Update instance repo from cookiecutter template

docs/conf.py

@@ -55,6 +55,7 @@
     "sphinx.ext.napoleon",
     "sphinxcontrib.bibtex",
     "sphinx_autodoc_typehints",
+    "sphinx_tabs.tabs",
     "sphinx.ext.mathjax",
     "IPython.sphinxext.ipython_console_highlighting",
     "sphinxext.opengraph",

docs/contributing.md

@@ -13,15 +13,33 @@ If not, please refer to the [scanpy developer guide][].
 
 In addition to the packages needed to _use_ this package,
 you need additional python packages to [run tests](#writing-tests) and [build the documentation](#docs-building).
-It's easy to install them using `pip`:
+
+:::::{tabs}
+::::{group-tab} Hatch
+The easiest way is to get familiar with [hatch environments][], with which these tasks are simply:
+
+```bash
+hatch test  # defined in the table [tool.hatch.envs.hatch-test] in pyproject.toml
+hatch run docs:build  # defined in the table [tool.hatch.envs.docs]
+```
+
+::::
+
+::::{group-tab} Pip
+If you prefer managing environments manually, you can use `pip`:
 
 ```bash
 cd cookiecutter-scverse-instance
-python -m venv .venv
+python3 -m venv .venv
 source .venv/bin/activate
 pip install -e ".[dev,test,doc]"
 ```
 
+::::
+:::::
+
+[hatch environments]: https://hatch.pypa.io/latest/tutorials/environment/basic-usage/
+
 ## Code-style
 
 This package uses [pre-commit][] to enforce consistent code-styles.
@@ -62,16 +80,40 @@ Consider enabling this option for [ruff][ruff-editors] and [prettier][prettier-e
 
 ## Writing tests
 
-This package uses the [pytest][] for automated testing.
+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
+```
+
 Alternatively, you can run all tests from the command line by executing
 
+:::::{tabs}
+::::{group-tab} Hatch
+
+```bash
+hatch test  # test with the highest supported Python version
+# or
+hatch test --all  # test with all supported Python versions
+```
+
+::::
+
+::::{group-tab} Pip
+
 ```bash
+source .venv/bin/activate
 pytest
 ```
 
+::::
+:::::
+
 in the root of the repository.
 
 [pytest]: https://docs.pytest.org/
@@ -120,7 +162,7 @@ This project uses [sphinx][] with the following features:
 -   [sphinx-autodoc-typehints][], to automatically reference annotated input and output types
 -   Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
 
-See the scanpy’s {doc}`scanpy:dev/documentation` for more information on how to write your own.
+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
@@ -151,8 +193,24 @@ please check out [this feature request][issue-render-notebooks] in the `cookiecu
 
 #### Building the docs locally
 
+:::::{tabs}
+::::{group-tab} Hatch
+
 ```bash
+hatch docs:build
+hatch docs:open
+```
+
+::::
+
+::::{group-tab} Pip
+
+```bash
+source .venv/bin/activate
 cd docs
 make html
-open _build/html/index.html
+(xdg-)open _build/html/index.html
 ```
+
+::::
+:::::

pyproject.toml

@@ -42,6 +42,7 @@ optional-dependencies.doc = [
   "sphinx-autodoc-typehints",
   "sphinx-book-theme>=1",
   "sphinx-copybutton",
+  "sphinx-tabs",
   "sphinxcontrib-bibtex>=1",
   "sphinxext-opengraph",
 ]
@@ -54,6 +55,19 @@ urls.Documentation = "https://cookiecutter-scverse-instance.readthedocs.io/"
 urls.Homepage = "https://github.com/scverse/cookiecutter-scverse-instance"
 urls.Source = "https://github.com/scverse/cookiecutter-scverse-instance"
 
+[tool.hatch.envs.default]
+installer = "uv"
+features = [ "dev" ]
+
+[tool.hatch.envs.docs]
+extra-features = [ "doc" ]
+scripts.build = "sphinx-build -M html docs docs/_build {args}"
+scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
+scripts.clean = "git clean -fdX -- {args:docs}"
+
+[tool.hatch.envs.hatch-test]
+features = [ "test" ]
+
 [tool.ruff]
 line-length = 120
 src = [ "src" ]