Merge pull request #72 from databio/partial_processing #107

	name: test coverage

	on:
	push:
	branches: [master, dev]

	jobs:
	cli-coverage-report:
	strategy:
	matrix:
	python-version: ["3.10"]
	os: [ ubuntu-latest ] # can't use macOS when using service containers or container jobs
	runs-on: ${{ matrix.os }}
	services:
	postgres:
	image: postgres
	env:
	POSTGRES_USER: postgres
	POSTGRES_PASSWORD: docker
	POSTGRES_DB: bedbase
	POSTGRES_HOST: localhost
	ports:
	- 5432:5432
	options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5

	steps:
	- uses: actions/checkout@v2

	- uses: actions/setup-python@v1
	with:
	python-version: '3.10'

	- name: Install dev dependencies
	run: if [ -f requirements/requirements-dev.txt ]; then pip install -r requirements/requirements-dev.txt; fi

	- name: Install test dependencies
	run: if [ -f requirements/requirements-test.txt ]; then pip install -r requirements/requirements-test.txt; fi

	- run: pip install .

	- name: Run tests
	run: coverage run -m pytest

	- name: build coverage
	run: coverage html -i

	- run: smokeshow upload htmlcov
	env:
	SMOKESHOW_GITHUB_STATUS_DESCRIPTION: Coverage {coverage-percentage}
	SMOKESHOW_GITHUB_COVERAGE_THRESHOLD: 35
	SMOKESHOW_GITHUB_CONTEXT: coverage
	SMOKESHOW_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	SMOKESHOW_GITHUB_PR_HEAD_SHA: ${{ github.event.pull_request.head.sha }}
	SMOKESHOW_AUTH_KEY: ${{ secrets.SMOKESHOW_AUTH_KEY }}

Provide feedback