setup.sh

#!/usr/bin/env bash
#
# Setup script for "Brief Introduction to Data Analysis with R"
# Installs all required dependencies for building course materials
#

set -e

# Colors for output
RED='\033[0;31m'
GREEN='\033[0;32m'
YELLOW='\033[1;33m'
NC='\033[0m' # No Color

echo "======================================"
echo "Setup: Brief Introduction to Data Analysis with R"
echo "======================================"
echo ""

# Detect OS
OS="unknown"
if [[ "$OSTYPE" == "darwin"* ]]; then
    OS="macos"
elif [[ -f /etc/debian_version ]]; then
    OS="debian"
elif [[ -f /etc/redhat-release ]]; then
    OS="redhat"
elif [[ "$OSTYPE" == "msys" || "$OSTYPE" == "cygwin" ]]; then
    OS="windows"
fi

# Detect architecture
ARCH=$(uname -m)
IS_ARM=false
if [[ "$ARCH" == "arm64" || "$ARCH" == "aarch64" ]]; then
    IS_ARM=true
fi

echo "Detected OS: $OS"
echo "Architecture: $ARCH"
if [ "$IS_ARM" = true ]; then
    echo -e "${YELLOW}Note: ARM architecture detected${NC}"
fi
echo ""

# Function to check if a command exists
command_exists() {
    command -v "$1" >/dev/null 2>&1
}

# Function to print status
print_status() {
    if [ "$2" = "ok" ]; then
        echo -e "  $1: ${GREEN}OK${NC}"
    elif [ "$2" = "missing" ]; then
        echo -e "  $1: ${RED}MISSING${NC}"
    elif [ "$2" = "optional" ]; then
        echo -e "  $1: ${YELLOW}MISSING (optional)${NC}"
    fi
}

# ============================================================
# Step 1: Check/Install R
# ============================================================
echo "Step 1: Checking R installation..."

if command_exists R && command_exists Rscript; then
    R_VERSION=$(R --version 2>/dev/null | head -1)
    print_status "R" "ok"
    echo "         $R_VERSION"
else
    print_status "R" "missing"
    echo ""
    echo "R is required. Install it with:"
    echo ""
    case $OS in
        macos)
            if [ "$IS_ARM" = true ]; then
                echo "  Apple Silicon (ARM64) detected."
                echo ""
                echo "  Option 1 (Homebrew - recommended for ARM):"
                echo "    brew install r"
                echo ""
                echo "  Option 2 (Official ARM installer):"
                echo "    Download the arm64 build from https://cran.r-project.org/bin/macosx/"
                echo "    (Look for 'R-x.x.x-arm64.pkg')"
            else
                echo "  Option 1 (Homebrew):"
                echo "    brew install r"
                echo ""
                echo "  Option 2 (Official installer):"
                echo "    Download from https://cran.r-project.org/bin/macosx/"
            fi
            ;;
        debian)
            if [ "$IS_ARM" = true ]; then
                echo "  ARM64 Linux detected."
                echo ""
            fi
            echo "  sudo apt update"
            echo "  sudo apt install -y r-base r-base-dev"
            if [ "$IS_ARM" = true ]; then
                echo ""
                echo "  Note: Some R packages may need to compile from source on ARM."
                echo "  This may take longer but should work automatically."
            fi
            ;;
        redhat)
            echo "  sudo dnf install -y R"
            ;;
        windows)
            echo "  Download and install from https://cran.r-project.org/bin/windows/base/"
            ;;
        *)
            echo "  Download from https://cran.r-project.org/"
            ;;
    esac
    echo ""

