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

Create a conda virtual environment as explained here and install Harpy.

conda activate harpy
pip install -e '.[testing,docs]'

This development environment is supported for:

To run unit tests, run the following from the root of the project:

pytest

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

Do a type test:

mypy --ignore-missing-imports src/

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

pre-commit install
pre-commit run -a