pairwise[from-xtc] PASSED [ 25%] 162s tests/test_mdconvert.py::test_pairwise[from-dcd] PASSED [ 25%] 170s tests/test_mdconvert.py::test_pairwise[from-trr] PASSED [ 25%] 186s tests/test_mdconvert.py::test_pairwise[from-nc] PASSED [ 25%] 194s tests/test_mdconvert.py::test_pairwise[from-pdb] PASSED [ 25%] 202s tests/test_mdconvert.py::test_pairwise[from-h5] PASSED [ 25%] 211s tests/test_mdconvert.py::test_pairwise[from-lh5] PASSED [ 25%] 218s tests/test_mdconvert.py::test_pairwise[from-netcdf] PASSED [ 26%] 219s tests/test_mdcrd.py::test_read_0 PASSED [ 26%] 219s 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tests/test_mol2.py::test_load_all_mol2[li.mol2] PASSED [ 27%] 219s tests/test_mol2.py::test_load_all_mol2[lysozyme-ligand-tripos.mol2] PASSED [ 27%] 219s tests/test_mol2.py::test_load_all_mol2[imatinib.mol2] PASSED [ 27%] 219s tests/test_mol2.py::test_load_all_mol2[status-bits.mol2] PASSED [ 27%] 219s tests/test_mol2.py::test_load_all_mol2[adp.mol2] PASSED [ 28%] 219s tests/test_mol2.py::test_load_all_mol2[water_acn.mol2] PASSED [ 28%] 219s tests/test_mol2.py::test_mol2_n_residues PASSED [ 28%] 219s tests/test_neighborlist.py::test_nonperiodic PASSED [ 28%] 219s tests/test_neighborlist.py::test_periodic PASSED [ 28%] 220s tests/test_neighborlist.py::test_triclinic PASSED [ 28%] 220s tests/test_neighbors.py::test_compute_neighbors_1 PASSED [ 28%] 220s tests/test_neighbors.py::test_compute_neighbors_2 PASSED [ 28%] 221s tests/test_neighbors.py::test_compute_neighbors_3 PASSED [ 28%] 221s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_after_close PASSED [ 28%] 221s tests/test_netcdf.py::TestNetCDFNetCDF4::test_shape PASSED [ 28%] 221s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_1 PASSED [ 29%] 221s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_2 PASSED [ 29%] 221s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_3 PASSED [ 29%] 221s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_1 PASSED [ 29%] 221s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_2 PASSED [ 29%] 221s tests/test_netcdf.py::TestNetCDFNetCDF4::test_ragged_1 PASSED [ 29%] 221s tests/test_netcdf.py::TestNetCDFNetCDF4::test_ragged_2 PASSED [ 29%] 221s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_25 PASSED [ 29%] 221s tests/test_netcdf.py::TestNetCDFNetCDF4::test_write_3 PASSED [ 29%] 221s tests/test_netcdf.py::TestNetCDFNetCDF4::test_n_atoms PASSED [ 29%] 221s tests/test_netcdf.py::TestNetCDFNetCDF4::test_do_overwrite PASSED [ 29%] 221s tests/test_netcdf.py::TestNetCDFNetCDF4::test_do_not_overwrite PASSED [ 29%] 221s tests/test_netcdf.py::TestNetCDFNetCDF4::test_trajectory_save_load PASSED [ 30%] 221s tests/test_netcdf.py::TestNetCDFScipy::test_read_after_close PASSED [ 30%] 221s tests/test_netcdf.py::TestNetCDFScipy::test_shape PASSED [ 30%] 221s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_1 PASSED [ 30%] 221s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_2 PASSED [ 30%] 221s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_3 PASSED [ 30%] 221s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_1 PASSED [ 30%] 221s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_2 PASSED [ 30%] 221s tests/test_netcdf.py::TestNetCDFScipy::test_ragged_1 PASSED [ 30%] 221s tests/test_netcdf.py::TestNetCDFScipy::test_ragged_2 PASSED [ 30%] 221s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_25 PASSED [ 30%] 221s tests/test_netcdf.py::TestNetCDFScipy::test_write_3 PASSED [ 31%] 221s tests/test_netcdf.py::TestNetCDFScipy::test_n_atoms PASSED [ 31%] 221s tests/test_netcdf.py::TestNetCDFScipy::test_do_overwrite PASSED [ 31%] 221s tests/test_netcdf.py::TestNetCDFScipy::test_do_not_overwrite PASSED [ 31%] 221s tests/test_netcdf.py::TestNetCDFScipy::test_trajectory_save_load PASSED [ 31%] 221s tests/test_netcdf.py::test_cpptraj SKIPPED (This test requires cpptr...) [ 31%] 221s tests/test_nmr.py::test_spartaplus SKIPPED (SPARTA+ binary not found) [ 31%] 221s tests/test_nmr.py::test_ppm SKIPPED (PPM binary not found) [ 31%] 221s tests/test_nmr.py::test_shiftx2 SKIPPED (SHIFTX2 binary not found or...) [ 31%] 221s tests/test_nmr.py::test_2_scalar_couplings PASSED [ 31%] 221s tests/test_nmr.py::test_3_scalar_couplings PASSED [ 31%] 221s tests/test_order.py::test_nematic_order PASSED [ 32%] 221s tests/test_order.py::test_director PASSED [ 32%] 221s tests/test_order.py::test_inertia PASSED [ 32%] 221s tests/test_order.py::test_nematic_order_args PASSED [ 32%] 221s tests/test_order.py::test_order_from_traj PASSED [ 32%] 221s tests/test_order.py::test_directors_angle_from_traj PASSED [ 32%] 221s tests/test_pdb.py::test_pdbread PASSED [ 32%] 221s tests/test_pdb.py::test_pdbread_with_input_top PASSED [ 32%] 221s tests/test_pdb.py::test_pdbwrite PASSED [ 32%] 221s tests/test_pdb.py::test_load_multiframe PASSED [ 32%] 222s tests/test_pdb.py::test_4ZUO PASSED [ 32%] 222s tests/test_pdb.py::test_2EQQ_0 PASSED [ 33%] 223s tests/test_pdb.py::test_1vii_solvated_with_ligand PASSED [ 33%] 223s tests/test_pdb.py::test_write_large PASSED [ 33%] 223s tests/test_pdb.py::test_write_large_2 PASSED [ 33%] 223s tests/test_pdb.py::test_pdbstructure_0 PASSED [ 33%] 223s tests/test_pdb.py::test_pdbstructure_1 PASSED [ 33%] 223s tests/test_pdb.py::test_pdbstructure_2 PASSED [ 33%] 223s tests/test_pdb.py::test_pdbstructure_3 PASSED [ 33%] 224s tests/test_pdb.py::test_pdb_from_url FAILED [ 33%] 224s tests/test_pdb.py::test_3nch_conect PASSED [ 33%] 226s tests/test_pdb.py::test_3nch_serial_resSeq PASSED [ 33%] 226s tests/test_pdb.py::test_1ncw PASSED [ 33%] 226s tests/test_pdb.py::test_1vii_url_and_gz FAILED [ 34%] 226s tests/test_pdb.py::test_segment_id PASSED [ 34%] 226s tests/test_pdb.py::test_bfactors PASSED [ 34%] 229s tests/test_pdb.py::test_hex PASSED [ 34%] 230s tests/test_pdb.py::test_dummy_pdb_box_detection PASSED [ 34%] 230s tests/test_pdb.py::test_multichain_load_cycle PASSED [ 34%] 230s tests/test_pdb.py::test_multichain_load_cycle_noter PASSED [ 34%] 230s tests/test_pdb.py::test_load_pdb_input_top PASSED [ 34%] 230s tests/test_pdb.py::test_chimera_indexing PASSED [ 34%] 230s tests/test_pdb.py::test_vmd_indexing PASSED [ 34%] 230s tests/test_pdbx.py::test_convert SKIPPED (test_pdbx.py needs OpenMM.) [ 34%] 230s tests/test_prmtop.py::test_load_prmtop PASSED [ 35%] 230s tests/test_prmtop.py::test_load_chamber_prmtop PASSED [ 35%] 230s tests/test_psf.py::test_load_psf PASSED [ 35%] 233s tests/test_psf.py::test_multichain_psf PASSED [ 35%] 233s tests/test_psf.py::test_load_mdcrd_with_psf PASSED [ 35%] 233s tests/test_psf.py::test_against_vmd[1vii.pdb] SKIPPED (This test req...) [ 35%] 233s tests/test_psf.py::test_against_vmd[2EQQ.pdb] SKIPPED (This test req...) [ 35%] 233s tests/test_quaternion.py::test_quaternion_0 PASSED [ 35%] 233s tests/test_quaternion.py::test_quaternion_1 PASSED [ 35%] 233s tests/test_quaternion.py::test_quaternion_2 PASSED [ 35%] 236s tests/test_rdf.py::test_rdf_norm PASSED [ 35%] 236s tests/test_rdf.py::test_compare_rdf_to_gromacs SKIPPED (Binning does...) [ 36%] 236s tests/test_rdf.py::test_rdf_t[True-True] PASSED [ 36%] 239s tests/test_rdf.py::test_rdf_t[True-False] PASSED [ 36%] 239s tests/test_rdf.py::test_rdf_t[False-True] PASSED [ 36%] 240s tests/test_rdf.py::test_rdf_t[False-False] PASSED [ 36%] 240s tests/test_rdf.py::test_rdf_t_norm[0] PASSED [ 36%] 240s tests/test_rdf.py::test_rdf_t_norm[2] PASSED [ 36%] 241s tests/test_rdf.py::test_rdf_t_norm[4] PASSED [ 36%] 241s tests/test_rdf.py::test_compare_rdf_t_at_0[True-True] PASSED [ 36%] 242s tests/test_rdf.py::test_compare_rdf_t_at_0[True-False] PASSED [ 36%] 242s tests/test_rdf.py::test_compare_rdf_t_at_0[False-True] PASSED [ 36%] 242s tests/test_rdf.py::test_compare_rdf_t_at_0[False-False] PASSED [ 37%] 242s tests/test_rdf.py::test_amber_rdf_t[True-True] PASSED [ 37%] 242s tests/test_rdf.py::test_amber_rdf_t[True-False] PASSED [ 37%] 243s tests/test_rdf.py::test_amber_rdf_t[False-True] PASSED [ 37%] 243s tests/test_rdf.py::test_amber_rdf_t[False-False] PASSED [ 37%] 243s tests/test_rdf.py::test_compare_gromacs_rdf_t SKIPPED (Binning does ...) [ 37%] 243s tests/test_rdf.py::test_compare_rdf_t_master PASSED [ 37%] 243s tests/test_rdf.py::test_compare_n_concurrent_pairs PASSED [ 37%] 243s tests/test_reporter.py::test_reporter SKIPPED (test_reporter.py need...) [ 37%] 243s tests/test_reporter.py::test_reporter_subset SKIPPED (test_reporter....) [ 37%] 243s tests/test_reporter.py::test_xtc_reporter_append SKIPPED (test_repor...) [ 37%] 243s tests/test_restart.py::test_read_after_close PASSED [ 37%] 243s tests/test_restart.py::test_shape PASSED [ 38%] 243s tests/test_restart.py::test_shape_2 PASSED [ 38%] 243s tests/test_restart.py::test_read_write_1 PASSED [ 38%] 243s tests/test_restart.py::test_read_write_2 PASSED [ 38%] 243s tests/test_restart.py::test_read_write_3 PASSED [ 38%] 244s tests/test_restart.py::test_read_write_4 PASSED [ 38%] 244s tests/test_rmsd.py::test_trajectory_rmsd PASSED [ 38%] 244s tests/test_rmsd.py::test_precentered_1 PASSED [ 38%] 244s tests/test_rmsd.py::test_precentered_2 PASSED [ 38%] 244s tests/test_rmsd.py::test_superpose_0 PASSED [ 38%] 244s tests/test_rmsd.py::test_superpose_1 