(chore): generate 1.11.0 release notes (#3466)

docs/release-notes/1.11.0.md

@@ -0,0 +1,53 @@
+(v1.11.0)=
+### 1.11.0 {small}`2025-02-14`
+
+Release candidates:
+
+- (v1.11.0rc2)=
+  {guilabel}`rc2` 2025-01-24
+- (v1.11.0rc1)=
+  {guilabel}`rc1` 2024-12-20
+
+### Features
+
+- {guilabel}`rc1` {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`)
+- {guilabel}`rc1` Add `layer` argument to {func}`scanpy.tl.score_genes` and {func}`scanpy.tl.score_genes_cell_cycle` {smaller}`L Zappia` ({pr}`2921`)
+- {guilabel}`rc1` Prevent `raw` conflict with `layer` in {func}`~scanpy.tl.score_genes` {smaller}`S Dicks` ({pr}`3155`)
+- {guilabel}`rc1` Add support for `median` as an aggregation function to {func}`~scanpy.get.aggregate`. 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`)
+- {guilabel}`rc1` Add `key_added` argument to {func}`~scanpy.pp.pca`, {func}`~scanpy.tl.tsne` and {func}`~scanpy.tl.umap` {smaller}`P Angerer` ({pr}`3184`)
+- {guilabel}`rc1` Support running {func}`scanpy.pp.pca` on sparse Dask arrays with the `'covariance_eigh'` solver {smaller}`P Angerer` ({pr}`3263`)
+- {guilabel}`rc1` Use upstreamed {class}`~sklearn.decomposition.PCA` implementation for {class}`~scipy.sparse.csr_array` and {class}`~scipy.sparse.csr_matrix` (see scikit-learn {ref}`sklearn:changes_1_4`) {smaller}`P Angerer` ({pr}`3267`)
+- {guilabel}`rc1` Add explicit support to {func}`scanpy.pp.pca` for `svd_solver='covariance_eigh'` {smaller}`P Angerer` ({pr}`3296`)
+- {guilabel}`rc1` Add support for {class}`dask.array.Array` to {func}`scanpy.pp.calculate_qc_metrics` {smaller}`I Gold` ({pr}`3307`)
+- {guilabel}`rc1` Support `layer` parameter in {func}`scanpy.pl.highest_expr_genes` {smaller}`P Angerer` ({pr}`3324`)
+- {guilabel}`rc1` Run numba functions single-threaded when called from inside of a {class}`~multiprocessing.pool.ThreadPool` {smaller}`P Angerer` ({pr}`3335`)
+- {guilabel}`rc1` Switch {func}`~scanpy.logging.print_header` and {func}`~scanpy.logging.print_versions` to {mod}`session_info2` {smaller}`P Angerer` ({pr}`3384`)
+- {guilabel}`rc1` Add sampling probabilities/mask parameter `p` to {func}`~scanpy.pp.sample` {smaller}`P Angerer` ({pr}`3410`)
+
+### Performance
+
+- {guilabel}`rc1` Speed up {func}`~scanpy.pp.regress_out` {smaller}`P Ashish, P Angerer & S Dicks` ({pr}`3284`)
+
+### Documentation
+
+- {guilabel}`rc1` Improve {func}`~scanpy.external.pp.harmony_integrate` docs {smaller}`D Kühl` ({pr}`3362`)
+- {guilabel}`rc1` Raise {exc}`FutureWarning` when calling deprecated {mod}`scanpy.pp` functions {smaller}`P Angerer` ({pr}`3380`)
+- {guilabel}`rc1` {smaller}`P Angerer` ({pr}`3407`)
+
+  | 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` |
+
+- {guilabel}`rc2` Fix reference in {mod}`scanpy.pp` page {smaller}`D Kazemi` ({pr}`3418`)
+
+### Bug fixes
+
+- {guilabel}`rc1` Upper-bound {mod}`sklearn` `<1.6.0` due to {issue}`dask/dask-ml#1002` {smaller}`Ilan Gold` ({pr}`3393`)
+- {guilabel}`rc2` Fix {func}`~scanpy.tl.rank_genes_groups` compatibility with data >10M cells {smaller}`P Angerer` ({pr}`3426`)
+- {guilabel}`rc2` Fix {func}`scanpy.pl.rank_genes_groups`’s `ax` parameter {smaller}`P Angerer` ({pr}`3428`)
+
+### Development Process
+
+- {guilabel}`rc2` Fix version number inference in development environments (CI and local) {smaller}`P Angerer` ({pr}`3441`)

pyproject.toml

@@ -268,6 +268,7 @@ exempt-modules = [  ]
 strict = true
 
 [tool.towncrier]
+name = "scanpy"
 package = "scanpy"
 directory = "docs/release-notes"
 filename = "docs/release-notes/{version}.md"