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Contributing guide

Scanpy provides extensive developer documentation, 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.

:::::{tabs} ::::{group-tab} Hatch The easiest way is to get familiar with hatch environments, with which these tasks are simply:

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:

cd cell-annotator
python3 -m venv .venv
source .venv/bin/activate
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

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 ruff and prettier.

(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

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

hatch test  # test with the highest supported Python version
# or
hatch test --all  # test with all supported Python versions

::::

::::{group-tab} Pip

source .venv/bin/activate
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.

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, 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.

Writing documentation

Please write documentation for new or changed features and use-cases. This project uses sphinx with the following features:

See scanpy’s {doc}scanpy:dev/documentation for more information on how to write your own.

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 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

(docs-building)=

Building the docs locally

:::::{tabs} ::::{group-tab} Hatch

hatch run docs:build
hatch run docs:open

::::

::::{group-tab} Pip

source .venv/bin/activate
cd docs
make html
(xdg-)open _build/html/index.html

:::: :::::