0s autopkgtest [04:01:15]: starting date and time: 2025-11-01 04:01:15+0000 0s autopkgtest [04:01:15]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [04:01:15]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.mbjf27iv/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:netcdf4-python --apt-upgrade mdtraj --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=netcdf4-python/1.7.3-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-4.secgroup --name adt-resolute-amd64-mdtraj-20251101-040115-juju-7f2275-prod-proposed-migration-environment-15-967a32ae-c19a-4c89-be3a-741eb3a25af1 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-mdtraj-20251101-040115-juju-7f2275-prod-proposed-migration-environment-15-967a32ae-c19a-4c89-be3a-741eb3a25af1 from image adt/ubuntu-resolute-amd64-server-20251031.img (UUID eaf9d537-af66-471e-af1e-6f7da9a9a444)... 32s autopkgtest [04:01:47]: testbed dpkg architecture: amd64 32s autopkgtest [04:01:47]: testbed apt version: 3.1.11 32s autopkgtest [04:01:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 33s autopkgtest [04:01:48]: testbed release detected to be: None 33s autopkgtest [04:01:48]: updating testbed package index (apt update) 33s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 33s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 33s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 33s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 33s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [150 kB] 33s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [50.7 kB] 34s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 34s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [2702 kB] 34s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [144 kB] 34s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [227 kB] 34s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [5124 B] 34s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [64.6 kB] 34s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3744 B] 34s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 34s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [808 kB] 34s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1944 kB] 34s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [53.1 kB] 34s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [38.8 kB] 34s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [14.7 kB] 34s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [1944 B] 35s Fetched 6307 kB in 1s (7526 kB/s) 35s Reading package lists... 36s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 36s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 36s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 36s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 36s Reading package lists... 36s Reading package lists... 37s Building dependency tree... 37s Reading state information... 37s Calculating upgrade... 37s The following packages will be upgraded: 37s gcc-15-base gcc-15-base:i386 libatomic1 libfribidi0 libgcc-s1 libgcc-s1:i386 37s libstdc++6 publicsuffix 37s 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 37s Need to get 1275 kB of archives. 37s After this operation, 14.3 kB of additional disk space will be used. 37s Get:1 http://ftpmaster.internal/ubuntu resolute/main i386 gcc-15-base i386 15.2.0-7ubuntu1 [58.4 kB] 37s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-base amd64 15.2.0-7ubuntu1 [58.4 kB] 37s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-s1 amd64 15.2.0-7ubuntu1 [78.0 kB] 37s Get:4 http://ftpmaster.internal/ubuntu resolute/main i386 libgcc-s1 i386 15.2.0-7ubuntu1 [94.1 kB] 37s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++6 amd64 15.2.0-7ubuntu1 [813 kB] 37s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libatomic1 amd64 15.2.0-7ubuntu1 [10.5 kB] 37s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libfribidi0 amd64 1.0.16-3 [26.5 kB] 37s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 publicsuffix all 20251016.1743-0.1 [136 kB] 37s dpkg-preconfigure: unable to re-open stdin: No such file or directory 37s Fetched 1275 kB in 0s (5247 kB/s) 37s (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 ... 78534 files and directories currently installed.) 37s Preparing to unpack .../gcc-15-base_15.2.0-7ubuntu1_amd64.deb ... 37s De-configuring gcc-15-base:i386 (15.2.0-5ubuntu1), to allow configuration of gcc-15-base:amd64 (15.2.0-7ubuntu1) ... 37s Unpacking gcc-15-base:amd64 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 37s Preparing to unpack .../gcc-15-base_15.2.0-7ubuntu1_i386.deb ... 37s Unpacking gcc-15-base:i386 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 37s Preparing to unpack .../libgcc-s1_15.2.0-7ubuntu1_i386.deb ... 37s De-configuring libgcc-s1:amd64 (15.2.0-5ubuntu1), to allow configuration of libgcc-s1:i386 (15.2.0-7ubuntu1) ... 37s Unpacking libgcc-s1:i386 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 37s Preparing to unpack .../libgcc-s1_15.2.0-7ubuntu1_amd64.deb ... 37s Unpacking libgcc-s1:amd64 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 37s Setting up gcc-15-base:amd64 (15.2.0-7ubuntu1) ... 37s Setting up libgcc-s1:amd64 (15.2.0-7ubuntu1) ... 37s (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 ... 78534 files and directories currently installed.) 38s Preparing to unpack .../libstdc++6_15.2.0-7ubuntu1_amd64.deb ... 38s Unpacking libstdc++6:amd64 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 38s Preparing to unpack .../libatomic1_15.2.0-7ubuntu1_amd64.deb ... 38s Unpacking libatomic1:amd64 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 38s Preparing to unpack .../libfribidi0_1.0.16-3_amd64.deb ... 38s Unpacking libfribidi0:amd64 (1.0.16-3) over (1.0.16-1) ... 38s Preparing to unpack .../publicsuffix_20251016.1743-0.1_all.deb ... 38s Unpacking publicsuffix (20251016.1743-0.1) over (20250328.1952-0.1) ... 38s Setting up libfribidi0:amd64 (1.0.16-3) ... 38s Setting up libatomic1:amd64 (15.2.0-7ubuntu1) ... 38s Setting up gcc-15-base:i386 (15.2.0-7ubuntu1) ... 38s Setting up publicsuffix (20251016.1743-0.1) ... 38s Setting up libstdc++6:amd64 (15.2.0-7ubuntu1) ... 38s Setting up libgcc-s1:i386 (15.2.0-7ubuntu1) ... 38s Processing triggers for libc-bin (2.42-0ubuntu3) ... 38s autopkgtest [04:01:53]: upgrading testbed (apt dist-upgrade and autopurge) 38s Reading package lists... 38s Building dependency tree... 38s Reading state information... 38s Calculating upgrade... 38s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 38s Reading package lists... 38s Building dependency tree... 38s Reading state information... 39s Solving dependencies... 39s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 41s autopkgtest [04:01:56]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025 41s autopkgtest [04:01:56]: @@@@@@@@@@@@@@@@@@@@ apt-source mdtraj 43s Get:1 http://ftpmaster.internal/ubuntu resolute/universe mdtraj 1.10.3-2build1 (dsc) [2701 B] 43s Get:2 http://ftpmaster.internal/ubuntu resolute/universe mdtraj 1.10.3-2build1 (tar) [22.0 MB] 43s Get:3 http://ftpmaster.internal/ubuntu resolute/universe mdtraj 1.10.3-2build1 (diff) [297 kB] 43s gpgv: Signature made Tue Mar 4 15:08:42 2025 UTC 43s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 43s gpgv: Can't check signature: No public key 43s dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.10.3-2build1.dsc: no acceptable signature found 43s autopkgtest [04:01:58]: testing package mdtraj version 1.10.3-2build1 44s autopkgtest [04:01:59]: build not needed 49s autopkgtest [04:02:04]: test command1: preparing testbed 50s Reading package lists... 50s Building dependency tree... 50s Reading state information... 50s Solving dependencies... 50s The following NEW packages will be installed: 50s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx gdb 50s libaec0 libbabeltrace1 libblas3 libblosc1 libblosc2-4 libdeflate0 50s libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 50s libhdf5-310 libhdf5-hl-310 libimagequant0 libipt2 libjbig0 libjpeg-turbo8 50s libjpeg8 liblapack3 liblcms2-2 liblerc4 liblzo2-2 libnetcdf22 libnorm1t64 50s libopenjp2-7 libpgm-5.3-0t64 libqhull-r8.0 libraqm0 libsharpyuv0 50s libsnappy1v5 libsodium23 libsource-highlight-common libsource-highlight4t64 50s libsz2 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 50s libxft2 libxrender1 libxslt1.1 libxss1 libzmq5 libzopfli1 50s python-matplotlib-data python-tables-data python3-asttokens python3-brotli 50s python3-cftime python3-comm python3-contourpy python3-coverage 50s python3-cpuinfo python3-cycler python3-dateutil python3-debugpy 50s python3-decorator python3-executing python3-fastjsonschema python3-fonttools 50s python3-fs python3-gsd python3-iniconfig python3-ipykernel python3-ipython 50s python3-jedi python3-joblib python3-jupyter-client python3-jupyter-core 50s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 50s python3-matplotlib-inline python3-mdtraj python3-mpmath python3-nbformat 50s python3-nest-asyncio python3-netcdf4 python3-networkx python3-numexpr 50s python3-numpy python3-numpy-dev python3-packaging python3-pandas 50s python3-pandas-lib python3-parso python3-pexpect python3-pil 50s python3-pil.imagetk python3-platformdirs python3-pluggy 50s python3-prompt-toolkit python3-psutil python3-ptyprocess python3-pure-eval 50s python3-pytest python3-pytz python3-scipy python3-sklearn 50s python3-sklearn-lib python3-stack-data python3-sympy python3-tables 50s python3-tables-lib python3-threadpoolctl python3-tk python3-tornado 50s python3-traitlets python3-typeshed python3-ufolib2 python3-unicodedata2 50s python3-wcwidth python3-zmq python3-zopfli python3.13-tk python3.14-tk 50s tk8.6-blt2.5 unicode-data x11-common 50s 0 upgraded, 128 newly installed, 0 to remove and 0 not upgraded. 50s Need to get 124 MB of archives. 50s After this operation, 611 MB of additional disk space will be used. 50s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 50s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-6build1 [263 kB] 50s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-7ubuntu1 [939 kB] 50s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-6build1 [2762 kB] 51s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 51s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1036 kB] 51s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 51s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 51s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB] 51s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB] 51s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 51s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 51s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 51s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 51s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 51s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [694 kB] 51s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 blt amd64 2.5.3+dfsg-8 [4824 B] 51s Get:18 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-lyx all 2.4.4-1 [171 kB] 51s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libbabeltrace1 amd64 1.5.11-4build3 [166 kB] 51s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libipt2 amd64 2.1.2-3 [49.2 kB] 51s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libsource-highlight-common all 3.1.9-4.3build1 [64.2 kB] 51s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libsource-highlight4t64 amd64 3.1.9-4.3build1 [258 kB] 51s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 gdb amd64 16.3-1ubuntu2 [4218 kB] 52s Get:24 http://ftpmaster.internal/ubuntu resolute/universe amd64 libaec0 amd64 1.1.4-2 [22.9 kB] 52s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libsnappy1v5 amd64 1.2.2-2 [30.8 kB] 52s Get:26 http://ftpmaster.internal/ubuntu resolute/universe amd64 libblosc1 amd64 1.21.5+ds-2 [35.8 kB] 52s Get:27 http://ftpmaster.internal/ubuntu resolute/universe amd64 libblosc2-4 amd64 2.17.1+ds-2 [173 kB] 52s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 52s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-7ubuntu1 [151 kB] 52s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 52s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.1.0-1 [535 kB] 52s Get:32 http://ftpmaster.internal/ubuntu resolute/universe amd64 libsz2 amd64 1.1.4-2 [5516 B] 52s Get:33 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhdf5-310 amd64 1.14.5+repack-3build1 [1411 kB] 52s Get:34 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhdf5-hl-310 amd64 1.14.5+repack-3build1 [59.8 kB] 52s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 52s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 52s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 52s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 52s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 52s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 liblzo2-2 amd64 2.10-3build1 [57.5 kB] 52s Get:41 http://ftpmaster.internal/ubuntu resolute/universe amd64 libnetcdf22 amd64 1:4.9.3-1build1 [561 kB] 52s Get:42 http://ftpmaster.internal/ubuntu resolute/universe amd64 libnorm1t64 amd64 1.5.9+dfsg-4 [158 kB] 52s Get:43 http://ftpmaster.internal/ubuntu resolute/universe amd64 libpgm-5.3-0t64 amd64 5.3.128~dfsg-2.1build1 [167 kB] 52s Get:44 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 52s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libraqm0 amd64 0.10.3-1 [15.4 kB] 52s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 52s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libsodium23 amd64 1.0.18-1build3 [161 kB] 52s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 52s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 52s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 52s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 52s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 52s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libxslt1.1 amd64 1.1.43-0.3 [172 kB] 52s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 libzmq5 amd64 4.3.5-1build2 [260 kB] 52s Get:55 http://ftpmaster.internal/ubuntu resolute/universe amd64 libzopfli1 amd64 1.0.3-3 [141 kB] 52s Get:56 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-matplotlib-data all 3.10.7+dfsg1-1 [2930 kB] 52s Get:57 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-tables-data all 3.10.2-3build1 [49.7 kB] 52s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-asttokens all 3.0.0-2 [20.5 kB] 52s Get:59 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-brotli amd64 1.1.0-2build6 [340 kB] 52s Get:60 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cftime amd64 1.6.5-1 [521 kB] 52s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 52s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-comm all 0.2.1-1 [7016 B] 52s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-contourpy amd64 1.3.1-1build2 [265 kB] 52s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-coverage amd64 7.8.2+dfsg1-1 [157 kB] 52s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cpuinfo all 9.0.0+git20221119-3 [21.7 kB] 52s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cycler all 0.12.1-2 [9850 B] 52s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-dateutil all 2.9.0-4 [80.3 kB] 52s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-debugpy amd64 1.8.12+ds-1ubuntu1 [778 kB] 52s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-decorator all 5.2.1-2 [28.1 kB] 52s Get:70 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-executing all 2.2.0-0.2 [25.0 kB] 52s Get:71 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fastjsonschema all 2.21.1-1 [20.4 kB] 52s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-platformdirs all 4.3.7-1 [16.9 kB] 52s Get:73 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fs all 2.4.16-7 [90.8 kB] 52s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-lxml amd64 6.0.1-1build1 [2336 kB] 52s Get:75 