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: debi...@lists.debian.org
Usertags: needs-update
User: debian...@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

[picca]

To reproduce the problem

Python3.10:

:~/$ python3.10
Python 3.10.8 (main, Nov 4 2022, 09:21:25) [GCC 12.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scitbx_linalg_ext
>>>


Python3.11

:~/$ python3.11
Python 3.11.0+ (main, Nov 4 2022, 09:23:33) [GCC 12.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scitbx_linalg_ext
Traceback (most recent call last):
File "<stdin>", line 1, in <module>

SystemError: initialization of scitbx_linalg_ext raised unreported
exception
>>>

This extension is using boost_python, something changed in the way
Python 3.11 import modules ?

or python_boost3.11 does not produce Python3.11 usable extension ?