Update instance repo (PR 498 -- chore: zizmor for pre-commit)

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "/home/runner/work/cookiecutter-scverse/cookiecutter-scverse",
-  "commit": "6cca9704e02edc716fa4665258aa2eb4518be78e",
+  "commit": "cb7f635331b7fbf10150a978f8e18b0e082aa8cd",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -13,6 +13,7 @@
       "github_repo": "cookiecutter-scverse-instance",
       "license": "BSD 3-Clause License",
       "ide_integration": true,
+      "issue_categorization": "labels",
       "_copy_without_render": [
         ".github/workflows/build.yaml",
         ".github/workflows/test.yaml",
@@ -36,7 +37,7 @@
         "trim_blocks": true
       },
       "_template": "/home/runner/work/cookiecutter-scverse/cookiecutter-scverse",
-      "_commit": "6cca9704e02edc716fa4665258aa2eb4518be78e"
+      "_commit": "cb7f635331b7fbf10150a978f8e18b0e082aa8cd"
     }
   },
   "directory": null

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -1,6 +1,6 @@
 name: Bug report
 description: Report something that is broken or incorrect
-type: Bug
+labels: bug
 body:
   - type: markdown
     attributes:

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,6 +1,6 @@
 name: Feature request
 description: Propose a new feature for cookiecutter-scverse-instance
-type: Enhancement
+labels: enhancement
 body:
   - type: textarea
     id: description

.github/workflows/test.yaml

@@ -48,6 +48,7 @@ jobs:
     needs: get-environments
     permissions:
        id-token: write  # for codecov OIDC
+       contents: read
 
     strategy:
       fail-fast: false
@@ -80,12 +81,12 @@ jobs:
         run: uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto
       - name: generate coverage report
         run: |
-          # See https://coverage.readthedocs.io/en/latest/config.html#run-patch
+          # See https://coverage.readthedocs.io/page/config.html#run-patch
           test -f .coverage || uvx hatch run ${{ matrix.env.name }}:cov-combine
           uvx hatch run ${{ matrix.env.name }}:cov-report   # report visibly
           uvx hatch run ${{ matrix.env.name }}:coverage xml # create report for upload
       - name: Upload coverage
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v6
         with:
           fail_ci_if_error: true
           use_oidc: true

.pre-commit-config.yaml

@@ -7,16 +7,16 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.4.13
+    rev: v2.5.2
     hooks:
       - id: biome-format
         exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.21.1
+    rev: v2.25.1
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.12
+    rev: v0.15.20
     hooks:
       - id: ruff-check
         types_or: [python, pyi, jupyter]
@@ -36,3 +36,8 @@ repos:
       # Check that there are no merge conflicts (could be generated by template sync)
       - id: check-merge-conflict
         args: [--assume-in-merge]
+
+  - repo: https://github.com/zizmorcore/zizmor-pre-commit
+    rev: v1.24.1
+    hooks:
+      - id: zizmor

.readthedocs.yaml

@@ -1,4 +1,4 @@
-# https://docs.readthedocs.io/en/stable/config-file/v2.html
+# https://docs.readthedocs.io/page/config-file/v2.html
 version: 2
 build:
   os: ubuntu-24.04

CHANGELOG.md

@@ -5,8 +5,8 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog][],
 and this project adheres to [Semantic Versioning][].
 
-[keep a changelog]: https://keepachangelog.com/en/1.0.0/
-[semantic versioning]: https://semver.org/spec/v2.0.0.html
+[keep a changelog]: https://keepachangelog.com/
+[semantic versioning]: https://semver.org/
 
 ## [Unreleased]
 

README.md

@@ -4,7 +4,7 @@
 [![Documentation][badge-docs]][documentation]
 
 [badge-tests]: https://img.shields.io/github/actions/workflow/status/scverse/cookiecutter-scverse-instance/test.yaml?branch=main
-[badge-docs]: https://img.shields.io/readthedocs/cookiecutter-scverse-instance
+[badge-docs]: https://app.readthedocs.org/projects/cookiecutter-scverse-instance/badge/
 
 An example repo generated from the `cookiecutter-scverse` template.
 
