# 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][]. [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](#writing-tests) and [build the documentation](#docs-building). :::::{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 scMagnify 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. 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]. [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 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/ ### 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. ## 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 > 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, 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][]. [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: - 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 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][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` (docs-building)= #### Building the docs locally :::::{tabs} ::::{group-tab} Hatch ```bash hatch run docs:build hatch run docs:open ``` :::: ::::{group-tab} Pip ```bash source .venv/bin/activate cd docs make html (xdg-)open _build/html/index.html ``` :::: :::::