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-lz4 amd64 4.4.4+dfsg-3 [27.5 kB] 52s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-scipy amd64 1.15.3-1ubuntu1 [20.3 MB] 53s Get:77 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 53s Get:78 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sympy all 1.13.3-5 [4229 kB] 53s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 53s Get:80 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-unicodedata2 amd64 16.0.0+ds-1build1 [400 kB] 53s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-zopfli amd64 0.2.3.post1-1 [10.8 kB] 53s Get:82 http://ftpmaster.internal/ubuntu resolute/universe amd64 unicode-data all 16.0.0-1 [9513 kB] 53s Get:83 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fonttools amd64 4.57.0-2build1 [1731 kB] 53s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-gsd amd64 4.0.0-1 [244 kB] 53s Get:85 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 53s Get:86 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-parso all 0.8.4-1 [67.6 kB] 53s Get:87 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-typeshed all 0.0~git20241223.ea91db2-3 [1554 kB] 53s Get:88 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-jedi all 0.19.1+ds1-1 [693 kB] 53s Get:89 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-matplotlib-inline all 0.1.7-1 [9186 B] 53s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 53s Get:91 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-prompt-toolkit all 3.0.51-2 [257 kB] 53s Get:92 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pure-eval all 0.2.3-1 [11.4 kB] 53s Get:93 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-stack-data all 0.6.3-1 [22.0 kB] 53s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-ptyprocess all 0.7.0-6 [14.8 kB] 53s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pexpect all 4.9-3 [48.1 kB] 53s Get:96 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ipython all 8.35.0-1 [575 kB] 53s Get:97 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-jupyter-core all 5.7.2-5 [28.1 kB] 53s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-psutil amd64 7.1.0-1ubuntu1 [191 kB] 53s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-tornado amd64 6.5.2-3 [304 kB] 53s Get:100 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-zmq amd64 27.1.0-1 [234 kB] 53s Get:101 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-jupyter-client all 8.6.3-3 [78.4 kB] 53s Get:102 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-nest-asyncio all 1.5.4-1 [6256 B] 53s Get:103 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-packaging all 25.0-1 [52.8 kB] 53s Get:104 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ipykernel all 6.29.5-2 [82.7 kB] 53s Get:105 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-joblib all 1.4.2-4 [205 kB] 53s Get:106 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-kiwisolver amd64 1.4.10~rc0-1 [65.5 kB] 53s Get:107 http://ftpmaster.internal/ubuntu resolute/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [188 kB] 53s Get:108 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pil amd64 11.3.0-1ubuntu2 [504 kB] 53s Get:109 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-tk amd64 3.14.0-4 [108 kB] 53s Get:110 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-tk amd64 3.13.9-1 [108 kB] 53s Get:111 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-tk amd64 3.13.9-1 [8946 B] 53s Get:112 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pil.imagetk amd64 11.3.0-1ubuntu2 [9804 B] 53s Get:113 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-matplotlib amd64 3.10.7+dfsg1-1 [17.2 MB] 53s Get:114 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 python3-netcdf4 amd64 1.7.3-1 [908 kB] 54s Get:115 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 54s Get:116 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pytz all 2025.2-4 [32.3 kB] 54s Get:117 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas-lib amd64 2.3.3+dfsg-1ubuntu1 [7668 kB] 54s Get:118 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas all 2.3.3+dfsg-1ubuntu1 [2948 kB] 54s Get:119 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-numexpr amd64 2.13.0-1 [139 kB] 54s Get:120 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-tables-lib amd64 3.10.2-3build1 [805 kB] 54s Get:121 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-tables all 3.10.2-3build1 [354 kB] 54s Get:122 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mdtraj amd64 1.10.3-2build1 [1126 kB] 54s Get:123 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-nbformat all 5.9.1-1 [41.2 kB] 54s Get:124 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pluggy all 1.6.0-1 [21.0 kB] 54s Get:125 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytest all 8.3.5-2 [252 kB] 54s Get:126 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 54s Get:127 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-8 [4359 kB] 54s Get:128 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sklearn all 1.4.2+dfsg-8 [2258 kB] 54s Fetched 124 MB in 4s (29.9 MB/s) 54s Selecting previously unselected package python3-numpy-dev:amd64. 54s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78534 files and directories currently installed.) 54s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 54s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 54s Selecting previously unselected package libblas3:amd64. 54s Preparing to unpack .../001-libblas3_3.12.1-6build1_amd64.deb ... 54s Unpacking libblas3:amd64 (3.12.1-6build1) ... 54s Selecting previously unselected package libgfortran5:amd64. 54s Preparing to unpack .../002-libgfortran5_15.2.0-7ubuntu1_amd64.deb ... 54s Unpacking libgfortran5:amd64 (15.2.0-7ubuntu1) ... 54s Selecting previously unselected package liblapack3:amd64. 54s Preparing to unpack .../003-liblapack3_3.12.1-6build1_amd64.deb ... 54s Unpacking liblapack3:amd64 (3.12.1-6build1) ... 54s Selecting previously unselected package python3-numpy. 54s Preparing to unpack .../004-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 54s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 55s Selecting previously unselected package libtcl8.6:amd64. 55s Preparing to unpack .../005-libtcl8.6_8.6.17+dfsg-1_amd64.deb ... 55s Unpacking libtcl8.6:amd64 (8.6.17+dfsg-1) ... 55s Selecting previously unselected package fonts-dejavu-mono. 55s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ... 55s Unpacking fonts-dejavu-mono (2.37-8) ... 55s Selecting previously unselected package fonts-dejavu-core. 55s Preparing to unpack .../007-fonts-dejavu-core_2.37-8_all.deb ... 55s Unpacking fonts-dejavu-core (2.37-8) ... 55s Selecting previously unselected package fontconfig-config. 55s Preparing to unpack .../008-fontconfig-config_2.15.0-2.3ubuntu1_amd64.deb ... 55s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 55s Selecting previously unselected package libfontconfig1:amd64. 55s Preparing to unpack .../009-libfontconfig1_2.15.0-2.3ubuntu1_amd64.deb ... 55s Unpacking libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 55s Selecting previously unselected package libxrender1:amd64. 55s Preparing to unpack .../010-libxrender1_1%3a0.9.12-1_amd64.deb ... 55s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 55s Selecting previously unselected package libxft2:amd64. 55s Preparing to unpack .../011-libxft2_2.3.6-1build1_amd64.deb ... 55s Unpacking libxft2:amd64 (2.3.6-1build1) ... 55s Selecting previously unselected package x11-common. 55s Preparing to unpack .../012-x11-common_1%3a7.7+24ubuntu1_all.deb ... 55s Unpacking x11-common (1:7.7+24ubuntu1) ... 55s Selecting previously unselected package libxss1:amd64. 55s Preparing to unpack .../013-libxss1_1%3a1.2.3-1build3_amd64.deb ... 55s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 55s Selecting previously unselected package libtk8.6:amd64. 55s Preparing to unpack .../014-libtk8.6_8.6.17-1_amd64.deb ... 55s Unpacking libtk8.6:amd64 (8.6.17-1) ... 55s Selecting previously unselected package tk8.6-blt2.5. 55s Preparing to unpack .../015-tk8.6-blt2.5_2.5.3+dfsg-8_amd64.deb ... 55s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 55s Selecting previously unselected package blt. 55s Preparing to unpack .../016-blt_2.5.3+dfsg-8_amd64.deb ... 55s Unpacking blt (2.5.3+dfsg-8) ... 55s Selecting previously unselected package fonts-lyx. 55s Preparing to unpack .../017-fonts-lyx_2.4.4-1_all.deb ... 55s Unpacking fonts-lyx (2.4.4-1) ... 55s Selecting previously unselected package libbabeltrace1:amd64. 55s Preparing to unpack .../018-libbabeltrace1_1.5.11-4build3_amd64.deb ... 55s Unpacking libbabeltrace1:amd64 (1.5.11-4build3) ... 55s Selecting previously unselected package libipt2. 55s Preparing to unpack .../019-libipt2_2.1.2-3_amd64.deb ... 55s Unpacking libipt2 (2.1.2-3) ... 55s Selecting previously unselected package libsource-highlight-common. 55s Preparing to unpack .../020-libsource-highlight-common_3.1.9-4.3build1_all.deb ... 55s Unpacking libsource-highlight-common (3.1.9-4.3build1) ... 55s Selecting previously unselected package libsource-highlight4t64:amd64. 55s Preparing to unpack .../021-libsource-highlight4t64_3.1.9-4.3build1_amd64.deb ... 55s Unpacking libsource-highlight4t64:amd64 (3.1.9-4.3build1) ... 55s Selecting previously unselected package gdb. 55s Preparing to unpack .../022-gdb_16.3-1ubuntu2_amd64.deb ... 55s Unpacking gdb (16.3-1ubuntu2) ... 55s Selecting previously unselected package libaec0:amd64. 55s Preparing to unpack .../023-libaec0_1.1.4-2_amd64.deb ... 55s Unpacking libaec0:amd64 (1.1.4-2) ... 55s Selecting previously unselected package libsnappy1v5:amd64. 55s Preparing to unpack .../024-libsnappy1v5_1.2.2-2_amd64.deb ... 55s Unpacking libsnappy1v5:amd64 (1.2.2-2) ... 55s Selecting previously unselected package libblosc1:amd64. 55s Preparing to unpack .../025-libblosc1_1.21.5+ds-2_amd64.deb ... 55s Unpacking libblosc1:amd64 (1.21.5+ds-2) ... 55s Selecting previously unselected package libblosc2-4:amd64. 55s Preparing to unpack .../026-libblosc2-4_2.17.1+ds-2_amd64.deb ... 55s Unpacking libblosc2-4:amd64 (2.17.1+ds-2) ... 55s Selecting previously unselected package libdeflate0:amd64. 55s Preparing to unpack .../027-libdeflate0_1.23-2_amd64.deb ... 55s Unpacking libdeflate0:amd64 (1.23-2) ... 55s Selecting previously unselected package libgomp1:amd64. 55s Preparing to unpack .../028-libgomp1_15.2.0-7ubuntu1_amd64.deb ... 55s Unpacking libgomp1:amd64 (15.2.0-7ubuntu1) ... 55s Selecting previously unselected package libgraphite2-3:amd64. 55s Preparing to unpack .../029-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 55s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 55s Selecting previously unselected package libharfbuzz0b:amd64. 55s Preparing to unpack .../030-libharfbuzz0b_12.1.0-1_amd64.deb ... 55s Unpacking libharfbuzz0b:amd64 (12.1.0-1) ... 55s Selecting previously unselected package libsz2:amd64. 55s Preparing to unpack .../031-libsz2_1.1.4-2_amd64.deb ... 55s Unpacking libsz2:amd64 (1.1.4-2) ... 55s Selecting previously unselected package libhdf5-310:amd64. 55s Preparing to unpack .../032-libhdf5-310_1.14.5+repack-3build1_amd64.deb ... 55s Unpacking libhdf5-310:amd64 (1.14.5+repack-3build1) ... 55s Selecting previously unselected package libhdf5-hl-310:amd64. 55s Preparing to unpack .../033-libhdf5-hl-310_1.14.5+repack-3build1_amd64.deb ... 55s Unpacking libhdf5-hl-310:amd64 (1.14.5+repack-3build1) ... 55s Selecting previously unselected package libimagequant0:amd64. 55s Preparing to unpack .../034-libimagequant0_2.18.0-1build1_amd64.deb ... 55s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 55s Selecting previously unselected package libjpeg-turbo8:amd64. 55s Preparing to unpack .../035-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 55s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 55s Selecting previously unselected package libjpeg8:amd64. 55s Preparing to unpack .../036-libjpeg8_8c-2ubuntu11_amd64.deb ... 55s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 55s Selecting previously unselected package liblcms2-2:amd64. 55s Preparing to unpack .../037-liblcms2-2_2.16-2_amd64.deb ... 55s Unpacking liblcms2-2:amd64 (2.16-2) ... 55s Selecting previously unselected package liblerc4:amd64. 55s Preparing to unpack .../038-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 55s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 55s Selecting previously unselected package liblzo2-2:amd64. 55s Preparing to unpack .../039-liblzo2-2_2.10-3build1_amd64.deb ... 55s Unpacking liblzo2-2:amd64 (2.10-3build1) ... 55s Selecting previously unselected package libnetcdf22:amd64. 55s Preparing to unpack .../040-libnetcdf22_1%3a4.9.3-1build1_amd64.deb ... 55s Unpacking libnetcdf22:amd64 (1:4.9.3-1build1) ... 55s Selecting previously unselected package libnorm1t64:amd64. 55s Preparing to unpack .../041-libnorm1t64_1.5.9+dfsg-4_amd64.deb ... 55s Unpacking libnorm1t64:amd64 (1.5.9+dfsg-4) ... 55s Selecting previously unselected package libpgm-5.3-0t64:amd64. 55s Preparing to unpack .../042-libpgm-5.3-0t64_5.3.128~dfsg-2.1build1_amd64.deb ... 55s Unpacking libpgm-5.3-0t64:amd64 (5.3.128~dfsg-2.1build1) ... 55s Selecting previously unselected package libqhull-r8.0:amd64. 55s Preparing to unpack .../043-libqhull-r8.0_2020.2-6build1_amd64.deb ... 55s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 55s Selecting previously unselected package libraqm0:amd64. 55s Preparing to unpack .../044-libraqm0_0.10.3-1_amd64.deb ... 55s Unpacking libraqm0:amd64 (0.10.3-1) ... 55s Selecting previously unselected package libsharpyuv0:amd64. 55s Preparing to unpack .../045-libsharpyuv0_1.5.0-0.1_amd64.deb ... 55s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 55s Selecting previously unselected package libsodium23:amd64. 55s Preparing to unpack .../046-libsodium23_1.0.18-1build3_amd64.deb ... 55s Unpacking libsodium23:amd64 (1.0.18-1build3) ... 55s Selecting previously unselected package libjbig0:amd64. 55s Preparing to unpack .../047-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 55s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 55s Selecting previously unselected package libwebp7:amd64. 55s Preparing to unpack .../048-libwebp7_1.5.0-0.1_amd64.deb ... 55s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 55s Selecting previously unselected package libtiff6:amd64. 55s Preparing to unpack .../049-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 55s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 55s Selecting previously unselected package libwebpdemux2:amd64. 55s Preparing to unpack .../050-libwebpdemux2_1.5.0-0.1_amd64.deb ... 55s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 55s Selecting previously unselected package libwebpmux3:amd64. 55s Preparing to unpack .../051-libwebpmux3_1.5.0-0.1_amd64.deb ... 55s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 55s Selecting previously unselected package libxslt1.1:amd64. 55s Preparing to unpack .../052-libxslt1.1_1.1.43-0.3_amd64.deb ... 55s Unpacking libxslt1.1:amd64 (1.1.43-0.3) ... 55s Selecting previously unselected package libzmq5:amd64. 55s Preparing to unpack .../053-libzmq5_4.3.5-1build2_amd64.deb ... 55s Unpacking libzmq5:amd64 (4.3.5-1build2) ... 55s Selecting previously unselected package libzopfli1. 55s Preparing to unpack .../054-libzopfli1_1.0.3-3_amd64.deb ... 55s Unpacking libzopfli1 (1.0.3-3) ... 55s Selecting previously unselected package python-matplotlib-data. 55s Preparing to unpack .../055-python-matplotlib-data_3.10.7+dfsg1-1_all.deb ... 55s Unpacking python-matplotlib-data (3.10.7+dfsg1-1) ... 55s Selecting previously unselected package python-tables-data. 55s Preparing to unpack .../056-python-tables-data_3.10.2-3build1_all.deb ... 55s Unpacking python-tables-data (3.10.2-3build1) ... 55s Selecting previously unselected package python3-asttokens. 