omicverse 2.2.2

omicverse 2.2.2

on Python PyPI

omicverse 2.2.2 — https://pypi.org/project/omicverse/2.2.2/ · pip install -U omicverse

⚠️ Breaking changes

• inferCNV now requires a platform. ov.single.CNV(method='infercnv').run() needs platform='10x'/'smartseq2' (or explicit cutoff=), else a clear ValueError (#822).
• Vendored gseapy removed — GSEA/ORA are now native; ov.bulk no longer imports gseapy or PyComplexHeatmap (#836).

Highlights

• From-scratch NumPy GSEA + hypergeometric ORA (#836) — single-process, no loky dead-lock, ES bit-exact vs gseapy, ~5× faster, progress bars; offline gene-set caching; geneset_plot_multi rendered with Marsilea.
• ov.single.Augur (#825) — cell-type prioritization (AUC / Lin's CCC).
• ov.space SPLIT purification (#828) — spatial signal purification.
• CNV heatmap & inferCNV (#822) — chromosome tiling fix, p/q arm split, phase 2/3 outputs, platform guard.
• ov.set_seed (#807/#820), unified QC workflow (#808/#819), reusable parametric-UMAP model (#809/#821), UpSet plots (#823), custom clone-size bins (#810/#818).

Compatibility fixes

matplotlib ≥3.9 get_cmap (#836), NumPy 2 / pyscenic (#829), COSG dotplot (#830), flowsig/pkg_resources (#832), PyG CUDA devices (#833).

Full notes: https://github.com/omicverse/omicverse-tutorials/blob/main/docs/Release_notes.md