Squidpy 1.3.0 (2023-06-16)

Features

• Add squidpy.tl.var_by_distance() to calculate distances to anchor points and store results in a design matrix.

• Add squidpy.pl.var_by_distance() to visualize variables such as gene expression by distance to an anchor point. @LLehner #591

Bugfixes

• Fix pandas inf squidpy.pl.ligrec(). @michalk8 #625

• Remove column assignment to improve compatibility with new cell metadata. @cornhundred #648

• Fix squidpy.pl.extract() on views. @michalk8 #663

• Set coordinates’ index type to same as in anndata.AnnData.obs in squidpy.read.vizgen() and squidpy.read.visium(). @michalk8 #665

• Update cell metadata index conversion. @djlee1 #679

• Fix previously updated cell metadata index conversion. @dfhannum #692

Miscellaneous

• Update pre-commits and unpin numba and numpy. @giovp #643

• Add :attr: option to squidpy.gr.spatial_autocorr() to select values from anndata.AnnData.obs or anndata.AnnData.obsm. @michalk8 #664

• Add attr option to squidpy.gr.spatial_autocorr() to select values from anndata.AnnData.obs or anndata.AnnData.obsm. @michalk8 #672

• Add percentile option to squidpy.gr.spatial_neighbors() to filter neighbor graph using percentile of distances threshold. @LLehner #690

• Add spatialdata.SpatialData as possible input for graph functions. @LLehner #701

Documentation

• Fix CI badges and tox. @michalk8 #627

• Changed tutorial directory structure. @LLehner #113

• Updated the quality control tutorials for Vizgen, Xenium and Nanostring. @pakiessling #110

• Improved example for squidpy.tl.var_by_distance() and squidpy.pl.var_by_distance(). @LLehner #115