General report with coverage over the entire genome when no genes or gene panels are provided #1114

	name: tests & coverage

	on: [ pull_request ]

	jobs:
	build:
	runs-on: ubuntu-latest
	steps:
	- name: Check out git repository
	uses: actions/checkout@v4

	- name: Install d4tools
	uses: baptiste0928/cargo-install@v3
	with:
	crate: d4tools
	git: https://github.com/38/d4-format.git
	tag: v0.3.10

	- name: Set up python
	id: setup-python
	uses: actions/setup-python@v5
	with:
	python-version: '3.11'

	# install & configure poetry
	- name: Install Poetry
	uses: snok/install-poetry@v1
	with:
	version: 1.7.1
	virtualenvs-create: true
	virtualenvs-in-project: true
	installer-parallel: true

	# load cached venv if cache exists
	- name: Load cached venv
	id: cached-poetry-dependencies
	uses: actions/cache@v4
	with:
	path: .venv
	key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}

	# install dependencies if cache does not exist
	- name: Install dependencies
	if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
	run: poetry install --no-interaction

	# install root project, if required
	- name: Install project
	run: poetry install --no-interaction

	- name: Test with pytest
	run:
	poetry run pytest --cov=./ --cov-report=xml

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v4
	with:
	flags: unittests
	files: ./coverage.xml
	name: codecov-umbrella
	fail_ci_if_error: true
	verbose: true
	env:
	CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

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