check-and-transform-R-notebooks.yml

name: Check R Notebooks

on:
  pull_request:
    branches:
      - main
  schedule:
    - cron: '0 12 * * 0'  # Runs every Sunday at 12 PM UTC

concurrency:
  group: test-R-notebooks-${{ github.ref }}
  cancel-in-progress: true

jobs:
  test-R-notebooks:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        directory: ['PM1', 'PM2', 'PM3', 'PM4', 'PM5', 'CM1', 'CM2', 'CM3', 'AC1', 'AC2', 'T']
    steps:
      - name: Checkout repository
        uses: actions/checkout@v3
        with:
          fetch-depth: ${{ github.event_name == 'pull_request' && 2 || 0 }}

      - name: Find changed notebooks in PR
        if: github.event_name == 'pull_request'
        id: find_notebooks_pr
        run: |
          # git fetch origin ${{ github.event.pull_request.base.ref }} ${{ github.event.pull_request.head.ref }}
          # git diff --name-only origin/${{ github.event.pull_request.base.ref }}...origin/${{ github.event.pull_request.head.ref }} > changed_files.txt
          git diff --name-only -r HEAD^1 HEAD > changed_files.txt
          if grep -q -E '^${{ matrix.directory }}/.*\.Rmd$' changed_files.txt; then
            echo "Changing directly the .Rmd files is prohibited. You should only be changing the .irnb files"
            echo "The .Rmd files will be automatically generated and updated when the PR is merged in the main branch"
            echo "It seems that you changed directly the following files:"
            grep -E '^${{ matrix.directory }}/.*\.Rmd$' changed_files.txt
            exit 1
          fi
          grep -E '^${{ matrix.directory }}/.*\.irnb$|\.github/workflows/check-and-transform-R-notebooks.yml$' changed_files.txt > changed_notebooks.txt || echo "No notebooks changed" > changed_notebooks.txt

      - name: Find changed notebooks in Push
        if: github.event_name == 'push'
        id: find_notebooks_push
        run: |
          git diff --name-only ${{ github.event.before }} ${{ github.event.after }} > changed_files.txt
          grep  -E '^${{ matrix.directory }}/.*\.irnb$|\.github/workflows/check-and-transform-R-notebooks.yml$' changed_files.txt > changed_notebooks.txt || echo "No notebooks changed" > changed_notebooks.txt

      - name: Check if any notebooks changed in PR or Push
        if: (github.event_name == 'push') || (github.event_name == 'pull_request')
        id: check_notebooks
        run: |
          cat changed_notebooks.txt
          if grep -q -E '^${{ matrix.directory }}/.*\.irnb$|\.github/workflows/check-and-transform-R-notebooks.yml$' changed_notebooks.txt; then
            echo "notebooks_changed=true" >> $GITHUB_ENV
          else
            echo "notebooks_changed=false" >> $GITHUB_ENV
            echo "No R notebooks changed in folder ${{ matrix.directory }} in this PR."
          fi

      - name: Set notebooks changed to true for schedule
        if: "! ((github.event_name == 'push') || (github.event_name == 'pull_request'))"
        id: set_check_notebooks_true
        run: |
          # we run all folders if it is the weekly scheduled run to
          # check if something broke due to changes in dependencies
          echo "notebooks_changed=true" >> $GITHUB_ENV

      - name: Install system dependencies
        if: env.notebooks_changed == 'true'
        run: |
          sudo apt-get update
          sudo apt-get install -y libcurl4-openssl-dev

      - name: Set up Python
        if: env.notebooks_changed == 'true'
        uses: actions/setup-python@v2
        with:
          python-version: '3.10'  # Specify your Python version here

      - name: Install Python dependencies
        if: env.notebooks_changed == 'true'
        run: |
          python -m pip install --upgrade pip
          pip install nbstripout
          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
        shell: bash

      - name: Set up R
        if: env.notebooks_changed == 'true'
        uses: r-lib/actions/setup-r@v2

      - name: Install rmarkdown, knitr, and lintr packages
        if: env.notebooks_changed == 'true'
        run: |
          R -e 'install.packages(c("rmarkdown", "knitr", "lintr", "xfun", "remotes"), repos="https://cloud.r-project.org")'

      - name: Strip outputs from .irnb files
        if: env.notebooks_changed == 'true'
        run: |
          for notebook in ${{ matrix.directory }}/*.irnb; do
            ipynb_notebook="${notebook%.irnb}.ipynb"
            mv "$notebook" "$ipynb_notebook"
            nbstripout "$ipynb_notebook"
            mv "$ipynb_notebook" "$notebook"
          done

