0s autopkgtest [02:57:59]: starting date and time: 2025-02-19 02:57:59+0000 0s autopkgtest [02:57:59]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [02:57:59]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.shf4puv0/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:numpy,src:python-gsd --apt-upgrade mdtraj --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=numpy/1:2.2.3+ds-1 python-gsd/3.4.2-2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-18.secgroup --name adt-plucky-arm64-mdtraj-20250219-025758-juju-7f2275-prod-proposed-migration-environment-15-0cacc2f4-568f-4c7f-bec2-862ef5a90772 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 147s autopkgtest [03:00:26]: testbed dpkg architecture: arm64 147s autopkgtest [03:00:26]: testbed apt version: 2.9.29 147s autopkgtest [03:00:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup 147s autopkgtest [03:00:26]: testbed release detected to be: None 148s autopkgtest [03:00:27]: updating testbed package index (apt update) 149s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 149s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 149s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 149s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 149s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [79.1 kB] 149s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.6 kB] 149s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [788 kB] 149s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 149s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [97.6 kB] 149s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [7960 B] 149s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [698 kB] 149s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [12.1 kB] 150s Fetched 1811 kB in 1s (1899 kB/s) 150s Reading package lists... 151s + lsb_release --codename --short 151s + RELEASE=plucky 151s + cat 151s + [ plucky != trusty ] 151s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 151s Reading package lists... 151s Building dependency tree... 151s Reading state information... 152s Calculating upgrade... 152s The following packages will be upgraded: 152s dhcpcd-base 152s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 152s Need to get 216 kB of archives. 152s After this operation, 0 B of additional disk space will be used. 152s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 dhcpcd-base arm64 1:10.1.0-7 [216 kB] 153s Fetched 216 kB in 0s (521 kB/s) 153s (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 ... 116620 files and directories currently installed.) 153s Preparing to unpack .../dhcpcd-base_1%3a10.1.0-7_arm64.deb ... 153s Unpacking dhcpcd-base (1:10.1.0-7) over (1:10.1.0-6) ... 153s Setting up dhcpcd-base (1:10.1.0-7) ... 153s Processing triggers for man-db (2.13.0-1) ... 155s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 155s + /usr/lib/apt/apt-helper analyze-pattern ?true 155s + uname -r 155s + sed s/\./\\./g 155s + running_kernel_pattern=^linux-.*6\.12\.0-15-generic.* 155s + apt list ?obsolete 155s + tail -n+2 155s + cut+ grep -v ^linux-.*6\.12\.0-15-generic.* 155s -d/ -f1 155s + true 155s + obsolete_pkgs= 155s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove 155s Reading package lists... 156s Building dependency tree... 156s Reading state information... 156s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 156s + grep -q trusty /etc/lsb-release 156s + [ ! -d /usr/share/doc/unattended-upgrades ] 156s + [ ! -d /usr/share/doc/lxd ] 156s + [ ! -d /usr/share/doc/lxd-client ] 156s + [ ! -d /usr/share/doc/snapd ] 156s + type iptables 156s + cat 156s + chmod 755 /etc/rc.local 156s + . /etc/rc.local 156s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 156s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 156s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 156s + uname -m 156s + [ aarch64 = ppc64le ] 156s + [ -d /run/systemd/system ] 156s + systemd-detect-virt --quiet --vm 156s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 156s + cat 156s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 156s + echo COMPRESS=lz4 156s autopkgtest [03:00:35]: upgrading testbed (apt dist-upgrade and autopurge) 156s Reading package lists... 157s Building dependency tree... 157s Reading state information... 157s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 157s Starting 2 pkgProblemResolver with broken count: 0 157s Done 158s Entering ResolveByKeep 158s 159s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 159s Reading package lists... 159s Building dependency tree... 159s Reading state information... 160s Starting pkgProblemResolver with broken count: 0 160s Starting 2 pkgProblemResolver with broken count: 0 160s Done 160s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 163s autopkgtest [03:00:42]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 15:49:33 UTC 2025 163s autopkgtest [03:00:42]: @@@@@@@@@@@@@@@@@@@@ apt-source mdtraj 167s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.3-2 (dsc) [2677 B] 167s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.3-2 (tar) [22.0 MB] 167s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.3-2 (diff) [300 kB] 167s gpgv: Signature made Tue Feb 11 15:16:54 2025 UTC 167s gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA 167s gpgv: Can't check signature: No public key 167s dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.10.3-2.dsc: no acceptable signature found 167s autopkgtest [03:00:46]: testing package mdtraj version 1.10.3-2 169s autopkgtest [03:00:48]: build not needed 174s autopkgtest [03:00:53]: test command1: preparing testbed 174s Reading package lists... 175s Building dependency tree... 175s Reading state information... 175s Starting pkgProblemResolver with broken count: 0 175s Starting 2 pkgProblemResolver with broken count: 0 175s Done 176s The following NEW packages will be installed: 176s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx gdb 176s libaec0 libbabeltrace1 libblas3 libblosc1 libblosc2-4 libdebuginfod-common 176s libdebuginfod1t64 libdeflate0 libfontconfig1 libgfortran5 libgomp1 176s libgraphite2-3 libharfbuzz0b libhdf5-310 libhdf5-hl-310 libimagequant0 176s libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 176s liblbfgsb0 liblcms2-2 liblerc4 libnetcdf22 libnorm1t64 libopenjp2-7 176s libpgm-5.3-0t64 libqhull-r8.0 libraqm0 libsharpyuv0 libsnappy1v5 libsodium23 176s libsource-highlight-common libsource-highlight4t64 libsz2 libtcl8.6 libtiff6 176s libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 176s libxss1 libzmq5 python-matplotlib-data python-tables-data python3-asttokens 176s python3-brotli python3-cftime python3-comm python3-contourpy 176s python3-coverage python3-cpuinfo python3-cycler python3-dateutil 176s python3-debugpy python3-decorator python3-executing python3-fastjsonschema 176s python3-fonttools python3-fs python3-gsd python3-iniconfig python3-ipykernel 176s python3-ipython python3-jedi python3-joblib python3-jupyter-client 176s python3-jupyter-core python3-kiwisolver python3-lxml python3-lz4 176s python3-matplotlib python3-matplotlib-inline python3-mdtraj python3-mpmath 176s python3-nbformat python3-nest-asyncio python3-netcdf4 python3-networkx 176s python3-numexpr python3-numpy python3-numpy-dev python3-packaging 176s python3-pandas python3-pandas-lib python3-parso python3-pexpect python3-pil 176s python3-pil.imagetk python3-platformdirs python3-pluggy 176s python3-prompt-toolkit python3-psutil python3-ptyprocess python3-pure-eval 176s python3-pytest python3-pytz python3-scipy python3-sklearn 176s python3-sklearn-lib python3-stack-data python3-sympy python3-tables 176s python3-tables-lib python3-threadpoolctl python3-tk python3-tornado 176s python3-traitlets python3-typeshed python3-tz python3-ufolib2 176s python3-unicodedata2 python3-wcwidth python3-zmq python3.12 176s python3.12-minimal python3.12-tk python3.13-tk tk8.6-blt2.5 unicode-data 176s x11-common 176s 0 upgraded, 132 newly installed, 0 to remove and 0 not upgraded. 176s Need to get 115 MB of archives. 176s After this operation, 614 MB of additional disk space will be used. 176s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-minimal arm64 3.12.9-1 [2236 kB] 177s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebuginfod-common all 0.192-4 [15.4 kB] 177s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12 arm64 3.12.9-1 [671 kB] 177s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 177s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 177s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 177s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 177s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 177s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 177s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 177s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 177s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 177s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 177s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 177s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 177s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.3-1 [171 kB] 177s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libbabeltrace1 arm64 1.5.11-4build1 [159 kB] 177s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebuginfod1t64 arm64 0.192-4 [20.8 kB] 177s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libsource-highlight-common all 3.1.9-4.3build1 [64.2 kB] 177s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libsource-highlight4t64 arm64 3.1.9-4.3build1 [243 kB] 177s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 gdb arm64 16.2-1ubuntu1 [7653 kB] 177s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 177s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 177s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libsnappy1v5 arm64 1.2.1-1 [30.4 kB] 177s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 libblosc1 arm64 1.21.5+ds-1build1 [25.7 kB] 177s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 libblosc2-4 arm64 2.16.0+ds-1 [158 kB] 177s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 177s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250213-1ubuntu1 [443 kB] 177s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250213-1ubuntu1 [146 kB] 177s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 177s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 177s Get:32 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 177s Get:33 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-310 arm64 1.14.5+repack-3 [1331 kB] 177s Get:34 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [59.8 kB] 177s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 177s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 177s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 177s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 177s Get:39 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 177s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 178s Get:41 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 178s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 178s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 178s Get:44 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnetcdf22 arm64 1:4.9.3-1 [504 kB] 178s Get:45 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnorm1t64 arm64 1.5.9+dfsg-3.1build1 [150 kB] 178s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpgm-5.3-0t64 arm64 5.3.128~dfsg-2.1build1 [162 kB] 178s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 178s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 178s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 178s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libsodium23 arm64 1.0.18-1build3 [119 kB] 178s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 178s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 178s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 178s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 178s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 178s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu2 [168 kB] 178s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 libzmq5 arm64 4.3.5-1build2 [247 kB] 178s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3ubuntu2 [2929 kB] 178s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-tables-data all 3.10.2-2 [49.6 kB] 178s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-asttokens all 3.0.0-1 [20.4 kB] 178s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build3 [342 kB] 178s Get:62 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-1 [145 kB] 178s Get:63 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-numpy arm64 1:2.2.3+ds-1 [4583 kB] 178s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cftime arm64 1.6.4-1build2 [289 kB] 178s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 178s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-comm all 0.2.1-1 [7016 B] 178s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.1-1 [216 kB] 178s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-coverage arm64 7.4.4+dfsg1-0ubuntu3 [150 kB] 178s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cpuinfo all 9.0.0+git20221119-3 [21.7 kB] 178s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 178s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB] 178s Get:72 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-debugpy arm64 1.8.8+ds-2ubuntu1 [1054 kB] 178s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 178s Get:74 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-executing all 2.2.0-0.1 [25.0 kB] 178s Get:75 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fastjsonschema all 2.21.1-1 [20.4 kB] 178s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pytz all 2025.1-3 [162 kB] 178s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2025.1-3 [1866 B] 178s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB] 178s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-6 [90.7 kB] 178s Get:80 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.1-1 [1600 kB] 178s Get:81 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.4.0+dfsg-1 [27.3 kB] 178s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-4ubuntu1 [19.5 MB] 179s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 179s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 179s Get:85 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 179s Get:86 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build2 [360 kB] 179s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 179s Get:88 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.55.3-2 [1615 kB] 179s Get:89 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-gsd arm64 3.4.2-2 [232 kB] 179s Get:90 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 179s Get:91 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-parso all 0.8.4-1 [67.6 kB] 179s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-typeshed all 0.0~git20241223.ea91db2-1 [1548 kB] 179s Get:93 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-jedi all 0.19.1+ds1-1 [693 kB] 179s Get:94 