0s autopkgtest [12:34:11]: starting date and time: 2026-01-24 12:34:11+0000 0s autopkgtest [12:34:11]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [12:34:11]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.3oa26goz/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-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-11.secgroup --name adt-resolute-amd64-propka-20260124-123411-juju-7f2275-prod-proposed-migration-environment-15-b1edc68a-1afd-4973-b2b5-ff51cfc21ff4 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-amd64-propka-20260124-123411-juju-7f2275-prod-proposed-migration-environment-15-b1edc68a-1afd-4973-b2b5-ff51cfc21ff4 from image adt/ubuntu-resolute-amd64-server-20260124.img (UUID 46811f22-3700-43f4-953b-ee3c613d71bb)... 76s autopkgtest [12:35:27]: testbed dpkg architecture: amd64 76s autopkgtest [12:35:27]: testbed apt version: 3.1.13 76s autopkgtest [12:35:27]: @@@@@@@@@@@@@@@@@@@@ test bed setup 76s autopkgtest [12:35:27]: testbed release detected to be: None 78s autopkgtest [12:35:28]: updating testbed package index (apt update) 78s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 78s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 78s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 78s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 78s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [998 kB] 78s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [92.3 kB] 78s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [24.3 kB] 78s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 78s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [98.2 kB] 78s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [115 kB] 78s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [3712 B] 78s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [12.3 kB] 78s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3696 B] 78s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 78s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [385 kB] 78s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [905 kB] 78s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [24.9 kB] 78s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [12.4 kB] 78s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4704 B] 78s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [824 B] 79s Fetched 2806 kB in 1s (2751 kB/s) 79s Reading package lists... 80s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 80s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 80s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 80s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 80s Reading package lists... 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s Calculating upgrade... 80s The following packages were automatically installed and are no longer required: 80s python3.13 python3.13-minimal 80s Use 'sudo apt autoremove' to remove them. 81s The following NEW packages will be installed: 81s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 81s The following packages will be upgraded: 81s libpython3-stdlib python3 python3-gdbm python3-minimal rust-coreutils 81s 5 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 81s Need to get 10.4 MB of archives. 81s After this operation, 25.2 MB of additional disk space will be used. 81s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 81s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-minimal amd64 3.14.2-1 [2563 kB] 81s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.14.2-1 [28.2 kB] 81s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.14.2-1 [22.9 kB] 81s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 81s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14 amd64 3.14.2-1 [816 kB] 81s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.14.2-1 [10.9 kB] 81s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 rust-coreutils amd64 0.5.0-0ubuntu1 [3628 kB] 81s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-gdbm amd64 3.14.2-1 [11.1 kB] 82s dpkg-preconfigure: unable to re-open stdin: No such file or directory 82s Fetched 10.4 MB in 1s (12.6 MB/s) 82s Selecting previously unselected package libpython3.14-minimal:amd64. 82s (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 ... 124177 files and directories currently installed.) 82s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_amd64.deb ... 82s Unpacking libpython3.14-minimal:amd64 (3.14.2-1) ... 82s Selecting previously unselected package python3.14-minimal. 82s Preparing to unpack .../python3.14-minimal_3.14.2-1_amd64.deb ... 82s Unpacking python3.14-minimal (3.14.2-1) ... 82s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 82s Setting up python3.14-minimal (3.14.2-1) ... 83s (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 ... 124519 files and directories currently installed.) 83s Preparing to unpack .../python3-minimal_3.14.2-1_amd64.deb ... 83s Unpacking python3-minimal (3.14.2-1) over (3.13.9-3) ... 83s Setting up python3-minimal (3.14.2-1) ... 83s (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 ... 124519 files and directories currently installed.) 83s Preparing to unpack .../python3_3.14.2-1_amd64.deb ... 83s running python pre-rtupdate hooks for python3.14... 83s Unpacking python3 (3.14.2-1) over (3.13.9-3) ... 83s Selecting previously unselected package libpython3.14-stdlib:amd64. 83s Preparing to unpack .../libpython3.14-stdlib_3.14.2-1_amd64.deb ... 83s Unpacking libpython3.14-stdlib:amd64 (3.14.2-1) ... 83s Selecting previously unselected package python3.14. 83s Preparing to unpack .../python3.14_3.14.2-1_amd64.deb ... 83s Unpacking python3.14 (3.14.2-1) ... 83s Preparing to unpack .../libpython3-stdlib_3.14.2-1_amd64.deb ... 83s Unpacking libpython3-stdlib:amd64 (3.14.2-1) over (3.13.9-3) ... 83s Preparing to unpack .../rust-coreutils_0.5.0-0ubuntu1_amd64.deb ... 83s Unpacking rust-coreutils (0.5.0-0ubuntu1) over (0.2.2-0ubuntu2) ... 83s Setting up rust-coreutils (0.5.0-0ubuntu1) ... 83s (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 ... 124980 files and directories currently installed.) 83s Preparing to unpack .../python3-gdbm_3.14.2-1_amd64.deb ... 83s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-3) ... 83s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 83s Setting up python3.14 (3.14.2-1) ... 84s Setting up libpython3-stdlib:amd64 (3.14.2-1) ... 84s Setting up python3-gdbm (3.14.2-1) ... 84s Setting up python3 (3.14.2-1) ... 84s running python rtupdate hooks for python3.14... 84s running python post-rtupdate hooks for python3.14... 84s Processing triggers for man-db (2.13.1-1) ... 84s Processing triggers for systemd (259-1ubuntu2) ... 84s autopkgtest [12:35:35]: upgrading testbed (apt dist-upgrade and autopurge) 85s Reading package lists... 85s Building dependency tree... 85s Reading state information... 85s Calculating upgrade... 