0s autopkgtest [11:59:27]: starting date and time: 2025-02-19 11:59:27+0000 0s autopkgtest [11:59:27]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [11:59:27]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /var/tmp/autopkgtest-work.vle5ic9e/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:sphinx --apt-upgrade mdtraj --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/8.1.3-5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-4.secgroup --name adt-plucky-arm64-mdtraj-20250219-115927-juju-7f2275-prod-proposed-migration-environment-15-d563b619-0353-4225-9e8f-d7ec1f16f008 --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/ 139s autopkgtest [12:01:46]: testbed dpkg architecture: arm64 139s autopkgtest [12:01:46]: testbed apt version: 2.9.29 140s autopkgtest [12:01:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 140s autopkgtest [12:01:47]: testbed release detected to be: None 141s autopkgtest [12:01:48]: updating testbed package index (apt update) 141s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 141s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 141s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 141s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 141s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 141s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [750 kB] 142s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 142s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 142s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [93.3 kB] 142s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [7960 B] 142s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [686 kB] 142s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [11.2 kB] 142s Fetched 1752 kB in 1s (1784 kB/s) 143s Reading package lists... 143s + lsb_release --codename --short 143s + RELEASE=plucky 143s + cat 143s + [ plucky != trusty ] 143s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 143s Reading package lists... 144s Building dependency tree... 144s Reading state information... 144s Calculating upgrade... 145s The following NEW packages will be installed: 145s libapt-pkg7.0 145s The following packages will be upgraded: 145s apt apt-utils iproute2 liblsof0 libp11-kit0 lsof rsyslog 145s 7 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 145s Need to get 4842 kB of archives. 145s After this operation, 3409 kB of additional disk space will be used. 145s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libapt-pkg7.0 arm64 2.9.30 [1023 kB] 146s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 apt arm64 2.9.30 [1364 kB] 146s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 apt-utils arm64 2.9.30 [207 kB] 146s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 iproute2 arm64 6.13.0-1ubuntu1 [1158 kB] 146s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libp11-kit0 arm64 0.25.5-2ubuntu3 [280 kB] 146s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 rsyslog arm64 8.2412.0-2ubuntu1 [521 kB] 146s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 lsof arm64 4.99.4+dfsg-1 [236 kB] 146s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsof0 arm64 4.99.4+dfsg-1 [53.9 kB] 146s Preconfiguring packages ... 146s Fetched 4842 kB in 1s (5864 kB/s) 147s Selecting previously unselected package libapt-pkg7.0:arm64. 147s (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.) 147s Preparing to unpack .../libapt-pkg7.0_2.9.30_arm64.deb ... 147s Unpacking libapt-pkg7.0:arm64 (2.9.30) ... 147s Setting up libapt-pkg7.0:arm64 (2.9.30) ... 147s (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 ... 116669 files and directories currently installed.) 147s Preparing to unpack .../archives/apt_2.9.30_arm64.deb ... 147s Unpacking apt (2.9.30) over (2.9.29) ... 147s Setting up apt (2.9.30) ... 148s (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 ... 116669 files and directories currently installed.) 148s Preparing to unpack .../0-apt-utils_2.9.30_arm64.deb ... 148s Unpacking apt-utils (2.9.30) over (2.9.29) ... 148s Preparing to unpack .../1-iproute2_6.13.0-1ubuntu1_arm64.deb ... 148s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 148s Preparing to unpack .../2-libp11-kit0_0.25.5-2ubuntu3_arm64.deb ... 148s Unpacking libp11-kit0:arm64 (0.25.5-2ubuntu3) over (0.25.5-2ubuntu2) ... 148s Preparing to unpack .../3-rsyslog_8.2412.0-2ubuntu1_arm64.deb ... 149s Unpacking rsyslog (8.2412.0-2ubuntu1) over (8.2412.0-1ubuntu1) ... 149s Preparing to unpack .../4-lsof_4.99.4+dfsg-1_arm64.deb ... 149s Unpacking lsof (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 149s Preparing to unpack .../5-liblsof0_4.99.4+dfsg-1_arm64.deb ... 149s Unpacking liblsof0 (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 149s Setting up apt-utils (2.9.30) ... 149s Setting up liblsof0 (4.99.4+dfsg-1) ... 149s Setting up iproute2 (6.13.0-1ubuntu1) ... 149s Setting up rsyslog (8.2412.0-2ubuntu1) ... 149s info: The user `syslog' is already a member of `adm'. 151s Setting up libp11-kit0:arm64 (0.25.5-2ubuntu3) ... 151s Setting up lsof (4.99.4+dfsg-1) ... 151s Processing triggers for man-db (2.13.0-1) ... 154s Processing triggers for libc-bin (2.40-4ubuntu1) ... 154s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 154s + /usr/lib/apt/apt-helper analyze-pattern ?true 154s + uname -r 154s + sed s/\./\\./g 154s + running_kernel_pattern=^linux-.*6\.12\.0-15-generic.* 154s + apt list ?obsolete 154s + tail -n+2 154s + cut -d/ -f1 154s + grep -v ^linux-.*6\.12\.0-15-generic.* 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 [12:02:03]: upgrading testbed (apt dist-upgrade and autopurge) 157s Reading package lists... 157s Building dependency tree... 157s Reading state information... 158s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 158s Starting 2 pkgProblemResolver with broken count: 0 158s Done 159s Entering ResolveByKeep 159s 159s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 160s Reading package lists... 160s Building dependency tree... 160s Reading state information... 160s Starting pkgProblemResolver with broken count: 0 161s Starting 2 pkgProblemResolver with broken count: 0 161s Done 161s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 162s autopkgtest [12:02:09]: rebooting testbed after setup commands that affected boot 196s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 203s autopkgtest [12:02:50]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 15:49:33 UTC 2025 205s autopkgtest [12:02:52]: @@@@@@@@@@@@@@@@@@@@ apt-source mdtraj 212s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.3-2 (dsc) [2677 B] 212s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.3-2 (tar) [22.0 MB] 212s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.3-2 (diff) [300 kB] 212s gpgv: Signature made Tue Feb 11 15:16:54 2025 UTC 212s gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA 212s gpgv: Can't check signature: No public key 212s dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.10.3-2.dsc: no acceptable signature found 213s autopkgtest [12:03:00]: testing package mdtraj version 1.10.3-2 216s autopkgtest [12:03:03]: build not needed 232s autopkgtest [12:03:19]: test command1: preparing testbed 233s Reading package lists... 233s Building dependency tree... 233s Reading state information... 233s Starting pkgProblemResolver with broken count: 0 233s Starting 2 pkgProblemResolver with broken count: 0 233s Done 234s The following NEW packages will be installed: 234s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx gdb 234s libaec0 libbabeltrace1 libblas3 libblosc1 libblosc2-4 libdebuginfod-common 234s libdebuginfod1t64 libdeflate0 libfontconfig1 libgfortran5 libgomp1 234s libgraphite2-3 libharfbuzz0b libhdf5-310 libhdf5-hl-310 libimagequant0 234s libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 234s liblbfgsb0 liblcms2-2 liblerc4 libnetcdf22 libnorm1t64 libopenjp2-7 234s libpgm-5.3-0t64 libqhull-r8.0 libraqm0 libsharpyuv0 libsnappy1v5 libsodium23 234s libsource-highlight-common libsource-highlight4t64 libsz2 libtcl8.6 libtiff6 234s libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 234s libxss1 libzmq5 python-matplotlib-data python-tables-data python3-asttokens 234s python3-brotli python3-cftime python3-comm python3-contourpy 234s python3-coverage python3-cpuinfo python3-cycler python3-dateutil 234s python3-debugpy python3-decorator python3-executing python3-fastjsonschema 234s python3-fonttools python3-fs python3-gsd python3-iniconfig python3-ipykernel 234s python3-ipython python3-jedi python3-joblib python3-jupyter-client 234s python3-jupyter-core python3-kiwisolver python3-lxml python3-lz4 234s python3-matplotlib python3-matplotlib-inline python3-mdtraj python3-mpmath 234s python3-nbformat python3-nest-asyncio python3-netcdf4 python3-networkx 234s python3-numexpr python3-numpy python3-packaging python3-pandas 234s python3-pandas-lib python3-parso python3-pexpect python3-pil 234s python3-pil.imagetk python3-platformdirs python3-pluggy 234s python3-prompt-toolkit python3-psutil python3-ptyprocess python3-pure-eval 234s python3-pytest python3-pytz python3-scipy python3-sklearn 234s python3-sklearn-lib python3-stack-data python3-sympy python3-tables 234s python3-tables-lib python3-threadpoolctl python3-tk python3-tornado 234s python3-traitlets python3-typeshed python3-tz python3-ufolib2 234s python3-unicodedata2 python3-wcwidth python3-zmq python3.12 234s python3.12-minimal python3.12-tk python3.13-tk tk8.6-blt2.5 unicode-data 234s x11-common 235s 0 upgraded, 131 newly installed, 0 to remove and 0 not upgraded. 235s Need to get 114 MB of archives. 235s After this operation, 610 MB of additional disk space will be used. 235s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-minimal arm64 3.12.9-1 [2236 kB] 236s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebuginfod-common all 0.192-4 [15.4 kB] 236s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12 arm64 3.12.9-1 [671 kB] 236s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 236s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 236s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 237s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 237s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 237s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 237s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 237s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 237s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 237s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 237s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 237s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 237s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.3-1 [171 kB] 237s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libbabeltrace1 arm64 1.5.11-4build1 [159 kB] 237s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebuginfod1t64 arm64 0.192-4 [20.8 kB] 237s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libsource-highlight-common all 3.1.9-4.3build1 [64.2 kB] 237s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libsource-highlight4t64 arm64 3.1.9-4.3build1 [243 kB] 237s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 gdb arm64 16.2-1ubuntu1 [7653 kB] 238s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 238s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 238s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libsnappy1v5 arm64 1.2.1-1 [30.4 kB] 238s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 libblosc1 arm64 1.21.5+ds-1build1 [25.7 kB] 238s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 libblosc2-4 arm64 2.16.0+ds-1 [158 kB] 238s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 238s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250213-1ubuntu1 [443 kB] 238s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250213-1ubuntu1 [146 kB] 238s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 238s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 238s Get:32 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 238s Get:33 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-310 arm64 1.14.5+repack-3 [1331 kB] 238s Get:34 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [59.8 kB] 238s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 238s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 238s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 238s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 238s Get:39 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 238s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 238s Get:41 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 238s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 238s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 238s Get:44 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnetcdf22 arm64 1:4.9.3-1 [504 kB] 239s Get:45 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnorm1t64 arm64 1.5.9+dfsg-3.1build1 [150 kB] 239s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpgm-5.3-0t64 arm64 5.3.128~dfsg-2.1build1 [162 kB] 239s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 239s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 239s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 239s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libsodium23 arm64 1.0.18-1build3 [119 kB] 239s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 239s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 239s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 239s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 239s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 239s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu2 [168 kB] 239s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 libzmq5 arm64 4.3.5-1build2 [247 kB] 239s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3ubuntu2 [2929 kB] 240s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-tables-data all 3.10.2-2 [49.6 kB] 240s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-asttokens all 3.0.0-1 [20.4 kB] 240s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build3 [342 kB] 240s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-13 [4148 kB] 240s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cftime arm64 1.6.4-1build2 [289 kB] 240s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 240s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-comm all 0.2.1-1 [7016 B] 240s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.1-1 [216 kB] 240s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-coverage arm64 7.4.4+dfsg1-0ubuntu3 [150 kB] 240s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cpuinfo all 9.0.0+git20221119-3 [21.7 kB] 240s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 240s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB] 240s Get:71 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-debugpy arm64 1.8.8+ds-2ubuntu1 [1054 kB] 241s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 241s Get:73 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-executing all 2.2.0-0.1 [25.0 kB] 241s Get:74 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fastjsonschema all 2.21.1-1 [20.4 kB] 241s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pytz all 2025.1-3 [162 kB] 241s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2025.1-3 [1866 B] 241s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB] 241s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-6 [90.7 kB] 241s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.1-1 [1600 kB] 241s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.4.0+dfsg-1 [27.3 kB] 241s Get:81 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-4ubuntu1 [19.5 MB] 244s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 244s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 244s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 244s Get:85 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build2 [360 kB] 244s Get:86 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 246s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.55.3-2 [1615 kB] 246s Get:88 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-gsd arm64 3.3.0-1build2 [229 kB] 246s Get:89 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 246s Get:90 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-parso all 0.8.4-1 [67.6 kB] 246s Get:91 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-typeshed all 0.0~git20241223.ea91db2-1 [1548 kB] 246s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-jedi all 0.19.1+ds1-1 [693 kB] 246s Get:93 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 246s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 246s Get:95 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-prompt-toolkit all 3.0.50-1 [257 kB] 247s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pure-eval all 0.2.3-1 [11.4 kB] 247s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-stack-data all 0.6.3-1 [22.0 kB] 247s Get:98 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-ptyprocess all 0.7.0-6 [14.8 kB] 247s Get:99 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pexpect all 4.9-3 [48.1 kB] 247s Get:100 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ipython all 8.30.0-2 [569 kB] 247s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-jupyter-core all 5.7.2-5 [28.1 kB] 247s Get:102 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-psutil arm64 5.9.8-2build3 [196 kB] 247s Get:103 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tornado arm64 6.4.2-1 [299 kB] 247s Get:104 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-zmq arm64 26.2.1-1 [215 kB] 247s Get:105 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-jupyter-client all 8.6.3-2 [78.5 kB] 247s Get:106 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-nest-asyncio all 1.5.4-1 [6256 B] 247s Get:107 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 247s Get:108 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ipykernel all 6.29.5-2 [82.7 kB] 247s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-joblib all 1.4.2-2 [205 kB] 248s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-3 [62.5 kB] 248s Get:111 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu3 [182 kB] 248s Get:112 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 11.1.0-5 [491 kB] 248s Get:113 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.9-1 [115 kB] 248s Get:114 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.2-1 [106 kB] 248s Get:115 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.13.1-1 [9770 B] 248s Get:116 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 11.1.0-5 [9948 B] 248s Get:117 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3ubuntu2 [4616 kB] 249s Get:118 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-netcdf4 arm64 1.7.2-1build3 [797 kB] 249s Get:119 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 250s Get:120 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-8 [6925 kB] 251s Get:121 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-8 [3112 kB] 251s Get:122 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-numexpr arm64 2.10.2-1build1 [124 kB] 251s Get:123 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tables-lib arm64 3.10.2-2 [738 kB] 251s Get:124 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tables all 3.10.2-2 [354 kB] 251s Get:125 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mdtraj arm64 1.10.3-2 [1552 kB] 251s Get:126 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-nbformat all 5.9.1-1 [41.2 kB] 251s Get:127 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 251s Get:128 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.4-1 [252 kB] 251s Get:129 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 251s Get:130 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-7build1 [6372 kB] 251s Get:131 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn all 1.4.2+dfsg-7build1 [2258 kB] 252s Preconfiguring packages ... 252s Fetched 114 MB in 17s (6741 kB/s) 252s Selecting previously unselected package python3.12-minimal. 253s (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 ... 116670 files and directories currently installed.) 253s Preparing to unpack .../000-python3.12-minimal_3.12.9-1_arm64.deb ... 253s Unpacking python3.12-minimal (3.12.9-1) ... 253s Selecting previously unselected package libdebuginfod-common. 253s Preparing to unpack .../001-libdebuginfod-common_0.192-4_all.deb ... 253s Unpacking libdebuginfod-common (0.192-4) ... 253s Selecting previously unselected package python3.12. 253s Preparing to unpack .../002-python3.12_3.12.9-1_arm64.deb ... 253s Unpacking python3.12 (3.12.9-1) ... 253s Selecting previously unselected package libtcl8.6:arm64. 253s Preparing to unpack .../003-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... 253s Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... 253s Selecting previously unselected package fonts-dejavu-mono. 253s Preparing to unpack .../004-fonts-dejavu-mono_2.37-8_all.deb ... 253s Unpacking fonts-dejavu-mono (2.37-8) ... 253s Selecting previously unselected package fonts-dejavu-core. 253s Preparing to unpack .../005-fonts-dejavu-core_2.37-8_all.deb ... 253s Unpacking fonts-dejavu-core (2.37-8) ... 253s Selecting previously unselected package fontconfig-config. 253s Preparing to unpack .../006-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 253s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 253s Selecting previously unselected package libfontconfig1:arm64. 254s Preparing to unpack .../007-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 254s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 254s Selecting previously unselected package libxrender1:arm64. 254s Preparing to unpack .../008-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 254s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 254s Selecting previously unselected package libxft2:arm64. 254s Preparing to unpack .../009-libxft2_2.3.6-1build1_arm64.deb ... 254s Unpacking libxft2:arm64 (2.3.6-1build1) ... 254s Selecting previously unselected package x11-common. 254s Preparing to unpack .../010-x11-common_1%3a7.7+23ubuntu3_all.deb ... 254s Unpacking x11-common (1:7.7+23ubuntu3) ... 254s Selecting previously unselected package libxss1:arm64. 254s Preparing to unpack .../011-libxss1_1%3a1.2.3-1build3_arm64.deb ... 254s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 254s Selecting previously unselected package libtk8.6:arm64. 254s Preparing to unpack .../012-libtk8.6_8.6.16-1_arm64.deb ... 254s Unpacking libtk8.6:arm64 (8.6.16-1) ... 254s Selecting previously unselected package tk8.6-blt2.5. 254s Preparing to unpack .../013-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ... 254s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 254s Selecting previously unselected package blt. 254s Preparing to unpack .../014-blt_2.5.3+dfsg-7build1_arm64.deb ... 254s Unpacking blt (2.5.3+dfsg-7build1) ... 254s Selecting previously unselected package fonts-lyx. 254s Preparing to unpack .../015-fonts-lyx_2.4.3-1_all.deb ... 254s Unpacking fonts-lyx (2.4.3-1) ... 254s Selecting previously unselected package libbabeltrace1:arm64. 254s Preparing to unpack .../016-libbabeltrace1_1.5.11-4build1_arm64.deb ... 254s Unpacking libbabeltrace1:arm64 (1.5.11-4build1) ... 254s Selecting previously unselected package libdebuginfod1t64:arm64. 254s Preparing to unpack .../017-libdebuginfod1t64_0.192-4_arm64.deb ... 254s Unpacking libdebuginfod1t64:arm64 (0.192-4) ... 254s Selecting previously unselected package libsource-highlight-common. 254s Preparing to unpack .../018-libsource-highlight-common_3.1.9-4.3build1_all.deb ... 254s Unpacking libsource-highlight-common (3.1.9-4.3build1) ... 254s Selecting previously unselected package libsource-highlight4t64:arm64. 254s Preparing to unpack .../019-libsource-highlight4t64_3.1.9-4.3build1_arm64.deb ... 254s Unpacking libsource-highlight4t64:arm64 (3.1.9-4.3build1) ... 254s Selecting previously unselected package gdb. 254s Preparing to unpack .../020-gdb_16.2-1ubuntu1_arm64.deb ... 254s Unpacking gdb (16.2-1ubuntu1) ... 255s Selecting previously unselected package libaec0:arm64. 255s Preparing to unpack .../021-libaec0_1.1.3-1_arm64.deb ... 255s Unpacking libaec0:arm64 (1.1.3-1) ... 255s Selecting previously unselected package libblas3:arm64. 255s Preparing to unpack .../022-libblas3_3.12.1-2_arm64.deb ... 255s Unpacking libblas3:arm64 (3.12.1-2) ... 255s Selecting previously unselected package libsnappy1v5:arm64. 255s Preparing to unpack .../023-libsnappy1v5_1.2.1-1_arm64.deb ... 255s Unpacking libsnappy1v5:arm64 (1.2.1-1) ... 255s Selecting previously unselected package libblosc1:arm64. 255s Preparing to unpack .../024-libblosc1_1.21.5+ds-1build1_arm64.deb ... 255s Unpacking libblosc1:arm64 (1.21.5+ds-1build1) ... 255s Selecting previously unselected package libblosc2-4:arm64. 255s Preparing to unpack .../025-libblosc2-4_2.16.0+ds-1_arm64.deb ... 255s Unpacking libblosc2-4:arm64 (2.16.0+ds-1) ... 255s Selecting previously unselected package libdeflate0:arm64. 255s Preparing to unpack .../026-libdeflate0_1.23-1_arm64.deb ... 255s Unpacking libdeflate0:arm64 (1.23-1) ... 255s Selecting previously unselected package libgfortran5:arm64. 255s Preparing to unpack .../027-libgfortran5_15-20250213-1ubuntu1_arm64.deb ... 255s Unpacking libgfortran5:arm64 (15-20250213-1ubuntu1) ... 255s Selecting previously unselected package libgomp1:arm64. 255s Preparing to unpack .../028-libgomp1_15-20250213-1ubuntu1_arm64.deb ... 255s Unpacking libgomp1:arm64 (15-20250213-1ubuntu1) ... 255s Selecting previously unselected package libgraphite2-3:arm64. 255s Preparing to unpack .../029-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 255s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 255s Selecting previously unselected package libharfbuzz0b:arm64. 255s Preparing to unpack .../030-libharfbuzz0b_10.2.0-1_arm64.deb ... 255s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 255s Selecting previously unselected package libsz2:arm64. 255s Preparing to unpack .../031-libsz2_1.1.3-1_arm64.deb ... 255s Unpacking libsz2:arm64 (1.1.3-1) ... 255s Selecting previously unselected package libhdf5-310:arm64. 255s Preparing to unpack .../032-libhdf5-310_1.14.5+repack-3_arm64.deb ... 255s Unpacking libhdf5-310:arm64 (1.14.5+repack-3) ... 255s Selecting previously unselected package libhdf5-hl-310:arm64. 255s Preparing to unpack .../033-libhdf5-hl-310_1.14.5+repack-3_arm64.deb ... 255s Unpacking libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 255s Selecting previously unselected package libimagequant0:arm64. 255s Preparing to unpack .../034-libimagequant0_2.18.0-1build1_arm64.deb ... 255s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 255s Selecting previously unselected package libjpeg-turbo8:arm64. 255s Preparing to unpack .../035-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 255s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 255s Selecting previously unselected package libjpeg8:arm64. 255s Preparing to unpack .../036-libjpeg8_8c-2ubuntu11_arm64.deb ... 255s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 255s Selecting previously unselected package libjs-jquery. 255s Preparing to unpack .../037-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 255s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 255s Selecting previously unselected package libjs-jquery-ui. 255s Preparing to unpack .../038-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 255s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 256s Selecting previously unselected package liblapack3:arm64. 256s Preparing to unpack .../039-liblapack3_3.12.1-2_arm64.deb ... 256s Unpacking liblapack3:arm64 (3.12.1-2) ... 256s Selecting previously unselected package liblbfgsb0:arm64. 256s Preparing to unpack .../040-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 256s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 256s Selecting previously unselected package liblcms2-2:arm64. 256s Preparing to unpack .../041-liblcms2-2_2.16-2_arm64.deb ... 256s Unpacking liblcms2-2:arm64 (2.16-2) ... 256s Selecting previously unselected package liblerc4:arm64. 256s Preparing to unpack .../042-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 256s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 256s Selecting previously unselected package libnetcdf22:arm64. 256s Preparing to unpack .../043-libnetcdf22_1%3a4.9.3-1_arm64.deb ... 256s Unpacking libnetcdf22:arm64 (1:4.9.3-1) ... 256s Selecting previously unselected package libnorm1t64:arm64. 256s Preparing to unpack .../044-libnorm1t64_1.5.9+dfsg-3.1build1_arm64.deb ... 256s Unpacking libnorm1t64:arm64 (1.5.9+dfsg-3.1build1) ... 256s Selecting previously unselected package libpgm-5.3-0t64:arm64. 256s Preparing to unpack .../045-libpgm-5.3-0t64_5.3.128~dfsg-2.1build1_arm64.deb ... 256s Unpacking libpgm-5.3-0t64:arm64 (5.3.128~dfsg-2.1build1) ... 256s Selecting previously unselected package libqhull-r8.0:arm64. 256s Preparing to unpack .../046-libqhull-r8.0_2020.2-6build1_arm64.deb ... 256s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 256s Selecting previously unselected package libraqm0:arm64. 256s Preparing to unpack .../047-libraqm0_0.10.2-1_arm64.deb ... 256s Unpacking libraqm0:arm64 (0.10.2-1) ... 256s Selecting previously unselected package libsharpyuv0:arm64. 256s Preparing to unpack .../048-libsharpyuv0_1.5.0-0.1_arm64.deb ... 256s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 256s Selecting previously unselected package libsodium23:arm64. 256s Preparing to unpack .../049-libsodium23_1.0.18-1build3_arm64.deb ... 256s Unpacking libsodium23:arm64 (1.0.18-1build3) ... 256s Selecting previously unselected package libjbig0:arm64. 256s Preparing to unpack .../050-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 256s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 256s Selecting previously unselected package libwebp7:arm64. 256s Preparing to unpack .../051-libwebp7_1.5.0-0.1_arm64.deb ... 256s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 256s Selecting previously unselected package libtiff6:arm64. 256s Preparing to unpack .../052-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 256s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 256s Selecting previously unselected package libwebpdemux2:arm64. 256s Preparing to unpack .../053-libwebpdemux2_1.5.0-0.1_arm64.deb ... 256s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 256s Selecting previously unselected package libwebpmux3:arm64. 256s Preparing to unpack .../054-libwebpmux3_1.5.0-0.1_arm64.deb ... 256s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 256s Selecting previously unselected package libxslt1.1:arm64. 256s Preparing to unpack .../055-libxslt1.1_1.1.39-0exp1ubuntu2_arm64.deb ... 256s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ... 256s Selecting previously unselected package libzmq5:arm64. 256s Preparing to unpack .../056-libzmq5_4.3.5-1build2_arm64.deb ... 256s Unpacking libzmq5:arm64 (4.3.5-1build2) ... 256s Selecting previously unselected package python-matplotlib-data. 257s Preparing to unpack .../057-python-matplotlib-data_3.8.3-3ubuntu2_all.deb ... 257s Unpacking python-matplotlib-data (3.8.3-3ubuntu2) ... 