Preserve h5py.Dataset filter settings on export

[oruebel]

Motivation

Fix #152 Preserve h5py.Dataset filter settings on export

How to test the behavior?

• Add unit tests
• Add functions to ZarrDataIO to wrap h5py.Dataset and infer filter settings
• Update ZarrIO to wrap h5py.Dataset on write to preserve filter settings

Checklist

• Did you update CHANGELOG.md with your changes?
• Have you checked our Contributing document?
• Have you ensured the PR clearly describes the problem and the solution?
• Is your contribution compliant with our coding style? This can be checked running ruff from the source directory.
• Have you checked to ensure that there aren't other open Pull Requests for the same change?
• Have you included the relevant issue number using "Fix #XXX" notation where XXX is the issue number? By including "Fix #XXX" you allow GitHub to close issue #XXX when the PR is merged.

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (9692a98) 84.51% compared to head (4bdb47a) 85.07%.

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #153      +/-   ##
==========================================
+ Coverage   84.51%   85.07%   +0.56%     
==========================================
  Files           5        5              
  Lines        1104     1146      +42     
  Branches      296      311      +15     
==========================================
+ Hits          933      975      +42     
  Misses        115      115              
  Partials       56       56              

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[oruebel]

@sinha-r @rly this PR is related to the cloud project to allow conversion from HDF5 to Zarr while preserving chunking and compression settings if possible

[oruebel]

@rly @mavaylon1 can you please review

[rly]

The code looks good to me. There are a bunch of branches in the code that translates the compression. I know it's tedious, but could you write tests for those branches? That would help make sure those lines work as intended and prevent our code coverage from dropping 1% to 83.4%. We might want to include hdmf-zarr in our core packages for the U24 at some point.

[oruebel]

There are a bunch of branches in the code that translates the compression. I know it's tedious, but could you write tests for those branches?

The main reason I didn't add tests for all the branches is because in order to cover those cases I believe we need to install custom HDF5 compressors, i.e., add hdf5_plugins as a dependency just to run tests and szip may not be possible to test because it requires a license. In principle, we just need a HDF5 dataset that looks like it uses those filters, but I'm not sure if we can "fake" that easily.

[rly]

add hdf5_plugins as a dependency just to run tests

I think that is OK. It would be added to https://github.com/hdmf-dev/hdmf-zarr/blob/dev/requirements-dev.txt

szip may not be possible to test because it requires a license

We can just exclude that one from coverage

[oruebel]

@rly Can you please take another look. I added a new unit test module for ZarrDataIO. As mentioned above, I had to add hdf5plugin as a requirement for these tests. I added @unittest.skipIf to the test cases that use hdf5plugin just in case the library is not installed. The tests now cover 100% of the patch.

[rly]

Thanks! Looks good to me.