[Debichem-devel] Bug#1028995: mdtraj: (autopkgtest) needs update for Python 3.11

[Graham Inggs]

Source: mdtraj
Version: 1.9.7-4
Severity: serious
User: debian-ci at lists.debian.org
Usertags: needs-update
User: debian-python at lists.debian.org
Usertags: python3.11
Control: affects -1 src:python3-defaults

Hi Maintainer

The autopkgtests of mdtraj fail with Python 3.11 as the default
version (and Python 3.10 still supported) [1].  I've copied what I
hope is the relevant part of the log below.

Regards
Graham


[1] https://ci.debian.net/packages/m/mdtraj/testing/amd64/


Fatal Python error: Segmentation fault

Current thread 0x00007f9669eda040 (most recent call first):
  File "/usr/lib/python3/dist-packages/mdtraj/core/trajectory.py",
line 2062 in image_molecules
  File "/tmp/autopkgtest-lxc.czx2fspl/downtmp/build.1n0/src/tests/test_trajectory.py",
line 732 in test_image_molecules
  File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195 in
pytest_pyfunc_call
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in
_multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1789 in runtest
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 167 in
pytest_runtest_call
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in
_multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 260 in <lambda>
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 339 in from_call
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 259 in
call_runtest_hook
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 220 in
call_and_report
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 131 in
runtestprotocol
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 112 in
pytest_runtest_protocol
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in
_multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 349 in
pytest_runtestloop
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in
_multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 324 in _main
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 270 in
wrap_session
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 317 in
pytest_cmdline_main
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in
_multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py",
line 167 in main
  File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py",
line 190 in console_main
  File "/usr/bin/pytest-3", line 33 in <module>