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[python] Ingest somacore classes #3307

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[python] Ingest somacore classes #3307

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@ryan-williams ryan-williams commented Nov 7, 2024

Accompanying SOMA "core" changes: single-cell-data/SOMA#244

It can be awkward having some implementations in that repo:

  • I'm experimenting with a dask kwarg to ExperimentAxisQuery.to_anndata; EAQ impl has lived in the core repo, to date, but arguably should not
  • @bkmartinjr has been working on improved "fast CSR" algorithms, which were previously implemented and used in the SOMA core repo, but arguably belong in an implementation repo like this one.

Changes:
Move files and classes from single-cell-data/SOMA to this repo:

  • _query.py:
    • Axis
    • AxisIndexer
    • AxisQueryResult
    • ExperimentAxisQuery
    • MatrixAxisQuery
    • JoinIDCache
  • _fast_csr.py
  • _eager_iter.py

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codecov bot commented Nov 7, 2024

Codecov Report

Attention: Patch coverage is 88.33333% with 56 lines in your changes missing coverage. Please review.

Project coverage is 85.41%. Comparing base (b959b8b) to head (6013020).

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #3307      +/-   ##
==========================================
+ Coverage   85.14%   85.41%   +0.26%     
==========================================
  Files          53       56       +3     
  Lines        5568     6040     +472     
==========================================
+ Hits         4741     5159     +418     
- Misses        827      881      +54     
Flag Coverage Δ
python 85.41% <88.33%> (+0.26%) ⬆️

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

Components Coverage Δ
python_api 85.41% <88.33%> (+0.26%) ⬆️
libtiledbsoma ∅ <ø> (∅)

@ryan-williams ryan-williams marked this pull request as ready for review November 8, 2024 14:00
@johnkerl johnkerl changed the title Ingest somacore classes [python] Ingest somacore classes Nov 13, 2024
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Looks like straightforward code motion (as intended!) -- looks good to me

Holding off on approval until we get the somacore PR merged & a release tagged

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