Update template to v0.8.0

.cruft.json

@@ -13,6 +13,7 @@
       "github_repo": "pycea",
       "license": "BSD 3-Clause License",
       "ide_integration": true,
+      "issue_categorization": "",
       "_copy_without_render": [
         ".github/workflows/build.yaml",
         ".github/workflows/test.yaml",

.github/dependabot.yml

@@ -0,0 +1,12 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly
+    cooldown:
+      default-days: 7
+    groups:
+      actions-deps:
+        patterns:
+          - "*"

.github/workflows/build.yaml

@@ -18,6 +18,7 @@ jobs:
         with:
           filter: blob:none
           fetch-depth: 0
+          persist-credentials: false
       - name: Install uv
         uses: astral-sh/setup-uv@v7
       - name: Build package

.github/workflows/release.yaml

@@ -5,6 +5,8 @@ on:
     types: [published]
 
 # Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+permissions: {}
+
 jobs:
   release:
     name: Upload release to PyPI
@@ -13,15 +15,17 @@ jobs:
       name: pypi
       url: https://pypi.org/p/pycea-lineage
     permissions:
+      contents: read
       id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
       - uses: actions/checkout@v5
         with:
           filter: blob:none
           fetch-depth: 0
+          persist-credentials: false
       - name: Install uv
         uses: astral-sh/setup-uv@v7
       - name: Build package
         run: uv build
       - name: Publish package distributions to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0

.github/workflows/test.yaml

@@ -19,14 +19,15 @@ jobs:
   # Check [[tool.hatch.envs.hatch-test.matrix]] in pyproject.toml and https://hatch.pypa.io/latest/environment/ for
   # more details.
   get-environments:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-slim
     outputs:
       envs: ${{ steps.get-envs.outputs.envs }}
     steps:
       - uses: actions/checkout@v5
         with:
           filter: blob:none
           fetch-depth: 0
+          persist-credentials: false
       - name: Install uv
         uses: astral-sh/setup-uv@v7
       - name: Get test environments
@@ -58,20 +59,23 @@ jobs:
 
     name: ${{ matrix.env.label }}
     runs-on: ${{ matrix.os }}
-    
+
     continue-on-error: ${{ matrix.env.allow_failure }}
 
     steps:
       - uses: actions/checkout@v5
         with:
           filter: blob:none
           fetch-depth: 0
+          persist-credentials: false
       - name: Install uv
         uses: astral-sh/setup-uv@v7
         with:
           python-version: ${{ matrix.env.python }}
       - name: create hatch environment
         run: uvx hatch env create ${{ matrix.env.name }}
+      - name: list all all installed package versions
+        run: uvx hatch run ${{ matrix.env.name }}:uv pip list
       - name: run tests using hatch
         env:
           MPLBACKEND: agg
@@ -80,7 +84,7 @@ 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
@@ -104,6 +108,6 @@ jobs:
       - test
     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) }}

.pre-commit-config.yaml

@@ -36,3 +36,9 @@ 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
+        args: [--no-progress, --fix]

.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

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
@@ -62,6 +62,7 @@
     "sphinx_design",
     "IPython.sphinxext.ipython_console_highlighting",
     "sphinxext.opengraph",
+    "scverse_misc.sphinx_ext",
     *[p.stem for p in (HERE / "extensions").glob("*.py")],
 ]
 
