Merge branch 'main' into copilot/convert-repo-to-quarto-website #13
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| # GitHub Copilot Setup Steps for rme | |
| # | |
| # This workflow configures the GitHub Copilot coding agent's environment | |
| # by preinstalling R, Quarto, TinyTeX, 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 >= 3.5 (as specified in DESCRIPTION, prefer latest release) | |
| # - Quarto CLI for rendering the website | |
| # - TinyTeX for PDF output | |
| # - JAGS for Bayesian analysis (rjags and runjags packages) | |
| # - All package dependencies managed via renv | |
| 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 renv.lock | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| # Install system dependencies required for R packages | |
| # See .github/copilot-instructions.md "System Dependencies" and "JAGS Dependencies" sections | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y \ | |
| jags \ | |
| libcurl4-openssl-dev \ | |
| libssl-dev \ | |
| libxml2-dev \ | |
| libfontconfig1-dev \ | |
| libharfbuzz-dev \ | |
| libfribidi-dev \ | |
| libfreetype6-dev \ | |
| libpng-dev \ | |
| libtiff5-dev \ | |
| libjpeg-dev | |
| # 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 >= 3.5 required (see DESCRIPTION and .github/copilot-instructions.md) | |
| # Using 'release' to get the latest R version | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 'release' | |
| use-public-rspm: true | |
| # Set up Quarto - required for rendering the website | |
| # See .github/copilot-instructions.md "Quarto Rendering" section | |
| - name: Set up Quarto | |
| uses: quarto-dev/quarto-actions/setup@v2 | |
| with: | |
| tinytex: true | |
| # Install R dependencies using renv | |
| # This project uses renv for package management | |
| # See .github/copilot-instructions.md "R Package Management" section | |
| - name: Install R dependencies via renv | |
| uses: r-lib/actions/setup-renv@v2 | |
| with: | |
| cache-version: 1 | |
| # Verify R environment is properly configured | |
| # See .github/copilot-instructions.md sections on development setup | |
| - 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 (>= 3.5) | |
| r_version <- paste(R.version$major, R.version$minor, sep = ".") | |
| cat("Checking R version >= 3.5... ") | |
| if (getRversion() >= "3.5") { | |
| cat("PASSED (", r_version, ")\n\n", sep = "") | |
| } else { | |
| cat("FAILED (", r_version, ")\n\n", sep = "") | |
| stop("R version must be >= 3.5") | |
| } | |
| # Display key installed packages from DESCRIPTION | |
| cat("Key installed packages:\n") | |
| key_packages <- c("arm", "arsenal", "cards", "cardx", "cvTools", "dobson", | |
| "forcats", "fs", "glmmTMB", "glmnet", "gtsummary", "here", | |
| "insight", "knitr", "latex2exp", "olsrr", "pander", "printr", | |
| "reactable", "rlang", "rmarkdown", "stringr", "table1", "tibble", | |
| "webshot2", "tidyverse", "rjags", "runjags", "ggplot2", "dplyr", | |
| "tidyr", "spelling", "gh", "lintr", "purrr", "pkgdown") | |
| 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") | |
| ' | |
| # Verify Quarto is installed and working | |
| echo "" | |
| echo "=== Quarto Status ===" | |
| quarto --version | |
| quarto list tools | |
| # Verify JAGS is installed | |
| echo "" | |
| echo "=== JAGS Status ===" | |
| if which jags > /dev/null 2>&1; then | |
| echo "JAGS found in PATH" | |
| jags -v 2>&1 || echo "JAGS installed but version check failed" | |
| else | |
| echo "JAGS not found in PATH" | |
| fi | |
| # Verify renv is active | |
| echo "" | |
| echo "=== renv Status ===" | |
| Rscript -e 'cat("renv active:", !is.null(renv::project()), "\n")' | |
| Rscript -e 'cat("renv library path:", .libPaths()[1], "\n")' | |
| echo "" | |
| echo "Development environment setup complete!" |