Add signature reversal scoring to enrichment

[daveringelberg]

PR Checklist

• Referenced issue is linked
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

Description of changes

This adds a first CMap-style signature reversal workflow to pt.tl.Enrichment.

Given perturbation-level AnnData with perturbations as observations and genes as variables, users can provide either up/down query gene sets or a signed query signature. The method scores each perturbation by how strongly it opposes the query signature and stores the results back on the AnnData object.

This addresses the signature reversal part of #1036. It does not address Bliss/Loewe synergy, dose-response, or genetic interaction workflows.

Technical details

• adds Enrichment.signature_reversal
• stores reversal score, connectivity score, and rank in adata.obs
• stores query metadata and result keys in adata.uns
• supports .X, an optional layer, and optional gene-symbol matching through adata.var
• documents signature reversal under the Enrichment tools section
• adds compact tests for up/down gene sets and signed query signatures
• adds no new dependency

Testing

• ruff check src\pertpy\tools\_enrichment.py tests\tools\test_enrichment.py
• ruff format --check src\pertpy\tools\_enrichment.py tests\tools\test_enrichment.py
• pytest tests\tools\test_enrichment.py -q -p no:cacheprovider

Addresses part of #1036.

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 79.78%. Comparing base (c2831c5) to head (ace13a9).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1082      +/-   ##
==========================================
+ Coverage   79.45%   79.78%   +0.32%     
==========================================
  Files          53       53              
  Lines        7546     7667     +121     
==========================================
+ Hits         5996     6117     +121     
  Misses       1550     1550              

Files with missing lines	Coverage Δ
src/pertpy/tools/_enrichment.py	83.33% <100.00%> (+16.94%)	⬆️

... and 2 files with indirect coverage changes

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[daveringelberg]

It looks like the ReadTheDocs failure is unrelated to this PR. The warnings seem to come from external intersphinx/scvi-lightning references.

[daveringelberg]

After a further pass, the implementation now uses raw CMap WTCS. The remaining ReadTheDocs failure is caused by the same external issue noted above.

[Zethson]

Thanks! I'll have a look at the RTD failure soon.