fix/only-close-biofiofile-on-exit-if-not-open-on-entry

[tlambert03]

Description

fixes the issue mentioned by @NHPatterson described in #339 (comment), wherein dask.compute() closes a BioFile after reading. (It should only close if the file was not already open when __enter__ was called)

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!

[codecov-commenter]

Codecov Report

Merging #341 (103fc96) into main (2595aca) will decrease coverage by 0.27%.
The diff coverage is 82.85%.

@@            Coverage Diff             @@
##             main     #341      +/-   ##
==========================================
- Coverage   93.96%   93.68%   -0.28%     
==========================================
  Files          47       47              
  Lines        3548     3565      +17     
==========================================
+ Hits         3334     3340       +6     
- Misses        214      225      +11     

Impacted Files	Coverage Δ
aicsimageio/utils/dask_proxy.py	86.04% <68.42%> (-13.96%)	⬇️
aicsimageio/readers/bioformats_reader.py	85.47% <100.00%> (-0.07%)	⬇️
...icsimageio/tests/readers/test_bioformats_reader.py	100.00% <100.00%> (ø)
aicsimageio/tests/utils/test_dask_proxy.py	100.00% <100.00%> (ø)
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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[tlambert03]

argh... now I'm running into leaked file handles in tests again 😂 ok, need a bit more time with this one

[evamaxfield]

argh... now I'm running into leaked file handles in tests again joy ok, need a bit more time with this one

I am going to retrigger CI because tiff reader is failing even though there are no changes to it...

[evamaxfield]

Oh yea. Okay there is a bug somewhere. I am assuming the tiff reader failures are happening because of leftover file opens from some other tests. 🤷

[toloudis]

windows ftw

[evamaxfield]

Happy to merge this, looks like Sphinx released an update today that broke our docs: https://pypi.org/project/Sphinx/ so ignore that build.

[tlambert03]

thanks! lemme clean up one comment first