@@ -52,6 +52,6 @@ If you found a bug, please use the [issue tracker][].
 [issue tracker]: https://github.com/scverse/cookiecutter-scverse-instance/issues
 [tests]: https://github.com/scverse/cookiecutter-scverse-instance/actions/workflows/test.yaml
 [documentation]: https://cookiecutter-scverse-instance.readthedocs.io
-[changelog]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/changelog.html
-[api documentation]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/api.html
+[changelog]: https://cookiecutter-scverse-instance.readthedocs.io/page/changelog.html
+[api documentation]: https://cookiecutter-scverse-instance.readthedocs.io/page/api.html
 [pypi]: https://pypi.org/project/cookiecutter-scverse-instance

docs/conf.py

@@ -2,7 +2,7 @@
 
 # This file only contains a selection of the most common options. For a full
 # list see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
+# https://www.sphinx-doc.org/page/usage/configuration.html
 
 # -- Path setup --------------------------------------------------------------
 import shutil
@@ -97,8 +97,8 @@
 
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3", None),
-    "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
-    "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
+    "anndata": ("https://anndata.scverse.org/en/stable/", None),
+    "scanpy": ("https://scanpy.scverse.org/en/stable/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
 }
 

docs/contributing.md

@@ -9,7 +9,7 @@ the [scientific Python tutorials][], or the [scanpy developer guide][].
 
 [pyopensci tutorials]: https://www.pyopensci.org/learn.html
 [scientific Python tutorials]: https://learn.scientific-python.org/development/tutorials/
-[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html
+[scanpy developer guide]: https://scanpy.scverse.org/page/dev/
 
 :::{tip} The *hatch* project manager
 
@@ -138,21 +138,22 @@ The `.venv` directory is typically automatically discovered by IDEs such as VS C
 
 ## Code-style
 
-This package uses [pre-commit][] to enforce consistent code-styles.
-On every commit, pre-commit checks will either automatically fix issues with the code, or raise an error message.
+This package uses [pre-commit][]-style hooks to enforce consistent code-styles.
+We recommend running them with [prek][], a fast, drop-in replacement for `pre-commit` that reads the same `.pre-commit-config.yaml`.
+On every commit, the checks will either automatically fix issues with the code, or raise an error message.
 See [pre-commit checks](template_usage.md#pre-commit-checks) for a full list of checks enabled for this repository.
 
-To enable pre-commit locally, simply run
+To enable the checks locally, install [prek][] (e.g. with `uv tool install prek`) and run
 
 ```bash
-pre-commit install
+prek install
 ```
 
 in the root of the repository.
-Pre-commit will automatically download all dependencies when it is run for the first time.
+prek will automatically download all dependencies when it is run for the first time.
 
 Alternatively, you can rely on the [pre-commit.ci][] service enabled on GitHub.
-If you didn’t run `pre-commit` before pushing changes to GitHub it will automatically commit fixes to your pull request, or show an error message.
+If you didn’t run the checks before pushing changes to GitHub it will automatically commit fixes to your pull request, or show an error message.
 
 If pre-commit.ci added a commit on a branch you still have been working on locally, simply use
 
