First commit #1

	# This workflow will install Python dependencies, run tests and lint with a single version of Python
	# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

	name: CR-SeqGEM-RL

	on:
	push:
	branches: [ "main" ]
	pull_request:
	branches: [ "main" ]

	permissions:
	contents: read

	jobs:
	build:

	runs-on: ubuntu-latest
	# Do not ignore bash profile files. From:
	# https://github.com/marketplace/actions/setup-miniconda
	defaults:
	run:
	shell: bash -l {0}

	steps:
	- uses: actions/checkout@v4
	- name: Set up Python 3.9.19
	uses: actions/setup-python@v3
	with:
	python-version: "3.9.19"

	- name: Install clasp
	run: sudo apt-get install clasp

	- name: Install gringo
	run: sudo apt-get install gringo

	- name: Install libtinfo5
	run: sudo apt-get install libtinfo5

	- name: Install dependencies
	run: \|
	# $CONDA is an environment variable pointing to the root of the miniconda directory
	$CONDA/bin/conda env update --file environment.yml --name base

	- name: Lint with flake8
	run: \|
	$CONDA/bin/conda install flake8
	# stop the build if there are Python syntax errors or undefined names
	$CONDA/bin/flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
	# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
	$CONDA/bin/flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics

	- name: Test with pytest
	run: \|
	conda install pytest
	$CONDA/bin/pytest ./tests/

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