55s Preparing to unpack .../057-python3-asttokens_3.0.0-2_all.deb ... 55s Unpacking python3-asttokens (3.0.0-2) ... 55s Selecting previously unselected package python3-brotli. 55s Preparing to unpack .../058-python3-brotli_1.1.0-2build6_amd64.deb ... 55s Unpacking python3-brotli (1.1.0-2build6) ... 55s Selecting previously unselected package python3-cftime. 55s Preparing to unpack .../059-python3-cftime_1.6.5-1_amd64.deb ... 55s Unpacking python3-cftime (1.6.5-1) ... 55s Selecting previously unselected package python3-traitlets. 55s Preparing to unpack .../060-python3-traitlets_5.14.3+really5.14.3-1_all.deb ... 55s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ... 55s Selecting previously unselected package python3-comm. 55s Preparing to unpack .../061-python3-comm_0.2.1-1_all.deb ... 55s Unpacking python3-comm (0.2.1-1) ... 55s Selecting previously unselected package python3-contourpy. 55s Preparing to unpack .../062-python3-contourpy_1.3.1-1build2_amd64.deb ... 55s Unpacking python3-contourpy (1.3.1-1build2) ... 55s Selecting previously unselected package python3-coverage. 55s Preparing to unpack .../063-python3-coverage_7.8.2+dfsg1-1_amd64.deb ... 55s Unpacking python3-coverage (7.8.2+dfsg1-1) ... 55s Selecting previously unselected package python3-cpuinfo. 55s Preparing to unpack .../064-python3-cpuinfo_9.0.0+git20221119-3_all.deb ... 55s Unpacking python3-cpuinfo (9.0.0+git20221119-3) ... 55s Selecting previously unselected package python3-cycler. 55s Preparing to unpack .../065-python3-cycler_0.12.1-2_all.deb ... 55s Unpacking python3-cycler (0.12.1-2) ... 55s Selecting previously unselected package python3-dateutil. 56s Preparing to unpack .../066-python3-dateutil_2.9.0-4_all.deb ... 56s Unpacking python3-dateutil (2.9.0-4) ... 56s Selecting previously unselected package python3-debugpy. 56s Preparing to unpack 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python3-fs (2.4.16-7) ... 56s Selecting previously unselected package python3-lxml:amd64. 56s Preparing to unpack .../073-python3-lxml_6.0.1-1build1_amd64.deb ... 56s Unpacking python3-lxml:amd64 (6.0.1-1build1) ... 56s Selecting previously unselected package python3-lz4. 56s Preparing to unpack .../074-python3-lz4_4.4.4+dfsg-3_amd64.deb ... 56s Unpacking python3-lz4 (4.4.4+dfsg-3) ... 56s Selecting previously unselected package python3-scipy. 56s Preparing to unpack .../075-python3-scipy_1.15.3-1ubuntu1_amd64.deb ... 56s Unpacking python3-scipy (1.15.3-1ubuntu1) ... 56s Selecting previously unselected package python3-mpmath. 56s Preparing to unpack .../076-python3-mpmath_1.3.0-1_all.deb ... 56s Unpacking python3-mpmath (1.3.0-1) ... 56s Selecting previously unselected package python3-sympy. 56s Preparing to unpack .../077-python3-sympy_1.13.3-5_all.deb ... 56s Unpacking python3-sympy (1.13.3-5) ... 56s Selecting previously unselected package python3-ufolib2. 56s Preparing to unpack .../078-python3-ufolib2_0.17.1+dfsg1-1_all.deb ... 56s Unpacking python3-ufolib2 (0.17.1+dfsg1-1) ... 56s Selecting previously unselected package python3-unicodedata2. 56s Preparing to unpack .../079-python3-unicodedata2_16.0.0+ds-1build1_amd64.deb ... 56s Unpacking python3-unicodedata2 (16.0.0+ds-1build1) ... 56s Selecting previously unselected package python3-zopfli. 56s Preparing to unpack .../080-python3-zopfli_0.2.3.post1-1_amd64.deb ... 56s Unpacking python3-zopfli (0.2.3.post1-1) ... 56s Selecting previously unselected package unicode-data. 56s Preparing to unpack .../081-unicode-data_16.0.0-1_all.deb ... 56s Unpacking unicode-data (16.0.0-1) ... 56s Selecting previously unselected package python3-fonttools. 56s Preparing to unpack .../082-python3-fonttools_4.57.0-2build1_amd64.deb ... 56s Unpacking python3-fonttools (4.57.0-2build1) ... 56s Selecting previously unselected package python3-gsd. 56s Preparing to unpack .../083-python3-gsd_4.0.0-1_amd64.deb ... 56s Unpacking python3-gsd (4.0.0-1) ... 56s Selecting previously unselected package python3-iniconfig. 56s Preparing to unpack .../084-python3-iniconfig_1.1.1-2_all.deb ... 56s Unpacking python3-iniconfig (1.1.1-2) ... 56s Selecting previously unselected package python3-parso. 56s Preparing to unpack .../085-python3-parso_0.8.4-1_all.deb ... 56s Unpacking python3-parso (0.8.4-1) ... 56s Selecting previously unselected package python3-typeshed. 56s Preparing to unpack .../086-python3-typeshed_0.0~git20241223.ea91db2-3_all.deb ... 56s Unpacking python3-typeshed (0.0~git20241223.ea91db2-3) ... 57s Selecting previously unselected package python3-jedi. 57s Preparing to unpack .../087-python3-jedi_0.19.1+ds1-1_all.deb ... 57s Unpacking python3-jedi (0.19.1+ds1-1) ... 57s Selecting previously unselected package python3-matplotlib-inline. 57s Preparing to unpack .../088-python3-matplotlib-inline_0.1.7-1_all.deb ... 57s Unpacking python3-matplotlib-inline (0.1.7-1) ... 57s Selecting previously unselected package python3-wcwidth. 57s Preparing to unpack .../089-python3-wcwidth_0.2.13+dfsg1-1_all.deb ... 57s Unpacking python3-wcwidth (0.2.13+dfsg1-1) ... 57s Selecting previously unselected package python3-prompt-toolkit. 57s Preparing to unpack .../090-python3-prompt-toolkit_3.0.51-2_all.deb ... 57s Unpacking python3-prompt-toolkit (3.0.51-2) ... 57s Selecting previously unselected package python3-pure-eval. 57s Preparing to unpack .../091-python3-pure-eval_0.2.3-1_all.deb ... 57s Unpacking python3-pure-eval (0.2.3-1) ... 57s Selecting previously unselected package python3-stack-data. 57s Preparing to unpack .../092-python3-stack-data_0.6.3-1_all.deb ... 57s Unpacking python3-stack-data (0.6.3-1) ... 57s Selecting previously unselected package python3-ptyprocess. 57s Preparing to unpack .../093-python3-ptyprocess_0.7.0-6_all.deb ... 57s Unpacking python3-ptyprocess (0.7.0-6) ... 57s Selecting previously unselected package python3-pexpect. 57s Preparing to unpack .../094-python3-pexpect_4.9-3_all.deb ... 57s Unpacking python3-pexpect (4.9-3) ... 57s Selecting previously unselected package python3-ipython. 57s Preparing to unpack .../095-python3-ipython_8.35.0-1_all.deb ... 57s Unpacking python3-ipython (8.35.0-1) ... 57s Selecting previously unselected package python3-jupyter-core. 57s Preparing to unpack .../096-python3-jupyter-core_5.7.2-5_all.deb ... 57s Unpacking python3-jupyter-core (5.7.2-5) ... 57s Selecting previously unselected package python3-psutil. 57s Preparing to unpack .../097-python3-psutil_7.1.0-1ubuntu1_amd64.deb ... 57s Unpacking python3-psutil (7.1.0-1ubuntu1) ... 57s Selecting previously unselected package python3-tornado. 57s Preparing to unpack .../098-python3-tornado_6.5.2-3_amd64.deb ... 57s Unpacking python3-tornado (6.5.2-3) ... 57s Selecting previously unselected package python3-zmq. 57s Preparing to unpack .../099-python3-zmq_27.1.0-1_amd64.deb ... 57s Unpacking python3-zmq (27.1.0-1) ... 57s Selecting previously unselected package python3-jupyter-client. 57s Preparing to unpack .../100-python3-jupyter-client_8.6.3-3_all.deb ... 57s Unpacking python3-jupyter-client (8.6.3-3) ... 57s Selecting previously unselected package python3-nest-asyncio. 57s Preparing to unpack .../101-python3-nest-asyncio_1.5.4-1_all.deb ... 57s Unpacking python3-nest-asyncio (1.5.4-1) ... 57s Selecting previously unselected package python3-packaging. 57s Preparing to unpack .../102-python3-packaging_25.0-1_all.deb ... 57s Unpacking python3-packaging (25.0-1) ... 57s Selecting previously unselected package python3-ipykernel. 57s Preparing to unpack .../103-python3-ipykernel_6.29.5-2_all.deb ... 57s Unpacking python3-ipykernel (6.29.5-2) ... 57s Selecting previously unselected package python3-joblib. 57s Preparing to unpack .../104-python3-joblib_1.4.2-4_all.deb ... 57s Unpacking python3-joblib (1.4.2-4) ... 57s Selecting previously unselected package python3-kiwisolver. 57s Preparing to unpack .../105-python3-kiwisolver_1.4.10~rc0-1_amd64.deb ... 57s Unpacking python3-kiwisolver (1.4.10~rc0-1) ... 57s Selecting previously unselected package libopenjp2-7:amd64. 57s Preparing to unpack .../106-libopenjp2-7_2.5.3-2.1_amd64.deb ... 57s Unpacking libopenjp2-7:amd64 (2.5.3-2.1) ... 57s Selecting previously unselected package python3-pil:amd64. 57s Preparing to unpack .../107-python3-pil_11.3.0-1ubuntu2_amd64.deb ... 57s Unpacking python3-pil:amd64 (11.3.0-1ubuntu2) ... 57s Selecting previously unselected package python3.14-tk. 57s Preparing to unpack .../108-python3.14-tk_3.14.0-4_amd64.deb ... 57s Unpacking python3.14-tk (3.14.0-4) ... 57s Selecting previously unselected package python3.13-tk. 57s Preparing to unpack .../109-python3.13-tk_3.13.9-1_amd64.deb ... 57s Unpacking python3.13-tk (3.13.9-1) ... 57s Selecting previously unselected package python3-tk:amd64. 57s Preparing to unpack .../110-python3-tk_3.13.9-1_amd64.deb ... 57s Unpacking python3-tk:amd64 (3.13.9-1) ... 57s Selecting previously unselected package python3-pil.imagetk:amd64. 57s Preparing to unpack .../111-python3-pil.imagetk_11.3.0-1ubuntu2_amd64.deb ... 57s Unpacking python3-pil.imagetk:amd64 (11.3.0-1ubuntu2) ... 57s Selecting previously unselected package python3-matplotlib. 57s Preparing to unpack .../112-python3-matplotlib_3.10.7+dfsg1-1_amd64.deb ... 57s Unpacking python3-matplotlib (3.10.7+dfsg1-1) ... 57s Selecting previously unselected package python3-netcdf4. 57s Preparing to unpack .../113-python3-netcdf4_1.7.3-1_amd64.deb ... 57s Unpacking python3-netcdf4 (1.7.3-1) ... 57s Selecting previously unselected package python3-networkx. 57s Preparing to unpack .../114-python3-networkx_3.2.1-4ubuntu1_all.deb ... 57s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 57s Selecting previously unselected package python3-pytz. 57s Preparing to unpack .../115-python3-pytz_2025.2-4_all.deb ... 57s Unpacking python3-pytz (2025.2-4) ... 57s Selecting previously unselected package python3-pandas-lib:amd64. 57s Preparing to unpack .../116-python3-pandas-lib_2.3.3+dfsg-1ubuntu1_amd64.deb ... 57s Unpacking python3-pandas-lib:amd64 (2.3.3+dfsg-1ubuntu1) ... 58s Selecting previously unselected package python3-pandas. 58s Preparing to unpack .../117-python3-pandas_2.3.3+dfsg-1ubuntu1_all.deb ... 58s Unpacking python3-pandas (2.3.3+dfsg-1ubuntu1) ... 58s Selecting previously unselected package python3-numexpr. 58s Preparing to unpack .../118-python3-numexpr_2.13.0-1_amd64.deb ... 58s Unpacking python3-numexpr (2.13.0-1) ... 58s Selecting previously unselected package python3-tables-lib. 58s Preparing to unpack .../119-python3-tables-lib_3.10.2-3build1_amd64.deb ... 58s Unpacking python3-tables-lib (3.10.2-3build1) ... 58s Selecting previously unselected package python3-tables. 58s Preparing to unpack .../120-python3-tables_3.10.2-3build1_all.deb ... 58s Unpacking python3-tables (3.10.2-3build1) ... 58s Selecting previously unselected package python3-mdtraj. 58s 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python3-sklearn-lib:amd64 (1.4.2+dfsg-8) ... 58s Selecting previously unselected package python3-sklearn. 58s Preparing to unpack .../127-python3-sklearn_1.4.2+dfsg-8_all.deb ... 58s Unpacking python3-sklearn (1.4.2+dfsg-8) ... 58s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 58s Setting up liblcms2-2:amd64 (2.16-2) ... 58s Setting up python3-iniconfig (1.1.1-2) ... 58s Setting up python3-tornado (6.5.2-3) ... 58s Setting up libnorm1t64:amd64 (1.5.9+dfsg-4) ... 58s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 58s Setting up python3-pure-eval (0.2.3-1) ... 58s Setting up libsodium23:amd64 (1.0.18-1build3) ... 58s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 58s Setting up libxrender1:amd64 (1:0.9.12-1) ... 58s Setting up python3-joblib (1.4.2-4) ... 58s Setting up python3-parso (0.8.4-1) ... 58s Setting up python3-lz4 (4.4.4+dfsg-3) ... 59s Setting up python3-asttokens (3.0.0-2) ... 59s Setting up python3-unicodedata2 (16.0.0+ds-1build1) ... 59s Setting up fonts-lyx (2.4.4-1) ... 59s Setting up python3-threadpoolctl (3.1.0-1) ... 59s Setting up x11-common (1:7.7+24ubuntu1) ... 59s Setting up libdeflate0:amd64 (1.23-2) ... 59s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 59s Setting up python3-coverage (7.8.2+dfsg1-1) ... 59s Setting up liblzo2-2:amd64 (2.10-3build1) ... 59s Setting up python3-pytz (2025.2-4) ... 59s Setting up libgomp1:amd64 (15.2.0-7ubuntu1) ... 59s Setting up python3-networkx (3.2.1-4ubuntu1) ... 60s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 60s Setting up libaec0:amd64 (1.1.4-2) ... 60s Setting up python3-platformdirs (4.3.7-1) ... 60s Setting up python3-psutil (7.1.0-1ubuntu1) ... 60s Setting up libsource-highlight-common (3.1.9-4.3build1) ... 60s Setting up libsnappy1v5:amd64 (1.2.2-2) ... 60s Setting up python3-fs (2.4.16-7) ... 60s Setting up unicode-data (16.0.0-1) ... 60s Setting up libpgm-5.3-0t64:amd64 (5.3.128~dfsg-2.1build1) ... 60s Setting up python3-decorator (5.2.1-2) ... 60s Setting up libblosc2-4:amd64 (2.17.1+ds-2) ... 60s Setting up libblas3:amd64 (3.12.1-6build1) ... 60s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 60s Setting up python3-packaging (25.0-1) ... 60s Setting up python3-wcwidth (0.2.13+dfsg1-1) ... 60s Setting up libzopfli1 (1.0.3-3) ... 60s Setting up python3-typeshed (0.0~git20241223.ea91db2-3) ... 60s Setting up python3-executing (2.2.0-0.2) ... 60s Setting up python3-nest-asyncio (1.5.4-1) ... 61s Setting up python3-brotli (1.1.0-2build6) ... 61s Setting up python3-cycler (0.12.1-2) ... 61s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 61s Setting up fonts-dejavu-mono (2.37-8) ... 61s Setting up python3-kiwisolver (1.4.10~rc0-1) ... 61s Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 61s Setting up libtcl8.6:amd64 (8.6.17+dfsg-1) ... 61s Setting up libipt2 (2.1.2-3) ... 61s Setting up fonts-dejavu-core (2.37-8) ... 61s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 61s Setting up python3-cpuinfo (9.0.0+git20221119-3) ... 61s Setting up libbabeltrace1:amd64 (1.5.11-4build3) ... 61s Setting up libgfortran5:amd64 (15.2.0-7ubuntu1) ... 61s Setting up python3-pluggy (1.6.0-1) ... 61s Setting up libwebp7:amd64 (1.5.0-0.1) ... 61s Setting up python3-fastjsonschema (2.21.1-1) ... 61s Setting up python3-traitlets (5.14.3+really5.14.3-1) ... 61s Setting up libxslt1.1:amd64 (1.1.43-0.3) ... 61s Setting up libblosc1:amd64 (1.21.5+ds-2) ... 61s Setting up libopenjp2-7:amd64 (2.5.3-2.1) ... 61s Setting up libharfbuzz0b:amd64 (12.1.0-1) ... 61s Setting up python3-dateutil (2.9.0-4) ... 61s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 61s Setting up python3-mpmath (1.3.0-1) ... 61s Setting up python-matplotlib-data (3.10.7+dfsg1-1) ... 61s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 61s Setting up python3-stack-data (0.6.3-1) ... 62s Setting up python-tables-data (3.10.2-3build1) ... 62s Setting up python3-jupyter-core (5.7.2-5) ... 62s Setting up libsz2:amd64 (1.1.4-2) ... 62s Setting up python3-ptyprocess (0.7.0-6) ... 62s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 62s Setting up python3-prompt-toolkit (3.0.51-2) ... 62s Setting up python3-sympy (1.13.3-5) ... 65s Setting up liblapack3:amd64 (3.12.1-6build1) ... 65s 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 65s Setting up libzmq5:amd64 (4.3.5-1build2) ... 65s Setting up python3-jedi (0.19.1+ds1-1) ... 65s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 66s Setting up python3-pytest (8.3.5-2) ... 66s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 66s Setting up libsource-highlight4t64:amd64 (3.1.9-4.3build1) ... 66s Setting up python3-nbformat (5.9.1-1) ... 66s Setting up python3-zopfli (0.2.3.post1-1) ... 66s Setting up python3-matplotlib-inline (0.1.7-1) ... 66s Setting up python3-comm (0.2.1-1) ... 66s Setting up gdb (16.3-1ubuntu2) ... 66s Setting up python3-pexpect (4.9-3) ... 66s Setting up python3-zmq (27.1.0-1) ... 66s Setting up libraqm0:amd64 (0.10.3-1) ... 66s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 67s Setting up libhdf5-310:amd64 (1.14.5+repack-3build1) ... 