0s autopkgtest [17:06:46]: starting date and time: 2024-07-12 17:06:46+0000 0s autopkgtest [17:06:46]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [17:06:46]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ggjfl2xa/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade mdtraj --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.39-3.1ubuntu3 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-86.secgroup --name adt-oracular-amd64-mdtraj-20240712-170645-juju-7f2275-prod-proposed-migration-environment-2-948a4456-bdf2-46db-81ab-82e8a8c9b326 --image adt/ubuntu-oracular-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 115s autopkgtest [17:08:41]: testbed dpkg architecture: amd64 115s autopkgtest [17:08:41]: testbed apt version: 2.9.6 115s autopkgtest [17:08:41]: @@@@@@@@@@@@@@@@@@@@ test bed setup 118s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 118s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [334 kB] 118s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [46.6 kB] 118s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B] 118s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 118s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [70.9 kB] 118s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [98.2 kB] 118s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 c-n-f Metadata [2104 B] 118s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [6244 B] 118s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [34.9 kB] 118s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 c-n-f Metadata [368 B] 118s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [368 kB] 118s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [224 kB] 118s Get:14 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 c-n-f Metadata [9228 B] 118s Get:15 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3052 B] 118s Get:16 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [7644 B] 118s Get:17 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 c-n-f Metadata [276 B] 120s Fetched 1342 kB in 0s (5600 kB/s) 120s Reading package lists... 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 139s Calculating upgrade... 139s The following packages will be upgraded: 139s binutils binutils-common binutils-x86-64-linux-gnu gir1.2-glib-2.0 139s inetutils-telnet libbinutils libc-bin libc-dev-bin libc-devtools libc6 139s libc6-dev libctf-nobfd0 libctf0 libglib2.0-0t64 libglib2.0-data libgprofng0 139s libnghttp2-14 libnss3 libsframe1 libssl3t64 locales openssh-client 139s openssh-server openssh-sftp-server openssl telnet 139s 26 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 139s Need to get 22.8 MB of archives. 139s After this operation, 444 kB of additional disk space will be used. 139s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-devtools amd64 2.39-3.1ubuntu3 [29.3 kB] 139s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6-dev amd64 2.39-3.1ubuntu3 [2120 kB] 139s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-dev-bin amd64 2.39-3.1ubuntu3 [20.4 kB] 139s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6 amd64 2.39-3.1ubuntu3 [3262 kB] 139s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-bin amd64 2.39-3.1ubuntu3 [680 kB] 139s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 libssl3t64 amd64 3.2.2-1ubuntu1 [2138 kB] 139s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 openssh-sftp-server amd64 1:9.6p1-3ubuntu17 [37.1 kB] 139s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 openssh-server amd64 1:9.6p1-3ubuntu17 [509 kB] 139s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 openssh-client amd64 1:9.6p1-3ubuntu17 [905 kB] 139s Get:10 http://ftpmaster.internal/ubuntu oracular/main amd64 gir1.2-glib-2.0 amd64 2.80.4-1ubuntu1 [182 kB] 139s Get:11 http://ftpmaster.internal/ubuntu oracular/main amd64 libglib2.0-0t64 amd64 2.80.4-1ubuntu1 [1545 kB] 139s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 libglib2.0-data all 2.80.4-1ubuntu1 [49.3 kB] 139s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 locales all 2.39-3.1ubuntu3 [4220 kB] 139s Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 openssl amd64 3.2.2-1ubuntu1 [1122 kB] 139s Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 inetutils-telnet amd64 2:2.5-5ubuntu1 [105 kB] 139s Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 libnghttp2-14 amd64 1.62.1-2 [75.1 kB] 139s Get:17 http://ftpmaster.internal/ubuntu oracular/main amd64 telnet all 0.17+2.5-5ubuntu1 [3688 B] 139s Get:18 http://ftpmaster.internal/ubuntu oracular/main amd64 libgprofng0 amd64 2.42.50.20240710-1ubuntu1 [860 kB] 139s Get:19 http://ftpmaster.internal/ubuntu oracular/main amd64 libctf0 amd64 2.42.50.20240710-1ubuntu1 [95.6 kB] 139s Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 libctf-nobfd0 amd64 2.42.50.20240710-1ubuntu1 [97.6 kB] 139s Get:21 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils-x86-64-linux-gnu amd64 2.42.50.20240710-1ubuntu1 [2477 kB] 139s Get:22 http://ftpmaster.internal/ubuntu oracular/main amd64 libbinutils amd64 2.42.50.20240710-1ubuntu1 [574 kB] 139s Get:23 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils amd64 2.42.50.20240710-1ubuntu1 [18.1 kB] 139s Get:24 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils-common amd64 2.42.50.20240710-1ubuntu1 [243 kB] 139s Get:25 http://ftpmaster.internal/ubuntu oracular/main amd64 libsframe1 amd64 2.42.50.20240710-1ubuntu1 [14.4 kB] 139s Get:26 http://ftpmaster.internal/ubuntu oracular/main amd64 libnss3 amd64 2:3.102-1 [1399 kB] 140s Preconfiguring packages ... 140s Fetched 22.8 MB in 0s (120 MB/s) 140s (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 ... 74487 files and directories currently installed.) 140s Preparing to unpack .../libc-devtools_2.39-3.1ubuntu3_amd64.deb ... 140s Unpacking libc-devtools (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 140s Preparing to unpack .../libc6-dev_2.39-3.1ubuntu3_amd64.deb ... 140s Unpacking libc6-dev:amd64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 140s Preparing to unpack .../libc-dev-bin_2.39-3.1ubuntu3_amd64.deb ... 140s Unpacking libc-dev-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 140s Preparing to unpack .../libc6_2.39-3.1ubuntu3_amd64.deb ... 140s Unpacking libc6:amd64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 141s Setting up libc6:amd64 (2.39-3.1ubuntu3) ... 141s Error: Could not restart systemd, systemd binary not working 141s (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 ... 74487 files and directories currently installed.) 141s Preparing to unpack .../libc-bin_2.39-3.1ubuntu3_amd64.deb ... 141s Unpacking libc-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 141s Setting up libc-bin (2.39-3.1ubuntu3) ... 141s (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 ... 74487 files and directories currently installed.) 141s Preparing to unpack .../libssl3t64_3.2.2-1ubuntu1_amd64.deb ... 141s Unpacking libssl3t64:amd64 (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ... 141s Setting up libssl3t64:amd64 (3.2.2-1ubuntu1) ... 141s (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 ... 74487 files and directories currently installed.) 141s Preparing to unpack .../00-openssh-sftp-server_1%3a9.6p1-3ubuntu17_amd64.deb ... 141s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 141s Preparing to unpack .../01-openssh-server_1%3a9.6p1-3ubuntu17_amd64.deb ... 141s Unpacking openssh-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 141s Preparing to unpack .../02-openssh-client_1%3a9.6p1-3ubuntu17_amd64.deb ... 141s Unpacking openssh-client (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 141s Preparing to unpack .../03-gir1.2-glib-2.0_2.80.4-1ubuntu1_amd64.deb ... 141s Unpacking gir1.2-glib-2.0:amd64 (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ... 141s Preparing to unpack .../04-libglib2.0-0t64_2.80.4-1ubuntu1_amd64.deb ... 141s Unpacking libglib2.0-0t64:amd64 (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ... 141s Preparing to unpack .../05-libglib2.0-data_2.80.4-1ubuntu1_all.deb ... 141s Unpacking libglib2.0-data (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ... 141s Preparing to unpack .../06-locales_2.39-3.1ubuntu3_all.deb ... 141s Unpacking locales (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 142s Preparing to unpack .../07-openssl_3.2.2-1ubuntu1_amd64.deb ... 142s Unpacking openssl (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ... 142s Preparing to unpack .../08-inetutils-telnet_2%3a2.5-5ubuntu1_amd64.deb ... 142s Unpacking inetutils-telnet (2:2.5-5ubuntu1) over (2:2.5-3ubuntu4) ... 142s Preparing to unpack .../09-libnghttp2-14_1.62.1-2_amd64.deb ... 142s Unpacking libnghttp2-14:amd64 (1.62.1-2) over (1.62.1-1) ... 142s Preparing to unpack .../10-telnet_0.17+2.5-5ubuntu1_all.deb ... 142s Unpacking telnet (0.17+2.5-5ubuntu1) over (0.17+2.5-3ubuntu4) ... 142s Preparing to unpack .../11-libgprofng0_2.42.50.20240710-1ubuntu1_amd64.deb ... 142s Unpacking libgprofng0:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 142s Preparing to unpack .../12-libctf0_2.42.50.20240710-1ubuntu1_amd64.deb ... 142s Unpacking libctf0:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 142s Preparing to unpack .../13-libctf-nobfd0_2.42.50.20240710-1ubuntu1_amd64.deb ... 142s Unpacking libctf-nobfd0:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 142s Preparing to unpack .../14-binutils-x86-64-linux-gnu_2.42.50.20240710-1ubuntu1_amd64.deb ... 142s Unpacking binutils-x86-64-linux-gnu (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 142s Preparing to unpack .../15-libbinutils_2.42.50.20240710-1ubuntu1_amd64.deb ... 142s Unpacking libbinutils:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 142s Preparing to unpack .../16-binutils_2.42.50.20240710-1ubuntu1_amd64.deb ... 142s Unpacking binutils (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 142s Preparing to unpack .../17-binutils-common_2.42.50.20240710-1ubuntu1_amd64.deb ... 142s Unpacking binutils-common:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 142s Preparing to unpack .../18-libsframe1_2.42.50.20240710-1ubuntu1_amd64.deb ... 142s Unpacking libsframe1:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 142s Preparing to unpack .../19-libnss3_2%3a3.102-1_amd64.deb ... 142s Unpacking libnss3:amd64 (2:3.102-1) over (2:3.101-1) ... 142s Setting up openssh-client (1:9.6p1-3ubuntu17) ... 142s Setting up binutils-common:amd64 (2.42.50.20240710-1ubuntu1) ... 142s Setting up libnghttp2-14:amd64 (1.62.1-2) ... 142s Setting up inetutils-telnet (2:2.5-5ubuntu1) ... 142s Setting up libctf-nobfd0:amd64 (2.42.50.20240710-1ubuntu1) ... 142s Setting up libnss3:amd64 (2:3.102-1) ... 142s Setting up locales (2.39-3.1ubuntu3) ... 143s Generating locales (this might take a while)... 144s en_US.UTF-8... done 144s Generation complete. 144s Setting up libsframe1:amd64 (2.42.50.20240710-1ubuntu1) ... 144s Setting up libglib2.0-0t64:amd64 (2.80.4-1ubuntu1) ... 144s No schema files found: doing nothing. 144s Setting up libglib2.0-data (2.80.4-1ubuntu1) ... 144s Setting up gir1.2-glib-2.0:amd64 (2.80.4-1ubuntu1) ... 144s Setting up libbinutils:amd64 (2.42.50.20240710-1ubuntu1) ... 144s Setting up libc-dev-bin (2.39-3.1ubuntu3) ... 144s Setting up openssl (3.2.2-1ubuntu1) ... 144s Installing new version of config file /etc/ssl/openssl.cnf ... 144s Setting up libc-devtools (2.39-3.1ubuntu3) ... 144s Setting up libctf0:amd64 (2.42.50.20240710-1ubuntu1) ... 144s Setting up openssh-sftp-server (1:9.6p1-3ubuntu17) ... 144s Setting up telnet (0.17+2.5-5ubuntu1) ... 144s Setting up openssh-server (1:9.6p1-3ubuntu17) ... 144s Installing new version of config file /etc/pam.d/sshd ... 146s Setting up libgprofng0:amd64 (2.42.50.20240710-1ubuntu1) ... 146s Setting up libc6-dev:amd64 (2.39-3.1ubuntu3) ... 146s Setting up binutils-x86-64-linux-gnu (2.42.50.20240710-1ubuntu1) ... 146s Setting up binutils (2.42.50.20240710-1ubuntu1) ... 146s Processing triggers for libc-bin (2.39-3.1ubuntu3) ... 146s Processing triggers for ufw (0.36.2-6) ... 146s Processing triggers for systemd (256-1ubuntu1) ... 146s Processing triggers for man-db (2.12.1-2) ... 148s Reading package lists... 148s Building dependency tree... 148s Reading state information... 149s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 149s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 149s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 149s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 150s Reading package lists... 150s Reading package lists... 150s Building dependency tree... 150s Reading state information... 151s Calculating upgrade... 151s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 151s Reading package lists... 151s Building dependency tree... 151s Reading state information... 152s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 153s autopkgtest [17:09:19]: rebooting testbed after setup commands that affected boot 181s autopkgtest [17:09:47]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024 198s autopkgtest [17:10:04]: @@@@@@@@@@@@@@@@@@@@ apt-source mdtraj 202s Get:1 http://ftpmaster.internal/ubuntu oracular/universe mdtraj 1.9.9-1ubuntu2 (dsc) [2701 B] 202s Get:2 http://ftpmaster.internal/ubuntu oracular/universe mdtraj 1.9.9-1ubuntu2 (tar) [21.7 MB] 202s Get:3 http://ftpmaster.internal/ubuntu oracular/universe mdtraj 1.9.9-1ubuntu2 (diff) [296 kB] 203s gpgv: Signature made Mon Apr 1 06:57:01 2024 UTC 203s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 203s gpgv: Can't check signature: No public key 203s dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.9.9-1ubuntu2.dsc: no acceptable signature found 203s autopkgtest [17:10:09]: testing package mdtraj version 1.9.9-1ubuntu2 207s autopkgtest [17:10:13]: build not needed 241s autopkgtest [17:10:47]: test command1: preparing testbed 285s Reading package lists... 285s Building dependency tree... 285s Reading state information... 286s Starting pkgProblemResolver with broken count: 0 286s Starting 2 pkgProblemResolver with broken count: 0 286s Done 286s The following additional packages will be installed: 286s blt fonts-lyx gdb libaec0 libbabeltrace1 libblas3 libblosc1 libblosc2-3 286s libdebuginfod-common libdebuginfod1t64 libgfortran5 libgomp1 libgraphite2-3 286s libharfbuzz0b libhdf5-103-1t64 libimagequant0 libipt2 libjs-jquery 286s libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 libnorm1t64 libopenjp2-7 286s libpgm-5.3-0t64 libpython3.12t64 libqhull-r8.0 libraqm0 libsnappy1v5 286s libsodium23 libsource-highlight-common libsource-highlight4t64 libsz2 286s libtcl8.6 libtk8.6 libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 286s libxss1 libzmq5 python-matplotlib-data python-tables-data python3-appdirs 286s python3-asttokens python3-astunparse python3-brotli python3-comm 286s python3-contourpy python3-coverage python3-cpuinfo python3-cycler 286s python3-dateutil python3-debugpy python3-decorator python3-entrypoints 286s python3-executing python3-fastjsonschema python3-fonttools python3-fs 286s python3-iniconfig python3-ipykernel python3-ipython python3-jedi 286s python3-joblib python3-jupyter-client python3-jupyter-core 286s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 286s python3-matplotlib-inline python3-mdtraj python3-mpmath python3-nbformat 286s python3-nest-asyncio python3-networkx python3-numexpr python3-numpy 286s python3-packaging python3-pandas python3-pandas-lib python3-parso 286s python3-pexpect python3-pil python3-pil.imagetk python3-platformdirs 286s python3-pluggy python3-prompt-toolkit python3-psutil python3-ptyprocess 286s python3-pure-eval python3-py python3-pytest python3-scipy python3-sklearn 286s python3-sklearn-lib python3-stack-data python3-sympy python3-tables 286s python3-tables-lib python3-threadpoolctl python3-tk python3-tornado 286s python3-traitlets python3-typeshed python3-ufolib2 python3-unicodedata2 286s python3-wcwidth python3-zmq tk8.6-blt2.5 unicode-data x11-common 286s Suggested packages: 286s blt-demo gdb-doc gdbserver libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 286s python-coverage-doc python-cycler-doc python-fastjsonschema-doc 286s python-ipython-doc python3-pip python-lxml-doc cm-super-minimal dvipng 286s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 286s librsvg2-common python3-cairocffi python3-gi-cairo python3-gobject 286s python3-pyqt5 python3-sip texlive-extra-utils texlive-latex-extra 286s python-mdtraj-doc python-mpmath-doc python3-gmpy2 python3-gdal python3-pydot 286s python3-pygraphviz gcc gfortran python-numpy-doc python3-dev 286s python-pandas-doc python3-statsmodels python-pexpect-doc python-pil-doc 286s subversion python-scipy-doc python3-dap python-sklearn-doc 286s texlive-fonts-extra python-sympy-doc python3-netcdf4 python-tables-doc 286s vitables tix python3-tk-dbg python3-pycurl python-tornado-doc 286s python3-twisted 286s Recommended packages: 286s libc-dbg javascript-common python3-simplejson python3-bs4 python3-cssselect 286s python3-html5lib python3-bottleneck python3-odf python3-openpyxl 286s python3-numba python3-olefile g++ | c++-compiler isympy-common 286s The following NEW packages will be installed: 286s autopkgtest-satdep blt fonts-lyx gdb libaec0 libbabeltrace1 libblas3 286s libblosc1 libblosc2-3 libdebuginfod-common libdebuginfod1t64 libgfortran5 286s libgomp1 libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libimagequant0 286s libipt2 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 286s libnorm1t64 libopenjp2-7 libpgm-5.3-0t64 libpython3.12t64 libqhull-r8.0 286s libraqm0 libsnappy1v5 libsodium23 libsource-highlight-common 286s libsource-highlight4t64 libsz2 libtcl8.6 libtk8.6 libwebpdemux2 libwebpmux3 286s libxft2 libxrender1 libxslt1.1 libxss1 libzmq5 python-matplotlib-data 286s python-tables-data python3-appdirs python3-asttokens python3-astunparse 286s python3-brotli python3-comm python3-contourpy python3-coverage 286s python3-cpuinfo python3-cycler python3-dateutil python3-debugpy 286s python3-decorator python3-entrypoints python3-executing 286s python3-fastjsonschema python3-fonttools python3-fs python3-iniconfig 286s python3-ipykernel python3-ipython python3-jedi python3-joblib 286s python3-jupyter-client python3-jupyter-core python3-kiwisolver python3-lxml 286s python3-lz4 python3-matplotlib python3-matplotlib-inline python3-mdtraj 286s python3-mpmath python3-nbformat python3-nest-asyncio python3-networkx 286s python3-numexpr python3-numpy python3-packaging python3-pandas 286s python3-pandas-lib python3-parso python3-pexpect python3-pil 286s python3-pil.imagetk python3-platformdirs python3-pluggy 286s python3-prompt-toolkit python3-psutil python3-ptyprocess python3-pure-eval 286s python3-py python3-pytest python3-scipy python3-sklearn python3-sklearn-lib 286s python3-stack-data python3-sympy python3-tables python3-tables-lib 286s python3-threadpoolctl python3-tk python3-tornado python3-traitlets 286s python3-typeshed python3-ufolib2 python3-unicodedata2 python3-wcwidth 286s python3-zmq tk8.6-blt2.5 unicode-data x11-common 286s 0 upgraded, 115 newly installed, 0 to remove and 0 not upgraded. 