0s autopkgtest [00:21:40]: starting date and time: 2024-06-08 00:21:40+0000 0s autopkgtest [00:21:40]: git checkout: 433ed4cb Merge branch 'skia/nova_flock' into 'ubuntu/5.34+prod' 0s autopkgtest [00:21:40]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.8wxlrrjo/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest,src:astropy --apt-upgrade mdtraj --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.2.2-1ubuntu1 astropy/6.0.1-4' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@lcy02-12.secgroup --name adt-oracular-amd64-mdtraj-20240608-002140-juju-7f2275-prod-proposed-migration-environment-3-5ab103c8-eebc-42ac-bf52-7b931e451b24 --image adt/ubuntu-oracular-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 152s autopkgtest [00:24:12]: testbed dpkg architecture: amd64 152s autopkgtest [00:24:12]: testbed apt version: 2.9.3 152s autopkgtest [00:24:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup 152s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 153s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [44.3 kB] 153s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [339 kB] 153s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7972 B] 153s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2852 B] 153s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [37.8 kB] 153s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [65.6 kB] 153s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [27.4 kB] 153s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [9340 B] 153s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [124 kB] 153s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [300 kB] 153s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [9280 B] 153s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3368 B] 153s Fetched 1081 kB in 0s (3979 kB/s) 153s Reading package lists... 154s Reading package lists... 155s Building dependency tree... 155s Reading state information... 155s Calculating upgrade... 155s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 155s Reading package lists... 155s Building dependency tree... 155s Reading state information... 156s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 156s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 156s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 156s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 156s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 157s Reading package lists... 157s Reading package lists... 157s Building dependency tree... 157s Reading state information... 158s Calculating upgrade... 158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 158s Reading package lists... 158s Building dependency tree... 158s Reading state information... 159s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 160s autopkgtest [00:24:20]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024 160s autopkgtest [00:24:20]: @@@@@@@@@@@@@@@@@@@@ apt-source mdtraj 161s Get:1 http://ftpmaster.internal/ubuntu oracular/universe mdtraj 1.9.9-1ubuntu2 (dsc) [2701 B] 161s Get:2 http://ftpmaster.internal/ubuntu oracular/universe mdtraj 1.9.9-1ubuntu2 (tar) [21.7 MB] 161s Get:3 http://ftpmaster.internal/ubuntu oracular/universe mdtraj 1.9.9-1ubuntu2 (diff) [296 kB] 161s gpgv: Signature made Mon Apr 1 06:57:01 2024 UTC 161s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 161s gpgv: Can't check signature: No public key 161s dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.9.9-1ubuntu2.dsc: no acceptable signature found 162s autopkgtest [00:24:22]: testing package mdtraj version 1.9.9-1ubuntu2 163s autopkgtest [00:24:23]: build not needed 164s autopkgtest [00:24:24]: test command1: preparing testbed 164s Reading package lists... 165s Building dependency tree... 165s Reading state information... 165s Starting pkgProblemResolver with broken count: 0 165s Starting 2 pkgProblemResolver with broken count: 0 165s Done 165s The following additional packages will be installed: 165s blt fonts-lyx gdb libaec0 libbabeltrace1 libblas3 libblosc1 libblosc2-3 165s libdebuginfod-common libdebuginfod1t64 libgfortran5 libgomp1 libgraphite2-3 165s libharfbuzz0b libhdf5-103-1t64 libimagequant0 libipt2 libjs-jquery 165s libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 libnorm1t64 libopenjp2-7 165s libpgm-5.3-0t64 libpython3.12t64 libqhull-r8.0 libraqm0 libsnappy1v5 165s libsodium23 libsource-highlight-common libsource-highlight4t64 libsz2 165s libtcl8.6 libtk8.6 libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 165s libxss1 libzmq5 python-matplotlib-data python-tables-data python3-appdirs 165s python3-asttokens python3-astunparse python3-brotli python3-bytecode 165s python3-comm python3-contourpy python3-coverage python3-cpuinfo 165s python3-cycler python3-dateutil python3-debugpy python3-decorator 165s python3-entrypoints python3-executing python3-fastjsonschema 165s python3-fonttools python3-fs python3-iniconfig python3-ipykernel 165s python3-ipython python3-jedi python3-joblib python3-jupyter-client 165s python3-jupyter-core python3-kiwisolver python3-lxml python3-lz4 165s python3-matplotlib python3-matplotlib-inline python3-mdtraj python3-mpmath 165s python3-nbformat python3-nest-asyncio python3-networkx python3-numexpr 165s python3-numpy python3-packaging python3-pandas python3-pandas-lib 165s python3-parso python3-pexpect python3-pil python3-pil.imagetk 165s python3-platformdirs python3-pluggy python3-prompt-toolkit python3-psutil 165s python3-ptyprocess python3-pure-eval python3-py python3-pydevd 165s python3-pytest python3-scipy python3-sklearn python3-sklearn-lib 165s python3-stack-data python3-sympy python3-tables python3-tables-lib 165s python3-threadpoolctl python3-tk python3-tornado python3-traitlets 165s python3-typeshed python3-ufolib2 python3-unicodedata2 python3-wcwidth 165s python3-zmq tk8.6-blt2.5 unicode-data x11-common 165s Suggested packages: 165s blt-demo gdb-doc gdbserver libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 165s python-bytecode-doc python-coverage-doc python-cycler-doc 165s python-fastjsonschema-doc python-ipython-doc python3-pip python-lxml-doc 165s cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 165s inkscape ipython3 librsvg2-common python3-cairocffi python3-gi-cairo 165s python3-gobject python3-pyqt5 python3-sip texlive-extra-utils 165s texlive-latex-extra python-mdtraj-doc python-mpmath-doc python3-gmpy2 165s python3-gdal python3-pydot python3-pygraphviz gcc gfortran python-numpy-doc 165s python3-dev python-pandas-doc python3-statsmodels python-pexpect-doc 165s python-pil-doc subversion pydevd python-scipy-doc python3-dap 165s python-sklearn-doc texlive-fonts-extra python-sympy-doc python3-netcdf4 165s python-tables-doc vitables tix python3-tk-dbg python3-pycurl 165s python-tornado-doc python3-twisted 165s Recommended packages: 165s libc-dbg javascript-common python3-simplejson python3-bs4 python3-cssselect 165s python3-html5lib python3-bottleneck python3-odf python3-openpyxl 165s python3-numba python3-olefile g++ | c++-compiler isympy-common 165s The following NEW packages will be installed: 165s autopkgtest-satdep blt fonts-lyx gdb libaec0 libbabeltrace1 libblas3 165s libblosc1 libblosc2-3 libdebuginfod-common libdebuginfod1t64 libgfortran5 165s libgomp1 libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libimagequant0 165s libipt2 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 165s libnorm1t64 libopenjp2-7 libpgm-5.3-0t64 libpython3.12t64 libqhull-r8.0 165s libraqm0 libsnappy1v5 libsodium23 libsource-highlight-common 165s libsource-highlight4t64 libsz2 libtcl8.6 libtk8.6 libwebpdemux2 libwebpmux3 165s libxft2 libxrender1 libxslt1.1 libxss1 libzmq5 python-matplotlib-data 165s python-tables-data python3-appdirs python3-asttokens python3-astunparse 165s python3-brotli python3-bytecode python3-comm python3-contourpy 165s python3-coverage python3-cpuinfo python3-cycler python3-dateutil 165s python3-debugpy python3-decorator python3-entrypoints python3-executing 165s python3-fastjsonschema python3-fonttools python3-fs python3-iniconfig 165s python3-ipykernel python3-ipython python3-jedi python3-joblib 165s python3-jupyter-client python3-jupyter-core python3-kiwisolver python3-lxml 165s python3-lz4 python3-matplotlib python3-matplotlib-inline python3-mdtraj 165s python3-mpmath python3-nbformat python3-nest-asyncio python3-networkx 165s python3-numexpr python3-numpy python3-packaging python3-pandas 165s python3-pandas-lib python3-parso python3-pexpect python3-pil 165s python3-pil.imagetk python3-platformdirs python3-pluggy 165s python3-prompt-toolkit python3-psutil python3-ptyprocess python3-pure-eval 165s python3-py python3-pydevd python3-pytest python3-scipy python3-sklearn 165s python3-sklearn-lib python3-stack-data python3-sympy python3-tables 165s python3-tables-lib python3-threadpoolctl python3-tk python3-tornado 165s python3-traitlets python3-typeshed python3-ufolib2 python3-unicodedata2 165s python3-wcwidth python3-zmq tk8.6-blt2.5 unicode-data x11-common 165s 0 upgraded, 117 newly installed, 0 to remove and 0 not upgraded. 165s Need to get 97.3 MB/97.3 MB of archives. 165s After this operation, 463 MB of additional disk space will be used. 165s Get:1 /tmp/autopkgtest.hoy8Kc/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [764 B] 165s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libdebuginfod-common all 0.191-1 [14.6 kB] 165s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1build1 [988 kB] 165s Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 165s Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 165s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 165s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 165s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 libtk8.6 amd64 8.6.14-1build1 [779 kB] 165s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 165s Get:10 http://ftpmaster.internal/ubuntu oracular/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 165s Get:11 http://ftpmaster.internal/ubuntu oracular/universe amd64 fonts-lyx all 2.4.0-1 [171 kB] 165s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 libbabeltrace1 amd64 1.5.11-3build3 [164 kB] 166s Get:13 http://ftpmaster.internal/ubuntu oracular/main amd64 libdebuginfod1t64 amd64 0.191-1 [17.1 kB] 166s Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 libipt2 amd64 2.0.6-1build1 [45.7 kB] 166s Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 libpython3.12t64 amd64 3.12.3-1 [2339 kB] 166s Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 libsource-highlight-common all 3.1.9-4.3build1 [64.2 kB] 166s Get:17 http://ftpmaster.internal/ubuntu oracular/main amd64 libsource-highlight4t64 amd64 3.1.9-4.3build1 [258 kB] 166s Get:18 http://ftpmaster.internal/ubuntu oracular/main amd64 gdb amd64 15.0.50.20240403-0ubuntu1 [4010 kB] 166s Get:19 http://ftpmaster.internal/ubuntu oracular/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 166s Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas3 amd64 3.12.0-3build1 [238 kB] 166s Get:21 http://ftpmaster.internal/ubuntu oracular/main amd64 libsnappy1v5 amd64 1.2.1-1 [30.4 kB] 166s Get:22 http://ftpmaster.internal/ubuntu oracular/universe amd64 libblosc1 amd64 1.21.5+ds-1build1 [36.2 kB] 166s Get:23 http://ftpmaster.internal/ubuntu oracular/universe amd64 libblosc2-3 amd64 2.14.4+ds-2 [164 kB] 166s Get:24 http://ftpmaster.internal/ubuntu oracular/main amd64 libgfortran5 amd64 14.1.0-1ubuntu1 [928 kB] 166s Get:25 http://ftpmaster.internal/ubuntu oracular/main amd64 libgomp1 amd64 14.1.0-1ubuntu1 [148 kB] 166s Get:26 http://ftpmaster.internal/ubuntu oracular/main amd64 libgraphite2-3 amd64 1.3.14-2build1 [73.0 kB] 166s Get:27 http://ftpmaster.internal/ubuntu oracular/main amd64 libharfbuzz0b amd64 8.3.0-2build2 [469 kB] 166s Get:28 http://ftpmaster.internal/ubuntu oracular/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 166s Get:29 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.1ubuntu4 [1270 kB] 166s Get:30 http://ftpmaster.internal/ubuntu oracular/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 166s Get:31 http://ftpmaster.internal/ubuntu oracular/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 166s Get:32 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 166s Get:33 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack3 amd64 3.12.0-3build1 [2650 kB] 166s Get:34 http://ftpmaster.internal/ubuntu oracular/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 166s Get:35 http://ftpmaster.internal/ubuntu oracular/main amd64 liblcms2-2 amd64 2.14-2build1 [161 kB] 166s Get:36 http://ftpmaster.internal/ubuntu oracular/universe amd64 libnorm1t64 amd64 1.5.9+dfsg-3.1build1 [154 kB] 166s Get:37 http://ftpmaster.internal/ubuntu oracular/universe amd64 libpgm-5.3-0t64 amd64 5.3.128~dfsg-2.1build1 [167 kB] 166s Get:38 http://ftpmaster.internal/ubuntu oracular/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 166s Get:39 http://ftpmaster.internal/ubuntu oracular/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 166s Get:40 http://ftpmaster.internal/ubuntu oracular/main amd64 libsodium23 amd64 1.0.18-1build3 [161 kB] 166s Get:41 http://ftpmaster.internal/ubuntu oracular/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 166s Get:42 http://ftpmaster.internal/ubuntu oracular/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 166s Get:43 http://ftpmaster.internal/ubuntu oracular/main amd64 libxslt1.1 amd64 1.1.39-0exp1build1 [167 kB] 166s Get:44 http://ftpmaster.internal/ubuntu oracular/universe amd64 libzmq5 amd64 4.3.5-1build2 [260 kB] 166s Get:45 http://ftpmaster.internal/ubuntu oracular/universe amd64 python-matplotlib-data all 3.6.3-2ubuntu1 [2937 kB] 166s Get:46 http://ftpmaster.internal/ubuntu oracular/universe amd64 python-tables-data all 3.9.2-2build1 [49.3 kB] 166s Get:47 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 166s Get:48 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-asttokens all 2.4.1-1 [20.9 kB] 166s Get:49 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-astunparse all 1.6.3-2 [13.5 kB] 166s Get:50 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 166s Get:51 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-bytecode all 0.15.1-3 [44.7 kB] 166s Get:52 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-traitlets all 5.5.0-2 [85.0 kB] 166s Get:53 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-comm all 0.2.1-1 [7016 B] 166s Get:54 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-numpy amd64 1:1.26.4+ds-10 [4437 kB] 166s Get:55 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-contourpy amd64 1.0.7-3 [181 kB] 166s Get:56 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-coverage amd64 7.4.4+dfsg1-0ubuntu2 [147 kB] 166s Get:57 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-cpuinfo all 9.0.0+git20221119-1 [21.4 kB] 166s Get:58 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 166s Get:59 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 166s Get:60 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pydevd amd64 2.10.0+ds-10ubuntu1 [637 kB] 166s Get:61 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-debugpy all 1.8.0+ds-4ubuntu4 [67.6 kB] 166s Get:62 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 166s Get:63 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-entrypoints all 0.4-2 [7146 B] 166s Get:64 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-executing all 2.0.1-0.1 [23.3 kB] 166s Get:65 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-fastjsonschema all 2.19.1-1 [19.7 kB] 166s Get:66 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-scipy amd64 1.11.4-10 [15.5 MB] 166s Get:67 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB] 166s Get:68 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 166s Get:69 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-sympy all 1.12-8 [3966 kB] 166s Get:70 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 166s Get:71 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-lxml amd64 5.2.1-1 [1243 kB] 166s Get:72 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 166s Get:73 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build1 [362 kB] 166s Get:74 http://ftpmaster.internal/ubuntu oracular/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 166s Get:75 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 166s Get:76 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 166s Get:77 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-parso all 0.8.3-1 [67.2 kB] 166s Get:78 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-typeshed all 0.0~git20231111.6764465-3 [1274 kB] 166s Get:79 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-jedi all 0.19.1+ds1-1 [693 kB] 166s Get:80 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 166s Get:81 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-ptyprocess all 0.7.0-5 [15.1 kB] 166s Get:82 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-pexpect all 4.9-2 [48.1 kB] 166s Get:83 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-wcwidth all 0.2.5+dfsg1-1.1ubuntu1 [22.5 kB] 166s Get:84 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-prompt-toolkit all 3.0.46-1 [256 kB] 166s Get:85 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pure-eval all 0.2.2-2 [11.1 kB] 166s Get:86 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-stack-data all 0.6.3-1 [22.0 kB] 166s Get:87 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-ipython all 8.20.0-1ubuntu1 [561 kB] 166s Get:88 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-platformdirs all 4.2.1-1 [16.3 kB] 166s Get:89 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-jupyter-core all 5.3.2-2 [25.5 kB] 166s Get:90 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-nest-asyncio all 1.5.4-1 [6256 B] 166s Get:91 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-tornado amd64 6.4.0-2 [297 kB] 166s Get:92 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-py all 1.11.0-2 [72.7 kB] 166s Get:93 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-zmq amd64 24.0.1-5build1 [286 kB] 166s Get:94 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-jupyter-client all 7.4.9-2ubuntu1 [90.5 kB] 166s Get:95 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-packaging all 24.0-1 [41.1 kB] 166s Get:96 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-psutil amd64 5.9.8-2build2 [195 kB] 166s Get:97 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-ipykernel all 6.29.3-1ubuntu1 [82.6 kB] 166s Get:98 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-joblib all 1.3.2-2 [208 kB] 166s Get:99 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-kiwisolver amd64 1.4.5-1 [51.0 kB] 166s Get:100 http://ftpmaster.internal/ubuntu oracular/main amd64 libopenjp2-7 amd64 2.5.0-2build3 [173 kB] 166s Get:101 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-pil amd64 10.3.0-2 [457 kB] 166s Get:102 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-tk amd64 3.12.3-0ubuntu1 [102 kB] 166s Get:103 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pil.imagetk amd64 10.3.0-2 [9224 B] 166s Get:104 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-matplotlib amd64 3.6.3-2ubuntu1 [6080 kB] 166s Get:105 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 166s Get:106 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pandas-lib amd64 2.1.4+dfsg-8 [4450 kB] 166s Get:107 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pandas all 2.1.4+dfsg-8 [3042 kB] 166s Get:108 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-numexpr amd64 2.10.0-2 [86.2 kB] 166s Get:109 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-tables-lib amd64 3.9.2-2build1 [520 kB] 166s Get:110 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-tables all 3.9.2-2build1 [344 kB] 166s Get:111 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-mdtraj amd64 1.9.9-1ubuntu2 [1140 kB] 166s Get:112 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-nbformat all 5.9.1-1 [41.2 kB] 166s Get:113 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 166s Get:114 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 python3-pytest all 8.2.2-1ubuntu1 [250 kB] 166s Get:115 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 166s Get:116 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-1 [3795 kB] 166s Get:117 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-sklearn all 1.4.2+dfsg-1 [2261 kB] 167s Preconfiguring packages ... 