[Debian-med-packaging] Bug#1093353: python-mne: FTBFS: Segmentation fault
Étienne Mollier
emollier at debian.org
Tue Feb 4 21:02:51 GMT 2025
Control: tags -1 + confirmed
Control: retitle -1 python-mne: FTBFS: NumPy 2.0 AttributeError and other issues
The original error looks to have gone away when #1092354
affecting python3-vtk9 has been resolved:
> mne/commands/tests/test_commands.py::test_sys_info Fatal Python error: Segmentation fault
>
> Current thread 0x00007f24f9b14080 (most recent call first):
> File "<frozen importlib._bootstrap>", line 488 in _call_with_frames_removed
[…]
> File "<frozen importlib._bootstrap>", line 1360 in _find_and_load
> File "/usr/lib/python3/dist-packages/vtk.py", line 4 in <module>
> File "<frozen importlib._bootstrap>", line 488 in _call_with_frames_removed
[…]
> Segmentation fault
However, my build attempt of python-mne reported a new bunch of
test failures, some of which look related to the migration to
numpy 2.0, example:
______________________________ test_search_light _______________________________
joblib.externals.loky.process_executor._RemoteTraceback:
"""
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/joblib/externals/loky/backend/queues.py", line 159, in _feed
obj_ = dumps(obj, reducers=reducers)
File "/usr/lib/python3/dist-packages/joblib/externals/loky/backend/reduction.py", line 215, in dumps
dump(obj, buf, reducers=reducers, protocol=protocol)
~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/joblib/externals/loky/backend/reduction.py", line 208, in dump
_LokyPickler(file, reducers=reducers, protocol=protocol).dump(obj)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
File "/usr/lib/python3/dist-packages/joblib/externals/cloudpickle/cloudpickle_fast.py", line 632, in dump
return Pickler.dump(self, obj)
~~~~~~~~~~~~^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/joblib/_memmapping_reducer.py", line 385, in __call__
return _reduce_memmap_backed(a, m)
File "/usr/lib/python3/dist-packages/joblib/_memmapping_reducer.py", line 269, in _reduce_memmap_backed
a_start, a_end = np.byte_bounds(a)
^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 400, in __getattr__
raise AttributeError(
...<3 lines>...
)
AttributeError: `np.byte_bounds` was removed in the NumPy 2.0 release. Now it's available under `np.lib.array_utils.byte_bounds`
"""
The above exception was the direct cause of the following exception:
mne/decoding/tests/test_search_light.py:150: in test_search_light
score_njobs = sl.fit(X, y).score(X, y)
mne/decoding/search_light.py:103: in fit
estimators = parallel(
/usr/lib/python3/dist-packages/joblib/parallel.py:1952: in __call__
return output if self.return_generator else list(output)
/usr/lib/python3/dist-packages/joblib/parallel.py:1595: in _get_outputs
yield from self._retrieve()
/usr/lib/python3/dist-packages/joblib/parallel.py:1699: in _retrieve
self._raise_error_fast()
/usr/lib/python3/dist-packages/joblib/parallel.py:1734: in _raise_error_fast
error_job.get_result(self.timeout)
/usr/lib/python3/dist-packages/joblib/parallel.py:736: in get_result
return self._return_or_raise()
/usr/lib/python3/dist-packages/joblib/parallel.py:754: in _return_or_raise
raise self._result
E _pickle.PicklingError: Could not pickle the task to send it to the workers.
Some others look to stem from another issue having to do with
doctest perhaps:
______________________ [doctest] mne.utils.docs.copy_doc _______________________
5093 >>> class A:
5094 ... def m1():
5095 ... '''Docstring for m1'''
5096 ... pass
5097 >>> class B (A):
5098 ... @copy_doc(A.m1)
5099 ... def m1():
5100 ... ''' this gets appended'''
5101 ... pass
5102 >>> print(B.m1.__doc__)
Expected:
Docstring for m1 this gets appended
Got:
Docstring for m1this gets appended
/build/reproducible-path/python-mne-1.8.0/mne/utils/docs.py:5102: DocTestFailure
___________ [doctest] mne.utils.docs.copy_function_doc_to_method_doc ___________
5162 >>> class A:
5163 ... @copy_function_doc_to_method_doc(plot_function)
5164 ... def plot(self, a, b):
5165 ... '''
5166 ... Notes
5167 ... -----
5168 ... .. versionadded:: 0.13.0
5169 ... '''
5170 ... plot_function(self, a, b)
5171 >>> print(A.plot.__doc__)
Differences (unified diff with -expected +actual):
@@ -1,13 +1,13 @@
Docstring for plotting function.
<BLANKLINE>
- Parameters
- ----------
- a : int
- Some parameter
- b : int
- Some parameter
+Parameters
+----------
+a : int
+ Some parameter
+b : int
+ Some parameter
<BLANKLINE>
- Notes
- -----
- .. versionadded:: 0.13.0
+Notes
+-----
+.. versionadded:: 0.13.0
<BLANKLINE>
/build/reproducible-path/python-mne-1.8.0/mne/utils/docs.py:5171: DocTestFailure
_____________________ test_copy_function_doc_to_method_doc _____________________
mne/utils/tests/test_docs.py:196: in test_copy_function_doc_to_method_doc
assert (
E AssertionError: assert 'Docstring fo...Parameter b\n' == 'Docstring fo...r b\n '
E
E Docstring for f1.
E
E + Parameters
E + ----------
E + a : int
E - Parameters...
E
E ...Full output truncated (12 lines hidden), use '-vv' to show
- generated xml file: /build/reproducible-path/python-mne-1.8.0/junit-results.xml -
Have a nice day, :)
--
.''`. Étienne Mollier <emollier at debian.org>
: :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
`. `' sent from /dev/pts/2, please excuse my verbosity
`- on air: Kaprekar's Constant - Ghost Planes
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