ericdatakelly/sgkit

Statistical genetics toolkit

sgkit

Statistical genetics toolkit

Developer documentation

Build and test

From a Python virtual environment run:

pip install -r requirements.txt -r requirements-dev.txt
pytest

To check code coverage and get a coverage report, run

pytest --cov=sgkit --cov-report term-missing

To check that the documentation builds without warnings, run

cd docs
make clean html SPHINXOPTS="-W --keep-going"

Code standards

Use pre-commit to check or enforce the coding standards. Install the git hook using:

pre-commit install

To manually enforce (or check) the source code adheres to our coding standards:

pre-commit run --all-files

To run specific tool (black/flake8/isort/mypy etc):

pre-commit run black --all-files

Notes:

• if you skip --all-files checks are incremental