67s Setting up python3-lxml:amd64 (6.0.1-1build1) ... 67s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 67s Setting up python3-jupyter-client (8.6.3-3) ... 67s Setting up python3-contourpy (1.3.1-1build2) ... 67s Setting up libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 67s Setting up libhdf5-hl-310:amd64 (1.14.5+repack-3build1) ... 67s Setting up libxft2:amd64 (2.3.6-1build1) ... 67s Setting up python3-scipy (1.15.3-1ubuntu1) ... 70s Setting up python3-tables-lib (3.10.2-3build1) ... 70s Setting up libtk8.6:amd64 (8.6.17-1) ... 70s Setting up python3-pandas-lib:amd64 (2.3.3+dfsg-1ubuntu1) ... 70s Setting up libnetcdf22:amd64 (1:4.9.3-1build1) ... 70s Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-8) ... 70s Setting up python3-gsd (4.0.0-1) ... 70s Setting up python3-debugpy (1.8.12+ds-1ubuntu1) ... 70s Setting up python3.13-tk (3.13.9-1) ... 70s Setting up python3-pil:amd64 (11.3.0-1ubuntu2) ... 71s Setting up python3-pandas (2.3.3+dfsg-1ubuntu1) ... 73s Setting up python3-ipython (8.35.0-1) ... 73s Setting up python3-ipykernel (6.29.5-2) ... 74s Setting up python3-sklearn (1.4.2+dfsg-8) ... 75s Setting up python3-cftime (1.6.5-1) ... 75s Setting up python3-numexpr (2.13.0-1) ... 75s Setting up python3-netcdf4 (1.7.3-1) ... 75s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 75s Setting up python3.14-tk (3.14.0-4) ... 75s Setting up blt (2.5.3+dfsg-8) ... 75s Setting up python3-tk:amd64 (3.13.9-1) ... 75s Setting up python3-tables (3.10.2-3build1) ... 75s Setting up python3-mdtraj (1.10.3-2build1) ... 75s Setting up python3-pil.imagetk:amd64 (11.3.0-1ubuntu2) ... 75s Setting up python3-fonttools (4.57.0-2build1) ... 76s Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... 76s Setting up python3-matplotlib (3.10.7+dfsg1-1) ... 77s Processing triggers for libc-bin (2.42-0ubuntu3) ... 77s Processing triggers for man-db (2.13.1-1) ... 78s autopkgtest [04:02:33]: test command1: pytest-3 -k 'not (nmr.ipynb or test_image_molecules) and not (test_3 or test_pdb_from_url or test_1vii_url_and_gz)' 78s autopkgtest [04:02:33]: test command1: [----------------------- 79s ============================= test session starts ============================== 79s platform linux -- Python 3.13.9, pytest-8.3.5, pluggy-1.6.0 -- /usr/bin/python3 79s cachedir: .pytest_cache 79s rootdir: /tmp/autopkgtest.qPicin/build.7Dk/src 79s configfile: pyproject.toml 79s testpaths: tests, examples 79s plugins: typeguard-4.4.2 79s collecting ... collected 1145 items / 12 deselected / 1133 selected 79s 79s tests/test_alignment.py::test_rmsd_zero PASSED [ 0%] 79s tests/test_alignment.py::test_rmsd_nonzero PASSED [ 0%] 79s 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[ 3%] 81s tests/test_dihedral.py::test_dihedral_2chains PASSED [ 4%] 81s tests/test_dihedral.py::test_generator PASSED [ 4%] 81s tests/test_distance.py::test_generator PASSED [ 4%] 81s tests/test_distance.py::test_0 PASSED [ 4%] 81s tests/test_distance.py::test_compute_distances_core_nonperiodic PASSED [ 4%] 82s tests/test_distance.py::test_compute_distances_core_periodic PASSED [ 4%] 82s tests/test_distance.py::test_1 PASSED [ 4%] 82s tests/test_distance.py::test_2 PASSED [ 4%] 82s tests/test_distance.py::test_0p PASSED [ 4%] 82s tests/test_distance.py::test_1p PASSED [ 4%] 83s tests/test_distance.py::test_2p PASSED [ 4%] 83s tests/test_distance.py::test_4 PASSED [ 5%] 83s tests/test_distance.py::test_5 PASSED [ 5%] 84s tests/test_distance.py::test_6 PASSED [ 5%] 84s tests/test_distance.py::test_7 PASSED [ 5%] 84s tests/test_distance.py::test_closest_contact PASSED [ 5%] 84s tests/test_distance.py::test_distance_nan PASSED [ 5%] 84s tests/test_distance.py::test_closest_contact_nan_pos PASSED [ 5%] 84s tests/test_distance.py::test_distance_t_inputs PASSED [ 5%] 84s tests/test_distance.py::test_distances_t PASSED [ 5%] 84s tests/test_distance.py::test_distances_t_at_0 PASSED [ 5%] 84s tests/test_distance.py::test_amber_t PASSED [ 5%] 84s tests/test_docstrings.py::test_docstrings[mdtraj._lprmsd] PASSED [ 6%] 84s tests/test_docstrings.py::test_docstrings[mdtraj._rmsd] PASSED [ 6%] 84s tests/test_docstrings.py::test_docstrings[mdtraj._version] SKIPPED (...) [ 6%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.core.element] PASSED [ 6%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.core.residue_names] PASSED [ 6%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.core.selection] PASSED [ 6%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.core.topology] PASSED [ 6%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.core.trajectory] PASSED [ 6%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.amberrst] PASSED [ 6%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.arc] PASSED [ 6%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.dcd] PASSED [ 6%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.dtr] PASSED [ 6%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.gro] PASSED [ 7%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.gsd] PASSED [ 7%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.hdf5] SKIPPED [ 7%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.hoomdxml] PASSED [ 7%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.lammpstrj] PASSED [ 7%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.lh5] SKIPPED [ 7%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.mdcrd] PASSED [ 7%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.mol2] PASSED [ 7%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.netcdf] PASSED [ 7%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.openmmxml] PASSED [ 7%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdb.pdbfile] PASSED [ 7%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdb.pdbstructure] SKIPPED [ 8%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdbx] PASSED [ 8%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.prmtop] PASSED [ 8%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.psf] PASSED [ 8%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.registry] PASSED [ 8%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.trr] PASSED [ 8%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.xtc] PASSED [ 8%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.formats.xyzfile] PASSED [ 8%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.geometry._geometry] PASSED [ 8%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.alignment] PASSED [ 8%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.angle] PASSED [ 8%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.contact] PASSED [ 9%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.dihedral] PASSED [ 9%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.distance] PASSED [ 9%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.drid] PASSED [ 9%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.dssp] PASSED [ 9%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.hbond] PASSED [ 9%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.internal] PASSED [ 9%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.neighborlist] PASSED [ 9%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.neighbors] PASSED [ 9%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.order] PASSED [ 9%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.rdf] PASSED [ 9%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.rg] PASSED [ 9%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.sasa] PASSED [ 10%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.shape] PASSED [ 10%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.thermodynamic_properties] PASSED [ 10%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.io] SKIPPED (Skip c...) [ 10%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.nmr.scalar_couplings] PASSED [ 10%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.nmr.shift_wrappers] PASSED [ 10%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.basereporter] PASSED [ 10%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.dcdreporter] PASSED [ 10%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.hdf5reporter] PASSED [ 10%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.netcdfreporter] PASSED [ 10%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.xtcreporter] PASSED [ 10%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.scripts.mdconvert] SKIPPED [ 11%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.scripts.mdinspect] SKIPPED [ 11%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.testing.docscrape] SKIPPED [ 11%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.testing.docstrings] PASSED [ 11%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.testing.testing] PASSED [ 11%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.utils.contextmanagers] PASSED [ 11%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.utils.delay_import] PASSED [ 11%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.utils.rotation] PASSED [ 11%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.utils.singleton] PASSED [ 11%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.basedimension] PASSED [ 11%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.baseunit] SKIPPED [ 11%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.constants] PASSED [ 12%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.mymatrix] SKIPPED [ 12%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.prefix] SKIPPED [ 12%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.quantity] SKIPPED [ 12%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.standard_dimensions] PASSED [ 12%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit] SKIPPED [ 12%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_definitions] SKIPPED [ 12%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_math] SKIPPED [ 12%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_operators] SKIPPED [ 12%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unitcell] PASSED [ 12%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.utils.validation] PASSED [ 12%] 84s tests/test_docstrings.py::test_docstrings[mdtraj.utils.zipped] PASSED [ 12%] 84s tests/test_drid.py::test_drid_1 PASSED [ 13%] 84s tests/test_drid.py::test_drid_2 PASSED [ 13%] 84s tests/test_dssp.py::test_1[1bpi.pdb] PASSED [ 13%] 84s tests/test_dssp.py::test_1[1vii.pdb] PASSED [ 13%] 84s tests/test_dssp.py::test_1[4ZUO.pdb] PASSED [ 13%] 84s 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tests/test_dtr.py::test_read_closed PASSED [ 15%] 86s tests/test_dtr.py::test_tell PASSED [ 15%] 86s tests/test_element.py::test_immutable PASSED [ 15%] 86s tests/test_element.py::test_element_0 PASSED [ 15%] 86s tests/test_element.py::test_element_pickle PASSED [ 15%] 86s tests/test_geometry.py::test_rg PASSED [ 15%] 86s tests/test_geometry.py::test_distances PASSED [ 15%] 86s tests/test_geometry.py::test_center_of_mass PASSED [ 15%] 86s tests/test_geometry.py::test_center_of_geometry PASSED [ 15%] 86s tests/test_geometry.py::test_dihedral_indices PASSED [ 16%] 86s tests/test_geometry.py::test_dihedral_index_offset_generation PASSED [ 16%] 86s tests/test_geometry.py::test_dihedral_0 PASSED [ 16%] 86s tests/test_geometry.py::test_dihedral_1 PASSED [ 16%] 86s tests/test_geometry.py::test_dihedral_triclinic PASSED [ 16%] 86s tests/test_geometry.py::test_angle_0 PASSED [ 16%] 86s tests/test_geometry.py::test_angle_periodic_0 PASSED [ 16%] 86s tests/test_geometry.py::test_angle_triclinic_0 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[ 37%] 164s tests/test_rdf.py::test_compare_rdf_t_master PASSED [ 37%] 164s tests/test_rdf.py::test_compare_n_concurrent_pairs PASSED [ 37%] 164s tests/test_reporter.py::test_reporter SKIPPED (test_reporter.py need...) [ 37%] 164s tests/test_reporter.py::test_reporter_subset SKIPPED (test_reporter....) [ 37%] 164s tests/test_reporter.py::test_xtc_reporter_append SKIPPED (test_repor...) [ 37%] 164s tests/test_restart.py::test_read_after_close PASSED [ 37%] 164s tests/test_restart.py::test_shape PASSED [ 37%] 164s tests/test_restart.py::test_shape_2 PASSED [ 38%] 164s tests/test_restart.py::test_read_write_1 PASSED [ 38%] 164s tests/test_restart.py::test_read_write_2 PASSED [ 38%] 164s tests/test_restart.py::test_read_write_3 PASSED [ 38%] 165s tests/test_restart.py::test_read_write_4 PASSED [ 38%] 165s tests/test_rmsd.py::test_trajectory_rmsd PASSED [ 38%] 165s tests/test_rmsd.py::test_precentered_1 PASSED [ 38%] 165s tests/test_rmsd.py::test_precentered_2 PASSED [ 38%] 165s tests/test_rmsd.py::test_superpose_0 PASSED [ 38%] 165s tests/test_rmsd.py::test_superpose_1 PASSED [ 38%] 165s tests/test_rmsd.py::test_superpose_2 PASSED [ 38%] 165s tests/test_rmsd.py::test_superpose_refinds PASSED [ 39%] 165s tests/test_rmsd.py::test_rmsd_atom_indices PASSED [ 39%] 165s tests/test_rmsd.py::test_rmsd_ref_ainds PASSED [ 39%] 165s tests/test_rmsd.py::test_average_structure PASSED [ 39%] 165s tests/test_rmsd.py::test_trajectory_rmsf PASSED [ 39%] 165s tests/test_rmsd.py::test_trajectory_rmsf_aligned PASSED [ 39%] 165s tests/test_rmsd.py::test_rmsd_atom_indices_vs_ref_indices PASSED [ 39%] 165s tests/test_rmsd_memmap.py::test_1 PASSED [ 39%] 165s tests/test_rmsd_memmap.py::test_2 PASSED [ 39%] 165s tests/test_sasa.py::test_sasa_0 PASSED [ 39%] 165s tests/test_sasa.py::test_sasa_1 PASSED [ 39%] 165s tests/test_sasa.py::test_sasa_2 PASSED [ 39%] 165s tests/test_sasa.py::test_sasa_3 PASSED [ 40%] 166s tests/test_sasa.py::test_sasa_4 PASSED [ 40%] 166s tests/test_sasa.py::test_sasa_5 PASSED [ 40%] 166s tests/test_sasa.py::test_sasa_6 PASSED [ 40%] 166s tests/test_sasa.py::test_sasa_7 PASSED [ 40%] 166s tests/test_selection.py::test_range PASSED [ 40%] 166s tests/test_selection.py::test_unary_2 PASSED [ 40%] 166s tests/test_selection.py::test_unary_3 PASSED [ 40%] 166s tests/test_selection.py::test_binary_1 PASSED [ 40%] 166s tests/test_selection.py::test_binary_2 PASSED [ 40%] 166s tests/test_selection.py::test_simple PASSED [ 40%] 166s tests/test_selection.py::test_alias PASSED [ 41%] 166s tests/test_selection.py::test_unary_1 PASSED [ 41%] 166s tests/test_selection.py::test_binary_selection_operator PASSED [ 41%] 166s tests/test_selection.py::test_raises PASSED [ 41%] 166s tests/test_selection.py::test_raises2 PASSED [ 41%] 166s tests/test_selection.py::test_bool PASSED [ 41%] 166s tests/test_selection.py::test_nested_bool PASSED [ 41%] 166s tests/test_selection.py::test_values PASSED [ 41%] 166s tests/test_selection.py::test_element PASSED [ 41%] 166s tests/test_selection.py::test_not PASSED [ 41%] 167s tests/test_selection.py::test_re PASSED [ 41%] 167s tests/test_selection.py::test_within SKIPPED (failed to parse selection) [ 42%] 167s tests/test_selection.py::test_quotes PASSED [ 42%] 167s tests/test_selection.py::test_top PASSED [ 42%] 167s tests/test_selection.py::test_top_2 PASSED [ 42%] 167s tests/test_selection.py::test_backbone PASSED [ 42%] 167s tests/test_selection.py::test_sidechain PASSED [ 42%] 167s tests/test_selection.py::test_literal PASSED [ 42%] 167s tests/test_selection.py::test_in PASSED [ 42%] 167s tests/test_shape.py::test_gyration PASSED [ 42%] 167s tests/test_shape.py::test_principal_moments PASSED [ 42%] 167s tests/test_shape.py::test_asphericity PASSED [ 42%] 167s tests/test_shape.py::test_shape_metrics PASSED [ 42%] 167s tests/test_thermodynamic_properties.py::test_volume PASSED [ 43%] 167s tests/test_thermodynamic_properties.py::test_density PASSED [ 43%] 167s tests/test_thermodynamic_properties.py::test_dipole_moments PASSED [ 43%] 167s tests/test_thermodynamic_properties.py::test_static_dielectric PASSED [ 43%] 167s tests/test_thermodynamic_properties.py::test_kappa PASSED [ 43%] 167s tests/test_thermodynamic_properties.py::test_alpha SKIPPED (Thermal ...) [ 43%] 167s tests/test_topology.py::test_topology_openmm SKIPPED (needs OpenMM) [ 43%] 167s