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adds niche-level aucell enrichment, generalize package, repro fixes#5

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teslajoy merged 6 commits into
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feature/redesign
May 27, 2026
Merged

adds niche-level aucell enrichment, generalize package, repro fixes#5
teslajoy merged 6 commits into
mainfrom
feature/redesign

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teslajoy added 6 commits May 19, 2026 06:00
…rovenance

- new _join_meta helper joins any non-key meta columns into cluster_embeddings;
  no hardcoded column names. used by both niche-pipeline and end2end.
- niche-pipeline: --niche-meta-key (default niche_id) replaces the hardcoded
  subarray/patient lookup; all non-key meta columns are now joined.
- end2end: --n-jobs (parallel enrich), --reactome-dir (offline/hpc),
  --meta + --meta-key (generic schema-free join), run_provenance.json,
  cluster_embeddings.parquet output, enrichment json -> parquet.
- verified end2end --gene-sets with arbitrary meta column names round-trips
  values into cluster_embeddings.parquet (no schema assumptions remain).
@teslajoy teslajoy merged commit 31430b7 into main May 27, 2026
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