AttributeError: 'PosixPath' object has no attribute 'lower'

[yarikoptic]

Building backport for debian stable (buster) with python 3.7 leads to test_copy_header to error with

____________________________ test_copy_header[True] ____________________________

tmp_path = PosixPath('/tmp/pytest-of-pbuilder/pytest-0/test_copy_header_True_0')
keep_dtype = True

    @pytest.mark.parametrize("keep_dtype", (True, False))
    def test_copy_header(tmp_path, keep_dtype):
        """Cover copy_header."""
        fname1 = tmp_path / "reference.nii.gz"
        fname2 = tmp_path / "target.nii.gz"
    
        nii = nb.Nifti1Image(np.zeros((10, 10, 10), dtype="uint8"), None, None)
        nii.set_qform(np.diag((1.0, 2.0, 3.0, 1.0)), code=2)
        nii.set_sform(np.diag((1.0, 2.0, 3.0, 1.0)), code=1)
        nii.to_filename(str(fname1))
    
        nii.set_data_dtype("float32")
        nii.set_qform(np.eye(4), code=1)
        nii.to_filename(str(fname2))
    
>       copied = nb.load(copy_header(fname1, fname2, keep_dtype=keep_dtype))

/build/nipype-1.6.0/nipype/utils/tests/test_imagemanip.py:24: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/build/nipype-1.6.0/nipype/utils/imagemanip.py:7: in copy_header
    hdr_img = nb.load(header_file)
/usr/lib/python3/dist-packages/nibabel/loadsave.py:47: in load
    is_valid, sniff = image_klass.path_maybe_image(filename, sniff)
/usr/lib/python3/dist-packages/nibabel/filebasedimages.py:500: in path_maybe_image
    klass._compressed_suffixes)
/usr/lib/python3/dist-packages/nibabel/filename_parser.py:265: in splitext_addext
    if endswith(filename, ext):
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

whole = PosixPath('/tmp/pytest-of-pbuilder/pytest-0/test_copy_header_True_0/reference.nii.gz')
end = '.gz'

    def _iendswith(whole, end):
>       return whole.lower().endswith(end.lower())
E       AttributeError: 'PosixPath' object has no attribute 'lower'

/usr/lib/python3/dist-packages/nibabel/filename_parser.py:223: AttributeError

[yarikoptic]

d'oh -- just now realized that it is coming from nibabel, surprised that this code path was not triggered by any of its unittests. Transferring to nibabel

[effigies]

What version of nibabel? nibabel.load should handle pathlib.Paths as of 3.0.

[effigies]

Looks like the problem is that test in nipype assumes nibabel 3+, but nipype's minimum nibabel is 2.1.

@satra @oesteban Which seems more worthwhile, updating the minimum nibabel, or guarding accidental uses of Paths?

[yarikoptic]

oh right -- I have missed that I did not have 3.x yet there, my bad, thank you @effigies !

[effigies]

Going to move this to nipype, since it is a dependency issue there. There is nothing to do in nibabel, since there is no plan to backport Path support to 2.5.x.

[oesteban]

Which seems more worthwhile, updating the minimum nibabel

I think to update nibabel's minimum version is the right call here.

[effigies]

3.0 is only a year old. But I suppose if somebody can upgrade to nipype 1.6+, they can upgrade to nibabel 3.0+.