Provide token for codecov upload #51

	name: CI
	on: [push, pull_request, release] # runs on all branches
	env:
	PYTHON_VERSION: 3.12

	jobs:
	test:
	runs-on: ubuntu-latest

	steps:

	- uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: ${{ env.PYTHON_VERSION }}

	- name: Install and configure Poetry
	uses: snok/install-poetry@v1
	with:
	virtualenvs-create: false

	- name: Install biopeaks
	run: poetry install --no-interaction --with main,dev

	- name: Install system dependencies for headless testing
	run: sudo ./.devcontainer/install_system_dependencies.sh

	- name: Test and collect coverage
	run: pytest -v --cov-config=.coveragerc --cov-report=xml --cov=biopeaks

	- name: Upload coverage report
	uses: codecov/codecov-action@v4
	with:
	file: ./coverage.xml
	token: ${{ secrets.CODECOV_TOKEN }}


	build_distribution:

	needs: test
	runs-on: ubuntu-latest
	if: github.event_name == 'release' && github.event.action == 'published'

	steps:

	- uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: ${{ env.PYTHON_VERSION }}

	- name: Install and configure Poetry
	uses: snok/install-poetry@v1
	with:
	virtualenvs-create: false

	- name: Build and upload distribution
	env:
	PYPI_USERNAME: ${{ secrets.PYPI_USERNAME }}
	PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
	run: \|
	poetry publish -u $PYPI_USERNAME -p $PYPI_PASSWORD --build

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