167s Fetched 97.3 MB in 1s (125 MB/s) 167s Selecting previously unselected package libdebuginfod-common. 167s (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 ... 74365 files and directories currently installed.) 167s Preparing to unpack .../000-libdebuginfod-common_0.191-1_all.deb ... 167s Unpacking libdebuginfod-common (0.191-1) ... 167s Selecting previously unselected package libtcl8.6:amd64. 167s Preparing to unpack .../001-libtcl8.6_8.6.14+dfsg-1build1_amd64.deb ... 167s Unpacking libtcl8.6:amd64 (8.6.14+dfsg-1build1) ... 167s Selecting previously unselected package libxrender1:amd64. 167s Preparing to unpack .../002-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 167s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 167s Selecting previously unselected package libxft2:amd64. 167s Preparing to unpack .../003-libxft2_2.3.6-1build1_amd64.deb ... 167s Unpacking libxft2:amd64 (2.3.6-1build1) ... 167s Selecting previously unselected package x11-common. 167s Preparing to unpack .../004-x11-common_1%3a7.7+23ubuntu3_all.deb ... 167s Unpacking x11-common (1:7.7+23ubuntu3) ... 167s Selecting previously unselected package libxss1:amd64. 167s Preparing to unpack .../005-libxss1_1%3a1.2.3-1build3_amd64.deb ... 167s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 167s Selecting previously unselected package libtk8.6:amd64. 167s Preparing to unpack .../006-libtk8.6_8.6.14-1build1_amd64.deb ... 167s Unpacking libtk8.6:amd64 (8.6.14-1build1) ... 167s Selecting previously unselected package tk8.6-blt2.5. 167s Preparing to unpack .../007-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 167s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 167s Selecting previously unselected package blt. 167s Preparing to unpack .../008-blt_2.5.3+dfsg-7build1_amd64.deb ... 167s Unpacking blt (2.5.3+dfsg-7build1) ... 167s Selecting previously unselected package fonts-lyx. 167s Preparing to unpack .../009-fonts-lyx_2.4.0-1_all.deb ... 167s Unpacking fonts-lyx (2.4.0-1) ... 167s Selecting previously unselected package libbabeltrace1:amd64. 167s Preparing to unpack .../010-libbabeltrace1_1.5.11-3build3_amd64.deb ... 167s Unpacking libbabeltrace1:amd64 (1.5.11-3build3) ... 167s Selecting previously unselected package libdebuginfod1t64:amd64. 167s Preparing to unpack .../011-libdebuginfod1t64_0.191-1_amd64.deb ... 167s Unpacking libdebuginfod1t64:amd64 (0.191-1) ... 167s Selecting previously unselected package libipt2. 167s Preparing to unpack .../012-libipt2_2.0.6-1build1_amd64.deb ... 167s Unpacking libipt2 (2.0.6-1build1) ... 167s Selecting previously unselected package libpython3.12t64:amd64. 167s Preparing to unpack .../013-libpython3.12t64_3.12.3-1_amd64.deb ... 167s Unpacking libpython3.12t64:amd64 (3.12.3-1) ... 168s Selecting previously unselected package libsource-highlight-common. 168s Preparing to unpack .../014-libsource-highlight-common_3.1.9-4.3build1_all.deb ... 168s Unpacking libsource-highlight-common (3.1.9-4.3build1) ... 168s Selecting previously unselected package libsource-highlight4t64:amd64. 168s Preparing to unpack .../015-libsource-highlight4t64_3.1.9-4.3build1_amd64.deb ... 168s Unpacking libsource-highlight4t64:amd64 (3.1.9-4.3build1) ... 168s Selecting previously unselected package gdb. 168s Preparing to unpack .../016-gdb_15.0.50.20240403-0ubuntu1_amd64.deb ... 168s Unpacking gdb (15.0.50.20240403-0ubuntu1) ... 168s Selecting previously unselected package libaec0:amd64. 168s Preparing to unpack .../017-libaec0_1.1.3-1_amd64.deb ... 168s Unpacking libaec0:amd64 (1.1.3-1) ... 168s Selecting previously unselected package libblas3:amd64. 168s Preparing to unpack .../018-libblas3_3.12.0-3build1_amd64.deb ... 168s Unpacking libblas3:amd64 (3.12.0-3build1) ... 168s Selecting previously unselected package libsnappy1v5:amd64. 168s Preparing to unpack .../019-libsnappy1v5_1.2.1-1_amd64.deb ... 168s Unpacking libsnappy1v5:amd64 (1.2.1-1) ... 168s Selecting previously unselected package libblosc1:amd64. 168s Preparing to unpack .../020-libblosc1_1.21.5+ds-1build1_amd64.deb ... 168s Unpacking libblosc1:amd64 (1.21.5+ds-1build1) ... 168s Selecting previously unselected package libblosc2-3:amd64. 168s Preparing to unpack .../021-libblosc2-3_2.14.4+ds-2_amd64.deb ... 168s Unpacking libblosc2-3:amd64 (2.14.4+ds-2) ... 168s Selecting previously unselected package libgfortran5:amd64. 168s Preparing to unpack .../022-libgfortran5_14.1.0-1ubuntu1_amd64.deb ... 168s Unpacking libgfortran5:amd64 (14.1.0-1ubuntu1) ... 168s Selecting previously unselected package libgomp1:amd64. 168s Preparing to unpack .../023-libgomp1_14.1.0-1ubuntu1_amd64.deb ... 168s Unpacking libgomp1:amd64 (14.1.0-1ubuntu1) ... 168s Selecting previously unselected package libgraphite2-3:amd64. 168s Preparing to unpack .../024-libgraphite2-3_1.3.14-2build1_amd64.deb ... 168s Unpacking libgraphite2-3:amd64 (1.3.14-2build1) ... 168s Selecting previously unselected package libharfbuzz0b:amd64. 168s Preparing to unpack .../025-libharfbuzz0b_8.3.0-2build2_amd64.deb ... 168s Unpacking libharfbuzz0b:amd64 (8.3.0-2build2) ... 168s Selecting previously unselected package libsz2:amd64. 168s Preparing to unpack .../026-libsz2_1.1.3-1_amd64.deb ... 168s Unpacking libsz2:amd64 (1.1.3-1) ... 168s Selecting previously unselected package libhdf5-103-1t64:amd64. 168s Preparing to unpack .../027-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu4_amd64.deb ... 168s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-3.1ubuntu4) ... 168s Selecting previously unselected package libimagequant0:amd64. 168s Preparing to unpack .../028-libimagequant0_2.18.0-1build1_amd64.deb ... 168s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 168s Selecting previously unselected package libjs-jquery. 168s Preparing to unpack .../029-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 168s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 168s Selecting previously unselected package libjs-jquery-ui. 168s Preparing to unpack .../030-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 168s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 168s Selecting previously unselected package liblapack3:amd64. 168s Preparing to unpack .../031-liblapack3_3.12.0-3build1_amd64.deb ... 168s Unpacking liblapack3:amd64 (3.12.0-3build1) ... 168s Selecting previously unselected package liblbfgsb0:amd64. 168s Preparing to unpack .../032-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 168s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 168s Selecting previously unselected package liblcms2-2:amd64. 168s Preparing to unpack .../033-liblcms2-2_2.14-2build1_amd64.deb ... 168s Unpacking liblcms2-2:amd64 (2.14-2build1) ... 168s Selecting previously unselected package libnorm1t64:amd64. 168s Preparing to unpack .../034-libnorm1t64_1.5.9+dfsg-3.1build1_amd64.deb ... 168s Unpacking libnorm1t64:amd64 (1.5.9+dfsg-3.1build1) ... 168s Selecting previously unselected package libpgm-5.3-0t64:amd64. 168s Preparing to unpack .../035-libpgm-5.3-0t64_5.3.128~dfsg-2.1build1_amd64.deb ... 168s Unpacking libpgm-5.3-0t64:amd64 (5.3.128~dfsg-2.1build1) ... 168s Selecting previously unselected package libqhull-r8.0:amd64. 168s Preparing to unpack .../036-libqhull-r8.0_2020.2-6build1_amd64.deb ... 168s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 169s Selecting previously unselected package libraqm0:amd64. 169s Preparing to unpack .../037-libraqm0_0.10.1-1build1_amd64.deb ... 169s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 169s Selecting previously unselected package libsodium23:amd64. 169s Preparing to unpack .../038-libsodium23_1.0.18-1build3_amd64.deb ... 169s Unpacking libsodium23:amd64 (1.0.18-1build3) ... 169s Selecting previously unselected package libwebpdemux2:amd64. 169s Preparing to unpack .../039-libwebpdemux2_1.4.0-0.1_amd64.deb ... 169s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 169s Selecting previously unselected package libwebpmux3:amd64. 169s Preparing to unpack .../040-libwebpmux3_1.4.0-0.1_amd64.deb ... 169s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 169s Selecting previously unselected package libxslt1.1:amd64. 169s Preparing to unpack .../041-libxslt1.1_1.1.39-0exp1build1_amd64.deb ... 169s Unpacking libxslt1.1:amd64 (1.1.39-0exp1build1) ... 169s Selecting previously unselected package libzmq5:amd64. 169s Preparing to unpack .../042-libzmq5_4.3.5-1build2_amd64.deb ... 169s Unpacking libzmq5:amd64 (4.3.5-1build2) ... 169s Selecting previously unselected package python-matplotlib-data. 169s Preparing to unpack .../043-python-matplotlib-data_3.6.3-2ubuntu1_all.deb ... 169s Unpacking python-matplotlib-data (3.6.3-2ubuntu1) ... 169s Selecting previously unselected package python-tables-data. 169s Preparing to unpack .../044-python-tables-data_3.9.2-2build1_all.deb ... 169s Unpacking python-tables-data (3.9.2-2build1) ... 169s Selecting previously unselected package python3-appdirs. 169s Preparing to unpack .../045-python3-appdirs_1.4.4-4_all.deb ... 169s Unpacking python3-appdirs (1.4.4-4) ... 169s Selecting previously unselected package python3-asttokens. 169s Preparing to unpack .../046-python3-asttokens_2.4.1-1_all.deb ... 169s Unpacking python3-asttokens (2.4.1-1) ... 169s Selecting previously unselected package python3-astunparse. 169s Preparing to unpack .../047-python3-astunparse_1.6.3-2_all.deb ... 169s Unpacking python3-astunparse (1.6.3-2) ... 169s Selecting previously unselected package python3-brotli. 169s Preparing to unpack .../048-python3-brotli_1.1.0-2build2_amd64.deb ... 169s Unpacking python3-brotli (1.1.0-2build2) ... 169s Selecting previously unselected package python3-bytecode. 169s Preparing to unpack .../049-python3-bytecode_0.15.1-3_all.deb ... 169s Unpacking python3-bytecode (0.15.1-3) ... 169s Selecting previously unselected package python3-traitlets. 169s Preparing to unpack .../050-python3-traitlets_5.5.0-2_all.deb ... 169s Unpacking python3-traitlets (5.5.0-2) ... 169s Selecting previously unselected package python3-comm. 169s Preparing to unpack .../051-python3-comm_0.2.1-1_all.deb ... 169s Unpacking python3-comm (0.2.1-1) ... 169s Selecting previously unselected package python3-numpy. 169s Preparing to unpack .../052-python3-numpy_1%3a1.26.4+ds-10_amd64.deb ... 169s Unpacking python3-numpy (1:1.26.4+ds-10) ... 169s Selecting previously unselected package python3-contourpy. 169s Preparing to unpack .../053-python3-contourpy_1.0.7-3_amd64.deb ... 169s Unpacking python3-contourpy (1.0.7-3) ... 169s Selecting previously unselected package python3-coverage. 169s Preparing to unpack .../054-python3-coverage_7.4.4+dfsg1-0ubuntu2_amd64.deb ... 169s Unpacking python3-coverage (7.4.4+dfsg1-0ubuntu2) ... 169s Selecting previously unselected package python3-cpuinfo. 169s Preparing to unpack .../055-python3-cpuinfo_9.0.0+git20221119-1_all.deb ... 169s Unpacking python3-cpuinfo (9.0.0+git20221119-1) ... 169s Selecting previously unselected package python3-cycler. 169s Preparing to unpack .../056-python3-cycler_0.12.1-1_all.deb ... 169s Unpacking python3-cycler (0.12.1-1) ... 169s Selecting previously unselected package python3-dateutil. 169s Preparing to unpack .../057-python3-dateutil_2.9.0-2_all.deb ... 169s Unpacking python3-dateutil (2.9.0-2) ... 169s Selecting previously unselected package python3-pydevd. 169s Preparing to unpack .../058-python3-pydevd_2.10.0+ds-10ubuntu1_amd64.deb ... 169s Unpacking python3-pydevd (2.10.0+ds-10ubuntu1) ... 169s Selecting previously unselected package python3-debugpy. 169s Preparing to unpack .../059-python3-debugpy_1.8.0+ds-4ubuntu4_all.deb ... 169s Unpacking python3-debugpy (1.8.0+ds-4ubuntu4) ... 170s Selecting previously unselected package python3-decorator. 170s Preparing to unpack .../060-python3-decorator_5.1.1-5_all.deb ... 170s Unpacking python3-decorator (5.1.1-5) ... 170s Selecting previously unselected package python3-entrypoints. 170s Preparing to unpack .../061-python3-entrypoints_0.4-2_all.deb ... 170s Unpacking python3-entrypoints (0.4-2) ... 170s Selecting previously unselected package python3-executing. 170s Preparing to unpack .../062-python3-executing_2.0.1-0.1_all.deb ... 170s Unpacking python3-executing (2.0.1-0.1) ... 170s Selecting previously unselected package python3-fastjsonschema. 170s Preparing to unpack .../063-python3-fastjsonschema_2.19.1-1_all.deb ... 170s Unpacking python3-fastjsonschema (2.19.1-1) ... 170s Selecting previously unselected package python3-scipy. 170s Preparing to unpack .../064-python3-scipy_1.11.4-10_amd64.deb ... 170s Unpacking python3-scipy (1.11.4-10) ... 170s Selecting previously unselected package python3-ufolib2. 170s Preparing to unpack .../065-python3-ufolib2_0.16.0+dfsg1-1_all.deb ... 170s Unpacking python3-ufolib2 (0.16.0+dfsg1-1) ... 170s Selecting previously unselected package python3-mpmath. 170s Preparing to unpack .../066-python3-mpmath_1.3.0-1_all.deb ... 170s Unpacking python3-mpmath (1.3.0-1) ... 170s Selecting previously unselected package python3-sympy. 170s Preparing to unpack .../067-python3-sympy_1.12-8_all.deb ... 170s Unpacking python3-sympy (1.12-8) ... 170s Selecting previously unselected package python3-fs. 170s Preparing to unpack .../068-python3-fs_2.4.16-4_all.deb ... 170s Unpacking python3-fs (2.4.16-4) ... 171s Selecting previously unselected package python3-lxml:amd64. 171s Preparing to unpack .../069-python3-lxml_5.2.1-1_amd64.deb ... 171s Unpacking python3-lxml:amd64 (5.2.1-1) ... 171s Selecting previously unselected package python3-lz4. 171s Preparing to unpack .../070-python3-lz4_4.0.2+dfsg-1build4_amd64.deb ... 171s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 171s Selecting previously unselected package python3-unicodedata2. 171s Preparing to unpack .../071-python3-unicodedata2_15.1.0+ds-1build1_amd64.deb ... 171s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 171s Selecting previously unselected package unicode-data. 171s Preparing to unpack .../072-unicode-data_15.1.0-1_all.deb ... 171s Unpacking unicode-data (15.1.0-1) ... 171s Selecting previously unselected package python3-fonttools. 171s Preparing to unpack .../073-python3-fonttools_4.46.0-1build2_amd64.deb ... 171s Unpacking python3-fonttools (4.46.0-1build2) ... 171s Selecting previously unselected package python3-iniconfig. 171s Preparing to unpack .../074-python3-iniconfig_1.1.1-2_all.deb ... 171s Unpacking python3-iniconfig (1.1.1-2) ... 171s Selecting previously unselected package python3-parso. 171s Preparing to unpack .../075-python3-parso_0.8.3-1_all.deb ... 171s Unpacking python3-parso (0.8.3-1) ... 171s Selecting previously unselected package python3-typeshed. 171s Preparing to unpack .../076-python3-typeshed_0.0~git20231111.6764465-3_all.deb ... 171s Unpacking python3-typeshed (0.0~git20231111.6764465-3) ... 172s Selecting previously unselected package python3-jedi. 172s Preparing to unpack .../077-python3-jedi_0.19.1+ds1-1_all.deb ... 172s Unpacking python3-jedi (0.19.1+ds1-1) ... 172s Selecting previously unselected package python3-matplotlib-inline. 172s Preparing to unpack .../078-python3-matplotlib-inline_0.1.6-2_all.deb ... 172s Unpacking python3-matplotlib-inline (0.1.6-2) ... 172s Selecting previously unselected package python3-ptyprocess. 172s Preparing to unpack .../079-python3-ptyprocess_0.7.0-5_all.deb ... 172s Unpacking python3-ptyprocess (0.7.0-5) ... 172s Selecting previously unselected package python3-pexpect. 172s Preparing to unpack .../080-python3-pexpect_4.9-2_all.deb ... 172s Unpacking python3-pexpect (4.9-2) ... 172s Selecting previously unselected package python3-wcwidth. 172s Preparing to unpack .../081-python3-wcwidth_0.2.5+dfsg1-1.1ubuntu1_all.deb ... 172s Unpacking python3-wcwidth (0.2.5+dfsg1-1.1ubuntu1) ... 172s Selecting previously unselected package python3-prompt-toolkit. 172s Preparing to unpack .../082-python3-prompt-toolkit_3.0.46-1_all.deb ... 172s Unpacking python3-prompt-toolkit (3.0.46-1) ... 172s Selecting previously unselected package python3-pure-eval. 172s Preparing to unpack .../083-python3-pure-eval_0.2.2-2_all.deb ... 172s Unpacking python3-pure-eval (0.2.2-2) ... 172s Selecting previously unselected package python3-stack-data. 172s Preparing to unpack .../084-python3-stack-data_0.6.3-1_all.deb ... 172s Unpacking python3-stack-data (0.6.3-1) ... 172s Selecting previously unselected package python3-ipython. 172s Preparing to unpack .../085-python3-ipython_8.20.0-1ubuntu1_all.deb ... 172s Unpacking python3-ipython (8.20.0-1ubuntu1) ... 172s Selecting previously unselected package python3-platformdirs. 172s Preparing to unpack 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python3-kiwisolver. 173s Preparing to unpack .../097-python3-kiwisolver_1.4.5-1_amd64.deb ... 173s Unpacking python3-kiwisolver (1.4.5-1) ... 173s Selecting previously unselected package libopenjp2-7:amd64. 173s Preparing to unpack .../098-libopenjp2-7_2.5.0-2build3_amd64.deb ... 173s Unpacking libopenjp2-7:amd64 (2.5.0-2build3) ... 173s Selecting previously unselected package python3-pil:amd64. 173s Preparing to unpack .../099-python3-pil_10.3.0-2_amd64.deb ... 173s Unpacking python3-pil:amd64 (10.3.0-2) ... 173s Selecting previously unselected package python3-tk:amd64. 173s Preparing to unpack .../100-python3-tk_3.12.3-0ubuntu1_amd64.deb ... 173s Unpacking python3-tk:amd64 (3.12.3-0ubuntu1) ... 173s Selecting previously unselected package python3-pil.imagetk:amd64. 173s Preparing to unpack .../101-python3-pil.imagetk_10.3.0-2_amd64.deb ... 173s Unpacking python3-pil.imagetk:amd64 (10.3.0-2) ... 173s Selecting previously unselected package python3-matplotlib. 173s Preparing to unpack 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up python3-tornado (6.4.0-2) ... 176s Setting up libnorm1t64:amd64 (1.5.9+dfsg-3.1build1) ... 176s Setting up python3-pure-eval (0.2.2-2) ... 176s Setting up python3-astunparse (1.6.3-2) ... 176s Setting up libsodium23:amd64 (1.0.18-1build3) ... 