0s autopkgtest [19:44:21]: starting date and time: 2026-01-22 19:44:21+0000 0s autopkgtest [19:44:21]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [19:44:21]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.kfi1vxcm/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-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-arm64-4.secgroup --name adt-resolute-arm64-propka-20260122-194421-juju-7f2275-prod-proposed-migration-environment-2-959d3e6a-80cd-4f9c-9780-20eaed215191 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-arm64-propka-20260122-194421-juju-7f2275-prod-proposed-migration-environment-2-959d3e6a-80cd-4f9c-9780-20eaed215191 from image adt/ubuntu-resolute-arm64-server-20260122.img (UUID ed27afc7-5f46-4e8b-ad73-864280a0ddbb)... 72s autopkgtest [19:45:33]: testbed dpkg architecture: arm64 72s autopkgtest [19:45:33]: testbed apt version: 3.1.12 73s autopkgtest [19:45:34]: @@@@@@@@@@@@@@@@@@@@ test bed setup 73s autopkgtest [19:45:34]: testbed release detected to be: None 73s autopkgtest [19:45:34]: updating testbed package index (apt update) 74s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 74s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 74s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 74s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 74s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 74s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [80.9 kB] 75s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [815 kB] 75s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [19.2 kB] 75s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [103 kB] 75s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [3316 B] 75s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [7876 B] 75s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [120 B] 75s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [639 kB] 75s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [16.2 kB] 75s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [4636 B] 75s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [460 B] 78s Fetched 1818 kB in 2s (1056 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... 81s Building dependency tree... 81s Reading state information... 81s Calculating upgrade... 81s The following packages were automatically installed and are no longer required: 81s python3.13 python3.13-minimal 81s 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 82s 4 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 82s Need to get 6705 kB of archives. 82s After this operation, 26.0 MB of additional disk space will be used. 82s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-minimal arm64 3.14.2-1 [917 kB] 82s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-minimal arm64 3.14.2-1 [2548 kB] 82s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-gdbm arm64 3.14.2-1 [11.1 kB] 82s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-minimal arm64 3.14.2-1 [28.2 kB] 82s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3 arm64 3.14.2-1 [22.9 kB] 82s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-stdlib arm64 3.14.2-1 [2351 kB] 82s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14 arm64 3.14.2-1 [816 kB] 82s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-stdlib arm64 3.14.2-1 [10.9 kB] 82s dpkg-preconfigure: unable to re-open stdin: No such file or directory 82s Fetched 6705 kB in 1s (12.9 MB/s) 82s Selecting previously unselected package libpython3.14-minimal:arm64. 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 ... 135223 files and directories currently installed.) 83s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_arm64.deb ... 83s Unpacking libpython3.14-minimal:arm64 (3.14.2-1) ... 83s Selecting previously unselected package python3.14-minimal. 83s Preparing to unpack .../python3.14-minimal_3.14.2-1_arm64.deb ... 83s Unpacking python3.14-minimal (3.14.2-1) ... 83s Preparing to unpack .../python3-gdbm_3.14.2-1_arm64.deb ... 83s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-1) ... 83s Setting up libpython3.14-minimal:arm64 (3.14.2-1) ... 83s Setting up python3.14-minimal (3.14.2-1) ... 84s (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 ... 135565 files and directories currently installed.) 84s Preparing to unpack .../python3-minimal_3.14.2-1_arm64.deb ... 84s Unpacking python3-minimal (3.14.2-1) over (3.13.7-1) ... 84s Setting up python3-minimal (3.14.2-1) ... 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 ... 135565 files and directories currently installed.) 85s Preparing to unpack .../python3_3.14.2-1_arm64.deb ... 85s running python pre-rtupdate hooks for python3.14... 85s Unpacking python3 (3.14.2-1) over (3.13.7-1) ... 85s Selecting previously unselected package libpython3.14-stdlib:arm64. 85s Preparing to unpack .../libpython3.14-stdlib_3.14.2-1_arm64.deb ... 85s Unpacking libpython3.14-stdlib:arm64 (3.14.2-1) ... 85s Selecting previously unselected package python3.14. 85s Preparing to unpack .../python3.14_3.14.2-1_arm64.deb ... 85s Unpacking python3.14 (3.14.2-1) ... 85s Preparing to unpack .../libpython3-stdlib_3.14.2-1_arm64.deb ... 85s Unpacking libpython3-stdlib:arm64 (3.14.2-1) over (3.13.7-1) ... 85s Setting up libpython3.14-stdlib:arm64 (3.14.2-1) ... 85s Setting up python3.14 (3.14.2-1) ... 86s Setting up libpython3-stdlib:arm64 (3.14.2-1) ... 86s Setting up python3-gdbm (3.14.2-1) ... 86s Setting up python3 (3.14.2-1) ... 86s running python rtupdate hooks for python3.14... 86s running python post-rtupdate hooks for python3.14... 87s Processing triggers for man-db (2.13.1-1) ... 87s Processing triggers for systemd (259-1ubuntu2) ... 87s autopkgtest [19:45:48]: upgrading testbed (apt dist-upgrade and autopurge) 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 88s Calculating upgrade... 88s The following packages were automatically installed and are no longer required: 88s python3.13 python3.13-minimal 88s Use 'sudo apt autoremove' to remove them. 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 89s Solving dependencies... 90s The following packages will be REMOVED: 90s python3.13* python3.13-minimal* 90s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 90s After this operation, 7766 kB disk space will be freed. 90s (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 ... 135995 files and directories currently installed.) 90s Removing python3.13 (3.13.11-1) ... 90s Removing python3.13-minimal (3.13.11-1) ... 91s Processing triggers for man-db (2.13.1-1) ... 91s Processing triggers for systemd (259-1ubuntu2) ... 91s (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 ... 135968 files and directories currently installed.) 91s Purging configuration files for python3.13-minimal (3.13.11-1) ... 