Makefile

tests = tests
module = atropos
#pytestops = --full-trace
#pytestops = -v -s
repo = jdidion/$(module)
desc = Release $(version)

BUILD =
TEST =

all: clean install test

# install prerequisites
init:
	pip install cython pytest pytest-timeout twine

build:
	python setup.py build_ext -i
	python setup.py sdist bdist_wheel

install: clean build
	python setup.py install $(installargs)

test:
	pytest $(pytestops) $(tests)

docs:
	make -C doc html

readme:
	pandoc --from=markdown --to=rst --output=README.rst README.md
	pandoc --from=markdown --to=rst --output=CHANGES.rst CHANGES.md

lint:
	pylint $(module)

clean:
	rm -Rf __pycache__
	rm -Rf **/__pycache__/*
	rm -Rf **/*.c
	rm -Rf **/*.so
	rm -Rf **/*.pyc
	rm -Rf dist
	rm -Rf build
	rm -Rf .adapters
	rm -Rf atropos.egg-info

docker:
	# build
	docker build -f Dockerfile -t $(repo):$(version) .
	# add alternate tags
	docker tag $(repo):$(version) $(repo):latest
	# push to Docker Hub
	docker login -u jdidion && \
	docker push $(repo)

tag:
	git tag $(version)

release: clean tag install test
	echo "Releasing version $(version)"
	# release
	twine upload -u "__token__" -p "$(pypi_token)" dist/*.whl dist/*.tar.gz
	# push new tag after successful build
	git push origin --tags
	# create release in GitHub
	curl -v -i -X POST \
		-H "Content-Type:application/json" \
		-H "Authorization: token $(token)" \
		https://api.github.com/repos/$(repo)/releases \
		-d '{ \
		  "tag_name":"$(version)", \
		  "target_commitish": "master", \
		  "name": "$(version)", \
		  "body": "$(desc)", \
		  "draft": false, \
		  "prerelease": false \
		}'

# build a package with the files needed to run the workflows
workflow:
	mkdir -p dist
	tar -C paper -czf dist/atropos-paper-workflow.tgz \
		workflow/simulated.nf \
		workflow/rnaseq.nf \
		workflow/wgbs.nf \
		workflow/nextflow.config \
		workflow/run-workflows.sh \
		workflow/bin \
		containers/data/simulated/art_profiles.txt \
		containers/tools/tool-names.txt