176s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 176s Setting up python3-py (1.11.0-2) ... 176s Setting up libdebuginfod-common (0.191-1) ... 176s Setting up python3-joblib (1.3.2-2) ... 177s Setting up python3-parso (0.8.3-1) ... 177s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 177s Setting up python3-asttokens (2.4.1-1) ... 177s Setting up python3-unicodedata2 (15.1.0+ds-1build1) ... 177s Setting up fonts-lyx (2.4.0-1) ... 177s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 177s Setting up python3-threadpoolctl (3.1.0-1) ... 177s Setting up x11-common (1:7.7+23ubuntu3) ... 178s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 178s Setting up python3-coverage (7.4.4+dfsg1-0ubuntu2) ... 178s Setting up libgomp1:amd64 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180s Setting up python3-executing (2.0.1-0.1) ... 180s Setting up python3-nest-asyncio (1.5.4-1) ... 181s Setting up python3-brotli (1.1.0-2build2) ... 181s Setting up python3-cycler (0.12.1-1) ... 181s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 181s Setting up python3-bytecode (0.15.1-3) ... 181s Setting up python3-kiwisolver (1.4.5-1) ... 181s Setting up libtcl8.6:amd64 (8.6.14+dfsg-1build1) ... 181s Setting up libipt2 (2.0.6-1build1) ... 181s Setting up python3-cpuinfo (9.0.0+git20221119-1) ... 181s Setting up libbabeltrace1:amd64 (1.5.11-3build3) ... 181s Setting up libgfortran5:amd64 (14.1.0-1ubuntu1) ... 181s Setting up python3-pluggy (1.5.0-1) ... 181s Setting up python3-fastjsonschema (2.19.1-1) ... 181s Setting up python3-traitlets (5.5.0-2) ... 182s Setting up libxslt1.1:amd64 (1.1.39-0exp1build1) ... 182s Setting up libblosc1:amd64 (1.21.5+ds-1build1) ... 182s Setting up libopenjp2-7:amd64 (2.5.0-2build3) ... 182s Setting up libharfbuzz0b:amd64 (8.3.0-2build2) ... 182s Setting up python3-dateutil (2.9.0-2) ... 182s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 182s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 182s Setting up python3-mpmath (1.3.0-1) ... 182s Setting up python-matplotlib-data (3.6.3-2ubuntu1) ... 182s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 182s Setting up python3-appdirs (1.4.4-4) ... 183s Setting up python3-stack-data (0.6.3-1) ... 183s Setting up python-tables-data (3.9.2-2build1) ... 183s Setting up python3-jupyter-core (5.3.2-2) ... 183s Setting up libsz2:amd64 (1.1.3-1) ... 183s Setting up python3-ptyprocess (0.7.0-5) ... 183s Setting up python3-prompt-toolkit (3.0.46-1) ... 183s Setting up python3-sympy (1.12-8) ... 189s Setting up libdebuginfod1t64:amd64 (0.191-1) ... 189s Setting up liblapack3:amd64 (3.12.0-3build1) ... 189s 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 189s Setting up libxft2:amd64 (2.3.6-1build1) ... 189s Setting up libzmq5:amd64 (4.3.5-1build2) ... 189s Setting up python3-jedi (0.19.1+ds1-1) ... 190s Setting up python3-pytest (8.2.2-1ubuntu1) ... 190s Setting up libtk8.6:amd64 (8.6.14-1build1) ... 190s Setting up libsource-highlight4t64:amd64 (3.1.9-4.3build1) ... 190s Setting up python3-nbformat (5.9.1-1) ... 190s Setting up python3-matplotlib-inline (0.1.6-2) ... 190s Setting up python3-comm (0.2.1-1) ... 190s Setting up python3-fs (2.4.16-4) ... 191s Setting up gdb (15.0.50.20240403-0ubuntu1) ... 191s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 191s Setting up python3-pexpect (4.9-2) ... 191s Setting up python3-zmq (24.0.1-5build1) ... 191s Setting up libraqm0:amd64 (0.10.1-1build1) ... 191s Setting up python3-numpy (1:1.26.4+ds-10) ... 193s Setting up python3-lxml:amd64 (5.2.1-1) ... 193s Setting up python3-jupyter-client (7.4.9-2ubuntu1) ... 193s Setting up python3-contourpy (1.0.7-3) ... 194s Setting up python3-pydevd (2.10.0+ds-10ubuntu1) ... 194s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-3.1ubuntu4) ... 194s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 194s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 194s Setting up python3-scipy (1.11.4-10) ... 198s Setting up python3-tables-lib (3.9.2-2build1) ... 198s Setting up blt (2.5.3+dfsg-7build1) ... 198s Setting up python3-pandas-lib:amd64 (2.1.4+dfsg-8) ... 198s Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-1) ... 198s Setting up python3-tk:amd64 (3.12.3-0ubuntu1) ... 198s Setting up python3-debugpy (1.8.0+ds-4ubuntu4) ... 198s Setting up python3-pil:amd64 (10.3.0-2) ... 198s Setting up python3-pandas (2.1.4+dfsg-8) ... 203s Setting up python3-pil.imagetk:amd64 (10.3.0-2) ... 203s Setting up python3-ipython (8.20.0-1ubuntu1) ... 204s Setting up python3-ipykernel (6.29.3-1ubuntu1) ... 204s Setting up python3-sklearn (1.4.2+dfsg-1) ... 206s Setting up python3-numexpr (2.10.0-2) ... 206s Setting up python3-tables (3.9.2-2build1) ... 207s Setting up python3-mdtraj (1.9.9-1ubuntu2) ... 207s /usr/lib/python3/dist-packages/mdtraj/formats/amberrst.py:271: SyntaxWarning: invalid escape sequence '\g' 207s """Read data from an AMBER ASCII restart file 207s /usr/lib/python3/dist-packages/mdtraj/formats/amberrst.py:534: SyntaxWarning: invalid escape sequence '\g' 207s """Read data from an AMBER NetCDF restart file 207s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:394: SyntaxWarning: invalid escape sequence '\d' 207s time = float(findall('t= *(\d+\.\d+)',comment)[-1]) 207s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:500: SyntaxWarning: invalid escape sequence '\.' 207s return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) 207s /usr/lib/python3/dist-packages/mdtraj/formats/gsd.py:228: SyntaxWarning: invalid escape sequence '\g' 207s """Write one or more frames of data to a gsd file. 207s /usr/lib/python3/dist-packages/mdtraj/formats/lammpstrj.py:237: SyntaxWarning: invalid escape sequence '\g' 207s """Read data from a lammpstrj file. 207s /usr/lib/python3/dist-packages/mdtraj/formats/lammpstrj.py:429: SyntaxWarning: invalid escape sequence '\g' 207s """Write the box lines in the header of a frame. 207s /usr/lib/python3/dist-packages/mdtraj/formats/lammpstrj.py:476: SyntaxWarning: invalid escape sequence '\g' 207s """Write one or more frames of data to a lammpstrj file. 207s /usr/lib/python3/dist-packages/mdtraj/formats/mol2.py:215: SyntaxWarning: invalid escape sequence '\s' 207s index_col=0, header=None, sep="\s+", engine='python') 207s /usr/lib/python3/dist-packages/mdtraj/formats/mol2.py:222: SyntaxWarning: invalid escape sequence '\s' 207s atoms_frame = pd.read_csv(csv, sep="\s+", engine='python', header=None) 207s /usr/lib/python3/dist-packages/mdtraj/formats/netcdf.py:217: SyntaxWarning: invalid escape sequence '\g' 207s """Read data from a molecular dynamics trajectory in the AMBER NetCDF 207s /usr/lib/python3/dist-packages/mdtraj/formats/netcdf.py:323: SyntaxWarning: invalid escape sequence '\g' 207s """Write one or more frames of a molecular dynamics trajectory to disk 207s /usr/lib/python3/dist-packages/mdtraj/formats/prmtop.py:63: SyntaxWarning: invalid escape sequence '\.' 207s FORMAT_RE_PATTERN = re.compile("([0-9]+)([a-zA-Z]+)([0-9]+)\.?([0-9]*)") 207s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:44: SyntaxWarning: invalid escape sequence '\s' 207s """Compute the distance between pairs of residues in a trajectory. 207s /usr/lib/python3/dist-packages/mdtraj/geometry/hbond.py:251: SyntaxWarning: invalid escape sequence '\c' 207s """Compute the Kabsch-Sander hydrogen bond energy between each pair 207s /usr/lib/python3/dist-packages/mdtraj/geometry/internal.py:370: SyntaxWarning: invalid escape sequence '\p' 207s """Calculate the Wilson B matrix, which collects the derivatives of the 207s /usr/lib/python3/dist-packages/mdtraj/geometry/shape.py:80: SyntaxWarning: invalid escape sequence '\l' 207s """Compute the asphericity of a trajectory. 207s /usr/lib/python3/dist-packages/mdtraj/geometry/shape.py:105: SyntaxWarning: invalid escape sequence '\l' 207s """Compute the acylindricity of a trajectory. 207s /usr/lib/python3/dist-packages/mdtraj/geometry/shape.py:130: SyntaxWarning: invalid escape sequence '\k' 207s """Compute the relative shape anisotropy of a trajectory. 207s /usr/lib/python3/dist-packages/mdtraj/nmr/shift_wrappers.py:214: SyntaxWarning: invalid escape sequence '\s' 207s d = pd.read_table("./bb_details.dat", index_col=False, header=None, sep="\s+").drop([3], axis=1) 207s /usr/lib/python3/dist-packages/mdtraj/nmr/shift_wrappers.py:292: SyntaxWarning: invalid escape sequence '\s' 207s d = pd.read_table("./trj%d_pred.tab" % i, names=names, header=None, sep="\s+", skiprows=lines_to_skip) 207s /usr/lib/python3/dist-packages/mdtraj/testing/docscrape.py:305: SyntaxWarning: invalid escape sequence '\w' 207s if re.compile('^([\w., ]+=)?\s*[\w\.]+\(.*\)$').match(summary_str): 207s /usr/lib/python3/dist-packages/mdtraj/testing/docscrape.py:345: SyntaxWarning: invalid escape sequence '\*' 207s return [self['Signature'].replace('*','\*')] + [''] 207s /usr/lib/python3/dist-packages/mdtraj/testing/docscrape.py:464: SyntaxWarning: invalid escape sequence '\*' 207s argspec = argspec.replace('*','\*') 207s /usr/lib/python3/dist-packages/mdtraj/testing/docscrape.py:482: SyntaxWarning: invalid escape sequence '\*' 207s signature = self['Signature'].replace('*', '\*') 207s /usr/lib/python3/dist-packages/mdtraj/testing/docstrings.py:126: SyntaxWarning: invalid escape sequence '\d' 207s m = re.search('takes at most (\d+) positional arguments', str(e)) 207s Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... 207s Setting up python3-fonttools (4.46.0-1build2) ... 208s Setting up python3-matplotlib (3.6.3-2ubuntu1) ... 210s Setting up autopkgtest-satdep (0) ... 210s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 210s Processing triggers for man-db (2.12.1-1) ... 216s (Reading database ... 96357 files and directories currently installed.) 216s Removing autopkgtest-satdep (0) ... 216s autopkgtest [00:25:16]: test command1: pytest-3 -k 'not nmr.ipynb and not test_image_molecules' 216s autopkgtest [00:25:16]: test command1: [----------------------- 216s ============================= test session starts ============================== 216s platform linux -- Python 3.12.3, pytest-8.2.2, pluggy-1.5.0 -- /usr/bin/python3 216s cachedir: .pytest_cache 216s rootdir: /tmp/autopkgtest.hoy8Kc/build.SoL/src 216s configfile: pytest.ini 216s testpaths: tests, examples 219s collecting ... collected 1221 items / 2 deselected / 1219 selected 219s 219s tests/test_alignment.py::test_rmsd_zero PASSED [ 0%] 219s tests/test_alignment.py::test_rmsd_nonzero PASSED [ 0%] 219s tests/test_alignment.py::test_transform PASSED [ 0%] 219s tests/test_alignment.py::test_transform2 PASSED [ 0%] 220s tests/test_angles.py::test_angle_pbc_0 PASSED [ 0%] 220s 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tests/test_hoomdxml.py::test_correct_ordering PASSED [ 21%] 245s tests/test_io.py::test_overwrite_1 PASSED [ 21%] 245s tests/test_io.py::test_overwrite_2 PASSED [ 21%] 245s tests/test_io.py::test_io::test_load_1 PASSED [ 21%] 245s tests/test_io.py::test_io::test_load_2 PASSED [ 21%] 245s tests/test_io.py::test_io::test_load_3 PASSED [ 21%] 245s tests/test_io.py::test_io::test_save PASSED [ 21%] 245s tests/test_io.py::test_io_int::test_load_1 PASSED [ 21%] 245s tests/test_io.py::test_io_int::test_load_2 PASSED [ 21%] 245s tests/test_io.py::test_io_int::test_load_3 PASSED [ 21%] 245s tests/test_io.py::test_io_int::test_save PASSED [ 21%] 245s tests/test_io.py::test_groups PASSED [ 22%] 245s tests/test_lammpstrj.py::test_read_0 PASSED [ 22%] 245s tests/test_lammpstrj.py::test_read_1 PASSED [ 22%] 245s tests/test_lammpstrj.py::test_read_write_0 PASSED [ 22%] 246s tests/test_lammpstrj.py::test_mdwrite PASSED [ 22%] 246s tests/test_lammpstrj.py::test_multiread PASSED [ 22%] 246s tests/test_lammpstrj.py::test_seek PASSED [ 22%] 246s tests/test_lammpstrj.py::test_custom PASSED [ 22%] 246s tests/test_lh5.py::test_write_coordinates PASSED [ 22%] 246s tests/test_lh5.py::test_write_coordinates_reshape PASSED [ 22%] 246s tests/test_lh5.py::test_write_multiple PASSED [ 22%] 246s tests/test_lh5.py::test_topology PASSED [ 22%] 246s tests/test_lh5.py::test_read_slice_0 PASSED [ 23%] 246s tests/test_lh5.py::test_vsite_elements PASSED [ 23%] 246s tests/test_lh5.py::test_do_overwrite_0 PASSED [ 23%] 246s tests/test_lh5.py::test_do_overwrite_1 PASSED [ 23%] 246s tests/test_load.py::test_load_single PASSED [ 23%] 247s tests/test_load.py::test_load_single_list PASSED [ 23%] 247s tests/test_load.py::test_load_many_list PASSED [ 23%] 247s tests/test_load.py::test_load_atom_indices_multiple_files PASSED [ 23%] 247s tests/test_lprmsd.py::test_munkres_0 PASSED [ 23%] 247s tests/test_lprmsd.py::test_lprmsd_null PASSED [ 23%] 247s tests/test_lprmsd.py::test_lprmsd_0 PASSED [ 23%] 247s tests/test_lprmsd.py::test_lprmsd_1 PASSED [ 23%] 247s tests/test_lprmsd.py::test_lprmsd_2 PASSED [ 24%] 248s tests/test_lprmsd.py::test_lprmsd_3 PASSED [ 24%] 248s tests/test_lprmsd.py::test_lprmsd_4 PASSED [ 24%] 248s tests/test_lprmsd.py::test_lprmsd_5 PASSED [ 24%] 249s tests/test_mdconvert.py::test_index PASSED [ 24%] 251s tests/test_mdconvert.py::test_slice PASSED [ 24%] 274s tests/test_mdconvert.py::test_pairwise[from-xtc] PASSED [ 24%] 296s tests/test_mdconvert.py::test_pairwise[from-dcd] PASSED [ 24%] 319s tests/test_mdconvert.py::test_pairwise[from-binpos] PASSED [ 24%] 341s tests/test_mdconvert.py::test_pairwise[from-trr] PASSED [ 24%] 363s tests/test_mdconvert.py::test_pairwise[from-nc] PASSED [ 24%] 386s tests/test_mdconvert.py::test_pairwise[from-pdb] PASSED [ 24%] 434s tests/test_mdconvert.py::test_pairwise[from-h5] PASSED [ 25%] 483s tests/test_mdconvert.py::test_pairwise[from-lh5] PASSED [ 25%] 505s tests/test_mdconvert.py::test_pairwise[from-netcdf] PASSED [ 25%] 505s tests/test_mdconvert.py::test_mdconvert_alanine PASSED [ 25%] 505s tests/test_mdcrd.py::test_read_0 PASSED [ 25%] 505s tests/test_mdcrd.py::test_read_1 PASSED [ 25%] 505s tests/test_mdcrd.py::test_read_write_0 PASSED [ 25%] 505s tests/test_mdcrd.py::test_read_write_1 PASSED [ 25%] 506s tests/test_mdcrd.py::test_read_write_2 PASSED [ 25%] 506s tests/test_mdcrd.py::test_multiread PASSED [ 25%] 506s tests/test_mdcrd.py::test_seek PASSED [ 25%] 506s tests/test_mdcrd.py::test_atom_indices_0 PASSED [ 25%] 506s tests/test_mdcrd.py::test_atom_indices_1 PASSED [ 26%] 506s tests/test_mol2.py::test_load_mol2 PASSED [ 26%] 506s tests/test_mol2.py::test_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb SKIPPED [ 26%] 506s tests/test_mol2.py::test_mol2_dataframe PASSED [ 26%] 506s tests/test_mol2.py::test_mol2_dataframe_status PASSED [ 26%] 506s tests/test_mol2.py::test_mol2_warnings PASSED [ 26%] 506s tests/test_mol2.py::test_mol2_status_bits PASSED [ 26%] 506s tests/test_mol2.py::test_mol2_without_bonds PASSED [ 26%] 506s tests/test_mol2.py::test_mol2_element_name PASSED [ 26%] 506s tests/test_mol2.py::test_load_all_mol2[li.mol2] PASSED [ 26%] 506s tests/test_mol2.py::test_load_all_mol2[lysozyme-ligand-tripos.mol2] PASSED [ 26%] 506s tests/test_mol2.py::test_load_all_mol2[imatinib.mol2] PASSED [ 26%] 506s tests/test_mol2.py::test_load_all_mol2[status-bits.mol2] PASSED [ 26%] 506s tests/test_mol2.py::test_load_all_mol2[adp.mol2] PASSED [ 27%] 506s tests/test_mol2.py::test_load_all_mol2[water_acn.mol2] PASSED [ 27%] 506s tests/test_mol2.py::test_mol2_n_residues PASSED [ 27%] 506s tests/test_neighborlist.py::test_nonperiodic PASSED [ 27%] 506s tests/test_neighborlist.py::test_periodic PASSED [ 27%] 507s tests/test_neighborlist.py::test_triclinic PASSED [ 27%] 507s tests/test_neighbors.py::test_compute_neighbors_1 PASSED [ 27%] 507s tests/test_neighbors.py::test_compute_neighbors_2 PASSED [ 27%] 509s tests/test_neighbors.py::test_compute_neighbors_3 PASSED [ 27%] 509s tests/test_netcdf.py::test_read_after_close PASSED [ 27%] 509s tests/test_netcdf.py::test_shape PASSED [ 27%] 509s tests/test_netcdf.py::test_read_chunk_1 PASSED [ 27%] 509s tests/test_netcdf.py::test_read_chunk_2 PASSED [ 28%] 509s tests/test_netcdf.py::test_read_chunk_3 PASSED [ 28%] 509s tests/test_netcdf.py::test_read_write_1 PASSED [ 28%] 509s tests/test_netcdf.py::test_read_write_2 PASSED [ 28%] 509s tests/test_netcdf.py::test_ragged_1 PASSED [ 28%] 509s tests/test_netcdf.py::test_ragged_2 PASSED [ 28%] 509s tests/test_netcdf.py::test_read_write_25 PASSED [ 28%] 509s tests/test_netcdf.py::test_write_3 PASSED [ 28%] 509s tests/test_netcdf.py::test_n_atoms PASSED [ 28%] 509s tests/test_netcdf.py::test_do_overwrite PASSED [ 28%] 509s tests/test_netcdf.py::test_trajectory_save_load PASSED [ 28%] 509s tests/test_netcdf.py::test_cpptraj SKIPPED (This test requires cpptr...) [ 28%] 509s tests/test_nmr.py::test_spartaplus SKIPPED (SPARTA+ binary not found) [ 29%] 509s tests/test_nmr.py::test_ppm SKIPPED (PPM binary not found) [ 29%] 509s tests/test_nmr.py::test_shiftx2 SKIPPED (SHIFTX2 binary not found or...) [ 29%] 509s tests/test_nmr.py::test_2_scalar_couplings PASSED [ 29%] 509s tests/test_nmr.py::test_3_scalar_couplings PASSED [ 29%] 509s tests/test_order.py::test_nematic_order PASSED [ 29%] 509s tests/test_order.py::test_director PASSED [ 29%] 509s tests/test_order.py::test_inertia PASSED [ 29%] 509s tests/test_order.py::test_nematic_order_args PASSED [ 29%] 509s tests/test_order.py::test_order_from_traj PASSED [ 29%] 509s tests/test_order.py::test_directors_angle_from_traj PASSED [ 29%] 509s tests/test_pdb.py::test_pdbread PASSED [ 29%] 509s tests/test_pdb.py::test_pdbread_with_input_top PASSED [ 30%] 509s tests/test_pdb.py::test_pdbwrite PASSED [ 30%] 509s tests/test_pdb.py::test_load_multiframe PASSED [ 30%] 509s tests/test_pdb.py::test_4ZUO PASSED [ 30%] 510s tests/test_pdb.py::test_2EQQ_0 PASSED [ 30%] 511s tests/test_pdb.py::test_1vii_solvated_with_ligand PASSED [ 30%] 511s tests/test_pdb.py::test_write_large PASSED [ 30%] 511s tests/test_pdb.py::test_write_large_2 PASSED [ 30%] 511s tests/test_pdb.py::test_pdbstructure_0 PASSED [ 30%] 511s tests/test_pdb.py::test_pdbstructure_1 PASSED [ 30%] 511s tests/test_pdb.py::test_pdbstructure_2 PASSED [ 30%] 511s tests/test_pdb.py::test_pdbstructure_3 PASSED [ 30%] 514s tests/test_pdb.py::test_pdb_from_url PASSED [ 31%] 515s tests/test_pdb.py::test_3nch_conect PASSED [ 31%] 517s tests/test_pdb.py::test_3nch_serial_resSeq PASSED [ 31%] 517s tests/test_pdb.py::test_1ncw PASSED [ 31%] 519s tests/test_pdb.py::test_1vii_url_and_gz PASSED [ 31%] 519s tests/test_pdb.py::test_segment_id PASSED [ 31%] 519s tests/test_pdb.py::test_bfactors PASSED [ 31%] 523s tests/test_pdb.py::test_hex PASSED [ 31%] 523s tests/test_pdb.py::test_dummy_pdb_box_detection PASSED [ 31%] 523s tests/test_pdb.py::test_multichain_load_cycle PASSED [ 31%] 523s tests/test_pdb.py::test_load_pdb_input_top PASSED [ 31%] 523s tests/test_pdbx.py::test_convert SKIPPED (test_pdbx.py needs OpenMM.) [ 31%] 523s tests/test_prmtop.py::test_load_prmtop PASSED [ 31%] 523s tests/test_prmtop.py::test_load_binpos_w_prmtop PASSED [ 32%] 523s tests/test_prmtop.py::test_load_chamber_prmtop PASSED [ 32%] 523s tests/test_psf.py::test_load_psf PASSED [ 32%] 528s tests/test_psf.py::test_multichain_psf PASSED [ 32%] 528s tests/test_psf.py::test_load_mdcrd_with_psf PASSED [ 32%] 528s tests/test_psf.py::test_against_vmd[1vii.pdb] SKIPPED (This test req...) [ 32%] 