.gitignore
.readthedocs.yaml
LICENSE
MANIFEST.in
README.md
pyproject.toml
.github/workflows/ci.yml
.github/workflows/docker-pr.yml
.github/workflows/docker.yml
.github/workflows/docs.yml
.github/workflows/pypi-release.yml
docker/Dockerfile
docker/README.md
docker/docker-compose.yml
docker/requirements.txt
examples/demo/README.md
examples/demo/evidence_table.tsv
examples/demo/make_evidence_table.py
examples/demo/run.sh
examples/demo/sample_card.json
examples/demo/expected/audit_log.tsv
examples/demo/expected/claims.proposed.tsv
examples/demo/expected/distilled.tsv
examples/demo/expected/distilled.with_modules.tsv
examples/demo/expected/evidence.normalized.tsv
examples/demo/expected/modules.tsv
examples/demo/expected/report.jsonl
examples/demo/expected/report.md
examples/demo/expected/risk_coverage.tsv
examples/demo/expected/run_meta.json
examples/demo/expected/sample_card.normalized.json
examples/demo/expected/sample_card.raw.json
examples/demo/expected/term_gene_edges.tsv
examples/demo/expected/term_modules.tsv
examples/demo/inputs/fgsea_results.tsv
resources/README.md
resources/context_lexicon.tsv
resources/gene_id_maps/build_ensembl_to_symbol_from_gtf.sh
resources/gene_id_maps/build_entrez_id_map.sh
resources/gene_id_maps/ensembl_id_map.tsv.gz
resources/gene_id_maps/id_map.tsv.gz
src/llm_pathway_curator/__init__.py
src/llm_pathway_curator/_shared.py
src/llm_pathway_curator/audit.py
src/llm_pathway_curator/audit_reasons.py
src/llm_pathway_curator/backends.py
src/llm_pathway_curator/calibrate.py
src/llm_pathway_curator/claim_schema.py
src/llm_pathway_curator/cli.py
src/llm_pathway_curator/distill.py
src/llm_pathway_curator/llm_claims.py
src/llm_pathway_curator/masking.py
src/llm_pathway_curator/modules.py
src/llm_pathway_curator/noise_lists.py
src/llm_pathway_curator/pipeline.py
src/llm_pathway_curator/ranked.py
src/llm_pathway_curator/report.py
src/llm_pathway_curator/sample_card.py
src/llm_pathway_curator/schema.py
src/llm_pathway_curator/select.py
src/llm_pathway_curator/utils.py
src/llm_pathway_curator/viz_ranked.py
src/llm_pathway_curator.egg-info/PKG-INFO
src/llm_pathway_curator.egg-info/SOURCES.txt
src/llm_pathway_curator.egg-info/dependency_links.txt
src/llm_pathway_curator.egg-info/entry_points.txt
src/llm_pathway_curator.egg-info/requires.txt
src/llm_pathway_curator.egg-info/top_level.txt
src/llm_pathway_curator/adapters/README.md
src/llm_pathway_curator/adapters/__init__.py
src/llm_pathway_curator/adapters/fgsea.py
src/llm_pathway_curator/adapters/metascape.py
tests/test_demo_cli.py
tests/test_import.py
tests/test_shared_gate_mode.py
tests/test_smoke_adapters.py