PASSED [ 38%] 244s tests/test_rmsd.py::test_superpose_2 PASSED [ 39%] 244s tests/test_rmsd.py::test_superpose_refinds PASSED [ 39%] 244s tests/test_rmsd.py::test_rmsd_atom_indices PASSED [ 39%] 244s tests/test_rmsd.py::test_rmsd_ref_ainds PASSED [ 39%] 244s tests/test_rmsd.py::test_average_structure PASSED [ 39%] 244s tests/test_rmsd.py::test_trajectory_rmsf PASSED [ 39%] 244s tests/test_rmsd.py::test_trajectory_rmsf_aligned PASSED [ 39%] 244s tests/test_rmsd.py::test_rmsd_atom_indices_vs_ref_indices PASSED [ 39%] 244s tests/test_rmsd_memmap.py::test_1 PASSED [ 39%] 244s tests/test_rmsd_memmap.py::test_2 PASSED [ 39%] 244s tests/test_sasa.py::test_sasa_0 PASSED [ 39%] 244s tests/test_sasa.py::test_sasa_1 PASSED [ 40%] 244s tests/test_sasa.py::test_sasa_2 PASSED [ 40%] 245s tests/test_sasa.py::test_sasa_3 PASSED [ 40%] 245s tests/test_sasa.py::test_sasa_4 PASSED [ 40%] 245s tests/test_sasa.py::test_sasa_5 PASSED [ 40%] 246s tests/test_sasa.py::test_sasa_6 PASSED [ 40%] 246s tests/test_sasa.py::test_sasa_7 PASSED [ 40%] 246s tests/test_selection.py::test_range PASSED [ 40%] 246s tests/test_selection.py::test_unary_2 PASSED [ 40%] 246s tests/test_selection.py::test_unary_3 PASSED [ 40%] 246s tests/test_selection.py::test_binary_1 PASSED [ 40%] 246s tests/test_selection.py::test_binary_2 PASSED [ 40%] 246s tests/test_selection.py::test_simple PASSED [ 41%] 246s tests/test_selection.py::test_alias PASSED [ 41%] 246s tests/test_selection.py::test_unary_1 PASSED [ 41%] 246s tests/test_selection.py::test_binary_selection_operator PASSED [ 41%] 246s tests/test_selection.py::test_raises PASSED [ 41%] 246s tests/test_selection.py::test_raises2 PASSED [ 41%] 246s tests/test_selection.py::test_bool PASSED [ 41%] 246s tests/test_selection.py::test_nested_bool PASSED [ 41%] 246s tests/test_selection.py::test_values PASSED [ 41%] 246s tests/test_selection.py::test_element PASSED [ 41%] 246s tests/test_selection.py::test_not PASSED [ 41%] 246s tests/test_selection.py::test_re PASSED [ 42%] 246s tests/test_selection.py::test_within SKIPPED (failed to parse selection) [ 42%] 246s tests/test_selection.py::test_quotes PASSED [ 42%] 247s tests/test_selection.py::test_top PASSED [ 42%] 247s tests/test_selection.py::test_top_2 PASSED [ 42%] 247s tests/test_selection.py::test_backbone PASSED [ 42%] 247s tests/test_selection.py::test_sidechain PASSED [ 42%] 247s tests/test_selection.py::test_literal PASSED [ 42%] 247s tests/test_selection.py::test_in PASSED [ 42%] 247s tests/test_shape.py::test_gyration PASSED [ 42%] 247s tests/test_shape.py::test_principal_moments PASSED [ 42%] 248s tests/test_shape.py::test_asphericity PASSED [ 43%] 248s tests/test_shape.py::test_shape_metrics PASSED [ 43%] 248s tests/test_thermodynamic_properties.py::test_volume PASSED [ 43%] 248s tests/test_thermodynamic_properties.py::test_density PASSED [ 43%] 248s tests/test_thermodynamic_properties.py::test_dipole_moments PASSED [ 43%] 248s tests/test_thermodynamic_properties.py::test_static_dielectric PASSED [ 43%] 248s tests/test_thermodynamic_properties.py::test_kappa PASSED [ 43%] 248s tests/test_thermodynamic_properties.py::test_alpha SKIPPED (Thermal ...) [ 43%] 248s tests/test_topology.py::test_topology_openmm SKIPPED (needs OpenMM) [ 43%] 248s tests/test_topology.py::test_topology_openmm_boxes SKIPPED (needs Op...) [ 43%] 248s tests/test_topology.py::test_topology_pandas PASSED [ 43%] 248s tests/test_topology.py::test_topology_pandas_TIP4PEW PASSED [ 44%] 248s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq PASSED [ 44%] 248s tests/test_topology.py::test_topology_numbers PASSED [ 44%] 248s tests/test_topology.py::test_topology_unique_elements_bpti PASSED [ 44%] 248s tests/test_topology.py::test_chain PASSED [ 44%] 248s tests/test_topology.py::test_residue PASSED [ 44%] 248s tests/test_topology.py::test_segment_id PASSED [ 44%] 248s tests/test_topology.py::test_nonconsective_resSeq PASSED [ 44%] 249s tests/test_topology.py::test_pickle PASSED [ 44%] 249s tests/test_topology.py::test_atoms_by_name PASSED [ 44%] 249s tests/test_topology.py::test_select_atom_indices PASSED [ 44%] 249s tests/test_topology.py::test_top_dataframe_openmm_roundtrip SKIPPED [ 44%] 249s tests/test_topology.py::test_n_bonds PASSED [ 45%] 249s tests/test_topology.py::test_load_unknown_topology PASSED [ 45%] 249s tests/test_topology.py::test_unique_pairs PASSED [ 45%] 249s tests/test_topology.py::test_select_pairs PASSED [ 45%] 249s tests/test_topology.py::test_to_fasta PASSED [ 45%] 250s tests/test_topology.py::test_subset PASSED [ 45%] 250s tests/test_topology.py::test_subset_re_index_residues PASSED [ 45%] 250s tests/test_topology.py::test_molecules PASSED [ 45%] 250s tests/test_topology.py::test_copy_and_hash PASSED [ 45%] 250s tests/test_topology.py::test_topology_sliced_residue_indices PASSED [ 45%] 250s tests/test_topology.py::test_topology_join PASSED [ 45%] 250s tests/test_topology.py::test_topology_join_keep_resSeq PASSED [ 46%] 250s tests/test_trajectory.py::test_mismatch PASSED [ 46%] 250s tests/test_trajectory.py::test_box PASSED [ 46%] 250s tests/test_trajectory.py::test_load_pdb_box PASSED [ 46%] 251s tests/test_trajectory.py::test_load_pdb_gz PASSED [ 46%] 251s tests/test_trajectory.py::test_box_load_save[nc] PASSED [ 46%] 251s tests/test_trajectory.py::test_box_load_save[h5] PASSED [ 46%] 251s tests/test_trajectory.py::test_box_load_save[xtc] PASSED [ 46%] 251s tests/test_trajectory.py::test_box_load_save[trr] PASSED [ 46%] 251s tests/test_trajectory.py::test_box_load_save[dcd] PASSED [ 46%] 251s tests/test_trajectory.py::test_box_load_save[mdcrd] PASSED [ 46%] 251s tests/test_trajectory.py::test_box_load_save[dtr] PASSED [ 47%] 251s tests/test_trajectory.py::test_box_load_save[xyz] SKIPPED (xyz does ...) [ 47%] 251s tests/test_trajectory.py::test_box_load_save[xyz.gz] SKIPPED (xyz.gz...) [ 47%] 251s tests/test_trajectory.py::test_box_load_save[lammpstrj] PASSED [ 47%] 251s tests/test_trajectory.py::test_box_load_save[lh5] SKIPPED (lh5 does ...) [ 47%] 251s tests/test_trajectory.py::test_box_load_save[pdb] SKIPPED (pdb does ...) [ 47%] 251s tests/test_trajectory.py::test_box_load_save[pdb.gz] SKIPPED (pdb.gz...) [ 47%] 251s tests/test_trajectory.py::test_box_load_save[ncrst] PASSED [ 47%] 251s tests/test_trajectory.py::test_box_load_save[rst7] PASSED [ 47%] 251s tests/test_trajectory.py::test_box_load_save[gro] PASSED [ 47%] 251s tests/test_trajectory.py::test_slice PASSED [ 47%] 251s tests/test_trajectory.py::test_slice2 PASSED [ 48%] 251s tests/test_trajectory.py::test_read_path[nc] PASSED [ 48%] 251s tests/test_trajectory.py::test_read_path[h5] PASSED [ 48%] 251s tests/test_trajectory.py::test_read_path[xtc] PASSED [ 48%] 251s tests/test_trajectory.py::test_read_path[trr] PASSED [ 48%] 251s tests/test_trajectory.py::test_read_path[dcd] PASSED [ 48%] 251s tests/test_trajectory.py::test_read_path[mdcrd] PASSED [ 48%] 251s tests/test_trajectory.py::test_read_path[dtr] PASSED [ 48%] 251s tests/test_trajectory.py::test_read_path[xyz] PASSED [ 48%] 251s tests/test_trajectory.py::test_read_path[xyz.gz] PASSED [ 48%] 251s tests/test_trajectory.py::test_read_path[lammpstrj] PASSED [ 48%] 251s tests/test_trajectory.py::test_read_path[lh5] PASSED [ 48%] 251s tests/test_trajectory.py::test_read_path[pdb] PASSED [ 49%] 251s tests/test_trajectory.py::test_read_path[pdb.gz] PASSED [ 49%] 251s tests/test_trajectory.py::test_read_path[ncrst] XFAIL (These referen...) [ 49%] 251s tests/test_trajectory.py::test_read_path[rst7] XFAIL (These referenc...) [ 49%] 251s tests/test_trajectory.py::test_read_path[gro] PASSED [ 49%] 251s tests/test_trajectory.py::test_write_path[nc] PASSED [ 49%] 251s tests/test_trajectory.py::test_write_path[h5] PASSED [ 49%] 251s tests/test_trajectory.py::test_write_path[xtc] PASSED [ 49%] 251s tests/test_trajectory.py::test_write_path[trr] PASSED [ 49%] 251s tests/test_trajectory.py::test_write_path[dcd] PASSED [ 49%] 251s tests/test_trajectory.py::test_write_path[mdcrd] SKIPPED (mdcrd can ...) [ 49%] 251s tests/test_trajectory.py::test_write_path[dtr] PASSED [ 50%] 251s tests/test_trajectory.py::test_write_path[xyz] PASSED [ 50%] 251s tests/test_trajectory.py::test_write_path[xyz.gz] PASSED [ 50%] 251s tests/test_trajectory.py::test_write_path[lammpstrj] PASSED [ 50%] 251s tests/test_trajectory.py::test_write_path[lh5] PASSED [ 50%] 251s tests/test_trajectory.py::test_write_path[pdb] PASSED [ 50%] 251s tests/test_trajectory.py::test_write_path[pdb.gz] PASSED [ 50%] 251s tests/test_trajectory.py::test_write_path[ncrst] SKIPPED (ncrst can ...) [ 50%] 251s tests/test_trajectory.py::test_write_path[rst7] SKIPPED (rst7 can on...) [ 50%] 251s tests/test_trajectory.py::test_write_path[gro] PASSED [ 50%] 251s tests/test_trajectory.py::test_read_write[nc-nc] PASSED [ 50%] 252s tests/test_trajectory.py::test_read_write[nc-h5] PASSED [ 51%] 252s tests/test_trajectory.py::test_read_write[nc-xtc] PASSED [ 51%] 252s tests/test_trajectory.py::test_read_write[nc-trr] PASSED [ 51%] 252s tests/test_trajectory.py::test_read_write[nc-dcd] PASSED [ 51%] 252s tests/test_trajectory.py::test_read_write[nc-mdcrd] SKIPPED (mdcrd c...) [ 51%] 253s tests/test_trajectory.py::test_read_write[nc-dtr] PASSED [ 51%] 253s tests/test_trajectory.py::test_read_write[nc-xyz] PASSED [ 51%] 253s tests/test_trajectory.py::test_read_write[nc-xyz.gz] PASSED [ 51%] 254s tests/test_trajectory.py::test_read_write[nc-lammpstrj] PASSED [ 51%] 254s tests/test_trajectory.py::test_read_write[nc-lh5] PASSED [ 51%] 254s tests/test_trajectory.py::test_read_write[nc-pdb] PASSED [ 51%] 255s tests/test_trajectory.py::test_read_write[nc-pdb.gz] PASSED [ 51%] 255s tests/test_trajectory.py::test_read_write[nc-ncrst] SKIPPED (ncrst c...) [ 52%] 255s tests/test_trajectory.py::test_read_write[nc-rst7] SKIPPED (rst7 can...) [ 52%] 255s tests/test_trajectory.py::test_read_write[nc-gro] PASSED [ 52%] 255s tests/test_trajectory.py::test_read_write[h5-nc] PASSED [ 52%] 255s tests/test_trajectory.py::test_read_write[h5-h5] PASSED [ 52%] 255s tests/test_trajectory.py::test_read_write[h5-xtc] PASSED [ 52%] 255s tests/test_trajectory.py::test_read_write[h5-trr] PASSED [ 52%] 255s tests/test_trajectory.py::test_read_write[h5-dcd] PASSED [ 52%] 255s tests/test_trajectory.py::test_read_write[h5-mdcrd] SKIPPED (mdcrd c...) [ 52%] 256s tests/test_trajectory.py::test_read_write[h5-dtr] PASSED [ 52%] 256s tests/test_trajectory.py::test_read_write[h5-xyz] PASSED [ 52%] 256s tests/test_trajectory.py::test_read_write[h5-xyz.gz] PASSED [ 53%] 256s tests/test_trajectory.py::test_read_write[h5-lammpstrj] PASSED [ 53%] 256s tests/test_trajectory.py::test_read_write[h5-lh5] PASSED [ 53%] 257s tests/test_trajectory.py::test_read_write[h5-pdb] PASSED [ 53%] 257s tests/test_trajectory.py::test_read_write[h5-pdb.gz] PASSED [ 53%] 257s tests/test_trajectory.py::test_read_write[h5-ncrst] SKIPPED (ncrst c...) [ 53%] 257s tests/test_trajectory.py::test_read_write[h5-rst7] SKIPPED (rst7 can...) [ 53%] 257s tests/test_trajectory.py::test_read_write[h5-gro] PASSED [ 53%] 257s tests/test_trajectory.py::test_read_write[xtc-nc] PASSED [ 53%] 257s tests/test_trajectory.py::test_read_write[xtc-h5] PASSED [ 53%] 257s tests/test_trajectory.py::test_read_write[xtc-xtc] PASSED [ 53%] 257s tests/test_trajectory.py::test_read_write[xtc-trr] PASSED [ 54%] 257s tests/test_trajectory.py::test_read_write[xtc-dcd] PASSED [ 54%] 257s tests/test_trajectory.py::test_read_write[xtc-mdcrd] SKIPPED (mdcrd ...) [ 54%] 258s tests/test_trajectory.py::test_read_write[xtc-dtr] PASSED [ 54%] 258s tests/test_trajectory.py::test_read_write[xtc-xyz] PASSED [ 54%] 258s tests/test_trajectory.py::test_read_write[xtc-xyz.gz] PASSED [ 54%] 259s tests/test_trajectory.py::test_read_write[xtc-lammpstrj] PASSED [ 54%] 259s tests/test_trajectory.py::test_read_write[xtc-lh5] PASSED [ 54%] 259s tests/test_trajectory.py::test_read_write[xtc-pdb] PASSED [ 54%] 259s tests/test_trajectory.py::test_read_write[xtc-pdb.gz] PASSED [ 54%] 259s tests/test_trajectory.py::test_read_write[xtc-ncrst] SKIPPED (ncrst ...) [ 54%] 259s tests/test_trajectory.py::test_read_write[xtc-rst7] SKIPPED (rst7 ca...) [ 55%] 259s tests/test_trajectory.py::test_read_write[xtc-gro] PASSED [ 55%] 260s tests/test_trajectory.py::test_read_write[trr-nc] PASSED [ 55%] 260s tests/test_trajectory.py::test_read_write[trr-h5] PASSED [ 55%] 260s tests/test_trajectory.py::test_read_write[trr-xtc] PASSED [ 55%] 260s tests/test_trajectory.py::test_read_write[trr-trr] PASSED [ 55%] 260s tests/test_trajectory.py::test_read_write[trr-dcd] PASSED [ 55%] 260s tests/test_trajectory.py::test_read_write[trr-mdcrd] SKIPPED (mdcrd ...) [ 55%] 260s tests/test_trajectory.py::test_read_write[trr-dtr] PASSED [ 55%] 260s tests/test_trajectory.py::test_read_write[trr-xyz] PASSED [ 55%] 261s tests/test_trajectory.py::test_read_write[trr-xyz.gz] PASSED [ 55%] 261s tests/test_trajectory.py::test_read_write[trr-lammpstrj] PASSED [ 55%] 261s tests/test_trajectory.py::test_read_write[trr-lh5] PASSED [ 56%] 261s tests/test_trajectory.py::test_read_write[trr-pdb] PASSED [ 56%] 261s tests/test_trajectory.py::test_read_write[trr-pdb.gz] PASSED [ 56%] 261s tests/test_trajectory.py::test_read_write[trr-ncrst] SKIPPED (ncrst ...) [ 56%] 261s tests/test_trajectory.py::test_read_write[trr-rst7] SKIPPED (rst7 ca...) [ 56%] 261s tests/test_trajectory.py::test_read_write[trr-gro] PASSED [ 56%] 261s tests/test_trajectory.py::test_read_write[dcd-nc] PASSED [ 56%] 261s tests/test_trajectory.py::test_read_write[dcd-h5] PASSED [ 56%] 261s tests/test_trajectory.py::test_read_write[dcd-xtc] PASSED [ 56%] 261s tests/test_trajectory.py::test_read_write[dcd-trr] PASSED [ 56%] 262s tests/test_trajectory.py::test_read_write[dcd-dcd] PASSED [ 56%] 262s tests/test_trajectory.py::test_read_write[dcd-mdcrd] SKIPPED (mdcrd ...) [ 57%] 262s tests/test_trajectory.py::test_read_write[dcd-dtr] PASSED [ 57%] 262s tests/test_trajectory.py::test_read_write[dcd-xyz] PASSED [ 57%] 262s tests/test_trajectory.py::test_read_write[dcd-xyz.gz] PASSED [ 57%] 263s tests/test_trajectory.py::test_read_write[dcd-lammpstrj] PASSED [ 57%] 263s tests/test_trajectory.py::test_read_write[dcd-lh5] PASSED [ 57%] 263s tests/test_trajectory.py::test_read_write[dcd-pdb] PASSED [ 57%] 263s tests/test_trajectory.py::test_read_write[dcd-pdb.gz] PASSED [ 57%] 263s tests/test_trajectory.py::test_read_write[dcd-ncrst] SKIPPED (ncrst ...) [ 57%] 263s tests/test_trajectory.py::test_read_write[dcd-rst7] SKIPPED (rst7 ca...) [ 57%] 263s tests/test_trajectory.py::test_read_write[dcd-gro] PASSED [ 57%] 264s tests/test_trajectory.py::test_read_write[mdcrd-nc] PASSED [ 58%] 264s tests/test_trajectory.py::test_read_write[mdcrd-h5] PASSED [ 58%] 264s tests/test_trajectory.py::test_read_write[mdcrd-xtc] PASSED [ 58%] 264s tests/test_trajectory.py::test_read_write[mdcrd-trr] PASSED [ 58%] 264s tests/test_trajectory.py::test_read_write[mdcrd-dcd] PASSED [ 58%] 264s tests/test_trajectory.py::test_read_write[mdcrd-mdcrd] SKIPPED (mdcr...) [ 58%] 264s tests/test_trajectory.py::test_read_write[mdcrd-dtr] SKIPPED (dtr ne...) [ 58%] 264s tests/test_trajectory.py::test_read_write[mdcrd-xyz] PASSED [ 58%] 264s tests/test_trajectory.py::test_read_write[mdcrd-xyz.gz] PASSED [ 58%] 264s tests/test_trajectory.py::test_read_write[mdcrd-lammpstrj] SKIPPED (...) [ 58%] 264s tests/test_trajectory.py::test_read_write[mdcrd-lh5] PASSED [ 58%] 265s tests/test_trajectory.py::test_read_write[mdcrd-pdb] PASSED [ 59%] 266s tests/test_trajectory.py::test_read_write[mdcrd-pdb.gz] PASSED [ 59%] 266s tests/test_trajectory.py::test_read_write[mdcrd-ncrst] SKIPPED (ncrs...) [ 59%] 266s tests/test_trajectory.py::test_read_write[mdcrd-rst7] SKIPPED (rst7 ...) [ 59%] 266s tests/test_trajectory.py::test_read_write[mdcrd-gro] PASSED [ 59%] 266s tests/test_trajectory.py::test_read_write[dtr-nc] PASSED [ 59%] 266s tests/test_trajectory.py::test_read_write[dtr-h5] PASSED [ 59%] 266s tests/test_trajectory.py::test_read_write[dtr-xtc] PASSED [ 59%] 266s tests/test_trajectory.py::test_read_write[dtr-trr] PASSED [ 59%] 266s tests/test_trajectory.py::test_read_write[dtr-dcd] PASSED [ 59%] 266s tests/test_trajectory.py::test_read_write[dtr-mdcrd] SKIPPED (mdcrd ...) [ 59%] 267s tests/test_trajectory.py::test_read_write[dtr-dtr] PASSED [ 59%] 267s tests/test_trajectory.py::test_read_write[dtr-xyz] PASSED [ 60%] 267s tests/test_trajectory.py::test_read_write[dtr-xyz.gz] PASSED [ 60%] 267s tests/test_trajectory.py::test_read_write[dtr-lammpstrj] PASSED [ 60%] 267s tests/test_trajectory.py::test_read_write[dtr-lh5] PASSED [ 60%] 267s tests/test_trajectory.py::test_read_write[dtr-pdb] PASSED [ 60%] 268s tests/test_trajectory.py::test_read_write[dtr-pdb.gz] PASSED [ 60%] 268s tests/test_trajectory.py::test_read_write[dtr-ncrst] SKIPPED (ncrst ...) [ 60%] 268s tests/test_trajectory.py::test_read_write[dtr-rst7] SKIPPED (rst7 ca...) [ 60%] 268s tests/test_trajectory.py::test_read_write[dtr-gro] PASSED [ 60%] 268s tests/test_trajectory.py::test_read_write[xyz-nc] PASSED [ 60%] 268s tests/test_trajectory.py::test_read_write[xyz-h5] PASSED [ 60%] 268s tests/test_trajectory.py::test_read_write[xyz-xtc] PASSED [ 61%] 268s tests/test_trajectory.py::test_read_write[xyz-trr] PASSED [ 61%] 268s tests/test_trajectory.py::test_read_write[xyz-dcd] PASSED [ 61%] 268s tests/test_trajectory.py::test_read_write[xyz-mdcrd] SKIPPED (mdcrd ...) [ 61%] 268s tests/test_trajectory.py::test_read_write[xyz-dtr] SKIPPED (dtr need...) [ 61%] 268s tests/test_trajectory.py::test_read_write[xyz-xyz] PASSED [ 61%] 268s tests/test_trajectory.py::test_read_write[xyz-xyz.gz] PASSED [ 61%] 268s tests/test_trajectory.py::test_read_write[xyz-lammpstrj] SKIPPED (la...) [ 61%] 268s tests/test_trajectory.py::test_read_write[xyz-lh5] PASSED [ 61%] 269s tests/test_trajectory.py::test_read_write[xyz-pdb] PASSED [ 61%] 269s tests/test_trajectory.py::test_read_write[xyz-pdb.gz] PASSED [ 61%] 269s tests/test_trajectory.py::test_read_write[xyz-ncrst] SKIPPED (ncrst ...) [ 62%] 269s tests/test_trajectory.py::test_read_write[xyz-rst7] SKIPPED (rst7 ca...) [ 62%] 269s tests/test_trajectory.py::test_read_write[xyz-gro] PASSED [ 62%] 269s tests/test_trajectory.py::test_read_write[xyz.gz-nc] PASSED [ 62%] 269s