257s Selecting previously unselected package python-tables-data. 257s Preparing to unpack .../058-python-tables-data_3.10.2-2_all.deb ... 257s Unpacking python-tables-data (3.10.2-2) ... 257s Selecting previously unselected package python3-asttokens. 257s Preparing to unpack .../059-python3-asttokens_3.0.0-1_all.deb ... 257s Unpacking python3-asttokens (3.0.0-1) ... 257s Selecting previously unselected package python3-brotli. 257s Preparing to unpack .../060-python3-brotli_1.1.0-2build3_arm64.deb ... 257s Unpacking python3-brotli (1.1.0-2build3) ... 257s Selecting previously unselected package python3-numpy. 257s Preparing to unpack .../061-python3-numpy_1%3a1.26.4+ds-13_arm64.deb ... 257s Unpacking python3-numpy (1:1.26.4+ds-13) ... 257s Selecting previously unselected package python3-cftime. 257s Preparing to unpack .../062-python3-cftime_1.6.4-1build2_arm64.deb ... 257s Unpacking python3-cftime (1.6.4-1build2) ... 257s Selecting previously unselected package python3-traitlets. 257s Preparing to unpack .../063-python3-traitlets_5.14.3+really5.14.3-1_all.deb ... 257s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ... 257s Selecting previously unselected package python3-comm. 257s Preparing to unpack .../064-python3-comm_0.2.1-1_all.deb ... 257s Unpacking python3-comm (0.2.1-1) ... 257s Selecting previously unselected package python3-contourpy. 257s Preparing to unpack .../065-python3-contourpy_1.3.1-1_arm64.deb ... 257s Unpacking python3-contourpy (1.3.1-1) ... 257s Selecting previously unselected package python3-coverage. 257s Preparing to unpack .../066-python3-coverage_7.4.4+dfsg1-0ubuntu3_arm64.deb ... 257s Unpacking python3-coverage (7.4.4+dfsg1-0ubuntu3) ... 257s Selecting previously unselected package python3-cpuinfo. 257s Preparing to unpack .../067-python3-cpuinfo_9.0.0+git20221119-3_all.deb ... 257s Unpacking python3-cpuinfo (9.0.0+git20221119-3) ... 257s Selecting previously unselected package python3-cycler. 257s Preparing to unpack .../068-python3-cycler_0.12.1-1_all.deb ... 257s Unpacking python3-cycler (0.12.1-1) ... 257s Selecting previously unselected package python3-dateutil. 257s Preparing to unpack .../069-python3-dateutil_2.9.0-3_all.deb ... 257s Unpacking python3-dateutil (2.9.0-3) ... 257s Selecting previously unselected package python3-debugpy. 257s Preparing to unpack .../070-python3-debugpy_1.8.8+ds-2ubuntu1_arm64.deb ... 257s Unpacking python3-debugpy (1.8.8+ds-2ubuntu1) ... 257s Selecting previously unselected package python3-decorator. 258s Preparing to unpack .../071-python3-decorator_5.1.1-5_all.deb ... 258s Unpacking python3-decorator (5.1.1-5) ... 258s Selecting previously unselected package python3-executing. 258s Preparing to unpack .../072-python3-executing_2.2.0-0.1_all.deb ... 258s Unpacking python3-executing (2.2.0-0.1) ... 258s Selecting previously unselected package python3-fastjsonschema. 258s Preparing to unpack .../073-python3-fastjsonschema_2.21.1-1_all.deb ... 258s Unpacking python3-fastjsonschema (2.21.1-1) ... 258s Selecting previously unselected package python3-pytz. 258s Preparing to unpack .../074-python3-pytz_2025.1-3_all.deb ... 258s Unpacking python3-pytz (2025.1-3) ... 258s Selecting previously unselected package python3-tz. 258s Preparing to unpack .../075-python3-tz_2025.1-3_all.deb ... 258s Unpacking python3-tz (2025.1-3) ... 258s Selecting previously unselected package python3-platformdirs. 258s Preparing to unpack .../076-python3-platformdirs_4.3.6-1_all.deb ... 258s Unpacking python3-platformdirs (4.3.6-1) ... 258s Selecting previously unselected package python3-fs. 258s Preparing to unpack .../077-python3-fs_2.4.16-6_all.deb ... 258s Unpacking python3-fs (2.4.16-6) ... 258s Selecting previously unselected package python3-lxml:arm64. 258s Preparing to unpack .../078-python3-lxml_5.3.1-1_arm64.deb ... 258s Unpacking python3-lxml:arm64 (5.3.1-1) ... 258s Selecting previously unselected package python3-lz4. 258s Preparing to unpack .../079-python3-lz4_4.4.0+dfsg-1_arm64.deb ... 258s Unpacking python3-lz4 (4.4.0+dfsg-1) ... 258s Selecting previously unselected package python3-scipy. 258s Preparing to unpack .../080-python3-scipy_1.14.1-4ubuntu1_arm64.deb ... 258s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 259s Selecting previously unselected package python3-mpmath. 259s Preparing to unpack .../081-python3-mpmath_1.3.0-1_all.deb ... 259s Unpacking python3-mpmath (1.3.0-1) ... 259s Selecting previously unselected package python3-sympy. 259s Preparing to unpack .../082-python3-sympy_1.13.3-1_all.deb ... 259s Unpacking python3-sympy (1.13.3-1) ... 259s Selecting previously unselected package python3-ufolib2. 259s Preparing to unpack .../083-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 259s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 259s Selecting previously unselected package python3-unicodedata2. 259s Preparing to unpack .../084-python3-unicodedata2_15.1.0+ds-1build2_arm64.deb ... 259s Unpacking python3-unicodedata2 (15.1.0+ds-1build2) ... 259s Selecting previously unselected package unicode-data. 259s Preparing to unpack .../085-unicode-data_15.1.0-1_all.deb ... 259s Unpacking unicode-data (15.1.0-1) ... 260s Selecting previously unselected package python3-fonttools. 260s Preparing to unpack .../086-python3-fonttools_4.55.3-2_arm64.deb ... 260s Unpacking python3-fonttools (4.55.3-2) ... 260s Selecting previously unselected package python3-gsd. 260s Preparing to unpack .../087-python3-gsd_3.3.0-1build2_arm64.deb ... 260s Unpacking python3-gsd (3.3.0-1build2) ... 260s Selecting previously unselected package python3-iniconfig. 260s Preparing to unpack .../088-python3-iniconfig_1.1.1-2_all.deb ... 260s Unpacking python3-iniconfig (1.1.1-2) ... 260s Selecting previously unselected package python3-parso. 260s Preparing to unpack .../089-python3-parso_0.8.4-1_all.deb ... 260s Unpacking python3-parso (0.8.4-1) ... 260s Selecting previously unselected package python3-typeshed. 260s Preparing to unpack .../090-python3-typeshed_0.0~git20241223.ea91db2-1_all.deb ... 260s Unpacking python3-typeshed (0.0~git20241223.ea91db2-1) ... 260s Selecting previously unselected package python3-jedi. 260s Preparing to unpack .../091-python3-jedi_0.19.1+ds1-1_all.deb ... 260s Unpacking python3-jedi (0.19.1+ds1-1) ... 261s Selecting previously unselected package python3-matplotlib-inline. 261s Preparing to unpack .../092-python3-matplotlib-inline_0.1.6-2_all.deb ... 261s Unpacking python3-matplotlib-inline (0.1.6-2) ... 261s Selecting previously unselected package python3-wcwidth. 261s Preparing to unpack .../093-python3-wcwidth_0.2.13+dfsg1-1_all.deb ... 261s Unpacking python3-wcwidth (0.2.13+dfsg1-1) ... 261s Selecting previously unselected package python3-prompt-toolkit. 261s Preparing to unpack .../094-python3-prompt-toolkit_3.0.50-1_all.deb ... 261s Unpacking python3-prompt-toolkit (3.0.50-1) ... 261s Selecting previously unselected package python3-pure-eval. 261s Preparing to unpack .../095-python3-pure-eval_0.2.3-1_all.deb ... 261s Unpacking python3-pure-eval (0.2.3-1) ... 261s Selecting previously unselected package python3-stack-data. 261s Preparing to unpack .../096-python3-stack-data_0.6.3-1_all.deb ... 261s Unpacking python3-stack-data (0.6.3-1) ... 261s Selecting previously unselected package python3-ptyprocess. 261s Preparing to unpack .../097-python3-ptyprocess_0.7.0-6_all.deb ... 261s Unpacking python3-ptyprocess (0.7.0-6) ... 261s Selecting previously unselected package python3-pexpect. 261s Preparing to unpack .../098-python3-pexpect_4.9-3_all.deb ... 261s Unpacking python3-pexpect (4.9-3) ... 261s Selecting previously unselected package python3-ipython. 261s Preparing to unpack .../099-python3-ipython_8.30.0-2_all.deb ... 261s Unpacking python3-ipython (8.30.0-2) ... 261s Selecting previously unselected package python3-jupyter-core. 261s Preparing to unpack .../100-python3-jupyter-core_5.7.2-5_all.deb ... 261s Unpacking python3-jupyter-core (5.7.2-5) ... 261s Selecting previously unselected package python3-psutil. 261s Preparing to unpack .../101-python3-psutil_5.9.8-2build3_arm64.deb ... 261s Unpacking python3-psutil (5.9.8-2build3) ... 261s Selecting previously unselected package python3-tornado. 261s Preparing to unpack .../102-python3-tornado_6.4.2-1_arm64.deb ... 261s Unpacking python3-tornado (6.4.2-1) ... 261s Selecting previously unselected package python3-zmq. 261s Preparing to unpack .../103-python3-zmq_26.2.1-1_arm64.deb ... 261s Unpacking python3-zmq (26.2.1-1) ... 261s Selecting previously unselected package python3-jupyter-client. 261s Preparing to unpack .../104-python3-jupyter-client_8.6.3-2_all.deb ... 261s Unpacking python3-jupyter-client (8.6.3-2) ... 261s Selecting previously unselected package python3-nest-asyncio. 262s Preparing to unpack .../105-python3-nest-asyncio_1.5.4-1_all.deb ... 262s Unpacking python3-nest-asyncio (1.5.4-1) ... 262s Selecting previously unselected package python3-packaging. 262s Preparing to unpack .../106-python3-packaging_24.2-1_all.deb ... 262s Unpacking python3-packaging (24.2-1) ... 262s Selecting previously unselected package python3-ipykernel. 262s Preparing to unpack .../107-python3-ipykernel_6.29.5-2_all.deb ... 262s Unpacking python3-ipykernel (6.29.5-2) ... 262s Selecting previously unselected package python3-joblib. 262s Preparing to unpack .../108-python3-joblib_1.4.2-2_all.deb ... 262s Unpacking python3-joblib (1.4.2-2) ... 262s Selecting previously unselected package python3-kiwisolver. 262s Preparing to unpack .../109-python3-kiwisolver_1.4.7-3_arm64.deb ... 262s Unpacking python3-kiwisolver (1.4.7-3) ... 262s Selecting previously unselected package libopenjp2-7:arm64. 262s Preparing to unpack .../110-libopenjp2-7_2.5.0-2ubuntu3_arm64.deb ... 262s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu3) ... 262s Selecting previously unselected package python3-pil:arm64. 262s Preparing to unpack .../111-python3-pil_11.1.0-5_arm64.deb ... 262s Unpacking python3-pil:arm64 (11.1.0-5) ... 262s Selecting previously unselected package python3.12-tk. 262s Preparing to unpack .../112-python3.12-tk_3.12.9-1_arm64.deb ... 262s Unpacking python3.12-tk (3.12.9-1) ... 262s Selecting previously unselected package python3.13-tk. 262s Preparing to unpack .../113-python3.13-tk_3.13.2-1_arm64.deb ... 262s Unpacking python3.13-tk (3.13.2-1) ... 262s Selecting previously unselected package python3-tk:arm64. 262s Preparing to unpack .../114-python3-tk_3.13.1-1_arm64.deb ... 262s Unpacking python3-tk:arm64 (3.13.1-1) ... 262s Selecting previously unselected package python3-pil.imagetk:arm64. 262s Preparing to unpack .../115-python3-pil.imagetk_11.1.0-5_arm64.deb ... 262s Unpacking python3-pil.imagetk:arm64 (11.1.0-5) ... 262s Selecting previously unselected package python3-matplotlib. 262s Preparing to unpack .../116-python3-matplotlib_3.8.3-3ubuntu2_arm64.deb ... 262s Unpacking python3-matplotlib (3.8.3-3ubuntu2) ... 263s Selecting previously unselected package python3-netcdf4. 263s Preparing to unpack .../117-python3-netcdf4_1.7.2-1build3_arm64.deb ... 263s Unpacking python3-netcdf4 (1.7.2-1build3) ... 263s Selecting previously unselected package python3-networkx. 263s Preparing to unpack .../118-python3-networkx_3.2.1-4ubuntu1_all.deb ... 263s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 263s Selecting previously unselected package python3-pandas-lib:arm64. 263s Preparing to unpack .../119-python3-pandas-lib_2.2.3+dfsg-8_arm64.deb ... 263s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-8) ... 264s Selecting previously unselected package python3-pandas. 264s Preparing to unpack .../120-python3-pandas_2.2.3+dfsg-8_all.deb ... 264s Unpacking python3-pandas (2.2.3+dfsg-8) ... 264s Selecting previously unselected package python3-numexpr. 264s Preparing to unpack .../121-python3-numexpr_2.10.2-1build1_arm64.deb ... 264s Unpacking python3-numexpr (2.10.2-1build1) ... 264s Selecting previously unselected package python3-tables-lib. 264s Preparing to unpack .../122-python3-tables-lib_3.10.2-2_arm64.deb ... 264s Unpacking python3-tables-lib (3.10.2-2) ... 264s Selecting previously unselected package python3-tables. 264s Preparing to unpack .../123-python3-tables_3.10.2-2_all.deb ... 264s Unpacking python3-tables (3.10.2-2) ... 264s Selecting previously unselected package python3-mdtraj. 264s Preparing to unpack .../124-python3-mdtraj_1.10.3-2_arm64.deb ... 264s Unpacking python3-mdtraj (1.10.3-2) ... 264s Selecting previously unselected package python3-nbformat. 264s Preparing to unpack .../125-python3-nbformat_5.9.1-1_all.deb ... 264s Unpacking python3-nbformat (5.9.1-1) ... 264s Selecting previously unselected package python3-pluggy. 264s Preparing to unpack .../126-python3-pluggy_1.5.0-1_all.deb ... 264s Unpacking python3-pluggy (1.5.0-1) ... 264s Selecting previously unselected package python3-pytest. 264s Preparing to unpack .../127-python3-pytest_8.3.4-1_all.deb ... 264s Unpacking python3-pytest (8.3.4-1) ... 265s Selecting previously unselected package python3-threadpoolctl. 265s Preparing to unpack .../128-python3-threadpoolctl_3.1.0-1_all.deb ... 265s Unpacking python3-threadpoolctl (3.1.0-1) ... 265s Selecting previously unselected package python3-sklearn-lib:arm64. 265s Preparing to unpack .../129-python3-sklearn-lib_1.4.2+dfsg-7build1_arm64.deb ... 265s Unpacking python3-sklearn-lib:arm64 (1.4.2+dfsg-7build1) ... 265s Selecting previously unselected package python3-sklearn. 265s Preparing to unpack .../130-python3-sklearn_1.4.2+dfsg-7build1_all.deb ... 265s Unpacking python3-sklearn (1.4.2+dfsg-7build1) ... 265s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 265s Setting up liblcms2-2:arm64 (2.16-2) ... 265s Setting up python3-iniconfig (1.1.1-2) ... 265s Setting up python3.12-minimal (3.12.9-1) ... 267s Setting up python3-tornado (6.4.2-1) ... 268s Setting up libnorm1t64:arm64 (1.5.9+dfsg-3.1build1) ... 268s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 268s Setting up python3-pure-eval (0.2.3-1) ... 268s Setting up libsodium23:arm64 (1.0.18-1build3) ... 268s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 268s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 268s Setting up libdebuginfod-common (0.192-4) ... 268s Setting up python3-joblib (1.4.2-2) ... 268s Setting up python3-parso (0.8.4-1) ... 269s Setting up python3-lz4 (4.4.0+dfsg-1) ... 269s Setting up python3-asttokens (3.0.0-1) ... 270s Setting up python3-unicodedata2 (15.1.0+ds-1build2) ... 270s Setting up fonts-lyx (2.4.3-1) ... 270s Setting up python3.12 (3.12.9-1) ... 271s Setting up python3-threadpoolctl (3.1.0-1) ... 272s Setting up x11-common (1:7.7+23ubuntu3) ... 272s Setting up libdeflate0:arm64 (1.23-1) ... 272s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 272s Setting up python3-coverage (7.4.4+dfsg1-0ubuntu3) ... 273s Setting up python3-pytz (2025.1-3) ... 273s Setting up libgomp1:arm64 (15-20250213-1ubuntu1) ... 273s Setting up python3-networkx (3.2.1-4ubuntu1) ... 276s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 276s Setting up libaec0:arm64 (1.1.3-1) ... 276s Setting up python3-platformdirs (4.3.6-1) ... 276s Setting up python3-psutil (5.9.8-2build3) ... 277s Setting up libsource-highlight-common (3.1.9-4.3build1) ... 277s Setting up python3-tz (2025.1-3) ... 277s Setting up libsnappy1v5:arm64 (1.2.1-1) ... 277s Setting up python3-fs (2.4.16-6) ... 277s Setting up unicode-data (15.1.0-1) ... 277s Setting up libpgm-5.3-0t64:arm64 (5.3.128~dfsg-2.1build1) ... 277s Setting up python3-decorator (5.1.1-5) ... 277s Setting up libblosc2-4:arm64 (2.16.0+ds-1) ... 277s Setting up libblas3:arm64 (3.12.1-2) ... 277s 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 277s Setting up python3-packaging (24.2-1) ... 