528s tests/test_psf.py::test_against_vmd[2EQQ.pdb] SKIPPED (This test req...) [ 32%] 528s tests/test_quaternion.py::test_quaternion_0 PASSED [ 32%] 528s tests/test_quaternion.py::test_quaternion_1 PASSED [ 32%] 528s tests/test_quaternion.py::test_quaternion_2 PASSED [ 32%] 532s tests/test_rdf.py::test_rdf_norm PASSED [ 32%] 532s tests/test_rdf.py::test_compare_rdf_to_gromacs SKIPPED (Binning does...) [ 32%] 532s tests/test_rdf.py::test_rdf_t[True-True] PASSED [ 33%] 537s tests/test_rdf.py::test_rdf_t[True-False] PASSED [ 33%] 537s tests/test_rdf.py::test_rdf_t[False-True] PASSED [ 33%] 538s tests/test_rdf.py::test_rdf_t[False-False] PASSED [ 33%] 538s tests/test_rdf.py::test_rdf_t_norm[0] PASSED [ 33%] 539s tests/test_rdf.py::test_rdf_t_norm[2] PASSED [ 33%] 539s tests/test_rdf.py::test_rdf_t_norm[4] PASSED [ 33%] 539s tests/test_rdf.py::test_compare_rdf_t_at_0[True-True] PASSED [ 33%] 541s tests/test_rdf.py::test_compare_rdf_t_at_0[True-False] PASSED [ 33%] 541s tests/test_rdf.py::test_compare_rdf_t_at_0[False-True] PASSED [ 33%] 541s tests/test_rdf.py::test_compare_rdf_t_at_0[False-False] PASSED [ 33%] 541s tests/test_rdf.py::test_amber_rdf_t[True-True] PASSED [ 33%] 542s tests/test_rdf.py::test_amber_rdf_t[True-False] PASSED [ 34%] 542s tests/test_rdf.py::test_amber_rdf_t[False-True] PASSED [ 34%] 542s tests/test_rdf.py::test_amber_rdf_t[False-False] PASSED [ 34%] 542s tests/test_rdf.py::test_compare_gromacs_rdf_t SKIPPED (Binning does ...) [ 34%] 542s tests/test_rdf.py::test_compare_rdf_t_master PASSED [ 34%] 542s tests/test_rdf.py::test_compare_n_concurrent_pairs PASSED [ 34%] 542s tests/test_reporter.py::test_reporter SKIPPED (test_reporter.py need...) [ 34%] 542s tests/test_reporter.py::test_reporter_subset SKIPPED (test_reporter....) [ 34%] 542s tests/test_reporter.py::test_xtc_reporter_append SKIPPED (test_repor...) [ 34%] 542s tests/test_restart.py::test_read_after_close PASSED [ 34%] 542s tests/test_restart.py::test_shape PASSED [ 34%] 542s tests/test_restart.py::test_shape_2 PASSED [ 34%] 542s tests/test_restart.py::test_read_write_1 PASSED [ 35%] 542s tests/test_restart.py::test_read_write_2 PASSED [ 35%] 543s tests/test_restart.py::test_read_write_3 PASSED [ 35%] 543s tests/test_restart.py::test_read_write_4 PASSED [ 35%] 543s tests/test_rmsd.py::test_trajectory_rmsd PASSED [ 35%] 543s tests/test_rmsd.py::test_precentered_1 PASSED [ 35%] 544s tests/test_rmsd.py::test_precentered_2 PASSED [ 35%] 544s tests/test_rmsd.py::test_superpose_0 PASSED [ 35%] 544s tests/test_rmsd.py::test_superpose_1 PASSED [ 35%] 544s tests/test_rmsd.py::test_superpose_2 PASSED [ 35%] 544s tests/test_rmsd.py::test_superpose_refinds PASSED [ 35%] 544s tests/test_rmsd.py::test_rmsd_atom_indices PASSED [ 35%] 544s tests/test_rmsd.py::test_rmsd_ref_ainds PASSED [ 36%] 544s tests/test_rmsd.py::test_average_structure PASSED [ 36%] 544s tests/test_rmsd.py::test_trajectory_rmsf PASSED [ 36%] 544s tests/test_rmsd.py::test_trajectory_rmsf_aligned PASSED [ 36%] 544s tests/test_rmsd.py::test_rmsd_atom_indices_vs_ref_indices PASSED [ 36%] 544s tests/test_rmsd_memmap.py::test_1 PASSED [ 36%] 544s tests/test_rmsd_memmap.py::test_2 PASSED [ 36%] 544s tests/test_sasa.py::test_sasa_0 PASSED [ 36%] 544s tests/test_sasa.py::test_sasa_1 PASSED [ 36%] 545s tests/test_sasa.py::test_sasa_2 PASSED [ 36%] 545s tests/test_sasa.py::test_sasa_3 PASSED [ 36%] 546s tests/test_sasa.py::test_sasa_4 PASSED [ 36%] 546s tests/test_sasa.py::test_sasa_5 PASSED [ 36%] 546s tests/test_selection.py::test_range PASSED [ 37%] 546s tests/test_selection.py::test_unary_2 PASSED [ 37%] 546s tests/test_selection.py::test_unary_3 PASSED [ 37%] 546s tests/test_selection.py::test_binary_1 PASSED [ 37%] 546s tests/test_selection.py::test_binary_2 PASSED [ 37%] 546s tests/test_selection.py::test_simple PASSED [ 37%] 546s tests/test_selection.py::test_alias PASSED [ 37%] 546s tests/test_selection.py::test_unary_1 PASSED [ 37%] 546s tests/test_selection.py::test_binary_selection_operator PASSED [ 37%] 546s tests/test_selection.py::test_raises PASSED [ 37%] 546s tests/test_selection.py::test_raises2 PASSED [ 37%] 546s tests/test_selection.py::test_bool PASSED [ 37%] 546s tests/test_selection.py::test_nested_bool PASSED [ 38%] 546s tests/test_selection.py::test_values PASSED [ 38%] 546s tests/test_selection.py::test_element PASSED [ 38%] 546s tests/test_selection.py::test_not PASSED [ 38%] 546s tests/test_selection.py::test_re PASSED [ 38%] 546s tests/test_selection.py::test_quotes PASSED [ 38%] 546s tests/test_selection.py::test_top PASSED [ 38%] 547s tests/test_selection.py::test_top_2 PASSED [ 38%] 547s tests/test_selection.py::test_backbone PASSED [ 38%] 547s tests/test_selection.py::test_sidechain PASSED [ 38%] 547s tests/test_selection.py::test_literal PASSED [ 38%] 547s tests/test_selection.py::test_in PASSED [ 38%] 547s tests/test_shape.py::test_gyration PASSED [ 39%] 548s tests/test_shape.py::test_principal_moments PASSED [ 39%] 548s tests/test_shape.py::test_asphericity PASSED [ 39%] 548s tests/test_shape.py::test_shape_metrics PASSED [ 39%] 548s tests/test_thermodynamic_properties.py::test_volume PASSED [ 39%] 548s tests/test_thermodynamic_properties.py::test_density PASSED [ 39%] 548s tests/test_thermodynamic_properties.py::test_dipole_moments PASSED [ 39%] 548s tests/test_thermodynamic_properties.py::test_static_dielectric PASSED [ 39%] 548s tests/test_thermodynamic_properties.py::test_kappa PASSED [ 39%] 548s tests/test_thermodynamic_properties.py::test_alpha SKIPPED (Thermal ...) [ 39%] 548s tests/test_tng.py::test_load_trajectory PASSED [ 39%] 548s tests/test_tng.py::test_load_topology SKIPPED (Fails on macOS + Pyth...) [ 39%] 549s tests/test_tng.py::test_write PASSED [ 40%] 549s tests/test_topology.py::test_topology_openmm SKIPPED (needs OpenMM) [ 40%] 549s tests/test_topology.py::test_topology_openmm_boxes SKIPPED (needs Op...) [ 40%] 549s tests/test_topology.py::test_topology_pandas PASSED [ 40%] 549s tests/test_topology.py::test_topology_pandas_TIP4PEW PASSED [ 40%] 549s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq PASSED [ 40%] 549s tests/test_topology.py::test_topology_numbers PASSED [ 40%] 549s tests/test_topology.py::test_topology_unique_elements_bpti PASSED [ 40%] 549s tests/test_topology.py::test_chain PASSED [ 40%] 549s tests/test_topology.py::test_residue PASSED [ 40%] 549s tests/test_topology.py::test_segment_id PASSED [ 40%] 549s tests/test_topology.py::test_nonconsective_resSeq PASSED [ 40%] 549s tests/test_topology.py::test_pickle PASSED [ 41%] 549s tests/test_topology.py::test_atoms_by_name PASSED [ 41%] 549s tests/test_topology.py::test_select_atom_indices PASSED [ 41%] 549s tests/test_topology.py::test_top_dataframe_openmm_roundtrip SKIPPED [ 41%] 549s tests/test_topology.py::test_n_bonds PASSED [ 41%] 549s tests/test_topology.py::test_load_unknown_topology PASSED [ 41%] 549s tests/test_topology.py::test_unique_pairs PASSED [ 41%] 550s tests/test_topology.py::test_select_pairs PASSED [ 41%] 550s tests/test_topology.py::test_to_fasta PASSED [ 41%] 551s tests/test_topology.py::test_subset PASSED [ 41%] 551s tests/test_topology.py::test_subset_re_index_residues PASSED [ 41%] 551s tests/test_topology.py::test_molecules PASSED [ 41%] 551s tests/test_topology.py::test_copy_and_hash PASSED [ 42%] 551s tests/test_topology.py::test_topology_sliced_residue_indices PASSED [ 42%] 551s tests/test_topology.py::test_topology_join PASSED [ 42%] 551s tests/test_topology.py::test_topology_join_keep_resSeq PASSED [ 42%] 552s tests/test_trajectory.py::test_mismatch PASSED [ 42%] 552s tests/test_trajectory.py::test_box PASSED [ 42%] 552s tests/test_trajectory.py::test_load_pdb_box PASSED [ 42%] 552s tests/test_trajectory.py::test_load_pdb_gz PASSED [ 42%] 552s tests/test_trajectory.py::test_box_load_save[nc] PASSED [ 42%] 552s tests/test_trajectory.py::test_box_load_save[h5] PASSED [ 42%] 552s tests/test_trajectory.py::test_box_load_save[xtc] PASSED [ 42%] 552s tests/test_trajectory.py::test_box_load_save[trr] PASSED [ 42%] 552s tests/test_trajectory.py::test_box_load_save[dcd] PASSED [ 42%] 552s tests/test_trajectory.py::test_box_load_save[mdcrd] PASSED [ 43%] 552s tests/test_trajectory.py::test_box_load_save[binpos] SKIPPED (binpos...) [ 43%] 552s tests/test_trajectory.py::test_box_load_save[dtr] PASSED [ 43%] 552s tests/test_trajectory.py::test_box_load_save[xyz] SKIPPED (xyz does ...) [ 43%] 552s tests/test_trajectory.py::test_box_load_save[xyz.gz] SKIPPED (xyz.gz...) [ 43%] 552s tests/test_trajectory.py::test_box_load_save[lammpstrj] PASSED [ 43%] 552s tests/test_trajectory.py::test_box_load_save[tng] PASSED [ 43%] 552s tests/test_trajectory.py::test_box_load_save[lh5] SKIPPED (lh5 does ...) [ 43%] 552s tests/test_trajectory.py::test_box_load_save[pdb] SKIPPED (pdb does ...) [ 43%] 552s tests/test_trajectory.py::test_box_load_save[pdb.gz] SKIPPED (pdb.gz...) [ 43%] 552s tests/test_trajectory.py::test_box_load_save[ncrst] PASSED [ 43%] 552s tests/test_trajectory.py::test_box_load_save[rst7] PASSED [ 43%] 552s tests/test_trajectory.py::test_box_load_save[gro] PASSED [ 44%] 552s tests/test_trajectory.py::test_slice PASSED [ 44%] 552s tests/test_trajectory.py::test_slice2 PASSED [ 44%] 552s tests/test_trajectory.py::test_read_path[nc] PASSED [ 44%] 552s tests/test_trajectory.py::test_read_path[h5] PASSED [ 44%] 552s tests/test_trajectory.py::test_read_path[xtc] PASSED [ 44%] 552s tests/test_trajectory.py::test_read_path[trr] PASSED [ 44%] 552s tests/test_trajectory.py::test_read_path[dcd] PASSED [ 44%] 552s tests/test_trajectory.py::test_read_path[mdcrd] PASSED [ 44%] 552s tests/test_trajectory.py::test_read_path[binpos] PASSED [ 44%] 552s tests/test_trajectory.py::test_read_path[dtr] PASSED [ 44%] 552s tests/test_trajectory.py::test_read_path[xyz] PASSED [ 44%] 552s tests/test_trajectory.py::test_read_path[xyz.gz] PASSED [ 45%] 552s tests/test_trajectory.py::test_read_path[lammpstrj] PASSED [ 45%] 552s tests/test_trajectory.py::test_read_path[tng] PASSED [ 45%] 552s tests/test_trajectory.py::test_read_path[lh5] PASSED [ 45%] 552s tests/test_trajectory.py::test_read_path[pdb] PASSED [ 45%] 552s tests/test_trajectory.py::test_read_path[pdb.gz] PASSED [ 45%] 553s tests/test_trajectory.py::test_read_path[ncrst] XFAIL (These referen...) [ 45%] 553s tests/test_trajectory.py::test_read_path[rst7] XFAIL (These referenc...) [ 45%] 553s tests/test_trajectory.py::test_read_path[gro] PASSED [ 45%] 553s tests/test_trajectory.py::test_write_path[nc] PASSED [ 45%] 553s tests/test_trajectory.py::test_write_path[h5] PASSED [ 45%] 553s tests/test_trajectory.py::test_write_path[xtc] PASSED [ 45%] 553s tests/test_trajectory.py::test_write_path[trr] PASSED [ 46%] 553s tests/test_trajectory.py::test_write_path[dcd] PASSED [ 46%] 553s tests/test_trajectory.py::test_write_path[mdcrd] SKIPPED (mdcrd can ...) [ 46%] 553s tests/test_trajectory.py::test_write_path[binpos] PASSED [ 46%] 553s tests/test_trajectory.py::test_write_path[dtr] PASSED [ 46%] 553s tests/test_trajectory.py::test_write_path[xyz] PASSED [ 46%] 553s tests/test_trajectory.py::test_write_path[xyz.gz] PASSED [ 46%] 553s tests/test_trajectory.py::test_write_path[lammpstrj] PASSED [ 46%] 553s tests/test_trajectory.py::test_write_path[tng] PASSED [ 46%] 553s tests/test_trajectory.py::test_write_path[lh5] PASSED [ 46%] 553s tests/test_trajectory.py::test_write_path[pdb] PASSED [ 46%] 553s tests/test_trajectory.py::test_write_path[pdb.gz] PASSED [ 46%] 553s tests/test_trajectory.py::test_write_path[ncrst] SKIPPED (ncrst can ...) [ 47%] 553s tests/test_trajectory.py::test_write_path[rst7] SKIPPED (rst7 can on...) [ 47%] 553s tests/test_trajectory.py::test_write_path[gro] PASSED [ 47%] 553s tests/test_trajectory.py::test_read_write[nc-nc] PASSED [ 47%] 553s tests/test_trajectory.py::test_read_write[nc-h5] PASSED [ 47%] 553s tests/test_trajectory.py::test_read_write[nc-xtc] PASSED [ 47%] 553s tests/test_trajectory.py::test_read_write[nc-trr] PASSED [ 47%] 553s tests/test_trajectory.py::test_read_write[nc-dcd] PASSED [ 47%] 553s tests/test_trajectory.py::test_read_write[nc-mdcrd] SKIPPED (mdcrd c...) [ 47%] 553s tests/test_trajectory.py::test_read_write[nc-binpos] PASSED [ 47%] 554s tests/test_trajectory.py::test_read_write[nc-dtr] PASSED [ 47%] 554s tests/test_trajectory.py::test_read_write[nc-xyz] PASSED [ 47%] 554s tests/test_trajectory.py::test_read_write[nc-xyz.gz] PASSED [ 47%] 554s tests/test_trajectory.py::test_read_write[nc-lammpstrj] PASSED [ 48%] 555s tests/test_trajectory.py::test_read_write[nc-tng] PASSED [ 48%] 555s tests/test_trajectory.py::test_read_write[nc-lh5] PASSED [ 48%] 555s tests/test_trajectory.py::test_read_write[nc-pdb] PASSED [ 48%] 556s tests/test_trajectory.py::test_read_write[nc-pdb.gz] PASSED [ 48%] 556s tests/test_trajectory.py::test_read_write[nc-ncrst] SKIPPED (ncrst c...) [ 48%] 556s tests/test_trajectory.py::test_read_write[nc-rst7] SKIPPED (rst7 can...) [ 48%] 556s tests/test_trajectory.py::test_read_write[nc-gro] PASSED [ 48%] 556s tests/test_trajectory.py::test_read_write[h5-nc] PASSED [ 48%] 556s tests/test_trajectory.py::test_read_write[h5-h5] PASSED [ 48%] 556s tests/test_trajectory.py::test_read_write[h5-xtc] PASSED [ 48%] 556s tests/test_trajectory.py::test_read_write[h5-trr] PASSED [ 48%] 556s tests/test_trajectory.py::test_read_write[h5-dcd] PASSED [ 49%] 556s tests/test_trajectory.py::test_read_write[h5-mdcrd] SKIPPED (mdcrd c...) [ 49%] 556s tests/test_trajectory.py::test_read_write[h5-binpos] PASSED [ 49%] 556s tests/test_trajectory.py::test_read_write[h5-dtr] PASSED [ 49%] 556s tests/test_trajectory.py::test_read_write[h5-xyz] PASSED [ 49%] 557s tests/test_trajectory.py::test_read_write[h5-xyz.gz] PASSED [ 49%] 557s tests/test_trajectory.py::test_read_write[h5-lammpstrj] PASSED [ 49%] 557s tests/test_trajectory.py::test_read_write[h5-tng] PASSED [ 49%] 557s tests/test_trajectory.py::test_read_write[h5-lh5] PASSED [ 49%] 557s tests/test_trajectory.py::test_read_write[h5-pdb] PASSED [ 49%] 558s tests/test_trajectory.py::test_read_write[h5-pdb.gz] PASSED [ 49%] 558s tests/test_trajectory.py::test_read_write[h5-ncrst] SKIPPED (ncrst c...) [ 49%] 558s tests/test_trajectory.py::test_read_write[h5-rst7] SKIPPED (rst7 can...) [ 50%] 558s tests/test_trajectory.py::test_read_write[h5-gro] PASSED [ 50%] 558s tests/test_trajectory.py::test_read_write[xtc-nc] PASSED [ 50%] 558s tests/test_trajectory.py::test_read_write[xtc-h5] PASSED [ 50%] 558s tests/test_trajectory.py::test_read_write[xtc-xtc] PASSED [ 50%] 558s tests/test_trajectory.py::test_read_write[xtc-trr] PASSED [ 50%] 558s tests/test_trajectory.py::test_read_write[xtc-dcd] PASSED [ 50%] 558s tests/test_trajectory.py::test_read_write[xtc-mdcrd] SKIPPED (mdcrd ...) [ 50%] 558s tests/test_trajectory.py::test_read_write[xtc-binpos] PASSED [ 50%] 559s tests/test_trajectory.py::test_read_write[xtc-dtr] PASSED [ 50%] 559s tests/test_trajectory.py::test_read_write[xtc-xyz] PASSED [ 50%] 559s tests/test_trajectory.py::test_read_write[xtc-xyz.gz] PASSED [ 50%] 559s tests/test_trajectory.py::test_read_write[xtc-lammpstrj] PASSED [ 51%] 559s tests/test_trajectory.py::test_read_write[xtc-tng] PASSED [ 51%] 559s tests/test_trajectory.py::test_read_write[xtc-lh5] PASSED [ 51%] 560s tests/test_trajectory.py::test_read_write[xtc-pdb] PASSED [ 51%] 560s tests/test_trajectory.py::test_read_write[xtc-pdb.gz] PASSED [ 51%] 560s tests/test_trajectory.py::test_read_write[xtc-ncrst] SKIPPED (ncrst ...) [ 51%] 560s tests/test_trajectory.py::test_read_write[xtc-rst7] SKIPPED (rst7 ca...) [ 51%] 560s tests/test_trajectory.py::test_read_write[xtc-gro] PASSED [ 51%] 560s tests/test_trajectory.py::test_read_write[trr-nc] PASSED [ 51%] 560s tests/test_trajectory.py::test_read_write[trr-h5] PASSED [ 51%] 560s tests/test_trajectory.py::test_read_write[trr-xtc] PASSED [ 51%] 560s tests/test_trajectory.py::test_read_write[trr-trr] PASSED [ 51%] 560s tests/test_trajectory.py::test_read_write[trr-dcd] PASSED [ 52%] 560s tests/test_trajectory.py::test_read_write[trr-mdcrd] SKIPPED (mdcrd ...) [ 52%] 560s tests/test_trajectory.py::test_read_write[trr-binpos] PASSED [ 52%] 561s tests/test_trajectory.py::test_read_write[trr-dtr] PASSED [ 52%] 561s tests/test_trajectory.py::test_read_write[trr-xyz] PASSED [ 52%] 561s tests/test_trajectory.py::test_read_write[trr-xyz.gz] PASSED [ 52%] 561s tests/test_trajectory.py::test_read_write[trr-lammpstrj] PASSED [ 52%] 561s tests/test_trajectory.py::test_read_write[trr-tng] PASSED [ 52%] 561s tests/test_trajectory.py::test_read_write[trr-lh5] PASSED [ 52%] 562s tests/test_trajectory.py::test_read_write[trr-pdb] PASSED [ 52%] 563s tests/test_trajectory.py::test_read_write[trr-pdb.gz] PASSED [ 52%] 563s tests/test_trajectory.py::test_read_write[trr-ncrst] SKIPPED (ncrst ...) [ 52%] 563s tests/test_trajectory.py::test_read_write[trr-rst7] SKIPPED (rst7 ca...) [ 52%] 563s tests/test_trajectory.py::test_read_write[trr-gro] PASSED [ 53%] 563s tests/test_trajectory.py::test_read_write[dcd-nc] PASSED [ 53%] 563s tests/test_trajectory.py::test_read_write[dcd-h5] PASSED [ 53%] 563s tests/test_trajectory.py::test_read_write[dcd-xtc] PASSED [ 53%] 563s tests/test_trajectory.py::test_read_write[dcd-trr] PASSED [ 53%] 563s tests/test_trajectory.py::test_read_write[dcd-dcd] PASSED [ 53%] 563s tests/test_trajectory.py::test_read_write[dcd-mdcrd] SKIPPED (mdcrd ...) [ 53%] 563s tests/test_trajectory.py::test_read_write[dcd-binpos] PASSED [ 53%] 564s tests/test_trajectory.py::test_read_write[dcd-dtr] PASSED [ 53%] 564s tests/test_trajectory.py::test_read_write[dcd-xyz] PASSED [ 53%] 564s tests/test_trajectory.py::test_read_write[dcd-xyz.gz] PASSED [ 53%] 564s tests/test_trajectory.py::test_read_write[dcd-lammpstrj] PASSED [ 53%] 564s tests/test_trajectory.py::test_read_write[dcd-tng] PASSED [ 54%] 564s tests/test_trajectory.py::test_read_write[dcd-lh5] PASSED [ 54%] 565s tests/test_trajectory.py::test_read_write[dcd-pdb] PASSED [ 54%] 565s tests/test_trajectory.py::test_read_write[dcd-pdb.gz] PASSED [ 54%] 565s tests/test_trajectory.py::test_read_write[dcd-ncrst] SKIPPED (ncrst ...) [ 54%] 565s tests/test_trajectory.py::test_read_write[dcd-rst7] SKIPPED (rst7 ca...) [ 54%] 565s tests/test_trajectory.py::test_read_write[dcd-gro] PASSED [ 54%] 565s tests/test_trajectory.py::test_read_write[mdcrd-nc] PASSED [ 54%] 565s tests/test_trajectory.py::test_read_write[mdcrd-h5] PASSED [ 54%] 565s tests/test_trajectory.py::test_read_write[mdcrd-xtc] PASSED [ 54%] 566s tests/test_trajectory.py::test_read_write[mdcrd-trr] PASSED [ 54%] 566s tests/test_trajectory.py::test_read_write[mdcrd-dcd] PASSED [ 54%] 566s tests/test_trajectory.py::test_read_write[mdcrd-mdcrd] SKIPPED (mdcr...) [ 55%] 566s tests/test_trajectory.py::test_read_write[mdcrd-binpos] PASSED [ 55%] 566s tests/test_trajectory.py::test_read_write[mdcrd-dtr] SKIPPED (dtr ne...) [ 55%] 566s tests/test_trajectory.py::test_read_write[mdcrd-xyz] PASSED [ 55%] 566s tests/test_trajectory.py::test_read_write[mdcrd-xyz.gz] PASSED [ 55%] 566s tests/test_trajectory.py::test_read_write[mdcrd-lammpstrj] SKIPPED (...) [ 55%] 566s tests/test_trajectory.py::test_read_write[mdcrd-tng] PASSED [ 55%] 566s