# Contributing guide

Scanpy provides extensive [developer documentation][scanpy developer guide], most of which applies to this repo, 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][].

## Cloning the repository

ehrapy consists of this main repository and a git submodule [ehrapy-tutorials](https://github.com/theislab/ehrapy-tutorials) which hosts tutorial notebooks.

Clone both using:

```bash

git clone --recurse-submodules https://github.com/theislab/ehrapy

```

More details on the tutorials submodule are described in the [Writing documentation](#writing-documentation) section.

## 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 ehrapy

pip install -e ".[dev,test,docs]"

```

## Code-style

This project 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 [black][black-editors]

and [prettier][prettier-editors].

[black-editors]: https://black.readthedocs.io/en/stable/integrations/editors.html

[prettier-editors]: https://prettier.io/docs/en/editors.html

## Writing tests

```{note}

Remember to first install the package with `pip install -e ".[dev,test,docs]"`

```

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 will automatically run the tests on all pull requests.

[scanpy-test-docs]: https://scanpy.readthedocs.io/en/latest/dev/testing.html#writing-tests

## Publishing a release

### Updating the version number

Before making a release, you need to update the version number. 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.

>

> Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.

Once you are done, run

```

git push --tags

```

to publish the created tag on GitHub.

### Building and publishing the package on PyPI

Python packages are not distributed as source code, but as _distributions_. The most common distribution format is the so-called _wheel_. To build a _wheel_, run

```bash

python -m build

```

This command creates a _source archive_ and a _wheel_, which are required for publishing your package to [PyPI][]. These files are created directly in the root of the repository.

Before uploading them to [PyPI][] you can check that your _distribution_ is valid by running:

```bash

twine check dist/*

```

and finally publishing it with:

```bash

twine upload dist/*

```

Provide your username and password when requested and then go check out your package on [PyPI][]!

For more information, follow the [Python packaging tutorial][].

It is possible to automate this with GitHub actions, see also [this feature request][pypi-feature-request]

in the cookiecutter-scverse template.

[python packaging tutorial]: https://packaging.python.org/en/latest/tutorials/packaging-projects/#generating-distribution-archives

[pypi-feature-request]: https://github.com/scverse/cookiecutter-scverse/issues/88

## 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

- Google-style docstrings

- 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/tutorials` directory using [myst-nb][].

Currently, only notebooks in `.ipynb` format are supported that will be included with both their input and output cells.

These notebooks come from [ehrapy-tutorials](https://github.com/theislab/ehrapy-tutorials) which is a git submodule of ehrapy.

#### Working with the git submodule

Whenever the tutorials are updated in the submodule, two pull requests need to be made.

Submit a pull request to [ehrapy-tutorials](https://github.com/theislab/ehrapy-tutorials) and ensure that the CI passes.

Further, submit a pull request on the ehrapy repository where the submodule also contains the commit and ensure that

the documentation as build by ReadTheDocs properly shows the updated notebooks.

Both pull requests need to be merged to ensure that no repository gets out of sync.

### 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/