0s autopkgtest [19:29:57]: starting date and time: 2026-01-22 19:29:57+0000 0s autopkgtest [19:29:57]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [19:29:57]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.nlcuvseb/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-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-ppc64el-8.secgroup --name adt-resolute-ppc64el-propka-20260122-192957-juju-7f2275-prod-proposed-migration-environment-15-ca7d9bf6-6784-445c-b10f-a3358a723b23 --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-ppc64el-propka-20260122-192957-juju-7f2275-prod-proposed-migration-environment-15-ca7d9bf6-6784-445c-b10f-a3358a723b23 from image adt/ubuntu-resolute-ppc64el-server-20260122.img (UUID 987e5803-394f-43eb-a969-151b6b75a57a)... 51s autopkgtest [19:30:48]: testbed dpkg architecture: ppc64el 51s autopkgtest [19:30:48]: testbed apt version: 3.1.12 51s autopkgtest [19:30:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 52s autopkgtest [19:30:49]: testbed release detected to be: None 52s autopkgtest [19:30:49]: updating testbed package index (apt update) 52s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 53s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 53s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 53s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 53s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [815 kB] 53s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [19.2 kB] 53s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [80.9 kB] 53s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 53s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [103 kB] 53s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [618 kB] 53s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [4644 B] 53s Fetched 1768 kB in 1s (2355 kB/s) 54s Reading package lists... 55s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 55s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 55s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 55s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 56s Reading package lists... 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Calculating upgrade... 56s The following packages were automatically installed and are no longer required: 56s python3.13 python3.13-minimal 56s Use 'sudo apt autoremove' to remove them. 56s The following NEW packages will be installed: 56s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 56s The following packages will be upgraded: 56s libpython3-stdlib python3 python3-gdbm python3-minimal 56s 4 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 56s Need to get 6966 kB of archives. 56s After this operation, 27.7 MB of additional disk space will be used. 56s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpython3.14-minimal ppc64el 3.14.2-1 [921 kB] 56s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3.14-minimal ppc64el 3.14.2-1 [2712 kB] 56s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3-gdbm ppc64el 3.14.2-1 [11.1 kB] 56s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3-minimal ppc64el 3.14.2-1 [28.2 kB] 56s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3 ppc64el 3.14.2-1 [22.9 kB] 56s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpython3.14-stdlib ppc64el 3.14.2-1 [2444 kB] 56s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3.14 ppc64el 3.14.2-1 [816 kB] 56s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libpython3-stdlib ppc64el 3.14.2-1 [10.9 kB] 57s dpkg-preconfigure: unable to re-open stdin: No such file or directory 57s Fetched 6966 kB in 0s (20.8 MB/s) 57s Selecting previously unselected package libpython3.14-minimal:ppc64el. 57s (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 ... 120824 files and directories currently installed.) 57s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_ppc64el.deb ... 57s Unpacking libpython3.14-minimal:ppc64el (3.14.2-1) ... 57s Selecting previously unselected package python3.14-minimal. 57s Preparing to unpack .../python3.14-minimal_3.14.2-1_ppc64el.deb ... 57s Unpacking python3.14-minimal (3.14.2-1) ... 58s Preparing to unpack .../python3-gdbm_3.14.2-1_ppc64el.deb ... 58s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-1) ... 58s Setting up libpython3.14-minimal:ppc64el (3.14.2-1) ... 58s Setting up python3.14-minimal (3.14.2-1) ... 59s (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 ... 121166 files and directories currently installed.) 59s Preparing to unpack .../python3-minimal_3.14.2-1_ppc64el.deb ... 59s Unpacking python3-minimal (3.14.2-1) over (3.13.7-1) ... 59s Setting up python3-minimal (3.14.2-1) ... 59s (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 ... 121166 files and directories currently installed.) 59s Preparing to unpack .../python3_3.14.2-1_ppc64el.deb ... 59s running python pre-rtupdate hooks for python3.14... 59s Unpacking python3 (3.14.2-1) over (3.13.7-1) ... 60s Selecting previously unselected package libpython3.14-stdlib:ppc64el. 60s Preparing to unpack .../libpython3.14-stdlib_3.14.2-1_ppc64el.deb ... 60s Unpacking libpython3.14-stdlib:ppc64el (3.14.2-1) ... 60s Selecting previously unselected package python3.14. 60s Preparing to unpack .../python3.14_3.14.2-1_ppc64el.deb ... 60s Unpacking python3.14 (3.14.2-1) ... 60s Preparing to unpack .../libpython3-stdlib_3.14.2-1_ppc64el.deb ... 60s Unpacking libpython3-stdlib:ppc64el (3.14.2-1) over (3.13.7-1) ... 60s Setting up libpython3.14-stdlib:ppc64el (3.14.2-1) ... 60s Setting up python3.14 (3.14.2-1) ... 61s Setting up libpython3-stdlib:ppc64el (3.14.2-1) ... 61s Setting up python3-gdbm (3.14.2-1) ... 61s Setting up python3 (3.14.2-1) ... 61s running python rtupdate hooks for python3.14... 61s running python post-rtupdate hooks for python3.14... 62s Processing triggers for man-db (2.13.1-1) ... 63s Processing triggers for systemd (259-1ubuntu2) ... 63s autopkgtest [19:31:00]: upgrading testbed (apt dist-upgrade and autopurge) 63s Reading package lists... 63s Building dependency tree... 63s Reading state information... 63s Calculating upgrade... 63s The following packages were automatically installed and are no longer required: 63s python3.13 python3.13-minimal 63s Use 'sudo apt autoremove' to remove them. 64s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 64s Reading package lists... 64s Building dependency tree... 64s Reading state information... 64s Solving dependencies... 64s The following packages will be REMOVED: 64s python3.13* python3.13-minimal* 64s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 64s After this operation, 9077 kB disk space will be freed. 64s (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 ... 121596 files and directories currently installed.) 64s Removing python3.13 (3.13.11-1) ... 64s Removing python3.13-minimal (3.13.11-1) ... 67s Processing triggers for man-db (2.13.1-1) ... 67s Processing triggers for systemd (259-1ubuntu2) ... 67s (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 ... 121569 files and directories currently installed.) 67s Purging configuration files for python3.13-minimal (3.13.11-1) ... 70s autopkgtest [19:31:07]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:45:54 UTC 2026 70s autopkgtest [19:31:07]: @@@@@@@@@@@@@@@@@@@@ apt-source propka 71s Get:1 http://ftpmaster.internal/ubuntu resolute/universe propka 3.5.1-2 (dsc) [2286 B] 71s Get:2 http://ftpmaster.internal/ubuntu resolute/universe propka 3.5.1-2 (tar) [376 kB] 71s Get:3 http://ftpmaster.internal/ubuntu resolute/universe propka 3.5.1-2 (diff) [5096 B] 72s gpgv: Signature made Wed Oct 16 14:47:53 2024 UTC 72s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 72s gpgv: issuer "emollier@debian.org" 72s gpgv: Can't check signature: No public key 72s dpkg-source: warning: cannot verify inline signature for ./propka_3.5.1-2.dsc: no acceptable signature found 72s autopkgtest [19:31:09]: testing package propka version 3.5.1-2 72s autopkgtest [19:31:09]: build not needed 73s autopkgtest [19:31:10]: test pybuild-autopkgtest: preparing testbed 73s Reading package lists... 