Merge pull request #245 from gp201/expanded_pathogens_docs #415

	name: freyja CI
	on:
	push:
	branches: [ main ]
	pull_request:

	jobs:
	testsuite:
	runs-on: ubuntu-latest

	steps:
	# Downloads a copy of the code in your repository before running CI tests
	- name: Check out repository code
	uses: actions/checkout@v2

	- name: Setup for conda
	uses: conda-incubator/setup-miniconda@v2
	with:
	auto-update-conda: true
	channels: bioconda,conda-forge
	channel-priority: true
	python-version: '3.10'
	activate-environment: test

	- name: Install
	shell: bash -l {0}
	run: \|
	conda install -n base conda-libmamba-solver
	conda config --set solver libmamba
	conda config --add channels bioconda
	conda config --add channels conda-forge
	conda install --yes --file ci/conda_requirements.txt
	pip install -e . --no-deps

	- name: Test
	shell: bash -l {0}
	run: \|
	conda activate test
	make test

	lint:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2
	- name: flake8
	uses: actions/setup-python@v2
	with:
	python-version: 3.7
	- name: install dependencies
	run: python -m pip install --upgrade pip
	- name: lint
	run: \|
	pip install -q flake8
	make lint

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