286s Need to get 98.1 MB/98.1 MB of archives. 286s After this operation, 468 MB of additional disk space will be used. 286s Get:1 /tmp/autopkgtest.34lqv9/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [768 B] 286s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libdebuginfod-common all 0.191-1 [14.6 kB] 286s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1build1 [988 kB] 286s Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 286s Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 286s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 286s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 286s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 libtk8.6 amd64 8.6.14-1build1 [779 kB] 286s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 286s Get:10 http://ftpmaster.internal/ubuntu oracular/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 286s Get:11 http://ftpmaster.internal/ubuntu oracular/universe amd64 fonts-lyx all 2.4.1-1 [171 kB] 286s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 libbabeltrace1 amd64 1.5.11-3build3 [164 kB] 286s Get:13 http://ftpmaster.internal/ubuntu oracular/main amd64 libdebuginfod1t64 amd64 0.191-1 [17.1 kB] 286s Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 libipt2 amd64 2.0.6-1build1 [45.7 kB] 286s Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 libpython3.12t64 amd64 3.12.4-1ubuntu1 [2341 kB] 286s Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 libsource-highlight-common all 3.1.9-4.3build1 [64.2 kB] 286s Get:17 http://ftpmaster.internal/ubuntu oracular/main amd64 libsource-highlight4t64 amd64 3.1.9-4.3build1 [258 kB] 286s Get:18 http://ftpmaster.internal/ubuntu oracular/main amd64 gdb amd64 15.1-0ubuntu1 [3890 kB] 286s Get:19 http://ftpmaster.internal/ubuntu oracular/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 286s Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas3 amd64 3.12.0-3build1 [238 kB] 286s Get:21 http://ftpmaster.internal/ubuntu oracular/main amd64 libsnappy1v5 amd64 1.2.1-1 [30.4 kB] 286s Get:22 http://ftpmaster.internal/ubuntu oracular/universe amd64 libblosc1 amd64 1.21.5+ds-1build1 [36.2 kB] 286s Get:23 http://ftpmaster.internal/ubuntu oracular/universe amd64 libblosc2-3 amd64 2.14.4+ds-2 [164 kB] 286s Get:24 http://ftpmaster.internal/ubuntu oracular/main amd64 libgfortran5 amd64 14.1.0-1ubuntu1 [928 kB] 287s Get:25 http://ftpmaster.internal/ubuntu oracular/main amd64 libgomp1 amd64 14.1.0-1ubuntu1 [148 kB] 287s Get:26 http://ftpmaster.internal/ubuntu oracular/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 287s Get:27 http://ftpmaster.internal/ubuntu oracular/main amd64 libharfbuzz0b amd64 8.3.0-2build2 [469 kB] 287s Get:28 http://ftpmaster.internal/ubuntu oracular/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 287s Get:29 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.1ubuntu4 [1270 kB] 287s Get:30 http://ftpmaster.internal/ubuntu oracular/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 287s Get:31 http://ftpmaster.internal/ubuntu oracular/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 287s Get:32 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 287s Get:33 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack3 amd64 3.12.0-3build1 [2650 kB] 287s Get:34 http://ftpmaster.internal/ubuntu oracular/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 287s Get:35 http://ftpmaster.internal/ubuntu oracular/main amd64 liblcms2-2 amd64 2.14-2build1 [161 kB] 287s Get:36 http://ftpmaster.internal/ubuntu oracular/universe amd64 libnorm1t64 amd64 1.5.9+dfsg-3.1build1 [154 kB] 287s Get:37 http://ftpmaster.internal/ubuntu oracular/universe amd64 libpgm-5.3-0t64 amd64 5.3.128~dfsg-2.1build1 [167 kB] 287s Get:38 http://ftpmaster.internal/ubuntu oracular/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 287s Get:39 http://ftpmaster.internal/ubuntu oracular/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 287s Get:40 http://ftpmaster.internal/ubuntu oracular/main amd64 libsodium23 amd64 1.0.18-1build3 [161 kB] 287s Get:41 http://ftpmaster.internal/ubuntu oracular/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 287s Get:42 http://ftpmaster.internal/ubuntu oracular/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 287s Get:43 http://ftpmaster.internal/ubuntu oracular/main amd64 libxslt1.1 amd64 1.1.39-0exp1build1 [167 kB] 287s Get:44 http://ftpmaster.internal/ubuntu oracular/universe amd64 libzmq5 amd64 4.3.5-1build2 [260 kB] 287s Get:45 http://ftpmaster.internal/ubuntu oracular/universe amd64 python-matplotlib-data all 3.6.3-2ubuntu1 [2937 kB] 287s Get:46 http://ftpmaster.internal/ubuntu oracular/universe amd64 python-tables-data all 3.9.2-2build1 [49.3 kB] 287s Get:47 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 287s Get:48 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-asttokens all 2.4.1-1 [20.9 kB] 287s Get:49 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-astunparse all 1.6.3-2 [13.5 kB] 287s Get:50 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 287s Get:51 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-traitlets all 5.5.0-2 [85.0 kB] 287s Get:52 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-comm all 0.2.1-1 [7016 B] 287s Get:53 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-numpy amd64 1:1.26.4+ds-10 [4437 kB] 287s Get:54 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-contourpy amd64 1.0.7-3 [181 kB] 287s Get:55 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-coverage amd64 7.4.4+dfsg1-0ubuntu2 [147 kB] 287s Get:56 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-cpuinfo all 9.0.0+git20221119-1 [21.4 kB] 287s Get:57 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 287s Get:58 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 287s Get:59 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-debugpy amd64 1.8.2+ds-4ubuntu1 [587 kB] 287s Get:60 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 287s Get:61 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-entrypoints all 0.4-2 [7146 B] 287s Get:62 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-executing all 2.0.1-0.1 [23.3 kB] 287s Get:63 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-fastjsonschema all 2.20.0-1 [20.1 kB] 287s Get:64 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-scipy amd64 1.12.0-2 [16.5 MB] 287s Get:65 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB] 287s Get:66 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 287s Get:67 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-sympy all 1.12-8 [3966 kB] 287s Get:68 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 287s Get:69 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-lxml amd64 5.2.2-1 [1243 kB] 287s Get:70 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 287s Get:71 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build1 [362 kB] 287s Get:72 http://ftpmaster.internal/ubuntu oracular/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 287s Get:73 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 287s Get:74 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 287s Get:75 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-parso all 0.8.3-1 [67.2 kB] 287s Get:76 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-typeshed all 0.0~git20231111.6764465-3 [1274 kB] 287s Get:77 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-jedi all 0.19.1+ds1-1 [693 kB] 287s Get:78 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 287s Get:79 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-ptyprocess all 0.7.0-5 [15.1 kB] 287s Get:80 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-pexpect all 4.9-2 [48.1 kB] 287s Get:81 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-wcwidth all 0.2.5+dfsg1-1.1ubuntu1 [22.5 kB] 287s Get:82 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-prompt-toolkit all 3.0.47-1 [256 kB] 287s Get:83 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pure-eval all 0.2.2-2 [11.1 kB] 287s Get:84 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-stack-data all 0.6.3-1 [22.0 kB] 287s Get:85 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-ipython all 8.20.0-1ubuntu1 [561 kB] 287s Get:86 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-platformdirs all 4.2.1-1 [16.3 kB] 287s Get:87 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-jupyter-core all 5.3.2-3 [25.6 kB] 287s Get:88 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-nest-asyncio all 1.5.4-1 [6256 B] 287s Get:89 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-tornado amd64 6.4.1-1 [298 kB] 287s Get:90 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-py all 1.11.0-2 [72.7 kB] 287s Get:91 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-zmq amd64 24.0.1-5build1 [286 kB] 287s Get:92 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-jupyter-client all 7.4.9-2ubuntu1 [90.5 kB] 287s Get:93 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-packaging all 24.1-1 [41.4 kB] 287s Get:94 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-psutil amd64 5.9.8-2build2 [195 kB] 287s Get:95 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-ipykernel all 6.29.5-1 [82.5 kB] 287s Get:96 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-joblib all 1.3.2-2 [208 kB] 287s Get:97 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-kiwisolver amd64 1.4.5-1 [51.0 kB] 287s Get:98 http://ftpmaster.internal/ubuntu oracular/main amd64 libopenjp2-7 amd64 2.5.0-2build3 [173 kB] 287s Get:99 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-pil amd64 10.4.0-1 [462 kB] 288s Get:100 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-tk amd64 3.12.3-0ubuntu1 [102 kB] 288s Get:101 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pil.imagetk amd64 10.4.0-1 [9264 B] 288s Get:102 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-matplotlib amd64 3.6.3-2ubuntu1 [6080 kB] 288s Get:103 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 288s Get:104 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pandas-lib amd64 2.1.4+dfsg-8 [4450 kB] 288s Get:105 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pandas all 2.1.4+dfsg-8 [3042 kB] 288s Get:106 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-numexpr amd64 2.10.1-2 [117 kB] 288s Get:107 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-tables-lib amd64 3.9.2-2build1 [520 kB] 288s Get:108 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-tables all 3.9.2-2build1 [344 kB] 288s Get:109 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-mdtraj amd64 1.9.9-1ubuntu2 [1140 kB] 288s Get:110 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-nbformat all 5.9.1-1 [41.2 kB] 288s Get:111 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 288s Get:112 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pytest all 7.4.4-1 [305 kB] 288s Get:113 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 288s Get:114 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-3 [3786 kB] 288s Get:115 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-sklearn all 1.4.2+dfsg-3 [2257 kB] 289s Preconfiguring packages ... 289s Fetched 98.1 MB in 2s (45.2 MB/s) 289s Selecting previously unselected package libdebuginfod-common. 289s (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 ... 74486 files and directories currently installed.) 289s Preparing to unpack .../000-libdebuginfod-common_0.191-1_all.deb ... 289s Unpacking libdebuginfod-common (0.191-1) ... 289s Selecting previously unselected package libtcl8.6:amd64. 289s Preparing to unpack .../001-libtcl8.6_8.6.14+dfsg-1build1_amd64.deb ... 289s Unpacking libtcl8.6:amd64 (8.6.14+dfsg-1build1) ... 289s Selecting previously unselected package libxrender1:amd64. 289s Preparing to unpack .../002-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 289s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 289s Selecting previously unselected package libxft2:amd64. 289s Preparing to unpack .../003-libxft2_2.3.6-1build1_amd64.deb ... 289s Unpacking libxft2:amd64 (2.3.6-1build1) ... 289s Selecting previously unselected package x11-common. 289s Preparing to unpack .../004-x11-common_1%3a7.7+23ubuntu3_all.deb ... 289s Unpacking x11-common (1:7.7+23ubuntu3) ... 289s Selecting previously unselected package libxss1:amd64. 289s Preparing to unpack .../005-libxss1_1%3a1.2.3-1build3_amd64.deb ... 289s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 289s Selecting previously unselected package libtk8.6:amd64. 289s Preparing to unpack .../006-libtk8.6_8.6.14-1build1_amd64.deb ... 289s Unpacking libtk8.6:amd64 (8.6.14-1build1) ... 289s Selecting previously unselected package tk8.6-blt2.5. 289s Preparing to unpack .../007-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 289s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 290s Selecting previously unselected package blt. 290s Preparing to unpack .../008-blt_2.5.3+dfsg-7build1_amd64.deb ... 290s Unpacking blt (2.5.3+dfsg-7build1) ... 290s Selecting previously unselected package fonts-lyx. 290s Preparing to unpack .../009-fonts-lyx_2.4.1-1_all.deb ... 290s Unpacking fonts-lyx (2.4.1-1) ... 290s Selecting previously unselected package libbabeltrace1:amd64. 290s Preparing to unpack .../010-libbabeltrace1_1.5.11-3build3_amd64.deb ... 290s Unpacking libbabeltrace1:amd64 (1.5.11-3build3) ... 290s Selecting previously unselected package libdebuginfod1t64:amd64. 290s Preparing to unpack .../011-libdebuginfod1t64_0.191-1_amd64.deb ... 290s Unpacking libdebuginfod1t64:amd64 (0.191-1) ... 290s Selecting previously unselected package libipt2. 290s Preparing to unpack .../012-libipt2_2.0.6-1build1_amd64.deb ... 290s Unpacking libipt2 (2.0.6-1build1) ... 290s Selecting previously unselected package libpython3.12t64:amd64. 290s Preparing to unpack .../013-libpython3.12t64_3.12.4-1ubuntu1_amd64.deb ... 290s Unpacking libpython3.12t64:amd64 (3.12.4-1ubuntu1) ... 290s Selecting previously unselected package libsource-highlight-common. 290s Preparing to unpack .../014-libsource-highlight-common_3.1.9-4.3build1_all.deb ... 290s Unpacking libsource-highlight-common (3.1.9-4.3build1) ... 290s Selecting previously unselected package libsource-highlight4t64:amd64. 290s Preparing to unpack .../015-libsource-highlight4t64_3.1.9-4.3build1_amd64.deb ... 290s Unpacking libsource-highlight4t64:amd64 (3.1.9-4.3build1) ... 290s Selecting previously unselected package gdb. 290s Preparing to unpack .../016-gdb_15.1-0ubuntu1_amd64.deb ... 290s Unpacking gdb (15.1-0ubuntu1) ... 290s Selecting previously unselected package libaec0:amd64. 290s Preparing to unpack .../017-libaec0_1.1.3-1_amd64.deb ... 290s Unpacking libaec0:amd64 (1.1.3-1) ... 290s Selecting previously unselected package libblas3:amd64. 290s Preparing to unpack .../018-libblas3_3.12.0-3build1_amd64.deb ... 290s Unpacking libblas3:amd64 (3.12.0-3build1) ... 290s Selecting previously unselected package libsnappy1v5:amd64. 290s Preparing to unpack .../019-libsnappy1v5_1.2.1-1_amd64.deb ... 290s Unpacking libsnappy1v5:amd64 (1.2.1-1) ... 290s Selecting previously unselected package libblosc1:amd64. 290s Preparing to unpack .../020-libblosc1_1.21.5+ds-1build1_amd64.deb ... 290s Unpacking libblosc1:amd64 (1.21.5+ds-1build1) ... 290s Selecting previously unselected package libblosc2-3:amd64. 290s Preparing to unpack .../021-libblosc2-3_2.14.4+ds-2_amd64.deb ... 290s Unpacking libblosc2-3:amd64 (2.14.4+ds-2) ... 290s Selecting previously unselected package libgfortran5:amd64. 290s Preparing to unpack .../022-libgfortran5_14.1.0-1ubuntu1_amd64.deb ... 290s Unpacking libgfortran5:amd64 (14.1.0-1ubuntu1) ... 290s Selecting previously unselected package libgomp1:amd64. 290s Preparing to unpack .../023-libgomp1_14.1.0-1ubuntu1_amd64.deb ... 290s Unpacking libgomp1:amd64 (14.1.0-1ubuntu1) ... 290s Selecting previously unselected package libgraphite2-3:amd64. 290s Preparing to unpack .../024-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 290s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 290s Selecting previously unselected package libharfbuzz0b:amd64. 290s Preparing to unpack .../025-libharfbuzz0b_8.3.0-2build2_amd64.deb ... 290s Unpacking libharfbuzz0b:amd64 (8.3.0-2build2) ... 290s Selecting previously unselected package libsz2:amd64. 290s Preparing to unpack .../026-libsz2_1.1.3-1_amd64.deb ... 290s Unpacking libsz2:amd64 (1.1.3-1) ... 290s Selecting previously unselected package libhdf5-103-1t64:amd64. 290s Preparing to unpack .../027-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu4_amd64.deb ... 290s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-3.1ubuntu4) ... 290s Selecting previously unselected package libimagequant0:amd64. 290s Preparing to unpack .../028-libimagequant0_2.18.0-1build1_amd64.deb ... 290s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 290s Selecting previously unselected package libjs-jquery. 290s Preparing to unpack .../029-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 290s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 290s Selecting previously unselected package libjs-jquery-ui. 290s Preparing to unpack .../030-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 290s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 290s Selecting previously unselected package liblapack3:amd64. 290s Preparing to unpack .../031-liblapack3_3.12.0-3build1_amd64.deb ... 290s Unpacking liblapack3:amd64 (3.12.0-3build1) ... 291s Selecting previously unselected package liblbfgsb0:amd64. 291s Preparing to unpack .../032-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 291s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 291s Selecting previously unselected package liblcms2-2:amd64. 291s Preparing to unpack .../033-liblcms2-2_2.14-2build1_amd64.deb ... 291s Unpacking liblcms2-2:amd64 (2.14-2build1) ... 291s Selecting previously unselected package libnorm1t64:amd64. 291s Preparing to unpack .../034-libnorm1t64_1.5.9+dfsg-3.1build1_amd64.deb ... 291s Unpacking libnorm1t64:amd64 (1.5.9+dfsg-3.1build1) ... 291s Selecting previously unselected package libpgm-5.3-0t64:amd64. 291s Preparing to unpack .../035-libpgm-5.3-0t64_5.3.128~dfsg-2.1build1_amd64.deb ... 291s Unpacking libpgm-5.3-0t64:amd64 (5.3.128~dfsg-2.1build1) ... 291s Selecting previously unselected package libqhull-r8.0:amd64. 291s Preparing to unpack .../036-libqhull-r8.0_2020.2-6build1_amd64.deb ... 291s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 291s Selecting previously unselected package libraqm0:amd64. 291s Preparing to unpack .../037-libraqm0_0.10.1-1build1_amd64.deb ... 291s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 291s Selecting previously unselected package libsodium23:amd64. 291s Preparing to unpack .../038-libsodium23_1.0.18-1build3_amd64.deb ... 291s Unpacking libsodium23:amd64 (1.0.18-1build3) ... 291s Selecting previously unselected package libwebpdemux2:amd64. 291s Preparing to unpack .../039-libwebpdemux2_1.4.0-0.1_amd64.deb ... 