From 46d77ade20c68afb5213490de85f33b81b00dbf9 Mon Sep 17 00:00:00 2001
From: "Philipp A." <flying-sheep@web.de>
Date: Thu, 6 Aug 2026 14:29:29 +0200
Subject: [PATCH 1/3] Backport PR #4276 on branch 1.12.x (ci: run prek in GH
 actions)

---
 .github/dependabot.yml          | 24 +++++++-
 .github/workflows/benchmark.yml | 10 ++--
 .github/workflows/check-pr.yml  | 18 +++---
 .github/workflows/ci.yml        | 64 ++++++++++++++--------
 .github/workflows/publish.yml   | 12 ++--
 .pre-commit-config.yaml         | 97 ++++++++++++++++++---------------
 .vscode/settings.json           |  5 +-
 hatch.toml                      | 10 ++++
 8 files changed, 151 insertions(+), 89 deletions(-)

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
index abd2e5876f..18fa22a4ca 100644
--- a/.github/dependabot.yml
+++ b/.github/dependabot.yml
@@ -1,10 +1,30 @@
 version: 2
 updates:
-  - package-ecosystem: github-actions
+  - package-ecosystem: pre-commit
     directory: /
     schedule:
       interval: weekly
-  - package-ecosystem: pip
+    labels:
+      - no milestone
+    commit-message:
+      prefix: test
+    cooldown:
+      default-days: 7
+    groups:
+      pre-commit:
+        patterns:
+          - "*"
+  - package-ecosystem: github-actions
     directory: /
     schedule:
       interval: weekly
+    labels:
+      - no milestone
+    commit-message:
+      prefix: ci
+    cooldown:
+      default-days: 7
+    groups:
+      actions-deps:
+        patterns:
+          - "*"
diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml
index 51a2ff5d30..ef28f89140 100644
--- a/.github/workflows/benchmark.yml
+++ b/.github/workflows/benchmark.yml
@@ -9,6 +9,8 @@ on:
 env:
   FORCE_COLOR: "1"
 
+permissions: {}
+
 jobs:
   benchmark:
     runs-on: ${{ matrix.os }}
@@ -25,21 +27,21 @@ jobs:
       ASV_DIR: "./benchmarks"
 
     steps:
-      - uses: actions/checkout@v6
-        with: { fetch-depth: 0 } # no blob:none so ASV can compare commits
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with: { fetch-depth: 0, persist-credentials: false } # no blob:none so ASV can compare commits
 
       - name: Fetch main branch for `asv run`’s hash
         run: git fetch origin main:main
         if: ${{ github.ref_name != 'main' }}
 
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
         with:
           python-version: ${{ matrix.python }}
           cache: 'pip'
 
       - name: Cache datasets
-        uses: actions/cache@v5
+        uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
         with:
           path: |
             ~/.cache
diff --git a/.github/workflows/check-pr.yml b/.github/workflows/check-pr.yml
index 4643cd3678..8498f8f7d5 100644
--- a/.github/workflows/check-pr.yml
+++ b/.github/workflows/check-pr.yml
@@ -20,19 +20,23 @@ on:
       # code change (e.g. this workflow)
       - synchronize
 