94s autopkgtest [19:45:55]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:41:39 UTC 2026 94s autopkgtest [19:45:55]: @@@@@@@@@@@@@@@@@@@@ apt-source propka 97s Get:1 http://ftpmaster.internal/ubuntu resolute/universe propka 3.5.1-2 (dsc) [2286 B] 97s Get:2 http://ftpmaster.internal/ubuntu resolute/universe propka 3.5.1-2 (tar) [376 kB] 97s Get:3 http://ftpmaster.internal/ubuntu resolute/universe propka 3.5.1-2 (diff) [5096 B] 97s gpgv: Signature made Wed Oct 16 14:47:53 2024 UTC 97s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 97s gpgv: issuer "emollier@debian.org" 97s gpgv: Can't check signature: No public key 97s dpkg-source: warning: cannot verify inline signature for ./propka_3.5.1-2.dsc: no acceptable signature found 97s autopkgtest [19:45:58]: testing package propka version 3.5.1-2 97s autopkgtest [19:45:58]: build not needed 98s autopkgtest [19:45:59]: test pybuild-autopkgtest: preparing testbed 98s Reading package lists... 98s Building dependency tree... 98s Reading state information... 98s Solving dependencies... 99s The following NEW packages will be installed: 99s autoconf automake autopoint autotools-dev build-essential cpp cpp-15 99s cpp-15-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper debugedit 99s dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz 99s fonts-font-awesome fonts-lato fonts-mathjax g++ g++-15 99s g++-15-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-15 99s gcc-15-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext help2man 99s intltool-debian libarchive-zip-perl libasan8 libblas3 libcc1-0 99s libdebhelper-perl libfile-stripnondeterminism-perl libgcc-15-dev 99s libgfortran5 libgomp1 libhwasan0 libisl23 libitm1 libjs-jquery libjs-mathjax 99s libjson-perl liblapack3 liblsan0 libmpc3 libstdc++-15-dev libtool libtsan2 99s libubsan1 m4 po-debconf pybuild-plugin-autopkgtest python-propka-doc 99s python3-alabaster python3-all python3-defusedxml python3-docutils 99s python3-imagesize python3-iniconfig python3-numpy python3-numpy-dev 99s python3-pluggy python3-propka python3-pytest python3-roman-numerals 99s python3-snowballstemmer python3-sphinx python3-sphinx-rtd-theme 99s python3-sphinxcontrib.jquery python3.13 python3.13-minimal sgml-base 99s sphinx-common sphinx-rtd-theme-common xml-core 99s 0 upgraded, 78 newly installed, 0 to remove and 0 not upgraded. 99s Need to get 95.8 MB of archives. 99s After this operation, 363 MB of additional disk space will be used. 99s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.13-minimal arm64 3.13.11-1 [2346 kB] 99s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-lato all 2.015-1build1 [2779 kB] 99s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.3.5+ds-3 [366 kB] 99s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 99s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-11ubuntu1 [450 kB] 99s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 99s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.3.5+ds-3 [4569 kB] 99s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.13 arm64 3.13.11-1 [758 kB] 99s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 m4 arm64 1.4.20-2 [213 kB] 99s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 autoconf all 2.72-3.1ubuntu1 [384 kB] 99s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 autotools-dev all 20240727.1 [43.4 kB] 99s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 automake all 1:1.18.1-3build1 [582 kB] 99s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 autopoint all 0.23.2-1 [620 kB] 99s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libisl23 arm64 0.27-1build1 [676 kB] 99s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libmpc3 arm64 1.3.1-2 [55.6 kB] 99s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15-aarch64-linux-gnu arm64 15.2.0-11ubuntu1 [11.7 MB] 99s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15 arm64 15.2.0-11ubuntu1 [1030 B] 99s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [5736 B] 99s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp arm64 4:15.2.0-4ubuntu1 [22.4 kB] 99s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libcc1-0 arm64 15.2.0-11ubuntu1 [49.0 kB] 99s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-11ubuntu1 [147 kB] 99s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libitm1 arm64 15.2.0-11ubuntu1 [28.0 kB] 99s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 libasan8 arm64 15.2.0-11ubuntu1 [2920 kB] 99s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 liblsan0 arm64 15.2.0-11ubuntu1 [1316 kB] 100s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 libtsan2 arm64 15.2.0-11ubuntu1 [2690 kB] 100s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 libubsan1 arm64 15.2.0-11ubuntu1 [1176 kB] 100s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libhwasan0 arm64 15.2.0-11ubuntu1 [1638 kB] 100s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 libgcc-15-dev arm64 15.2.0-11ubuntu1 [2600 kB] 100s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15-aarch64-linux-gnu arm64 15.2.0-11ubuntu1 [23.1 MB] 100s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15 arm64 15.2.0-11ubuntu1 [517 kB] 100s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [1206 B] 100s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc arm64 4:15.2.0-4ubuntu1 [5016 B] 100s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libstdc++-15-dev arm64 15.2.0-11ubuntu1 [2547 kB] 100s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15-aarch64-linux-gnu arm64 15.2.0-11ubuntu1 [13.2 MB] 101s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15 arm64 15.2.0-11ubuntu1 [24.6 kB] 101s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [956 B] 101s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 g++ arm64 4:15.2.0-4ubuntu1 [1080 B] 101s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 build-essential arm64 12.12ubuntu2 [5254 B] 101s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libdebhelper-perl all 13.28ubuntu1 [97.4 kB] 101s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libtool all 2.5.4-9 [169 kB] 101s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 dh-autoreconf all 21 [12.5 kB] 101s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 101s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1build1 [20.6 kB] 101s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 dh-strip-nondeterminism all 1.15.0-1build1 [5110 B] 101s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 debugedit arm64 1:5.2-3 [49.1 kB] 101s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 dwz arm64 0.16-2 [113 kB] 101s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 gettext arm64 0.23.2-1 [998 kB] 101s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 intltool-debian all 0.35.0+20060710.6build1 [24.1 kB] 101s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 po-debconf all 1.0.22 [215 kB] 101s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 debhelper all 13.28ubuntu1 [916 kB] 101s Get:51 http://ftpmaster.internal/ubuntu resolute/universe arm64 dh-python all 7.20251231 [122 kB] 101s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 sgml-base all 1.31+nmu1 [11.0 kB] 101s Get:53 http://ftpmaster.internal/ubuntu resolute/main arm64 xml-core all 0.19build1 [20.3 kB] 101s Get:54 http://ftpmaster.internal/ubuntu resolute/main arm64 docutils-common all 0.22.4+dfsg-1 [130 kB] 101s Get:55 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1build1 [531 kB] 101s Get:56 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 101s Get:57 http://ftpmaster.internal/ubuntu