0s autopkgtest [12:20:48]: starting date and time: 2026-01-23 12:20:48+0000 0s autopkgtest [12:20:48]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [12:20:48]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.u4oq5f87/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade propka --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.14.2-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-s390x-18.secgroup --name adt-resolute-s390x-propka-20260123-122047-juju-7f2275-prod-proposed-migration-environment-15-03eb50cb-be21-4741-b3fb-f09ad0e70073 --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-s390x-propka-20260123-122047-juju-7f2275-prod-proposed-migration-environment-15-03eb50cb-be21-4741-b3fb-f09ad0e70073 from image adt/ubuntu-resolute-s390x-server-20260123.img (UUID 5f2e306c-5dfc-4ef6-8be2-414f657c7562)... 88s autopkgtest [12:22:16]: testbed dpkg architecture: s390x 88s autopkgtest [12:22:16]: testbed apt version: 3.1.13 88s autopkgtest [12:22:16]: @@@@@@@@@@@@@@@@@@@@ test bed setup 88s autopkgtest [12:22:16]: testbed release detected to be: None 89s autopkgtest [12:22:17]: updating testbed package index (apt update) 89s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 89s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 89s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 89s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 89s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 89s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.6 kB] 89s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1016 kB] 90s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [92.8 kB] 90s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [115 kB] 90s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [826 kB] 90s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [9152 B] 91s Fetched 2210 kB in 2s (1318 kB/s) 94s Reading package lists... 121s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 121s dpkg-preconfigure: unable to re-open stdin: No such file or directory 121s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 121s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 121s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 121s Reading package lists... 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Calculating upgrade... 121s The following packages were automatically installed and are no longer required: 121s python3.13 python3.13-minimal 121s Use 'sudo apt autoremove' to remove them. 121s The following NEW packages will be installed: 121s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 121s The following packages will be upgraded: 121s libpython3-stdlib python3 python3-gdbm python3-minimal 121s 4 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 121s Need to get 6689 kB of archives. 121s After this operation, 24.3 MB of additional disk space will be used. 121s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-minimal s390x 3.14.2-1 [917 kB] 121s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14-minimal s390x 3.14.2-1 [2510 kB] 121s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-minimal s390x 3.14.2-1 [28.2 kB] 121s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3 s390x 3.14.2-1 [22.9 kB] 121s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-stdlib s390x 3.14.2-1 [2373 kB] 121s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14 s390x 3.14.2-1 [816 kB] 121s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x libpython3-stdlib s390x 3.14.2-1 [10.9 kB] 121s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-gdbm s390x 3.14.2-1 [11.1 kB] 121s Fetched 6689 kB in 2s (2951 kB/s) 121s Selecting previously unselected package libpython3.14-minimal:s390x. 121s (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 ... 87685 files and directories currently installed.) 121s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_s390x.deb ... 121s Unpacking libpython3.14-minimal:s390x (3.14.2-1) ... 121s Selecting previously unselected package python3.14-minimal. 121s Preparing to unpack .../python3.14-minimal_3.14.2-1_s390x.deb ... 121s Unpacking python3.14-minimal (3.14.2-1) ... 121s Setting up libpython3.14-minimal:s390x (3.14.2-1) ... 121s Setting up python3.14-minimal (3.14.2-1) ... 121s (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 ... 88027 files and directories currently installed.) 121s Preparing to unpack .../python3-minimal_3.14.2-1_s390x.deb ... 121s Unpacking python3-minimal (3.14.2-1) over (3.13.9-3) ... 121s Setting up python3-minimal (3.14.2-1) ... 121s (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 ... 88027 files and directories currently installed.) 121s Preparing to unpack .../python3_3.14.2-1_s390x.deb ... 121s running python pre-rtupdate hooks for python3.14... 121s Unpacking python3 (3.14.2-1) over (3.13.9-3) ... 121s Selecting previously unselected package libpython3.14-stdlib:s390x. 121s Preparing to unpack .../libpython3.14-stdlib_3.14.2-1_s390x.deb ... 121s Unpacking libpython3.14-stdlib:s390x (3.14.2-1) ... 121s Selecting previously unselected package python3.14. 121s Preparing to unpack .../python3.14_3.14.2-1_s390x.deb ... 121s Unpacking python3.14 (3.14.2-1) ... 121s Preparing to unpack .../libpython3-stdlib_3.14.2-1_s390x.deb ... 121s Unpacking libpython3-stdlib:s390x (3.14.2-1) over (3.13.9-3) ... 121s Preparing to unpack .../python3-gdbm_3.14.2-1_s390x.deb ... 121s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-3) ... 121s Setting up libpython3.14-stdlib:s390x (3.14.2-1) ... 121s Setting up python3.14 (3.14.2-1) ... 121s Setting up libpython3-stdlib:s390x (3.14.2-1) ... 121s Setting up python3-gdbm (3.14.2-1) ... 121s Setting up python3 (3.14.2-1) ... 121s running python rtupdate hooks for python3.14... 121s running python post-rtupdate hooks for python3.14... 121s Processing triggers for man-db (2.13.1-1) ... 121s Processing triggers for systemd (259-1ubuntu2) ... 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Calculating upgrade... 121s The following packages were automatically installed and are no longer required: 121s python3.13 python3.13-minimal 121s Use 'sudo apt autoremove' to remove them. 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Solving dependencies... 121s The following packages will be REMOVED: 121s python3.13* python3.13-minimal* 121s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 121s After this operation, 8012 kB disk space will be freed. 121s (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 ... 88457 files and directories currently installed.) 121s Removing python3.13 (3.13.11-1) ... 121s Removing python3.13-minimal (3.13.11-1) ... 121s autopkgtest [12:22:45]: upgrading testbed (apt dist-upgrade and autopurge) 122s Processing triggers for man-db (2.13.1-1) ... 123s Processing triggers for systemd (259-1ubuntu2) ... 123s (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 ... 88430 files and directories currently installed.) 123s Purging configuration files for python3.13-minimal (3.13.11-1) ... 