      - name: Convert .irnb to .Rmd and .R
        if: env.notebooks_changed == 'true'
        run: |
          R -e '
            files <- list.files(path = "${{ matrix.directory }}", pattern = "\\.irnb$", full.names = TRUE, recursive = FALSE)
            lapply(files, function(input) {
              rmarkdown::convert_ipynb(input)
              rmd_file <- xfun::with_ext(input, "Rmd")
              knitr::purl(rmd_file, output = xfun::with_ext(input, "R"))
            })
          '

      - name: Lint .Rmd files
        if: env.notebooks_changed == 'true'
        id: lint
        run: |
          R -e '
            library(lintr)
            linters <- with_defaults(line_length_linter = line_length_linter(120),
                                     object_name_linter = object_name_linter(styles = c("snake_case", "CamelCase", "camelCase")),
                                     object_usage_linter = NULL)
            rmd_files <- list.files(path = "${{ matrix.directory }}", pattern = "\\.Rmd$", full.names = TRUE)
            results <- lapply(rmd_files, function(file) {
              lints <- lint(file, linters)
              if (length(lints) > 0) {
                cat("Warnings found during linting:\n")
                print(lints)
                stop("Linting failed with warnings")
              }
            })
          '

      - name: Execute R scripts and log output
        if: env.notebooks_changed == 'true'
        id: execute
        run: |
          log_file="${{ matrix.directory }}_r_script_execution.log"
          R -e '
            options(show.error.locations = TRUE)
            files <- list.files(path = "${{ matrix.directory }}", pattern = "\\.R$", full.names = TRUE, recursive = FALSE)
            log_con <- file("'$log_file'", open = "wt")
            sink(log_con, type = "output")
            sink(log_con, type = "message")
            errors <- list()
            for (gitrfile in files) {
              withCallingHandlers(
                withRestarts(
                  source(gitrfile),
                  muffleStop = function() NULL
                ),
                error = function(e) {
                  traceback_info <- sys.calls()
                  errors[[length(errors) + 1]] <<- list(gitrfile = gitrfile, location = capture.output(print(e$call)), message = e$message, traceback = traceback_info)
                  invokeRestart("muffleStop")
                  }
                )
            }
            sink(type = "output")
            sink(type = "message")
            close(log_con)
            if (length(errors) > 0) {
              for (error in errors) {
                cat("Error found in file:", error$gitrfile, "\n")
                cat("at line::", error$location, "\n")
                cat("Error message:", error$message, "\n")
                print("Traceback:\n")
                cat(paste(error$traceback, collapse = "\n"))
                print("\n")
              }
              quit(status = 1, save = "no")  # Exit with an error status if errors are found
            }
          ' 2>/dev/null
        env:
          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

      - name: Upload execution log
        if: env.notebooks_changed == 'true'
        uses: actions/upload-artifact@v2
        with:
          name: ${{ matrix.directory }}-r-script-execution-log
          path: ${{ matrix.directory }}_r_script_execution.log

      - name: Zip .R files
        if: env.notebooks_changed == 'true'
        run: |
          mkdir r_scripts
          mv ${{ matrix.directory }}/*.R r_scripts/
          zip -r ${{ matrix.directory }}_r_scripts.zip r_scripts

      - name: Upload artifact
        if: env.notebooks_changed == 'true'
        uses: actions/upload-artifact@v2
        with:
          name: ${{ matrix.directory }}-r-scripts
          path: ${{ matrix.directory }}_r_scripts.zip

      - name: Delete .R files and zip
        if: env.notebooks_changed == 'true'
        run: |
          rm -rf r_scripts
          rm ${{ matrix.directory }}_r_scripts.zip

      # - name: Check out the branch for pull request
      #   if: "(github.event_name == 'pull_request') && (env.notebooks_changed == 'true')"
      #   run: |
      #     git fetch --all
      #     git checkout ${{ github.event.pull_request.head.ref }}

      # - name: Check if there are any changes
      #   if: env.notebooks_changed == 'true'
      #   id: verify_diff
      #   run: |
      #     git pull
      #     git diff --quiet ${{ matrix.directory }}/*.irnb ${{ matrix.directory }}/*.Rmd || echo "changed=true" >> $GITHUB_OUTPUT

      # - name: Commit and push stripped .irnb and .Rmd files
      #   if: "(env.notebooks_changed == 'true') && (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
      #     git add ${{ matrix.directory }}/*.irnb ${{ matrix.directory }}/*.Rmd
      #     git commit -m 'Strip outputs from .irnb, convert to .Rmd, lint .Rmd files, and execute .R files in ${{ matrix.directory }} [skip ci]'
      #     git push --force-with-lease
      #   env:
      #     GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}