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Clean GSVA public nomenclature and provenance - #72

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maggiecam merged 2 commits into
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docs/issue-71-gsva-public-cleanup
Oct 2, 2026
Merged

maggiecam merged 2 commits into
mainfrom
docs/issue-71-gsva-public-cleanup

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Summary

  • remove internal template provenance and legacy NIDAP labels from the public
    OMIX GSVA README and source-level help
  • rename the canonical source to GSVA.R and stable outputs to
    gsva_results.csv and gsva_heatmap.png
  • register and link the Code Ocean deployment adapter
  • record OMIX module/interface identity in the run summary instead of internal
    template paths and checksums
  • add repository-wide contributor and module-contract rules for public module
    naming and provenance

Compatibility

The scientific implementation, methods, parameters, defaults, score-table
contents, and heatmap behavior are unchanged. Output filenames changed, so the
module advances from 0.1.0/interface 1 to 0.2.0/interface 2 while still in
development. The open deployment-adapter PR must be synchronized before it is
merged or released.

This implements the first GSVA phase of #71. The compatibility-aware audit of
older modules remains tracked there.

Validation

  • Rscript modules/OMIX-GSVA/tests/test-module-layout.R
  • Rscript modules/OMIX-GSVA/tests/test-gsva-cli.R
  • Rscript tests/test-monorepo-layout.R
  • git diff --check

@maggiecam
maggiecam merged commit 13b8715 into main Oct 2, 2026
4 checks passed
@maggiecam
maggiecam deleted the docs/issue-71-gsva-public-cleanup branch October 2, 2026 14:14
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