73s Building dependency tree... 73s Reading state information... 73s Solving dependencies... 73s The following NEW packages will be installed: 73s autoconf automake autopoint autotools-dev build-essential cpp cpp-15 73s cpp-15-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu debhelper debugedit 73s dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz 73s fonts-font-awesome fonts-lato fonts-mathjax g++ g++-15 73s g++-15-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-15 73s gcc-15-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gettext help2man 73s intltool-debian libarchive-zip-perl libasan8 libblas3 libcc1-0 73s libdebhelper-perl libfile-stripnondeterminism-perl libgcc-15-dev 73s libgfortran5 libgomp1 libisl23 libitm1 libjs-jquery libjs-mathjax 73s libjson-perl liblapack3 liblsan0 libmpc3 libquadmath0 libstdc++-15-dev 73s libtool libtsan2 libubsan1 m4 po-debconf pybuild-plugin-autopkgtest 73s python-propka-doc python3-alabaster python3-all python3-defusedxml 73s python3-docutils python3-imagesize python3-iniconfig python3-numpy 73s python3-numpy-dev python3-pluggy python3-propka python3-pytest 73s python3-roman-numerals python3-snowballstemmer python3-sphinx 73s python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3.13 73s python3.13-minimal sgml-base sphinx-common sphinx-rtd-theme-common xml-core 73s 0 upgraded, 78 newly installed, 0 to remove and 0 not upgraded. 73s Need to get 95.2 MB of archives. 73s After this operation, 375 MB of additional disk space will be used. 73s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3.13-minimal ppc64el 3.13.11-1 [2571 kB] 73s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-lato all 2.015-1build1 [2779 kB] 73s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-numpy-dev ppc64el 1:2.3.5+ds-3 [153 kB] 73s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-7ubuntu1 [291 kB] 73s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-11ubuntu1 [620 kB] 74s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack3 ppc64el 3.12.1-7ubuntu1 [2960 kB] 74s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-numpy ppc64el 1:2.3.5+ds-3 [5722 kB] 74s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3.13 ppc64el 3.13.11-1 [758 kB] 74s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el m4 ppc64el 1.4.20-2 [236 kB] 74s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el autoconf all 2.72-3.1ubuntu1 [384 kB] 74s Get:11 http://ftpmaster.internal/ubuntu resolute/main ppc64el autotools-dev all 20240727.1 [43.4 kB] 74s Get:12 http://ftpmaster.internal/ubuntu resolute/main ppc64el automake all 1:1.18.1-3build1 [582 kB] 74s Get:13 http://ftpmaster.internal/ubuntu resolute/main ppc64el autopoint all 0.23.2-1 [620 kB] 74s Get:14 http://ftpmaster.internal/ubuntu resolute/main ppc64el libisl23 ppc64el 0.27-1build1 [893 kB] 74s Get:15 http://ftpmaster.internal/ubuntu resolute/main ppc64el libmpc3 ppc64el 1.3.1-2 [62.5 kB] 74s Get:16 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp-15-powerpc64le-linux-gnu ppc64el 15.2.0-11ubuntu1 [11.4 MB] 74s Get:17 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp-15 ppc64el 15.2.0-11ubuntu1 [1038 B] 74s Get:18 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [5746 B] 74s Get:19 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp ppc64el 4:15.2.0-4ubuntu1 [22.4 kB] 74s Get:20 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcc1-0 ppc64el 15.2.0-11ubuntu1 [49.0 kB] 74s Get:21 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgomp1 ppc64el 15.2.0-11ubuntu1 [169 kB] 74s Get:22 http://ftpmaster.internal/ubuntu resolute/main ppc64el libitm1 ppc64el 15.2.0-11ubuntu1 [32.2 kB] 74s Get:23 http://ftpmaster.internal/ubuntu resolute/main ppc64el libasan8 ppc64el 15.2.0-11ubuntu1 [3006 kB] 74s Get:24 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblsan0 ppc64el 15.2.0-11ubuntu1 [1374 kB] 75s Get:25 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtsan2 ppc64el 15.2.0-11ubuntu1 [2728 kB] 75s Get:26 http://ftpmaster.internal/ubuntu resolute/main ppc64el libubsan1 ppc64el 15.2.0-11ubuntu1 [1231 kB] 75s Get:27 http://ftpmaster.internal/ubuntu resolute/main ppc64el libquadmath0 ppc64el 15.2.0-11ubuntu1 [160 kB] 75s Get:28 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgcc-15-dev ppc64el 15.2.0-11ubuntu1 [1670 kB] 75s Get:29 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc-15-powerpc64le-linux-gnu ppc64el 15.2.0-11ubuntu1 [22.4 MB] 75s Get:30 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc-15 ppc64el 15.2.0-11ubuntu1 [528 kB] 75s Get:31 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [1220 B] 75s Get:32 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc ppc64el 4:15.2.0-4ubuntu1 [5032 B] 75s Get:33 http://ftpmaster.internal/ubuntu resolute/main ppc64el libstdc++-15-dev ppc64el 15.2.0-11ubuntu1 [2745 kB] 76s Get:34 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++-15-powerpc64le-linux-gnu ppc64el 15.2.0-11ubuntu1 [13.0 MB] 76s Get:35 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++-15 ppc64el 15.2.0-11ubuntu1 [24.6 kB] 76s Get:36 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [970 B] 76s Get:37 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++ ppc64el 4:15.2.0-4ubuntu1 [1092 B] 76s Get:38 http://ftpmaster.internal/ubuntu resolute/main ppc64el build-essential ppc64el 12.12ubuntu2 [5256 B] 76s Get:39 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdebhelper-perl all 13.28ubuntu1 [97.4 kB] 76s Get:40 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtool all 2.5.4-9 [169 kB] 76s Get:41 http://ftpmaster.internal/ubuntu resolute/main ppc64el dh-autoreconf all 21 [12.5 kB] 76s Get:42 http://ftpmaster.internal/ubuntu resolute/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] 76s Get:43 http://ftpmaster.internal/ubuntu resolute/main ppc64el libfile-stripnondeterminism-perl all 1.15.0-1build1 [20.6 kB] 76s Get:44 http://ftpmaster.internal/ubuntu resolute/main ppc64el dh-strip-nondeterminism all 1.15.0-1build1 [5110 B] 76s Get:45 http://ftpmaster.internal/ubuntu resolute/main ppc64el debugedit ppc64el 1:5.2-3 [57.3 kB] 76s Get:46 http://ftpmaster.internal/ubuntu resolute/main ppc64el dwz ppc64el 0.16-2 [142 kB] 76s Get:47 http://ftpmaster.internal/ubuntu resolute/main ppc64el gettext ppc64el 0.23.2-1 [1177 kB] 76s Get:48 http://ftpmaster.internal/ubuntu resolute/main ppc64el intltool-debian all 0.35.0+20060710.6build1 [24.1 kB] 76s Get:49 http://ftpmaster.internal/ubuntu resolute/main ppc64el po-debconf all 1.0.22 [215 kB] 76s Get:50 http://ftpmaster.internal/ubuntu resolute/main ppc64el debhelper all 13.28ubuntu1 [916 kB] 76s Get:51 http://ftpmaster.internal/ubuntu resolute/universe ppc64el dh-python all 7.20251231 [122 kB] 76s Get:52 http://ftpmaster.internal/ubuntu resolute/main ppc64el sgml-base all 1.31+nmu1 [11.0 kB] 76s Get:53 http://ftpmaster.internal/ubuntu resolute/main ppc64el xml-core all 0.19build1 [20.3 kB] 76s Get:54 http://ftpmaster.internal/ubuntu resolute/main ppc64el docutils-common all 0.22.4+dfsg-1 [130 kB] 76s Get:55 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1build1 [531 kB] 76s Get:56 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 76s Get:57 http://ftpmaster.internal/ubuntu resolute/universe ppc64el help2man ppc64el 1.49.3 [201 kB] 76s Get:58 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 76s Get:59 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjson-perl all 4.10000-1 [81.9 kB] 76s Get:60 http://ftpmaster.internal/ubuntu