tests/test_trajectory.py::test_read_write[mdcrd-lh5] PASSED [ 55%] 567s tests/test_trajectory.py::test_read_write[mdcrd-pdb] PASSED [ 55%] 568s tests/test_trajectory.py::test_read_write[mdcrd-pdb.gz] PASSED [ 55%] 568s tests/test_trajectory.py::test_read_write[mdcrd-ncrst] SKIPPED (ncrs...) [ 55%] 568s tests/test_trajectory.py::test_read_write[mdcrd-rst7] SKIPPED (rst7 ...) [ 55%] 569s tests/test_trajectory.py::test_read_write[mdcrd-gro] PASSED [ 56%] 569s tests/test_trajectory.py::test_read_write[binpos-nc] PASSED [ 56%] 569s tests/test_trajectory.py::test_read_write[binpos-h5] PASSED [ 56%] 569s tests/test_trajectory.py::test_read_write[binpos-xtc] PASSED [ 56%] 569s tests/test_trajectory.py::test_read_write[binpos-trr] PASSED [ 56%] 569s tests/test_trajectory.py::test_read_write[binpos-dcd] PASSED [ 56%] 569s tests/test_trajectory.py::test_read_write[binpos-mdcrd] SKIPPED (mdc...) [ 56%] 569s tests/test_trajectory.py::test_read_write[binpos-binpos] PASSED [ 56%] 569s tests/test_trajectory.py::test_read_write[binpos-dtr] SKIPPED (dtr n...) [ 56%] 569s tests/test_trajectory.py::test_read_write[binpos-xyz] PASSED [ 56%] 569s tests/test_trajectory.py::test_read_write[binpos-xyz.gz] PASSED [ 56%] 569s tests/test_trajectory.py::test_read_write[binpos-lammpstrj] SKIPPED [ 56%] 569s tests/test_trajectory.py::test_read_write[binpos-tng] PASSED [ 57%] 569s tests/test_trajectory.py::test_read_write[binpos-lh5] PASSED [ 57%] 569s tests/test_trajectory.py::test_read_write[binpos-pdb] PASSED [ 57%] 570s tests/test_trajectory.py::test_read_write[binpos-pdb.gz] PASSED [ 57%] 570s tests/test_trajectory.py::test_read_write[binpos-ncrst] SKIPPED (ncr...) [ 57%] 570s tests/test_trajectory.py::test_read_write[binpos-rst7] SKIPPED (rst7...) [ 57%] 570s tests/test_trajectory.py::test_read_write[binpos-gro] PASSED [ 57%] 570s tests/test_trajectory.py::test_read_write[dtr-nc] PASSED [ 57%] 570s tests/test_trajectory.py::test_read_write[dtr-h5] PASSED [ 57%] 570s tests/test_trajectory.py::test_read_write[dtr-xtc] PASSED [ 57%] 570s tests/test_trajectory.py::test_read_write[dtr-trr] PASSED [ 57%] 570s tests/test_trajectory.py::test_read_write[dtr-dcd] PASSED [ 57%] 570s tests/test_trajectory.py::test_read_write[dtr-mdcrd] SKIPPED (mdcrd ...) [ 57%] 570s tests/test_trajectory.py::test_read_write[dtr-binpos] PASSED [ 58%] 571s tests/test_trajectory.py::test_read_write[dtr-dtr] PASSED [ 58%] 571s tests/test_trajectory.py::test_read_write[dtr-xyz] PASSED [ 58%] 571s tests/test_trajectory.py::test_read_write[dtr-xyz.gz] PASSED [ 58%] 571s tests/test_trajectory.py::test_read_write[dtr-lammpstrj] PASSED [ 58%] 571s tests/test_trajectory.py::test_read_write[dtr-tng] PASSED [ 58%] 571s tests/test_trajectory.py::test_read_write[dtr-lh5] PASSED [ 58%] 572s tests/test_trajectory.py::test_read_write[dtr-pdb] PASSED [ 58%] 572s tests/test_trajectory.py::test_read_write[dtr-pdb.gz] PASSED [ 58%] 572s tests/test_trajectory.py::test_read_write[dtr-ncrst] SKIPPED (ncrst ...) [ 58%] 572s tests/test_trajectory.py::test_read_write[dtr-rst7] SKIPPED (rst7 ca...) [ 58%] 573s tests/test_trajectory.py::test_read_write[dtr-gro] PASSED [ 58%] 573s tests/test_trajectory.py::test_read_write[xyz-nc] PASSED [ 59%] 573s tests/test_trajectory.py::test_read_write[xyz-h5] PASSED [ 59%] 573s tests/test_trajectory.py::test_read_write[xyz-xtc] PASSED [ 59%] 573s tests/test_trajectory.py::test_read_write[xyz-trr] PASSED [ 59%] 573s tests/test_trajectory.py::test_read_write[xyz-dcd] PASSED [ 59%] 573s tests/test_trajectory.py::test_read_write[xyz-mdcrd] SKIPPED (mdcrd ...) [ 59%] 573s tests/test_trajectory.py::test_read_write[xyz-binpos] PASSED [ 59%] 573s tests/test_trajectory.py::test_read_write[xyz-dtr] SKIPPED (dtr need...) [ 59%] 573s tests/test_trajectory.py::test_read_write[xyz-xyz] PASSED [ 59%] 573s tests/test_trajectory.py::test_read_write[xyz-xyz.gz] PASSED [ 59%] 573s tests/test_trajectory.py::test_read_write[xyz-lammpstrj] SKIPPED (la...) [ 59%] 573s tests/test_trajectory.py::test_read_write[xyz-tng] PASSED [ 59%] 573s tests/test_trajectory.py::test_read_write[xyz-lh5] PASSED [ 60%] 574s tests/test_trajectory.py::test_read_write[xyz-pdb] PASSED [ 60%] 574s tests/test_trajectory.py::test_read_write[xyz-pdb.gz] PASSED [ 60%] 574s tests/test_trajectory.py::test_read_write[xyz-ncrst] SKIPPED (ncrst ...) [ 60%] 574s tests/test_trajectory.py::test_read_write[xyz-rst7] SKIPPED (rst7 ca...) [ 60%] 574s tests/test_trajectory.py::test_read_write[xyz-gro] PASSED [ 60%] 575s tests/test_trajectory.py::test_read_write[xyz.gz-nc] PASSED [ 60%] 575s tests/test_trajectory.py::test_read_write[xyz.gz-h5] PASSED [ 60%] 575s tests/test_trajectory.py::test_read_write[xyz.gz-xtc] PASSED [ 60%] 575s tests/test_trajectory.py::test_read_write[xyz.gz-trr] PASSED [ 60%] 575s tests/test_trajectory.py::test_read_write[xyz.gz-dcd] PASSED [ 60%] 575s tests/test_trajectory.py::test_read_write[xyz.gz-mdcrd] SKIPPED (mdc...) [ 60%] 575s tests/test_trajectory.py::test_read_write[xyz.gz-binpos] PASSED [ 61%] 575s tests/test_trajectory.py::test_read_write[xyz.gz-dtr] SKIPPED (dtr n...) [ 61%] 575s tests/test_trajectory.py::test_read_write[xyz.gz-xyz] PASSED [ 61%] 575s tests/test_trajectory.py::test_read_write[xyz.gz-xyz.gz] PASSED [ 61%] 575s tests/test_trajectory.py::test_read_write[xyz.gz-lammpstrj] SKIPPED [ 61%] 575s tests/test_trajectory.py::test_read_write[xyz.gz-tng] PASSED [ 61%] 575s tests/test_trajectory.py::test_read_write[xyz.gz-lh5] PASSED [ 61%] 576s tests/test_trajectory.py::test_read_write[xyz.gz-pdb] PASSED [ 61%] 576s tests/test_trajectory.py::test_read_write[xyz.gz-pdb.gz] PASSED [ 61%] 576s tests/test_trajectory.py::test_read_write[xyz.gz-ncrst] SKIPPED (ncr...) [ 61%] 576s tests/test_trajectory.py::test_read_write[xyz.gz-rst7] SKIPPED (rst7...) [ 61%] 576s tests/test_trajectory.py::test_read_write[xyz.gz-gro] PASSED [ 61%] 576s tests/test_trajectory.py::test_read_write[lammpstrj-nc] PASSED [ 62%] 576s tests/test_trajectory.py::test_read_write[lammpstrj-h5] PASSED [ 62%] 576s tests/test_trajectory.py::test_read_write[lammpstrj-xtc] PASSED [ 62%] 576s tests/test_trajectory.py::test_read_write[lammpstrj-trr] PASSED [ 62%] 576s tests/test_trajectory.py::test_read_write[lammpstrj-dcd] PASSED [ 62%] 576s tests/test_trajectory.py::test_read_write[lammpstrj-mdcrd] SKIPPED (...) [ 62%] 576s tests/test_trajectory.py::test_read_write[lammpstrj-binpos] PASSED [ 62%] 577s tests/test_trajectory.py::test_read_write[lammpstrj-dtr] PASSED [ 62%] 577s tests/test_trajectory.py::test_read_write[lammpstrj-xyz] PASSED [ 62%] 577s tests/test_trajectory.py::test_read_write[lammpstrj-xyz.gz] PASSED [ 62%] 578s tests/test_trajectory.py::test_read_write[lammpstrj-lammpstrj] PASSED [ 62%] 578s tests/test_trajectory.py::test_read_write[lammpstrj-tng] PASSED [ 62%] 578s tests/test_trajectory.py::test_read_write[lammpstrj-lh5] PASSED [ 63%] 578s tests/test_trajectory.py::test_read_write[lammpstrj-pdb] PASSED [ 63%] 579s tests/test_trajectory.py::test_read_write[lammpstrj-pdb.gz] PASSED [ 63%] 579s tests/test_trajectory.py::test_read_write[lammpstrj-ncrst] SKIPPED (...) [ 63%] 579s tests/test_trajectory.py::test_read_write[lammpstrj-rst7] SKIPPED (r...) [ 63%] 579s tests/test_trajectory.py::test_read_write[lammpstrj-gro] PASSED [ 63%] 579s tests/test_trajectory.py::test_read_write[tng-nc] PASSED [ 63%] 579s tests/test_trajectory.py::test_read_write[tng-h5] PASSED [ 63%] 579s tests/test_trajectory.py::test_read_write[tng-xtc] PASSED [ 63%] 579s tests/test_trajectory.py::test_read_write[tng-trr] PASSED [ 63%] 579s tests/test_trajectory.py::test_read_write[tng-dcd] PASSED [ 63%] 579s tests/test_trajectory.py::test_read_write[tng-mdcrd] SKIPPED (mdcrd ...) [ 63%] 579s tests/test_trajectory.py::test_read_write[tng-binpos] PASSED [ 63%] 580s tests/test_trajectory.py::test_read_write[tng-dtr] PASSED [ 64%] 580s tests/test_trajectory.py::test_read_write[tng-xyz] PASSED [ 64%] 580s tests/test_trajectory.py::test_read_write[tng-xyz.gz] PASSED [ 64%] 581s tests/test_trajectory.py::test_read_write[tng-lammpstrj] PASSED [ 64%] 581s tests/test_trajectory.py::test_read_write[tng-tng] PASSED [ 64%] 581s tests/test_trajectory.py::test_read_write[tng-lh5] PASSED [ 64%] 581s tests/test_trajectory.py::test_read_write[tng-pdb] PASSED [ 64%] 582s tests/test_trajectory.py::test_read_write[tng-pdb.gz] PASSED [ 64%] 582s tests/test_trajectory.py::test_read_write[tng-ncrst] SKIPPED (ncrst ...) [ 64%] 582s tests/test_trajectory.py::test_read_write[tng-rst7] SKIPPED (rst7 ca...) [ 64%] 582s tests/test_trajectory.py::test_read_write[tng-gro] PASSED [ 64%] 582s tests/test_trajectory.py::test_read_write[lh5-nc] PASSED [ 64%] 582s tests/test_trajectory.py::test_read_write[lh5-h5] PASSED [ 65%] 582s tests/test_trajectory.py::test_read_write[lh5-xtc] PASSED [ 65%] 582s tests/test_trajectory.py::test_read_write[lh5-trr] PASSED [ 65%] 582s tests/test_trajectory.py::test_read_write[lh5-dcd] PASSED [ 65%] 582s tests/test_trajectory.py::test_read_write[lh5-mdcrd] SKIPPED (mdcrd ...) [ 65%] 582s tests/test_trajectory.py::test_read_write[lh5-binpos] PASSED [ 65%] 582s tests/test_trajectory.py::test_read_write[lh5-dtr] SKIPPED (dtr need...) [ 65%] 582s tests/test_trajectory.py::test_read_write[lh5-xyz] PASSED [ 65%] 582s tests/test_trajectory.py::test_read_write[lh5-xyz.gz] PASSED [ 65%] 582s tests/test_trajectory.py::test_read_write[lh5-lammpstrj] SKIPPED (la...) [ 65%] 582s tests/test_trajectory.py::test_read_write[lh5-tng] PASSED [ 65%] 582s tests/test_trajectory.py::test_read_write[lh5-lh5] PASSED [ 65%] 583s tests/test_trajectory.py::test_read_write[lh5-pdb] PASSED [ 66%] 583s tests/test_trajectory.py::test_read_write[lh5-pdb.gz] PASSED [ 66%] 583s tests/test_trajectory.py::test_read_write[lh5-ncrst] SKIPPED (ncrst ...) [ 66%] 583s tests/test_trajectory.py::test_read_write[lh5-rst7] SKIPPED (rst7 ca...) [ 66%] 583s tests/test_trajectory.py::test_read_write[lh5-gro] PASSED [ 66%] 584s tests/test_trajectory.py::test_read_write[pdb-nc] PASSED [ 66%] 584s tests/test_trajectory.py::test_read_write[pdb-h5] PASSED [ 66%] 584s tests/test_trajectory.py::test_read_write[pdb-xtc] PASSED [ 66%] 584s tests/test_trajectory.py::test_read_write[pdb-trr] PASSED [ 66%] 584s tests/test_trajectory.py::test_read_write[pdb-dcd] PASSED [ 66%] 584s tests/test_trajectory.py::test_read_write[pdb-mdcrd] SKIPPED (mdcrd ...) [ 66%] 585s tests/test_trajectory.py::test_read_write[pdb-binpos] PASSED [ 66%] 586s tests/test_trajectory.py::test_read_write[pdb-dtr] PASSED [ 67%] 586s tests/test_trajectory.py::test_read_write[pdb-xyz] PASSED [ 67%] 586s tests/test_trajectory.py::test_read_write[pdb-xyz.gz] PASSED [ 67%] 587s tests/test_trajectory.py::test_read_write[pdb-lammpstrj] PASSED [ 67%] 587s tests/test_trajectory.py::test_read_write[pdb-tng] PASSED [ 67%] 587s tests/test_trajectory.py::test_read_write[pdb-lh5] PASSED [ 67%] 588s tests/test_trajectory.py::test_read_write[pdb-pdb] PASSED [ 67%] 588s tests/test_trajectory.py::test_read_write[pdb-pdb.gz] PASSED [ 67%] 588s tests/test_trajectory.py::test_read_write[pdb-ncrst] SKIPPED (ncrst ...) [ 67%] 588s tests/test_trajectory.py::test_read_write[pdb-rst7] SKIPPED (rst7 ca...) [ 67%] 589s tests/test_trajectory.py::test_read_write[pdb-gro] PASSED [ 67%] 589s tests/test_trajectory.py::test_read_write[pdb.gz-nc] PASSED [ 67%] 589s tests/test_trajectory.py::test_read_write[pdb.gz-h5] PASSED [ 68%] 589s tests/test_trajectory.py::test_read_write[pdb.gz-xtc] PASSED [ 68%] 590s tests/test_trajectory.py::test_read_write[pdb.gz-trr] PASSED [ 68%] 590s tests/test_trajectory.py::test_read_write[pdb.gz-dcd] PASSED [ 68%] 590s tests/test_trajectory.py::test_read_write[pdb.gz-mdcrd] SKIPPED (mdc...) [ 68%] 590s tests/test_trajectory.py::test_read_write[pdb.gz-binpos] PASSED [ 68%] 591s tests/test_trajectory.py::test_read_write[pdb.gz-dtr] PASSED [ 68%] 591s tests/test_trajectory.py::test_read_write[pdb.gz-xyz] PASSED [ 68%] 592s tests/test_trajectory.py::test_read_write[pdb.gz-xyz.gz] PASSED [ 68%] 592s tests/test_trajectory.py::test_read_write[pdb.gz-lammpstrj] PASSED [ 68%] 592s tests/test_trajectory.py::test_read_write[pdb.gz-tng] PASSED [ 68%] 592s tests/test_trajectory.py::test_read_write[pdb.gz-lh5] PASSED [ 68%] 593s tests/test_trajectory.py::test_read_write[pdb.gz-pdb] PASSED [ 68%] 594s tests/test_trajectory.py::test_read_write[pdb.gz-pdb.gz] PASSED [ 69%] 594s tests/test_trajectory.py::test_read_write[pdb.gz-ncrst] SKIPPED (ncr...) [ 69%] 594s tests/test_trajectory.py::test_read_write[pdb.gz-rst7] SKIPPED (rst7...) [ 69%] 594s tests/test_trajectory.py::test_read_write[pdb.gz-gro] PASSED [ 69%] 594s tests/test_trajectory.py::test_read_write[ncrst-nc] XFAIL (These ref...) [ 69%] 594s tests/test_trajectory.py::test_read_write[ncrst-h5] XFAIL (These ref...) [ 69%] 594s tests/test_trajectory.py::test_read_write[ncrst-xtc] XFAIL (These re...) [ 69%] 594s tests/test_trajectory.py::test_read_write[ncrst-trr] XFAIL (These re...) [ 69%] 594s tests/test_trajectory.py::test_read_write[ncrst-dcd] XFAIL (These re...) [ 69%] 594s tests/test_trajectory.py::test_read_write[ncrst-mdcrd] XFAIL (These ...) [ 69%] 594s tests/test_trajectory.py::test_read_write[ncrst-binpos] XFAIL (These...) [ 69%] 594s tests/test_trajectory.py::test_read_write[ncrst-dtr] XFAIL (These re...) [ 69%] 595s tests/test_trajectory.py::test_read_write[ncrst-xyz] XFAIL (These re...) [ 70%] 595s tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] XFAIL (These...) [ 70%] 595s tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] XFAIL (Th...) [ 70%] 595s tests/test_trajectory.py::test_read_write[ncrst-tng] XFAIL (These re...) [ 70%] 595s tests/test_trajectory.py::test_read_write[ncrst-lh5] XFAIL (These re...) [ 70%] 595s tests/test_trajectory.py::test_read_write[ncrst-pdb] XFAIL (These re...) [ 70%] 595s tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] XFAIL (These...) [ 70%] 595s tests/test_trajectory.py::test_read_write[ncrst-ncrst] XFAIL (These ...) [ 70%] 595s tests/test_trajectory.py::test_read_write[ncrst-rst7] XFAIL (These r...) [ 70%] 595s tests/test_trajectory.py::test_read_write[ncrst-gro] XFAIL (These re...) [ 70%] 595s tests/test_trajectory.py::test_read_write[rst7-nc] XFAIL (These refe...) [ 70%] 595s tests/test_trajectory.py::test_read_write[rst7-h5] XFAIL (These refe...) [ 70%] 595s tests/test_trajectory.py::test_read_write[rst7-xtc] XFAIL (These ref...) [ 71%] 595s tests/test_trajectory.py::test_read_write[rst7-trr] XFAIL (These ref...) [ 71%] 595s tests/test_trajectory.py::test_read_write[rst7-dcd] XFAIL (These ref...) [ 71%] 595s tests/test_trajectory.py::test_read_write[rst7-mdcrd] XFAIL (These r...) [ 71%] 595s tests/test_trajectory.py::test_read_write[rst7-binpos] XFAIL (These ...) [ 71%] 595s tests/test_trajectory.py::test_read_write[rst7-dtr] XFAIL (These ref...) [ 71%] 595s tests/test_trajectory.py::test_read_write[rst7-xyz] XFAIL (These ref...) [ 71%] 595s tests/test_trajectory.py::test_read_write[rst7-xyz.gz] XFAIL (These ...) [ 71%] 595s tests/test_trajectory.py::test_read_write[rst7-lammpstrj] XFAIL (The...) [ 71%] 595s tests/test_trajectory.py::test_read_write[rst7-tng] XFAIL (These ref...) [ 71%] 595s tests/test_trajectory.py::test_read_write[rst7-lh5] XFAIL (These ref...) [ 71%] 595s tests/test_trajectory.py::test_read_write[rst7-pdb] XFAIL (These ref...) [ 71%] 595s tests/test_trajectory.py::test_read_write[rst7-pdb.gz] XFAIL (These ...) [ 72%] 595s tests/test_trajectory.py::test_read_write[rst7-ncrst] XFAIL (These r...) [ 72%] 595s tests/test_trajectory.py::test_read_write[rst7-rst7] XFAIL (These re...) [ 72%] 595s tests/test_trajectory.py::test_read_write[rst7-gro] XFAIL (These ref...) [ 72%] 595s tests/test_trajectory.py::test_read_write[gro-nc] PASSED [ 72%] 595s tests/test_trajectory.py::test_read_write[gro-h5] PASSED [ 72%] 595s tests/test_trajectory.py::test_read_write[gro-xtc] PASSED [ 72%] 595s tests/test_trajectory.py::test_read_write[gro-trr] PASSED [ 72%] 595s tests/test_trajectory.py::test_read_write[gro-dcd] PASSED [ 72%] 595s tests/test_trajectory.py::test_read_write[gro-mdcrd] SKIPPED (mdcrd ...) [ 72%] 595s tests/test_trajectory.py::test_read_write[gro-binpos] PASSED [ 72%] 596s tests/test_trajectory.py::test_read_write[gro-dtr] PASSED [ 72%] 596s tests/test_trajectory.py::test_read_write[gro-xyz] PASSED [ 73%] 597s tests/test_trajectory.py::test_read_write[gro-xyz.gz] PASSED [ 73%] 597s tests/test_trajectory.py::test_read_write[gro-lammpstrj] PASSED [ 73%] 597s tests/test_trajectory.py::test_read_write[gro-tng] PASSED [ 73%] 597s tests/test_trajectory.py::test_read_write[gro-lh5] PASSED [ 73%] 598s tests/test_trajectory.py::test_read_write[gro-pdb] PASSED [ 73%] 598s tests/test_trajectory.py::test_read_write[gro-pdb.gz] PASSED [ 73%] 598s tests/test_trajectory.py::test_read_write[gro-ncrst] SKIPPED (ncrst ...) [ 73%] 598s tests/test_trajectory.py::test_read_write[gro-rst7] SKIPPED (rst7 ca...) [ 73%] 598s tests/test_trajectory.py::test_read_write[gro-gro] PASSED [ 73%] 598s tests/test_trajectory.py::test_load[nc] PASSED [ 73%] 598s tests/test_trajectory.py::test_load[h5] PASSED [ 73%] 598s tests/test_trajectory.py::test_load[xtc] PASSED [ 73%] 598s tests/test_trajectory.py::test_load[trr] PASSED [ 74%] 598s tests/test_trajectory.py::test_load[dcd] PASSED [ 74%] 599s tests/test_trajectory.py::test_load[mdcrd] PASSED [ 74%] 599s tests/test_trajectory.py::test_load[binpos] PASSED [ 74%] 599s tests/test_trajectory.py::test_load[dtr] PASSED [ 74%] 599s tests/test_trajectory.py::test_load[xyz] PASSED [ 74%] 599s tests/test_trajectory.py::test_load[xyz.gz] PASSED [ 74%] 599s tests/test_trajectory.py::test_load[lammpstrj] PASSED [ 74%] 599s tests/test_trajectory.py::test_load[tng] PASSED [ 74%] 599s tests/test_trajectory.py::test_load[lh5] PASSED [ 74%] 601s tests/test_trajectory.py::test_load[pdb] PASSED [ 74%] 602s tests/test_trajectory.py::test_load[pdb.gz] PASSED [ 74%] 602s tests/test_trajectory.py::test_load[ncrst] XFAIL (These reference fi...) [ 75%] 602s tests/test_trajectory.py::test_load[rst7] XFAIL (These reference fil...) [ 75%] 603s tests/test_trajectory.py::test_load[gro] PASSED [ 75%] 603s tests/test_trajectory.py::test_hdf5 PASSED [ 75%] 603s tests/test_trajectory.py::test_center PASSED [ 75%] 603s tests/test_trajectory.py::test_center_aind PASSED [ 75%] 603s tests/test_trajectory.py::test_float_atom_indices_exception[nc] PASSED [ 75%] 603s tests/test_trajectory.py::test_float_atom_indices_exception[h5] PASSED [ 75%] 603s tests/test_trajectory.py::test_float_atom_indices_exception[xtc] PASSED [ 75%] 603s tests/test_trajectory.py::test_float_atom_indices_exception[trr] PASSED [ 75%] 603s tests/test_trajectory.py::test_float_atom_indices_exception[dcd] PASSED [ 75%] 603s tests/test_trajectory.py::test_float_atom_indices_exception[mdcrd] PASSED [ 75%] 603s tests/test_trajectory.py::test_float_atom_indices_exception[binpos] PASSED [ 76%] 603s tests/test_trajectory.py::test_float_atom_indices_exception[dtr] PASSED [ 76%] 603s tests/test_trajectory.py::test_float_atom_indices_exception[xyz] PASSED [ 76%] 603s tests/test_trajectory.py::test_float_atom_indices_exception[xyz.gz] PASSED [ 76%] 603s tests/test_trajectory.py::test_float_atom_indices_exception[lammpstrj] PASSED [ 76%] 603s tests/test_trajectory.py::test_float_atom_indices_exception[tng] PASSED [ 76%] 603s tests/test_trajectory.py::test_float_atom_indices_exception[lh5] PASSED [ 76%] 603s tests/test_trajectory.py::test_float_atom_indices_exception[pdb] PASSED [ 76%] 603s tests/test_trajectory.py::test_float_atom_indices_exception[pdb.gz] PASSED [ 76%] 603s tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] XFAIL [ 76%] 603s tests/test_trajectory.py::test_float_atom_indices_exception[rst7] XFAIL [ 76%] 603s tests/test_trajectory.py::test_float_atom_indices_exception[gro] PASSED [ 76%] 603s tests/test_trajectory.py::test_restrict_atoms PASSED [ 77%] 603s tests/test_trajectory.py::test_restrict_atoms_not_inplace PASSED [ 77%] 603s tests/test_trajectory.py::test_array_vs_matrix PASSED [ 77%] 603s tests/test_trajectory.py::test_pdb_unitcell_loadsave PASSED [ 77%] 603s tests/test_trajectory.py::test_load_combination[nc] PASSED [ 77%] 603s tests/test_trajectory.py::test_load_combination[h5] PASSED [ 77%] 603s tests/test_trajectory.py::test_load_combination[xtc] PASSED [ 77%] 603s tests/test_trajectory.py::test_load_combination[trr] PASSED [ 77%] 603s tests/test_trajectory.py::test_load_combination[dcd] PASSED [ 77%] 603s tests/test_trajectory.py::test_load_combination[mdcrd] PASSED [ 77%] 603s tests/test_trajectory.py::test_load_combination[binpos] PASSED [ 77%] 603s tests/test_trajectory.py::test_load_combination[dtr] PASSED [ 77%] 603s tests/test_trajectory.py::test_load_combination[xyz] PASSED [ 78%] 603s tests/test_trajectory.py::test_load_combination[xyz.gz] PASSED [ 78%] 603s tests/test_trajectory.py::test_load_combination[lammpstrj] PASSED [ 78%] 603s tests/test_trajectory.py::test_load_combination[tng] PASSED [ 78%] 603s tests/test_trajectory.py::test_load_combination[lh5] PASSED [ 78%] 604s tests/test_trajectory.py::test_load_combination[pdb] PASSED [ 78%] 605s tests/test_trajectory.py::test_load_combination[pdb.gz] PASSED [ 78%] 605s tests/test_trajectory.py::test_load_combination[ncrst] XFAIL (These ...) [ 78%] 605s tests/test_trajectory.py::test_load_combination[rst7] XFAIL (These r...) [ 78%] 605s tests/test_trajectory.py::test_load_combination[gro] PASSED [ 78%] 605s tests/test_trajectory.py::test_no_topology PASSED [ 78%] 605s tests/test_trajectory.py::test_join PASSED [ 78%] 605s tests/test_trajectory.py::test_md_join PASSED [ 78%] 605s tests/test_trajectory.py::test_stack_1 PASSED [ 79%] 605s tests/test_trajectory.py::test_stack_2 PASSED [ 79%] 605s tests/test_trajectory.py::test_seek_read_mode[nc] PASSED [ 79%] 605s tests/test_trajectory.py::test_seek_read_mode[h5] PASSED [ 79%] 605s tests/test_trajectory.py::test_seek_read_mode[xtc] PASSED [ 79%] 605s tests/test_trajectory.py::test_seek_read_mode[trr] PASSED [ 79%] 605s tests/test_trajectory.py::test_seek_read_mode[dcd] PASSED [ 79%] 605s tests/test_trajectory.py::test_seek_read_mode[mdcrd] PASSED [ 79%] 605s tests/test_trajectory.py::test_seek_read_mode[binpos] PASSED [ 79%] 605s tests/test_trajectory.py::test_seek_read_mode[dtr] PASSED [ 79%] 605s tests/test_trajectory.py::test_seek_read_mode[xyz] PASSED [ 79%] 605s tests/test_trajectory.py::test_seek_read_mode[xyz.gz] XFAIL (This is...) [ 79%] 605s tests/test_trajectory.py::test_seek_read_mode[lammpstrj] PASSED [ 80%] 605s tests/test_trajectory.py::test_seek_read_mode[tng] PASSED [ 80%] 605s tests/test_trajectory.py::test_seek_read_mode[lh5] PASSED [ 80%] 605s tests/test_trajectory.py::test_seek_read_mode[pdb] XFAIL (PDB Files ...) [ 80%] 605s tests/test_trajectory.py::test_seek_read_mode[pdb.gz] XFAIL (PDB Fil...) [ 80%] 605s tests/test_trajectory.py::test_seek_read_mode[ncrst] XFAIL (These re...) [ 80%] 605s tests/test_trajectory.py::test_seek_read_mode[rst7] XFAIL (These ref...) [ 80%] 605s tests/test_trajectory.py::test_seek_read_mode[gro] XFAIL (This is br...) [ 80%] 605s tests/test_trajectory.py::test_load_frame[nc] PASSED [ 80%] 605s tests/test_trajectory.py::test_load_frame[h5] PASSED [ 80%] 605s tests/test_trajectory.py::test_load_frame[xtc] PASSED [ 80%] 605s tests/test_trajectory.py::test_load_frame[trr] PASSED [ 80%] 605s tests/test_trajectory.py::test_load_frame[dcd] PASSED [ 81%] 605s tests/test_trajectory.py::test_load_frame[mdcrd] PASSED [ 81%] 605s tests/test_trajectory.py::test_load_frame[binpos] PASSED [ 81%] 606s tests/test_trajectory.py::test_load_frame[dtr] XFAIL (DTR doesn't lo...) [ 81%] 606s tests/test_trajectory.py::test_load_frame[xyz] PASSED [ 81%] 606s tests/test_trajectory.py::test_load_frame[xyz.gz] PASSED [ 81%] 606s tests/test_trajectory.py::test_load_frame[lammpstrj] PASSED [ 81%] 606s tests/test_trajectory.py::test_load_frame[tng] PASSED [ 81%] 606s tests/test_trajectory.py::test_load_frame[lh5] PASSED [ 81%] 606s tests/test_trajectory.py::test_load_frame[pdb] PASSED [ 81%] 606s tests/test_trajectory.py::test_load_frame[pdb.gz] PASSED [ 81%] 606s tests/test_trajectory.py::test_load_frame[ncrst] XFAIL (These refere...) [ 81%] 606s tests/test_trajectory.py::test_load_frame[rst7] XFAIL (These referen...) [ 82%] 606s tests/test_trajectory.py::test_load_frame[gro] XFAIL (Gro doesn't im...) [ 82%] 607s tests/test_trajectory.py::test_load_frame_2eqq PASSED [ 82%] 607s tests/test_trajectory.py::test_iterload[nc] PASSED [ 82%] 607s tests/test_trajectory.py::test_iterload[h5] PASSED [ 82%] 607s tests/test_trajectory.py::test_iterload[xtc] PASSED [ 82%] 607s tests/test_trajectory.py::test_iterload[trr] PASSED [ 82%] 607s tests/test_trajectory.py::test_iterload[dcd] PASSED [ 82%] 607s tests/test_trajectory.py::test_iterload[mdcrd] PASSED [ 82%] 607s tests/test_trajectory.py::test_iterload[binpos] PASSED [ 82%] 607s tests/test_trajectory.py::test_iterload[dtr] XFAIL (This is broken w...) [ 82%] 607s tests/test_trajectory.py::test_iterload[xyz] PASSED [ 82%] 607s tests/test_trajectory.py::test_iterload[xyz.gz] PASSED [ 83%] 607s tests/test_trajectory.py::test_iterload[lammpstrj] PASSED [ 83%] 607s tests/test_trajectory.py::test_iterload[tng] PASSED [ 83%] 607s tests/test_trajectory.py::test_iterload[lh5] PASSED [ 83%] 607s tests/test_trajectory.py::test_iterload[pdb] PASSED [ 83%] 607s tests/test_trajectory.py::test_iterload[pdb.gz] PASSED [ 83%] 607s tests/test_trajectory.py::test_iterload[ncrst] SKIPPED (Only 1 frame...) [ 83%] 607s tests/test_trajectory.py::test_iterload[rst7] SKIPPED (Only 1 frame ...) [ 83%] 607s tests/test_trajectory.py::test_iterload[gro] PASSED [ 83%] 608s tests/test_trajectory.py::test_iterload_skip[nc] PASSED [ 83%] 611s tests/test_trajectory.py::test_iterload_skip[h5] PASSED [ 83%] 612s tests/test_trajectory.py::test_iterload_skip[xtc] PASSED [ 83%] 614s tests/test_trajectory.py::test_iterload_skip[trr] PASSED [ 84%] 615s tests/test_trajectory.py::test_iterload_skip[dcd] PASSED [ 84%] 617s tests/test_trajectory.py::test_iterload_skip[mdcrd] PASSED [ 84%] 618s tests/test_trajectory.py::test_iterload_skip[binpos] PASSED [ 84%] 618s tests/test_trajectory.py::test_iterload_skip[dtr] PASSED [ 84%] 619s tests/test_trajectory.py::test_iterload_skip[xyz] PASSED [ 84%] 620s tests/test_trajectory.py::test_iterload_skip[xyz.gz] PASSED [ 84%] 622s tests/test_trajectory.py::test_iterload_skip[lammpstrj] PASSED [ 84%] 623s tests/test_trajectory.py::test_iterload_skip[tng] PASSED [ 84%] 625s tests/test_trajectory.py::test_iterload_skip[lh5] PASSED [ 84%] 625s tests/test_trajectory.py::test_iterload_skip[pdb] XFAIL (PDB Iterloa...) [ 84%] 625s tests/test_trajectory.py::test_iterload_skip[pdb.gz] XFAIL (PDB Iter...) [ 84%] 625s tests/test_trajectory.py::test_iterload_skip[ncrst] XFAIL (These ref...) [ 84%] 625s tests/test_trajectory.py::test_iterload_skip[rst7] XFAIL (These refe...) [ 85%] 625s tests/test_trajectory.py::test_iterload_skip[gro] XFAIL (Not impleme...) [ 85%] 625s tests/test_trajectory.py::test_iterload_chunk_dcd PASSED [ 85%] 625s tests/test_trajectory.py::test_save_load[nc] PASSED [ 85%] 625s tests/test_trajectory.py::test_save_load[h5] PASSED [ 85%] 625s tests/test_trajectory.py::test_save_load[xtc] PASSED [ 85%] 625s tests/test_trajectory.py::test_save_load[trr] PASSED [ 85%] 625s tests/test_trajectory.py::test_save_load[dcd] PASSED [ 85%] 625s tests/test_trajectory.py::test_save_load[mdcrd] PASSED [ 85%] 625s tests/test_trajectory.py::test_save_load[binpos] PASSED [ 85%] 626s tests/test_trajectory.py::test_save_load[dtr] PASSED [ 85%] 626s tests/test_trajectory.py::test_save_load[xyz] PASSED [ 85%] 626s tests/test_trajectory.py::test_save_load[xyz.gz] PASSED [ 86%] 626s tests/test_trajectory.py::test_save_load[lammpstrj] PASSED [ 86%] 626s tests/test_trajectory.py::test_save_load[tng] PASSED [ 86%] 626s tests/test_trajectory.py::test_save_load[lh5] PASSED [ 86%] 626s tests/test_trajectory.py::test_save_load[pdb] PASSED [ 86%] 626s tests/test_trajectory.py::test_save_load[pdb.gz] PASSED [ 86%] 626s tests/test_trajectory.py::test_save_load[ncrst] PASSED [ 86%] 626s tests/test_trajectory.py::test_save_load[rst7] PASSED [ 86%] 626s tests/test_trajectory.py::test_save_load[gro] PASSED [ 86%] 626s tests/test_trajectory.py::test_force_overwrite[nc] PASSED [ 86%] 626s tests/test_trajectory.py::test_force_overwrite[h5] PASSED [ 86%] 626s tests/test_trajectory.py::test_force_overwrite[xtc] PASSED [ 86%] 626s tests/test_trajectory.py::test_force_overwrite[trr] PASSED [ 87%] 626s tests/test_trajectory.py::test_force_overwrite[dcd] PASSED [ 87%] 626s tests/test_trajectory.py::test_force_overwrite[mdcrd] PASSED [ 87%] 626s tests/test_trajectory.py::test_force_overwrite[binpos] PASSED [ 87%] 626s tests/test_trajectory.py::test_force_overwrite[dtr] XFAIL (This is b...) [ 87%] 626s tests/test_trajectory.py::test_force_overwrite[xyz] PASSED [ 87%] 626s tests/test_trajectory.py::test_force_overwrite[xyz.gz] PASSED [ 87%] 626s tests/test_trajectory.py::test_force_overwrite[lammpstrj] PASSED [ 87%] 626s tests/test_trajectory.py::test_force_overwrite[tng] PASSED [ 87%] 626s tests/test_trajectory.py::test_force_overwrite[lh5] PASSED [ 87%] 626s tests/test_trajectory.py::test_force_overwrite[pdb] PASSED [ 87%] 626s tests/test_trajectory.py::test_force_overwrite[pdb.gz] PASSED [ 87%] 626s tests/test_trajectory.py::test_force_overwrite[ncrst] PASSED [ 88%] 626s tests/test_trajectory.py::test_force_overwrite[rst7] PASSED [ 88%] 626s tests/test_trajectory.py::test_force_overwrite[gro] PASSED [ 88%] 626s tests/test_trajectory.py::test_force_noverwrite[nc] PASSED [ 88%] 626s tests/test_trajectory.py::test_force_noverwrite[h5] PASSED [ 88%] 626s tests/test_trajectory.py::test_force_noverwrite[xtc] PASSED [ 88%] 626s tests/test_trajectory.py::test_force_noverwrite[trr] PASSED [ 88%] 626s tests/test_trajectory.py::test_force_noverwrite[dcd] PASSED [ 88%] 626s tests/test_trajectory.py::test_force_noverwrite[mdcrd] PASSED [ 88%] 626s tests/test_trajectory.py::test_force_noverwrite[binpos] PASSED [ 88%] 626s tests/test_trajectory.py::test_force_noverwrite[dtr] PASSED [ 88%] 626s tests/test_trajectory.py::test_force_noverwrite[xyz] PASSED [ 88%] 626s tests/test_trajectory.py::test_force_noverwrite[xyz.gz] PASSED [ 89%] 626s tests/test_trajectory.py::test_force_noverwrite[lammpstrj] PASSED [ 89%] 626s tests/test_trajectory.py::test_force_noverwrite[tng] PASSED [ 89%] 626s tests/test_trajectory.py::test_force_noverwrite[lh5] PASSED [ 89%] 626s tests/test_trajectory.py::test_force_noverwrite[pdb] PASSED [ 89%] 626s tests/test_trajectory.py::test_force_noverwrite[pdb.gz] PASSED [ 89%] 626s tests/test_trajectory.py::test_force_noverwrite[ncrst] PASSED [ 89%] 626s tests/test_trajectory.py::test_force_noverwrite[rst7] PASSED [ 89%] 626s tests/test_trajectory.py::test_force_noverwrite[gro] PASSED [ 89%] 626s tests/test_trajectory.py::test_open_and_load PASSED [ 89%] 626s tests/test_trajectory.py::test_length PASSED [ 89%] 626s tests/test_trajectory.py::test_unitcell[nc] PASSED [ 89%] 626s tests/test_trajectory.py::test_unitcell[h5] PASSED [ 89%] 626s tests/test_trajectory.py::test_unitcell[xtc] PASSED [ 90%] 626s tests/test_trajectory.py::test_unitcell[trr] PASSED [ 90%] 626s tests/test_trajectory.py::test_unitcell[dcd] PASSED [ 90%] 626s tests/test_trajectory.py::test_unitcell[mdcrd] PASSED [ 90%] 626s tests/test_trajectory.py::test_unitcell[binpos] PASSED [ 90%] 626s tests/test_trajectory.py::test_unitcell[dtr] XFAIL (dtr seems to nee...) [ 90%] 626s tests/test_trajectory.py::test_unitcell[xyz] PASSED [ 90%] 626s tests/test_trajectory.py::test_unitcell[xyz.gz] PASSED [ 90%] 626s tests/test_trajectory.py::test_unitcell[lammpstrj] XFAIL (lammpstrj ...) [ 90%] 626s tests/test_trajectory.py::test_unitcell[tng] PASSED [ 90%] 626s tests/test_trajectory.py::test_unitcell[lh5] PASSED [ 90%] 626s tests/test_trajectory.py::test_unitcell[pdb] PASSED [ 90%] 626s tests/test_trajectory.py::test_unitcell[pdb.gz] PASSED [ 91%] 626s tests/test_trajectory.py::test_unitcell[ncrst] XFAIL (ncrst seems to...) [ 91%] 626s tests/test_trajectory.py::test_unitcell[rst7] XFAIL (rst7 seems to n...) [ 91%] 626s tests/test_trajectory.py::test_unitcell[gro] PASSED [ 91%] 626s tests/test_trajectory.py::test_chunk0_iterload PASSED [ 91%] 627s tests/test_trajectory.py::test_hashing PASSED [ 91%] 627s tests/test_trajectory.py::test_smooth PASSED [ 91%] 627s tests/test_trajectory.py::test_load_pdb_no_standard_names PASSED [ 91%] 627s tests/test_trajectory.py::test_load_with_atom_indices PASSED [ 91%] 627s tests/test_trajectory.py::test_load_with_frame PASSED [ 91%] 627s tests/test_trajectory.py::test_add_remove_atoms PASSED [ 91%] 627s tests/test_trr.py::test_1 PASSED [ 91%] 627s tests/test_trr.py::test_read_stride PASSED [ 92%] 627s tests/test_trr.py::test_read_stride_n_frames PASSED [ 92%] 627s tests/test_trr.py::test_read_stride_offsets PASSED [ 92%] 627s tests/test_trr.py::test_read_stride_n_frames_offsets PASSED [ 92%] 627s tests/test_trr.py::test_read_stride_switching PASSED [ 92%] 627s tests/test_trr.py::test_write_read PASSED [ 92%] 627s tests/test_trr.py::test_read_atomindices_1 PASSED [ 92%] 627s tests/test_trr.py::test_read_atomindices_2 PASSED [ 92%] 627s tests/test_trr.py::test_deficient_shape PASSED [ 92%] 627s tests/test_trr.py::test_ragged_1 PASSED [ 92%] 627s tests/test_trr.py::test_ragged_2 PASSED [ 92%] 627s tests/test_trr.py::test_malformed PASSED [ 92%] 627s tests/test_trr.py::test_tell PASSED [ 93%] 627s tests/test_trr.py::test_seek PASSED [ 93%] 627s tests/test_trr.py::test_get_velocities PASSED [ 93%] 627s tests/test_trr.py::test_get_forces PASSED [ 93%] 627s tests/test_trr.py::test_get_velocities_and_forces PASSED [ 93%] 627s tests/test_trr.py::test_get_velocities_forces_atom_indices_1 PASSED [ 93%] 627s tests/test_trr.py::test_get_velocities_forces_atom_indices_2 PASSED [ 93%] 627s tests/test_trr.py::test_read_velocities_do_not_exist PASSED [ 93%] 627s tests/test_trr.py::test_read_forces_do_not_exist PASSED [ 93%] 627s tests/test_utils.py::test_unitcell_0 PASSED [ 93%] 627s tests/test_utils.py::test_unitcell_1 PASSED [ 93%] 627s tests/test_utils.py::test_ensure_type_1 PASSED [ 93%] 627s tests/test_utils.py::test_ensure_type_2 PASSED [ 94%] 627s tests/test_utils.py::test_ensure_type_25 PASSED [ 94%] 627s tests/test_utils.py::test_ensure_type_3 PASSED [ 94%] 627s tests/test_utils.py::test_ensure_type_4 PASSED [ 94%] 627s tests/test_utils.py::test_ensure_type_5 PASSED [ 94%] 627s tests/test_utils.py::test_ensure_type_6 PASSED [ 94%] 627s tests/test_utils.py::test_ensure_type_7 PASSED [ 94%] 627s tests/test_utils.py::test_ensure_type_8 PASSED [ 94%] 627s tests/test_utils.py::test_ensure_type_9 PASSED [ 94%] 627s tests/test_utils.py::test_ensure_type_10 PASSED [ 94%] 627s tests/test_utils.py::test_ensure_type_11 PASSED [ 94%] 627s tests/test_utils.py::test_ensure_type_12 PASSED [ 94%] 627s tests/test_utils.py::test_ensure_type_13 PASSED [ 94%] 627s tests/test_utils.py::test_ensure_type_14 PASSED [ 95%] 627s tests/test_utils.py::test_ensure_type_15 PASSED [ 95%] 627s tests/test_utils.py::test_delay_import_fail_1 PASSED [ 95%] 627s tests/test_utils.py::test_delay_import PASSED [ 95%] 627s tests/test_utils.py::test_unit_0 PASSED [ 95%] 627s tests/test_utils.py::test_unit_1 PASSED [ 95%] 627s tests/test_utils.py::test_unit_2 PASSED [ 95%] 627s tests/test_utils.py::test_unit_3 PASSED [ 95%] 627s tests/test_xml.py::test_xml PASSED [ 95%] 627s tests/test_xtc.py::test_read_chunk1 PASSED [ 95%] 628s tests/test_xtc.py::test_read_stride PASSED [ 95%] 628s tests/test_xtc.py::test_read_stride_n_frames PASSED [ 95%] 628s tests/test_xtc.py::test_read_stride_offsets PASSED [ 96%] 628s tests/test_xtc.py::test_read_stride_n_frames_offsets PASSED [ 96%] 628s tests/test_xtc.py::test_read_stride_switching_offsets PASSED [ 96%] 628s tests/test_xtc.py::test_read_atomindices_1 PASSED [ 96%] 628s tests/test_xtc.py::test_read_atomindices_w_stride PASSED [ 96%] 628s tests/test_xtc.py::test_read_atomindices_2 PASSED [ 96%] 628s tests/test_xtc.py::test_read_chunk2 PASSED [ 96%] 628s tests/test_xtc.py::test_read_chunk3 PASSED [ 96%] 628s tests/test_xtc.py::test_write_0 PASSED [ 96%] 628s tests/test_xtc.py::test_write_1 PASSED [ 96%] 628s tests/test_xtc.py::test_write_2 PASSED [ 96%] 628s tests/test_xtc.py::test_read_error_0 PASSED [ 96%] 628s tests/test_xtc.py::test_write_error_0 PASSED [ 97%] 628s tests/test_xtc.py::test_read_error_1 PASSED [ 97%] 628s tests/test_xtc.py::test_read_error_2 PASSED [ 97%] 628s tests/test_xtc.py::test_xtc_write_wierd_0 PASSED [ 97%] 628s tests/test_xtc.py::test_tell PASSED [ 97%] 628s tests/test_xtc.py::test_seek PASSED [ 97%] 628s tests/test_xtc.py::test_seek_natoms9 PASSED [ 97%] 628s tests/test_xtc.py::test_seek_out_of_bounds PASSED [ 97%] 628s tests/test_xtc.py::test_ragged_1 PASSED [ 97%] 628s tests/test_xtc.py::test_ragged_2 PASSED [ 97%] 628s tests/test_xtc.py::test_short_traj PASSED [ 97%] 628s tests/test_xtc.py::test_flush PASSED [ 97%] 628s tests/test_xyz.py::test_read_0 PASSED [ 98%] 628s tests/test_xyz.py::test_read_1 PASSED [ 98%] 628s tests/test_xyz.py::test_read_gz PASSED [ 98%] 628s tests/test_xyz.py::test_read_write PASSED [ 98%] 628s tests/test_xyz.py::test_mdwrite PASSED [ 98%] 628s tests/test_xyz.py::test_multiread PASSED [ 98%] 628s tests/test_xyz.py::test_seek PASSED [ 98%] 628s tests/test_xyz.py::test_len PASSED [ 98%] 628s tests/test_zipped.py::test_read_gz PASSED [ 98%] 628s tests/test_zipped.py::test_write_gz PASSED [ 98%] 628s tests/test_zipped.py::test_read_bz2 PASSED [ 98%] 628s tests/test_zipped.py::test_write_bz2 PASSED [ 98%] 764s examples/test_examples.py::test_example_notebook[two-pass-clustering.ipynb] PASSED [ 99%] 764s examples/test_examples.py::test_example_notebook[simulation-with-openmm.ipynb] SKIPPED [ 99%] 904s examples/test_examples.py::test_example_notebook[centroids.ipynb] PASSED [ 99%] 1042s examples/test_examples.py::test_example_notebook[rmsd-benchmark.ipynb] PASSED [ 99%] 1178s examples/test_examples.py::test_example_notebook[ramachandran-plot.ipynb] PASSED [ 99%] 1314s examples/test_examples.py::test_example_notebook[hbonds.ipynb] SKIPPED [ 99%] 1449s examples/test_examples.py::test_example_notebook[native-contact.ipynb] SKIPPED [ 99%] 1588s examples/test_examples.py::test_example_notebook[solvent-accessible-surface-area.ipynb] PASSED [ 