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

2022-12-24 Thread Graham Inggs 
Control: tags -1 + ftbfs

With #1025658 fixed in boost1.74, the autopkgtest of cctbx now fails as follows:

Testing dxtbx with python3.10:
= test session starts ==
platform linux -- Python 3.10.9, pytest-7.1.2, pluggy-1.0.0+repack
rootdir: /tmp/autopkgtest-lxc.1endj91b/downtmp/autopkgtest_tmp
plugins: mock-3.8.2, dials-data-2.4.0
collected 745 items / 2 skipped

tests/test_FormatCBFFull.py ss   [  0%]
tests/test_beam.py . [  0%]
tests/test_beamline_definitions.py ..[  0%]
tests/test_compression.py .  [  0%]
tests/test_crystal_model_equivalence.py .[  0%]
tests/test_datablock.py ss   [  1%]
tests/test_dataset_as_flex.py Fatal Python error: Segmentation fault


I suspected a rebuild might solve this, but cctbx now FTBFS with:

Processing: "/build/1st/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/libtbx_refresh.py"
  Generating C++ header files in:

"/build/1st/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include/scitbx/array_family"
  Generating C++ files in:

"/build/1st/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include/scitbx/array_family/boost_python"
  Using fable to convert scitbx/lbfgs.f
Updating entry points for scitbx
  1 entries for entry point pytest_randomly.random_seeder
Traceback (most recent call last):
  File "/build/1st/cctbx-2022.9+ds2+~3.11.2+ds1/libtbx/configure.py",
line 34, in 
if not run():
   ^
  File "/build/1st/cctbx-2022.9+ds2+~3.11.2+ds1/libtbx/configure.py",
line 29, in run
libtbx.env_config.cold_start(sys.argv)
  File "/build/1st/cctbx-2022.9+ds2+~3.11.2+ds1/libtbx/env_config.py",
line 3042, in cold_start
env.refresh()
  File "/build/1st/cctbx-2022.9+ds2+~3.11.2+ds1/libtbx/env_config.py",
line 2264, in refresh
module.process_libtbx_refresh_py()
  File "/build/1st/cctbx-2022.9+ds2+~3.11.2+ds1/libtbx/env_config.py",
line 2585, in process_libtbx_refresh_py
exec(to_str(fh.read()), global_vars)
  File "", line 25, in 
  File "/build/1st/cctbx-2022.9+ds2+~3.11.2+ds1/libtbx/pkg_utils.py",
line 242, in define_entry_points
setuptools.setup(
  File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line
86, in setup
_install_setup_requires(attrs)
  File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line
78, in _install_setup_requires
dist.parse_config_files(ignore_option_errors=True)
  File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 862,
in parse_config_files
self._parse_config_files(filenames=inifiles)
  File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 704,
in _parse_config_files
filenames = self.find_config_files()

  File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py",
line 337, in find_config_files
files = [str(path) for path in self._gen_paths() if os.path.isfile(path)]
^
  File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py",
line 337, in 
files = [str(path) for path in self._gen_paths() if os.path.isfile(path)]
^
  File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py",
line 346, in _gen_paths
sys_dir = pathlib.Path(sys.modules['distutils'].__file__).parent
   ~~~^
KeyError: 'distutils'

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

2022-12-06 Thread 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 "", line 1, in 
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 ?

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

2022-11-26 Thread Paul Gevers 

Source: cctbx
Version: 2022.9+ds2+~3.11.2+ds1-4
Severity: serious
Tags: sid bookworm
User: debian...@lists.debian.org
Usertags: needs-update
User: debian-pyt...@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:


   passfail
python3-defaults   from testing3.10.6-3
cctbx  from testing2022.9+ds2+~3.11.2+ds1-4
all others from testingfrom 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)
:1206: in _gcd_import
???
:1178: in _find_and_load
???
:1128: in _find_and_load_unlocked
???
:241: in _call_with_frames_removed
???
:1206: in _gcd_import
???
:1178: in _find_and_load
???
:1128: in _find_and_load_unlocked
???
:241: in _call_with_frames_removed
???
:1206: in _gcd_import
???
:1178: in _find_and_load
???
:1128: in _find_and_load_unlocked
???
:241: in _call_with_frames_removed
???
:1206: in _gcd_import
???
:1178: in _find_and_load
???
:1149: in _find_and_load_unlocked
???
:690: in _load_unlocked
???
:940: in exec_module
???
:241: in _call_with_frames_removed
???
/usr/lib/python3/dist-packages/smtbx/refinement/__init__.py:2: in 
from cctbx import xray
/usr/lib/python3/dist-packages/cctbx/xray/__init__.py:4: in 
from cctbx.xray.scatterer import *
/usr/lib/python3/dist-packages/cctbx/xray/scatterer.py:3: in 
import cctbx.eltbx.xray_scattering
/usr/lib/python3/dist-packages/cctbx/eltbx/xray_scattering/__init__.py:2: 
in 

import scitbx.math.gaussian # base class for gaussian
/usr/lib/python3/dist-packages/scitbx/math/__init__.py:8: in 
import scitbx.linalg.eigensystem
/usr/lib/python3/dist-packages/scitbx/linalg/__init__.py:2: in 
from scitbx.linalg.ext import *
/usr/lib/python3/dist-packages/scitbx/linalg/ext.py:3: in 
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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