Bug#1024859: cctbx: (autopkgtest) needs update for python3.11: initialization of scitbx_linalg_ext raised unreported exception

[Paul Gevers]

Source: cctbx
Version: 2022.9+ds2+~3.11.2+ds1-4
Severity: serious
Tags: sid bookworm
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

Dear maintainer(s),

We are in the transition of adding python3.11 as a supported Python 
version [0]. With a recent upload of python3-defaults the autopkgtest of 
cctbx fails in testing when that autopkgtest is run with the binary 
packages of python3-defaults from unstable. It passes when run with only 
packages from testing. In tabular form:

                        pass            fail
python3-defaults       from testing    3.10.6-3
cctbx                  from testing    2022.9+ds2+~3.11.2+ds1-4
all others             from testing    from testing

I copied some of the output at the bottom of this report.

Currently this regression is blocking the migration of python3-defaults 
to testing [1]. https://docs.python.org/3/whatsnew/3.11.html lists 
what's new in Python3.11, it may help to identify what needs to be updated.

More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation

Paul

[0] https://bugs.debian.org/1021984
[1] https://qa.debian.org/excuses.php?package=python3-defaults

https://ci.debian.net/data/autopkgtest/testing/amd64/c/cctbx/28708326/log.gz

Testing cctbx with python3.11:
Discovering pytest tests for smtbx:
refinement/constraints/tests/test_disorder.py: 1
refinement/constraints/tests/test_occupancies.py: 1
refinement/constraints/tests/test_rigid.py: 9
refinement/constraints/tests/test_same_group.py: 2

==================================== ERRORS 
====================================
_______ ERROR collecting refinement/constraints/tests/test_direction.py 
________
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
     return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1206: in _gcd_import
     ???
<frozen importlib._bootstrap>:1178: in _find_and_load
     ???
<frozen importlib._bootstrap>:1128: in _find_and_load_unlocked
     ???
<frozen importlib._bootstrap>:241: in _call_with_frames_removed
     ???
<frozen importlib._bootstrap>:1206: in _gcd_import
     ???
<frozen importlib._bootstrap>:1178: in _find_and_load
     ???
<frozen importlib._bootstrap>:1128: in _find_and_load_unlocked
     ???
<frozen importlib._bootstrap>:241: in _call_with_frames_removed
     ???
<frozen importlib._bootstrap>:1206: in _gcd_import
     ???
<frozen importlib._bootstrap>:1178: in _find_and_load
     ???
<frozen importlib._bootstrap>:1128: in _find_and_load_unlocked
     ???
<frozen importlib._bootstrap>:241: in _call_with_frames_removed
     ???
<frozen importlib._bootstrap>:1206: in _gcd_import
     ???
<frozen importlib._bootstrap>:1178: in _find_and_load
     ???
<frozen importlib._bootstrap>:1149: in _find_and_load_unlocked
     ???
<frozen importlib._bootstrap>:690: in _load_unlocked
     ???
<frozen importlib._bootstrap_external>:940: in exec_module
     ???
<frozen importlib._bootstrap>:241: in _call_with_frames_removed
     ???
/usr/lib/python3/dist-packages/smtbx/refinement/__init__.py:2: in <module>
     from cctbx import xray
/usr/lib/python3/dist-packages/cctbx/xray/__init__.py:4: in <module>
     from cctbx.xray.scatterer import *
/usr/lib/python3/dist-packages/cctbx/xray/scatterer.py:3: in <module>
     import cctbx.eltbx.xray_scattering
/usr/lib/python3/dist-packages/cctbx/eltbx/xray_scattering/__init__.py:2: 
in <module>
     import scitbx.math.gaussian # base class for gaussian
/usr/lib/python3/dist-packages/scitbx/math/__init__.py:8: in <module>
     import scitbx.linalg.eigensystem
/usr/lib/python3/dist-packages/scitbx/linalg/__init__.py:2: in <module>
     from scitbx.linalg.ext import *
/usr/lib/python3/dist-packages/scitbx/linalg/ext.py:3: in <module>
     bp.import_ext("scitbx_linalg_ext")
/usr/lib/python3/dist-packages/boost_adaptbx/boost/python.py:22: in 
import_ext
     try: mod = __import__(name)
E   SystemError: initialization of scitbx_linalg_ext raised unreported 
exception

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