test_resample fails with scipy 1.16

[drew-parsons]

nibabel is failing tests using scipy 1.16 on debian CI infrastructure, https://ci.debian.net/packages/n/nibabel/ (tests with scipy 1.16 are reported under the unstable links). The bug was reported to Debian at https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1109953

The failing tests are

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) =

It looks like it might be a problem with API changes. The error is

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

Full test log at https://ci.debian.net/data/autopkgtest/unstable/amd64/n/nibabel/63127756/log.gz

These tests were run with scipy 1.16.0, not the more recent 1.16.1.