Fix dockerfile installation problems #162

	# Tests that run on every PR

	name: Pull Request Checks

	on: [push, pull_request]

	jobs:
	black:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2
	name: Checkout repository

	- uses: actions/setup-python@v2
	name: Setup Python
	with:
	python-version: 3.9

	- name: Install black
	run: \|
	python -m pip install --upgrade pip
	pip install black
	- name: Run black
	run: \|
	black . --check
	# This job is copied over from `deploy.yaml`
	run-tests:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2

	# See: https://github.com/marketplace/actions/setup-conda
	- uses: s-weigand/setup-conda@v1
	with:
	conda-channels: "conda-forge"

	- name: Build environment
	run: \|
	conda env create -f environment.yml
	eval "$(conda shell.bash hook)"
	conda activate cellxgene-gateway
	pip install markupsafe==2.0.1 # temporary workaround for jinja2-2.11.3 calling soft_unicode in markupsafe
	python setup.py install

	- name: Run tests
	run: \|
	eval "$(conda shell.bash hook)"
	conda activate cellxgene-gateway
	coverage run -m unittest discover tests

	- name: Check coverage
	run: \|
	eval "$(conda shell.bash hook)"
	conda activate cellxgene-gateway
	coverage report --fail-under 41
	coverage xml -i

	- name: "Upload coverage to Codecov"
	uses: codecov/codecov-action@v1
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	files: ./coverage.xml
	flags: unittests
	env_vars: OS,PYTHON
	name: codecov-umbrella
	fail_ci_if_error: true
	path_to_write_report: ./codecov_report.txt
	verbose: true

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