admin/ship-mypy-type-annotations-drop-py37-add-py310-manage-test-dependencies-separate-for-each-tox-env

[evamaxfield]

Description

Ships type annotations with the library when installed. Now people can define functions based on our types and mypy will correctly resolve them.

This also massively overhauls the testing portions of our library. Extra readers and writers have been moved to their own subdirs in our tests dirs. And each extra reader and writer is tested independently from one another. This is to make it possible to avoid dependency overlap.

Specifically, this relates to how bfio doesn't support and doesn't plan on supporting tifffiles latest releases: PolusAI/bfio#35

However, this somewhat more naturally sets us up better for when we move to a plugin model.

The diff is quite large because of all of these changes but if you look at the codecov, our coverage only minimally changes 🎉

The testing code is now a bit odd imo but something to "not worry about because we actively are trying to make the build 🟢 so we can spend some time prototyping v5"

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 #325
Resolves #373

• 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 #397 (9e6e839) into main (2a62b4e) will increase coverage by 0.87%.
The diff coverage is 98.33%.

@@            Coverage Diff             @@
##             main     #397      +/-   ##
==========================================
+ Coverage   93.65%   94.52%   +0.87%     
==========================================
  Files          49       45       -4     
  Lines        3702     3728      +26     
==========================================
+ Hits         3467     3524      +57     
+ Misses        235      204      -31     

Impacted Files	Coverage Δ
aicsimageio/readers/czi_reader.py	96.19% <ø> (+0.97%)	⬆️
aicsimageio/tests/readers/test_ome_tiff_reader.py	96.33% <94.80%> (-3.67%)	⬇️
...eio/tests/readers/extra_readers/test_lif_reader.py	99.13% <98.27%> (ø)
aicsimageio/tests/readers/test_tiff_reader.py	99.03% <98.80%> (-0.97%)	⬇️
aicsimageio/readers/bioformats_reader.py	85.40% <100.00%> (-0.07%)	⬇️
aicsimageio/readers/dv_reader.py	92.85% <100.00%> (+4.76%)	⬆️
aicsimageio/readers/tiff_glob_reader.py	85.35% <100.00%> (+0.64%)	⬆️
...ts/readers/extra_readers/test_bioformats_reader.py	100.00% <100.00%> (ø)
...eio/tests/readers/extra_readers/test_czi_reader.py	98.14% <100.00%> (ø)
...tests/readers/extra_readers/test_default_reader.py	100.00% <100.00%> (ø)
... and 20 more

---

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[AetherUnbound]

Looks good! Just one note on what looks like some debug code.

[toloudis]

Sorry if I missed this, or forgot, but why can we drop 3.7? its end of life date is still more than 1 year away

[evamaxfield]

Sorry if I missed this, or forgot, but why can we drop 3.7? its end of life date is still more than 1 year away

numpy, dask, pandas, scipy, tifffile, have all dropped py37. I am following their cycle.

[toloudis]

Sorry if I missed this, or forgot, but why can we drop 3.7? its end of life date is still more than 1 year away

numpy, dask, pandas, scipy, tifffile, have all dropped py37. I am following their cycle.

Wonder if this PR is the place to add 3.10

[evamaxfield]

Sorry if I missed this, or forgot, but why can we drop 3.7? its end of life date is still more than 1 year away

numpy, dask, pandas, scipy, tifffile, have all dropped py37. I am following their cycle.

Wonder if this PR is the place to add 3.10

Yep I am going to do it here and close the other PR

[evamaxfield]

@toloudis @AetherUnbound if possible wanna give this a look over? It's ready!! and Jpype 1.4.0 was released so we can officially ship 3.10 too!

[toloudis]

😈

[toloudis]

Not looking forward to mergeing with other outstanding PRs but i like the changes.