Update instance repo (PR 578 -- chore(deps): bump the pre-commit group across 1 directory with 4 updates)

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "/home/runner/work/cookiecutter-scverse/cookiecutter-scverse",
-  "commit": "be7aa668a1f275bf9555e048fb2a3e2a02704778",
+  "commit": "a9da0ae1e14597665ffa6408828e30ad630c0fdf",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -37,7 +37,7 @@
         "trim_blocks": true
       },
       "_template": "/home/runner/work/cookiecutter-scverse/cookiecutter-scverse",
-      "_commit": "be7aa668a1f275bf9555e048fb2a3e2a02704778"
+      "_commit": "a9da0ae1e14597665ffa6408828e30ad630c0fdf"
     }
   },
   "directory": null

.github/workflows/autofix.yaml

@@ -26,4 +26,4 @@ jobs:
       - name: Run pre-commit hooks
         run: uvx prek run --all-files --show-diff-on-failure --color=always
       - uses: autofix-ci/action@c5b2d67aa2274e7b5a18224e8171550871fc7e4a # v1.3.4
-        if: '!cancelled()'
+        if: "!cancelled()"

.github/workflows/test.yaml

@@ -52,8 +52,8 @@ jobs:
   test:
     needs: get-environments
     permissions:
-       id-token: write  # for codecov OIDC
-       contents: read
+      id-token: write # for codecov OIDC
+      contents: read
 
     strategy:
       fail-fast: false
@@ -63,7 +63,7 @@ jobs:
 
     name: ${{ matrix.env.label }}
     runs-on: ${{ matrix.os }}
-    continue-on-error: ${{ contains(matrix.env.name, 'pre') }}  # make "all-green" pass even if pre-release job fails
+    continue-on-error: ${{ contains(matrix.env.name, 'pre') }} # make "all-green" pass even if pre-release job fails
     env:
       UV_PYTHON: ${{ matrix.env.python }}
 
@@ -102,6 +102,6 @@ jobs:
       - test
     runs-on: ubuntu-latest
     steps:
-        - uses: re-actors/alls-green@05ac9388f0aebcb5727afa17fcccfecd6f8ec5fe # v1.2.2
-          with:
-            jobs: ${{ toJSON(needs) }}
+      - uses: re-actors/alls-green@05ac9388f0aebcb5727afa17fcccfecd6f8ec5fe # v1.2.2
+        with:
+          jobs: ${{ toJSON(needs) }}

.pre-commit-config.yaml

@@ -7,18 +7,18 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.5.11
+    rev: v2.6.3
     hooks:
       - id: biome-format
         exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
         groups: [format]
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.29.2
+    rev: v2.30.3
     hooks:
       - id: pyproject-fmt
         groups: [format]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.16.5
+    rev: v0.17.2
     hooks:
       - id: ruff-check
         args: [--fix, --exit-non-zero-on-fix]
@@ -43,7 +43,7 @@ repos:
       - id: end-of-file-fixer
         groups: [format]
       - id: mixed-line-ending
-        exclude: ^\.cruft\.json$  # inconsistent file endings on windows - file never to be modified manually.
+        exclude: ^\.cruft\.json$ # inconsistent file endings on windows - file never to be modified manually.
         args: [--fix=lf]
         groups: [format]
       - id: trailing-whitespace
@@ -54,7 +54,7 @@ repos:
         args: [--assume-in-merge]
 
   - repo: https://github.com/zizmorcore/zizmor-pre-commit
-    rev: v1.30.0
+    rev: v1.31.1
     hooks:
       - id: zizmor
         args: [--no-progress, --fix]

biome.jsonc

@@ -1,5 +1,5 @@
 {
-    "$schema": "https://biomejs.dev/schemas/2.2.0/schema.json",
+    "$schema": "https://biomejs.dev/schemas/2.6.3/schema.json",
     "vcs": { "enabled": true, "clientKind": "git", "useIgnoreFile": true },
     "formatter": { "useEditorconfig": true },
     "overrides": [

docs/contributing.md

@@ -11,7 +11,7 @@ the [scientific Python tutorials][], or the [scanpy developer guide][].
 [scientific Python tutorials]: https://learn.scientific-python.org/development/tutorials/
 [scanpy developer guide]: https://scanpy.scverse.org/page/dev/
 