tests/test_trajectory.py::test_read_write[xyz.gz-h5] PASSED [ 62%] 269s tests/test_trajectory.py::test_read_write[xyz.gz-xtc] PASSED [ 62%] 269s tests/test_trajectory.py::test_read_write[xyz.gz-trr] PASSED [ 62%] 269s tests/test_trajectory.py::test_read_write[xyz.gz-dcd] PASSED [ 62%] 269s tests/test_trajectory.py::test_read_write[xyz.gz-mdcrd] SKIPPED (mdc...) [ 62%] 269s tests/test_trajectory.py::test_read_write[xyz.gz-dtr] SKIPPED (dtr n...) [ 62%] 269s tests/test_trajectory.py::test_read_write[xyz.gz-xyz] PASSED [ 62%] 270s tests/test_trajectory.py::test_read_write[xyz.gz-xyz.gz] PASSED [ 62%] 270s tests/test_trajectory.py::test_read_write[xyz.gz-lammpstrj] SKIPPED [ 63%] 270s tests/test_trajectory.py::test_read_write[xyz.gz-lh5] PASSED [ 63%] 270s tests/test_trajectory.py::test_read_write[xyz.gz-pdb] PASSED [ 63%] 270s tests/test_trajectory.py::test_read_write[xyz.gz-pdb.gz] PASSED [ 63%] 270s tests/test_trajectory.py::test_read_write[xyz.gz-ncrst] SKIPPED (ncr...) [ 63%] 270s tests/test_trajectory.py::test_read_write[xyz.gz-rst7] SKIPPED (rst7...) [ 63%] 270s tests/test_trajectory.py::test_read_write[xyz.gz-gro] PASSED [ 63%] 270s tests/test_trajectory.py::test_read_write[lammpstrj-nc] PASSED [ 63%] 270s tests/test_trajectory.py::test_read_write[lammpstrj-h5] PASSED [ 63%] 270s tests/test_trajectory.py::test_read_write[lammpstrj-xtc] PASSED [ 63%] 271s tests/test_trajectory.py::test_read_write[lammpstrj-trr] PASSED [ 63%] 271s tests/test_trajectory.py::test_read_write[lammpstrj-dcd] PASSED [ 64%] 271s tests/test_trajectory.py::test_read_write[lammpstrj-mdcrd] SKIPPED (...) [ 64%] 271s tests/test_trajectory.py::test_read_write[lammpstrj-dtr] PASSED [ 64%] 271s tests/test_trajectory.py::test_read_write[lammpstrj-xyz] PASSED [ 64%] 272s tests/test_trajectory.py::test_read_write[lammpstrj-xyz.gz] PASSED [ 64%] 272s tests/test_trajectory.py::test_read_write[lammpstrj-lammpstrj] PASSED [ 64%] 272s tests/test_trajectory.py::test_read_write[lammpstrj-lh5] PASSED [ 64%] 272s tests/test_trajectory.py::test_read_write[lammpstrj-pdb] PASSED [ 64%] 273s tests/test_trajectory.py::test_read_write[lammpstrj-pdb.gz] PASSED [ 64%] 273s tests/test_trajectory.py::test_read_write[lammpstrj-ncrst] SKIPPED (...) [ 64%] 273s tests/test_trajectory.py::test_read_write[lammpstrj-rst7] SKIPPED (r...) [ 64%] 273s tests/test_trajectory.py::test_read_write[lammpstrj-gro] PASSED [ 65%] 273s tests/test_trajectory.py::test_read_write[lh5-nc] PASSED [ 65%] 273s tests/test_trajectory.py::test_read_write[lh5-h5] PASSED [ 65%] 273s tests/test_trajectory.py::test_read_write[lh5-xtc] PASSED [ 65%] 273s tests/test_trajectory.py::test_read_write[lh5-trr] PASSED [ 65%] 273s tests/test_trajectory.py::test_read_write[lh5-dcd] PASSED [ 65%] 273s tests/test_trajectory.py::test_read_write[lh5-mdcrd] SKIPPED (mdcrd ...) [ 65%] 273s tests/test_trajectory.py::test_read_write[lh5-dtr] SKIPPED (dtr need...) [ 65%] 273s tests/test_trajectory.py::test_read_write[lh5-xyz] PASSED [ 65%] 273s tests/test_trajectory.py::test_read_write[lh5-xyz.gz] PASSED [ 65%] 273s tests/test_trajectory.py::test_read_write[lh5-lammpstrj] SKIPPED (la...) [ 65%] 273s tests/test_trajectory.py::test_read_write[lh5-lh5] PASSED [ 66%] 273s tests/test_trajectory.py::test_read_write[lh5-pdb] PASSED [ 66%] 274s tests/test_trajectory.py::test_read_write[lh5-pdb.gz] PASSED [ 66%] 274s tests/test_trajectory.py::test_read_write[lh5-ncrst] SKIPPED (ncrst ...) [ 66%] 274s tests/test_trajectory.py::test_read_write[lh5-rst7] SKIPPED (rst7 ca...) [ 66%] 274s tests/test_trajectory.py::test_read_write[lh5-gro] PASSED [ 66%] 274s tests/test_trajectory.py::test_read_write[pdb-nc] PASSED [ 66%] 274s tests/test_trajectory.py::test_read_write[pdb-h5] PASSED [ 66%] 275s tests/test_trajectory.py::test_read_write[pdb-xtc] PASSED [ 66%] 275s tests/test_trajectory.py::test_read_write[pdb-trr] PASSED [ 66%] 275s tests/test_trajectory.py::test_read_write[pdb-dcd] PASSED [ 66%] 275s tests/test_trajectory.py::test_read_write[pdb-mdcrd] SKIPPED (mdcrd ...) [ 66%] 276s tests/test_trajectory.py::test_read_write[pdb-dtr] PASSED [ 67%] 276s tests/test_trajectory.py::test_read_write[pdb-xyz] PASSED [ 67%] 276s tests/test_trajectory.py::test_read_write[pdb-xyz.gz] PASSED [ 67%] 277s tests/test_trajectory.py::test_read_write[pdb-lammpstrj] PASSED [ 67%] 277s tests/test_trajectory.py::test_read_write[pdb-lh5] PASSED [ 67%] 277s tests/test_trajectory.py::test_read_write[pdb-pdb] PASSED [ 67%] 278s tests/test_trajectory.py::test_read_write[pdb-pdb.gz] PASSED [ 67%] 278s tests/test_trajectory.py::test_read_write[pdb-ncrst] SKIPPED (ncrst ...) [ 67%] 278s tests/test_trajectory.py::test_read_write[pdb-rst7] SKIPPED (rst7 ca...) [ 67%] 278s tests/test_trajectory.py::test_read_write[pdb-gro] PASSED [ 67%] 279s tests/test_trajectory.py::test_read_write[pdb.gz-nc] PASSED [ 67%] 279s tests/test_trajectory.py::test_read_write[pdb.gz-h5] PASSED [ 68%] 279s tests/test_trajectory.py::test_read_write[pdb.gz-xtc] PASSED [ 68%] 279s tests/test_trajectory.py::test_read_write[pdb.gz-trr] PASSED [ 68%] 279s tests/test_trajectory.py::test_read_write[pdb.gz-dcd] PASSED [ 68%] 279s tests/test_trajectory.py::test_read_write[pdb.gz-mdcrd] SKIPPED (mdc...) [ 68%] 280s tests/test_trajectory.py::test_read_write[pdb.gz-dtr] PASSED [ 68%] 280s tests/test_trajectory.py::test_read_write[pdb.gz-xyz] PASSED [ 68%] 281s tests/test_trajectory.py::test_read_write[pdb.gz-xyz.gz] PASSED [ 68%] 281s tests/test_trajectory.py::test_read_write[pdb.gz-lammpstrj] PASSED [ 68%] 281s tests/test_trajectory.py::test_read_write[pdb.gz-lh5] PASSED [ 68%] 282s tests/test_trajectory.py::test_read_write[pdb.gz-pdb] PASSED [ 68%] 282s tests/test_trajectory.py::test_read_write[pdb.gz-pdb.gz] PASSED [ 69%] 282s tests/test_trajectory.py::test_read_write[pdb.gz-ncrst] SKIPPED (ncr...) [ 69%] 282s tests/test_trajectory.py::test_read_write[pdb.gz-rst7] SKIPPED (rst7...) [ 69%] 283s tests/test_trajectory.py::test_read_write[pdb.gz-gro] PASSED [ 69%] 283s tests/test_trajectory.py::test_read_write[ncrst-nc] XFAIL (These ref...) [ 69%] 283s tests/test_trajectory.py::test_read_write[ncrst-h5] XFAIL (These ref...) [ 69%] 283s tests/test_trajectory.py::test_read_write[ncrst-xtc] XFAIL (These re...) [ 69%] 283s tests/test_trajectory.py::test_read_write[ncrst-trr] XFAIL (These re...) [ 69%] 283s tests/test_trajectory.py::test_read_write[ncrst-dcd] XFAIL (These re...) [ 69%] 283s tests/test_trajectory.py::test_read_write[ncrst-mdcrd] XFAIL (These ...) [ 69%] 283s tests/test_trajectory.py::test_read_write[ncrst-dtr] XFAIL (These re...) [ 69%] 283s tests/test_trajectory.py::test_read_write[ncrst-xyz] XFAIL (These re...) [ 70%] 283s tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] XFAIL (These...) [ 70%] 283s tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] XFAIL (Th...) [ 70%] 283s tests/test_trajectory.py::test_read_write[ncrst-lh5] XFAIL (These re...) [ 70%] 283s tests/test_trajectory.py::test_read_write[ncrst-pdb] XFAIL (These re...) [ 70%] 283s tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] XFAIL (These...) [ 70%] 283s tests/test_trajectory.py::test_read_write[ncrst-ncrst] XFAIL (These ...) [ 70%] 283s tests/test_trajectory.py::test_read_write[ncrst-rst7] XFAIL (These r...) [ 70%] 283s tests/test_trajectory.py::test_read_write[ncrst-gro] XFAIL (These re...) [ 70%] 283s tests/test_trajectory.py::test_read_write[rst7-nc] XFAIL (These refe...) [ 70%] 283s tests/test_trajectory.py::test_read_write[rst7-h5] XFAIL (These refe...) [ 70%] 283s tests/test_trajectory.py::test_read_write[rst7-xtc] XFAIL (These ref...) [ 70%] 283s tests/test_trajectory.py::test_read_write[rst7-trr] XFAIL (These ref...) [ 71%] 283s tests/test_trajectory.py::test_read_write[rst7-dcd] XFAIL (These ref...) [ 71%] 283s tests/test_trajectory.py::test_read_write[rst7-mdcrd] XFAIL (These r...) [ 71%] 283s tests/test_trajectory.py::test_read_write[rst7-dtr] XFAIL (These ref...) [ 71%] 283s tests/test_trajectory.py::test_read_write[rst7-xyz] XFAIL (These ref...) [ 71%] 283s tests/test_trajectory.py::test_read_write[rst7-xyz.gz] XFAIL (These ...) [ 71%] 283s tests/test_trajectory.py::test_read_write[rst7-lammpstrj] XFAIL (The...) [ 71%] 283s tests/test_trajectory.py::test_read_write[rst7-lh5] XFAIL (These ref...) [ 71%] 283s tests/test_trajectory.py::test_read_write[rst7-pdb] XFAIL (These ref...) [ 71%] 283s tests/test_trajectory.py::test_read_write[rst7-pdb.gz] XFAIL (These ...) [ 71%] 283s tests/test_trajectory.py::test_read_write[rst7-ncrst] XFAIL (These r...) [ 71%] 283s tests/test_trajectory.py::test_read_write[rst7-rst7] XFAIL (These re...) [ 72%] 283s tests/test_trajectory.py::test_read_write[rst7-gro] XFAIL (These ref...) [ 72%] 283s tests/test_trajectory.py::test_read_write[gro-nc] PASSED [ 72%] 283s tests/test_trajectory.py::test_read_write[gro-h5] PASSED [ 72%] 283s tests/test_trajectory.py::test_read_write[gro-xtc] PASSED [ 72%] 283s tests/test_trajectory.py::test_read_write[gro-trr] PASSED [ 72%] 283s tests/test_trajectory.py::test_read_write[gro-dcd] PASSED [ 72%] 283s tests/test_trajectory.py::test_read_write[gro-mdcrd] SKIPPED (mdcrd ...) [ 72%] 284s tests/test_trajectory.py::test_read_write[gro-dtr] PASSED [ 72%] 284s tests/test_trajectory.py::test_read_write[gro-xyz] PASSED [ 72%] 285s tests/test_trajectory.py::test_read_write[gro-xyz.gz] PASSED [ 72%] 285s tests/test_trajectory.py::test_read_write[gro-lammpstrj] PASSED [ 73%] 285s tests/test_trajectory.py::test_read_write[gro-lh5] PASSED [ 73%] 285s tests/test_trajectory.py::test_read_write[gro-pdb] PASSED [ 73%] 286s tests/test_trajectory.py::test_read_write[gro-pdb.gz] PASSED [ 73%] 286s tests/test_trajectory.py::test_read_write[gro-ncrst] SKIPPED (ncrst ...) [ 73%] 286s tests/test_trajectory.py::test_read_write[gro-rst7] SKIPPED (rst7 ca...) [ 73%] 286s tests/test_trajectory.py::test_read_write[gro-gro] PASSED [ 73%] 286s tests/test_trajectory.py::test_load[nc] PASSED [ 73%] 286s tests/test_trajectory.py::test_load[h5] PASSED [ 73%] 286s tests/test_trajectory.py::test_load[xtc] PASSED [ 73%] 286s tests/test_trajectory.py::test_load[trr] PASSED [ 73%] 286s tests/test_trajectory.py::test_load[dcd] PASSED [ 74%] 286s tests/test_trajectory.py::test_load[mdcrd] PASSED [ 74%] 286s tests/test_trajectory.py::test_load[dtr] PASSED [ 74%] 286s tests/test_trajectory.py::test_load[xyz] PASSED [ 74%] 286s tests/test_trajectory.py::test_load[xyz.gz] PASSED [ 74%] 286s tests/test_trajectory.py::test_load[lammpstrj] PASSED [ 74%] 286s tests/test_trajectory.py::test_load[lh5] PASSED [ 74%] 288s tests/test_trajectory.py::test_load[pdb] PASSED [ 74%] 289s tests/test_trajectory.py::test_load[pdb.gz] PASSED [ 74%] 289s tests/test_trajectory.py::test_load[ncrst] XFAIL (These reference fi...) [ 74%] 289s tests/test_trajectory.py::test_load[rst7] XFAIL (These reference fil...) [ 74%] 289s tests/test_trajectory.py::test_load[gro] PASSED [ 74%] 289s tests/test_trajectory.py::test_hdf5 PASSED [ 75%] 289s tests/test_trajectory.py::test_center PASSED [ 75%] 289s tests/test_trajectory.py::test_center_aind PASSED [ 75%] 289s tests/test_trajectory.py::test_float_atom_indices_exception[nc] PASSED [ 75%] 289s tests/test_trajectory.py::test_float_atom_indices_exception[h5] PASSED [ 75%] 289s tests/test_trajectory.py::test_float_atom_indices_exception[xtc] PASSED [ 75%] 289s tests/test_trajectory.py::test_float_atom_indices_exception[trr] PASSED [ 75%] 289s tests/test_trajectory.py::test_float_atom_indices_exception[dcd] PASSED [ 75%] 289s tests/test_trajectory.py::test_float_atom_indices_exception[mdcrd] PASSED [ 75%] 289s tests/test_trajectory.py::test_float_atom_indices_exception[dtr] PASSED [ 75%] 289s tests/test_trajectory.py::test_float_atom_indices_exception[xyz] PASSED [ 75%] 289s tests/test_trajectory.py::test_float_atom_indices_exception[xyz.gz] PASSED [ 76%] 289s tests/test_trajectory.py::test_float_atom_indices_exception[lammpstrj] PASSED [ 76%] 289s tests/test_trajectory.py::test_float_atom_indices_exception[lh5] PASSED [ 76%] 289s tests/test_trajectory.py::test_float_atom_indices_exception[pdb] PASSED [ 76%] 289s tests/test_trajectory.py::test_float_atom_indices_exception[pdb.gz] PASSED [ 76%] 289s tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] XFAIL [ 76%] 289s tests/test_trajectory.py::test_float_atom_indices_exception[rst7] XFAIL [ 76%] 289s tests/test_trajectory.py::test_float_atom_indices_exception[gro] PASSED [ 76%] 289s tests/test_trajectory.py::test_restrict_atoms PASSED [ 76%] 289s tests/test_trajectory.py::test_restrict_atoms_not_inplace PASSED [ 76%] 289s tests/test_trajectory.py::test_array_vs_matrix PASSED [ 76%] 289s tests/test_trajectory.py::test_pdb_unitcell_loadsave PASSED [ 77%] 289s tests/test_trajectory.py::test_load_combination[nc] PASSED [ 77%] 289s tests/test_trajectory.py::test_load_combination[h5] PASSED [ 77%] 289s tests/test_trajectory.py::test_load_combination[xtc] PASSED [ 77%] 289s tests/test_trajectory.py::test_load_combination[trr] PASSED [ 77%] 289s tests/test_trajectory.py::test_load_combination[dcd] PASSED [ 77%] 289s tests/test_trajectory.py::test_load_combination[mdcrd] PASSED [ 77%] 289s tests/test_trajectory.py::test_load_combination[dtr] PASSED [ 77%] 289s tests/test_trajectory.py::test_load_combination[xyz] PASSED [ 77%] 289s tests/test_trajectory.py::test_load_combination[xyz.gz] PASSED [ 77%] 289s tests/test_trajectory.py::test_load_combination[lammpstrj] PASSED [ 77%] 289s tests/test_trajectory.py::test_load_combination[lh5] PASSED [ 77%] 290s tests/test_trajectory.py::test_load_combination[pdb] PASSED [ 78%] 290s tests/test_trajectory.py::test_load_combination[pdb.gz] PASSED [ 78%] 290s tests/test_trajectory.py::test_load_combination[ncrst] XFAIL (These ...) [ 78%] 290s tests/test_trajectory.py::test_load_combination[rst7] XFAIL (These r...) [ 78%] 291s tests/test_trajectory.py::test_load_combination[gro] PASSED [ 78%] 291s tests/test_trajectory.py::test_no_topology PASSED [ 78%] 291s tests/test_trajectory.py::test_join PASSED [ 78%] 291s tests/test_trajectory.py::test_md_join PASSED [ 78%] 291s tests/test_trajectory.py::test_stack_1 PASSED [ 78%] 291s tests/test_trajectory.py::test_stack_2 PASSED [ 78%] 291s tests/test_trajectory.py::test_seek_read_mode[nc] PASSED [ 78%] 291s tests/test_trajectory.py::test_seek_read_mode[h5] PASSED [ 79%] 291s tests/test_trajectory.py::test_seek_read_mode[xtc] PASSED [ 79%] 291s tests/test_trajectory.py::test_seek_read_mode[trr] PASSED [ 79%] 291s tests/test_trajectory.py::test_seek_read_mode[dcd] PASSED [ 79%] 291s tests/test_trajectory.py::test_seek_read_mode[mdcrd] PASSED [ 79%] 291s tests/test_trajectory.py::test_seek_read_mode[dtr] PASSED [ 79%] 291s tests/test_trajectory.py::test_seek_read_mode[xyz] PASSED [ 79%] 291s tests/test_trajectory.py::test_seek_read_mode[xyz.gz] XFAIL (This is...) [ 79%] 291s tests/test_trajectory.py::test_seek_read_mode[lammpstrj] PASSED [ 79%] 291s tests/test_trajectory.py::test_seek_read_mode[lh5] PASSED [ 79%] 291s tests/test_trajectory.py::test_seek_read_mode[pdb] XFAIL (PDB Files ...) [ 79%] 291s tests/test_trajectory.py::test_seek_read_mode[pdb.gz] XFAIL (PDB Fil...) [ 80%] 291s tests/test_trajectory.py::test_seek_read_mode[ncrst] XFAIL (These re...) [ 80%] 291s tests/test_trajectory.py::test_seek_read_mode[rst7] XFAIL (These ref...) [ 80%] 291s tests/test_trajectory.py::test_seek_read_mode[gro] XFAIL (This is br...) [ 80%] 291s tests/test_trajectory.py::test_load_frame[nc] PASSED [ 80%] 291s tests/test_trajectory.py::test_load_frame[h5] PASSED [ 80%] 291s tests/test_trajectory.py::test_load_frame[xtc] PASSED [ 80%] 291s tests/test_trajectory.py::test_load_frame[trr] PASSED [ 80%] 291s tests/test_trajectory.py::test_load_frame[dcd] PASSED [ 80%] 291s tests/test_trajectory.py::test_load_frame[mdcrd] PASSED [ 80%] 291s tests/test_trajectory.py::test_load_frame[dtr] XFAIL (DTR doesn't lo...) [ 80%] 291s tests/test_trajectory.py::test_load_frame[xyz] PASSED [ 81%] 291s tests/test_trajectory.py::test_load_frame[xyz.gz] PASSED [ 81%] 291s tests/test_trajectory.py::test_load_frame[lammpstrj] PASSED [ 81%] 291s tests/test_trajectory.py::test_load_frame[lh5] PASSED [ 81%] 292s tests/test_trajectory.py::test_load_frame[pdb] PASSED [ 81%] 292s tests/test_trajectory.py::test_load_frame[pdb.gz] PASSED [ 81%] 292s tests/test_trajectory.py::test_load_frame[ncrst] XFAIL (These refere...) [ 81%] 292s tests/test_trajectory.py::test_load_frame[rst7] XFAIL (These referen...) [ 81%] 292s tests/test_trajectory.py::test_load_frame[gro] XFAIL (Gro doesn't im...) [ 81%] 292s tests/test_trajectory.py::test_load_frame_2eqq PASSED [ 81%] 292s tests/test_trajectory.py::test_iterload[nc] PASSED [ 81%] 292s tests/test_trajectory.py::test_iterload[h5] PASSED [ 81%] 292s tests/test_trajectory.py::test_iterload[xtc] PASSED [ 82%] 292s tests/test_trajectory.py::test_iterload[trr] PASSED [ 82%] 292s tests/test_trajectory.py::test_iterload[dcd] PASSED [ 82%] 292s tests/test_trajectory.py::test_iterload[mdcrd] PASSED [ 82%] 292s tests/test_trajectory.py::test_iterload[dtr] XFAIL (This is broken w...) [ 82%] 292s tests/test_trajectory.py::test_iterload[xyz] PASSED [ 82%] 292s tests/test_trajectory.py::test_iterload[xyz.gz] PASSED [ 82%] 292s tests/test_trajectory.py::test_iterload[lammpstrj] PASSED [ 82%] 292s tests/test_trajectory.py::test_iterload[lh5] PASSED [ 82%] 292s tests/test_trajectory.py::test_iterload[pdb] PASSED [ 82%] 293s tests/test_trajectory.py::test_iterload[pdb.gz] PASSED [ 82%] 293s tests/test_trajectory.py::test_iterload[ncrst] SKIPPED (Only 1 frame...) [ 83%] 293s tests/test_trajectory.py::test_iterload[rst7] SKIPPED (Only 1 frame ...) [ 83%] 293s tests/test_trajectory.py::test_iterload[gro] PASSED [ 83%] 295s tests/test_trajectory.py::test_iterload_skip[nc] PASSED [ 83%] 297s tests/test_trajectory.py::test_iterload_skip[h5] PASSED [ 83%] 298s tests/test_trajectory.py::test_iterload_skip[xtc] PASSED [ 83%] 299s tests/test_trajectory.py::test_iterload_skip[trr] PASSED [ 83%] 300s tests/test_trajectory.py::test_iterload_skip[dcd] PASSED [ 83%] 301s tests/test_trajectory.py::test_iterload_skip[mdcrd] PASSED [ 83%] 301s tests/test_trajectory.py::test_iterload_skip[dtr] PASSED [ 83%] 302s tests/test_trajectory.py::test_iterload_skip[xyz] PASSED [ 83%] 303s