tests/test_topology.py::test_topology_openmm_preserve_chain_id_when_specified SKIPPED [ 43%] 167s tests/test_topology.py::test_topology_openmm_roundtrip_chain_id SKIPPED [ 43%] 167s tests/test_topology.py::test_topology_openmm_preserve_chain_id_even_when_empty SKIPPED [ 43%] 167s tests/test_topology.py::test_topology_openmm_boxes SKIPPED (needs Op...) [ 43%] 167s tests/test_topology.py::test_topology_openmm_formal_charges SKIPPED [ 44%] 167s tests/test_topology.py::test_topology_pandas PASSED [ 44%] 167s tests/test_topology.py::test_topology_pandas_TIP4PEW PASSED [ 44%] 167s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq PASSED [ 44%] 167s tests/test_topology.py::test_topology_numbers PASSED [ 44%] 167s tests/test_topology.py::test_topology_unique_elements_bpti PASSED [ 44%] 167s tests/test_topology.py::test_chain PASSED [ 44%] 168s tests/test_topology.py::test_residue PASSED [ 44%] 168s tests/test_topology.py::test_segment_id PASSED [ 44%] 168s tests/test_topology.py::test_nonconsective_resSeq PASSED [ 44%] 168s tests/test_topology.py::test_pickle PASSED [ 44%] 168s tests/test_topology.py::test_atoms_by_name PASSED [ 45%] 168s tests/test_topology.py::test_select_atom_indices PASSED [ 45%] 168s tests/test_topology.py::test_top_dataframe_openmm_roundtrip SKIPPED [ 45%] 168s tests/test_topology.py::test_n_bonds PASSED [ 45%] 168s tests/test_topology.py::test_load_unknown_topology PASSED [ 45%] 168s tests/test_topology.py::test_unique_pairs PASSED [ 45%] 168s tests/test_topology.py::test_select_pairs PASSED [ 45%] 168s tests/test_topology.py::test_to_fasta PASSED [ 45%] 168s tests/test_topology.py::test_subset PASSED [ 45%] 168s tests/test_topology.py::test_subset_re_index_residues PASSED [ 45%] 168s tests/test_topology.py::test_molecules PASSED [ 45%] 168s tests/test_topology.py::test_copy_and_hash PASSED [ 45%] 168s tests/test_topology.py::test_topology_sliced_residue_indices PASSED [ 46%] 168s tests/test_topology.py::test_topology_join PASSED [ 46%] 169s tests/test_topology.py::test_topology_join_keep_resSeq PASSED [ 46%] 169s tests/test_trajectory.py::test_mismatch PASSED [ 46%] 169s tests/test_trajectory.py::test_box PASSED [ 46%] 169s tests/test_trajectory.py::test_load_pdb_box PASSED [ 46%] 169s tests/test_trajectory.py::test_load_pdb_gz PASSED [ 46%] 169s tests/test_trajectory.py::test_box_load_save[nc] PASSED [ 46%] 169s tests/test_trajectory.py::test_box_load_save[h5] PASSED [ 46%] 169s tests/test_trajectory.py::test_box_load_save[xtc] PASSED [ 46%] 169s tests/test_trajectory.py::test_box_load_save[trr] PASSED [ 46%] 169s tests/test_trajectory.py::test_box_load_save[dcd] PASSED [ 47%] 169s tests/test_trajectory.py::test_box_load_save[mdcrd] PASSED [ 47%] 169s tests/test_trajectory.py::test_box_load_save[dtr] PASSED [ 47%] 169s tests/test_trajectory.py::test_box_load_save[xyz] SKIPPED (xyz does ...) [ 47%] 169s tests/test_trajectory.py::test_box_load_save[xyz.gz] SKIPPED (xyz.gz...) [ 47%] 169s tests/test_trajectory.py::test_box_load_save[lammpstrj] PASSED [ 47%] 169s tests/test_trajectory.py::test_box_load_save[lh5] SKIPPED (lh5 does ...) [ 47%] 169s tests/test_trajectory.py::test_box_load_save[pdb] SKIPPED (pdb does ...) [ 47%] 169s tests/test_trajectory.py::test_box_load_save[pdb.gz] SKIPPED (pdb.gz...) [ 47%] 169s tests/test_trajectory.py::test_box_load_save[ncrst] PASSED [ 47%] 169s tests/test_trajectory.py::test_box_load_save[rst7] PASSED [ 47%] 169s tests/test_trajectory.py::test_box_load_save[gro] PASSED [ 48%] 169s tests/test_trajectory.py::test_slice PASSED [ 48%] 169s tests/test_trajectory.py::test_slice2 PASSED [ 48%] 169s tests/test_trajectory.py::test_read_path[nc] PASSED [ 48%] 169s tests/test_trajectory.py::test_read_path[h5] PASSED [ 48%] 169s tests/test_trajectory.py::test_read_path[xtc] PASSED [ 48%] 169s tests/test_trajectory.py::test_read_path[trr] PASSED [ 48%] 169s tests/test_trajectory.py::test_read_path[dcd] PASSED [ 48%] 169s tests/test_trajectory.py::test_read_path[mdcrd] PASSED [ 48%] 169s tests/test_trajectory.py::test_read_path[dtr] PASSED [ 48%] 169s tests/test_trajectory.py::test_read_path[xyz] PASSED [ 48%] 169s tests/test_trajectory.py::test_read_path[xyz.gz] PASSED [ 48%] 169s tests/test_trajectory.py::test_read_path[lammpstrj] PASSED [ 49%] 169s tests/test_trajectory.py::test_read_path[lh5] PASSED [ 49%] 169s tests/test_trajectory.py::test_read_path[pdb] PASSED [ 49%] 169s tests/test_trajectory.py::test_read_path[pdb.gz] PASSED [ 49%] 169s tests/test_trajectory.py::test_read_path[ncrst] XFAIL (These referen...) [ 49%] 169s tests/test_trajectory.py::test_read_path[rst7] XFAIL (These referenc...) [ 49%] 169s tests/test_trajectory.py::test_read_path[gro] PASSED [ 49%] 169s tests/test_trajectory.py::test_write_path[nc] PASSED [ 49%] 169s tests/test_trajectory.py::test_write_path[h5] PASSED [ 49%] 169s tests/test_trajectory.py::test_write_path[xtc] PASSED [ 49%] 169s tests/test_trajectory.py::test_write_path[trr] PASSED [ 49%] 169s tests/test_trajectory.py::test_write_path[dcd] PASSED [ 50%] 169s tests/test_trajectory.py::test_write_path[mdcrd] SKIPPED (mdcrd can ...) [ 50%] 169s tests/test_trajectory.py::test_write_path[dtr] PASSED [ 50%] 169s tests/test_trajectory.py::test_write_path[xyz] PASSED [ 50%] 169s tests/test_trajectory.py::test_write_path[xyz.gz] PASSED [ 50%] 169s tests/test_trajectory.py::test_write_path[lammpstrj] PASSED [ 50%] 169s tests/test_trajectory.py::test_write_path[lh5] PASSED [ 50%] 169s tests/test_trajectory.py::test_write_path[pdb] PASSED [ 50%] 169s tests/test_trajectory.py::test_write_path[pdb.gz] PASSED [ 50%] 169s tests/test_trajectory.py::test_write_path[ncrst] SKIPPED (ncrst can ...) [ 50%] 169s tests/test_trajectory.py::test_write_path[rst7] SKIPPED (rst7 can on...) [ 50%] 169s tests/test_trajectory.py::test_write_path[gro] PASSED [ 51%] 169s tests/test_trajectory.py::test_read_write[nc-nc] PASSED [ 51%] 169s tests/test_trajectory.py::test_read_write[nc-h5] PASSED [ 51%] 169s tests/test_trajectory.py::test_read_write[nc-xtc] PASSED [ 51%] 169s tests/test_trajectory.py::test_read_write[nc-trr] PASSED [ 51%] 169s tests/test_trajectory.py::test_read_write[nc-dcd] PASSED [ 51%] 169s tests/test_trajectory.py::test_read_write[nc-mdcrd] SKIPPED (mdcrd c...) [ 51%] 170s tests/test_trajectory.py::test_read_write[nc-dtr] PASSED [ 51%] 170s tests/test_trajectory.py::test_read_write[nc-xyz] PASSED [ 51%] 171s tests/test_trajectory.py::test_read_write[nc-xyz.gz] PASSED [ 51%] 171s tests/test_trajectory.py::test_read_write[nc-lammpstrj] PASSED [ 51%] 171s tests/test_trajectory.py::test_read_write[nc-lh5] PASSED [ 51%] 171s tests/test_trajectory.py::test_read_write[nc-pdb] PASSED [ 52%] 171s tests/test_trajectory.py::test_read_write[nc-pdb.gz] PASSED [ 52%] 171s tests/test_trajectory.py::test_read_write[nc-ncrst] SKIPPED (ncrst c...) [ 52%] 171s tests/test_trajectory.py::test_read_write[nc-rst7] SKIPPED (rst7 can...) [ 52%] 172s tests/test_trajectory.py::test_read_write[nc-gro] PASSED [ 52%] 172s tests/test_trajectory.py::test_read_write[h5-nc] PASSED [ 52%] 172s tests/test_trajectory.py::test_read_write[h5-h5] PASSED [ 52%] 172s tests/test_trajectory.py::test_read_write[h5-xtc] PASSED [ 52%] 172s tests/test_trajectory.py::test_read_write[h5-trr] PASSED [ 52%] 172s tests/test_trajectory.py::test_read_write[h5-dcd] PASSED [ 52%] 172s tests/test_trajectory.py::test_read_write[h5-mdcrd] SKIPPED (mdcrd c...) [ 52%] 172s tests/test_trajectory.py::test_read_write[h5-dtr] PASSED [ 53%] 172s tests/test_trajectory.py::test_read_write[h5-xyz] PASSED [ 53%] 172s tests/test_trajectory.py::test_read_write[h5-xyz.gz] PASSED [ 53%] 172s tests/test_trajectory.py::test_read_write[h5-lammpstrj] PASSED [ 53%] 172s tests/test_trajectory.py::test_read_write[h5-lh5] PASSED [ 53%] 172s tests/test_trajectory.py::test_read_write[h5-pdb] PASSED [ 53%] 173s tests/test_trajectory.py::test_read_write[h5-pdb.gz] PASSED [ 53%] 173s tests/test_trajectory.py::test_read_write[h5-ncrst] SKIPPED (ncrst c...) [ 53%] 173s tests/test_trajectory.py::test_read_write[h5-rst7] SKIPPED (rst7 can...) [ 53%] 173s tests/test_trajectory.py::test_read_write[h5-gro] PASSED [ 53%] 173s tests/test_trajectory.py::test_read_write[xtc-nc] PASSED [ 53%] 173s tests/test_trajectory.py::test_read_write[xtc-h5] PASSED [ 54%] 173s tests/test_trajectory.py::test_read_write[xtc-xtc] PASSED [ 54%] 173s tests/test_trajectory.py::test_read_write[xtc-trr] PASSED [ 54%] 173s tests/test_trajectory.py::test_read_write[xtc-dcd] PASSED [ 54%] 173s tests/test_trajectory.py::test_read_write[xtc-mdcrd] SKIPPED (mdcrd ...) [ 54%] 173s tests/test_trajectory.py::test_read_write[xtc-dtr] PASSED [ 54%] 173s tests/test_trajectory.py::test_read_write[xtc-xyz] PASSED [ 54%] 173s tests/test_trajectory.py::test_read_write[xtc-xyz.gz] PASSED [ 54%] 173s tests/test_trajectory.py::test_read_write[xtc-lammpstrj] PASSED [ 54%] 173s tests/test_trajectory.py::test_read_write[xtc-lh5] PASSED [ 54%] 174s tests/test_trajectory.py::test_read_write[xtc-pdb] PASSED [ 54%] 174s tests/test_trajectory.py::test_read_write[xtc-pdb.gz] PASSED [ 54%] 174s tests/test_trajectory.py::test_read_write[xtc-ncrst] SKIPPED (ncrst ...) [ 55%] 174s tests/test_trajectory.py::test_read_write[xtc-rst7] SKIPPED (rst7 ca...) [ 55%] 174s tests/test_trajectory.py::test_read_write[xtc-gro] PASSED [ 55%] 174s tests/test_trajectory.py::test_read_write[trr-nc] PASSED [ 55%] 174s tests/test_trajectory.py::test_read_write[trr-h5] PASSED [ 55%] 174s tests/test_trajectory.py::test_read_write[trr-xtc] PASSED [ 55%] 174s tests/test_trajectory.py::test_read_write[trr-trr] PASSED [ 55%] 174s tests/test_trajectory.py::test_read_write[trr-dcd] PASSED [ 55%] 174s tests/test_trajectory.py::test_read_write[trr-mdcrd] SKIPPED (mdcrd ...) [ 55%] 174s tests/test_trajectory.py::test_read_write[trr-dtr] PASSED [ 55%] 174s tests/test_trajectory.py::test_read_write[trr-xyz] PASSED [ 55%] 175s tests/test_trajectory.py::test_read_write[trr-xyz.gz] PASSED [ 56%] 175s tests/test_trajectory.py::test_read_write[trr-lammpstrj] PASSED [ 56%] 175s tests/test_trajectory.py::test_read_write[trr-lh5] PASSED [ 56%] 175s tests/test_trajectory.py::test_read_write[trr-pdb] PASSED [ 56%] 175s tests/test_trajectory.py::test_read_write[trr-pdb.gz] PASSED [ 56%] 175s tests/test_trajectory.py::test_read_write[trr-ncrst] SKIPPED (ncrst ...) [ 56%] 175s tests/test_trajectory.py::test_read_write[trr-rst7] SKIPPED (rst7 ca...) [ 56%] 175s tests/test_trajectory.py::test_read_write[trr-gro] PASSED [ 56%] 175s tests/test_trajectory.py::test_read_write[dcd-nc] PASSED [ 56%] 175s tests/test_trajectory.py::test_read_write[dcd-h5] PASSED [ 56%] 175s tests/test_trajectory.py::test_read_write[dcd-xtc] PASSED [ 56%] 175s tests/test_trajectory.py::test_read_write[dcd-trr] PASSED [ 57%] 175s tests/test_trajectory.py::test_read_write[dcd-dcd] PASSED [ 57%] 175s tests/test_trajectory.py::test_read_write[dcd-mdcrd] SKIPPED (mdcrd ...) [ 57%] 175s tests/test_trajectory.py::test_read_write[dcd-dtr] PASSED [ 57%] 175s tests/test_trajectory.py::test_read_write[dcd-xyz] PASSED [ 57%] 176s tests/test_trajectory.py::test_read_write[dcd-xyz.gz] PASSED [ 57%] 176s tests/test_trajectory.py::test_read_write[dcd-lammpstrj] PASSED [ 57%] 176s tests/test_trajectory.py::test_read_write[dcd-lh5] PASSED [ 57%] 176s tests/test_trajectory.py::test_read_write[dcd-pdb] PASSED [ 57%] 176s tests/test_trajectory.py::test_read_write[dcd-pdb.gz] PASSED [ 57%] 176s tests/test_trajectory.py::test_read_write[dcd-ncrst] SKIPPED (ncrst ...) [ 57%] 176s tests/test_trajectory.py::test_read_write[dcd-rst7] SKIPPED (rst7 ca...) [ 57%] 176s tests/test_trajectory.py::test_read_write[dcd-gro] PASSED [ 58%] 176s tests/test_trajectory.py::test_read_write[mdcrd-nc] PASSED [ 58%] 176s tests/test_trajectory.py::test_read_write[mdcrd-h5] PASSED [ 58%] 176s tests/test_trajectory.py::test_read_write[mdcrd-xtc] PASSED [ 58%] 176s tests/test_trajectory.py::test_read_write[mdcrd-trr] PASSED [ 58%] 176s tests/test_trajectory.py::test_read_write[mdcrd-dcd] PASSED [ 58%] 176s tests/test_trajectory.py::test_read_write[mdcrd-mdcrd] SKIPPED (mdcr...) [ 58%] 176s tests/test_trajectory.py::test_read_write[mdcrd-dtr] SKIPPED (dtr ne...) [ 58%] 176s tests/test_trajectory.py::test_read_write[mdcrd-xyz] PASSED [ 58%] 177s tests/test_trajectory.py::test_read_write[mdcrd-xyz.gz] PASSED [ 58%] 177s tests/test_trajectory.py::test_read_write[mdcrd-lammpstrj] SKIPPED (...) [ 58%] 177s tests/test_trajectory.py::test_read_write[mdcrd-lh5] PASSED [ 59%] 177s tests/test_trajectory.py::test_read_write[mdcrd-pdb] PASSED [ 59%] 177s tests/test_trajectory.py::test_read_write[mdcrd-pdb.gz] PASSED [ 59%] 177s tests/test_trajectory.py::test_read_write[mdcrd-ncrst] SKIPPED (ncrs...) [ 59%] 177s tests/test_trajectory.py::test_read_write[mdcrd-rst7] SKIPPED (rst7 ...) [ 59%] 177s tests/test_trajectory.py::test_read_write[mdcrd-gro] PASSED [ 59%] 177s tests/test_trajectory.py::test_read_write[dtr-nc] PASSED [ 59%] 177s tests/test_trajectory.py::test_read_write[dtr-h5] PASSED [ 59%] 177s tests/test_trajectory.py::test_read_write[dtr-xtc] PASSED [ 59%] 177s tests/test_trajectory.py::test_read_write[dtr-trr] PASSED [ 59%] 177s tests/test_trajectory.py::test_read_write[dtr-dcd] PASSED [ 59%] 177s tests/test_trajectory.py::test_read_write[dtr-mdcrd] SKIPPED (mdcrd ...) [ 60%] 178s tests/test_trajectory.py::test_read_write[dtr-dtr] PASSED [ 60%] 178s tests/test_trajectory.py::test_read_write[dtr-xyz] PASSED [ 60%] 178s tests/test_trajectory.py::test_read_write[dtr-xyz.gz] PASSED [ 60%] 178s tests/test_trajectory.py::test_read_write[dtr-lammpstrj] PASSED [ 60%] 178s tests/test_trajectory.py::test_read_write[dtr-lh5] PASSED [ 60%] 178s tests/test_trajectory.py::test_read_write[dtr-pdb] PASSED [ 60%] 179s tests/test_trajectory.py::test_read_write[dtr-pdb.gz] PASSED [ 60%] 179s tests/test_trajectory.py::test_read_write[dtr-ncrst] SKIPPED (ncrst ...) [ 60%] 179s tests/test_trajectory.py::test_read_write[dtr-rst7] SKIPPED (rst7 ca...) [ 60%] 179s tests/test_trajectory.py::test_read_write[dtr-gro] PASSED [ 60%] 179s tests/test_trajectory.py::test_read_write[xyz-nc] PASSED [ 60%] 179s tests/test_trajectory.py::test_read_write[xyz-h5] PASSED [ 61%] 179s tests/test_trajectory.py::test_read_write[xyz-xtc] PASSED [ 61%] 179s tests/test_trajectory.py::test_read_write[xyz-trr] PASSED [ 61%] 179s tests/test_trajectory.py::test_read_write[xyz-dcd] PASSED [ 61%] 179s tests/test_trajectory.py::test_read_write[xyz-mdcrd] SKIPPED (mdcrd ...) [ 61%] 179s tests/test_trajectory.py::test_read_write[xyz-dtr] SKIPPED (dtr need...) [ 61%] 179s tests/test_trajectory.py::test_read_write[xyz-xyz] PASSED [ 61%] 179s tests/test_trajectory.py::test_read_write[xyz-xyz.gz] PASSED [ 61%] 179s tests/test_trajectory.py::test_read_write[xyz-lammpstrj] SKIPPED (la...) [ 61%] 179s tests/test_trajectory.py::test_read_write[xyz-lh5] PASSED [ 61%] 179s tests/test_trajectory.py::test_read_write[xyz-pdb] PASSED [ 61%] 179s tests/test_trajectory.py::test_read_write[xyz-pdb.gz] PASSED [ 62%] 179s tests/test_trajectory.py::test_read_write[xyz-ncrst] SKIPPED (ncrst ...) [ 62%] 179s tests/test_trajectory.py::test_read_write[xyz-rst7] SKIPPED (rst7 ca...) [ 62%] 179s tests/test_trajectory.py::test_read_write[xyz-gro] PASSED [ 62%] 179s tests/test_trajectory.py::test_read_write[xyz.gz-nc] PASSED [ 62%] 179s tests/test_trajectory.py::test_read_write[xyz.gz-h5] PASSED [ 62%] 179s tests/test_trajectory.py::test_read_write[xyz.gz-xtc] PASSED [ 62%] 179s tests/test_trajectory.py::test_read_write[xyz.gz-trr] PASSED [ 62%] 179s tests/test_trajectory.py::test_read_write[xyz.gz-dcd] PASSED [ 62%] 179s tests/test_trajectory.py::test_read_write[xyz.gz-mdcrd] SKIPPED (mdc...) [ 62%] 179s tests/test_trajectory.py::test_read_write[xyz.gz-dtr] SKIPPED (dtr n...) [ 62%] 179s tests/test_trajectory.py::test_read_write[xyz.gz-xyz] PASSED [ 63%] 180s tests/test_trajectory.py::test_read_write[xyz.gz-xyz.gz] PASSED [ 