feat(fine-mapping): GWAS Catalog fine-mapping manifest generator

[project-defiant]

Summary

Adds a FineMappingManifest dataset and a GWASCatalogFineMappingManifestGenerator step that joins the fine-mapping planner output with the GWAS Catalog study index to produce a single TSV manifest file — the input required by the downstream MultiSuSiE Nextflow pipeline.

What's new

• FineMappingManifest dataset (src/gentropy/dataset/fine_mapping.py) — new Dataset-derived class with columns runId, studyId, route, summarystatsLocation, majorAncestry, traitFromSourceMappedIds (comma-joined, sorted, deduped).
• GWASCatalogFineMappingManifestGenerator step (src/gentropy/finemapping_manifest.py) — filters the study index to GWAS Catalog studies with sumstats + LD population structure, resolves majorAncestry via LDAnnotator._get_major_population, joins with the planner output, and writes a single TSV via toPandas().to_csv(). Optional summary_statistics_glob overrides summarystatsLocation with live GCS paths.
• Hydra config (src/gentropy/config.py) — GWASCatalogFineMappingManifestConfig registered as step=gwas_catalog_finemapping_manifest.
• 4 tests (tests/gentropy/step/) — 2 orchestration (mocked) + 2 integration (real Spark): TSV content, schema, ancestry derivation, trait dedup/sort, missing-study warning.
• Constraint fixes (constraint.py, constraint_set.py) — HasAllowedMajorAncestry now guards against null/empty ldPopulationStructure before indexing; _compute_major_ancestry uses LDAnnotator._get_major_population directly; traitSet is array_sort(array_distinct(...)) for stable ordering.

Real-data run (GWAS Catalog, release 26.06 sumstats susie study index — 214,716 studies)

The manifest was generated against the full GWAS Catalog study index using the planner output from the preceding step.

Fine-mapping plan (gs://gwas_catalog_multi_ancestry_fine_mapping/plan/):

Metric	Value
Total studies in plan	214,716
Eligible runs (non-null runId)	5,288
Ineligible studies	202,640
Run sizes	pairs: 3,788 · triplets: 1,500
Ancestry combinations	AFR+NFE: 3,617 · EAS+NFE: 166 · AFR+EAS+NFE: 1,500 · AFR+EAS: 5

Manifest (gs://gwas_catalog_multi_ancestry_fine_mapping/manifest.tsv):

Metric	Value
Total rows	12,076
Distinct runs	5,288
Sumstat paths resolved via glob	gs://gwas_catalog_inputs/harmonised_summary_statistics/GCST*

A test manifest (4 triplet runs, 12 rows, traits EFO_0004309 / EFO_0004541 / EFO_0004611 / EFO_0004833) has been uploaded to gs://ot_orchestration/tests/multi_ancestry_fine_mapping/manifest.tsv for pipeline integration testing.