+permissions: {}
+
 jobs:
   # This job verifies that the milestone is present or not necessary
   # and determines if “check-relnotes” needs to be run.
   check-milestone:
     name: Check title, milestone, and labels
     runs-on: ubuntu-latest
+    permissions:
+      pull-requests: read # for amannn/action-semantic-pull-request
     steps:
       - name: Check if milestone or “no milestone” label is present
-        uses: flying-sheep/check@v1
+        uses: flying-sheep/check@e10bb11109d1434ab16729bd988d78d65d47e163 # v1.0.5
         with:
           success: ${{ github.event.pull_request.user.login == 'pre-commit-ci[bot]' || github.event.pull_request.milestone != null || contains(github.event.pull_request.labels.*.name, 'no milestone') }}
       - name: Check if the “Release notes” checkbox is checked and filled
-        uses: kaisugi/action-regex-match@v1.0.2
+        uses: kaisugi/action-regex-match@d67cd689755dc47c5362609e0a6e2e1c93fa721b # v1.0.2
         id: checked-relnotes
         with:
           text: ${{ github.event.pull_request.body }}
@@ -40,7 +44,7 @@ jobs:
           flags: m
       - name: Check PR title
         id: check-title
-        uses: amannn/action-semantic-pull-request@v6
+        uses: amannn/action-semantic-pull-request@48f256284bd46cdaab1048c3721360e808335d50 # v6.1.1
         env: # Needs repo options: “Squash and merge” with commit message set to “PR title”
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     outputs:
@@ -53,15 +57,15 @@ jobs:
     needs: check-milestone
     if: github.event.pull_request.user.login != 'pre-commit-ci[bot]' && needs.check-milestone.outputs.no-relnotes-reason == '' && !contains(fromJSON('["style","refactor","test","build","docs","ci"]'), needs.check-milestone.outputs.type)
     steps:
-      - uses: actions/checkout@v6
-        with: { filter: 'blob:none', fetch-depth: 0 }
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with: { filter: 'blob:none', fetch-depth: 0, persist-credentials: false }
       - name: Find out if a relevant release fragment is added
-        uses: dorny/paths-filter@v3
+        uses: dorny/paths-filter@7b450fff21473bca461d4b92ce414b9d0420d706 # v4.0.2
         id: changes
         with:
           filters: | # this is intentionally a string
             relnotes: 'docs/release-notes/${{ github.event.pull_request.number }}.${{ (contains(github.event.pull_request.title, '!') && 'breaking') || needs.check-milestone.outputs.type }}.md'
       - name: Check if a relevant release fragment is added
-        uses: flying-sheep/check@v1
+        uses: flying-sheep/check@e10bb11109d1434ab16729bd988d78d65d47e163 # v1.0.5
         with:
           success: ${{ steps.changes.outputs.relnotes }}
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2524cca620..3c3c249a88 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -15,16 +15,25 @@ env:
   # so because leidenalg 0.10.0 has them, we pre-compile things: https://github.com/vtraag/leidenalg/issues/173
   UV_COMPILE_BYTECODE: "1"
 
+permissions:
+  contents: read
+
 jobs:
   get-environments:
     runs-on: ubuntu-latest
     outputs:
       envs: ${{ steps.get-envs.outputs.envs }}
     steps:
-      - uses: actions/checkout@v6
-        with: { filter: 'blob:none', fetch-depth: 0 }
-      - uses: astral-sh/setup-uv@v7
-        with: { enable-cache: false }
+      - &clone
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          fetch-depth: 0
+          filter: blob:none
+          persist-credentials: false
+      - &setup-uv
+        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
+        with:
+          enable-cache: true
       - id: get-envs
         run: |
           ENVS_JSON=$(NO_COLOR=1 uvx hatch env show --json | jq -c 'to_entries
@@ -46,16 +55,13 @@ jobs:
         env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
     permissions:
       id-token: write  # for codecov OIDC
+    env:
+      UV_PYTHON: ${{ matrix.env.python }}
     steps:
-      - uses: actions/checkout@v6
-        with: { filter: 'blob:none', fetch-depth: 0 }
-
-      - uses: astral-sh/setup-uv@v7
-        with:
-          python-version: ${{ matrix.env.python }}
-
+      - *clone
+      - *setup-uv
       - name: Cache downloaded data
-        uses: actions/cache@v5
+        uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
         with:
           path: .pytest_cache/d/scanpy-data
           key: pytest
@@ -83,7 +89,7 @@ jobs:
 
       - name: Upload coverage data
         if: ${{ !cancelled() && matrix.env.test-type == 'coverage' }}
-        uses: codecov/codecov-action@v6
+        uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7.0.0
         with:
           flags: ${{ matrix.env.name }}
           files: test-data/coverage.xml
@@ -92,7 +98,7 @@ jobs:
 
