patch chipseeker env (#1024) #2747
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name: docs | |
on: | |
push: | |
jobs: | |
docs: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v3 | |
with: | |
persist-credentials: false | |
- uses: actions/setup-python@v3 | |
with: | |
python-version: 3.8 | |
- name: Install dependencies 🔨 & Build 🔧 | |
run: | | |
# setup mambaforge | |
wget -q -O Mambaforge.sh "https://github.com/conda-forge/miniforge/releases/download/4.11.0-1/Mambaforge-$(uname)-$(uname -m).sh" | |
bash Mambaforge.sh -b -p "${HOME}/conda" > /dev/null | |
source "${HOME}/conda/etc/profile.d/conda.sh" | |
source "${HOME}/conda/etc/profile.d/mamba.sh" | |
mamba activate | |
# load channels | |
$CONDA/bin/conda config --add channels bioconda | |
$CONDA/bin/conda config --add channels conda-forge | |
# install seq2science with added docs requirements | |
declare -a requirements=( | |
"graphviz>=7" | |
"importlib_metadata=4.11.4" | |
"m2r2>=0.3.3" | |
"networkx>=3" | |
"sphinx>=6" | |
"sphinx_rtd_theme>=1.2" | |
"sphinx-argparse>=0.4" | |
) | |
cp requirements.yaml doc_reqs.yaml | |
for pkg in "${requirements[@]}"; do | |
echo " - conda-forge::${pkg}" >> doc_reqs.yaml | |
done | |
mamba env create --name seq2science --file doc_reqs.yaml | |
rm doc_reqs.yaml | |
mamba activate seq2science | |
pip3 install . | |
# make the docs | |
python docs/scripts/schemas.py | |
python docs/scripts/rule_description.py | |
python docs/scripts/gen_dags.py | |
cp CHANGELOG.md docs/content | |
sphinx-build docs/ build -W | |
touch build/.nojekyll | |
# only deploy | |
- name: Deploy 📬 | |
uses: JamesIves/github-pages-deploy-action@releases/v3 | |
if: github.ref == 'refs/heads/master' | |
with: | |
ACCESS_TOKEN: ${{ secrets.AccessToken }} | |
BRANCH: gh-pages # The branch the action should deploy to. | |
FOLDER: build # The folder the action should deploy. |