resolute/universe ppc64el pybuild-plugin-autopkgtest all 7.20251231 [1748 B] 76s Get:61 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 76s Get:62 http://ftpmaster.internal/ubuntu resolute/main ppc64el sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 76s Get:63 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python-propka-doc all 3.5.1-2 [157 kB] 76s Get:64 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3-all ppc64el 3.14.2-1 [890 B] 76s Get:65 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-defusedxml all 0.7.1-3build1 [42.4 kB] 76s Get:66 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-roman-numerals all 4.1.0-1 [8660 B] 76s Get:67 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-docutils all 0.22.4+dfsg-1 [439 kB] 76s Get:68 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-imagesize all 1.4.1-1build1 [6900 B] 76s Get:69 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-iniconfig all 2.1.0-2 [6962 B] 76s Get:70 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pluggy all 1.6.0-2 [21.1 kB] 76s Get:71 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-propka all 3.5.1-2 [70.1 kB] 76s Get:72 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pytest all 9.0.2-2 [277 kB] 76s Get:73 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-snowballstemmer all 3.0.1-1 [65.9 kB] 77s Get:74 http://ftpmaster.internal/ubuntu resolute/main ppc64el sphinx-common all 8.2.3-12 [657 kB] 77s Get:75 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-alabaster all 0.7.16-0.1build1 [18.6 kB] 77s Get:76 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-sphinx all 8.2.3-12 [483 kB] 77s Get:77 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-sphinxcontrib.jquery all 4.1-6 [6856 B] 77s Get:78 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-sphinx-rtd-theme all 3.0.2+dfsg-3 [23.5 kB] 77s Fetched 95.2 MB in 4s (26.1 MB/s) 77s Selecting previously unselected package python3.13-minimal. 77s (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 ... 121571 files and directories currently installed.) 77s Preparing to unpack .../00-python3.13-minimal_3.13.11-1_ppc64el.deb ... 77s Unpacking python3.13-minimal (3.13.11-1) ... 77s Selecting previously unselected package fonts-lato. 77s Preparing to unpack .../01-fonts-lato_2.015-1build1_all.deb ... 77s Unpacking fonts-lato (2.015-1build1) ... 77s Selecting previously unselected package python3-numpy-dev:ppc64el. 77s Preparing to unpack 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libisl23:ppc64el (0.27-1build1) ... 78s Selecting previously unselected package libmpc3:ppc64el. 78s Preparing to unpack .../14-libmpc3_1.3.1-2_ppc64el.deb ... 78s Unpacking libmpc3:ppc64el (1.3.1-2) ... 78s Selecting previously unselected package cpp-15-powerpc64le-linux-gnu. 78s Preparing to unpack .../15-cpp-15-powerpc64le-linux-gnu_15.2.0-11ubuntu1_ppc64el.deb ... 78s Unpacking cpp-15-powerpc64le-linux-gnu (15.2.0-11ubuntu1) ... 78s Selecting previously unselected package cpp-15. 78s Preparing to unpack .../16-cpp-15_15.2.0-11ubuntu1_ppc64el.deb ... 78s Unpacking cpp-15 (15.2.0-11ubuntu1) ... 78s Selecting previously unselected package cpp-powerpc64le-linux-gnu. 78s Preparing to unpack .../17-cpp-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 78s Unpacking cpp-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 78s Selecting previously unselected package cpp. 78s Preparing to unpack .../18-cpp_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 78s Unpacking cpp (4:15.2.0-4ubuntu1) ... 78s 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gcc-15. 79s Preparing to unpack .../29-gcc-15_15.2.0-11ubuntu1_ppc64el.deb ... 79s Unpacking gcc-15 (15.2.0-11ubuntu1) ... 79s Selecting previously unselected package gcc-powerpc64le-linux-gnu. 79s Preparing to unpack .../30-gcc-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 79s Unpacking gcc-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 79s Selecting previously unselected package gcc. 79s Preparing to unpack .../31-gcc_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 79s Unpacking gcc (4:15.2.0-4ubuntu1) ... 79s Selecting previously unselected package libstdc++-15-dev:ppc64el. 79s Preparing to unpack .../32-libstdc++-15-dev_15.2.0-11ubuntu1_ppc64el.deb ... 79s Unpacking libstdc++-15-dev:ppc64el (15.2.0-11ubuntu1) ... 79s Selecting previously unselected package g++-15-powerpc64le-linux-gnu. 79s Preparing to unpack .../33-g++-15-powerpc64le-linux-gnu_15.2.0-11ubuntu1_ppc64el.deb ... 79s Unpacking g++-15-powerpc64le-linux-gnu (15.2.0-11ubuntu1) ... 79s Selecting previously unselected package g++-15. 79s Preparing to unpack .../34-g++-15_15.2.0-11ubuntu1_ppc64el.deb ... 79s Unpacking g++-15 (15.2.0-11ubuntu1) ... 79s Selecting previously unselected package g++-powerpc64le-linux-gnu. 79s Preparing to unpack .../35-g++-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 79s Unpacking g++-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 79s Selecting previously unselected package g++. 79s Preparing to unpack .../36-g++_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 79s Unpacking g++ (4:15.2.0-4ubuntu1) ... 79s Selecting previously unselected package build-essential. 79s Preparing to unpack .../37-build-essential_12.12ubuntu2_ppc64el.deb ... 79s Unpacking build-essential (12.12ubuntu2) ... 79s Selecting previously unselected package libdebhelper-perl. 79s Preparing to unpack .../38-libdebhelper-perl_13.28ubuntu1_all.deb ... 79s Unpacking libdebhelper-perl (13.28ubuntu1) ... 79s Selecting previously unselected package libtool. 79s Preparing to unpack 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debugedit (1:5.2-3) ... 79s Selecting previously unselected package dwz. 79s Preparing to unpack .../45-dwz_0.16-2_ppc64el.deb ... 79s Unpacking dwz (0.16-2) ... 80s Selecting previously unselected package gettext. 80s Preparing to unpack .../46-gettext_0.23.2-1_ppc64el.deb ... 80s Unpacking gettext (0.23.2-1) ... 80s Selecting previously unselected package intltool-debian. 80s Preparing to unpack .../47-intltool-debian_0.35.0+20060710.6build1_all.deb ... 80s Unpacking intltool-debian (0.35.0+20060710.6build1) ... 80s Selecting previously unselected package po-debconf. 80s Preparing to unpack .../48-po-debconf_1.0.22_all.deb ... 80s Unpacking po-debconf (1.0.22) ... 80s Selecting previously unselected package debhelper. 80s Preparing to unpack .../49-debhelper_13.28ubuntu1_all.deb ... 80s Unpacking debhelper (13.28ubuntu1) ... 80s Selecting previously unselected package dh-python. 80s Preparing to unpack .../50-dh-python_7.20251231_all.deb ... 80s Unpacking dh-python (7.20251231) ... 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81s Setting up dh-python (7.20251231) ... 81s Setting up python3-iniconfig (2.1.0-2) ... 82s Setting up python3-propka (3.5.1-2) ... 82s Setting up fonts-lato (2.015-1build1) ... 82s Setting up fonts-mathjax (2.7.9+dfsg-1build1) ... 82s Setting up libjs-mathjax (2.7.9+dfsg-1build1) ... 82s Setting up python3-defusedxml (0.7.1-3build1) ... 82s Setting up libarchive-zip-perl (1.68-1) ... 82s Setting up python3-alabaster (0.7.16-0.1build1) ... 82s Setting up libdebhelper-perl (13.28ubuntu1) ... 82s Setting up m4 (1.4.20-2) ... 82s Setting up libgomp1:ppc64el (15.2.0-11ubuntu1) ... 82s Setting up help2man (1.49.3) ... 82s Setting up autotools-dev (20240727.1) ... 82s Setting up libblas3:ppc64el (3.12.1-7ubuntu1) ... 82s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 82s Setting up python3-snowballstemmer (3.0.1-1) ... 83s Setting up libquadmath0:ppc64el 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libcc1-0:ppc64el (15.2.0-11ubuntu1) ... 84s Setting up liblsan0:ppc64el (15.2.0-11ubuntu1) ... 84s Setting up libitm1:ppc64el (15.2.0-11ubuntu1) ... 