126s autopkgtest [12:22:54]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP Mon Jan 12 15:39:23 UTC 2026 126s autopkgtest [12:22:54]: @@@@@@@@@@@@@@@@@@@@ apt-source propka 127s Get:1 http://ftpmaster.internal/ubuntu resolute/universe propka 3.5.1-2 (dsc) [2286 B] 127s Get:2 http://ftpmaster.internal/ubuntu resolute/universe propka 3.5.1-2 (tar) [376 kB] 127s Get:3 http://ftpmaster.internal/ubuntu resolute/universe propka 3.5.1-2 (diff) [5096 B] 128s gpgv: Signature made Wed Oct 16 14:47:53 2024 UTC 128s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 128s gpgv: issuer "emollier@debian.org" 128s gpgv: Can't check signature: No public key 128s dpkg-source: warning: cannot verify inline signature for ./propka_3.5.1-2.dsc: no acceptable signature found 128s autopkgtest [12:22:56]: testing package propka version 3.5.1-2 128s autopkgtest [12:22:56]: build not needed 128s autopkgtest [12:22:56]: test pybuild-autopkgtest: preparing testbed 128s Reading package lists... 129s Building dependency tree... 129s Reading state information... 130s Solving dependencies... 130s The following NEW packages will be installed: 130s autoconf automake autopoint autotools-dev build-essential cpp cpp-15 130s cpp-15-s390x-linux-gnu cpp-s390x-linux-gnu debhelper debugedit dh-autoreconf 130s dh-python dh-strip-nondeterminism docutils-common dwz fonts-font-awesome 130s fonts-lato fonts-mathjax g++ g++-15 g++-15-s390x-linux-gnu 130s g++-s390x-linux-gnu gcc gcc-15 gcc-15-s390x-linux-gnu gcc-s390x-linux-gnu 130s gettext help2man intltool-debian libarchive-zip-perl libasan8 libblas3 130s libcc1-0 libdebhelper-perl libfile-stripnondeterminism-perl libgcc-15-dev 130s libgfortran5 libgomp1 libisl23 libitm1 libjs-jquery libjs-mathjax 130s libjson-perl liblapack3 libmpc3 libstdc++-15-dev libtool libubsan1 m4 130s po-debconf pybuild-plugin-autopkgtest python-propka-doc python3-alabaster 130s python3-all python3-defusedxml python3-docutils python3-imagesize 130s python3-iniconfig python3-numpy python3-numpy-dev python3-pluggy 130s python3-propka python3-pytest python3-roman-numerals python3-snowballstemmer 130s python3-sphinx python3-sphinx-rtd-theme python3-sphinxcontrib.jquery 130s python3.13 python3.13-minimal sgml-base sphinx-common 130s sphinx-rtd-theme-common xml-core 130s 0 upgraded, 75 newly installed, 0 to remove and 0 not upgraded. 130s Need to get 84.1 MB of archives. 130s After this operation, 310 MB of additional disk space will be used. 130s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3.13-minimal s390x 3.13.11-1 [2405 kB] 131s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-lato all 2.015-1build1 [2779 kB] 131s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.3.5+ds-3 [146 kB] 131s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-7ubuntu1 [255 kB] 131s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-11ubuntu1 [629 kB] 131s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-7ubuntu1 [2983 kB] 131s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.3.5+ds-3 [5305 kB] 131s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x python3.13 s390x 3.13.11-1 [758 kB] 131s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x m4 s390x 1.4.20-2 [223 kB] 131s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x autoconf all 2.72-3.1ubuntu1 [384 kB] 131s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x autotools-dev all 20240727.1 [43.4 kB] 131s Get:12 http://ftpmaster.internal/ubuntu resolute/main s390x automake all 1:1.18.1-3build1 [582 kB] 131s Get:13 http://ftpmaster.internal/ubuntu resolute/main s390x autopoint all 0.23.2-1 [620 kB] 131s Get:14 http://ftpmaster.internal/ubuntu resolute/main s390x libisl23 s390x 0.27-1build1 [702 kB] 131s Get:15 http://ftpmaster.internal/ubuntu resolute/main s390x libmpc3 s390x 1.3.1-2 [57.4 kB] 131s Get:16 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-15-s390x-linux-gnu s390x 15.2.0-11ubuntu1 [10.2 MB] 131s Get:17 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-15 s390x 15.2.0-11ubuntu1 [1028 B] 131s Get:18 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [5746 B] 131s Get:19 http://ftpmaster.internal/ubuntu resolute/main s390x cpp s390x 4:15.2.0-4ubuntu1 [22.4 kB] 131s Get:20 http://ftpmaster.internal/ubuntu resolute/main s390x libcc1-0 s390x 15.2.0-11ubuntu1 [50.0 kB] 131s Get:21 http://ftpmaster.internal/ubuntu resolute/main s390x libgomp1 s390x 15.2.0-11ubuntu1 [154 kB] 131s Get:22 http://ftpmaster.internal/ubuntu resolute/main s390x libitm1 s390x 15.2.0-11ubuntu1 [30.9 kB] 131s Get:23 http://ftpmaster.internal/ubuntu resolute/main s390x libasan8 s390x 15.2.0-11ubuntu1 [2968 kB] 131s Get:24 http://ftpmaster.internal/ubuntu resolute/main s390x libubsan1 s390x 15.2.0-11ubuntu1 [1211 kB] 131s Get:25 http://ftpmaster.internal/ubuntu resolute/main s390x libgcc-15-dev s390x 15.2.0-11ubuntu1 [1045 kB] 132s Get:26 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15-s390x-linux-gnu s390x 15.2.0-11ubuntu1 [19.9 MB] 132s Get:27 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15 s390x 15.2.0-11ubuntu1 [517 kB] 132s Get:28 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [1208 B] 132s Get:29 http://ftpmaster.internal/ubuntu resolute/main s390x gcc s390x 4:15.2.0-4ubuntu1 [5018 B] 132s Get:30 http://ftpmaster.internal/ubuntu resolute/main s390x libstdc++-15-dev s390x 15.2.0-11ubuntu1 [2660 kB] 132s Get:31 http://ftpmaster.internal/ubuntu resolute/main s390x g++-15-s390x-linux-gnu s390x 15.2.0-11ubuntu1 [11.7 MB] 132s Get:32 http://ftpmaster.internal/ubuntu resolute/main s390x g++-15 s390x 15.2.0-11ubuntu1 [24.6 kB] 132s Get:33 http://ftpmaster.internal/ubuntu resolute/main s390x g++-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [956 B] 132s Get:34 http://ftpmaster.internal/ubuntu resolute/main s390x g++ s390x 4:15.2.0-4ubuntu1 [1078 B] 132s Get:35 http://ftpmaster.internal/ubuntu resolute/main s390x build-essential s390x 12.12ubuntu2 [5258 B] 132s Get:36 http://ftpmaster.internal/ubuntu resolute/main s390x libdebhelper-perl all 13.28ubuntu1 [97.4 kB] 132s Get:37 http://ftpmaster.internal/ubuntu resolute/main s390x libtool all 2.5.4-9 [169 kB] 132s Get:38 http://ftpmaster.internal/ubuntu resolute/main s390x dh-autoreconf all 21 [12.5 kB] 132s Get:39 http://ftpmaster.internal/ubuntu resolute/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] 132s Get:40 http://ftpmaster.internal/ubuntu resolute/main s390x libfile-stripnondeterminism-perl all 1.15.0-1build1 [20.6 kB] 132s Get:41 http://ftpmaster.internal/ubuntu resolute/main s390x dh-strip-nondeterminism all 1.15.0-1build1 [5110 B] 132s Get:42 http://ftpmaster.internal/ubuntu resolute/main s390x debugedit s390x 1:5.2-3 [52.8 kB] 132s Get:43 http://ftpmaster.internal/ubuntu resolute/main s390x dwz s390x 0.16-2 [121 kB] 132s Get:44 http://ftpmaster.internal/ubuntu resolute/main s390x gettext s390x 0.23.2-1 [1062 kB] 132s Get:45 http://ftpmaster.internal/ubuntu resolute/main s390x intltool-debian all 0.35.0+20060710.6build1 [24.1 kB] 132s Get:46 http://ftpmaster.internal/ubuntu resolute/main s390x po-debconf all 1.0.22 [215 kB] 132s Get:47 http://ftpmaster.internal/ubuntu resolute/main s390x debhelper all 13.28ubuntu1 [916 kB] 132s Get:48 http://ftpmaster.internal/ubuntu resolute/universe s390x dh-python all 7.20251231 [122 kB] 132s Get:49 http://ftpmaster.internal/ubuntu resolute/main s390x sgml-base all 1.31+nmu1 [11.0 kB] 132s Get:50 http://ftpmaster.internal/ubuntu resolute/main s390x xml-core all 0.19build1 [20.3 kB] 132s Get:51 http://ftpmaster.internal/ubuntu resolute/main