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

Fixed by the following commit, not in 0.19.2 release:

https://github.com/scikit-image/scikit-image/commit/6c4294c76ab1dcbd230d3c71414761248a83bce0

We believe that the bug you reported is fixed in the latest version of
skimage, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1010430@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Ole Streicher <olebole@debian.org> (supplier of updated skimage package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Wed, 08 Jun 2022 18:33:48 +0200
Source: skimage
Architecture: source
Version: 0.18.3-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers <debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Ole Streicher <olebole@debian.org>
Closes: 1009431 1010430
Changes:
 skimage (0.18.3-3) unstable; urgency=medium
 .
   * Remove use of deprecated kwargs from test_tifffile_kwarg_passthrough
     (Closes: #1010430)
   * handle PIL palettes with <256 colors (Closes: #1009431)
Checksums-Sha1:
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 38084aa1bcf6f38c248ab1d8b44e5fe019279c8b 25316 skimage_0.18.3-3.debian.tar.xz
Checksums-Sha256:
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 130d3ab231dedaa2bc6dce3e862065b2e58953c0239287fc652f8bc3ca9093f1 25316 skimage_0.18.3-3.debian.tar.xz
Files:
 3b2b1df1e8ec2fed472d8c06331875d6 2905 python optional skimage_0.18.3-3.dsc
 7f938c35c03c608bc32cc34f0f2b7ef0 25316 python optional skimage_0.18.3-3.debian.tar.xz
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We believe that the bug you reported is fixed in the latest version of
skimage, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1010430@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Ole Streicher <olebole@debian.org> (supplier of updated skimage package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Sat, 25 Jun 2022 19:45:33 +0200
Source: skimage
Architecture: source
Version: 0.19.3-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers <debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Ole Streicher <olebole@debian.org>
Closes: 1010430
Changes:
 skimage (0.19.3-1) unstable; urgency=medium
 .
   * New upstream version 0.19.3
   * Rediff patches. Drop patches applied upstream.
   * Drop versionized build deps where applicable
   * Push Standards-Version to 4.6.0. No changes needed
   * Add new build dependencies python3-pythran, python3-pooch
   * Skip more files that require pooch and internet
   * Remove use of deprecated kwargs from test_tifffile_kwarg_passthrough
     (Closes: #1010430)
Checksums-Sha1:
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 f80bc957d6f2bafc7c74e3b9e9972686279ef6c1 22978982 skimage_0.19.3.orig.tar.gz
 3cb6d9214c2f8b56b92aa114a804ac3e22bfc734 25296 skimage_0.19.3-1.debian.tar.xz
Checksums-Sha256:
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Files:
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