0s autopkgtest [19:44:02]: starting date and time: 2026-01-22 19:44:02+0000 0s autopkgtest [19:44:02]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [19:44:02]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.sl_fnami/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.56 lxd-armhf-10.145.243.56:autopkgtest/ubuntu/resolute/armhf 23s autopkgtest [19:44:25]: testbed dpkg architecture: armhf 25s autopkgtest [19:44:27]: testbed apt version: 3.1.12 29s autopkgtest [19:44:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup 31s autopkgtest [19:44:33]: testbed release detected to be: None 39s autopkgtest [19:44:41]: updating testbed package index (apt update) 41s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 41s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB] 42s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [124 kB] 42s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [124 kB] 42s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [19.2 kB] 42s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [80.9 kB] 42s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 42s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [815 kB] 42s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [97.4 kB] 42s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [571 kB] 42s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [3644 B] 42s Get:12 http://ftpmaster.internal/ubuntu resolute/multiverse Sources [310 kB] 42s Get:13 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.4 MB] 45s Get:14 http://ftpmaster.internal/ubuntu resolute/main Sources [1402 kB] 45s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1371 kB] 45s Get:16 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [14.9 MB] 46s Get:17 http://ftpmaster.internal/ubuntu resolute/multiverse armhf Packages [175 kB] 49s Fetched 41.6 MB in 8s (5528 kB/s) 50s Reading package lists... 56s autopkgtest [19:44:58]: upgrading testbed (apt dist-upgrade and autopurge) 57s Reading package lists... 58s Building dependency tree... 58s Reading state information... 58s Calculating upgrade... 59s The following packages were automatically installed and are no longer required: 59s libpython3.13-minimal libpython3.13-stdlib python3.13 python3.13-minimal 59s Use 'apt autoremove' to remove them. 59s The following NEW packages will be installed: 59s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 59s The following packages will be upgraded: 59s libpython3-stdlib python3 python3-gdbm python3-minimal 59s 4 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 59s Need to get 6219 kB of archives. 59s After this operation, 22.5 MB of additional disk space will be used. 59s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.14-minimal armhf 3.14.2-1 [905 kB] 59s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14-minimal armhf 3.14.2-1 [2155 kB] 60s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-gdbm armhf 3.14.2-1 [11.1 kB] 60s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-minimal armhf 3.14.2-1 [28.2 kB] 60s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3 armhf 3.14.2-1 [22.9 kB] 60s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.14-stdlib armhf 3.14.2-1 [2270 kB] 60s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14 armhf 3.14.2-1 [816 kB] 60s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libpython3-stdlib armhf 3.14.2-1 [10.9 kB] 60s Fetched 6219 kB in 1s (7110 kB/s) 60s Selecting previously unselected package libpython3.14-minimal:armhf. 60s (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 ... 66485 files and directories currently installed.) 60s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_armhf.deb ... 60s Unpacking libpython3.14-minimal:armhf (3.14.2-1) ... 60s Selecting previously unselected package python3.14-minimal. 60s Preparing to unpack .../python3.14-minimal_3.14.2-1_armhf.deb ... 60s Unpacking python3.14-minimal (3.14.2-1) ... 61s Preparing to unpack .../python3-gdbm_3.14.2-1_armhf.deb ... 61s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-1) ... 61s Setting up libpython3.14-minimal:armhf (3.14.2-1) ... 61s Setting up python3.14-minimal (3.14.2-1) ... 62s (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 ... 66827 files and directories currently installed.) 62s Preparing to unpack .../python3-minimal_3.14.2-1_armhf.deb ... 62s Unpacking python3-minimal (3.14.2-1) over (3.13.7-1) ... 62s Setting up python3-minimal (3.14.2-1) ... 62s (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 ... 66827 files and directories currently installed.) 62s Preparing to unpack .../python3_3.14.2-1_armhf.deb ... 62s Unpacking python3 (3.14.2-1) over (3.13.7-1) ... 62s Selecting previously unselected package libpython3.14-stdlib:armhf. 62s Preparing to unpack .../libpython3.14-stdlib_3.14.2-1_armhf.deb ... 62s Unpacking libpython3.14-stdlib:armhf (3.14.2-1) ... 63s Selecting previously unselected package python3.14. 63s Preparing to unpack .../python3.14_3.14.2-1_armhf.deb ... 63s Unpacking python3.14 (3.14.2-1) ... 63s Preparing to unpack .../libpython3-stdlib_3.14.2-1_armhf.deb ... 63s Unpacking libpython3-stdlib:armhf (3.14.2-1) over (3.13.7-1) ... 63s Setting up libpython3.14-stdlib:armhf (3.14.2-1) ... 63s Setting up python3.14 (3.14.2-1) ... 64s Setting up libpython3-stdlib:armhf (3.14.2-1) ... 64s Setting up python3-gdbm (3.14.2-1) ... 64s Setting up python3 (3.14.2-1) ... 64s Processing triggers for man-db (2.13.1-1) ... 65s Processing triggers for systemd (259-1ubuntu2) ... 67s Reading package lists... 68s Building dependency tree... 68s Reading state information... 68s Solving dependencies... 69s The following packages will be REMOVED: 69s libpython3.13-minimal* libpython3.13-stdlib* python3.13* python3.13-minimal* 69s 0 upgraded, 0 newly installed, 4 to remove and 0 not upgraded. 69s After this operation, 21.3 MB disk space will be freed. 69s (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 ... 67257 files and directories currently installed.) 69s Removing python3.13 (3.13.11-1) ... 69s Removing libpython3.13-stdlib:armhf (3.13.11-1) ... 69s Removing python3.13-minimal (3.13.11-1) ... 71s Removing libpython3.13-minimal:armhf (3.13.11-1) ... 71s Processing triggers for man-db (2.13.1-1) ... 72s Processing triggers for systemd (259-1ubuntu2) ... 72s (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 ... 66518 files and directories currently installed.) 72s Purging configuration files for libpython3.13-minimal:armhf (3.13.11-1) ... 72s Purging configuration files for python3.13-minimal (3.13.11-1) ... 74s autopkgtest [19:45:16]: rebooting testbed after setup commands that affected boot 118s autopkgtest [19:46:00]: testbed running kernel: Linux 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:00:09 UTC 2 147s autopkgtest [19:46:29]: @@@@@@@@@@@@@@@@@@@@ apt-source propka 161s Get:1 http://ftpmaster.internal/ubuntu resolute/universe propka 3.5.1-2 (dsc) [2286 B] 161s Get:2 http://ftpmaster.internal/ubuntu resolute/universe propka 3.5.1-2 (tar) [376 kB] 161s Get:3 http://ftpmaster.internal/ubuntu resolute/universe propka 3.5.1-2 (diff) [5096 B] 162s gpgv: Signature made Wed Oct 16 14:47:53 2024 UTC 162s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 162s gpgv: issuer "emollier@debian.org" 162s gpgv: Can't check signature: No public key 162s dpkg-source: warning: cannot verify inline signature for ./propka_3.5.1-2.dsc: no acceptable signature found 162s autopkgtest [19:46:44]: testing package propka version 3.5.1-2 164s autopkgtest [19:46:46]: build not needed 166s autopkgtest [19:46:48]: test pybuild-autopkgtest: preparing testbed 168s Reading package lists... 