85s The following packages were automatically installed and are no longer required: 85s python3.13 python3.13-minimal 85s Use 'sudo apt autoremove' to remove them. 85s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 85s Reading package lists... 85s Building dependency tree... 85s Reading state information... 85s Solving dependencies... 85s The following packages will be REMOVED: 85s python3.13* python3.13-minimal* 85s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 85s After this operation, 7860 kB disk space will be freed. 85s (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 ... 124978 files and directories currently installed.) 85s Removing python3.13 (3.13.11-1) ... 85s Removing python3.13-minimal (3.13.11-1) ... 86s Processing triggers for man-db (2.13.1-1) ... 86s Processing triggers for systemd (259-1ubuntu2) ... 86s (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 ... 124951 files and directories currently installed.) 86s Purging configuration files for python3.13-minimal (3.13.11-1) ... 88s autopkgtest [12:35:39]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:49:02 UTC 2026 88s autopkgtest [12:35:39]: @@@@@@@@@@@@@@@@@@@@ apt-source propka 90s Get:1 http://ftpmaster.internal/ubuntu resolute/universe propka 3.5.1-2 (dsc) [2286 B] 90s Get:2 http://ftpmaster.internal/ubuntu resolute/universe propka 3.5.1-2 (tar) [376 kB] 90s Get:3 http://ftpmaster.internal/ubuntu resolute/universe propka 3.5.1-2 (diff) [5096 B] 90s gpgv: Signature made Wed Oct 16 14:47:53 2024 UTC 90s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 90s gpgv: issuer "emollier@debian.org" 90s gpgv: Can't check signature: No public key 90s dpkg-source: warning: cannot verify inline signature for ./propka_3.5.1-2.dsc: no acceptable signature found 90s autopkgtest [12:35:41]: testing package propka version 3.5.1-2 90s autopkgtest [12:35:41]: build not needed 91s autopkgtest [12:35:42]: test pybuild-autopkgtest: preparing testbed 91s Reading package lists... 91s Building dependency tree... 91s Reading state information... 91s Solving dependencies... 91s The following NEW packages will be installed: 91s autoconf automake autopoint autotools-dev build-essential cpp cpp-15 91s cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu debhelper debugedit 91s dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz 91s fonts-font-awesome fonts-lato fonts-mathjax g++ g++-15 91s g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-15 91s gcc-15-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext help2man 91s intltool-debian libarchive-zip-perl libasan8 libblas3 libcc1-0 91s libdebhelper-perl libfile-stripnondeterminism-perl libgcc-15-dev 91s libgfortran5 libgomp1 libhwasan0 libisl23 libitm1 libjs-jquery libjs-mathjax 91s libjson-perl liblapack3 liblsan0 libmpc3 libquadmath0 libstdc++-15-dev 91s libtool libtsan2 libubsan1 m4 po-debconf pybuild-plugin-autopkgtest 91s python-propka-doc python3-alabaster python3-all python3-defusedxml 91s python3-docutils python3-imagesize python3-iniconfig python3-numpy 91s python3-numpy-dev python3-pluggy python3-propka python3-pytest 91s python3-roman-numerals python3-snowballstemmer python3-sphinx 91s python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3.13 91s python3.13-minimal sgml-base sphinx-common sphinx-rtd-theme-common xml-core 91s 0 upgraded, 79 newly installed, 0 to remove and 0 not upgraded. 91s Need to get 106 MB of archives. 91s After this operation, 393 MB of additional disk space will be used. 91s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-minimal amd64 3.13.11-1 [2408 kB] 92s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-lato all 2.015-1build1 [2779 kB] 93s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.3.5+ds-3 [147 kB] 93s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB] 93s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-11ubuntu1 [939 kB] 93s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB] 93s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.3.5+ds-3 [8129 kB] 93s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13 amd64 3.13.11-1 [758 kB] 93s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 m4 amd64 1.4.20-2 [217 kB] 93s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 autoconf all 2.72-3.1ubuntu1 [384 kB] 93s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 autotools-dev all 20240727.1 [43.4 kB] 93s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 automake all 1:1.18.1-3build1 [582 kB] 93s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 autopoint all 0.23.2-1 [620 kB] 94s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1build1 [691 kB] 94s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-2 [54.8 kB] 94s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-11ubuntu1 [12.9 MB] 94s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-11ubuntu1 [1030 B] 94s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B] 94s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB] 94s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 15.2.0-11ubuntu1 [47.4 kB] 94s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-11ubuntu1 [151 kB] 94s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 15.2.0-11ubuntu1 [29.5 kB] 94s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 15.2.0-11ubuntu1 [3070 kB] 94s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 15.2.0-11ubuntu1 [1360 kB] 94s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 15.2.0-11ubuntu1 [2757 kB] 94s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 15.2.0-11ubuntu1 [1210 kB] 94s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 15.2.0-11ubuntu1 [1685 kB] 94s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 15.2.0-11ubuntu1 [153 kB] 94s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-11ubuntu1 [2863 kB] 94s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-11ubuntu1 [25.4 MB] 95s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-11ubuntu1 [528 kB] 95s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B] 95s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B] 95s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-11ubuntu1 [2574 kB] 95s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-11ubuntu1 [14.4 MB] 95s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15 amd64 15.2.0-11ubuntu1 [24.6 kB] 95s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [966 B] 95s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 g++ amd64 4:15.2.0-4ubuntu1 [1100 B] 95s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 build-essential amd64 12.12ubuntu2 [5256 B] 95s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libdebhelper-perl all 13.28ubuntu1 [97.4 kB] 95s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libtool all 2.5.4-9 [169 kB] 95s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 