transform-notebooks.yml

name: Strip Python and R Notebooks from Outputs and Transform .irnb to .Rmd

on:
  push:
    branches:
      - main
      - gen-Rmd

concurrency:
  group: strip-transform-notebooks-${{ github.ref }}
  cancel-in-progress: true

jobs:
  strip-transform-notebooks:
    runs-on: ubuntu-latest

    steps:
    - name: Checkout repository
      uses: actions/checkout@v3
      with:
          fetch-depth: 0

    - name: Set up Python
      uses: actions/setup-python@v2
      with:
        python-version: '3.10'  # Use Python 3.10

    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install jupyter nbstripout
      shell: bash

    - name: Set up R
      uses: r-lib/actions/setup-r@v2

    - name: Install rmarkdown package
      run: |
        R -e 'install.packages(c("rmarkdown"), repos="https://cloud.r-project.org")'

    - name: Strip outputs from .ipynb files
      run: |
        dirs=(PM1 PM2 PM3 PM4 PM5 CM1 CM2 CM3 AC1 AC2 T)
        for dir in "${dirs[@]}"; do
        # Check if directory exists
        if [ -d "$dir" ]; then
            echo "Processing directory: $dir"
            # Loop over all .ipynb files in the directory (non-recursively)
            for notebook in "$dir"/*.ipynb; do
                # Check if there are any .ipynb files
                if [ -e "$notebook" ]; then
                    echo "Stripping output from notebook: $notebook"
                    nbstripout "$notebook"
                fi
            done
            for notebook in "$dir"/*.irnb; do
                # Check if there are any .irnb files
                if [ -e "$notebook" ]; then                    
                    echo "Stripping output from notebook: $notebook"
                    ipynb_notebook=$(mktemp --suffix=.ipynb)
                    mv "$notebook" "$ipynb_notebook"
                    nbstripout "$ipynb_notebook"
                    mv "$ipynb_notebook" "$notebook"
                fi
            done
            echo "Converting .irnb to .Rmd to update the .Rmd version"
            R -e "
              files <- list.files(path = '$dir', pattern = '\\\\.irnb$', full.names = TRUE, recursive = FALSE)
              lapply(files, function(input) {
                rmarkdown::convert_ipynb(input)
              })
            "
        else
            echo "Directory $dir does not exist."
        fi
        done

    - name: Check if there are any changes (e.g. stripped outputs)
      id: verify_diff
      run: |
        git pull
        git status --porcelain
        CHANGES=$(git status --porcelain)
        if [ -z "$CHANGES" ]; then
            echo "No changes were found"
        else
            echo "Found changes"
            echo "$CHANGES"
            echo "changed=true" >> $GITHUB_OUTPUT
            break 1
        fi

    - name: Commit and push stripped .ipynb files
      if: steps.verify_diff.outputs.changed == 'true'
      run: |
        git config --global user.name 'github-actions[bot]'
        git config --global user.email 'github-actions[bot]@users.noreply.github.com'
        git pull
        dirs=(PM1 PM2 PM3 PM4 PM5 CM1 CM2 CM3 AC1 AC2 T)
        for dir in "${dirs[@]}"; do
            # Check if directory exists
            if [ -d "$dir" ]; then
                echo "Adding changed files from directory: $dir"
                git add "$dir"/*.ipynb "$dir"/*.irnb "$dir"/*.Rmd
            else
                echo "Directory $dir does not exist."
            fi
        done
        git commit -m 'Strip outputs from .ipynb files [skip ci]'
        git push --force-with-lease
      env:
        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}