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 179s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 179s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-prompt-toolkit all 3.0.50-1 [257 kB] 179s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pure-eval all 0.2.3-1 [11.4 kB] 179s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-stack-data all 0.6.3-1 [22.0 kB] 179s Get:99 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-ptyprocess all 0.7.0-6 [14.8 kB] 179s Get:100 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pexpect all 4.9-3 [48.1 kB] 179s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ipython all 8.30.0-2 [569 kB] 179s Get:102 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-jupyter-core all 5.7.2-5 [28.1 kB] 179s Get:103 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-psutil arm64 5.9.8-2build3 [196 kB] 179s Get:104 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tornado arm64 6.4.2-1 [299 kB] 180s Get:105 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-zmq arm64 26.2.1-1 [215 kB] 180s Get:106 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-jupyter-client all 8.6.3-2 [78.5 kB] 180s Get:107 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-nest-asyncio all 1.5.4-1 [6256 B] 180s Get:108 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 180s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ipykernel all 6.29.5-2 [82.7 kB] 180s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-joblib all 1.4.2-2 [205 kB] 180s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-3 [62.5 kB] 180s Get:112 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu3 [182 kB] 180s Get:113 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 11.1.0-5 [491 kB] 180s Get:114 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.9-1 [115 kB] 180s Get:115 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.2-1 [106 kB] 180s Get:116 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.13.1-1 [9770 B] 180s Get:117 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 11.1.0-5 [9948 B] 180s Get:118 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3ubuntu2 [4616 kB] 180s Get:119 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-netcdf4 arm64 1.7.2-1build3 [797 kB] 180s Get:120 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 180s Get:121 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-8 [6925 kB] 180s Get:122 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-8 [3112 kB] 181s Get:123 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-numexpr arm64 2.10.2-1build1 [124 kB] 181s Get:124 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tables-lib arm64 3.10.2-2 [738 kB] 181s Get:125 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tables all 3.10.2-2 [354 kB] 181s Get:126 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mdtraj arm64 1.10.3-2 [1552 kB] 181s Get:127 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-nbformat all 5.9.1-1 [41.2 kB] 181s Get:128 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 181s Get:129 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.4-1 [252 kB] 181s Get:130 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 181s Get:131 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-7build1 [6372 kB] 181s Get:132 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn all 1.4.2+dfsg-7build1 [2258 kB] 181s Preconfiguring packages ... 182s Fetched 115 MB in 5s (23.4 MB/s) 182s Selecting previously unselected package python3.12-minimal. 182s (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 ... 116620 files and directories currently installed.) 182s Preparing to unpack .../000-python3.12-minimal_3.12.9-1_arm64.deb ... 182s Unpacking python3.12-minimal (3.12.9-1) ... 182s Selecting previously unselected package libdebuginfod-common. 182s Preparing to unpack .../001-libdebuginfod-common_0.192-4_all.deb ... 182s Unpacking libdebuginfod-common (0.192-4) ... 182s Selecting previously unselected package python3.12. 182s Preparing to unpack .../002-python3.12_3.12.9-1_arm64.deb ... 182s Unpacking python3.12 (3.12.9-1) ... 182s Selecting previously unselected package libtcl8.6:arm64. 182s Preparing to unpack .../003-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... 182s Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... 182s Selecting previously unselected package fonts-dejavu-mono. 182s Preparing to unpack .../004-fonts-dejavu-mono_2.37-8_all.deb ... 182s Unpacking fonts-dejavu-mono (2.37-8) ... 182s Selecting previously unselected package fonts-dejavu-core. 182s Preparing to unpack .../005-fonts-dejavu-core_2.37-8_all.deb ... 182s Unpacking fonts-dejavu-core (2.37-8) ... 182s Selecting previously unselected package fontconfig-config. 182s Preparing to unpack .../006-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 183s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 183s Selecting previously unselected package libfontconfig1:arm64. 183s Preparing to unpack .../007-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 183s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 183s Selecting previously unselected package libxrender1:arm64. 183s Preparing to unpack .../008-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 183s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 183s Selecting previously unselected package libxft2:arm64. 183s Preparing to unpack .../009-libxft2_2.3.6-1build1_arm64.deb ... 183s Unpacking libxft2:arm64 (2.3.6-1build1) ... 183s Selecting previously unselected package x11-common. 183s Preparing to unpack .../010-x11-common_1%3a7.7+23ubuntu3_all.deb ... 183s Unpacking x11-common (1:7.7+23ubuntu3) ... 183s Selecting previously unselected package libxss1:arm64. 183s Preparing to unpack .../011-libxss1_1%3a1.2.3-1build3_arm64.deb ... 183s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 183s Selecting previously unselected package libtk8.6:arm64. 183s Preparing to unpack .../012-libtk8.6_8.6.16-1_arm64.deb ... 183s Unpacking libtk8.6:arm64 (8.6.16-1) ... 183s Selecting previously unselected package tk8.6-blt2.5. 183s Preparing to unpack .../013-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ... 183s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 183s Selecting previously unselected package blt. 183s Preparing to unpack .../014-blt_2.5.3+dfsg-7build1_arm64.deb ... 183s Unpacking blt (2.5.3+dfsg-7build1) ... 183s Selecting previously unselected package fonts-lyx. 183s Preparing to unpack .../015-fonts-lyx_2.4.3-1_all.deb ... 183s Unpacking fonts-lyx (2.4.3-1) ... 183s Selecting previously unselected package libbabeltrace1:arm64. 183s Preparing to unpack .../016-libbabeltrace1_1.5.11-4build1_arm64.deb ... 183s Unpacking libbabeltrace1:arm64 (1.5.11-4build1) ... 183s Selecting previously unselected package libdebuginfod1t64:arm64. 183s Preparing to unpack .../017-libdebuginfod1t64_0.192-4_arm64.deb ... 183s Unpacking libdebuginfod1t64:arm64 (0.192-4) ... 183s Selecting previously unselected package libsource-highlight-common. 183s Preparing to unpack .../018-libsource-highlight-common_3.1.9-4.3build1_all.deb ... 183s Unpacking libsource-highlight-common (3.1.9-4.3build1) ... 183s Selecting previously unselected package libsource-highlight4t64:arm64. 183s Preparing to unpack .../019-libsource-highlight4t64_3.1.9-4.3build1_arm64.deb ... 183s Unpacking libsource-highlight4t64:arm64 (3.1.9-4.3build1) ... 183s Selecting previously unselected package gdb. 183s Preparing to unpack .../020-gdb_16.2-1ubuntu1_arm64.deb ... 183s Unpacking gdb (16.2-1ubuntu1) ... 184s Selecting previously unselected package libaec0:arm64. 184s Preparing to unpack .../021-libaec0_1.1.3-1_arm64.deb ... 184s Unpacking libaec0:arm64 (1.1.3-1) ... 184s Selecting previously unselected package libblas3:arm64. 184s Preparing to unpack .../022-libblas3_3.12.1-2_arm64.deb ... 184s Unpacking libblas3:arm64 (3.12.1-2) ... 184s Selecting previously unselected package libsnappy1v5:arm64. 184s Preparing to unpack .../023-libsnappy1v5_1.2.1-1_arm64.deb ... 184s Unpacking libsnappy1v5:arm64 (1.2.1-1) ... 184s Selecting previously unselected package libblosc1:arm64. 184s Preparing to unpack .../024-libblosc1_1.21.5+ds-1build1_arm64.deb ... 184s Unpacking libblosc1:arm64 (1.21.5+ds-1build1) ... 184s Selecting previously unselected package libblosc2-4:arm64. 184s Preparing to unpack .../025-libblosc2-4_2.16.0+ds-1_arm64.deb ... 184s Unpacking libblosc2-4:arm64 (2.16.0+ds-1) ... 184s Selecting previously unselected package libdeflate0:arm64. 184s Preparing to unpack .../026-libdeflate0_1.23-1_arm64.deb ... 184s Unpacking libdeflate0:arm64 (1.23-1) ... 184s Selecting previously unselected package libgfortran5:arm64. 184s Preparing to unpack .../027-libgfortran5_15-20250213-1ubuntu1_arm64.deb ... 184s Unpacking libgfortran5:arm64 (15-20250213-1ubuntu1) ... 184s Selecting previously unselected package libgomp1:arm64. 184s Preparing to unpack .../028-libgomp1_15-20250213-1ubuntu1_arm64.deb ... 184s Unpacking libgomp1:arm64 (15-20250213-1ubuntu1) ... 184s Selecting previously unselected package libgraphite2-3:arm64. 184s Preparing to unpack .../029-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 184s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 184s Selecting previously unselected package libharfbuzz0b:arm64. 184s Preparing to unpack .../030-libharfbuzz0b_10.2.0-1_arm64.deb ... 184s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 184s Selecting previously unselected package libsz2:arm64. 184s Preparing to unpack .../031-libsz2_1.1.3-1_arm64.deb ... 184s Unpacking libsz2:arm64 (1.1.3-1) ... 184s Selecting previously unselected package libhdf5-310:arm64. 184s Preparing to unpack .../032-libhdf5-310_1.14.5+repack-3_arm64.deb ... 184s Unpacking libhdf5-310:arm64 (1.14.5+repack-3) ... 184s Selecting previously unselected package libhdf5-hl-310:arm64. 184s Preparing to unpack .../033-libhdf5-hl-310_1.14.5+repack-3_arm64.deb ... 184s Unpacking libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 184s Selecting previously unselected package libimagequant0:arm64. 184s Preparing to unpack .../034-libimagequant0_2.18.0-1build1_arm64.deb ... 184s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 184s Selecting previously unselected package libjpeg-turbo8:arm64. 184s Preparing to unpack .../035-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 184s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 184s Selecting previously unselected package libjpeg8:arm64. 184s Preparing to unpack .../036-libjpeg8_8c-2ubuntu11_arm64.deb ... 184s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 184s Selecting previously unselected package libjs-jquery. 184s Preparing to unpack .../037-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 184s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 184s Selecting previously unselected package libjs-jquery-ui. 184s Preparing to unpack .../038-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 184s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 184s Selecting previously unselected package liblapack3:arm64. 184s Preparing to unpack .../039-liblapack3_3.12.1-2_arm64.deb ... 184s Unpacking liblapack3:arm64 (3.12.1-2) ... 185s Selecting previously unselected package liblbfgsb0:arm64. 185s Preparing to unpack .../040-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 185s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 185s Selecting previously unselected package liblcms2-2:arm64. 185s Preparing to unpack .../041-liblcms2-2_2.16-2_arm64.deb ... 185s Unpacking liblcms2-2:arm64 (2.16-2) ... 185s Selecting previously unselected package liblerc4:arm64. 185s Preparing to unpack .../042-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 185s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 185s Selecting previously unselected package libnetcdf22:arm64. 185s Preparing to unpack .../043-libnetcdf22_1%3a4.9.3-1_arm64.deb ... 185s Unpacking libnetcdf22:arm64 (1:4.9.3-1) ... 185s Selecting previously unselected package libnorm1t64:arm64. 185s Preparing to unpack .../044-libnorm1t64_1.5.9+dfsg-3.1build1_arm64.deb ... 185s Unpacking libnorm1t64:arm64 (1.5.9+dfsg-3.1build1) ... 185s Selecting previously unselected package libpgm-5.3-0t64:arm64. 185s Preparing to unpack .../045-libpgm-5.3-0t64_5.3.128~dfsg-2.1build1_arm64.deb ... 185s Unpacking libpgm-5.3-0t64:arm64 (5.3.128~dfsg-2.1build1) ... 185s Selecting previously unselected package libqhull-r8.0:arm64. 185s Preparing to unpack .../046-libqhull-r8.0_2020.2-6build1_arm64.deb ... 185s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 185s Selecting previously unselected package libraqm0:arm64. 185s Preparing to unpack .../047-libraqm0_0.10.2-1_arm64.deb ... 185s Unpacking libraqm0:arm64 (0.10.2-1) ... 185s Selecting previously unselected package libsharpyuv0:arm64. 185s Preparing to unpack .../048-libsharpyuv0_1.5.0-0.1_arm64.deb ... 185s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 185s Selecting previously unselected package libsodium23:arm64. 185s Preparing to unpack .../049-libsodium23_1.0.18-1build3_arm64.deb ... 185s Unpacking libsodium23:arm64 (1.0.18-1build3) ... 185s Selecting previously unselected package libjbig0:arm64. 185s Preparing to unpack .../050-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 185s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 185s Selecting previously unselected package libwebp7:arm64. 185s Preparing to unpack .../051-libwebp7_1.5.0-0.1_arm64.deb ... 185s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 185s Selecting previously unselected package libtiff6:arm64. 185s Preparing to unpack .../052-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 185s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 185s Selecting previously unselected package libwebpdemux2:arm64. 185s Preparing to unpack .../053-libwebpdemux2_1.5.0-0.1_arm64.deb ... 185s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 185s Selecting previously unselected package libwebpmux3:arm64. 185s Preparing to unpack .../054-libwebpmux3_1.5.0-0.1_arm64.deb ... 185s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 185s Selecting previously unselected package libxslt1.1:arm64. 185s Preparing to unpack .../055-libxslt1.1_1.1.39-0exp1ubuntu2_arm64.deb ... 185s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ... 185s Selecting previously unselected package libzmq5:arm64. 185s Preparing to unpack .../056-libzmq5_4.3.5-1build2_arm64.deb ... 185s Unpacking libzmq5:arm64 (4.3.5-1build2) ... 185s Selecting previously unselected package python-matplotlib-data. 185s Preparing to unpack .../057-python-matplotlib-data_3.8.3-3ubuntu2_all.deb ... 185s Unpacking python-matplotlib-data (3.8.3-3ubuntu2) ... 185s Selecting previously unselected package python-tables-data. 185s Preparing to unpack .../058-python-tables-data_3.10.2-2_all.deb ... 185s Unpacking python-tables-data (3.10.2-2) ... 185s Selecting previously unselected package python3-asttokens. 186s Preparing to unpack .../059-python3-asttokens_3.0.0-1_all.deb ... 186s Unpacking python3-asttokens (3.0.0-1) ... 186s Selecting previously unselected package python3-brotli. 