resolute/universe arm64 help2man arm64 1.49.3 [201 kB] 101s Get:58 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 101s Get:59 http://ftpmaster.internal/ubuntu resolute/main arm64 libjson-perl all 4.10000-1 [81.9 kB] 101s Get:60 http://ftpmaster.internal/ubuntu resolute/universe arm64 pybuild-plugin-autopkgtest all 7.20251231 [1748 B] 101s Get:61 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 101s Get:62 http://ftpmaster.internal/ubuntu resolute/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 101s Get:63 http://ftpmaster.internal/ubuntu resolute/universe arm64 python-propka-doc all 3.5.1-2 [157 kB] 101s Get:64 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-all arm64 3.14.2-1 [888 B] 101s Get:65 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-defusedxml all 0.7.1-3build1 [42.4 kB] 101s Get:66 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-roman-numerals all 4.1.0-1 [8660 B] 101s Get:67 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-docutils all 0.22.4+dfsg-1 [439 kB] 101s Get:68 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-imagesize all 1.4.1-1build1 [6900 B] 101s Get:69 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-iniconfig all 2.1.0-2 [6962 B] 101s Get:70 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pluggy all 1.6.0-2 [21.1 kB] 101s Get:71 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-propka all 3.5.1-2 [70.1 kB] 101s Get:72 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytest all 9.0.2-2 [277 kB] 101s Get:73 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-snowballstemmer all 3.0.1-1 [65.9 kB] 101s Get:74 http://ftpmaster.internal/ubuntu resolute/main arm64 sphinx-common all 8.2.3-12 [657 kB] 101s Get:75 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-alabaster all 0.7.16-0.1build1 [18.6 kB] 101s Get:76 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-sphinx all 8.2.3-12 [483 kB] 101s Get:77 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-sphinxcontrib.jquery all 4.1-6 [6856 B] 101s Get:78 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-sphinx-rtd-theme all 3.0.2+dfsg-3 [23.5 kB] 102s Fetched 95.8 MB in 3s (37.2 MB/s) 102s Selecting previously unselected package python3.13-minimal. 102s (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 ... 135970 files and directories currently installed.) 102s Preparing to unpack .../00-python3.13-minimal_3.13.11-1_arm64.deb ... 102s Unpacking python3.13-minimal (3.13.11-1) ... 102s Selecting previously unselected package fonts-lato. 102s Preparing to unpack .../01-fonts-lato_2.015-1build1_all.deb ... 102s Unpacking fonts-lato (2.015-1build1) ... 102s Selecting previously unselected package python3-numpy-dev:arm64. 102s Preparing to unpack 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(libblas.so.3-aarch64-linux-gnu) in auto mode 109s Setting up python3-snowballstemmer (3.0.1-1) ... 110s Setting up libmpc3:arm64 (1.3.1-2) ... 110s Setting up python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 110s Setting up autopoint (0.23.2-1) ... 110s Setting up libgfortran5:arm64 (15.2.0-11ubuntu1) ... 110s Setting up autoconf (2.72-3.1ubuntu1) ... 110s Setting up python3-pluggy (1.6.0-2) ... 110s Setting up libubsan1:arm64 (15.2.0-11ubuntu1) ... 110s Setting up dwz (0.16-2) ... 110s Setting up libhwasan0:arm64 (15.2.0-11ubuntu1) ... 110s Setting up libasan8:arm64 (15.2.0-11ubuntu1) ... 110s Setting up libjson-perl (4.10000-1) ... 110s Setting up debugedit (1:5.2-3) ... 110s Setting up python3-roman-numerals (4.1.0-1) ... 110s Setting up python3.13-minimal (3.13.11-1) ... 111s Setting up sgml-base (1.31+nmu1) ... 111s Setting up libtsan2:arm64 (15.2.0-11ubuntu1) ... 111s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 111s Setting up libisl23:arm64 (0.27-1build1) ... 111s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ... 111s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 111s Setting up libcc1-0:arm64 (15.2.0-11ubuntu1) ... 111s Setting up liblsan0:arm64 (15.2.0-11ubuntu1) ... 111s Setting up libitm1:arm64 (15.2.0-11ubuntu1) ... 111s Setting up python3-imagesize (1.4.1-1build1) ... 111s Setting up automake (1:1.18.1-3build1) ... 111s update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode 111s Setting up libfile-stripnondeterminism-perl (1.15.0-1build1) ... 111s Setting up cpp-15-aarch64-linux-gnu (15.2.0-11ubuntu1) ... 111s Setting up liblapack3:arm64 (3.12.1-7ubuntu1) ... 111s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 111s Setting up gettext (0.23.2-1) ... 111s Setting up libgcc-15-dev:arm64 (15.2.0-11ubuntu1) ... 111s Setting up python3.13 (3.13.11-1) ... 112s Setting up python3-pytest (9.0.2-2) ... 113s Setting up python3-all (3.14.2-1) ... 113s Setting up intltool-debian (0.35.0+20060710.6build1) ... 113s Setting up cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 113s Setting up libstdc++-15-dev:arm64 (15.2.0-11ubuntu1) ... 113s Setting up sphinx-common (8.2.3-12) ... 113s Setting up python3-numpy (1:2.3.5+ds-3) ... 117s Setting up dh-strip-nondeterminism (1.15.0-1build1) ... 117s Setting up python-propka-doc (3.5.1-2) ... 117s Setting up cpp-15 (15.2.0-11ubuntu1) ... 117s Setting up cpp (4:15.2.0-4ubuntu1) ... 117s Setting up xml-core (0.19build1) ... 117s Setting up gcc-15-aarch64-linux-gnu (15.2.0-11ubuntu1) ... 117s Setting up po-debconf (1.0.22) ... 117s Setting up gcc-15 (15.2.0-11ubuntu1) ... 117s Setting up g++-15-aarch64-linux-gnu (15.2.0-11ubuntu1) ... 117s Setting up g++-15 (15.2.0-11ubuntu1) ... 117s Setting up gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 117s Setting up libtool (2.5.4-9) ... 117s Setting up gcc (4:15.2.0-4ubuntu1) ... 117s Setting up dh-autoreconf (21) ... 117s Setting up g++-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 117s Setting up debhelper (13.28ubuntu1) ... 117s Setting up g++ (4:15.2.0-4ubuntu1) ... 117s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 117s Setting up build-essential (12.12ubuntu2) ... 117s Setting up pybuild-plugin-autopkgtest (7.20251231) ... 117s Processing triggers for install-info (7.2-5) ... 117s Processing triggers for libc-bin (2.42-2ubuntu4) ... 118s Processing triggers for systemd (259-1ubuntu2) ... 118s Processing triggers for man-db (2.13.1-1) ... 119s Processing triggers for sgml-base (1.31+nmu1) ... 119s Setting up docutils-common (0.22.4+dfsg-1) ... 119s Processing triggers for sgml-base (1.31+nmu1) ... 119s Setting up python3-docutils (0.22.4+dfsg-1) ... 120s Setting up python3-sphinx (8.2.3-12) ... 122s Setting up python3-sphinxcontrib.jquery (4.1-6) ... 122s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-3) ... 123s autopkgtest [19:46:24]: test pybuild-autopkgtest: pybuild-autopkgtest 123s autopkgtest [19:46:24]: test pybuild-autopkgtest: [----------------------- 124s pybuild-autopkgtest 124s I: pybuild base:384: cd /tmp/autopkgtest.dbAyJa/autopkgtest_tmp/build; python3.13 -m pytest -k 'not test_molecular_container' 125s ============================= test session starts ============================== 125s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 125s rootdir: /tmp/autopkgtest.dbAyJa/autopkgtest_tmp/build 125s plugins: typeguard-4.4.4 125s collected 49 items / 2 deselected / 47 selected 125s 127s tests/test_basic_regression.py ....... [ 14%] 127s tests/test_hybrid36.py .. [ 19%] 127s tests/test_input.py .. [ 23%] 127s tests/test_lib.py .. [ 27%] 127s tests/test_protonate.py . [ 29%] 129s tests/test_run.py ........ [ 46%] 130s tests/test_streamio.py ........ [ 63%] 130s tests/test_vector_algebra.py ............... [ 95%] 130s tests/test_version.py .. [100%] 130s 130s ======================= 47 passed, 2 deselected in 5.63s ======================= 130s I: pybuild base:384: cd /tmp/autopkgtest.dbAyJa/autopkgtest_tmp/build; python3.14 -m pytest -k 'not test_molecular_container' 131s ============================= test session starts ============================== 131s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 131s rootdir: /tmp/autopkgtest.dbAyJa/autopkgtest_tmp/build 131s plugins: typeguard-4.4.4 131s collected 49 items / 2 deselected / 47 selected 131s 131s tests/test_basic_regression.py FFFFFFF [ 14%] 131s tests/test_hybrid36.py .. [ 19%] 131s tests/test_input.py .. [ 23%] 131s tests/test_lib.py .. [ 27%] 131s tests/test_protonate.py . [ 29%] 131s tests/test_run.py FFFFFFFF [ 46%] 131s tests/test_streamio.py FFFFFFFF [ 63%] 131s tests/test_vector_algebra.py ............... [ 95%] 131s tests/test_version.py .. [100%] 131s 131s =================================== FAILURES =================================== 131s ________________ test_regression[sample-issue-140: no options] _________________ 131s 131s pdb = 'sample-issue-140' 131s options = ['/tmp/autopkgtest.dbAyJa/autopkgtest_tmp/build/tests/pdb/sample-issue-140.pdb'] 131s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_sample_issue_10') 131s 131s @pytest.mark.parametrize("pdb, options", [ 131s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 131s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 131s pytest.param('1HPX', [], id="1HPX: no options"), 131s pytest.param('4DFR', [], id="4DFR: no options"), 131s pytest.param('3SGB', [], id="3SGB: no options"), 131s pytest.param('3SGB-subset', [ 131s "--titrate_only", 131s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 131s id="3SGB: --titrate_only"), 131s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 131s def test_regression(pdb, options, tmp_path): 131s """Basic regression test of PROPKA functionality.""" 131s path_dict = get_test_dirs() 131s ref_path = None 131s 131s for ext in ["json", "dat"]: 131s ref_path = path_dict["results"] / f"{pdb}.{ext}" 131s if ref_path.is_file(): 131s ref_path = ref_path.resolve() 131s break 131s else: 131s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 131s str(ref_path))) 131s ref_path = None 131s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 131s if pdb_path.is_file(): 131s pdb_path = pdb_path.resolve() 131s else: 131s errstr = "Missing PDB file: {0:s}".format(pdb_path) 131s raise FileNotFoundError(errstr) 131s tmp_path = Path(tmp_path).resolve() 131s 131s > run_propka(options, pdb_path, tmp_path) 131s 131s tests/test_basic_regression.py:170: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s tests/test_basic_regression.py:77: in run_propka 131s parameters = read_parameter_file(args.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s ------------------------------ Captured log call ------------------------------- 131s 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. 131s __________________ test_regression[1FTJ-Chain-A: no options] ___________________ 131s 131s pdb = '1FTJ-Chain-A' 131s options = ['/tmp/autopkgtest.dbAyJa/autopkgtest_tmp/build/tests/pdb/1FTJ-Chain-A.pdb'] 131s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_1FTJ_Chain_A__0') 131s 131s @pytest.mark.parametrize("pdb, options", [ 131s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 131s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 131s pytest.param('1HPX', [], id="1HPX: no options"), 131s pytest.param('4DFR', [], id="4DFR: no options"), 131s pytest.param('3SGB', [], id="3SGB: no options"), 131s pytest.param('3SGB-subset', [ 131s "--titrate_only", 131s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 131s id="3SGB: --titrate_only"), 131s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 131s def test_regression(pdb, options, tmp_path): 131s """Basic regression test of PROPKA functionality.""" 131s path_dict = get_test_dirs() 131s ref_path = None 131s 131s for ext in ["json", "dat"]: 131s ref_path = path_dict["results"] / f"{pdb}.{ext}" 131s if ref_path.is_file(): 131s ref_path = ref_path.resolve() 131s break 131s else: 131s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 131s str(ref_path))) 131s ref_path = None 131s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 131s if pdb_path.is_file(): 131s pdb_path = pdb_path.resolve() 131s else: 131s errstr = "Missing PDB file: {0:s}".format(pdb_path) 131s raise FileNotFoundError(errstr) 131s tmp_path = Path(tmp_path).resolve() 131s 131s > run_propka(options, pdb_path, tmp_path) 131s 131s tests/test_basic_regression.py:170: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s tests/test_basic_regression.py:77: in run_propka 131s parameters = read_parameter_file(args.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s ------------------------------ Captured log call ------------------------------- 131s 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. 131s ______________________ test_regression[1HPX: no options] _______________________ 131s 131s pdb = '1HPX' 131s options = ['/tmp/autopkgtest.dbAyJa/autopkgtest_tmp/build/tests/pdb/1HPX.pdb'] 131s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_1HPX__no_optio0') 131s 131s @pytest.mark.parametrize("pdb, options", [ 131s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 131s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 131s pytest.param('1HPX', [], id="1HPX: no options"), 131s pytest.param('4DFR', [], id="4DFR: no options"), 131s pytest.param('3SGB', [], id="3SGB: no options"), 131s pytest.param('3SGB-subset', [ 131s "--titrate_only", 131s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 131s id="3SGB: --titrate_only"), 131s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 131s def test_regression(pdb, options, tmp_path): 131s """Basic regression test of PROPKA functionality.""" 131s path_dict = get_test_dirs() 131s ref_path = None 131s 131s for ext in ["json", "dat"]: 131s ref_path = path_dict["results"] / f"{pdb}.{ext}" 131s if ref_path.is_file(): 131s ref_path = ref_path.resolve() 131s break 131s else: 131s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 131s str(ref_path))) 131s ref_path = None 131s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 131s if pdb_path.is_file(): 131s pdb_path = pdb_path.resolve() 131s else: 131s errstr = "Missing PDB file: {0:s}".format(pdb_path) 131s raise FileNotFoundError(errstr) 131s tmp_path = Path(tmp_path).resolve() 131s 131s > run_propka(options, pdb_path, tmp_path) 131s 131s tests/test_basic_regression.py:170: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s tests/test_basic_regression.py:77: in run_propka 131s parameters = read_parameter_file(args.