Merge pull request #5 from UMCUGenetics/feature/default-fix-output-fix #53

	name: Test (pytest)

	on:
	push:
	branches:
	- "**"
	pull_request:
	workflow_dispatch:

	permissions:
	contents: write
	pull-requests: write

	jobs:
	pytest:
	runs-on: ubuntu-latest

	steps:
	- name: Check out repository
	uses: actions/checkout@v4

	- name: Install uv
	uses: astral-sh/setup-uv@v7
	with:
	enable-cache: true
	cache-suffix: "uv_cache"
	python-version: "3.13.0"

	- name: Install dependencies
	run: uv sync

	- name: Run tests
	run: \|
	set -o pipefail
	uv run pytest tests \
	--junitxml=pytest.xml \
	--cov=src \
	--cov-report=term-missing \
	--cov-fail-under=70 \| \
	tee pytest-coverage.txt

	- name: Add test coverage comment
	# Only comment on events from the same repository (skip forked PRs)
	if: github.event_name != 'pull_request' \|\| github.event.pull_request.head.repo.full_name == github.repository

	# Alternative for open source projects: https://github.com/codecov/example-python
	uses: MishaKav/pytest-coverage-comment@main
	with:
	pytest-coverage-path: ./pytest-coverage.txt
	junitxml-path: ./pytest.xml

	- name: Upload test reports
	if: always()
	uses: actions/upload-artifact@v4
	with:
	name: pytest-reports-3.13.0
	path: \|
	pytest.xml
	pytest-coverage.txt

Provide feedback