Adding code coverage (#1) #10

	# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
	# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

	name: Python package

	on:
	push:
	branches:
	pull_request:
	branches:

	jobs:
	build:

	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: ["3.9", "3.10", "3.11"]

	steps:
	- uses: actions/checkout@v4
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v3
	with:
	python-version: ${{ matrix.python-version }}
	- name: Cache pip
	uses: actions/cache@v3
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
	restore-keys: \|
	${{ runner.os }}-pip-
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	python -m pip install flake8 pytest-cov
	if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
	- name: Install package
	run: \|
	pip install -e .
	- name: Lint with flake8
	run: \|
	# stop the build if there are Python syntax errors or undefined names
	flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
	# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
	flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
	- name: Test with pytest and coverage
	run: \|
	pytest --cov=pCRscore
	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v2
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	directory: ./coverage/reports/

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