       - name: Upload test results
         if: ${{ !cancelled() }}
-        uses: codecov/codecov-action@v6
+        uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7.0.0
         with:
           report_type: test_results
           flags: ${{ matrix.env.name }}
@@ -102,7 +108,7 @@ jobs:
 
       - name: Publish debug artifacts
         if: ${{ !cancelled() }}
-        uses: actions/upload-artifact@v5
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
         with:
           name: debug-data-${{ matrix.env.name }}
           path: .pytest_cache/d/debug
@@ -110,25 +116,35 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
-        with: { filter: 'blob:none', fetch-depth: 0 }
-      - uses: actions/setup-python@v6
-        with:
-          python-version: "3.x"
-      - uses: astral-sh/setup-uv@v7
-        with:
-          enable-cache: true
+      - *clone
+      - *setup-uv
       - run: uvx --from build pyproject-build --sdist --wheel .
       - run: uvx twine check dist/*
 
+  lint:
+    name: Pre-commit checks
+    runs-on: ubuntu-latest
+    permissions: {}
+    steps:
+      - *clone
+      - *setup-uv
+      - run: uv tool install hatch
+      - name: Run pre-commit hooks
+        run: uvx prek run --all-files --show-diff-on-failure --color=always
+        env:
+          SKIP: no-commit-to-branch
+      - uses: autofix-ci/action@c5b2d67aa2274e7b5a18224e8171550871fc7e4a # v1.3.4
+        if: ${{ !cancelled() }}
+
   check:
     if: always()
     needs:
       - get-environments
       - test
       - build
+      - lint
     runs-on: ubuntu-latest
     steps:
-      - uses: re-actors/alls-green@release/v1
+      - uses: re-actors/alls-green@05ac9388f0aebcb5727afa17fcccfecd6f8ec5fe # v1.2.2
         with:
           jobs: ${{ toJSON(needs) }}
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 54d9359219..2b6a46b4a6 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -14,12 +14,14 @@ jobs:
     permissions:
       id-token: write # to authenticate as Trusted Publisher to pypi.org
     steps:
-      - uses: actions/checkout@v6
-        with: { filter: 'blob:none', fetch-depth: 0 }
-      - uses: actions/setup-python@v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with: { filter: 'blob:none', fetch-depth: 0, persist-credentials: false }
+      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
         with:
           python-version: "3.x"
-      - uses: astral-sh/setup-uv@v7
+      - uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
+        with:
+          enable-cache: false
       - run: uvx --from build pyproject-build --sdist --wheel .
       - run: uvx twine check dist/*
-      - uses: pypa/gh-action-pypi-publish@release/v1
+      - uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index bd3b7f026e..8ffe492d9d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,44 +1,55 @@
-ci:
-  autoupdate_commit_msg: "ci: pre-commit autoupdate"
-
 repos:
--   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.0
-    hooks:
-    -   id: ruff-check
-        args: ["--fix"]
-    -   id: ruff-format
-    # The following can be removed once PLR0917 is out of preview
-    -   name: ruff preview rules
-        id: ruff-check
-        args: ["--preview", "--select=PLR0917"]
--   repo: https://github.com/flying-sheep/bibfmt
-    rev: v4.3.0
-    hooks:
-    -   id: bibfmt
-        args:
-        - --sort-by-bibkey
-        - --drop=abstract
--   repo: https://github.com/biomejs/pre-commit
-    rev: v2.3.14
-    hooks:
-    -   id: biome-format
--   repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.15.1
-    hooks:
-    -   id: pyproject-fmt
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v6.0.0
-    hooks:
-    -   id: trailing-whitespace
-        exclude: tests/_data
-    -   id: end-of-file-fixer
-        exclude: tests/_data
-    -   id: check-added-large-files
-    -   id: check-case-conflict
-    -   id: check-toml
-    -   id: check-yaml
-    -   id: check-merge-conflict
-    -   id: detect-private-key
-    -   id: no-commit-to-branch
-        args: ["--branch=main"]
+- repo: https://github.com/flying-sheep/bibfmt
+  rev: v4.3.0
+  hooks:
+  - id: bibfmt
+    args:
+    - --sort-by-bibkey
+    - --drop=abstract
+    groups: [format]
+- repo: https://github.com/biomejs/pre-commit
+  rev: v2.5.6
+  hooks:
+  - id: biome-format
+    groups: [format]
+    exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
+- repo: https://github.com/tox-dev/pyproject-fmt
+  rev: v2.27.0
+  hooks:
+  - id: pyproject-fmt
+    groups: [format]
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.16.1
+  hooks:
+  - id: ruff-check
+    args: [--fix, --exit-non-zero-on-fix]
+  - id: ruff-format
+    groups: [format]
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v6.0.0
+  hooks:
+  - id: detect-private-key
+  - id: check-ast
+  - id: check-added-large-files
+  - id: check-toml
+  - id: check-yaml
+  - id: end-of-file-fixer
+    groups: [format]
+    exclude: tests/_data
+  - id: mixed-line-ending
+    groups: [format]
+    args: [--fix=lf]
+  - id: trailing-whitespace
+    groups: [format]
+    exclude: tests/_data
+  - id: check-case-conflict
+  # Check that there are no merge conflicts (could be generated by template sync)
+  - id: check-merge-conflict
+    args: [--assume-in-merge]
+  - id: no-commit-to-branch
+    args: [--branch=main]
+- repo: https://github.com/zizmorcore/zizmor-pre-commit
+  rev: v1.29.0
+  hooks:
+  - id: zizmor
+    args: [--no-progress, --fix]
diff --git a/.vscode/settings.json b/.vscode/settings.json
index fc4da964e2..b0648f1990 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -1,5 +1,5 @@
 {
-    "[python][toml][json][jsonc]": {
+    "[python][json][jsonc]": {
         "editor.formatOnSave": true,
         "editor.codeActionsOnSave": {
             "source.organizeImports": "explicit",
@@ -9,9 +9,6 @@
     "[python]": {
         "editor.defaultFormatter": "charliermarsh.ruff",
     },
-    "[toml]": {
-        "editor.defaultFormatter": "tamasfe.even-better-toml",
-    },
     "[json][jsonc]": {
         "editor.defaultFormatter": "biomejs.biome",
     },
diff --git a/hatch.toml b/hatch.toml
index 27a00a1677..30abcd0eed 100644
--- a/hatch.toml
+++ b/hatch.toml
@@ -14,6 +14,16 @@ scripts.create = "towncrier create {args}"
 scripts.build = "python3 ci/scripts/towncrier_automation.py {args}"
 scripts.clean = "git restore --source=HEAD --staged --worktree -- docs/release-notes"
 