84s Setting up python3-imagesize (1.4.1-1build1) ... 84s Setting up automake (1:1.18.1-3build1) ... 84s update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode 84s Setting up libfile-stripnondeterminism-perl (1.15.0-1build1) ... 84s Setting up liblapack3:ppc64el (3.12.1-7ubuntu1) ... 84s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 84s Setting up gettext (0.23.2-1) ... 84s Setting up libgcc-15-dev:ppc64el (15.2.0-11ubuntu1) ... 84s Setting up python3.13 (3.13.11-1) ... 86s Setting up python3-pytest (9.0.2-2) ... 86s Setting up python3-all (3.14.2-1) ... 86s Setting up intltool-debian (0.35.0+20060710.6build1) ... 86s Setting up cpp-15-powerpc64le-linux-gnu (15.2.0-11ubuntu1) ... 86s Setting up libstdc++-15-dev:ppc64el (15.2.0-11ubuntu1) ... 86s Setting up sphinx-common (8.2.3-12) ... 86s Setting up python3-numpy (1:2.3.5+ds-3) ... 90s Setting up dh-strip-nondeterminism (1.15.0-1build1) ... 90s Setting up python-propka-doc (3.5.1-2) ... 90s Setting up cpp-15 (15.2.0-11ubuntu1) ... 90s Setting up xml-core (0.19build1) ... 90s Setting up cpp-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 90s Setting up gcc-15-powerpc64le-linux-gnu (15.2.0-11ubuntu1) ... 90s Setting up po-debconf (1.0.22) ... 90s Setting up gcc-15 (15.2.0-11ubuntu1) ... 90s Setting up gcc-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 90s Setting up cpp (4:15.2.0-4ubuntu1) ... 90s Setting up g++-15-powerpc64le-linux-gnu (15.2.0-11ubuntu1) ... 90s Setting up libtool (2.5.4-9) ... 90s Setting up gcc (4:15.2.0-4ubuntu1) ... 90s Setting up dh-autoreconf (21) ... 90s Setting up g++-15 (15.2.0-11ubuntu1) ... 90s Setting up g++-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 90s Setting up debhelper (13.28ubuntu1) ... 90s Setting up g++ (4:15.2.0-4ubuntu1) ... 90s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 90s Setting up build-essential (12.12ubuntu2) ... 90s Setting up pybuild-plugin-autopkgtest (7.20251231) ... 90s Processing triggers for install-info (7.2-5) ... 90s Processing triggers for libc-bin (2.42-2ubuntu4) ... 90s Processing triggers for systemd (259-1ubuntu2) ... 90s Processing triggers for man-db (2.13.1-1) ... 92s Processing triggers for sgml-base (1.31+nmu1) ... 92s Setting up docutils-common (0.22.4+dfsg-1) ... 92s Processing triggers for sgml-base (1.31+nmu1) ... 92s Setting up python3-docutils (0.22.4+dfsg-1) ... 93s Setting up python3-sphinx (8.2.3-12) ... 95s Setting up python3-sphinxcontrib.jquery (4.1-6) ... 95s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-3) ... 96s autopkgtest [19:31:33]: test pybuild-autopkgtest: pybuild-autopkgtest 96s autopkgtest [19:31:33]: test pybuild-autopkgtest: [----------------------- 96s pybuild-autopkgtest 96s I: pybuild base:384: cd /tmp/autopkgtest.MagSSz/autopkgtest_tmp/build; python3.13 -m pytest -k 'not test_molecular_container' 97s ============================= test session starts ============================== 97s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 97s rootdir: /tmp/autopkgtest.MagSSz/autopkgtest_tmp/build 97s plugins: typeguard-4.4.4 97s collected 49 items / 2 deselected / 47 selected 97s 100s tests/test_basic_regression.py ....... [ 14%] 100s tests/test_hybrid36.py .. [ 19%] 100s tests/test_input.py .. [ 23%] 100s tests/test_lib.py .. [ 27%] 100s tests/test_protonate.py . [ 29%] 102s tests/test_run.py ........ [ 46%] 103s tests/test_streamio.py ........ [ 63%] 104s tests/test_vector_algebra.py ............... [ 95%] 104s tests/test_version.py .. [100%] 104s 104s ======================= 47 passed, 2 deselected in 6.80s ======================= 104s I: pybuild base:384: cd /tmp/autopkgtest.MagSSz/autopkgtest_tmp/build; python3.14 -m pytest -k 'not test_molecular_container' 104s ============================= test session starts ============================== 104s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 104s rootdir: /tmp/autopkgtest.MagSSz/autopkgtest_tmp/build 104s plugins: typeguard-4.4.4 104s collected 49 items / 2 deselected / 47 selected 104s 104s tests/test_basic_regression.py FFFFFFF [ 14%] 104s tests/test_hybrid36.py .. [ 19%] 104s tests/test_input.py .. [ 23%] 104s tests/test_lib.py .. [ 27%] 104s tests/test_protonate.py . [ 29%] 104s tests/test_run.py FFFFFFFF [ 46%] 105s tests/test_streamio.py FFFFFFFF [ 63%] 105s tests/test_vector_algebra.py ............... [ 95%] 105s tests/test_version.py .. [100%] 105s 105s =================================== FAILURES =================================== 105s ________________ test_regression[sample-issue-140: no options] _________________ 105s 105s pdb = 'sample-issue-140' 105s options = ['/tmp/autopkgtest.MagSSz/autopkgtest_tmp/build/tests/pdb/sample-issue-140.pdb'] 105s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_sample_issue_10') 105s 105s @pytest.mark.parametrize("pdb, options", [ 105s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 105s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 105s pytest.param('1HPX', [], id="1HPX: no options"), 105s pytest.param('4DFR', [], id="4DFR: no options"), 105s pytest.param('3SGB', [], id="3SGB: no options"), 105s pytest.param('3SGB-subset', [ 105s "--titrate_only", 105s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 105s id="3SGB: --titrate_only"), 105s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 105s def test_regression(pdb, options, tmp_path): 105s """Basic regression test of PROPKA functionality.""" 105s path_dict = get_test_dirs() 105s ref_path = None 105s 105s for ext in ["json", "dat"]: 105s ref_path = path_dict["results"] / f"{pdb}.{ext}" 105s if ref_path.is_file(): 105s ref_path = ref_path.resolve() 105s break 105s else: 105s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 105s str(ref_path))) 105s ref_path = None 105s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 105s if pdb_path.is_file(): 105s pdb_path = pdb_path.resolve() 105s else: 105s errstr = "Missing PDB file: {0:s}".format(pdb_path) 105s raise FileNotFoundError(errstr) 105s tmp_path = Path(tmp_path).resolve() 105s 105s > run_propka(options, pdb_path, tmp_path) 105s 105s tests/test_basic_regression.py:170: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s tests/test_basic_regression.py:77: in run_propka 105s parameters = read_parameter_file(args.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s ------------------------------ Captured log call ------------------------------- 105s 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. 105s __________________ test_regression[1FTJ-Chain-A: no options] ___________________ 105s 105s pdb = '1FTJ-Chain-A' 105s options = ['/tmp/autopkgtest.MagSSz/autopkgtest_tmp/build/tests/pdb/1FTJ-Chain-A.pdb'] 105s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_1FTJ_Chain_A__0') 105s 105s @pytest.mark.parametrize("pdb, options", [ 105s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 105s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 105s pytest.param('1HPX', [], id="1HPX: no options"), 105s pytest.param('4DFR', [], id="4DFR: no options"), 105s pytest.param('3SGB', [], id="3SGB: no options"), 105s pytest.param('3SGB-subset', [ 105s "--titrate_only", 105s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 105s id="3SGB: --titrate_only"), 105s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 105s def test_regression(pdb, options, tmp_path): 105s """Basic regression test of PROPKA functionality.""" 105s path_dict = get_test_dirs() 105s ref_path = None 105s 105s for ext in ["json", "dat"]: 105s ref_path = path_dict["results"] / f"{pdb}.