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s ------------------------------ Captured log call ------------------------------- 131s 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. 131s ______________________ test_regression[4DFR: no options] _______________________ 131s 131s pdb = '4DFR' 131s options = ['/tmp/autopkgtest.dbAyJa/autopkgtest_tmp/build/tests/pdb/4DFR.pdb'] 131s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_4DFR__no_optio0') 131s 131s @pytest.mark.parametrize("pdb, options", [ 131s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 131s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 131s pytest.param('1HPX', [], id="1HPX: no options"), 131s pytest.param('4DFR', [], id="4DFR: no options"), 131s pytest.param('3SGB', [], id="3SGB: no options"), 131s pytest.param('3SGB-subset', [ 131s "--titrate_only", 131s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 131s id="3SGB: --titrate_only"), 131s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 131s def test_regression(pdb, options, tmp_path): 131s """Basic regression test of PROPKA functionality.""" 131s path_dict = get_test_dirs() 131s ref_path = None 131s 131s for ext in ["json", "dat"]: 131s ref_path = path_dict["results"] / f"{pdb}.{ext}" 131s if ref_path.is_file(): 131s ref_path = ref_path.resolve() 131s break 131s else: 131s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 131s str(ref_path))) 131s ref_path = None 131s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 131s if pdb_path.is_file(): 131s pdb_path = pdb_path.resolve() 131s else: 131s errstr = "Missing PDB file: {0:s}".format(pdb_path) 131s raise FileNotFoundError(errstr) 131s tmp_path = Path(tmp_path).resolve() 131s 131s > run_propka(options, pdb_path, tmp_path) 131s 131s tests/test_basic_regression.py:170: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s tests/test_basic_regression.py:77: in run_propka 131s parameters = read_parameter_file(args.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s ------------------------------ Captured log call ------------------------------- 131s 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. 131s ______________________ test_regression[3SGB: no options] _______________________ 131s 131s pdb = '3SGB' 131s options = ['/tmp/autopkgtest.dbAyJa/autopkgtest_tmp/build/tests/pdb/3SGB.pdb'] 131s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_3SGB__no_optio0') 131s 131s @pytest.mark.parametrize("pdb, options", [ 131s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 131s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 131s pytest.param('1HPX', [], id="1HPX: no options"), 131s pytest.param('4DFR', [], id="4DFR: no options"), 131s pytest.param('3SGB', [], id="3SGB: no options"), 131s pytest.param('3SGB-subset', [ 131s "--titrate_only", 131s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 131s id="3SGB: --titrate_only"), 131s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 131s def test_regression(pdb, options, tmp_path): 131s """Basic regression test of PROPKA functionality.""" 131s path_dict = get_test_dirs() 131s ref_path = None 131s 131s for ext in ["json", "dat"]: 131s ref_path = path_dict["results"] / f"{pdb}.{ext}" 131s if ref_path.is_file(): 131s ref_path = ref_path.resolve() 131s break 131s else: 131s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 131s str(ref_path))) 131s ref_path = None 131s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 131s if pdb_path.is_file(): 131s pdb_path = pdb_path.resolve() 131s else: 131s errstr = "Missing PDB file: {0:s}".format(pdb_path) 131s raise FileNotFoundError(errstr) 131s tmp_path = Path(tmp_path).resolve() 131s 131s > run_propka(options, pdb_path, tmp_path) 131s 131s tests/test_basic_regression.py:170: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s tests/test_basic_regression.py:77: in run_propka 131s parameters = read_parameter_file(args.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s ------------------------------ Captured log call ------------------------------- 131s 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. 131s ____________________ test_regression[3SGB: --titrate_only] _____________________ 131s 131s pdb = '3SGB-subset' 131s 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.dbAyJa/autopkgtest_tmp/build/tests/pdb/3SGB-subset.pdb'] 131s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_3SGB____titrat0') 131s 131s @pytest.mark.parametrize("pdb, options", [ 131s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 131s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 131s pytest.param('1HPX', [], id="1HPX: no options"), 131s pytest.param('4DFR', [], id="4DFR: no options"), 131s pytest.param('3SGB', [], id="3SGB: no options"), 131s pytest.param('3SGB-subset', [ 131s "--titrate_only", 131s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 131s id="3SGB: --titrate_only"), 131s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 131s def test_regression(pdb, options, tmp_path): 131s """Basic regression test of PROPKA functionality.""" 131s path_dict = get_test_dirs() 131s ref_path = None 131s 131s for ext in ["json", "dat"]: 131s ref_path = path_dict["results"] / f"{pdb}.{ext}" 131s if ref_path.is_file(): 131s ref_path = ref_path.resolve() 131s break 131s else: 131s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 131s str(ref_path))) 131s ref_path = None 131s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 131s if pdb_path.is_file(): 131s pdb_path = pdb_path.resolve() 131s else: 131s errstr = "Missing PDB file: {0:s}".format(pdb_path) 131s raise FileNotFoundError(errstr) 131s tmp_path = Path(tmp_path).resolve() 131s 131s > run_propka(options, pdb_path, tmp_path) 131s 131s tests/test_basic_regression.py:170: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s tests/test_basic_regression.py:77: in run_propka 131s parameters = read_parameter_file(args.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s ------------------------------ Captured log call ------------------------------- 131s 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. 131s _____________________ test_regression[1HPX-warn: --quiet] ______________________ 131s 131s pdb = '1HPX-warn' 131s options = ['--quiet', '/tmp/autopkgtest.dbAyJa/autopkgtest_tmp/build/tests/pdb/1HPX-warn.pdb'] 131s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_1HPX_warn____q0') 131s 131s @pytest.mark.parametrize("pdb, options", [ 131s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 131s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 131s pytest.param('1HPX', [], id="1HPX: no options"), 131s pytest.param('4DFR', [], id="4DFR: no options"), 131s pytest.param('3SGB', [], id="3SGB: no options"), 131s pytest.param('3SGB-subset', [ 131s "--titrate_only", 131s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 131s id="3SGB: --titrate_only"), 131s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 131s def test_regression(pdb, options, tmp_path): 131s """Basic regression test of PROPKA functionality.""" 131s path_dict = get_test_dirs() 131s ref_path = None 131s 131s for ext in ["json", "dat"]: 131s ref_path = path_dict["results"] / f"{pdb}.