Casanovo Nextflow Workflow Documentation #627

	# This workflow will install Python dependencies, run tests and lint with a single version of Python
	# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

	name: tests

	on:
	push:
	branches:
	- main
	- dev
	pull_request:
	branches:
	- main
	- dev

	jobs:
	build:
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	os: [ubuntu-latest, windows-latest, macos-13]

	steps:
	- uses: actions/checkout@v4
	- name: Set up Python 3.10
	uses: actions/setup-python@v5
	with:
	python-version: "3.10"
	- name: Set up Java
	uses: actions/setup-java@v3
	with:
	distribution: 'zulu'
	java-version: '22'
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install flake8 pytest pytest-cov wheel
	pip install -e .[dev]
	- 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: Run unit and system tests
	run: \|
	pytest --cov=casanovo tests/
	- name: Upload coverage to codecov
	uses: codecov/codecov-action@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	fail_ci_if_error: true

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