add coverage reporting step #41

	# This workflow will install Python dependencies, run tests and lint with a single version of Python
	# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

	name: Python application

	on:
	push:
	branches: [ "Refactor_fgi_file_staging_unit_tests" ]
	pull_request:
	branches: [ "Refactor_fgi_file_staging_unit_tests" ]

	permissions:
	contents: read

	jobs:
	build_lint_test:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	- name: setup_mongodb
	uses: supercharge/[email protected]
	- name: Set up Python 3.9
	uses: actions/setup-python@v3
	with:
	python-version: "3.9"
	- name: Install Poetry
	uses: snok/install-poetry@v1
	- name: Install dependencies
	run: \|
	poetry install
	- name: Test with pytest
	run: \|
	poetry run pytest ./tests --junit-xml=pytest.xml --cov-report=term --cov-report=html \
	--cov-report=xml --cov=nmdc_automation
	- name: Pytest coverage comment
	uses: MishaKav/pytest-coverage-comment@main
	with:
	pytest-xml-coverage-path: ./coverage.xml
	junitxml-path: ./pytest.xml

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