s390x docutils-common all 0.22.4+dfsg-1 [130 kB] 133s Get:52 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1build1 [531 kB] 133s Get:53 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 133s Get:54 http://ftpmaster.internal/ubuntu resolute/universe s390x help2man s390x 1.49.3 [201 kB] 133s Get:55 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 133s Get:56 http://ftpmaster.internal/ubuntu resolute/main s390x libjson-perl all 4.10000-1 [81.9 kB] 133s Get:57 http://ftpmaster.internal/ubuntu resolute/universe s390x pybuild-plugin-autopkgtest all 7.20251231 [1748 B] 133s Get:58 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 133s Get:59 http://ftpmaster.internal/ubuntu resolute/main s390x sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 133s Get:60 http://ftpmaster.internal/ubuntu resolute/universe s390x python-propka-doc all 3.5.1-2 [157 kB] 133s Get:61 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-all s390x 3.14.2-1 [890 B] 133s Get:62 http://ftpmaster.internal/ubuntu resolute/main s390x python3-defusedxml all 0.7.1-3build1 [42.4 kB] 133s Get:63 http://ftpmaster.internal/ubuntu resolute/main s390x python3-roman-numerals all 4.1.0-1 [8660 B] 133s Get:64 http://ftpmaster.internal/ubuntu resolute/main s390x python3-docutils all 0.22.4+dfsg-1 [439 kB] 133s Get:65 http://ftpmaster.internal/ubuntu resolute/main s390x python3-imagesize all 1.4.1-1build1 [6900 B] 133s Get:66 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-iniconfig all 2.1.0-2 [6962 B] 133s Get:67 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pluggy all 1.6.0-2 [21.1 kB] 133s Get:68 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-propka all 3.5.1-2 [70.1 kB] 133s Get:69 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pytest all 9.0.2-2 [277 kB] 133s Get:70 http://ftpmaster.internal/ubuntu resolute/main s390x python3-snowballstemmer all 3.0.1-1 [65.9 kB] 133s Get:71 http://ftpmaster.internal/ubuntu resolute/main s390x sphinx-common all 8.2.3-12 [657 kB] 133s Get:72 http://ftpmaster.internal/ubuntu resolute/main s390x python3-alabaster all 0.7.16-0.1build1 [18.6 kB] 133s Get:73 http://ftpmaster.internal/ubuntu resolute/main s390x python3-sphinx all 8.2.3-12 [483 kB] 133s Get:74 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-sphinxcontrib.jquery all 4.1-6 [6856 B] 133s Get:75 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-sphinx-rtd-theme all 3.0.2+dfsg-3 [23.5 kB] 135s Fetched 84.1 MB in 3s (33.1 MB/s) 135s Selecting previously unselected package python3.13-minimal. 135s (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 ... 88432 files and directories currently installed.) 135s Preparing to unpack .../00-python3.13-minimal_3.13.11-1_s390x.deb ... 135s Unpacking python3.13-minimal (3.13.11-1) ... 135s Selecting previously unselected package fonts-lato. 135s Preparing to unpack .../01-fonts-lato_2.015-1build1_all.deb ... 135s Unpacking fonts-lato (2.015-1build1) ... 136s Selecting previously unselected package python3-numpy-dev:s390x. 136s Preparing to unpack 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up debugedit (1:5.2-3) ... 159s Setting up python3-roman-numerals (4.1.0-1) ... 159s Setting up python3.13-minimal (3.13.11-1) ... 162s Setting up sgml-base (1.31+nmu1) ... 162s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 162s Setting up libisl23:s390x (0.27-1build1) ... 162s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ... 162s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 162s Setting up libcc1-0:s390x (15.2.0-11ubuntu1) ... 162s Setting up libitm1:s390x (15.2.0-11ubuntu1) ... 162s Setting up python3-imagesize (1.4.1-1build1) ... 162s Setting up automake (1:1.18.1-3build1) ... 162s update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode 162s Setting up libfile-stripnondeterminism-perl (1.15.0-1build1) ... 162s Setting up liblapack3:s390x (3.12.1-7ubuntu1) ... 162s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 162s Setting up gettext (0.23.2-1) ... 162s Setting up libgcc-15-dev:s390x (15.2.0-11ubuntu1) ... 162s Setting up python3.13 (3.13.11-1) ... 166s Setting up python3-pytest (9.0.2-2) ... 169s Setting up python3-all (3.14.2-1) ... 169s Setting up intltool-debian (0.35.0+20060710.6build1) ... 169s Setting up libstdc++-15-dev:s390x (15.2.0-11ubuntu1) ... 169s Setting up sphinx-common (8.2.3-12) ... 169s Setting up python3-numpy (1:2.3.5+ds-3) ... 185s Setting up dh-strip-nondeterminism (1.15.0-1build1) ... 185s Setting up python-propka-doc (3.5.1-2) ... 185s Setting up xml-core (0.19build1) ... 186s Setting up cpp-15-s390x-linux-gnu (15.2.0-11ubuntu1) ... 186s Setting up gcc-15-s390x-linux-gnu (15.2.0-11ubuntu1) ... 186s Setting up g++-15-s390x-linux-gnu (15.2.0-11ubuntu1) ... 186s Setting up cpp-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 186s Setting up po-debconf (1.0.22) ... 186s Setting up gcc-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 186s Setting up cpp-15 (15.2.0-11ubuntu1) ... 186s Setting up cpp (4:15.2.0-4ubuntu1) ... 186s Setting up g++-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 186s Setting up gcc-15 (15.2.0-11ubuntu1) ... 186s Setting up g++-15 (15.2.0-11ubuntu1) ... 186s Setting up libtool (2.5.4-9) ... 186s Setting up gcc (4:15.2.0-4ubuntu1) ... 186s Setting up dh-autoreconf (21) ... 186s Setting up g++ (4:15.2.0-4ubuntu1) ... 186s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 186s Setting up build-essential (12.12ubuntu2) ... 186s Setting up debhelper (13.28ubuntu1) ... 186s Setting up pybuild-plugin-autopkgtest (7.20251231) ... 186s Processing triggers for install-info (7.2-5) ... 187s Processing triggers for libc-bin (2.42-2ubuntu4) ... 187s Processing triggers for systemd (259-1ubuntu2) ... 187s Processing triggers for man-db (2.13.1-1) ... 190s Processing triggers for sgml-base (1.31+nmu1) ... 190s Setting up docutils-common (0.22.4+dfsg-1) ... 190s Processing triggers for sgml-base (1.31+nmu1) ... 190s Setting up python3-docutils (0.22.4+dfsg-1) ... 191s Setting up python3-sphinx (8.2.3-12) ... 196s Setting up python3-sphinxcontrib.jquery (4.1-6) ... 197s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-3) ... 198s autopkgtest [12:24:06]: test pybuild-autopkgtest: pybuild-autopkgtest 198s autopkgtest [12:24:06]: test pybuild-autopkgtest: [----------------------- 199s pybuild-autopkgtest 199s I: pybuild base:384: cd /tmp/autopkgtest.QjIrgy/autopkgtest_tmp/build; python3.13 -m pytest -k 'not test_molecular_container' 200s ============================= test session starts ============================== 200s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 200s rootdir: /tmp/autopkgtest.QjIrgy/autopkgtest_tmp/build 200s plugins: typeguard-4.4.4 200s collected 49 items / 2 deselected / 47 selected 200s 211s tests/test_basic_regression.py ....... [ 14%] 211s tests/test_hybrid36.py .. [ 19%] 211s tests/test_input.py .. [ 23%] 211s tests/test_lib.py .. [ 27%] 211s tests/test_protonate.py . [ 29%] 219s tests/test_run.py ........ [ 46%] 223s tests/test_streamio.py ........ [ 63%] 223s tests/test_vector_algebra.py ............... [ 95%] 223s tests/test_version.py .. [100%] 223s 223s ====================== 47 passed, 2 deselected in 23.06s ======================= 223s I: pybuild base:384: cd /tmp/autopkgtest.QjIrgy/autopkgtest_tmp/build; python3.14 -m pytest -k 'not test_molecular_container' 225s ============================= test session starts ============================== 225s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 225s rootdir: /tmp/autopkgtest.QjIrgy/autopkgtest_tmp/build 225s plugins: typeguard-4.4.4 225s collected 49 items / 2 deselected / 47 selected 225s 226s tests/test_basic_regression.py FFFFFFF [ 14%] 226s tests/test_hybrid36.py .. [ 19%] 226s tests/test_input.py .. [ 23%] 226s tests/test_lib.py .. [ 27%] 226s tests/test_protonate.py . [ 29%] 226s tests/test_run.py FFFFFFFF [ 46%] 227s tests/test_streamio.py FFFFFFFF [ 63%] 227s tests/test_vector_algebra.py ............... [ 95%] 227s tests/test_version.py .. [100%] 227s 227s =================================== FAILURES =================================== 227s ________________ test_regression[sample-issue-140: no options] _________________ 227s 227s pdb = 'sample-issue-140' 227s options = ['/tmp/autopkgtest.QjIrgy/autopkgtest_tmp/build/tests/pdb/sample-issue-140.pdb'] 227s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_sample_issue_10') 227s 227s @pytest.mark.parametrize("pdb, options", [ 227s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 227s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 227s pytest.param('1HPX', [], id="1HPX: no options"), 227s pytest.param('4DFR', [], id="4DFR: no options"), 227s pytest.param('3SGB', [], id="3SGB: no options"), 227s pytest.param('3SGB-subset', [ 227s "--titrate_only", 227s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 227s id="3SGB: --titrate_only"), 227s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 227s def test_regression(pdb, options, tmp_path): 227s """Basic regression test of PROPKA functionality.""" 227s path_dict = get_test_dirs() 227s ref_path = None 227s 227s for ext in ["json", "dat"]: 227s ref_path = path_dict["results"] / f"{pdb}.{ext}" 227s if ref_path.is_file(): 227s ref_path = ref_path.resolve() 227s break 227s else: 227s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 227s str(ref_path))) 227s ref_path = None 227s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 227s if pdb_path.is_file(): 227s pdb_path = pdb_path.resolve() 227s else: 227s errstr = "Missing PDB file: {0:s}".format(pdb_path) 227s raise FileNotFoundError(errstr) 227s tmp_path = Path(tmp_path).resolve() 227s 227s > run_propka(options, pdb_path, tmp_path) 227s 227s tests/test_basic_regression.py:170: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s tests/test_basic_regression.py:77: in run_propka 227s parameters = read_parameter_file(args.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s ------------------------------ Captured log call ------------------------------- 227s WARNING tests.test_basic_regression:test_basic_regression.py:73 Working in tmpdir /tmp/pytest-of-ubuntu/pytest-1/test_regression_sample_issue_10 because of PROPKA file output; need to fix this. 227s __________________ test_regression[1FTJ-Chain-A: no options] ___________________ 227s 227s pdb = '1FTJ-Chain-A' 227s options = ['/tmp/autopkgtest.QjIrgy/autopkgtest_tmp/build/tests/pdb/1FTJ-Chain-A.pdb'] 227s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_1FTJ_Chain_A__0') 227s 227s @pytest.mark.parametrize("pdb, options", [ 227s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 227s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 227s pytest.param('1HPX', [], id="1HPX: no options"), 227s pytest.param('4DFR', [], id="4DFR: no options"), 227s pytest.param('3SGB', [], id="3SGB: no options"), 227s pytest.param('3SGB-subset', [ 227s "--titrate_only", 227s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 227s id="3SGB: --titrate_only"), 227s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 227s def test_regression(pdb, options, tmp_path): 227s """Basic regression test of PROPKA functionality.""" 227s path_dict = get_test_dirs() 227s ref_path = None 227s 227s for ext in ["json", "dat"]: 227s ref_path = path_dict["results"] / f"{pdb}.{ext}" 227s if ref_path.is_file(): 227s ref_path = ref_path.resolve() 227s break 227s else: 227s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 227s str(ref_path))) 227s ref_path = None 227s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 227s if pdb_path.is_file(): 227s pdb_path = pdb_path.resolve() 227s else: 227s errstr = "Missing PDB file: {0:s}".format(pdb_path) 227s raise FileNotFoundError(errstr) 227s tmp_path = Path(tmp_path).resolve() 227s 227s > run_propka(options, pdb_path, tmp_path) 227s 227s tests/test_basic_regression.py:170: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s tests/test_basic_regression.py:77: in run_propka 227s parameters = read_parameter_file(args.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s ------------------------------ Captured log call ------------------------------- 227s WARNING tests.test_basic_regression:test_basic_regression.py:73 Working in tmpdir /tmp/pytest-of-ubuntu/pytest-1/test_regression_1FTJ_Chain_A__0 because of PROPKA file output; need to fix this. 227s ______________________ test_regression[1HPX: no options] _______________________ 227s 227s pdb = '1HPX' 227s options = ['/tmp/autopkgtest.QjIrgy/autopkgtest_tmp/build/tests/pdb/1HPX.pdb'] 227s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_1HPX__no_optio0') 227s 227s @pytest.mark.parametrize("pdb, options", [ 227s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 227s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 227s pytest.param('1HPX', [], id="1HPX: no options"), 227s pytest.param('4DFR', [], id="4DFR: no options"), 227s pytest.param('3SGB', [], id="3SGB: no options"), 227s pytest.param('3SGB-subset', [ 227s "--titrate_only", 227s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 227s id="3SGB: --titrate_only"), 227s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 227s def test_regression(pdb, options, tmp_path): 227s """Basic regression test of PROPKA functionality.""" 227s path_dict = get_test_dirs() 227s ref_path = None 227s 227s for ext in ["json", "dat"]: 227s ref_path = path_dict["results"] / f"{pdb}.{ext}" 227s if ref_path.is_file(): 227s ref_path = ref_path.resolve() 227s break 227s else: 227s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 227s str(ref_path))) 227s ref_path = None 227s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 227s if pdb_path.is_file(): 227s pdb_path = pdb_path.resolve() 227s else: 227s errstr = "Missing PDB file: {0:s}".format(pdb_path) 227s raise FileNotFoundError(errstr) 227s tmp_path = Path(tmp_path).resolve() 227s 227s > run_propka(options, pdb_path, tmp_path) 227s 227s tests/test_basic_regression.py:170: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s tests/test_basic_regression.py:77: in run_propka 227s parameters = read_parameter_file(args.