{ext}" 105s if ref_path.is_file(): 105s ref_path = ref_path.resolve() 105s break 105s else: 105s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 105s str(ref_path))) 105s ref_path = None 105s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 105s if pdb_path.is_file(): 105s pdb_path = pdb_path.resolve() 105s else: 105s errstr = "Missing PDB file: {0:s}".format(pdb_path) 105s raise FileNotFoundError(errstr) 105s tmp_path = Path(tmp_path).resolve() 105s 105s > run_propka(options, pdb_path, tmp_path) 105s 105s tests/test_basic_regression.py:170: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s tests/test_basic_regression.py:77: in run_propka 105s parameters = read_parameter_file(args.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s ------------------------------ Captured log call ------------------------------- 105s 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. 105s ______________________ test_regression[1HPX: no options] _______________________ 105s 105s pdb = '1HPX' 105s options = ['/tmp/autopkgtest.MagSSz/autopkgtest_tmp/build/tests/pdb/1HPX.pdb'] 105s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_1HPX__no_optio0') 105s 105s @pytest.mark.parametrize("pdb, options", [ 105s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 105s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 105s pytest.param('1HPX', [], id="1HPX: no options"), 105s pytest.param('4DFR', [], id="4DFR: no options"), 105s pytest.param('3SGB', [], id="3SGB: no options"), 105s pytest.param('3SGB-subset', [ 105s "--titrate_only", 105s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 105s id="3SGB: --titrate_only"), 105s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 105s def test_regression(pdb, options, tmp_path): 105s """Basic regression test of PROPKA functionality.""" 105s path_dict = get_test_dirs() 105s ref_path = None 105s 105s for ext in ["json", "dat"]: 105s ref_path = path_dict["results"] / f"{pdb}.{ext}" 105s if ref_path.is_file(): 105s ref_path = ref_path.resolve() 105s break 105s else: 105s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 105s str(ref_path))) 105s ref_path = None 105s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 105s if pdb_path.is_file(): 105s pdb_path = pdb_path.resolve() 105s else: 105s errstr = "Missing PDB file: {0:s}".format(pdb_path) 105s raise FileNotFoundError(errstr) 105s tmp_path = Path(tmp_path).resolve() 105s 105s > run_propka(options, pdb_path, tmp_path) 105s 105s tests/test_basic_regression.py:170: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s tests/test_basic_regression.py:77: in run_propka 105s parameters = read_parameter_file(args.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s ------------------------------ Captured log call ------------------------------- 105s 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. 105s ______________________ test_regression[4DFR: no options] _______________________ 105s 105s pdb = '4DFR' 105s options = ['/tmp/autopkgtest.MagSSz/autopkgtest_tmp/build/tests/pdb/4DFR.pdb'] 105s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_4DFR__no_optio0') 105s 105s @pytest.mark.parametrize("pdb, options", [ 105s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 105s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 105s pytest.param('1HPX', [], id="1HPX: no options"), 105s pytest.param('4DFR', [], id="4DFR: no options"), 105s pytest.param('3SGB', [], id="3SGB: no options"), 105s pytest.param('3SGB-subset', [ 105s "--titrate_only", 105s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 105s id="3SGB: --titrate_only"), 105s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 105s def test_regression(pdb, options, tmp_path): 105s """Basic regression test of PROPKA functionality.""" 105s path_dict = get_test_dirs() 105s ref_path = None 105s 105s for ext in ["json", "dat"]: 105s ref_path = path_dict["results"] / f"{pdb}.{ext}" 105s if ref_path.is_file(): 105s ref_path = ref_path.resolve() 105s break 105s else: 105s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 105s str(ref_path))) 105s ref_path = None 105s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 105s if pdb_path.is_file(): 105s pdb_path = pdb_path.resolve() 105s else: 105s errstr = "Missing PDB file: {0:s}".format(pdb_path) 105s raise FileNotFoundError(errstr) 105s tmp_path = Path(tmp_path).resolve() 105s 105s > run_propka(options, pdb_path, tmp_path) 105s 105s tests/test_basic_regression.py:170: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s tests/test_basic_regression.py:77: in run_propka 105s parameters = read_parameter_file(args.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s ------------------------------ Captured log call ------------------------------- 105s 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. 105s ______________________ test_regression[3SGB: no options] _______________________ 105s 105s pdb = '3SGB' 105s options = ['/tmp/autopkgtest.MagSSz/autopkgtest_tmp/build/tests/pdb/3SGB.pdb'] 105s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_3SGB__no_optio0') 105s 105s @pytest.mark.parametrize("pdb, options", [ 105s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 105s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 105s pytest.param('1HPX', [], id="1HPX: no options"), 105s pytest.param('4DFR', [], id="4DFR: no options"), 105s pytest.param('3SGB', [], id="3SGB: no options"), 105s pytest.param('3SGB-subset', [ 105s "--titrate_only", 105s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 105s id="3SGB: --titrate_only"), 105s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 105s def test_regression(pdb, options, tmp_path): 105s """Basic regression test of PROPKA functionality.""" 105s path_dict = get_test_dirs() 105s ref_path = None 105s 105s for ext in ["json", "dat"]: 105s ref_path = path_dict["results"] / f"{pdb}.{ext}" 105s if ref_path.is_file(): 105s ref_path = ref_path.resolve() 105s break 105s else: 105s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 105s str(ref_path))) 105s ref_path = None 105s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 105s if pdb_path.is_file(): 105s pdb_path = pdb_path.resolve() 105s else: 105s errstr = "Missing PDB file: {0:s}".format(pdb_path) 105s raise FileNotFoundError(errstr) 105s tmp_path = Path(tmp_path).resolve() 105s 105s > run_propka(options, pdb_path, tmp_path) 105s 105s tests/test_basic_regression.py:170: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s tests/test_basic_regression.py:77: in run_propka 105s parameters = read_parameter_file(args.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s ------------------------------ Captured log call ------------------------------- 105s 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. 105s ____________________ test_regression[3SGB: --titrate_only] _____________________ 105s 105s pdb = '3SGB-subset' 105s 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.MagSSz/autopkgtest_tmp/build/tests/pdb/3SGB-subset.pdb'] 105s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_3SGB____titrat0') 105s 105s @pytest.mark.parametrize("pdb, options", [ 105s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 105s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 105s pytest.param('1HPX', [], id="1HPX: no options"), 105s pytest.param('4DFR', [], id="4DFR: no options"), 105s pytest.param('3SGB', [], id="3SGB: no options"), 105s pytest.param('3SGB-subset', [ 105s "--titrate_only", 105s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 105s id="3SGB: --titrate_only"), 105s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 105s def test_regression(pdb, options, tmp_path): 105s """Basic regression test of PROPKA functionality.""" 105s path_dict = get_test_dirs() 105s ref_path = None 105s 105s for ext in ["json", "dat"]: 105s ref_path = path_dict["results"] / f"{pdb}.