{ext}" 131s if ref_path.is_file(): 131s ref_path = ref_path.resolve() 131s break 131s else: 131s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 131s str(ref_path))) 131s ref_path = None 131s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 131s if pdb_path.is_file(): 131s pdb_path = pdb_path.resolve() 131s else: 131s errstr = "Missing PDB file: {0:s}".format(pdb_path) 131s raise FileNotFoundError(errstr) 131s tmp_path = Path(tmp_path).resolve() 131s 131s > run_propka(options, pdb_path, tmp_path) 131s 131s tests/test_basic_regression.py:170: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s tests/test_basic_regression.py:77: in run_propka 131s parameters = read_parameter_file(args.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s ------------------------------ Captured log call ------------------------------- 131s 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. 131s __________________ test_single_file[1FTJ-Chain-A: no options] __________________ 131s 131s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_file_1FTJ_Chain_A_0') 131s pdb = '1FTJ-Chain-A', options = () 131s 131s @pytest.mark.parametrize("pdb, options", [ 131s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 131s pytest.param('3SGB-subset', ( 131s "--titrate_only", 131s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 131s id="3SGB: --titrate_only"), 131s pytest.param('1HPX-warn', ('--quiet',), id="1HPX-warn: --quiet"), 131s ]) 131s def test_single_file(tmpdir, pdb, options): 131s """Basic regression test using propka.run.single and local file for the 131s input PDB file""" 131s ref_path, pdb_path = get_paths(pdb) 131s filename = str(pdb_path) 131s 131s with tmpdir.as_cwd(): 131s > pkrun.single(filename, options) 131s 131s tests/test_run.py:31: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s /usr/lib/python3/dist-packages/propka/run.py:118: in single 131s parameters = read_parameter_file(options.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s ____________________ test_single_file[3SGB: --titrate_only] ____________________ 131s 131s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_file_3SGB____titra0') 131s pdb = '3SGB-subset' 131s 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') 131s 131s @pytest.mark.parametrize("pdb, options", [ 131s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 131s pytest.param('3SGB-subset', ( 131s "--titrate_only", 131s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 131s id="3SGB: --titrate_only"), 131s pytest.param('1HPX-warn', ('--quiet',), id="1HPX-warn: --quiet"), 131s ]) 131s def test_single_file(tmpdir, pdb, options): 131s """Basic regression test using propka.run.single and local file for the 131s input PDB file""" 131s ref_path, pdb_path = get_paths(pdb) 131s filename = str(pdb_path) 131s 131s with tmpdir.as_cwd(): 131s > pkrun.single(filename, options) 131s 131s tests/test_run.py:31: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s /usr/lib/python3/dist-packages/propka/run.py:118: in single 131s parameters = read_parameter_file(options.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s _____________________ test_single_file[1HPX-warn: --quiet] _____________________ 131s 131s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_file_1HPX_warn____0') 131s pdb = '1HPX-warn', options = ('--quiet',) 131s 131s @pytest.mark.parametrize("pdb, options", [ 131s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 131s pytest.param('3SGB-subset', ( 131s "--titrate_only", 131s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 131s id="3SGB: --titrate_only"), 131s pytest.param('1HPX-warn', ('--quiet',), id="1HPX-warn: --quiet"), 131s ]) 131s def test_single_file(tmpdir, pdb, options): 131s """Basic regression test using propka.run.single and local file for the 131s input PDB file""" 131s ref_path, pdb_path = get_paths(pdb) 131s filename = str(pdb_path) 131s 131s with tmpdir.as_cwd(): 131s > pkrun.single(filename, options) 131s 131s tests/test_run.py:31: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s /usr/lib/python3/dist-packages/propka/run.py:118: in single 131s parameters = read_parameter_file(options.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s _______________ test_single_filestream[1FTJ-Chain-A: no options] _______________ 131s 131s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_filestream_1FTJ_Ch0') 131s pdb = '1FTJ-Chain-A', options = () 131s 131s @pytest.mark.parametrize("pdb, options", [ 131s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 131s pytest.param('3SGB-subset', ( 131s "--titrate_only", 131s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 131s id="3SGB: --titrate_only"), 131s pytest.param('1HPX-warn',('--quiet',), id="1HPX-warn: --quiet"), 131s ]) 131s def test_single_filestream(tmpdir, pdb, options): 131s """Basic regression test using StringIO streams for the input PDB file""" 131s ref_path, pdb_path = get_paths(pdb) 131s filename = f"{pdb}.pdb" 131s 131s with open(pdb_path, 'r') as writer: 131s filestream = StringIO(writer.read()) 131s 131s with tmpdir.as_cwd(): 131s > pkrun.single(filename, options, stream=filestream) 131s 131s tests/test_run.py:53: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s /usr/lib/python3/dist-packages/propka/run.py:118: in single 131s parameters = read_parameter_file(options.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s _________________ test_single_filestream[3SGB: --titrate_only] _________________ 131s 131s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_filestream_3SGB___0') 131s pdb = '3SGB-subset' 131s 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') 131s 131s @pytest.mark.parametrize("pdb, options", [ 131s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 131s pytest.param('3SGB-subset', ( 131s "--titrate_only", 131s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 131s id="3SGB: --titrate_only"), 131s pytest.param('1HPX-warn',('--quiet',), id="1HPX-warn: --quiet"), 131s ]) 131s def test_single_filestream(tmpdir, pdb, options): 131s """Basic regression test using StringIO streams for the input PDB file""" 131s ref_path, pdb_path = get_paths(pdb) 131s filename = f"{pdb}.pdb" 131s 131s with open(pdb_path, 'r') as writer: 131s filestream = StringIO(writer.read()) 131s 131s with tmpdir.as_cwd(): 131s > pkrun.single(filename, options, stream=filestream) 131s 131s tests/test_run.py:53: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s /usr/lib/python3/dist-packages/propka/run.py:118: in single 131s parameters = read_parameter_file(options.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s __________________ test_single_filestream[1HPX-warn: --quiet] __________________ 131s 131s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_filestream_1HPX_wa0') 131s pdb = '1HPX-warn', options = ('--quiet',) 131s 131s @pytest.mark.parametrize("pdb, options", [ 131s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 131s pytest.param('3SGB-subset', ( 131s "--titrate_only", 131s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 131s id="3SGB: --titrate_only"), 131s pytest.param('1HPX-warn',('--quiet',), id="1HPX-warn: --quiet"), 131s ]) 131s def test_single_filestream(tmpdir, pdb, options): 131s """Basic regression test using StringIO streams for the input PDB file""" 131s ref_path, pdb_path = get_paths(pdb) 131s filename = f"{pdb}.pdb" 131s 131s with open(pdb_path, 'r') as writer: 131s filestream = StringIO(writer.read()) 131s 131s with tmpdir.as_cwd(): 131s > pkrun.single(filename, options, stream=filestream) 131s 131s tests/test_run.py:53: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s /usr/lib/python3/dist-packages/propka/run.py:118: in single 131s parameters = read_parameter_file(options.