[Debian-med-packaging] Bug#1109953: nibabel: tests failing with scipy 1.16

[Drew Parsons]

Source: nibabel
Version: 5.3.2-2
Severity: normal

scipy 1.16 has been uploaded to experimental.
nibabel tests are failing with it, possibly due to a change in API.

176s =========================== short test summary info ============================
176s FAILED nibabel/tests/test_processing.py::test_resample_from_to - Failed: DID ...
176s FAILED nibabel/tests/test_processing.py::test_resample_to_output - Failed: DI...
176s = 2 failed, 5362 passed, 108 skipped, 11 xfailed, 1 xpassed, 26950 warnings in 137.68s (0:02:17) =

nibabel is expecting a UserWarning which is not emitted, so test_resample* fails:

176s ___________________________ test_resample_to_output ____________________________
176s 
176s caplog = <_pytest.logging.LogCaptureFixture object at 0x7fb89afd3110>
176s 
176s     @needs_scipy
176s     def test_resample_to_output(caplog):
176s         # Test routine to sample images to output space
176s         # Image aligned to output axes - no-op
176s         data = np.arange(24, dtype='int32').reshape((2, 3, 4))
176s         img = Nifti1Image(data, np.eye(4))
176s         # Check default resampling
176s         img2 = resample_to_output(img)
176s         assert_array_equal(img2.shape, (2, 3, 4))
176s         assert_array_equal(img2.affine, np.eye(4))
176s         assert_array_equal(img2.dataobj, data)
176s         # Check resampling with different voxel size specifications
176s         for vox_sizes in (None, 1, [1, 1, 1]):
176s             img2 = resample_to_output(img, vox_sizes)
176s             assert_array_equal(img2.shape, (2, 3, 4))
176s             assert_array_equal(img2.affine, np.eye(4))
176s             assert_array_equal(img2.dataobj, data)
176s         img2 = resample_to_output(img, vox_sizes)
176s         # Check 2D works
176s         img_2d = Nifti1Image(data[0], np.eye(4))
176s         for vox_sizes in (None, 1, (1, 1), (1, 1, 1)):
176s             img3 = resample_to_output(img_2d, vox_sizes)
176s             assert_array_equal(img3.shape, (3, 4, 1))
176s             assert_array_equal(img3.affine, np.eye(4))
176s             assert_array_equal(img3.dataobj, data[0][..., None])
176s         # Even 1D
176s         img_1d = Nifti1Image(data[0, 0], np.eye(4))
176s         img3 = resample_to_output(img_1d)
176s         assert_array_equal(img3.shape, (4, 1, 1))
176s         assert_array_equal(img3.affine, np.eye(4))
176s         assert_array_equal(img3.dataobj, data[0, 0][..., None, None])
176s         # But 4D does not
176s         img_4d = Nifti1Image(data.reshape(2, 3, 2, 2), np.eye(4))
176s         with pytest.raises(ValueError):
176s             resample_to_output(img_4d)
176s         # Run vox2vox_out tests, checking output shape, coordinate transform
176s         for in_shape, in_aff, vox, out_shape, out_aff in get_outspace_params():
176s             # Allow for expansion of image shape from < 3D
176s             in_n_dim = len(in_shape)
176s             if in_n_dim < 3:
176s                 in_shape = in_shape + (1,) * (3 - in_n_dim)
176s                 if not vox is None:
176s                     vox = vox + (1,) * (3 - in_n_dim)
176s                 assert len(out_shape) == in_n_dim
176s                 out_shape = out_shape + (1,) * (3 - in_n_dim)
176s             img = Nifti1Image(np.ones(in_shape), in_aff)
176s             out_img = resample_to_output(img, vox)
176s             assert_all_in(in_shape, in_aff, out_img.shape, out_img.affine)
176s             assert out_img.shape == out_shape
176s             assert_almost_equal(out_img.affine, out_aff)
176s         # Check data is as expected with some transforms
176s         # Flip first axis
176s         out_img = resample_to_output(Nifti1Image(data, np.diag([-1, 1, 1, 1])))
176s         assert_array_equal(out_img.dataobj, np.flipud(data))
176s         # Subsample voxels
176s         out_img = resample_to_output(Nifti1Image(data, np.diag([4, 5, 6, 1])))
176s >       with pytest.warns(UserWarning):  # Suppress scipy warning
176s E       Failed: DID NOT WARN. No warnings of type (<class 'UserWarning'>,) were emitted.
176s E        Emitted warnings: [].
176s 
176s nibabel/tests/test_processing.py:278: Failed


This bug will become RC serious later, after scipy 1.16 is uploaded to
unstable.


-- System Information:
Debian Release: 13.0
  APT prefers unstable-debug
  APT policy: (500, 'unstable-debug'), (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 6.12.38+deb13-amd64 (SMP w/8 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_WARN, TAINT_OOT_MODULE
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8), LANGUAGE=en_AU:en
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Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled