Run tests in GitHub Actions #1

	name: Test

	on:
	push:
	branches: [ master ]
	paths:
	- '.github/workflows/test.yml'
	- '**.py'
	pull_request:

	jobs:
	test:
	name: Tests
	runs-on: ubuntu-24.04
	steps:
	- uses: actions/checkout@v4
	- name: Spin up ChRIS
	uses: FNNDSC/miniChRIS-docker@master
	with:
	# for testing, we need to create plugin instances, but we don't need the plugins to actually run.
	services: chris
	- name: Build
	run: docker compose build
	- name: Test
	id: test
	continue-on-error: true # we want to upload coverage, even on failure
	run: docker compose run -T test pytest --color=yes --cov=chrisomatic --cov-report=xml
	- name: Copy coverage.xml from container
	run: docker cp "$(docker compose ps -a test -q \| tail -n 1):/app/coverage.xml" coverage.xml
	- name: Upload test coverage to Codecov
	uses: codecov/codecov-action@v4
	with:
	files: ./coverage.xml
	flags: unittests
	fail_ci_if_error: true
	token: ${{ secrets.CODECOV_TOKEN }}
	- name: Run example
	run: \|
	set +e
	docker compose run -T test sh -c '
	export PYTHONPATH=$PWD
	/app/scripts/create_example.py \| coverage run python -m chrisomatic.cli -
	'
	if [ "$?" = '0' ]; then
	echo "::error::Expected run to fail, but it did not.
	exit 1
	fi
	docker compose run -T test coverage xml -o - > simulation_coverage.xml
	- name: Upload simulation coverage to Codecov
	uses: codecov/codecov-action@v4
	with:
	files: ./simulation_coverage.xml
	flags: simulation
	fail_ci_if_error: true
	token: ${{ secrets.CODECOV_TOKEN }}

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