-:::{tip} The *hatch* project manager
+:::{tip} The _hatch_ project manager
 
 We highly recommend to familiarize yourself with [`hatch`][hatch].
 Hatch is a Python project manager that

docs/template_usage.md

@@ -172,7 +172,7 @@ To set this up, login to [PyPI][], and proceed depending on whether you already
 - If yes, navigate to the project. In the left sidebar, choose "Publishing", then proceed to add the repository details.
 - If not, go to your [PyPI publishing settings][] and fill out the “Add a new pending publisher” form.
 
-Enter everything *exactly* as it is displayed on GitHub (i.e. use the correct casing for your repository name).
+Enter everything _exactly_ as it is displayed on GitHub (i.e. use the correct casing for your repository name).
 The "Workflow name" needs to bet set to `release.yaml`.
 Set "Environment name" to “pypi” to match `environment: pypi` in `.github/workflows/release.yaml`.
 For more details, please refer to the official [PyPI guide for setting up trusted publishing][trusted publisher].
@@ -182,7 +182,6 @@ the project will be published only once you release your package for the first t
 
 [github-releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/about-releases
 [pypi-trusted-publishing-guide]: https://docs.pypi.org/trusted-publishers/adding-a-publisher/
-
 [PyPI]: https://pypi.org/
 [PyPI publishing settings]: https://pypi.org/manage/account/publishing/
 [trusted publisher]: https://docs.pypi.org/trusted-publishers/
@@ -218,38 +217,38 @@ The following pre-commit hooks are for code style and format:
   code formatter for non-Python files (e.g. JSON).
 - [ruff][] formatting (`ruff-format`) which implements all rules of the also widely used [Black formatter](https://github.com/psf/black)
 - [ruff][] based checks:
-    - [isort](https://beta.ruff.rs/docs/rules/#isort-i) (rule category: `I`):
-      sort module imports into sections and types.
-    - [pydocstyle](https://beta.ruff.rs/docs/rules/#pydocstyle-d) (rule category: `D`):
-      pydocstyle extension of flake8.
-    - [flake8-tidy-imports](https://beta.ruff.rs/docs/rules/#flake8-tidy-imports-tid) (rule category: `TID`):
-      tidy module imports.
-    - [flake8-comprehensions](https://beta.ruff.rs/docs/rules/#flake8-comprehensions-c4) (rule category: `C4`):
-      write better list/set/dict comprehensions.
-    - [pyupgrade](https://beta.ruff.rs/docs/rules/#pyupgrade-up) (rule category: `UP`):
-      upgrade syntax for newer versions of the language.
+  - [isort](https://beta.ruff.rs/docs/rules/#isort-i) (rule category: `I`):
+    sort module imports into sections and types.
+  - [pydocstyle](https://beta.ruff.rs/docs/rules/#pydocstyle-d) (rule category: `D`):
+    pydocstyle extension of flake8.
+  - [flake8-tidy-imports](https://beta.ruff.rs/docs/rules/#flake8-tidy-imports-tid) (rule category: `TID`):
+    tidy module imports.
+  - [flake8-comprehensions](https://beta.ruff.rs/docs/rules/#flake8-comprehensions-c4) (rule category: `C4`):
+    write better list/set/dict comprehensions.
+  - [pyupgrade](https://beta.ruff.rs/docs/rules/#pyupgrade-up) (rule category: `UP`):
+    upgrade syntax for newer versions of the language.
 - [pyproject-fmt][] formats the `pyproject.toml` file in a consistent way.
 
