copilot-setup-steps.yml

# GitHub Copilot Setup Steps for serodynamics
#
# This workflow configures the GitHub Copilot coding agent's environment
# by preinstalling R, JAGS, and all required dependencies.
#
# See: https://docs.github.com/en/copilot/how-tos/use-copilot-agents/coding-agent/customize-the-agent-environment
# For detailed setup instructions, see .github/copilot-instructions.md
#
# This workflow aligns with the setup requirements documented in .github/copilot-instructions.md:
# - R version >= 4.1.0 (as specified in DESCRIPTION)
# - JAGS 4.3.1 system library and R interface
# - All package dependencies (Imports, Suggests, and development needs)

name: "Copilot Setup Steps"

# Automatically run the setup steps when they are changed to allow for easy validation,
# and allow manual testing through the repository's "Actions" tab
on:
  workflow_dispatch:
  push:
    paths:
      - .github/workflows/copilot-setup-steps.yml
  pull_request:
    paths:
      - .github/workflows/copilot-setup-steps.yml

jobs:
  # The job MUST be called `copilot-setup-steps` or it will not be picked up by Copilot.
  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:
      contents: read
    
    # Timeout after 55 minutes (max is 59 for copilot-setup-steps)
    timeout-minutes: 55
    
    steps:
      # Checkout code - Copilot will do this automatically if we don't,
      # but we need it to install dependencies from DESCRIPTION
      - name: Checkout code
        uses: actions/checkout@v4
      
      # Install system dependencies required for R packages
      # See .github/copilot-instructions.md "Verify Development Environment" section
      - name: Install system dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y \
            libcurl4-openssl-dev \
            libssl-dev \
            libxml2-dev \
            libfontconfig1-dev \
            libharfbuzz-dev \
            libfribidi-dev \
            libfreetype6-dev \
            libpng-dev \
            libtiff5-dev \
            libjpeg-dev
      
      # Install JAGS (Just Another Gibbs Sampler) - REQUIRED for this package
      # Version 4.3.1 as documented in .github/copilot-instructions.md
      - name: Install JAGS
        run: |
          sudo apt-get install -y jags
          echo "JAGS installed successfully"
      
      # Set up pandoc for documentation
      - name: Set up Pandoc
        uses: r-lib/actions/setup-pandoc@v2
      
      # Set up R using the standard GitHub Actions setup
      # R version >= 4.1.0 required (see DESCRIPTION and .github/copilot-instructions.md)
      - name: Set up R
        uses: r-lib/actions/setup-r@HEAD
        with:
          r-version: 'release'
          use-public-rspm: true
      
      # Install R dependencies with caching for faster subsequent runs
      - name: Install R dependencies
        uses: r-lib/actions/setup-r-dependencies@HEAD
        with:
          extra-packages: |
            any::devtools
            any::rcmdcheck
            any::lintr
            any::spelling
            any::rmarkdown
          needs: check
      
      # Install rjags from source to ensure proper linking with JAGS
      # See .github/copilot-instructions.md "JAGS Installation" section
      - name: Install rjags
        run: |
          install.packages("rjags",
                    repos = "https://cloud.r-project.org",
                    type = "source",
                    verbose = TRUE)
          withr::local_options(warn = 2)
          library(rjags)
          library(runjags)
          runjags::findjags()
          runjags::testjags()
        shell: Rscript {0}
      
      # Verify JAGS installation
      # See .github/copilot-instructions.md "JAGS Installation" section for details
      - name: Verify JAGS installation
        run: |
          echo "=== Verifying JAGS Installation ==="
          echo "System JAGS command:"
          which jags || echo "Warning: jags command not found in PATH"
          echo ""
          echo "R JAGS interface packages:"
          Rscript -e 'cat("rjags version:", as.character(packageVersion("rjags")), "\n")'
          Rscript -e 'cat("runjags version:", as.character(packageVersion("runjags")), "\n")'
          echo ""
          echo "JAGS location (from runjags):"
          Rscript -e 'print(runjags::findjags())'
          echo ""
          echo "Running JAGS test:"
          Rscript -e 'runjags::testjags()'
      
      # Verify R environment is properly configured
      # See .github/copilot-instructions.md "Verify Development Environment" section
      - name: Verify development environment
        run: |
          echo "=== R Development Environment Status ==="
          Rscript -e '
            cat("R version:", R.version.string, "\n\n")
            
            # Check R version meets minimum requirement (>= 4.1.0)
            r_version <- paste(R.version$major, R.version$minor, sep = ".")
            cat("Checking R version >= 4.1.0... ")
            if (getRversion() >= "4.1.0") {
              cat("PASSED (", r_version, ")\n\n", sep = "")
            } else {
              cat("FAILED (", r_version, ")\n\n", sep = "")
              stop("R version must be >= 4.1.0")
            }
            
            # Display key installed packages
            cat("Key installed packages:\n")
            key_packages <- c("devtools", "rjags", "runjags", "rcmdcheck", "lintr", "spelling", "testthat")
            for (pkg in key_packages) {
              if (requireNamespace(pkg, quietly = TRUE)) {
                cat("  -", pkg, ":", as.character(packageVersion(pkg)), "\n")
              } else {
                cat("  -", pkg, ": NOT INSTALLED\n")
              }
            }
            
            cat("\nTotal packages installed:", nrow(installed.packages()), "\n")
            cat("\nDevelopment environment setup complete!\n")
          '