bugfix/pass-series-index-in-biofile-init

[evamaxfield]

Description

Somehow slipped through multiple layers of testing and review. The set_scene function in the BioformatsReader was named set_series (which makes sense from the Bioformats API but not consistent with AICSImageIO standard.

Above was incorrect. This PR now actually fixes this. The only problem was that the current scene index of the Reader wasn't being passed down to the BioFile object init during reads.

It also adds a parameter to our multi scene checking function that will check if the data between the two comparison scenes is different or not. By default, this check does not run so as to not make us have to go back and update all of our old tests but potentially useful in the future.

Note: These changes should not be merged until #397 is merged

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 [gh-], adds tiff file format support

Resolves #400

• Provide relevant tests for your feature or bug fix.
• Provide or update documentation for any feature added by your pull request.

Thanks for contributing!

[codecov-commenter]

Codecov Report

Merging #401 (cf482e1) into main (ae4fde0) will decrease coverage by 0.08%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main     #401      +/-   ##
==========================================
- Coverage   94.66%   94.57%   -0.09%     
==========================================
  Files          45       45              
  Lines        3728     3741      +13     
==========================================
+ Hits         3529     3538       +9     
- Misses        199      203       +4     

Impacted Files	Coverage Δ
...ts/readers/extra_readers/test_bioformats_reader.py	100.00% <ø> (ø)
aicsimageio/readers/bioformats_reader.py	85.59% <100.00%> (+0.18%)	⬆️
aicsimageio/tests/image_container_test_utils.py	100.00% <100.00%> (ø)
aicsimageio/tests/conftest.py	92.30% <0.00%> (-3.85%)	⬇️
...eio/tests/readers/extra_readers/test_czi_reader.py	98.14% <0.00%> (-1.86%)	⬇️
aicsimageio/readers/ome_tiff_reader.py	98.16% <0.00%> (-0.92%)	⬇️
aicsimageio/readers/czi_reader.py	96.19% <0.00%> (-0.35%)	⬇️
aicsimageio/aics_image.py	88.17% <0.00%> (+0.49%)	⬆️

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[AetherUnbound]

Ah drat! Nice deprecation warning, this looks good 👍🏼

[evamaxfield]

@tlambert03 @AetherUnbound @toloudis this PR is ready for review! The two bugs were, the BioFile init not being provided the series index and there was a resource-backend-dask-array bug where the open was starting a new file handle / loci object and not setting the scene on open.

[evamaxfield]

Also, lol, I have no idea what is going on with credentials @tlambert03 this PR works and your PR doesn't... I wonder if GitHub changed GH Actions secrets access permissions...

[AetherUnbound]

Also, lol, I have no idea what is going on with credentials @tlambert03 this PR works and your PR doesn't... I wonder if GitHub changed GH Actions secrets access permissions...

Oh, I should have realized 😅 If @tlambert03 is submitting a PR from a fork, then the GH actions don't have the same permissions unfortunately. See: https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/enabling-features-for-your-repository/managing-github-actions-settings-for-a-repository and https://github.community/t/how-to-use-github-token-for-prs-from-forks/16818

When we encountered this issue, we set up a separate ACCESS_TOKEN in the repositories that would allow the actions to run successfully I believe: WordPress/openverse#199

[AetherUnbound]

Looks good!

[evamaxfield]

Oh, I should have realized sweat_smile If @tlambert03 is submitting a PR from a fork, then the GH actions don't have the same permissions unfortunately. See: https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/enabling-features-for-your-repository/managing-github-actions-settings-for-a-repository and https://github.community/t/how-to-use-github-token-for-prs-from-forks/16818

When we encountered this issue, we set up a separate ACCESS_TOKEN in the repositories that would allow the actions to run successfully I believe: WordPress/openverse#199

We already have very permissive action / action secret usage.

Plus talley has already PRed to this repo numerous times... 🤷‍♀️ 🤷‍♀️

[AetherUnbound]

Oof, okay yea I'm not sure then 😓