Add integration tests #1025

	# 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: CI

	on:
	push:

	permissions:
	contents: read

	jobs:
	build_lint_test:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3

	- name: Ensure Docker configuration directory exists
	run: \|
	sudo mkdir -p /etc/docker

	- name: Set up Docker Hub mirror
	run: \|
	echo '{"registry-mirrors": ["https://docker.mirrors.ustc.edu.cn"]}' \| sudo tee /etc/docker/daemon.json
	sudo systemctl restart docker

	- 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: Lint with flake8
	run: \|
	poetry run flake8 nmdc_automation --exit-zero --statistics --tee --output-file flake8stats.txt

	- name: Test with pytest
	run: \|
	poetry run pytest -m "not integration" ./tests --junit-xml=pytest.xml --cov-report=term \
	--cov-report=xml --cov=nmdc_automation --local-badge-output-dir badges/

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