291s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 291s Selecting previously unselected package libwebpmux3:amd64. 291s Preparing to unpack .../040-libwebpmux3_1.4.0-0.1_amd64.deb ... 291s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 291s Selecting previously unselected package libxslt1.1:amd64. 291s Preparing to unpack .../041-libxslt1.1_1.1.39-0exp1build1_amd64.deb ... 291s Unpacking libxslt1.1:amd64 (1.1.39-0exp1build1) ... 291s Selecting previously unselected package libzmq5:amd64. 291s Preparing to unpack .../042-libzmq5_4.3.5-1build2_amd64.deb ... 291s Unpacking libzmq5:amd64 (4.3.5-1build2) ... 291s Selecting previously unselected package python-matplotlib-data. 291s Preparing to unpack .../043-python-matplotlib-data_3.6.3-2ubuntu1_all.deb ... 291s Unpacking python-matplotlib-data (3.6.3-2ubuntu1) ... 291s Selecting previously unselected package python-tables-data. 291s Preparing to unpack .../044-python-tables-data_3.9.2-2build1_all.deb ... 291s Unpacking python-tables-data (3.9.2-2build1) ... 291s Selecting previously unselected package python3-appdirs. 291s Preparing to unpack .../045-python3-appdirs_1.4.4-4_all.deb ... 291s Unpacking python3-appdirs (1.4.4-4) ... 291s Selecting previously unselected package python3-asttokens. 291s Preparing to unpack .../046-python3-asttokens_2.4.1-1_all.deb ... 291s Unpacking python3-asttokens (2.4.1-1) ... 291s Selecting previously unselected package python3-astunparse. 291s Preparing to unpack .../047-python3-astunparse_1.6.3-2_all.deb ... 291s Unpacking python3-astunparse (1.6.3-2) ... 291s Selecting previously unselected package python3-brotli. 291s Preparing to unpack .../048-python3-brotli_1.1.0-2build2_amd64.deb ... 291s Unpacking python3-brotli (1.1.0-2build2) ... 291s Selecting previously unselected package python3-traitlets. 291s Preparing to unpack .../049-python3-traitlets_5.5.0-2_all.deb ... 291s Unpacking python3-traitlets (5.5.0-2) ... 291s Selecting previously unselected package python3-comm. 291s Preparing to unpack .../050-python3-comm_0.2.1-1_all.deb ... 291s Unpacking python3-comm (0.2.1-1) ... 291s Selecting previously unselected package python3-numpy. 291s Preparing to unpack .../051-python3-numpy_1%3a1.26.4+ds-10_amd64.deb ... 291s Unpacking python3-numpy (1:1.26.4+ds-10) ... 291s Selecting previously unselected package python3-contourpy. 291s Preparing to unpack .../052-python3-contourpy_1.0.7-3_amd64.deb ... 291s Unpacking python3-contourpy (1.0.7-3) ... 291s Selecting previously unselected package python3-coverage. 291s Preparing to unpack .../053-python3-coverage_7.4.4+dfsg1-0ubuntu2_amd64.deb ... 291s Unpacking python3-coverage (7.4.4+dfsg1-0ubuntu2) ... 291s Selecting previously unselected package python3-cpuinfo. 291s Preparing to unpack .../054-python3-cpuinfo_9.0.0+git20221119-1_all.deb ... 291s Unpacking python3-cpuinfo (9.0.0+git20221119-1) ... 291s Selecting previously unselected package python3-cycler. 291s Preparing to unpack .../055-python3-cycler_0.12.1-1_all.deb ... 291s Unpacking python3-cycler (0.12.1-1) ... 291s Selecting previously unselected package python3-dateutil. 291s Preparing to unpack .../056-python3-dateutil_2.9.0-2_all.deb ... 291s Unpacking python3-dateutil (2.9.0-2) ... 291s Selecting previously unselected package python3-debugpy. 291s Preparing to unpack .../057-python3-debugpy_1.8.2+ds-4ubuntu1_amd64.deb ... 291s Unpacking python3-debugpy (1.8.2+ds-4ubuntu1) ... 292s Selecting previously unselected package python3-decorator. 292s Preparing to unpack .../058-python3-decorator_5.1.1-5_all.deb ... 292s Unpacking python3-decorator (5.1.1-5) ... 292s Selecting previously unselected package python3-entrypoints. 292s Preparing to unpack .../059-python3-entrypoints_0.4-2_all.deb ... 292s Unpacking python3-entrypoints (0.4-2) ... 292s Selecting previously unselected package python3-executing. 292s Preparing to unpack .../060-python3-executing_2.0.1-0.1_all.deb ... 292s Unpacking python3-executing (2.0.1-0.1) ... 292s Selecting previously unselected package python3-fastjsonschema. 292s Preparing to unpack .../061-python3-fastjsonschema_2.20.0-1_all.deb ... 292s Unpacking python3-fastjsonschema (2.20.0-1) ... 292s Selecting previously unselected package python3-scipy. 292s Preparing to unpack .../062-python3-scipy_1.12.0-2_amd64.deb ... 292s Unpacking python3-scipy (1.12.0-2) ... 292s Selecting previously unselected package python3-ufolib2. 292s Preparing to unpack .../063-python3-ufolib2_0.16.0+dfsg1-1_all.deb ... 292s Unpacking python3-ufolib2 (0.16.0+dfsg1-1) ... 292s Selecting previously unselected package python3-mpmath. 292s Preparing to unpack .../064-python3-mpmath_1.3.0-1_all.deb ... 292s Unpacking python3-mpmath (1.3.0-1) ... 292s Selecting previously unselected package python3-sympy. 292s Preparing to unpack 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293s Selecting previously unselected package python3-fonttools. 293s Preparing to unpack .../071-python3-fonttools_4.46.0-1build2_amd64.deb ... 293s Unpacking python3-fonttools (4.46.0-1build2) ... 293s Selecting previously unselected package python3-iniconfig. 293s Preparing to unpack .../072-python3-iniconfig_1.1.1-2_all.deb ... 293s Unpacking python3-iniconfig (1.1.1-2) ... 293s Selecting previously unselected package python3-parso. 293s Preparing to unpack .../073-python3-parso_0.8.3-1_all.deb ... 293s Unpacking python3-parso (0.8.3-1) ... 293s Selecting previously unselected package python3-typeshed. 293s Preparing to unpack .../074-python3-typeshed_0.0~git20231111.6764465-3_all.deb ... 293s Unpacking python3-typeshed (0.0~git20231111.6764465-3) ... 294s Selecting previously unselected package python3-jedi. 294s Preparing to unpack .../075-python3-jedi_0.19.1+ds1-1_all.deb ... 294s Unpacking python3-jedi (0.19.1+ds1-1) ... 294s Selecting previously unselected package python3-matplotlib-inline. 294s Preparing to unpack .../076-python3-matplotlib-inline_0.1.6-2_all.deb ... 294s Unpacking python3-matplotlib-inline (0.1.6-2) ... 294s Selecting previously unselected package python3-ptyprocess. 294s Preparing to unpack .../077-python3-ptyprocess_0.7.0-5_all.deb ... 294s Unpacking python3-ptyprocess (0.7.0-5) ... 294s Selecting previously unselected package python3-pexpect. 294s Preparing to unpack .../078-python3-pexpect_4.9-2_all.deb ... 294s Unpacking python3-pexpect (4.9-2) ... 294s Selecting previously unselected package python3-wcwidth. 294s Preparing to unpack .../079-python3-wcwidth_0.2.5+dfsg1-1.1ubuntu1_all.deb ... 294s Unpacking python3-wcwidth (0.2.5+dfsg1-1.1ubuntu1) ... 294s Selecting previously unselected package python3-prompt-toolkit. 294s Preparing to unpack .../080-python3-prompt-toolkit_3.0.47-1_all.deb ... 294s Unpacking python3-prompt-toolkit (3.0.47-1) ... 294s Selecting previously unselected package python3-pure-eval. 294s 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(24.1-1) ... 295s Selecting previously unselected package python3-psutil. 295s Preparing to unpack .../092-python3-psutil_5.9.8-2build2_amd64.deb ... 295s Unpacking python3-psutil (5.9.8-2build2) ... 295s Selecting previously unselected package python3-ipykernel. 295s Preparing to unpack .../093-python3-ipykernel_6.29.5-1_all.deb ... 295s Unpacking python3-ipykernel (6.29.5-1) ... 295s Selecting previously unselected package python3-joblib. 295s Preparing to unpack .../094-python3-joblib_1.3.2-2_all.deb ... 295s Unpacking python3-joblib (1.3.2-2) ... 295s Selecting previously unselected package python3-kiwisolver. 295s Preparing to unpack .../095-python3-kiwisolver_1.4.5-1_amd64.deb ... 295s Unpacking python3-kiwisolver (1.4.5-1) ... 295s Selecting previously unselected package libopenjp2-7:amd64. 295s Preparing to unpack .../096-libopenjp2-7_2.5.0-2build3_amd64.deb ... 295s Unpacking libopenjp2-7:amd64 (2.5.0-2build3) ... 295s Selecting previously unselected package python3-pil:amd64. 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296s Unpacking python3-mdtraj (1.9.9-1ubuntu2) ... 296s Selecting previously unselected package python3-nbformat. 296s Preparing to unpack .../108-python3-nbformat_5.9.1-1_all.deb ... 296s Unpacking python3-nbformat (5.9.1-1) ... 296s Selecting previously unselected package python3-pluggy. 297s Preparing to unpack .../109-python3-pluggy_1.5.0-1_all.deb ... 297s Unpacking python3-pluggy (1.5.0-1) ... 297s Selecting previously unselected package python3-pytest. 297s Preparing to unpack .../110-python3-pytest_7.4.4-1_all.deb ... 297s Unpacking python3-pytest (7.4.4-1) ... 297s Selecting previously unselected package python3-threadpoolctl. 297s Preparing to unpack .../111-python3-threadpoolctl_3.1.0-1_all.deb ... 297s Unpacking python3-threadpoolctl (3.1.0-1) ... 297s Selecting previously unselected package python3-sklearn-lib:amd64. 297s Preparing to unpack .../112-python3-sklearn-lib_1.4.2+dfsg-3_amd64.deb ... 297s Unpacking python3-sklearn-lib:amd64 (1.4.2+dfsg-3) ... 297s Selecting previously unselected package python3-sklearn. 297s Preparing to unpack .../113-python3-sklearn_1.4.2+dfsg-3_all.deb ... 297s Unpacking python3-sklearn (1.4.2+dfsg-3) ... 297s Selecting previously unselected package autopkgtest-satdep. 297s Preparing to unpack .../114-1-autopkgtest-satdep.deb ... 297s Unpacking autopkgtest-satdep (0) ... 297s Setting up python3-entrypoints (0.4-2) ... 297s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 297s Setting up liblcms2-2:amd64 (2.14-2build1) ... 297s Setting up python3-iniconfig (1.1.1-2) ... 297s Setting up python3-tornado (6.4.1-1) ... 298s Setting up libnorm1t64:amd64 (1.5.9+dfsg-3.1build1) ... 298s Setting up python3-pure-eval (0.2.2-2) ... 298s Setting up python3-astunparse (1.6.3-2) ... 298s Setting up libsodium23:amd64 (1.0.18-1build3) ... 298s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 298s Setting up python3-py (1.11.0-2) ... 298s Setting up libdebuginfod-common (0.191-1) ... 298s Setting up python3-joblib (1.3.2-2) 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(1.8.2+ds-4ubuntu1) ... 320s Setting up python3-pil:amd64 (10.4.0-1) ... 320s Setting up python3-pandas (2.1.4+dfsg-8) ... 325s Setting up python3-pil.imagetk:amd64 (10.4.0-1) ... 325s Setting up python3-ipython (8.20.0-1ubuntu1) ... 326s Setting up python3-ipykernel (6.29.5-1) ... 326s Setting up python3-sklearn (1.4.2+dfsg-3) ... 328s Setting up python3-numexpr (2.10.1-2) ... 328s Setting up python3-tables (3.9.2-2build1) ... 329s Setting up python3-mdtraj (1.9.9-1ubuntu2) ... 329s /usr/lib/python3/dist-packages/mdtraj/formats/amberrst.py:271: SyntaxWarning: invalid escape sequence '\g' 329s """Read data from an AMBER ASCII restart file 329s /usr/lib/python3/dist-packages/mdtraj/formats/amberrst.py:534: SyntaxWarning: invalid escape sequence '\g' 329s """Read data from an AMBER NetCDF restart file 329s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:394: SyntaxWarning: invalid escape sequence '\d' 329s time = float(findall('t= *(\d+\.\d+)',comment)[-1]) 329s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:500: SyntaxWarning: invalid escape sequence '\.' 329s return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) 329s /usr/lib/python3/dist-packages/mdtraj/formats/gsd.py:228: SyntaxWarning: invalid escape sequence '\g' 329s """Write one or more frames of data to a gsd file. 329s /usr/lib/python3/dist-packages/mdtraj/formats/lammpstrj.py:237: SyntaxWarning: invalid escape sequence '\g' 329s """Read data from a lammpstrj file. 329s /usr/lib/python3/dist-packages/mdtraj/formats/lammpstrj.py:429: SyntaxWarning: invalid escape sequence '\g' 329s """Write the box lines in the header of a frame. 329s /usr/lib/python3/dist-packages/mdtraj/formats/lammpstrj.py:476: SyntaxWarning: invalid escape sequence '\g' 329s """Write one or more frames of data to a lammpstrj file. 329s /usr/lib/python3/dist-packages/mdtraj/formats/mol2.py:215: SyntaxWarning: invalid escape sequence '\s' 329s index_col=0, header=None, sep="\s+", engine='python') 329s /usr/lib/python3/dist-packages/mdtraj/formats/mol2.py:222: SyntaxWarning: invalid escape sequence '\s' 329s atoms_frame = pd.read_csv(csv, sep="\s+", engine='python', header=None) 329s /usr/lib/python3/dist-packages/mdtraj/formats/netcdf.py:217: SyntaxWarning: invalid escape sequence '\g' 329s """Read data from a molecular dynamics trajectory in the AMBER NetCDF 329s /usr/lib/python3/dist-packages/mdtraj/formats/netcdf.py:323: SyntaxWarning: invalid escape sequence '\g' 329s """Write one or more frames of a molecular dynamics trajectory to disk 329s /usr/lib/python3/dist-packages/mdtraj/formats/prmtop.py:63: SyntaxWarning: invalid escape sequence '\.' 329s FORMAT_RE_PATTERN = re.compile("([0-9]+)([a-zA-Z]+)([0-9]+)\.?([0-9]*)") 329s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:44: SyntaxWarning: invalid escape sequence '\s' 329s """Compute the distance between pairs of residues in a trajectory. 329s /usr/lib/python3/dist-packages/mdtraj/geometry/hbond.py:251: SyntaxWarning: invalid escape sequence '\c' 329s """Compute the Kabsch-Sander hydrogen bond energy between each pair 329s /usr/lib/python3/dist-packages/mdtraj/geometry/internal.py:370: SyntaxWarning: invalid escape sequence '\p' 329s """Calculate the Wilson B matrix, which collects the derivatives of the 329s /usr/lib/python3/dist-packages/mdtraj/geometry/shape.py:80: SyntaxWarning: invalid escape sequence '\l' 329s """Compute the asphericity of a trajectory. 329s /usr/lib/python3/dist-packages/mdtraj/geometry/shape.py:105: SyntaxWarning: invalid escape sequence '\l' 329s """Compute the acylindricity of a trajectory. 329s /usr/lib/python3/dist-packages/mdtraj/geometry/shape.py:130: SyntaxWarning: invalid escape sequence '\k' 329s """Compute the relative shape anisotropy of a trajectory. 329s /usr/lib/python3/dist-packages/mdtraj/nmr/shift_wrappers.py:214: SyntaxWarning: invalid escape sequence '\s' 329s d = pd.read_table("./bb_details.dat", index_col=False, header=None, sep="\s+").drop([3], axis=1) 329s /usr/lib/python3/dist-packages/mdtraj/nmr/shift_wrappers.py:292: SyntaxWarning: invalid escape sequence '\s' 329s d = pd.read_table("./trj%d_pred.tab" % i, names=names, header=None, sep="\s+", skiprows=lines_to_skip) 329s /usr/lib/python3/dist-packages/mdtraj/testing/docscrape.py:305: SyntaxWarning: invalid escape sequence '\w' 329s if re.compile('^([\w., ]+=)?\s*[\w\.]+\(.*\)$').match(summary_str): 329s /usr/lib/python3/dist-packages/mdtraj/testing/docscrape.py:345: SyntaxWarning: invalid escape sequence '\*' 329s return [self['Signature'].replace('*','\*')] + [''] 329s /usr/lib/python3/dist-packages/mdtraj/testing/docscrape.py:464: SyntaxWarning: invalid escape sequence '\*' 329s argspec = argspec.replace('*','\*') 329s /usr/lib/python3/dist-packages/mdtraj/testing/docscrape.py:482: SyntaxWarning: invalid escape sequence '\*' 329s signature = self['Signature'].replace('*', '\*') 329s /usr/lib/python3/dist-packages/mdtraj/testing/docstrings.py:126: SyntaxWarning: invalid escape sequence '\d' 329s m = re.search('takes at most (\d+) positional arguments', str(e)) 329s Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... 329s Setting up python3-fonttools (4.46.0-1build2) ... 330s Setting up python3-matplotlib (3.6.3-2ubuntu1) ... 331s Setting up autopkgtest-satdep (0) ... 331s Processing triggers for libc-bin (2.39-3.1ubuntu3) ... 331s Processing triggers for man-db (2.12.1-2) ... 340s (Reading database ... 96520 files and directories currently installed.) 340s Removing autopkgtest-satdep (0) ... 341s autopkgtest [17:12:27]: test command1: pytest-3 -k 'not nmr.ipynb and not test_image_molecules' 341s autopkgtest [17:12:27]: test command1: [----------------------- 342s ============================= test session starts ============================== 342s platform linux -- Python 3.12.4, pytest-7.4.4, pluggy-1.5.0 -- /usr/bin/python3 342s cachedir: .pytest_cache 342s rootdir: /tmp/autopkgtest.34lqv9/build.kEU/src 342s configfile: pytest.ini 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tests/test_docstrings.py::test_docstrings[mdtraj.formats.xyzfile] PASSED [ 9%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.geometry._geometry] PASSED [ 9%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.alignment] PASSED [ 9%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.angle] PASSED [ 9%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.contact] PASSED [ 9%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.dihedral] PASSED [ 9%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.distance] PASSED [ 9%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.drid] PASSED [ 9%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.dssp] PASSED [ 9%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.hbond] PASSED [ 9%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.internal] PASSED [ 9%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.neighborlist] PASSED [ 9%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.neighbors] PASSED [ 10%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.order] PASSED [ 10%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.rdf] PASSED [ 10%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.rg] PASSED [ 10%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.sasa] PASSED [ 10%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.shape] PASSED [ 10%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.geometry.thermodynamic_properties] PASSED [ 10%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.io] SKIPPED (Skip c...) [ 10%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.nmr.scalar_couplings] PASSED [ 10%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.nmr.shift_wrappers] PASSED [ 10%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.basereporter] PASSED [ 10%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.dcdreporter] PASSED [ 10%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.hdf5reporter] PASSED [ 10%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.netcdfreporter] PASSED [ 11%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.xtcreporter] PASSED [ 11%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.scripts.mdconvert] SKIPPED [ 11%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.scripts.mdinspect] SKIPPED [ 11%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.testing.docscrape] SKIPPED [ 11%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.testing.docstrings] PASSED [ 11%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.testing.testing] PASSED [ 11%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.utils.contextmanagers] PASSED [ 11%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.utils.delay_import] PASSED [ 11%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.utils.rotation] PASSED [ 11%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.utils.singleton] PASSED [ 11%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.utils.six] SKIPPED [ 11%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.basedimension] PASSED [ 12%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.baseunit] SKIPPED [ 12%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.constants] PASSED [ 12%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.mymatrix] SKIPPED [ 12%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.prefix] SKIPPED [ 12%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.quantity] SKIPPED [ 12%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.standard_dimensions] PASSED [ 12%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit] SKIPPED [ 12%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_definitions] SKIPPED [ 12%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_math] SKIPPED [ 12%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_operators] SKIPPED [ 12%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unitcell] PASSED [ 12%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.utils.validation] PASSED [ 13%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.utils.zipped] PASSED [ 13%] 355s tests/test_docstrings.py::test_docstrings[mdtraj.version] PASSED [ 13%] 355s tests/test_drid.py::test_drid_1 PASSED [ 13%] 355s tests/test_drid.py::test_drid_2 PASSED [ 13%] 355s tests/test_dssp.py::test_1 SKIPPED (This test requires mkdssp to be ...) [ 13%] 355s tests/test_dssp.py::test_2 SKIPPED (This test requires mkdssp to be ...) [ 13%] 355s tests/test_dssp.py::test_3 SKIPPED (This test requires mkdssp to be ...) [ 13%] 356s tests/test_dssp.py::test_4 PASSED [ 13%] 356s tests/test_dssp.py::test_5 PASSED [ 13%] 356s tests/test_dssp.py::test_7 PASSED [ 13%] 356s tests/test_dtr.py::test_read PASSED [ 13%] 356s tests/test_dtr.py::test_read_1 PASSED [ 14%] 356s tests/test_dtr.py::test_read_2 PASSED [ 14%] 356s tests/test_dtr.py::test_read_3 PASSED [ 14%] 356s tests/test_dtr.py::test_read_stride PASSED [ 14%] 356s tests/test_dtr.py::test_read_4 PASSED [ 14%] 356s tests/test_dtr.py::test_read_5 PASSED [ 14%] 356s tests/test_dtr.py::test_read_6 PASSED [ 14%] 356s tests/test_dtr.py::test_read_7 PASSED [ 14%] 356s tests/test_dtr.py::test_read_8 PASSED [ 14%] 358s tests/test_dtr.py::test_write_1 PASSED [ 14%] 361s tests/test_dtr.py::test_write_2 PASSED [ 14%] 361s tests/test_dtr.py::test_write_3 PASSED [ 14%] 361s tests/test_dtr.py::test_write_4 PASSED [ 15%] 361s tests/test_dtr.py::test_seek PASSED [ 15%] 361s tests/test_dtr.py::test_read_closed PASSED [ 15%] 361s tests/test_dtr.py::test_tell PASSED [ 15%] 361s tests/test_element.py::test_immutable PASSED [ 15%] 361s tests/test_element.py::test_element_0 PASSED [ 15%] 361s tests/test_element.py::test_element_pickle PASSED [ 15%] 361s tests/test_geometry.py::test_rg PASSED [ 15%] 361s tests/test_geometry.py::test_distances PASSED [ 15%] 361s tests/test_geometry.py::test_center_of_mass PASSED [ 15%] 361s tests/test_geometry.py::test_center_of_geometry PASSED [ 15%] 361s tests/test_geometry.py::test_dihedral_indices PASSED [ 15%] 361s tests/test_geometry.py::test_dihedral_index_offset_generation PASSED [ 15%] 361s tests/test_geometry.py::test_dihedral_0 PASSED [ 16%] 361s tests/test_geometry.py::test_dihedral_1 PASSED [ 16%] 361s tests/test_geometry.py::test_dihedral_triclinic PASSED [ 16%] 361s tests/test_geometry.py::test_angle_0 PASSED [ 16%] 361s tests/test_geometry.py::test_angle_periodic_0 PASSED [ 16%] 361s tests/test_geometry.py::test_angle_triclinic_0 PASSED [ 16%] 361s tests/test_geometry.py::test_angle_1 PASSED [ 16%] 361s tests/test_geometry.py::test_dihedral_performance SKIPPED (Not doing...) [ 16%] 361s tests/test_geometry.py::test_angle_performance SKIPPED (Not doing pe...) [ 16%] 361s tests/test_geometry.py::test_angle_nan PASSED [ 16%] 362s tests/test_geometry.py::test_angle_pbc PASSED [ 16%] 365s tests/test_geometry.py::test_dihedral_pbc PASSED [ 16%] 365s tests/test_geometry.py::test_dihedral_pbc_fails1 PASSED [ 17%] 365s tests/test_geometry.py::test_dihedral_pbc_fails2 PASSED [ 17%] 365s tests/test_geometry.py::test_angle_pbc_fails1 PASSED [ 17%] 366s tests/test_geometry.py::test_no_indices PASSED [ 17%] 366s tests/test_gro.py::test_read_write PASSED [ 17%] 367s tests/test_gro.py::test_read_write_precision PASSED [ 17%] 367s tests/test_gro.py::test_no_whitespace_gro PASSED [ 17%] 367s tests/test_gro.py::test_load PASSED [ 17%] 367s tests/test_gro.py::test_load_with_given_top PASSED [ 17%] 368s tests/test_gro.py::test_against_gmx PASSED [ 17%] 368s tests/test_gsd.py::test_read SKIPPED (gsd module is not available) [ 17%] 368s tests/test_gsd.py::test_read_start SKIPPED (gsd module is not available) [ 17%] 368s tests/test_gsd.py::test_read_frame SKIPPED (gsd module is not available) [ 18%] 368s tests/test_gsd.py::test_read_stride SKIPPED (gsd module is not avail...) [ 18%] 368s tests/test_gsd.py::test_read_variable_top_error SKIPPED (gsd module ...) [ 18%] 368s tests/test_gsd.py::test_write SKIPPED (gsd module is not available) [ 18%] 368s tests/test_gsd.py::test_write_frame SKIPPED (gsd module is not avail...) [ 18%] 368s tests/test_hbonds.py::test_hbonds PASSED [ 18%] 368s tests/test_hbonds.py::test_hbonds_against_dssp SKIPPED (This test re...) [ 18%] 368s tests/test_hbonds.py::test_baker_hubbard_0 PASSED [ 18%] 368s tests/test_hbonds.py::test_baker_hubbard_1 PASSED [ 18%] 369s tests/test_hbonds.py::test_baker_hubbard_2 PASSED [ 18%] 369s tests/test_hbonds.py::test_baker_hubbard_3 PASSED [ 18%] 369s tests/test_hbonds.py::test_wernet_nilsson_0 PASSED [ 18%] 369s tests/test_hbonds.py::test_wernet_nilsson_1 PASSED [ 19%] 369s tests/test_hdf5.py::test_write_coordinates PASSED [ 19%] 369s tests/test_hdf5.py::test_write_coordinates_reshape PASSED [ 19%] 369s tests/test_hdf5.py::test_write_multiple PASSED [ 19%] 370s tests/test_hdf5.py::test_write_inconsistent PASSED [ 19%] 370s tests/test_hdf5.py::test_write_inconsistent_2 PASSED [ 19%] 370s tests/test_hdf5.py::test_write_units SKIPPED (requires openmm.units) [ 19%] 370s tests/test_hdf5.py::test_write_units2 PASSED [ 19%] 370s tests/test_hdf5.py::test_write_units_mismatch SKIPPED (requires open...) [ 19%] 370s tests/test_hdf5.py::test_topology PASSED [ 19%] 370s tests/test_hdf5.py::test_constraints PASSED [ 19%] 370s tests/test_hdf5.py::test_constraints2 PASSED [ 19%] 370s tests/test_hdf5.py::test_read_0 PASSED [ 20%] 370s tests/test_hdf5.py::test_read_1 SKIPPED (requires openmm.units) [ 20%] 370s tests/test_hdf5.py::test_read_slice_0 PASSED [ 20%] 370s tests/test_hdf5.py::test_read_slice_1 PASSED [ 20%] 370s tests/test_hdf5.py::test_read_slice_2 PASSED [ 20%] 370s tests/test_hdf5.py::test_read_slice_3 PASSED [ 20%] 370s tests/test_hdf5.py::test_do_overwrite PASSED [ 20%] 370s tests/test_hdf5.py::test_vsite_elements PASSED [ 20%] 370s tests/test_hdf5.py::test_dont_overwrite PASSED [ 20%] 370s tests/test_hdf5.py::test_attributes PASSED [ 20%] 370s tests/test_hdf5.py::test_append PASSED [ 20%] 372s tests/test_hoomdxml.py::test_load PASSED [ 20%] 372s tests/test_hoomdxml.py::test_load_no_chains PASSED [ 21%] 372s tests/test_hoomdxml.py::test_load_no_ions PASSED [ 21%] 372s tests/test_hoomdxml.py::test_correct_ordering PASSED [ 21%] 372s tests/test_io.py::test_overwrite_1 PASSED [ 21%] 372s tests/test_io.py::test_overwrite_2 PASSED [ 21%] 372s tests/test_io.py::test_io::test_load_1 PASSED [ 21%] 372s tests/test_io.py::test_io::test_load_2 PASSED [ 21%] 372s tests/test_io.py::test_io::test_load_3 PASSED [ 21%] 372s tests/test_io.py::test_io::test_save PASSED [ 21%] 372s tests/test_io.py::test_io_int::test_load_1 PASSED [ 21%] 372s tests/test_io.py::test_io_int::test_load_2 PASSED [ 21%] 372s tests/test_io.py::test_io_int::test_load_3 PASSED [ 21%] 372s tests/test_io.py::test_io_int::test_save PASSED [ 21%] 372s tests/test_io.py::test_groups PASSED [ 22%] 372s tests/test_lammpstrj.py::test_read_0 PASSED [ 22%] 372s tests/test_lammpstrj.py::test_read_1 PASSED [ 22%] 372s tests/test_lammpstrj.py::test_read_write_0 PASSED [ 22%] 372s tests/test_lammpstrj.py::test_mdwrite PASSED [ 22%] 372s tests/test_lammpstrj.py::test_multiread PASSED [ 22%] 372s tests/test_lammpstrj.py::test_seek PASSED [ 22%] 372s tests/test_lammpstrj.py::test_custom PASSED [ 22%] 372s tests/test_lh5.py::test_write_coordinates PASSED [ 22%] 372s tests/test_lh5.py::test_write_coordinates_reshape PASSED [ 22%] 372s tests/test_lh5.py::test_write_multiple PASSED [ 22%] 372s tests/test_lh5.py::test_topology PASSED [ 22%] 372s tests/test_lh5.py::test_read_slice_0 PASSED [ 23%] 372s tests/test_lh5.py::test_vsite_elements PASSED [ 23%] 372s tests/test_lh5.py::test_do_overwrite_0 PASSED [ 23%] 372s tests/test_lh5.py::test_do_overwrite_1 PASSED [ 23%] 373s tests/test_load.py::test_load_single PASSED [ 23%] 373s tests/test_load.py::test_load_single_list PASSED [ 23%] 374s tests/test_load.py::test_load_many_list PASSED [ 23%] 374s tests/test_load.py::test_load_atom_indices_multiple_files PASSED [ 23%] 374s tests/test_lprmsd.py::test_munkres_0 PASSED [ 23%] 374s tests/test_lprmsd.py::test_lprmsd_null PASSED [ 23%] 374s tests/test_lprmsd.py::test_lprmsd_0 PASSED [ 23%] 374s tests/test_lprmsd.py::test_lprmsd_1 PASSED [ 23%] 374s tests/test_lprmsd.py::test_lprmsd_2 PASSED [ 24%] 374s tests/test_lprmsd.py::test_lprmsd_3 PASSED [ 24%] 374s tests/test_lprmsd.py::test_lprmsd_4 PASSED [ 24%] 374s tests/test_lprmsd.py::test_lprmsd_5 PASSED [ 24%] 376s tests/test_mdconvert.py::test_index PASSED [ 24%] 378s tests/test_mdconvert.py::test_slice PASSED [ 24%] 401s tests/test_mdconvert.py::test_pairwise[from-xtc] PASSED [ 24%] 424s tests/test_mdconvert.py::test_pairwise[from-dcd] PASSED [ 24%] 446s tests/test_mdconvert.py::test_pairwise[from-binpos] PASSED [ 24%] 469s tests/test_mdconvert.py::test_pairwise[from-trr] PASSED [ 24%] 492s tests/test_mdconvert.py::test_pairwise[from-nc] PASSED [ 24%] 515s tests/test_mdconvert.py::test_pairwise[from-pdb] PASSED [ 24%] 565s tests/test_mdconvert.py::test_pairwise[from-h5] PASSED [ 25%] 614s tests/test_mdconvert.py::test_pairwise[from-lh5] PASSED [ 25%] 637s tests/test_mdconvert.py::test_pairwise[from-netcdf] PASSED [ 25%] 637s tests/test_mdconvert.py::test_mdconvert_alanine PASSED [ 25%] 637s tests/test_mdcrd.py::test_read_0 PASSED [ 25%] 637s tests/test_mdcrd.py::test_read_1 PASSED [ 25%] 637s tests/test_mdcrd.py::test_read_write_0 PASSED [ 25%] 637s tests/test_mdcrd.py::test_read_write_1 PASSED [ 25%] 637s tests/test_mdcrd.py::test_read_write_2 PASSED [ 25%] 637s tests/test_mdcrd.py::test_multiread PASSED [ 25%] 637s tests/test_mdcrd.py::test_seek PASSED [ 25%] 637s tests/test_mdcrd.py::test_atom_indices_0 PASSED [ 25%] 638s tests/test_mdcrd.py::test_atom_indices_1 PASSED [ 26%] 638s tests/test_mol2.py::test_load_mol2 PASSED [ 26%] 638s tests/test_mol2.py::test_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb SKIPPED [ 26%] 638s tests/test_mol2.py::test_mol2_dataframe PASSED [ 26%] 638s tests/test_mol2.py::test_mol2_dataframe_status PASSED [ 26%] 638s tests/test_mol2.py::test_mol2_warnings PASSED [ 26%] 638s tests/test_mol2.py::test_mol2_status_bits PASSED [ 26%] 638s tests/test_mol2.py::test_mol2_without_bonds PASSED [ 26%] 645s tests/test_mol2.py::test_mol2_element_name PASSED [ 26%] 645s tests/test_mol2.py::test_load_all_mol2[li.mol2] PASSED [ 26%] 645s tests/test_mol2.py::test_load_all_mol2[lysozyme-ligand-tripos.mol2] PASSED [ 26%] 645s tests/test_mol2.py::test_load_all_mol2[imatinib.mol2] PASSED [ 26%] 645s tests/test_mol2.py::test_load_all_mol2[status-bits.mol2] PASSED [ 26%] 645s tests/test_mol2.py::test_load_all_mol2[adp.mol2] PASSED [ 27%] 645s tests/test_mol2.py::test_load_all_mol2[water_acn.mol2] PASSED [ 27%] 645s tests/test_mol2.py::test_mol2_n_residues PASSED [ 27%] 645s tests/test_neighborlist.py::test_nonperiodic PASSED [ 27%] 645s tests/test_neighborlist.py::test_periodic PASSED [ 27%] 645s tests/test_neighborlist.py::test_triclinic PASSED [ 27%] 645s tests/test_neighbors.py::test_compute_neighbors_1 PASSED [ 27%] 645s tests/test_neighbors.py::test_compute_neighbors_2 PASSED [ 27%] 645s tests/test_neighbors.py::test_compute_neighbors_3 PASSED [ 27%] 645s tests/test_netcdf.py::test_read_after_close PASSED [ 27%] 645s tests/test_netcdf.py::test_shape PASSED [ 27%] 645s tests/test_netcdf.py::test_read_chunk_1 PASSED [ 27%] 645s tests/test_netcdf.py::test_read_chunk_2 PASSED [ 28%] 645s tests/test_netcdf.py::test_read_chunk_3 PASSED [ 28%] 645s tests/test_netcdf.py::test_read_write_1 PASSED [ 28%] 645s tests/test_netcdf.py::test_read_write_2 PASSED [ 28%] 645s tests/test_netcdf.py::test_ragged_1 PASSED [ 28%] 645s tests/test_netcdf.py::test_ragged_2 PASSED [ 28%] 645s tests/test_netcdf.py::test_read_write_25 PASSED [ 28%] 645s tests/test_netcdf.py::test_write_3 PASSED [ 28%] 645s tests/test_netcdf.py::test_n_atoms PASSED [ 28%] 645s tests/test_netcdf.py::test_do_overwrite PASSED [ 28%] 645s tests/test_netcdf.py::test_trajectory_save_load PASSED [ 28%] 645s tests/test_netcdf.py::test_cpptraj SKIPPED (This test requires cpptr...) [ 28%] 645s tests/test_nmr.py::test_spartaplus SKIPPED (SPARTA+ binary not found) [ 29%] 645s tests/test_nmr.py::test_ppm SKIPPED (PPM binary not found) [ 29%] 645s tests/test_nmr.py::test_shiftx2 SKIPPED (SHIFTX2 binary not found or...) [ 29%] 645s tests/test_nmr.py::test_2_scalar_couplings PASSED [ 29%] 645s tests/test_nmr.py::test_3_scalar_couplings PASSED [ 29%] 645s tests/test_order.py::test_nematic_order PASSED [ 29%] 645s tests/test_order.py::test_director PASSED [ 29%] 645s tests/test_order.py::test_inertia PASSED [ 29%] 645s tests/test_order.py::test_nematic_order_args PASSED [ 29%] 645s tests/test_order.py::test_order_from_traj PASSED [ 29%] 645s tests/test_order.py::test_directors_angle_from_traj PASSED [ 29%] 645s tests/test_pdb.py::test_pdbread PASSED [ 29%] 645s tests/test_pdb.py::test_pdbread_with_input_top PASSED [ 30%] 645s tests/test_pdb.py::test_pdbwrite PASSED [ 30%] 645s tests/test_pdb.py::test_load_multiframe PASSED [ 30%] 645s tests/test_pdb.py::test_4ZUO PASSED [ 30%] 645s tests/test_pdb.py::test_2EQQ_0 PASSED [ 30%] 645s tests/test_pdb.py::test_1vii_solvated_with_ligand PASSED [ 30%] 645s tests/test_pdb.py::test_write_large PASSED [ 30%] 645s tests/test_pdb.py::test_write_large_2 PASSED [ 30%] 645s tests/test_pdb.py::test_pdbstructure_0 PASSED [ 30%] 645s tests/test_pdb.py::test_pdbstructure_1 PASSED [ 30%] 645s tests/test_pdb.py::test_pdbstructure_2 PASSED [ 30%] 645s tests/test_pdb.py::test_pdbstructure_3 PASSED [ 30%] 646s tests/test_pdb.py::test_pdb_from_url PASSED [ 31%] 647s tests/test_pdb.py::test_3nch_conect PASSED [ 31%] 649s tests/test_pdb.py::test_3nch_serial_resSeq PASSED [ 31%] 650s tests/test_pdb.py::test_1ncw PASSED [ 31%] 651s tests/test_pdb.py::test_1vii_url_and_gz PASSED [ 31%] 651s tests/test_pdb.py::test_segment_id PASSED [ 31%] 651s tests/test_pdb.py::test_bfactors PASSED [ 31%] 656s tests/test_pdb.py::test_hex PASSED [ 31%] 656s tests/test_pdb.py::test_dummy_pdb_box_detection PASSED [ 31%] 656s tests/test_pdb.py::test_multichain_load_cycle PASSED [ 31%] 656s tests/test_pdb.py::test_load_pdb_input_top PASSED [ 31%] 656s tests/test_pdbx.py::test_convert SKIPPED (test_pdbx.py needs OpenMM.) [ 31%] 656s tests/test_prmtop.py::test_load_prmtop PASSED [ 31%] 656s tests/test_prmtop.py::test_load_binpos_w_prmtop PASSED [ 32%] 656s tests/test_prmtop.py::test_load_chamber_prmtop PASSED [ 32%] 656s tests/test_psf.py::test_load_psf PASSED [ 32%] 661s tests/test_psf.py::test_multichain_psf PASSED [ 32%] 661s tests/test_psf.py::test_load_mdcrd_with_psf PASSED [ 32%] 661s tests/test_psf.py::test_against_vmd[1vii.pdb] SKIPPED (This test req...) [ 32%] 661s tests/test_psf.py::test_against_vmd[2EQQ.pdb] SKIPPED (This test req...) [ 32%] 661s tests/test_quaternion.py::test_quaternion_0 PASSED [ 32%] 661s tests/test_quaternion.py::test_quaternion_1 PASSED [ 32%] 661s tests/test_quaternion.py::test_quaternion_2 PASSED [ 32%] 665s tests/test_rdf.py::test_rdf_norm PASSED [ 32%] 665s tests/test_rdf.py::test_compare_rdf_to_gromacs SKIPPED (Binning does...) [ 32%] 665s tests/test_rdf.py::test_rdf_t[True-True] PASSED [ 33%] 671s tests/test_rdf.py::test_rdf_t[True-False] PASSED [ 33%] 671s tests/test_rdf.py::test_rdf_t[False-True] PASSED [ 33%] 671s tests/test_rdf.py::test_rdf_t[False-False] PASSED [ 33%] 672s tests/test_rdf.py::test_rdf_t_norm[0] PASSED [ 33%] 672s tests/test_rdf.py::test_rdf_t_norm[2] PASSED [ 33%] 673s tests/test_rdf.py::test_rdf_t_norm[4] PASSED [ 33%] 673s tests/test_rdf.py::test_compare_rdf_t_at_0[True-True] PASSED [ 33%] 674s tests/test_rdf.py::test_compare_rdf_t_at_0[True-False] PASSED [ 33%] 674s tests/test_rdf.py::test_compare_rdf_t_at_0[False-True] PASSED [ 33%] 675s tests/test_rdf.py::test_compare_rdf_t_at_0[False-False] PASSED [ 33%] 675s tests/test_rdf.py::test_amber_rdf_t[True-True] PASSED [ 33%] 675s tests/test_rdf.py::test_amber_rdf_t[True-False] PASSED [ 34%] 675s tests/test_rdf.py::test_amber_rdf_t[False-True] PASSED [ 34%] 676s tests/test_rdf.py::test_amber_rdf_t[False-False] PASSED [ 34%] 676s tests/test_rdf.py::test_compare_gromacs_rdf_t SKIPPED (Binning does ...) [ 34%] 676s tests/test_rdf.py::test_compare_rdf_t_master PASSED [ 34%] 676s tests/test_rdf.py::test_compare_n_concurrent_pairs PASSED [ 34%] 676s tests/test_reporter.py::test_reporter SKIPPED (test_reporter.py need...) [ 34%] 676s tests/test_reporter.py::test_reporter_subset SKIPPED (test_reporter....) [ 34%] 676s tests/test_reporter.py::test_xtc_reporter_append SKIPPED (test_repor...) [ 34%] 676s tests/test_restart.py::test_read_after_close PASSED [ 34%] 676s tests/test_restart.py::test_shape PASSED [ 34%] 676s tests/test_restart.py::test_shape_2 PASSED [ 34%] 676s tests/test_restart.py::test_read_write_1 PASSED [ 35%] 676s tests/test_restart.py::test_read_write_2 PASSED [ 35%] 676s tests/test_restart.py::test_read_write_3 PASSED [ 35%] 677s tests/test_restart.py::test_read_write_4 PASSED [ 35%] 677s tests/test_rmsd.py::test_trajectory_rmsd PASSED [ 35%] 677s tests/test_rmsd.py::test_precentered_1 PASSED [ 35%] 677s tests/test_rmsd.py::test_precentered_2 PASSED [ 35%] 677s tests/test_rmsd.py::test_superpose_0 PASSED [ 35%] 677s tests/test_rmsd.py::test_superpose_1 PASSED [ 35%] 677s tests/test_rmsd.py::test_superpose_2 PASSED [ 35%] 677s tests/test_rmsd.py::test_superpose_refinds PASSED [ 35%] 677s tests/test_rmsd.py::test_rmsd_atom_indices PASSED [ 35%] 677s tests/test_rmsd.py::test_rmsd_ref_ainds PASSED [ 36%] 678s tests/test_rmsd.py::test_average_structure PASSED [ 36%] 678s tests/test_rmsd.py::test_trajectory_rmsf PASSED [ 36%] 678s tests/test_rmsd.py::test_trajectory_rmsf_aligned PASSED [ 36%] 678s tests/test_rmsd.py::test_rmsd_atom_indices_vs_ref_indices PASSED [ 36%] 678s tests/test_rmsd_memmap.py::test_1 PASSED [ 36%] 678s tests/test_rmsd_memmap.py::test_2 PASSED [ 36%] 678s tests/test_sasa.py::test_sasa_0 PASSED [ 36%] 678s tests/test_sasa.py::test_sasa_1 PASSED [ 36%] 678s tests/test_sasa.py::test_sasa_2 PASSED [ 36%] 678s tests/test_sasa.py::test_sasa_3 PASSED [ 36%] 679s tests/test_sasa.py::test_sasa_4 PASSED [ 36%] 679s tests/test_sasa.py::test_sasa_5 PASSED [ 36%] 679s