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s ------------------------------ Captured log call ------------------------------- 227s WARNING tests.test_basic_regression:test_basic_regression.py:73 Working in tmpdir /tmp/pytest-of-ubuntu/pytest-1/test_regression_1HPX__no_optio0 because of PROPKA file output; need to fix this. 227s ______________________ test_regression[4DFR: no options] _______________________ 227s 227s pdb = '4DFR' 227s options = ['/tmp/autopkgtest.QjIrgy/autopkgtest_tmp/build/tests/pdb/4DFR.pdb'] 227s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_4DFR__no_optio0') 227s 227s @pytest.mark.parametrize("pdb, options", [ 227s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 227s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 227s pytest.param('1HPX', [], id="1HPX: no options"), 227s pytest.param('4DFR', [], id="4DFR: no options"), 227s pytest.param('3SGB', [], id="3SGB: no options"), 227s pytest.param('3SGB-subset', [ 227s "--titrate_only", 227s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 227s id="3SGB: --titrate_only"), 227s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 227s def test_regression(pdb, options, tmp_path): 227s """Basic regression test of PROPKA functionality.""" 227s path_dict = get_test_dirs() 227s ref_path = None 227s 227s for ext in ["json", "dat"]: 227s ref_path = path_dict["results"] / f"{pdb}.{ext}" 227s if ref_path.is_file(): 227s ref_path = ref_path.resolve() 227s break 227s else: 227s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 227s str(ref_path))) 227s ref_path = None 227s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 227s if pdb_path.is_file(): 227s pdb_path = pdb_path.resolve() 227s else: 227s errstr = "Missing PDB file: {0:s}".format(pdb_path) 227s raise FileNotFoundError(errstr) 227s tmp_path = Path(tmp_path).resolve() 227s 227s > run_propka(options, pdb_path, tmp_path) 227s 227s tests/test_basic_regression.py:170: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s tests/test_basic_regression.py:77: in run_propka 227s parameters = read_parameter_file(args.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s ------------------------------ Captured log call ------------------------------- 227s WARNING tests.test_basic_regression:test_basic_regression.py:73 Working in tmpdir /tmp/pytest-of-ubuntu/pytest-1/test_regression_4DFR__no_optio0 because of PROPKA file output; need to fix this. 227s ______________________ test_regression[3SGB: no options] _______________________ 227s 227s pdb = '3SGB' 227s options = ['/tmp/autopkgtest.QjIrgy/autopkgtest_tmp/build/tests/pdb/3SGB.pdb'] 227s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_3SGB__no_optio0') 227s 227s @pytest.mark.parametrize("pdb, options", [ 227s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 227s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 227s pytest.param('1HPX', [], id="1HPX: no options"), 227s pytest.param('4DFR', [], id="4DFR: no options"), 227s pytest.param('3SGB', [], id="3SGB: no options"), 227s pytest.param('3SGB-subset', [ 227s "--titrate_only", 227s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 227s id="3SGB: --titrate_only"), 227s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 227s def test_regression(pdb, options, tmp_path): 227s """Basic regression test of PROPKA functionality.""" 227s path_dict = get_test_dirs() 227s ref_path = None 227s 227s for ext in ["json", "dat"]: 227s ref_path = path_dict["results"] / f"{pdb}.{ext}" 227s if ref_path.is_file(): 227s ref_path = ref_path.resolve() 227s break 227s else: 227s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 227s str(ref_path))) 227s ref_path = None 227s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 227s if pdb_path.is_file(): 227s pdb_path = pdb_path.resolve() 227s else: 227s errstr = "Missing PDB file: {0:s}".format(pdb_path) 227s raise FileNotFoundError(errstr) 227s tmp_path = Path(tmp_path).resolve() 227s 227s > run_propka(options, pdb_path, tmp_path) 227s 227s tests/test_basic_regression.py:170: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s tests/test_basic_regression.py:77: in run_propka 227s parameters = read_parameter_file(args.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s ------------------------------ Captured log call ------------------------------- 227s WARNING tests.test_basic_regression:test_basic_regression.py:73 Working in tmpdir /tmp/pytest-of-ubuntu/pytest-1/test_regression_3SGB__no_optio0 because of PROPKA file output; need to fix this. 227s ____________________ test_regression[3SGB: --titrate_only] _____________________ 227s 227s pdb = '3SGB-subset' 227s options = ['--titrate_only', 'E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139', '/tmp/autopkgtest.QjIrgy/autopkgtest_tmp/build/tests/pdb/3SGB-subset.pdb'] 227s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_3SGB____titrat0') 227s 227s @pytest.mark.parametrize("pdb, options", [ 227s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 227s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 227s pytest.param('1HPX', [], id="1HPX: no options"), 227s pytest.param('4DFR', [], id="4DFR: no options"), 227s pytest.param('3SGB', [], id="3SGB: no options"), 227s pytest.param('3SGB-subset', [ 227s "--titrate_only", 227s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 227s id="3SGB: --titrate_only"), 227s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 227s def test_regression(pdb, options, tmp_path): 227s """Basic regression test of PROPKA functionality.""" 227s path_dict = get_test_dirs() 227s ref_path = None 227s 227s for ext in ["json", "dat"]: 227s ref_path = path_dict["results"] / f"{pdb}.{ext}" 227s if ref_path.is_file(): 227s ref_path = ref_path.resolve() 227s break 227s else: 227s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 227s str(ref_path))) 227s ref_path = None 227s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 227s if pdb_path.is_file(): 227s pdb_path = pdb_path.resolve() 227s else: 227s errstr = "Missing PDB file: {0:s}".format(pdb_path) 227s raise FileNotFoundError(errstr) 227s tmp_path = Path(tmp_path).resolve() 227s 227s > run_propka(options, pdb_path, tmp_path) 227s 227s tests/test_basic_regression.py:170: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s tests/test_basic_regression.py:77: in run_propka 227s parameters = read_parameter_file(args.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s ------------------------------ Captured log call ------------------------------- 227s WARNING tests.test_basic_regression:test_basic_regression.py:73 Working in tmpdir /tmp/pytest-of-ubuntu/pytest-1/test_regression_3SGB____titrat0 because of PROPKA file output; need to fix this. 227s _____________________ test_regression[1HPX-warn: --quiet] ______________________ 227s 227s pdb = '1HPX-warn' 227s options = ['--quiet', '/tmp/autopkgtest.QjIrgy/autopkgtest_tmp/build/tests/pdb/1HPX-warn.pdb'] 227s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_1HPX_warn____q0') 227s 227s @pytest.mark.parametrize("pdb, options", [ 227s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 227s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 227s pytest.param('1HPX', [], id="1HPX: no options"), 227s pytest.param('4DFR', [], id="4DFR: no options"), 227s pytest.param('3SGB', [], id="3SGB: no options"), 227s pytest.param('3SGB-subset', [ 227s "--titrate_only", 227s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 227s id="3SGB: --titrate_only"), 227s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 227s def test_regression(pdb, options, tmp_path): 227s """Basic regression test of PROPKA functionality.""" 227s path_dict = get_test_dirs() 227s ref_path = None 227s 227s for ext in ["json", "dat"]: 227s ref_path = path_dict["results"] / f"{pdb}.