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docs/update-biofile-docstring-add-bf-options-param#322

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evamaxfield merged 2 commits into
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Sep 27, 2021
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docs/update-biofile-docstring-add-bf-options-param#322
evamaxfield merged 2 commits into
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@tlambert03

@tlambert03 tlambert03 commented Sep 27, 2021

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Description

Just wanted to clarify the expected dimensions on the objects returned by the (lower level) BioFile.to_numpy and to_dask. Also, rather than hardcode the 'nativend2.chunkmap' = False, this just lets the user use any of the options declared here with the new options parameter. Lastly, I added a few parameters (original_meta, memoize, options) to the main BioformatsReader.__init__ to expose some of the underlying options.

Pull request recommendations:

  • Name your pull request your-development-type/short-description. Ex: feature/read-tiff-files
  • Link to any relevant issue in the PR description. Ex: Resolves [Fix release #12], adds tiff file format support
  • Provide relevant tests for your feature or bug fix.
  • Provide or update documentation for any feature added by your pull request.

Thanks for contributing!

@evamaxfield evamaxfield left a comment

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Perfect. Thanks!

Will wait for builds to pass then merge.

@evamaxfield evamaxfield changed the title Update BioFile docstrings, expose options docs/update-biofile-docstring-add-bf-options-param Sep 27, 2021
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codecov-commenter commented Sep 27, 2021

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Codecov Report

Merging #322 (f2874ad) into main (afd24fb) will decrease coverage by 0.29%.
The diff coverage is 72.72%.

Impacted file tree graph

@@            Coverage Diff             @@
##             main     #322      +/-   ##
==========================================
- Coverage   94.59%   94.30%   -0.30%     
==========================================
  Files          40       40              
  Lines        3016     3018       +2     
==========================================
- Hits         2853     2846       -7     
- Misses        163      172       +9     
Impacted Files Coverage Δ
aicsimageio/readers/bioformats_reader.py 82.52% <72.72%> (-1.79%) ⬇️
aicsimageio/tests/conftest.py 92.30% <0.00%> (-3.85%) ⬇️
aicsimageio/tests/readers/test_czi_reader.py 96.29% <0.00%> (-3.71%) ⬇️
aicsimageio/readers/ome_tiff_reader.py 98.13% <0.00%> (-0.94%) ⬇️
aicsimageio/readers/czi_reader.py 95.43% <0.00%> (-0.36%) ⬇️

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@evamaxfield evamaxfield merged commit 5f5b4b7 into AllenCellModeling:main Sep 27, 2021
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3 participants