help:

@echo "available commands"

@echo " - lint : run linting and flaking"

@echo " - test : run all unit tests"

@echo " - doc : build the documentation"

@echo " - install : install the package"

@echo " - install-dev : install the package in dev mode"

@echo " - cythonize : cythonize all pyx files"

@echo " - clean : clean the repo"

clean:

rm -rf docs/build

rm -rf htmlcov

rm -rf .coverage*

rm -rf docs/source/scphylo*

rm -rf docs/source/auto_examples

rm -rf docs/source/gen_modules

lint:

pre-commit run --all-files

test:

rm -rf htmlcov

pytest --disable-warnings --cov=scphylo --cov-report=html ./tests

rm -rf .coverage*

doc:

rm -rf docs/source/scphylo*

rm -rf docs/source/auto_examples

rm -rf docs/source/gen_modules

cd docs && $(MAKE) clean html

cd docs/build/html && python -m http.server 8080

install:

python -m pip install .

install-dev:

git fetch

python -m pip install -e '.[dev,docs]'

pre-commit install

cythonize:

CYTHONIZE=1 pip install -e .