{ext}" 227s if ref_path.is_file(): 227s ref_path = ref_path.resolve() 227s break 227s else: 227s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 227s str(ref_path))) 227s ref_path = None 227s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 227s if pdb_path.is_file(): 227s pdb_path = pdb_path.resolve() 227s else: 227s errstr = "Missing PDB file: {0:s}".format(pdb_path) 227s raise FileNotFoundError(errstr) 227s tmp_path = Path(tmp_path).resolve() 227s 227s > run_propka(options, pdb_path, tmp_path) 227s 227s tests/test_basic_regression.py:170: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s tests/test_basic_regression.py:77: in run_propka 227s parameters = read_parameter_file(args.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s ------------------------------ Captured log call ------------------------------- 227s WARNING tests.test_basic_regression:test_basic_regression.py:73 Working in tmpdir /tmp/pytest-of-ubuntu/pytest-1/test_regression_1HPX_warn____q0 because of PROPKA file output; need to fix this. 227s __________________ test_single_file[1FTJ-Chain-A: no options] __________________ 227s 227s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_file_1FTJ_Chain_A_0') 227s pdb = '1FTJ-Chain-A', options = () 227s 227s @pytest.mark.parametrize("pdb, options", [ 227s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 227s pytest.param('3SGB-subset', ( 227s "--titrate_only", 227s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 227s id="3SGB: --titrate_only"), 227s pytest.param('1HPX-warn', ('--quiet',), id="1HPX-warn: --quiet"), 227s ]) 227s def test_single_file(tmpdir, pdb, options): 227s """Basic regression test using propka.run.single and local file for the 227s input PDB file""" 227s ref_path, pdb_path = get_paths(pdb) 227s filename = str(pdb_path) 227s 227s with tmpdir.as_cwd(): 227s > pkrun.single(filename, options) 227s 227s tests/test_run.py:31: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s /usr/lib/python3/dist-packages/propka/run.py:118: in single 227s parameters = read_parameter_file(options.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s ____________________ test_single_file[3SGB: --titrate_only] ____________________ 227s 227s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_file_3SGB____titra0') 227s pdb = '3SGB-subset' 227s options = ('--titrate_only', 'E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139') 227s 227s @pytest.mark.parametrize("pdb, options", [ 227s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 227s pytest.param('3SGB-subset', ( 227s "--titrate_only", 227s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 227s id="3SGB: --titrate_only"), 227s pytest.param('1HPX-warn', ('--quiet',), id="1HPX-warn: --quiet"), 227s ]) 227s def test_single_file(tmpdir, pdb, options): 227s """Basic regression test using propka.run.single and local file for the 227s input PDB file""" 227s ref_path, pdb_path = get_paths(pdb) 227s filename = str(pdb_path) 227s 227s with tmpdir.as_cwd(): 227s > pkrun.single(filename, options) 227s 227s tests/test_run.py:31: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s /usr/lib/python3/dist-packages/propka/run.py:118: in single 227s parameters = read_parameter_file(options.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s _____________________ test_single_file[1HPX-warn: --quiet] _____________________ 227s 227s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_file_1HPX_warn____0') 227s pdb = '1HPX-warn', options = ('--quiet',) 227s 227s @pytest.mark.parametrize("pdb, options", [ 227s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 227s pytest.param('3SGB-subset', ( 227s "--titrate_only", 227s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 227s id="3SGB: --titrate_only"), 227s pytest.param('1HPX-warn', ('--quiet',), id="1HPX-warn: --quiet"), 227s ]) 227s def test_single_file(tmpdir, pdb, options): 227s """Basic regression test using propka.run.single and local file for the 227s input PDB file""" 227s ref_path, pdb_path = get_paths(pdb) 227s filename = str(pdb_path) 227s 227s with tmpdir.as_cwd(): 227s > pkrun.single(filename, options) 227s 227s tests/test_run.py:31: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s /usr/lib/python3/dist-packages/propka/run.py:118: in single 227s parameters = read_parameter_file(options.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s _______________ test_single_filestream[1FTJ-Chain-A: no options] _______________ 227s 227s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_filestream_1FTJ_Ch0') 227s pdb = '1FTJ-Chain-A', options = () 227s 227s @pytest.mark.parametrize("pdb, options", [ 227s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 227s pytest.param('3SGB-subset', ( 227s "--titrate_only", 227s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 227s id="3SGB: --titrate_only"), 227s pytest.param('1HPX-warn',('--quiet',), id="1HPX-warn: --quiet"), 227s ]) 227s def test_single_filestream(tmpdir, pdb, options): 227s """Basic regression test using StringIO streams for the input PDB file""" 227s ref_path, pdb_path = get_paths(pdb) 227s filename = f"{pdb}.pdb" 227s 227s with open(pdb_path, 'r') as writer: 227s filestream = StringIO(writer.read()) 227s 227s with tmpdir.as_cwd(): 227s > pkrun.single(filename, options, stream=filestream) 227s 227s tests/test_run.py:53: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s /usr/lib/python3/dist-packages/propka/run.py:118: in single 227s parameters = read_parameter_file(options.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s _________________ test_single_filestream[3SGB: --titrate_only] _________________ 227s 227s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_filestream_3SGB___0') 227s pdb = '3SGB-subset' 227s options = ('--titrate_only', 'E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139') 227s 227s @pytest.mark.parametrize("pdb, options", [ 227s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 227s pytest.param('3SGB-subset', ( 227s "--titrate_only", 227s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 227s id="3SGB: --titrate_only"), 227s pytest.param('1HPX-warn',('--quiet',), id="1HPX-warn: --quiet"), 227s ]) 227s def test_single_filestream(tmpdir, pdb, options): 227s """Basic regression test using StringIO streams for the input PDB file""" 227s ref_path, pdb_path = get_paths(pdb) 227s filename = f"{pdb}.pdb" 227s 227s with open(pdb_path, 'r') as writer: 227s filestream = StringIO(writer.read()) 227s 227s with tmpdir.as_cwd(): 227s > pkrun.single(filename, options, stream=filestream) 227s 227s tests/test_run.py:53: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s /usr/lib/python3/dist-packages/propka/run.py:118: in single 227s parameters = read_parameter_file(options.