dh-autoreconf all 21 [12.5 kB] 95s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 95s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1build1 [20.6 kB] 95s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 dh-strip-nondeterminism all 1.15.0-1build1 [5110 B] 95s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 debugedit amd64 1:5.2-3 [49.9 kB] 95s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 dwz amd64 0.16-2 [115 kB] 95s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 gettext amd64 0.23.2-1 [1019 kB] 95s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 intltool-debian all 0.35.0+20060710.6build1 [24.1 kB] 95s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 po-debconf all 1.0.22 [215 kB] 95s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 debhelper all 13.28ubuntu1 [916 kB] 95s Get:52 http://ftpmaster.internal/ubuntu resolute/universe amd64 dh-python all 7.20251231 [122 kB] 95s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 sgml-base all 1.31+nmu1 [11.0 kB] 95s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 xml-core all 0.19build1 [20.3 kB] 95s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 docutils-common all 0.22.4+dfsg-1 [130 kB] 95s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1build1 [531 kB] 95s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 95s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 help2man amd64 1.49.3 [201 kB] 95s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 95s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libjson-perl all 4.10000-1 [81.9 kB] 95s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 pybuild-plugin-autopkgtest all 7.20251231 [1748 B] 95s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 95s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 95s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-propka-doc all 3.5.1-2 [157 kB] 95s Get:65 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-all amd64 3.14.2-1 [890 B] 95s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-defusedxml all 0.7.1-3build1 [42.4 kB] 95s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-roman-numerals all 4.1.0-1 [8660 B] 95s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-docutils all 0.22.4+dfsg-1 [439 kB] 95s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-imagesize all 1.4.1-1build1 [6900 B] 95s Get:70 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-iniconfig all 2.1.0-2 [6962 B] 95s Get:71 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pluggy all 1.6.0-2 [21.1 kB] 95s Get:72 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-propka all 3.5.1-2 [70.1 kB] 95s Get:73 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytest all 9.0.2-2 [277 kB] 95s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-snowballstemmer all 3.0.1-1 [65.9 kB] 95s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 sphinx-common all 8.2.3-12 [657 kB] 95s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-alabaster all 0.7.16-0.1build1 [18.6 kB] 95s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-sphinx all 8.2.3-12 [483 kB] 95s Get:78 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sphinxcontrib.jquery all 4.1-6 [6856 B] 95s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sphinx-rtd-theme all 3.0.2+dfsg-3 [23.5 kB] 96s Fetched 106 MB in 4s (25.8 MB/s) 96s Selecting previously unselected package python3.13-minimal. 96s (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 ... 124953 files and directories currently installed.) 96s Preparing to unpack .../00-python3.13-minimal_3.13.11-1_amd64.deb ... 96s Unpacking python3.13-minimal (3.13.11-1) ... 96s Selecting previously unselected package fonts-lato. 96s Preparing to unpack .../01-fonts-lato_2.015-1build1_all.deb ... 96s Unpacking fonts-lato (2.015-1build1) ... 96s Selecting previously unselected package python3-numpy-dev:amd64. 96s Preparing to unpack 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98s Setting up dh-python (7.20251231) ... 98s Setting up python3-iniconfig (2.1.0-2) ... 98s Setting up python3-propka (3.5.1-2) ... 99s Setting up fonts-lato (2.015-1build1) ... 99s Setting up fonts-mathjax (2.7.9+dfsg-1build1) ... 99s Setting up libjs-mathjax (2.7.9+dfsg-1build1) ... 99s Setting up python3-defusedxml (0.7.1-3build1) ... 99s Setting up libarchive-zip-perl (1.68-1) ... 99s Setting up python3-alabaster (0.7.16-0.1build1) ... 99s Setting up libdebhelper-perl (13.28ubuntu1) ... 99s Setting up m4 (1.4.20-2) ... 99s Setting up libgomp1:amd64 (15.2.0-11ubuntu1) ... 99s Setting up help2man (1.49.3) ... 99s Setting up autotools-dev (20240727.1) ... 99s Setting up libblas3:amd64 (3.12.1-7ubuntu1) ... 99s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 99s Setting up python3-snowballstemmer (3.0.1-1) ... 99s Setting up libquadmath0:amd64 (15.2.0-11ubuntu1) ... 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test pybuild-autopkgtest: [----------------------- 107s pybuild-autopkgtest 107s I: pybuild base:384: cd /tmp/autopkgtest.lK2tJD/autopkgtest_tmp/build; python3.13 -m pytest -k 'not test_molecular_container' 107s ============================= test session starts ============================== 107s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 107s rootdir: /tmp/autopkgtest.lK2tJD/autopkgtest_tmp/build 107s plugins: typeguard-4.4.4 107s collected 49 items / 2 deselected / 47 selected 107s 109s tests/test_basic_regression.py ....... [ 14%] 109s tests/test_hybrid36.py .. [ 19%] 109s tests/test_input.py .. [ 23%] 109s tests/test_lib.py .. [ 27%] 109s tests/test_protonate.py . [ 29%] 110s tests/test_run.py ........ [ 46%] 111s tests/test_streamio.py ........ [ 63%] 111s tests/test_vector_algebra.py ............... [ 95%] 111s tests/test_version.py .. [100%] 111s 111s ======================= 47 passed, 2 deselected in 3.14s ======================= 111s I: pybuild base:384: cd /tmp/autopkgtest.lK2tJD/autopkgtest_tmp/build; python3.14 -m pytest -k 'not test_molecular_container' 111s ============================= test session starts ============================== 111s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 111s rootdir: /tmp/autopkgtest.lK2tJD/autopkgtest_tmp/build 111s plugins: typeguard-4.4.4 111s collected 49 items / 2 deselected / 47 selected 111s 111s tests/test_basic_regression.py FFFFFFF [ 14%] 111s tests/test_hybrid36.py .. [ 19%] 111s tests/test_input.py .. [ 23%] 111s tests/test_lib.py .. [ 27%] 111s tests/test_protonate.py . [ 29%] 111s tests/test_run.py FFFFFFFF [ 46%] 111s tests/test_streamio.py FFFFFFFF [ 63%] 111s tests/test_vector_algebra.py ............... [ 95%] 111s tests/test_version.py .. [100%] 111s 111s =================================== FAILURES =================================== 111s ________________ test_regression[sample-issue-140: no options] _________________ 111s 111s pdb = 'sample-issue-140' 111s options = ['/tmp/autopkgtest.lK2tJD/autopkgtest_tmp/build/tests/pdb/sample-issue-140.pdb'] 111s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_sample_issue_10') 111s 111s @pytest.mark.parametrize("pdb, options", [ 111s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 111s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 111s pytest.param('1HPX', [], id="1HPX: no options"), 111s pytest.param('4DFR', [], id="4DFR: no options"), 111s pytest.param('3SGB', [], id="3SGB: no options"), 111s pytest.param('3SGB-subset', [ 111s "--titrate_only", 111s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 111s id="3SGB: --titrate_only"), 111s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 111s def test_regression(pdb, options, tmp_path): 111s """Basic regression test of PROPKA functionality.""" 