99%] 1727s examples/test_examples.py::test_example_notebook[clustering.ipynb] PASSED [ 99%] 1866s examples/test_examples.py::test_example_notebook[iterload.ipynb] PASSED [ 99%] 2002s examples/test_examples.py::test_example_notebook[principal-components.ipynb] PASSED [ 99%] 2140s examples/test_examples.py::test_example_notebook[atom-selection.ipynb] PASSED [ 99%] 2275s examples/test_examples.py::test_example_notebook[rmsd-drift.ipynb] PASSED [100%] 2275s 2275s ================================== XFAILURES =================================== 2275s ____________________________ test_read_path[ncrst] _____________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s _____________________________ test_read_path[rst7] _____________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s __________________________ test_read_write[ncrst-nc] ___________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s __________________________ test_read_write[ncrst-h5] ___________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s __________________________ test_read_write[ncrst-xtc] __________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s __________________________ test_read_write[ncrst-trr] __________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s __________________________ test_read_write[ncrst-dcd] __________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s _________________________ test_read_write[ncrst-mdcrd] _________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s ________________________ test_read_write[ncrst-binpos] _________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s __________________________ test_read_write[ncrst-dtr] __________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s __________________________ test_read_write[ncrst-xyz] __________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s ________________________ test_read_write[ncrst-xyz.gz] _________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s _______________________ test_read_write[ncrst-lammpstrj] _______________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s __________________________ test_read_write[ncrst-tng] __________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s __________________________ test_read_write[ncrst-lh5] __________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s __________________________ test_read_write[ncrst-pdb] __________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s ________________________ test_read_write[ncrst-pdb.gz] _________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s _________________________ test_read_write[ncrst-ncrst] _________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s _________________________ test_read_write[ncrst-rst7] __________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s __________________________ test_read_write[ncrst-gro] __________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s ___________________________ test_read_write[rst7-nc] ___________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s ___________________________ test_read_write[rst7-h5] ___________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s __________________________ test_read_write[rst7-xtc] ___________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s __________________________ test_read_write[rst7-trr] ___________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s __________________________ test_read_write[rst7-dcd] ___________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s _________________________ test_read_write[rst7-mdcrd] __________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s _________________________ test_read_write[rst7-binpos] _________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s __________________________ test_read_write[rst7-dtr] ___________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s __________________________ test_read_write[rst7-xyz] ___________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s _________________________ test_read_write[rst7-xyz.gz] _________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s _______________________ test_read_write[rst7-lammpstrj] ________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s __________________________ test_read_write[rst7-tng] ___________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s __________________________ test_read_write[rst7-lh5] ___________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s __________________________ test_read_write[rst7-pdb] ___________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s _________________________ test_read_write[rst7-pdb.gz] _________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s _________________________ test_read_write[rst7-ncrst] __________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s __________________________ test_read_write[rst7-rst7] __________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s __________________________ test_read_write[rst7-gro] ___________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s _______________________________ test_load[ncrst] _______________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s _______________________________ test_load[rst7] ________________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s ___________________ test_float_atom_indices_exception[ncrst] ___________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s ___________________ test_float_atom_indices_exception[rst7] ____________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s _________________________ test_load_combination[ncrst] _________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s _________________________ test_load_combination[rst7] __________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s _________________________ test_seek_read_mode[xyz.gz] __________________________ 2275s 2275s ref_traj = TrajObj(fobj=, fext='xyz.gz', fn='frame0.xyz.gz') 2275s get_fn = ._get_fn at 0x77a89c234ea0> 2275s 2275s def test_seek_read_mode(ref_traj, get_fn): 2275s # Test the seek/tell capacity of the different TrajectoryFile objects in 2275s # read mode. Basically, we just seek around the files and read different 2275s # segments, keeping track of our location manually and checking with both 2275s # tell() and by checking that the right coordinates are actually returned 2275s fobj = ref_traj.fobj 2275s fn = ref_traj.fn 2275s 2275s if ref_traj.fobj is md.formats.PDBTrajectoryFile: 2275s pytest.xfail("PDB Files don't support seeking") 2275s if ref_traj.fext == 'xyz.gz': 2275s > pytest.xfail("This is broken") 2275s E _pytest.outcomes.XFailed: This is broken 2275s 2275s tests/test_trajectory.py:462: XFailed 2275s ___________________________ test_seek_read_mode[pdb] ___________________________ 2275s 2275s ref_traj = TrajObj(fobj=, fext='pdb', fn='frame0.pdb') 2275s get_fn = ._get_fn at 0x77a89c234ea0> 2275s 2275s def test_seek_read_mode(ref_traj, get_fn): 2275s # Test the seek/tell capacity of the different TrajectoryFile objects in 2275s # read mode. Basically, we just seek around the files and read different 2275s # segments, keeping track of our location manually and checking with both 2275s # tell() and by checking that the right coordinates are actually returned 2275s fobj = ref_traj.fobj 2275s fn = ref_traj.fn 2275s 2275s if ref_traj.fobj is md.formats.PDBTrajectoryFile: 2275s > pytest.xfail("PDB Files don't support seeking") 2275s E _pytest.outcomes.XFailed: PDB Files don't support seeking 2275s 2275s tests/test_trajectory.py:460: XFailed 2275s _________________________ test_seek_read_mode[pdb.gz] __________________________ 2275s 2275s ref_traj = TrajObj(fobj=, fext='pdb.gz', fn='frame0.pdb.gz') 2275s get_fn = ._get_fn at 0x77a89c234ea0> 2275s 2275s def test_seek_read_mode(ref_traj, get_fn): 2275s # Test the seek/tell capacity of the different TrajectoryFile objects in 2275s # read mode. Basically, we just seek around the files and read different 2275s # segments, keeping track of our location manually and checking with both 2275s # tell() and by checking that the right coordinates are actually returned 2275s fobj = ref_traj.fobj 2275s fn = ref_traj.fn 2275s 2275s if ref_traj.fobj is md.formats.PDBTrajectoryFile: 2275s > pytest.xfail("PDB Files don't support seeking") 2275s E _pytest.outcomes.XFailed: PDB Files don't support seeking 2275s 2275s tests/test_trajectory.py:460: XFailed 2275s __________________________ test_seek_read_mode[ncrst] __________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s __________________________ test_seek_read_mode[rst7] ___________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s ___________________________ test_seek_read_mode[gro] ___________________________ 2275s 2275s ref_traj = TrajObj(fobj=, fext='gro', fn='frame0.gro') 2275s get_fn = ._get_fn at 0x77a89c234ea0> 2275s 2275s def test_seek_read_mode(ref_traj, get_fn): 2275s # Test the seek/tell capacity of the different TrajectoryFile objects in 2275s # read mode. Basically, we just seek around the files and read different 2275s # segments, keeping track of our location manually and checking with both 2275s # tell() and by checking that the right coordinates are actually returned 2275s fobj = ref_traj.fobj 2275s fn = ref_traj.fn 2275s 2275s if ref_traj.fobj is md.formats.PDBTrajectoryFile: 2275s pytest.xfail("PDB Files don't support seeking") 2275s if ref_traj.fext == 'xyz.gz': 2275s pytest.xfail("This is broken") 2275s if ref_traj.fext == 'gro': 2275s > pytest.xfail("This is broken") 2275s E _pytest.outcomes.XFailed: This is broken 2275s 2275s tests/test_trajectory.py:464: XFailed 2275s _____________________________ test_load_frame[dtr] _____________________________ 2275s 2275s ref_traj = TrajObj(fobj=, fext='dtr', fn='frame0.dtr') 2275s get_fn = ._get_fn at 0x77a89c234ea0> 2275s 2275s def test_load_frame(ref_traj, get_fn): 2275s if ref_traj.fobj is md.formats.GroTrajectoryFile: 2275s pytest.xfail("Gro doesn't implement seek") 2275s trajectory = md.load(get_fn(ref_traj.fn), top=get_fn('native.pdb')) 2275s rand = np.random.randint(len(trajectory)) 2275s frame = md.load_frame(get_fn(ref_traj.fn), index=rand, top=get_fn('native.pdb')) 2275s 2275s if ref_traj.fobj is md.formats.DTRTrajectoryFile: 2275s > pytest.xfail("DTR doesn't load a single frame properly") 2275s E _pytest.outcomes.XFailed: DTR doesn't load a single frame properly 2275s 2275s tests/test_trajectory.py:521: XFailed 2275s ____________________________ test_load_frame[ncrst] ____________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s ____________________________ test_load_frame[rst7] _____________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s _____________________________ test_load_frame[gro] _____________________________ 2275s 2275s ref_traj = TrajObj(fobj=, fext='gro', fn='frame0.gro') 2275s get_fn = ._get_fn at 0x77a89c234ea0> 2275s 2275s def test_load_frame(ref_traj, get_fn): 2275s if ref_traj.fobj is md.formats.GroTrajectoryFile: 2275s > pytest.xfail("Gro doesn't implement seek") 2275s E _pytest.outcomes.XFailed: Gro doesn't implement seek 2275s 2275s tests/test_trajectory.py:515: XFailed 2275s ______________________________ test_iterload[dtr] ______________________________ 2275s 2275s write_traj = TrajObj(fobj=, fext='dtr', fn='/tmp/pytest-of-ubuntu/pytest-0/test_iterload_dtr_0/traj.dtr') 2275s get_fn = ._get_fn at 0x77a89c234ea0> 2275s 2275s def test_iterload(write_traj, get_fn): 2275s if write_traj.fext == 'dtr': 2275s > pytest.xfail("This is broken with dtr") 2275s E _pytest.outcomes.XFailed: This is broken with dtr 2275s 2275s tests/test_trajectory.py:537: XFailed 2275s ___________________________ test_iterload_skip[pdb] ____________________________ 2275s 2275s ref_traj = TrajObj(fobj=, fext='pdb', fn='frame0.pdb') 2275s get_fn = ._get_fn at 0x77a89c234ea0> 2275s 2275s def test_iterload_skip(ref_traj, get_fn): 2275s if ref_traj.fobj is md.formats.PDBTrajectoryFile: 2275s > pytest.xfail("PDB Iterloads an extra frame!!") 2275s E _pytest.outcomes.XFailed: PDB Iterloads an extra frame!! 2275s 2275s tests/test_trajectory.py:557: XFailed 2275s __________________________ test_iterload_skip[pdb.gz] __________________________ 2275s 2275s ref_traj = TrajObj(fobj=, fext='pdb.gz', fn='frame0.pdb.gz') 2275s get_fn = ._get_fn at 0x77a89c234ea0> 2275s 2275s def test_iterload_skip(ref_traj, get_fn): 2275s if ref_traj.fobj is md.formats.PDBTrajectoryFile: 2275s > pytest.xfail("PDB Iterloads an extra frame!!") 2275s E _pytest.outcomes.XFailed: PDB Iterloads an extra frame!! 2275s 2275s tests/test_trajectory.py:557: XFailed 2275s __________________________ test_iterload_skip[ncrst] ___________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s ___________________________ test_iterload_skip[rst7] ___________________________ 2275s 2275s request = > 2275s 2275s @pytest.fixture(params=file_objs, ids=lambda x: x[1]) 2275s def ref_traj(request): 2275s fobj, fext = request.param 2275s if (on_win and on_py3): 2275s if fext == 'lh5': 2275s pytest.skip("lh5 is not supported on Windows + Py3") 2275s 2275s if fext in ['ncrst', 'rst7']: 2275s > pytest.xfail("These reference files don't exist yet") 2275s E _pytest.outcomes.XFailed: These reference files don't exist yet 2275s 2275s tests/test_trajectory.py:73: XFailed 2275s ___________________________ test_iterload_skip[gro] ____________________________ 2275s 2275s ref_traj = TrajObj(fobj=, fext='gro', fn='frame0.gro') 2275s get_fn = ._get_fn at 0x77a89c234ea0> 2275s 2275s def test_iterload_skip(ref_traj, get_fn): 2275s if ref_traj.fobj is md.formats.PDBTrajectoryFile: 2275s pytest.xfail("PDB Iterloads an extra frame!!") 2275s if ref_traj.fobj is md.formats.GroTrajectoryFile: 2275s > pytest.xfail("Not implemented for some reason") 2275s E _pytest.outcomes.XFailed: Not implemented for some reason 2275s 2275s tests/test_trajectory.py:559: XFailed 2275s __________________________ test_force_overwrite[dtr] ___________________________ 2275s 2275s write_traj = TrajObj(fobj=, fext='dtr', fn='/tmp/pytest-of-ubuntu/pytest-0/test_force_overwrite_dtr_0/traj.dtr') 2275s get_fn = ._get_fn at 0x77a89c234ea0> 2275s 2275s def test_force_overwrite(write_traj, get_fn): 2275s if write_traj.fext == 'dtr': 2275s > pytest.xfail("This is broken with dtr") 2275s E _pytest.outcomes.XFailed: This is broken with dtr 2275s 2275s tests/test_trajectory.py:615: XFailed 2275s ______________________________ test_unitcell[dtr] ______________________________ 2275s 2275s write_traj = TrajObj(fobj=, fext='dtr', fn='/tmp/pytest-of-ubuntu/pytest-0/test_unitcell_dtr_0/traj.dtr') 2275s get_fn = ._get_fn at 0x77a89c234ea0> 2275s 2275s def test_unitcell(write_traj, get_fn): 2275s # make sure that bogus unitcell vecotrs are not saved 2275s 2275s if write_traj.fext in ['rst7', 'ncrst', 'lammpstrj', 'dtr']: 2275s > pytest.xfail('{} seems to need unit vectors'.format(write_traj.fext)) 2275s E _pytest.outcomes.XFailed: dtr seems to need unit vectors 2275s 2275s tests/test_trajectory.py:665: XFailed 2275s ___________________________ test_unitcell[lammpstrj] ___________________________ 2275s 2275s write_traj = TrajObj(fobj=, fext='lammpstrj', fn='/tmp/pytest-of-ubuntu/pytest-0/test_unitcell_lammpstrj_0/traj.lammpstrj') 2275s get_fn = ._get_fn at 0x77a89c234ea0> 2275s 2275s def test_unitcell(write_traj, get_fn): 2275s # make sure that bogus unitcell vecotrs are not saved 2275s 2275s if write_traj.fext in ['rst7', 'ncrst', 'lammpstrj', 'dtr']: 2275s > pytest.xfail('{} seems to need unit vectors'.format(write_traj.fext)) 2275s E _pytest.outcomes.XFailed: lammpstrj seems to need unit vectors 2275s 2275s tests/test_trajectory.py:665: XFailed 2275s _____________________________ test_unitcell[ncrst] _____________________________ 2275s 2275s write_traj = TrajObj(fobj=, fext='ncrst', fn='/tmp/pytest-of-ubuntu/pytest-0/test_unitcell_ncrst_0/traj.ncrst') 2275s get_fn = ._get_fn at 0x77a89c234ea0> 2275s 2275s def test_unitcell(write_traj, get_fn): 2275s # make sure that bogus unitcell vecotrs are not saved 2275s 2275s if write_traj.fext in ['rst7', 'ncrst', 'lammpstrj', 'dtr']: 2275s > pytest.xfail('{} seems to need unit vectors'.format(write_traj.fext)) 2275s E _pytest.outcomes.XFailed: ncrst seems to need unit vectors 2275s 2275s tests/test_trajectory.py:665: XFailed 2275s _____________________________ test_unitcell[rst7] ______________________________ 2275s 2275s write_traj = TrajObj(fobj=, fext='rst7', fn='/tmp/pytest-of-ubuntu/pytest-0/test_unitcell_rst7_0/traj.rst7') 2275s get_fn = ._get_fn at 0x77a89c234ea0> 2275s 2275s def test_unitcell(write_traj, get_fn): 2275s # make sure that bogus unitcell vecotrs are not saved 2275s 2275s if write_traj.fext in ['rst7', 'ncrst', 'lammpstrj', 'dtr']: 2275s > pytest.xfail('{} seems to need unit vectors'.format(write_traj.fext)) 2275s E _pytest.outcomes.XFailed: rst7 seems to need unit vectors 2275s 2275s tests/test_trajectory.py:665: XFailed 2275s =============================== warnings summary =============================== 2275s ../../../../usr/lib/python3/dist-packages/mdtraj/utils/unit/__init__.py:57 2275s /usr/lib/python3/dist-packages/mdtraj/utils/unit/__init__.py:57: DeprecationWarning: ast.Num is deprecated and will be removed in Python 3.14; use ast.Constant instead 2275s ast.Pow, ast.Div, ast.Mult, ast.Num] 2275s 2275s ../../../../usr/lib/python3/dist-packages/mdtraj/formats/__init__.py:6 2275s /usr/lib/python3/dist-packages/mdtraj/formats/__init__.py:6: DeprecationWarning: 'xdrlib' is deprecated and slated for removal in Python 3.13 2275s from .xtc import XTCTrajectoryFile 2275s 2275s ../../../../usr/lib/python3/dist-packages/mdtraj/geometry/order.py:25 2275s /usr/lib/python3/dist-packages/mdtraj/geometry/order.py:25: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2275s from pkg_resources import parse_version 2275s 2275s ../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871 2275s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('mpl_toolkits')`. 2275s Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages 2275s declare_namespace(pkg) 2275s 2275s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:27 2275s /usr/lib/python3/dist-packages/jupyter_client/connect.py:27: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 2275s given by the platformdirs library. To remove this warning and 2275s see the appropriate new directories, set the environment variable 2275s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 2275s The use of platformdirs will be the default in `jupyter_core` v6 2275s from jupyter_core.paths import jupyter_data_dir 2275s 2275s examples/test_examples.py:26 2275s /tmp/autopkgtest.hoy8Kc/build.SoL/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 2275s examples = [pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 2275s 2275s tests/test_angles.py::test_angle_pbc_0 2275s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting unitcell_vectors dtype=float64 to 2275s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2275s 2275s tests/test_arc.py::test_read_arctraj 2275s tests/test_order.py::test_nematic_order 2275s tests/test_order.py::test_director 2275s tests/test_order.py::test_inertia 2275s tests/test_order.py::test_nematic_order_args 2275s tests/test_shape.py::test_gyration 2275s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:198: RuntimeWarning: divide by zero encountered in divide 2275s particle_density = traj.top.n_atoms / traj.unitcell_volumes[0] 2275s 2275s tests/test_arc.py: 1 warning 2275s tests/test_gro.py: 3 warnings 2275s tests/test_order.py: 4 warnings 2275s tests/test_pdb.py: 1 warning 2275s tests/test_shape.py: 4 warnings 2275s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:200: UserWarning: Unlikely unit cell vectors detected in PDB file likely resulting from a dummy CRYST1 record. Discarding unit cell vectors. 