CellNiche v0.1.8

CellNiche v0.1.8

This release improves the usability and robustness of CellNiche after publication.

Added

• Added multi-slice support using precomputed Squidpy spatial graphs.
• Added multi_slice and connectivity_key config options.
• Added embedding_type: "embedding" support for using precomputed embeddings from adata.obsm[embedding_key].
• Added a multi-slice tutorial notebook.

Fixed

• Fixed embedding_type="expr" to use adata.X as model input.
• Fixed phenoLabels handling so it is required only for pheno and pheno_expr.
• Fixed n_hvg handling during HVG selection.
• Cleaned package metadata and removed generated build/cache files.

Notes

For multi-slice datasets, users should precompute a sample-aware spatial graph using Squidpy, for example with sq.gr.spatial_neighbors(..., library_key="sample"), and then set:

multi_slice: true
connectivity_key: "spatial"