A grade level changes #3

	name: CI

	on:
	push:
	branches: [ main, master ]
	pull_request:
	branches: [ main, master ]

	jobs:
	test:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: [3.6, 3.7, 3.8, 3.9, "3.10", "3.11"]

	steps:
	- uses: actions/checkout@v3

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}

	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install -r requirements.txt
	pip install -r requirements-dev.txt

	- name: Lint (flake8)
	run: \|
	flake8 src tests

	- name: Type check (mypy)
	run: \|
	mypy src

	- name: Run unit tests
	run: \|
	pytest tests/ -v --cov=fasta_aa_extractor --cov-report=term --cov-report=xml

	- name: Run integration test
	run: \|
	python -m fasta_aa_extractor.cli --genome examples/ECS34.fasta --coords examples/ECS34.tsv --isolate ECS34

	- name: Check output
	run: \|
	ls -la Extracted_Proteins.zip
	unzip -l Extracted_Proteins.zip \| wc -l

	- name: Upload coverage reports
	uses: codecov/codecov-action@v3
	with:
	file: ./coverage.xml
	flags: unittests
	name: codecov-umbrella
	if: matrix.python-version == '3.11'

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