+[envs.hatch-check-fmt]
+dependencies = [ "prek" ]
+scripts.format-check = "echo 'try `hatch check fmt --fix`'; false"
+scripts.format-fix = "prek run -a --group=format"
+
+[envs.hatch-check-code]
+dependencies = [ "prek" ]
+lint-check = "echo 'try `hatch check code --fix`'; false"
+scripts.lint-fix = "prek run -a --no-group=format"
+
 [envs.hatch-test]
 python = "3.14"
 default-args = [  ]

From 797fe9a0036fac9bd36d0ef3dc32da3ae84a6fab Mon Sep 17 00:00:00 2001
From: "autofix-ci[bot]" <114827586+autofix-ci[bot]@users.noreply.github.com>
Date: Thu, 6 Aug 2026 13:00:05 +0000
Subject: [PATCH 2/3] [autofix.ci] apply automated fixes

---
 docs/extensions/myst_ignore_mime_types.py    |  2 +-
 pyproject.toml                               | 32 ++++++++++----------
 src/scanpy/_utils/__init__.py                |  3 +-
 src/scanpy/experimental/pp/_normalization.py |  2 +-
 src/scanpy/plotting/_baseplot_class.py       |  2 +-
 src/scanpy/plotting/_dotplot.py              | 10 +++---
 src/scanpy/plotting/_matrixplot.py           |  6 ++--
 src/scanpy/plotting/_stacked_violin.py       | 10 +++---
 src/scanpy/plotting/_tools/scatterplots.py   |  8 ++---
 src/scanpy/preprocessing/_pca/__init__.py    |  2 +-
 src/scanpy/preprocessing/_simple.py          |  2 +-
 src/scanpy/readwrite.py                      |  6 ++--
 12 files changed, 42 insertions(+), 43 deletions(-)

diff --git a/docs/extensions/myst_ignore_mime_types.py b/docs/extensions/myst_ignore_mime_types.py
index 762b9e31c4..d90c47db07 100644
--- a/docs/extensions/myst_ignore_mime_types.py
+++ b/docs/extensions/myst_ignore_mime_types.py
@@ -31,7 +31,7 @@ class _Ignore(MimeRenderPlugin):
     @staticmethod
     def handle_mime(
         renderer: NbElementRenderer, data: MimeData, inline: bool
-    ) -> None | list[nodes.Element]:
+    ) -> list[nodes.Element] | None:
         if data.mime_type in ignore:
             return []  # returning a list instead of `None` means “we handled it”
         return None
diff --git a/pyproject.toml b/pyproject.toml
index cfd52e1908..5201c2f766 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -148,9 +148,9 @@ test-min = [
 ]
 
 [tool.hatch]
-build.targets.wheel.packages = [ "src/testing", "src/scanpy" ]
 version.source = "vcs"
 version.raw-options.version_scheme = "release-branch-semver"
+build.targets.wheel.packages = [ "src/scanpy", "src/testing" ]
 
 [tool.ruff]
 src = [ "src" ]
@@ -241,7 +241,6 @@ expand_tables = [
 ]
 
 [tool.pytest]
-strict = true
 addopts = [
     "--import-mode=importlib",
     "--strict-markers",
@@ -249,14 +248,6 @@ addopts = [
     "-ptesting.scanpy._pytest",
     "--pyargs",
 ]
-testpaths = [ "./tests", "./ci", "scanpy" ]
-norecursedirs = [ "tests/_images" ]
-junit_family = "xunit1"
-markers = [
-    "internet: tests which rely on internet resources (enable with `--internet-tests`)",
-    "gpu: tests that use a GPU (unused, required by anndata.tests.helpers)",
-    "array_api: tests that use array_api (unused, required by anndata.tests.helpers)",
-]
 filterwarnings = [
     "error",
     # Umap warns when tensorflow isn’t installed.
@@ -284,6 +275,15 @@ filterwarnings = [
     # everybody uses this zarr 3 feature, including us, XArray, lots of data out there …
     "ignore:Consolidated metadata is currently not part:UserWarning",
 ]
+junit_family = "xunit1"
+markers = [
+    "internet: tests which rely on internet resources (enable with `--internet-tests`)",
+    "gpu: tests that use a GPU (unused, required by anndata.tests.helpers)",
+    "array_api: tests that use array_api (unused, required by anndata.tests.helpers)",
+]
+norecursedirs = [ "tests/_images" ]
+strict = true
+testpaths = [ "./tests", "./ci", "scanpy" ]
 
 [tool.coverage]
 run.concurrency = [ "multiprocessing" ]
@@ -304,19 +304,19 @@ xml.output = "test-data/coverage.xml"
 [tool.towncrier]
 name = "scanpy"
 package = "scanpy"
+package_dir = "src"
 directory = "docs/release-notes"
 filename = "docs/release-notes/{version}.md"
-single_file = false
-package_dir = "src"
-issue_format = "{{pr}}`{issue}`"
 title_format = "(v{version})=\n### {version} {{small}}`{project_date}`"
+issue_format = "{{pr}}`{issue}`"
+single_file = false
+fragment.breaking.name = "Breaking changes"  # add `!` to commit type (e.g. “feature!:”)
+fragment.chore.name = "Miscellaneous changes"
+fragment.docs.name = "Documentation"
 # Valid fragments should be a subset of conventional commit types (except for `breaking`):
 # https://github.com/commitizen/conventional-commit-types/blob/master/index.json
 # style, refactor, test, build, ci: should not go into changelog
 fragment.feat.name = "Features"
 fragment.fix.name = "Bug fixes"
-fragment.docs.name = "Documentation"
 fragment.perf.name = "Performance"
-fragment.chore.name = "Miscellaneous changes"
 fragment.revert.name = "Revert"
-fragment.breaking.name = "Breaking changes"  # add `!` to commit type (e.g. “feature!:”)
diff --git a/src/scanpy/_utils/__init__.py b/src/scanpy/_utils/__init__.py
index 9a0380b1f3..ab0398c9ac 100644
--- a/src/scanpy/_utils/__init__.py
+++ b/src/scanpy/_utils/__init__.py
@@ -78,7 +78,6 @@
     "get_literal_vals",
     "indent",
     "is_backed_type",
-    "is_backed_type",
     "raise_not_implemented_error_if_backed_type",
     "renamed_arg",
     "sanitize_anndata",
@@ -268,7 +267,7 @@ def check_array_function_arguments(**kwargs):
 
