GitHub action test example workflow (#167) #12

	name: Python Package using Conda

	on: [push]

	jobs:
	build-linux:
	runs-on: ubuntu-latest
	strategy:
	max-parallel: 5

	steps:
	- uses: actions/checkout@v3
	- name: Set up Python 3.10
	uses: actions/setup-python@v3
	with:
	python-version: '3.10'
	- name: Add conda to system path
	run: \|
	# $CONDA is an environment variable pointing to the root of the miniconda directory
	echo $CONDA/bin >> $GITHUB_PATH
	- name: Install dependencies
	run: \|
	conda install -c conda-forge -c bioconda snakemake pip mamba
	pip install .
	- name: Deploy panoptes
	run: \|
	panoptes &
	- name: Test panoptes
	run: \|
	response=$(curl http://127.0.0.1:5000/api/service-info)
	if [ "$response" = "{\"status\":\"running\"}" ]; then
	echo "Success";
	exit 0;
	else
	echo "Fail";
	exit 1;
	fi
	- name: Run test workflow
	run: \|
	snakemake --version
	cd ..
	git clone https://github.com/panoptes-organization/snakemake_example_workflow.git
	cd snakemake_example_workflow
	ls
	bash run_local.sh

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