docs-auto.yml

name: ODK data, Run analysis, and Deploy
on:
  # Keep the push trigger for manual updates
  push:
    branches: [main]
  # Add scheduled runs at 11am and 12pm UTC daily
  schedule:
    - cron: '0 8 * * *'   # 11am EAT (8am UTC)
    - cron: '0 9 * * *'   # 12pm EAT (9am UTC)
    # Allow manual triggering
  workflow_dispatch:

env:
  # `BASE_URL` determines the website is served from, including CSS & JS assets
  BASE_URL: /${{ github.event.repository.name }}

# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
permissions:
  contents: read
  pages: write
  id-token: write

# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
concurrency:
  group: 'pages'
  cancel-in-progress: false

jobs:
  deploy:
    environment:
      name: github-pages
      url: ${{ steps.deployment.outputs.page_url }}
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      
      # Set up Python for ODK data processing
      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: '3.10'
          
      - name: Install Python dependencies
        run: |
          python -m pip install --upgrade pip
          pip install papermill plotly pandas requests ipykernel
          python -m ipykernel install --user --name python3
      
      # Pull data from ODK
      - name: Pull data from ODK
        run: python .github/pull_odk_data.py
        env:
          ODK_EMAIL: ${{ secrets.ODK_EMAIL }}
          ODK_PASSWORD: ${{ secrets.ODK_PASSWORD }}
      
      # Execute the notebook with papermill
      - name: Execute notebook with papermill
        run: |
          # Adjust the path to your notebook
          papermill sampling/odk/morpho-id-auto.ipynb docs/anokin-site/notebooks/morpho-id.ipynb
      
      # Setup Node.js for MyST
      - uses: actions/setup-node@v4
        with:
          node-version: 18.x
      
      - name: Install MyST Markdown
        run: npm install -g mystmd
      
      - name: Build HTML Assets
        run: cd docs/anokin-site && myst build --html
      
      - name: Debug Build Output
        run: ls -R docs/anokin-site/_build/html
      
      - name: Upload artifact
        uses: actions/upload-pages-artifact@v3
        with:
          path: 'docs/anokin-site/_build/html'
      
      - name: Deploy to GitHub Pages
        id: deployment
        uses: actions/deploy-pages@v4