    # Offer to install on supported systems
    if [[ "$OS" == "debian" ]]; then
        read -p "Install R now? [y/N] " -n 1 -r
        echo
        if [[ $REPLY =~ ^[Yy]$ ]]; then
            sudo apt update
            sudo apt install -y r-base r-base-dev
        else
            echo "Please install R and run this script again."
            exit 1
        fi
    elif [[ "$OS" == "macos" ]] && command_exists brew; then
        read -p "Install R via Homebrew now? [y/N] " -n 1 -r
        echo
        if [[ $REPLY =~ ^[Yy]$ ]]; then
            brew install r
        else
            echo "Please install R and run this script again."
            exit 1
        fi
    else
        echo "Please install R and run this script again."
        exit 1
    fi
fi

echo ""

# ============================================================
# Step 2: Check/Install Pandoc (required for rmarkdown)
# ============================================================
echo "Step 2: Checking Pandoc installation..."

if command_exists pandoc; then
    PANDOC_VERSION=$(pandoc --version | head -1)
    print_status "Pandoc" "ok"
    echo "         $PANDOC_VERSION"
else
    print_status "Pandoc" "missing"
    echo ""
    echo "Pandoc is required for rendering R Markdown. Install it with:"
    echo ""
    case $OS in
        macos)
            echo "  brew install pandoc"
            ;;
        debian)
            echo "  sudo apt install -y pandoc"
            ;;
        redhat)
            echo "  sudo dnf install -y pandoc"
            ;;
        windows)
            echo "  Download from https://pandoc.org/installing.html"
            ;;
        *)
            echo "  Download from https://pandoc.org/installing.html"
            ;;
    esac
    echo ""

    # Offer to install on supported systems
    if [[ "$OS" == "debian" ]]; then
        read -p "Install Pandoc now? [y/N] " -n 1 -r
        echo
        if [[ $REPLY =~ ^[Yy]$ ]]; then
            sudo apt install -y pandoc
        else
            echo "Please install Pandoc and run this script again."
            exit 1
        fi
    elif [[ "$OS" == "macos" ]] && command_exists brew; then
        read -p "Install Pandoc via Homebrew now? [y/N] " -n 1 -r
        echo
        if [[ $REPLY =~ ^[Yy]$ ]]; then
            brew install pandoc
        else
            echo "Please install Pandoc and run this script again."
            exit 1
        fi
    else
        echo "Please install Pandoc and run this script again."
        exit 1
    fi
fi

echo ""

# ============================================================
# Step 3: Check/Install LaTeX (for PDF output)
# ============================================================
echo "Step 3: Checking LaTeX installation (for PDF output)..."

if command_exists pdflatex; then
    print_status "LaTeX" "ok"
else
    print_status "LaTeX" "missing"
    echo ""
    echo "LaTeX is required for PDF output. Installing TinyTeX (lightweight LaTeX distribution)..."
    echo ""

    # Install TinyTeX via R
    Rscript --vanilla -e "
    if (!requireNamespace('tinytex', quietly = TRUE)) {
        install.packages('tinytex', repos = 'https://cloud.r-project.org', quiet = TRUE)
    }
    cat('Installing TinyTeX (this may take a few minutes)...\n')
    tinytex::install_tinytex(force = TRUE)
    "

    # Add TinyTeX to PATH for this session
    if [ -d "$HOME/bin" ]; then
        export PATH="$HOME/bin:$PATH"
    fi
    if [ -d "$HOME/.TinyTeX/bin/"* ]; then
        export PATH="$HOME/.TinyTeX/bin/"*":$PATH"
    fi

    # Verify installation
    if command_exists pdflatex; then
        echo -e "${GREEN}TinyTeX installed successfully${NC}"
    else
        echo -e "${YELLOW}TinyTeX installed but pdflatex not in PATH yet.${NC}"
        echo "You may need to restart your terminal or run:"
        echo "  export PATH=\"\$HOME/bin:\$PATH\""
    fi
fi

# Install additional LaTeX packages needed for the course materials
if command_exists tlmgr || [ -f "$HOME/.TinyTeX/bin/"*/tlmgr ]; then
    echo "Installing required LaTeX packages..."
    Rscript --vanilla -e "
    if (requireNamespace('tinytex', quietly = TRUE)) {
        tinytex::tlmgr_install(c('collection-fontsrecommended', 'fancyhdr', 'booktabs', 'caption', 'float', 'lastpage', 'geometry', 'babel-german'))
    }
    " 2>/dev/null || true
fi

echo ""

