CI #134

	name: CI
	on:
	push:
	pull_request:
	schedule:
	- cron: "0 0 1 * *" # run monthly
	jobs:
	build:
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	modes: ["s", "p"]
	schedulers: ["gridengine", "slurm"]
	env:
	REGISTRY: ghcr.io
	NAME: ${{ matrix.schedulers }}-${{ matrix.modes }}
	IMAGE: ${{ github.repository_owner }}/sv-callers-${{ matrix.schedulers }}
	TAG: "1.2.2"
	ARGS: 0 ${{ matrix.modes }} ${{ matrix.schedulers }}
	steps:
	- name: Checkout repo
	uses: actions/checkout@v2
	- name: Set up Python
	uses: actions/setup-python@v1
	with:
	python-version: "3.7"
	- name: Python info
	run: \|
	which python
	python --version
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install -r test-requirements.txt
	- name: Show pip list
	run: pip list
	- name: Run unit tests
	run: \|
	pytest --cov=helper_functions --cov-report=xml
	mv coverage.xml ${{ github.workspace }}
	working-directory: workflow
	- name: Log into registry
	uses: docker/login-action@v1
	with:
	registry: ${{ env.REGISTRY }}
	username: ${{ github.actor }}
	password: ${{ secrets.GITHUB_TOKEN }}
	- name: Run workflow
	run: \|
	docker run -d -p 10000:22 --name $NAME ${REGISTRY}/${IMAGE,,}:${TAG}
	sleep 10
	docker ps -a
	docker exec -u xenon -t $NAME bash -c "cd sv-callers && ./run.sh $ARGS"
	- name: Upload coverage report to Codacy
	uses: codacy/codacy-coverage-reporter-action@master
	with:
	project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
	coverage-reports: coverage.xml

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