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s ______________________________ test_single_nopka _______________________________ 131s 131s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_nopka0') 131s 131s def test_single_nopka(tmpdir): 131s """Basic test to check that the pKa file is not written when write_pka is 131s `False`""" 131s pdb = "1FTJ-Chain-A" 131s ref_path, pdb_path = get_paths(pdb) 131s filename = f"{pdb}.pdb" 131s 131s with open(pdb_path, 'r') as writer: 131s filestream = StringIO(writer.read()) 131s 131s > pkrun.single(filename, stream=filestream, write_pka=False) 131s 131s tests/test_run.py:70: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s /usr/lib/python3/dist-packages/propka/run.py:118: in single 131s parameters = read_parameter_file(options.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s _______________________ test_single_extra_files_logwarn ________________________ 131s 131s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_extra_files_logwar0') 131s caplog = <_pytest.logging.LogCaptureFixture object at 0xeb6bbc6c8830> 131s 131s def test_single_extra_files_logwarn(tmpdir, caplog): 131s """Tests that a logging warning is thrown if passing files via optargs""" 131s pdb = "1FTJ-Chain-A" 131s options = ('-f foo.pdb bar.pdb', '-f test.pdb test2.pdb') 131s ref_path, pdb_path = get_paths(pdb) 131s filename = str(pdb_path) 131s 131s with tmpdir.as_cwd(): 131s > pkrun.single(filename, options) 131s 131s tests/test_run.py:82: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s /usr/lib/python3/dist-packages/propka/run.py:118: in single 131s parameters = read_parameter_file(options.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s _______________ test_textio_filestream[1FTJ-Chain-A: no options] _______________ 131s 131s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_textio_filestream_1FTJ_Ch0') 131s pdb = '1FTJ-Chain-A', options = ['1FTJ-Chain-A.pdb'] 131s 131s @pytest.mark.parametrize("pdb, options", [ 131s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 131s pytest.param('3SGB-subset', [ 131s "--titrate_only", 131s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 131s id="3SGB: --titrate_only"), 131s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 131s ]) 131s def test_textio_filestream(tmpdir, pdb, options): 131s """Basic regression test using TextIO streams for the input PDB file""" 131s # Get the relevant paths 131s ref_path, pdb_path = get_paths(pdb) 131s filename = f"{pdb}.pdb" 131s 131s filestream = open(pdb_path, 'r') 131s 131s with tmpdir.as_cwd(): 131s > run_propka_stream(options, filestream, filename) 131s 131s tests/test_streamio.py:60: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s tests/test_streamio.py:36: in run_propka_stream 131s parameters = read_parameter_file(args.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s _________________ test_textio_filestream[3SGB: --titrate_only] _________________ 131s 131s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_textio_filestream_3SGB___0') 131s pdb = '3SGB-subset' 131s 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'] 131s 131s @pytest.mark.parametrize("pdb, options", [ 131s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 131s pytest.param('3SGB-subset', [ 131s "--titrate_only", 131s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 131s id="3SGB: --titrate_only"), 131s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 131s ]) 131s def test_textio_filestream(tmpdir, pdb, options): 131s """Basic regression test using TextIO streams for the input PDB file""" 131s # Get the relevant paths 131s ref_path, pdb_path = get_paths(pdb) 131s filename = f"{pdb}.pdb" 131s 131s filestream = open(pdb_path, 'r') 131s 131s with tmpdir.as_cwd(): 131s > run_propka_stream(options, filestream, filename) 131s 131s tests/test_streamio.py:60: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s tests/test_streamio.py:36: in run_propka_stream 131s parameters = read_parameter_file(args.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s __________________ test_textio_filestream[1HPX-warn: --quiet] __________________ 131s 131s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_textio_filestream_1HPX_wa0') 131s pdb = '1HPX-warn', options = ['--quiet', '1HPX-warn.pdb'] 131s 131s @pytest.mark.parametrize("pdb, options", [ 131s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 131s pytest.param('3SGB-subset', [ 131s "--titrate_only", 131s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 131s id="3SGB: --titrate_only"), 131s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 131s ]) 131s def test_textio_filestream(tmpdir, pdb, options): 131s """Basic regression test using TextIO streams for the input PDB file""" 131s # Get the relevant paths 131s ref_path, pdb_path = get_paths(pdb) 131s filename = f"{pdb}.pdb" 131s 131s filestream = open(pdb_path, 'r') 131s 131s with tmpdir.as_cwd(): 131s > run_propka_stream(options, filestream, filename) 131s 131s tests/test_streamio.py:60: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s tests/test_streamio.py:36: in run_propka_stream 131s parameters = read_parameter_file(args.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s ______________ test_stringio_filestream[1FTJ-Chain-A: no options] ______________ 131s 131s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_stringio_filestream_1FTJ_0') 131s pdb = '1FTJ-Chain-A', options = ['1FTJ-Chain-A.pdb'] 131s 131s @pytest.mark.parametrize("pdb, options", [ 131s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 131s pytest.param('3SGB-subset', [ 131s "--titrate_only", 131s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 131s id="3SGB: --titrate_only"), 131s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 131s ]) 131s def test_stringio_filestream(tmpdir, pdb, options): 131s """Basic regression test using StringIO streams for the input PDB file""" 131s # Get the relevant paths 131s ref_path, pdb_path = get_paths(pdb) 131s filename = f"{pdb}.pdb" 131s 131s with open(pdb_path, 'r') as writer: 131s filestream = StringIO(writer.read()) 131s 131s with tmpdir.as_cwd(): 131s > run_propka_stream(options, filestream, filename) 131s 131s tests/test_streamio.py:84: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s tests/test_streamio.py:36: in run_propka_stream 131s parameters = read_parameter_file(args.