168s Building dependency tree... 168s Reading state information... 168s Solving dependencies... 169s The following NEW packages will be installed: 169s autoconf automake autopoint autotools-dev build-essential cpp cpp-15 169s cpp-15-arm-linux-gnueabihf cpp-arm-linux-gnueabihf debhelper debugedit 169s dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz 169s fonts-font-awesome fonts-lato fonts-mathjax g++ g++-15 169s g++-15-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-15 169s gcc-15-arm-linux-gnueabihf gcc-arm-linux-gnueabihf gettext help2man 169s intltool-debian libarchive-zip-perl libasan8 libblas3 libc-dev-bin libc6-dev 169s libcc1-0 libcrypt-dev libdebhelper-perl libdw1t64 169s libfile-stripnondeterminism-perl libgcc-15-dev libgfortran5 libgomp1 169s libisl23 libjs-jquery libjs-mathjax libjson-perl liblapack3 libmpc3 169s libpython3.13-minimal libpython3.13-stdlib libstdc++-15-dev libtool 169s libubsan1 linux-libc-dev m4 po-debconf pybuild-plugin-autopkgtest 169s python-propka-doc python3-alabaster python3-all python3-defusedxml 169s python3-docutils python3-imagesize python3-iniconfig python3-numpy 169s python3-numpy-dev python3-pluggy python3-propka python3-pytest 169s python3-roman-numerals python3-snowballstemmer python3-sphinx 169s python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3.13 169s python3.13-minimal rpcsvc-proto sgml-base sphinx-common 169s sphinx-rtd-theme-common xml-core 169s 0 upgraded, 82 newly installed, 0 to remove and 0 not upgraded. 169s Need to get 87.1 MB of archives. 169s After this operation, 301 MB of additional disk space will be used. 169s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.13-minimal armhf 3.13.11-1 [875 kB] 170s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf python3.13-minimal armhf 3.13.11-1 [2055 kB] 170s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-lato all 2.015-1build1 [2779 kB] 170s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy-dev armhf 1:2.3.5+ds-3 [141 kB] 170s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7ubuntu1 [133 kB] 170s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-11ubuntu1 [334 kB] 170s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-7ubuntu1 [2090 kB] 170s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy armhf 1:2.3.5+ds-3 [4729 kB] 170s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.13-stdlib armhf 3.13.11-1 [1960 kB] 170s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf python3.13 armhf 3.13.11-1 [758 kB] 170s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf m4 armhf 1.4.20-2 [212 kB] 170s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf autoconf all 2.72-3.1ubuntu1 [384 kB] 170s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf autotools-dev all 20240727.1 [43.4 kB] 170s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf automake all 1:1.18.1-3build1 [582 kB] 170s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf autopoint all 0.23.2-1 [620 kB] 170s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf libc-dev-bin armhf 2.42-2ubuntu4 [21.8 kB] 170s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf linux-libc-dev armhf 6.18.0-9.9 [1819 kB] 170s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf libcrypt-dev armhf 1:4.5.1-1 [128 kB] 170s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf rpcsvc-proto armhf 1.4.3-1 [62.3 kB] 170s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf libc6-dev armhf 2.42-2ubuntu4 [1416 kB] 170s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf libisl23 armhf 0.27-1build1 [553 kB] 170s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf libmpc3 armhf 1.3.1-2 [47.0 kB] 170s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-15-arm-linux-gnueabihf armhf 15.2.0-11ubuntu1 [10.1 MB] 171s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-15 armhf 15.2.0-11ubuntu1 [1032 B] 171s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [5756 B] 171s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf cpp armhf 4:15.2.0-4ubuntu1 [22.4 kB] 171s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf libcc1-0 armhf 15.2.0-11ubuntu1 [43.5 kB] 171s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf libgomp1 armhf 15.2.0-11ubuntu1 [129 kB] 171s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf libasan8 armhf 15.2.0-11ubuntu1 [2947 kB] 171s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf libubsan1 armhf 15.2.0-11ubuntu1 [1187 kB] 171s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf libgcc-15-dev armhf 15.2.0-11ubuntu1 [898 kB] 171s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15-arm-linux-gnueabihf armhf 15.2.0-11ubuntu1 [19.5 MB] 171s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15 armhf 15.2.0-11ubuntu1 [497 kB] 171s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [1220 B] 171s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf gcc armhf 4:15.2.0-4ubuntu1 [5022 B] 171s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf libstdc++-15-dev armhf 15.2.0-11ubuntu1 [2638 kB] 171s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf g++-15-arm-linux-gnueabihf armhf 15.2.0-11ubuntu1 [11.4 MB] 172s Get:38 http://ftpmaster.internal/ubuntu resolute/main armhf g++-15 armhf 15.2.0-11ubuntu1 [24.6 kB] 172s Get:39 http://ftpmaster.internal/ubuntu resolute/main armhf g++-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [968 B] 172s Get:40 http://ftpmaster.internal/ubuntu resolute/main armhf g++ armhf 4:15.2.0-4ubuntu1 [1086 B] 172s Get:41 http://ftpmaster.internal/ubuntu resolute/main armhf build-essential armhf 12.12ubuntu2 [5256 B] 172s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf libdebhelper-perl all 13.28ubuntu1 [97.4 kB] 172s Get:43 http://ftpmaster.internal/ubuntu resolute/main armhf libtool all 2.5.4-9 [169 kB] 172s Get:44 http://ftpmaster.internal/ubuntu resolute/main armhf dh-autoreconf all 21 [12.5 kB] 172s Get:45 http://ftpmaster.internal/ubuntu resolute/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] 172s Get:46 http://ftpmaster.internal/ubuntu resolute/main armhf libfile-stripnondeterminism-perl all 1.15.0-1build1 [20.6 kB] 172s Get:47 http://ftpmaster.internal/ubuntu resolute/main armhf dh-strip-nondeterminism all 1.15.0-1build1 [5110 B] 172s Get:48 http://ftpmaster.internal/ubuntu resolute/main armhf libdw1t64 armhf 0.194-1 [254 kB] 172s Get:49 http://ftpmaster.internal/ubuntu resolute/main armhf debugedit armhf 1:5.2-3 [48.9 kB] 172s Get:50 http://ftpmaster.internal/ubuntu resolute/main armhf dwz armhf 0.16-2 [114 kB] 172s Get:51 http://ftpmaster.internal/ubuntu resolute/main armhf gettext armhf 0.23.2-1 [1059 kB] 172s Get:52 http://ftpmaster.internal/ubuntu resolute/main