63%] 180s tests/test_trajectory.py::test_read_write[xyz.gz-lammpstrj] SKIPPED [ 63%] 180s tests/test_trajectory.py::test_read_write[xyz.gz-lh5] PASSED [ 63%] 180s tests/test_trajectory.py::test_read_write[xyz.gz-pdb] PASSED [ 63%] 180s tests/test_trajectory.py::test_read_write[xyz.gz-pdb.gz] PASSED [ 63%] 180s tests/test_trajectory.py::test_read_write[xyz.gz-ncrst] SKIPPED (ncr...) [ 63%] 180s tests/test_trajectory.py::test_read_write[xyz.gz-rst7] SKIPPED (rst7...) [ 63%] 180s tests/test_trajectory.py::test_read_write[xyz.gz-gro] PASSED [ 63%] 180s tests/test_trajectory.py::test_read_write[lammpstrj-nc] PASSED [ 63%] 180s tests/test_trajectory.py::test_read_write[lammpstrj-h5] PASSED [ 63%] 180s tests/test_trajectory.py::test_read_write[lammpstrj-xtc] PASSED [ 63%] 180s tests/test_trajectory.py::test_read_write[lammpstrj-trr] PASSED [ 64%] 180s tests/test_trajectory.py::test_read_write[lammpstrj-dcd] PASSED [ 64%] 180s tests/test_trajectory.py::test_read_write[lammpstrj-mdcrd] SKIPPED (...) [ 64%] 181s tests/test_trajectory.py::test_read_write[lammpstrj-dtr] PASSED [ 64%] 181s tests/test_trajectory.py::test_read_write[lammpstrj-xyz] PASSED [ 64%] 181s tests/test_trajectory.py::test_read_write[lammpstrj-xyz.gz] PASSED [ 64%] 181s tests/test_trajectory.py::test_read_write[lammpstrj-lammpstrj] PASSED [ 64%] 181s tests/test_trajectory.py::test_read_write[lammpstrj-lh5] PASSED [ 64%] 181s tests/test_trajectory.py::test_read_write[lammpstrj-pdb] PASSED [ 64%] 181s tests/test_trajectory.py::test_read_write[lammpstrj-pdb.gz] PASSED [ 64%] 181s tests/test_trajectory.py::test_read_write[lammpstrj-ncrst] SKIPPED (...) [ 64%] 181s tests/test_trajectory.py::test_read_write[lammpstrj-rst7] SKIPPED (r...) [ 65%] 181s tests/test_trajectory.py::test_read_write[lammpstrj-gro] PASSED [ 65%] 181s tests/test_trajectory.py::test_read_write[lh5-nc] PASSED [ 65%] 181s tests/test_trajectory.py::test_read_write[lh5-h5] PASSED [ 65%] 181s tests/test_trajectory.py::test_read_write[lh5-xtc] PASSED [ 65%] 181s tests/test_trajectory.py::test_read_write[lh5-trr] PASSED [ 65%] 181s tests/test_trajectory.py::test_read_write[lh5-dcd] PASSED [ 65%] 181s tests/test_trajectory.py::test_read_write[lh5-mdcrd] SKIPPED (mdcrd ...) [ 65%] 181s tests/test_trajectory.py::test_read_write[lh5-dtr] SKIPPED (dtr need...) [ 65%] 181s tests/test_trajectory.py::test_read_write[lh5-xyz] PASSED [ 65%] 182s tests/test_trajectory.py::test_read_write[lh5-xyz.gz] PASSED [ 65%] 182s tests/test_trajectory.py::test_read_write[lh5-lammpstrj] SKIPPED (la...) [ 66%] 182s tests/test_trajectory.py::test_read_write[lh5-lh5] PASSED [ 66%] 182s tests/test_trajectory.py::test_read_write[lh5-pdb] PASSED [ 66%] 182s tests/test_trajectory.py::test_read_write[lh5-pdb.gz] PASSED [ 66%] 182s tests/test_trajectory.py::test_read_write[lh5-ncrst] SKIPPED (ncrst ...) [ 66%] 182s tests/test_trajectory.py::test_read_write[lh5-rst7] SKIPPED (rst7 ca...) [ 66%] 182s tests/test_trajectory.py::test_read_write[lh5-gro] PASSED [ 66%] 182s tests/test_trajectory.py::test_read_write[pdb-nc] PASSED [ 66%] 182s tests/test_trajectory.py::test_read_write[pdb-h5] PASSED [ 66%] 182s tests/test_trajectory.py::test_read_write[pdb-xtc] PASSED [ 66%] 182s tests/test_trajectory.py::test_read_write[pdb-trr] PASSED [ 66%] 182s tests/test_trajectory.py::test_read_write[pdb-dcd] PASSED [ 66%] 182s tests/test_trajectory.py::test_read_write[pdb-mdcrd] SKIPPED (mdcrd ...) [ 67%] 183s tests/test_trajectory.py::test_read_write[pdb-dtr] PASSED [ 67%] 183s tests/test_trajectory.py::test_read_write[pdb-xyz] PASSED [ 67%] 183s tests/test_trajectory.py::test_read_write[pdb-xyz.gz] PASSED [ 67%] 183s tests/test_trajectory.py::test_read_write[pdb-lammpstrj] PASSED [ 67%] 183s tests/test_trajectory.py::test_read_write[pdb-lh5] PASSED [ 67%] 184s tests/test_trajectory.py::test_read_write[pdb-pdb] PASSED [ 67%] 184s tests/test_trajectory.py::test_read_write[pdb-pdb.gz] PASSED [ 67%] 184s tests/test_trajectory.py::test_read_write[pdb-ncrst] SKIPPED (ncrst ...) [ 67%] 184s tests/test_trajectory.py::test_read_write[pdb-rst7] SKIPPED (rst7 ca...) [ 67%] 184s tests/test_trajectory.py::test_read_write[pdb-gro] PASSED [ 67%] 184s tests/test_trajectory.py::test_read_write[pdb.gz-nc] PASSED [ 68%] 184s tests/test_trajectory.py::test_read_write[pdb.gz-h5] PASSED [ 68%] 184s tests/test_trajectory.py::test_read_write[pdb.gz-xtc] PASSED [ 68%] 184s tests/test_trajectory.py::test_read_write[pdb.gz-trr] PASSED [ 68%] 184s tests/test_trajectory.py::test_read_write[pdb.gz-dcd] PASSED [ 68%] 184s tests/test_trajectory.py::test_read_write[pdb.gz-mdcrd] SKIPPED (mdc...) [ 68%] 185s tests/test_trajectory.py::test_read_write[pdb.gz-dtr] PASSED [ 68%] 185s tests/test_trajectory.py::test_read_write[pdb.gz-xyz] PASSED [ 68%] 185s tests/test_trajectory.py::test_read_write[pdb.gz-xyz.gz] PASSED [ 68%] 185s tests/test_trajectory.py::test_read_write[pdb.gz-lammpstrj] PASSED [ 68%] 185s tests/test_trajectory.py::test_read_write[pdb.gz-lh5] PASSED [ 68%] 186s tests/test_trajectory.py::test_read_write[pdb.gz-pdb] PASSED [ 69%] 186s tests/test_trajectory.py::test_read_write[pdb.gz-pdb.gz] PASSED [ 69%] 186s tests/test_trajectory.py::test_read_write[pdb.gz-ncrst] SKIPPED (ncr...) [ 69%] 186s tests/test_trajectory.py::test_read_write[pdb.gz-rst7] SKIPPED (rst7...) [ 69%] 186s tests/test_trajectory.py::test_read_write[pdb.gz-gro] PASSED [ 69%] 186s tests/test_trajectory.py::test_read_write[ncrst-nc] XFAIL (These ref...) [ 69%] 186s tests/test_trajectory.py::test_read_write[ncrst-h5] XFAIL (These ref...) [ 69%] 186s tests/test_trajectory.py::test_read_write[ncrst-xtc] XFAIL (These re...) [ 69%] 186s tests/test_trajectory.py::test_read_write[ncrst-trr] XFAIL (These re...) [ 69%] 186s tests/test_trajectory.py::test_read_write[ncrst-dcd] XFAIL (These re...) [ 69%] 186s tests/test_trajectory.py::test_read_write[ncrst-mdcrd] XFAIL (These ...) [ 69%] 186s tests/test_trajectory.py::test_read_write[ncrst-dtr] XFAIL (These re...) [ 69%] 186s tests/test_trajectory.py::test_read_write[ncrst-xyz] XFAIL (These re...) [ 70%] 186s tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] XFAIL (These...) [ 70%] 186s tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] XFAIL (Th...) [ 70%] 186s tests/test_trajectory.py::test_read_write[ncrst-lh5] XFAIL (These re...) [ 70%] 186s tests/test_trajectory.py::test_read_write[ncrst-pdb] XFAIL (These re...) [ 70%] 186s tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] XFAIL (These...) [ 70%] 186s tests/test_trajectory.py::test_read_write[ncrst-ncrst] XFAIL (These ...) [ 70%] 186s tests/test_trajectory.py::test_read_write[ncrst-rst7] XFAIL (These r...) [ 70%] 186s tests/test_trajectory.py::test_read_write[ncrst-gro] XFAIL (These re...) [ 70%] 186s tests/test_trajectory.py::test_read_write[rst7-nc] XFAIL (These refe...) [ 70%] 186s tests/test_trajectory.py::test_read_write[rst7-h5] XFAIL (These refe...) [ 70%] 186s tests/test_trajectory.py::test_read_write[rst7-xtc] XFAIL (These ref...) [ 71%] 186s tests/test_trajectory.py::test_read_write[rst7-trr] XFAIL (These ref...) [ 71%] 186s tests/test_trajectory.py::test_read_write[rst7-dcd] XFAIL (These ref...) [ 71%] 186s tests/test_trajectory.py::test_read_write[rst7-mdcrd] XFAIL (These r...) [ 71%] 186s tests/test_trajectory.py::test_read_write[rst7-dtr] XFAIL (These ref...) [ 71%] 186s tests/test_trajectory.py::test_read_write[rst7-xyz] XFAIL (These ref...) [ 71%] 186s tests/test_trajectory.py::test_read_write[rst7-xyz.gz] XFAIL (These ...) [ 71%] 186s tests/test_trajectory.py::test_read_write[rst7-lammpstrj] XFAIL (The...) [ 71%] 186s tests/test_trajectory.py::test_read_write[rst7-lh5] XFAIL (These ref...) [ 71%] 186s tests/test_trajectory.py::test_read_write[rst7-pdb] XFAIL (These ref...) [ 71%] 186s tests/test_trajectory.py::test_read_write[rst7-pdb.gz] XFAIL (These ...) [ 71%] 186s tests/test_trajectory.py::test_read_write[rst7-ncrst] XFAIL (These r...) [ 72%] 186s tests/test_trajectory.py::test_read_write[rst7-rst7] XFAIL (These re...) [ 72%] 186s tests/test_trajectory.py::test_read_write[rst7-gro] XFAIL (These ref...) [ 72%] 186s tests/test_trajectory.py::test_read_write[gro-nc] PASSED [ 72%] 186s tests/test_trajectory.py::test_read_write[gro-h5] PASSED [ 72%] 186s tests/test_trajectory.py::test_read_write[gro-xtc] PASSED [ 72%] 186s tests/test_trajectory.py::test_read_write[gro-trr] PASSED [ 72%] 187s tests/test_trajectory.py::test_read_write[gro-dcd] PASSED [ 72%] 187s tests/test_trajectory.py::test_read_write[gro-mdcrd] SKIPPED (mdcrd ...) [ 72%] 187s tests/test_trajectory.py::test_read_write[gro-dtr] PASSED [ 72%] 187s tests/test_trajectory.py::test_read_write[gro-xyz] PASSED [ 72%] 187s tests/test_trajectory.py::test_read_write[gro-xyz.gz] PASSED [ 72%] 187s tests/test_trajectory.py::test_read_write[gro-lammpstrj] PASSED [ 73%] 187s tests/test_trajectory.py::test_read_write[gro-lh5] PASSED [ 73%] 187s tests/test_trajectory.py::test_read_write[gro-pdb] PASSED [ 73%] 188s tests/test_trajectory.py::test_read_write[gro-pdb.gz] PASSED [ 73%] 188s tests/test_trajectory.py::test_read_write[gro-ncrst] SKIPPED (ncrst ...) [ 73%] 188s tests/test_trajectory.py::test_read_write[gro-rst7] SKIPPED (rst7 ca...) [ 73%] 188s tests/test_trajectory.py::test_read_write[gro-gro] PASSED [ 73%] 188s tests/test_trajectory.py::test_load[nc] PASSED [ 73%] 188s tests/test_trajectory.py::test_load[h5] PASSED [ 73%] 188s tests/test_trajectory.py::test_load[xtc] PASSED [ 73%] 188s tests/test_trajectory.py::test_load[trr] PASSED [ 73%] 188s tests/test_trajectory.py::test_load[dcd] PASSED [ 74%] 188s tests/test_trajectory.py::test_load[mdcrd] PASSED [ 74%] 188s tests/test_trajectory.py::test_load[dtr] PASSED [ 74%] 188s tests/test_trajectory.py::test_load[xyz] PASSED [ 74%] 188s tests/test_trajectory.py::test_load[xyz.gz] PASSED [ 74%] 188s tests/test_trajectory.py::test_load[lammpstrj] PASSED [ 74%] 188s tests/test_trajectory.py::test_load[lh5] PASSED [ 74%] 189s tests/test_trajectory.py::test_load[pdb] PASSED [ 74%] 189s tests/test_trajectory.py::test_load[pdb.gz] PASSED [ 74%] 189s tests/test_trajectory.py::test_load[ncrst] XFAIL (These reference fi...) [ 74%] 189s tests/test_trajectory.py::test_load[rst7] XFAIL (These reference fil...) [ 74%] 189s tests/test_trajectory.py::test_load[gro] PASSED [ 75%] 189s tests/test_trajectory.py::test_hdf5 PASSED [ 75%] 190s tests/test_trajectory.py::test_center PASSED [ 75%] 190s tests/test_trajectory.py::test_center_aind PASSED [ 75%] 190s tests/test_trajectory.py::test_float_atom_indices_exception[nc] PASSED [ 75%] 190s tests/test_trajectory.py::test_float_atom_indices_exception[h5] PASSED [ 75%] 190s tests/test_trajectory.py::test_float_atom_indices_exception[xtc] PASSED [ 75%] 190s tests/test_trajectory.py::test_float_atom_indices_exception[trr] PASSED [ 75%] 190s tests/test_trajectory.py::test_float_atom_indices_exception[dcd] PASSED [ 75%] 190s tests/test_trajectory.py::test_float_atom_indices_exception[mdcrd] PASSED [ 75%] 190s tests/test_trajectory.py::test_float_atom_indices_exception[dtr] PASSED [ 75%] 190s tests/test_trajectory.py::test_float_atom_indices_exception[xyz] PASSED [ 75%] 190s tests/test_trajectory.py::test_float_atom_indices_exception[xyz.gz] PASSED [ 76%] 190s tests/test_trajectory.py::test_float_atom_indices_exception[lammpstrj] PASSED [ 76%] 190s tests/test_trajectory.py::test_float_atom_indices_exception[lh5] PASSED [ 76%] 190s tests/test_trajectory.py::test_float_atom_indices_exception[pdb] PASSED [ 76%] 190s tests/test_trajectory.py::test_float_atom_indices_exception[pdb.gz] PASSED [ 76%] 190s tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] XFAIL [ 76%] 190s tests/test_trajectory.py::test_float_atom_indices_exception[rst7] XFAIL [ 76%] 190s tests/test_trajectory.py::test_float_atom_indices_exception[gro] PASSED [ 76%] 190s tests/test_trajectory.py::test_restrict_atoms PASSED [ 76%] 190s tests/test_trajectory.py::test_restrict_atoms_not_inplace PASSED [ 76%] 190s tests/test_trajectory.py::test_array_vs_matrix PASSED [ 76%] 190s tests/test_trajectory.py::test_pdb_unitcell_loadsave PASSED [ 77%] 190s tests/test_trajectory.py::test_load_combination[nc] PASSED [ 77%] 190s tests/test_trajectory.py::test_load_combination[h5] PASSED [ 77%] 190s tests/test_trajectory.py::test_load_combination[xtc] PASSED [ 77%] 190s tests/test_trajectory.py::test_load_combination[trr] PASSED [ 77%] 190s tests/test_trajectory.py::test_load_combination[dcd] PASSED [ 77%] 190s tests/test_trajectory.py::test_load_combination[mdcrd] PASSED [ 77%] 190s tests/test_trajectory.py::test_load_combination[dtr] PASSED [ 77%] 190s tests/test_trajectory.py::test_load_combination[xyz] PASSED [ 77%] 190s tests/test_trajectory.py::test_load_combination[xyz.gz] PASSED [ 77%] 190s tests/test_trajectory.py::test_load_combination[lammpstrj] PASSED [ 77%] 190s tests/test_trajectory.py::test_load_combination[lh5] PASSED [ 78%] 190s tests/test_trajectory.py::test_load_combination[pdb] PASSED [ 78%] 190s tests/test_trajectory.py::test_load_combination[pdb.gz] PASSED [ 78%] 190s tests/test_trajectory.py::test_load_combination[ncrst] XFAIL (These ...) [ 78%] 190s tests/test_trajectory.py::test_load_combination[rst7] XFAIL (These r...) [ 78%] 190s tests/test_trajectory.py::test_load_combination[gro] PASSED [ 78%] 190s tests/test_trajectory.py::test_no_topology PASSED [ 78%] 190s tests/test_trajectory.py::test_join PASSED [ 78%] 190s tests/test_trajectory.py::test_md_join PASSED [ 78%] 190s tests/test_trajectory.py::test_stack_1 PASSED [ 78%] 190s tests/test_trajectory.py::test_stack_2 PASSED [ 78%] 190s tests/test_trajectory.py::test_seek_read_mode[nc] PASSED [ 78%] 190s tests/test_trajectory.py::test_seek_read_mode[h5] PASSED [ 79%] 190s tests/test_trajectory.py::test_seek_read_mode[xtc] PASSED [ 79%] 190s tests/test_trajectory.py::test_seek_read_mode[trr] PASSED [ 79%] 190s tests/test_trajectory.py::test_seek_read_mode[dcd] PASSED [ 79%] 190s tests/test_trajectory.py::test_seek_read_mode[mdcrd] PASSED [ 79%] 190s tests/test_trajectory.py::test_seek_read_mode[dtr] PASSED [ 79%] 191s tests/test_trajectory.py::test_seek_read_mode[xyz] PASSED [ 79%] 191s tests/test_trajectory.py::test_seek_read_mode[xyz.gz] XFAIL (This is...) [ 79%] 191s tests/test_trajectory.py::test_seek_read_mode[lammpstrj] PASSED [ 79%] 191s tests/test_trajectory.py::test_seek_read_mode[lh5] PASSED [ 79%] 191s tests/test_trajectory.py::test_seek_read_mode[pdb] XFAIL (PDB Files ...) [ 79%] 191s tests/test_trajectory.py::test_seek_read_mode[pdb.gz] XFAIL (PDB Fil...) [ 80%] 191s tests/test_trajectory.py::test_seek_read_mode[ncrst] XFAIL (These re...) [ 80%] 191s tests/test_trajectory.py::test_seek_read_mode[rst7] XFAIL (These ref...) [ 80%] 191s tests/test_trajectory.py::test_seek_read_mode[gro] XFAIL (This is br...) [ 80%] 191s tests/test_trajectory.py::test_load_frame[nc] PASSED [ 80%] 191s tests/test_trajectory.py::test_load_frame[h5] PASSED [ 80%] 191s tests/test_trajectory.py::test_load_frame[xtc] PASSED [ 80%] 191s tests/test_trajectory.py::test_load_frame[trr] PASSED [ 80%] 191s tests/test_trajectory.py::test_load_frame[dcd] PASSED [ 80%] 191s tests/test_trajectory.py::test_load_frame[mdcrd] PASSED [ 80%] 191s tests/test_trajectory.py::test_load_frame[dtr] XFAIL (DTR doesn't lo...) [ 80%] 191s tests/test_trajectory.py::test_load_frame[xyz] PASSED [ 81%] 191s tests/test_trajectory.py::test_load_frame[xyz.gz] PASSED [ 81%] 191s tests/test_trajectory.py::test_load_frame[lammpstrj] PASSED [ 81%] 191s tests/test_trajectory.py::test_load_frame[lh5] PASSED [ 81%] 191s tests/test_trajectory.py::test_load_frame[pdb] PASSED [ 81%] 191s tests/test_trajectory.py::test_load_frame[pdb.gz] PASSED [ 81%] 191s tests/test_trajectory.py::test_load_frame[ncrst] XFAIL (These refere...) [ 81%] 191s tests/test_trajectory.py::test_load_frame[rst7] XFAIL (These referen...) [ 81%] 191s tests/test_trajectory.py::test_load_frame[gro] XFAIL (Gro doesn't im...) [ 81%] 191s tests/test_trajectory.py::test_load_frame_2eqq PASSED [ 81%] 191s tests/test_trajectory.py::test_iterload[nc] PASSED [ 81%] 191s tests/test_trajectory.py::test_iterload[h5] PASSED [ 81%] 191s tests/test_trajectory.py::test_iterload[xtc] PASSED [ 82%] 191s tests/test_trajectory.py::test_iterload[trr] PASSED [ 82%] 191s tests/test_trajectory.py::test_iterload[dcd] PASSED [ 82%] 191s tests/test_trajectory.py::test_iterload[mdcrd] PASSED [ 82%] 191s tests/test_trajectory.py::test_iterload[dtr] XFAIL (This is broken w...) [ 82%] 191s tests/test_trajectory.py::test_iterload[xyz] PASSED [ 82%] 191s tests/test_trajectory.py::test_iterload[xyz.gz] PASSED [ 82%] 191s tests/test_trajectory.py::test_iterload[lammpstrj] PASSED [ 82%] 191s tests/test_trajectory.py::test_iterload[lh5] PASSED [ 82%] 191s tests/test_trajectory.py::test_iterload[pdb] PASSED [ 82%] 191s tests/test_trajectory.py::test_iterload[pdb.gz] PASSED [ 82%] 191s tests/test_trajectory.py::test_iterload[ncrst] SKIPPED (Only 1 frame...) [ 83%] 191s tests/test_trajectory.py::test_iterload[rst7] SKIPPED (Only 1 frame ...) [ 83%] 191s tests/test_trajectory.py::test_iterload[gro] PASSED [ 83%] 193s tests/test_trajectory.py::test_iterload_skip[nc] PASSED [ 83%] 194s tests/test_trajectory.py::test_iterload_skip[h5] PASSED [ 83%] 195s tests/test_trajectory.py::test_iterload_skip[xtc] PASSED [ 83%] 195s tests/test_trajectory.py::test_iterload_skip[trr] PASSED [ 83%] 196s tests/test_trajectory.py::test_iterload_skip[dcd] PASSED [ 83%] 196s tests/test_trajectory.py::test_iterload_skip[mdcrd] PASSED [ 83%] 196s tests/test_trajectory.py::test_iterload_skip[dtr] PASSED [ 83%] 197s tests/test_trajectory.py::test_iterload_skip[xyz] PASSED [ 83%] 198s tests/test_trajectory.py::test_iterload_skip[xyz.gz] PASSED [ 84%] 198s tests/test_trajectory.py::test_iterload_skip[lammpstrj] PASSED [ 84%] 199s tests/test_trajectory.py::test_iterload_skip[lh5] PASSED [ 84%] 199s tests/test_trajectory.py::test_iterload_skip[pdb] XFAIL (PDB Iterloa...) [ 84%] 199s tests/test_trajectory.py::test_iterload_skip[pdb.gz] XFAIL (PDB Iter...) [ 84%] 199s tests/test_trajectory.py::test_iterload_skip[ncrst] XFAIL (These ref...) [ 84%] 199s tests/test_trajectory.py::test_iterload_skip[rst7] XFAIL (These refe...) [ 84%] 199s tests/test_trajectory.py::test_iterload_skip[gro] XFAIL (Not impleme...) [ 84%] 199s tests/test_trajectory.py::test_iterload_chunk_dcd PASSED [ 84%] 199s tests/test_trajectory.py::test_save_load[nc] PASSED [ 84%] 199s tests/test_trajectory.py::test_save_load[h5] PASSED [ 84%] 199s tests/test_trajectory.py::test_save_load[xtc] PASSED [ 84%] 199s tests/test_trajectory.py::test_save_load[trr] PASSED [ 85%] 199s tests/test_trajectory.py::test_save_load[dcd] PASSED [ 85%] 199s tests/test_trajectory.py::test_save_load[mdcrd] PASSED [ 85%] 199s tests/test_trajectory.py::test_save_load[dtr] PASSED [ 85%] 199s tests/test_trajectory.py::test_save_load[xyz] PASSED [ 85%] 199s tests/test_trajectory.py::test_save_load[xyz.gz] PASSED [ 85%] 199s tests/test_trajectory.py::test_save_load[lammpstrj] PASSED [ 85%] 199s tests/test_trajectory.py::test_save_load[lh5] PASSED [ 85%] 199s tests/test_trajectory.py::test_save_load[pdb] PASSED [ 85%] 199s tests/test_trajectory.py::test_save_load[pdb.gz] PASSED [ 85%] 199s tests/test_trajectory.py::test_save_load[ncrst] PASSED [ 85%] 199s tests/test_trajectory.py::test_save_load[rst7] PASSED [ 86%] 199s tests/test_trajectory.py::test_save_load[gro] PASSED [ 86%] 199s tests/test_trajectory.py::test_force_overwrite[nc] PASSED [ 86%] 199s tests/test_trajectory.py::test_force_overwrite[h5] PASSED [ 86%] 199s tests/test_trajectory.py::test_force_overwrite[xtc] PASSED [ 86%] 199s tests/test_trajectory.py::test_force_overwrite[trr] PASSED [ 86%] 199s tests/test_trajectory.py::test_force_overwrite[dcd] PASSED [ 86%] 199s tests/test_trajectory.py::test_force_overwrite[mdcrd] PASSED [ 86%] 199s tests/test_trajectory.py::test_force_overwrite[dtr] XFAIL (This is b...) [ 86%] 199s tests/test_trajectory.py::test_force_overwrite[xyz] PASSED [ 86%] 199s tests/test_trajectory.py::test_force_overwrite[xyz.gz] PASSED [ 86%] 199s tests/test_trajectory.py::test_force_overwrite[lammpstrj] PASSED [ 87%] 199s tests/test_trajectory.py::test_force_overwrite[lh5] PASSED [ 87%] 199s tests/test_trajectory.py::test_force_overwrite[pdb] PASSED [ 87%] 199s tests/test_trajectory.py::test_force_overwrite[pdb.gz] PASSED [ 87%] 199s tests/test_trajectory.py::test_force_overwrite[ncrst] PASSED [ 87%] 199s tests/test_trajectory.py::test_force_overwrite[rst7] PASSED [ 87%] 199s tests/test_trajectory.py::test_force_overwrite[gro] PASSED [ 87%] 199s tests/test_trajectory.py::test_force_noverwrite[nc] PASSED [ 87%] 199s tests/test_trajectory.py::test_force_noverwrite[h5] PASSED [ 87%] 199s tests/test_trajectory.py::test_force_noverwrite[xtc] PASSED [ 87%] 199s tests/test_trajectory.py::test_force_noverwrite[trr] PASSED [ 87%] 199s tests/test_trajectory.py::test_force_noverwrite[dcd] PASSED [ 87%] 199s tests/test_trajectory.py::test_force_noverwrite[mdcrd] PASSED [ 88%] 199s tests/test_trajectory.py::test_force_noverwrite[dtr] PASSED [ 88%] 199s tests/test_trajectory.py::test_force_noverwrite[xyz] PASSED [ 88%] 199s tests/test_trajectory.py::test_force_noverwrite[xyz.gz] PASSED [ 88%] 199s tests/test_trajectory.py::test_force_noverwrite[lammpstrj] PASSED [ 88%] 199s tests/test_trajectory.py::test_force_noverwrite[lh5] PASSED [ 88%] 199s tests/test_trajectory.py::test_force_noverwrite[pdb] PASSED [ 88%] 199s tests/test_trajectory.py::test_force_noverwrite[pdb.gz] PASSED [ 88%] 199s tests/test_trajectory.py::test_force_noverwrite[ncrst] PASSED [ 88%] 199s tests/test_trajectory.py::test_force_noverwrite[rst7] PASSED [ 88%] 199s tests/test_trajectory.py::test_force_noverwrite[gro] PASSED [ 88%] 199s tests/test_trajectory.py::test_open_and_load PASSED [ 89%] 199s tests/test_trajectory.py::test_length PASSED [ 89%] 199s tests/test_trajectory.py::test_unitcell[nc] PASSED [ 89%] 199s tests/test_trajectory.py::test_unitcell[h5] PASSED [ 89%] 199s tests/test_trajectory.py::test_unitcell[xtc] PASSED [ 89%] 199s tests/test_trajectory.py::test_unitcell[trr] PASSED [ 89%] 199s tests/test_trajectory.py::test_unitcell[dcd] PASSED [ 89%] 199s tests/test_trajectory.py::test_unitcell[mdcrd] PASSED [ 89%] 199s tests/test_trajectory.py::test_unitcell[dtr] XFAIL (dtr seems to nee...) [ 89%] 199s tests/test_trajectory.py::test_unitcell[xyz] PASSED [ 89%] 199s tests/test_trajectory.py::test_unitcell[xyz.gz] PASSED [ 89%] 199s tests/test_trajectory.py::test_unitcell[lammpstrj] XFAIL (lammpstrj ...) [ 90%] 199s tests/test_trajectory.py::test_unitcell[lh5] PASSED [ 90%] 199s tests/test_trajectory.py::test_unitcell[pdb] PASSED [ 90%] 199s tests/test_trajectory.py::test_unitcell[pdb.gz] PASSED [ 90%] 199s tests/test_trajectory.py::test_unitcell[ncrst] XFAIL (ncrst seems to...) [ 90%] 199s tests/test_trajectory.py::test_unitcell[rst7] XFAIL (rst7 seems to n...) [ 90%] 199s tests/test_trajectory.py::test_unitcell[gro] PASSED [ 90%] 199s tests/test_trajectory.py::test_chunk0_iterload PASSED [ 90%] 200s tests/test_trajectory.py::test_hashing PASSED [ 90%] 200s tests/test_trajectory.py::test_smooth PASSED [ 90%] 200s tests/test_trajectory.py::test_load_pdb_no_standard_names PASSED [ 90%] 200s tests/test_trajectory.py::test_load_with_atom_indices PASSED [ 90%] 200s tests/test_trajectory.py::test_atom_slicing PASSED [ 91%] 200s tests/test_trajectory.py::test_load_with_frame PASSED [ 91%] 200s tests/test_trajectory.py::test_add_remove_atoms PASSED [ 91%] 200s tests/test_trr.py::test_1 PASSED [ 91%] 200s tests/test_trr.py::test_read_stride PASSED [ 91%] 200s tests/test_trr.py::test_read_stride_n_frames PASSED [ 91%] 200s tests/test_trr.py::test_read_stride_offsets PASSED [ 91%] 200s tests/test_trr.py::test_read_stride_n_frames_offsets PASSED [ 91%] 200s tests/test_trr.py::test_read_stride_switching PASSED [ 91%] 200s tests/test_trr.py::test_write_read PASSED [ 91%] 200s tests/test_trr.py::test_read_atomindices_1 PASSED [ 91%] 200s tests/test_trr.py::test_read_atomindices_2 PASSED [ 92%] 200s tests/test_trr.py::test_deficient_shape PASSED [ 92%] 200s tests/test_trr.py::test_ragged_1 PASSED [ 92%] 200s tests/test_trr.py::test_ragged_2 PASSED [ 92%] 200s tests/test_trr.py::test_malformed PASSED [ 92%] 200s tests/test_trr.py::test_tell PASSED [ 92%] 200s tests/test_trr.py::test_seek PASSED [ 92%] 200s tests/test_trr.py::test_get_velocities PASSED [ 92%] 200s tests/test_trr.py::test_get_forces PASSED [ 92%] 200s tests/test_trr.py::test_get_velocities_and_forces PASSED [ 92%] 200s tests/test_trr.py::test_get_velocities_forces_atom_indices_1 PASSED [ 92%] 200s tests/test_trr.py::test_get_velocities_forces_atom_indices_2 PASSED [ 93%] 200s tests/test_trr.py::test_read_velocities_do_not_exist PASSED [ 93%] 200s tests/test_trr.py::test_read_forces_do_not_exist PASSED [ 93%] 200s tests/test_utils.py::test_unitcell_0 PASSED [ 93%] 200s tests/test_utils.py::test_unitcell_1 PASSED [ 93%] 200s tests/test_utils.py::test_ensure_type_1 PASSED [ 93%] 200s tests/test_utils.py::test_ensure_type_2 PASSED [ 93%] 200s tests/test_utils.py::test_ensure_type_25 PASSED [ 93%] 200s tests/test_utils.py::test_ensure_type_3 PASSED [ 93%] 200s tests/test_utils.py::test_ensure_type_4 PASSED [ 93%] 200s tests/test_utils.py::test_ensure_type_5 PASSED [ 93%] 200s tests/test_utils.py::test_ensure_type_6 PASSED [ 93%] 200s tests/test_utils.py::test_ensure_type_7 PASSED [ 94%] 200s tests/test_utils.py::test_ensure_type_8 PASSED [ 94%] 200s tests/test_utils.py::test_ensure_type_9 PASSED [ 94%] 200s tests/test_utils.py::test_ensure_type_10 PASSED [ 94%] 200s tests/test_utils.py::test_ensure_type_11 PASSED [ 94%] 200s tests/test_utils.py::test_ensure_type_12 PASSED [ 94%] 200s tests/test_utils.py::test_ensure_type_13 PASSED [ 94%] 200s tests/test_utils.py::test_ensure_type_14 PASSED [ 94%] 200s tests/test_utils.py::test_ensure_type_15 PASSED [ 94%] 200s tests/test_utils.py::test_delay_import_fail_1 PASSED [ 94%] 200s tests/test_utils.py::test_delay_import PASSED [ 94%] 200s tests/test_utils.py::test_unit_0 PASSED [ 95%] 200s tests/test_utils.py::test_unit_1 PASSED [ 95%] 200s tests/test_utils.py::test_unit_2 PASSED [ 95%] 200s tests/test_utils.py::test_unit_3 PASSED [ 95%] 200s tests/test_xml.py::test_xml PASSED [ 95%] 200s tests/test_xtc.py::test_read_chunk1 PASSED [ 95%] 200s tests/test_xtc.py::test_read_stride PASSED [ 95%] 200s tests/test_xtc.py::test_read_stride_n_frames PASSED [ 95%] 200s tests/test_xtc.py::test_read_stride_offsets PASSED [ 95%] 200s tests/test_xtc.py::test_read_stride_n_frames_offsets PASSED [ 95%] 200s tests/test_xtc.py::test_read_stride_switching_offsets PASSED [ 95%] 200s tests/test_xtc.py::test_read_atomindices_1 PASSED [ 96%] 200s tests/test_xtc.py::test_read_atomindices_w_stride PASSED [ 96%] 200s tests/test_xtc.py::test_read_atomindices_2 PASSED [ 96%] 200s tests/test_xtc.py::test_read_chunk2 PASSED [ 96%] 200s tests/test_xtc.py::test_read_chunk3 PASSED [ 96%] 200s tests/test_xtc.py::test_write_0 PASSED [ 96%] 200s tests/test_xtc.py::test_write_1 PASSED [ 96%] 200s tests/test_xtc.py::test_write_2 PASSED [ 96%] 200s tests/test_xtc.py::test_read_error_0 PASSED [ 96%] 200s tests/test_xtc.py::test_write_error_0 PASSED [ 96%] 200s tests/test_xtc.py::test_read_error_1 PASSED [ 96%] 200s tests/test_xtc.py::test_read_error_2 PASSED [ 96%] 200s tests/test_xtc.py::test_xtc_write_wierd_0 PASSED [ 97%] 200s tests/test_xtc.py::test_tell PASSED [ 97%] 200s tests/test_xtc.py::test_seek PASSED [ 97%] 200s tests/test_xtc.py::test_seek_natoms9 PASSED [ 97%] 200s tests/test_xtc.py::test_seek_out_of_bounds PASSED [ 97%] 200s tests/test_xtc.py::test_ragged_1 PASSED [ 97%] 200s tests/test_xtc.py::test_ragged_2 PASSED [ 97%] 200s tests/test_xtc.py::test_short_traj PASSED [ 97%] 200s tests/test_xtc.py::test_flush PASSED [ 97%] 200s tests/test_xyz.py::test_read_0 PASSED [ 97%] 200s tests/test_xyz.py::test_read_1 PASSED [ 97%] 200s tests/test_xyz.py::test_read_gz PASSED [ 98%] 200s tests/test_xyz.py::test_read_write PASSED [ 98%] 200s tests/test_xyz.py::test_mdwrite PASSED [ 98%] 200s tests/test_xyz.py::test_multiread PASSED [ 98%] 200s tests/test_xyz.py::test_seek PASSED [ 98%] 200s tests/test_xyz.py::test_len PASSED [ 98%] 200s tests/test_zipped.py::test_read_gz PASSED [ 98%] 200s tests/test_zipped.py::test_write_gz PASSED [ 98%] 200s tests/test_zipped.py::test_read_bz2 PASSED [ 98%] 200s tests/test_zipped.py::test_write_bz2 PASSED [ 98%] 335s examples/test_examples.py::test_example_notebook[iterload.ipynb] PASSED [ 98%] 335s examples/test_examples.py::test_example_notebook[simulation-with-openmm.ipynb] SKIPPED [ 99%] 470s examples/test_examples.py::test_example_notebook[atom-selection.ipynb] PASSED [ 99%] 605s examples/test_examples.py::test_example_notebook[rmsd-benchmark.ipynb] PASSED [ 99%] 740s examples/test_examples.py::test_example_notebook[rmsd-drift.ipynb] PASSED [ 99%] 875s examples/test_examples.py::test_example_notebook[native-contact.ipynb] SKIPPED [ 99%] 1011s examples/test_examples.py::test_example_notebook[centroids.ipynb] PASSED [ 99%] 1146s examples/test_examples.py::test_example_notebook[two-pass-clustering.ipynb] PASSED [ 99%] 1282s examples/test_examples.py::test_example_notebook[principal-components.ipynb] PASSED [ 99%] 1416s examples/test_examples.py::test_example_notebook[solvent-accessible-surface-area.ipynb] PASSED [ 99%] 1550s examples/test_examples.py::test_example_notebook[hbonds.ipynb] SKIPPED [ 99%] 1687s examples/test_examples.py::test_example_notebook[ramachandran-plot.ipynb] PASSED [ 99%] 1822s examples/test_examples.py::test_example_notebook[clustering.ipynb] PASSED [100%] 1822s 1822s =============================== warnings summary =============================== 1822s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:56 1822s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:56: DeprecationWarning: Name.__init__ got an unexpected keyword argument 'SINGLETON'. Support for arbitrary keyword arguments is deprecated and will be removed in Python 3.15. 1822s THIS_ATOM = ast.Name(id="atom", ctx=ast.Load(), SINGLETON=True) 1822s 1822s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:57 1822s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:57: DeprecationWarning: Name.__init__ got an unexpected keyword argument 'SINGLETON'. Support for arbitrary keyword arguments is deprecated and will be removed in Python 3.15. 1822s RE_MODULE = ast.Name(id="re", ctx=ast.Load(), SINGLETON=True) 1822s 1822s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 1822s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 1822s given by the platformdirs library. To remove this warning and 1822s see the appropriate new directories, set the environment variable 1822s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 1822s The use of platformdirs will be the default in `jupyter_core` v6 1822s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 1822s 1822s examples/test_examples.py:26 1822s /tmp/autopkgtest.qPicin/build.7Dk/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 1822s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 1822s 1822s tests/test_contact.py::test_contact_0 1822s tests/test_contact.py::test_contact_4 1822s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:220: UserWarning: selected topology includes at least one glycine residue, which has no heavy atoms in its sidechain. The distances involving glycine residues will be computed using the sidechain hydrogen instead. 