186s Preparing to unpack .../060-python3-brotli_1.1.0-2build3_arm64.deb ... 186s Unpacking python3-brotli (1.1.0-2build3) ... 186s Selecting previously unselected package python3-numpy-dev:arm64. 186s Preparing to unpack .../061-python3-numpy-dev_1%3a2.2.3+ds-1_arm64.deb ... 186s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-1) ... 186s Selecting previously unselected package python3-numpy. 186s Preparing to unpack .../062-python3-numpy_1%3a2.2.3+ds-1_arm64.deb ... 186s Unpacking python3-numpy (1:2.2.3+ds-1) ... 186s Selecting previously unselected package python3-cftime. 186s Preparing to unpack .../063-python3-cftime_1.6.4-1build2_arm64.deb ... 186s Unpacking python3-cftime (1.6.4-1build2) ... 186s Selecting previously unselected package python3-traitlets. 186s Preparing to unpack .../064-python3-traitlets_5.14.3+really5.14.3-1_all.deb ... 186s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ... 186s Selecting previously unselected package python3-comm. 186s Preparing to unpack .../065-python3-comm_0.2.1-1_all.deb ... 186s Unpacking python3-comm (0.2.1-1) ... 186s Selecting previously unselected package python3-contourpy. 186s Preparing to unpack .../066-python3-contourpy_1.3.1-1_arm64.deb ... 186s Unpacking python3-contourpy (1.3.1-1) ... 186s Selecting previously unselected package python3-coverage. 186s Preparing to unpack .../067-python3-coverage_7.4.4+dfsg1-0ubuntu3_arm64.deb ... 186s Unpacking python3-coverage (7.4.4+dfsg1-0ubuntu3) ... 186s Selecting previously unselected package python3-cpuinfo. 186s Preparing to unpack .../068-python3-cpuinfo_9.0.0+git20221119-3_all.deb ... 186s Unpacking python3-cpuinfo (9.0.0+git20221119-3) ... 186s Selecting previously unselected package python3-cycler. 186s Preparing to unpack .../069-python3-cycler_0.12.1-1_all.deb ... 186s Unpacking python3-cycler (0.12.1-1) ... 186s Selecting previously unselected package python3-dateutil. 186s Preparing to unpack .../070-python3-dateutil_2.9.0-3_all.deb ... 186s Unpacking python3-dateutil (2.9.0-3) ... 186s Selecting previously unselected package python3-debugpy. 186s Preparing to unpack .../071-python3-debugpy_1.8.8+ds-2ubuntu1_arm64.deb ... 186s Unpacking python3-debugpy (1.8.8+ds-2ubuntu1) ... 186s Selecting previously unselected package python3-decorator. 186s Preparing to unpack .../072-python3-decorator_5.1.1-5_all.deb ... 186s Unpacking python3-decorator (5.1.1-5) ... 186s Selecting previously unselected package python3-executing. 186s Preparing to unpack .../073-python3-executing_2.2.0-0.1_all.deb ... 186s Unpacking python3-executing (2.2.0-0.1) ... 186s Selecting previously unselected package python3-fastjsonschema. 186s Preparing to unpack .../074-python3-fastjsonschema_2.21.1-1_all.deb ... 186s Unpacking python3-fastjsonschema (2.21.1-1) ... 186s Selecting previously unselected package python3-pytz. 187s Preparing to unpack .../075-python3-pytz_2025.1-3_all.deb ... 187s Unpacking python3-pytz (2025.1-3) ... 187s Selecting previously unselected package python3-tz. 187s Preparing to unpack .../076-python3-tz_2025.1-3_all.deb ... 187s Unpacking python3-tz (2025.1-3) ... 187s Selecting previously unselected package python3-platformdirs. 187s Preparing to unpack .../077-python3-platformdirs_4.3.6-1_all.deb ... 187s Unpacking python3-platformdirs (4.3.6-1) ... 187s Selecting previously unselected package python3-fs. 187s Preparing to unpack .../078-python3-fs_2.4.16-6_all.deb ... 187s Unpacking python3-fs (2.4.16-6) ... 187s Selecting previously unselected package python3-lxml:arm64. 187s Preparing to unpack .../079-python3-lxml_5.3.1-1_arm64.deb ... 187s Unpacking python3-lxml:arm64 (5.3.1-1) ... 187s Selecting previously unselected package python3-lz4. 187s Preparing to unpack .../080-python3-lz4_4.4.0+dfsg-1_arm64.deb ... 187s Unpacking python3-lz4 (4.4.0+dfsg-1) ... 187s Selecting previously unselected package python3-scipy. 187s Preparing to unpack .../081-python3-scipy_1.14.1-4ubuntu1_arm64.deb ... 187s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 188s Selecting previously unselected package python3-mpmath. 188s Preparing to unpack .../082-python3-mpmath_1.3.0-1_all.deb ... 188s Unpacking python3-mpmath (1.3.0-1) ... 188s Selecting previously unselected package python3-sympy. 188s Preparing to unpack .../083-python3-sympy_1.13.3-1_all.deb ... 188s Unpacking python3-sympy (1.13.3-1) ... 188s Selecting previously unselected package python3-ufolib2. 188s Preparing to unpack .../084-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 188s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 188s Selecting previously unselected package python3-unicodedata2. 188s Preparing to unpack .../085-python3-unicodedata2_15.1.0+ds-1build2_arm64.deb ... 188s Unpacking python3-unicodedata2 (15.1.0+ds-1build2) ... 188s Selecting previously unselected package unicode-data. 188s Preparing to unpack .../086-unicode-data_15.1.0-1_all.deb ... 188s Unpacking unicode-data (15.1.0-1) ... 188s Selecting previously unselected package python3-fonttools. 188s Preparing to unpack .../087-python3-fonttools_4.55.3-2_arm64.deb ... 188s Unpacking python3-fonttools (4.55.3-2) ... 188s Selecting previously unselected package python3-gsd. 188s Preparing to unpack .../088-python3-gsd_3.4.2-2_arm64.deb ... 188s Unpacking python3-gsd (3.4.2-2) ... 188s Selecting previously unselected package python3-iniconfig. 188s Preparing to unpack .../089-python3-iniconfig_1.1.1-2_all.deb ... 188s Unpacking python3-iniconfig (1.1.1-2) ... 188s Selecting previously unselected package python3-parso. 188s Preparing to unpack .../090-python3-parso_0.8.4-1_all.deb ... 188s Unpacking python3-parso (0.8.4-1) ... 189s Selecting previously unselected package python3-typeshed. 189s Preparing to unpack .../091-python3-typeshed_0.0~git20241223.ea91db2-1_all.deb ... 189s Unpacking python3-typeshed (0.0~git20241223.ea91db2-1) ... 189s Selecting previously unselected package python3-jedi. 189s Preparing to unpack .../092-python3-jedi_0.19.1+ds1-1_all.deb ... 189s Unpacking python3-jedi (0.19.1+ds1-1) ... 189s Selecting previously unselected package python3-matplotlib-inline. 189s Preparing to unpack .../093-python3-matplotlib-inline_0.1.6-2_all.deb ... 189s Unpacking python3-matplotlib-inline (0.1.6-2) ... 189s Selecting previously unselected package python3-wcwidth. 189s Preparing to unpack .../094-python3-wcwidth_0.2.13+dfsg1-1_all.deb ... 189s Unpacking python3-wcwidth (0.2.13+dfsg1-1) ... 189s Selecting previously unselected package python3-prompt-toolkit. 189s Preparing to unpack .../095-python3-prompt-toolkit_3.0.50-1_all.deb ... 189s Unpacking python3-prompt-toolkit (3.0.50-1) ... 189s Selecting previously unselected package python3-pure-eval. 189s Preparing to unpack .../096-python3-pure-eval_0.2.3-1_all.deb ... 189s Unpacking python3-pure-eval (0.2.3-1) ... 190s Selecting previously unselected package python3-stack-data. 190s Preparing to unpack .../097-python3-stack-data_0.6.3-1_all.deb ... 190s Unpacking python3-stack-data (0.6.3-1) ... 190s Selecting previously unselected package python3-ptyprocess. 190s Preparing to unpack .../098-python3-ptyprocess_0.7.0-6_all.deb ... 190s Unpacking python3-ptyprocess (0.7.0-6) ... 190s Selecting previously unselected package python3-pexpect. 190s Preparing to unpack .../099-python3-pexpect_4.9-3_all.deb ... 190s Unpacking python3-pexpect (4.9-3) ... 190s Selecting previously unselected package python3-ipython. 190s Preparing to unpack .../100-python3-ipython_8.30.0-2_all.deb ... 190s Unpacking python3-ipython (8.30.0-2) ... 190s Selecting previously unselected package python3-jupyter-core. 190s Preparing to unpack .../101-python3-jupyter-core_5.7.2-5_all.deb ... 190s Unpacking python3-jupyter-core (5.7.2-5) ... 190s Selecting previously unselected package python3-psutil. 190s Preparing to unpack .../102-python3-psutil_5.9.8-2build3_arm64.deb ... 190s Unpacking python3-psutil (5.9.8-2build3) ... 190s Selecting previously unselected package python3-tornado. 190s 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python3-ipykernel (6.29.5-2) ... 190s Selecting previously unselected package python3-joblib. 190s Preparing to unpack .../109-python3-joblib_1.4.2-2_all.deb ... 190s Unpacking python3-joblib (1.4.2-2) ... 190s Selecting previously unselected package python3-kiwisolver. 190s Preparing to unpack .../110-python3-kiwisolver_1.4.7-3_arm64.deb ... 190s Unpacking python3-kiwisolver (1.4.7-3) ... 190s Selecting previously unselected package libopenjp2-7:arm64. 190s Preparing to unpack .../111-libopenjp2-7_2.5.0-2ubuntu3_arm64.deb ... 190s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu3) ... 190s Selecting previously unselected package python3-pil:arm64. 190s Preparing to unpack .../112-python3-pil_11.1.0-5_arm64.deb ... 190s Unpacking python3-pil:arm64 (11.1.0-5) ... 190s Selecting previously unselected package python3.12-tk. 190s Preparing to unpack .../113-python3.12-tk_3.12.9-1_arm64.deb ... 190s Unpacking python3.12-tk (3.12.9-1) ... 190s Selecting previously unselected package python3.13-tk. 190s Preparing to unpack .../114-python3.13-tk_3.13.2-1_arm64.deb ... 190s Unpacking python3.13-tk (3.13.2-1) ... 190s Selecting previously unselected package python3-tk:arm64. 190s Preparing to unpack .../115-python3-tk_3.13.1-1_arm64.deb ... 190s Unpacking python3-tk:arm64 (3.13.1-1) ... 190s Selecting previously unselected package python3-pil.imagetk:arm64. 191s Preparing to unpack .../116-python3-pil.imagetk_11.1.0-5_arm64.deb ... 191s Unpacking python3-pil.imagetk:arm64 (11.1.0-5) ... 191s Selecting previously unselected package python3-matplotlib. 191s Preparing to unpack .../117-python3-matplotlib_3.8.3-3ubuntu2_arm64.deb ... 191s Unpacking python3-matplotlib (3.8.3-3ubuntu2) ... 191s Selecting previously unselected package python3-netcdf4. 191s Preparing to unpack .../118-python3-netcdf4_1.7.2-1build3_arm64.deb ... 191s Unpacking python3-netcdf4 (1.7.2-1build3) ... 191s Selecting previously unselected package python3-networkx. 191s Preparing to unpack .../119-python3-networkx_3.2.1-4ubuntu1_all.deb ... 191s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 191s Selecting previously unselected package python3-pandas-lib:arm64. 191s Preparing to unpack .../120-python3-pandas-lib_2.2.3+dfsg-8_arm64.deb ... 191s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-8) ... 192s Selecting previously unselected package python3-pandas. 192s Preparing to unpack .../121-python3-pandas_2.2.3+dfsg-8_all.deb ... 192s Unpacking python3-pandas (2.2.3+dfsg-8) ... 192s Selecting previously unselected package python3-numexpr. 192s Preparing to unpack .../122-python3-numexpr_2.10.2-1build1_arm64.deb ... 192s Unpacking python3-numexpr (2.10.2-1build1) ... 192s Selecting previously unselected package python3-tables-lib. 192s Preparing to unpack .../123-python3-tables-lib_3.10.2-2_arm64.deb ... 192s Unpacking python3-tables-lib (3.10.2-2) ... 192s Selecting previously unselected package python3-tables. 192s Preparing to unpack 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previously unselected package python3-sklearn-lib:arm64. 192s Preparing to unpack .../130-python3-sklearn-lib_1.4.2+dfsg-7build1_arm64.deb ... 192s Unpacking python3-sklearn-lib:arm64 (1.4.2+dfsg-7build1) ... 193s Selecting previously unselected package python3-sklearn. 193s Preparing to unpack .../131-python3-sklearn_1.4.2+dfsg-7build1_all.deb ... 193s Unpacking python3-sklearn (1.4.2+dfsg-7build1) ... 193s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 193s Setting up liblcms2-2:arm64 (2.16-2) ... 193s Setting up python3-iniconfig (1.1.1-2) ... 193s Setting up python3.12-minimal (3.12.9-1) ... 194s Setting up python3-tornado (6.4.2-1) ... 195s Setting up libnorm1t64:arm64 (1.5.9+dfsg-3.1build1) ... 195s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 195s Setting up python3-pure-eval (0.2.3-1) ... 195s Setting up libsodium23:arm64 (1.0.18-1build3) ... 195s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 195s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 195s Setting up libdebuginfod-common (0.192-4) ... 195s Setting up python3-joblib (1.4.2-2) ... 196s Setting up python3-parso (0.8.4-1) ... 196s Setting up python3-lz4 (4.4.0+dfsg-1) ... 196s Setting up python3-asttokens (3.0.0-1) ... 197s Setting up python3-unicodedata2 (15.1.0+ds-1build2) ... 197s Setting up fonts-lyx (2.4.3-1) ... 197s Setting up python3.12 (3.12.9-1) ... 198s Setting up python3-threadpoolctl (3.1.0-1) ... 199s Setting up x11-common (1:7.7+23ubuntu3) ... 199s Setting up libdeflate0:arm64 (1.23-1) ... 199s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 199s Setting up python3-coverage (7.4.4+dfsg1-0ubuntu3) ... 199s Setting up python3-pytz (2025.1-3) ... 200s Setting up libgomp1:arm64 (15-20250213-1ubuntu1) ... 200s Setting up python3-networkx (3.2.1-4ubuntu1) ... 202s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 202s Setting up libaec0:arm64 (1.1.3-1) ... 202s Setting up python3-platformdirs (4.3.6-1) ... 203s Setting up python3-psutil (5.9.8-2build3) ... 203s Setting up libsource-highlight-common (3.1.9-4.3build1) ... 203s Setting up python3-tz (2025.1-3) ... 203s Setting up libsnappy1v5:arm64 (1.2.1-1) ... 203s Setting up python3-fs (2.4.16-6) ... 204s Setting up unicode-data (15.1.0-1) ... 204s Setting up libpgm-5.3-0t64:arm64 (5.3.128~dfsg-2.1build1) ... 204s Setting up python3-decorator (5.1.1-5) ... 204s Setting up libblosc2-4:arm64 (2.16.0+ds-1) ... 204s Setting up libblas3:arm64 (3.12.1-2) ... 204s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 204s Setting up python3-packaging (24.2-1) ... 204s Setting up python3-wcwidth (0.2.13+dfsg1-1) ... 204s Setting up python3-typeshed (0.0~git20241223.ea91db2-1) ... 204s Setting up python3-executing (2.2.0-0.1) ... 205s Setting up python3-nest-asyncio (1.5.4-1) ... 205s Setting up python3-brotli (1.1.0-2build3) ... 205s Setting up python3-cycler (0.12.1-1) ... 205s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 205s Setting up fonts-dejavu-mono (2.37-8) ... 205s Setting up python3-kiwisolver (1.4.7-3) ... 205s Setting up python3-numpy-dev:arm64 (1:2.2.3+ds-1) ... 205s Setting up libtcl8.6:arm64 (8.6.16+dfsg-1) ... 205s Setting up fonts-dejavu-core (2.37-8) ... 205s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 205s Setting up python3-cpuinfo (9.0.0+git20221119-3) ... 206s Setting up libbabeltrace1:arm64 (1.5.11-4build1) ... 206s Setting up libgfortran5:arm64 (15-20250213-1ubuntu1) ... 206s Setting up python3-pluggy (1.5.0-1) ... 206s Setting up libwebp7:arm64 (1.5.0-0.1) ... 206s Setting up python3-fastjsonschema (2.21.1-1) ... 206s Setting up python3-traitlets (5.14.3+really5.14.3-1) ... 206s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ... 206s Setting up libblosc1:arm64 (1.21.5+ds-1build1) ... 206s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu3) ... 206s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 206s Setting up python3-dateutil (2.9.0-3) ... 207s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 207s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 207s Setting up python3-mpmath (1.3.0-1) ... 208s Setting up python-matplotlib-data (3.8.3-3ubuntu2) ... 