Fix links (#309)

{{cookiecutter.project_name}}/docs/conf.py

@@ -93,6 +93,7 @@
 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),
     "numpy": ("https://numpy.org/doc/stable/", None),
 }
 

{{cookiecutter.project_name}}/docs/contributing.md

@@ -1,19 +1,24 @@
 # Contributing guide
 
 Scanpy provides extensive [developer documentation][scanpy developer guide], most of which applies to this project, too.
-This document will not reproduce the entire content from there. Instead, it aims at summarizing the most important
-information to get you started on contributing.
+This document will not reproduce the entire content from there.
+Instead, it aims at summarizing the most important information to get you started on contributing.
 
-We assume that you are already familiar with git and with making pull requests on GitHub. If not, please refer
-to the [scanpy developer guide][].
+We assume that you are already familiar with git and with making pull requests on GitHub.
+If not, please refer to the [scanpy developer guide][].
+
+[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html
 
 ## Installing dev dependencies
 
-In addition to the packages needed to _use_ this package, you need additional python packages to _run tests_ and _build
-the documentation_. It's easy to install them using `pip`:
+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`:
 
 ```bash
 cd {{ cookiecutter.project_name }}
+python -m venv .venv
+source .venv/bin/activate
 pip install -e ".[dev,test,doc]"
 ```
 
@@ -31,10 +36,11 @@ To enable pre-commit locally, simply run
 pre-commit install
 ```
 
-in the root of the repository. Pre-commit will automatically download all dependencies when it is run for the first time.
+in the root of the repository.
+Pre-commit 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.
+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 pre-commit.ci added a commit on a branch you still have been working on locally, simply use
 
@@ -45,88 +51,105 @@ 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.
 
-Finally, most editors have an _autoformat on save_ feature. Consider enabling this option for [ruff][ruff-editors]
-and [prettier][prettier-editors].
+Finally, most editors have an _autoformat on save_ feature.
+Consider enabling this option for [ruff][ruff-editors] and [prettier][prettier-editors].
 
+[pre-commit]: https://pre-commit.com/
+[pre-commit.ci]: https://pre-commit.ci/
 [ruff-editors]: https://docs.astral.sh/ruff/integrations/
+
 [prettier-editors]: https://prettier.io/docs/en/editors.html
 
-## Writing tests
+(writing-tests)=
 
-```{note}
-Remember to first install the package with `pip install -e '.[dev,test]'`
-```
+## Writing tests
 
-This package uses the [pytest][] for automated testing. Please [write tests][scanpy-test-docs] for every function added
-to the package.
+This package uses the [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. Alternatively, you can run all tests from the
-command line by executing
+Most IDEs integrate with pytest and provide a GUI to run tests.
+Alternatively, you can run all tests from the command line by executing
 
