Adjusted run annotations import script to be accession agnostic #1221

	name: Testing

	on: [push, pull_request]
	env:
	EMG_CONFIG: ${{ github.workspace }}/ci/configuration.yaml

	jobs:
	build:

	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: [3.9]

	steps:
	- uses: actions/checkout@v3

	- name: 🐍 - Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}

	- name: 💾 Start MongoDB
	uses: supercharge/[email protected]
	with:
	mongodb-version: 4.0.6

	- name: ⚙️ - Checking environment
	run: \|
	python -V
	sudo systemctl start mysql
	mysql --version
	mysql -uroot -proot -e 'CREATE DATABASE emg;'
	mysql -uroot -proot -e "SET GLOBAL sql_mode = 'STRICT_TRANS_TABLES'"

	- name: 🔧 - Install Dependencies
	run: \|
	pip install .[tests]
	pip freeze

	- name: Check for unmigrated code changes
	run: \|
	python emgcli/manage.py makemigrations --noinput --check --dry-run

	- name: 🧪 - Testing
	run: \|
	cat $EMG_CONFIG
	pytest

	# TODO: disabled until black formatting completed and all flake issues fixed
	# - name: Flake
	# continue-on-error: true
	# run: \|
	# flake8 --version
	# flake8 -v .

	- name: 📮 - Slack Notification
	uses: rtCamp/action-slack-notify@v2
	continue-on-error: true
	if: github.ref == 'refs/heads/master' \|\| github.ref == 'refs/heads/develop'
	env:
	SLACK_COLOR: "${{ job.status == 'success' && 'good' \|\| 'danger' }}"
	SLACK_USERNAME: "Github Actions API"
	SLACK_ICON_EMOJI: ":octocat:"
	SLACK_TITLE: "CI API results in GitHub Actions"
	SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }}
	SLACK_CHANNEL: "#metagenomics-notify"
	MSG_MINIMAL: Actions URL

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