v0.3.7

What's Changed

• Replace deprecated np.in1d with np.isin by @marcovarrone in #113

Full Changelog: v0.3.6...v0.3.7

v0.3.6

What's Changed

• Allow saving shape_metrics plot by @marcovarrone in #104
• Fix datasets import failing by developing standalone dataset system by @marcovarrone in #111

Full Changelog: v0.3.5...v0.3.6

v0.3.5

What's Changed

• Relative Component Size (RCS) metric by @LukasHats in #66
• Use separate tables for SpatialData boundaries object by @marcovarrone in #92
• Match color between cell components and their boundaries in pl.boundaries by @marcovarrone in #94
• Make all CellCharter's generated data serializable by @marcovarrone in #95

New Contributors

• @LukasHats made their first contribution in #66

Full Changelog: v0.3.4...v0.3.5

v0.3.4

What's Changed

• Lower bound squidpy, relax deps and update installation instructions by @marcovarrone in #81
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #79

Full Changelog: v0.3.3...v0.3.4

v0.3.3

What's Changed

• Fix scipy error by @marcovarrone in #76
• Fix boundaries TypeError
• Fix boundaries shape plotting
• Retry test data download if first time fails
• Fix requirements conflict

Full Changelog: v0.3.2...v0.3.3

v0.3.2

What's Changed

• Fix differential neighborhood enrichment memory leak by @marcovarrone in #57
• Use Git LFS for test data by @marcovarrone in #58
• Add cc.tl.TRVAE to docs

Full Changelog: v0.3.1...v0.3.2

v0.3.1

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #50
• Reduce INFO and WARNING logging on .fit and .predict for tl.Cluster and tl.ClusterAutoK.
• Add property peaks to tl.ClusterAutoK to find all peaks in the stability curve.
• Change pl.enrichment legend from log2 fold change to log2FC.

Full Changelog: v0.3.0...v0.3.1

v0.3.0

What's Changed

• Replace pycave and lightkit with torchgmm by @marcovarrone in #49
• Extend Python compatibility to >= 3.8, <3.13
• Extend PyTorch compatibility to >= 1.12.0
• Misc fixes

Full Changelog: v0.2.3...v0.3.0

v0.2.3

• Bug fix pl.enrichment
• Add fontsize parameter to plotting functions
• Bug fix gr.diff_nhood_enrichment if conditions had different clusters
  Full Changelog: v0.2.2...v0.2.3

v0.2.2

What's Changed

• Raise ValueError on sparse array by @marcovarrone in #44
• Complete rewrite of the pl.enrichment and adding the permutation-based computation of gr.enrichment to estimate pvalues by @marcovarrone in #47
  • Removed dependency of pl.enrichment with scanpy's dotplot.
  • p-values are shown by color (parameter pvalues)
  • Possibility to select a significance threshold (parameter significance )
  • Show also depleted label-group pairs (parameter enriched_only)
  • Show only significant pairs based on the significance threshold (parameter significant_only)
• Fix issue with diff_nhood_enrichment when more than two conditions are present by @grst in #45

Full Changelog: v0.2.1...v0.2.2