1822s warnings.warn( 1822s 1822s tests/test_contact.py::test_contact_3 1822s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:271: RuntimeWarning: overflow encountered in exp 1822s np.exp( 1822s 1822s tests/test_contact.py::test_contact_3 1822s /tmp/autopkgtest.qPicin/build.7Dk/src/tests/test_contact.py:115: RuntimeWarning: divide by zero encountered in scalar divide 1822s beta / np.log(np.sum(np.exp(beta / maps[t, r0, r1]))), 1822s 1822s tests/test_dcd.py::test_do_overwrite 1822s tests/test_dcd.py::test_ragged_1 1822s tests/test_dcd.py::test_ragged_2 1822s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting xyz dtype=float64 to 1822s warnings.warn( 1822s 1822s tests/test_distance.py::test_6 1822s :488: RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject 1822s 1822s tests/test_drid.py::test_drid_2 1822s /tmp/autopkgtest.qPicin/build.7Dk/src/tests/test_drid.py:62: RuntimeWarning: divide by zero encountered in divide 1822s recip = 1 / squareform(pdist(t.xyz[i])) 1822s 1822s tests/test_dssp.py::test_1[1vii.pdb] 1822s tests/test_gro.py::test_read_write 1822s tests/test_gro.py::test_read_write_precision 1822s tests/test_gro.py::test_load 1822s tests/test_shape.py::test_principal_moments 1822s tests/test_shape.py::test_asphericity 1822s tests/test_shape.py::test_shape_metrics 1822s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:208: UserWarning: Unlikely unit cell vectors detected in PDB file likely resulting from a dummy CRYST1 record. Discarding unit cell vectors. 1822s warnings.warn( 1822s 1822s tests/test_geometry.py::test_dihedral_indices 1822s tests/test_geometry.py::test_dihedral_indices 1822s /usr/lib/python3/dist-packages/mdtraj/geometry/dihedral.py:237: DeprecationWarning: Passing a Trajectory object to _atom_sequence isdeprecated. Please pass a Topology object 1822s warnings.warn( 1822s 1822s tests/test_gro.py::test_load 1822s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq 1822s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:364: UserWarning: WARNING: two consecutive residues with same number (GST, HST) 1822s warnings.warn( 1822s 1822s tests/test_pdb.py::test_blank_indexing 1822s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:204: UserWarning: Need to guess atom number starting from atom 100000. 1822s warnings.warn(f'Need to guess atom number {num_str} starting from atom {pdbstructure._next_atom_number}.') 1822s 1822s tests/test_pdb.py::test_blank_indexing 1822s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:271: UserWarning: Need to guess residue number string starting from residue10000, atom 100000. 1822s warnings.warn(f'Need to guess residue number string {num_str} starting from residue{pdbstructure._next_residue_number}, atom {pdbstructure._next_atom_number}.') 1822s 1822s tests/test_rdf.py::test_rdf_norm 1822s tests/test_rdf.py::test_rdf_t_norm[0] 1822s tests/test_rdf.py::test_rdf_t_norm[2] 1822s tests/test_rdf.py::test_rdf_t_norm[4] 1822s tests/test_selection.py::test_re 1822s tests/test_selection.py::test_re 1822s tests/test_topology.py::test_select_pairs 1822s tests/test_topology.py::test_select_pairs 1822s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:199: DeprecationWarning: Call.__init__ got an unexpected keyword argument 'starargs'. Support for arbitrary keyword arguments is deprecated and will be removed in Python 3.15. 1822s left=ast.Call( 1822s 1822s tests/test_rdf.py::test_rdf_norm 1822s tests/test_rdf.py::test_rdf_t_norm[0] 1822s tests/test_rdf.py::test_rdf_t_norm[2] 1822s tests/test_rdf.py::test_rdf_t_norm[4] 1822s tests/test_selection.py::test_re 1822s tests/test_selection.py::test_re 1822s tests/test_topology.py::test_select_pairs 1822s tests/test_topology.py::test_select_pairs 1822s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:199: DeprecationWarning: Call.__init__ got an unexpected keyword argument 'kwargs'. Support for arbitrary keyword arguments is deprecated and will be removed in Python 3.15. 1822s left=ast.Call( 1822s 1822s tests/test_trajectory.py::test_float_atom_indices_exception[gro] 1822s tests/test_trajectory.py::test_atom_slicing 1822s /usr/lib/python3/dist-packages/mdtraj/core/topology.py:84: UserWarning: atom_indices are not monotonically increasing 1822s warnings.warn("atom_indices are not monotonically increasing") 1822s 1822s tests/test_utils.py::test_ensure_type_8 1822s tests/test_utils.py::test_ensure_type_9 1822s tests/test_utils.py::test_ensure_type_13 1822s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=float64 to 1822s warnings.warn( 1822s 1822s tests/test_utils.py::test_ensure_type_11 1822s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=int64 to 1822s warnings.warn( 1822s 1822s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1822s =========================== short test summary info ============================ 1822s SKIPPED [1] tests/test_dihedral.py:56: pymol executable not found 1822s SKIPPED [1] tests/test_dihedral.py:181: pymol executable not found 1822s SKIPPED [16] tests/test_docstrings.py:38: Skip checking certain modules' docstrings 1822s SKIPPED [1] tests/test_geometry.py:300: Not doing performance testing 1822s SKIPPED [1] tests/test_geometry.py:322: Not doing performance testing 1822s SKIPPED [1] tests/test_hdf5.py:104: requires openmm.units 1822s SKIPPED [1] tests/test_hdf5.py:156: requires openmm.units 1822s SKIPPED [1] tests/test_hdf5.py:223: requires openmm.units 1822s SKIPPED [1] tests/test_mol2.py:59: Requires obabel 1822s SKIPPED [1] tests/test_netcdf.py:271: This test requires cpptraj from AmberTools to be installed (http://ambermd.org) 1822s SKIPPED [1] tests/test_nmr.py:11: SPARTA+ binary not found 1822s SKIPPED [1] tests/test_nmr.py:26: PPM binary not found 1822s SKIPPED [1] tests/test_nmr.py:42: SHIFTX2 binary not found or running on travis. 1822s SKIPPED [1] tests/test_pdbx.py:43: test_pdbx.py needs OpenMM. 1822s SKIPPED [2] tests/test_psf.py:93: This test requires the VMD executable: http://www.ks.uiuc.edu/Research/vmd/ 1822s SKIPPED [1] tests/test_rdf.py:64: Binning does not match up with gromacs currently. 1822s SKIPPED [1] tests/test_rdf.py:200: Binning does not match up with gromacs currently. 1822s SKIPPED [1] tests/test_reporter.py:58: test_reporter.py needs OpenMM. 1822s SKIPPED [1] tests/test_reporter.py:145: test_reporter.py needs OpenMM. 1822s SKIPPED [1] tests/test_reporter.py:245: test_reporter.py needs OpenMM. 1822s SKIPPED [1] tests/test_selection.py:267: failed to parse selection 1822s SKIPPED [1] tests/test_thermodynamic_properties.py:161: Thermal expansion test doesn't work. 1822s SKIPPED [1] tests/test_topology.py:45: needs OpenMM 1822s SKIPPED [1] tests/test_topology.py:62: needs OpenMM 1822s SKIPPED [1] tests/test_topology.py:72: needs OpenMM 1822s SKIPPED [1] tests/test_topology.py:81: needs OpenMM 1822s SKIPPED [1] tests/test_topology.py:91: needs OpenMM 1822s SKIPPED [1] tests/test_topology.py:97: needs OpenMM 1822s SKIPPED [1] tests/test_topology.py:247: needs OpenMM 1822s SKIPPED [1] tests/test_trajectory.py:129: xyz does not store box information 1822s SKIPPED [1] tests/test_trajectory.py:129: xyz.gz does not store box information 1822s SKIPPED [1] tests/test_trajectory.py:129: lh5 does not store box information 1822s SKIPPED [1] tests/test_trajectory.py:129: pdb does not store box information 1822s SKIPPED [1] tests/test_trajectory.py:129: pdb.gz does not store box information 1822s SKIPPED [1] tests/test_trajectory.py:226: mdcrd can only store rectilinear boxes 1822s SKIPPED [1] tests/test_trajectory.py:224: ncrst can only store 1 frame per file 1822s SKIPPED [1] tests/test_trajectory.py:224: rst7 can only store 1 frame per file 1822s SKIPPED [14] tests/test_trajectory.py:248: mdcrd can only store rectilinear boxes 1822s SKIPPED [14] tests/test_trajectory.py:246: ncrst can only store 1 frame per file 1822s SKIPPED [14] tests/test_trajectory.py:246: rst7 can only store 1 frame per file 1822s SKIPPED [4] tests/test_trajectory.py:256: dtr needs to write unitcells 1822s SKIPPED [4] tests/test_trajectory.py:256: lammpstrj needs to write unitcells 1822s SKIPPED [2] tests/test_trajectory.py:640: Only 1 frame per file format 1822s SKIPPED [1] examples/test_examples.py:77: Openmm required for example notebook `simulation-with-openmm.ipynb` 1822s SKIPPED [2] examples/test_examples.py:77: Network access required 1822s XFAIL tests/test_trajectory.py::test_read_path[ncrst] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_path[rst7] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[ncrst-nc] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[ncrst-h5] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xtc] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[ncrst-trr] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dcd] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[ncrst-mdcrd] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dtr] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lh5] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[ncrst-ncrst] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[ncrst-rst7] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[ncrst-gro] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[rst7-nc] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[rst7-h5] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[rst7-xtc] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[rst7-trr] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[rst7-dcd] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[rst7-mdcrd] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[rst7-dtr] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz.gz] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[rst7-lammpstrj] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[rst7-lh5] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb.gz] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[rst7-ncrst] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[rst7-rst7] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_read_write[rst7-gro] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_load[ncrst] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_load[rst7] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[rst7] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_load_combination[ncrst] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_load_combination[rst7] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_seek_read_mode[xyz.gz] - reason: This is broken 1822s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb] - reason: PDB Files don't support seeking 1822s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb.gz] - reason: PDB Files don't support seeking 1822s XFAIL tests/test_trajectory.py::test_seek_read_mode[ncrst] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_seek_read_mode[rst7] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_seek_read_mode[gro] - reason: This is broken 1822s XFAIL tests/test_trajectory.py::test_load_frame[dtr] - reason: DTR doesn't load a single frame properly 1822s XFAIL tests/test_trajectory.py::test_load_frame[ncrst] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_load_frame[rst7] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_load_frame[gro] - reason: Gro doesn't implement seek 1822s XFAIL tests/test_trajectory.py::test_iterload[dtr] - reason: This is broken with dtr 1822s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb] - reason: PDB Iterloads an extra frame!! 1822s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb.gz] - reason: PDB Iterloads an extra frame!! 1822s XFAIL tests/test_trajectory.py::test_iterload_skip[ncrst] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_iterload_skip[rst7] - reason: These reference files don't exist yet 1822s XFAIL tests/test_trajectory.py::test_iterload_skip[gro] - reason: Not implemented for some reason 1822s XFAIL tests/test_trajectory.py::test_force_overwrite[dtr] - reason: This is broken with dtr 1822s XFAIL tests/test_trajectory.py::test_unitcell[dtr] - reason: dtr seems to need unit vectors 1822s XFAIL tests/test_trajectory.py::test_unitcell[lammpstrj] - reason: lammpstrj seems to need unit vectors 1822s XFAIL tests/test_trajectory.py::test_unitcell[ncrst] - reason: ncrst seems to need unit vectors 1822s XFAIL tests/test_trajectory.py::test_unitcell[rst7] - reason: rst7 seems to need unit vectors 1822s = 964 passed, 108 skipped, 12 deselected, 61 xfailed, 48 warnings in 1743.15s (0:29:03) = 1822s autopkgtest [04:31:37]: test command1: -----------------------] 1823s command1 PASS 1823s autopkgtest [04:31:38]: test command1: - - - - - - - - - - results - - - - - - - - - - 1823s autopkgtest [04:31:38]: test command2: preparing testbed 1823s Reading package lists... 1823s Building dependency tree... 1823s Reading state information... 1823s Solving dependencies... 1823s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1824s autopkgtest [04:31:39]: test command2: pytest-3 -k 'test_3 or test_pdb_from_url or test_1vii_url_and_gz' 1824s autopkgtest [04:31:39]: test command2: [----------------------- 1825s ============================= test session starts ============================== 1825s platform linux -- Python 3.13.9, pytest-8.3.5, pluggy-1.6.0 -- /usr/bin/python3 1825s cachedir: .pytest_cache 1825s rootdir: /tmp/autopkgtest.qPicin/build.7Dk/src 1825s configfile: pyproject.toml 1825s testpaths: tests, examples 1825s plugins: typeguard-4.4.2 1825s collecting ... collected 1145 items / 1135 deselected / 10 selected 1825s 1825s tests/test_distance.py::test_3 PASSED [ 10%] 1825s tests/test_distance.py::test_3p PASSED [ 20%] 1826s tests/test_dssp.py::test_3[1GAI] PASSED [ 30%] 1827s tests/test_dssp.py::test_3[6gsv] PASSED [ 40%] 1827s tests/test_dssp.py::test_3[2AAC] PASSED [ 50%] 1827s tests/test_nmr.py::test_3_scalar_couplings PASSED [ 60%] 1829s tests/test_pdb.py::test_pdb_from_url PASSED [ 70%] 1829s tests/test_pdb.py::test_3nch_conect PASSED [ 80%] 1830s tests/test_pdb.py::test_3nch_serial_resSeq PASSED [ 90%] 1831s tests/test_pdb.py::test_1vii_url_and_gz PASSED [100%] 1831s 1831s =============================== warnings summary =============================== 1831s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:56 1831s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:56: DeprecationWarning: Name.__init__ got an unexpected keyword argument 'SINGLETON'. Support for arbitrary keyword arguments is deprecated and will be removed in Python 3.15. 1831s THIS_ATOM = ast.Name(id="atom", ctx=ast.Load(), SINGLETON=True) 1831s 1831s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:57 1831s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:57: DeprecationWarning: Name.__init__ got an unexpected keyword argument 'SINGLETON'. Support for arbitrary keyword arguments is deprecated and will be removed in Python 3.15. 1831s RE_MODULE = ast.Name(id="re", ctx=ast.Load(), SINGLETON=True) 1831s 1831s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 1831s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 1831s given by the platformdirs library. To remove this warning and 1831s see the appropriate new directories, set the environment variable 1831s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 1831s The use of platformdirs will be the default in `jupyter_core` v6 1831s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 1831s 1831s examples/test_examples.py:26 1831s /tmp/autopkgtest.qPicin/build.7Dk/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 1831s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 1831s 1831s tests/test_pdb.py::test_1vii_url_and_gz 1831s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:208: UserWarning: Unlikely unit cell vectors detected in PDB file likely resulting from a dummy CRYST1 record. Discarding unit cell vectors. 1831s warnings.warn( 1831s 1831s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1831s =============== 10 passed, 1135 deselected, 5 warnings in 6.40s ================ 1831s autopkgtest [04:31:46]: test command2: -----------------------] 1832s autopkgtest [04:31:47]: test command2: - - - - - - - - - - results - - - - - - - - - - 1832s command2 PASS 1832s autopkgtest [04:31:47]: @@@@@@@@@@@@@@@@@@@@ summary 1832s command1 PASS 1832s command2 PASS