armhf intltool-debian all 0.35.0+20060710.6build1 [24.1 kB] 172s Get:53 http://ftpmaster.internal/ubuntu resolute/main armhf po-debconf all 1.0.22 [215 kB] 172s Get:54 http://ftpmaster.internal/ubuntu resolute/main armhf debhelper all 13.28ubuntu1 [916 kB] 172s Get:55 http://ftpmaster.internal/ubuntu resolute/universe armhf dh-python all 7.20251231 [122 kB] 172s Get:56 http://ftpmaster.internal/ubuntu resolute/main armhf sgml-base all 1.31+nmu1 [11.0 kB] 172s Get:57 http://ftpmaster.internal/ubuntu resolute/main armhf xml-core all 0.19build1 [20.3 kB] 172s Get:58 http://ftpmaster.internal/ubuntu resolute/main armhf docutils-common all 0.22.4+dfsg-1 [130 kB] 172s Get:59 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1build1 [531 kB] 172s Get:60 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 172s Get:61 http://ftpmaster.internal/ubuntu resolute/universe armhf help2man armhf 1.49.3 [200 kB] 172s Get:62 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 172s Get:63 http://ftpmaster.internal/ubuntu resolute/main armhf libjson-perl all 4.10000-1 [81.9 kB] 172s Get:64 http://ftpmaster.internal/ubuntu resolute/universe armhf pybuild-plugin-autopkgtest all 7.20251231 [1748 B] 172s Get:65 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 172s Get:66 http://ftpmaster.internal/ubuntu resolute/main armhf sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 172s Get:67 http://ftpmaster.internal/ubuntu resolute/universe armhf python-propka-doc all 3.5.1-2 [157 kB] 172s Get:68 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-all armhf 3.14.2-1 [888 B] 172s Get:69 http://ftpmaster.internal/ubuntu resolute/main armhf python3-defusedxml all 0.7.1-3build1 [42.4 kB] 172s Get:70 http://ftpmaster.internal/ubuntu resolute/main armhf python3-roman-numerals all 4.1.0-1 [8660 B] 172s Get:71 http://ftpmaster.internal/ubuntu resolute/main armhf python3-docutils all 0.22.4+dfsg-1 [439 kB] 172s Get:72 http://ftpmaster.internal/ubuntu resolute/main armhf python3-imagesize all 1.4.1-1build1 [6900 B] 172s Get:73 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-iniconfig all 2.1.0-2 [6962 B] 172s Get:74 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pluggy all 1.6.0-2 [21.1 kB] 172s Get:75 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-propka all 3.5.1-2 [70.1 kB] 172s Get:76 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pytest all 9.0.2-2 [277 kB] 172s Get:77 http://ftpmaster.internal/ubuntu resolute/main armhf python3-snowballstemmer all 3.0.1-1 [65.9 kB] 172s Get:78 http://ftpmaster.internal/ubuntu resolute/main armhf sphinx-common all 8.2.3-12 [657 kB] 172s Get:79 http://ftpmaster.internal/ubuntu resolute/main armhf python3-alabaster all 0.7.16-0.1build1 [18.6 kB] 172s Get:80 http://ftpmaster.internal/ubuntu resolute/main armhf python3-sphinx all 8.2.3-12 [483 kB] 172s Get:81 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-sphinxcontrib.jquery all 4.1-6 [6856 B] 172s Get:82 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-sphinx-rtd-theme all 3.0.2+dfsg-3 [23.5 kB] 173s Fetched 87.1 MB in 3s (26.0 MB/s) 173s Selecting previously unselected package libpython3.13-minimal:armhf. 173s (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 ... 66518 files and directories currently installed.) 173s Preparing to unpack .../00-libpython3.13-minimal_3.13.11-1_armhf.deb ... 173s Unpacking libpython3.13-minimal:armhf (3.13.11-1) ... 173s Selecting previously unselected package python3.13-minimal. 173s Preparing to unpack .../01-python3.13-minimal_3.13.11-1_armhf.deb ... 173s Unpacking python3.13-minimal (3.13.11-1) ... 173s Selecting previously unselected package fonts-lato. 173s Preparing to unpack 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183s Setting up python3-numpy-dev:armhf (1:2.3.5+ds-3) ... 183s Setting up autopoint (0.23.2-1) ... 183s Setting up libgfortran5:armhf (15.2.0-11ubuntu1) ... 183s Setting up autoconf (2.72-3.1ubuntu1) ... 183s Setting up python3-pluggy (1.6.0-2) ... 183s Setting up libubsan1:armhf (15.2.0-11ubuntu1) ... 183s Setting up dwz (0.16-2) ... 183s Setting up libcrypt-dev:armhf (1:4.5.1-1) ... 183s Setting up libasan8:armhf (15.2.0-11ubuntu1) ... 183s Setting up libjson-perl (4.10000-1) ... 183s Setting up debugedit (1:5.2-3) ... 183s Setting up python3-roman-numerals (4.1.0-1) ... 183s Setting up python3.13-minimal (3.13.11-1) ... 184s Setting up sgml-base (1.31+nmu1) ... 184s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 184s Setting up libisl23:armhf (0.27-1build1) ... 184s Setting up libc-dev-bin (2.42-2ubuntu4) ... 184s Setting up cpp-15-arm-linux-gnueabihf (15.2.0-11ubuntu1) ... 184s Setting up libpython3.13-stdlib:armhf (3.13.11-1) ... 184s Setting up fonts-font-awesome 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Setting up python3-all (3.14.2-1) ... 187s Setting up intltool-debian (0.35.0+20060710.6build1) ... 187s Setting up sphinx-common (8.2.3-12) ... 187s Setting up python3-numpy (1:2.3.5+ds-3) ... 192s Setting up dh-strip-nondeterminism (1.15.0-1build1) ... 192s Setting up python-propka-doc (3.5.1-2) ... 192s Setting up cpp-15 (15.2.0-11ubuntu1) ... 192s Setting up cpp (4:15.2.0-4ubuntu1) ... 192s Setting up xml-core (0.19build1) ... 192s Setting up libc6-dev:armhf (2.42-2ubuntu4) ... 192s Setting up gcc-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 192s Setting up po-debconf (1.0.22) ... 192s Setting up gcc-15 (15.2.0-11ubuntu1) ... 192s Setting up libstdc++-15-dev:armhf (15.2.0-11ubuntu1) ... 192s Setting up libtool (2.5.4-9) ... 192s Setting up g++-15-arm-linux-gnueabihf (15.2.0-11ubuntu1) ... 192s Setting up gcc (4:15.2.0-4ubuntu1) ... 192s Setting up dh-autoreconf (21) ... 192s Setting up g++-15 (15.2.0-11ubuntu1) ... 192s Setting up g++-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 192s Setting up debhelper (13.28ubuntu1) ... 192s Setting up g++ (4:15.2.0-4ubuntu1) ... 192s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 192s Setting up build-essential (12.12ubuntu2) ... 192s Setting up pybuild-plugin-autopkgtest (7.20251231) ... 192s Processing triggers for install-info (7.2-5) ... 192s Processing triggers for libc-bin (2.42-2ubuntu4) ... 192s Processing triggers for systemd (259-1ubuntu2) ... 193s Processing triggers for man-db (2.13.1-1) ... 194s Processing triggers for sgml-base (1.31+nmu1) ... 194s Setting up docutils-common (0.22.4+dfsg-1) ... 194s Processing triggers for sgml-base (1.31+nmu1) ... 195s Setting up python3-docutils (0.22.4+dfsg-1) ... 196s Setting up python3-sphinx (8.2.3-12) ... 198s Setting up python3-sphinxcontrib.jquery (4.1-6) ... 198s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-3) ... 209s autopkgtest [19:47:31]: test pybuild-autopkgtest: pybuild-autopkgtest 209s autopkgtest [19:47:31]: test pybuild-autopkgtest: [----------------------- 211s pybuild-autopkgtest 211s I: pybuild base:384: cd /tmp/autopkgtest.78MxMH/autopkgtest_tmp/build; python3.13 -m pytest -k 'not test_molecular_container' 212s ============================= test session starts ============================== 212s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 212s rootdir: /tmp/autopkgtest.78MxMH/autopkgtest_tmp/build 212s plugins: typeguard-4.4.4 212s collected 49 items / 2 deselected / 47 selected 212s 216s tests/test_basic_regression.py ....... [ 14%] 216s tests/test_hybrid36.py .. [ 19%] 216s tests/test_input.py .. [ 23%] 216s tests/test_lib.py .. [ 27%] 216s tests/test_protonate.py . [ 29%] 219s tests/test_run.py ........ [ 46%] 220s tests/test_streamio.py ........ [ 63%] 220s tests/test_vector_algebra.py ............... [ 95%] 220s tests/test_version.py .. [100%] 220s 220s ======================= 47 passed, 2 deselected in 7.68s ======================= 220s I: pybuild base:384: cd /tmp/autopkgtest.78MxMH/autopkgtest_tmp/build; python3.14 -m pytest -k 'not test_molecular_container' 221s ============================= test session starts ============================== 221s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 221s rootdir: /tmp/autopkgtest.78MxMH/autopkgtest_tmp/build 221s plugins: typeguard-4.4.4 221s collected 49 items / 2 deselected / 47 selected 221s 221s tests/test_basic_regression.py FFFFFFF [ 14%] 221s tests/test_hybrid36.py .. [ 19%] 221s tests/test_input.py .. [ 23%] 221s tests/test_lib.py .. [ 27%] 221s tests/test_protonate.py . [ 29%] 221s tests/test_run.py FFFFFFFF [ 46%] 221s tests/test_streamio.py FFFFFFFF [ 63%] 221s tests/test_vector_algebra.py ............... [ 95%] 222s tests/test_version.py .. [100%] 222s 222s =================================== FAILURES =================================== 222s ________________ test_regression[sample-issue-140: no options] _________________ 222s 222s pdb = 'sample-issue-140' 222s options = ['/tmp/autopkgtest.78MxMH/autopkgtest_tmp/build/tests/pdb/sample-issue-140.pdb'] 222s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_sample_issue_10') 222s 222s @pytest.mark.parametrize("pdb, options", [ 222s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 222s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 222s pytest.param('1HPX', [], id="1HPX: no options"), 222s pytest.param('4DFR', [], id="4DFR: no options"), 222s pytest.param('3SGB', [], id="3SGB: no options"), 222s pytest.param('3SGB-subset', [ 222s "--titrate_only", 222s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 222s id="3SGB: --titrate_only"), 222s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 222s def test_regression(pdb, options, tmp_path): 222s """Basic regression test of PROPKA functionality.""" 222s path_dict = get_test_dirs() 222s ref_path = None 222s 222s for ext in ["json", "dat"]: 222s ref_path = path_dict["results"] / f"{pdb}.{ext}" 222s if ref_path.is_file(): 222s ref_path = ref_path.resolve() 222s break 222s else: 222s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 222s str(ref_path))) 222s ref_path = None 222s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 222s if pdb_path.is_file(): 222s pdb_path = pdb_path.resolve() 222s else: 222s errstr = "Missing PDB file: {0:s}".format(pdb_path) 222s raise FileNotFoundError(errstr) 222s tmp_path = Path(tmp_path).resolve() 222s 222s > run_propka(options, pdb_path, tmp_path) 222s 222s tests/test_basic_regression.py:170: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s tests/test_basic_regression.py:77: in run_propka 222s parameters = read_parameter_file(args.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s ------------------------------ Captured log call ------------------------------- 222s 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. 222s __________________ test_regression[1FTJ-Chain-A: no options] ___________________ 222s 222s pdb = '1FTJ-Chain-A' 222s options = ['/tmp/autopkgtest.78MxMH/autopkgtest_tmp/build/tests/pdb/1FTJ-Chain-A.pdb'] 222s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_1FTJ_Chain_A__0') 222s 222s @pytest.mark.parametrize("pdb, options", [ 222s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 222s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 222s pytest.param('1HPX', [], id="1HPX: no options"), 222s pytest.param('4DFR', [], id="4DFR: no options"), 222s pytest.param('3SGB', [], id="3SGB: no options"), 222s pytest.param('3SGB-subset', [ 222s "--titrate_only", 222s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 222s id="3SGB: --titrate_only"), 222s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 222s def test_regression(pdb, options, tmp_path): 222s """Basic regression test of PROPKA functionality.""" 222s path_dict = get_test_dirs() 222s ref_path = None 222s 222s for ext in ["json", "dat"]: 222s ref_path = path_dict["results"] / f"{pdb}.{ext}" 222s if ref_path.is_file(): 222s ref_path = ref_path.resolve() 222s break 222s else: 222s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 222s str(ref_path))) 222s ref_path = None 222s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 222s if pdb_path.is_file(): 222s pdb_path = pdb_path.resolve() 222s else: 222s errstr = "Missing PDB file: {0:s}".format(pdb_path) 222s raise FileNotFoundError(errstr) 222s tmp_path = Path(tmp_path).resolve() 222s 222s > run_propka(options, pdb_path, tmp_path) 222s 222s tests/test_basic_regression.py:170: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s tests/test_basic_regression.py:77: in run_propka 222s parameters = read_parameter_file(args.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s ------------------------------ Captured log call ------------------------------- 222s 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. 222s ______________________ test_regression[1HPX: no options] _______________________ 222s 222s pdb = '1HPX' 222s options = ['/tmp/autopkgtest.78MxMH/autopkgtest_tmp/build/tests/pdb/1HPX.pdb'] 222s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_1HPX__no_optio0') 222s 222s @pytest.mark.parametrize("pdb, options", [ 222s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 222s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 222s pytest.param('1HPX', [], id="1HPX: no options"), 222s pytest.param('4DFR', [], id="4DFR: no options"), 222s pytest.param('3SGB', [], id="3SGB: no options"), 222s pytest.param('3SGB-subset', [ 222s "--titrate_only", 222s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 222s id="3SGB: --titrate_only"), 222s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 222s def test_regression(pdb, options, tmp_path): 222s """Basic regression test of PROPKA functionality.""" 222s path_dict = get_test_dirs() 222s ref_path = None 222s 222s for ext in ["json", "dat"]: 222s ref_path = path_dict["results"] / f"{pdb}.{ext}" 222s if ref_path.is_file(): 222s ref_path = ref_path.resolve() 222s break 222s else: 222s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 222s str(ref_path))) 222s ref_path = None 222s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 222s if pdb_path.is_file(): 222s pdb_path = pdb_path.resolve() 222s else: 222s errstr = "Missing PDB file: {0:s}".format(pdb_path) 222s raise FileNotFoundError(errstr) 222s tmp_path = Path(tmp_path).resolve() 222s 222s > run_propka(options, pdb_path, tmp_path) 222s 222s tests/test_basic_regression.py:170: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s tests/test_basic_regression.py:77: in run_propka 222s parameters = read_parameter_file(args.