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Merge pull request #317 from d-morrison/copilot/adapt-copilot-setup-steps
Add copilot-setup-steps workflow for automated environment configuration
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‎.github/workflows/copilot-setup-steps.yml‎

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# GitHub Copilot Setup Steps for rme
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#
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# This workflow configures the GitHub Copilot coding agent's environment
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# by preinstalling R, Quarto, TinyTeX, and all required dependencies.
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#
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# See: https://docs.github.com/en/copilot/how-tos/use-copilot-agents/coding-agent/customize-the-agent-environment
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# For detailed setup instructions, see .github/copilot-instructions.md
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#
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# This workflow aligns with the setup requirements documented in .github/copilot-instructions.md:
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# - R version >= 3.5 (as specified in DESCRIPTION, prefer latest release)
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# - Quarto CLI for rendering the website
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# - TinyTeX for PDF output
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# - JAGS for Bayesian analysis (rjags and runjags packages)
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# - All package dependencies managed via renv
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name: "Copilot Setup Steps"
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# Automatically run the setup steps when they are changed to allow for easy validation,
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# and allow manual testing through the repository's "Actions" tab
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on:
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workflow_dispatch:
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push:
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paths:
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- .github/workflows/copilot-setup-steps.yml
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pull_request:
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paths:
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- .github/workflows/copilot-setup-steps.yml
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jobs:
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# The job MUST be called `copilot-setup-steps` or it will not be picked up by Copilot.
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copilot-setup-steps:
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runs-on: ubuntu-latest
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# Set the permissions to the lowest permissions possible needed for your steps.
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# Copilot will be given its own token for its operations.
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permissions:
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contents: read
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# Timeout after 55 minutes (max is 59 for copilot-setup-steps)
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timeout-minutes: 55
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steps:
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# Checkout code - Copilot will do this automatically if we don't,
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# but we need it to install dependencies from renv.lock
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- name: Checkout code
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uses: actions/checkout@v4
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# Install system dependencies required for R packages
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# See .github/copilot-instructions.md "System Dependencies" and "JAGS Dependencies" sections
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- name: Install system dependencies
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run: |
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sudo apt-get update
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sudo apt-get install -y \
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jags \
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libcurl4-openssl-dev \
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libssl-dev \
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libxml2-dev \
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libfontconfig1-dev \
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libharfbuzz-dev \
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libfribidi-dev \
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libfreetype6-dev \
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libpng-dev \
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libtiff5-dev \
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libjpeg-dev
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# Set up pandoc for documentation
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- name: Set up Pandoc
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uses: r-lib/actions/setup-pandoc@v2
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# Set up R using the standard GitHub Actions setup
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# R version >= 3.5 required (see DESCRIPTION and .github/copilot-instructions.md)
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# Using 'release' to get the latest R version
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- name: Set up R
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uses: r-lib/actions/setup-r@v2
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with:
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r-version: 'release'
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use-public-rspm: true
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# Set up Quarto - required for rendering the website
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# See .github/copilot-instructions.md "Quarto Rendering" section
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- name: Set up Quarto
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uses: quarto-dev/quarto-actions/setup@v2
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with:
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tinytex: true
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# Install R dependencies using renv
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# This project uses renv for package management
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# See .github/copilot-instructions.md "R Package Management" section
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- name: Install R dependencies via renv
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uses: r-lib/actions/setup-renv@v2
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with:
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cache-version: 1
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# Verify R environment is properly configured
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# See .github/copilot-instructions.md sections on development setup
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- name: Verify development environment
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run: |
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echo "=== R Development Environment Status ==="
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Rscript -e '
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cat("R version:", R.version.string, "\n\n")
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# Check R version meets minimum requirement (>= 3.5)
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r_version <- paste(R.version$major, R.version$minor, sep = ".")
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cat("Checking R version >= 3.5... ")
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if (getRversion() >= "3.5") {
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cat("PASSED (", r_version, ")\n\n", sep = "")
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} else {
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cat("FAILED (", r_version, ")\n\n", sep = "")
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stop("R version must be >= 3.5")
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}
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# Display key installed packages from DESCRIPTION
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cat("Key installed packages:\n")
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key_packages <- c("arm", "arsenal", "cards", "cardx", "cvTools", "dobson",
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"forcats", "fs", "glmmTMB", "glmnet", "gtsummary", "here",
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"insight", "knitr", "latex2exp", "olsrr", "pander", "printr",
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"reactable", "rlang", "rmarkdown", "stringr", "table1", "tibble",
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"webshot2", "tidyverse", "rjags", "runjags", "ggplot2", "dplyr",
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"tidyr", "spelling", "gh", "lintr", "purrr", "pkgdown")
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for (pkg in key_packages) {
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if (requireNamespace(pkg, quietly = TRUE)) {
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cat(" -", pkg, ":", as.character(packageVersion(pkg)), "\n")
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} else {
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cat(" -", pkg, ": NOT INSTALLED\n")
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}
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}
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cat("\nTotal packages installed:", nrow(installed.packages()), "\n")
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'
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# Verify Quarto is installed and working
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echo ""
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echo "=== Quarto Status ==="
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quarto --version
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quarto list tools
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# Verify JAGS is installed
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echo ""
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echo "=== JAGS Status ==="
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if which jags > /dev/null 2>&1; then
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echo "JAGS found in PATH"
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jags -v 2>&1 || echo "JAGS installed but version check failed"
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else
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echo "JAGS not found in PATH"
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fi
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# Verify renv is active
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echo ""
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echo "=== renv Status ==="
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Rscript -e 'cat("renv active:", !is.null(renv::project()), "\n")'
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Rscript -e 'cat("renv library path:", .libPaths()[1], "\n")'
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echo ""
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echo "Development environment setup complete!"

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