Create test_env.yml #29

	name: Run Pytest on Push

	on:
	push:
	paths:
	- '.github/workflows/pytest.yml'
	- '.github/envs/test_env.yml'
	branches:
	- '*'

	jobs:
	build:
	runs-on: ubuntu-latest
	defaults:
	run:
	shell: bash -l {0}

	strategy:
	fail-fast: false

	steps:
	- uses: actions/checkout@v3

	- name: Set up Conda
	uses: conda-incubator/setup-miniconda@v2
	with:
	mamba-version: "*"
	channels: conda-forge,bioconda,defaults
	auto-activate-base: false
	activate-environment: test_env
	environment-file: .github/envs/test_env.yml

	- name: Install apt dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install -y gcc g++ bowtie2 samtools libsys-hostname-long-perl

	- name: Install dependencies
	run: \|
	conda create -n test_env -c defaults -c conda-forge -c bioconda -y --debug -c bioconda pip trimmomatic flash numpy cython jinja2 tbb=2020.2 pyparsing=2.3.1 scipy matplotlib pandas plotly
	conda init

	- name: Install Pytest
	run: \|
	pip install pytest pytest-cov

	- name: Install CRISPResso
	run: \|
	pip install .

	- name: Run Pytest
	run: \|
	pytest --cov CRISPResso2

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