tests/test_selection.py::test_range PASSED [ 37%] 679s tests/test_selection.py::test_unary_2 PASSED [ 37%] 679s tests/test_selection.py::test_unary_3 PASSED [ 37%] 679s tests/test_selection.py::test_binary_1 PASSED [ 37%] 679s tests/test_selection.py::test_binary_2 PASSED [ 37%] 679s tests/test_selection.py::test_simple PASSED [ 37%] 679s tests/test_selection.py::test_alias PASSED [ 37%] 679s tests/test_selection.py::test_unary_1 PASSED [ 37%] 680s tests/test_selection.py::test_binary_selection_operator PASSED [ 37%] 680s tests/test_selection.py::test_raises PASSED [ 37%] 680s tests/test_selection.py::test_raises2 PASSED [ 37%] 680s tests/test_selection.py::test_bool PASSED [ 37%] 680s tests/test_selection.py::test_nested_bool PASSED [ 38%] 680s tests/test_selection.py::test_values PASSED [ 38%] 680s tests/test_selection.py::test_element PASSED [ 38%] 680s tests/test_selection.py::test_not PASSED [ 38%] 680s tests/test_selection.py::test_re PASSED [ 38%] 680s tests/test_selection.py::test_quotes PASSED [ 38%] 680s tests/test_selection.py::test_top PASSED [ 38%] 680s tests/test_selection.py::test_top_2 PASSED [ 38%] 680s tests/test_selection.py::test_backbone PASSED [ 38%] 681s tests/test_selection.py::test_sidechain PASSED [ 38%] 681s tests/test_selection.py::test_literal PASSED [ 38%] 681s tests/test_selection.py::test_in PASSED [ 38%] 681s tests/test_shape.py::test_gyration PASSED [ 39%] 681s tests/test_shape.py::test_principal_moments PASSED [ 39%] 681s tests/test_shape.py::test_asphericity PASSED [ 39%] 682s tests/test_shape.py::test_shape_metrics PASSED [ 39%] 682s tests/test_thermodynamic_properties.py::test_volume PASSED [ 39%] 682s tests/test_thermodynamic_properties.py::test_density PASSED [ 39%] 682s tests/test_thermodynamic_properties.py::test_dipole_moments PASSED [ 39%] 682s tests/test_thermodynamic_properties.py::test_static_dielectric PASSED [ 39%] 682s tests/test_thermodynamic_properties.py::test_kappa PASSED [ 39%] 682s tests/test_thermodynamic_properties.py::test_alpha SKIPPED (Thermal ...) [ 39%] 682s tests/test_tng.py::test_load_trajectory PASSED [ 39%] 682s tests/test_tng.py::test_load_topology SKIPPED (Fails on macOS + Pyth...) [ 39%] 682s tests/test_tng.py::test_write PASSED [ 40%] 682s tests/test_topology.py::test_topology_openmm SKIPPED (needs OpenMM) [ 40%] 682s tests/test_topology.py::test_topology_openmm_boxes SKIPPED (needs Op...) [ 40%] 682s tests/test_topology.py::test_topology_pandas PASSED [ 40%] 683s tests/test_topology.py::test_topology_pandas_TIP4PEW PASSED [ 40%] 683s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq PASSED [ 40%] 683s tests/test_topology.py::test_topology_numbers PASSED [ 40%] 683s tests/test_topology.py::test_topology_unique_elements_bpti PASSED [ 40%] 683s tests/test_topology.py::test_chain PASSED [ 40%] 683s tests/test_topology.py::test_residue PASSED [ 40%] 683s tests/test_topology.py::test_segment_id PASSED [ 40%] 683s tests/test_topology.py::test_nonconsective_resSeq PASSED [ 40%] 683s tests/test_topology.py::test_pickle PASSED [ 41%] 683s tests/test_topology.py::test_atoms_by_name PASSED [ 41%] 683s tests/test_topology.py::test_select_atom_indices PASSED [ 41%] 683s tests/test_topology.py::test_top_dataframe_openmm_roundtrip SKIPPED [ 41%] 683s tests/test_topology.py::test_n_bonds PASSED [ 41%] 683s tests/test_topology.py::test_load_unknown_topology PASSED [ 41%] 683s tests/test_topology.py::test_unique_pairs PASSED [ 41%] 684s tests/test_topology.py::test_select_pairs PASSED [ 41%] 684s tests/test_topology.py::test_to_fasta PASSED [ 41%] 684s tests/test_topology.py::test_subset PASSED [ 41%] 685s tests/test_topology.py::test_subset_re_index_residues PASSED [ 41%] 685s tests/test_topology.py::test_molecules PASSED [ 41%] 685s tests/test_topology.py::test_copy_and_hash PASSED [ 42%] 685s tests/test_topology.py::test_topology_sliced_residue_indices PASSED [ 42%] 685s tests/test_topology.py::test_topology_join PASSED [ 42%] 685s tests/test_topology.py::test_topology_join_keep_resSeq PASSED [ 42%] 686s tests/test_trajectory.py::test_mismatch PASSED [ 42%] 686s tests/test_trajectory.py::test_box PASSED [ 42%] 686s tests/test_trajectory.py::test_load_pdb_box PASSED [ 42%] 686s tests/test_trajectory.py::test_load_pdb_gz PASSED [ 42%] 686s tests/test_trajectory.py::test_box_load_save[nc] PASSED [ 42%] 686s tests/test_trajectory.py::test_box_load_save[h5] PASSED [ 42%] 686s tests/test_trajectory.py::test_box_load_save[xtc] PASSED [ 42%] 686s tests/test_trajectory.py::test_box_load_save[trr] PASSED [ 42%] 686s tests/test_trajectory.py::test_box_load_save[dcd] PASSED [ 42%] 686s tests/test_trajectory.py::test_box_load_save[mdcrd] PASSED [ 43%] 686s tests/test_trajectory.py::test_box_load_save[binpos] SKIPPED (binpos...) [ 43%] 686s tests/test_trajectory.py::test_box_load_save[dtr] PASSED [ 43%] 686s tests/test_trajectory.py::test_box_load_save[xyz] SKIPPED (xyz does ...) [ 43%] 686s tests/test_trajectory.py::test_box_load_save[xyz.gz] SKIPPED (xyz.gz...) [ 43%] 686s tests/test_trajectory.py::test_box_load_save[lammpstrj] PASSED [ 43%] 686s tests/test_trajectory.py::test_box_load_save[tng] PASSED [ 43%] 686s tests/test_trajectory.py::test_box_load_save[lh5] SKIPPED (lh5 does ...) [ 43%] 686s tests/test_trajectory.py::test_box_load_save[pdb] SKIPPED (pdb does ...) [ 43%] 686s tests/test_trajectory.py::test_box_load_save[pdb.gz] SKIPPED (pdb.gz...) [ 43%] 686s tests/test_trajectory.py::test_box_load_save[ncrst] PASSED [ 43%] 686s tests/test_trajectory.py::test_box_load_save[rst7] PASSED [ 43%] 686s tests/test_trajectory.py::test_box_load_save[gro] PASSED [ 44%] 686s tests/test_trajectory.py::test_slice PASSED [ 44%] 686s tests/test_trajectory.py::test_slice2 PASSED [ 44%] 686s tests/test_trajectory.py::test_read_path[nc] PASSED [ 44%] 686s tests/test_trajectory.py::test_read_path[h5] PASSED [ 44%] 686s tests/test_trajectory.py::test_read_path[xtc] PASSED [ 44%] 686s tests/test_trajectory.py::test_read_path[trr] PASSED [ 44%] 686s tests/test_trajectory.py::test_read_path[dcd] PASSED [ 44%] 686s tests/test_trajectory.py::test_read_path[mdcrd] PASSED [ 44%] 686s tests/test_trajectory.py::test_read_path[binpos] PASSED [ 44%] 686s tests/test_trajectory.py::test_read_path[dtr] PASSED [ 44%] 686s tests/test_trajectory.py::test_read_path[xyz] PASSED [ 44%] 686s tests/test_trajectory.py::test_read_path[xyz.gz] PASSED [ 45%] 686s tests/test_trajectory.py::test_read_path[lammpstrj] PASSED [ 45%] 686s tests/test_trajectory.py::test_read_path[tng] PASSED [ 45%] 686s tests/test_trajectory.py::test_read_path[lh5] PASSED [ 45%] 686s tests/test_trajectory.py::test_read_path[pdb] PASSED [ 45%] 687s tests/test_trajectory.py::test_read_path[pdb.gz] PASSED [ 45%] 687s tests/test_trajectory.py::test_read_path[ncrst] XFAIL (These referen...) [ 45%] 687s tests/test_trajectory.py::test_read_path[rst7] XFAIL (These referenc...) [ 45%] 687s tests/test_trajectory.py::test_read_path[gro] PASSED [ 45%] 687s tests/test_trajectory.py::test_write_path[nc] PASSED [ 45%] 687s tests/test_trajectory.py::test_write_path[h5] PASSED [ 45%] 687s tests/test_trajectory.py::test_write_path[xtc] PASSED [ 45%] 687s tests/test_trajectory.py::test_write_path[trr] PASSED [ 46%] 687s tests/test_trajectory.py::test_write_path[dcd] PASSED [ 46%] 687s tests/test_trajectory.py::test_write_path[mdcrd] SKIPPED (mdcrd can ...) [ 46%] 687s tests/test_trajectory.py::test_write_path[binpos] PASSED [ 46%] 687s tests/test_trajectory.py::test_write_path[dtr] PASSED [ 46%] 687s tests/test_trajectory.py::test_write_path[xyz] PASSED [ 46%] 687s tests/test_trajectory.py::test_write_path[xyz.gz] PASSED [ 46%] 687s tests/test_trajectory.py::test_write_path[lammpstrj] PASSED [ 46%] 687s tests/test_trajectory.py::test_write_path[tng] PASSED [ 46%] 687s tests/test_trajectory.py::test_write_path[lh5] PASSED [ 46%] 687s tests/test_trajectory.py::test_write_path[pdb] PASSED [ 46%] 687s tests/test_trajectory.py::test_write_path[pdb.gz] PASSED [ 46%] 687s tests/test_trajectory.py::test_write_path[ncrst] SKIPPED (ncrst can ...) [ 47%] 687s tests/test_trajectory.py::test_write_path[rst7] SKIPPED (rst7 can on...) [ 47%] 687s tests/test_trajectory.py::test_write_path[gro] PASSED [ 47%] 687s tests/test_trajectory.py::test_read_write[nc-nc] PASSED [ 47%] 687s tests/test_trajectory.py::test_read_write[nc-h5] PASSED [ 47%] 687s tests/test_trajectory.py::test_read_write[nc-xtc] PASSED [ 47%] 687s tests/test_trajectory.py::test_read_write[nc-trr] PASSED [ 47%] 688s tests/test_trajectory.py::test_read_write[nc-dcd] PASSED [ 47%] 688s tests/test_trajectory.py::test_read_write[nc-mdcrd] SKIPPED (mdcrd c...) [ 47%] 688s tests/test_trajectory.py::test_read_write[nc-binpos] PASSED [ 47%] 689s tests/test_trajectory.py::test_read_write[nc-dtr] PASSED [ 47%] 689s tests/test_trajectory.py::test_read_write[nc-xyz] PASSED [ 47%] 689s tests/test_trajectory.py::test_read_write[nc-xyz.gz] PASSED [ 47%] 689s tests/test_trajectory.py::test_read_write[nc-lammpstrj] PASSED [ 48%] 689s tests/test_trajectory.py::test_read_write[nc-tng] PASSED [ 48%] 689s tests/test_trajectory.py::test_read_write[nc-lh5] PASSED [ 48%] 690s tests/test_trajectory.py::test_read_write[nc-pdb] PASSED [ 48%] 690s tests/test_trajectory.py::test_read_write[nc-pdb.gz] PASSED [ 48%] 690s tests/test_trajectory.py::test_read_write[nc-ncrst] SKIPPED (ncrst c...) [ 48%] 690s tests/test_trajectory.py::test_read_write[nc-rst7] SKIPPED (rst7 can...) [ 48%] 690s tests/test_trajectory.py::test_read_write[nc-gro] PASSED [ 48%] 690s tests/test_trajectory.py::test_read_write[h5-nc] PASSED [ 48%] 690s tests/test_trajectory.py::test_read_write[h5-h5] PASSED [ 48%] 690s tests/test_trajectory.py::test_read_write[h5-xtc] PASSED [ 48%] 690s tests/test_trajectory.py::test_read_write[h5-trr] PASSED [ 48%] 690s tests/test_trajectory.py::test_read_write[h5-dcd] PASSED [ 49%] 690s tests/test_trajectory.py::test_read_write[h5-mdcrd] SKIPPED (mdcrd c...) [ 49%] 690s tests/test_trajectory.py::test_read_write[h5-binpos] PASSED [ 49%] 692s tests/test_trajectory.py::test_read_write[h5-dtr] PASSED [ 49%] 692s tests/test_trajectory.py::test_read_write[h5-xyz] PASSED [ 49%] 692s tests/test_trajectory.py::test_read_write[h5-xyz.gz] PASSED [ 49%] 692s tests/test_trajectory.py::test_read_write[h5-lammpstrj] PASSED [ 49%] 692s tests/test_trajectory.py::test_read_write[h5-tng] PASSED [ 49%] 692s tests/test_trajectory.py::test_read_write[h5-lh5] PASSED [ 49%] 693s tests/test_trajectory.py::test_read_write[h5-pdb] PASSED [ 49%] 693s tests/test_trajectory.py::test_read_write[h5-pdb.gz] PASSED [ 49%] 693s tests/test_trajectory.py::test_read_write[h5-ncrst] SKIPPED (ncrst c...) [ 49%] 693s tests/test_trajectory.py::test_read_write[h5-rst7] SKIPPED (rst7 can...) [ 50%] 694s tests/test_trajectory.py::test_read_write[h5-gro] PASSED [ 50%] 694s tests/test_trajectory.py::test_read_write[xtc-nc] PASSED [ 50%] 694s tests/test_trajectory.py::test_read_write[xtc-h5] PASSED [ 50%] 694s tests/test_trajectory.py::test_read_write[xtc-xtc] PASSED [ 50%] 694s tests/test_trajectory.py::test_read_write[xtc-trr] PASSED [ 50%] 694s tests/test_trajectory.py::test_read_write[xtc-dcd] PASSED [ 50%] 694s tests/test_trajectory.py::test_read_write[xtc-mdcrd] SKIPPED (mdcrd ...) [ 50%] 694s tests/test_trajectory.py::test_read_write[xtc-binpos] PASSED [ 50%] 695s tests/test_trajectory.py::test_read_write[xtc-dtr] PASSED [ 50%] 695s tests/test_trajectory.py::test_read_write[xtc-xyz] PASSED [ 50%] 695s tests/test_trajectory.py::test_read_write[xtc-xyz.gz] PASSED [ 50%] 695s tests/test_trajectory.py::test_read_write[xtc-lammpstrj] PASSED [ 51%] 695s tests/test_trajectory.py::test_read_write[xtc-tng] PASSED [ 51%] 695s tests/test_trajectory.py::test_read_write[xtc-lh5] PASSED [ 51%] 696s tests/test_trajectory.py::test_read_write[xtc-pdb] PASSED [ 51%] 697s tests/test_trajectory.py::test_read_write[xtc-pdb.gz] PASSED [ 51%] 697s tests/test_trajectory.py::test_read_write[xtc-ncrst] SKIPPED (ncrst ...) [ 51%] 697s tests/test_trajectory.py::test_read_write[xtc-rst7] SKIPPED (rst7 ca...) [ 51%] 697s tests/test_trajectory.py::test_read_write[xtc-gro] PASSED [ 51%] 697s tests/test_trajectory.py::test_read_write[trr-nc] PASSED [ 51%] 697s tests/test_trajectory.py::test_read_write[trr-h5] PASSED [ 51%] 697s tests/test_trajectory.py::test_read_write[trr-xtc] PASSED [ 51%] 697s tests/test_trajectory.py::test_read_write[trr-trr] PASSED [ 51%] 697s tests/test_trajectory.py::test_read_write[trr-dcd] PASSED [ 52%] 697s tests/test_trajectory.py::test_read_write[trr-mdcrd] SKIPPED (mdcrd ...) [ 52%] 697s tests/test_trajectory.py::test_read_write[trr-binpos] PASSED [ 52%] 698s tests/test_trajectory.py::test_read_write[trr-dtr] PASSED [ 52%] 698s tests/test_trajectory.py::test_read_write[trr-xyz] PASSED [ 52%] 699s tests/test_trajectory.py::test_read_write[trr-xyz.gz] PASSED [ 52%] 699s tests/test_trajectory.py::test_read_write[trr-lammpstrj] PASSED [ 52%] 699s tests/test_trajectory.py::test_read_write[trr-tng] PASSED [ 52%] 699s tests/test_trajectory.py::test_read_write[trr-lh5] PASSED [ 52%] 699s tests/test_trajectory.py::test_read_write[trr-pdb] PASSED [ 52%] 700s tests/test_trajectory.py::test_read_write[trr-pdb.gz] PASSED [ 52%] 700s tests/test_trajectory.py::test_read_write[trr-ncrst] SKIPPED (ncrst ...) [ 52%] 700s tests/test_trajectory.py::test_read_write[trr-rst7] SKIPPED (rst7 ca...) [ 52%] 700s tests/test_trajectory.py::test_read_write[trr-gro] PASSED [ 53%] 700s tests/test_trajectory.py::test_read_write[dcd-nc] PASSED [ 53%] 700s tests/test_trajectory.py::test_read_write[dcd-h5] PASSED [ 53%] 700s tests/test_trajectory.py::test_read_write[dcd-xtc] PASSED [ 53%] 700s tests/test_trajectory.py::test_read_write[dcd-trr] PASSED [ 53%] 700s tests/test_trajectory.py::test_read_write[dcd-dcd] PASSED [ 53%] 700s tests/test_trajectory.py::test_read_write[dcd-mdcrd] SKIPPED (mdcrd ...) [ 53%] 700s tests/test_trajectory.py::test_read_write[dcd-binpos] PASSED [ 53%] 701s tests/test_trajectory.py::test_read_write[dcd-dtr] PASSED [ 53%] 702s tests/test_trajectory.py::test_read_write[dcd-xyz] PASSED [ 53%] 702s tests/test_trajectory.py::test_read_write[dcd-xyz.gz] PASSED [ 53%] 702s tests/test_trajectory.py::test_read_write[dcd-lammpstrj] PASSED [ 53%] 702s tests/test_trajectory.py::test_read_write[dcd-tng] PASSED [ 54%] 702s tests/test_trajectory.py::test_read_write[dcd-lh5] PASSED [ 54%] 702s tests/test_trajectory.py::test_read_write[dcd-pdb] PASSED [ 54%] 703s tests/test_trajectory.py::test_read_write[dcd-pdb.gz] PASSED [ 54%] 703s tests/test_trajectory.py::test_read_write[dcd-ncrst] SKIPPED (ncrst ...) [ 54%] 703s tests/test_trajectory.py::test_read_write[dcd-rst7] SKIPPED (rst7 ca...) [ 54%] 703s tests/test_trajectory.py::test_read_write[dcd-gro] PASSED [ 54%] 703s tests/test_trajectory.py::test_read_write[mdcrd-nc] PASSED [ 54%] 703s tests/test_trajectory.py::test_read_write[mdcrd-h5] PASSED [ 54%] 703s tests/test_trajectory.py::test_read_write[mdcrd-xtc] PASSED [ 54%] 703s tests/test_trajectory.py::test_read_write[mdcrd-trr] PASSED [ 54%] 703s tests/test_trajectory.py::test_read_write[mdcrd-dcd] PASSED [ 54%] 703s tests/test_trajectory.py::test_read_write[mdcrd-mdcrd] SKIPPED (mdcr...) [ 55%] 703s tests/test_trajectory.py::test_read_write[mdcrd-binpos] PASSED [ 55%] 703s tests/test_trajectory.py::test_read_write[mdcrd-dtr] SKIPPED (dtr ne...) [ 55%] 704s tests/test_trajectory.py::test_read_write[mdcrd-xyz] PASSED [ 55%] 704s tests/test_trajectory.py::test_read_write[mdcrd-xyz.gz] PASSED [ 55%] 704s tests/test_trajectory.py::test_read_write[mdcrd-lammpstrj] SKIPPED (...) [ 55%] 704s tests/test_trajectory.py::test_read_write[mdcrd-tng] PASSED [ 55%] 704s tests/test_trajectory.py::test_read_write[mdcrd-lh5] PASSED [ 55%] 705s tests/test_trajectory.py::test_read_write[mdcrd-pdb] PASSED [ 55%] 706s tests/test_trajectory.py::test_read_write[mdcrd-pdb.gz] PASSED [ 55%] 706s tests/test_trajectory.py::test_read_write[mdcrd-ncrst] SKIPPED (ncrs...) [ 55%] 706s tests/test_trajectory.py::test_read_write[mdcrd-rst7] SKIPPED (rst7 ...) [ 55%] 707s tests/test_trajectory.py::test_read_write[mdcrd-gro] PASSED [ 56%] 707s tests/test_trajectory.py::test_read_write[binpos-nc] PASSED [ 56%] 707s tests/test_trajectory.py::test_read_write[binpos-h5] PASSED [ 56%] 707s tests/test_trajectory.py::test_read_write[binpos-xtc] PASSED [ 56%] 707s tests/test_trajectory.py::test_read_write[binpos-trr] PASSED [ 56%] 707s tests/test_trajectory.py::test_read_write[binpos-dcd] PASSED [ 56%] 707s tests/test_trajectory.py::test_read_write[binpos-mdcrd] SKIPPED (mdc...) [ 56%] 707s tests/test_trajectory.py::test_read_write[binpos-binpos] PASSED [ 56%] 707s tests/test_trajectory.py::test_read_write[binpos-dtr] SKIPPED (dtr n...) [ 56%] 707s tests/test_trajectory.py::test_read_write[binpos-xyz] PASSED [ 56%] 707s tests/test_trajectory.py::test_read_write[binpos-xyz.gz] PASSED [ 56%] 707s tests/test_trajectory.py::test_read_write[binpos-lammpstrj] SKIPPED [ 56%] 707s tests/test_trajectory.py::test_read_write[binpos-tng] PASSED [ 57%] 707s tests/test_trajectory.py::test_read_write[binpos-lh5] PASSED [ 57%] 707s tests/test_trajectory.py::test_read_write[binpos-pdb] PASSED [ 57%] 708s tests/test_trajectory.py::test_read_write[binpos-pdb.gz] PASSED [ 57%] 708s tests/test_trajectory.py::test_read_write[binpos-ncrst] SKIPPED (ncr...) [ 57%] 708s tests/test_trajectory.py::test_read_write[binpos-rst7] SKIPPED (rst7...) [ 57%] 708s tests/test_trajectory.py::test_read_write[binpos-gro] PASSED [ 57%] 708s tests/test_trajectory.py::test_read_write[dtr-nc] PASSED [ 57%] 708s tests/test_trajectory.py::test_read_write[dtr-h5] PASSED [ 57%] 708s tests/test_trajectory.py::test_read_write[dtr-xtc] PASSED [ 57%] 708s tests/test_trajectory.py::test_read_write[dtr-trr] PASSED [ 57%] 708s tests/test_trajectory.py::test_read_write[dtr-dcd] PASSED [ 57%] 708s tests/test_trajectory.py::test_read_write[dtr-mdcrd] SKIPPED (mdcrd ...) [ 57%] 708s tests/test_trajectory.py::test_read_write[dtr-binpos] PASSED [ 58%] 710s tests/test_trajectory.py::test_read_write[dtr-dtr] PASSED [ 58%] 710s tests/test_trajectory.py::test_read_write[dtr-xyz] PASSED [ 58%] 710s tests/test_trajectory.py::test_read_write[dtr-xyz.gz] PASSED [ 58%] 710s tests/test_trajectory.py::test_read_write[dtr-lammpstrj] PASSED [ 58%] 710s tests/test_trajectory.py::test_read_write[dtr-tng] PASSED [ 58%] 710s tests/test_trajectory.py::test_read_write[dtr-lh5] PASSED [ 58%] 711s tests/test_trajectory.py::test_read_write[dtr-pdb] PASSED [ 58%] 711s tests/test_trajectory.py::test_read_write[dtr-pdb.gz] PASSED [ 58%] 711s tests/test_trajectory.py::test_read_write[dtr-ncrst] SKIPPED (ncrst ...) [ 58%] 711s tests/test_trajectory.py::test_read_write[dtr-rst7] SKIPPED (rst7 ca...) [ 58%] 711s tests/test_trajectory.py::test_read_write[dtr-gro] PASSED [ 58%] 711s tests/test_trajectory.py::test_read_write[xyz-nc] PASSED [ 59%] 711s tests/test_trajectory.py::test_read_write[xyz-h5] PASSED [ 59%] 711s tests/test_trajectory.py::test_read_write[xyz-xtc] PASSED [ 59%] 