Fix CI #166

	# 786
	# https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

	name: aldy-test
	on:
	push:
	branches: [ master ]
	tags:
	- '*'
	pull_request:
	branches: [ master ]
	jobs:
	build:
	runs-on: ubuntu-20.04
	strategy:
	matrix:
	python-version: ['3.7', '3.11', '3.12']
	permissions:
	id-token: write
	steps:
	- uses: actions/checkout@v4
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install dependencies
	run: \|
	sudo apt-get install libgfortran4 samtools
	python -m pip install --upgrade pip
	python -m pip install flake8 pytest pytest-cov codecov black
	python -m pip install setuptools wheel twine numpy cython
	python -m pip install .
	- name: Format with black
	run: black aldy
	- name: Lint with flake8
	run: flake8 aldy
	- name: Run Aldy tests
	run: \|
	mkdir -p tmp
	cd tmp
	aldy test
	cd ..
	- name: Run code coverage tests
	run: \|
	python setup.py build_ext --inplace
	pytest --cov=./ -v aldy
	- name: Upload code coverage data
	uses: codecov/[email protected]
	- name: Build package
	run: \|
	python setup.py sdist
	- name: Publish on TestPyPI
	if: matrix.python-version == '3.7'
	uses: pypa/gh-action-pypi-publish@release/v1
	with:
	repository-url: https://test.pypi.org/legacy/
	skip-existing: true
	attestations: false
	- name: Publish package
	if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') && matrix.python-version == '3.7'
	uses: pypa/gh-action-pypi-publish@release/v1

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