Ivirshup/census builder spatial

[ivirshup]

x* #1092

To install from this branch

gh pr checkout 1245
pip install -e tools/cellxgene_census_builder

TODO

• Update source datasets links to ones which use schema v5.1.0
• Update builder
  • Don't include normalized layer
  • Figure out what set of genes to use
  • populate spatial collection
    • Add a scene per ingested dataset
      • Add images
        • Remove alpha channel from datasets that have it, and report the one weird dataset
      • Add obsl["loc"], data frame containing ["soma_joinid", "x", "y"]
        • Add radius
      • Add scene as Scene object once that is available: Add the new Scene collection to the python-spec single-cell-data/SOMA#202
      • Use MultiscaleImage (or whatever it ends up being called) for the images
  • Add obs_scene table
  • Add var_scene table
  • Allow writing duplicates to loc
  • Filter out objects with .uns["spatial"]["is_single"]==False (current filtering code seems to rely only on columns in obs)
• Tests
  • Check equivalence of written data to input anndata
    • loc
    • images

[codecov]

Codecov Report

Attention: Patch coverage is 79.50530% with 58 lines in your changes missing coverage. Please review.

Project coverage is 91.00%. Comparing base (1f55385) to head (a8a2898).
Report is 4 commits behind head on main.

Files with missing lines	Patch %	Lines
.../cellxgene_census_builder/build_soma/build_soma.py	41.30%	54 Missing ⚠️
...ne_census_builder/build_soma/experiment_builder.py	93.33%	2 Missing ⚠️
...cellxgene_census_builder/build_soma/consolidate.py	75.00%	1 Missing ⚠️
...ols/cellxgene_census_builder/tests/test_spatial.py	99.13%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1245      +/-   ##
==========================================
- Coverage   91.35%   91.00%   -0.35%     
==========================================
  Files          82       83       +1     
  Lines        6480     6706     +226     
==========================================
+ Hits         5920     6103     +183     
- Misses        560      603      +43     

Flag	Coverage Δ
unittests	91.00% <79.50%> (-0.35%)	⬇️

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