DependencyFix/Upgrade ome-types to 0.3.4

[Armavica]

Description

In version 0.3.4, ome-types restricts pydantic to < 2.0.

This upgrade prevents aicsimageio from importing ome-types 0.3.3, which will crash with pydantic 2.0 (released yesterday), making aicsimageio unusable.

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!

[codecov-commenter]

Codecov Report

Patch coverage has no change and project coverage change: -0.05% ⚠️

Comparison is base (2e88f68) 94.03% compared to head (5f6b8ea) 93.98%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #522      +/-   ##
==========================================
- Coverage   94.03%   93.98%   -0.05%     
==========================================
  Files          53       53              
  Lines        4659     4658       -1     
==========================================
- Hits         4381     4378       -3     
- Misses        278      280       +2     

Files Changed	Coverage Δ
aicsimageio/tests/readers/test_ome_tiff_reader.py	95.45% <ø> (ø)
aicsimageio/tests/writers/test_ome_tiff_writer.py	100.00% <ø> (ø)

... and 1 file with indirect coverage changes

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[tlambert03]

fwiw, ome-types v0.4.0 will also be compatible with pydantic2. (not that this shouldn't still be merged)

[Armavica]

Great! Then I let you decide what makes more sense, considering aicsimageio's release schedule. In the meantime, I had to add the restriction pydantic < 2.0 in my library, in order to avoid the incompatibility with ome-types 0.3.3, and it fixed the issue on my side. So it is not a problem for me to wait for a release of aicsimageio with ome-types 0.4.0 if you think that makes more sense.

[tlambert03]

merge?

[toloudis]

The last commit caused build breakage. It changes dependency versions.

[toloudis]

I may have got the merge wrong. The only change we want here is ome types >= 0.3.4 correct?

[tlambert03]

yeah, that should work

[toloudis]

Will make sure tests pass and then merge asap

[toloudis]

I'm wondering if 0.3.4 raises a different exception than 0.4.0+ for trying to parse "bad ome string".

aicsimageio/aicsimageio/tests/writers/test_ome_tiff_writer.py

Line 164 in 2e88f68

pytest.param(

[tlambert03]

ah, yes that's possible. do you need to be asserting the specific exception type of an external library? (if it changed the behavior of your usage, it would make sense, but here it kinda just seems like you're testing an external library)

[toloudis]

Cleaning this up revealed one more test that has different results in ome-types 0.3.4 vs 0.4.1. This now has to do with our ome-tiff metadata parsing and where we detect whether or not we need to do our own auto-cleanup. I'm tempted to just remove the test cases for this since they fail (expectedly) for 0.3.4 and pass (unexpectedly) for 0.4.1.
@SeanLeRoy @BrianWhitneyAI @evamaxfield What do you think? This is in test_ome_tiff_reader.py test_known_errors_without_cleaning .

[tlambert03]

Yeah I also noticed that in my tests... that aicsimagio was essentially asserting that something would be an error forever 😀

Lots of things were improved that will probably ultimately remove your need for the special cleanup.

I agree just remove the cases.

[toloudis]

I agree just remove the cases.

Gonna do it. 😀

[evamaxfield]

Fully supportive of removing the tests! I think I remember when those tests were added and they were around the same time as our work on fixing some bad metadata cases and such iirc. Thanks for all the work and thoughts on this everyone!