278s Setting up python3-wcwidth (0.2.13+dfsg1-1) ... 278s Setting up python3-typeshed (0.0~git20241223.ea91db2-1) ... 278s Setting up python3-executing (2.2.0-0.1) ... 278s Setting up python3-nest-asyncio (1.5.4-1) ... 278s Setting up python3-brotli (1.1.0-2build3) ... 279s Setting up python3-cycler (0.12.1-1) ... 279s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 279s Setting up fonts-dejavu-mono (2.37-8) ... 279s Setting up python3-kiwisolver (1.4.7-3) ... 279s Setting up libtcl8.6:arm64 (8.6.16+dfsg-1) ... 279s Setting up fonts-dejavu-core (2.37-8) ... 279s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 279s Setting up python3-cpuinfo (9.0.0+git20221119-3) ... 279s Setting up libbabeltrace1:arm64 (1.5.11-4build1) ... 279s Setting up libgfortran5:arm64 (15-20250213-1ubuntu1) ... 280s Setting up python3-pluggy (1.5.0-1) ... 280s Setting up libwebp7:arm64 (1.5.0-0.1) ... 280s Setting up python3-fastjsonschema (2.21.1-1) ... 280s Setting up python3-traitlets (5.14.3+really5.14.3-1) ... 280s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ... 280s Setting up libblosc1:arm64 (1.21.5+ds-1build1) ... 280s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu3) ... 280s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 280s Setting up python3-dateutil (2.9.0-3) ... 281s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 281s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 281s Setting up python3-mpmath (1.3.0-1) ... 282s Setting up python-matplotlib-data (3.8.3-3ubuntu2) ... 282s Setting up libwebpmux3:arm64 (1.5.0-0.1) ... 282s Setting up python3-stack-data (0.6.3-1) ... 282s Setting up python-tables-data (3.10.2-2) ... 282s Setting up python3-jupyter-core (5.7.2-5) ... 282s Setting up libsz2:arm64 (1.1.3-1) ... 282s Setting up python3-ptyprocess (0.7.0-6) ... 282s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 282s Setting up python3-prompt-toolkit (3.0.50-1) ... 283s Setting up python3-sympy (1.13.3-1) ... 298s Setting up libdebuginfod1t64:arm64 (0.192-4) ... 298s Setting up liblapack3:arm64 (3.12.1-2) ... 298s 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 298s Setting up libzmq5:arm64 (4.3.5-1build2) ... 298s Setting up python3-jedi (0.19.1+ds1-1) ... 299s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 299s Setting up python3-pytest (8.3.4-1) ... 300s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 300s Setting up libsource-highlight4t64:arm64 (3.1.9-4.3build1) ... 300s Setting up python3-nbformat (5.9.1-1) ... 300s Setting up python3-matplotlib-inline (0.1.6-2) ... 300s Setting up python3-comm (0.2.1-1) ... 300s Setting up gdb (16.2-1ubuntu1) ... 300s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 300s Setting up python3-pexpect (4.9-3) ... 301s Setting up python3-zmq (26.2.1-1) ... 301s Setting up libraqm0:arm64 (0.10.2-1) ... 301s Setting up python3-numpy (1:1.26.4+ds-13) ... 305s Setting up libhdf5-310:arm64 (1.14.5+repack-3) ... 305s Setting up python3-lxml:arm64 (5.3.1-1) ... 306s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 306s Setting up python3-jupyter-client (8.6.3-2) ... 306s Setting up python3-contourpy (1.3.1-1) ... 306s Setting up libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 306s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 306s Setting up libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 306s Setting up libxft2:arm64 (2.3.6-1build1) ... 306s Setting up python3-scipy (1.14.1-4ubuntu1) ... 314s Setting up python3-tables-lib (3.10.2-2) ... 314s Setting up libtk8.6:arm64 (8.6.16-1) ... 314s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-8) ... 314s Setting up python3.12-tk (3.12.9-1) ... 314s Setting up libnetcdf22:arm64 (1:4.9.3-1) ... 314s Setting up python3-sklearn-lib:arm64 (1.4.2+dfsg-7build1) ... 314s Setting up python3-gsd (3.3.0-1build2) ... 314s Setting up python3-debugpy (1.8.8+ds-2ubuntu1) ... 316s Setting up python3.13-tk (3.13.2-1) ... 316s Setting up python3-pil:arm64 (11.1.0-5) ... 316s Setting up python3-pandas (2.2.3+dfsg-8) ... 328s Setting up python3-ipython (8.30.0-2) ... 328s Setting up python3-ipykernel (6.29.5-2) ... 329s Setting up python3-sklearn (1.4.2+dfsg-7build1) ... 333s Setting up python3-cftime (1.6.4-1build2) ... 333s Setting up python3-numexpr (2.10.2-1build1) ... 334s Setting up python3-netcdf4 (1.7.2-1build3) ... 334s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 334s Setting up blt (2.5.3+dfsg-7build1) ... 334s Setting up python3-tk:arm64 (3.13.1-1) ... 334s Setting up python3-tables (3.10.2-2) ... 335s Setting up python3-mdtraj (1.10.3-2) ... 336s Setting up python3-pil.imagetk:arm64 (11.1.0-5) ... 336s Setting up python3-fonttools (4.55.3-2) ... 338s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 338s Setting up python3-matplotlib (3.8.3-3ubuntu2) ... 342s Processing triggers for libc-bin (2.40-4ubuntu1) ... 342s Processing triggers for systemd (257.2-3ubuntu1) ... 342s Processing triggers for man-db (2.13.0-1) ... 344s autopkgtest [12:05:11]: 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)' 344s autopkgtest [12:05:11]: test command1: [----------------------- 346s ============================= test session starts ============================== 346s platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 -- /usr/bin/python3 346s cachedir: .pytest_cache 346s rootdir: /tmp/autopkgtest.3VyOX4/build.ex9/src 346s configfile: pyproject.toml 346s testpaths: tests, examples 346s plugins: typeguard-4.4.1 347s collecting ... collected 1145 items / 12 deselected / 1133 selected 347s 347s tests/test_alignment.py::test_rmsd_zero PASSED [ 0%] 347s tests/test_alignment.py::test_rmsd_nonzero PASSED [ 0%] 347s tests/test_alignment.py::test_transform PASSED [ 0%] 347s tests/test_alignment.py::test_transform2 PASSED [ 0%] 348s tests/test_angles.py::test_angle_pbc_0 PASSED [ 0%] 348s tests/test_angles.py::test_generator PASSED [ 0%] 348s tests/test_angles.py::test_angle_180[True] PASSED [ 0%] 348s tests/test_angles.py::test_angle_180[False] PASSED [ 0%] 348s tests/test_arc.py::test_read_0 PASSED [ 0%] 348s tests/test_arc.py::test_read_arctraj PASSED [ 0%] 348s tests/test_arc.py::test_read_pbc PASSED [ 0%] 348s tests/test_capi.py::test_1 PASSED [ 1%] 348s tests/test_contact.py::test_contact_0 PASSED [ 1%] 348s tests/test_contact.py::test_contact_1 PASSED [ 1%] 349s tests/test_contact.py::test_contact_2 PASSED [ 1%] 349s tests/test_contact.py::test_contact_3 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[ 3%] 350s tests/test_dihedral.py::test_dihedral_2chains PASSED [ 4%] 350s tests/test_dihedral.py::test_generator PASSED [ 4%] 350s tests/test_distance.py::test_generator PASSED [ 4%] 350s tests/test_distance.py::test_0 PASSED [ 4%] 350s tests/test_distance.py::test_compute_distances_core_nonperiodic PASSED [ 4%] 352s tests/test_distance.py::test_compute_distances_core_periodic PASSED [ 4%] 352s tests/test_distance.py::test_1 PASSED [ 4%] 352s tests/test_distance.py::test_2 PASSED [ 4%] 353s tests/test_distance.py::test_0p PASSED [ 4%] 354s tests/test_distance.py::test_1p PASSED [ 4%] 356s tests/test_distance.py::test_2p PASSED [ 4%] 357s tests/test_distance.py::test_4 PASSED [ 5%] 357s tests/test_distance.py::test_5 PASSED [ 5%] 357s tests/test_distance.py::test_6 PASSED [ 5%] 357s tests/test_distance.py::test_7 PASSED [ 5%] 357s tests/test_distance.py::test_closest_contact PASSED [ 5%] 357s tests/test_distance.py::test_distance_nan PASSED [ 5%] 357s tests/test_distance.py::test_closest_contact_nan_pos PASSED [ 5%] 357s tests/test_distance.py::test_distance_t_inputs PASSED [ 5%] 358s tests/test_distance.py::test_distances_t PASSED [ 5%] 358s tests/test_distance.py::test_distances_t_at_0 PASSED [ 5%] 358s tests/test_distance.py::test_amber_t PASSED [ 5%] 358s tests/test_docstrings.py::test_docstrings[mdtraj._lprmsd] PASSED [ 6%] 358s tests/test_docstrings.py::test_docstrings[mdtraj._rmsd] PASSED [ 6%] 358s tests/test_docstrings.py::test_docstrings[mdtraj._version] SKIPPED (...) [ 6%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.core.element] PASSED [ 6%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.core.residue_names] PASSED [ 6%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.core.selection] PASSED [ 6%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.core.topology] PASSED [ 6%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.core.trajectory] PASSED [ 6%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.amberrst] PASSED [ 6%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.arc] PASSED [ 6%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.dcd] PASSED [ 6%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.dtr] PASSED [ 6%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.gro] PASSED [ 7%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.gsd] PASSED [ 7%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.hdf5] SKIPPED [ 7%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.hoomdxml] PASSED [ 7%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.lammpstrj] PASSED [ 7%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.lh5] SKIPPED [ 7%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.mdcrd] PASSED [ 7%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.mol2] PASSED [ 7%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.netcdf] PASSED [ 7%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.openmmxml] PASSED [ 7%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdb.pdbfile] PASSED [ 7%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdb.pdbstructure] SKIPPED [ 8%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.pdbx] PASSED [ 8%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.prmtop] PASSED [ 8%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.psf] PASSED [ 8%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.registry] PASSED [ 8%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.trr] PASSED [ 8%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.xtc] PASSED [ 8%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.formats.xyzfile] PASSED [ 8%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.geometry._geometry] PASSED [ 8%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.alignment] PASSED [ 8%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.angle] PASSED [ 8%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.contact] PASSED [ 9%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.dihedral] PASSED [ 9%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.distance] PASSED [ 9%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.drid] PASSED [ 9%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.dssp] PASSED [ 9%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.hbond] PASSED [ 9%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.internal] PASSED [ 9%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.neighborlist] PASSED [ 9%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.neighbors] PASSED [ 9%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.order] PASSED [ 9%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.rdf] PASSED [ 9%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.rg] PASSED [ 9%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.sasa] PASSED [ 10%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.shape] PASSED [ 10%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.thermodynamic_properties] PASSED [ 10%] 358s tests/test_docstrings.py::test_docstrings[mdtraj.io] SKIPPED (Skip c...) 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[ 37%] 550s tests/test_rdf.py::test_compare_rdf_t_master SKIPPED (Expected failu...) [ 37%] 550s tests/test_rdf.py::test_compare_n_concurrent_pairs PASSED [ 37%] 550s tests/test_reporter.py::test_reporter SKIPPED (test_reporter.py need...) [ 37%] 550s tests/test_reporter.py::test_reporter_subset SKIPPED (test_reporter....) [ 37%] 550s tests/test_reporter.py::test_xtc_reporter_append SKIPPED (test_repor...) [ 37%] 550s tests/test_restart.py::test_read_after_close PASSED [ 37%] 550s tests/test_restart.py::test_shape PASSED [ 37%] 550s tests/test_restart.py::test_shape_2 PASSED [ 38%] 550s tests/test_restart.py::test_read_write_1 PASSED [ 38%] 550s tests/test_restart.py::test_read_write_2 PASSED [ 38%] 550s tests/test_restart.py::test_read_write_3 PASSED [ 38%] 551s tests/test_restart.py::test_read_write_4 PASSED [ 38%] 551s tests/test_rmsd.py::test_trajectory_rmsd PASSED [ 38%] 551s tests/test_rmsd.py::test_precentered_1 PASSED [ 38%] 551s tests/test_rmsd.py::test_precentered_2 PASSED [ 38%] 551s tests/test_rmsd.py::test_superpose_0 PASSED [ 38%] 551s tests/test_rmsd.py::test_superpose_1 PASSED [ 38%] 551s tests/test_rmsd.py::test_superpose_2 PASSED [ 38%] 551s tests/test_rmsd.py::test_superpose_refinds PASSED [ 39%] 551s tests/test_rmsd.py::test_rmsd_atom_indices PASSED [ 39%] 551s tests/test_rmsd.py::test_rmsd_ref_ainds PASSED [ 39%] 552s tests/test_rmsd.py::test_average_structure PASSED [ 39%] 552s tests/test_rmsd.py::test_trajectory_rmsf PASSED [ 39%] 552s tests/test_rmsd.py::test_trajectory_rmsf_aligned PASSED [ 39%] 552s tests/test_rmsd.py::test_rmsd_atom_indices_vs_ref_indices PASSED [ 39%] 552s tests/test_rmsd_memmap.py::test_1 PASSED [ 39%] 552s tests/test_rmsd_memmap.py::test_2 PASSED [ 39%] 552s tests/test_sasa.py::test_sasa_0 PASSED [ 39%] 552s tests/test_sasa.py::test_sasa_1 PASSED [ 39%] 552s tests/test_sasa.py::test_sasa_2 PASSED [ 39%] 552s tests/test_sasa.py::test_sasa_3 PASSED [ 40%] 553s tests/test_sasa.py::test_sasa_4 PASSED [ 40%] 553s tests/test_sasa.py::test_sasa_5 PASSED [ 40%] 553s tests/test_sasa.py::test_sasa_6 PASSED [ 40%] 554s tests/test_sasa.py::test_sasa_7 PASSED [ 40%] 554s tests/test_selection.py::test_range PASSED [ 40%] 554s tests/test_selection.py::test_unary_2 PASSED [ 40%] 554s tests/test_selection.py::test_unary_3 PASSED [ 40%] 554s tests/test_selection.py::test_binary_1 PASSED [ 40%] 554s tests/test_selection.py::test_binary_2 PASSED [ 40%] 554s tests/test_selection.py::test_simple PASSED [ 40%] 554s tests/test_selection.py::test_alias PASSED [ 41%] 554s tests/test_selection.py::test_unary_1 PASSED [ 41%] 554s tests/test_selection.py::test_binary_selection_operator PASSED [ 41%] 554s tests/test_selection.py::test_raises PASSED [ 41%] 554s tests/test_selection.py::test_raises2 PASSED [ 41%] 554s tests/test_selection.py::test_bool PASSED [ 41%] 554s tests/test_selection.py::test_nested_bool PASSED [ 41%] 554s tests/test_selection.py::test_values PASSED [ 41%] 554s tests/test_selection.py::test_element PASSED [ 41%] 554s tests/test_selection.py::test_not PASSED [ 41%] 554s tests/test_selection.py::test_re PASSED [ 41%] 554s tests/test_selection.py::test_within SKIPPED (failed to parse selection) [ 42%] 554s tests/test_selection.py::test_quotes PASSED [ 42%] 555s tests/test_selection.py::test_top PASSED [ 42%] 555s tests/test_selection.py::test_top_2 PASSED [ 42%] 555s tests/test_selection.py::test_backbone PASSED [ 42%] 555s tests/test_selection.py::test_sidechain PASSED [ 42%] 555s tests/test_selection.py::test_literal PASSED [ 42%] 555s tests/test_selection.py::test_in PASSED [ 42%] 555s tests/test_shape.py::test_gyration PASSED [ 42%] 556s tests/test_shape.py::test_principal_moments PASSED [ 42%] 556s tests/test_shape.py::test_asphericity PASSED [ 42%] 556s tests/test_shape.py::test_shape_metrics PASSED [ 42%] 557s tests/test_thermodynamic_properties.py::test_volume PASSED [ 43%] 557s tests/test_thermodynamic_properties.py::test_density PASSED [ 43%] 557s tests/test_thermodynamic_properties.py::test_dipole_moments PASSED [ 43%] 557s tests/test_thermodynamic_properties.py::test_static_dielectric