docs.yml

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.