711s tests/test_trajectory.py::test_read_write[xyz-trr] PASSED [ 59%] 711s tests/test_trajectory.py::test_read_write[xyz-dcd] PASSED [ 59%] 711s tests/test_trajectory.py::test_read_write[xyz-mdcrd] SKIPPED (mdcrd ...) [ 59%] 712s tests/test_trajectory.py::test_read_write[xyz-binpos] PASSED [ 59%] 712s tests/test_trajectory.py::test_read_write[xyz-dtr] SKIPPED (dtr need...) [ 59%] 712s tests/test_trajectory.py::test_read_write[xyz-xyz] PASSED [ 59%] 712s tests/test_trajectory.py::test_read_write[xyz-xyz.gz] PASSED [ 59%] 712s tests/test_trajectory.py::test_read_write[xyz-lammpstrj] SKIPPED (la...) [ 59%] 712s tests/test_trajectory.py::test_read_write[xyz-tng] PASSED [ 59%] 712s tests/test_trajectory.py::test_read_write[xyz-lh5] PASSED [ 60%] 712s tests/test_trajectory.py::test_read_write[xyz-pdb] PASSED [ 60%] 713s tests/test_trajectory.py::test_read_write[xyz-pdb.gz] PASSED [ 60%] 713s tests/test_trajectory.py::test_read_write[xyz-ncrst] SKIPPED (ncrst ...) [ 60%] 713s tests/test_trajectory.py::test_read_write[xyz-rst7] SKIPPED (rst7 ca...) [ 60%] 713s tests/test_trajectory.py::test_read_write[xyz-gro] PASSED [ 60%] 713s tests/test_trajectory.py::test_read_write[xyz.gz-nc] PASSED [ 60%] 713s tests/test_trajectory.py::test_read_write[xyz.gz-h5] PASSED [ 60%] 713s tests/test_trajectory.py::test_read_write[xyz.gz-xtc] PASSED [ 60%] 713s tests/test_trajectory.py::test_read_write[xyz.gz-trr] PASSED [ 60%] 713s tests/test_trajectory.py::test_read_write[xyz.gz-dcd] PASSED [ 60%] 713s tests/test_trajectory.py::test_read_write[xyz.gz-mdcrd] SKIPPED (mdc...) [ 60%] 713s tests/test_trajectory.py::test_read_write[xyz.gz-binpos] PASSED [ 61%] 713s tests/test_trajectory.py::test_read_write[xyz.gz-dtr] SKIPPED (dtr n...) [ 61%] 714s tests/test_trajectory.py::test_read_write[xyz.gz-xyz] PASSED [ 61%] 714s tests/test_trajectory.py::test_read_write[xyz.gz-xyz.gz] PASSED [ 61%] 714s tests/test_trajectory.py::test_read_write[xyz.gz-lammpstrj] SKIPPED [ 61%] 714s tests/test_trajectory.py::test_read_write[xyz.gz-tng] PASSED [ 61%] 714s tests/test_trajectory.py::test_read_write[xyz.gz-lh5] PASSED [ 61%] 714s tests/test_trajectory.py::test_read_write[xyz.gz-pdb] PASSED [ 61%] 715s tests/test_trajectory.py::test_read_write[xyz.gz-pdb.gz] PASSED [ 61%] 715s tests/test_trajectory.py::test_read_write[xyz.gz-ncrst] SKIPPED (ncr...) [ 61%] 715s tests/test_trajectory.py::test_read_write[xyz.gz-rst7] SKIPPED (rst7...) [ 61%] 715s tests/test_trajectory.py::test_read_write[xyz.gz-gro] PASSED [ 61%] 715s tests/test_trajectory.py::test_read_write[lammpstrj-nc] PASSED [ 62%] 715s tests/test_trajectory.py::test_read_write[lammpstrj-h5] PASSED [ 62%] 715s tests/test_trajectory.py::test_read_write[lammpstrj-xtc] PASSED [ 62%] 715s tests/test_trajectory.py::test_read_write[lammpstrj-trr] PASSED [ 62%] 715s tests/test_trajectory.py::test_read_write[lammpstrj-dcd] PASSED [ 62%] 715s tests/test_trajectory.py::test_read_write[lammpstrj-mdcrd] SKIPPED (...) [ 62%] 715s tests/test_trajectory.py::test_read_write[lammpstrj-binpos] PASSED [ 62%] 717s tests/test_trajectory.py::test_read_write[lammpstrj-dtr] PASSED [ 62%] 717s tests/test_trajectory.py::test_read_write[lammpstrj-xyz] PASSED [ 62%] 717s tests/test_trajectory.py::test_read_write[lammpstrj-xyz.gz] PASSED [ 62%] 717s tests/test_trajectory.py::test_read_write[lammpstrj-lammpstrj] PASSED [ 62%] 717s tests/test_trajectory.py::test_read_write[lammpstrj-tng] PASSED [ 62%] 717s tests/test_trajectory.py::test_read_write[lammpstrj-lh5] PASSED [ 63%] 718s tests/test_trajectory.py::test_read_write[lammpstrj-pdb] PASSED [ 63%] 718s tests/test_trajectory.py::test_read_write[lammpstrj-pdb.gz] PASSED [ 63%] 718s tests/test_trajectory.py::test_read_write[lammpstrj-ncrst] SKIPPED (...) [ 63%] 718s tests/test_trajectory.py::test_read_write[lammpstrj-rst7] SKIPPED (r...) [ 63%] 718s tests/test_trajectory.py::test_read_write[lammpstrj-gro] PASSED [ 63%] 718s tests/test_trajectory.py::test_read_write[tng-nc] PASSED [ 63%] 718s tests/test_trajectory.py::test_read_write[tng-h5] PASSED [ 63%] 718s tests/test_trajectory.py::test_read_write[tng-xtc] PASSED [ 63%] 718s tests/test_trajectory.py::test_read_write[tng-trr] PASSED [ 63%] 719s tests/test_trajectory.py::test_read_write[tng-dcd] PASSED [ 63%] 719s tests/test_trajectory.py::test_read_write[tng-mdcrd] SKIPPED (mdcrd ...) [ 63%] 719s tests/test_trajectory.py::test_read_write[tng-binpos] PASSED [ 63%] 720s tests/test_trajectory.py::test_read_write[tng-dtr] PASSED [ 64%] 720s tests/test_trajectory.py::test_read_write[tng-xyz] PASSED [ 64%] 720s tests/test_trajectory.py::test_read_write[tng-xyz.gz] PASSED [ 64%] 720s tests/test_trajectory.py::test_read_write[tng-lammpstrj] PASSED [ 64%] 720s tests/test_trajectory.py::test_read_write[tng-tng] PASSED [ 64%] 720s tests/test_trajectory.py::test_read_write[tng-lh5] PASSED [ 64%] 721s tests/test_trajectory.py::test_read_write[tng-pdb] PASSED [ 64%] 721s tests/test_trajectory.py::test_read_write[tng-pdb.gz] PASSED [ 64%] 721s tests/test_trajectory.py::test_read_write[tng-ncrst] SKIPPED (ncrst ...) [ 64%] 721s tests/test_trajectory.py::test_read_write[tng-rst7] SKIPPED (rst7 ca...) [ 64%] 722s tests/test_trajectory.py::test_read_write[tng-gro] PASSED [ 64%] 722s tests/test_trajectory.py::test_read_write[lh5-nc] PASSED [ 64%] 722s tests/test_trajectory.py::test_read_write[lh5-h5] PASSED [ 65%] 722s tests/test_trajectory.py::test_read_write[lh5-xtc] PASSED [ 65%] 722s tests/test_trajectory.py::test_read_write[lh5-trr] PASSED [ 65%] 722s tests/test_trajectory.py::test_read_write[lh5-dcd] PASSED [ 65%] 722s tests/test_trajectory.py::test_read_write[lh5-mdcrd] SKIPPED (mdcrd ...) [ 65%] 722s tests/test_trajectory.py::test_read_write[lh5-binpos] PASSED [ 65%] 722s tests/test_trajectory.py::test_read_write[lh5-dtr] SKIPPED (dtr need...) [ 65%] 722s tests/test_trajectory.py::test_read_write[lh5-xyz] PASSED [ 65%] 722s tests/test_trajectory.py::test_read_write[lh5-xyz.gz] PASSED [ 65%] 722s tests/test_trajectory.py::test_read_write[lh5-lammpstrj] SKIPPED (la...) [ 65%] 722s tests/test_trajectory.py::test_read_write[lh5-tng] PASSED [ 65%] 722s tests/test_trajectory.py::test_read_write[lh5-lh5] PASSED [ 65%] 722s tests/test_trajectory.py::test_read_write[lh5-pdb] PASSED [ 66%] 723s tests/test_trajectory.py::test_read_write[lh5-pdb.gz] PASSED [ 66%] 723s tests/test_trajectory.py::test_read_write[lh5-ncrst] SKIPPED (ncrst ...) [ 66%] 723s tests/test_trajectory.py::test_read_write[lh5-rst7] SKIPPED (rst7 ca...) [ 66%] 723s tests/test_trajectory.py::test_read_write[lh5-gro] PASSED [ 66%] 723s tests/test_trajectory.py::test_read_write[pdb-nc] PASSED [ 66%] 723s tests/test_trajectory.py::test_read_write[pdb-h5] PASSED [ 66%] 724s tests/test_trajectory.py::test_read_write[pdb-xtc] PASSED [ 66%] 724s tests/test_trajectory.py::test_read_write[pdb-trr] PASSED [ 66%] 724s tests/test_trajectory.py::test_read_write[pdb-dcd] PASSED [ 66%] 724s tests/test_trajectory.py::test_read_write[pdb-mdcrd] SKIPPED (mdcrd ...) [ 66%] 724s tests/test_trajectory.py::test_read_write[pdb-binpos] PASSED [ 66%] 726s tests/test_trajectory.py::test_read_write[pdb-dtr] PASSED [ 67%] 726s tests/test_trajectory.py::test_read_write[pdb-xyz] PASSED [ 67%] 727s tests/test_trajectory.py::test_read_write[pdb-xyz.gz] PASSED [ 67%] 727s tests/test_trajectory.py::test_read_write[pdb-lammpstrj] PASSED [ 67%] 727s tests/test_trajectory.py::test_read_write[pdb-tng] PASSED [ 67%] 727s tests/test_trajectory.py::test_read_write[pdb-lh5] PASSED [ 67%] 728s tests/test_trajectory.py::test_read_write[pdb-pdb] PASSED [ 67%] 729s tests/test_trajectory.py::test_read_write[pdb-pdb.gz] PASSED [ 67%] 729s tests/test_trajectory.py::test_read_write[pdb-ncrst] SKIPPED (ncrst ...) [ 67%] 729s tests/test_trajectory.py::test_read_write[pdb-rst7] SKIPPED (rst7 ca...) [ 67%] 729s tests/test_trajectory.py::test_read_write[pdb-gro] PASSED [ 67%] 729s tests/test_trajectory.py::test_read_write[pdb.gz-nc] PASSED [ 67%] 729s tests/test_trajectory.py::test_read_write[pdb.gz-h5] PASSED [ 68%] 730s tests/test_trajectory.py::test_read_write[pdb.gz-xtc] PASSED [ 68%] 730s tests/test_trajectory.py::test_read_write[pdb.gz-trr] PASSED [ 68%] 730s tests/test_trajectory.py::test_read_write[pdb.gz-dcd] PASSED [ 68%] 730s tests/test_trajectory.py::test_read_write[pdb.gz-mdcrd] SKIPPED (mdc...) [ 68%] 730s tests/test_trajectory.py::test_read_write[pdb.gz-binpos] PASSED [ 68%] 732s tests/test_trajectory.py::test_read_write[pdb.gz-dtr] PASSED [ 68%] 732s tests/test_trajectory.py::test_read_write[pdb.gz-xyz] PASSED [ 68%] 733s tests/test_trajectory.py::test_read_write[pdb.gz-xyz.gz] PASSED [ 68%] 733s tests/test_trajectory.py::test_read_write[pdb.gz-lammpstrj] PASSED [ 68%] 733s tests/test_trajectory.py::test_read_write[pdb.gz-tng] PASSED [ 68%] 734s tests/test_trajectory.py::test_read_write[pdb.gz-lh5] PASSED [ 68%] 734s tests/test_trajectory.py::test_read_write[pdb.gz-pdb] PASSED [ 68%] 735s tests/test_trajectory.py::test_read_write[pdb.gz-pdb.gz] PASSED [ 69%] 735s tests/test_trajectory.py::test_read_write[pdb.gz-ncrst] SKIPPED (ncr...) [ 69%] 735s tests/test_trajectory.py::test_read_write[pdb.gz-rst7] SKIPPED (rst7...) [ 69%] 735s tests/test_trajectory.py::test_read_write[pdb.gz-gro] PASSED [ 69%] 735s tests/test_trajectory.py::test_read_write[ncrst-nc] XFAIL (These ref...) [ 69%] 735s tests/test_trajectory.py::test_read_write[ncrst-h5] XFAIL (These ref...) [ 69%] 735s tests/test_trajectory.py::test_read_write[ncrst-xtc] XFAIL (These re...) [ 69%] 735s tests/test_trajectory.py::test_read_write[ncrst-trr] XFAIL (These re...) [ 69%] 735s tests/test_trajectory.py::test_read_write[ncrst-dcd] XFAIL (These re...) [ 69%] 735s tests/test_trajectory.py::test_read_write[ncrst-mdcrd] XFAIL (These ...) [ 69%] 735s tests/test_trajectory.py::test_read_write[ncrst-binpos] XFAIL (These...) [ 69%] 735s tests/test_trajectory.py::test_read_write[ncrst-dtr] XFAIL (These re...) [ 69%] 736s tests/test_trajectory.py::test_read_write[ncrst-xyz] XFAIL (These re...) [ 70%] 736s tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] XFAIL (These...) [ 70%] 736s tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] XFAIL (Th...) [ 70%] 736s tests/test_trajectory.py::test_read_write[ncrst-tng] XFAIL (These re...) [ 70%] 736s tests/test_trajectory.py::test_read_write[ncrst-lh5] XFAIL (These re...) [ 70%] 736s tests/test_trajectory.py::test_read_write[ncrst-pdb] XFAIL (These re...) [ 70%] 736s tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] XFAIL (These...) [ 70%] 736s tests/test_trajectory.py::test_read_write[ncrst-ncrst] XFAIL (These ...) [ 70%] 736s tests/test_trajectory.py::test_read_write[ncrst-rst7] XFAIL (These r...) [ 70%] 736s tests/test_trajectory.py::test_read_write[ncrst-gro] XFAIL (These re...) [ 70%] 736s tests/test_trajectory.py::test_read_write[rst7-nc] XFAIL (These refe...) [ 70%] 736s tests/test_trajectory.py::test_read_write[rst7-h5] XFAIL (These refe...) [ 70%] 736s tests/test_trajectory.py::test_read_write[rst7-xtc] XFAIL (These ref...) [ 71%] 736s tests/test_trajectory.py::test_read_write[rst7-trr] XFAIL (These ref...) [ 71%] 736s tests/test_trajectory.py::test_read_write[rst7-dcd] XFAIL (These ref...) [ 71%] 736s tests/test_trajectory.py::test_read_write[rst7-mdcrd] XFAIL (These r...) [ 71%] 736s tests/test_trajectory.py::test_read_write[rst7-binpos] XFAIL (These ...) [ 71%] 736s tests/test_trajectory.py::test_read_write[rst7-dtr] XFAIL (These ref...) [ 71%] 736s tests/test_trajectory.py::test_read_write[rst7-xyz] XFAIL (These ref...) [ 71%] 736s tests/test_trajectory.py::test_read_write[rst7-xyz.gz] XFAIL (These ...) [ 71%] 736s tests/test_trajectory.py::test_read_write[rst7-lammpstrj] XFAIL (The...) [ 71%] 736s tests/test_trajectory.py::test_read_write[rst7-tng] XFAIL (These ref...) [ 71%] 736s tests/test_trajectory.py::test_read_write[rst7-lh5] XFAIL (These ref...) [ 71%] 736s tests/test_trajectory.py::test_read_write[rst7-pdb] XFAIL (These ref...) [ 71%] 736s tests/test_trajectory.py::test_read_write[rst7-pdb.gz] XFAIL (These ...) [ 72%] 736s tests/test_trajectory.py::test_read_write[rst7-ncrst] XFAIL (These r...) [ 72%] 736s tests/test_trajectory.py::test_read_write[rst7-rst7] XFAIL (These re...) [ 72%] 736s tests/test_trajectory.py::test_read_write[rst7-gro] XFAIL (These ref...) [ 72%] 736s tests/test_trajectory.py::test_read_write[gro-nc] PASSED [ 72%] 736s tests/test_trajectory.py::test_read_write[gro-h5] PASSED [ 72%] 736s tests/test_trajectory.py::test_read_write[gro-xtc] PASSED [ 72%] 736s tests/test_trajectory.py::test_read_write[gro-trr] PASSED [ 72%] 736s tests/test_trajectory.py::test_read_write[gro-dcd] PASSED [ 72%] 736s tests/test_trajectory.py::test_read_write[gro-mdcrd] SKIPPED (mdcrd ...) [ 72%] 736s tests/test_trajectory.py::test_read_write[gro-binpos] PASSED [ 72%] 738s tests/test_trajectory.py::test_read_write[gro-dtr] PASSED [ 72%] 738s tests/test_trajectory.py::test_read_write[gro-xyz] PASSED [ 73%] 738s tests/test_trajectory.py::test_read_write[gro-xyz.gz] PASSED [ 73%] 738s tests/test_trajectory.py::test_read_write[gro-lammpstrj] PASSED [ 73%] 739s tests/test_trajectory.py::test_read_write[gro-tng] PASSED [ 73%] 739s tests/test_trajectory.py::test_read_write[gro-lh5] PASSED [ 73%] 739s tests/test_trajectory.py::test_read_write[gro-pdb] PASSED [ 73%] 740s tests/test_trajectory.py::test_read_write[gro-pdb.gz] PASSED [ 73%] 740s tests/test_trajectory.py::test_read_write[gro-ncrst] SKIPPED (ncrst ...) [ 73%] 740s tests/test_trajectory.py::test_read_write[gro-rst7] SKIPPED (rst7 ca...) [ 73%] 740s tests/test_trajectory.py::test_read_write[gro-gro] PASSED [ 73%] 740s tests/test_trajectory.py::test_load[nc] PASSED [ 73%] 740s tests/test_trajectory.py::test_load[h5] PASSED [ 73%] 740s tests/test_trajectory.py::test_load[xtc] PASSED [ 73%] 740s tests/test_trajectory.py::test_load[trr] PASSED [ 74%] 740s tests/test_trajectory.py::test_load[dcd] PASSED [ 74%] 740s tests/test_trajectory.py::test_load[mdcrd] PASSED [ 74%] 740s tests/test_trajectory.py::test_load[binpos] PASSED [ 74%] 740s tests/test_trajectory.py::test_load[dtr] PASSED [ 74%] 741s tests/test_trajectory.py::test_load[xyz] PASSED [ 74%] 741s tests/test_trajectory.py::test_load[xyz.gz] PASSED [ 74%] 741s tests/test_trajectory.py::test_load[lammpstrj] PASSED [ 74%] 741s tests/test_trajectory.py::test_load[tng] PASSED [ 74%] 741s tests/test_trajectory.py::test_load[lh5] PASSED [ 74%] 743s tests/test_trajectory.py::test_load[pdb] PASSED [ 74%] 744s tests/test_trajectory.py::test_load[pdb.gz] PASSED [ 74%] 745s tests/test_trajectory.py::test_load[ncrst] XFAIL (These reference fi...) [ 75%] 745s tests/test_trajectory.py::test_load[rst7] XFAIL (These reference fil...) [ 75%] 745s tests/test_trajectory.py::test_load[gro] PASSED [ 75%] 745s tests/test_trajectory.py::test_hdf5 PASSED [ 75%] 745s tests/test_trajectory.py::test_center PASSED [ 75%] 745s tests/test_trajectory.py::test_center_aind PASSED [ 75%] 745s tests/test_trajectory.py::test_float_atom_indices_exception[nc] PASSED [ 75%] 745s tests/test_trajectory.py::test_float_atom_indices_exception[h5] PASSED [ 75%] 745s tests/test_trajectory.py::test_float_atom_indices_exception[xtc] PASSED [ 75%] 745s tests/test_trajectory.py::test_float_atom_indices_exception[trr] PASSED [ 75%] 745s tests/test_trajectory.py::test_float_atom_indices_exception[dcd] PASSED [ 75%] 745s tests/test_trajectory.py::test_float_atom_indices_exception[mdcrd] PASSED [ 75%] 745s tests/test_trajectory.py::test_float_atom_indices_exception[binpos] PASSED [ 76%] 745s tests/test_trajectory.py::test_float_atom_indices_exception[dtr] PASSED [ 76%] 745s tests/test_trajectory.py::test_float_atom_indices_exception[xyz] PASSED [ 76%] 745s tests/test_trajectory.py::test_float_atom_indices_exception[xyz.gz] PASSED [ 76%] 745s tests/test_trajectory.py::test_float_atom_indices_exception[lammpstrj] PASSED [ 76%] 745s tests/test_trajectory.py::test_float_atom_indices_exception[tng] PASSED [ 76%] 745s tests/test_trajectory.py::test_float_atom_indices_exception[lh5] PASSED [ 76%] 745s tests/test_trajectory.py::test_float_atom_indices_exception[pdb] PASSED [ 76%] 745s tests/test_trajectory.py::test_float_atom_indices_exception[pdb.gz] PASSED [ 76%] 745s tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] XFAIL [ 76%] 745s tests/test_trajectory.py::test_float_atom_indices_exception[rst7] XFAIL [ 76%] 745s tests/test_trajectory.py::test_float_atom_indices_exception[gro] PASSED [ 76%] 745s tests/test_trajectory.py::test_restrict_atoms PASSED [ 77%] 745s tests/test_trajectory.py::test_restrict_atoms_not_inplace PASSED [ 77%] 745s tests/test_trajectory.py::test_array_vs_matrix PASSED [ 77%] 745s tests/test_trajectory.py::test_pdb_unitcell_loadsave PASSED [ 77%] 745s tests/test_trajectory.py::test_load_combination[nc] PASSED [ 77%] 745s tests/test_trajectory.py::test_load_combination[h5] PASSED [ 77%] 745s tests/test_trajectory.py::test_load_combination[xtc] PASSED [ 77%] 745s tests/test_trajectory.py::test_load_combination[trr] PASSED [ 77%] 745s tests/test_trajectory.py::test_load_combination[dcd] PASSED [ 77%] 745s tests/test_trajectory.py::test_load_combination[mdcrd] PASSED [ 77%] 745s tests/test_trajectory.py::test_load_combination[binpos] PASSED [ 77%] 745s tests/test_trajectory.py::test_load_combination[dtr] PASSED [ 77%] 745s tests/test_trajectory.py::test_load_combination[xyz] PASSED [ 78%] 745s tests/test_trajectory.py::test_load_combination[xyz.gz] PASSED [ 78%] 746s tests/test_trajectory.py::test_load_combination[lammpstrj] PASSED [ 78%] 746s tests/test_trajectory.py::test_load_combination[tng] PASSED [ 78%] 746s tests/test_trajectory.py::test_load_combination[lh5] PASSED [ 78%] 746s tests/test_trajectory.py::test_load_combination[pdb] PASSED [ 78%] 747s tests/test_trajectory.py::test_load_combination[pdb.gz] PASSED [ 78%] 747s tests/test_trajectory.py::test_load_combination[ncrst] XFAIL (These ...) [ 78%] 747s tests/test_trajectory.py::test_load_combination[rst7] XFAIL (These r...) [ 78%] 747s tests/test_trajectory.py::test_load_combination[gro] PASSED [ 78%] 747s tests/test_trajectory.py::test_no_topology PASSED [ 78%] 747s tests/test_trajectory.py::test_join PASSED [ 78%] 747s tests/test_trajectory.py::test_md_join PASSED [ 78%] 747s tests/test_trajectory.py::test_stack_1 PASSED [ 79%] 747s tests/test_trajectory.py::test_stack_2 PASSED [ 79%] 747s tests/test_trajectory.py::test_seek_read_mode[nc] PASSED [ 79%] 747s tests/test_trajectory.py::test_seek_read_mode[h5] PASSED [ 79%] 747s tests/test_trajectory.py::test_seek_read_mode[xtc] PASSED [ 79%] 747s tests/test_trajectory.py::test_seek_read_mode[trr] PASSED [ 79%] 747s tests/test_trajectory.py::test_seek_read_mode[dcd] PASSED [ 79%] 747s tests/test_trajectory.py::test_seek_read_mode[mdcrd] PASSED [ 79%] 747s tests/test_trajectory.py::test_seek_read_mode[binpos] PASSED [ 79%] 747s tests/test_trajectory.py::test_seek_read_mode[dtr] PASSED [ 79%] 747s tests/test_trajectory.py::test_seek_read_mode[xyz] PASSED [ 79%] 747s