111s path_dict = get_test_dirs() 111s ref_path = None 111s 111s for ext in ["json", "dat"]: 111s ref_path = path_dict["results"] / f"{pdb}.{ext}" 111s if ref_path.is_file(): 111s ref_path = ref_path.resolve() 111s break 111s else: 111s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 111s str(ref_path))) 111s ref_path = None 111s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 111s if pdb_path.is_file(): 111s pdb_path = pdb_path.resolve() 111s else: 111s errstr = "Missing PDB file: {0:s}".format(pdb_path) 111s raise FileNotFoundError(errstr) 111s tmp_path = Path(tmp_path).resolve() 111s 111s > run_propka(options, pdb_path, tmp_path) 111s 111s tests/test_basic_regression.py:170: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s tests/test_basic_regression.py:77: in run_propka 111s parameters = read_parameter_file(args.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s ------------------------------ Captured log call ------------------------------- 111s 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. 111s __________________ test_regression[1FTJ-Chain-A: no options] ___________________ 111s 111s pdb = '1FTJ-Chain-A' 111s options = ['/tmp/autopkgtest.lK2tJD/autopkgtest_tmp/build/tests/pdb/1FTJ-Chain-A.pdb'] 111s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_1FTJ_Chain_A__0') 111s 111s @pytest.mark.parametrize("pdb, options", [ 111s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 111s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 111s pytest.param('1HPX', [], id="1HPX: no options"), 111s pytest.param('4DFR', [], id="4DFR: no options"), 111s pytest.param('3SGB', [], id="3SGB: no options"), 111s pytest.param('3SGB-subset', [ 111s "--titrate_only", 111s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 111s id="3SGB: --titrate_only"), 111s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 111s def test_regression(pdb, options, tmp_path): 111s """Basic regression test of PROPKA functionality.""" 111s path_dict = get_test_dirs() 111s ref_path = None 111s 111s for ext in ["json", "dat"]: 111s ref_path = path_dict["results"] / f"{pdb}.{ext}" 111s if ref_path.is_file(): 111s ref_path = ref_path.resolve() 111s break 111s else: 111s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 111s str(ref_path))) 111s ref_path = None 111s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 111s if pdb_path.is_file(): 111s pdb_path = pdb_path.resolve() 111s else: 111s errstr = "Missing PDB file: {0:s}".format(pdb_path) 111s raise FileNotFoundError(errstr) 111s tmp_path = Path(tmp_path).resolve() 111s 111s > run_propka(options, pdb_path, tmp_path) 111s 111s tests/test_basic_regression.py:170: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s tests/test_basic_regression.py:77: in run_propka 111s parameters = read_parameter_file(args.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s ------------------------------ Captured log call ------------------------------- 111s 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. 111s ______________________ test_regression[1HPX: no options] _______________________ 111s 111s pdb = '1HPX' 111s options = ['/tmp/autopkgtest.lK2tJD/autopkgtest_tmp/build/tests/pdb/1HPX.pdb'] 111s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_1HPX__no_optio0') 111s 111s @pytest.mark.parametrize("pdb, options", [ 111s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 111s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 111s pytest.param('1HPX', [], id="1HPX: no options"), 111s pytest.param('4DFR', [], id="4DFR: no options"), 111s pytest.param('3SGB', [], id="3SGB: no options"), 111s pytest.param('3SGB-subset', [ 111s "--titrate_only", 111s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 111s id="3SGB: --titrate_only"), 111s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 111s def test_regression(pdb, options, tmp_path): 111s """Basic regression test of PROPKA functionality.""" 111s path_dict = get_test_dirs() 111s ref_path = None 111s 111s for ext in ["json", "dat"]: 111s ref_path = path_dict["results"] / f"{pdb}.{ext}" 111s if ref_path.is_file(): 111s ref_path = ref_path.resolve() 111s break 111s else: 111s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 111s str(ref_path))) 111s ref_path = None 111s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 111s if pdb_path.is_file(): 111s pdb_path = pdb_path.resolve() 111s else: 111s errstr = "Missing PDB file: {0:s}".format(pdb_path) 111s raise FileNotFoundError(errstr) 111s tmp_path = Path(tmp_path).resolve() 111s 111s > run_propka(options, pdb_path, tmp_path) 111s 111s tests/test_basic_regression.py:170: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s tests/test_basic_regression.py:77: in run_propka 111s parameters = read_parameter_file(args.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s ------------------------------ Captured log call ------------------------------- 111s 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. 111s ______________________ test_regression[4DFR: no options] _______________________ 111s 111s pdb = '4DFR' 111s options = ['/tmp/autopkgtest.lK2tJD/autopkgtest_tmp/build/tests/pdb/4DFR.pdb'] 111s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_4DFR__no_optio0') 111s 111s @pytest.mark.parametrize("pdb, options", [ 111s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 111s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 111s pytest.param('1HPX', [], id="1HPX: no options"), 111s pytest.param('4DFR', [], id="4DFR: no options"), 111s pytest.param('3SGB', [], id="3SGB: no options"), 111s pytest.param('3SGB-subset', [ 111s "--titrate_only", 111s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 111s id="3SGB: --titrate_only"), 111s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 111s def test_regression(pdb, options, tmp_path): 111s """Basic regression test of PROPKA functionality.""" 111s path_dict = get_test_dirs() 111s ref_path = None 111s 111s for ext in ["json", "dat"]: 111s ref_path = path_dict["results"] / f"{pdb}.