 The following pre-commit hooks are for errors and inconsistencies:
 
 - [pre-commit-hooks](https://github.com/pre-commit/pre-commit-hooks): generic pre-commit hooks for text files.
-    - **detect-private-key**: checks for the existence of private keys.
-    - **check-ast**: check whether files parse as valid python.
-    - **end-of-file-fixer**: check files end in a newline and only a newline.
-    - **mixed-line-ending**: checks mixed line ending.
-    - **trailing-whitespace**: trims trailing whitespace.
-    - **check-case-conflict**: check files that would conflict with case-insensitive file systems.
+  - **detect-private-key**: checks for the existence of private keys.
+  - **check-ast**: check whether files parse as valid python.
+  - **end-of-file-fixer**: check files end in a newline and only a newline.
+  - **mixed-line-ending**: checks mixed line ending.
+  - **trailing-whitespace**: trims trailing whitespace.
+  - **check-case-conflict**: check files that would conflict with case-insensitive file systems.
 - [ruff][] based checks:
-    - [pyflakes](https://beta.ruff.rs/docs/rules/#pyflakes-f) (rule category: `F`):
-      various checks for errors.
-    - [pycodestyle](https://beta.ruff.rs/docs/rules/#pycodestyle-e-w) (rule category: `E`, `W`):
-      various checks for errors.
-    - [flake8-bugbear](https://beta.ruff.rs/docs/rules/#flake8-bugbear-b) (rule category: `B`):
-      find possible bugs and design issues in program.
-    - [flake8-blind-except](https://beta.ruff.rs/docs/rules/#flake8-blind-except-ble) (rule category: `BLE`):
-      checks for blind, catch-all `except` statements.
-    - [Ruff-specific rules](https://beta.ruff.rs/docs/rules/#ruff-specific-rules-ruf) (rule category: `RUF`):
-        - `RUF100`: remove unnecessary `# noqa` comments ()
+  - [pyflakes](https://beta.ruff.rs/docs/rules/#pyflakes-f) (rule category: `F`):
+    various checks for errors.
+  - [pycodestyle](https://beta.ruff.rs/docs/rules/#pycodestyle-e-w) (rule category: `E`, `W`):
+    various checks for errors.
+  - [flake8-bugbear](https://beta.ruff.rs/docs/rules/#flake8-bugbear-b) (rule category: `B`):
+    find possible bugs and design issues in program.
+  - [flake8-blind-except](https://beta.ruff.rs/docs/rules/#flake8-blind-except-ble) (rule category: `BLE`):
+    checks for blind, catch-all `except` statements.
+  - [Ruff-specific rules](https://beta.ruff.rs/docs/rules/#ruff-specific-rules-ruf) (rule category: `RUF`):
+    - `RUF100`: remove unnecessary `# noqa` comments ()
 - [mypy][]:
   static type checker that verifies the type annotations of the package under `src/` and the `tests/`.
 
@@ -456,29 +455,29 @@ Here's one way how to do it:
 2. Clone your repository a second time to `${REPO}_cookiecutterized`
 3. Initialize an empty repository from this cookiecutter template:
 
-    ```bash
-    mkdir template && cd template
-    uvx --with prek cruft create https://github.com/scverse/cookiecutter-scverse
-    ```
+   ```bash
+   mkdir template && cd template
+   uvx --with prek cruft create https://github.com/scverse/cookiecutter-scverse
+   ```
 
 4. remove everything from the existing repo
 
-    ```bash
-    cd ${REPO}_cookiecutterized
-    git switch -c cookiecutterize
-    git rm -r "*"
-    git add -A
-    git commit -m "clean repo"
-    ```
+   ```bash
+   cd ${REPO}_cookiecutterized
+   git switch -c cookiecutterize
+   git rm -r "*"
+   git add -A
+   git commit -m "clean repo"
+   ```
 
 5. move template over from generated folder
 
-    ```bash
-    # move everything, including hidden folders, excluding `.git`.
-    rsync -av --exclude='.git' ../template/$REPO/ ./
-    git add -A
-    git commit -m "init from template"
-    ```
+   ```bash
+   # move everything, including hidden folders, excluding `.git`.
+   rsync -av --exclude='.git' ../template/$REPO/ ./
+   git add -A
+   git commit -m "init from template"
+   ```
 
 6. Migrate your project: Move over files from `$REPO` to `${REPO}_cookiecutterized`.
    Omit files that are not needed anymore and manually merge files where required.

pyproject.toml

@@ -20,6 +20,7 @@ classifiers = [
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
   "Programming Language :: Python :: 3.14",
+  "Programming Language :: Python :: 3.15",
   "Typing :: Typed",
 ]
 dependencies = [