(chore): generate 1.11.0 release notes (#3412)

Author: flying-sheep

ci/scripts/towncrier_automation.py

@@ -92,7 +92,11 @@ def main(argv: Sequence[str] | None = None) -> None:
             f"--base={base_branch}",
             f"--title={pr_title}",
             f"--body={pr_description}",
-            *(["--label=no milestone"] if base_branch == "main" else []),
+            *(
+                ["--label=no milestone", "--label=Development Process 🚀"]
+                if base_branch == "main"
+                else []
+            ),
             *(["--dry-run"] if args.dry_run else []),
         ],
         check=True,

docs/release-notes/1.11.0.md

@@ -0,0 +1,38 @@
+(v1.11.0)=
+### 1.11.0 {small}`2024-12-20`
+
+### Features
+
+- {func}`~scanpy.pp.sample` supports both upsampling and downsampling of observations and variables. {func}`~scanpy.pp.subsample` is now deprecated. {smaller}`G Eraslan & P Angerer` ({pr}`943`)
+- Add `layer` argument to {func}`scanpy.tl.score_genes` and {func}`scanpy.tl.score_genes_cell_cycle` {smaller}`L Zappia` ({pr}`2921`)
+- Prevent `raw` conflict with `layer` in {func}`~scanpy.tl.score_genes` {smaller}`S Dicks` ({pr}`3155`)
+- Add support for `median` as an aggregation function to the `Aggregation` class in `scanpy.get._aggregated.py`. This allows for median-based aggregation of data (e.g., pseudobulk), complementing existing methods like mean- and sum-based aggregation {smaller}`M Dehkordi (Farhad)` ({pr}`3180`)
+- Add `key_added` argument to {func}`~scanpy.pp.pca`, {func}`~scanpy.tl.tsne` and {func}`~scanpy.tl.umap` {smaller}`P Angerer` ({pr}`3184`)
+- Support running {func}`scanpy.pp.pca` on sparse Dask arrays with the `'covariance_eigh'` solver {smaller}`P Angerer` ({pr}`3263`)
+- Use upstreamed {class}`~sklearn.decomposition.PCA` implementation for {class}`~scipy.sparse.csr_array` and {class}`~scipy.sparse.csr_matrix` (see {ref}`sklearn:changes_1_4`) {smaller}`P Angerer` ({pr}`3267`)
+- Add explicit support to {func}`scanpy.pp.pca` for `svd_solver='covariance_eigh'` {smaller}`P Angerer` ({pr}`3296`)
+- Add support {class}`dask.array.Array` to {func}`scanpy.pp.calculate_qc_metrics` {smaller}`I Gold` ({pr}`3307`)
+- Support `layer` parameter in {func}`scanpy.pl.highest_expr_genes` {smaller}`P Angerer` ({pr}`3324`)
+- Run numba functions single-threaded when called from inside of a ThreadPool {smaller}`P Angerer` ({pr}`3335`)
+- Switch {func}`~scanpy.logging.print_header` and {func}`~scanpy.logging.print_versions` to {mod}`session_info2` {smaller}`P Angerer` ({pr}`3384`)
+- Add sampling probabilities/mask parameter `p` to {func}`~scanpy.pp.sample` {smaller}`P Angerer` ({pr}`3410`)
+
+### Performance
+
+- Speed up {func}`~scanpy.pp.regress_out` {smaller}`P Ashish, P Angerer & S Dicks` ({pr}`3284`)
+
+### Documentation
+
+- Improve {func}`~scanpy.external.pp.harmony_integrate` docs {smaller}`D Kühl` ({pr}`3362`)
+- Raise {exc}`FutureWarning` when calling deprecated {mod}`scanpy.pp` functions {smaller}`P Angerer` ({pr}`3380`)
+- | Deprecate … | in favor of … |
+  | --- | --- |
+  | {func}`scanpy.read_visium` | {func}`squidpy.read.visium` |
+  | {func}`scanpy.datasets.visium_sge` | {func}`squidpy.datasets.visium` |
+  | {func}`scanpy.pl.spatial` | {func}`squidpy.pl.spatial_scatter` |
+
+  {smaller}`P Angerer` ({pr}`3407`)
+
+### Bug fixes
+
+- Upper-bound {mod}`sklearn` `<1.6.0` due to {issue}`dask/dask-ml#1002` {smaller}`Ilan Gold` ({pr}`3393`)