Contributing guide¶

Scanpy provides extensive developer documentation, 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.

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:

cd ehrapy
pip install -e ".[dev,test,doc]"

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

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

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 and prettier.

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 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

pytest

in the root of the repository. Continuous integration will automatically run the tests on all pull requests.

Publishing a release¶

Updating the version number¶

Before making a release, you need to update the version number. Please adhere to Semantic Versioning, in brief

Given a version number MAJOR.MINOR.PATCH, increment the:

MAJOR version when you make incompatible API changes,

MINOR version when you add functionality in a backwards compatible manner, and

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

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:

twine check dist/*

and finally publishing it with:

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 in the cookiecutter-scverse template.

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)
Sphinx autodoc typehints, to automatically reference annotated input and output types
Citations (like ) can be included with sphinxcontrib-bibtex

See the scanpy developer docs 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 pert-tutorials which is a git submodule of ehrapy.

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¶

cd docs
make html
open _build/html/index.html