CI-CD

Update CI-CD.yml #994

	name: CI-CD

	on: [push]

	jobs:
	build-linux:
	runs-on: ubuntu-latest
	strategy:
	max-parallel: 5

	steps:
	- uses: actions/checkout@v3

	- name: Set up Python 3.10
	uses: actions/setup-python@v3
	with:
	python-version: '3.10'

	- name: Add conda to system path
	run: \|
	# $CONDA is an environment variable pointing to the root of the miniconda directory
	echo $CONDA/bin >> $GITHUB_PATH

	- name: Install dependencies
	run: \|
	conda install -c conda-forge openmmdl

	- name: Install package and its entry points
	run: \|
	pip install .

	- name: Install linter and formatter
	run: \|
	python -m pip install shyaml flake8 black black-nb flake8-nb

	- name: Run black formatter
	run: \|
	black -l 99 .

	- name: Run flake8 linter
	run: \|
	flake8 . --count --select=E9,F63,F7,F82 --ignore=E501,W605,F821 --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: Install pytest and run tests
	run: \|
	pip install pytest pytest-cov
	pytest -vv --cov=openmmdl --cov-report=xml --cov-report=html --color=yes openmmdl/tests/
	coverage run -m pytest openmmdl/tests/
	coverage xml
	coverage report

	- name: Upload coverage reports to Codecov
	uses: codecov/codecov-action@v3
	with:
	file: ./coverage.xml # Specify the path to the XML coverage report
	flags: unittests
	version: "v0.1.15"
	env:
	CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

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