# ============================================================
# Step 4: Install R packages
# ============================================================
echo "Step 4: Installing R packages..."

if [ "$IS_ARM" = true ]; then
    echo -e "${YELLOW}Note: On ARM, some packages may compile from source (this may take a few minutes)${NC}"
    echo ""
fi

# Required packages (must match Makefile)
R_PACKAGES="knitr rmarkdown bookdown ggplot2 readxl haven stargazer ctv gridExtra"

Rscript --vanilla -e "
packages <- c('knitr', 'rmarkdown', 'bookdown', 'ggplot2', 'readxl', 'haven', 'stargazer', 'ctv', 'gridExtra')

# Ensure user library exists
user_lib <- Sys.getenv('R_LIBS_USER')
if (user_lib == '') {
    user_lib <- file.path(Sys.getenv('HOME'), 'R', paste0(R.version\$platform, '-library'), paste0(R.version\$major, '.', strsplit(R.version\$minor, '[.]')[[1]][1]))
}
if (!dir.exists(user_lib)) {
    dir.create(user_lib, recursive = TRUE, showWarnings = FALSE)
    cat('Created user library:', user_lib, '\n')
}
.libPaths(c(user_lib, .libPaths()))

installed <- rownames(installed.packages())
missing <- setdiff(packages, installed)

if (length(missing) > 0) {
    cat('Installing:', paste(missing, collapse=', '), '\n')
    cat('Library:', user_lib, '\n')
    install.packages(missing, lib = user_lib, repos = 'https://cloud.r-project.org', quiet = TRUE)
    cat('Done.\n')
} else {
    cat('All R packages already installed.\n')
}

# Verify installation
installed_after <- rownames(installed.packages())
still_missing <- setdiff(packages, installed_after)
if (length(still_missing) > 0) {
    cat('\nWarning: Failed to install:', paste(still_missing, collapse=', '), '\n')
    quit(status = 1)
}
"

echo ""

# ============================================================
# Step 5: Verify setup
# ============================================================
echo "Step 5: Verifying setup..."
echo ""
echo "System: $OS / $ARCH"
echo ""

# Check all dependencies
ALL_OK=true

if command_exists Rscript; then
    print_status "Rscript" "ok"
else
    print_status "Rscript" "missing"
    ALL_OK=false
fi

if command_exists pandoc; then
    print_status "Pandoc" "ok"
else
    print_status "Pandoc" "missing"
    ALL_OK=false
fi

if command_exists latexmk; then
    print_status "latexmk" "ok"
else
    print_status "latexmk (PDF)" "optional"
fi

# Check R packages
echo ""
echo "R packages:"
Rscript --vanilla -e "
packages <- c('knitr', 'rmarkdown', 'bookdown', 'ggplot2', 'readxl', 'haven', 'stargazer', 'ctv', 'gridExtra')
installed <- rownames(installed.packages())
for (p in packages) {
    status <- if (p %in% installed) '\033[0;32mOK\033[0m' else '\033[0;31mMISSING\033[0m'
    cat(sprintf('  %-12s %s\n', paste0(p, ':'), status))
}
"

echo ""
echo "======================================"
if [ "$ALL_OK" = true ]; then
    echo -e "${GREEN}Setup complete!${NC}"
    echo ""
    echo "Build commands:"
    echo "  make          # Build all materials (both languages)"
    echo "  make en       # Build English materials only"
    echo "  make de       # Build German materials only"
    echo "  make html     # Build HTML only (no LaTeX needed)"
    echo "  make -j4      # Parallel build (faster)"
else
    echo -e "${RED}Setup incomplete. Please resolve the issues above.${NC}"
    exit 1
fi
echo "======================================"