Merge pull request #10 from logsdon-lab/feature/cenplot #66

	name: CI

	on: [push, pull_request]

	jobs:
	test:
	runs-on: ubuntu-latest
	defaults:
	run:
	shell: bash -el {0}
	steps:
	# https://github.com/orgs/community/discussions/25678#discussioncomment-5242449
	- name: Delete huge unnecessary tools folder
	run: rm -rf /opt/hostedtoolcache

	- name: Checkout directory.
	uses: actions/checkout@v3
	with:
	lfs: 'true'

	- name: Setup Miniforge.
	uses: conda-incubator/setup-miniconda@v3
	with:
	miniforge-version: latest
	activate-environment: smk

	- name: Get date.
	id: get-date
	run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
	shell: bash

	- name: Cache conda env.
	uses: actions/cache@v3
	with:
	path: ${{ env.CONDA }}/envs
	key:
	conda-${{ runner.os }}--${{ runner.arch }}--${{
	steps.get-date.outputs.today }}-${{
	hashFiles('env.yaml') }}-${{ env.CACHE_NUMBER }}
	env:
	# Increase this value to reset cache if etc/example-environment.yml has not changed
	CACHE_NUMBER: 0
	id: cache

	- name: Update environment.
	run:
	conda env update -n smk -f 'env.yaml'
	if: steps.cache.outputs.cache-hit != 'true'

	- name: Test can generate Dockerfile.
	run: \|
	make dockerfile

	- name: Test scripts.
	run: \|
	pytest -vvv

	- name: Test run chr8 and chr21 workflow.
	run: \|
	snakemake -c 4 -p \
	--sdm conda \
	--configfile test/config/config.yaml \
	--show-failed-logs

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