tests/test_trajectory.py::test_iterload_skip[xyz.gz] PASSED [ 84%] 304s tests/test_trajectory.py::test_iterload_skip[lammpstrj] PASSED [ 84%] 305s tests/test_trajectory.py::test_iterload_skip[lh5] PASSED [ 84%] 305s tests/test_trajectory.py::test_iterload_skip[pdb] XFAIL (PDB Iterloa...) [ 84%] 305s tests/test_trajectory.py::test_iterload_skip[pdb.gz] XFAIL (PDB Iter...) [ 84%] 305s tests/test_trajectory.py::test_iterload_skip[ncrst] XFAIL (These ref...) [ 84%] 305s tests/test_trajectory.py::test_iterload_skip[rst7] XFAIL (These refe...) [ 84%] 305s tests/test_trajectory.py::test_iterload_skip[gro] XFAIL (Not impleme...) [ 84%] 305s tests/test_trajectory.py::test_iterload_chunk_dcd PASSED [ 84%] 305s tests/test_trajectory.py::test_save_load[nc] PASSED [ 84%] 305s tests/test_trajectory.py::test_save_load[h5] PASSED [ 84%] 305s tests/test_trajectory.py::test_save_load[xtc] PASSED [ 85%] 305s tests/test_trajectory.py::test_save_load[trr] PASSED [ 85%] 305s tests/test_trajectory.py::test_save_load[dcd] PASSED [ 85%] 305s tests/test_trajectory.py::test_save_load[mdcrd] PASSED [ 85%] 305s tests/test_trajectory.py::test_save_load[dtr] PASSED [ 85%] 305s tests/test_trajectory.py::test_save_load[xyz] PASSED [ 85%] 305s tests/test_trajectory.py::test_save_load[xyz.gz] PASSED [ 85%] 305s tests/test_trajectory.py::test_save_load[lammpstrj] PASSED [ 85%] 305s tests/test_trajectory.py::test_save_load[lh5] PASSED [ 85%] 305s tests/test_trajectory.py::test_save_load[pdb] PASSED [ 85%] 305s tests/test_trajectory.py::test_save_load[pdb.gz] PASSED [ 85%] 305s tests/test_trajectory.py::test_save_load[ncrst] PASSED [ 85%] 305s tests/test_trajectory.py::test_save_load[rst7] PASSED [ 86%] 305s tests/test_trajectory.py::test_save_load[gro] PASSED [ 86%] 306s tests/test_trajectory.py::test_force_overwrite[nc] PASSED [ 86%] 306s tests/test_trajectory.py::test_force_overwrite[h5] PASSED [ 86%] 306s tests/test_trajectory.py::test_force_overwrite[xtc] PASSED [ 86%] 306s tests/test_trajectory.py::test_force_overwrite[trr] PASSED [ 86%] 306s tests/test_trajectory.py::test_force_overwrite[dcd] PASSED [ 86%] 306s tests/test_trajectory.py::test_force_overwrite[mdcrd] PASSED [ 86%] 306s tests/test_trajectory.py::test_force_overwrite[dtr] XFAIL (This is b...) [ 86%] 306s tests/test_trajectory.py::test_force_overwrite[xyz] PASSED [ 86%] 306s tests/test_trajectory.py::test_force_overwrite[xyz.gz] PASSED [ 86%] 306s tests/test_trajectory.py::test_force_overwrite[lammpstrj] PASSED [ 87%] 306s tests/test_trajectory.py::test_force_overwrite[lh5] PASSED [ 87%] 306s tests/test_trajectory.py::test_force_overwrite[pdb] PASSED [ 87%] 306s tests/test_trajectory.py::test_force_overwrite[pdb.gz] PASSED [ 87%] 306s tests/test_trajectory.py::test_force_overwrite[ncrst] PASSED [ 87%] 306s tests/test_trajectory.py::test_force_overwrite[rst7] PASSED [ 87%] 306s tests/test_trajectory.py::test_force_overwrite[gro] PASSED [ 87%] 306s tests/test_trajectory.py::test_force_noverwrite[nc] PASSED [ 87%] 306s tests/test_trajectory.py::test_force_noverwrite[h5] PASSED [ 87%] 306s tests/test_trajectory.py::test_force_noverwrite[xtc] PASSED [ 87%] 306s tests/test_trajectory.py::test_force_noverwrite[trr] PASSED [ 87%] 306s tests/test_trajectory.py::test_force_noverwrite[dcd] PASSED [ 88%] 306s tests/test_trajectory.py::test_force_noverwrite[mdcrd] PASSED [ 88%] 306s tests/test_trajectory.py::test_force_noverwrite[dtr] PASSED [ 88%] 306s tests/test_trajectory.py::test_force_noverwrite[xyz] PASSED [ 88%] 306s tests/test_trajectory.py::test_force_noverwrite[xyz.gz] PASSED [ 88%] 306s tests/test_trajectory.py::test_force_noverwrite[lammpstrj] PASSED [ 88%] 306s tests/test_trajectory.py::test_force_noverwrite[lh5] PASSED [ 88%] 306s tests/test_trajectory.py::test_force_noverwrite[pdb] PASSED [ 88%] 306s tests/test_trajectory.py::test_force_noverwrite[pdb.gz] PASSED [ 88%] 306s tests/test_trajectory.py::test_force_noverwrite[ncrst] PASSED [ 88%] 306s tests/test_trajectory.py::test_force_noverwrite[rst7] PASSED [ 88%] 306s tests/test_trajectory.py::test_force_noverwrite[gro] PASSED [ 88%] 306s tests/test_trajectory.py::test_open_and_load PASSED [ 89%] 306s tests/test_trajectory.py::test_length PASSED [ 89%] 306s tests/test_trajectory.py::test_unitcell[nc] PASSED [ 89%] 306s tests/test_trajectory.py::test_unitcell[h5] PASSED [ 89%] 306s tests/test_trajectory.py::test_unitcell[xtc] PASSED [ 89%] 306s tests/test_trajectory.py::test_unitcell[trr] PASSED [ 89%] 306s tests/test_trajectory.py::test_unitcell[dcd] PASSED [ 89%] 306s tests/test_trajectory.py::test_unitcell[mdcrd] PASSED [ 89%] 306s tests/test_trajectory.py::test_unitcell[dtr] XFAIL (dtr seems to nee...) [ 89%] 306s tests/test_trajectory.py::test_unitcell[xyz] PASSED [ 89%] 306s tests/test_trajectory.py::test_unitcell[xyz.gz] PASSED [ 89%] 306s tests/test_trajectory.py::test_unitcell[lammpstrj] XFAIL (lammpstrj ...) [ 90%] 306s tests/test_trajectory.py::test_unitcell[lh5] PASSED [ 90%] 306s tests/test_trajectory.py::test_unitcell[pdb] PASSED [ 90%] 306s tests/test_trajectory.py::test_unitcell[pdb.gz] PASSED [ 90%] 306s tests/test_trajectory.py::test_unitcell[ncrst] XFAIL (ncrst seems to...) [ 90%] 306s tests/test_trajectory.py::test_unitcell[rst7] XFAIL (rst7 seems to n...) [ 90%] 306s tests/test_trajectory.py::test_unitcell[gro] PASSED [ 90%] 306s tests/test_trajectory.py::test_chunk0_iterload PASSED [ 90%] 306s tests/test_trajectory.py::test_hashing PASSED [ 90%] 306s tests/test_trajectory.py::test_smooth PASSED [ 90%] 306s tests/test_trajectory.py::test_load_pdb_no_standard_names PASSED [ 90%] 306s tests/test_trajectory.py::test_load_with_atom_indices PASSED [ 91%] 307s tests/test_trajectory.py::test_load_with_frame PASSED [ 91%] 307s tests/test_trajectory.py::test_add_remove_atoms PASSED [ 91%] 307s tests/test_trr.py::test_1 PASSED [ 91%] 307s tests/test_trr.py::test_read_stride PASSED [ 91%] 307s tests/test_trr.py::test_read_stride_n_frames PASSED [ 91%] 307s tests/test_trr.py::test_read_stride_offsets PASSED [ 91%] 307s tests/test_trr.py::test_read_stride_n_frames_offsets PASSED [ 91%] 307s tests/test_trr.py::test_read_stride_switching PASSED [ 91%] 307s tests/test_trr.py::test_write_read PASSED [ 91%] 307s tests/test_trr.py::test_read_atomindices_1 PASSED [ 91%] 307s tests/test_trr.py::test_read_atomindices_2 PASSED [ 92%] 307s tests/test_trr.py::test_deficient_shape PASSED [ 92%] 307s tests/test_trr.py::test_ragged_1 PASSED [ 92%] 307s tests/test_trr.py::test_ragged_2 PASSED [ 92%] 307s tests/test_trr.py::test_malformed PASSED [ 92%] 307s tests/test_trr.py::test_tell PASSED [ 92%] 307s tests/test_trr.py::test_seek PASSED [ 92%] 307s tests/test_trr.py::test_get_velocities PASSED [ 92%] 307s tests/test_trr.py::test_get_forces PASSED [ 92%] 307s tests/test_trr.py::test_get_velocities_and_forces PASSED [ 92%] 307s tests/test_trr.py::test_get_velocities_forces_atom_indices_1 PASSED [ 92%] 307s tests/test_trr.py::test_get_velocities_forces_atom_indices_2 PASSED [ 92%] 307s tests/test_trr.py::test_read_velocities_do_not_exist PASSED [ 93%] 307s tests/test_trr.py::test_read_forces_do_not_exist PASSED [ 93%] 307s tests/test_utils.py::test_unitcell_0 PASSED [ 93%] 307s tests/test_utils.py::test_unitcell_1 PASSED [ 93%] 307s tests/test_utils.py::test_ensure_type_1 PASSED [ 93%] 307s tests/test_utils.py::test_ensure_type_2 PASSED [ 93%] 307s tests/test_utils.py::test_ensure_type_25 PASSED [ 93%] 307s tests/test_utils.py::test_ensure_type_3 PASSED [ 93%] 307s tests/test_utils.py::test_ensure_type_4 PASSED [ 93%] 307s tests/test_utils.py::test_ensure_type_5 PASSED [ 93%] 307s tests/test_utils.py::test_ensure_type_6 PASSED [ 93%] 307s tests/test_utils.py::test_ensure_type_7 PASSED [ 94%] 307s tests/test_utils.py::test_ensure_type_8 PASSED [ 94%] 307s tests/test_utils.py::test_ensure_type_9 PASSED [ 94%] 307s tests/test_utils.py::test_ensure_type_10 PASSED [ 94%] 307s tests/test_utils.py::test_ensure_type_11 PASSED [ 94%] 307s tests/test_utils.py::test_ensure_type_12 PASSED [ 94%] 307s tests/test_utils.py::test_ensure_type_13 PASSED [ 94%] 307s tests/test_utils.py::test_ensure_type_14 PASSED [ 94%] 307s tests/test_utils.py::test_ensure_type_15 PASSED [ 94%] 307s tests/test_utils.py::test_delay_import_fail_1 PASSED [ 94%] 307s tests/test_utils.py::test_delay_import PASSED [ 94%] 307s tests/test_utils.py::test_unit_0 PASSED [ 95%] 307s tests/test_utils.py::test_unit_1 PASSED [ 95%] 307s tests/test_utils.py::test_unit_2 PASSED [ 95%] 307s tests/test_utils.py::test_unit_3 PASSED [ 95%] 307s tests/test_xml.py::test_xml PASSED [ 95%] 307s tests/test_xtc.py::test_read_chunk1 PASSED [ 95%] 307s tests/test_xtc.py::test_read_stride PASSED [ 95%] 307s tests/test_xtc.py::test_read_stride_n_frames PASSED [ 95%] 307s tests/test_xtc.py::test_read_stride_offsets PASSED [ 95%] 307s tests/test_xtc.py::test_read_stride_n_frames_offsets PASSED [ 95%] 307s tests/test_xtc.py::test_read_stride_switching_offsets PASSED [ 95%] 307s tests/test_xtc.py::test_read_atomindices_1 PASSED [ 96%] 307s tests/test_xtc.py::test_read_atomindices_w_stride PASSED [ 96%] 307s tests/test_xtc.py::test_read_atomindices_2 PASSED [ 96%] 307s tests/test_xtc.py::test_read_chunk2 PASSED [ 96%] 307s tests/test_xtc.py::test_read_chunk3 PASSED [ 96%] 307s tests/test_xtc.py::test_write_0 PASSED [ 96%] 307s tests/test_xtc.py::test_write_1 PASSED [ 96%] 307s tests/test_xtc.py::test_write_2 PASSED [ 96%] 307s tests/test_xtc.py::test_read_error_0 PASSED [ 96%] 307s tests/test_xtc.py::test_write_error_0 PASSED [ 96%] 307s tests/test_xtc.py::test_read_error_1 PASSED [ 96%] 307s tests/test_xtc.py::test_read_error_2 PASSED [ 96%] 307s tests/test_xtc.py::test_xtc_write_wierd_0 PASSED [ 97%] 307s tests/test_xtc.py::test_tell PASSED [ 97%] 307s tests/test_xtc.py::test_seek PASSED [ 97%] 307s tests/test_xtc.py::test_seek_natoms9 PASSED [ 97%] 307s tests/test_xtc.py::test_seek_out_of_bounds PASSED [ 97%] 307s tests/test_xtc.py::test_ragged_1 PASSED [ 97%] 307s tests/test_xtc.py::test_ragged_2 PASSED [ 97%] 307s tests/test_xtc.py::test_short_traj PASSED [ 97%] 307s tests/test_xtc.py::test_flush PASSED [ 97%] 307s tests/test_xyz.py::test_read_0 PASSED [ 97%] 307s tests/test_xyz.py::test_read_1 PASSED [ 97%] 307s tests/test_xyz.py::test_read_gz PASSED [ 98%] 307s tests/test_xyz.py::test_read_write PASSED [ 98%] 307s tests/test_xyz.py::test_mdwrite PASSED [ 98%] 307s tests/test_xyz.py::test_multiread PASSED [ 98%] 307s tests/test_xyz.py::test_seek PASSED [ 98%] 307s tests/test_xyz.py::test_len PASSED [ 98%] 307s tests/test_zipped.py::test_read_gz PASSED [ 98%] 307s tests/test_zipped.py::test_write_gz PASSED [ 98%] 307s tests/test_zipped.py::test_read_bz2 PASSED [ 98%] 307s tests/test_zipped.py::test_write_bz2 PASSED [ 98%] 309s examples/test_examples.py::test_example_notebook[two-pass-clustering.ipynb] PASSED [ 98%] 310s examples/test_examples.py::test_example_notebook[rmsd-benchmark.ipynb] PASSED [ 99%] 310s examples/test_examples.py::test_example_notebook[hbonds.ipynb] SKIPPED [ 99%] 311s examples/test_examples.py::test_example_notebook[rmsd-drift.ipynb] PASSED [ 99%] 311s examples/test_examples.py::test_example_notebook[native-contact.ipynb] SKIPPED [ 99%] 312s examples/test_examples.py::test_example_notebook[atom-selection.ipynb] PASSED [ 99%] 314s examples/test_examples.py::test_example_notebook[centroids.ipynb] PASSED [ 99%] 314s examples/test_examples.py::test_example_notebook[simulation-with-openmm.ipynb] SKIPPED [ 99%] 315s examples/test_examples.py::test_example_notebook[ramachandran-plot.ipynb] PASSED [ 99%] 316s examples/test_examples.py::test_example_notebook[iterload.ipynb] PASSED [ 99%] 317s examples/test_examples.py::test_example_notebook[clustering.ipynb] PASSED [ 99%] 319s examples/test_examples.py::test_example_notebook[solvent-accessible-surface-area.ipynb] PASSED [ 99%] 321s examples/test_examples.py::test_example_notebook[principal-components.ipynb] PASSED [100%] 321s 321s =================================== FAILURES =================================== 321s ______________________________ test_pdb_from_url _______________________________ 321s 321s def test_pdb_from_url(): 321s # load pdb from URL 321s > t1 = load_pdb("http://www.rcsb.org/pdb/files/4ZUO.pdb.gz") 321s 321s tests/test_pdb.py:212: 321s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 321s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:152: in load_pdb 321s with PDBTrajectoryFile(filename, standard_names=standard_names, top=top) as f: 321s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:282: in __init__ 321s self._file = urlopen(filename) 321s /usr/lib/python3.12/urllib/request.py:215: in urlopen 321s return opener.open(url, data, timeout) 321s /usr/lib/python3.12/urllib/request.py:521: in open 321s response = meth(req, response) 321s /usr/lib/python3.12/urllib/request.py:630: in http_response 321s response = self.parent.error( 321s /usr/lib/python3.12/urllib/request.py:559: in error 321s return self._call_chain(*args) 321s /usr/lib/python3.12/urllib/request.py:492: in _call_chain 321s result = func(*args) 321s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 321s 321s self = 321s req = 321s fp = , code = 403 321s msg = 'Forbidden', hdrs = 321s 321s def http_error_default(self, req, fp, code, msg, hdrs): 321s > raise HTTPError(req.full_url, code, msg, hdrs, fp) 321s E urllib.error.HTTPError: HTTP Error 403: Forbidden 321s 321s /usr/lib/python3.12/urllib/request.py:639: HTTPError 321s _____________________________ test_1vii_url_and_gz _____________________________ 321s 321s get_fn = ._get_fn at 0x7135ce679940> 321s 321s def test_1vii_url_and_gz(get_fn): 321s > t1 = load_pdb("http://www.rcsb.org/pdb/files/1vii.pdb.gz") 321s 321s tests/test_pdb.py:259: 321s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 321s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:152: in load_pdb 321s with PDBTrajectoryFile(filename, standard_names=standard_names, top=top) as f: 321s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:282: in __init__ 321s self._file = urlopen(filename) 321s /usr/lib/python3.12/urllib/request.py:215: in urlopen 321s return opener.open(url, data, timeout) 321s /usr/lib/python3.12/urllib/request.py:521: in open 321s response = meth(req, response) 321s /usr/lib/python3.12/urllib/request.py:630: in http_response 321s response = self.parent.error( 321s /usr/lib/python3.12/urllib/request.py:559: in error 321s return self._call_chain(*args) 321s /usr/lib/python3.12/urllib/request.py:492: in _call_chain 321s result = func(*args) 321s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 321s 321s self = 321s req = 321s fp = , code = 403 321s msg = 'Forbidden', hdrs = 321s 321s def http_error_default(self, req, fp, code, msg, hdrs): 321s > raise HTTPError(req.full_url, code, msg, hdrs, fp) 321s E urllib.error.HTTPError: HTTP Error 403: Forbidden 321s 321s /usr/lib/python3.12/urllib/request.py:639: HTTPError 321s =============================== warnings summary =============================== 321s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 321s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 321s given by the platformdirs library. To remove this warning and 321s see the appropriate new directories, set the environment variable 321s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 321s The use of platformdirs will be the default in `jupyter_core` v6 321s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 321s 321s examples/test_examples.py:26 321s /tmp/autopkgtest.rpGlbR/build.G5Q/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 321s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 321s 321s tests/test_arc.py::test_read_arctraj 321s tests/test_order.py::test_nematic_order 321s tests/test_order.py::test_director 321s tests/test_order.py::test_inertia 321s tests/test_order.py::test_nematic_order_args 321s tests/test_shape.py::test_gyration 321s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:204: RuntimeWarning: divide by zero encountered in divide 321s particle_density = traj.top.n_atoms / traj.unitcell_volumes[0] 321s 321s tests/test_arc.py: 1 warning 321s tests/test_gro.py: 3 warnings 321s tests/test_order.py: 4 warnings 321s tests/test_shape.py: 4 warnings 321s /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. 321s warnings.warn( 321s 321s tests/test_contact.py::test_contact_0 321s tests/test_contact.py::test_contact_4 321s /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. 321s warnings.warn( 321s 321s tests/test_contact.py::test_contact_3 321s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:271: RuntimeWarning: overflow encountered in exp 321s np.exp( 321s 321s tests/test_contact.py::test_contact_3 321s /tmp/autopkgtest.rpGlbR/build.G5Q/src/tests/test_contact.py:114: RuntimeWarning: divide by zero encountered in divide 321s assert np.allclose( 321s 321s tests/test_dcd.py::test_do_overwrite 321s tests/test_dcd.py::test_ragged_1 321s tests/test_dcd.py::test_ragged_2 321s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting xyz dtype=float64 to 321s warnings.warn( 321s 321s tests/test_distance.py::test_6 321s :488: RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject 321s 321s tests/test_drid.py::test_drid_2 321s /tmp/autopkgtest.rpGlbR/build.G5Q/src/tests/test_drid.py:62: RuntimeWarning: divide by zero encountered in divide 321s recip = 1 / squareform(pdist(t.xyz[i])) 321s 321s tests/test_geometry.py::test_dihedral_indices 321s tests/test_geometry.py::test_dihedral_indices 321s /usr/lib/python3/dist-packages/mdtraj/geometry/dihedral.py:237: DeprecationWarning: Passing a Trajectory object to _atom_sequence isdeprecated. Please pass a Topology object 321s warnings.warn( 321s 321s tests/test_gro.py::test_load 321s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq 321s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:364: UserWarning: WARNING: two consecutive residues with same number (GST, HST) 321s warnings.warn( 321s 321s tests/test_trajectory.py::test_float_atom_indices_exception[gro] 321s /usr/lib/python3/dist-packages/mdtraj/core/topology.py:84: UserWarning: atom_indices are not monotonically increasing 321s warnings.warn("atom_indices are not monotonically increasing") 321s 321s tests/test_trajectory.py::test_array_vs_matrix 321s /tmp/autopkgtest.rpGlbR/build.G5Q/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. 