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Fix/enrichment nan and bidirectional similarity#2

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malbiruk merged 4 commits into
mainfrom
fix/enrichment-nan-and-bidirectional-similarity
Jun 4, 2026
Merged

Fix/enrichment nan and bidirectional similarity#2
malbiruk merged 4 commits into
mainfrom
fix/enrichment-nan-and-bidirectional-similarity

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@malbiruk malbiruk commented Jun 4, 2026

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amirfeizi and others added 4 commits June 1, 2026 20:46
Correctness fixes:
- Return NaN for RR/OR when either comparison group is empty instead of
  misleading continuity-corrected effect sizes.
- Match EFO similarity pairs in both orientations in matching and disease
  expansion (handles inline or one-sided lookup tables).

New features:
- Add two-sided Fisher's exact test p_value to enrichment results
  (statistics.fisher_exact_pvalue, exposed in API/CLI/MCP output).
- Add create_matched_pairs_df() audit export with gene, ct_efo_id,
  ge_efo_id, similarity, and match_type columns.
- Add validate(return_matched_pairs=True) and CLI --save-matched-pairs
  (optional output.save_matched_pairs in YAML config).
- Improve CLI summary: show p-value column and render undefined RR/CI as N/A.

CI:
- Add GitHub Actions workflow (.github/workflows/ci.yml) running ruff and
  pytest on Python 3.11, 3.12, and 3.13.

Tests: 130 passed.
@malbiruk malbiruk merged commit 00a69d4 into main Jun 4, 2026
3 checks passed
@malbiruk malbiruk deleted the fix/enrichment-nan-and-bidirectional-similarity branch June 4, 2026 10:22
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2 participants