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[python] Outgest obsp/varp as dense #3362

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@johnkerl johnkerl commented Nov 21, 2024

Issue and/or context: #3360

Changes:

Outgest these as dense.

Notes for Reviewer:

Closed on feedback from @ivirshup (see below). I'll repurpose the tracking task #3360 to have us outgest sparse in all cases.

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codecov bot commented Nov 21, 2024

Codecov Report

Attention: Patch coverage is 60.00000% with 2 lines in your changes missing coverage. Please review.

Project coverage is 85.77%. Comparing base (ca00d5b) to head (b2aadda).
Report is 6 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #3362      +/-   ##
==========================================
+ Coverage   85.64%   85.77%   +0.12%     
==========================================
  Files          57       57              
  Lines        6201     6194       -7     
==========================================
+ Hits         5311     5313       +2     
+ Misses        890      881       -9     
Flag Coverage Δ
python 85.77% <60.00%> (+0.12%) ⬆️

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Components Coverage Δ
python_api 85.77% <60.00%> (+0.12%) ⬆️
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@johnkerl johnkerl changed the title [python] Outgest obsp/varp as dense [WIP] [python] Outgest obsp/varp as dense Nov 21, 2024
@johnkerl johnkerl marked this pull request as ready for review November 21, 2024 18:20
@ivirshup
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That is a problem in the anndata docs, these should definitely be sparse.

These are typically things like nearest neighbor networks. So number of cells X number of cells with like ~15 entries per row. Very sparse!

@johnkerl
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cc @aaronwolen and @bkmartinjr -- I'll cancel this.

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This just means that the ExperimentAxisQuery is wrong then - one does sparse, one does dense

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