v2.3.0

What's Changed

• docs: adopt agent-neutral AGENTS.md + REVIEW_GUIDE.md pattern by @Marius1311 in #1319
• Support .obsm proportion frames in plot_macrostate_composition by @Marius1311 in #1321
• fix(io): pass element positionally to anndata write_basic by @Marius1311 in #1322
• fix(pl): drop deprecated N argument to ListedColormap by @Marius1311 in #1330
• fix(cytotrace): handle None layer key in invalid-layer error message by @Marius1311 in #1324
• test(model): compare ExtensionArray model attrs element-wise by @Marius1311 in #1325
• test(plotting): make image comparison robust to transparent backgrounds by @Marius1311 in #1323
• Bump the actions group across 1 directory with 2 updates by @dependabot[bot] in #1320
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #1318
• fix(deps): replace deprecated numpy.core / scipy.ndimage.filters imports by @Marius1311 in #1331
• docs(install): note PETSc/SLEPc unavailable on Windows conda-forge by @Marius1311 in #1332
• fix(rtk): recompute transition matrix when conn_weight changes by @Marius1311 in #1333
• fix(gpcca): clearer error when no macrostate meets stability threshold by @Marius1311 in #1334
• fix(pl): reuse fitted models passed back to gene_trends by @Marius1311 in #1335
• feat(estimators): support omitting missing values in lineage drivers by @Marius1311 in #1336
• test: install moscot in the test dependency group by @Marius1311 in #1338
• deprecate(rtk): deprecate RealTimeKernel.from_wot (removed in v3) by @Marius1311 in #1339
• Support .obsm proportion frames for macrostate naming by @Marius1311 in #1326
• test: centralize skip markers and enable strict markers/config by @Marius1311 in #1341
• docs: clarify that PETSc/SLEPc + R tests run in a dedicated CI job by @Marius1311 in #1342
• test(plotting): pilot image-test refactor for gene-trend & GPCCA (#1328) by @Marius1311 in #1337
• ci(test): upload rendered plotting figures as an artifact by @Marius1311 in #1343
• Explain why the coarse stationary distribution is missing in GPCCA by @Marius1311 in #1345
• test(plotting): migrate CFLARE, driver-correlation & macrostate-composition (#1328) by @Marius1311 in #1344
• fix(models): support BaseModel.prepare() with lineage=None when no lineages computed by @Marius1311 in #1346
• docs(kernels): document how to save plot_projection figures by @Marius1311 in #1347
• test(plotting): migrate cluster-trends & heatmap (#1328) by @Marius1311 in #1348
• Add agg option for fate probabilities towards aggregated terminal states (#1000) by @Marius1311 in #1349
• feat(estimators): add which="initial_and_terminal" to plot_macrostates by @Marius1311 in #1351
• test(plotting): migrate model/lineage family (#1328) by @Marius1311 in #1350
• test(plotting): raise the smoke-test floor to a non-blank check (#1328) by @Marius1311 in #1352
• test(plotting): promote over-smoked knobs to real introspection (#1328) by @Marius1311 in #1354
• test(plotting): migrate projection/flow family (#1328) by @Marius1311 in #1353
• test(plotting): migrate log-odds (#1328) by @Marius1311 in #1355
• Add Signal API to plot obs/obsm quantities along trajectories (#1202) by @Marius1311 in #1357
• test(plotting): migrate aggregate-fate-probabilities (#1328) by @Marius1311 in #1356
• test(plotting): migrate plotting tests off deprecated data_key/use_raw (#1328) by @Marius1311 in #1358
• test(plotting): replace bilinear-resize fallback; fix dpi propagation (#1327) by @Marius1311 in #1359
• test(plotting): regenerate stale baselines on Linux; un-xfail (#1328) by @Marius1311 in #1360
• test(plotting): migrate fitted-model tests (#1328) by @Marius1311 in #1361

New Contributors

• @dependabot[bot] made their first contribution in #1320

Full Changelog: v2.2.0...v2.3.0