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ci.yml
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name: ci
on:
push:
branches:
- master
- main
- final-cleanup
- rename-repo-astral
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