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s ________________ test_stringio_filestream[3SGB: --titrate_only] ________________ 131s 131s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_stringio_filestream_3SGB_0') 131s pdb = '3SGB-subset' 131s 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'] 131s 131s @pytest.mark.parametrize("pdb, options", [ 131s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 131s pytest.param('3SGB-subset', [ 131s "--titrate_only", 131s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 131s id="3SGB: --titrate_only"), 131s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 131s ]) 131s def test_stringio_filestream(tmpdir, pdb, options): 131s """Basic regression test using StringIO streams for the input PDB file""" 131s # Get the relevant paths 131s ref_path, pdb_path = get_paths(pdb) 131s filename = f"{pdb}.pdb" 131s 131s with open(pdb_path, 'r') as writer: 131s filestream = StringIO(writer.read()) 131s 131s with tmpdir.as_cwd(): 131s > run_propka_stream(options, filestream, filename) 131s 131s tests/test_streamio.py:84: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s tests/test_streamio.py:36: in run_propka_stream 131s parameters = read_parameter_file(args.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s _________________ test_stringio_filestream[1HPX-warn: --quiet] _________________ 131s 131s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_stringio_filestream_1HPX_0') 131s pdb = '1HPX-warn', options = ['--quiet', '1HPX-warn.pdb'] 131s 131s @pytest.mark.parametrize("pdb, options", [ 131s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 131s pytest.param('3SGB-subset', [ 131s "--titrate_only", 131s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 131s id="3SGB: --titrate_only"), 131s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 131s ]) 131s def test_stringio_filestream(tmpdir, pdb, options): 131s """Basic regression test using StringIO streams for the input PDB file""" 131s # Get the relevant paths 131s ref_path, pdb_path = get_paths(pdb) 131s filename = f"{pdb}.pdb" 131s 131s with open(pdb_path, 'r') as writer: 131s filestream = StringIO(writer.read()) 131s 131s with tmpdir.as_cwd(): 131s > run_propka_stream(options, filestream, filename) 131s 131s tests/test_streamio.py:84: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s tests/test_streamio.py:36: in run_propka_stream 131s parameters = read_parameter_file(args.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s __________________________ test_valuerror_nofiletype ___________________________ 131s 131s def test_valuerror_nofiletype(): 131s """Tests for raised ValueError when an unknown filename is passed to 131s read_molecule_file""" 131s pdb = "1FTJ-Chain-A" 131s options = [] 131s 131s ref_path, pdb_path = get_paths(pdb) 131s 131s with open(pdb_path, 'r') as writer: 131s filestream = StringIO(writer.read()) 131s 131s errmsg = "Unknown input file type" 131s with pytest.raises(ValueError, match=errmsg): 131s > run_propka_stream(options, filestream, filename="test.dat") 131s 131s tests/test_streamio.py:103: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s tests/test_streamio.py:36: in run_propka_stream 131s parameters = read_parameter_file(args.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s ____________________________ test_valuerror_notpdb _____________________________ 131s 131s def test_valuerror_notpdb(): 131s """Tests for raised ValueError when a stream object that isn't a PDB 131s is passed to read_molecule_file""" 131s pdb = "1FTJ-Chain-A" 131s options = [] 131s 131s ref_path, pdb_path = get_paths(pdb) 131s 131s filestream = StringIO() 131s 131s errmsg = "The pdb file does not seem to contain any " 131s with pytest.raises(ValueError, match=errmsg): 131s > run_propka_stream(options, filestream, filename="test.pdb") 131s 131s tests/test_streamio.py:118: 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s tests/test_streamio.py:36: in run_propka_stream 131s parameters = read_parameter_file(args.parameters, Parameters()) 131s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 131s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 131s parameters.parse_line(line) 131s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 131s 131s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 131s ^^^^^^^^^^^^^^^^^^^^ 131s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 131s 131s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 131s =========================== short test summary info ============================ 131s FAILED tests/test_basic_regression.py::test_regression[sample-issue-140: no options] 131s FAILED tests/test_basic_regression.py::test_regression[1FTJ-Chain-A: no options] 131s FAILED tests/test_basic_regression.py::test_regression[1HPX: no options] - At... 131s FAILED tests/test_basic_regression.py::test_regression[4DFR: no options] - At... 131s FAILED tests/test_basic_regression.py::test_regression[3SGB: no options] - At... 131s FAILED tests/test_basic_regression.py::test_regression[3SGB: --titrate_only] 131s FAILED tests/test_basic_regression.py::test_regression[1HPX-warn: --quiet] - ... 131s FAILED tests/test_run.py::test_single_file[1FTJ-Chain-A: no options] - Attrib... 131s FAILED tests/test_run.py::test_single_file[3SGB: --titrate_only] - AttributeE... 131s FAILED tests/test_run.py::test_single_file[1HPX-warn: --quiet] - AttributeErr... 131s FAILED tests/test_run.py::test_single_filestream[1FTJ-Chain-A: no options] - ... 131s FAILED tests/test_run.py::test_single_filestream[3SGB: --titrate_only] - Attr... 131s FAILED tests/test_run.py::test_single_filestream[1HPX-warn: --quiet] - Attrib... 131s FAILED tests/test_run.py::test_single_nopka - AttributeError: 'Parameters' ob... 131s FAILED tests/test_run.py::test_single_extra_files_logwarn - AttributeError: '... 131s FAILED tests/test_streamio.py::test_textio_filestream[1FTJ-Chain-A: no options] 131s FAILED tests/test_streamio.py::test_textio_filestream[3SGB: --titrate_only] 131s FAILED tests/test_streamio.py::test_textio_filestream[1HPX-warn: --quiet] - A... 131s FAILED tests/test_streamio.py::test_stringio_filestream[1FTJ-Chain-A: no options] 131s FAILED tests/test_streamio.py::test_stringio_filestream[3SGB: --titrate_only] 131s FAILED tests/test_streamio.py::test_stringio_filestream[1HPX-warn: --quiet] 131s FAILED tests/test_streamio.py::test_valuerror_nofiletype - AttributeError: 'P... 131s FAILED tests/test_streamio.py::test_valuerror_notpdb - AttributeError: 'Param... 131s ================= 23 failed, 24 passed, 2 deselected in 0.63s ================== 131s E: pybuild pybuild:483: test: plugin distutils failed with: exit code=1: cd /tmp/autopkgtest.dbAyJa/autopkgtest_tmp/build; python3.14 -m pytest -k 'not test_molecular_container' 131s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.13 3.14" returned exit code 13 132s make: *** [/tmp/a4B4vsuQXX/run:4: pybuild-autopkgtest] Error 25 132s pybuild-autopkgtest: error: /tmp/a4B4vsuQXX/run pybuild-autopkgtest returned exit code 2 132s autopkgtest [19:46:33]: test pybuild-autopkgtest: -----------------------] 132s pybuild-autopkgtest FAIL non-zero exit status 25 132s autopkgtest [19:46:33]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 133s autopkgtest [19:46:34]: @@@@@@@@@@@@@@@@@@@@ summary 133s pybuild-autopkgtest FAIL non-zero exit status 25