warnings from skimage.io module in test suite

[grlee77]

Description

The following test suite warnings were observed for the main branch while working on #5336

skimage/io/tests/test_collection.py::TestImageCollection::test_concatenate
skimage/io/tests/test_collection.py::TestImageCollection::test_concatenate_mismatched_image_shapes
skimage/io/tests/test_collection.py::TestImageCollection::test_getitem
skimage/io/tests/test_collection.py::TestImageCollection::test_multiimage_imagecollection
skimage/io/tests/test_collection.py::TestImageCollection::test_slicing
  /home/lee8rx/my_git/pyir/scikit-image/skimage/io/collection.py:292: ResourceWarning: unclosed file <_io.BufferedReader name='/home/lee8rx/.cache/scikit-image/main/data/brick.png'>
    raise

skimage/io/tests/test_collection.py::TestImageCollection::test_concatenate
skimage/io/tests/test_collection.py::TestImageCollection::test_multiimage_imagecollection
  /home/lee8rx/my_git/pyir/scikit-image/skimage/io/collection.py:292: ResourceWarning: unclosed file <_io.BufferedReader name='/home/lee8rx/.cache/scikit-image/main/data/moon.png'>
    raise

skimage/io/tests/test_collection.py::TestImageCollection::test_concatenate_mismatched_image_shapes
skimage/io/tests/test_collection.py::TestImageCollection::test_getitem
skimage/io/tests/test_collection.py::TestImageCollection::test_slicing
  /home/lee8rx/my_git/pyir/scikit-image/skimage/io/collection.py:292: ResourceWarning: unclosed file <_io.BufferedReader name='/home/lee8rx/.cache/scikit-image/main/data/color.png'>
    raise

skimage/io/tests/test_imageio.py::test_imageio_truncated_jpg
  /home/lee8rx/my_git/pyir/scikit-image/skimage/io/tests/test_imageio.py:41: ResourceWarning: unclosed file <_io.BufferedReader name='/home/lee8rx/.cache/scikit-image/main/data/truncated.jpg'>
    imread(fetch('data/truncated.jpg'))

skimage/io/tests/test_tifffile.py::test_tifffile_kwarg_passthrough
  /home/lee8rx/miniconda3/envs/skimage_dev/lib/python3.8/site-packages/tifffile/tifffile.py:2876: DeprecationWarning: TiffFile: the 'fastij' argument is ignored
    warnings.warn(

skimage/io/tests/test_tifffile.py::test_tifffile_kwarg_passthrough
  /home/lee8rx/miniconda3/envs/skimage_dev/lib/python3.8/site-packages/tifffile/tifffile.py:2876: DeprecationWarning: TiffFile: the 'multifile' argument is ignored
    warnings.warn(

skimage/io/tests/test_tifffile.py::test_tifffile_kwarg_passthrough
  /home/lee8rx/miniconda3/envs/skimage_dev/lib/python3.8/site-packages/tifffile/tifffile.py:2876: DeprecationWarning: TiffFile: the 'multifile_close' argument is ignored
    warnings.warn(

[mkcor]

On current main there are no more ResourceWarnings but the DeprecationWarnings related to TiffFile (version 2022.2.9) in skimage.io have grown to:

scikit-image/skimage/io/tests/test_pil.py::test_imread_separate_channels
  /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/tifffile/tifffile.py:984: DeprecationWarning: <tifffile.TiffWriter.write> data with shape (3, 16, 8) and dtype 'float64' are stored as RGB with separate component planes. Future versions will store such data as MINISBLACK in separate pages by default unless the 'photometric' and 'planarconfig' parameters are specified.
    result = tif.write(data, shape, dtype, **kwargs)

scikit-image/skimage/io/tests/test_tifffile.py::test_tifffile_kwarg_passthrough
  /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/tifffile/tifffile.py:908: DeprecationWarning: <tifffile.TiffFile> the 'fastij' argument is ignored
    with TiffFile(files, **kwargs_file) as tif:

scikit-image/skimage/io/tests/test_tifffile.py::test_tifffile_kwarg_passthrough
  /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/tifffile/tifffile.py:908: DeprecationWarning: <tifffile.TiffFile> the 'multifile' argument is ignored
    with TiffFile(files, **kwargs_file) as tif:

scikit-image/skimage/io/tests/test_tifffile.py::test_tifffile_kwarg_passthrough
  /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/tifffile/tifffile.py:908: DeprecationWarning: <tifffile.TiffFile> the 'multifile_close' argument is ignored
    with TiffFile(files, **kwargs_file) as tif:

