Add AnnData as format

[flying-sheep]

Description

Add AnnData as supported format

TODO

• Check if AnnData can interact with buffers
• Add to optional feature dependencies (extras)
• Sample h5ad file
• Unit tests
• Documentation
  • Python: Run build.py for new docstrings
• Changelog entry

[sir-sigurd]

This needs tests and changelog entry.

Might makes to add anndata as extra dependency, see

quilt/api/python/setup.py

Line 70 in 9c1d054

extras_require={

.

Also it would be useful if you provide sample .h5ad file.

[flying-sheep]

I think this looks good. I can’t run gendocs though, I get

Starting pydocmd_main...
Started generating documentation...
Traceback (most recent call last):
  File "/home/phil/Dev/Python/Misc/Quilt/gendocs/build.py", line 90, in <module>
    pydocmd_main()
  File "/home/phil/Dev/Python/Misc/Quilt/.venv/lib/python3.10/site-packages/pydocmd/__main__.py", line 251, in main
    loader.load_section(section)
  File "/home/phil/Dev/Python/Misc/Quilt/.venv/lib/python3.10/site-packages/pydocmd/loader.py", line 87, in load_section
    sig = get_function_signature(obj, scope if inspect.isclass(scope) else None)
  File "/home/phil/Dev/Python/Misc/Quilt/.venv/lib/python3.10/site-packages/pydocmd/loader.py", line 138, in get_function_signature
    sig = str(inspect.signature(function))
  File "/usr/lib/python3.10/inspect.py", line 3247, in signature
    return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
  File "/usr/lib/python3.10/inspect.py", line 2995, in from_callable
    return _signature_from_callable(obj, sigcls=cls,
  File "/usr/lib/python3.10/inspect.py", line 2392, in _signature_from_callable
    raise TypeError('{!r} is not a callable object'.format(obj))
TypeError: <classmethod(<function Package.install at 0x7f29436355a0>)> is not a callable object

[codecov]

Codecov Report

Merging #2974 (ab5c024) into master (2313e3a) will increase coverage by 0.12%.
The diff coverage is 90.38%.

@@            Coverage Diff             @@
##           master    #2974      +/-   ##
==========================================
+ Coverage   35.14%   35.27%   +0.12%     
==========================================
  Files         679      679              
  Lines       29616    29658      +42     
  Branches     4400     4400              
==========================================
+ Hits        10410    10462      +52     
+ Misses      18013    18003      -10     
  Partials     1193     1193              

Flag	Coverage Δ
api-python	91.17% <90.38%> (+0.23%)	⬆️
catalog	8.87% <ø> (ø)
lambda	86.07% <ø> (ø)

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

Impacted Files	Coverage Δ
api/python/setup.py	0.00% <ø> (ø)
api/python/quilt3/formats.py	85.20% <86.48%> (+3.34%)	⬆️
api/python/tests/test_formats.py	100.00% <100.00%> (ø)

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[flying-sheep]

OK, done!

[flying-sheep]

those tests are pretty flaky, I didn’t touch lambda and now it fails …

[robnewman]

@sir-sigurd Can you please review the PR?