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SUMO 1.2.2

New

• Pretrained artifacts for fast demos/tests Added cached, pre-trained demo objects (simulated outputs and factor structures) to speed up examples, vignettes, and CI cold starts.
• Optional backend support: basilisk & reticulate Introduced backend hooks for isolated Python environments via basilisk and interoperability via reticulate (aka “reticulare” in earlier notes). Includes auto-detection and clearer setup guidance.
• Demo mode in simulate_twoOmicsData() multiomics_demo = "SHOW" provides a ready-to-run two-factor toy example for quick multi-omics walkthroughs.

Enhancements

• Legacy → standard conversion pipeline Polished as_multiomics() to reliably upgrade legacy simulate_twoOmicsData() outputs into the current schema (omics, per-omic list_betas, signal_annotation$features, factor_map, etc.), including:

  • normalization of factor-score names (alpha{n}),
  • mapping delta{n} → beta{n} for omic 2,
  • inference of sample/feature annotations when explicit indices are missing,
  • robust split of concatenated_datasets back into omic1/omic2 using counts or omic1_/omic2_ prefixes.

• Internal helpers made non-exported (with docs scaffolding) %||% for defaults and .is_multiomics_like() for schema checks are now internal, with roxygen headers (no code changes).

• Stronger standardization & resilience Automatic row/column naming for omics matrices; safer handling of empty/NA index vectors; improved messages for sample-partition constraints; sturdier concatenated-split heuristics.

Documentation

• Vignette updates Expanded “Getting Started” and migration guidance: using demo mode, converting legacy objects with as_multiomics(), and configuring basilisk/reticulate backends.
• Function docs Roxygen scaffolding added for the internal utilities and converter while preserving the original function bodies.

Fixes

• Consistent delta→beta mapping across omics.
• Deterministic naming and factor-label normalization.
• More informative errors when sample segments are too small or factors are unmapped.

Breaking Changes

• None. Legacy outputs remain supported; call as_multiomics() to standardize them for downstream workflows.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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