docs: generate 1.12.0 release notes (#3951)

Author: flying-sheep

docs/release-notes/1.12.0.md

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+(v1.12.0)=
+### 1.12.0 {small}`2026-01-23`
+
+Release candidates:
+
+- (v1.12.0rc1)=
+  {guilabel}`rc1` 2025-11-10
+
+#### Breaking changes
+
+- {guilabel}`rc1` Adopt the Scientific Python [deprecation schedule](https://scientific-python.org/specs/spec-0000/):
+  remove Python ≤3.11 support and officially add Python 3.13 and 3.14 support, require anndata≥0.10 {smaller}`P Angerer` ({pr}`3485`, {pr}`3874`)
+
+#### Features
+
+- {guilabel}`rc1` Added `n_components` parameter to {func}`~scanpy.tl.tsne` {smaller}`Kitsune` ({pr}`2803`)
+- {guilabel}`rc1` {func}`scanpy.pp.highly_variable_genes` flavors `seurat_v3` and `seurat_v3_paper` are now `dask`-compatible {smaller}`I Gold` ({pr}`3340`)
+- {guilabel}`rc1` Add {mod}`zarr` support and `convert_strings_to_categoricals` parameter to {func}`scanpy.write` {smaller}`P Angerer` ({pr}`3498`)
+- {guilabel}`rc1` Add support for {class}`scipy.sparse.csr_array` and {class}`scipy.sparse.csc_array` {smaller}`P Angerer` ({pr}`3563`)
+- {guilabel}`rc1` Added a new `compressed` parameter to {func}`~scanpy.read_10x_mtx` to support reading uncompressed matrix files produced by tools like STARsolo {smaller}`T Kuthuru` ({pr}`3564`)
+- {guilabel}`rc1` Make {func}`scanpy.get.aggregate` {doc}`dask:index` compatible with all aggregations except median {smaller}`I Gold` ({pr}`3700`)
+- {guilabel}`rc1` Add `filter_unexpressed_genes` parameter to {func}`scanpy.pp.highly_variable_genes` {smaller}`M Mueller` ({pr}`3767`)
+- {guilabel}`rc1` Add column `"n_obs_aggregated"` to {func}`scanpy.get.aggregate` output to show the total number of observations aggregated per group {smaller}`R Disa` ({pr}`3824`)
+- {guilabel}`rc1` Add `method='jaccard'` for generating connectivities in {func}`scanpy.pp.neighbors` {smaller}`J Pintar` ({pr}`3831`)
+- {guilabel}`rc1` Add in `csc`-in-{doc}`dask:index` support for {func}`scanpy.get.aggregate` {smaller}`I Gold` ({pr}`3872`)
+- {guilabel}`rc1` Raised warnings now always point at user code, not internal scanpy code {smaller}`P Angerer` ({pr}`3876`)
+- Add modularity scoring via {func}`scanpy.metrics.modularity` with support for directed/undirected graphs {smaller}`A. Karesh` ({pr}`3613`)
+- Added `distances` parameter to {func}`scanpy.pp.neighbors`, allowing to compute graphs from a precomputed distance matrix {smaller}`A. Karesh` ({pr}`3627`)
+- {func}`scanpy.pl.dotplot` now supports a `group_colors` parameter for custom per-group coloring with perceptually uniform color gradients via OKLab interpolation. {smaller}`R Baber` ({pr}`3764`)
+- Allow specifying graphs in {mod}`scanpy.metrics` functions {smaller}`P Angerer` ({pr}`3898`)
+
+#### Miscellaneous changes
+
+- {guilabel}`rc1` Replaced several internal utilities with their {mod}`fast_array_utils` counterparts {smaller}`P Angerer` ({pr}`3598`)
+- {guilabel}`rc1` Deprecate {func}`scanpy.tl.louvain` {smaller}`P Angerer` ({pr}`3658`)
+- {guilabel}`rc1` Deprecate `save` parameter of plotting functions. {smaller}`zethson` ({pr}`3675`)
+- {guilabel}`rc1` Remove support for the experimental and unmaintained `zappy` library {smaller}`P Angerer` ({pr}`3884`)
+- Remove development extras (`scanpy[test,dev]`) in favor of dependency groups {smaller}`P Angerer` ({pr}`3905`)
+
+#### Documentation
+
+- {guilabel}`rc1` Update tutorial {doc}`/tutorials/experimental/dask` for {mod}`anndata` 0.12 (see {pr}`scverse/scanpy-tutorials#186`) {smaller}`I Gold` ({pr}`3675`)
+- {guilabel}`rc1` Add a warning message to {func}`~scanpy.tl.rank_genes_groups` that it is not appropriate for most use-cases {smaller}`G Sturm` ({pr}`3792`)
+- Remove a few falsely advertised parameters from {func}`scanpy.pl.scatter` {smaller}`P Angerer` ({pr}`3894`)
+- Document array type support for most functions in {mod}`~scanpy.pp` and {mod}`~scanpy.tl` {smaller}`P Angerer` ({pr}`3895`)
+- Add cruft config & update authors {smaller}`zethson` ({pr}`3896`)
+
+#### Bug fixes
+
+- {guilabel}`rc1` Raise fewer redundant warnings, mainly in {mod}`scanpy.pl` and {mod}`scanpy.datasets` functions {smaller}`P Angerer` ({pr}`3724`)
+- {guilabel}`rc1` Fix `swap_axes` argument used with `standard_scale` in {func}`scanpy.pl.dotplot` {smaller}`I Gold` ({pr}`3851`)
+- {guilabel}`rc1` Allow operating on {attr}`~anndata.AnnData.obsm` arrays in {func}`scanpy.pp.normalize_total` and {func}`scanpy.pp.pca` {smaller}`P Angerer` ({pr}`3863`)
+- {guilabel}`rc1` Fix {func}`~scanpy.pl.dpt_groups_pseudotime` {smaller}`P Angerer` ({pr}`3864`)
+- Fix {func}`scanpy.get.aggregate` when a `by` column misses data {smaller}`P Angerer` ({pr}`3906`)
+- Fix compatibility with pandas 3.0 {smaller}`P Angerer` ({pr}`3929`)
+- Allow {func}`scanpy.read_10x_mtx` to read numeric gene IDs {smaller}`P Angerer` ({pr}`3932`)
+- Ensure {func}`scanpy.pp.scrublet` preserves (categorical) data types within `.obs` {smaller}`etlioglu` ({pr}`3939`)