Fix chunking bug with compound dtypes

[pauladkisson]

Fixes #1122

Comapare Dev Tests after the fix: https://github.com/catalystneuro/neuroconv/actions/runs/12960177532/job/36153641201 (2 failed -- see #1188)

To Dev Tests before: https://github.com/catalystneuro/neuroconv/actions/runs/12995279932/job/36241639533 (8 failed)

[pauladkisson]

@rly, lmk what you think

[pauladkisson]

@h-mayorquin, this is ready for review. Basically I use the hdmf.build.builders.BaseBuilder to check if a neurodata object would have a compound dtype. Most of the complexity is introduced by the need to find a match between the neurodata object and its location in the builder, which is outlined in the docstrings. Lmk what you think!

[h-mayorquin]

I did a first reading. Two things:

• I think, we should update hdmf on the pyproject to the latest version or greater.
• Looking at the tests that were failing before they seem related to the pixel mask. Can we create a more direct test of this in the dataset configuration tests? I think it would be better to have something more unit-test-like that would fail quicker if we break this (or if we can to refactor). Can we build something simpler with pixel-mask so we don't rely on the full segmentation conversion test?

[pauladkisson]

I think, we should update hdmf on the pyproject to the latest version or greater.

I updated to include everything <4, which zarr-related issues. Should be able to add hdmf 4.0 soon -- see: #1191

[pauladkisson]

Looking at the tests that were failing before they seem related to the pixel mask. Can we create a more direct test of this in the dataset configuration tests? I think it would be better to have something more unit-test-like that would fail quicker if we break this (or if we can to refactor). Can we build something simpler with pixel-mask so we don't rely on the full segmentation conversion test?

Definitely needs some unit tests. I'll put together some.

[pauladkisson]

From Meeting: move has_compound_dtype inside get_data_shape

[pauladkisson]

From Meeting: move has_compound_dtype inside get_data_shape

Actually, get_data_shape comes from hdmf.utils, so no way to move that in this PR. Also, if I remember correctly, they use get_data_shape in ways that would make incorporating this compound_dtype fix difficult.

[pauladkisson]

@h-mayorquin, i added tests, so this should be good to go!

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 89.72%. Comparing base (96dfdff) to head (23c0c89).
Report is 32 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1146      +/-   ##
==========================================
- Coverage   90.69%   89.72%   -0.98%     
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  Files         129      129              
  Lines        8189     8415     +226     
==========================================
+ Hits         7427     7550     +123     
- Misses        762      865     +103     

Flag	Coverage Δ
unittests	89.72% <100.00%> (-0.98%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
..._helpers/_configuration_models/_base_dataset_io.py	98.80% <100.00%> (+2.03%)	⬆️
...roconv/tools/nwb_helpers/_dataset_configuration.py	93.67% <100.00%> (+0.16%)	⬆️

... and 20 files with indirect coverage changes