feat(enrichr): retrieve gene sets incl. MSigDB collections (#139)#241
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feat(enrichr): retrieve gene sets incl. MSigDB collections (#139)#241Elarwei001 wants to merge 2 commits into
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Add `gget.enrichr_library()` (CLI: `gget enrichr --get_library`) to fetch the
gene sets (members) of any Enrichr gene-set library — the recommended way to
retrieve MSigDB gene sets (e.g. MSigDB_Hallmark_2020) without MSigDB login.
- Returns a long-format DataFrame (gene_set, gene), or a {gene_set: [genes]}
dict with json=True. `gene_set=` returns a single set; `species` selects the
non-human Enrichr variants.
- CLI: new --get_library/-gl and --gene_set/-gs; genes/--database made optional
in library mode (still enforced for enrichment). Backward compatible.
- Detects Enrichr's HTML-404 (HTTP 200) response for unknown libraries.
- Tests + fixtures (live Enrichr) and docs.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## dev #241 +/- ##
==========================================
+ Coverage 56.14% 56.62% +0.48%
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Files 29 29
Lines 9244 9285 +41
==========================================
+ Hits 5190 5258 +68
+ Misses 4054 4027 -27 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Add a network-free TestEnrichrLibraryOffline class that mocks requests to cover enrichr_library: invalid species, verbose logging, blank-line parsing, bad/empty library errors, gene_set filter + not-found, and the json/json+save/CSV-save branches. All PR-added lines now covered. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Resolves #139
Summary
gget enrichr: Added support for retrieving gene sets, including MSigDB collections (fixes issue 139).Testing
Unit tests added/extended in
tests/test_enrichr.pywith fixture entries intests/fixtures/test_enrichr.json; run with pytest.