OMIX_Test

Prototype OMIX monorepo for modular analysis modules with shared starter environments.

This repo is organized so each analysis module can be developed, tested, and released independently while sharing a small set of cached starter environments.

Repository Layout

OMIX_Test/
├── core/                     # Shared R utilities used by modules
├── starter-environments/     # Shared Docker/renv environments
├── modules/                  # Independent analysis modules
├── tests/                    # Repo-level contract tests
└── .github/workflows/        # CI for module checks and starter environments

Starter Environments

Environment	Purpose	Example modules
r-base	Base R, renv, common system libraries	shared utility modules
r-visualization	Plotting and visualization packages	volcano, heatmap, PCA, Venn, tSNE/UMAP, limma stats
r-pathway	Pathway and gene-set packages	GSVA, GSEA, L2P single, L2P multi
r-singlecell	Single-cell packages	future single-cell modules

Starter environments are intended to be built once, cached in GHCR, and referenced by module runtime builds.

Modules

Each module owns its own code, tests, schemas, app-panel config, and runtime entrypoint. The starter environment is declared in module.yml.

Current starter modules:

• volcano
• heatmap
• pca
• pca3d
• venn_diagram
• tsne_umap
• stats_limma
• pathway_gsva
• pathway_gsea
• pathway_l2p_single
• pathway_l2p_multi

The first platform-ready runtime examples are:

• modules/volcano/runtime/
• modules/pathway_l2p_single/runtime/
• modules/pathway_l2p_multi/runtime/

All other modules are placeholders until these first examples are validated in Code Ocean.

Code Ocean Sync

Each runtime bundle can be sparse-synced into a standalone Code Ocean root. The OMIX monorepo remains the source of truth, and reverse sync is guarded so Code Ocean-side edits return only to the matching module runtime directory.

See:

• docs/code-ocean-sync.md for the step-by-step sync workflow
• docs/code-ocean-sync-flow.mmd for the Mermaid/Lucidchart diagram

Module Contract

Every module should contain:

modules/<module>/
├── R/
├── tests/
├── schemas/
├── app-panel/
├── code/
├── module.yml
├── README.md
└── CHANGELOG.md

See docs/module-contract.md for the expected manifest fields.

Local Checks

Validate the current scaffold with:

Rscript tests/test-module-contract.R

Development Flow

1. Edit one module under modules/<module>/.
2. Commit and push.
3. CI validates the module contract and reports changed modules.
4. Module-specific build/test jobs can build only the changed runtime.
5. Starter environments rebuild only when files under starter-environments/ change.