docs.yml

name: Deploy Documentation

on:
  workflow_dispatch:
    inputs:
      branch:
        description: "Branch to run action on"
        required: false
        default: "main"

permissions:
  contents: write
  pages: write
  id-token: write

jobs:
  deploy:
    runs-on: ubuntu-latest

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
        with:
          fetch-depth: 0

      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: '3.11'
          cache: 'pip'

      - name: Install MkDocs and plugins
        run: |
          python -m pip install --upgrade pip
          pip install mkdocs \
                      mkdocs-material \
                      mkdocstrings \
                      mkdocstrings-python \
                      pymdown-extensions \
                      pygments \
                      mkdocs-git-revision-date-localized-plugin

      - name: Configure Git
        run: |
          git config --global user.name "GitHub Actions"
          git config --global user.email "actions@github.com"

      - name: Build documentation
        run: mkdocs build --strict
        env:
          GOOGLE_ANALYTICS_KEY: ${{ secrets.GOOGLE_ANALYTICS_KEY }}

      - name: Check for broken links
        run: |
          if [ -f ./site/404.html ]; then
            echo "🔍 Checking for broken links..."
            if grep -r "404.html" ./site/; then
              echo "❌ Broken links found."
              exit 1
            fi
          fi

      - name: Deploy to GitHub Pages
        uses: peaceiris/actions-gh-pages@v3
        with:
          github_token: ${{ secrets.GITHUB_TOKEN }}
          publish_dir: ./site
          force_orphan: true
          user_name: 'github-actions[bot]'
          user_email: 'github-actions[bot]@users.noreply.github.com'
          commit_message: 'docs: update documentation'

      - name: Check deployment status
        run: |
          SITE_URL="https://holobiomicslab.github.io/MetaboT/"
          for i in {1..10}; do
            HTTP_STATUS=$(curl -s -o /dev/null -w "%{http_code}" --max-time 10 $SITE_URL)
            if [ "$HTTP_STATUS" -eq 200 ]; then
              echo "✅ Documentation deployed successfully at $SITE_URL"
              exit 0
            fi
            echo "⌛ Waiting for GitHub Pages... ($i)"
            sleep 15
          done
          echo "❌ Deployment check failed after waiting."
          exit 1