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s ------------------------------ Captured log call ------------------------------- 222s 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. 222s ______________________ test_regression[4DFR: no options] _______________________ 222s 222s pdb = '4DFR' 222s options = ['/tmp/autopkgtest.78MxMH/autopkgtest_tmp/build/tests/pdb/4DFR.pdb'] 222s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_4DFR__no_optio0') 222s 222s @pytest.mark.parametrize("pdb, options", [ 222s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 222s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 222s pytest.param('1HPX', [], id="1HPX: no options"), 222s pytest.param('4DFR', [], id="4DFR: no options"), 222s pytest.param('3SGB', [], id="3SGB: no options"), 222s pytest.param('3SGB-subset', [ 222s "--titrate_only", 222s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 222s id="3SGB: --titrate_only"), 222s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 222s def test_regression(pdb, options, tmp_path): 222s """Basic regression test of PROPKA functionality.""" 222s path_dict = get_test_dirs() 222s ref_path = None 222s 222s for ext in ["json", "dat"]: 222s ref_path = path_dict["results"] / f"{pdb}.{ext}" 222s if ref_path.is_file(): 222s ref_path = ref_path.resolve() 222s break 222s else: 222s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 222s str(ref_path))) 222s ref_path = None 222s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 222s if pdb_path.is_file(): 222s pdb_path = pdb_path.resolve() 222s else: 222s errstr = "Missing PDB file: {0:s}".format(pdb_path) 222s raise FileNotFoundError(errstr) 222s tmp_path = Path(tmp_path).resolve() 222s 222s > run_propka(options, pdb_path, tmp_path) 222s 222s tests/test_basic_regression.py:170: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s tests/test_basic_regression.py:77: in run_propka 222s parameters = read_parameter_file(args.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s ------------------------------ Captured log call ------------------------------- 222s 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. 222s ______________________ test_regression[3SGB: no options] _______________________ 222s 222s pdb = '3SGB' 222s options = ['/tmp/autopkgtest.78MxMH/autopkgtest_tmp/build/tests/pdb/3SGB.pdb'] 222s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_3SGB__no_optio0') 222s 222s @pytest.mark.parametrize("pdb, options", [ 222s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 222s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 222s pytest.param('1HPX', [], id="1HPX: no options"), 222s pytest.param('4DFR', [], id="4DFR: no options"), 222s pytest.param('3SGB', [], id="3SGB: no options"), 222s pytest.param('3SGB-subset', [ 222s "--titrate_only", 222s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 222s id="3SGB: --titrate_only"), 222s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 222s def test_regression(pdb, options, tmp_path): 222s """Basic regression test of PROPKA functionality.""" 222s path_dict = get_test_dirs() 222s ref_path = None 222s 222s for ext in ["json", "dat"]: 222s ref_path = path_dict["results"] / f"{pdb}.{ext}" 222s if ref_path.is_file(): 222s ref_path = ref_path.resolve() 222s break 222s else: 222s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 222s str(ref_path))) 222s ref_path = None 222s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 222s if pdb_path.is_file(): 222s pdb_path = pdb_path.resolve() 222s else: 222s errstr = "Missing PDB file: {0:s}".format(pdb_path) 222s raise FileNotFoundError(errstr) 222s tmp_path = Path(tmp_path).resolve() 222s 222s > run_propka(options, pdb_path, tmp_path) 222s 222s tests/test_basic_regression.py:170: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s tests/test_basic_regression.py:77: in run_propka 222s parameters = read_parameter_file(args.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s ------------------------------ Captured log call ------------------------------- 222s 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. 222s ____________________ test_regression[3SGB: --titrate_only] _____________________ 222s 222s pdb = '3SGB-subset' 222s 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.78MxMH/autopkgtest_tmp/build/tests/pdb/3SGB-subset.pdb'] 222s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_3SGB____titrat0') 222s 222s @pytest.mark.parametrize("pdb, options", [ 222s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 222s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 222s pytest.param('1HPX', [], id="1HPX: no options"), 222s pytest.param('4DFR', [], id="4DFR: no options"), 222s pytest.param('3SGB', [], id="3SGB: no options"), 222s pytest.param('3SGB-subset', [ 222s "--titrate_only", 222s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 222s id="3SGB: --titrate_only"), 222s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 222s def test_regression(pdb, options, tmp_path): 222s """Basic regression test of PROPKA functionality.""" 222s path_dict = get_test_dirs() 222s ref_path = None 222s 222s for ext in ["json", "dat"]: 222s ref_path = path_dict["results"] / f"{pdb}.{ext}" 222s if ref_path.is_file(): 222s ref_path = ref_path.resolve() 222s break 222s else: 222s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 222s str(ref_path))) 222s ref_path = None 222s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 222s if pdb_path.is_file(): 222s pdb_path = pdb_path.resolve() 222s else: 222s errstr = "Missing PDB file: {0:s}".format(pdb_path) 222s raise FileNotFoundError(errstr) 222s tmp_path = Path(tmp_path).resolve() 222s 222s > run_propka(options, pdb_path, tmp_path) 222s 222s tests/test_basic_regression.py:170: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s tests/test_basic_regression.py:77: in run_propka 222s parameters = read_parameter_file(args.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s ------------------------------ Captured log call ------------------------------- 222s 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. 222s _____________________ test_regression[1HPX-warn: --quiet] ______________________ 222s 222s pdb = '1HPX-warn' 222s options = ['--quiet', '/tmp/autopkgtest.78MxMH/autopkgtest_tmp/build/tests/pdb/1HPX-warn.pdb'] 222s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_1HPX_warn____q0') 222s 222s @pytest.mark.parametrize("pdb, options", [ 222s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 222s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 222s pytest.param('1HPX', [], id="1HPX: no options"), 222s pytest.param('4DFR', [], id="4DFR: no options"), 222s pytest.param('3SGB', [], id="3SGB: no options"), 222s pytest.param('3SGB-subset', [ 222s "--titrate_only", 222s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 222s id="3SGB: --titrate_only"), 222s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 222s def test_regression(pdb, options, tmp_path): 222s """Basic regression test of PROPKA functionality.""" 222s path_dict = get_test_dirs() 222s ref_path = None 222s 222s for ext in ["json", "dat"]: 222s ref_path = path_dict["results"] / f"{pdb}.