scikit-image/skimage/io/tests/test_tifffile.py::TestSave::test_imsave_roundtrip[False-float32-shape1]
scikit-image/skimage/io/tests/test_tifffile.py::TestSave::test_imsave_roundtrip[True-float32-shape1]
  /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/tifffile/tifffile.py:984: DeprecationWarning: <tifffile.TiffWriter.write> data with shape (10, 10, 3) and dtype 'float32' are stored as RGB with contiguous samples. Future versions will store such data as MINISBLACK in separate pages by default unless the 'photometric' parameter is specified.
    result = tif.write(data, shape, dtype, **kwargs)

scikit-image/skimage/io/tests/test_tifffile.py::TestSave::test_imsave_roundtrip[False-float32-shape2]
scikit-image/skimage/io/tests/test_tifffile.py::TestSave::test_imsave_roundtrip[True-float32-shape2]
  /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/tifffile/tifffile.py:984: DeprecationWarning: <tifffile.TiffWriter.write> data with shape (10, 10, 4) and dtype 'float32' are stored as RGB with contiguous samples. Future versions will store such data as MINISBLACK in separate pages by default unless the 'photometric' parameter is specified.
    result = tif.write(data, shape, dtype, **kwargs)

scikit-image/skimage/io/tests/test_tifffile.py::TestSave::test_imsave_roundtrip[False-int16-shape1]
scikit-image/skimage/io/tests/test_tifffile.py::TestSave::test_imsave_roundtrip[True-int16-shape1]
  /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/tifffile/tifffile.py:984: DeprecationWarning: <tifffile.TiffWriter.write> data with shape (10, 10, 3) and dtype 'int16' are stored as RGB with contiguous samples. Future versions will store such data as MINISBLACK in separate pages by default unless the 'photometric' parameter is specified.
    result = tif.write(data, shape, dtype, **kwargs)

scikit-image/skimage/io/tests/test_tifffile.py::TestSave::test_imsave_roundtrip[False-int16-shape2]
scikit-image/skimage/io/tests/test_tifffile.py::TestSave::test_imsave_roundtrip[True-int16-shape2]
  /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/tifffile/tifffile.py:984: DeprecationWarning: <tifffile.TiffWriter.write> data with shape (10, 10, 4) and dtype 'int16' are stored as RGB with contiguous samples. Future versions will store such data as MINISBLACK in separate pages by default unless the 'photometric' parameter is specified.
    result = tif.write(data, shape, dtype, **kwargs)

scikit-image/skimage/io/tests/test_tifffile.py::TestSave::test_imsave_roundtrip[False-float64-shape1]
scikit-image/skimage/io/tests/test_tifffile.py::TestSave::test_imsave_roundtrip[True-float64-shape1]
  /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/tifffile/tifffile.py:984: DeprecationWarning: <tifffile.TiffWriter.write> data with shape (10, 10, 3) and dtype 'float64' are stored as RGB with contiguous samples. Future versions will store such data as MINISBLACK in separate pages by default unless the 'photometric' parameter is specified.
    result = tif.write(data, shape, dtype, **kwargs)

scikit-image/skimage/io/tests/test_tifffile.py::TestSave::test_imsave_roundtrip[False-float64-shape2]
scikit-image/skimage/io/tests/test_tifffile.py::TestSave::test_imsave_roundtrip[True-float64-shape2]
  /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/tifffile/tifffile.py:984: DeprecationWarning: <tifffile.TiffWriter.write> data with shape (10, 10, 4) and dtype 'float64' are stored as RGB with contiguous samples. Future versions will store such data as MINISBLACK in separate pages by default unless the 'photometric' parameter is specified.
    result = tif.write(data, shape, dtype, **kwargs)

[grlee77]

Thanks @mkcor, to summarize these, it looks like most are of this type.

DeprecationWarning: <tifffile.TiffWriter.write> 
data with shape (3, 16, 8) and dtype 'float64' are stored as RGB with separate component planes.
Future versions will store such data as MINISBLACK in separate pages by default unless the
'photometric' and 'planarconfig' parameters are specified.

We need to decide if we should be adding one of these new kwargs for backwards compatibility or if our policy is just to dispatch to whatever the tifffile defaults are when writing unless the user supplies kwargs. Do other @skimage/core devs more familiar with skimage.io have an opinion here?

The others just look like we are testing with some deprecated kwargs, so we should be able to address that pretty easily in the test suite.:
DeprecationWarning: <tifffile.TiffFile> the 'fastij' argument is ignored
DeprecationWarning: <tifffile.TiffFile> the 'multifile' argument is ignored
DeprecationWarning: <tifffile.TiffFile> the 'multifile_close' argument is ignored