@@ -87,6 +88,9 @@
 nb_execution_mode = "off"
 nb_merge_streams = True
 typehints_defaults = "braces"
+always_use_bars_union = (
+    True  # use `|` instead of `Union` in types even when building with Python ≤3.14
+)
 # Render @typing.overload'd functions as a single entry (the implementation).
 # Otherwise sphinx-autodoc-typehints emits every overload signature, which both
 # drops the short description from the API summary table and clutters each
@@ -100,16 +104,14 @@
 }
 
 intersphinx_mapping = {
-    # TODO: replace `3.13` with `3` once ReadTheDocs supports building with Python 3.14
-    "python": ("https://docs.python.org/3.13", None),
     "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
     "cycler": ("https://matplotlib.org/cycler/", None),
     "matplotlib": ("https://matplotlib.org/stable/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
     "networkx": ("https://networkx.org/documentation/stable/", None),
     "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
     "python": ("https://docs.python.org/3", None),
-    "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
+    "scanpy": ("https://scanpy.scverse.org/en/stable/", None),
     "scipy": ("https://docs.scipy.org/doc/scipy/reference/", None),
     "squidpy": ("https://squidpy.readthedocs.io/en/stable/", None),
     "treedata": ("https://treedata.readthedocs.io/en/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
 
@@ -45,11 +45,21 @@ hatch test  # defined in the table [tool.hatch.envs.hatch-test] in pyproject.tom
 hatch run docs:build  # defined in the table [tool.hatch.envs.docs]
 ```
 
-When using an IDE such as VS Code,
-you’ll have to point the editor at the paths to the virtual environments manually.
-The environment you typically want to use as your main development environment is the `hatch-test`
-environment with the latest Python version.
+### VS Code
 
+If you are using VS code, install the [hatch-code][] extension.
+Additionally, make sure that the `vscode-python-environments` extension is installed (should be by default)
+and `"python.useEnvironmentsExtension": true` is activated in your `settings.json`.
+
+Next, open the "Python Environment Managers" sidebar.
+You can do so by opening the command palette (Ctrl+Shift+P) and searching for `Python: Focus on Environment Managers View`.
+It will show a collapsible list where you can expand "Hatch"
+and activate an environment by clicking on the checkmark next to it.
+As the main development environment, we recommend to use `hatch-test` with the latest supported Python version.
+
+### Other IDEs
+
+For other IDEs, you’ll have to point the editor at the paths to the virtual environments manually.
 To get a list of all environments for your projects, run
 
 ```bash
@@ -87,10 +97,8 @@ Then, obtain the path to the environment using
 hatch env find hatch-test.py3.14-stable
 ```
 
-In case you are using VScode, now open the command palette (Ctrl+Shift+P) and search for `Python: Select Interpreter`.
-Choose `Enter Interpreter Path` and paste the path to the virtual environment from above.
+and manually point it to the python binary.
 
-In this future, this may become easier through a hatch vscode extension.
 
 ::::
 
@@ -103,7 +111,7 @@ This can have undesired side-effects,
 such as requiring to install a lower version of a library your project depends on,
 only because an outdated sphinx plugin pins an older version.
 
-To initalize a virtual environment in the `.venv` directory of your project, simply run
+To initialize a virtual environment in the `.venv` directory of your project, simply run
 
 ```bash
 uv sync --all-extras
@@ -131,24 +139,26 @@ The `.venv` directory is typically automatically discovered by IDEs such as VS C
 :::::
 
 [hatch environments]: https://hatch.pypa.io/latest/tutorials/environment/basic-usage/
+[hatch-code]: https://marketplace.visualstudio.com/items?itemName=PyPA.hatch
 [uv]: https://docs.astral.sh/uv/
 
 ## 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.
 
-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
 
@@ -157,12 +167,13 @@ 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/
@@ -175,12 +186,8 @@ This package uses [pytest][] for automated testing.
 Please write {doc}`scanpy:dev/testing` for every function added to the package.
 
 Most IDEs integrate with pytest and provide a GUI to run tests.
-Just point yours to one of the environments returned by
-
-```bash
-hatch env create hatch-test  # create test environments for all supported versions
-hatch env find hatch-test  # list all possible test environment paths
-```
+If you set up your virtual environments as described in [installing dev dependencies](#installing-dev-dependencies),
+test cases should be automatically discovered by your IDE.
 
 Alternatively, you can run all tests from the command line by executing
 
@@ -268,11 +275,11 @@ 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