tests/test_trajectory.py::test_seek_read_mode[xyz.gz] XFAIL (This is...) [ 79%] 748s tests/test_trajectory.py::test_seek_read_mode[lammpstrj] PASSED [ 80%] 748s tests/test_trajectory.py::test_seek_read_mode[tng] PASSED [ 80%] 748s tests/test_trajectory.py::test_seek_read_mode[lh5] PASSED [ 80%] 748s tests/test_trajectory.py::test_seek_read_mode[pdb] XFAIL (PDB Files ...) [ 80%] 748s tests/test_trajectory.py::test_seek_read_mode[pdb.gz] XFAIL (PDB Fil...) [ 80%] 748s tests/test_trajectory.py::test_seek_read_mode[ncrst] XFAIL (These re...) [ 80%] 748s tests/test_trajectory.py::test_seek_read_mode[rst7] XFAIL (These ref...) [ 80%] 748s tests/test_trajectory.py::test_seek_read_mode[gro] XFAIL (This is br...) [ 80%] 748s tests/test_trajectory.py::test_load_frame[nc] PASSED [ 80%] 748s tests/test_trajectory.py::test_load_frame[h5] PASSED [ 80%] 748s tests/test_trajectory.py::test_load_frame[xtc] PASSED [ 80%] 748s tests/test_trajectory.py::test_load_frame[trr] PASSED [ 80%] 748s tests/test_trajectory.py::test_load_frame[dcd] PASSED [ 81%] 748s tests/test_trajectory.py::test_load_frame[mdcrd] PASSED [ 81%] 748s tests/test_trajectory.py::test_load_frame[binpos] PASSED [ 81%] 748s tests/test_trajectory.py::test_load_frame[dtr] XFAIL (DTR doesn't lo...) [ 81%] 748s tests/test_trajectory.py::test_load_frame[xyz] PASSED [ 81%] 748s tests/test_trajectory.py::test_load_frame[xyz.gz] PASSED [ 81%] 748s tests/test_trajectory.py::test_load_frame[lammpstrj] PASSED [ 81%] 748s tests/test_trajectory.py::test_load_frame[tng] PASSED [ 81%] 748s tests/test_trajectory.py::test_load_frame[lh5] PASSED [ 81%] 749s tests/test_trajectory.py::test_load_frame[pdb] PASSED [ 81%] 749s tests/test_trajectory.py::test_load_frame[pdb.gz] PASSED [ 81%] 749s tests/test_trajectory.py::test_load_frame[ncrst] XFAIL (These refere...) [ 81%] 749s tests/test_trajectory.py::test_load_frame[rst7] XFAIL (These referen...) [ 82%] 749s tests/test_trajectory.py::test_load_frame[gro] XFAIL (Gro doesn't im...) [ 82%] 749s tests/test_trajectory.py::test_load_frame_2eqq PASSED [ 82%] 749s tests/test_trajectory.py::test_iterload[nc] PASSED [ 82%] 749s tests/test_trajectory.py::test_iterload[h5] PASSED [ 82%] 749s tests/test_trajectory.py::test_iterload[xtc] PASSED [ 82%] 749s tests/test_trajectory.py::test_iterload[trr] PASSED [ 82%] 749s tests/test_trajectory.py::test_iterload[dcd] PASSED [ 82%] 750s tests/test_trajectory.py::test_iterload[mdcrd] PASSED [ 82%] 750s tests/test_trajectory.py::test_iterload[binpos] PASSED [ 82%] 750s tests/test_trajectory.py::test_iterload[dtr] XFAIL (This is broken w...) [ 82%] 750s tests/test_trajectory.py::test_iterload[xyz] PASSED [ 82%] 750s tests/test_trajectory.py::test_iterload[xyz.gz] PASSED [ 83%] 750s tests/test_trajectory.py::test_iterload[lammpstrj] PASSED [ 83%] 750s tests/test_trajectory.py::test_iterload[tng] PASSED [ 83%] 750s tests/test_trajectory.py::test_iterload[lh5] PASSED [ 83%] 750s tests/test_trajectory.py::test_iterload[pdb] PASSED [ 83%] 750s tests/test_trajectory.py::test_iterload[pdb.gz] PASSED [ 83%] 750s tests/test_trajectory.py::test_iterload[ncrst] SKIPPED (Only 1 frame...) [ 83%] 750s tests/test_trajectory.py::test_iterload[rst7] SKIPPED (Only 1 frame ...) [ 83%] 750s tests/test_trajectory.py::test_iterload[gro] PASSED [ 83%] 751s tests/test_trajectory.py::test_iterload_skip[nc] PASSED [ 83%] 753s tests/test_trajectory.py::test_iterload_skip[h5] PASSED [ 83%] 754s tests/test_trajectory.py::test_iterload_skip[xtc] PASSED [ 83%] 755s tests/test_trajectory.py::test_iterload_skip[trr] PASSED [ 84%] 756s tests/test_trajectory.py::test_iterload_skip[dcd] PASSED [ 84%] 759s tests/test_trajectory.py::test_iterload_skip[mdcrd] PASSED [ 84%] 760s tests/test_trajectory.py::test_iterload_skip[binpos] PASSED [ 84%] 760s tests/test_trajectory.py::test_iterload_skip[dtr] PASSED [ 84%] 761s tests/test_trajectory.py::test_iterload_skip[xyz] PASSED [ 84%] 762s tests/test_trajectory.py::test_iterload_skip[xyz.gz] PASSED [ 84%] 763s tests/test_trajectory.py::test_iterload_skip[lammpstrj] PASSED [ 84%] 764s tests/test_trajectory.py::test_iterload_skip[tng] PASSED [ 84%] 766s tests/test_trajectory.py::test_iterload_skip[lh5] PASSED [ 84%] 766s tests/test_trajectory.py::test_iterload_skip[pdb] XFAIL (PDB Iterloa...) [ 84%] 766s tests/test_trajectory.py::test_iterload_skip[pdb.gz] XFAIL (PDB Iter...) [ 84%] 766s tests/test_trajectory.py::test_iterload_skip[ncrst] XFAIL (These ref...) [ 84%] 766s tests/test_trajectory.py::test_iterload_skip[rst7] XFAIL (These refe...) [ 85%] 766s tests/test_trajectory.py::test_iterload_skip[gro] XFAIL (Not impleme...) [ 85%] 766s tests/test_trajectory.py::test_iterload_chunk_dcd PASSED [ 85%] 766s tests/test_trajectory.py::test_save_load[nc] PASSED [ 85%] 766s tests/test_trajectory.py::test_save_load[h5] PASSED [ 85%] 766s tests/test_trajectory.py::test_save_load[xtc] PASSED [ 85%] 766s tests/test_trajectory.py::test_save_load[trr] PASSED [ 85%] 766s tests/test_trajectory.py::test_save_load[dcd] PASSED [ 85%] 766s tests/test_trajectory.py::test_save_load[mdcrd] PASSED [ 85%] 766s tests/test_trajectory.py::test_save_load[binpos] PASSED [ 85%] 766s tests/test_trajectory.py::test_save_load[dtr] PASSED [ 85%] 766s tests/test_trajectory.py::test_save_load[xyz] PASSED [ 85%] 766s tests/test_trajectory.py::test_save_load[xyz.gz] PASSED [ 86%] 766s tests/test_trajectory.py::test_save_load[lammpstrj] PASSED [ 86%] 766s tests/test_trajectory.py::test_save_load[tng] PASSED [ 86%] 766s tests/test_trajectory.py::test_save_load[lh5] PASSED [ 86%] 766s tests/test_trajectory.py::test_save_load[pdb] PASSED [ 86%] 766s tests/test_trajectory.py::test_save_load[pdb.gz] PASSED [ 86%] 766s tests/test_trajectory.py::test_save_load[ncrst] PASSED [ 86%] 766s tests/test_trajectory.py::test_save_load[rst7] PASSED [ 86%] 766s tests/test_trajectory.py::test_save_load[gro] PASSED [ 86%] 766s tests/test_trajectory.py::test_force_overwrite[nc] PASSED [ 86%] 766s tests/test_trajectory.py::test_force_overwrite[h5] PASSED [ 86%] 766s tests/test_trajectory.py::test_force_overwrite[xtc] PASSED [ 86%] 766s tests/test_trajectory.py::test_force_overwrite[trr] PASSED [ 87%] 766s tests/test_trajectory.py::test_force_overwrite[dcd] PASSED [ 87%] 766s tests/test_trajectory.py::test_force_overwrite[mdcrd] PASSED [ 87%] 766s tests/test_trajectory.py::test_force_overwrite[binpos] PASSED [ 87%] 766s tests/test_trajectory.py::test_force_overwrite[dtr] XFAIL (This is b...) [ 87%] 766s tests/test_trajectory.py::test_force_overwrite[xyz] PASSED [ 87%] 766s tests/test_trajectory.py::test_force_overwrite[xyz.gz] PASSED [ 87%] 766s tests/test_trajectory.py::test_force_overwrite[lammpstrj] PASSED [ 87%] 766s tests/test_trajectory.py::test_force_overwrite[tng] PASSED [ 87%] 766s tests/test_trajectory.py::test_force_overwrite[lh5] PASSED [ 87%] 766s tests/test_trajectory.py::test_force_overwrite[pdb] PASSED [ 87%] 766s tests/test_trajectory.py::test_force_overwrite[pdb.gz] PASSED [ 87%] 766s tests/test_trajectory.py::test_force_overwrite[ncrst] PASSED [ 88%] 766s tests/test_trajectory.py::test_force_overwrite[rst7] PASSED [ 88%] 766s tests/test_trajectory.py::test_force_overwrite[gro] PASSED [ 88%] 766s tests/test_trajectory.py::test_force_noverwrite[nc] PASSED [ 88%] 766s tests/test_trajectory.py::test_force_noverwrite[h5] PASSED [ 88%] 766s tests/test_trajectory.py::test_force_noverwrite[xtc] PASSED [ 88%] 766s tests/test_trajectory.py::test_force_noverwrite[trr] PASSED [ 88%] 766s tests/test_trajectory.py::test_force_noverwrite[dcd] PASSED [ 88%] 766s tests/test_trajectory.py::test_force_noverwrite[mdcrd] PASSED [ 88%] 767s tests/test_trajectory.py::test_force_noverwrite[binpos] PASSED [ 88%] 767s tests/test_trajectory.py::test_force_noverwrite[dtr] PASSED [ 88%] 767s tests/test_trajectory.py::test_force_noverwrite[xyz] PASSED [ 88%] 767s tests/test_trajectory.py::test_force_noverwrite[xyz.gz] PASSED [ 89%] 767s tests/test_trajectory.py::test_force_noverwrite[lammpstrj] PASSED [ 89%] 767s tests/test_trajectory.py::test_force_noverwrite[tng] PASSED [ 89%] 767s tests/test_trajectory.py::test_force_noverwrite[lh5] PASSED [ 89%] 767s tests/test_trajectory.py::test_force_noverwrite[pdb] PASSED [ 89%] 767s tests/test_trajectory.py::test_force_noverwrite[pdb.gz] PASSED [ 89%] 767s tests/test_trajectory.py::test_force_noverwrite[ncrst] PASSED [ 89%] 767s tests/test_trajectory.py::test_force_noverwrite[rst7] PASSED [ 89%] 767s tests/test_trajectory.py::test_force_noverwrite[gro] PASSED [ 89%] 767s tests/test_trajectory.py::test_open_and_load PASSED [ 89%] 767s tests/test_trajectory.py::test_length PASSED [ 89%] 767s tests/test_trajectory.py::test_unitcell[nc] PASSED [ 89%] 767s tests/test_trajectory.py::test_unitcell[h5] PASSED [ 89%] 767s tests/test_trajectory.py::test_unitcell[xtc] PASSED [ 90%] 767s tests/test_trajectory.py::test_unitcell[trr] PASSED [ 90%] 767s tests/test_trajectory.py::test_unitcell[dcd] PASSED [ 90%] 767s tests/test_trajectory.py::test_unitcell[mdcrd] PASSED [ 90%] 767s tests/test_trajectory.py::test_unitcell[binpos] PASSED [ 90%] 767s tests/test_trajectory.py::test_unitcell[dtr] XFAIL (dtr seems to nee...) [ 90%] 767s tests/test_trajectory.py::test_unitcell[xyz] PASSED [ 90%] 767s tests/test_trajectory.py::test_unitcell[xyz.gz] PASSED [ 90%] 767s tests/test_trajectory.py::test_unitcell[lammpstrj] XFAIL (lammpstrj ...) [ 90%] 767s tests/test_trajectory.py::test_unitcell[tng] PASSED [ 90%] 767s tests/test_trajectory.py::test_unitcell[lh5] PASSED [ 90%] 767s tests/test_trajectory.py::test_unitcell[pdb] PASSED [ 90%] 767s tests/test_trajectory.py::test_unitcell[pdb.gz] PASSED [ 91%] 767s tests/test_trajectory.py::test_unitcell[ncrst] XFAIL (ncrst seems to...) [ 91%] 767s tests/test_trajectory.py::test_unitcell[rst7] XFAIL (rst7 seems to n...) [ 91%] 767s tests/test_trajectory.py::test_unitcell[gro] PASSED [ 91%] 767s tests/test_trajectory.py::test_chunk0_iterload PASSED [ 91%] 768s tests/test_trajectory.py::test_hashing PASSED [ 91%] 768s tests/test_trajectory.py::test_smooth PASSED [ 91%] 768s tests/test_trajectory.py::test_load_pdb_no_standard_names PASSED [ 91%] 768s tests/test_trajectory.py::test_load_with_atom_indices PASSED [ 91%] 768s tests/test_trajectory.py::test_load_with_frame PASSED [ 91%] 768s tests/test_trajectory.py::test_add_remove_atoms PASSED [ 91%] 768s tests/test_trr.py::test_1 PASSED [ 91%] 768s tests/test_trr.py::test_read_stride PASSED [ 92%] 768s tests/test_trr.py::test_read_stride_n_frames PASSED [ 92%] 768s tests/test_trr.py::test_read_stride_offsets PASSED [ 92%] 768s tests/test_trr.py::test_read_stride_n_frames_offsets PASSED [ 92%] 768s tests/test_trr.py::test_read_stride_switching PASSED [ 92%] 768s tests/test_trr.py::test_write_read PASSED [ 92%] 768s tests/test_trr.py::test_read_atomindices_1 PASSED [ 92%] 768s tests/test_trr.py::test_read_atomindices_2 PASSED [ 92%] 768s tests/test_trr.py::test_deficient_shape PASSED [ 92%] 768s tests/test_trr.py::test_ragged_1 PASSED [ 92%] 768s tests/test_trr.py::test_ragged_2 PASSED [ 92%] 768s tests/test_trr.py::test_malformed PASSED [ 92%] 768s tests/test_trr.py::test_tell PASSED [ 93%] 768s tests/test_trr.py::test_seek PASSED [ 93%] 768s tests/test_trr.py::test_get_velocities PASSED [ 93%] 768s tests/test_trr.py::test_get_forces PASSED [ 93%] 768s tests/test_trr.py::test_get_velocities_and_forces PASSED [ 93%] 768s tests/test_trr.py::test_get_velocities_forces_atom_indices_1 PASSED [ 93%] 768s tests/test_trr.py::test_get_velocities_forces_atom_indices_2 PASSED [ 93%] 768s tests/test_trr.py::test_read_velocities_do_not_exist PASSED [ 93%] 768s tests/test_trr.py::test_read_forces_do_not_exist PASSED [ 93%] 768s tests/test_utils.py::test_unitcell_0 PASSED [ 93%] 768s tests/test_utils.py::test_unitcell_1 PASSED [ 93%] 768s tests/test_utils.py::test_ensure_type_1 PASSED [ 93%] 768s tests/test_utils.py::test_ensure_type_2 PASSED [ 94%] 768s tests/test_utils.py::test_ensure_type_25 PASSED [ 94%] 768s tests/test_utils.py::test_ensure_type_3 PASSED [ 94%] 768s tests/test_utils.py::test_ensure_type_4 PASSED [ 94%] 768s tests/test_utils.py::test_ensure_type_5 PASSED [ 94%] 768s tests/test_utils.py::test_ensure_type_6 PASSED [ 94%] 768s tests/test_utils.py::test_ensure_type_7 PASSED [ 94%] 768s tests/test_utils.py::test_ensure_type_8 PASSED [ 94%] 768s tests/test_utils.py::test_ensure_type_9 PASSED [ 94%] 768s tests/test_utils.py::test_ensure_type_10 PASSED [ 94%] 768s tests/test_utils.py::test_ensure_type_11 PASSED [ 94%] 768s tests/test_utils.py::test_ensure_type_12 PASSED [ 94%] 768s tests/test_utils.py::test_ensure_type_13 PASSED [ 94%] 768s tests/test_utils.py::test_ensure_type_14 PASSED [ 95%] 768s tests/test_utils.py::test_ensure_type_15 PASSED [ 95%] 768s tests/test_utils.py::test_delay_import_fail_1 PASSED [ 95%] 768s tests/test_utils.py::test_delay_import PASSED [ 95%] 768s tests/test_utils.py::test_unit_0 PASSED [ 95%] 768s tests/test_utils.py::test_unit_1 PASSED [ 95%] 768s tests/test_utils.py::test_unit_2 PASSED [ 95%] 768s tests/test_utils.py::test_unit_3 PASSED [ 95%] 768s tests/test_xml.py::test_xml PASSED [ 95%] 769s tests/test_xtc.py::test_read_chunk1 PASSED [ 95%] 769s tests/test_xtc.py::test_read_stride PASSED [ 95%] 769s tests/test_xtc.py::test_read_stride_n_frames PASSED [ 95%] 769s tests/test_xtc.py::test_read_stride_offsets PASSED [ 96%] 769s tests/test_xtc.py::test_read_stride_n_frames_offsets PASSED [ 96%] 769s tests/test_xtc.py::test_read_stride_switching_offsets PASSED [ 96%] 769s tests/test_xtc.py::test_read_atomindices_1 PASSED [ 96%] 769s tests/test_xtc.py::test_read_atomindices_w_stride PASSED [ 96%] 769s tests/test_xtc.py::test_read_atomindices_2 PASSED [ 96%] 769s tests/test_xtc.py::test_read_chunk2 PASSED [ 96%] 769s tests/test_xtc.py::test_read_chunk3 PASSED [ 96%] 769s tests/test_xtc.py::test_write_0 PASSED [ 96%] 769s tests/test_xtc.py::test_write_1 PASSED [ 96%] 769s tests/test_xtc.py::test_write_2 PASSED [ 96%] 769s tests/test_xtc.py::test_read_error_0 PASSED [ 96%] 769s tests/test_xtc.py::test_write_error_0 PASSED [ 97%] 769s tests/test_xtc.py::test_read_error_1 PASSED [ 97%] 769s tests/test_xtc.py::test_read_error_2 PASSED [ 97%] 769s tests/test_xtc.py::test_xtc_write_wierd_0 PASSED [ 97%] 769s tests/test_xtc.py::test_tell PASSED [ 97%] 769s tests/test_xtc.py::test_seek PASSED [ 97%] 769s tests/test_xtc.py::test_seek_natoms9 PASSED [ 97%] 769s tests/test_xtc.py::test_seek_out_of_bounds PASSED [ 97%] 769s tests/test_xtc.py::test_ragged_1 PASSED [ 97%] 769s tests/test_xtc.py::test_ragged_2 PASSED [ 97%] 769s tests/test_xtc.py::test_short_traj PASSED [ 97%] 769s tests/test_xtc.py::test_flush PASSED [ 97%] 769s tests/test_xyz.py::test_read_0 PASSED [ 98%] 769s tests/test_xyz.py::test_read_1 PASSED [ 98%] 769s tests/test_xyz.py::test_read_gz PASSED [ 98%] 769s tests/test_xyz.py::test_read_write PASSED [ 98%] 769s tests/test_xyz.py::test_mdwrite PASSED [ 98%] 769s tests/test_xyz.py::test_multiread PASSED [ 98%] 769s tests/test_xyz.py::test_seek PASSED [ 98%] 769s tests/test_xyz.py::test_len PASSED [ 98%] 769s tests/test_zipped.py::test_read_gz PASSED [ 98%] 769s tests/test_zipped.py::test_write_gz PASSED [ 98%] 769s tests/test_zipped.py::test_read_bz2 PASSED [ 98%] 769s tests/test_zipped.py::test_write_bz2 PASSED [ 98%] 905s examples/test_examples.py::test_example_notebook[two-pass-clustering.ipynb] PASSED [ 99%] 905s examples/test_examples.py::test_example_notebook[simulation-with-openmm.ipynb] SKIPPED [ 99%] 1045s examples/test_examples.py::test_example_notebook[centroids.ipynb] PASSED [ 99%] 1183s examples/test_examples.py::test_example_notebook[rmsd-benchmark.ipynb] PASSED [ 99%] 1320s examples/test_examples.py::test_example_notebook[ramachandran-plot.ipynb] PASSED [ 99%] 1455s examples/test_examples.py::test_example_notebook[hbonds.ipynb] SKIPPED [ 99%] 1590s examples/test_examples.py::test_example_notebook[native-contact.ipynb] SKIPPED [ 99%] 1729s examples/test_examples.py::test_example_notebook[solvent-accessible-surface-area.ipynb] PASSED [ 99%] 1868s examples/test_examples.py::test_example_notebook[clustering.ipynb] PASSED [ 99%] 2007s examples/test_examples.py::test_example_notebook[iterload.ipynb] PASSED [ 99%] 2143s examples/test_examples.py::test_example_notebook[principal-components.ipynb] PASSED [ 99%] 2281s examples/test_examples.py::test_example_notebook[atom-selection.ipynb] PASSED [ 99%] 2416s examples/test_examples.py::test_example_notebook[rmsd-drift.ipynb] PASSED [100%] 2416s 2416s =============================== warnings summary =============================== 2416s ../../../../usr/lib/python3/dist-packages/mdtraj/utils/unit/__init__.py:57 2416s /usr/lib/python3/dist-packages/mdtraj/utils/unit/__init__.py:57: DeprecationWarning: ast.Num is deprecated and will be removed in Python 3.14; use ast.Constant instead 2416s ast.Pow, ast.Div, ast.Mult, ast.Num] 2416s 2416s ../../../../usr/lib/python3/dist-packages/mdtraj/formats/__init__.py:6 2416s /usr/lib/python3/dist-packages/mdtraj/formats/__init__.py:6: DeprecationWarning: 'xdrlib' is deprecated and slated for removal in Python 3.13 2416s from .xtc import XTCTrajectoryFile 2416s 2416s ../../../../usr/lib/python3/dist-packages/mdtraj/geometry/order.py:25 2416s /usr/lib/python3/dist-packages/mdtraj/geometry/order.py:25: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2416s from pkg_resources import parse_version 2416s 2416s ../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871 2416s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('mpl_toolkits')`. 2416s Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages 2416s declare_namespace(pkg) 2416s 2416s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:27 2416s /usr/lib/python3/dist-packages/jupyter_client/connect.py:27: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 2416s given by the platformdirs library. To remove this warning and 2416s see the appropriate new directories, set the environment variable 2416s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 2416s The use of platformdirs will be the default in `jupyter_core` v6 2416s from jupyter_core.paths import jupyter_data_dir 2416s 2416s examples/test_examples.py:26 2416s /tmp/autopkgtest.34lqv9/build.kEU/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 2416s examples = [pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 2416s 2416s tests/test_angles.py::test_angle_pbc_0 2416s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting unitcell_vectors dtype=float64 to 2416s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2416s 2416s tests/test_arc.py::test_read_arctraj 2416s tests/test_order.py::test_nematic_order 2416s tests/test_order.py::test_director 2416s tests/test_order.py::test_inertia 2416s tests/test_order.py::test_nematic_order_args 2416s tests/test_shape.py::test_gyration 2416s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:198: RuntimeWarning: divide by zero encountered in divide 2416s particle_density = traj.top.n_atoms / traj.unitcell_volumes[0] 2416s 2416s tests/test_arc.py: 1 warning 2416s tests/test_gro.py: 3 warnings 2416s tests/test_order.py: 4 warnings 2416s tests/test_pdb.py: 1 warning 2416s tests/test_shape.py: 4 warnings 2416s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:200: UserWarning: Unlikely unit cell vectors detected in PDB file likely resulting from a dummy CRYST1 record. Discarding unit cell vectors. 