{ext}" 105s if ref_path.is_file(): 105s ref_path = ref_path.resolve() 105s break 105s else: 105s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 105s str(ref_path))) 105s ref_path = None 105s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 105s if pdb_path.is_file(): 105s pdb_path = pdb_path.resolve() 105s else: 105s errstr = "Missing PDB file: {0:s}".format(pdb_path) 105s raise FileNotFoundError(errstr) 105s tmp_path = Path(tmp_path).resolve() 105s 105s > run_propka(options, pdb_path, tmp_path) 105s 105s tests/test_basic_regression.py:170: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s tests/test_basic_regression.py:77: in run_propka 105s parameters = read_parameter_file(args.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s ------------------------------ Captured log call ------------------------------- 105s 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. 105s _____________________ test_regression[1HPX-warn: --quiet] ______________________ 105s 105s pdb = '1HPX-warn' 105s options = ['--quiet', '/tmp/autopkgtest.MagSSz/autopkgtest_tmp/build/tests/pdb/1HPX-warn.pdb'] 105s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_1HPX_warn____q0') 105s 105s @pytest.mark.parametrize("pdb, options", [ 105s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 105s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 105s pytest.param('1HPX', [], id="1HPX: no options"), 105s pytest.param('4DFR', [], id="4DFR: no options"), 105s pytest.param('3SGB', [], id="3SGB: no options"), 105s pytest.param('3SGB-subset', [ 105s "--titrate_only", 105s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 105s id="3SGB: --titrate_only"), 105s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 105s def test_regression(pdb, options, tmp_path): 105s """Basic regression test of PROPKA functionality.""" 105s path_dict = get_test_dirs() 105s ref_path = None 105s 105s for ext in ["json", "dat"]: 105s ref_path = path_dict["results"] / f"{pdb}.{ext}" 105s if ref_path.is_file(): 105s ref_path = ref_path.resolve() 105s break 105s else: 105s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 105s str(ref_path))) 105s ref_path = None 105s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 105s if pdb_path.is_file(): 105s pdb_path = pdb_path.resolve() 105s else: 105s errstr = "Missing PDB file: {0:s}".format(pdb_path) 105s raise FileNotFoundError(errstr) 105s tmp_path = Path(tmp_path).resolve() 105s 105s > run_propka(options, pdb_path, tmp_path) 105s 105s tests/test_basic_regression.py:170: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s tests/test_basic_regression.py:77: in run_propka 105s parameters = read_parameter_file(args.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s ------------------------------ Captured log call ------------------------------- 105s 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. 105s __________________ test_single_file[1FTJ-Chain-A: no options] __________________ 105s 105s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_file_1FTJ_Chain_A_0') 105s pdb = '1FTJ-Chain-A', options = () 105s 105s @pytest.mark.parametrize("pdb, options", [ 105s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 105s pytest.param('3SGB-subset', ( 105s "--titrate_only", 105s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 105s id="3SGB: --titrate_only"), 105s pytest.param('1HPX-warn', ('--quiet',), id="1HPX-warn: --quiet"), 105s ]) 105s def test_single_file(tmpdir, pdb, options): 105s """Basic regression test using propka.run.single and local file for the 105s input PDB file""" 105s ref_path, pdb_path = get_paths(pdb) 105s filename = str(pdb_path) 105s 105s with tmpdir.as_cwd(): 105s > pkrun.single(filename, options) 105s 105s tests/test_run.py:31: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s /usr/lib/python3/dist-packages/propka/run.py:118: in single 105s parameters = read_parameter_file(options.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s ____________________ test_single_file[3SGB: --titrate_only] ____________________ 105s 105s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_file_3SGB____titra0') 105s pdb = '3SGB-subset' 105s 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') 105s 105s @pytest.mark.parametrize("pdb, options", [ 105s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 105s pytest.param('3SGB-subset', ( 105s "--titrate_only", 105s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 105s id="3SGB: --titrate_only"), 105s pytest.param('1HPX-warn', ('--quiet',), id="1HPX-warn: --quiet"), 105s ]) 105s def test_single_file(tmpdir, pdb, options): 105s """Basic regression test using propka.run.single and local file for the 105s input PDB file""" 105s ref_path, pdb_path = get_paths(pdb) 105s filename = str(pdb_path) 105s 105s with tmpdir.as_cwd(): 105s > pkrun.single(filename, options) 105s 105s tests/test_run.py:31: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s /usr/lib/python3/dist-packages/propka/run.py:118: in single 105s parameters = read_parameter_file(options.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s _____________________ test_single_file[1HPX-warn: --quiet] _____________________ 105s 105s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_file_1HPX_warn____0') 105s pdb = '1HPX-warn', options = ('--quiet',) 105s 105s @pytest.mark.parametrize("pdb, options", [ 105s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 105s pytest.param('3SGB-subset', ( 105s "--titrate_only", 105s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 105s id="3SGB: --titrate_only"), 105s pytest.param('1HPX-warn', ('--quiet',), id="1HPX-warn: --quiet"), 105s ]) 105s def test_single_file(tmpdir, pdb, options): 105s """Basic regression test using propka.run.single and local file for the 105s input PDB file""" 105s ref_path, pdb_path = get_paths(pdb) 105s filename = str(pdb_path) 105s 105s with tmpdir.as_cwd(): 105s > pkrun.single(filename, options) 105s 105s tests/test_run.py:31: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s /usr/lib/python3/dist-packages/propka/run.py:118: in single 105s parameters = read_parameter_file(options.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s _______________ test_single_filestream[1FTJ-Chain-A: no options] _______________ 105s 105s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_filestream_1FTJ_Ch0') 105s pdb = '1FTJ-Chain-A', options = () 105s 105s @pytest.mark.parametrize("pdb, options", [ 105s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 105s pytest.param('3SGB-subset', ( 105s "--titrate_only", 105s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 105s id="3SGB: --titrate_only"), 105s pytest.param('1HPX-warn',('--quiet',), id="1HPX-warn: --quiet"), 105s ]) 105s def test_single_filestream(tmpdir, pdb, options): 105s """Basic regression test using StringIO streams for the input PDB file""" 105s ref_path, pdb_path = get_paths(pdb) 105s filename = f"{pdb}.pdb" 105s 105s with open(pdb_path, 'r') as writer: 105s filestream = StringIO(writer.read()) 105s 105s with tmpdir.as_cwd(): 105s > pkrun.single(filename, options, stream=filestream) 105s 105s tests/test_run.py:53: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s /usr/lib/python3/dist-packages/propka/run.py:118: in single 105s parameters = read_parameter_file(options.