2275s warnings.warn('Unlikely unit cell vectors detected in PDB file likely ' 2275s 2275s tests/test_arc.py: 1 warning 2275s tests/test_dihedral.py: 1 warning 2275s tests/test_geometry.py: 2 warnings 2275s tests/test_hdf5.py: 1 warning 2275s tests/test_lprmsd.py: 1 warning 2275s tests/test_mdconvert.py: 9 warnings 2275s tests/test_mol2.py: 1 warning 2275s tests/test_nmr.py: 1 warning 2275s tests/test_rmsd.py: 8 warnings 2275s tests/test_rmsd_memmap.py: 2 warnings 2275s tests/test_sasa.py: 3 warnings 2275s tests/test_topology.py: 2 warnings 2275s tests/test_trajectory.py: 85 warnings 2275s /usr/lib/python3/dist-packages/mdtraj/core/trajectory.py:439: UserWarning: top= kwargs ignored since this file parser does not support it 2275s warnings.warn('top= kwargs ignored since this file parser does not support it') 2275s 2275s tests/test_contact.py::test_contact_0 2275s tests/test_contact.py::test_contact_4 2275s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:199: 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. 2275s warnings.warn('selected topology includes at least one glycine residue, which has no heavy atoms in its sidechain. The distances involving glycine residues ' 2275s 2275s tests/test_contact.py::test_contact_3 2275s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:227: RuntimeWarning: overflow encountered in exp 2275s np.log(np.sum(np.exp(soft_min_beta/ 2275s 2275s tests/test_contact.py::test_contact_3 2275s /tmp/autopkgtest.hoy8Kc/build.SoL/src/tests/test_contact.py:106: RuntimeWarning: divide by zero encountered in divide 2275s assert np.allclose(beta / np.log(np.sum(np.exp(beta / maps[t, r0, r1]))), dists[t, i]) 2275s 2275s tests/test_dcd.py::test_do_overwrite 2275s tests/test_dcd.py::test_ragged_1 2275s tests/test_dcd.py::test_ragged_2 2275s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting xyz dtype=float64 to 2275s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2275s 2275s tests/test_distance.py: 6 warnings 2275s tests/test_mdconvert.py: 112 warnings 2275s tests/test_neighbors.py: 2 warnings 2275s tests/test_netcdf.py: 46 warnings 2275s tests/test_rdf.py: 8 warnings 2275s tests/test_restart.py: 4 warnings 2275s tests/test_trajectory.py: 196 warnings 2275s /usr/lib/python3/dist-packages/mdtraj/formats/netcdf.py:130: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. 2275s if StrictVersion(import_('scipy.version').short_version) < StrictVersion('0.12.0'): 2275s 2275s tests/test_drid.py::test_drid_2 2275s /tmp/autopkgtest.hoy8Kc/build.SoL/src/tests/test_drid.py:61: RuntimeWarning: divide by zero encountered in divide 2275s recip = 1 / squareform(pdist(t.xyz[i])) 2275s 2275s tests/test_geometry.py: 1 warning 2275s tests/test_hoomdxml.py: 1 warning 2275s tests/test_neighbors.py: 2 warnings 2275s tests/test_rdf.py: 38 warnings 2275s tests/test_selection.py: 73 warnings 2275s tests/test_topology.py: 17 warnings 2275s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:385: DeprecationWarning: ast.Num is deprecated and will be removed in Python 3.14; use ast.Constant instead 2275s if isinstance(astnode, ast.Num) or isinstance(astnode, ast.Str): 2275s 2275s tests/test_geometry.py: 2 warnings 2275s tests/test_hoomdxml.py: 1 warning 2275s tests/test_neighbors.py: 2 warnings 2275s tests/test_rdf.py: 38 warnings 2275s tests/test_selection.py: 73 warnings 2275s tests/test_topology.py: 17 warnings 2275s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:385: DeprecationWarning: ast.Str is deprecated and will be removed in Python 3.14; use ast.Constant instead 2275s if isinstance(astnode, ast.Num) or isinstance(astnode, ast.Str): 2275s 2275s tests/test_geometry.py::test_dihedral_indices 2275s tests/test_geometry.py::test_dihedral_indices 2275s /usr/lib/python3/dist-packages/mdtraj/geometry/dihedral.py:203: DeprecationWarning: Passing a Trajectory object to _atom_sequence isdeprecated. Please pass a Topology object 2275s warnings.warn("Passing a Trajectory object to _atom_sequence is" 2275s 2275s tests/test_gro.py::test_load 2275s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq 2275s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:322: UserWarning: WARNING: two consecutive residues with same number (GST, HST) 2275s warnings.warn("WARNING: two consecutive residues with same number (%s, %s)" % (thisresname, old_resname)) 2275s 2275s tests/test_hdf5.py::test_read_0 2275s tests/test_hdf5.py::test_read_slice_0 2275s tests/test_hdf5.py::test_read_slice_2 2275s tests/test_hdf5.py::test_read_slice_3 2275s /usr/lib/python3/dist-packages/tables/path.py:137: NaturalNameWarning: object name is a Python keyword: 'lambda'; you will not be able to use natural naming to access this object; using ``getattr()`` will still work, though 2275s check_attribute_name(name) 2275s 2275s tests/test_rdf.py: 7 warnings 2275s tests/test_selection.py: 14 warnings 2275s tests/test_topology.py: 5 warnings 2275s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:62: DeprecationWarning: ast.NameConstant is deprecated and will be removed in Python 3.14; use ast.Constant instead 2275s return ast.NameConstant(value=_safe_names[node.id], kind=None) 2275s 2275s tests/test_rdf.py: 32 warnings 2275s tests/test_selection.py: 23 warnings 2275s tests/test_topology.py: 12 warnings 2275s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:68: DeprecationWarning: ast.Str is deprecated and will be removed in Python 3.14; use ast.Constant instead 2275s return ast.Str(s=node.id, kind=None) 2275s 2275s tests/test_rdf.py: 32 warnings 2275s tests/test_selection.py: 23 warnings 2275s tests/test_topology.py: 12 warnings 2275s /usr/lib/python3.12/ast.py:587: DeprecationWarning: Attribute s is deprecated and will be removed in Python 3.14; use value instead 2275s return Constant(*args, **kwargs) 2275s 2275s tests/test_restart.py: 1014 warnings 2275s tests/test_trajectory.py: 12 warnings 2275s /usr/lib/python3/dist-packages/mdtraj/formats/amberrst.py:465: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. 2275s if StrictVersion(import_('scipy.version').short_version) < StrictVersion('0.12.0'): 2275s 2275s tests/test_restart.py::test_read_write_1 2275s /usr/lib/python3/dist-packages/mdtraj/formats/amberrst.py:354: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) 2275s time = float(time) 2275s 2275s tests/test_restart.py::test_read_write_2 2275s /usr/lib/python3/dist-packages/mdtraj/formats/amberrst.py:692: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) 2275s time = float(time) 2275s 2275s tests/test_trajectory.py::test_box_load_save[dtr] 2275s tests/test_trajectory.py::test_read_write[dcd-dtr] 2275s tests/test_trajectory.py::test_read_write[lammpstrj-dtr] 2275s tests/test_trajectory.py::test_read_write[pdb-dtr] 2275s tests/test_trajectory.py::test_read_write[pdb.gz-dtr] 2275s tests/test_trajectory.py::test_save_load[dtr] 2275s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting times dtype=int64 to 2275s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2275s 2275s tests/test_trajectory.py::test_write_path[dtr] 2275s tests/test_trajectory.py::test_read_write[h5-dtr] 2275s tests/test_trajectory.py::test_read_write[xtc-dtr] 2275s tests/test_trajectory.py::test_read_write[trr-dtr] 2275s tests/test_trajectory.py::test_read_write[tng-dtr] 2275s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting times dtype=float32 to 2275s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2275s 2275s tests/test_trajectory.py::test_read_write[nc-dtr] 2275s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting times dtype=>f4 to 2275s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2275s 2275s tests/test_trajectory.py::test_float_atom_indices_exception[gro] 2275s /usr/lib/python3/dist-packages/mdtraj/core/topology.py:91: UserWarning: atom_indices are not monotonically increasing 2275s warnings.warn('atom_indices are not monotonically increasing') 2275s 2275s tests/test_trajectory.py::test_array_vs_matrix 2275s /tmp/autopkgtest.hoy8Kc/build.SoL/src/tests/test_trajectory.py:352: 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. 2275s xyz_mat = np.matrix(xyz) 2275s 2275s tests/test_utils.py::test_ensure_type_8 2275s tests/test_utils.py::test_ensure_type_9 2275s tests/test_utils.py::test_ensure_type_13 2275s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting dtype=float64 to 2275s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2275s 2275s tests/test_utils.py::test_ensure_type_11 2275s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting dtype=int64 to 2275s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2275s 2275s tests/test_utils.py::test_unit_3 2275s tests/test_utils.py::test_unit_3 2275s /usr/lib/python3/dist-packages/mdtraj/utils/unit/__init__.py:60: DeprecationWarning: ast.Num is deprecated and will be removed in Python 3.14; use ast.Constant instead 2275s if not any(isinstance(node, a) for a in self.allowed_ops): 2275s 2275s examples/test_examples.py::test_example_notebook[two-pass-clustering.ipynb] 2275s /usr/lib/python3/dist-packages/jupyter_client/utils.py:18: DeprecationWarning: There is no current event loop 2275s loop = asyncio.get_event_loop_policy().get_event_loop() 2275s 2275s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 2275s =========================== short test summary info ============================ 2275s SKIPPED [1] tests/test_dihedral.py:48: pymol executable not found 2275s SKIPPED [1] tests/test_dihedral.py:149: pymol executable not found 2275s SKIPPED [16] tests/test_docstrings.py:36: Skip checking certain modules' docstrings 2275s SKIPPED [1] tests/test_dssp.py:44: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 2275s SKIPPED [1] tests/test_dssp.py:52: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 2275s SKIPPED [1] tests/test_dssp.py:59: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 2275s SKIPPED [1] tests/test_geometry.py:243: Not doing performance testing 2275s SKIPPED [1] tests/test_geometry.py:261: Not doing performance testing 2275s SKIPPED [1] tests/test_gsd.py:30: gsd module is not available 2275s SKIPPED [1] tests/test_gsd.py:41: gsd module is not available 2275s SKIPPED [1] tests/test_gsd.py:51: gsd module is not available 2275s SKIPPED [1] tests/test_gsd.py:61: gsd module is not available 2275s SKIPPED [1] tests/test_gsd.py:75: gsd module is not available 2275s SKIPPED [1] tests/test_gsd.py:82: gsd module is not available 2275s SKIPPED [1] tests/test_gsd.py:94: gsd module is not available 2275s SKIPPED [1] tests/test_hbonds.py:43: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 2275s SKIPPED [1] tests/test_hdf5.py:99: requires openmm.units 2275s SKIPPED [1] tests/test_hdf5.py:133: requires openmm.units 2275s SKIPPED [1] tests/test_hdf5.py:186: requires openmm.units 2275s SKIPPED [1] tests/test_mol2.py:55: Requires obabel 2275s SKIPPED [1] tests/test_netcdf.py:248: This test requires cpptraj from AmberTools to be installed (http://ambermd.org) 2275s SKIPPED [1] tests/test_nmr.py:11: SPARTA+ binary not found 2275s SKIPPED [1] tests/test_nmr.py:24: PPM binary not found 2275s SKIPPED [1] tests/test_nmr.py:38: SHIFTX2 binary not found or Python 2 not found or runningn on travis. 2275s SKIPPED [1] tests/test_pdbx.py:39: test_pdbx.py needs OpenMM. 2275s SKIPPED [2] tests/test_psf.py:92: This test requires the VMD executable: http://www.ks.uiuc.edu/Research/vmd/ 2275s SKIPPED [1] tests/test_rdf.py:66: Binning does not match up with gromacs currently. 2275s SKIPPED [1] tests/test_rdf.py:153: Binning does not match up with gromacs currently. 2275s SKIPPED [1] tests/test_reporter.py:47: test_reporter.py needs OpenMM. 2275s SKIPPED [1] tests/test_reporter.py:121: test_reporter.py needs OpenMM. 2275s SKIPPED [1] tests/test_reporter.py:201: test_reporter.py needs OpenMM. 2275s SKIPPED [1] tests/test_thermodynamic_properties.py:154: Thermal expansion test doesn't work. 2275s SKIPPED [1] tests/test_tng.py:20: Fails on macOS + Python 3.11, need to investigate. 2275s SKIPPED [1] tests/test_topology.py:42: needs OpenMM 2275s SKIPPED [1] tests/test_topology.py:59: needs OpenMM 2275s SKIPPED [1] tests/test_topology.py:187: needs OpenMM 2275s SKIPPED [1] tests/test_trajectory.py:128: binpos does not store box information 2275s SKIPPED [1] tests/test_trajectory.py:128: xyz does not store box information 2275s SKIPPED [1] tests/test_trajectory.py:128: xyz.gz does not store box information 2275s SKIPPED [1] tests/test_trajectory.py:128: lh5 does not store box information 2275s SKIPPED [1] tests/test_trajectory.py:128: pdb does not store box information 2275s SKIPPED [1] tests/test_trajectory.py:128: pdb.gz does not store box information 2275s SKIPPED [1] tests/test_trajectory.py:200: mdcrd can only store rectilinear boxes 2275s SKIPPED [1] tests/test_trajectory.py:198: ncrst can only store 1 frame per file 2275s SKIPPED [1] tests/test_trajectory.py:198: rst7 can only store 1 frame per file 2275s SKIPPED [16] tests/test_trajectory.py:212: mdcrd can only store rectilinear boxes 2275s SKIPPED [16] tests/test_trajectory.py:210: ncrst can only store 1 frame per file 2275s SKIPPED [16] tests/test_trajectory.py:210: rst7 can only store 1 frame per file 2275s SKIPPED [5] tests/test_trajectory.py:219: dtr needs to write unitcells 2275s SKIPPED [5] tests/test_trajectory.py:219: lammpstrj needs to write unitcells 2275s SKIPPED [2] tests/test_trajectory.py:541: Only 1 frame per file format 2275s SKIPPED [1] examples/test_examples.py:71: Openmm required for example notebook `simulation-with-openmm.ipynb` 2275s SKIPPED [2] examples/test_examples.py:71: Network access required 2275s XFAIL tests/test_trajectory.py::test_read_path[ncrst] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_path[rst7] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[ncrst-nc] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[ncrst-h5] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xtc] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[ncrst-trr] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dcd] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[ncrst-mdcrd] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[ncrst-binpos] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dtr] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[ncrst-tng] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lh5] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[ncrst-ncrst] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[ncrst-rst7] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[ncrst-gro] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[rst7-nc] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[rst7-h5] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[rst7-xtc] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[rst7-trr] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[rst7-dcd] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[rst7-mdcrd] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[rst7-binpos] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[rst7-dtr] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz.gz] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[rst7-lammpstrj] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[rst7-tng] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[rst7-lh5] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb.gz] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[rst7-ncrst] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[rst7-rst7] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_read_write[rst7-gro] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_load[ncrst] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_load[rst7] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[rst7] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_load_combination[ncrst] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_load_combination[rst7] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_seek_read_mode[xyz.gz] - reason: This is broken 2275s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb] - reason: PDB Files don't support seeking 2275s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb.gz] - reason: PDB Files don't support seeking 2275s XFAIL tests/test_trajectory.py::test_seek_read_mode[ncrst] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_seek_read_mode[rst7] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_seek_read_mode[gro] - reason: This is broken 2275s XFAIL tests/test_trajectory.py::test_load_frame[dtr] - reason: DTR doesn't load a single frame properly 2275s XFAIL tests/test_trajectory.py::test_load_frame[ncrst] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_load_frame[rst7] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_load_frame[gro] - reason: Gro doesn't implement seek 2275s XFAIL tests/test_trajectory.py::test_iterload[dtr] - reason: This is broken with dtr 2275s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb] - reason: PDB Iterloads an extra frame!! 2275s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb.gz] - reason: PDB Iterloads an extra frame!! 2275s XFAIL tests/test_trajectory.py::test_iterload_skip[ncrst] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_iterload_skip[rst7] - reason: These reference files don't exist yet 2275s XFAIL tests/test_trajectory.py::test_iterload_skip[gro] - reason: Not implemented for some reason 2275s XFAIL tests/test_trajectory.py::test_force_overwrite[dtr] - reason: This is broken with dtr 2275s XFAIL tests/test_trajectory.py::test_unitcell[dtr] - reason: dtr seems to need unit vectors 2275s XFAIL tests/test_trajectory.py::test_unitcell[lammpstrj] - reason: lammpstrj seems to need unit vectors 2275s XFAIL tests/test_trajectory.py::test_unitcell[ncrst] - reason: ncrst seems to need unit vectors 2275s XFAIL tests/test_trajectory.py::test_unitcell[rst7] - reason: rst7 seems to need unit vectors 2275s = 1030 passed, 124 skipped, 2 deselected, 65 xfailed, 2007 warnings in 2058.66s (0:34:18) = 2276s autopkgtest [00:59:36]: test command1: -----------------------] 2276s autopkgtest [00:59:36]: test command1: - - - - - - - - - - results - - - - - - - - - - 2276s command1 PASS 2276s autopkgtest [00:59:36]: @@@@@@@@@@@@@@@@@@@@ summary 2276s command1 PASS 2287s nova [W] Skipping flock for amd64 2287s Creating nova instance adt-oracular-amd64-mdtraj-20240608-002140-juju-7f2275-prod-proposed-migration-environment-3-5ab103c8-eebc-42ac-bf52-7b931e451b24 from image adt/ubuntu-oracular-amd64-server-20240607.img (UUID d996b44c-1e10-4875-aeab-5b4c434d75a2)...