{ext}" 111s if ref_path.is_file(): 111s ref_path = ref_path.resolve() 111s break 111s else: 111s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 111s str(ref_path))) 111s ref_path = None 111s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 111s if pdb_path.is_file(): 111s pdb_path = pdb_path.resolve() 111s else: 111s errstr = "Missing PDB file: {0:s}".format(pdb_path) 111s raise FileNotFoundError(errstr) 111s tmp_path = Path(tmp_path).resolve() 111s 111s > run_propka(options, pdb_path, tmp_path) 111s 111s tests/test_basic_regression.py:170: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s tests/test_basic_regression.py:77: in run_propka 111s parameters = read_parameter_file(args.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s ------------------------------ Captured log call ------------------------------- 111s 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. 111s ______________________ test_regression[3SGB: no options] _______________________ 111s 111s pdb = '3SGB' 111s options = ['/tmp/autopkgtest.lK2tJD/autopkgtest_tmp/build/tests/pdb/3SGB.pdb'] 111s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_3SGB__no_optio0') 111s 111s @pytest.mark.parametrize("pdb, options", [ 111s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 111s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 111s pytest.param('1HPX', [], id="1HPX: no options"), 111s pytest.param('4DFR', [], id="4DFR: no options"), 111s pytest.param('3SGB', [], id="3SGB: no options"), 111s pytest.param('3SGB-subset', [ 111s "--titrate_only", 111s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 111s id="3SGB: --titrate_only"), 111s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 111s def test_regression(pdb, options, tmp_path): 111s """Basic regression test of PROPKA functionality.""" 111s path_dict = get_test_dirs() 111s ref_path = None 111s 111s for ext in ["json", "dat"]: 111s ref_path = path_dict["results"] / f"{pdb}.{ext}" 111s if ref_path.is_file(): 111s ref_path = ref_path.resolve() 111s break 111s else: 111s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 111s str(ref_path))) 111s ref_path = None 111s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 111s if pdb_path.is_file(): 111s pdb_path = pdb_path.resolve() 111s else: 111s errstr = "Missing PDB file: {0:s}".format(pdb_path) 111s raise FileNotFoundError(errstr) 111s tmp_path = Path(tmp_path).resolve() 111s 111s > run_propka(options, pdb_path, tmp_path) 111s 111s tests/test_basic_regression.py:170: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s tests/test_basic_regression.py:77: in run_propka 111s parameters = read_parameter_file(args.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s ------------------------------ Captured log call ------------------------------- 111s 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. 111s ____________________ test_regression[3SGB: --titrate_only] _____________________ 111s 111s pdb = '3SGB-subset' 111s 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.lK2tJD/autopkgtest_tmp/build/tests/pdb/3SGB-subset.pdb'] 111s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_3SGB____titrat0') 111s 111s @pytest.mark.parametrize("pdb, options", [ 111s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 111s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 111s pytest.param('1HPX', [], id="1HPX: no options"), 111s pytest.param('4DFR', [], id="4DFR: no options"), 111s pytest.param('3SGB', [], id="3SGB: no options"), 111s pytest.param('3SGB-subset', [ 111s "--titrate_only", 111s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 111s id="3SGB: --titrate_only"), 111s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 111s def test_regression(pdb, options, tmp_path): 111s """Basic regression test of PROPKA functionality.""" 111s path_dict = get_test_dirs() 111s ref_path = None 111s 111s for ext in ["json", "dat"]: 111s ref_path = path_dict["results"] / f"{pdb}.{ext}" 111s if ref_path.is_file(): 111s ref_path = ref_path.resolve() 111s break 111s else: 111s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 111s str(ref_path))) 111s ref_path = None 111s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 111s if pdb_path.is_file(): 111s pdb_path = pdb_path.resolve() 111s else: 111s errstr = "Missing PDB file: {0:s}".format(pdb_path) 111s raise FileNotFoundError(errstr) 111s tmp_path = Path(tmp_path).resolve() 111s 111s > run_propka(options, pdb_path, tmp_path) 111s 111s tests/test_basic_regression.py:170: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s tests/test_basic_regression.py:77: in run_propka 111s parameters = read_parameter_file(args.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s ------------------------------ Captured log call ------------------------------- 111s 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. 111s _____________________ test_regression[1HPX-warn: --quiet] ______________________ 111s 111s pdb = '1HPX-warn' 111s options = ['--quiet', '/tmp/autopkgtest.lK2tJD/autopkgtest_tmp/build/tests/pdb/1HPX-warn.pdb'] 111s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_1HPX_warn____q0') 111s 111s @pytest.mark.parametrize("pdb, options", [ 111s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 111s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 111s pytest.param('1HPX', [], id="1HPX: no options"), 111s pytest.param('4DFR', [], id="4DFR: no options"), 111s pytest.param('3SGB', [], id="3SGB: no options"), 111s pytest.param('3SGB-subset', [ 111s "--titrate_only", 111s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 111s id="3SGB: --titrate_only"), 111s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 111s def test_regression(pdb, options, tmp_path): 111s """Basic regression test of PROPKA functionality.""" 111s path_dict = get_test_dirs() 111s ref_path = None 111s 111s for ext in ["json", "dat"]: 111s ref_path = path_dict["results"] / f"{pdb}.{ext}" 111s if ref_path.is_file(): 111s ref_path = ref_path.resolve() 111s break 111s else: 111s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 111s str(ref_path))) 111s ref_path = None 111s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 111s if pdb_path.is_file(): 111s pdb_path = pdb_path.resolve() 111s else: 111s errstr = "Missing PDB file: {0:s}".format(pdb_path) 111s raise FileNotFoundError(errstr) 111s tmp_path = Path(tmp_path).resolve() 111s 111s > run_propka(options, pdb_path, tmp_path) 111s 111s tests/test_basic_regression.py:170: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s tests/test_basic_regression.py:77: in run_propka 111s parameters = read_parameter_file(args.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s ------------------------------ Captured log call ------------------------------- 111s 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. 