Changelog

All notable changes to this project will be documented in this file.

Release

[1.0.0] - 2026-05-25

First public release

Unreleased

[0.0.5] - 2026-04-01

Fixed

• Fix aggregation of fate probabilities when cluster_key is categorical preventing the inclusion of unused categories

• Fix muon.MuData copy mechanism in atlas.pp.preprocessing: if copy = True performs deep copy and preserves all information in the new MuData instance

Added

• Renamed atlas.tl.PalantirExtension.compute_diffusion_map in atlas.tl.PalantirExtension.compute_diffusion_maps

Removed

• Removed atlas.tl.PalantirExtension.compute_diffusion_map

[0.0.6] - 2026-04-09

Fixed

• Fixed new MuData creation in atlas.pp.preprocessing with safe MuData copy and replacing del data.mod["atac"]

Added

• Added function _safe_mudata

[0.0.7] - 2026-04-10

Changed

• Changed KeyError into warning in atlas.tl.evaluate.terminal_pseudotime_enrichment when no terminal states are found. In this case np.NaN is returned.

[0.0.8] - 2026-04-13

Changed

• Added count_reads parameter to atlas.pp.preprocessing. The parameter is used in activity computation using muon.

• Parameter n_neighbors in atlas.pp.preprocessing updated to include None and adopt standard behavior for mu.pp.neighbors.

• Parameter knn_rna and knn_act in atlas.pp.neighbors set to 15 as in sc.pp.neighbors default version 1.12.0.

• Parameter n_pcs_rna and n_pcs_act in atlas.pp.preprocessing set to 50 as in sc.pp.pca default version 1.12.0.

[0.0.9] - 2026-04-20

Changed

• Changed plot size in atlas.pl.plot_trends and adjusted for labels and legend.

[0.0.11] - 2026-05-18

Added

• Added backend parameter to atlas.tl.CellRankExtension.compute_transition_matrix. The parameter is used for parallelization.

• Added backend parameter to atlas.tl.CellRankExtension.run. The parameter is used for parallelization.

[0.0.12] - 2026-05-20

Changed

• Fixed plot fate probabilities when a single fate is found

[0.1.0] - 2026-05-23

Package release on github