docs: document array type support

[flying-sheep]

• [x] Closes #3892
• [x] Tests included or not required because:

• [ ] Release notes not necessary because:

I double-checked everything in #2578 and mostly winged it for the rest.

Would be nice if one of you could take a look if I mis-specified something.

• I didn’t check if some flavors of highly_variable_genes supports only CSR. Any idea?
• I tried to document things that implicitly convert to csr as “not supporting csc”, except when that’s conditional (i.e sc.pp.scale supports CSC if you don’t specify mask_obs, so that’s detailed in mask_obs).

[codecov[bot]]

Codecov Report

:white_check_mark: All modified and coverable lines are covered by tests. :white_check_mark: Project coverage is 76.80%. Comparing base (b85d814) to head (c9c352b). :warning: Report is 1 commits behind head on main. :white_check_mark: All tests successful. No failed tests found.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3895      +/-   ##
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+ Coverage   76.77%   76.80%   +0.03%     
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  Files         116      117       +1     
  Lines       12398    12440      +42     
==========================================
+ Hits         9518     9554      +36     
- Misses       2880     2886       +6     

Flag	Coverage Δ
hatch-test.pre	76.80% <100.00%> (+0.03%)	:arrow_up:

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Files with missing lines	Coverage Δ
src/scanpy/_utils/_docs.py	100.00% <100.00%> (ø)
...c/scanpy/experimental/pp/_highly_variable_genes.py	18.44% <ø> (ø)
src/scanpy/get/_aggregated.py	92.78% <ø> (ø)
src/scanpy/neighbors/__init__.py	80.05% <ø> (ø)
src/scanpy/preprocessing/_combat.py	88.46% <ø> (ø)
src/scanpy/preprocessing/_highly_variable_genes.py	94.71% <ø> (ø)
src/scanpy/preprocessing/_normalization.py	94.66% <ø> (ø)
src/scanpy/preprocessing/_pca/__init__.py	90.65% <ø> (ø)
src/scanpy/preprocessing/_qc.py	95.83% <ø> (ø)
src/scanpy/preprocessing/_scale.py	91.20% <ø> (ø)
... and 15 more

... and 1 file with indirect coverage changes

[grst]

How hard would it be to make an overview page that lists all functions in a single table?

[ilan-gold]

@flying-sheep I'll try to look tomorrow more closely but I do like @grst's suggestion. That being said, I don't think it should be instead of what is here, this is really cool!

[flying-sheep]

Can you draft how that would look like? Tables for something like PCA are already quite big, and I can’t imagine how to lay out one big table in a way that it would be clear what’s going on.

[grst]

I had in mind something like this

✅ = supported ❌ = not supported ⚡= supported in dask

Function	numpy.ndarray	csr_array	csr_matrix	csc_array	csc_matrix
sc.tl.pca	✅⚡	✅⚡	✅⚡	✅	✅
sc.tl.tsne	✅	✅	✅	❌	❌
sc.tl.umap	✅⚡	✅	✅	❌	❌
...

[Intron7]

@flying-sheep I have not checked how this work or not. But do umap and tsne work with sp_matrix and arrays?

[flying-sheep]

Yes! In umap, doing sc.pp.neighbors(adata, use_rep="X") results in X being passed to simplicial_set_embedding, which will do a TruncatedSVD on it.

TSNE calls validate_data(self, X, accept_sparse=["csr", "csc", "coo"], ...) which very likely also means it supports it.

Thanks, thinking like this is exactly the reason I requested your reviews! Could have easily been that I messed this up.

[grst]

The table leads to horizontal scrolling for me

Also not sure if the top of the API page is the best place to place it? Maybe even have a dedicated page for it?