{ext}" 222s if ref_path.is_file(): 222s ref_path = ref_path.resolve() 222s break 222s else: 222s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 222s str(ref_path))) 222s ref_path = None 222s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 222s if pdb_path.is_file(): 222s pdb_path = pdb_path.resolve() 222s else: 222s errstr = "Missing PDB file: {0:s}".format(pdb_path) 222s raise FileNotFoundError(errstr) 222s tmp_path = Path(tmp_path).resolve() 222s 222s > run_propka(options, pdb_path, tmp_path) 222s 222s tests/test_basic_regression.py:170: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s tests/test_basic_regression.py:77: in run_propka 222s parameters = read_parameter_file(args.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s ------------------------------ Captured log call ------------------------------- 222s 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. 222s __________________ test_single_file[1FTJ-Chain-A: no options] __________________ 222s 222s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_file_1FTJ_Chain_A_0') 222s pdb = '1FTJ-Chain-A', options = () 222s 222s @pytest.mark.parametrize("pdb, options", [ 222s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 222s pytest.param('3SGB-subset', ( 222s "--titrate_only", 222s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 222s id="3SGB: --titrate_only"), 222s pytest.param('1HPX-warn', ('--quiet',), id="1HPX-warn: --quiet"), 222s ]) 222s def test_single_file(tmpdir, pdb, options): 222s """Basic regression test using propka.run.single and local file for the 222s input PDB file""" 222s ref_path, pdb_path = get_paths(pdb) 222s filename = str(pdb_path) 222s 222s with tmpdir.as_cwd(): 222s > pkrun.single(filename, options) 222s 222s tests/test_run.py:31: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s /usr/lib/python3/dist-packages/propka/run.py:118: in single 222s parameters = read_parameter_file(options.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s ____________________ test_single_file[3SGB: --titrate_only] ____________________ 222s 222s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_file_3SGB____titra0') 222s pdb = '3SGB-subset' 222s 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') 222s 222s @pytest.mark.parametrize("pdb, options", [ 222s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 222s pytest.param('3SGB-subset', ( 222s "--titrate_only", 222s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 222s id="3SGB: --titrate_only"), 222s pytest.param('1HPX-warn', ('--quiet',), id="1HPX-warn: --quiet"), 222s ]) 222s def test_single_file(tmpdir, pdb, options): 222s """Basic regression test using propka.run.single and local file for the 222s input PDB file""" 222s ref_path, pdb_path = get_paths(pdb) 222s filename = str(pdb_path) 222s 222s with tmpdir.as_cwd(): 222s > pkrun.single(filename, options) 222s 222s tests/test_run.py:31: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s /usr/lib/python3/dist-packages/propka/run.py:118: in single 222s parameters = read_parameter_file(options.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s _____________________ test_single_file[1HPX-warn: --quiet] _____________________ 222s 222s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_file_1HPX_warn____0') 222s pdb = '1HPX-warn', options = ('--quiet',) 222s 222s @pytest.mark.parametrize("pdb, options", [ 222s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 222s pytest.param('3SGB-subset', ( 222s "--titrate_only", 222s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 222s id="3SGB: --titrate_only"), 222s pytest.param('1HPX-warn', ('--quiet',), id="1HPX-warn: --quiet"), 222s ]) 222s def test_single_file(tmpdir, pdb, options): 222s """Basic regression test using propka.run.single and local file for the 222s input PDB file""" 222s ref_path, pdb_path = get_paths(pdb) 222s filename = str(pdb_path) 222s 222s with tmpdir.as_cwd(): 222s > pkrun.single(filename, options) 222s 222s tests/test_run.py:31: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s /usr/lib/python3/dist-packages/propka/run.py:118: in single 222s parameters = read_parameter_file(options.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s _______________ test_single_filestream[1FTJ-Chain-A: no options] _______________ 222s 222s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_filestream_1FTJ_Ch0') 222s pdb = '1FTJ-Chain-A', options = () 222s 222s @pytest.mark.parametrize("pdb, options", [ 222s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 222s pytest.param('3SGB-subset', ( 222s "--titrate_only", 222s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 222s id="3SGB: --titrate_only"), 222s pytest.param('1HPX-warn',('--quiet',), id="1HPX-warn: --quiet"), 222s ]) 222s def test_single_filestream(tmpdir, pdb, options): 222s """Basic regression test using StringIO streams for the input PDB file""" 222s ref_path, pdb_path = get_paths(pdb) 222s filename = f"{pdb}.pdb" 222s 222s with open(pdb_path, 'r') as writer: 222s filestream = StringIO(writer.read()) 222s 222s with tmpdir.as_cwd(): 222s > pkrun.single(filename, options, stream=filestream) 222s 222s tests/test_run.py:53: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s /usr/lib/python3/dist-packages/propka/run.py:118: in single 222s parameters = read_parameter_file(options.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s _________________ test_single_filestream[3SGB: --titrate_only] _________________ 222s 222s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_filestream_3SGB___0') 222s pdb = '3SGB-subset' 222s 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') 222s 222s @pytest.mark.parametrize("pdb, options", [ 222s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 222s pytest.param('3SGB-subset', ( 222s "--titrate_only", 222s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 222s id="3SGB: --titrate_only"), 222s pytest.param('1HPX-warn',('--quiet',), id="1HPX-warn: --quiet"), 222s ]) 222s def test_single_filestream(tmpdir, pdb, options): 222s """Basic regression test using StringIO streams for the input PDB file""" 222s ref_path, pdb_path = get_paths(pdb) 222s filename = f"{pdb}.pdb" 222s 222s with open(pdb_path, 'r') as writer: 222s filestream = StringIO(writer.read()) 222s 222s with tmpdir.as_cwd(): 222s > pkrun.single(filename, options, stream=filestream) 222s 222s tests/test_run.py:53: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s /usr/lib/python3/dist-packages/propka/run.py:118: in single 222s parameters = read_parameter_file(options.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s __________________ test_single_filestream[1HPX-warn: --quiet] __________________ 222s 222s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_filestream_1HPX_wa0') 222s pdb = '1HPX-warn', options = ('--quiet',) 222s 222s @pytest.mark.parametrize("pdb, options", [ 222s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 222s pytest.param('3SGB-subset', ( 222s "--titrate_only", 222s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 222s id="3SGB: --titrate_only"), 222s pytest.param('1HPX-warn',('--quiet',), id="1HPX-warn: --quiet"), 222s ]) 222s def test_single_filestream(tmpdir, pdb, options): 222s """Basic regression test using StringIO streams for the input PDB file""" 222s ref_path, pdb_path = get_paths(pdb) 222s filename = f"{pdb}.pdb" 222s 222s with open(pdb_path, 'r') as writer: 222s filestream = StringIO(writer.read()) 222s 222s with tmpdir.as_cwd(): 222s > pkrun.single(filename, options, stream=filestream) 222s 222s tests/test_run.py:53: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s /usr/lib/python3/dist-packages/propka/run.py:118: in single 222s parameters = read_parameter_file(options.