# 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.

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][].

## 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`:

```bash
cd scirpy
pip install -e ".[dev,test,doc]"
```

## 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.

To enable pre-commit locally, simply run

```bash
pre-commit install
```

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.

If pre-commit.ci added a commit on a branch you still have been working on locally, simply use

```bash
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].

[ruff-editors]: https://docs.astral.sh/ruff/integrations/
[prettier-editors]: https://prettier.io/docs/en/editors.html

## Writing tests

```{note}
Remember to first install the package with `pip install -e '.[dev,test]'`
```

This package uses the [pytest][] for automated testing. Please [write tests][scanpy-test-docs] 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

```bash
pytest
```

in the root of the repository.

### 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

## Making a release

1. **Review and update the changelog.** Make sure the changelog is up-to-date and change the top line from `[Unreleased]` to the version number you intend to publish.
2. **Create a release on GitHub.** 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][].

**That's it!** The release will be built automatically and published on PyPI using GitHub actions using the [trusted publishing workflow](https://docs.pypi.org/trusted-publishers/).
Scirpy uses [hatch-vcs](https://github.com/ofek/hatch-vcs) to automaticlly retrieve the version number from the git tag. Therefore, it is not necessary to bump versions in the code.

## Writing documentation

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
- [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
- 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.

### 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 reponsibility 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.

#### 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`

#### Building the docs locally

```bash
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