 def check_use_raw(
     adata: AnnData,
-    use_raw: None | bool,  # noqa: FBT001
+    use_raw: bool | None,  # noqa: FBT001
     *,
     layer: str | None = None,
 ) -> bool:
diff --git a/src/scanpy/experimental/pp/_normalization.py b/src/scanpy/experimental/pp/_normalization.py
index cb34b9902b..eac0f28d7b 100644
--- a/src/scanpy/experimental/pp/_normalization.py
+++ b/src/scanpy/experimental/pp/_normalization.py
@@ -168,7 +168,7 @@ def normalize_pearson_residuals_pca(
     n_comps: int | None = 50,
     random_state: float = 0,
     kwargs_pca: Mapping[str, Any] = MappingProxyType({}),
-    mask_var: np.ndarray | str | None | Empty = _empty,
+    mask_var: np.ndarray | str | Empty | None = _empty,
     use_highly_variable: bool | None = None,
     check_values: bool = True,
     inplace: bool = True,
diff --git a/src/scanpy/plotting/_baseplot_class.py b/src/scanpy/plotting/_baseplot_class.py
index 20ecb30809..f8236d8a04 100644
--- a/src/scanpy/plotting/_baseplot_class.py
+++ b/src/scanpy/plotting/_baseplot_class.py
@@ -410,7 +410,7 @@ def add_totals(
         return self
 
     @old_positionals("cmap")
-    def style(self, *, cmap: Colormap | str | None | Empty = _empty) -> Self:
+    def style(self, *, cmap: Colormap | str | Empty | None = _empty) -> Self:
         r"""Set visual style parameters.
 
         Parameters
diff --git a/src/scanpy/plotting/_dotplot.py b/src/scanpy/plotting/_dotplot.py
index b903e781f3..6ea356f4ae 100644
--- a/src/scanpy/plotting/_dotplot.py
+++ b/src/scanpy/plotting/_dotplot.py
@@ -350,14 +350,14 @@ def _prepare_dot_data(
     def style(  # noqa: PLR0913
         self,
         *,
-        cmap: Colormap | str | None | Empty = _empty,
+        cmap: Colormap | str | Empty | None = _empty,
         color_on: Literal["dot", "square"] | Empty = _empty,
-        dot_max: float | None | Empty = _empty,
-        dot_min: float | None | Empty = _empty,
+        dot_max: float | Empty | None = _empty,
+        dot_min: float | Empty | None = _empty,
         smallest_dot: float | Empty = _empty,
         largest_dot: float | Empty = _empty,
-        dot_edge_color: ColorLike | None | Empty = _empty,
-        dot_edge_lw: float | None | Empty = _empty,
+        dot_edge_color: ColorLike | Empty | None = _empty,
+        dot_edge_lw: float | Empty | None = _empty,
         size_exponent: float | Empty = _empty,
         grid: bool | Empty = _empty,
         x_padding: float | Empty = _empty,
diff --git a/src/scanpy/plotting/_matrixplot.py b/src/scanpy/plotting/_matrixplot.py
index e803bdc1eb..9146124787 100644
--- a/src/scanpy/plotting/_matrixplot.py
+++ b/src/scanpy/plotting/_matrixplot.py
@@ -198,9 +198,9 @@ def __init__(  # noqa: PLR0913
 
     def style(
         self,
-        cmap: Colormap | str | None | Empty = _empty,
-        edge_color: ColorLike | None | Empty = _empty,
-        edge_lw: float | None | Empty = _empty,
+        cmap: Colormap | str | Empty | None = _empty,
+        edge_color: ColorLike | Empty | None = _empty,
+        edge_lw: float | Empty | None = _empty,
     ) -> Self:
         r"""Modify plot visual parameters.
 
diff --git a/src/scanpy/plotting/_stacked_violin.py b/src/scanpy/plotting/_stacked_violin.py
index 19d6aa7a97..9899afa0d9 100644
--- a/src/scanpy/plotting/_stacked_violin.py
+++ b/src/scanpy/plotting/_stacked_violin.py
@@ -273,15 +273,15 @@ def __init__(  # noqa: PLR0913
     def style(  # noqa: PLR0913
         self,
         *,
-        cmap: Colormap | str | None | Empty = _empty,
+        cmap: Colormap | str | Empty | None = _empty,
         stripplot: bool | Empty = _empty,
         jitter: float | bool | Empty = _empty,
         jitter_size: float | Empty = _empty,
-        linewidth: float | None | Empty = _empty,
-        row_palette: str | None | Empty = _empty,
+        linewidth: float | Empty | None = _empty,
+        row_palette: str | Empty | None = _empty,
         density_norm: DensityNorm | Empty = _empty,
         yticklabels: bool | Empty = _empty,
-        ylim: tuple[float, float] | None | Empty = _empty,
+        ylim: tuple[float, float] | Empty | None = _empty,
         x_padding: float | Empty = _empty,
         y_padding: float | Empty = _empty,
         # deprecated
@@ -700,7 +700,7 @@ def stacked_violin(  # noqa: PLR0913
     density_norm: DensityNorm | Empty = _empty,
     yticklabels: bool = StackedViolin.DEFAULT_PLOT_YTICKLABELS,
     # deprecated
-    order: Sequence[str] | None | Empty = _empty,
+    order: Sequence[str] | Empty | None = _empty,
     scale: DensityNorm | Empty = _empty,
     save: bool | str | None = None,
     **kwds,
diff --git a/src/scanpy/plotting/_tools/scatterplots.py b/src/scanpy/plotting/_tools/scatterplots.py
index 46cb969f5e..0679fd69c3 100644
--- a/src/scanpy/plotting/_tools/scatterplots.py
+++ b/src/scanpy/plotting/_tools/scatterplots.py
@@ -978,8 +978,8 @@ def spatial(  # noqa: PLR0913
     *,
     basis: str = "spatial",
     img: np.ndarray | None = None,
-    img_key: str | None | Empty = _empty,
-    library_id: str | None | Empty = _empty,
+    img_key: str | Empty | None = _empty,
+    library_id: str | Empty | None = _empty,
     crop_coord: tuple[int, int, int, int] | None = None,
     alpha_img: float = 1.0,
     bw: bool | None = False,
@@ -1366,7 +1366,7 @@ def _check_scale_factor(
 
 
 def _check_spatial_data(
-    uns: Mapping, library_id: str | None | Empty
+    uns: Mapping, library_id: str | Empty | None
 ) -> tuple[str | None, Mapping | None]:
     """Given a mapping, try and extract a library id/ mapping with spatial data.
 
@@ -1391,7 +1391,7 @@ def _check_spatial_data(
 def _check_img(
     spatial_data: Mapping | None,
     img: np.ndarray | None,
-    img_key: None | str | Empty,
+    img_key: str | Empty | None,
     *,
     bw: bool = False,
 ) -> tuple[np.ndarray | None, str | None]:
diff --git a/src/scanpy/preprocessing/_pca/__init__.py b/src/scanpy/preprocessing/_pca/__init__.py
index f12229d842..67e2f448e2 100644
--- a/src/scanpy/preprocessing/_pca/__init__.py
+++ b/src/scanpy/preprocessing/_pca/__init__.py
@@ -66,7 +66,7 @@ def pca(  # noqa: PLR0912, PLR0913, PLR0915
     chunk_size: int | None = None,
     random_state: _LegacyRandom = 0,
     return_info: bool = False,
-    mask_var: NDArray[np.bool] | str | None | Empty = _empty,
+    mask_var: NDArray[np.bool] | str | Empty | None = _empty,
     use_highly_variable: bool | None = None,
     dtype: DTypeLike = "float32",
     key_added: str | None = None,
diff --git a/src/scanpy/preprocessing/_simple.py b/src/scanpy/preprocessing/_simple.py
index 379562847e..30b5e69113 100644
--- a/src/scanpy/preprocessing/_simple.py
+++ b/src/scanpy/preprocessing/_simple.py
@@ -896,7 +896,7 @@ def sample(  # noqa: PLR0912
     replace: bool = False,
     axis: Literal["obs", 0, "var", 1] = "obs",
     p: str | NDArray[np.bool] | NDArray[np.floating] | None = None,
-) -> AnnData | None | tuple[np.ndarray | CSBase | DaskArray, NDArray[np.int64]]:
+) -> AnnData | tuple[np.ndarray | CSBase | DaskArray, NDArray[np.int64]] | None:
     r"""Sample observations or variables with or without replacement.
 
     .. array-support:: pp.sample
diff --git a/src/scanpy/readwrite.py b/src/scanpy/readwrite.py
index 4f1d6b2b0e..c935cc6e2f 100644
--- a/src/scanpy/readwrite.py
+++ b/src/scanpy/readwrite.py
@@ -99,7 +99,7 @@ def read(
     first_column_names: bool = False,
     backup_url: str | None = None,
     cache: bool = False,
-    cache_compression: Literal["gzip", "lzf"] | None | Empty = _empty,
+    cache_compression: Literal["gzip", "lzf"] | Empty | None = _empty,
     **kwargs,
 ) -> AnnData:
     """Read file and return :class:`~anndata.AnnData` object.
@@ -538,7 +538,7 @@ def read_10x_mtx(
     var_names: Literal["gene_symbols", "gene_ids"] = "gene_symbols",
     make_unique: bool = True,
     cache: bool = False,
-    cache_compression: Literal["gzip", "lzf"] | None | Empty = _empty,
+    cache_compression: Literal["gzip", "lzf"] | Empty | None = _empty,
     gex_only: bool = True,
     prefix: str | None = None,
     compressed: bool = True,
@@ -607,7 +607,7 @@ def _read_10x_mtx(
     var_names: Literal["gene_symbols", "gene_ids"] = "gene_symbols",
     make_unique: bool = True,
     cache: bool = False,
-    cache_compression: Literal["gzip", "lzf"] | None | Empty = _empty,
+    cache_compression: Literal["gzip", "lzf"] | Empty | None = _empty,
     prefix: str = "",
     is_legacy: bool,
     compressed: bool = True,

From 2e3ffdc95db52775461a43bbb7293026dd072f23 Mon Sep 17 00:00:00 2001
From: Phil Schaf <flying-sheep@web.de>
Date: Thu, 6 Aug 2026 15:33:38 +0200
Subject: [PATCH 3/3] fix broken ref

---
 tests/plotting/legacy/test_plotting_utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/plotting/legacy/test_plotting_utils.py b/tests/plotting/legacy/test_plotting_utils.py
index 8ea20bbda2..5ac5a58d9d 100644
--- a/tests/plotting/legacy/test_plotting_utils.py
+++ b/tests/plotting/legacy/test_plotting_utils.py
@@ -9,8 +9,8 @@
 from matplotlib import colormaps
 
 from scanpy.plotting._anndata import _check_if_annotations
+from scanpy.plotting._tools.scatterplots import _get_palette
 from scanpy.plotting._utils import validate_palette
-from scanpy.plotting.legacy._tools.scatterplots import _get_palette
 
 if TYPE_CHECKING:
     from typing import Any, Literal