1.0.1 🌈

🚀 Features

• Add support for gamma parameter in MMD distance (#825) @Zethson
• Run notebooks in CI (#815) @Zethson

🐛 Bug Fixes

• Fix milo output writing (#821) @Zethson

1.0.0 🌈

Changes

🚀 Features

• Simplify guide assignment tutorial (#796) @Zethson
• Add pydeseq2 solver to milo (#795) @Zethson

0.11.5 🌈

🚀 Features

• Move to trusted publishing (#790) @Zethson
• Add conda-forge to installation instructions (#789) @Zethson
• fix seaborn 0.14 compat & testing dependencies & speed up tests (#787) @Zethson
• Support > 2 colors in pt.tl.Sccoda.plot_boxplots (#784) @mschilli87

🐛 Bug Fixes

• Fix LIL support for AnnData 0.12 (#792) @Zethson
• Fix compatibility with rpy 3.6.0 in milo (#791) @seohyonkim

0.11.4 🌈

Changes

🧰 Maintenance

• Remove decoupler (#783) @Zethson

0.11.3 🌈

Changes

🚀 Features

• add about page (#770) @Zethson
• Simplify Metadata errors (#765) @Zethson
• Standardize scCODA plot palette interface (#773) @mschilli87

🐛 Bug Fixes

• Add statmod installation instructions (#776) @Zethson

0.11.2 🌈

Changes

🚀 Features

• Simplify Metadata errors (#765) @Zethson

0.11.1 🌈

Changes

• fix scCODA not requiring tcoda extra (#762) @Zethson

🧰 Maintenance

• Restructure documentation (#762) @Zethson

0.11.0 🌈

Changes

🚀 Features

• Improve CI test setup & speed up mixscape (#757) @Zethson
• Speed up mixscape (#756) @Zethson
• Optimize mixscape (#735) @Zethson
• Cleaner mixscape (#746) @eroell
• Speedup Mixscape's lda function (#754) @eroell
• skip milotests properly & cache metadata (#752) @Zethson
• Sparse threshold max assignment (#744) @Zethson
• Speedup import times (#743) @stefanpeidli
• Add sparse threshold guide assignment & fix docstrings (#737) @Zethson
• More robust download (#721) @Zethson
• Support Python 3.13 (#720) @Zethson
• PRISM drug response metadata annotation (#716) @Lilly-May
• improve CellLine metadata module UX (#717) @JiriBruthans
• Switch from ete3 to ete4 (#618) @dengzq1234
• Move pynndescent import out of for-loop (#761) @eroell
• Cleaner CinemaOT (#745) @eroell

🐛 Bug Fixes

• Change how guide assignment model saves params from uns to var (#758) @stefanpeidli
• A ton of doc improvements & fix mudata warnings & Augur interface (#759) @Zethson
• Change cell_wise_metric from "sqeuclidean" to "euclidean" for edist (#733) @stefanpeidli
• Check only for numeric in statsmodels (#725) @grst
• Remove leidenalg from requirements (#729) @Zethson
• Remove pyenchant (#728) @Zethson
• Fix coda plot axes (#739) @mschilli87

🧰 Maintenance

• A ton of doc improvements & fix mudata warnings & Augur interface (#759) @Zethson
• Additional pre-commit checks (#748) @Zethson
• mixscape dropdown (#740) @Zethson
• fix docstrings (#737) @Zethson

0.10.0 🌈

Changes

🚀 Features

• Allow Custom Feature Spaces in Dialogue (#712) @grpinto
• Add Poisson-Gauss Mixture model for Guide Assignment (#709) @stefanpeidli
• Add perturbation signature calculation from replicate control cells (#695) @Lilly-May
• Optimize test speed (#699) @Zethson
• Optimize MeanVarDistributionDistance (#697) @Zethson

🐛 Bug Fixes

• Align Mixscape with Seurat’s implementation (#710) @Lilly-May
• Fix empty figure returns when show=True in plotting functions (#703) @Lilly-May
• Fix probability data type (#696) @Zethson
• Mixscape reproducibility (#683) @Lilly-May

0.9.5 🌈

Changes

🚀 Features

• Augur scsim warnings (#670) @Zethson
• Add uncertainty score in KNN label_transfer in PerturbationSpace (#658) @stefanpeidli
• Incorporate use case tutorials (#665) @Lilly-May
• Add plots for DE analysis and unify plotting API (#654) @Lilly-May
• Switch to formulaic-contrasts (#682) @grst @emdann
• Remove anndata pin (#653) @Lilly-May

🐛 Bug Fixes

• Fix jax random array (#686) @Zethson
• Fixed plotting for mixscape.plot_barplot and sccoda.plot_effects_barplot (#667) @Lilly-May
• Remove explicit anndata in dependencies (#666) @Zethson
• Fix legend position for pt.tl.Mixscape.plot_barplot (#660) @Lilly-May