[python] Add get_obs

[ivirshup]

Fixes #1037

TODO:

• Add get_var
• Docs
• Confirm argument names

[codecov]

Codecov Report

Attention: Patch coverage is 97.67442% with 1 lines in your changes are missing coverage. Please review.

Project coverage is 91.16%. Comparing base (e36addb) to head (f2db37f).

Files	Patch %	Lines
...lxgene_census/src/cellxgene_census/_get_anndata.py	93.75%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1151      +/-   ##
==========================================
+ Coverage   91.12%   91.16%   +0.04%     
==========================================
  Files          77       77              
  Lines        5857     5896      +39     
==========================================
+ Hits         5337     5375      +38     
- Misses        520      521       +1     

Flag	Coverage Δ
unittests	91.16% <97.67%> (+0.04%)	⬆️

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[prathapsridharan]

Overall this looks good to me. I have one question about the implementation in the test case.

@pablo-gar @ebezzi - Can y'all take a look too please?

[prathapsridharan]

LGTM but please wait for @ebezzi and @pablo-gar to review as well before merging to main

[pablo-gar]

@prathapsridharan @ebezzi I see a pattern in the file structure in api/python/cellxgene_census/src/cellxgene_census whereby the SOMAExperiment helpers are under _experiment.py, the anndata helpers are _get_anndata.py

Would it make sense to have the proposed helpers in this PR under a new _axis_metadata.py or _get_axis_metadata.py file?

I defer to you both as this touches dev eng design.

LGTM otherwise

[prathapsridharan]

get_obs and get_var to me seems consistent when put together with anndata related functions. And the same applies to helper functions needed in service of get_anndata, get_obs, get_var.

I think we can shift things around later if needed but for now this organization seems fine to me

[ebezzi]

Typo in the docs, but otherwise LGTM.

[ivirshup]

Thanks for the catch! Applied your changes.