1.1.0 🌈 release

🚀 Features

• milo: speed up pydeseq2 da_nhoods ~100x via poscounts size factors (#992) @Zethson
• Guide RNA assignment: crispat-matching JAX MAP fit (10–30× faster) (#987) @Zethson
• DIALOGUE: from-scratch port of the R reference (PMD + HLM + iterative NNLS) (#988) @Zethson
• PyDESeq2: optional apeGLM LFC shrinkage (#985) @Zethson
• Add layout option to coda plot_boxplots (#718) (#932) @emekaokoli19

🐛 Bug Fixes

• scCODA: fix run_hmc TypeError; clarify log2-fold-change sign (#993) @Zethson
• scCODA/tascCODA: make make_arviz stateless (#991) @Zethson
• scCODA: unify covariate index format across get_effect_df / summary / credible_effects (#989) @Zethson
• Reject all-zero contrasts in test_contrasts (#981) @Zethson
• Fix PseudobulkSpace.compute losing X with anndata main (#979) @Zethson
• Fix plot_effects_umap KeyError on Sccoda output (#780) (#971) @LiudengZhang
• Fix marker positions: calculate marker positions from DataFrame, not rendered labels (#970) @kimjune01
• Fix plot_multicomparison_fc ValueError with default figsize (#965) @kimjune01
• Fix minor bugs (#960) @Zethson
• Fix add and subtract (#959) @Zethson

🧰 Maintenance

• Milo cleanup: address #181 (#986) @Zethson
• Refresh tools API page (#983) @Zethson
• Resolve scgen test warnings (#982) @Zethson
• Upgrade R (#943) @Zethson
• Use pooch for dataset downloads (#980) @Zethson

1.0.6 🌈

🚀 Features

• Support Python 3.14 (#893) @Zethson

🐛 Bug Fixes

• Correct neighbors_key docstring for make_nhoods (#940) @Zethson
• Fix augur low frequency cell type behavior (#938) @Zethson
• Fix replogle_2022_k562_essential URL (#917) @Zethson
• Fix reshaping (#909) @Zethson
• fillna(1) spatialfdr (#913) @ktpolanski

🧰 Maintenance

• Mention paper in README (#935) @Zethson

1.0.5 🌈

🐛 Bug Fixes

• fix use raw & docs build (#906) @Zethson
• Add relative abundance warning (#900) @Zethson
• Fix PyDESeq2 layer handling in fit() (#895) @giovp

🧰 Maintenance

• Update citation (#899) @Zethson
• Update the exampledataset URLs to point to cloudfront (#898) @grst

1.0.4 🌈

Changes

🚀 Features

• Speedup For EDistance-like distances (#880) @selmanozleyen
• add milo-edger extra (#874) @mschilli87
• ci: fix isort formatting (#878) @flying-sheep
• Add permutation test (#726) @maltekuehl

🐛 Bug Fixes

• Remove cmap default in GuideAssignment.heatmap (#887) @Zethson
• fix: adapt fixture usage to newer pytest versions (#879) @flying-sheep
• remove decoupler mention (#869) @Zethson
• unpin R version in CI (#863) @Zethson
• Fix harded control key in plot_heatmap (#862) @Zethson

🧰 Maintenance

• switch to template (#866) @Zethson
• Add dataset cache back (#885) @Zethson
• metadata to scverse AWS (#860) @Zethson

1.0.3 🌈

🚀 Features

• Support layers for Augur load (#852) @Zethson
• Improve mixscape parameter names (#848) @Zethson
• Replace figshare & zenodo URLs with scverse URLs (#849) @Zethson
• Remove scvi-tools dependency (#844) @Zethson

1.0.2 🌈

Changes

🐛 Bug Fixes

• Fixed GDSC and PRISM annotation warnings (#835) @Lilly-May
• Fix: Validate 'type' parameter in Tasccoda.load (#839) @JuanTejedor
• Partial fixes for make_arviz (#834) @jpintar
• Fix setting of rng_key in make_arviz (#831) @jpintar

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