@@ -161,12 +162,13 @@ git pull --rebase
 ```
 
 to integrate the changes into yours.
-While the [pre-commit.ci][] is useful, we strongly encourage installing and running pre-commit locally first to understand its usage.
+While the [pre-commit.ci][] is useful, we strongly encourage installing and running the checks locally first to understand their usage.
 
 Finally, most editors have an _autoformat on save_ feature.
 Consider enabling this option for [ruff][ruff-editors] and [biome][biome-editors].
 
 [pre-commit]: https://pre-commit.com/
+[prek]: https://prek.j178.dev/
 [pre-commit.ci]: https://pre-commit.ci/
 [ruff-editors]: https://docs.astral.sh/ruff/integrations/
 [biome-editors]: https://biomejs.dev/guides/integrate-in-editor/
@@ -275,11 +277,11 @@ This project uses [sphinx][] with the following features:
 
 See scanpy’s {doc}`scanpy:dev/documentation` for more information on how to write your own.
 
-[sphinx]: https://www.sphinx-doc.org/en/master/
-[myst]: https://myst-parser.readthedocs.io/en/latest/intro.html
-[myst-nb]: https://myst-nb.readthedocs.io/en/latest/
-[numpydoc-napoleon]: https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html
-[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
+[sphinx]: https://www.sphinx-doc.org/
+[myst]: https://myst-parser.readthedocs.io/page/intro.html
+[myst-nb]: https://myst-nb.readthedocs.io/
+[numpydoc-napoleon]: https://www.sphinx-doc.org/page/usage/extensions/napoleon.html
+[numpydoc]: https://numpydoc.readthedocs.io/page/format.html
 [sphinx-autodoc-typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
 
 ### Tutorials with myst-nb and jupyter notebooks

docs/notebooks/example.ipynb

@@ -45,7 +45,10 @@
     "\n",
     "Again, check the raw markdown of this cell to see how each of these links are specified.\n",
     "\n",
-    "You can read more about this in the [intersphinx page](https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html) and the [myst page](https://myst-parser.readthedocs.io/en/v0.15.1/syntax/syntax.html#roles-an-in-line-extension-point)."
+    "You can read more about this in the [intersphinx page] and the [myst page].\n",
+    "\n",
+    "[intersphinx page]: https://www.sphinx-doc.org/page/usage/extensions/intersphinx.html\n",
+    "[myst page]: https://myst-parser.readthedocs.io/page/syntax/roles-and-directives.html#roles-an-in-line-extension-point"
    ]
   },
   {

docs/template_usage.md

@@ -48,7 +48,7 @@ While the repository at this point can be directly used, there are few remaining
 
 Modern Python package management uses a `pyproject.toml` that was first introduced in [PEP 518](https://peps.python.org/pep-0518/).
 This file contains build system requirements and information, which are used by pip to build the package, and tool configurations.
-For more details please have a look at [pip's description of the pyproject.toml file](https://pip.pypa.io/en/stable/reference/build-system/pyproject-toml/).
+For more details please have a look at [pip's description of the pyproject.toml file](https://pip.pypa.io/page/reference/build-system/).
 It also serves as a single point of truth to define test environments and how docs are built by leveraging
 the [hatch][] project manager, but more about that in the [contributing guide](contributing.md).
 
@@ -113,10 +113,10 @@ On the RTD dashboard choose "Import a Project" and follow the instructions to ad
   For more information, please refer to the [official RTD documentation][rtd-prs].
 
 If your project is private, there are ways to enable docs rendering on [readthedocs.org][] but it is more cumbersome and requires a different RTD subscription.
-See a guide [here](https://docs.readthedocs.io/en/stable/guides/importing-private-repositories.html).
+See a guide [here](https://docs.readthedocs.io/page/guides/importing-private-repositories.html).
 
 [readthedocs.org]: https://readthedocs.org/
-[rtd-prs]: https://docs.readthedocs.io/en/stable/pull-requests.html
+[rtd-prs]: https://docs.readthedocs.io/page/pull-requests.html
 
