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[r][python] Create an AnnData -> SOMA -> Seurat test #1263

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merged 3 commits into from
Apr 25, 2023

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@ebezzi ebezzi commented Apr 19, 2023

Issue and/or context:
#1184

Changes:
Adds an AnnData -> SOMA -> Seurat using the existing python/R framework

Notes for Reviewer:

  1. It is possible to add more assertions if desired (e.g. on the X layer)
  2. It is possible to replicate the tests on different artifacts. This one uses a stripped down version of pbmc3k that was already in the repo
  3. Right now, the R side requires a query since to_seurat is only available at a query level. Eventually it will be available on SOMAExperiment ([r] [WIP] Port to_seurat() to SOMAExperiment #1261) and this test should be updated to be simpler.
  4. Right now we can only do one "trip" of the test, since Seurat -> SOMA isn't in main yet (it's here though). Once this is merged we can add the other test.

@ebezzi ebezzi requested review from johnkerl and mojaveazure April 19, 2023 14:26
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codecov-commenter commented Apr 19, 2023

Codecov Report

Patch coverage has no change and project coverage change: -40.02 ⚠️

Comparison is base (85d9ed1) 91.24% compared to head (b4242d2) 51.22%.

❗ Current head b4242d2 differs from pull request most recent head 9a7dae1. Consider uploading reports for the commit 9a7dae1 to get more accurate results

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Additional details and impacted files
@@             Coverage Diff             @@
##             main    #1263       +/-   ##
===========================================
- Coverage   91.24%   51.22%   -40.02%     
===========================================
  Files          30       63       +33     
  Lines        2306     4816     +2510     
===========================================
+ Hits         2104     2467      +363     
- Misses        202     2349     +2147     
Flag Coverage Δ
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LGTM! :)

@ebezzi ebezzi merged commit e22e1d4 into main Apr 25, 2023
@johnkerl johnkerl deleted the ebezzi/anndata-seurat-roundtrip-testing branch April 25, 2023 17:23
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3 participants