Bug#1071782: skimage: autopkgtest needs update for new version of pytest on s390x

[Paul Gevers]

Source: skimage
Version: 0.22.0-3
Severity: serious
X-Debbugs-CC: pytest at packages.debian.org
Tags: sid trixie
User: debian-ci at lists.debian.org
Usertags: needs-update
Control: affects -1 src:pytest

Dear maintainer(s),

With a recent upload of pytest the autopkgtest of skimage fails in 
testing on s390x when that autopkgtest is run with the binary packages 
of pytest from unstable. It passes when run with only packages from 
testing. In tabular form:

                        pass            fail
pytest                 from testing    8.1.2-1
skimage                from testing    0.22.0-3
all others             from testing    from testing

I copied some of the output at the bottom of this report. I'll note that 
s390x is our only big endian architecture with autopgktest.

Currently this regression is blocking the migration of pytest to testing 
[1]. Of course, pytest shouldn't just break your autopkgtest (or even 
worse, your package), but due to the nature of the package pytest I 
suspect that your package just needs to update to the new situation.

If this is a real problem in your package (and not only in your 
autopkgtest), the right binary package(s) from pytest should really add 
a versioned Breaks on the unfixed version of (one of your) package(s). 
Note: the Breaks is nice even if the issue is only in the autopkgtest as 
it helps the migration software to figure out the right versions to 
combine in the tests.

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

Paul

[1] https://qa.debian.org/excuses.php?package=pytest

https://ci.debian.net/data/autopkgtest/testing/s390x/s/skimage/46978110/log.gz

=================================== FAILURES 
===================================
300s ______________________________ test_imread_handle 
______________________________
300s 300s     def test_imread_handle():
300s         expected = np.load(fetch('data/chessboard_GRAY_U8.npy'))
300s         with open(fetch('data/chessboard_GRAY_U16.tif'), 'rb') as fh:
300s             img = imread(fh)
300s >       assert img.dtype == np.uint16
300s E       AssertionError: assert dtype('<u2') == <class 'numpy.uint16'>
300s E        +  where dtype('<u2') = array([[255, 255, 255, ...,   0, 
0,   0],\n       [255, 255, 255, ...,   0,   0,   0],\n       [255, 255, 
255, ...,   0,   0,   0],\n       ...,\n       [  0,   0,   0, ..., 255, 
255, 255],\n       [  0,   0,   0, ..., 255, 255, 255],\n       [  0, 
0,   0, ..., 255, 255, 255]], dtype='<u2').dtype
300s E        +  and   <class 'numpy.uint16'> = np.uint16
300s 300s 
/usr/lib/python3/dist-packages/skimage/io/tests/test_tifffile.py:48: 
AssertionError
300s =============================== warnings summary 
===============================
300s filters/tests/test_unsharp_mask.py: 480 warnings
300s 
/usr/lib/python3/dist-packages/skimage/filters/tests/test_unsharp_mask.py:26: 
RuntimeWarning: invalid value encountered in cast
300s     array = ((array + offset) * 128).astype(dtype)
300s 300s io/tests/test_pil.py::test_png_round_trip
300s io/tests/test_pil.py::test_imsave_filelike
300s 
/usr/lib/python3/dist-packages/skimage/io/_plugins/pil_plugin.py:105: 
DeprecationWarning: The binary mode of fromstring is deprecated, as it 
behaves surprisingly on unicode inputs. Use frombuffer instead
300s     frame = np.fromstring(frame.tobytes(), dtype)
300s 300s measure/tests/test_fit.py::test_ellipse_parameter_stability
300s   /usr/lib/python3/dist-packages/skimage/measure/fit.py:526: 
RuntimeWarning: divide by zero encountered in scalar divide
300s     phi = 0.5 * np.arctan((2. * b) / (a - c))
300s 300s 
transform/tests/test_pyramids.py::test_pyramid_dtype_support[pyramid_gaussian-uint8]
300s 
transform/tests/test_pyramids.py::test_pyramid_dtype_support[pyramid_laplacian-uint8]
300s 
/usr/lib/python3/dist-packages/skimage/transform/tests/test_pyramids.py:208: 
RuntimeWarning: invalid value encountered in cast
300s     img = np.random.randn(32, 8).astype(dtype)
300s 300s 
../../../../usr/lib/python3/dist-packages/_pytest/cacheprovider.py:446
300s   /usr/lib/python3/dist-packages/_pytest/cacheprovider.py:446: 
PytestCacheWarning: could not create cache path 
/usr/lib/python3/dist-packages/skimage/.pytest_cache/v/cache/nodeids: 
[Errno 13] Permission denied: 
'/usr/lib/python3/dist-packages/skimage/.pytest_cache'
300s     config.cache.set("cache/nodeids", sorted(self.cached_nodeids))
300s 300s 
../../../../usr/lib/python3/dist-packages/_pytest/cacheprovider.py:398
300s   /usr/lib/python3/dist-packages/_pytest/cacheprovider.py:398: 
PytestCacheWarning: could not create cache path 
/usr/lib/python3/dist-packages/skimage/.pytest_cache/v/cache/lastfailed: 
[Errno 13] Permission denied: 
'/usr/lib/python3/dist-packages/skimage/.pytest_cache'
300s     config.cache.set("cache/lastfailed", self.lastfailed)
300s 300s ../../../../usr/lib/python3/dist-packages/_pytest/stepwise.py:57
300s   /usr/lib/python3/dist-packages/_pytest/stepwise.py:57: 
PytestCacheWarning: could not create cache path 
/usr/lib/python3/dist-packages/skimage/.pytest_cache/v/cache/stepwise: 
[Errno 13] Permission denied: 
'/usr/lib/python3/dist-packages/skimage/.pytest_cache'
300s     session.config.cache.set(STEPWISE_CACHE_DIR, [])
300s 300s -- Docs: 
https://docs.pytest.org/en/stable/how-to/capture-warnings.html
300s =========================== short test summary info 
============================
300s FAILED 
../../../../usr/lib/python3/dist-packages/skimage/io/tests/test_tifffile.py::test_imread_handle
300s = 1 failed, 7880 passed, 120 skipped, 91 xfailed, 27 xpassed, 488 
warnings in 195.50s (0:03:15) =
300s autopkgtest [16:16:32]: test python3

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