Add ability for indexed sequence file to be uploaded and used in an assembly #678

	name: Pull Request

	on: pull_request

	jobs:
	build:
	name: Strict lint and test
	runs-on: ubuntu-latest
	steps:
	- name: Check out
	uses: actions/checkout@v4
	- name: Use Node.js 18.x
	uses: actions/setup-node@v4
	with:
	node-version: 18
	cache: yarn
	- name: Install
	run: yarn --immutable
	# Have to build shared before linting so type-based lint rules can
	# run correctly
	- name: Build shared
	run: yarn build
	working-directory: packages/apollo-shared
	- name: Lint codebase
	run:
	yarn eslint --report-unused-disable-directives --max-warnings 0 --ext
	.js,.ts,.jsx,.tsx .
	- name: Run Jest tests
	run: yarn test
	- name: Get latest JBrowse
	run: yarn run jbrowse create --nightly .jbrowse
	working-directory: packages/jbrowse-plugin-apollo
	- name: Start MongoDB
	uses: supercharge/[email protected]
	with:
	mongodb-version: 7
	mongodb-replica-set: test-rs
	- name: Run Cypress tests
	run: yarn run test:e2e
	working-directory: packages/jbrowse-plugin-apollo
	- name: Start apollo
	run: \|
	yarn --cwd packages/apollo-shared start &
	ALLOW_ROOT_USER=true ROOT_USER_NAME=admin ROOT_USER_PASSWORD=pass yarn --cwd packages/apollo-collaboration-server start &
	- name: Run CLI tests
	run: python3 ./test/test.py TestCLI
	working-directory: packages/apollo-cli
	# - name: Run docker tests
	# working-directory: packages/apollo-cli
	# run: python3 ./test/test_docker.py
	- name: Upload coverage reports to Codecov
	uses: codecov/codecov-action@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }}

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