Merge branch 'main' of https://github.com/mskcc/igo-demux #641

	# 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: Python application

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

	jobs:
	build:

	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v2
	- name: Set up Python 3.9
	uses: actions/setup-python@v2
	with:
	python-version: "3.9"
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install flake8 pytest
	pip install pandas
	AIRFLOW_VERSION=2.2.3
	PYTHON_VERSION=3.9
	CONSTRAINT_URL="https://raw.githubusercontent.com/apache/airflow/constraints-${AIRFLOW_VERSION}/constraints-${PYTHON_VERSION}.txt"
	pip install "apache-airflow==${AIRFLOW_VERSION}" --constraint "${CONSTRAINT_URL}"
	pip install apache-airflow[cncf.kubernetes]
	pip install virtualenv
	pip install pytest-cov
	if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
	- 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 collect coverage
	run: \|
	pytest --cov=./ --cov-report=xml
	- name: Upload coverage reports to Codecov with GitHub Action
	uses: codecov/codecov-action@v3

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