321s xyz_mat = np.matrix(xyz) 321s 321s tests/test_utils.py::test_ensure_type_8 321s tests/test_utils.py::test_ensure_type_9 321s tests/test_utils.py::test_ensure_type_13 321s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=float64 to 321s warnings.warn( 321s 321s tests/test_utils.py::test_ensure_type_11 321s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=int64 to 321s warnings.warn( 321s 321s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 321s =========================== short test summary info ============================ 321s SKIPPED [1] tests/test_dihedral.py:56: pymol executable not found 321s SKIPPED [1] tests/test_dihedral.py:181: pymol executable not found 321s SKIPPED [15] tests/test_docstrings.py:37: Skip checking certain modules' docstrings 321s SKIPPED [1] tests/test_dssp.py:48: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 321s SKIPPED [1] tests/test_dssp.py:56: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 321s SKIPPED [1] tests/test_dssp.py:63: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 321s SKIPPED [1] tests/test_geometry.py:300: Not doing performance testing 321s SKIPPED [1] tests/test_geometry.py:322: Not doing performance testing 321s SKIPPED [1] tests/test_hbonds.py:44: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 321s SKIPPED [1] tests/test_hdf5.py:103: requires openmm.units 321s SKIPPED [1] tests/test_hdf5.py:154: requires openmm.units 321s SKIPPED [1] tests/test_hdf5.py:221: requires openmm.units 321s SKIPPED [1] tests/test_mol2.py:59: Requires obabel 321s SKIPPED [1] tests/test_netcdf.py:271: This test requires cpptraj from AmberTools to be installed (http://ambermd.org) 321s SKIPPED [1] tests/test_nmr.py:11: SPARTA+ binary not found 321s SKIPPED [1] tests/test_nmr.py:26: PPM binary not found 321s SKIPPED [1] tests/test_nmr.py:42: SHIFTX2 binary not found or running on travis. 321s SKIPPED [1] tests/test_pdbx.py:43: test_pdbx.py needs OpenMM. 321s SKIPPED [2] tests/test_psf.py:93: This test requires the VMD executable: http://www.ks.uiuc.edu/Research/vmd/ 321s SKIPPED [1] tests/test_rdf.py:64: Binning does not match up with gromacs currently. 321s SKIPPED [1] tests/test_rdf.py:200: Binning does not match up with gromacs currently. 321s SKIPPED [1] tests/test_reporter.py:58: test_reporter.py needs OpenMM. 321s SKIPPED [1] tests/test_reporter.py:145: test_reporter.py needs OpenMM. 321s SKIPPED [1] tests/test_reporter.py:245: test_reporter.py needs OpenMM. 321s SKIPPED [1] tests/test_selection.py:267: failed to parse selection 321s SKIPPED [1] tests/test_thermodynamic_properties.py:161: Thermal expansion test doesn't work. 321s SKIPPED [1] tests/test_topology.py:44: needs OpenMM 321s SKIPPED [1] tests/test_topology.py:61: needs OpenMM 321s SKIPPED [1] tests/test_topology.py:192: needs OpenMM 321s SKIPPED [1] tests/test_trajectory.py:129: xyz does not store box information 321s SKIPPED [1] tests/test_trajectory.py:129: xyz.gz does not store box information 321s SKIPPED [1] tests/test_trajectory.py:129: lh5 does not store box information 321s SKIPPED [1] tests/test_trajectory.py:129: pdb does not store box information 321s SKIPPED [1] tests/test_trajectory.py:129: pdb.gz does not store box information 321s SKIPPED [1] tests/test_trajectory.py:226: mdcrd can only store rectilinear boxes 321s SKIPPED [1] tests/test_trajectory.py:224: ncrst can only store 1 frame per file 321s SKIPPED [1] tests/test_trajectory.py:224: rst7 can only store 1 frame per file 321s SKIPPED [14] tests/test_trajectory.py:248: mdcrd can only store rectilinear boxes 321s SKIPPED [14] tests/test_trajectory.py:246: ncrst can only store 1 frame per file 321s SKIPPED [14] tests/test_trajectory.py:246: rst7 can only store 1 frame per file 321s SKIPPED [4] tests/test_trajectory.py:256: dtr needs to write unitcells 321s SKIPPED [4] tests/test_trajectory.py:256: lammpstrj needs to write unitcells 321s SKIPPED [2] tests/test_trajectory.py:640: Only 1 frame per file format 321s SKIPPED [2] examples/test_examples.py:77: Network access required 321s SKIPPED [1] examples/test_examples.py:77: Openmm required for example notebook `simulation-with-openmm.ipynb` 321s XFAIL tests/test_trajectory.py::test_read_path[ncrst] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_path[rst7] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[ncrst-nc] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[ncrst-h5] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xtc] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[ncrst-trr] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dcd] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[ncrst-mdcrd] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dtr] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lh5] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[ncrst-ncrst] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[ncrst-rst7] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[ncrst-gro] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[rst7-nc] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[rst7-h5] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[rst7-xtc] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[rst7-trr] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[rst7-dcd] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[rst7-mdcrd] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[rst7-dtr] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz.gz] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[rst7-lammpstrj] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[rst7-lh5] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb.gz] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[rst7-ncrst] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[rst7-rst7] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_read_write[rst7-gro] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_load[ncrst] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_load[rst7] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[rst7] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_load_combination[ncrst] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_load_combination[rst7] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_seek_read_mode[xyz.gz] - reason: This is broken 321s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb] - reason: PDB Files don't support seeking 321s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb.gz] - reason: PDB Files don't support seeking 321s XFAIL tests/test_trajectory.py::test_seek_read_mode[ncrst] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_seek_read_mode[rst7] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_seek_read_mode[gro] - reason: This is broken 321s XFAIL tests/test_trajectory.py::test_load_frame[dtr] - reason: DTR doesn't load a single frame properly 321s XFAIL tests/test_trajectory.py::test_load_frame[ncrst] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_load_frame[rst7] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_load_frame[gro] - reason: Gro doesn't implement seek 321s XFAIL tests/test_trajectory.py::test_iterload[dtr] - reason: This is broken with dtr 321s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb] - reason: PDB Iterloads an extra frame!! 321s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb.gz] - reason: PDB Iterloads an extra frame!! 321s XFAIL tests/test_trajectory.py::test_iterload_skip[ncrst] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_iterload_skip[rst7] - reason: These reference files don't exist yet 321s XFAIL tests/test_trajectory.py::test_iterload_skip[gro] - reason: Not implemented for some reason 321s XFAIL tests/test_trajectory.py::test_force_overwrite[dtr] - reason: This is broken with dtr 321s XFAIL tests/test_trajectory.py::test_unitcell[dtr] - reason: dtr seems to need unit vectors 321s XFAIL tests/test_trajectory.py::test_unitcell[lammpstrj] - reason: lammpstrj seems to need unit vectors 321s XFAIL tests/test_trajectory.py::test_unitcell[ncrst] - reason: ncrst seems to need unit vectors 321s XFAIL tests/test_trajectory.py::test_unitcell[rst7] - reason: rst7 seems to need unit vectors 321s FAILED tests/test_pdb.py::test_pdb_from_url - urllib.error.HTTPError: HTTP Er... 321s FAILED tests/test_pdb.py::test_1vii_url_and_gz - urllib.error.HTTPError: HTTP... 321s = 2 failed, 957 passed, 107 skipped, 2 deselected, 61 xfailed, 39 warnings in 198.09s (0:03:18) = 321s autopkgtest [08:59:18]: test command1: -----------------------] 322s command1 FAIL non-zero exit status 1 322s autopkgtest [08:59:19]: test command1: - - - - - - - - - - results - - - - - - - - - - 323s autopkgtest [08:59:20]: @@@@@@@@@@@@@@@@@@@@ summary 323s command1 FAIL non-zero exit status 1 344s nova [W] Skipping flock for amd64 344s Creating nova instance adt-plucky-amd64-mdtraj-20241113-085357-juju-7f2275-prod-proposed-migration-environment-20-2582060d-857b-4159-ab7a-828362947049 from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 62c21ac4-2290-4c8d-8313-dddd18eacff4)...