remove_deleted_tutorials.yml

name: Remove Deleted Tutorials

on:
  push:
    branches: [ master ]
    paths:
      - '**.mlx'

permissions:
  contents: write
  
jobs:
  remove-deleted-files:
    runs-on: self-hosted
    steps:
      - name: Checkout Source Repo
        uses: actions/checkout@v4
        with:
          repository: '${{ github.repository_owner }}/COBRA.tutorials'
          token: ${{ secrets.GITHUB_TOKEN }}
          fetch-depth: 0

      - name: Clone the destination repository
        shell: bash
        run: |
          rm -rf cobratoolbox
          echo "Cloning the destination repository: git@github.com:opencobra/cobratoolbox.git"
          git clone --depth 1 --branch gh-pages "https://x-access-token:${{ secrets.DEST_REPO_TOKEN }}@github.com/opencobra/cobratoolbox.git"

      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: '3.x'

      - name: Install Python dependencies
        shell: bash
        run: |
          python -m pip install --upgrade pip
          pip install beautifulsoup4

      - name: Detect Deleted mlx Files
        id: getDeletedFiles
        shell: bash
        run: |
          echo "Looking for last sync commit..."

          last_sync_commit=$(git log --grep="removed .pdf, .html and .m files" -n 1 --pretty=format:%H)

          if [[ -z "$last_sync_commit" ]]; then
            echo "No previous deletion sync commit found. Checking all history for deletions."
            # Look back further for any sync commit
            last_sync_commit=$(git log --grep="created .pdf, .mlx and .m files" -n 1 --pretty=format:%H)
          fi

          if [[ -z "$last_sync_commit" ]]; then
            echo "No sync commit found. Cannot determine deletions. Exiting."
            exit 0
          fi

          echo "Last sync commit: $last_sync_commit"
          changed_status=$(git diff --name-status "$last_sync_commit"..HEAD -- '*.mlx' || true)
          echo "Detected .mlx status rows (D/R only relevant for deletion):"
          echo "$changed_status" | grep -E '^(D|R[0-9]+)\s' || echo "None"

          deleted_files=$(echo "$changed_status" | awk -F '\t' '
            $1 == "D" { print $2 }
            $1 ~ /^R[0-9]+$/ { print $2 }
          ' | sort -u)

          if [[ -z "$deleted_files" ]]; then
            echo "No .mlx files deleted or renamed since last sync. Exiting."
            exit 0
          fi

          deleted_files=$(echo "$deleted_files" | tr '\n' ' ')
          echo "Found deleted files: $deleted_files"
          echo "deleted_files=$deleted_files" >> "$GITHUB_ENV"

      - name: Remove Deleted Files from Website
        shell: bash
        run: |
          if [[ -z "${deleted_files:-}" ]]; then
            echo "No files to delete. Skipping."
            exit 0
          fi

          cd cobratoolbox

          for file in $deleted_files; do
            if [[ $file != "" ]]; then
              echo "Processing deletion: $file"
              
              # Remove only HTML file from website
              HTML_FILE_NAME=$(basename "$file" .mlx).html
              HTML_FILE_PATH="stable/tutorials/$(dirname "$file")/$HTML_FILE_NAME"
              
              if [[ -f "$HTML_FILE_PATH" ]]; then
                echo "Removing $HTML_FILE_PATH from website"
                git rm "$HTML_FILE_PATH" || rm -f "$HTML_FILE_PATH"
              else
                echo "HTML file not found: $HTML_FILE_PATH"
              fi

              # Update index to remove entry and remove tutorial wrapper file
              echo "Updating cobratoolbox index to remove deleted tutorial..."
              python stable/remove_from_index.py "stable/tutorials/$(dirname "$file")/$HTML_FILE_NAME" || echo "Index update failed or script not found"
            fi
          done

          cd ..

      - name: Pushing the changes to website
        shell: bash
        run: |
          git config --global user.name "github-actions[bot]"
          git config --global user.email "github-actions[bot]@users.noreply.github.com"

          cd cobratoolbox
          
          # Add any remaining untracked deletions
          git add -A
          
          if git diff --cached --quiet && git diff --quiet; then
            echo "No changes to commit in cobratoolbox"
          else
            git commit -m "Remove deleted tutorials from source repo" || echo "Commit failed"
            git push "https://x-access-token:${{ secrets.DEST_REPO_TOKEN }}@github.com/opencobra/cobratoolbox.git" gh-pages
          fi
          
          cd ..

          rm -rf cobratoolbox

          echo "Deletion workflow completed."