 (github-actions)=
 
@@ -179,6 +179,9 @@ the project will be published only once you release your package for the first t
 This template uses a number of pre-commit checks.
 In this section we'll detail what is used, where they're defined, and how to modify these checks.
 
+To run the checks locally, we recommend [prek][], a fast, drop-in replacement for `pre-commit` that reads the same `.pre-commit-config.yaml`.
+Install it (e.g. with `uv tool install prek`) and run `prek install` once to set up the git hook, then `prek run --all-files` to check the whole repository.
+
 
 ### Pre-commit CI
 
@@ -299,8 +302,9 @@ add it to Ruff’s [`external = [...]`][ruff-external] setting to prevent `RUF10
 
 [biome]: https://biomejs.dev/
 [pre-commit]: https://pre-commit.com/
+[prek]: https://prek.j178.dev/
 [pre-commit.ci]: https://pre-commit.ci/
-[pyproject-fmt]: https://pyproject-fmt.readthedocs.io/en/latest/index.html
+[pyproject-fmt]: https://pyproject-fmt.readthedocs.io/
 [ruff]: https://docs.astral.sh/ruff/
 [ruff-config]: https://docs.astral.sh/ruff/configuration/
 [ruff-error-suppression]: https://docs.astral.sh/ruff/linter/#error-suppression
@@ -322,7 +326,7 @@ there may also be good reasons to choose a different approach, e.g. using an obj
 
 [anndata]: https://github.com/scverse/anndata
 [mudata]: https://github.com/scverse/mudata
-[scanpy-api]: https://scanpy.readthedocs.io/en/stable/usage-principles.html
+[scanpy-api]: https://scanpy.scverse.org/page/usage-principles.html
 [spatialdata]: https://github.com/scverse/spatialdata
 
 (vcs-based-versioning)=
@@ -393,7 +397,7 @@ The following hints may be useful to work with the template sync:
 
 If you prefer to check for and apply the pre-release template updates manually, or if you are working on a private repository not tracked by the bot, you can use cruft. Simply:
 
-- Make sure cruft and pre-commit are installed.
+- Make sure cruft and prek are installed.
 - Make sure your git directory is clean (no unstaged/uncommitted files).
 - Run `cruft update` in the root of your repository.
 
@@ -417,7 +421,7 @@ Here's one way how to do it:
 
     ```bash
     mkdir template && cd template
-    uvx --with pre-commit cruft create https://github.com/scverse/cookiecutter-scverse
+    uvx --with prek cruft create https://github.com/scverse/cookiecutter-scverse
     ```
 
 4. remove everything from the existing repo

pyproject.toml

@@ -34,7 +34,7 @@ urls.Source = "https://github.com/scverse/cookiecutter-scverse-instance"
 
 [dependency-groups]
 dev = [
-  "pre-commit",
+  "prek",
   "twine>=4.0.2",
 ]
 test = [
@@ -60,11 +60,10 @@ doc = [
 [tool.hatch]
 envs.default.installer = "uv"
 envs.default.dependency-groups = [ "dev" ]
-envs.docs.dependency-groups = [ "doc" ]
 envs.docs.scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
-envs.docs.scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
 envs.docs.scripts.clean = "git clean -fdX -- {args:docs}"
-envs.hatch-test.dependency-groups = [ "dev", "test" ]
+envs.docs.scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
+envs.docs.dependency-groups = [ "doc" ]
 envs.hatch-test.matrix = [
   # Test the lowest and highest supported Python versions with normal deps
   { deps = [ "stable" ], python = [ "3.11", "3.14" ] },
@@ -74,8 +73,9 @@ envs.hatch-test.matrix = [
 # If the matrix variable `deps` is set to "pre",
 # set the environment variable `UV_PRERELEASE` to "allow".
 envs.hatch-test.overrides.matrix.deps.env-vars = [
-  { key = "UV_PRERELEASE", value = "allow", if = [ "pre" ] },
+  { value = "allow", key = "UV_PRERELEASE", if = [ "pre" ] },
 ]
+envs.hatch-test.dependency-groups = [ "dev", "test" ]
 
 [tool.ruff]
 line-length = 120
@@ -116,11 +116,11 @@ lint.per-file-ignores."tests/*" = [ "D" ]
 lint.pydocstyle.convention = "numpy"
 
 [tool.pytest]
-strict = true
-testpaths = [ "tests" ]
 addopts = [
   "--import-mode=importlib", # allow using test files with same name
 ]
+strict = true
+testpaths = [ "tests" ]
 
 [tool.coverage]
 run.omit = [