From a28fe88ec08cc144189f6cc1497a5f067b96ce7b Mon Sep 17 00:00:00 2001 From: "Philipp A." Date: Fri, 14 Feb 2025 10:46:17 +0100 Subject: [PATCH] (chore): generate 1.11.0 release notes (#3466) --- docs/release-notes/1.11.0.md | 53 +++++++++++++++++++++++++++++++++ docs/release-notes/1.11.0rc1.md | 38 ----------------------- docs/release-notes/1.11.0rc2.md | 15 ---------- pyproject.toml | 1 + 4 files changed, 54 insertions(+), 53 deletions(-) create mode 100644 docs/release-notes/1.11.0.md delete mode 100644 docs/release-notes/1.11.0rc1.md delete mode 100644 docs/release-notes/1.11.0rc2.md diff --git a/docs/release-notes/1.11.0.md b/docs/release-notes/1.11.0.md new file mode 100644 index 0000000000..d84884ccd7 --- /dev/null +++ b/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`) diff --git a/docs/release-notes/1.11.0rc1.md b/docs/release-notes/1.11.0rc1.md deleted file mode 100644 index 4d189fdafb..0000000000 --- a/docs/release-notes/1.11.0rc1.md +++ /dev/null @@ -1,38 +0,0 @@ -(v1.11.0rc1)= -### 1.11.0rc1 {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 {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`) -- 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 scikit-learn {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 for {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 {class}`~multiprocessing.pool.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`) diff --git a/docs/release-notes/1.11.0rc2.md b/docs/release-notes/1.11.0rc2.md deleted file mode 100644 index 04a0141ade..0000000000 --- a/docs/release-notes/1.11.0rc2.md +++ /dev/null @@ -1,15 +0,0 @@ -(v1.11.0rc2)= -### 1.11.0rc2 {small}`2025-01-24` - -### Bug fixes - -- Fix {func}`~scanpy.tl.rank_genes_groups` compatibility with data >10M cells {smaller}`P Angerer` ({pr}`3426`) -- Fix {func}`scanpy.pl.rank_genes_groups`’s `ax` parameter {smaller}`P Angerer` ({pr}`3428`) - -### Development Process - -- Fix version number inference in development environments (CI and local) {smaller}`P Angerer` ({pr}`3441`) - -### Documentation - -- Fix reference in {mod}`scanpy.pp` page {smaller}`D Kazemi` ({pr}`3418`) diff --git a/pyproject.toml b/pyproject.toml index 379f51d8c6..7ba5bd70c6 100644 --- a/pyproject.toml +++ b/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"