Bug#1010430: tifffile breaks skimage autopkgtest: asarray() got an unexpected keyword argument 'multifile'

[Paul Gevers]

Source: tifffile, skimage
Control: found -1 tifffile/20220426-1
Control: found -1 skimage/0.18.3-2
Severity: serious
Tags: sid bookworm
User: debian...@lists.debian.org
Usertags: breaks needs-update

Dear maintainer(s),



                       pass            fail
tifffile               from testing    20220426-1
skimage                from testing    0.18.3-2
all others             from testing    from testing

I copied some of the output at the bottom of this report.



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=tifffile

https://ci.debian.net/data/autopkgtest/testing/amd64/s/skimage/21268058/log.gz



    def test_tifffile_kwarg_passthrough ():

With a recent upload of tifffile the autopkgtest of skimage fails in testing when that autopkgtest is run with the binary packages of tifffile from unstable. It passes when run with only packages from testing. In tabular form: Currently this regression is blocking the migration of tifffile to testing [1]. Due to the nature of this issue, I filed this bug report against both packages. Can you please investigate the situation and reassign the bug to the right package? _______________________ test_tifffile_kwarg_passthrough ________________________

      img = imread(fetch('data/multipage.tif'), key=[1],

                     multifile=False, multifile_close=True, fastij=True,
                     is_ome=True)


    img = call_plugin('imread', fname, plugin=plugin, **plugin_args)

    return func(*args, **kwargs)

    return tifffile_imread(fname, **kwargs)

files = '/usr/lib/python3/dist-packages/skimage/data/../data/multipage.tif'
aszarr = False

kwargs_file = {'is_ome': True}, kwargs_seq = {}
tif = <tifffile.TiffFile 'multipage.tif'>

    def imread(
        files: str
        | os.PathLike
        | FileHandle
        | BinaryIO
        | Sequence[str | os.PathLike]
        | None = None,
        *,
        aszarr: bool = False,
        **kwargs,
    ) -> numpy.ndarray | ZarrTiffStore | ZarrFileSequenceStore:

        functions for documentation.
            Parameters
        ----------
        files : path-like, binary stream, or sequence
            File name, seekable binary stream, glob pattern, or sequence of
            file names. May be None (default) if 'container' is specified.
        aszarr : bool
            If True, return file sequences, series, or single pages as
            zarr storage instead of numpy array (experimental).
        **kwargs
            Optional extra arguments.

            TiffFile or TiffSequence.imread.

            and 'categories' are passed to TiffSequence.
            Other parameters are passed to the asarray or aszarr functions.

            provided.
            Returns
        -------
        numpy.ndarray or zarr storage
            Image data from the specified pages.
            Zarr storage instances must be closed after use.
            See TiffPage.asarray for operations that are applied (or not)
            to the raw data stored in the file.
            """
        kwargs_file = parse_kwargs(
            kwargs,
            'name',
            'offset',
            'size',
            # private
            '_multifile',
            '_useframes',
            # is_flags
            *(key for key in kwargs if key[:3] == 'is_'),
        )
        kwargs_seq = parse_kwargs(
            kwargs,
            'imread',
            'container',
            'sort',
            'pattern',
            'axesorder',
            'categories',
        )
            if kwargs_seq.get('container', None) is None:
            if isinstance(files, str) and ('*' in files or '?' in files):
                files = glob.glob(files)
            if not files:
                raise ValueError('no files found')
                if (
                isinstance(files, collections.abc.Sequence)
                and not isinstance(files, str)
                and len(files) == 1
            ):
                files = files[0]
                if isinstance(files, str) or not isinstance(
                files, collections.abc.Sequence
            ):
                with TiffFile(files, **kwargs_file) as tif:
                    if aszarr:
                        return tif.aszarr(**kwargs)

/usr/lib/python3/dist-packages/skimage/io/tests/test_tifffile.py:41: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ /usr/lib/python3/dist-packages/skimage/io/_io.py:48: in imread /usr/lib/python3/dist-packages/skimage/io/manage_plugins.py:207: in call_plugin /usr/lib/python3/dist-packages/skimage/io/_plugins/tifffile_plugin.py:30: in imread _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ kwargs = {'fastij': True, 'key': [1], 'multifile': False, 'multifile_close': True} """Return image data from TIFF file(s) as numpy array or zarr storage. Refer to the TiffFile and TiffSequence classes and their asarray Parameters 'name', 'offset', 'size', and 'is_' flags are passed to Parameters 'imread', 'container', 'sort', 'pattern', 'axesorder', The first image series in the file is returned if no arguments are

                  return tif.asarray(**kwargs)

E TypeError: asarray() got an unexpected keyword argument 'multifile'

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