pertpy 1.2.0

1.2.0 🌈

on Python PyPI

🚀 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