PASSED [ 43%] 557s tests/test_thermodynamic_properties.py::test_kappa PASSED [ 43%] 557s tests/test_thermodynamic_properties.py::test_alpha SKIPPED (Thermal ...) [ 43%] 557s tests/test_topology.py::test_topology_openmm SKIPPED (needs OpenMM) [ 43%] 557s tests/test_topology.py::test_topology_openmm_preserve_chain_id_when_specified SKIPPED [ 43%] 557s tests/test_topology.py::test_topology_openmm_roundtrip_chain_id SKIPPED [ 43%] 557s tests/test_topology.py::test_topology_openmm_preserve_chain_id_even_when_empty SKIPPED [ 43%] 557s tests/test_topology.py::test_topology_openmm_boxes SKIPPED (needs Op...) [ 43%] 557s tests/test_topology.py::test_topology_openmm_formal_charges SKIPPED [ 44%] 557s tests/test_topology.py::test_topology_pandas PASSED [ 44%] 557s tests/test_topology.py::test_topology_pandas_TIP4PEW PASSED [ 44%] 557s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq PASSED [ 44%] 557s tests/test_topology.py::test_topology_numbers PASSED [ 44%] 557s tests/test_topology.py::test_topology_unique_elements_bpti PASSED [ 44%] 557s tests/test_topology.py::test_chain PASSED [ 44%] 557s tests/test_topology.py::test_residue PASSED [ 44%] 557s tests/test_topology.py::test_segment_id PASSED [ 44%] 557s tests/test_topology.py::test_nonconsective_resSeq PASSED [ 44%] 557s tests/test_topology.py::test_pickle PASSED [ 44%] 557s tests/test_topology.py::test_atoms_by_name PASSED [ 45%] 557s tests/test_topology.py::test_select_atom_indices PASSED [ 45%] 557s tests/test_topology.py::test_top_dataframe_openmm_roundtrip SKIPPED [ 45%] 557s tests/test_topology.py::test_n_bonds PASSED [ 45%] 557s tests/test_topology.py::test_load_unknown_topology PASSED [ 45%] 557s tests/test_topology.py::test_unique_pairs PASSED [ 45%] 558s tests/test_topology.py::test_select_pairs PASSED [ 45%] 558s tests/test_topology.py::test_to_fasta PASSED [ 45%] 558s tests/test_topology.py::test_subset PASSED [ 45%] 559s tests/test_topology.py::test_subset_re_index_residues PASSED [ 45%] 559s tests/test_topology.py::test_molecules PASSED [ 45%] 559s tests/test_topology.py::test_copy_and_hash PASSED [ 45%] 559s tests/test_topology.py::test_topology_sliced_residue_indices PASSED [ 46%] 559s tests/test_topology.py::test_topology_join PASSED [ 46%] 559s tests/test_topology.py::test_topology_join_keep_resSeq PASSED [ 46%] 559s tests/test_trajectory.py::test_mismatch PASSED [ 46%] 559s tests/test_trajectory.py::test_box PASSED [ 46%] 559s tests/test_trajectory.py::test_load_pdb_box PASSED [ 46%] 559s tests/test_trajectory.py::test_load_pdb_gz PASSED [ 46%] 559s tests/test_trajectory.py::test_box_load_save[nc] PASSED [ 46%] 559s tests/test_trajectory.py::test_box_load_save[h5] PASSED [ 46%] 559s tests/test_trajectory.py::test_box_load_save[xtc] PASSED [ 46%] 559s tests/test_trajectory.py::test_box_load_save[trr] PASSED [ 46%] 559s tests/test_trajectory.py::test_box_load_save[dcd] PASSED [ 47%] 560s tests/test_trajectory.py::test_box_load_save[mdcrd] PASSED [ 47%] 560s tests/test_trajectory.py::test_box_load_save[dtr] PASSED [ 47%] 560s tests/test_trajectory.py::test_box_load_save[xyz] SKIPPED (xyz does ...) [ 47%] 560s tests/test_trajectory.py::test_box_load_save[xyz.gz] SKIPPED (xyz.gz...) [ 47%] 560s tests/test_trajectory.py::test_box_load_save[lammpstrj] PASSED [ 47%] 560s tests/test_trajectory.py::test_box_load_save[lh5] SKIPPED (lh5 does ...) [ 47%] 560s tests/test_trajectory.py::test_box_load_save[pdb] SKIPPED (pdb does ...) [ 47%] 560s tests/test_trajectory.py::test_box_load_save[pdb.gz] SKIPPED (pdb.gz...) [ 47%] 560s tests/test_trajectory.py::test_box_load_save[ncrst] PASSED [ 47%] 560s tests/test_trajectory.py::test_box_load_save[rst7] PASSED [ 47%] 560s tests/test_trajectory.py::test_box_load_save[gro] PASSED [ 48%] 560s tests/test_trajectory.py::test_slice PASSED [ 48%] 560s tests/test_trajectory.py::test_slice2 PASSED [ 48%] 560s tests/test_trajectory.py::test_read_path[nc] PASSED [ 48%] 560s tests/test_trajectory.py::test_read_path[h5] PASSED [ 48%] 560s tests/test_trajectory.py::test_read_path[xtc] PASSED [ 48%] 560s tests/test_trajectory.py::test_read_path[trr] PASSED [ 48%] 560s tests/test_trajectory.py::test_read_path[dcd] PASSED [ 48%] 560s tests/test_trajectory.py::test_read_path[mdcrd] PASSED [ 48%] 560s tests/test_trajectory.py::test_read_path[dtr] PASSED [ 48%] 560s tests/test_trajectory.py::test_read_path[xyz] PASSED [ 48%] 560s tests/test_trajectory.py::test_read_path[xyz.gz] PASSED [ 48%] 560s tests/test_trajectory.py::test_read_path[lammpstrj] PASSED [ 49%] 560s tests/test_trajectory.py::test_read_path[lh5] PASSED [ 49%] 560s tests/test_trajectory.py::test_read_path[pdb] PASSED [ 49%] 560s tests/test_trajectory.py::test_read_path[pdb.gz] PASSED [ 49%] 560s tests/test_trajectory.py::test_read_path[ncrst] XFAIL (These referen...) [ 49%] 560s tests/test_trajectory.py::test_read_path[rst7] XFAIL (These referenc...) [ 49%] 560s tests/test_trajectory.py::test_read_path[gro] PASSED [ 49%] 560s tests/test_trajectory.py::test_write_path[nc] PASSED [ 49%] 560s tests/test_trajectory.py::test_write_path[h5] PASSED [ 49%] 560s tests/test_trajectory.py::test_write_path[xtc] PASSED [ 49%] 560s tests/test_trajectory.py::test_write_path[trr] PASSED [ 49%] 560s tests/test_trajectory.py::test_write_path[dcd] PASSED [ 50%] 560s tests/test_trajectory.py::test_write_path[mdcrd] SKIPPED (mdcrd can ...) [ 50%] 561s tests/test_trajectory.py::test_write_path[dtr] PASSED [ 50%] 561s tests/test_trajectory.py::test_write_path[xyz] PASSED [ 50%] 561s tests/test_trajectory.py::test_write_path[xyz.gz] PASSED [ 50%] 561s tests/test_trajectory.py::test_write_path[lammpstrj] PASSED [ 50%] 561s tests/test_trajectory.py::test_write_path[lh5] PASSED [ 50%] 561s tests/test_trajectory.py::test_write_path[pdb] PASSED [ 50%] 561s tests/test_trajectory.py::test_write_path[pdb.gz] PASSED [ 50%] 561s tests/test_trajectory.py::test_write_path[ncrst] SKIPPED (ncrst can ...) [ 50%] 561s tests/test_trajectory.py::test_write_path[rst7] SKIPPED (rst7 can on...) [ 50%] 561s tests/test_trajectory.py::test_write_path[gro] PASSED [ 51%] 561s tests/test_trajectory.py::test_read_write[nc-nc] PASSED [ 51%] 561s tests/test_trajectory.py::test_read_write[nc-h5] PASSED [ 51%] 561s tests/test_trajectory.py::test_read_write[nc-xtc] PASSED [ 51%] 561s tests/test_trajectory.py::test_read_write[nc-trr] PASSED [ 51%] 561s tests/test_trajectory.py::test_read_write[nc-dcd] PASSED [ 51%] 561s tests/test_trajectory.py::test_read_write[nc-mdcrd] SKIPPED (mdcrd c...) [ 51%] 565s tests/test_trajectory.py::test_read_write[nc-dtr] PASSED [ 51%] 565s tests/test_trajectory.py::test_read_write[nc-xyz] PASSED [ 51%] 566s tests/test_trajectory.py::test_read_write[nc-xyz.gz] PASSED [ 51%] 566s tests/test_trajectory.py::test_read_write[nc-lammpstrj] PASSED [ 51%] 566s tests/test_trajectory.py::test_read_write[nc-lh5] PASSED [ 51%] 567s tests/test_trajectory.py::test_read_write[nc-pdb] PASSED [ 52%] 568s tests/test_trajectory.py::test_read_write[nc-pdb.gz] PASSED [ 52%] 568s tests/test_trajectory.py::test_read_write[nc-ncrst] SKIPPED (ncrst c...) [ 52%] 568s tests/test_trajectory.py::test_read_write[nc-rst7] SKIPPED (rst7 can...) [ 52%] 568s tests/test_trajectory.py::test_read_write[nc-gro] PASSED [ 52%] 568s tests/test_trajectory.py::test_read_write[h5-nc] PASSED [ 52%] 568s tests/test_trajectory.py::test_read_write[h5-h5] PASSED [ 52%] 568s tests/test_trajectory.py::test_read_write[h5-xtc] PASSED [ 52%] 568s tests/test_trajectory.py::test_read_write[h5-trr] PASSED [ 52%] 568s tests/test_trajectory.py::test_read_write[h5-dcd] PASSED [ 52%] 568s tests/test_trajectory.py::test_read_write[h5-mdcrd] SKIPPED (mdcrd c...) [ 52%] 571s tests/test_trajectory.py::test_read_write[h5-dtr] PASSED [ 53%] 571s tests/test_trajectory.py::test_read_write[h5-xyz] PASSED [ 53%] 571s tests/test_trajectory.py::test_read_write[h5-xyz.gz] PASSED [ 53%] 571s tests/test_trajectory.py::test_read_write[h5-lammpstrj] PASSED [ 53%] 572s tests/test_trajectory.py::test_read_write[h5-lh5] PASSED [ 53%] 572s tests/test_trajectory.py::test_read_write[h5-pdb] PASSED [ 53%] 572s tests/test_trajectory.py::test_read_write[h5-pdb.gz] PASSED [ 53%] 572s tests/test_trajectory.py::test_read_write[h5-ncrst] SKIPPED (ncrst c...) [ 53%] 572s tests/test_trajectory.py::test_read_write[h5-rst7] SKIPPED (rst7 can...) [ 53%] 572s tests/test_trajectory.py::test_read_write[h5-gro] PASSED [ 53%] 572s tests/test_trajectory.py::test_read_write[xtc-nc] PASSED [ 53%] 572s tests/test_trajectory.py::test_read_write[xtc-h5] PASSED [ 54%] 572s tests/test_trajectory.py::test_read_write[xtc-xtc] PASSED [ 54%] 572s tests/test_trajectory.py::test_read_write[xtc-trr] PASSED [ 54%] 572s tests/test_trajectory.py::test_read_write[xtc-dcd] PASSED [ 54%] 572s tests/test_trajectory.py::test_read_write[xtc-mdcrd] SKIPPED (mdcrd ...) [ 54%] 577s tests/test_trajectory.py::test_read_write[xtc-dtr] PASSED [ 54%] 577s tests/test_trajectory.py::test_read_write[xtc-xyz] PASSED [ 54%] 577s tests/test_trajectory.py::test_read_write[xtc-xyz.gz] PASSED [ 54%] 577s tests/test_trajectory.py::test_read_write[xtc-lammpstrj] PASSED [ 54%] 577s tests/test_trajectory.py::test_read_write[xtc-lh5] PASSED [ 54%] 577s tests/test_trajectory.py::test_read_write[xtc-pdb] PASSED [ 54%] 577s tests/test_trajectory.py::test_read_write[xtc-pdb.gz] PASSED [ 54%] 577s tests/test_trajectory.py::test_read_write[xtc-ncrst] SKIPPED (ncrst ...) [ 55%] 577s tests/test_trajectory.py::test_read_write[xtc-rst7] SKIPPED (rst7 ca...) [ 55%] 577s tests/test_trajectory.py::test_read_write[xtc-gro] PASSED [ 55%] 577s tests/test_trajectory.py::test_read_write[trr-nc] PASSED [ 55%] 577s tests/test_trajectory.py::test_read_write[trr-h5] PASSED [ 55%] 577s tests/test_trajectory.py::test_read_write[trr-xtc] PASSED [ 55%] 577s tests/test_trajectory.py::test_read_write[trr-trr] PASSED [ 55%] 577s tests/test_trajectory.py::test_read_write[trr-dcd] PASSED [ 55%] 577s tests/test_trajectory.py::test_read_write[trr-mdcrd] SKIPPED (mdcrd ...) [ 55%] 579s tests/test_trajectory.py::test_read_write[trr-dtr] PASSED [ 55%] 579s tests/test_trajectory.py::test_read_write[trr-xyz] PASSED [ 55%] 579s tests/test_trajectory.py::test_read_write[trr-xyz.gz] PASSED [ 56%] 579s tests/test_trajectory.py::test_read_write[trr-lammpstrj] PASSED [ 56%] 579s tests/test_trajectory.py::test_read_write[trr-lh5] PASSED [ 56%] 580s tests/test_trajectory.py::test_read_write[trr-pdb] PASSED [ 56%] 580s tests/test_trajectory.py::test_read_write[trr-pdb.gz] PASSED [ 56%] 580s tests/test_trajectory.py::test_read_write[trr-ncrst] SKIPPED (ncrst ...) [ 56%] 580s tests/test_trajectory.py::test_read_write[trr-rst7] SKIPPED (rst7 ca...) [ 56%] 580s tests/test_trajectory.py::test_read_write[trr-gro] PASSED [ 56%] 581s tests/test_trajectory.py::test_read_write[dcd-nc] PASSED [ 56%] 581s tests/test_trajectory.py::test_read_write[dcd-h5] PASSED [ 56%] 581s tests/test_trajectory.py::test_read_write[dcd-xtc] PASSED [ 56%] 581s tests/test_trajectory.py::test_read_write[dcd-trr] PASSED [ 57%] 581s tests/test_trajectory.py::test_read_write[dcd-dcd] PASSED [ 57%] 581s tests/test_trajectory.py::test_read_write[dcd-mdcrd] SKIPPED (mdcrd ...) [ 57%] 583s tests/test_trajectory.py::test_read_write[dcd-dtr] PASSED [ 57%] 583s tests/test_trajectory.py::test_read_write[dcd-xyz] PASSED [ 57%] 583s tests/test_trajectory.py::test_read_write[dcd-xyz.gz] PASSED [ 57%] 583s tests/test_trajectory.py::test_read_write[dcd-lammpstrj] PASSED [ 57%] 583s tests/test_trajectory.py::test_read_write[dcd-lh5] PASSED [ 57%] 584s tests/test_trajectory.py::test_read_write[dcd-pdb] PASSED [ 57%] 584s tests/test_trajectory.py::test_read_write[dcd-pdb.gz] PASSED [ 57%] 584s tests/test_trajectory.py::test_read_write[dcd-ncrst] SKIPPED (ncrst ...) [ 57%] 584s tests/test_trajectory.py::test_read_write[dcd-rst7] SKIPPED (rst7 ca...) [ 57%] 584s tests/test_trajectory.py::test_read_write[dcd-gro] PASSED [ 58%] 585s tests/test_trajectory.py::test_read_write[mdcrd-nc] PASSED [ 58%] 585s tests/test_trajectory.py::test_read_write[mdcrd-h5] PASSED [ 58%] 585s tests/test_trajectory.py::test_read_write[mdcrd-xtc] PASSED [ 58%] 585s tests/test_trajectory.py::test_read_write[mdcrd-trr] PASSED [ 58%] 585s tests/test_trajectory.py::test_read_write[mdcrd-dcd] PASSED [ 58%] 585s tests/test_trajectory.py::test_read_write[mdcrd-mdcrd] SKIPPED (mdcr...) [ 58%] 585s tests/test_trajectory.py::test_read_write[mdcrd-dtr] SKIPPED (dtr ne...) [ 58%] 585s tests/test_trajectory.py::test_read_write[mdcrd-xyz] PASSED [ 58%] 585s tests/test_trajectory.py::test_read_write[mdcrd-xyz.gz] PASSED [ 58%] 585s tests/test_trajectory.py::test_read_write[mdcrd-lammpstrj] SKIPPED (...) [ 58%] 585s tests/test_trajectory.py::test_read_write[mdcrd-lh5] PASSED [ 59%] 586s tests/test_trajectory.py::test_read_write[mdcrd-pdb] PASSED [ 59%] 587s tests/test_trajectory.py::test_read_write[mdcrd-pdb.gz] PASSED [ 59%] 587s tests/test_trajectory.py::test_read_write[mdcrd-ncrst] SKIPPED (ncrs...) [ 59%] 587s tests/test_trajectory.py::test_read_write[mdcrd-rst7] SKIPPED (rst7 ...) [ 59%] 587s tests/test_trajectory.py::test_read_write[mdcrd-gro] PASSED [ 59%] 587s tests/test_trajectory.py::test_read_write[dtr-nc] PASSED [ 59%] 587s tests/test_trajectory.py::test_read_write[dtr-h5] PASSED [ 59%] 587s tests/test_trajectory.py::test_read_write[dtr-xtc] PASSED [ 59%] 587s tests/test_trajectory.py::test_read_write[dtr-trr] PASSED [ 59%] 588s tests/test_trajectory.py::test_read_write[dtr-dcd] PASSED [ 59%] 588s tests/test_trajectory.py::test_read_write[dtr-mdcrd] SKIPPED (mdcrd ...) [ 60%] 590s tests/test_trajectory.py::test_read_write[dtr-dtr] PASSED [ 60%] 590s tests/test_trajectory.py::test_read_write[dtr-xyz] PASSED [ 60%] 590s tests/test_trajectory.py::test_read_write[dtr-xyz.gz] PASSED [ 60%] 590s tests/test_trajectory.py::test_read_write[dtr-lammpstrj] PASSED [ 60%] 590s tests/test_trajectory.py::test_read_write[dtr-lh5] PASSED [ 60%] 591s tests/test_trajectory.py::test_read_write[dtr-pdb] PASSED [ 60%] 591s tests/test_trajectory.py::test_read_write[dtr-pdb.gz] PASSED [ 60%] 591s tests/test_trajectory.py::test_read_write[dtr-ncrst] SKIPPED (ncrst ...) [ 60%] 591s tests/test_trajectory.py::test_read_write[dtr-rst7] SKIPPED (rst7 ca...) [ 60%] 591s tests/test_trajectory.py::test_read_write[dtr-gro] PASSED [ 60%] 591s tests/test_trajectory.py::test_read_write[xyz-nc] PASSED [ 60%] 591s tests/test_trajectory.py::test_read_write[xyz-h5] PASSED [ 61%] 591s tests/test_trajectory.py::test_read_write[xyz-xtc] PASSED [ 61%] 591s tests/test_trajectory.py::test_read_write[xyz-trr] PASSED [ 61%] 592s tests/test_trajectory.py::test_read_write[xyz-dcd] PASSED [ 61%] 592s tests/test_trajectory.py::test_read_write[xyz-mdcrd] SKIPPED (mdcrd ...) [ 61%] 592s tests/test_trajectory.py::test_read_write[xyz-dtr] SKIPPED (dtr need...) [ 61%] 592s tests/test_trajectory.py::test_read_write[xyz-xyz] PASSED [ 61%] 592s tests/test_trajectory.py::test_read_write[xyz-xyz.gz] PASSED [ 61%] 592s tests/test_trajectory.py::test_read_write[xyz-lammpstrj] SKIPPED (la...) [ 61%] 592s tests/test_trajectory.py::test_read_write[xyz-lh5] PASSED [ 61%] 592s tests/test_trajectory.py::test_read_write[xyz-pdb] PASSED [ 61%] 593s tests/test_trajectory.py::test_read_write[xyz-pdb.gz] PASSED [ 62%] 593s tests/test_trajectory.py::test_read_write[xyz-ncrst] SKIPPED (ncrst ...) [ 62%] 593s tests/test_trajectory.py::test_read_write[xyz-rst7] SKIPPED (rst7 ca...) [ 62%] 593s tests/test_trajectory.py::test_read_write[xyz-gro] PASSED [ 62%] 593s tests/test_trajectory.py::test_read_write[xyz.gz-nc] PASSED [ 62%] 593s tests/test_trajectory.py::test_read_write[xyz.gz-h5] PASSED [ 62%] 593s