Contribute

Workflow

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

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

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

Merge requests to develop should be squashed-and-merged, while merge requests (from develop) to main should be merged. This is to keep the history clean.

Environment

If you contribute to the development of FitMultiCell, consider installing developer requirements, for e.g. local testing, 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 defaults. tox creates virtual images in a .tox/ subfolder.

GitLab CI/CD

For automatic continuous integration testing, we use GitLab CI/CD All tests are run there on pull requests and required to pass. The configuration is specified in .gitlab-ci.yml.

Documentation

To make FitMultiCell easily usable, we try to provide good documentation, including code annotation and usage examples. The documentation is hosted at https://fitmulticell.readthedocs.io/en/latest/, a version for the develop branch at https://fitmulticell.readthedocs.io/en/develop/. These are updated automatically on merges to the main and develop branches. To create the documentation locally, run:

tox -e doc

The documentation is then undre doc/_build. Alternatively, install the requirements via:

pip install .[doc]

and then compile the documentation via:

cd doc
make html

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

Unit tests

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

tox -e base

You can also run only specific tests, see e.g. the pytest documentation for details. 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