208s Setting up libwebpmux3:arm64 (1.5.0-0.1) ... 208s Setting up python3-stack-data (0.6.3-1) ... 208s Setting up python-tables-data (3.10.2-2) ... 208s Setting up python3-jupyter-core (5.7.2-5) ... 208s Setting up libsz2:arm64 (1.1.3-1) ... 208s Setting up python3-ptyprocess (0.7.0-6) ... 209s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 209s Setting up python3-prompt-toolkit (3.0.50-1) ... 210s Setting up python3-sympy (1.13.3-1) ... 223s Setting up libdebuginfod1t64:arm64 (0.192-4) ... 223s Setting up liblapack3:arm64 (3.12.1-2) ... 223s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 223s Setting up libzmq5:arm64 (4.3.5-1build2) ... 223s Setting up python3-jedi (0.19.1+ds1-1) ... 223s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 224s Setting up python3-pytest (8.3.4-1) ... 224s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 224s Setting up libsource-highlight4t64:arm64 (3.1.9-4.3build1) ... 224s Setting up python3-nbformat (5.9.1-1) ... 224s Setting up python3-matplotlib-inline (0.1.6-2) ... 225s Setting up python3-comm (0.2.1-1) ... 227s Setting up gdb (16.2-1ubuntu1) ... 227s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 227s Setting up python3-pexpect (4.9-3) ... 227s Setting up python3-zmq (26.2.1-1) ... 227s Setting up libraqm0:arm64 (0.10.2-1) ... 227s Setting up python3-numpy (1:2.2.3+ds-1) ... 229s Setting up libhdf5-310:arm64 (1.14.5+repack-3) ... 229s Setting up python3-lxml:arm64 (5.3.1-1) ... 230s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 230s Setting up python3-jupyter-client (8.6.3-2) ... 230s Setting up python3-contourpy (1.3.1-1) ... 230s Setting up libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 230s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 230s Setting up libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 230s Setting up libxft2:arm64 (2.3.6-1build1) ... 230s Setting up python3-scipy (1.14.1-4ubuntu1) ... 237s Setting up python3-tables-lib (3.10.2-2) ... 237s Setting up libtk8.6:arm64 (8.6.16-1) ... 237s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-8) ... 237s Setting up python3.12-tk (3.12.9-1) ... 238s Setting up libnetcdf22:arm64 (1:4.9.3-1) ... 238s Setting up python3-sklearn-lib:arm64 (1.4.2+dfsg-7build1) ... 238s Setting up python3-gsd (3.4.2-2) ... 238s Setting up python3-debugpy (1.8.8+ds-2ubuntu1) ... 239s Setting up python3.13-tk (3.13.2-1) ... 239s Setting up python3-pil:arm64 (11.1.0-5) ... 240s Setting up python3-pandas (2.2.3+dfsg-8) ... 250s Setting up python3-ipython (8.30.0-2) ... 251s Setting up python3-ipykernel (6.29.5-2) ... 252s Setting up python3-sklearn (1.4.2+dfsg-7build1) ... 256s Setting up python3-cftime (1.6.4-1build2) ... 256s Setting up python3-numexpr (2.10.2-1build1) ... 256s Setting up python3-netcdf4 (1.7.2-1build3) ... 257s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 257s Setting up blt (2.5.3+dfsg-7build1) ... 257s Setting up python3-tk:arm64 (3.13.1-1) ... 257s Setting up python3-tables (3.10.2-2) ... 258s Setting up python3-mdtraj (1.10.3-2) ... 259s Setting up python3-pil.imagetk:arm64 (11.1.0-5) ... 259s Setting up python3-fonttools (4.55.3-2) ... 261s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 261s Setting up python3-matplotlib (3.8.3-3ubuntu2) ... 265s Processing triggers for libc-bin (2.40-4ubuntu1) ... 265s Processing triggers for systemd (257.2-3ubuntu1) ... 265s Processing triggers for man-db (2.13.0-1) ... 267s autopkgtest [03:02:26]: 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)' 267s autopkgtest [03:02:26]: test command1: [----------------------- 268s ============================= test session starts ============================== 268s platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 -- /usr/bin/python3 268s cachedir: .pytest_cache 268s rootdir: /tmp/autopkgtest.pzKnhO/build.Zfy/src 268s configfile: pyproject.toml 268s testpaths: tests, examples 268s plugins: typeguard-4.4.1 270s collecting ... collected 1145 items / 12 deselected / 1133 selected 270s 270s tests/test_alignment.py::test_rmsd_zero PASSED [ 0%] 270s tests/test_alignment.py::test_rmsd_nonzero PASSED [ 0%] 270s tests/test_alignment.py::test_transform PASSED [ 0%] 270s tests/test_alignment.py::test_transform2 PASSED [ 0%] 270s tests/test_angles.py::test_angle_pbc_0 PASSED [ 0%] 270s tests/test_angles.py::test_generator PASSED [ 0%] 270s tests/test_angles.py::test_angle_180[True] PASSED [ 0%] 270s tests/test_angles.py::test_angle_180[False] PASSED [ 0%] 270s tests/test_arc.py::test_read_0 PASSED [ 0%] 270s tests/test_arc.py::test_read_arctraj PASSED [ 0%] 270s tests/test_arc.py::test_read_pbc 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[ 6%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.core.element] PASSED [ 6%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.core.residue_names] PASSED [ 6%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.core.selection] PASSED [ 6%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.core.topology] PASSED [ 6%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.core.trajectory] PASSED [ 6%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.amberrst] PASSED [ 6%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.arc] PASSED [ 6%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.dcd] PASSED [ 6%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.dtr] PASSED [ 6%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.gro] PASSED [ 7%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.gsd] PASSED [ 7%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.hdf5] SKIPPED [ 7%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.hoomdxml] PASSED [ 7%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.lammpstrj] PASSED [ 7%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.lh5] SKIPPED [ 7%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.mdcrd] PASSED [ 7%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.mol2] PASSED [ 7%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.netcdf] PASSED [ 7%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.openmmxml] PASSED [ 7%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdb.pdbfile] PASSED [ 7%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdb.pdbstructure] SKIPPED [ 8%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdbx] PASSED [ 8%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.prmtop] PASSED [ 8%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.psf] PASSED [ 8%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.registry] PASSED [ 8%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.trr] PASSED [ 8%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.xtc] PASSED [ 8%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.formats.xyzfile] PASSED [ 8%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.geometry._geometry] PASSED [ 8%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.alignment] PASSED [ 8%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.angle] PASSED [ 8%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.contact] PASSED [ 9%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.dihedral] PASSED [ 9%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.distance] PASSED [ 9%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.drid] PASSED [ 9%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.dssp] PASSED [ 9%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.hbond] PASSED [ 9%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.internal] PASSED [ 9%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.neighborlist] PASSED [ 9%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.neighbors] PASSED [ 9%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.order] PASSED [ 9%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.rdf] PASSED [ 9%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.rg] PASSED [ 9%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.sasa] PASSED [ 10%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.shape] PASSED [ 10%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.thermodynamic_properties] PASSED [ 10%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.io] SKIPPED (Skip c...) [ 10%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.nmr.scalar_couplings] PASSED [ 10%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.nmr.shift_wrappers] PASSED [ 10%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.basereporter] PASSED [ 10%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.dcdreporter] PASSED [ 10%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.hdf5reporter] PASSED [ 10%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.netcdfreporter] PASSED [ 10%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.xtcreporter] PASSED [ 10%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.scripts.mdconvert] SKIPPED [ 11%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.scripts.mdinspect] SKIPPED [ 11%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.testing.docscrape] SKIPPED [ 11%] 280s tests/test_docstrings.py::test_docstrings[mdtraj.testing.docstrings] PASSED [ 11%] 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[ 43%] 476s tests/test_topology.py::test_topology_openmm_formal_charges SKIPPED [ 44%] 476s tests/test_topology.py::test_topology_pandas PASSED [ 44%] 477s tests/test_topology.py::test_topology_pandas_TIP4PEW PASSED [ 44%] 477s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq PASSED [ 44%] 477s tests/test_topology.py::test_topology_numbers PASSED [ 44%] 477s tests/test_topology.py::test_topology_unique_elements_bpti PASSED [ 44%] 477s tests/test_topology.py::test_chain PASSED [ 44%] 477s tests/test_topology.py::test_residue PASSED [ 44%] 477s tests/test_topology.py::test_segment_id PASSED [ 44%] 477s tests/test_topology.py::test_nonconsective_resSeq PASSED [ 44%] 477s tests/test_topology.py::test_pickle PASSED [ 44%] 477s tests/test_topology.py::test_atoms_by_name PASSED [ 45%] 477s tests/test_topology.py::test_select_atom_indices PASSED [ 45%] 477s tests/test_topology.py::test_top_dataframe_openmm_roundtrip SKIPPED [ 45%] 477s tests/test_topology.py::test_n_bonds PASSED [ 45%] 477s tests/test_topology.py::test_load_unknown_topology PASSED [ 45%] 477s tests/test_topology.py::test_unique_pairs PASSED [ 45%] 478s tests/test_topology.py::test_select_pairs PASSED [ 45%] 478s tests/test_topology.py::test_to_fasta PASSED [ 45%] 479s tests/test_topology.py::test_subset PASSED [ 45%] 479s tests/test_topology.py::test_subset_re_index_residues PASSED [ 45%] 479s tests/test_topology.py::test_molecules PASSED [ 45%] 479s tests/test_topology.py::test_copy_and_hash PASSED [ 45%] 479s tests/test_topology.py::test_topology_sliced_residue_indices PASSED [ 46%] 479s tests/test_topology.py::test_topology_join PASSED [ 46%] 479s tests/test_topology.py::test_topology_join_keep_resSeq PASSED [ 46%] 479s tests/test_trajectory.py::test_mismatch PASSED [ 46%] 479s tests/test_trajectory.py::test_box PASSED [ 46%] 479s tests/test_trajectory.py::test_load_pdb_box PASSED [ 46%] 479s tests/test_trajectory.py::test_load_pdb_gz PASSED [ 46%] 479s tests/test_trajectory.py::test_box_load_save[nc] PASSED [ 46%] 480s tests/test_trajectory.py::test_box_load_save[h5] PASSED [ 46%] 480s tests/test_trajectory.py::test_box_load_save[xtc] PASSED [ 46%] 480s tests/test_trajectory.py::test_box_load_save[trr] PASSED [ 46%] 480s tests/test_trajectory.py::test_box_load_save[dcd] PASSED [ 47%] 480s tests/test_trajectory.py::test_box_load_save[mdcrd] PASSED [ 47%] 480s tests/test_trajectory.py::test_box_load_save[dtr] PASSED [ 47%] 480s tests/test_trajectory.py::test_box_load_save[xyz] SKIPPED (xyz does ...) [ 47%] 480s tests/test_trajectory.py::test_box_load_save[xyz.gz] SKIPPED (xyz.gz...) [ 47%] 480s tests/test_trajectory.py::test_box_load_save[lammpstrj] PASSED [ 47%] 480s tests/test_trajectory.py::test_box_load_save[lh5] SKIPPED (lh5 does ...) [ 47%] 480s tests/test_trajectory.py::test_box_load_save[pdb] SKIPPED (pdb does ...) [ 47%] 480s tests/test_trajectory.py::test_box_load_save[pdb.gz] SKIPPED (pdb.gz...) [ 47%] 480s tests/test_trajectory.py::test_box_load_save[ncrst] PASSED [ 47%] 480s tests/test_trajectory.py::test_box_load_save[rst7] PASSED [ 47%] 480s tests/test_trajectory.py::test_box_load_save[gro] PASSED [ 48%] 480s tests/test_trajectory.py::test_slice PASSED [ 48%] 480s tests/test_trajectory.py::test_slice2 PASSED [ 48%] 480s tests/test_trajectory.py::test_read_path[nc] PASSED [ 48%] 480s tests/test_trajectory.py::test_read_path[h5] PASSED [ 48%] 480s tests/test_trajectory.py::test_read_path[xtc] PASSED [ 48%] 480s tests/test_trajectory.py::test_read_path[trr] PASSED [ 48%] 480s tests/test_trajectory.py::test_read_path[dcd] PASSED [ 48%] 480s tests/test_trajectory.py::test_read_path[mdcrd] PASSED [ 48%] 480s tests/test_trajectory.py::test_read_path[dtr] PASSED [ 48%] 480s tests/test_trajectory.py::test_read_path[xyz] PASSED [ 48%] 480s tests/test_trajectory.py::test_read_path[xyz.gz] PASSED [ 48%] 480s tests/test_trajectory.py::test_read_path[lammpstrj] PASSED [ 49%] 480s tests/test_trajectory.py::test_read_path[lh5] PASSED [ 49%] 480s tests/test_trajectory.py::test_read_path[pdb] PASSED [ 49%] 480s tests/test_trajectory.py::test_read_path[pdb.gz] PASSED [ 49%] 480s tests/test_trajectory.py::test_read_path[ncrst] XFAIL (These referen...) [ 49%] 480s tests/test_trajectory.py::test_read_path[rst7] XFAIL (These referenc...) [ 49%] 480s tests/test_trajectory.py::test_read_path[gro] PASSED [ 49%] 480s tests/test_trajectory.py::test_write_path[nc] PASSED [ 49%] 480s tests/test_trajectory.py::test_write_path[h5] PASSED [ 49%] 480s tests/test_trajectory.py::test_write_path[xtc] PASSED [ 49%] 480s tests/test_trajectory.py::test_write_path[trr] PASSED [ 49%] 480s tests/test_trajectory.py::test_write_path[dcd] PASSED [ 50%] 480s tests/test_trajectory.py::test_write_path[mdcrd] SKIPPED (mdcrd can ...) [ 50%] 481s tests/test_trajectory.py::test_write_path[dtr] PASSED [ 50%] 481s tests/test_trajectory.py::test_write_path[xyz] PASSED [ 50%] 481s tests/test_trajectory.py::test_write_path[xyz.gz] PASSED [ 50%] 481s tests/test_trajectory.py::test_write_path[lammpstrj] PASSED [ 50%] 481s tests/test_trajectory.py::test_write_path[lh5] PASSED [ 50%] 481s tests/test_trajectory.py::test_write_path[pdb] PASSED [ 50%] 481s tests/test_trajectory.py::test_write_path[pdb.gz] PASSED [ 50%] 481s tests/test_trajectory.py::test_write_path[ncrst] SKIPPED (ncrst can ...) [ 50%] 481s tests/test_trajectory.py::test_write_path[rst7] SKIPPED (rst7 can on...) [ 50%] 481s tests/test_trajectory.py::test_write_path[gro] PASSED [ 51%] 481s tests/test_trajectory.py::test_read_write[nc-nc] PASSED [ 51%] 481s tests/test_trajectory.py::test_read_write[nc-h5] PASSED [ 51%] 481s tests/test_trajectory.py::test_read_write[nc-xtc] PASSED [ 51%] 481s tests/test_trajectory.py::test_read_write[nc-trr] PASSED [ 51%] 481s tests/test_trajectory.py::test_read_write[nc-dcd] PASSED [ 51%] 481s tests/test_trajectory.py::test_read_write[nc-mdcrd] SKIPPED (mdcrd c...) [ 51%] 484s tests/test_trajectory.py::test_read_write[nc-dtr] PASSED [ 51%] 485s tests/test_trajectory.py::test_read_write[nc-xyz] PASSED [ 51%] 485s tests/test_trajectory.py::test_read_write[nc-xyz.gz] PASSED [ 51%] 485s tests/test_trajectory.py::test_read_write[nc-lammpstrj] PASSED [ 51%] 485s tests/test_trajectory.py::test_read_write[nc-lh5] PASSED [ 51%] 486s tests/test_trajectory.py::test_read_write[nc-pdb] PASSED [ 52%] 487s tests/test_trajectory.py::test_read_write[nc-pdb.gz] PASSED [ 52%] 487s tests/test_trajectory.py::test_read_write[nc-ncrst] SKIPPED (ncrst c...) [ 52%] 487s tests/test_trajectory.py::test_read_write[nc-rst7] SKIPPED (rst7 can...) [ 52%] 487s tests/test_trajectory.py::test_read_write[nc-gro] PASSED [ 52%] 487s tests/test_trajectory.py::test_read_write[h5-nc] PASSED [ 52%] 487s tests/test_trajectory.py::test_read_write[h5-h5] PASSED [ 52%] 487s tests/test_trajectory.py::test_read_write[h5-xtc] PASSED [ 52%] 487s tests/test_trajectory.py::test_read_write[h5-trr] PASSED [ 52%] 487s tests/test_trajectory.py::test_read_write[h5-dcd] PASSED [ 52%] 487s tests/test_trajectory.py::test_read_write[h5-mdcrd] SKIPPED (mdcrd c...) [ 52%] 489s tests/test_trajectory.py::test_read_write[h5-dtr] PASSED [ 53%] 489s tests/test_trajectory.py::test_read_write[h5-xyz] PASSED [ 53%] 490s tests/test_trajectory.py::test_read_write[h5-xyz.gz] PASSED [ 53%] 490s tests/test_trajectory.py::test_read_write[h5-lammpstrj] PASSED [ 53%] 490s tests/test_trajectory.py::test_read_write[h5-lh5] PASSED [ 53%] 490s tests/test_trajectory.py::test_read_write[h5-pdb] PASSED [ 53%] 490s tests/test_trajectory.py::test_read_write[h5-pdb.gz] PASSED [ 53%] 490s tests/test_trajectory.py::test_read_write[h5-ncrst] SKIPPED (ncrst c...) [ 53%] 490s tests/test_trajectory.py::test_read_write[h5-rst7] SKIPPED (rst7 can...) [ 53%] 490s tests/test_trajectory.py::test_read_write[h5-gro] PASSED [ 53%] 491s tests/test_trajectory.py::test_read_write[xtc-nc] PASSED [ 53%] 491s tests/test_trajectory.py::test_read_write[xtc-h5] PASSED [ 54%] 491s tests/test_trajectory.py::test_read_write[xtc-xtc] PASSED [ 54%] 491s tests/test_trajectory.py::test_read_write[xtc-trr] PASSED [ 54%] 491s tests/test_trajectory.py::test_read_write[xtc-dcd] PASSED [ 54%] 491s tests/test_trajectory.py::test_read_write[xtc-mdcrd] SKIPPED (mdcrd ...) [ 54%] 493s tests/test_trajectory.py::test_read_write[xtc-dtr] PASSED [ 54%] 493s tests/test_trajectory.py::test_read_write[xtc-xyz] PASSED [ 54%] 493s tests/test_trajectory.py::test_read_write[xtc-xyz.gz] PASSED [ 54%] 493s tests/test_trajectory.py::test_read_write[xtc-lammpstrj] PASSED [ 54%] 493s tests/test_trajectory.py::test_read_write[xtc-lh5] PASSED [ 54%] 494s tests/test_trajectory.py::test_read_write[xtc-pdb] PASSED [ 54%] 494s tests/test_trajectory.py::test_read_write[xtc-pdb.gz] PASSED [ 54%] 494s tests/test_trajectory.py::test_read_write[xtc-ncrst] SKIPPED (ncrst ...) [ 55%] 494s tests/test_trajectory.py::test_read_write[xtc-rst7] SKIPPED (rst7 ca...) [ 55%] 494s tests/test_trajectory.py::test_read_write[xtc-gro] PASSED [ 55%] 494s tests/test_trajectory.py::test_read_write[trr-nc] PASSED [ 55%] 494s tests/test_trajectory.py::test_read_write[trr-h5] PASSED [ 55%] 494s tests/test_trajectory.py::test_read_write[trr-xtc] PASSED [ 55%] 494s tests/test_trajectory.py::test_read_write[trr-trr] PASSED [ 55%] 494s tests/test_trajectory.py::test_read_write[trr-dcd] PASSED [ 55%] 494s tests/test_trajectory.py::test_read_write[trr-mdcrd] SKIPPED (mdcrd ...) [ 55%] 496s tests/test_trajectory.py::test_read_write[trr-dtr] PASSED [ 55%] 496s tests/test_trajectory.py::test_read_write[trr-xyz] PASSED [ 55%] 496s tests/test_trajectory.py::test_read_write[trr-xyz.gz] PASSED [ 56%] 497s tests/test_trajectory.py::test_read_write[trr-lammpstrj] PASSED [ 56%] 497s tests/test_trajectory.py::test_read_write[trr-lh5] PASSED [ 56%] 497s tests/test_trajectory.py::test_read_write[trr-pdb] PASSED [ 56%] 497s tests/test_trajectory.py::test_read_write[trr-pdb.gz] PASSED [ 56%] 497s tests/test_trajectory.py::test_read_write[trr-ncrst] SKIPPED (ncrst ...) [ 56%] 497s tests/test_trajectory.py::test_read_write[trr-rst7] SKIPPED (rst7 ca...) [ 56%] 497s tests/test_trajectory.py::test_read_write[trr-gro] PASSED [ 56%] 497s tests/test_trajectory.py::test_read_write[dcd-nc] PASSED [ 56%] 497s tests/test_trajectory.py::test_read_write[dcd-h5] PASSED [ 56%] 497s tests/test_trajectory.py::test_read_write[dcd-xtc] PASSED [ 56%] 497s tests/test_trajectory.py::test_read_write[dcd-trr] PASSED [ 57%] 497s tests/test_trajectory.py::test_read_write[dcd-dcd] PASSED [ 57%] 497s tests/test_trajectory.py::test_read_write[dcd-mdcrd] SKIPPED (mdcrd ...) [ 57%] 499s tests/test_trajectory.py::test_read_write[dcd-dtr] PASSED [ 57%] 499s tests/test_trajectory.py::test_read_write[dcd-xyz] PASSED [ 57%] 500s tests/test_trajectory.py::test_read_write[dcd-xyz.gz] PASSED [ 57%] 500s tests/test_trajectory.py::test_read_write[dcd-lammpstrj] PASSED [ 57%] 500s tests/test_trajectory.py::test_read_write[dcd-lh5] PASSED [ 57%] 500s tests/test_trajectory.py::test_read_write[dcd-pdb] PASSED [ 57%] 501s tests/test_trajectory.py::test_read_write[dcd-pdb.gz] PASSED [ 57%] 501s tests/test_trajectory.py::test_read_write[dcd-ncrst] SKIPPED (ncrst ...) [ 57%] 501s tests/test_trajectory.py::test_read_write[dcd-rst7] SKIPPED (rst7 ca...) [ 57%] 501s tests/test_trajectory.py::test_read_write[dcd-gro] PASSED [ 58%] 501s tests/test_trajectory.py::test_read_write[mdcrd-nc] PASSED [ 58%] 501s tests/test_trajectory.py::test_read_write[mdcrd-h5] PASSED [ 58%] 501s tests/test_trajectory.py::test_read_write[mdcrd-xtc] PASSED [ 58%] 501s tests/test_trajectory.py::test_read_write[mdcrd-trr] PASSED [ 58%] 501s tests/test_trajectory.py::test_read_write[mdcrd-dcd] PASSED [ 58%] 501s tests/test_trajectory.py::test_read_write[mdcrd-mdcrd] SKIPPED (mdcr...) [ 58%] 501s tests/test_trajectory.py::test_read_write[mdcrd-dtr] SKIPPED (dtr ne...) [ 58%] 501s tests/test_trajectory.py::test_read_write[mdcrd-xyz] PASSED [ 58%] 502s tests/test_trajectory.py::test_read_write[mdcrd-xyz.gz] PASSED [ 58%] 502s tests/test_trajectory.py::test_read_write[mdcrd-lammpstrj] SKIPPED (...) [ 58%] 502s tests/test_trajectory.py::test_read_write[mdcrd-lh5] PASSED [ 59%] 502s tests/test_trajectory.py::test_read_write[mdcrd-pdb] PASSED [ 59%] 503s tests/test_trajectory.py::test_read_write[mdcrd-pdb.gz] PASSED [ 59%] 503s tests/test_trajectory.py::test_read_write[mdcrd-ncrst] SKIPPED (ncrs...) [ 59%] 503s tests/test_trajectory.py::test_read_write[mdcrd-rst7] SKIPPED (rst7 ...) [ 59%] 503s tests/test_trajectory.py::test_read_write[mdcrd-gro] PASSED [ 59%] 503s tests/test_trajectory.py::test_read_write[dtr-nc] PASSED [ 59%] 503s tests/test_trajectory.py::test_read_write[dtr-h5] PASSED [ 59%] 503s tests/test_trajectory.py::test_read_write[dtr-xtc] PASSED [ 59%] 503s tests/test_trajectory.py::test_read_write[dtr-trr] PASSED [ 59%] 503s tests/test_trajectory.py::test_read_write[dtr-dcd] PASSED [ 59%] 503s tests/test_trajectory.py::test_read_write[dtr-mdcrd] SKIPPED (mdcrd ...) [ 60%] 505s tests/test_trajectory.py::test_read_write[dtr-dtr] PASSED [ 60%] 505s tests/test_trajectory.py::test_read_write[dtr-xyz] PASSED [ 60%] 505s tests/test_trajectory.py::test_read_write[dtr-xyz.gz] PASSED [ 60%] 505s tests/test_trajectory.py::test_read_write[dtr-lammpstrj] PASSED [ 60%] 505s tests/test_trajectory.py::test_read_write[dtr-lh5] PASSED [ 60%] 506s tests/test_trajectory.py::test_read_write[dtr-pdb] PASSED [ 60%] 506s tests/test_trajectory.py::test_read_write[dtr-pdb.gz] PASSED [ 60%] 506s tests/test_trajectory.py::test_read_write[dtr-ncrst] SKIPPED (ncrst ...) [ 60%] 506s tests/test_trajectory.py::test_read_write[dtr-rst7] SKIPPED (rst7 ca...) [ 60%] 506s tests/test_trajectory.py::test_read_write[dtr-gro] PASSED [ 60%] 506s tests/test_trajectory.py::test_read_write[xyz-nc] PASSED [ 60%] 506s tests/test_trajectory.py::test_read_write[xyz-h5] PASSED [ 61%] 506s tests/test_trajectory.py::test_read_write[xyz-xtc] PASSED [ 61%] 506s tests/test_trajectory.py::test_read_write[xyz-trr] PASSED [ 61%] 506s tests/test_trajectory.py::test_read_write[xyz-dcd] PASSED [ 61%] 506s tests/test_trajectory.py::test_read_write[xyz-mdcrd] SKIPPED (mdcrd ...) [ 61%] 506s tests/test_trajectory.py::test_read_write[xyz-dtr] SKIPPED (dtr need...) [ 61%] 507s tests/test_trajectory.py::test_read_write[xyz-xyz] PASSED [ 61%] 507s tests/test_trajectory.py::test_read_write[xyz-xyz.gz] PASSED [ 61%] 507s tests/test_trajectory.py::test_read_write[xyz-lammpstrj] SKIPPED (la...) [ 61%] 507s tests/test_trajectory.py::test_read_write[xyz-lh5] PASSED [ 61%] 507s tests/test_trajectory.py::test_read_write[xyz-pdb] PASSED [ 61%] 507s tests/test_trajectory.py::test_read_write[xyz-pdb.gz] PASSED [ 62%] 507s tests/test_trajectory.py::test_read_write[xyz-ncrst] SKIPPED (ncrst ...) [ 62%] 507s tests/test_trajectory.py::test_read_write[xyz-rst7] SKIPPED (rst7 ca...) [ 62%] 508s tests/test_trajectory.py::test_read_write[xyz-gro] PASSED [ 62%] 508s tests/test_trajectory.py::test_read_write[xyz.gz-nc] PASSED [ 62%] 508s tests/test_trajectory.py::test_read_write[xyz.gz-h5] PASSED [ 62%] 508s tests/test_trajectory.py::test_read_write[xyz.gz-xtc] PASSED [ 62%] 508s tests/test_trajectory.py::test_read_write[xyz.gz-trr] PASSED [ 62%] 508s tests/test_trajectory.py::test_read_write[xyz.gz-dcd] PASSED [ 62%] 508s tests/test_trajectory.py::test_read_write[xyz.gz-mdcrd] SKIPPED (mdc...) [ 62%] 508s tests/test_trajectory.py::test_read_write[xyz.gz-dtr] SKIPPED (dtr n...) [ 62%] 508s tests/test_trajectory.py::test_read_write[xyz.gz-xyz] PASSED [ 63%] 508s tests/test_trajectory.py::test_read_write[xyz.gz-xyz.gz] PASSED [ 63%] 508s tests/test_trajectory.py::test_read_write[xyz.gz-lammpstrj] SKIPPED [ 63%] 508s tests/test_trajectory.py::test_read_write[xyz.gz-lh5] PASSED [ 63%] 508s tests/test_trajectory.py::test_read_write[xyz.gz-pdb] PASSED [ 63%] 509s tests/test_trajectory.py::test_read_write[xyz.gz-pdb.gz] PASSED [ 63%] 509s tests/test_trajectory.py::test_read_write[xyz.gz-ncrst] SKIPPED (ncr...) [ 63%] 509s tests/test_trajectory.py::test_read_write[xyz.gz-rst7] SKIPPED (rst7...) [ 63%] 509s tests/test_trajectory.py::test_read_write[xyz.gz-gro] PASSED [ 63%] 509s tests/test_trajectory.py::test_read_write[lammpstrj-nc] PASSED [ 63%] 509s tests/test_trajectory.py::test_read_write[lammpstrj-h5] PASSED [ 63%] 509s tests/test_trajectory.py::test_read_write[lammpstrj-xtc] PASSED [ 63%] 509s tests/test_trajectory.py::test_read_write[lammpstrj-trr] PASSED [ 64%] 509s tests/test_trajectory.py::test_read_write[lammpstrj-dcd] PASSED [ 64%] 509s tests/test_trajectory.py::test_read_write[lammpstrj-mdcrd] SKIPPED (...) [ 64%] 511s tests/test_trajectory.py::test_read_write[lammpstrj-dtr] PASSED [ 64%] 511s tests/test_trajectory.py::test_read_write[lammpstrj-xyz] PASSED [ 64%] 512s tests/test_trajectory.py::test_read_write[lammpstrj-xyz.gz] PASSED [ 64%] 512s tests/test_trajectory.py::test_read_write[lammpstrj-lammpstrj] PASSED [ 64%] 512s tests/test_trajectory.py::test_read_write[lammpstrj-lh5] PASSED [ 64%] 512s tests/test_trajectory.py::test_read_write[lammpstrj-pdb] PASSED [ 64%] 512s tests/test_trajectory.py::test_read_write[lammpstrj-pdb.gz] PASSED [ 64%] 513s tests/test_trajectory.py::test_read_write[lammpstrj-ncrst] SKIPPED (...) [ 64%] 513s tests/test_trajectory.py::test_read_write[lammpstrj-rst7] SKIPPED (r...) [ 65%] 513s tests/test_trajectory.py::test_read_write[lammpstrj-gro] PASSED [ 65%] 513s tests/test_trajectory.py::test_read_write[lh5-nc] PASSED [ 65%] 513s tests/test_trajectory.py::test_read_write[lh5-h5] PASSED [ 65%] 513s tests/test_trajectory.py::test_read_write[lh5-xtc] PASSED [ 65%] 513s tests/test_trajectory.py::test_read_write[lh5-trr] PASSED [ 65%] 513s tests/test_trajectory.py::test_read_write[lh5-dcd] PASSED [ 65%] 513s tests/test_trajectory.py::test_read_write[lh5-mdcrd] SKIPPED (mdcrd ...) [ 65%] 513s tests/test_trajectory.py::test_read_write[lh5-dtr] SKIPPED (dtr need...) [ 65%] 513s tests/test_trajectory.py::test_read_write[lh5-xyz] PASSED [ 65%] 513s tests/test_trajectory.py::test_read_write[lh5-xyz.gz] PASSED [ 65%] 513s tests/test_trajectory.py::test_read_write[lh5-lammpstrj] SKIPPED (la...) [ 66%] 513s tests/test_trajectory.py::test_read_write[lh5-lh5] PASSED [ 66%] 513s tests/test_trajectory.py::test_read_write[lh5-pdb] PASSED [ 66%] 514s tests/test_trajectory.py::test_read_write[lh5-pdb.gz] PASSED [ 66%] 514s tests/test_trajectory.py::test_read_write[lh5-ncrst] SKIPPED (ncrst ...) [ 66%] 514s tests/test_trajectory.py::test_read_write[lh5-rst7] SKIPPED (rst7 ca...) [ 66%] 514s tests/test_trajectory.py::test_read_write[lh5-gro] PASSED [ 66%] 514s tests/test_trajectory.py::test_read_write[pdb-nc] PASSED [ 66%] 514s tests/test_trajectory.py::test_read_write[pdb-h5] PASSED [ 66%] 514s tests/test_trajectory.py::test_read_write[pdb-xtc] PASSED [ 66%] 515s tests/test_trajectory.py::test_read_write[pdb-trr] PASSED [ 66%] 515s tests/test_trajectory.py::test_read_write[pdb-dcd] PASSED [ 66%] 515s tests/test_trajectory.py::test_read_write[pdb-mdcrd] SKIPPED (mdcrd ...) [ 67%] 517s tests/test_trajectory.py::test_read_write[pdb-dtr] PASSED [ 67%] 517s tests/test_trajectory.py::test_read_write[pdb-xyz] PASSED [ 67%] 518s tests/test_trajectory.py::test_read_write[pdb-xyz.gz] PASSED [ 67%] 518s tests/test_trajectory.py::test_read_write[pdb-lammpstrj] PASSED [ 67%] 518s tests/test_trajectory.py::test_read_write[pdb-lh5] PASSED [ 67%] 518s tests/test_trajectory.py::test_read_write[pdb-pdb] PASSED [ 67%] 519s tests/test_trajectory.py::test_read_write[pdb-pdb.gz] PASSED [ 67%] 519s tests/test_trajectory.py::test_read_write[pdb-ncrst] SKIPPED (ncrst ...) [ 67%] 519s tests/test_trajectory.py::test_read_write[pdb-rst7] SKIPPED (rst7 ca...) [ 67%] 519s tests/test_trajectory.py::test_read_write[pdb-gro] PASSED [ 67%] 520s tests/test_trajectory.py::test_read_write[pdb.gz-nc] PASSED [ 68%] 520s tests/test_trajectory.py::test_read_write[pdb.gz-h5] PASSED [ 68%] 520s tests/test_trajectory.py::test_read_write[pdb.gz-xtc] PASSED [ 68%] 520s tests/test_trajectory.py::test_read_write[pdb.gz-trr] PASSED [ 68%] 520s tests/test_trajectory.py::test_read_write[pdb.gz-dcd] PASSED [ 68%] 520s tests/test_trajectory.py::test_read_write[pdb.gz-mdcrd] SKIPPED (mdc...) [ 68%] 522s tests/test_trajectory.py::test_read_write[pdb.gz-dtr] PASSED [ 68%] 523s tests/test_trajectory.py::test_read_write[pdb.gz-xyz] PASSED [ 68%] 523s tests/test_trajectory.py::test_read_write[pdb.gz-xyz.gz] PASSED [ 68%] 523s tests/test_trajectory.py::test_read_write[pdb.gz-lammpstrj] PASSED [ 68%] 524s tests/test_trajectory.py::test_read_write[pdb.gz-lh5] PASSED [ 68%] 524s tests/test_trajectory.py::test_read_write[pdb.gz-pdb] PASSED [ 69%] 524s tests/test_trajectory.py::test_read_write[pdb.gz-pdb.gz] PASSED [ 69%] 524s tests/test_trajectory.py::test_read_write[pdb.gz-ncrst] SKIPPED (ncr...) [ 69%] 524s tests/test_trajectory.py::test_read_write[pdb.gz-rst7] SKIPPED (rst7...) [ 69%] 525s tests/test_trajectory.py::test_read_write[pdb.gz-gro] PASSED [ 69%] 525s tests/test_trajectory.py::test_read_write[ncrst-nc] XFAIL (These ref...) [ 69%] 525s tests/test_trajectory.py::test_read_write[ncrst-h5] XFAIL (These ref...) [ 69%] 525s tests/test_trajectory.py::test_read_write[ncrst-xtc] XFAIL (These re...) [ 69%] 525s tests/test_trajectory.py::test_read_write[ncrst-trr] XFAIL (These re...) [ 69%] 525s tests/test_trajectory.py::test_read_write[ncrst-dcd] XFAIL (These re...) [ 69%] 525s tests/test_trajectory.py::test_read_write[ncrst-mdcrd] XFAIL (These ...) [ 69%] 525s tests/test_trajectory.py::test_read_write[ncrst-dtr] XFAIL (These re...) [ 69%] 525s tests/test_trajectory.py::test_read_write[ncrst-xyz] XFAIL (These re...) [ 70%] 525s tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] XFAIL (These...) [ 70%] 525s tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] XFAIL (Th...) [ 70%] 525s tests/test_trajectory.py::test_read_write[ncrst-lh5] XFAIL (These re...) [ 70%] 525s tests/test_trajectory.py::test_read_write[ncrst-pdb] XFAIL (These re...) [ 70%] 525s tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] XFAIL (These...) [ 70%] 525s tests/test_trajectory.py::test_read_write[ncrst-ncrst] XFAIL (These ...) [ 70%] 525s tests/test_trajectory.py::test_read_write[ncrst-rst7] XFAIL (These r...) [ 70%] 525s tests/test_trajectory.py::test_read_write[ncrst-gro] XFAIL (These re...) [ 70%] 525s tests/test_trajectory.py::test_read_write[rst7-nc] XFAIL (These refe...) [ 70%] 525s tests/test_trajectory.py::test_read_write[rst7-h5] XFAIL (These refe...) [ 70%] 525s tests/test_trajectory.py::test_read_write[rst7-xtc] XFAIL (These ref...) [ 71%] 525s tests/test_trajectory.py::test_read_write[rst7-trr] XFAIL (These ref...) [ 71%] 525s tests/test_trajectory.py::test_read_write[rst7-dcd] XFAIL (These ref...) [ 71%] 525s tests/test_trajectory.py::test_read_write[rst7-mdcrd] XFAIL (These r...) [ 71%] 525s tests/test_trajectory.py::test_read_write[rst7-dtr] XFAIL (These ref...) [ 71%] 525s tests/test_trajectory.py::test_read_write[rst7-xyz] XFAIL (These ref...) [ 71%] 525s tests/test_trajectory.py::test_read_write[rst7-xyz.gz] XFAIL (These ...) [ 71%] 525s tests/test_trajectory.py::test_read_write[rst7-lammpstrj] XFAIL (The...) [ 71%] 526s tests/test_trajectory.py::test_read_write[rst7-lh5] XFAIL (These ref...) [ 71%] 526s tests/test_trajectory.py::test_read_write[rst7-pdb] XFAIL (These ref...) [ 71%] 526s tests/test_trajectory.py::test_read_write[rst7-pdb.gz] XFAIL (These ...) [ 71%] 526s tests/test_trajectory.py::test_read_write[rst7-ncrst] XFAIL (These r...) [ 72%] 526s tests/test_trajectory.py::test_read_write[rst7-rst7] XFAIL (These re...) [ 72%] 526s tests/test_trajectory.py::test_read_write[rst7-gro] XFAIL (These ref...) [ 72%] 526s tests/test_trajectory.py::test_read_write[gro-nc] PASSED [ 72%] 526s tests/test_trajectory.py::test_read_write[gro-h5] PASSED [ 72%] 526s tests/test_trajectory.py::test_read_write[gro-xtc] PASSED [ 72%] 526s tests/test_trajectory.py::test_read_write[gro-trr] PASSED [ 72%] 526s tests/test_trajectory.py::test_read_write[gro-dcd] PASSED [ 72%] 526s tests/test_trajectory.py::test_read_write[gro-mdcrd] SKIPPED (mdcrd ...) [ 72%] 528s tests/test_trajectory.py::test_read_write[gro-dtr] PASSED [ 72%] 528s tests/test_trajectory.py::test_read_write[gro-xyz] PASSED [ 72%] 528s tests/test_trajectory.py::test_read_write[gro-xyz.gz] PASSED [ 72%] 528s tests/test_trajectory.py::test_read_write[gro-lammpstrj] PASSED [ 73%] 528s tests/test_trajectory.py::test_read_write[gro-lh5] PASSED [ 73%] 529s tests/test_trajectory.py::test_read_write[gro-pdb] PASSED [ 73%] 529s tests/test_trajectory.py::test_read_write[gro-pdb.gz] PASSED [ 73%] 529s tests/test_trajectory.py::test_read_write[gro-ncrst] SKIPPED (ncrst ...) [ 73%] 529s tests/test_trajectory.py::test_read_write[gro-rst7] SKIPPED (rst7 ca...) [ 73%] 529s tests/test_trajectory.py::test_read_write[gro-gro] PASSED [ 73%] 529s tests/test_trajectory.py::test_load[nc] PASSED [ 73%] 529s tests/test_trajectory.py::test_load[h5] PASSED [ 73%] 529s tests/test_trajectory.py::test_load[xtc] PASSED [ 73%] 529s tests/test_trajectory.py::test_load[trr] PASSED [ 73%] 529s tests/test_trajectory.py::test_load[dcd] PASSED [ 74%] 530s tests/test_trajectory.py::test_load[mdcrd] PASSED [ 74%] 530s tests/test_trajectory.py::test_load[dtr] PASSED [ 74%] 530s tests/test_trajectory.py::test_load[xyz] PASSED [ 74%] 530s tests/test_trajectory.py::test_load[xyz.gz] PASSED [ 74%] 530s tests/test_trajectory.py::test_load[lammpstrj] PASSED [ 74%] 530s tests/test_trajectory.py::test_load[lh5] PASSED [ 74%] 531s tests/test_trajectory.py::test_load[pdb] PASSED [ 74%] 533s tests/test_trajectory.py::test_load[pdb.gz] PASSED [ 74%] 533s tests/test_trajectory.py::test_load[ncrst] XFAIL (These reference fi...) [ 74%] 533s tests/test_trajectory.py::test_load[rst7] XFAIL (These reference fil...) [ 74%] 533s tests/test_trajectory.py::test_load[gro] PASSED [ 75%] 533s tests/test_trajectory.py::test_hdf5 PASSED [ 75%] 533s tests/test_trajectory.py::test_center PASSED [ 75%] 533s tests/test_trajectory.py::test_center_aind PASSED [ 75%] 533s tests/test_trajectory.py::test_float_atom_indices_exception[nc] PASSED [ 75%] 533s tests/test_trajectory.py::test_float_atom_indices_exception[h5] PASSED [ 75%] 533s tests/test_trajectory.py::test_float_atom_indices_exception[xtc] PASSED [ 75%] 533s tests/test_trajectory.py::test_float_atom_indices_exception[trr] PASSED [ 75%] 533s tests/test_trajectory.py::test_float_atom_indices_exception[dcd] PASSED [ 75%] 533s tests/test_trajectory.py::test_float_atom_indices_exception[mdcrd] PASSED [ 75%] 533s tests/test_trajectory.py::test_float_atom_indices_exception[dtr] PASSED [ 75%] 533s tests/test_trajectory.py::test_float_atom_indices_exception[xyz] PASSED [ 75%] 533s tests/test_trajectory.py::test_float_atom_indices_exception[xyz.gz] PASSED [ 76%] 533s tests/test_trajectory.py::test_float_atom_indices_exception[lammpstrj] PASSED [ 76%] 533s tests/test_trajectory.py::test_float_atom_indices_exception[lh5] PASSED [ 76%] 533s tests/test_trajectory.py::test_float_atom_indices_exception[pdb] PASSED [ 76%] 533s tests/test_trajectory.py::test_float_atom_indices_exception[pdb.gz] PASSED [ 76%] 533s tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] XFAIL [ 76%] 533s tests/test_trajectory.py::test_float_atom_indices_exception[rst7] XFAIL [ 76%] 533s tests/test_trajectory.py::test_float_atom_indices_exception[gro] PASSED [ 76%] 533s tests/test_trajectory.py::test_restrict_atoms PASSED [ 76%] 533s tests/test_trajectory.py::test_restrict_atoms_not_inplace PASSED [ 76%] 533s tests/test_trajectory.py::test_array_vs_matrix PASSED [ 76%] 533s tests/test_trajectory.py::test_pdb_unitcell_loadsave PASSED [ 77%] 533s tests/test_trajectory.py::test_load_combination[nc] PASSED [ 77%] 533s tests/test_trajectory.py::test_load_combination[h5] PASSED [ 77%] 533s tests/test_trajectory.py::test_load_combination[xtc] PASSED [ 77%] 533s tests/test_trajectory.py::test_load_combination[trr] PASSED [ 77%] 533s tests/test_trajectory.py::test_load_combination[dcd] PASSED [ 77%] 533s tests/test_trajectory.py::test_load_combination[mdcrd] PASSED [ 77%] 533s tests/test_trajectory.py::test_load_combination[dtr] PASSED [ 77%] 533s tests/test_trajectory.py::test_load_combination[xyz] PASSED [ 77%] 533s tests/test_trajectory.py::test_load_combination[xyz.gz] PASSED [ 77%] 534s tests/test_trajectory.py::test_load_combination[lammpstrj] PASSED [ 77%] 534s tests/test_trajectory.py::test_load_combination[lh5] PASSED [ 78%] 534s tests/test_trajectory.py::test_load_combination[pdb] PASSED [ 78%] 534s tests/test_trajectory.py::test_load_combination[pdb.gz] PASSED [ 78%] 534s tests/test_trajectory.py::test_load_combination[ncrst] XFAIL (These ...) [ 78%] 535s tests/test_trajectory.py::test_load_combination[rst7] XFAIL (These r...) [ 78%] 535s tests/test_trajectory.py::test_load_combination[gro] PASSED [ 78%] 535s tests/test_trajectory.py::test_no_topology PASSED [ 78%] 535s tests/test_trajectory.py::test_join PASSED [ 78%] 535s tests/test_trajectory.py::test_md_join PASSED [ 78%] 535s tests/test_trajectory.py::test_stack_1 PASSED [ 78%] 535s tests/test_trajectory.py::test_stack_2 PASSED [ 78%] 535s tests/test_trajectory.py::test_seek_read_mode[nc] PASSED [ 78%] 535s tests/test_trajectory.py::test_seek_read_mode[h5] PASSED [ 79%] 535s tests/test_trajectory.py::test_seek_read_mode[xtc] PASSED [ 79%] 535s tests/test_trajectory.py::test_seek_read_mode[trr] PASSED [ 79%] 535s tests/test_trajectory.py::test_seek_read_mode[dcd] PASSED [ 79%] 535s tests/test_trajectory.py::test_seek_read_mode[mdcrd] PASSED [ 79%] 535s tests/test_trajectory.py::test_seek_read_mode[dtr] PASSED [ 79%] 535s tests/test_trajectory.py::test_seek_read_mode[xyz] PASSED [ 79%] 535s tests/test_trajectory.py::test_seek_read_mode[xyz.gz] XFAIL (This is...) [ 79%] 535s tests/test_trajectory.py::test_seek_read_mode[lammpstrj] PASSED [ 79%] 535s tests/test_trajectory.py::test_seek_read_mode[lh5] PASSED [ 79%] 535s tests/test_trajectory.py::test_seek_read_mode[pdb] XFAIL (PDB Files ...) [ 79%] 535s tests/test_trajectory.py::test_seek_read_mode[pdb.gz] XFAIL (PDB Fil...) [ 80%] 535s tests/test_trajectory.py::test_seek_read_mode[ncrst] XFAIL (These re...) [ 80%] 535s tests/test_trajectory.py::test_seek_read_mode[rst7] XFAIL (These ref...) [ 80%] 535s tests/test_trajectory.py::test_seek_read_mode[gro] XFAIL (This is br...) [ 80%] 535s tests/test_trajectory.py::test_load_frame[nc] PASSED [ 80%] 535s tests/test_trajectory.py::test_load_frame[h5] PASSED [ 80%] 535s tests/test_trajectory.py::test_load_frame[xtc] PASSED [ 80%] 535s tests/test_trajectory.py::test_load_frame[trr] PASSED [ 80%] 535s tests/test_trajectory.py::test_load_frame[dcd] PASSED [ 80%] 536s tests/test_trajectory.py::test_load_frame[mdcrd] PASSED [ 80%] 536s tests/test_trajectory.py::test_load_frame[dtr] XFAIL (DTR doesn't lo...) [ 80%] 536s tests/test_trajectory.py::test_load_frame[xyz] PASSED [ 81%] 536s tests/test_trajectory.py::test_load_frame[xyz.gz] PASSED [ 81%] 536s tests/test_trajectory.py::test_load_frame[lammpstrj] PASSED [ 81%] 536s tests/test_trajectory.py::test_load_frame[lh5] PASSED [ 81%] 536s tests/test_trajectory.py::test_load_frame[pdb] PASSED [ 81%] 536s tests/test_trajectory.py::test_load_frame[pdb.gz] PASSED [ 81%] 536s tests/test_trajectory.py::test_load_frame[ncrst] XFAIL (These refere...) [ 81%] 536s tests/test_trajectory.py::test_load_frame[rst7] XFAIL (These referen...) [ 81%] 536s tests/test_trajectory.py::test_load_frame[gro] XFAIL (Gro doesn't im...) [ 81%] 537s tests/test_trajectory.py::test_load_frame_2eqq PASSED [ 81%] 537s tests/test_trajectory.py::test_iterload[nc] PASSED [ 81%] 537s tests/test_trajectory.py::test_iterload[h5] PASSED [ 81%] 537s tests/test_trajectory.py::test_iterload[xtc] PASSED [ 82%] 537s tests/test_trajectory.py::test_iterload[trr] PASSED [ 82%] 537s tests/test_trajectory.py::test_iterload[dcd] PASSED [ 82%] 537s tests/test_trajectory.py::test_iterload[mdcrd] PASSED [ 82%] 537s tests/test_trajectory.py::test_iterload[dtr] XFAIL (This is broken w...) [ 82%] 537s tests/test_trajectory.py::test_iterload[xyz] PASSED [ 82%] 537s tests/test_trajectory.py::test_iterload[xyz.gz] PASSED [ 82%] 537s tests/test_trajectory.py::test_iterload[lammpstrj] PASSED [ 82%] 537s tests/test_trajectory.py::test_iterload[lh5] PASSED [ 82%] 537s tests/test_trajectory.py::test_iterload[pdb] PASSED [ 82%] 537s tests/test_trajectory.py::test_iterload[pdb.gz] PASSED [ 82%] 537s tests/test_trajectory.py::test_iterload[ncrst] SKIPPED (Only 1 frame...) [ 83%] 537s tests/test_trajectory.py::test_iterload[rst7] SKIPPED (Only 1 frame ...) [ 83%] 537s tests/test_trajectory.py::test_iterload[gro] PASSED [ 83%] 541s tests/test_trajectory.py::test_iterload_skip[nc] PASSED [ 83%] 543s tests/test_trajectory.py::test_iterload_skip[h5] PASSED [ 83%] 545s tests/test_trajectory.py::test_iterload_skip[xtc] PASSED [ 83%] 546s tests/test_trajectory.py::test_iterload_skip[trr] PASSED [ 83%] 547s tests/test_trajectory.py::test_iterload_skip[dcd] PASSED [ 83%] 549s tests/test_trajectory.py::test_iterload_skip[mdcrd] PASSED [ 83%] 549s tests/test_trajectory.py::test_iterload_skip[dtr] PASSED [ 83%] 550s tests/test_trajectory.py::test_iterload_skip[xyz] PASSED [ 83%] 551s tests/test_trajectory.py::test_iterload_skip[xyz.gz] PASSED [ 84%] 552s tests/test_trajectory.py::test_iterload_skip[lammpstrj] PASSED [ 84%] 554s tests/test_trajectory.py::test_iterload_skip[lh5] PASSED [ 84%] 554s tests/test_trajectory.py::test_iterload_skip[pdb] XFAIL (PDB Iterloa...) [ 84%] 554s tests/test_trajectory.py::test_iterload_skip[pdb.gz] XFAIL (PDB Iter...) [ 84%] 554s tests/test_trajectory.py::test_iterload_skip[ncrst] XFAIL (These ref...) [ 84%] 554s tests/test_trajectory.py::test_iterload_skip[rst7] XFAIL (These refe...) [ 84%] 554s tests/test_trajectory.py::test_iterload_skip[gro] XFAIL (Not impleme...) [ 84%] 555s tests/test_trajectory.py::test_iterload_chunk_dcd PASSED [ 84%] 555s tests/test_trajectory.py::test_save_load[nc] PASSED [ 84%] 555s tests/test_trajectory.py::test_save_load[h5] PASSED [ 84%] 555s tests/test_trajectory.py::test_save_load[xtc] PASSED [ 84%] 555s tests/test_trajectory.py::test_save_load[trr] PASSED [ 85%] 555s tests/test_trajectory.py::test_save_load[dcd] PASSED [ 85%] 555s tests/test_trajectory.py::test_save_load[mdcrd] PASSED [ 85%] 555s tests/test_trajectory.py::test_save_load[dtr] PASSED [ 85%] 555s tests/test_trajectory.py::test_save_load[xyz] PASSED [ 85%] 555s tests/test_trajectory.py::test_save_load[xyz.gz] PASSED [ 85%] 555s tests/test_trajectory.py::test_save_load[lammpstrj] PASSED [ 85%] 555s tests/test_trajectory.py::test_save_load[lh5] PASSED [ 85%] 555s tests/test_trajectory.py::test_save_load[pdb] PASSED [ 85%] 555s tests/test_trajectory.py::test_save_load[pdb.gz] PASSED [ 85%] 555s tests/test_trajectory.py::test_save_load[ncrst] PASSED [ 85%] 555s tests/test_trajectory.py::test_save_load[rst7] PASSED [ 86%] 555s tests/test_trajectory.py::test_save_load[gro] PASSED [ 86%] 555s tests/test_trajectory.py::test_force_overwrite[nc] PASSED [ 86%] 555s tests/test_trajectory.py::test_force_overwrite[h5] PASSED [ 86%] 555s tests/test_trajectory.py::test_force_overwrite[xtc] PASSED [ 86%] 555s tests/test_trajectory.py::test_force_overwrite[trr] PASSED [ 86%] 555s tests/test_trajectory.py::test_force_overwrite[dcd] PASSED [ 86%] 555s tests/test_trajectory.py::test_force_overwrite[mdcrd] PASSED [ 86%] 555s tests/test_trajectory.py::test_force_overwrite[dtr] XFAIL (This is b...) [ 86%] 555s tests/test_trajectory.py::test_force_overwrite[xyz] PASSED [ 86%] 555s tests/test_trajectory.py::test_force_overwrite[xyz.gz] PASSED [ 86%] 555s tests/test_trajectory.py::test_force_overwrite[lammpstrj] PASSED [ 87%] 555s tests/test_trajectory.py::test_force_overwrite[lh5] PASSED [ 87%] 555s tests/test_trajectory.py::test_force_overwrite[pdb] PASSED [ 87%] 555s tests/test_trajectory.py::test_force_overwrite[pdb.gz] PASSED [ 87%] 555s tests/test_trajectory.py::test_force_overwrite[ncrst] PASSED [ 87%] 555s tests/test_trajectory.py::test_force_overwrite[rst7] PASSED [ 87%] 555s tests/test_trajectory.py::test_force_overwrite[gro] PASSED [ 87%] 555s tests/test_trajectory.py::test_force_noverwrite[nc] PASSED [ 87%] 555s tests/test_trajectory.py::test_force_noverwrite[h5] PASSED [ 87%] 555s tests/test_trajectory.py::test_force_noverwrite[xtc] PASSED [ 87%] 555s tests/test_trajectory.py::test_force_noverwrite[trr] PASSED [ 87%] 555s tests/test_trajectory.py::test_force_noverwrite[dcd] PASSED [ 87%] 555s tests/test_trajectory.py::test_force_noverwrite[mdcrd] PASSED [ 88%] 555s tests/test_trajectory.py::test_force_noverwrite[dtr] PASSED [ 88%] 555s tests/test_trajectory.py::test_force_noverwrite[xyz] PASSED [ 88%] 555s tests/test_trajectory.py::test_force_noverwrite[xyz.gz] PASSED [ 88%] 555s tests/test_trajectory.py::test_force_noverwrite[lammpstrj] PASSED [ 88%] 555s tests/test_trajectory.py::test_force_noverwrite[lh5] PASSED [ 88%] 555s tests/test_trajectory.py::test_force_noverwrite[pdb] PASSED [ 88%] 555s tests/test_trajectory.py::test_force_noverwrite[pdb.gz] PASSED [ 88%] 555s tests/test_trajectory.py::test_force_noverwrite[ncrst] PASSED [ 88%] 555s tests/test_trajectory.py::test_force_noverwrite[rst7] PASSED [ 88%] 555s tests/test_trajectory.py::test_force_noverwrite[gro] PASSED [ 88%] 555s tests/test_trajectory.py::test_open_and_load PASSED [ 89%] 555s tests/test_trajectory.py::test_length PASSED [ 89%] 555s tests/test_trajectory.py::test_unitcell[nc] PASSED [ 89%] 555s tests/test_trajectory.py::test_unitcell[h5] PASSED [ 89%] 555s tests/test_trajectory.py::test_unitcell[xtc] PASSED [ 89%] 555s tests/test_trajectory.py::test_unitcell[trr] PASSED [ 89%] 555s tests/test_trajectory.py::test_unitcell[dcd] PASSED [ 89%] 555s tests/test_trajectory.py::test_unitcell[mdcrd] PASSED [ 89%] 555s tests/test_trajectory.py::test_unitcell[dtr] XFAIL (dtr seems to nee...) [ 89%] 555s tests/test_trajectory.py::test_unitcell[xyz] PASSED [ 89%] 555s tests/test_trajectory.py::test_unitcell[xyz.gz] PASSED [ 89%] 555s tests/test_trajectory.py::test_unitcell[lammpstrj] XFAIL (lammpstrj ...) [ 90%] 556s tests/test_trajectory.py::test_unitcell[lh5] PASSED [ 90%] 556s tests/test_trajectory.py::test_unitcell[pdb] PASSED [ 90%] 556s tests/test_trajectory.py::test_unitcell[pdb.gz] PASSED [ 90%] 556s tests/test_trajectory.py::test_unitcell[ncrst] XFAIL (ncrst seems to...) [ 90%] 556s tests/test_trajectory.py::test_unitcell[rst7] XFAIL (rst7 seems to n...) [ 90%] 556s tests/test_trajectory.py::test_unitcell[gro] PASSED [ 90%] 556s tests/test_trajectory.py::test_chunk0_iterload PASSED [ 90%] 556s tests/test_trajectory.py::test_hashing PASSED [ 90%] 556s tests/test_trajectory.py::test_smooth PASSED [ 90%] 556s tests/test_trajectory.py::test_load_pdb_no_standard_names PASSED [ 90%] 556s tests/test_trajectory.py::test_load_with_atom_indices PASSED [ 90%] 556s tests/test_trajectory.py::test_atom_slicing PASSED [ 91%] 556s tests/test_trajectory.py::test_load_with_frame PASSED [ 91%] 556s tests/test_trajectory.py::test_add_remove_atoms PASSED [ 91%] 556s tests/test_trr.py::test_1 PASSED [ 91%] 556s tests/test_trr.py::test_read_stride PASSED [ 91%] 556s tests/test_trr.py::test_read_stride_n_frames PASSED [ 91%] 556s tests/test_trr.py::test_read_stride_offsets PASSED [ 91%] 556s tests/test_trr.py::test_read_stride_n_frames_offsets PASSED [ 91%] 556s tests/test_trr.py::test_read_stride_switching PASSED [ 91%] 556s tests/test_trr.py::test_write_read PASSED [ 91%] 556s tests/test_trr.py::test_read_atomindices_1 PASSED [ 91%] 556s tests/test_trr.py::test_read_atomindices_2 PASSED [ 92%] 556s tests/test_trr.py::test_deficient_shape PASSED [ 92%] 556s tests/test_trr.py::test_ragged_1 PASSED [ 92%] 556s tests/test_trr.py::test_ragged_2 PASSED [ 92%] 556s tests/test_trr.py::test_malformed PASSED [ 92%] 556s tests/test_trr.py::test_tell PASSED [ 92%] 556s tests/test_trr.py::test_seek PASSED [ 92%] 556s tests/test_trr.py::test_get_velocities PASSED [ 92%] 556s tests/test_trr.py::test_get_forces PASSED [ 92%] 557s tests/test_trr.py::test_get_velocities_and_forces PASSED [ 92%] 557s tests/test_trr.py::test_get_velocities_forces_atom_indices_1 PASSED [ 92%] 557s tests/test_trr.py::test_get_velocities_forces_atom_indices_2 PASSED [ 93%] 557s tests/test_trr.py::test_read_velocities_do_not_exist PASSED [ 93%] 557s tests/test_trr.py::test_read_forces_do_not_exist PASSED [ 93%] 557s tests/test_utils.py::test_unitcell_0 PASSED [ 93%] 557s tests/test_utils.py::test_unitcell_1 PASSED [ 93%] 557s tests/test_utils.py::test_ensure_type_1 PASSED [ 93%] 557s tests/test_utils.py::test_ensure_type_2 PASSED [ 93%] 557s tests/test_utils.py::test_ensure_type_25 PASSED [ 93%] 557s tests/test_utils.py::test_ensure_type_3 PASSED [ 93%] 557s tests/test_utils.py::test_ensure_type_4 PASSED [ 93%] 557s tests/test_utils.py::test_ensure_type_5 PASSED [ 93%] 557s tests/test_utils.py::test_ensure_type_6 PASSED [ 93%] 557s tests/test_utils.py::test_ensure_type_7 PASSED [ 94%] 557s tests/test_utils.py::test_ensure_type_8 PASSED [ 94%] 557s tests/test_utils.py::test_ensure_type_9 PASSED [ 94%] 557s tests/test_utils.py::test_ensure_type_10 PASSED [ 94%] 557s tests/test_utils.py::test_ensure_type_11 PASSED [ 94%] 557s tests/test_utils.py::test_ensure_type_12 PASSED [ 94%] 557s tests/test_utils.py::test_ensure_type_13 PASSED [ 94%] 557s tests/test_utils.py::test_ensure_type_14 PASSED [ 94%] 557s tests/test_utils.py::test_ensure_type_15 PASSED [ 94%] 557s tests/test_utils.py::test_delay_import_fail_1 PASSED [ 94%] 557s tests/test_utils.py::test_delay_import PASSED [ 94%] 557s tests/test_utils.py::test_unit_0 PASSED [ 95%] 557s tests/test_utils.py::test_unit_1 PASSED [ 95%] 557s tests/test_utils.py::test_unit_2 PASSED [ 95%] 557s tests/test_utils.py::test_unit_3 PASSED [ 95%] 557s tests/test_xml.py::test_xml PASSED [ 95%] 557s tests/test_xtc.py::test_read_chunk1 PASSED [ 95%] 557s tests/test_xtc.py::test_read_stride PASSED [ 95%] 557s tests/test_xtc.py::test_read_stride_n_frames PASSED [ 95%] 557s tests/test_xtc.py::test_read_stride_offsets PASSED [ 95%] 557s tests/test_xtc.py::test_read_stride_n_frames_offsets PASSED [ 95%] 557s tests/test_xtc.py::test_read_stride_switching_offsets PASSED [ 95%] 557s tests/test_xtc.py::test_read_atomindices_1 PASSED [ 96%] 557s tests/test_xtc.py::test_read_atomindices_w_stride PASSED [ 96%] 557s tests/test_xtc.py::test_read_atomindices_2 PASSED [ 96%] 557s tests/test_xtc.py::test_read_chunk2 PASSED [ 96%] 557s tests/test_xtc.py::test_read_chunk3 PASSED [ 96%] 557s tests/test_xtc.py::test_write_0 PASSED [ 96%] 557s tests/test_xtc.py::test_write_1 PASSED [ 96%] 557s tests/test_xtc.py::test_write_2 PASSED [ 96%] 557s tests/test_xtc.py::test_read_error_0 PASSED [ 96%] 557s tests/test_xtc.py::test_write_error_0 PASSED [ 96%] 557s tests/test_xtc.py::test_read_error_1 PASSED [ 96%] 557s tests/test_xtc.py::test_read_error_2 PASSED [ 96%] 557s tests/test_xtc.py::test_xtc_write_wierd_0 PASSED [ 97%] 557s tests/test_xtc.py::test_tell PASSED [ 97%] 557s tests/test_xtc.py::test_seek PASSED [ 97%] 557s tests/test_xtc.py::test_seek_natoms9 PASSED [ 97%] 557s tests/test_xtc.py::test_seek_out_of_bounds PASSED [ 97%] 557s tests/test_xtc.py::test_ragged_1 PASSED [ 97%] 557s tests/test_xtc.py::test_ragged_2 PASSED [ 97%] 557s tests/test_xtc.py::test_short_traj PASSED [ 97%] 557s tests/test_xtc.py::test_flush PASSED [ 97%] 557s tests/test_xyz.py::test_read_0 PASSED [ 97%] 557s tests/test_xyz.py::test_read_1 PASSED [ 97%] 557s tests/test_xyz.py::test_read_gz PASSED [ 98%] 557s tests/test_xyz.py::test_read_write PASSED [ 98%] 557s tests/test_xyz.py::test_mdwrite PASSED [ 98%] 557s tests/test_xyz.py::test_multiread PASSED [ 98%] 557s tests/test_xyz.py::test_seek PASSED [ 98%] 557s tests/test_xyz.py::test_len PASSED [ 98%] 557s tests/test_zipped.py::test_read_gz PASSED [ 98%] 557s tests/test_zipped.py::test_write_gz PASSED [ 98%] 557s tests/test_zipped.py::test_read_bz2 PASSED [ 98%] 557s tests/test_zipped.py::test_write_bz2 PASSED [ 98%] 559s examples/test_examples.py::test_example_notebook[iterload.ipynb] PASSED [ 98%] 562s examples/test_examples.py::test_example_notebook[principal-components.ipynb] PASSED [ 99%] 564s examples/test_examples.py::test_example_notebook[rmsd-drift.ipynb] PASSED [ 99%] 566s examples/test_examples.py::test_example_notebook[atom-selection.ipynb] PASSED [ 99%] 566s examples/test_examples.py::test_example_notebook[hbonds.ipynb] SKIPPED [ 99%] 568s examples/test_examples.py::test_example_notebook[solvent-accessible-surface-area.ipynb] PASSED [ 99%] 571s examples/test_examples.py::test_example_notebook[ramachandran-plot.ipynb] PASSED [ 99%] 573s examples/test_examples.py::test_example_notebook[clustering.ipynb] PASSED [ 99%] 574s examples/test_examples.py::test_example_notebook[two-pass-clustering.ipynb] PASSED [ 99%] 576s examples/test_examples.py::test_example_notebook[rmsd-benchmark.ipynb] PASSED [ 99%] 576s examples/test_examples.py::test_example_notebook[native-contact.ipynb] SKIPPED [ 99%] 578s examples/test_examples.py::test_example_notebook[centroids.ipynb] PASSED [ 99%] 578s examples/test_examples.py::test_example_notebook[simulation-with-openmm.ipynb] SKIPPED [100%] 578s 578s =============================== warnings summary =============================== 578s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:56 578s /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. 578s THIS_ATOM = ast.Name(id="atom", ctx=ast.Load(), SINGLETON=True) 578s 578s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:57 578s /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. 578s RE_MODULE = ast.Name(id="re", ctx=ast.Load(), SINGLETON=True) 578s 578s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 578s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 578s given by the platformdirs library. To remove this warning and 578s see the appropriate new directories, set the environment variable 578s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 578s The use of platformdirs will be the default in `jupyter_core` v6 578s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 578s 578s examples/test_examples.py:26 578s /tmp/autopkgtest.pzKnhO/build.Zfy/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 578s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 578s 578s tests/test_contact.py::test_contact_0 578s tests/test_contact.py::test_contact_4 578s /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. 578s warnings.warn( 578s 578s tests/test_contact.py::test_contact_3 578s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:271: RuntimeWarning: overflow encountered in exp 578s np.exp( 578s 578s tests/test_contact.py::test_contact_3 578s /tmp/autopkgtest.pzKnhO/build.Zfy/src/tests/test_contact.py:115: RuntimeWarning: divide by zero encountered in scalar divide 578s beta / np.log(np.sum(np.exp(beta / maps[t, r0, r1]))), 578s 578s tests/test_dcd.py::test_do_overwrite 578s tests/test_dcd.py::test_ragged_1 578s tests/test_dcd.py::test_ragged_2 578s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting xyz dtype=float64 to 578s warnings.warn( 578s 578s tests/test_distance.py::test_6 578s :488: RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject 578s 578s tests/test_drid.py::test_drid_2 578s /tmp/autopkgtest.pzKnhO/build.Zfy/src/tests/test_drid.py:62: RuntimeWarning: divide by zero encountered in divide 578s recip = 1 / squareform(pdist(t.xyz[i])) 578s 578s tests/test_dssp.py::test_1[1vii.pdb] 578s tests/test_gro.py::test_read_write 578s tests/test_gro.py::test_read_write_precision 578s tests/test_gro.py::test_load 578s tests/test_shape.py::test_principal_moments 578s tests/test_shape.py::test_asphericity 578s tests/test_shape.py::test_shape_metrics 578s /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. 578s warnings.warn( 578s 578s tests/test_geometry.py::test_dihedral_indices 578s tests/test_geometry.py::test_dihedral_indices 578s /usr/lib/python3/dist-packages/mdtraj/geometry/dihedral.py:237: DeprecationWarning: Passing a Trajectory object to _atom_sequence isdeprecated. Please pass a Topology object 578s warnings.warn( 578s 578s tests/test_gro.py::test_load 578s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq 578s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:364: UserWarning: WARNING: two consecutive residues with same number (GST, HST) 578s warnings.warn( 578s 578s tests/test_pdb.py::test_blank_indexing 578s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:204: UserWarning: Need to guess atom number starting from atom 100000. 578s warnings.warn(f'Need to guess atom number {num_str} starting from atom {pdbstructure._next_atom_number}.') 578s 578s tests/test_pdb.py::test_blank_indexing 578s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:271: UserWarning: Need to guess residue number string starting from residue10000, atom 100000. 578s warnings.warn(f'Need to guess residue number string {num_str} starting from residue{pdbstructure._next_residue_number}, atom {pdbstructure._next_atom_number}.') 578s 578s tests/test_rdf.py::test_rdf_norm 578s tests/test_rdf.py::test_rdf_t_norm[0] 578s tests/test_rdf.py::test_rdf_t_norm[2] 578s tests/test_rdf.py::test_rdf_t_norm[4] 578s tests/test_selection.py::test_re 578s tests/test_selection.py::test_re 578s tests/test_topology.py::test_select_pairs 578s tests/test_topology.py::test_select_pairs 578s /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. 578s left=ast.Call( 578s 578s tests/test_rdf.py::test_rdf_norm 578s tests/test_rdf.py::test_rdf_t_norm[0] 578s tests/test_rdf.py::test_rdf_t_norm[2] 578s tests/test_rdf.py::test_rdf_t_norm[4] 578s tests/test_selection.py::test_re 578s tests/test_selection.py::test_re 578s tests/test_topology.py::test_select_pairs 578s tests/test_topology.py::test_select_pairs 578s /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. 578s left=ast.Call( 578s 578s tests/test_trajectory.py::test_float_atom_indices_exception[gro] 578s tests/test_trajectory.py::test_atom_slicing 578s /usr/lib/python3/dist-packages/mdtraj/core/topology.py:84: UserWarning: atom_indices are not monotonically increasing 578s warnings.warn("atom_indices are not monotonically increasing") 578s 578s tests/test_utils.py::test_ensure_type_8 578s tests/test_utils.py::test_ensure_type_9 578s tests/test_utils.py::test_ensure_type_13 578s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=float64 to 578s warnings.warn( 578s 578s tests/test_utils.py::test_ensure_type_11 578s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=int64 to 578s warnings.warn( 578s 578s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 578s =========================== short test summary info ============================ 578s SKIPPED [1] tests/test_dihedral.py:56: pymol executable not found 578s SKIPPED [1] tests/test_dihedral.py:181: pymol executable not found 578s SKIPPED [16] tests/test_docstrings.py:38: Skip checking certain modules' docstrings 578s SKIPPED [1] tests/test_geometry.py:300: Not doing performance testing 578s SKIPPED [1] tests/test_geometry.py:322: Not doing performance testing 578s SKIPPED [1] tests/test_hdf5.py:104: requires openmm.units 578s SKIPPED [1] tests/test_hdf5.py:156: requires openmm.units 578s SKIPPED [1] tests/test_hdf5.py:223: requires openmm.units 578s SKIPPED [1] tests/test_mol2.py:59: Requires obabel 578s SKIPPED [1] tests/test_netcdf.py:271: This test requires cpptraj from AmberTools to be installed (http://ambermd.org) 578s SKIPPED [1] tests/test_nmr.py:11: SPARTA+ binary not found 578s SKIPPED [1] tests/test_nmr.py:26: PPM binary not found 578s SKIPPED [1] tests/test_nmr.py:42: SHIFTX2 binary not found or running on travis. 