celloracle_weekly_build_and_test #45

	name: celloracle_weekly_build_and_test

	on:
	schedule:
	- cron: '0 9 * * 0'
	workflow_dispatch:

	jobs:
	build_and_test:
	runs-on: ubuntu-20.04
	timeout-minutes: 60
	steps:
	- uses: actions/checkout@v2
	- name: Setup conda, install packages, and test celloracle
	run: \|
	sudo apt-get update
	sudo apt-get install -y bedtools
	wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
	bash miniconda.sh -b -p $HOME/miniconda
	source "$HOME/miniconda/etc/profile.d/conda.sh"
	hash -r
	conda config --set always_yes yes --set changeps1 no
	#conda update -q conda
	# Useful for debugging any issues with conda
	conda info -a
	# Create env
	conda create -q -n test-environment python=3.8
	# command to install dependencies
	conda activate test-environment
	conda install cython==0.29.35 numpy pytest

	conda list
	ls /home/runner/miniconda
	ls /home/runner/miniconda/bin

	python --version

	which pip
	#Install fa2 for tutorial
	pip install fa2
	# Install CellOracle
	git clone https://github.com/morris-lab/CellOracle.git
	cd CellOracle
	pip install .
	# command to run tests
	pytest -v

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