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✨ Support CELLxGENE 7.0.0#3466

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Zethson wants to merge 22 commits intomainfrom
feature/cxg_7
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✨ Support CELLxGENE 7.0.0#3466
Zethson wants to merge 22 commits intomainfrom
feature/cxg_7

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@Zethson
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@Zethson Zethson commented Jan 15, 2026

We simplify CELLxGENE integration by removing pinned ontology version support in favor of curating against latest versions.

In the future, we support users to

  1. Validate with BioHub's cellxgene-schema tool
  2. Then use LaminDB's CELLxGENE integration to ingest validated artifacts & register metadata

This is achieved by

Remaining TODOs

  • update ontology versions on cxg
  • Update guide

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
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You are unblocked via laminlabs/bionty#359.

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
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codecov bot commented Feb 5, 2026

Codecov Report

❌ Patch coverage is 95.00000% with 2 lines in your changes missing coverage. Please review.
βœ… Project coverage is 89.97%. Comparing base (aec1051) to head (507dfae).
⚠️ Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
lamindb/examples/cellxgene/_cellxgene.py 94.59% 2 Missing ⚠️
Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##             main    #3466      +/-   ##
==========================================
- Coverage   90.48%   89.97%   -0.51%     
==========================================
  Files          94       86       -8     
  Lines       13711    13301     -410     
==========================================
- Hits        12406    11968     -438     
- Misses       1305     1333      +28     
Files with missing lines Coverage Ξ”
lamindb/curators/__init__.py 100.00% <100.00%> (ΓΈ)
lamindb/curators/core.py 84.49% <100.00%> (-0.32%) ⬇️
lamindb/examples/cellxgene/_cellxgene.py 91.02% <94.59%> (-7.86%) ⬇️

... and 9 files with indirect coverage changes

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  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
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github-actions bot commented Feb 5, 2026

Deployment URL: https://e70fbb45.lamindb.pages.dev

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
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