v1.8.4

What's Changed

⚠️ Breaking Changes

• Fix: seed sequence permutation tests and make results independent of n_jobs by @selmanozleyen in #1234
• Move make_stitched_labels from experimental.im to experimental.tl by @timtreis in #1254
• refactor: convert experimental parameters to TypedDicts (1/4) by @selmanozleyen in #1279
• fix(gr): take the percentile threshold over edges only by @Marius1311 in #1309
• refactor: add StainReference transform methods (2/4) by @selmanozleyen in #1280

Added

• [3/3] cp_measure features + coordinate alignment for calculate_image_features by @timtreis in #1216
• Initial framework of the niche refactor by @shashkat in #1245
• Add COZI to nhood_enrichment() by @chiarasch in #1023
• Incorporating feedback on niche refactor by @shashkat in #1284
• Multi-slide pooled fit_stain_reference by @timtreis in #1209

Deprecated

• chore: switch to rngs by @selmanozleyen in #1270
• Make most arguments keyword-only, enforced by PLR0917 (#1288) by @selmanozleyen in #1297
• perf: centrality_scores as a numba BFS, drop parallelize by @selmanozleyen in #1302

Fixed

• fix: ci's and scanpy 1.13 plot compat by @selmanozleyen in #1253
• fix: ensure radius values stored in AnnData.uns are writable by @selmanozleyen in #1249
• fix: avoid obs_vector FutureWarning in spatial_scatter by @timtreis in #1265
• fix: reap leaked dask workers in process-based featurization by @timtreis in #1268
• fix: reproducible niche Leiden clustering + expose flavor/random_state/n_iterations by @timtreis in #1266
• fix: read images and scalefactors from adata.uns[spatial_key] by @FarisHrvat in #1304
• fix: preserve SpatialData input when copying spatial neighbors by @Georicl in #1292
• fix: clear the warnings CI emits by @selmanozleyen in #1310
• Fix spatial_key handling in var_by_distance by @Georicl in #1325

Other Changes

• chore(deps): bump the actions-deps group across 1 directory with 3 updates and pin pynndescent < 0.7 by @dependabot[bot] in #1316

New Contributors

• @jberg5 made their first contribution in #1236
• @shashkat made their first contribution in #1245
• @chiarasch made their first contribution in #1023
• @Georicl made their first contribution in #1290
• @Marius1311 made their first contribution in #1309
• @FarisHrvat made their first contribution in #1304
• @dependabot[bot] made their first contribution in #1294

Full Changelog: v1.8.3...v1.8.4