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Duplicated from  Paper2Agent/alphagenome_agent

anne-voigt

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Paper2Agent_decoupleRpy

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Running

decoupler_load_and_visualize_data called sc.pl.umap(color="leiden") unconditionally and crashed on any h5ad lacking X_umap/leiden — exactly the Loveless raw-count subsets (gse155698_steele, gse205013_werba, biodata-registry 0.1.8).

• _ensure_umap(): reuses precomputed embeddings (pbmc3k unchanged); else runs a bounded normalize+log1p -> pca -> neighbors -> leiden(igraph) -> umap pipeline. Never hard-fails: on failure the plot is skipped and the loaded AnnData + metadata are still returned with a note.
• Grouping detection covers R make.names atlas cols (Clusters, ...); leiden uses flavor="igraph" (no leidenalg dep on the Space).
• Sits on top of the existing _load_adata seam, so the Loveless subsets load AND visualize end-to-end.
• tests/test_rna_sc_load.py (4 green).

Opening as a PR only — not merged, no deploy. Folds into the pending 0.1.8 factory-rebuild.