admin/include-fsspec-dep-for-czi-in-readme

[evamaxfield]

Description

Sorta solves #431?? We can't really fully solve it because forcing everyone to upgrade their fsspec envs may result in dependency management for them. The only reader that broke with the recent fsspec change was CZI. So updating the CZI install docs to include the fsspec upgrade.

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

Thanks for contributing!

cc @psobolewskiPhD

[codecov-commenter]

Codecov Report

Merging #433 (97fc79f) into main (fc1e710) will decrease coverage by 0.11%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##             main     #433      +/-   ##
==========================================
- Coverage   94.03%   93.92%   -0.12%     
==========================================
  Files          46       46              
  Lines        3972     3997      +25     
==========================================
+ Hits         3735     3754      +19     
- Misses        237      243       +6     

Impacted Files	Coverage Δ
aicsimageio/readers/czi_reader.py	94.33% <ø> (-0.89%)	⬇️
aicsimageio/readers/lif_reader.py	98.34% <ø> (ø)
aicsimageio/readers/array_like_reader.py	97.45% <0.00%> (-2.55%)	⬇️
aicsimageio/tests/test_transforms.py	99.00% <0.00%> (+0.03%)	⬆️
aicsimageio/transforms.py	99.01% <0.00%> (+0.08%)	⬆️

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[AetherUnbound]

That works!

[psobolewskiPhD]

Better than nothing for sure, but a fresh install will get fsspec 2022.7.1 anyways, by default.
Edit: err, not necessarily I guess if some other packages has a different pin.

So it's just situations where someone upgrades aicsimageio that will trigger the issue. Still having it spelled out in the README makes tracking it down easier.

BTW Is it worth carving an if installer=czi and mentioning fsspec here:

aicsimageio/aicsimageio/aics_image.py

Lines 214 to 234 in 93559b1

	for format_ext, readers in FORMAT_IMPLEMENTATIONS.items():
	if path.lower().endswith(f".{format_ext}"):
	if readers[0] in READER_TO_INSTALL:
	installer = READER_TO_INSTALL[readers[0]]
	raise exceptions.UnsupportedFileFormatError(
	"AICSImage",
	path,
	msg_extra=(
	f"File extension suggests format: '{format_ext}'. "
	f"Install extra format dependency with: "
	f"`pip install {installer}`. "
	f"See all known format extensions and their "
	f"extra install name with "
	f"`aicsimageio.formats.FORMAT_IMPLEMENTATIONS`. "
	f"If the extra dependency is already installed this "
	f"error may have raised because the file is "
	f"corrupt or similar issue. For potentially more "
	f"information and to help debug, try loading the file "
	f"directly with the desired file format reader "
	f"instead of with the AICSImage object."
	),

[evamaxfield]

BTW Is it worth carving an if installer=czi and mentioning fsspec here:

Great recommendation. Will do that tonight!

[toloudis]

this line is giving me pause. You can install [czi] and not get czi support? I'm not sure if this is helping.