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s ______________________________ test_single_nopka _______________________________ 222s 222s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_nopka0') 222s 222s def test_single_nopka(tmpdir): 222s """Basic test to check that the pKa file is not written when write_pka is 222s `False`""" 222s pdb = "1FTJ-Chain-A" 222s ref_path, pdb_path = get_paths(pdb) 222s filename = f"{pdb}.pdb" 222s 222s with open(pdb_path, 'r') as writer: 222s filestream = StringIO(writer.read()) 222s 222s > pkrun.single(filename, stream=filestream, write_pka=False) 222s 222s tests/test_run.py:70: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s /usr/lib/python3/dist-packages/propka/run.py:118: in single 222s parameters = read_parameter_file(options.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s _______________________ test_single_extra_files_logwarn ________________________ 222s 222s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_extra_files_logwar0') 222s caplog = <_pytest.logging.LogCaptureFixture object at 0xf25b2c68> 222s 222s def test_single_extra_files_logwarn(tmpdir, caplog): 222s """Tests that a logging warning is thrown if passing files via optargs""" 222s pdb = "1FTJ-Chain-A" 222s options = ('-f foo.pdb bar.pdb', '-f test.pdb test2.pdb') 222s ref_path, pdb_path = get_paths(pdb) 222s filename = str(pdb_path) 222s 222s with tmpdir.as_cwd(): 222s > pkrun.single(filename, options) 222s 222s tests/test_run.py:82: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s /usr/lib/python3/dist-packages/propka/run.py:118: in single 222s parameters = read_parameter_file(options.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s _______________ test_textio_filestream[1FTJ-Chain-A: no options] _______________ 222s 222s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_textio_filestream_1FTJ_Ch0') 222s pdb = '1FTJ-Chain-A', options = ['1FTJ-Chain-A.pdb'] 222s 222s @pytest.mark.parametrize("pdb, options", [ 222s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 222s pytest.param('3SGB-subset', [ 222s "--titrate_only", 222s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 222s id="3SGB: --titrate_only"), 222s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 222s ]) 222s def test_textio_filestream(tmpdir, pdb, options): 222s """Basic regression test using TextIO streams for the input PDB file""" 222s # Get the relevant paths 222s ref_path, pdb_path = get_paths(pdb) 222s filename = f"{pdb}.pdb" 222s 222s filestream = open(pdb_path, 'r') 222s 222s with tmpdir.as_cwd(): 222s > run_propka_stream(options, filestream, filename) 222s 222s tests/test_streamio.py:60: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s tests/test_streamio.py:36: in run_propka_stream 222s parameters = read_parameter_file(args.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s _________________ test_textio_filestream[3SGB: --titrate_only] _________________ 222s 222s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_textio_filestream_3SGB___0') 222s pdb = '3SGB-subset' 222s 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'] 222s 222s @pytest.mark.parametrize("pdb, options", [ 222s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 222s pytest.param('3SGB-subset', [ 222s "--titrate_only", 222s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 222s id="3SGB: --titrate_only"), 222s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 222s ]) 222s def test_textio_filestream(tmpdir, pdb, options): 222s """Basic regression test using TextIO streams for the input PDB file""" 222s # Get the relevant paths 222s ref_path, pdb_path = get_paths(pdb) 222s filename = f"{pdb}.pdb" 222s 222s filestream = open(pdb_path, 'r') 222s 222s with tmpdir.as_cwd(): 222s > run_propka_stream(options, filestream, filename) 222s 222s tests/test_streamio.py:60: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s tests/test_streamio.py:36: in run_propka_stream 222s parameters = read_parameter_file(args.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s __________________ test_textio_filestream[1HPX-warn: --quiet] __________________ 222s 222s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_textio_filestream_1HPX_wa0') 222s pdb = '1HPX-warn', options = ['--quiet', '1HPX-warn.pdb'] 222s 222s @pytest.mark.parametrize("pdb, options", [ 222s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 222s pytest.param('3SGB-subset', [ 222s "--titrate_only", 222s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 222s id="3SGB: --titrate_only"), 222s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 222s ]) 222s def test_textio_filestream(tmpdir, pdb, options): 222s """Basic regression test using TextIO streams for the input PDB file""" 222s # Get the relevant paths 222s ref_path, pdb_path = get_paths(pdb) 222s filename = f"{pdb}.pdb" 222s 222s filestream = open(pdb_path, 'r') 222s 222s with tmpdir.as_cwd(): 222s > run_propka_stream(options, filestream, filename) 222s 222s tests/test_streamio.py:60: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s tests/test_streamio.py:36: in run_propka_stream 222s parameters = read_parameter_file(args.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s ______________ test_stringio_filestream[1FTJ-Chain-A: no options] ______________ 222s 222s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_stringio_filestream_1FTJ_0') 222s pdb = '1FTJ-Chain-A', options = ['1FTJ-Chain-A.pdb'] 222s 222s @pytest.mark.parametrize("pdb, options", [ 222s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 222s pytest.param('3SGB-subset', [ 222s "--titrate_only", 222s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 222s id="3SGB: --titrate_only"), 222s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 222s ]) 222s def test_stringio_filestream(tmpdir, pdb, options): 222s """Basic regression test using StringIO streams for the input PDB file""" 222s # Get the relevant paths 222s ref_path, pdb_path = get_paths(pdb) 222s filename = f"{pdb}.pdb" 222s 222s with open(pdb_path, 'r') as writer: 222s filestream = StringIO(writer.read()) 222s 222s with tmpdir.as_cwd(): 222s > run_propka_stream(options, filestream, filename) 222s 222s tests/test_streamio.py:84: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s tests/test_streamio.py:36: in run_propka_stream 222s parameters = read_parameter_file(args.