NEWS

SUMO 1.2.2 (2025-10-14)

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.

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.

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.

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.

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