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