111s __________________ test_single_file[1FTJ-Chain-A: no options] __________________ 111s 111s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_file_1FTJ_Chain_A_0') 111s pdb = '1FTJ-Chain-A', options = () 111s 111s @pytest.mark.parametrize("pdb, options", [ 111s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 111s pytest.param('3SGB-subset', ( 111s "--titrate_only", 111s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 111s id="3SGB: --titrate_only"), 111s pytest.param('1HPX-warn', ('--quiet',), id="1HPX-warn: --quiet"), 111s ]) 111s def test_single_file(tmpdir, pdb, options): 111s """Basic regression test using propka.run.single and local file for the 111s input PDB file""" 111s ref_path, pdb_path = get_paths(pdb) 111s filename = str(pdb_path) 111s 111s with tmpdir.as_cwd(): 111s > pkrun.single(filename, options) 111s 111s tests/test_run.py:31: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s /usr/lib/python3/dist-packages/propka/run.py:118: in single 111s parameters = read_parameter_file(options.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s ____________________ test_single_file[3SGB: --titrate_only] ____________________ 111s 111s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_file_3SGB____titra0') 111s pdb = '3SGB-subset' 111s 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') 111s 111s @pytest.mark.parametrize("pdb, options", [ 111s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 111s pytest.param('3SGB-subset', ( 111s "--titrate_only", 111s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 111s id="3SGB: --titrate_only"), 111s pytest.param('1HPX-warn', ('--quiet',), id="1HPX-warn: --quiet"), 111s ]) 111s def test_single_file(tmpdir, pdb, options): 111s """Basic regression test using propka.run.single and local file for the 111s input PDB file""" 111s ref_path, pdb_path = get_paths(pdb) 111s filename = str(pdb_path) 111s 111s with tmpdir.as_cwd(): 111s > pkrun.single(filename, options) 111s 111s tests/test_run.py:31: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s /usr/lib/python3/dist-packages/propka/run.py:118: in single 111s parameters = read_parameter_file(options.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s _____________________ test_single_file[1HPX-warn: --quiet] _____________________ 111s 111s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_file_1HPX_warn____0') 111s pdb = '1HPX-warn', options = ('--quiet',) 111s 111s @pytest.mark.parametrize("pdb, options", [ 111s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 111s pytest.param('3SGB-subset', ( 111s "--titrate_only", 111s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 111s id="3SGB: --titrate_only"), 111s pytest.param('1HPX-warn', ('--quiet',), id="1HPX-warn: --quiet"), 111s ]) 111s def test_single_file(tmpdir, pdb, options): 111s """Basic regression test using propka.run.single and local file for the 111s input PDB file""" 111s ref_path, pdb_path = get_paths(pdb) 111s filename = str(pdb_path) 111s 111s with tmpdir.as_cwd(): 111s > pkrun.single(filename, options) 111s 111s tests/test_run.py:31: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s /usr/lib/python3/dist-packages/propka/run.py:118: in single 111s parameters = read_parameter_file(options.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s _______________ test_single_filestream[1FTJ-Chain-A: no options] _______________ 111s 111s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_filestream_1FTJ_Ch0') 111s pdb = '1FTJ-Chain-A', options = () 111s 111s @pytest.mark.parametrize("pdb, options", [ 111s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 111s pytest.param('3SGB-subset', ( 111s "--titrate_only", 111s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 111s id="3SGB: --titrate_only"), 111s pytest.param('1HPX-warn',('--quiet',), id="1HPX-warn: --quiet"), 111s ]) 111s def test_single_filestream(tmpdir, pdb, options): 111s """Basic regression test using StringIO streams for the input PDB file""" 111s ref_path, pdb_path = get_paths(pdb) 111s filename = f"{pdb}.pdb" 111s 111s with open(pdb_path, 'r') as writer: 111s filestream = StringIO(writer.read()) 111s 111s with tmpdir.as_cwd(): 111s > pkrun.single(filename, options, stream=filestream) 111s 111s tests/test_run.py:53: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s /usr/lib/python3/dist-packages/propka/run.py:118: in singE: pybuild pybuild:483: test: plugin distutils failed with: exit code=1: cd /tmp/autopkgtest.lK2tJD/autopkgtest_tmp/build; python3.14 -m pytest -k 'not test_molecular_container' 111s le 111s parameters = read_parameter_file(options.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s _________________ test_single_filestream[3SGB: --titrate_only] _________________ 111s 111s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_filestream_3SGB___0') 111s pdb = '3SGB-subset' 111s 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') 111s 111s @pytest.mark.parametrize("pdb, options", [ 111s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 111s pytest.param('3SGB-subset', ( 111s "--titrate_only", 111s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 111s id="3SGB: --titrate_only"), 111s pytest.param('1HPX-warn',('--quiet',), id="1HPX-warn: --quiet"), 111s ]) 111s def test_single_filestream(tmpdir, pdb, options): 111s """Basic regression test using StringIO streams for the input PDB file""" 111s ref_path, pdb_path = get_paths(pdb) 111s filename = f"{pdb}.pdb" 111s 111s with open(pdb_path, 'r') as writer: 111s filestream = StringIO(writer.read()) 111s 111s with tmpdir.as_cwd(): 111s > pkrun.single(filename, options, stream=filestream) 111s 111s tests/test_run.py:53: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s /usr/lib/python3/dist-packages/propka/run.py:118: in single 111s parameters = read_parameter_file(options.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s __________________ test_single_filestream[1HPX-warn: --quiet] __________________ 111s 111s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_filestream_1HPX_wa0') 111s pdb = '1HPX-warn', options = ('--quiet',) 111s 111s @pytest.mark.parametrize("pdb, options", [ 111s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 111s pytest.param('3SGB-subset', ( 111s "--titrate_only", 111s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 111s id="3SGB: --titrate_only"), 111s pytest.param('1HPX-warn',('--quiet',), id="1HPX-warn: --quiet"), 111s ]) 111s def test_single_filestream(tmpdir, pdb, options): 111s """Basic regression test using StringIO streams for the input PDB file""" 111s ref_path, pdb_path = get_paths(pdb) 111s filename = f"{pdb}.pdb" 111s 111s with open(pdb_path, 'r') as writer: 111s filestream = StringIO(writer.read()) 111s 111s with tmpdir.as_cwd(): 111s > pkrun.single(filename, options, stream=filestream) 111s 111s tests/test_run.py:53: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s /usr/lib/python3/dist-packages/propka/run.py:118: in single 111s parameters = read_parameter_file(options.