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s _________________ test_single_filestream[3SGB: --titrate_only] _________________ 105s 105s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_filestream_3SGB___0') 105s pdb = '3SGB-subset' 105s 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') 105s 105s @pytest.mark.parametrize("pdb, options", [ 105s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 105s pytest.param('3SGB-subset', ( 105s "--titrate_only", 105s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 105s id="3SGB: --titrate_only"), 105s pytest.param('1HPX-warn',('--quiet',), id="1HPX-warn: --quiet"), 105s ]) 105s def test_single_filestream(tmpdir, pdb, options): 105s """Basic regression test using StringIO streams for the input PDB file""" 105s ref_path, pdb_path = get_paths(pdb) 105s filename = f"{pdb}.pdb" 105s 105s with open(pdb_path, 'r') as writer: 105s filestream = StringIO(writer.read()) 105s 105s with tmpdir.as_cwd(): 105s > pkrun.single(filename, options, stream=filestream) 105s 105s tests/test_run.py:53: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s /usr/lib/python3/dist-packages/propka/run.py:118: in single 105s parameters = read_parameter_file(options.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s __________________ test_single_filestream[1HPX-warn: --quiet] __________________ 105s 105s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_filestream_1HPX_wa0') 105s pdb = '1HPX-warn', options = ('--quiet',) 105s 105s @pytest.mark.parametrize("pdb, options", [ 105s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 105s pytest.param('3SGB-subset', ( 105s "--titrate_only", 105s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 105s id="3SGB: --titrate_only"), 105s pytest.param('1HPX-warn',('--quiet',), id="1HPX-warn: --quiet"), 105s ]) 105s def test_single_filestream(tmpdir, pdb, options): 105s """Basic regression test using StringIO streams for the input PDB file""" 105s ref_path, pdb_path = get_paths(pdb) 105s filename = f"{pdb}.pdb" 105s 105s with open(pdb_path, 'r') as writer: 105s filestream = StringIO(writer.read()) 105s 105s with tmpdir.as_cwd(): 105s > pkrun.single(filename, options, stream=filestream) 105s 105s tests/test_run.py:53: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s /usr/lib/python3/dist-packages/propka/run.py:118: in single 105s parameters = read_parameter_file(options.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s ______________________________ test_single_nopka _______________________________ 105s 105s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_nopka0') 105s 105s def test_single_nopka(tmpdir): 105s """Basic test to check that the pKa file is not written when write_pka is 105s `False`""" 105s pdb = "1FTJ-Chain-A" 105s ref_path, pdb_path = get_paths(pdb) 105s filename = f"{pdb}.pdb" 105s 105s with open(pdb_path, 'r') as writer: 105s filestream = StringIO(writer.read()) 105s 105s > pkrun.single(filename, stream=filestream, write_pka=False) 105s 105s tests/test_run.py:70: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s /usr/lib/python3/dist-packages/propka/run.py:118: in single 105s parameters = read_parameter_file(options.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s _______________________ test_single_extra_files_logwarn ________________________ 105s 105s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_extra_files_logwar0') 105s caplog = <_pytest.logging.LogCaptureFixture object at 0x6723081fc830> 105s 105s def test_single_extra_files_logwarn(tmpdir, caplog): 105s """Tests that a logging warning is thrown if passing files via optargs""" 105s pdb = "1FTJ-Chain-A" 105s options = ('-f foo.pdb bar.pdb', '-f test.pdb test2.pdb') 105s ref_path, pdb_path = get_paths(pdb) 105s filename = str(pdb_path) 105s 105s with tmpdir.as_cwd(): 105s > pkrun.single(filename, options) 105s 105s tests/test_run.py:82: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s /usr/lib/python3/dist-packages/propka/run.py:118: in single 105s parameters = read_parameter_file(options.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s _______________ test_textio_filestream[1FTJ-Chain-A: no options] _______________ 105s 105s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_textio_filestream_1FTJ_Ch0') 105s pdb = '1FTJ-Chain-A', options = ['1FTJ-Chain-A.pdb'] 105s 105s @pytest.mark.parametrize("pdb, options", [ 105s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 105s pytest.param('3SGB-subset', [ 105s "--titrate_only", 105s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 105s id="3SGB: --titrate_only"), 105s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 105s ]) 105s def test_textio_filestream(tmpdir, pdb, options): 105s """Basic regression test using TextIO streams for the input PDB file""" 105s # Get the relevant paths 105s ref_path, pdb_path = get_paths(pdb) 105s filename = f"{pdb}.pdb" 105s 105s filestream = open(pdb_path, 'r') 105s 105s with tmpdir.as_cwd(): 105s > run_propka_stream(options, filestream, filename) 105s 105s tests/test_streamio.py:60: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s tests/test_streamio.py:36: in run_propka_stream 105s parameters = read_parameter_file(args.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s _________________ test_textio_filestream[3SGB: --titrate_only] _________________ 105s 105s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_textio_filestream_3SGB___0') 105s pdb = '3SGB-subset' 105s 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'] 105s 105s @pytest.mark.parametrize("pdb, options", [ 105s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 105s pytest.param('3SGB-subset', [ 105s "--titrate_only", 105s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 105s id="3SGB: --titrate_only"), 105s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 105s ]) 105s def test_textio_filestream(tmpdir, pdb, options): 105s """Basic regression test using TextIO streams for the input PDB file""" 105s # Get the relevant paths 105s ref_path, pdb_path = get_paths(pdb) 105s filename = f"{pdb}.pdb" 105s 105s filestream = open(pdb_path, 'r') 105s 105s with tmpdir.as_cwd(): 105s > run_propka_stream(options, filestream, filename) 105s 105s tests/test_streamio.py:60: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s tests/test_streamio.py:36: in run_propka_stream 105s parameters = read_parameter_file(args.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s __________________ test_textio_filestream[1HPX-warn: --quiet] __________________ 105s 105s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_textio_filestream_1HPX_wa0') 105s pdb = '1HPX-warn', options = ['--quiet', '1HPX-warn.pdb'] 105s 105s @pytest.mark.parametrize("pdb, options", [ 105s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 105s pytest.param('3SGB-subset', [ 105s "--titrate_only", 105s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 105s id="3SGB: --titrate_only"), 105s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 105s ]) 105s def test_textio_filestream(tmpdir, pdb, options): 105s """Basic regression test using TextIO streams for the input PDB file""" 105s # Get the relevant paths 105s ref_path, pdb_path = get_paths(pdb) 105s filename = f"{pdb}.pdb" 105s 105s filestream = open(pdb_path, 'r') 105s 105s with tmpdir.as_cwd(): 105s > run_propka_stream(options, filestream, filename) 105s 105s tests/test_streamio.py:60: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s tests/test_streamio.py:36: in run_propka_stream 105s parameters = read_parameter_file(args.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s ______________ test_stringio_filestream[1FTJ-Chain-A: no options] ______________ 105s 105s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_stringio_filestream_1FTJ_0') 105s pdb = '1FTJ-Chain-A', options = ['1FTJ-Chain-A.pdb'] 105s 105s @pytest.mark.parametrize("pdb, options", [ 105s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 105s pytest.param('3SGB-subset', [ 105s "--titrate_only", 105s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 105s id="3SGB: --titrate_only"), 105s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 105s ]) 105s def test_stringio_filestream(tmpdir, pdb, options): 105s """Basic regression test using StringIO streams for the input PDB file""" 105s # Get the relevant paths 105s ref_path, pdb_path = get_paths(pdb) 105s filename = f"{pdb}.pdb" 105s 105s with open(pdb_path, 'r') as writer: 105s filestream = StringIO(writer.read()) 105s 105s with tmpdir.as_cwd(): 105s > run_propka_stream(options, filestream, filename) 105s 105s tests/test_streamio.py:84: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s tests/test_streamio.py:36: in run_propka_stream 105s parameters = read_parameter_file(args.