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s __________________ test_single_filestream[1HPX-warn: --quiet] __________________ 227s 227s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_filestream_1HPX_wa0') 227s pdb = '1HPX-warn', options = ('--quiet',) 227s 227s @pytest.mark.parametrize("pdb, options", [ 227s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 227s pytest.param('3SGB-subset', ( 227s "--titrate_only", 227s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 227s id="3SGB: --titrate_only"), 227s pytest.param('1HPX-warn',('--quiet',), id="1HPX-warn: --quiet"), 227s ]) 227s def test_single_filestream(tmpdir, pdb, options): 227s """Basic regression test using StringIO streams for the input PDB file""" 227s ref_path, pdb_path = get_paths(pdb) 227s filename = f"{pdb}.pdb" 227s 227s with open(pdb_path, 'r') as writer: 227s filestream = StringIO(writer.read()) 227s 227s with tmpdir.as_cwd(): 227s > pkrun.single(filename, options, stream=filestream) 227s 227s tests/test_run.py:53: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s /usr/lib/python3/dist-packages/propka/run.py:118: in single 227s parameters = read_parameter_file(options.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s ______________________________ test_single_nopka _______________________________ 227s 227s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_nopka0') 227s 227s def test_single_nopka(tmpdir): 227s """Basic test to check that the pKa file is not written when write_pka is 227s `False`""" 227s pdb = "1FTJ-Chain-A" 227s ref_path, pdb_path = get_paths(pdb) 227s filename = f"{pdb}.pdb" 227s 227s with open(pdb_path, 'r') as writer: 227s filestream = StringIO(writer.read()) 227s 227s > pkrun.single(filename, stream=filestream, write_pka=False) 227s 227s tests/test_run.py:70: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s /usr/lib/python3/dist-packages/propka/run.py:118: in single 227s parameters = read_parameter_file(options.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s _______________________ test_single_extra_files_logwarn ________________________ 227s 227s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_extra_files_logwar0') 227s caplog = <_pytest.logging.LogCaptureFixture object at 0x3ffa7cc8830> 227s 227s def test_single_extra_files_logwarn(tmpdir, caplog): 227s """Tests that a logging warning is thrown if passing files via optargs""" 227s pdb = "1FTJ-Chain-A" 227s options = ('-f foo.pdb bar.pdb', '-f test.pdb test2.pdb') 227s ref_path, pdb_path = get_paths(pdb) 227s filename = str(pdb_path) 227s 227s with tmpdir.as_cwd(): 227s > pkrun.single(filename, options) 227s 227s tests/test_run.py:82: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s /usr/lib/python3/dist-packages/propka/run.py:118: in single 227s parameters = read_parameter_file(options.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s _______________ test_textio_filestream[1FTJ-Chain-A: no options] _______________ 227s 227s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_textio_filestream_1FTJ_Ch0') 227s pdb = '1FTJ-Chain-A', options = ['1FTJ-Chain-A.pdb'] 227s 227s @pytest.mark.parametrize("pdb, options", [ 227s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 227s pytest.param('3SGB-subset', [ 227s "--titrate_only", 227s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 227s id="3SGB: --titrate_only"), 227s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 227s ]) 227s def test_textio_filestream(tmpdir, pdb, options): 227s """Basic regression test using TextIO streams for the input PDB file""" 227s # Get the relevant paths 227s ref_path, pdb_path = get_paths(pdb) 227s filename = f"{pdb}.pdb" 227s 227s filestream = open(pdb_path, 'r') 227s 227s with tmpdir.as_cwd(): 227s > run_propka_stream(options, filestream, filename) 227s 227s tests/test_streamio.py:60: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s tests/test_streamio.py:36: in run_propka_stream 227s parameters = read_parameter_file(args.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s _________________ test_textio_filestream[3SGB: --titrate_only] _________________ 227s 227s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_textio_filestream_3SGB___0') 227s pdb = '3SGB-subset' 227s options = ['--titrate_only', 'E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139', '3SGB-subset.pdb'] 227s 227s @pytest.mark.parametrize("pdb, options", [ 227s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 227s pytest.param('3SGB-subset', [ 227s "--titrate_only", 227s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 227s id="3SGB: --titrate_only"), 227s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 227s ]) 227s def test_textio_filestream(tmpdir, pdb, options): 227s """Basic regression test using TextIO streams for the input PDB file""" 227s # Get the relevant paths 227s ref_path, pdb_path = get_paths(pdb) 227s filename = f"{pdb}.pdb" 227s 227s filestream = open(pdb_path, 'r') 227s 227s with tmpdir.as_cwd(): 227s > run_propka_stream(options, filestream, filename) 227s 227s tests/test_streamio.py:60: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s tests/test_streamio.py:36: in run_propka_stream 227s parameters = read_parameter_file(args.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s __________________ test_textio_filestream[1HPX-warn: --quiet] __________________ 227s 227s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_textio_filestream_1HPX_wa0') 227s pdb = '1HPX-warn', options = ['--quiet', '1HPX-warn.pdb'] 227s 227s @pytest.mark.parametrize("pdb, options", [ 227s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 227s pytest.param('3SGB-subset', [ 227s "--titrate_only", 227s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 227s id="3SGB: --titrate_only"), 227s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 227s ]) 227s def test_textio_filestream(tmpdir, pdb, options): 227s """Basic regression test using TextIO streams for the input PDB file""" 227s # Get the relevant paths 227s ref_path, pdb_path = get_paths(pdb) 227s filename = f"{pdb}.pdb" 227s 227s filestream = open(pdb_path, 'r') 227s 227s with tmpdir.as_cwd(): 227s > run_propka_stream(options, filestream, filename) 227s 227s tests/test_streamio.py:60: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s tests/test_streamio.py:36: in run_propka_stream 227s parameters = read_parameter_file(args.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s ______________ test_stringio_filestream[1FTJ-Chain-A: no options] ______________ 227s 227s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_stringio_filestream_1FTJ_0') 227s pdb = '1FTJ-Chain-A', options = ['1FTJ-Chain-A.pdb'] 227s 227s @pytest.mark.parametrize("pdb, options", [ 227s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 227s pytest.param('3SGB-subset', [ 227s "--titrate_only", 227s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 227s id="3SGB: --titrate_only"), 227s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 227s ]) 227s def test_stringio_filestream(tmpdir, pdb, options): 227s """Basic regression test using StringIO streams for the input PDB file""" 227s # Get the relevant paths 227s ref_path, pdb_path = get_paths(pdb) 227s filename = f"{pdb}.pdb" 227s 227s with open(pdb_path, 'r') as writer: 227s filestream = StringIO(writer.read()) 227s 227s with tmpdir.as_cwd(): 227s > run_propka_stream(options, filestream, filename) 227s 227s tests/test_streamio.py:84: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s tests/test_streamio.py:36: in run_propka_stream 227s parameters = read_parameter_file(args.