renderNotebooks.yaml

# Github action that renders R markdown when PR is opened
# All R markdown is run in container/rmd.Dockerfile 

on:
  pull_request:
    types: [opened, reopened, edited]
  push:
  workflow_dispatch:

name: render-notebooks

jobs:
  render-rmarkdown:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

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


      - name: Check if Dockerfile changed
        id: dockerfile-check
        run: |
          if git diff --name-only HEAD^ HEAD | grep -q 'container/rmd.Dockerfile'; then
            echo "dockerfile_changed=true" >> $GITHUB_ENV
          else
            echo "dockerfile_changed=false" >> $GITHUB_ENV
          fi

      - name: Extract metadata (tags, labels) for Rmd Docker
        id: meta_rmd
        uses: docker/metadata-action@v5.3.0
        with:
          images: bcgsc/long-pog-rmd

      - name: Build and push Docker image
        if: env.dockerfile_changed == 'true'
        uses: docker/build-push-action@v5
        with:
          file: container/rmd.Dockerfile
          context: .
          push: true 
          tags: ${{ steps.meta_rmd.outputs.tags }}
          labels: ${{ steps.meta_rmd.outputs.labels }}


      - name: Check for changed R Markdown files
        id: check_rmd_files
        run: |
          CHANGED_RMD_FILES=$(git diff --name-only HEAD^ HEAD -- '*.Rmd' '*.rmd')
          if [ -n "$CHANGED_RMD_FILES" ]; then
            echo "Changed R Markdown files:"
            echo "$CHANGED_RMD_FILES"
            echo "::set-output name=has_changed::true"
            echo "$CHANGED_RMD_FILES" > changed_rmd_files.txt
          else
            echo "No changed R Markdown files found."
            echo "::set-output name=has_changed::false"
          fi
        
      - name: Run Docker container to compile changed R Markdown files
        if: steps.check_rmd_files.outputs.has_changed == 'true'
        uses: addnab/docker-run-action@v3
        with:
          image: ${{ steps.meta_rmd.outputs.tags }}
          options: |
            -v ${{ github.workspace }}:/workspace \
            -v /tmp/cache:/root/.cache \
            --rm -u root
          run: |
            CHANGED_RMD_FILES=$(cat changed_rmd_files.txt)
            for RMD in $CHANGED_RMD_FILES; do
              Rscript -e 'for (f in commandArgs(TRUE)) if (file.exists(f)) rmarkdown::render(f, output_format = "all")' /workspace/$RMD
            done


      - uses: stefanzweifel/git-auto-commit-action@v5


  render_jupyter:
    runs-on: ubuntu-latest
    needs: render-rmarkdown

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


    
    - name: Check if Dockerfile changed
      id: dockerfile-check
      run: |
          if git diff --name-only HEAD^ HEAD | grep -q 'container/jupyter.Dockerfile'; then
            echo "dockerfile_changed=true" >> $GITHUB_ENV
          else
            echo "dockerfile_changed=false" >> $GITHUB_ENV
          fi

    - name: Extract metadata (tags, labels) for Jupyter Docker
      id: meta_jupyter
      uses: docker/metadata-action@v5.3.0
      with:
        images: bcgsc/long-pog-jupyter

    - name: Build and push Docker image
      if: env.dockerfile_changed == 'true'
      uses: docker/build-push-action@v5
      with:
        file: container/jupyter.Dockerfile
        context: .
        push: true
        tags: ${{ steps.meta_jupyter.outputs.tags }}
        labels: ${{ steps.meta_jupyter.outputs.labels }}



    - name: Check for changed Jupyter Notebook files
      id: check_ipynb_files
      run: |
        CHANGED_IPYNB_FILES=$(git diff --name-only HEAD^ HEAD -- '*.ipynb')
        if [ -n "$CHANGED_IPYNB_FILES" ]; then
          echo "Changed Jupyter Notebook files:"
          echo "$CHANGED_IPYNB_FILES"
          echo "::set-output name=has_changed::true"
          echo "$CHANGED_IPYNB_FILES" > changed_ipynb_files.txt
        else
          echo "No changed Jupyter Notebook files found."
          echo "::set-output name=has_changed::false"
        fi
      
    - name: Run Docker container to compile changed Jupyter Notebooks
      if: steps.check_ipynb_files.outputs.has_changed == 'true'
      uses: addnab/docker-run-action@v3
      with:
        image: ${{ steps.meta_jupyter.outputs.tags }}
        options: |
          -v ${{ github.workspace }}:/workspace \
          -v /tmp/cache:/root/.cache \
          --rm -u root
        run: |
          CHANGED_IPYNB_FILES=$(cat changed_ipynb_files.txt)
          for NOTEBOOK in $CHANGED_IPYNB_FILES; do
            jupyter nbconvert --to html --execute /workspace/$NOTEBOOK
            jupyter nbconvert --to markdown --execute /workspace/$NOTEBOOK
          done


    - uses: stefanzweifel/git-auto-commit-action@v5