--- Begin Message ---
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 = False
kwargs = {'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)
return tif.asarray(**kwargs)
E TypeError: asarray() got an unexpected keyword
argument 'multifile'
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
