- Add
rsc.gr.calculate_nichewith flavorsneighborhood,utag, andcellcharter. Mirrorssquidpy.gr.calculate_niche{pr}644{smaller}S Dicks - Add a minimal full-covariance GMM (
squidpy_gpu._gmm.gmm_fit_predict) used by thecellcharter{pr}644{smaller}S Dicks tl.leidenandtl.louvainnow record the final modularity value inadata.uns[key_added]["modularity"](scalar for a single resolution, list for multiple resolutions) {pr}648{smaller}J Pintar
- Fixes
tl.rank_genes_groupsreturning NaN/zerologfoldchanges/pvalswithgroups=[subset]andreference='rest'{pr}651{smaller}S Dicks - Fixes
pp.bbknnconnectivities diverging from upstreambbknn: per-batch neighbours are now sorted by distance beforefuzzy_simplicial_set(so weights no longer collapse near 1.0), and the defaulttrimmatches upstream (10 * neighbors_within_batch * n_batches). Trimming kernel no longer crashes for largetrim, and a new block-cooperative sort kernel is auto-dispatched for largetrimfor substantial speedups {pr}659{smaller}S Dicks - Fixes float64 precision loss in
pp.normalize_pearson_residualson CSR/CSC input {pr}658{smaller}A Mikaeili & S Dicks
- Tidy
_check_gpu_Xreturn value on the canonicalizing branch {pr}664{smaller}S Dicks adata.uns[key_added]["params"]["resolution"]is now stored as a scalarfloatwhen a single resolution is passed totl.leidenandtl.louvainto match behaviour in Scanpy, and as alistwhen multiple resolutions are passed. Previously it was always stored as a list. {pr}648. {smaller}J Pintar- Drop dependency on
cuml.thirdparty_adapters.check_array(removed in cuml 26.06);init_posvalidation intl.umapandtl.draw_graphis now handled locally {pr}660{smaller}S Dicks - Unify cuBLAS handle creation across GMM and harmony {pr}
662{smaller}S Dicks