Development

Development#

Setting up a development environment#

First clone the GitHub repo and set it as the current directory:

git clone https://github.com/saeyslab/harpy.git
cd harpy

Install Harpy:

uv venv --python=3.12 # set python version
source .venv/bin/activate # activate the virtual environment
uv pip install -e '.[dev]' # use uv to pip install dependencies
python -c 'import harpy; print(harpy.__version__)' # check if the package is installed
# make changes
python -m pytest # run the tests

If you update the pyproject.toml, please also update the the uv lock file:

# update the lock file
uv lock
# check if lock file was updated correctly.
uv lock --check

This development environment is supported for:

  • CentOS

  • Ubuntu

  • MacOS with an M1/M2 Pro

  • Windows 11

Continuous integration will automatically run the tests on all pull requests.

Type testing#

Do a type test:

mypy --ignore-missing-imports src/

Automated commit checks#

Install a pre-commit hook to run all configured checks in .pre-commit-config.yaml:

pre-commit install
pre-commit run -a