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

v0.2.1

What's Changed

• Installation of cellcharter report import error from spatialdata coredata extent by @marcovarrone in #25
• Update template to v0.3.0 by @scverse-bot in #20
• Order diff nhood by @marcovarrone in #27
• Update template to v0.3.1 by @scverse-bot in #28
• Set pyro-ppl version dependency by @marcovarrone in #31
• Update docs by @marcovarrone in #36
• Fix plot_boundaries by @marcovarrone in #37
• Update template to v0.4.0 by @scverse-bot in #40
• Fix get_cmap import from matplotlib by @marcovarrone in #42
• Fix boundaries for NaN values by @marcovarrone in #43

Full Changelog: v0.2.0...v0.2.1

v0.2.0

The official version used in the Nature Genetics paper.