2416s warnings.warn('Unlikely unit cell vectors detected in PDB file likely ' 2416s 2416s tests/test_arc.py: 1 warning 2416s tests/test_dihedral.py: 1 warning 2416s tests/test_geometry.py: 2 warnings 2416s tests/test_hdf5.py: 1 warning 2416s tests/test_lprmsd.py: 1 warning 2416s tests/test_mdconvert.py: 9 warnings 2416s tests/test_mol2.py: 1 warning 2416s tests/test_nmr.py: 1 warning 2416s tests/test_rmsd.py: 8 warnings 2416s tests/test_rmsd_memmap.py: 2 warnings 2416s tests/test_sasa.py: 3 warnings 2416s tests/test_topology.py: 2 warnings 2416s tests/test_trajectory.py: 85 warnings 2416s /usr/lib/python3/dist-packages/mdtraj/core/trajectory.py:439: UserWarning: top= kwargs ignored since this file parser does not support it 2416s warnings.warn('top= kwargs ignored since this file parser does not support it') 2416s 2416s tests/test_contact.py::test_contact_0 2416s tests/test_contact.py::test_contact_4 2416s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:199: UserWarning: selected topology includes at least one glycine residue, which has no heavy atoms in its sidechain. The distances involving glycine residues will be computed using the sidechain hydrogen instead. 2416s warnings.warn('selected topology includes at least one glycine residue, which has no heavy atoms in its sidechain. The distances involving glycine residues ' 2416s 2416s tests/test_contact.py::test_contact_3 2416s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:227: RuntimeWarning: overflow encountered in exp 2416s np.log(np.sum(np.exp(soft_min_beta/ 2416s 2416s tests/test_contact.py::test_contact_3 2416s /tmp/autopkgtest.34lqv9/build.kEU/src/tests/test_contact.py:106: RuntimeWarning: divide by zero encountered in divide 2416s assert np.allclose(beta / np.log(np.sum(np.exp(beta / maps[t, r0, r1]))), dists[t, i]) 2416s 2416s tests/test_dcd.py::test_do_overwrite 2416s tests/test_dcd.py::test_ragged_1 2416s tests/test_dcd.py::test_ragged_2 2416s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting xyz dtype=float64 to 2416s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2416s 2416s tests/test_distance.py: 6 warnings 2416s tests/test_mdconvert.py: 112 warnings 2416s tests/test_neighbors.py: 2 warnings 2416s tests/test_netcdf.py: 46 warnings 2416s tests/test_rdf.py: 8 warnings 2416s tests/test_restart.py: 4 warnings 2416s tests/test_trajectory.py: 196 warnings 2416s /usr/lib/python3/dist-packages/mdtraj/formats/netcdf.py:130: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. 2416s if StrictVersion(import_('scipy.version').short_version) < StrictVersion('0.12.0'): 2416s 2416s tests/test_drid.py::test_drid_2 2416s /tmp/autopkgtest.34lqv9/build.kEU/src/tests/test_drid.py:61: RuntimeWarning: divide by zero encountered in divide 2416s recip = 1 / squareform(pdist(t.xyz[i])) 2416s 2416s tests/test_geometry.py: 1 warning 2416s tests/test_hoomdxml.py: 1 warning 2416s tests/test_neighbors.py: 2 warnings 2416s tests/test_rdf.py: 38 warnings 2416s tests/test_selection.py: 73 warnings 2416s tests/test_topology.py: 17 warnings 2416s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:385: DeprecationWarning: ast.Num is deprecated and will be removed in Python 3.14; use ast.Constant instead 2416s if isinstance(astnode, ast.Num) or isinstance(astnode, ast.Str): 2416s 2416s tests/test_geometry.py: 2 warnings 2416s tests/test_hoomdxml.py: 1 warning 2416s tests/test_neighbors.py: 2 warnings 2416s tests/test_rdf.py: 38 warnings 2416s tests/test_selection.py: 73 warnings 2416s tests/test_topology.py: 17 warnings 2416s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:385: DeprecationWarning: ast.Str is deprecated and will be removed in Python 3.14; use ast.Constant instead 2416s if isinstance(astnode, ast.Num) or isinstance(astnode, ast.Str): 2416s 2416s tests/test_geometry.py::test_dihedral_indices 2416s tests/test_geometry.py::test_dihedral_indices 2416s /usr/lib/python3/dist-packages/mdtraj/geometry/dihedral.py:203: DeprecationWarning: Passing a Trajectory object to _atom_sequence isdeprecated. Please pass a Topology object 2416s warnings.warn("Passing a Trajectory object to _atom_sequence is" 2416s 2416s tests/test_gro.py::test_load 2416s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq 2416s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:322: UserWarning: WARNING: two consecutive residues with same number (GST, HST) 2416s warnings.warn("WARNING: two consecutive residues with same number (%s, %s)" % (thisresname, old_resname)) 2416s 2416s tests/test_hdf5.py::test_read_0 2416s tests/test_hdf5.py::test_read_slice_0 2416s tests/test_hdf5.py::test_read_slice_2 2416s tests/test_hdf5.py::test_read_slice_3 2416s /usr/lib/python3/dist-packages/tables/path.py:137: NaturalNameWarning: object name is a Python keyword: 'lambda'; you will not be able to use natural naming to access this object; using ``getattr()`` will still work, though 2416s check_attribute_name(name) 2416s 2416s tests/test_rdf.py: 7 warnings 2416s tests/test_selection.py: 14 warnings 2416s tests/test_topology.py: 5 warnings 2416s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:62: DeprecationWarning: ast.NameConstant is deprecated and will be removed in Python 3.14; use ast.Constant instead 2416s return ast.NameConstant(value=_safe_names[node.id], kind=None) 2416s 2416s tests/test_rdf.py: 32 warnings 2416s tests/test_selection.py: 23 warnings 2416s tests/test_topology.py: 12 warnings 2416s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:68: DeprecationWarning: ast.Str is deprecated and will be removed in Python 3.14; use ast.Constant instead 2416s return ast.Str(s=node.id, kind=None) 2416s 2416s tests/test_rdf.py: 32 warnings 2416s tests/test_selection.py: 23 warnings 2416s tests/test_topology.py: 12 warnings 2416s /usr/lib/python3.12/ast.py:587: DeprecationWarning: Attribute s is deprecated and will be removed in Python 3.14; use value instead 2416s return Constant(*args, **kwargs) 2416s 2416s tests/test_restart.py: 1014 warnings 2416s tests/test_trajectory.py: 12 warnings 2416s /usr/lib/python3/dist-packages/mdtraj/formats/amberrst.py:465: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. 2416s if StrictVersion(import_('scipy.version').short_version) < StrictVersion('0.12.0'): 2416s 2416s tests/test_restart.py::test_read_write_1 2416s /usr/lib/python3/dist-packages/mdtraj/formats/amberrst.py:354: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) 2416s time = float(time) 2416s 2416s tests/test_restart.py::test_read_write_2 2416s /usr/lib/python3/dist-packages/mdtraj/formats/amberrst.py:692: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) 2416s time = float(time) 2416s 2416s tests/test_trajectory.py::test_box_load_save[dtr] 2416s tests/test_trajectory.py::test_read_write[dcd-dtr] 2416s tests/test_trajectory.py::test_read_write[lammpstrj-dtr] 2416s tests/test_trajectory.py::test_read_write[pdb-dtr] 2416s tests/test_trajectory.py::test_read_write[pdb.gz-dtr] 2416s tests/test_trajectory.py::test_save_load[dtr] 2416s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting times dtype=int64 to 2416s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2416s 2416s tests/test_trajectory.py::test_write_path[dtr] 2416s tests/test_trajectory.py::test_read_write[h5-dtr] 2416s tests/test_trajectory.py::test_read_write[xtc-dtr] 2416s tests/test_trajectory.py::test_read_write[trr-dtr] 2416s tests/test_trajectory.py::test_read_write[tng-dtr] 2416s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting times dtype=float32 to 2416s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2416s 2416s tests/test_trajectory.py::test_read_write[nc-dtr] 2416s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting times dtype=>f4 to 2416s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2416s 2416s tests/test_trajectory.py::test_float_atom_indices_exception[gro] 2416s /usr/lib/python3/dist-packages/mdtraj/core/topology.py:91: UserWarning: atom_indices are not monotonically increasing 2416s warnings.warn('atom_indices are not monotonically increasing') 2416s 2416s tests/test_trajectory.py::test_array_vs_matrix 2416s /tmp/autopkgtest.34lqv9/build.kEU/src/tests/test_trajectory.py:352: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 2416s xyz_mat = np.matrix(xyz) 2416s 2416s tests/test_utils.py::test_ensure_type_8 2416s tests/test_utils.py::test_ensure_type_9 2416s tests/test_utils.py::test_ensure_type_13 2416s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting dtype=float64 to 2416s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2416s 2416s tests/test_utils.py::test_ensure_type_11 2416s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting dtype=int64 to 2416s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2416s 2416s tests/test_utils.py::test_unit_3 2416s tests/test_utils.py::test_unit_3 2416s /usr/lib/python3/dist-packages/mdtraj/utils/unit/__init__.py:60: DeprecationWarning: ast.Num is deprecated and will be removed in Python 3.14; use ast.Constant instead 2416s if not any(isinstance(node, a) for a in self.allowed_ops): 2416s 2416s examples/test_examples.py::test_example_notebook[two-pass-clustering.ipynb] 2416s /usr/lib/python3/dist-packages/jupyter_client/utils.py:18: DeprecationWarning: There is no current event loop 2416s loop = asyncio.get_event_loop_policy().get_event_loop() 2416s 2416s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 2416s =========================== short test summary info ============================ 2416s SKIPPED [1] tests/test_dihedral.py:48: pymol executable not found 2416s SKIPPED [1] tests/test_dihedral.py:149: pymol executable not found 2416s SKIPPED [16] tests/test_docstrings.py:36: Skip checking certain modules' docstrings 2416s SKIPPED [1] tests/test_dssp.py:44: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 2416s SKIPPED [1] tests/test_dssp.py:52: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 2416s SKIPPED [1] tests/test_dssp.py:59: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 2416s SKIPPED [1] tests/test_geometry.py:243: Not doing performance testing 2416s SKIPPED [1] tests/test_geometry.py:261: Not doing performance testing 2416s SKIPPED [1] tests/test_gsd.py:30: gsd module is not available 2416s SKIPPED [1] tests/test_gsd.py:41: gsd module is not available 2416s SKIPPED [1] tests/test_gsd.py:51: gsd module is not available 2416s SKIPPED [1] tests/test_gsd.py:61: gsd module is not available 2416s SKIPPED [1] tests/test_gsd.py:75: gsd module is not available 2416s SKIPPED [1] tests/test_gsd.py:82: gsd module is not available 2416s SKIPPED [1] tests/test_gsd.py:94: gsd module is not available 2416s SKIPPED [1] tests/test_hbonds.py:43: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 2416s SKIPPED [1] tests/test_hdf5.py:99: requires openmm.units 2416s SKIPPED [1] tests/test_hdf5.py:133: requires openmm.units 2416s SKIPPED [1] tests/test_hdf5.py:186: requires openmm.units 2416s SKIPPED [1] tests/test_mol2.py:55: Requires obabel 2416s SKIPPED [1] tests/test_netcdf.py:248: This test requires cpptraj from AmberTools to be installed (http://ambermd.org) 2416s SKIPPED [1] tests/test_nmr.py:11: SPARTA+ binary not found 2416s SKIPPED [1] tests/test_nmr.py:24: PPM binary not found 2416s SKIPPED [1] tests/test_nmr.py:38: SHIFTX2 binary not found or Python 2 not found or runningn on travis. 2416s SKIPPED [1] tests/test_pdbx.py:39: test_pdbx.py needs OpenMM. 2416s SKIPPED [2] tests/test_psf.py:92: This test requires the VMD executable: http://www.ks.uiuc.edu/Research/vmd/ 2416s SKIPPED [1] tests/test_rdf.py:66: Binning does not match up with gromacs currently. 2416s SKIPPED [1] tests/test_rdf.py:153: Binning does not match up with gromacs currently. 2416s SKIPPED [1] tests/test_reporter.py:47: test_reporter.py needs OpenMM. 2416s SKIPPED [1] tests/test_reporter.py:121: test_reporter.py needs OpenMM. 2416s SKIPPED [1] tests/test_reporter.py:201: test_reporter.py needs OpenMM. 2416s SKIPPED [1] tests/test_thermodynamic_properties.py:154: Thermal expansion test doesn't work. 2416s SKIPPED [1] tests/test_tng.py:20: Fails on macOS + Python 3.11, need to investigate. 2416s SKIPPED [1] tests/test_topology.py:42: needs OpenMM 2416s SKIPPED [1] tests/test_topology.py:59: needs OpenMM 2416s SKIPPED [1] tests/test_topology.py:187: needs OpenMM 2416s SKIPPED [1] tests/test_trajectory.py:128: binpos does not store box information 2416s SKIPPED [1] tests/test_trajectory.py:128: xyz does not store box information 2416s SKIPPED [1] tests/test_trajectory.py:128: xyz.gz does not store box information 2416s SKIPPED [1] tests/test_trajectory.py:128: lh5 does not store box information 2416s SKIPPED [1] tests/test_trajectory.py:128: pdb does not store box information 2416s SKIPPED [1] tests/test_trajectory.py:128: pdb.gz does not store box information 2416s SKIPPED [1] tests/test_trajectory.py:200: mdcrd can only store rectilinear boxes 2416s SKIPPED [1] tests/test_trajectory.py:198: ncrst can only store 1 frame per file 2416s SKIPPED [1] tests/test_trajectory.py:198: rst7 can only store 1 frame per file 2416s SKIPPED [16] tests/test_trajectory.py:212: mdcrd can only store rectilinear boxes 2416s SKIPPED [16] tests/test_trajectory.py:210: ncrst can only store 1 frame per file 2416s SKIPPED [16] tests/test_trajectory.py:210: rst7 can only store 1 frame per file 2416s SKIPPED [5] tests/test_trajectory.py:219: dtr needs to write unitcells 2416s SKIPPED [5] tests/test_trajectory.py:219: lammpstrj needs to write unitcells 2416s SKIPPED [2] tests/test_trajectory.py:541: Only 1 frame per file format 2416s SKIPPED [1] examples/test_examples.py:71: Openmm required for example notebook `simulation-with-openmm.ipynb` 2416s SKIPPED [2] examples/test_examples.py:71: Network access required 2416s XFAIL tests/test_trajectory.py::test_read_path[ncrst] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_path[rst7] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[ncrst-nc] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[ncrst-h5] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xtc] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[ncrst-trr] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dcd] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[ncrst-mdcrd] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[ncrst-binpos] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dtr] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[ncrst-tng] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lh5] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[ncrst-ncrst] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[ncrst-rst7] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[ncrst-gro] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[rst7-nc] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[rst7-h5] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[rst7-xtc] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[rst7-trr] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[rst7-dcd] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[rst7-mdcrd] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[rst7-binpos] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[rst7-dtr] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz.gz] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[rst7-lammpstrj] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[rst7-tng] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[rst7-lh5] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb.gz] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[rst7-ncrst] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[rst7-rst7] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_read_write[rst7-gro] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_load[ncrst] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_load[rst7] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[rst7] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_load_combination[ncrst] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_load_combination[rst7] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_seek_read_mode[xyz.gz] - reason: This is broken 2416s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb] - reason: PDB Files don't support seeking 2416s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb.gz] - reason: PDB Files don't support seeking 2416s XFAIL tests/test_trajectory.py::test_seek_read_mode[ncrst] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_seek_read_mode[rst7] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_seek_read_mode[gro] - reason: This is broken 2416s XFAIL tests/test_trajectory.py::test_load_frame[dtr] - reason: DTR doesn't load a single frame properly 2416s XFAIL tests/test_trajectory.py::test_load_frame[ncrst] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_load_frame[rst7] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_load_frame[gro] - reason: Gro doesn't implement seek 2416s XFAIL tests/test_trajectory.py::test_iterload[dtr] - reason: This is broken with dtr 2416s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb] - reason: PDB Iterloads an extra frame!! 2416s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb.gz] - reason: PDB Iterloads an extra frame!! 2416s XFAIL tests/test_trajectory.py::test_iterload_skip[ncrst] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_iterload_skip[rst7] - reason: These reference files don't exist yet 2416s XFAIL tests/test_trajectory.py::test_iterload_skip[gro] - reason: Not implemented for some reason 2416s XFAIL tests/test_trajectory.py::test_force_overwrite[dtr] - reason: This is broken with dtr 2416s XFAIL tests/test_trajectory.py::test_unitcell[dtr] - reason: dtr seems to need unit vectors 2416s XFAIL tests/test_trajectory.py::test_unitcell[lammpstrj] - reason: lammpstrj seems to need unit vectors 2416s XFAIL tests/test_trajectory.py::test_unitcell[ncrst] - reason: ncrst seems to need unit vectors 2416s XFAIL tests/test_trajectory.py::test_unitcell[rst7] - reason: rst7 seems to need unit vectors 2416s = 1030 passed, 124 skipped, 2 deselected, 65 xfailed, 2007 warnings in 2074.11s (0:34:34) = 2417s autopkgtest [17:47:03]: test command1: -----------------------] 2418s autopkgtest [17:47:04]: test command1: - - - - - - - - - - results - - - - - - - - - - 2418s command1 PASS 2418s autopkgtest [17:47:04]: @@@@@@@@@@@@@@@@@@@@ summary 2418s command1 PASS 2490s nova [W] Skipping flock for amd64 2490s Creating nova instance adt-oracular-amd64-mdtraj-20240712-170645-juju-7f2275-prod-proposed-migration-environment-2-948a4456-bdf2-46db-81ab-82e8a8c9b326 from image adt/ubuntu-oracular-amd64-server-20240711.img (UUID 4d65b1cc-a829-44fc-a8ac-cdd52093f9db)...