tests/test_trajectory.py::test_read_write[xyz.gz-xtc] PASSED [ 62%] 593s tests/test_trajectory.py::test_read_write[xyz.gz-trr] PASSED [ 62%] 593s tests/test_trajectory.py::test_read_write[xyz.gz-dcd] PASSED [ 62%] 593s tests/test_trajectory.py::test_read_write[xyz.gz-mdcrd] SKIPPED (mdc...) [ 62%] 593s tests/test_trajectory.py::test_read_write[xyz.gz-dtr] SKIPPED (dtr n...) [ 62%] 593s tests/test_trajectory.py::test_read_write[xyz.gz-xyz] PASSED [ 63%] 594s tests/test_trajectory.py::test_read_write[xyz.gz-xyz.gz] PASSED [ 63%] 594s tests/test_trajectory.py::test_read_write[xyz.gz-lammpstrj] SKIPPED [ 63%] 594s tests/test_trajectory.py::test_read_write[xyz.gz-lh5] PASSED [ 63%] 594s tests/test_trajectory.py::test_read_write[xyz.gz-pdb] PASSED [ 63%] 595s tests/test_trajectory.py::test_read_write[xyz.gz-pdb.gz] PASSED [ 63%] 595s tests/test_trajectory.py::test_read_write[xyz.gz-ncrst] SKIPPED (ncr...) [ 63%] 595s tests/test_trajectory.py::test_read_write[xyz.gz-rst7] SKIPPED (rst7...) [ 63%] 595s tests/test_trajectory.py::test_read_write[xyz.gz-gro] PASSED [ 63%] 595s tests/test_trajectory.py::test_read_write[lammpstrj-nc] PASSED [ 63%] 595s tests/test_trajectory.py::test_read_write[lammpstrj-h5] PASSED [ 63%] 595s tests/test_trajectory.py::test_read_write[lammpstrj-xtc] PASSED [ 63%] 595s tests/test_trajectory.py::test_read_write[lammpstrj-trr] PASSED [ 64%] 595s tests/test_trajectory.py::test_read_write[lammpstrj-dcd] PASSED [ 64%] 595s tests/test_trajectory.py::test_read_write[lammpstrj-mdcrd] SKIPPED (...) [ 64%] 598s tests/test_trajectory.py::test_read_write[lammpstrj-dtr] PASSED [ 64%] 598s tests/test_trajectory.py::test_read_write[lammpstrj-xyz] PASSED [ 64%] 599s tests/test_trajectory.py::test_read_write[lammpstrj-xyz.gz] PASSED [ 64%] 599s tests/test_trajectory.py::test_read_write[lammpstrj-lammpstrj] PASSED [ 64%] 599s tests/test_trajectory.py::test_read_write[lammpstrj-lh5] PASSED [ 64%] 599s tests/test_trajectory.py::test_read_write[lammpstrj-pdb] PASSED [ 64%] 600s tests/test_trajectory.py::test_read_write[lammpstrj-pdb.gz] PASSED [ 64%] 600s tests/test_trajectory.py::test_read_write[lammpstrj-ncrst] SKIPPED (...) [ 64%] 600s tests/test_trajectory.py::test_read_write[lammpstrj-rst7] SKIPPED (r...) [ 65%] 600s tests/test_trajectory.py::test_read_write[lammpstrj-gro] PASSED [ 65%] 600s tests/test_trajectory.py::test_read_write[lh5-nc] PASSED [ 65%] 600s tests/test_trajectory.py::test_read_write[lh5-h5] PASSED [ 65%] 600s tests/test_trajectory.py::test_read_write[lh5-xtc] PASSED [ 65%] 600s tests/test_trajectory.py::test_read_write[lh5-trr] PASSED [ 65%] 600s tests/test_trajectory.py::test_read_write[lh5-dcd] PASSED [ 65%] 600s tests/test_trajectory.py::test_read_write[lh5-mdcrd] SKIPPED (mdcrd ...) [ 65%] 600s tests/test_trajectory.py::test_read_write[lh5-dtr] SKIPPED (dtr need...) [ 65%] 600s tests/test_trajectory.py::test_read_write[lh5-xyz] PASSED [ 65%] 600s tests/test_trajectory.py::test_read_write[lh5-xyz.gz] PASSED [ 65%] 601s tests/test_trajectory.py::test_read_write[lh5-lammpstrj] SKIPPED (la...) [ 66%] 601s tests/test_trajectory.py::test_read_write[lh5-lh5] PASSED [ 66%] 601s tests/test_trajectory.py::test_read_write[lh5-pdb] PASSED [ 66%] 601s tests/test_trajectory.py::test_read_write[lh5-pdb.gz] PASSED [ 66%] 601s tests/test_trajectory.py::test_read_write[lh5-ncrst] SKIPPED (ncrst ...) [ 66%] 601s tests/test_trajectory.py::test_read_write[lh5-rst7] SKIPPED (rst7 ca...) [ 66%] 601s tests/test_trajectory.py::test_read_write[lh5-gro] PASSED [ 66%] 602s tests/test_trajectory.py::test_read_write[pdb-nc] PASSED [ 66%] 602s tests/test_trajectory.py::test_read_write[pdb-h5] PASSED [ 66%] 602s tests/test_trajectory.py::test_read_write[pdb-xtc] PASSED [ 66%] 602s tests/test_trajectory.py::test_read_write[pdb-trr] PASSED [ 66%] 602s tests/test_trajectory.py::test_read_write[pdb-dcd] PASSED [ 66%] 602s tests/test_trajectory.py::test_read_write[pdb-mdcrd] SKIPPED (mdcrd ...) [ 67%] 605s tests/test_trajectory.py::test_read_write[pdb-dtr] PASSED [ 67%] 605s tests/test_trajectory.py::test_read_write[pdb-xyz] PASSED [ 67%] 606s tests/test_trajectory.py::test_read_write[pdb-xyz.gz] PASSED [ 67%] 606s tests/test_trajectory.py::test_read_write[pdb-lammpstrj] PASSED [ 67%] 606s tests/test_trajectory.py::test_read_write[pdb-lh5] PASSED [ 67%] 607s tests/test_trajectory.py::test_read_write[pdb-pdb] PASSED [ 67%] 608s tests/test_trajectory.py::test_read_write[pdb-pdb.gz] PASSED [ 67%] 608s tests/test_trajectory.py::test_read_write[pdb-ncrst] SKIPPED (ncrst ...) [ 67%] 608s tests/test_trajectory.py::test_read_write[pdb-rst7] SKIPPED (rst7 ca...) [ 67%] 608s tests/test_trajectory.py::test_read_write[pdb-gro] PASSED [ 67%] 608s tests/test_trajectory.py::test_read_write[pdb.gz-nc] PASSED [ 68%] 608s tests/test_trajectory.py::test_read_write[pdb.gz-h5] PASSED [ 68%] 609s tests/test_trajectory.py::test_read_write[pdb.gz-xtc] PASSED [ 68%] 609s tests/test_trajectory.py::test_read_write[pdb.gz-trr] PASSED [ 68%] 609s tests/test_trajectory.py::test_read_write[pdb.gz-dcd] PASSED [ 68%] 609s tests/test_trajectory.py::test_read_write[pdb.gz-mdcrd] SKIPPED (mdc...) [ 68%] 612s tests/test_trajectory.py::test_read_write[pdb.gz-dtr] PASSED [ 68%] 612s tests/test_trajectory.py::test_read_write[pdb.gz-xyz] PASSED [ 68%] 612s tests/test_trajectory.py::test_read_write[pdb.gz-xyz.gz] PASSED [ 68%] 613s tests/test_trajectory.py::test_read_write[pdb.gz-lammpstrj] PASSED [ 68%] 613s tests/test_trajectory.py::test_read_write[pdb.gz-lh5] PASSED [ 68%] 613s tests/test_trajectory.py::test_read_write[pdb.gz-pdb] PASSED [ 69%] 614s tests/test_trajectory.py::test_read_write[pdb.gz-pdb.gz] PASSED [ 69%] 614s tests/test_trajectory.py::test_read_write[pdb.gz-ncrst] SKIPPED (ncr...) [ 69%] 614s tests/test_trajectory.py::test_read_write[pdb.gz-rst7] SKIPPED (rst7...) [ 69%] 614s tests/test_trajectory.py::test_read_write[pdb.gz-gro] PASSED [ 69%] 615s tests/test_trajectory.py::test_read_write[ncrst-nc] XFAIL (These ref...) [ 69%] 615s tests/test_trajectory.py::test_read_write[ncrst-h5] XFAIL (These ref...) [ 69%] 615s tests/test_trajectory.py::test_read_write[ncrst-xtc] XFAIL (These re...) [ 69%] 615s tests/test_trajectory.py::test_read_write[ncrst-trr] XFAIL (These re...) [ 69%] 615s tests/test_trajectory.py::test_read_write[ncrst-dcd] XFAIL (These re...) [ 69%] 615s tests/test_trajectory.py::test_read_write[ncrst-mdcrd] XFAIL (These ...) [ 69%] 615s tests/test_trajectory.py::test_read_write[ncrst-dtr] XFAIL (These re...) [ 69%] 615s tests/test_trajectory.py::test_read_write[ncrst-xyz] XFAIL (These re...) [ 70%] 615s tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] XFAIL (These...) [ 70%] 615s tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] XFAIL (Th...) [ 70%] 615s tests/test_trajectory.py::test_read_write[ncrst-lh5] XFAIL (These re...) [ 70%] 615s tests/test_trajectory.py::test_read_write[ncrst-pdb] XFAIL (These re...) [ 70%] 615s tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] XFAIL (These...) [ 70%] 615s tests/test_trajectory.py::test_read_write[ncrst-ncrst] XFAIL (These ...) [ 70%] 615s tests/test_trajectory.py::test_read_write[ncrst-rst7] XFAIL (These r...) [ 70%] 615s tests/test_trajectory.py::test_read_write[ncrst-gro] XFAIL (These re...) [ 70%] 615s tests/test_trajectory.py::test_read_write[rst7-nc] XFAIL (These refe...) [ 70%] 615s tests/test_trajectory.py::test_read_write[rst7-h5] XFAIL (These refe...) [ 70%] 615s tests/test_trajectory.py::test_read_write[rst7-xtc] XFAIL (These ref...) [ 71%] 615s tests/test_trajectory.py::test_read_write[rst7-trr] XFAIL (These ref...) [ 71%] 615s tests/test_trajectory.py::test_read_write[rst7-dcd] XFAIL (These ref...) [ 71%] 615s tests/test_trajectory.py::test_read_write[rst7-mdcrd] XFAIL (These r...) [ 71%] 615s tests/test_trajectory.py::test_read_write[rst7-dtr] XFAIL (These ref...) [ 71%] 615s tests/test_trajectory.py::test_read_write[rst7-xyz] XFAIL (These ref...) [ 71%] 615s tests/test_trajectory.py::test_read_write[rst7-xyz.gz] XFAIL (These ...) [ 71%] 615s tests/test_trajectory.py::test_read_write[rst7-lammpstrj] XFAIL (The...) [ 71%] 615s tests/test_trajectory.py::test_read_write[rst7-lh5] XFAIL (These ref...) [ 71%] 615s tests/test_trajectory.py::test_read_write[rst7-pdb] XFAIL (These ref...) [ 71%] 615s tests/test_trajectory.py::test_read_write[rst7-pdb.gz] XFAIL (These ...) [ 71%] 615s tests/test_trajectory.py::test_read_write[rst7-ncrst] XFAIL (These r...) [ 72%] 615s tests/test_trajectory.py::test_read_write[rst7-rst7] XFAIL (These re...) [ 72%] 615s tests/test_trajectory.py::test_read_write[rst7-gro] XFAIL (These ref...) [ 72%] 615s tests/test_trajectory.py::test_read_write[gro-nc] PASSED [ 72%] 615s tests/test_trajectory.py::test_read_write[gro-h5] PASSED [ 72%] 616s tests/test_trajectory.py::test_read_write[gro-xtc] PASSED [ 72%] 616s tests/test_trajectory.py::test_read_write[gro-trr] PASSED [ 72%] 616s tests/test_trajectory.py::test_read_write[gro-dcd] PASSED [ 72%] 616s tests/test_trajectory.py::test_read_write[gro-mdcrd] SKIPPED (mdcrd ...) [ 72%] 618s tests/test_trajectory.py::test_read_write[gro-dtr] PASSED [ 72%] 618s tests/test_trajectory.py::test_read_write[gro-xyz] PASSED [ 72%] 618s tests/test_trajectory.py::test_read_write[gro-xyz.gz] PASSED [ 72%] 618s tests/test_trajectory.py::test_read_write[gro-lammpstrj] PASSED [ 73%] 618s tests/test_trajectory.py::test_read_write[gro-lh5] PASSED [ 73%] 619s tests/test_trajectory.py::test_read_write[gro-pdb] PASSED [ 73%] 619s tests/test_trajectory.py::test_read_write[gro-pdb.gz] PASSED [ 73%] 619s tests/test_trajectory.py::test_read_write[gro-ncrst] SKIPPED (ncrst ...) [ 73%] 620s tests/test_trajectory.py::test_read_write[gro-rst7] SKIPPED (rst7 ca...) [ 73%] 620s tests/test_trajectory.py::test_read_write[gro-gro] PASSED [ 73%] 620s tests/test_trajectory.py::test_load[nc] PASSED [ 73%] 620s tests/test_trajectory.py::test_load[h5] PASSED [ 73%] 620s tests/test_trajectory.py::test_load[xtc] PASSED [ 73%] 620s tests/test_trajectory.py::test_load[trr] PASSED [ 73%] 620s tests/test_trajectory.py::test_load[dcd] PASSED [ 74%] 620s tests/test_trajectory.py::test_load[mdcrd] PASSED [ 74%] 620s tests/test_trajectory.py::test_load[dtr] PASSED [ 74%] 620s tests/test_trajectory.py::test_load[xyz] PASSED [ 74%] 620s tests/test_trajectory.py::test_load[xyz.gz] PASSED [ 74%] 621s tests/test_trajectory.py::test_load[lammpstrj] PASSED [ 74%] 621s tests/test_trajectory.py::test_load[lh5] PASSED [ 74%] 622s tests/test_trajectory.py::test_load[pdb] PASSED [ 74%] 623s tests/test_trajectory.py::test_load[pdb.gz] PASSED [ 74%] 623s tests/test_trajectory.py::test_load[ncrst] XFAIL (These reference fi...) [ 74%] 623s tests/test_trajectory.py::test_load[rst7] XFAIL (These reference fil...) [ 74%] 624s tests/test_trajectory.py::test_load[gro] PASSED [ 75%] 624s tests/test_trajectory.py::test_hdf5 PASSED [ 75%] 624s tests/test_trajectory.py::test_center PASSED [ 75%] 624s tests/test_trajectory.py::test_center_aind PASSED [ 75%] 624s tests/test_trajectory.py::test_float_atom_indices_exception[nc] PASSED [ 75%] 624s tests/test_trajectory.py::test_float_atom_indices_exception[h5] PASSED [ 75%] 624s tests/test_trajectory.py::test_float_atom_indices_exception[xtc] PASSED [ 75%] 624s tests/test_trajectory.py::test_float_atom_indices_exception[trr] PASSED [ 75%] 624s tests/test_trajectory.py::test_float_atom_indices_exception[dcd] PASSED [ 75%] 624s tests/test_trajectory.py::test_float_atom_indices_exception[mdcrd] PASSED [ 75%] 624s tests/test_trajectory.py::test_float_atom_indices_exception[dtr] PASSED [ 75%] 624s tests/test_trajectory.py::test_float_atom_indices_exception[xyz] PASSED [ 75%] 624s tests/test_trajectory.py::test_float_atom_indices_exception[xyz.gz] PASSED [ 76%] 624s tests/test_trajectory.py::test_float_atom_indices_exception[lammpstrj] PASSED [ 76%] 624s tests/test_trajectory.py::test_float_atom_indices_exception[lh5] PASSED [ 76%] 624s tests/test_trajectory.py::test_float_atom_indices_exception[pdb] PASSED [ 76%] 624s tests/test_trajectory.py::test_float_atom_indices_exception[pdb.gz] PASSED [ 76%] 624s tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] XFAIL [ 76%] 624s tests/test_trajectory.py::test_float_atom_indices_exception[rst7] XFAIL [ 76%] 624s tests/test_trajectory.py::test_float_atom_indices_exception[gro] PASSED [ 76%] 624s tests/test_trajectory.py::test_restrict_atoms PASSED [ 76%] 624s tests/test_trajectory.py::test_restrict_atoms_not_inplace PASSED [ 76%] 624s tests/test_trajectory.py::test_array_vs_matrix PASSED [ 76%] 624s tests/test_trajectory.py::test_pdb_unitcell_loadsave PASSED [ 77%] 624s tests/test_trajectory.py::test_load_combination[nc] PASSED [ 77%] 624s tests/test_trajectory.py::test_load_combination[h5] PASSED [ 77%] 624s tests/test_trajectory.py::test_load_combination[xtc] PASSED [ 77%] 624s tests/test_trajectory.py::test_load_combination[trr] PASSED [ 77%] 624s tests/test_trajectory.py::test_load_combination[dcd] PASSED [ 77%] 624s tests/test_trajectory.py::test_load_combination[mdcrd] PASSED [ 77%] 624s tests/test_trajectory.py::test_load_combination[dtr] PASSED [ 77%] 624s tests/test_trajectory.py::test_load_combination[xyz] PASSED [ 77%] 624s tests/test_trajectory.py::test_load_combination[xyz.gz] PASSED [ 77%] 624s tests/test_trajectory.py::test_load_combination[lammpstrj] PASSED [ 77%] 624s tests/test_trajectory.py::test_load_combination[lh5] PASSED [ 78%] 625s tests/test_trajectory.py::test_load_combination[pdb] PASSED [ 78%] 625s tests/test_trajectory.py::test_load_combination[pdb.gz] PASSED [ 78%] 625s tests/test_trajectory.py::test_load_combination[ncrst] XFAIL (These ...) [ 78%] 625s tests/test_trajectory.py::test_load_combination[rst7] XFAIL (These r...) [ 78%] 625s tests/test_trajectory.py::test_load_combination[gro] PASSED [ 78%] 625s tests/test_trajectory.py::test_no_topology PASSED [ 78%] 625s tests/test_trajectory.py::test_join PASSED [ 78%] 625s tests/test_trajectory.py::test_md_join PASSED [ 78%] 625s tests/test_trajectory.py::test_stack_1 PASSED [ 78%] 625s tests/test_trajectory.py::test_stack_2 PASSED [ 78%] 625s tests/test_trajectory.py::test_seek_read_mode[nc] PASSED [ 78%] 626s tests/test_trajectory.py::test_seek_read_mode[h5] PASSED [ 79%] 626s tests/test_trajectory.py::test_seek_read_mode[xtc] PASSED [ 79%] 626s tests/test_trajectory.py::test_seek_read_mode[trr] PASSED [ 79%] 626s tests/test_trajectory.py::test_seek_read_mode[dcd] PASSED [ 79%] 626s tests/test_trajectory.py::test_seek_read_mode[mdcrd] PASSED [ 79%] 626s tests/test_trajectory.py::test_seek_read_mode[dtr] PASSED [ 79%] 626s tests/test_trajectory.py::test_seek_read_mode[xyz] PASSED [ 79%] 626s tests/test_trajectory.py::test_seek_read_mode[xyz.gz] XFAIL (This is...) [ 79%] 626s tests/test_trajectory.py::test_seek_read_mode[lammpstrj] PASSED [ 79%] 626s tests/test_trajectory.py::test_seek_read_mode[lh5] PASSED [ 79%] 626s tests/test_trajectory.py::test_seek_read_mode[pdb] XFAIL (PDB Files ...) [ 79%] 626s tests/test_trajectory.py::test_seek_read_mode[pdb.gz] XFAIL (PDB Fil...) [ 80%] 626s tests/test_trajectory.py::test_seek_read_mode[ncrst] XFAIL (These re...) [ 80%] 626s tests/test_trajectory.py::test_seek_read_mode[rst7] XFAIL (These ref...) [ 80%] 626s tests/test_trajectory.py::test_seek_read_mode[gro] XFAIL (This is br...) [ 80%] 626s tests/test_trajectory.py::test_load_frame[nc] PASSED [ 80%] 626s tests/test_trajectory.py::test_load_frame[h5] PASSED [ 80%] 626s tests/test_trajectory.py::test_load_frame[xtc] PASSED [ 80%] 626s tests/test_trajectory.py::test_load_frame[trr] PASSED [ 80%] 626s tests/test_trajectory.py::test_load_frame[dcd] PASSED [ 80%] 626s tests/test_trajectory.py::test_load_frame[mdcrd] PASSED [ 80%] 626s tests/test_trajectory.py::test_load_frame[dtr] XFAIL (DTR doesn't lo...) [ 80%] 626s tests/test_trajectory.py::test_load_frame[xyz] PASSED [ 81%] 626s tests/test_trajectory.py::test_load_frame[xyz.gz] PASSED [ 81%] 626s tests/test_trajectory.py::test_load_frame[lammpstrj] PASSED [ 81%] 626s tests/test_trajectory.py::test_load_frame[lh5] PASSED [ 81%] 627s tests/test_trajectory.py::test_load_frame[pdb] PASSED [ 81%] 627s tests/test_trajectory.py::test_load_frame[pdb.gz] PASSED [ 81%] 627s tests/test_trajectory.py::test_load_frame[ncrst] XFAIL (These refere...) [ 81%] 627s tests/test_trajectory.py::test_load_frame[rst7] XFAIL (These referen...) [ 81%] 627s tests/test_trajectory.py::test_load_frame[gro] XFAIL (Gro doesn't im...) [ 81%] 627s tests/test_trajectory.py::test_load_frame_2eqq PASSED [ 81%] 627s tests/test_trajectory.py::test_iterload[nc] PASSED [ 81%] 628s tests/test_trajectory.py::test_iterload[h5] PASSED [ 81%] 628s tests/test_trajectory.py::test_iterload[xtc] PASSED [ 82%] 628s tests/test_trajectory.py::test_iterload[trr] PASSED [ 82%] 628s tests/test_trajectory.py::test_iterload[dcd] PASSED [ 82%] 628s tests/test_trajectory.py::test_iterload[mdcrd] PASSED [ 82%] 628s tests/test_trajectory.py::test_iterload[dtr] XFAIL (This is broken w...) [ 82%] 628s tests/test_trajectory.py::test_iterload[xyz] PASSED [ 82%] 628s tests/test_trajectory.py::test_iterload[xyz.gz] PASSED [ 82%] 628s tests/test_trajectory.py::test_iterload[lammpstrj] PASSED [ 82%] 628s tests/test_trajectory.py::test_iterload[lh5] PASSED [ 82%] 628s tests/test_trajectory.py::test_iterload[pdb] PASSED [ 82%] 628s tests/test_trajectory.py::test_iterload[pdb.gz] PASSED [ 82%] 628s tests/test_trajectory.py::test_iterload[ncrst] SKIPPED (Only 1 frame...) [ 83%] 628s tests/test_trajectory.py::test_iterload[rst7] SKIPPED (Only 1 frame ...) [ 83%] 628s tests/test_trajectory.py::test_iterload[gro] PASSED [ 83%] 632s tests/test_trajectory.py::test_iterload_skip[nc] PASSED [ 83%] 635s tests/test_trajectory.py::test_iterload_skip[h5] PASSED [ 83%] 636s tests/test_trajectory.py::test_iterload_skip[xtc] PASSED [ 83%] 637s tests/test_trajectory.py::test_iterload_skip[trr] PASSED [ 83%] 638s tests/test_trajectory.py::test_iterload_skip[dcd] PASSED [ 83%] 640s tests/test_trajectory.py::test_iterload_skip[mdcrd] PASSED [ 83%] 640s tests/test_trajectory.py::test_iterload_skip[dtr] PASSED [ 83%] 641s tests/test_trajectory.py::test_iterload_skip[xyz] PASSED [ 83%] 642s tests/test_trajectory.py::test_iterload_skip[xyz.gz] PASSED [ 84%] 644s tests/test_trajectory.py::test_iterload_skip[lammpstrj] PASSED [ 84%] 646s tests/test_trajectory.py::test_iterload_skip[lh5] PASSED [ 84%] 646s tests/test_trajectory.py::test_iterload_skip[pdb] XFAIL (PDB Iterloa...) [ 84%] 646s tests/test_trajectory.py::test_iterload_skip[pdb.gz] XFAIL (PDB Iter...) [ 84%] 646s tests/test_trajectory.py::test_iterload_skip[ncrst] XFAIL (These ref...) [ 84%] 646s tests/test_trajectory.py::test_iterload_skip[rst7] XFAIL (These refe...) [ 84%] 646s tests/test_trajectory.py::test_iterload_skip[gro] XFAIL (Not impleme...) [ 84%] 646s tests/test_trajectory.py::test_iterload_chunk_dcd PASSED [ 84%] 646s tests/test_trajectory.py::test_save_load[nc] PASSED [ 84%] 646s tests/test_trajectory.py::test_save_load[h5] PASSED [ 84%] 646s tests/test_trajectory.py::test_save_load[xtc] PASSED [ 84%] 646s tests/test_trajectory.py::test_save_load[trr] PASSED [ 85%] 646s tests/test_trajectory.py::test_save_load[dcd] PASSED [ 85%] 646s tests/test_trajectory.py::test_save_load[mdcrd] PASSED [ 85%] 646s tests/test_trajectory.py::test_save_load[dtr] PASSED [ 85%] 646s tests/test_trajectory.py::test_save_load[xyz] PASSED [ 85%] 646s tests/test_trajectory.py::test_save_load[xyz.gz] PASSED [ 85%] 646s tests/test_trajectory.py::test_save_load[lammpstrj] PASSED [ 85%] 646s tests/test_trajectory.py::test_save_load[lh5] PASSED [ 85%] 646s tests/test_trajectory.py::test_save_load[pdb] PASSED [ 85%] 646s tests/test_trajectory.py::test_save_load[pdb.gz] PASSED [ 85%] 646s tests/test_trajectory.py::test_save_load[ncrst] PASSED [ 85%] 646s tests/test_trajectory.py::test_save_load[rst7] PASSED [ 86%] 646s tests/test_trajectory.py::test_save_load[gro] PASSED [ 86%] 646s tests/test_trajectory.py::test_force_overwrite[nc] PASSED [ 86%] 646s tests/test_trajectory.py::test_force_overwrite[h5] PASSED [ 86%] 646s tests/test_trajectory.py::test_force_overwrite[xtc] PASSED [ 86%] 646s tests/test_trajectory.py::test_force_overwrite[trr] PASSED [ 86%] 646s tests/test_trajectory.py::test_force_overwrite[dcd] PASSED [ 86%] 646s tests/test_trajectory.py::test_force_overwrite[mdcrd] PASSED [ 86%] 646s tests/test_trajectory.py::test_force_overwrite[dtr] XFAIL (This is b...) [ 86%] 646s tests/test_trajectory.py::test_force_overwrite[xyz] PASSED [ 86%] 646s tests/test_trajectory.py::test_force_overwrite[xyz.gz] PASSED [ 86%] 646s tests/test_trajectory.py::test_force_overwrite[lammpstrj] PASSED [ 87%] 646s tests/test_trajectory.py::test_force_overwrite[lh5] PASSED [ 87%] 646s tests/test_trajectory.py::test_force_overwrite[pdb] PASSED [ 87%] 646s tests/test_trajectory.py::test_force_overwrite[pdb.gz] PASSED [ 87%] 646s tests/test_trajectory.py::test_force_overwrite[ncrst] PASSED [ 87%] 646s tests/test_trajectory.py::test_force_overwrite[rst7] PASSED [ 87%] 646s tests/test_trajectory.py::test_force_overwrite[gro] PASSED [ 87%] 646s tests/test_trajectory.py::test_force_noverwrite[nc] PASSED [ 87%] 646s tests/test_trajectory.py::test_force_noverwrite[h5] PASSED [ 87%] 646s tests/test_trajectory.py::test_force_noverwrite[xtc] PASSED [ 87%] 646s tests/test_trajectory.py::test_force_noverwrite[trr] PASSED [ 87%] 646s tests/test_trajectory.py::test_force_noverwrite[dcd] PASSED [ 87%] 646s tests/test_trajectory.py::test_force_noverwrite[mdcrd] PASSED [ 88%] 646s tests/test_trajectory.py::test_force_noverwrite[dtr] PASSED [ 88%] 646s tests/test_trajectory.py::test_force_noverwrite[xyz] PASSED [ 88%] 646s tests/test_trajectory.py::test_force_noverwrite[xyz.gz] PASSED [ 88%] 646s tests/test_trajectory.py::test_force_noverwrite[lammpstrj] PASSED [ 88%] 646s tests/test_trajectory.py::test_force_noverwrite[lh5] PASSED [ 88%] 647s tests/test_trajectory.py::test_force_noverwrite[pdb] PASSED [ 88%] 647s tests/test_trajectory.py::test_force_noverwrite[pdb.gz] PASSED [ 88%] 647s tests/test_trajectory.py::test_force_noverwrite[ncrst] PASSED [ 88%] 647s tests/test_trajectory.py::test_force_noverwrite[rst7] PASSED [ 88%] 647s tests/test_trajectory.py::test_force_noverwrite[gro] PASSED [ 88%] 647s tests/test_trajectory.py::test_open_and_load PASSED [ 89%] 647s tests/test_trajectory.py::test_length PASSED [ 89%] 647s tests/test_trajectory.py::test_unitcell[nc] PASSED [ 89%] 647s tests/test_trajectory.py::test_unitcell[h5] PASSED [ 89%] 647s tests/test_trajectory.py::test_unitcell[xtc] PASSED [ 89%] 647s tests/test_trajectory.py::test_unitcell[trr] PASSED [ 89%] 647s tests/test_trajectory.py::test_unitcell[dcd] PASSED [ 89%] 647s tests/test_trajectory.py::test_unitcell[mdcrd] PASSED [ 89%] 647s tests/test_trajectory.py::test_unitcell[dtr] XFAIL (dtr seems to nee...) [ 89%] 647s tests/test_trajectory.py::test_unitcell[xyz] PASSED [ 89%] 647s tests/test_trajectory.py::test_unitcell[xyz.gz] PASSED [ 89%] 647s tests/test_trajectory.py::test_unitcell[lammpstrj] XFAIL (lammpstrj ...) [ 90%] 647s tests/test_trajectory.py::test_unitcell[lh5] PASSED [ 90%] 647s tests/test_trajectory.py::test_unitcell[pdb] PASSED [ 90%] 647s tests/test_trajectory.py::test_unitcell[pdb.gz] PASSED [ 90%] 647s tests/test_trajectory.py::test_unitcell[ncrst] XFAIL (ncrst seems to...) [ 90%] 647s tests/test_trajectory.py::test_unitcell[rst7] XFAIL (rst7 seems to n...) [ 90%] 647s tests/test_trajectory.py::test_unitcell[gro] PASSED [ 90%] 647s tests/test_trajectory.py::test_chunk0_iterload PASSED [ 90%] 647s tests/test_trajectory.py::test_hashing PASSED [ 90%] 647s tests/test_trajectory.py::test_smooth PASSED [ 90%] 647s tests/test_trajectory.py::test_load_pdb_no_standard_names PASSED [ 90%] 647s tests/test_trajectory.py::test_load_with_atom_indices PASSED [ 90%] 648s tests/test_trajectory.py::test_atom_slicing PASSED [ 91%] 648s tests/test_trajectory.py::test_load_with_frame PASSED [ 91%] 648s tests/test_trajectory.py::test_add_remove_atoms PASSED [ 91%] 648s tests/test_trr.py::test_1 PASSED [ 91%] 648s tests/test_trr.py::test_read_stride PASSED [ 91%] 648s tests/test_trr.py::test_read_stride_n_frames PASSED [ 91%] 648s tests/test_trr.py::test_read_stride_offsets PASSED [ 91%] 648s tests/test_trr.py::test_read_stride_n_frames_offsets PASSED [ 91%] 648s tests/test_trr.py::test_read_stride_switching PASSED [ 91%] 648s tests/test_trr.py::test_write_read PASSED [ 91%] 648s tests/test_trr.py::test_read_atomindices_1 PASSED [ 91%] 648s tests/test_trr.py::test_read_atomindices_2 PASSED [ 92%] 648s tests/test_trr.py::test_deficient_shape PASSED [ 92%] 648s tests/test_trr.py::test_ragged_1 PASSED [ 92%] 648s tests/test_trr.py::test_ragged_2 PASSED [ 92%] 648s tests/test_trr.py::test_malformed PASSED [ 92%] 648s tests/test_trr.py::test_tell PASSED [ 92%] 648s tests/test_trr.py::test_seek PASSED [ 92%] 648s tests/test_trr.py::test_get_velocities PASSED [ 92%] 648s tests/test_trr.py::test_get_forces PASSED [ 92%] 648s tests/test_trr.py::test_get_velocities_and_forces PASSED [ 92%] 648s tests/test_trr.py::test_get_velocities_forces_atom_indices_1 PASSED [ 92%] 648s tests/test_trr.py::test_get_velocities_forces_atom_indices_2 PASSED [ 93%] 648s tests/test_trr.py::test_read_velocities_do_not_exist PASSED [ 93%] 648s tests/test_trr.py::test_read_forces_do_not_exist PASSED [ 93%] 648s tests/test_utils.py::test_unitcell_0 PASSED [ 93%] 648s tests/test_utils.py::test_unitcell_1 PASSED [ 93%] 648s tests/test_utils.py::test_ensure_type_1 PASSED [ 93%] 648s tests/test_utils.py::test_ensure_type_2 PASSED [ 93%] 648s tests/test_utils.py::test_ensure_type_25 PASSED [ 93%] 648s tests/test_utils.py::test_ensure_type_3 PASSED [ 93%] 648s tests/test_utils.py::test_ensure_type_4 PASSED [ 93%] 648s tests/test_utils.py::test_ensure_type_5 PASSED [ 93%] 648s tests/test_utils.py::test_ensure_type_6 PASSED [ 93%] 648s tests/test_utils.py::test_ensure_type_7 PASSED [ 94%] 648s tests/test_utils.py::test_ensure_type_8 PASSED [ 94%] 648s tests/test_utils.py::test_ensure_type_9 PASSED [ 94%] 648s tests/test_utils.py::test_ensure_type_10 PASSED [ 94%] 648s tests/test_utils.py::test_ensure_type_11 PASSED [ 94%] 648s tests/test_utils.py::test_ensure_type_12 PASSED [ 94%] 648s tests/test_utils.py::test_ensure_type_13 PASSED [ 94%] 648s tests/test_utils.py::test_ensure_type_14 PASSED [ 94%] 648s tests/test_utils.py::test_ensure_type_15 PASSED [ 94%] 648s tests/test_utils.py::test_delay_import_fail_1 PASSED [ 94%] 648s tests/test_utils.py::test_delay_import PASSED [ 94%] 648s tests/test_utils.py::test_unit_0 PASSED [ 95%] 648s tests/test_utils.py::test_unit_1 PASSED [ 95%] 648s tests/test_utils.py::test_unit_2 PASSED [ 95%] 648s tests/test_utils.py::test_unit_3 PASSED [ 95%] 648s tests/test_xml.py::test_xml PASSED [ 95%] 648s tests/test_xtc.py::test_read_chunk1 PASSED [ 95%] 648s tests/test_xtc.py::test_read_stride PASSED [ 95%] 648s tests/test_xtc.py::test_read_stride_n_frames PASSED [ 95%] 648s tests/test_xtc.py::test_read_stride_offsets PASSED [ 95%] 648s tests/test_xtc.py::test_read_stride_n_frames_offsets PASSED [ 95%] 648s tests/test_xtc.py::test_read_stride_switching_offsets PASSED [ 95%] 648s tests/test_xtc.py::test_read_atomindices_1 PASSED [ 96%] 648s tests/test_xtc.py::test_read_atomindices_w_stride PASSED [ 96%] 648s tests/test_xtc.py::test_read_atomindices_2 PASSED [ 96%] 648s tests/test_xtc.py::test_read_chunk2 PASSED [ 96%] 648s tests/test_xtc.py::test_read_chunk3 PASSED [ 96%] 648s tests/test_xtc.py::test_write_0 PASSED [ 96%] 648s tests/test_xtc.py::test_write_1 PASSED [ 96%] 648s tests/test_xtc.py::test_write_2 PASSED [ 96%] 648s tests/test_xtc.py::test_read_error_0 PASSED [ 96%] 648s tests/test_xtc.py::test_write_error_0 PASSED [ 96%] 648s tests/test_xtc.py::test_read_error_1 PASSED [ 96%] 648s tests/test_xtc.py::test_read_error_2 PASSED [ 96%] 648s tests/test_xtc.py::test_xtc_write_wierd_0 PASSED [ 97%] 648s tests/test_xtc.py::test_tell PASSED [ 97%] 648s tests/test_xtc.py::test_seek PASSED [ 97%] 648s tests/test_xtc.py::test_seek_natoms9 PASSED [ 97%] 648s tests/test_xtc.py::test_seek_out_of_bounds PASSED [ 97%] 648s tests/test_xtc.py::test_ragged_1 PASSED [ 97%] 648s tests/test_xtc.py::test_ragged_2 PASSED [ 97%] 648s tests/test_xtc.py::test_short_traj PASSED [ 97%] 648s tests/test_xtc.py::test_flush PASSED [ 97%] 648s tests/test_xyz.py::test_read_0 PASSED [ 97%] 649s tests/test_xyz.py::test_read_1 PASSED [ 97%] 649s tests/test_xyz.py::test_read_gz PASSED [ 98%] 649s tests/test_xyz.py::test_read_write PASSED [ 98%] 649s tests/test_xyz.py::test_mdwrite PASSED [ 98%] 649s tests/test_xyz.py::test_multiread PASSED [ 98%] 649s tests/test_xyz.py::test_seek PASSED [ 98%] 649s tests/test_xyz.py::test_len PASSED [ 98%] 649s tests/test_zipped.py::test_read_gz PASSED [ 98%] 649s tests/test_zipped.py::test_write_gz PASSED [ 98%] 649s tests/test_zipped.py::test_read_bz2 PASSED [ 98%] 649s tests/test_zipped.py::test_write_bz2 PASSED [ 98%] 651s examples/test_examples.py::test_example_notebook[iterload.ipynb] PASSED [ 98%] 655s examples/test_examples.py::test_example_notebook[principal-components.ipynb] PASSED [ 99%] 657s examples/test_examples.py::test_example_notebook[rmsd-drift.ipynb] PASSED [ 99%] 658s examples/test_examples.py::test_example_notebook[atom-selection.ipynb] PASSED [ 99%] 658s examples/test_examples.py::test_example_notebook[hbonds.ipynb] SKIPPED [ 99%] 661s examples/test_examples.py::test_example_notebook[solvent-accessible-surface-area.ipynb] PASSED [ 99%] 664s examples/test_examples.py::test_example_notebook[ramachandran-plot.ipynb] PASSED [ 99%] 666s examples/test_examples.py::test_example_notebook[clustering.ipynb] PASSED [ 99%] 667s examples/test_examples.py::test_example_notebook[two-pass-clustering.ipynb] PASSED [ 99%] 670s examples/test_examples.py::test_example_notebook[rmsd-benchmark.ipynb] PASSED [ 99%] 670s examples/test_examples.py::test_example_notebook[native-contact.ipynb] SKIPPED [ 99%] 672s examples/test_examples.py::test_example_notebook[centroids.ipynb] PASSED [ 99%] 672s examples/test_examples.py::test_example_notebook[simulation-with-openmm.ipynb] SKIPPED [100%] 672s 672s =============================== warnings summary =============================== 672s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:56 672s /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. 672s THIS_ATOM = ast.Name(id="atom", ctx=ast.Load(), SINGLETON=True) 672s 672s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:57 672s /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. 672s RE_MODULE = ast.Name(id="re", ctx=ast.Load(), SINGLETON=True) 672s 672s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 672s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 672s given by the platformdirs library. To remove this warning and 672s see the appropriate new directories, set the environment variable 672s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 672s The use of platformdirs will be the default in `jupyter_core` v6 672s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 672s 672s examples/test_examples.py:26 672s /tmp/autopkgtest.3VyOX4/build.ex9/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 672s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 672s 672s tests/test_contact.py::test_contact_0 672s tests/test_contact.py::test_contact_4 672s /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. 