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s ______________________________ test_single_nopka _______________________________ 111s 111s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_nopka0') 111s 111s def test_single_nopka(tmpdir): 111s """Basic test to check that the pKa file is not written when write_pka is 111s `False`""" 111s pdb = "1FTJ-Chain-A" 111s ref_path, pdb_path = get_paths(pdb) 111s filename = f"{pdb}.pdb" 111s 111s with open(pdb_path, 'r') as writer: 111s filestream = StringIO(writer.read()) 111s 111s > pkrun.single(filename, stream=filestream, write_pka=False) 111s 111s tests/test_run.py:70: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s /usr/lib/python3/dist-packages/propka/run.py:118: in single 111s parameters = read_parameter_file(options.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s _______________________ test_single_extra_files_logwarn ________________________ 111s 111s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_extra_files_logwar0') 111s caplog = <_pytest.logging.LogCaptureFixture object at 0x76fef69d0830> 111s 111s def test_single_extra_files_logwarn(tmpdir, caplog): 111s """Tests that a logging warning is thrown if passing files via optargs""" 111s pdb = "1FTJ-Chain-A" 111s options = ('-f foo.pdb bar.pdb', '-f test.pdb test2.pdb') 111s ref_path, pdb_path = get_paths(pdb) 111s filename = str(pdb_path) 111s 111s with tmpdir.as_cwd(): 111s > pkrun.single(filename, options) 111s 111s tests/test_run.py:82: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s /usr/lib/python3/dist-packages/propka/run.py:118: in single 111s parameters = read_parameter_file(options.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s _______________ test_textio_filestream[1FTJ-Chain-A: no options] _______________ 111s 111s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_textio_filestream_1FTJ_Ch0') 111s pdb = '1FTJ-Chain-A', options = ['1FTJ-Chain-A.pdb'] 111s 111s @pytest.mark.parametrize("pdb, options", [ 111s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 111s pytest.param('3SGB-subset', [ 111s "--titrate_only", 111s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 111s id="3SGB: --titrate_only"), 111s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 111s ]) 111s def test_textio_filestream(tmpdir, pdb, options): 111s """Basic regression test using TextIO streams for the input PDB file""" 111s # Get the relevant paths 111s ref_path, pdb_path = get_paths(pdb) 111s filename = f"{pdb}.pdb" 111s 111s filestream = open(pdb_path, 'r') 111s 111s with tmpdir.as_cwd(): 111s > run_propka_stream(options, filestream, filename) 111s 111s tests/test_streamio.py:60: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s tests/test_streamio.py:36: in run_propka_stream 111s parameters = read_parameter_file(args.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s _________________ test_textio_filestream[3SGB: --titrate_only] _________________ 111s 111s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_textio_filestream_3SGB___0') 111s pdb = '3SGB-subset' 111s 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'] 111s 111s @pytest.mark.parametrize("pdb, options", [ 111s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 111s pytest.param('3SGB-subset', [ 111s "--titrate_only", 111s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 111s id="3SGB: --titrate_only"), 111s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 111s ]) 111s def test_textio_filestream(tmpdir, pdb, options): 111s """Basic regression test using TextIO streams for the input PDB file""" 111s # Get the relevant paths 111s ref_path, pdb_path = get_paths(pdb) 111s filename = f"{pdb}.pdb" 111s 111s filestream = open(pdb_path, 'r') 111s 111s with tmpdir.as_cwd(): 111s > run_propka_stream(options, filestream, filename) 111s 111s tests/test_streamio.py:60: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s tests/test_streamio.py:36: in run_propka_stream 111s parameters = read_parameter_file(args.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s __________________ test_textio_filestream[1HPX-warn: --quiet] __________________ 111s 111s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_textio_filestream_1HPX_wa0') 111s pdb = '1HPX-warn', options = ['--quiet', '1HPX-warn.pdb'] 111s 111s @pytest.mark.parametrize("pdb, options", [ 111s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 111s pytest.param('3SGB-subset', [ 111s "--titrate_only", 111s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 111s id="3SGB: --titrate_only"), 111s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 111s ]) 111s def test_textio_filestream(tmpdir, pdb, options): 111s """Basic regression test using TextIO streams for the input PDB file""" 111s # Get the relevant paths 111s ref_path, pdb_path = get_paths(pdb) 111s filename = f"{pdb}.pdb" 111s 111s filestream = open(pdb_path, 'r') 111s 111s with tmpdir.as_cwd(): 111s > run_propka_stream(options, filestream, filename) 111s 111s tests/test_streamio.py:60: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s tests/test_streamio.py:36: in run_propka_stream 111s parameters = read_parameter_file(args.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s ______________ test_stringio_filestream[1FTJ-Chain-A: no options] ______________ 111s 111s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_stringio_filestream_1FTJ_0') 111s pdb = '1FTJ-Chain-A', options = ['1FTJ-Chain-A.pdb'] 111s 111s @pytest.mark.parametrize("pdb, options", [ 111s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 111s pytest.param('3SGB-subset', [ 111s "--titrate_only", 111s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 111s id="3SGB: --titrate_only"), 111s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 111s ]) 111s def test_stringio_filestream(tmpdir, pdb, options): 111s """Basic regression test using StringIO streams for the input PDB file""" 111s # Get the relevant paths 111s ref_path, pdb_path = get_paths(pdb) 111s filename = f"{pdb}.pdb" 111s 111s with open(pdb_path, 'r') as writer: 111s filestream = StringIO(writer.read()) 111s 111s with tmpdir.as_cwd(): 111s > run_propka_stream(options, filestream, filename) 111s 111s tests/test_streamio.py:84: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s tests/test_streamio.py:36: in run_propka_stream 111s parameters = read_parameter_file(args.