Tests ome zarr models py

[will-moore]

Fixes #460

Use ome-zarr-models-py to validate data written in tests.

[will-moore]

There are 25 failing tests with that last commit, although they are all passing locally, where I have:

$ pip freeze | grep zarr
-e git+ssh://[email protected]/ome/ome-zarr-py.git@99c9a7ef917187b9368e6496c0266602f055c8de#egg=ome_zarr
ome-zarr-models==0.1.8
pydantic-zarr==0.7.0
zarr==2.18.4

The errors are all like this:

pydantic.errors.PydanticUserError: `HCS` is not fully defined; you should define `ArraySpec`, then call `HCS.model_rebuild()`.

pydantic.errors.PydanticUserError: `Well` is not fully defined; you should define `ArraySpec`, then call `Well.model_rebuild()`.

pydantic.errors.PydanticUserError: `Labels` is not fully defined; you should define `ArraySpec`, then call `Labels.model_rebuild()`.

@dstansby - Any ideas what might be causing these?

[dstansby]

Oh no, I know exactly what's causing that... fixed in ome-zarr-models/ome-zarr-models-py#212, I've just tagged a new release. Let me know if it's not fixed in ome-zarr-models 0.1.9

[will-moore]

Great, thanks. Re-ran the tests and they passed 👍

[jburel]

@will-moore Looks good

[jburel]

@dstansby we would like to push out a release candidate with #413 included.
This will obviously clash with this PR.
Do you have a timeline for support of version 0.5 in ome-zarr-models-py?

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 87.02%. Comparing base (7df023e) to head (e508895).
⚠️ Report is 50 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #461      +/-   ##
==========================================
+ Coverage   87.00%   87.02%   +0.01%     
==========================================
  Files          13       13              
  Lines        1770     1772       +2     
==========================================
+ Hits         1540     1542       +2     
  Misses        230      230              

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[will-moore]

ome-zarr-models/ome-zarr-models-py#211 has been fixed in https://github.com/ome-zarr-models/ome-zarr-models-py/releases/tag/v0.1.10 so last commit removes the workaround. Tests still passing.

[dstansby]

Do you have a timeline for support of version 0.5 in ome-zarr-models-py?

It's in progress, see https://github.com/ome-zarr-models/ome-zarr-models-py/milestone/1. Not sure on a timeline, maybe a couple of weeks? PRs welcome to fix the outstanding issues 😄

[joshmoore]

The clean diff of this looks great! will-moore/ome-zarr-py@ome-zarr-v0.5_writing...will-moore:ome-zarr-py:tests_ome-zarr-models-py

[will-moore]

The 4 tests failing now are due to Models05HCS.from_zarr(self.root_v3) failing validation:

  E       pydantic_core._pydantic_core.ValidationError: 1 validation error for HCS
  E       attributes.ome.plate.version

Reported at ome-zarr-models/ome-zarr-models-py#218 but this is actually due to a bug in the spec, see ome/ngff#322

Possible solutions:

• Ignore/skip the ValidationError in these 4 tests
• Update ome-zarr-py to write the plate.version = "0.5" for v0.5 to match what the spec requires

[will-moore]

Tests green now @jburel

[jburel]

https://github.com/ome-zarr-models/ome-zarr-models-py/tree/v1.0.0 is now out. Description should be updated

[will-moore]

@jburel Done

[will-moore]

@jburel @joshmoore Good to merge?