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Constrain Seurat Pseudobulk feature-ID contract - #74

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maggiecam merged 1 commit into
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fix/issue-68-pseudobulk-feature-id
Oct 2, 2026
Merged

maggiecam merged 1 commit into
mainfrom
fix/issue-68-pseudobulk-feature-id

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Summary

  • constrain feature_id_column to the implemented downstream-safe value
    GeneName in the canonical schema
  • reject an invalid CLI value before any Seurat object conversion begins
  • clarify the fixed handoff contract in function help and the README
  • link the deployment adapter that is currently under review

Compatibility and versioning

This corrects a schema/implementation mismatch identified during independent
review of NIDAP-Community/OMIX-Seurat-Pseudobulk#1. The implementation already
rejected every value other than GeneName, so this is a compatible patch from
module 0.4.0 to 0.4.1 and interface version 1 remains unchanged. Aggregation,
matrix values, manifests, output names, and downstream routing are unchanged.

Supports #68.

Validation

  • Rscript modules/OMIX-Seurat-Pseudobulk/tests/test-module-layout.R
  • Rscript modules/OMIX-Seurat-Pseudobulk/tests/test-seurat-pseudobulk.R
  • Rscript tests/test-monorepo-layout.R
  • git diff --check

The broader Seurat-to-DEG integration test was invoked but skipped locally
because OmixSeurat is not installed in the current host library; published
runtime validation remains a separate CI/deployment gate.

@maggiecam
maggiecam merged commit e3cc933 into main Oct 2, 2026
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