copilot-setup-steps.yaml

name: Copilot Agent Setup

# Configure the environment for GitHub Copilot coding agent
# This ensures R is available when the agent works on this repository
# Uses native R installation (containers may cause compatibility issues with Copilot's setup)

on:
  workflow_dispatch:
  workflow_call:

jobs:
  copilot-setup-steps:
    runs-on: ubuntu-latest

    # Set the permissions to the lowest permissions possible needed for your steps.
    # Copilot will be given its own token for its operations.
    permissions:
      # If you want to clone the repository as part of your setup steps, for example to install dependencies, you'll need the `contents: read` permission. If you don't clone the repository in your setup steps, Copilot will do this for you automatically after the steps complete.
      contents: read

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Set up R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: 'release'

      - name: Install R dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          cache-version: 1

      - name: Verify R installation
        run: |
          R --version
          R -e "sessionInfo()"
      
      # Additional steps for the Copilot agent would be invoked here
      # The agent will have access to R in this environment