To make yaml2sbml easily usable, we try to provide good documentation,
including code annotation and usage examples.
The documentation is hosted on
yaml2sbml.readthedocs.io
and updated automatically every time the main branch is updated.
To create the documentation locally, first install the requirements via:
pip install .[doc]
and then compile the documentation via:
cd doc make html
We use the virtual testing tool tox
for all unit tests, format and quality checks and notebooks.
Its configuration is specified in tox.ini. To run it locally, first
install:
pip install tox
and then simply execute:
tox
To run only selected tests (see tox.ini for what is tested), use e.g.:
tox -e pyroma,flake8
For continuous integration testing we use GitHub Actions. All tests are run there on pull requests and required to pass. The configuration is specified in .github/workflows/ci.yml.
Unit tests are located in the tests folder. All files starting with
test_ contain tests and are automatically run on GitHub Actions.
Run them locally via:
tox -e unittests
which boils mostly down to:
python3 -m pytest tests
You can also run only specific tests.
Unit tests can be written with pytest or unittest.
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 given in .flake8.
You can run it locally via:
tox -e flake8
If you start working on a new feature or a fix, please create an issue on GitHub shortly describing the issue and assign yourself.
To get your code merged, please:
- create a pull request to develop
- if not already done in a commit message, use the pull request description to reference and automatically close the respective issue (see https://help.github.com/articles/closing-issues-using-keywords/)
- check that all tests pass
- check that the documentation is up-to-date
- request a code review