add step tests and refactoring #172

	---

	name: Pull Request Actions

	on: [push]

	jobs:
	docker-image-push:
	runs-on: ubuntu-latest
	name: Create staging docker image
	steps:
	- name: Check out git repository
	uses: actions/checkout@v3

	- name: Extract branch name and remove illegal chars
	id: get_branch_name
	shell: bash
	run: echo "branch=$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")" >> $GITHUB_OUTPUT

	- name: Login to Docker Hub
	uses: docker/login-action@v2
	with:
	username: ${{ secrets.DOCKER_USERNAME }}
	password: ${{ secrets.DOCKER_PASSWORD }}

	- name: Set up Docker Buildx
	id: buildx
	uses: docker/setup-buildx-action@v2

	- name: Build and push
	id: docker_build
	uses: docker/build-push-action@v3
	with:
	context: ./
	file: ./Dockerfile
	push: true
	tags: "clinicalgenomics/arnold-stage:${{steps.get_branch_name.outputs.branch}}, clinicalgenomics/arnold-stage:latest"

	tests-coverage:
	runs-on: ubuntu-latest
	name: Test and coveralls
	steps:
	- name: Set up Python
	uses: actions/setup-python@v2
	with:
	python-version: 3.11

	- name: Check out arnold
	uses: actions/checkout@v2
	with:
	repository: "Clinical-Genomics/arnold"

	- name: Install arnold dependencies
	run: \|
	pip install -r requirements.txt -r requirements-dev.txt .

	- name: Install coveralls dependencies
	run: \|
	pip install pytest-cov coveralls

	- name: Test with pytest & Coveralls
	run: \|
	pytest --cov=arnold/
	coveralls
	env:
	GITHUB: 1
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}

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