Merge pull request #31 from TurakhiaLab/documentation #71

	name: ci

	on:
	push:
	branches:
	- master
	- main
	- final-cleanup
	- rename-repo-astral
	- video_embed

	permissions:
	contents: write

	jobs:
	deploy:
	name: Deploy Job
	runs-on: ubuntu-latest
	steps:
	- name: Checkout Code
	uses: actions/checkout@v3

	- name: Set up Python
	uses: actions/setup-python@v4
	with:
	python-version: 3.x

	- name: Cache dependencies
	uses: actions/cache@v2
	with:
	key: ${{ github.ref }}
	path: .cache

	- name: Download and Unzip Genomes
	run: \|
	mkdir -p test/test_data
	while IFS= read -r link; do
	file_name=$(basename "$link")
	wget -O "test/test_data/$file_name" "$link"
	done < test/input_genome_links.txt

	- name: Set up Conda
	uses: conda-incubator/setup-miniconda@v2
	with:
	miniforge-variant: Mambaforge
	channels: conda-forge, bioconda
	activate-environment: roadies_env_test
	environment-file: test/roadies_env_test.yaml

	- name: Run Tests
	shell: bash -l {0}
	run: \|
	chmod +x test/roadies_env_test.sh
	source test/roadies_env_test.sh
	pip3 install ete3 six numpy PyYAML
	python run_roadies.py --cores 32 --config test/test_config.yaml --mode accurate

	- name: Install dependencies for mkdocs
	run: \|
	pip install mkdocs-material
	pip install "mkdocs-material[imaging]"

	- run: mkdocs gh-deploy --force

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