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s ________________ test_stringio_filestream[3SGB: --titrate_only] ________________ 105s 105s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_stringio_filestream_3SGB_0') 105s pdb = '3SGB-subset' 105s 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'] 105s 105s @pytest.mark.parametrize("pdb, options", [ 105s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 105s pytest.param('3SGB-subset', [ 105s "--titrate_only", 105s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 105s id="3SGB: --titrate_only"), 105s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 105s ]) 105s def test_stringio_filestream(tmpdir, pdb, options): 105s """Basic regression test using StringIO streams for the input PDB file""" 105s # Get the relevant paths 105s ref_path, pdb_path = get_paths(pdb) 105s filename = f"{pdb}.pdb" 105s 105s with open(pdb_path, 'r') as writer: 105s filestream = StringIO(writer.read()) 105s 105s with tmpdir.as_cwd(): 105s > run_propka_stream(options, filestream, filename) 105s 105s tests/test_streamio.py:84: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s tests/test_streamio.py:36: in run_propka_stream 105s parameters = read_parameter_file(args.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s _________________ test_stringio_filestream[1HPX-warn: --quiet] _________________ 105s 105s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_stringio_filestream_1HPX_0') 105s pdb = '1HPX-warn', options = ['--quiet', '1HPX-warn.pdb'] 105s 105s @pytest.mark.parametrize("pdb, options", [ 105s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 105s pytest.param('3SGB-subset', [ 105s "--titrate_only", 105s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 105s id="3SGB: --titrate_only"), 105s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 105s ]) 105s def test_stringio_filestream(tmpdir, pdb, options): 105s """Basic regression test using StringIO streams for the input PDB file""" 105s # Get the relevant paths 105s ref_path, pdb_path = get_paths(pdb) 105s filename = f"{pdb}.pdb" 105s 105s with open(pdb_path, 'r') as writer: 105s filestream = StringIO(writer.read()) 105s 105s with tmpdir.as_cwd(): 105s > run_propka_stream(options, filestream, filename) 105s 105s tests/test_streamio.py:84: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s tests/test_streamio.py:36: in run_propka_stream 105s parameters = read_parameter_file(args.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s __________________________ test_valuerror_nofiletype ___________________________ 105s 105s def test_valuerror_nofiletype(): 105s """Tests for raised ValueError when an unknown filename is passed to 105s read_molecule_file""" 105s pdb = "1FTJ-Chain-A" 105s options = [] 105s 105s ref_path, pdb_path = get_paths(pdb) 105s 105s with open(pdb_path, 'r') as writer: 105s filestream = StringIO(writer.read()) 105s 105s errmsg = "Unknown input file type" 105s with pytest.raises(ValueError, match=errmsg): 105s > run_propka_stream(options, filestream, filename="test.dat") 105s 105s tests/test_streamio.py:103: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s tests/test_streamio.py:36: in run_propka_stream 105s parameters = read_parameter_file(args.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s ____________________________ test_valuerror_notpdb _____________________________ 105s 105s def test_valuerror_notpdb(): 105s """Tests for raised ValueError when a stream object that isn't a PDB 105s is passed to read_molecule_file""" 105s pdb = "1FTJ-Chain-A" 105s options = [] 105s 105s ref_path, pdb_path = get_paths(pdb) 105s 105s filestream = StringIO() 105s 105s errmsg = "The pdb file does not seem to contain any " 105s with pytest.raises(ValueError, match=errmsg): 105s > run_propka_stream(options, filestream, filename="test.pdb") 105s 105s tests/test_streamio.py:118: 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s tests/test_streamio.py:36: in run_propka_stream 105s parameters = read_parameter_file(args.parameters, Parameters()) 105s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 105s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 105s parameters.parse_line(line) 105s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 105s 105s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 105s ^^^^^^^^^^^^^^^^^^^^ 105s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 105s 105s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 105s =========================== short test summary info ============================ 105s FAILED tests/test_basic_regression.py::test_regression[sample-issue-140: no options] 105s FAILED tests/test_basic_regression.py::test_regression[1FTJ-Chain-A: no options] 105s FAILED tests/test_basic_regression.py::test_regression[1HPX: no options] - At... 105s FAILED tests/test_basic_regression.py::test_regression[4DFR: no options] - At... 105s FAILED tests/test_basic_regression.py::test_regression[3SGB: no options] - At... 105s FAILED tests/test_basic_regression.py::test_regression[3SGB: --titrate_only] 105s FAILED tests/test_basic_regression.py::test_regression[1HPX-warn: --quiet] - ... 105s FAILED tests/test_run.py::test_single_file[1FTJ-Chain-A: no options] - Attrib... 105s FAILED tests/test_run.py::test_single_file[3SGB: --titrate_only] - AttributeE... 105s FAILED tests/test_run.py::test_single_file[1HPX-warn: --quiet] - AttributeErr... 105s FAILED tests/test_run.py::test_single_filestream[1FTJ-Chain-A: no options] - ... 105s FAILED tests/test_run.py::test_single_filestream[3SGB: --titrate_only] - Attr... 105s FAILED tests/test_run.py::test_single_filestream[1HPX-warn: --quiet] - Attrib... 105s FAILED tests/test_run.py::test_single_nopka - AttributeError: 'Parameters' ob... 105s FAILED tests/test_run.py::test_single_extra_files_logwarn - AttributeError: '... 105s FAILED tests/test_streamio.py::test_textio_filestream[1FTJ-Chain-A: no options] 105s FAILED tests/test_streamio.py::test_textio_filestream[3SGB: --titrate_only] 105s FAILED tests/test_streamio.py::test_textio_filestream[1HPX-warn: --quiet] - A... 105s FAILED tests/test_streamio.py::test_stringio_filestream[1FTJ-Chain-A: no options] 105s FAILED tests/test_streamio.py::test_stringio_filestream[3SGB: --titrate_only] 105s FAILED tests/test_streamio.py::test_stringio_filestream[1HPX-warn: --quiet] 105s FAILED tests/test_streamio.py::test_valuerror_nofiletype - AttributeError: 'P... 105s FAILED tests/test_streamio.py::test_valuerror_notpdb - AttributeError: 'Param... 105s ================= 23 failed, 24 passed, 2 deselected in 0.65s ================== 105s E: pybuild pybuild:483: test: plugin distutils failed with: exit code=1: cd /tmp/autopkgtest.MagSSz/autopkgtest_tmp/build; python3.14 -m pytest -k 'not test_molecular_container' 105s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.13 3.14" returned exit code 13 105s make: *** [/tmp/pbaZpx0fQc/run:4: pybuild-autopkgtest] Error 25 105s pybuild-autopkgtest: error: /tmp/pbaZpx0fQc/run pybuild-autopkgtest returned exit code 2 105s autopkgtest [19:31:42]: test pybuild-autopkgtest: -----------------------] 105s autopkgtest [19:31:42]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 105s pybuild-autopkgtest FAIL non-zero exit status 25 106s autopkgtest [19:31:43]: @@@@@@@@@@@@@@@@@@@@ summary 106s pybuild-autopkgtest FAIL non-zero exit status 25