1.2.0 🌈

🚀 Features

• Rework perturbation spaces around a perturbation-level API (#1032) @Zethson
• Milo: add mixed models to differential abundance testing (#1069) @Zethson
• Milo: add neighbourhood grouping (#801) @MaximilianNuber, @Zethson
• Add plot_ma() for DGE results (#1066) @Zethson
• Add plot_credible option to plot_effects_umap() (#1063) @Zethson
• Add text and HTML representations to DE model classes (#1070) @Zethson
• Rename DistanceTest alpha to padj_threshold (#1062) @Zethson
• Vectorize and parallelize the DE methods that support it (#1051) @Zethson
• Speed up Augur predict() (#1043) @Zethson
• Show output filename in download progress (#1056) @corkang

🐛 Bug Fixes

• scGen: vendor JAX backend to support scvi-tools 1.5.0 (#1042) @Zethson,
• scGen: make the JAX implementation reproduce the PyTorch one (#1028) @Zethson
• Fix import of removed scanpy _get_obs_rep/_set_obs_rep (#1050) @Zethson
• pseudobulk: only transfer constant obs columns (#1061) @Zethson
• Correct the version of the Milo deprecations (#1064) @Zethson

🧰 Maintenance

• Adopt the src layout, VCS versioning and supply chain pinning (#1057) @Zethson
• Type check pertpy and tests with mypy (#1053) @Zethson
• Adopt anndata's mypy configuration (#1060) @Zethson
• Deduplicate metadata download boilerplate (#1027) @Zethson,
• Align dataset download progress (#1059) @corkang
• Add discoverability metadata (#1067) @Zethson
• Update template to v0.8.0 (#1045) @scverse-bot, @Zethson
• Bump tutorials submodule (#1040, #1065) @Zethson

1.1.1 🌈

Changes

🚀 Features

• mixscale: add continuous perturbation scoring (#945) @stefanm808
• Add MiloDE for neighbourhood-level differential expression (#1001) @Zethson
• Add plot_disp_ests() for dispersion-estimate visualisation (#1004) @LuisHeinzlmeier
• Add and rename significance thresholds (#974) @LuisHeinzlmeier

🐛 Bug Fixes

• tascCODA: fix no credible effects returned (theta collapse) (#1017) @Zethson
• tascCODA: fix always returning insignificant results (#1016) @Zethson
• PseudobulkSpace: fix all-NaN extra obs with groups_col (#1006) @Zethson
• perturbation_space: skip None-keyed layers in _combine (#1000) @Zethson
• plot_effects_barplot(): remove FutureWarning (#1013) @LuisHeinzlmeier
• coda: fix ImportError (#1014) @LuisHeinzlmeier

🧰 Maintenance

• perturbation_space: cleanup, safer defaults, kill stale-state bugs (#994) @Zethson
• Resolve test-suite warnings (#1018) @Zethson
• docs: refresh DE docstring pseudobulk examples (#996) @Zethson
• ci: bump codecov-action to v6 and fail CI on upload error (#1009) @timtreis

1.1.0 🌈

🚀 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