Example Python package

All design principles are explained in the developing.md file. The Python package template was created by Jakob Nybo Nissen and Henry Webel.

How to use

Can be used as GitHub template repository, see GitHub documentation.

You will need to find and replace occurences of

• python_package -> your_package_name

  • also the folder src/python_package

• RasmussenLab -> GitHub_user_name (or organization) with the name of your package and GitHub user name (or organization).

• look for First Last to see where to replace with your name

• choose a license, see GitHub documentation and Creative Commons. Replace LICENSE file with the license you choose.

• Update the CITATION.cff file with your information.

• once you change the code under src, please make sure to update

  • docs/tutorial/tutorial.ipynb (add your usage example)
  • tests/test_mockup.py (delete file and add your own tests following the naming conventions test_<filename>.py)

Development environment

Install package so that new code is picked up in a restared python interpreter:

pip install -e ".[dev]"

Then you want to run locally the commands which are check in the CI/CD pipeline (using GitHub Actions). You can type

# run unittests
pytest tests
# format code and sort imports
black .
isort .# lint code and check for obvious errors
ruff check src

Basic usage

works using this template

frompython_packageimporthello_worldprint (python_package.__version__)
print(hello_world(4))

Readthedocs

The documentation can be build using readthedocs automatically. See project on Readthedocs for the project based on this template. A new project needs to be registered on ReadTheDocs.

• make sure to enable build from PRs in the settings (advanded settings)
• checkout configuration file: .readthedocs.yaml