672s warnings.warn( 672s 672s tests/test_contact.py::test_contact_3 672s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:271: RuntimeWarning: overflow encountered in exp 672s np.exp( 672s 672s tests/test_contact.py::test_contact_3 672s /tmp/autopkgtest.3VyOX4/build.ex9/src/tests/test_contact.py:115: RuntimeWarning: divide by zero encountered in divide 672s beta / np.log(np.sum(np.exp(beta / maps[t, r0, r1]))), 672s 672s tests/test_dcd.py::test_do_overwrite 672s tests/test_dcd.py::test_ragged_1 672s tests/test_dcd.py::test_ragged_2 672s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting xyz dtype=float64 to 672s warnings.warn( 672s 672s tests/test_distance.py::test_6 672s :488: RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject 672s 672s tests/test_drid.py::test_drid_2 672s /tmp/autopkgtest.3VyOX4/build.ex9/src/tests/test_drid.py:62: RuntimeWarning: divide by zero encountered in divide 672s recip = 1 / squareform(pdist(t.xyz[i])) 672s 672s tests/test_dssp.py::test_1[1vii.pdb] 672s tests/test_gro.py::test_read_write 672s tests/test_gro.py::test_read_write_precision 672s tests/test_gro.py::test_load 672s tests/test_shape.py::test_principal_moments 672s tests/test_shape.py::test_asphericity 672s tests/test_shape.py::test_shape_metrics 672s /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. 672s warnings.warn( 672s 672s tests/test_geometry.py::test_dihedral_indices 672s tests/test_geometry.py::test_dihedral_indices 672s /usr/lib/python3/dist-packages/mdtraj/geometry/dihedral.py:237: DeprecationWarning: Passing a Trajectory object to _atom_sequence isdeprecated. Please pass a Topology object 672s warnings.warn( 672s 672s tests/test_gro.py::test_load 672s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq 672s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:364: UserWarning: WARNING: two consecutive residues with same number (GST, HST) 672s warnings.warn( 672s 672s tests/test_pdb.py::test_blank_indexing 672s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:204: UserWarning: Need to guess atom number starting from atom 100000. 672s warnings.warn(f'Need to guess atom number {num_str} starting from atom {pdbstructure._next_atom_number}.') 672s 672s tests/test_pdb.py::test_blank_indexing 672s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:271: UserWarning: Need to guess residue number string starting from residue10000, atom 100000. 672s warnings.warn(f'Need to guess residue number string {num_str} starting from residue{pdbstructure._next_residue_number}, atom {pdbstructure._next_atom_number}.') 672s 672s tests/test_rdf.py::test_rdf_norm 672s tests/test_rdf.py::test_rdf_t_norm[0] 672s tests/test_rdf.py::test_rdf_t_norm[2] 672s tests/test_rdf.py::test_rdf_t_norm[4] 672s tests/test_selection.py::test_re 672s tests/test_selection.py::test_re 672s tests/test_topology.py::test_select_pairs 672s tests/test_topology.py::test_select_pairs 672s /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. 672s left=ast.Call( 672s 672s tests/test_rdf.py::test_rdf_norm 672s tests/test_rdf.py::test_rdf_t_norm[0] 672s tests/test_rdf.py::test_rdf_t_norm[2] 672s tests/test_rdf.py::test_rdf_t_norm[4] 672s tests/test_selection.py::test_re 672s tests/test_selection.py::test_re 672s tests/test_topology.py::test_select_pairs 672s tests/test_topology.py::test_select_pairs 672s /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. 672s left=ast.Call( 672s 672s tests/test_trajectory.py::test_float_atom_indices_exception[gro] 672s tests/test_trajectory.py::test_atom_slicing 672s /usr/lib/python3/dist-packages/mdtraj/core/topology.py:84: UserWarning: atom_indices are not monotonically increasing 672s warnings.warn("atom_indices are not monotonically increasing") 672s 672s tests/test_utils.py::test_ensure_type_8 672s tests/test_utils.py::test_ensure_type_9 672s tests/test_utils.py::test_ensure_type_13 672s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=float64 to 672s warnings.warn( 672s 672s tests/test_utils.py::test_ensure_type_11 672s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=int64 to 672s warnings.warn( 672s 672s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 672s =========================== short test summary info ============================ 672s SKIPPED [1] tests/test_dihedral.py:56: pymol executable not found 672s SKIPPED [1] tests/test_dihedral.py:181: pymol executable not found 672s SKIPPED [16] tests/test_docstrings.py:38: Skip checking certain modules' docstrings 672s SKIPPED [1] tests/test_geometry.py:300: Not doing performance testing 672s SKIPPED [1] tests/test_geometry.py:322: Not doing performance testing 672s SKIPPED [1] tests/test_hdf5.py:104: requires openmm.units 672s SKIPPED [1] tests/test_hdf5.py:156: requires openmm.units 672s SKIPPED [1] tests/test_hdf5.py:223: requires openmm.units 672s SKIPPED [1] tests/test_mol2.py:59: Requires obabel 672s SKIPPED [1] tests/test_netcdf.py:271: This test requires cpptraj from AmberTools to be installed (http://ambermd.org) 672s SKIPPED [1] tests/test_nmr.py:11: SPARTA+ binary not found 672s SKIPPED [1] tests/test_nmr.py:26: PPM binary not found 672s SKIPPED [1] tests/test_nmr.py:42: SHIFTX2 binary not found or running on travis. 672s SKIPPED [1] tests/test_pdbx.py:43: test_pdbx.py needs OpenMM. 672s SKIPPED [2] tests/test_psf.py:93: This test requires the VMD executable: http://www.ks.uiuc.edu/Research/vmd/ 672s SKIPPED [1] tests/test_rdf.py:64: Binning does not match up with gromacs currently. 672s SKIPPED [1] tests/test_rdf.py:200: Binning does not match up with gromacs currently. 672s SKIPPED [1] tests/test_rdf.py:219: Expected failure for NumPy < 2.0 due to histogram output differences 672s SKIPPED [1] tests/test_reporter.py:58: test_reporter.py needs OpenMM. 672s SKIPPED [1] tests/test_reporter.py:145: test_reporter.py needs OpenMM. 672s SKIPPED [1] tests/test_reporter.py:245: test_reporter.py needs OpenMM. 672s SKIPPED [1] tests/test_selection.py:267: failed to parse selection 672s SKIPPED [1] tests/test_thermodynamic_properties.py:161: Thermal expansion test doesn't work. 672s SKIPPED [1] tests/test_topology.py:45: needs OpenMM 672s SKIPPED [1] tests/test_topology.py:62: needs OpenMM 672s SKIPPED [1] tests/test_topology.py:72: needs OpenMM 672s SKIPPED [1] tests/test_topology.py:81: needs OpenMM 672s SKIPPED [1] tests/test_topology.py:91: needs OpenMM 672s SKIPPED [1] tests/test_topology.py:97: needs OpenMM 672s SKIPPED [1] tests/test_topology.py:247: needs OpenMM 672s SKIPPED [1] tests/test_trajectory.py:129: xyz does not store box information 672s SKIPPED [1] tests/test_trajectory.py:129: xyz.gz does not store box information 672s SKIPPED [1] tests/test_trajectory.py:129: lh5 does not store box information 672s SKIPPED [1] tests/test_trajectory.py:129: pdb does not store box information 672s SKIPPED [1] tests/test_trajectory.py:129: pdb.gz does not store box information 672s SKIPPED [1] tests/test_trajectory.py:226: mdcrd can only store rectilinear boxes 672s SKIPPED [1] tests/test_trajectory.py:224: ncrst can only store 1 frame per file 672s SKIPPED [1] tests/test_trajectory.py:224: rst7 can only store 1 frame per file 672s SKIPPED [14] tests/test_trajectory.py:248: mdcrd can only store rectilinear boxes 672s SKIPPED [14] tests/test_trajectory.py:246: ncrst can only store 1 frame per file 672s SKIPPED [14] tests/test_trajectory.py:246: rst7 can only store 1 frame per file 672s SKIPPED [4] tests/test_trajectory.py:256: dtr needs to write unitcells 672s SKIPPED [4] tests/test_trajectory.py:256: lammpstrj needs to write unitcells 672s SKIPPED [2] tests/test_trajectory.py:640: Only 1 frame per file format 672s SKIPPED [2] examples/test_examples.py:77: Network access required 672s SKIPPED [1] examples/test_examples.py:77: Openmm required for example notebook `simulation-with-openmm.ipynb` 672s XFAIL tests/test_trajectory.py::test_read_path[ncrst] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_path[rst7] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[ncrst-nc] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[ncrst-h5] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xtc] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[ncrst-trr] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dcd] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[ncrst-mdcrd] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dtr] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lh5] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[ncrst-ncrst] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[ncrst-rst7] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[ncrst-gro] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[rst7-nc] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[rst7-h5] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[rst7-xtc] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[rst7-trr] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[rst7-dcd] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[rst7-mdcrd] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[rst7-dtr] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz.gz] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[rst7-lammpstrj] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[rst7-lh5] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb.gz] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[rst7-ncrst] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[rst7-rst7] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_read_write[rst7-gro] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_load[ncrst] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_load[rst7] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[rst7] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_load_combination[ncrst] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_load_combination[rst7] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_seek_read_mode[xyz.gz] - reason: This is broken 672s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb] - reason: PDB Files don't support seeking 672s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb.gz] - reason: PDB Files don't support seeking 672s XFAIL tests/test_trajectory.py::test_seek_read_mode[ncrst] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_seek_read_mode[rst7] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_seek_read_mode[gro] - reason: This is broken 672s XFAIL tests/test_trajectory.py::test_load_frame[dtr] - reason: DTR doesn't load a single frame properly 672s XFAIL tests/test_trajectory.py::test_load_frame[ncrst] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_load_frame[rst7] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_load_frame[gro] - reason: Gro doesn't implement seek 672s XFAIL tests/test_trajectory.py::test_iterload[dtr] - reason: This is broken with dtr 672s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb] - reason: PDB Iterloads an extra frame!! 672s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb.gz] - reason: PDB Iterloads an extra frame!! 672s XFAIL tests/test_trajectory.py::test_iterload_skip[ncrst] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_iterload_skip[rst7] - reason: These reference files don't exist yet 672s XFAIL tests/test_trajectory.py::test_iterload_skip[gro] - reason: Not implemented for some reason 672s XFAIL tests/test_trajectory.py::test_force_overwrite[dtr] - reason: This is broken with dtr 672s XFAIL tests/test_trajectory.py::test_unitcell[dtr] - reason: dtr seems to need unit vectors 672s XFAIL tests/test_trajectory.py::test_unitcell[lammpstrj] - reason: lammpstrj seems to need unit vectors 672s XFAIL tests/test_trajectory.py::test_unitcell[ncrst] - reason: ncrst seems to need unit vectors 672s XFAIL tests/test_trajectory.py::test_unitcell[rst7] - reason: rst7 seems to need unit vectors 672s = 963 passed, 109 skipped, 12 deselected, 61 xfailed, 48 warnings in 326.07s (0:05:26) = 673s autopkgtest [12:10:40]: test command1: -----------------------] 673s autopkgtest [12:10:40]: test command1: - - - - - - - - - - results - - - - - - - - - - 673s command1 PASS 674s autopkgtest [12:10:41]: test command2: preparing testbed 674s Reading package lists... 674s Building dependency tree... 674s Reading state information... 675s Starting pkgProblemResolver with broken count: 0 675s Starting 2 pkgProblemResolver with broken count: 0 675s Done 676s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 677s autopkgtest [12:10:44]: test command2: pytest-3 -k 'test_3 or test_pdb_from_url or test_1vii_url_and_gz' 677s autopkgtest [12:10:44]: test command2: [----------------------- 678s ============================= test session starts ============================== 678s platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 -- /usr/bin/python3 678s cachedir: .pytest_cache 678s rootdir: /tmp/autopkgtest.3VyOX4/build.ex9/src 678s configfile: pyproject.toml 678s testpaths: tests, examples 678s plugins: typeguard-4.4.1 679s collecting ... collected 1145 items / 1135 deselected / 10 selected 679s 679s tests/test_distance.py::test_3 PASSED [ 10%] 679s tests/test_distance.py::test_3p PASSED [ 20%] 683s tests/test_dssp.py::test_3[1GAI] PASSED [ 30%] 687s tests/test_dssp.py::test_3[6gsv] PASSED [ 40%] 691s tests/test_dssp.py::test_3[2AAC] PASSED [ 50%] 692s tests/test_nmr.py::test_3_scalar_couplings PASSED [ 60%] 701s tests/test_pdb.py::test_pdb_from_url PASSED [ 70%] 701s tests/test_pdb.py::test_3nch_conect PASSED [ 80%] 703s tests/test_pdb.py::test_3nch_serial_resSeq PASSED [ 90%] 709s tests/test_pdb.py::test_1vii_url_and_gz PASSED [100%] 709s 709s =============================== warnings summary =============================== 709s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:56 709s /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. 709s THIS_ATOM = ast.Name(id="atom", ctx=ast.Load(), SINGLETON=True) 709s 709s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:57 709s /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. 709s RE_MODULE = ast.Name(id="re", ctx=ast.Load(), SINGLETON=True) 709s 709s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 709s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 709s given by the platformdirs library. To remove this warning and 709s see the appropriate new directories, set the environment variable 709s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 709s The use of platformdirs will be the default in `jupyter_core` v6 709s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 709s 709s examples/test_examples.py:26 709s /tmp/autopkgtest.3VyOX4/build.ex9/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 709s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 709s 709s tests/test_pdb.py::test_1vii_url_and_gz 709s /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. 709s warnings.warn( 709s 709s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 709s =============== 10 passed, 1135 deselected, 5 warnings in 31.32s =============== 710s autopkgtest [12:11:17]: test command2: -----------------------] 710s command2 PASS 710s autopkgtest [12:11:17]: test command2: - - - - - - - - - - results - - - - - - - - - - 711s autopkgtest [12:11:18]: @@@@@@@@@@@@@@@@@@@@ summary 711s command1 PASS 711s command2 PASS 728s nova [W] Using flock in prodstack6-arm64 728s Creating nova instance adt-plucky-arm64-mdtraj-20250219-115927-juju-7f2275-prod-proposed-migration-environment-15-d563b619-0353-4225-9e8f-d7ec1f16f008 from image adt/ubuntu-plucky-arm64-server-20250219.img (UUID 02c92adb-9d9d-4b0e-b071-488d8ee6210f)... 728s nova [W] Timed out waiting for 95c78d00-e14e-45c1-bcff-23e635c218a6 to get deleted.