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CONTRIBUTE.rst

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Contribute

Workflow

If you start working on a new feature or a fix, please create an issue on GitHub briefly describing the issue and assign yourself. Your startpoint should always be the develop branch, which contains the latest updates.

Create an own branch or fork, on which you can implement your changes. To get your work merged, please:

  1. create a pull request to the develop branch with a meaningful summary,
  2. check that code changes are covered by tests, and all tests pass,
  3. check that the documentation is up-to-date,
  4. request a code review from the main developers.

Environment

If you contribute to the development of pyPESTO, install developer requirements via:

pip install -r requirements-dev.txt

This installs the tools described below.

Pre-commit hooks

Firstly, this installs a pre-commit tool. To add those hooks to the .git folder of your local clone such that they are run on every commit, run:

pre-commit install

When adding new hooks, consider manually running pre-commit run --all-files once as usually only the diff is checked. The configuration is specified in .pre-commit-config.yaml.

Should it be necessary to perform commits without pre-commit verification, use git commit --no-verify or the shortform -n.

Tox

Secondly, this installs the virtual testing tool tox, which we use for all tests, format and quality checks. Its configuration is specified in tox.ini. To run it locally, simply execute:

tox [-e flake8,doc]

with optional -e options specifying the environments to run, see tox.ini for details.

GitHub Actions

For automatic continuous integration testing, we use GitHub Actions. All tests are run there on pull requests and are required to pass. The configuration is specified in .github/workflows/ci.yml.

Documentation

To make pyPESTO easily usable, we try to provide good documentation, including code annotation and usage examples. The documentation is hosted at pypesto.readthedocs.io and updated automatically on merges to the main branches. To create the documentation locally, first install the requirements via:

pip install .[doc]

and then compile the documentation via:

cd doc
make html

The documentation is then under doc/_build.

Alternatively, the documentation can be compiled and tested via a single line:

tox -e doc

When adding code, all modules, classes, functions, parameters, code blocks should be properly documented.

For docstrings, we follow the numpy docstring standard. Check here for a detailed explanation.

Unit tests

Unit tests are located in the test folder. All files starting with test_ contain tests and are automatically run on GitHub Actions. Run them locally via e.g.:

tox -e base

with base covering basic tests, but some parts (optimize,petab,...) being in separate subfolders. This boils mostly down to e.g.:

pytest test/base

You can also run only specific tests.

Unit tests can be written with pytest or unittest.

Code changes should always be covered by unit tests. It might not always be easy to test code which is based on random sampling, but we still encourage general sanity and integration tests. We highly encourage a test-driven development style.

PEP8

We try to respect the PEP8 coding standards. We run flake8 as part of the tests. The flake8 plugins used are specified in tox.ini and the flake8 configuration is given in .flake8. You can run the checks locally via:

tox -e flake8