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),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:
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.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?
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_______________________ test_tifffile_kwarg_passthrough ________________________
def test_tifffile_kwarg_passthrough ():
img = imread(fetch('data/multipage.tif'), key=[1],
multifile=False, multifile_close=True, fastij=True, is_ome=True)/usr/lib/python3/dist-packages/skimage/io/tests/test_tifffile.py:41: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ /usr/lib/python3/dist-packages/skimage/io/_io.py:48: in imread
img = call_plugin('imread', fname, plugin=plugin, **plugin_args)/usr/lib/python3/dist-packages/skimage/io/manage_plugins.py:207: in call_plugin
return func(*args, **kwargs)/usr/lib/python3/dist-packages/skimage/io/_plugins/tifffile_plugin.py:30: in imread
return tifffile_imread(fname, **kwargs)_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
files = '/usr/lib/python3/dist-packages/skimage/data/../data/multipage.tif' aszarr = Falsekwargs = {'fastij': True, 'key': [1], 'multifile': False, 'multifile_close': True}
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:"""Return image data from TIFF file(s) as numpy array or zarr storage. Refer to the TiffFile and TiffSequence classes and their asarray
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.Parameters 'name', 'offset', 'size', and 'is_' flags are passed to
TiffFile or TiffSequence.imread.Parameters 'imread', 'container', 'sort', 'pattern', 'axesorder',
and 'categories' are passed to TiffSequence. Other parameters are passed to the asarray or aszarr functions.The first image series in the file is returned if no arguments are
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)
E TypeError: asarray() got an unexpected keyword argument 'multifile'return tif.asarray(**kwargs)
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