578s SKIPPED [1] tests/test_pdbx.py:43: test_pdbx.py needs OpenMM. 578s SKIPPED [2] tests/test_psf.py:93: This test requires the VMD executable: http://www.ks.uiuc.edu/Research/vmd/ 578s SKIPPED [1] tests/test_rdf.py:64: Binning does not match up with gromacs currently. 578s SKIPPED [1] tests/test_rdf.py:200: Binning does not match up with gromacs currently. 578s SKIPPED [1] tests/test_reporter.py:58: test_reporter.py needs OpenMM. 578s SKIPPED [1] tests/test_reporter.py:145: test_reporter.py needs OpenMM. 578s SKIPPED [1] tests/test_reporter.py:245: test_reporter.py needs OpenMM. 578s SKIPPED [1] tests/test_selection.py:267: failed to parse selection 578s SKIPPED [1] tests/test_thermodynamic_properties.py:161: Thermal expansion test doesn't work. 578s SKIPPED [1] tests/test_topology.py:45: needs OpenMM 578s SKIPPED [1] tests/test_topology.py:62: needs OpenMM 578s SKIPPED [1] tests/test_topology.py:72: needs OpenMM 578s SKIPPED [1] tests/test_topology.py:81: needs OpenMM 578s SKIPPED [1] tests/test_topology.py:91: needs OpenMM 578s SKIPPED [1] tests/test_topology.py:97: needs OpenMM 578s SKIPPED [1] tests/test_topology.py:247: needs OpenMM 578s SKIPPED [1] tests/test_trajectory.py:129: xyz does not store box information 578s SKIPPED [1] tests/test_trajectory.py:129: xyz.gz does not store box information 578s SKIPPED [1] tests/test_trajectory.py:129: lh5 does not store box information 578s SKIPPED [1] tests/test_trajectory.py:129: pdb does not store box information 578s SKIPPED [1] tests/test_trajectory.py:129: pdb.gz does not store box information 578s SKIPPED [1] tests/test_trajectory.py:226: mdcrd can only store rectilinear boxes 578s SKIPPED [1] tests/test_trajectory.py:224: ncrst can only store 1 frame per file 578s SKIPPED [1] tests/test_trajectory.py:224: rst7 can only store 1 frame per file 578s SKIPPED [14] tests/test_trajectory.py:248: mdcrd can only store rectilinear boxes 578s SKIPPED [14] tests/test_trajectory.py:246: ncrst can only store 1 frame per file 578s SKIPPED [14] tests/test_trajectory.py:246: rst7 can only store 1 frame per file 578s SKIPPED [4] tests/test_trajectory.py:256: dtr needs to write unitcells 578s SKIPPED [4] tests/test_trajectory.py:256: lammpstrj needs to write unitcells 578s SKIPPED [2] tests/test_trajectory.py:640: Only 1 frame per file format 578s SKIPPED [2] examples/test_examples.py:77: Network access required 578s SKIPPED [1] examples/test_examples.py:77: Openmm required for example notebook `simulation-with-openmm.ipynb` 578s XFAIL tests/test_trajectory.py::test_read_path[ncrst] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_path[rst7] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[ncrst-nc] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[ncrst-h5] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xtc] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[ncrst-trr] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dcd] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[ncrst-mdcrd] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dtr] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lh5] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[ncrst-ncrst] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[ncrst-rst7] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[ncrst-gro] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[rst7-nc] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[rst7-h5] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[rst7-xtc] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[rst7-trr] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[rst7-dcd] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[rst7-mdcrd] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[rst7-dtr] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz.gz] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[rst7-lammpstrj] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[rst7-lh5] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb.gz] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[rst7-ncrst] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[rst7-rst7] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_read_write[rst7-gro] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_load[ncrst] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_load[rst7] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[rst7] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_load_combination[ncrst] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_load_combination[rst7] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_seek_read_mode[xyz.gz] - reason: This is broken 578s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb] - reason: PDB Files don't support seeking 578s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb.gz] - reason: PDB Files don't support seeking 578s XFAIL tests/test_trajectory.py::test_seek_read_mode[ncrst] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_seek_read_mode[rst7] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_seek_read_mode[gro] - reason: This is broken 578s XFAIL tests/test_trajectory.py::test_load_frame[dtr] - reason: DTR doesn't load a single frame properly 578s XFAIL tests/test_trajectory.py::test_load_frame[ncrst] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_load_frame[rst7] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_load_frame[gro] - reason: Gro doesn't implement seek 578s XFAIL tests/test_trajectory.py::test_iterload[dtr] - reason: This is broken with dtr 578s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb] - reason: PDB Iterloads an extra frame!! 578s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb.gz] - reason: PDB Iterloads an extra frame!! 578s XFAIL tests/test_trajectory.py::test_iterload_skip[ncrst] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_iterload_skip[rst7] - reason: These reference files don't exist yet 578s XFAIL tests/test_trajectory.py::test_iterload_skip[gro] - reason: Not implemented for some reason 578s XFAIL tests/test_trajectory.py::test_force_overwrite[dtr] - reason: This is broken with dtr 578s XFAIL tests/test_trajectory.py::test_unitcell[dtr] - reason: dtr seems to need unit vectors 578s XFAIL tests/test_trajectory.py::test_unitcell[lammpstrj] - reason: lammpstrj seems to need unit vectors 578s XFAIL tests/test_trajectory.py::test_unitcell[ncrst] - reason: ncrst seems to need unit vectors 578s XFAIL tests/test_trajectory.py::test_unitcell[rst7] - reason: rst7 seems to need unit vectors 578s = 964 passed, 108 skipped, 12 deselected, 61 xfailed, 48 warnings in 309.44s (0:05:09) = 579s autopkgtest [03:07:38]: test command1: -----------------------] 579s command1 PASS 579s autopkgtest [03:07:38]: test command1: - - - - - - - - - - results - - - - - - - - - - 580s autopkgtest [03:07:39]: test command2: preparing testbed 580s Reading package lists... 580s Building dependency tree... 580s Reading state information... 581s Starting pkgProblemResolver with broken count: 0 581s Starting 2 pkgProblemResolver with broken count: 0 581s Done 581s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 582s autopkgtest [03:07:41]: test command2: pytest-3 -k 'test_3 or test_pdb_from_url or test_1vii_url_and_gz' 582s autopkgtest [03:07:41]: test command2: [----------------------- 583s ============================= test session starts ============================== 583s platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 -- /usr/bin/python3 583s cachedir: .pytest_cache 583s rootdir: /tmp/autopkgtest.pzKnhO/build.Zfy/src 583s configfile: pyproject.toml 583s testpaths: tests, examples 583s plugins: typeguard-4.4.1 584s collecting ... collected 1145 items / 1135 deselected / 10 selected 584s 584s tests/test_distance.py::test_3 PASSED [ 10%] 584s tests/test_distance.py::test_3p PASSED [ 20%] 587s tests/test_dssp.py::test_3[1GAI] FAILED [ 30%] 590s tests/test_dssp.py::test_3[6gsv] PASSED [ 40%] 593s tests/test_dssp.py::test_3[2AAC] PASSED [ 50%] 593s tests/test_nmr.py::test_3_scalar_couplings PASSED [ 60%] 598s tests/test_pdb.py::test_pdb_from_url PASSED [ 70%] 599s tests/test_pdb.py::test_3nch_conect PASSED [ 80%] 601s tests/test_pdb.py::test_3nch_serial_resSeq PASSED [ 90%] 605s tests/test_pdb.py::test_1vii_url_and_gz PASSED [100%] 605s 605s =================================== FAILURES =================================== 605s _________________________________ test_3[1GAI] _________________________________ 605s 605s get_fn = ._get_fn at 0xf72e6b780ae0> 605s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_3_1GAI_0'), pdbid = '1GAI' 605s 605s @pytest.mark.parametrize('pdbid', ["1GAI", "6gsv", "2AAC"]) 605s def test_3(get_fn, tmpdir, pdbid): 605s """This test checks dssp assignments on pdb files downloaded from rcsb""" 605s # 1COY gives a small error, due to a broken chain. 605s > t = md.load_pdb("http://www.rcsb.org/pdb/files/%s.pdb" % pdbid) 605s 605s tests/test_dssp.py:70: 605s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 605s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:151: in load_pdb 605s with PDBTrajectoryFile(filename, standard_names=standard_names, top=top) as f: 605s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:291: in __init__ 605s self._read_models() 605s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:629: in _read_models 605s pdb = PdbStructure(self._file, load_all_models=True) 605s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:376: in __init__ 605s self._load(input_stream) 605s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:392: in _load 605s self._add_atom(Atom(pdb_line, self)) 605s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 605s 605s self = 605s pdb_line = 'ATOM 2948 CG PHE A 420 13.00 28.09 61.890 1.00 63.92 82.14 4 \n' 605s pdbstructure = 605s 605s def __init__(self, pdb_line, pdbstructure=None): 605s """Create a new pdb.Atom from an ATOM or HETATM line. 605s 605s Example line: 605s ATOM 2209 CB TYR A 299 6.167 22.607 20.046 1.00 8.12 C 605s 00000000011111111112222222222333333333344444444445555555555666666666677777777778 605s 12345678901234567890123456789012345678901234567890123456789012345678901234567890 605s 605s ATOM line format description from 605s http://deposit.rcsb.org/adit/docs/pdb_atom_format.html: 605s 605s COLUMNS DATA TYPE CONTENTS 605s -------------------------------------------------------------------------------- 605s 1 - 6 Record name "ATOM " 605s 7 - 11 Integer Atom serial number. 605s 13 - 16 Atom Atom name. 605s 17 Character Alternate location indicator. 605s 18 - 20 Residue name Residue name. 605s 22 Character Chain identifier. 605s 23 - 26 Integer Residue sequence number. 605s 27 AChar Code for insertion of residues. 605s 31 - 38 Real(8.3) Orthogonal coordinates for X in Angstroms. 605s 39 - 46 Real(8.3) Orthogonal coordinates for Y in Angstroms. 605s 47 - 54 Real(8.3) Orthogonal coordinates for Z in Angstroms. 605s 55 - 60 Real(6.2) Occupancy (Default = 1.0). 605s 61 - 66 Real(6.2) Temperature factor (Default = 0.0). 605s 73 - 76 LString(4) Segment identifier, left-justified. 605s 77 - 78 LString(2) Element symbol, right-justified. 605s 79 - 80 LString(2) Charge on the atom. 605s 605s """ 605s # We might modify first/final status during _finalize() methods 605s self.is_first_atom_in_chain = False 605s self.is_final_atom_in_chain = False 605s self.is_first_residue_in_chain = False 605s self.is_final_residue_in_chain = False 605s # Start parsing fields from pdb line 605s self.record_name = pdb_line[0:6].strip() 605s 605s self.serial_number = _read_atom_number(pdb_line[6:11], pdbstructure=pdbstructure) 605s 605s self.name_with_spaces = pdb_line[12:16] 605s alternate_location_indicator = pdb_line[16] 605s 605s self.residue_name_with_spaces = pdb_line[17:20] 605s # In some MD codes, notably ffamber in gromacs, residue name has a fourth character in 605s # column 21 605s possible_fourth_character = pdb_line[20:21] 605s if possible_fourth_character != " ": 605s # Fourth character should only be there if official 3 are already full 605s if len(self.residue_name_with_spaces.strip()) != 3: 605s raise ValueError("Misaligned residue name: %s" % pdb_line) 605s self.residue_name_with_spaces += possible_fourth_character 605s self.residue_name = self.residue_name_with_spaces.strip() 605s 605s self.chain_id = pdb_line[21] 605s self.residue_number = _read_residue_number(pdb_line[22:26], pdbstructure, self) 605s 605s self.insertion_code = pdb_line[26] 605s # coordinates, occupancy, and temperature factor belong in Atom.Location object 605s x = float(pdb_line[30:38]) 605s > y = float(pdb_line[38:46]) 605s E ValueError: could not convert string to float: '28.09 6' 605s 605s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:974: ValueError 605s =============================== warnings summary =============================== 605s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:56 605s /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. 605s THIS_ATOM = ast.Name(id="atom", ctx=ast.Load(), SINGLETON=True) 605s 605s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:57 605s /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. 605s RE_MODULE = ast.Name(id="re", ctx=ast.Load(), SINGLETON=True) 605s 605s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 605s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 605s given by the platformdirs library. To remove this warning and 605s see the appropriate new directories, set the environment variable 605s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 605s The use of platformdirs will be the default in `jupyter_core` v6 605s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 605s 605s examples/test_examples.py:26 605s /tmp/autopkgtest.pzKnhO/build.Zfy/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 605s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 605s 605s tests/test_pdb.py::test_1vii_url_and_gz 605s /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. 605s warnings.warn( 605s 605s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 605s =========================== short test summary info ============================ 605s FAILED tests/test_dssp.py::test_3[1GAI] - ValueError: could not convert strin... 605s ========== 1 failed, 9 passed, 1135 deselected, 5 warnings in 21.77s =========== 606s autopkgtest [03:08:05]: test command2: -----------------------] 606s autopkgtest [03:08:05]: test command2: - - - - - - - - - - results - - - - - - - - - - 606s command2 FAIL non-zero exit status 1 607s autopkgtest [03:08:06]: @@@@@@@@@@@@@@@@@@@@ summary 607s command1 PASS 607s command2 FAIL non-zero exit status 1 615s nova [W] Using flock in prodstack6-arm64 615s Creating nova instance adt-plucky-arm64-mdtraj-20250219-025758-juju-7f2275-prod-proposed-migration-environment-15-0cacc2f4-568f-4c7f-bec2-862ef5a90772 from image adt/ubuntu-plucky-arm64-server-20250218.img (UUID db1e3557-ca0b-4978-8424-9ef955671030)... 615s nova [W] Timed out waiting for c029914e-543e-4db5-8c3d-30ae78a449f9 to get deleted.