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s ________________ test_stringio_filestream[3SGB: --titrate_only] ________________ 227s 227s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_stringio_filestream_3SGB_0') 227s pdb = '3SGB-subset' 227s options = ['--titrate_only', 'E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139', '3SGB-subset.pdb'] 227s 227s @pytest.mark.parametrize("pdb, options", [ 227s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 227s pytest.param('3SGB-subset', [ 227s "--titrate_only", 227s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 227s id="3SGB: --titrate_only"), 227s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 227s ]) 227s def test_stringio_filestream(tmpdir, pdb, options): 227s """Basic regression test using StringIO streams for the input PDB file""" 227s # Get the relevant paths 227s ref_path, pdb_path = get_paths(pdb) 227s filename = f"{pdb}.pdb" 227s 227s with open(pdb_path, 'r') as writer: 227s filestream = StringIO(writer.read()) 227s 227s with tmpdir.as_cwd(): 227s > run_propka_stream(options, filestream, filename) 227s 227s tests/test_streamio.py:84: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s tests/test_streamio.py:36: in run_propka_stream 227s parameters = read_parameter_file(args.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s _________________ test_stringio_filestream[1HPX-warn: --quiet] _________________ 227s 227s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_stringio_filestream_1HPX_0') 227s pdb = '1HPX-warn', options = ['--quiet', '1HPX-warn.pdb'] 227s 227s @pytest.mark.parametrize("pdb, options", [ 227s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 227s pytest.param('3SGB-subset', [ 227s "--titrate_only", 227s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 227s id="3SGB: --titrate_only"), 227s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 227s ]) 227s def test_stringio_filestream(tmpdir, pdb, options): 227s """Basic regression test using StringIO streams for the input PDB file""" 227s # Get the relevant paths 227s ref_path, pdb_path = get_paths(pdb) 227s filename = f"{pdb}.pdb" 227s 227s with open(pdb_path, 'r') as writer: 227s filestream = StringIO(writer.read()) 227s 227s with tmpdir.as_cwd(): 227s > run_propka_stream(options, filestream, filename) 227s 227s tests/test_streamio.py:84: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s tests/test_streamio.py:36: in run_propka_stream 227s parameters = read_parameter_file(args.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s __________________________ test_valuerror_nofiletype ___________________________ 227s 227s def test_valuerror_nofiletype(): 227s """Tests for raised ValueError when an unknown filename is passed to 227s read_molecule_file""" 227s pdb = "1FTJ-Chain-A" 227s options = [] 227s 227s ref_path, pdb_path = get_paths(pdb) 227s 227s with open(pdb_path, 'r') as writer: 227s filestream = StringIO(writer.read()) 227s 227s errmsg = "Unknown input file type" 227s with pytest.raises(ValueError, match=errmsg): 227s > run_propka_stream(options, filestream, filename="test.dat") 227s 227s tests/test_streamio.py:103: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s tests/test_streamio.py:36: in run_propka_stream 227s parameters = read_parameter_file(args.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s ____________________________ test_valuerror_notpdb _____________________________ 227s 227s def test_valuerror_notpdb(): 227s """Tests for raised ValueError when a stream object that isn't a PDB 227s is passed to read_molecule_file""" 227s pdb = "1FTJ-Chain-A" 227s options = [] 227s 227s ref_path, pdb_path = get_paths(pdb) 227s 227s filestream = StringIO() 227s 227s errmsg = "The pdb file does not seem to contain any " 227s with pytest.raises(ValueError, match=errmsg): 227s > run_propka_stream(options, filestream, filename="test.pdb") 227s 227s tests/test_streamio.py:118: 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s tests/test_streamio.py:36: in run_propka_stream 227s parameters = read_parameter_file(args.parameters, Parameters()) 227s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 227s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 227s parameters.parse_line(line) 227s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 227s 227s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 227s ^^^^^^^^^^^^^^^^^^^^ 227s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 227s 227s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 227s =========================== short test summary info ============================ 227s FAILED tests/test_basic_regression.py::test_regression[sample-issue-140: no options] 227s FAILED tests/test_basic_regression.py::test_regression[1FTJ-Chain-A: no options] 227s FAILED tests/test_basic_regression.py::test_regression[1HPX: no options] - At... 227s FAILED tests/test_basic_regression.py::test_regression[4DFR: no options] - At... 227s FAILED tests/test_basic_regression.py::test_regression[3SGB: no options] - At... 227s FAILED tests/test_basic_regression.py::test_regression[3SGB: --titrate_only] 227s FAILED tests/test_basic_regression.py::test_regression[1HPX-warn: --quiet] - ... 227s FAILED tests/test_run.py::test_single_file[1FTJ-Chain-A: no options] - Attrib... 227s FAILED tests/test_run.py::test_single_file[3SGB: --titrate_only] - AttributeE... 227s FAILED tests/test_run.py::test_single_file[1HPX-warn: --quiet] - AttributeErr... 227s FAILED tests/test_run.py::test_single_filestream[1FTJ-Chain-A: no options] - ... 227s FAILED tests/test_run.py::test_single_filestream[3SGB: --titrate_only] - Attr... 227s FAILED tests/test_run.py::test_single_filestream[1HPX-warn: --quiet] - Attrib... 227s FAILED tests/test_run.py::test_single_nopka - AttributeError: 'Parameters' ob... 227s FAILED tests/test_run.py::test_single_extra_files_logwarn - AttributeError: '... 227s FAILED tests/test_streamio.py::test_textio_filestream[1FTJ-Chain-A: no options] 227s FAILED tests/test_streamio.py::test_textio_filestream[3SGB: --titrate_only] 227s FAILED tests/test_streamio.py::test_textio_filestream[1HPX-warn: --quiet] - A... 227s FAILED tests/test_streamio.py::test_stringio_filestream[1FTJ-Chain-A: no options] 227s FAILED tests/test_streamio.py::test_stringio_filestream[3SGB: --titrate_only] 227s FAILED tests/test_streamio.py::test_stringio_filestream[1HPX-warn: --quiet] 227s FAILED tests/test_streamio.py::test_valuerror_nofiletype - AttributeError: 'P... 227s FAILED tests/test_streamio.py::test_valuerror_notpdb - AttributeError: 'Param... 227s ================= 23 failed, 24 passed, 2 deselected in 2.18s ================== 227s E: pybuild pybuild:483: test: plugin distutils failed with: exit code=1: cd /tmp/autopkgtest.QjIrgy/autopkgtest_tmp/build; python3.14 -m pytest -k 'not test_molecular_container' 227s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.13 3.14" returned exit code 13 227s make: *** [/tmp/QMrwsG10CX/run:4: pybuild-autopkgtest] Error 25 227s pybuild-autopkgtest: error: /tmp/QMrwsG10CX/run pybuild-autopkgtest returned exit code 2 227s autopkgtest [12:24:35]: test pybuild-autopkgtest: -----------------------] 228s autopkgtest [12:24:36]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 228s pybuild-autopkgtest FAIL non-zero exit status 25 228s autopkgtest [12:24:36]: @@@@@@@@@@@@@@@@@@@@ summary 228s pybuild-autopkgtest FAIL non-zero exit status 25