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s ________________ test_stringio_filestream[3SGB: --titrate_only] ________________ 222s 222s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_stringio_filestream_3SGB_0') 222s pdb = '3SGB-subset' 222s 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'] 222s 222s @pytest.mark.parametrize("pdb, options", [ 222s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 222s pytest.param('3SGB-subset', [ 222s "--titrate_only", 222s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 222s id="3SGB: --titrate_only"), 222s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 222s ]) 222s def test_stringio_filestream(tmpdir, pdb, options): 222s """Basic regression test using StringIO streams for the input PDB file""" 222s # Get the relevant paths 222s ref_path, pdb_path = get_paths(pdb) 222s filename = f"{pdb}.pdb" 222s 222s with open(pdb_path, 'r') as writer: 222s filestream = StringIO(writer.read()) 222s 222s with tmpdir.as_cwd(): 222s > run_propka_stream(options, filestream, filename) 222s 222s tests/test_streamio.py:84: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s tests/test_streamio.py:36: in run_propka_stream 222s parameters = read_parameter_file(args.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s _________________ test_stringio_filestream[1HPX-warn: --quiet] _________________ 222s 222s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_stringio_filestream_1HPX_0') 222s pdb = '1HPX-warn', options = ['--quiet', '1HPX-warn.pdb'] 222s 222s @pytest.mark.parametrize("pdb, options", [ 222s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 222s pytest.param('3SGB-subset', [ 222s "--titrate_only", 222s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 222s id="3SGB: --titrate_only"), 222s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 222s ]) 222s def test_stringio_filestream(tmpdir, pdb, options): 222s """Basic regression test using StringIO streams for the input PDB file""" 222s # Get the relevant paths 222s ref_path, pdb_path = get_paths(pdb) 222s filename = f"{pdb}.pdb" 222s 222s with open(pdb_path, 'r') as writer: 222s filestream = StringIO(writer.read()) 222s 222s with tmpdir.as_cwd(): 222s > run_propka_stream(options, filestream, filename) 222s 222s tests/test_streamio.py:84: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s tests/test_streamio.py:36: in run_propka_stream 222s parameters = read_parameter_file(args.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s __________________________ test_valuerror_nofiletype ___________________________ 222s 222s def test_valuerror_nofiletype(): 222s """Tests for raised ValueError when an unknown filename is passed to 222s read_molecule_file""" 222s pdb = "1FTJ-Chain-A" 222s options = [] 222s 222s ref_path, pdb_path = get_paths(pdb) 222s 222s with open(pdb_path, 'r') as writer: 222s filestream = StringIO(writer.read()) 222s 222s errmsg = "Unknown input file type" 222s with pytest.raises(ValueError, match=errmsg): 222s > run_propka_stream(options, filestream, filename="test.dat") 222s 222s tests/test_streamio.py:103: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s tests/test_streamio.py:36: in run_propka_stream 222s parameters = read_parameter_file(args.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s ____________________________ test_valuerror_notpdb _____________________________ 222s 222s def test_valuerror_notpdb(): 222s """Tests for raised ValueError when a stream object that isn't a PDB 222s is passed to read_molecule_file""" 222s pdb = "1FTJ-Chain-A" 222s options = [] 222s 222s ref_path, pdb_path = get_paths(pdb) 222s 222s filestream = StringIO() 222s 222s errmsg = "The pdb file does not seem to contain any " 222s with pytest.raises(ValueError, match=errmsg): 222s > run_propka_stream(options, filestream, filename="test.pdb") 222s 222s tests/test_streamio.py:118: 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s tests/test_streamio.py:36: in run_propka_stream 222s parameters = read_parameter_file(args.parameters, Parameters()) 222s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 222s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 222s parameters.parse_line(line) 222s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 222s 222s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 222s ^^^^^^^^^^^^^^^^^^^^ 222s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 222s 222s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 222s =========================== short test summary info ============================ 222s FAILED tests/test_basic_regression.py::test_regression[sample-issue-140: no options] 222s FAILED tests/test_basic_regression.py::test_regression[1FTJ-Chain-A: no options] 222s FAILED tests/test_basic_regression.py::test_regression[1HPX: no options] - At... 222s FAILED tests/test_basic_regression.py::test_regression[4DFR: no options] - At... 222s FAILED tests/test_basic_regression.py::test_regression[3SGB: no options] - At... 222s FAILED tests/test_basic_regression.py::test_regression[3SGB: --titrate_only] 222s FAILED tests/test_basic_regression.py::test_regression[1HPX-warn: --quiet] - ... 222s FAILED tests/test_run.py::test_single_file[1FTJ-Chain-A: no options] - Attrib... 222s FAILED tests/test_run.py::test_single_file[3SGB: --titrate_only] - AttributeE... 222s FAILED tests/test_run.py::test_single_file[1HPX-warn: --quiet] - AttributeErr... 222s FAILED tests/test_run.py::test_single_filestream[1FTJ-Chain-A: no options] - ... 222s FAILED tests/test_run.py::test_single_filestream[3SGB: --titrate_only] - Attr... 222s FAILED tests/test_run.py::test_single_filestream[1HPX-warn: --quiet] - Attrib... 222s FAILED tests/test_run.py::test_single_nopka - AttributeError: 'Parameters' ob... 222s FAILED tests/test_run.py::test_single_extra_files_logwarn - AttributeError: '... 222s FAILED tests/test_streamio.py::test_textio_filestream[1FTJ-Chain-A: no options] 222s FAILED tests/test_streamio.py::test_textio_filestream[3SGB: --titrate_only] 222s FAILED tests/test_streamio.py::test_textio_filestream[1HPX-warn: --quiet] - A... 222s FAILED tests/test_streamio.py::test_stringio_filestream[1FTJ-Chain-A: no options] 222s FAILED tests/test_streamio.py::test_stringio_filestream[3SGB: --titrate_only] 222s FAILED tests/test_streamio.py::test_stringio_filestream[1HPX-warn: --quiet] 222s FAILED tests/test_streamio.py::test_valuerror_nofiletype - AttributeError: 'P... 222s FAILED tests/test_streamio.py::test_valuerror_notpdb - AttributeError: 'Param... 222s ================= 23 failed, 24 passed, 2 deselected in 0.81s ================== 222s E: pybuild pybuild:483: test: plugin distutils failed with: exit code=1: cd /tmp/autopkgtest.78MxMH/autopkgtest_tmp/build; python3.14 -m pytest -k 'not test_molecular_container' 222s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.13 3.14" returned exit code 13 222s make: *** [/tmp/oZUMOg2mkR/run:4: pybuild-autopkgtest] Error 25 222s pybuild-autopkgtest: error: /tmp/oZUMOg2mkR/run pybuild-autopkgtest returned exit code 2 222s autopkgtest [19:47:44]: test pybuild-autopkgtest: -----------------------] 227s autopkgtest [19:47:49]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 227s pybuild-autopkgtest FAIL non-zero exit status 25 233s autopkgtest [19:47:55]: @@@@@@@@@@@@@@@@@@@@ summary 233s pybuild-autopkgtest FAIL non-zero exit status 25