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s ________________ test_stringio_filestream[3SGB: --titrate_only] ________________ 111s 111s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_stringio_filestream_3SGB_0') 111s pdb = '3SGB-subset' 111s 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'] 111s 111s @pytest.mark.parametrize("pdb, options", [ 111s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 111s pytest.param('3SGB-subset', [ 111s "--titrate_only", 111s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 111s id="3SGB: --titrate_only"), 111s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 111s ]) 111s def test_stringio_filestream(tmpdir, pdb, options): 111s """Basic regression test using StringIO streams for the input PDB file""" 111s # Get the relevant paths 111s ref_path, pdb_path = get_paths(pdb) 111s filename = f"{pdb}.pdb" 111s 111s with open(pdb_path, 'r') as writer: 111s filestream = StringIO(writer.read()) 111s 111s with tmpdir.as_cwd(): 111s > run_propka_stream(options, filestream, filename) 111s 111s tests/test_streamio.py:84: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s tests/test_streamio.py:36: in run_propka_stream 111s parameters = read_parameter_file(args.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s _________________ test_stringio_filestream[1HPX-warn: --quiet] _________________ 111s 111s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_stringio_filestream_1HPX_0') 111s pdb = '1HPX-warn', options = ['--quiet', '1HPX-warn.pdb'] 111s 111s @pytest.mark.parametrize("pdb, options", [ 111s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 111s pytest.param('3SGB-subset', [ 111s "--titrate_only", 111s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 111s id="3SGB: --titrate_only"), 111s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 111s ]) 111s def test_stringio_filestream(tmpdir, pdb, options): 111s """Basic regression test using StringIO streams for the input PDB file""" 111s # Get the relevant paths 111s ref_path, pdb_path = get_paths(pdb) 111s filename = f"{pdb}.pdb" 111s 111s with open(pdb_path, 'r') as writer: 111s filestream = StringIO(writer.read()) 111s 111s with tmpdir.as_cwd(): 111s > run_propka_stream(options, filestream, filename) 111s 111s tests/test_streamio.py:84: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s tests/test_streamio.py:36: in run_propka_stream 111s parameters = read_parameter_file(args.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s __________________________ test_valuerror_nofiletype ___________________________ 111s 111s def test_valuerror_nofiletype(): 111s """Tests for raised ValueError when an unknown filename is passed to 111s read_molecule_file""" 111s pdb = "1FTJ-Chain-A" 111s options = [] 111s 111s ref_path, pdb_path = get_paths(pdb) 111s 111s with open(pdb_path, 'r') as writer: 111s filestream = StringIO(writer.read()) 111s 111s errmsg = "Unknown input file type" 111s with pytest.raises(ValueError, match=errmsg): 111s > run_propka_stream(options, filestream, filename="test.dat") 111s 111s tests/test_streamio.py:103: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s tests/test_streamio.py:36: in run_propka_stream 111s parameters = read_parameter_file(args.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s ____________________________ test_valuerror_notpdb _____________________________ 111s 111s def test_valuerror_notpdb(): 111s """Tests for raised ValueError when a stream object that isn't a PDB 111s is passed to read_molecule_file""" 111s pdb = "1FTJ-Chain-A" 111s options = [] 111s 111s ref_path, pdb_path = get_paths(pdb) 111s 111s filestream = StringIO() 111s 111s errmsg = "The pdb file does not seem to contain any " 111s with pytest.raises(ValueError, match=errmsg): 111s > run_propka_stream(options, filestream, filename="test.pdb") 111s 111s tests/test_streamio.py:118: 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s tests/test_streamio.py:36: in run_propka_stream 111s parameters = read_parameter_file(args.parameters, Parameters()) 111s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 111s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 111s parameters.parse_line(line) 111s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 111s 111s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 111s ^^^^^^^^^^^^^^^^^^^^ 111s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 111s 111s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 111s =========================== short test summary info ============================ 111s FAILED tests/test_basic_regression.py::test_regression[sample-issue-140: no options] 111s FAILED tests/test_basic_regression.py::test_regression[1FTJ-Chain-A: no options] 111s FAILED tests/test_basic_regression.py::test_regression[1HPX: no options] - At... 111s FAILED tests/test_basic_regression.py::test_regression[4DFR: no options] - At... 111s FAILED tests/test_basic_regression.py::test_regression[3SGB: no options] - At... 111s FAILED tests/test_basic_regression.py::test_regression[3SGB: --titrate_only] 111s FAILED tests/test_basic_regression.py::test_regression[1HPX-warn: --quiet] - ... 111s FAILED tests/test_run.py::test_single_file[1FTJ-Chain-A: no options] - Attrib... 111s FAILED tests/test_run.py::test_single_file[3SGB: --titrate_only] - AttributeE... 111s FAILED tests/test_run.py::test_single_file[1HPX-warn: --quiet] - AttributeErr... 111s FAILED tests/test_run.py::test_single_filestream[1FTJ-Chain-A: no options] - ... 111s FAILED tests/test_run.py::test_single_filestream[3SGB: --titrate_only] - Attr... 111s FAILED tests/test_run.py::test_single_filestream[1HPX-warn: --quiet] - Attrib... 111s FAILED tests/test_run.py::test_single_nopka - AttributeError: 'Parameters' ob... 111s FAILED tests/test_run.py::test_single_extra_files_logwarn - AttributeError: '... 111s FAILED tests/test_streamio.py::test_textio_filestream[1FTJ-Chain-A: no options] 111s FAILED tests/test_streamio.py::test_textio_filestream[3SGB: --titrate_only] 111s FAILED tests/test_streamio.py::test_textio_filestream[1HPX-warn: --quiet] - A... 111s FAILED tests/test_streamio.py::test_stringio_filestream[1FTJ-Chain-A: no options] 111s FAILED tests/test_streamio.py::test_stringio_filestream[3SGB: --titrate_only] 111s FAILED tests/test_streamio.py::test_stringio_filestream[1HPX-warn: --quiet] 111s FAILED tests/test_streamio.py::test_valuerror_nofiletype - AttributeError: 'P... 111s FAILED tests/test_streamio.py::test_valuerror_notpdb - AttributeError: 'Param... 111s ================= 23 failed, 24 passed, 2 deselected in 0.31s ================== 111s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.13 3.14" returned exit code 13 111s make: *** [/tmp/d0wPTFnJiv/run:4: pybuild-autopkgtest] Error 25 111s pybuild-autopkgtest: error: /tmp/d0wPTFnJiv/run pybuild-autopkgtest returned exit code 2 112s autopkgtest [12:36:03]: test pybuild-autopkgtest: -----------------------] 112s autopkgtest [12:36:03]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 112s pybuild-autopkgtest FAIL non-zero exit status 25 112s autopkgtest [12:36:03]: @@@@@@@@@@@@@@@@@@@@ summary 112s pybuild-autopkgtest FAIL non-zero exit status 25