 ```bash
 pytest
 ```
 
 in the root of the repository.
 
+[pytest]: https://docs.pytest.org/
+
 ### Continuous integration
 
 Continuous integration will automatically run the tests on all pull requests and test
 against the minimum and maximum supported Python version.
 
-Additionally, there's a CI job that tests against pre-releases of all dependencies
-(if there are any). The purpose of this check is to detect incompatibilities
-of new package versions early on and gives you time to fix the issue or reach
-out to the developers of the dependency before the package is released to a wider audience.
-
-[scanpy-test-docs]: https://scanpy.readthedocs.io/en/latest/dev/testing.html#writing-tests
+Additionally, there's a CI job that tests against pre-releases of all dependencies (if there are any).
+The purpose of this check is to detect incompatibilities of new package versions early on and
+gives you time to fix the issue or reach out to the developers of the dependency before the package is released to a wider audience.
 
 ## Publishing a release
 
 ### Updating the version number
 
-Before making a release, you need to update the version number in the `pyproject.toml` file. Please adhere to [Semantic Versioning][semver], in brief
+Before making a release, you need to update the version number in the `pyproject.toml` file.
+Please adhere to [Semantic Versioning][semver], in brief
 
 > Given a version number MAJOR.MINOR.PATCH, increment the:
 >
-> 1.  MAJOR version when you make incompatible API changes,
-> 2.  MINOR version when you add functionality in a backwards compatible manner, and
-> 3.  PATCH version when you make backwards compatible bug fixes.
+> 1. MAJOR version when you make incompatible API changes,
+> 2. MINOR version when you add functionality in a backwards compatible manner, and
+> 3. PATCH version when you make backwards compatible bug fixes.
 >
 > Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.
 
 Once you are done, commit and push your changes and navigate to the "Releases" page of this project on GitHub.
-Specify `vX.X.X` as a tag name and create a release. For more information, see [managing GitHub releases][]. This will automatically create a git tag and trigger a Github workflow that creates a release on PyPI.
+Specify `vX.X.X` as a tag name and create a release.
+For more information, see [managing GitHub releases][].
+This will automatically create a git tag and trigger a Github workflow that creates a release on [PyPI][].
+
+[semver]: https://semver.org/
+[managing GitHub releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository
+[pypi]: https://pypi.org/
 
 ## Writing documentation
 
-Please write documentation for new or changed features and use-cases. This project uses [sphinx][] with the following features:
+Please write documentation for new or changed features and use-cases.
+This project uses [sphinx][] with the following features:
 
--   the [myst][] extension allows to write documentation in markdown/Markedly Structured Text
+-   The [myst][] extension allows to write documentation in markdown/Markedly Structured Text
 -   [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
 -   Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
--   [Sphinx autodoc typehints][], to automatically reference annotated input and output types
+-   [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 developer docs](https://scanpy.readthedocs.io/en/latest/dev/documentation.html) for more information
-on how to write documentation.
+See the 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-autodoc-typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
 
 ### Tutorials with myst-nb and jupyter notebooks
 
 The documentation is set-up to render jupyter notebooks stored in the `docs/notebooks` directory using [myst-nb][].
 Currently, only notebooks in `.ipynb` format are supported that will be included with both their input and output cells.
 It is your responsibility to update and re-run the notebook whenever necessary.
 
-If you are interested in automatically running notebooks as part of the continuous integration, please check
-out [this feature request](https://github.com/scverse/cookiecutter-scverse/issues/40) in the `cookiecutter-scverse`
-repository.
+If you are interested in automatically running notebooks as part of the continuous integration,
+please check out [this feature request][issue-render-notebooks] in the `cookiecutter-scverse` repository.
+
+[issue-render-notebooks]: https://github.com/scverse/cookiecutter-scverse/issues/40
 
 #### Hints
 
--   If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. Only
-    if you do so can sphinx automatically create a link to the external documentation.
--   If building the documentation fails because of a missing link that is outside your control, you can add an entry to
-    the `nitpick_ignore` list in `docs/conf.py`
+-   If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`.
+    Only if you do so can sphinx automatically create a link to the external documentation.
+-   If building the documentation fails because of a missing link that is outside your control,
+    you can add an entry to the `nitpick_ignore` list in `docs/conf.py`
+
+(docs-building)=
 
 #### Building the docs locally
 
@@ -135,29 +158,3 @@ cd docs
 make html
 open _build/html/index.html
 ```
-
-<!-- Links -->
-
-[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html
-[cookiecutter-scverse-instance]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html
-[github quickstart guide]: https://docs.github.com/en/get-started/quickstart/create-a-repo?tool=webui
-[codecov]: https://about.codecov.io/sign-up/
-[codecov docs]: https://docs.codecov.com/docs
-[codecov bot]: https://docs.codecov.com/docs/team-bot
-[codecov app]: https://github.com/apps/codecov
-[pre-commit.ci]: https://pre-commit.ci/
-[readthedocs.org]: https://readthedocs.org/
-[myst-nb]: https://myst-nb.readthedocs.io/en/latest/
-[jupytext]: https://jupytext.readthedocs.io/en/latest/
-[pre-commit]: https://pre-commit.com/
-[anndata]: https://github.com/scverse/anndata
-[mudata]: https://github.com/scverse/mudata
-[pytest]: https://docs.pytest.org/
-[semver]: https://semver.org/
-[sphinx]: https://www.sphinx-doc.org/en/master/
-[myst]: https://myst-parser.readthedocs.io/en/latest/intro.html
-[numpydoc-napoleon]: https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html
-[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
-[sphinx autodoc typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
-[pypi]: https://pypi.org/
-[managing GitHub releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository