SmartCane/r_app/package_manager.R

#' Package Manager for SmartCane Project
#' 
#' This script manages R package versions across development, testing, and production environments.
#' It uses renv for reproducible environments and ensures consistent package versions.
#' 
#' Usage:
#'   source("package_manager.R")
#' 
#' Author: SmartCane Team
#' Date: 2025-06-24

# =============================================================================
# CONFIGURATION
# =============================================================================

# Package requirements with your current working versions
REQUIRED_PACKAGES <- list(
  # Core data manipulation
  "dplyr" = "1.1.4",
  "here" = "1.0.1",
  "lubridate" = "1.9.4",
  "readr" = "2.1.5",
  "readxl" = "1.4.5",
  "stringr" = "1.5.1",
  "tidyr" = "1.3.1",
  "purrr" = "1.0.2",
  "magrittr" = "2.0.0",  # Adding this as it's commonly used
  
  # Spatial data
  "exactextractr" = "0.10.0",
  "raster" = "3.6.32",
  "sf" = "1.0.19",
  "terra" = "1.8.43",  # CRITICAL: for raster processing
  
  # Visualization - CRITICAL: tmap v4 for new syntax
  "ggplot2" = "3.5.1",
  "tmap" = "4.0",  # CRITICAL: for tm_scale_continuous() syntax
  "gridExtra" = "2.3",
  # Reporting
  "knitr" = "1.50",
  "rmarkdown" = "2.21.0",  # Adding this as it's needed for reports
  
  # Tidyverse meta-package
  "tidyverse" = "2.0.0",
  
  # Machine Learning & Statistics
  "caret" = "7.0.1",
  "CAST" = "1.0.3",
  "randomForest" = "4.7.1.2",
  "rsample" = "1.3.0",
  
  # Parallel processing
  "furrr" = "0.3.1",
  "future" = "1.40.0",
  "progressr" = "0.15.1",
  
  # Other utilities
  "reshape2" = "1.4.4",
  "zoo" = "1.8.13"
)

# Log file setup
LOG_FILE <- file.path(getwd(), "package_manager.log")
START_TIME <- Sys.time()

# =============================================================================
# UTILITY FUNCTIONS
# =============================================================================

#' Log message to both console and file
log_message <- function(message, level = "INFO") {
  timestamp <- format(Sys.time(), "%Y-%m-%d %H:%M:%S")
  formatted_msg <- sprintf("[%s] %s - %s", level, timestamp, message)
  
  # Print to console
  cat(formatted_msg, "\n")
  
  # Write to log file
  cat(formatted_msg, "\n", file = LOG_FILE, append = TRUE)
}

#' Check if package is installed
is_package_installed <- function(package) {
  package %in% rownames(installed.packages())
}

#' Get installed package version
get_package_version <- function(package) {
  if (is_package_installed(package)) {
    as.character(packageVersion(package))
  } else {
    NULL
  }
}

#' Compare version strings (returns TRUE if installed >= required)
version_meets_requirement <- function(installed, required) {
  if (is.null(installed)) return(FALSE)
  utils::compareVersion(installed, required) >= 0
}

#' Install or update package to minimum version
install_or_update_package <- function(package, required_version) {
  current_version <- get_package_version(package)
  
  if (is.null(current_version)) {
    log_message(sprintf("Installing %s (required: >= %s)", package, required_version))
    tryCatch({
      install.packages(package, dependencies = TRUE, quiet = TRUE)
      new_version <- get_package_version(package)
      log_message(sprintf("✓ Installed %s version %s", package, new_version), "SUCCESS")
      return(TRUE)
    }, error = function(e) {
      log_message(sprintf("✗ Failed to install %s: %s", package, e$message), "ERROR")
      return(FALSE)
    })
  } else if (!version_meets_requirement(current_version, required_version)) {
    log_message(sprintf("Updating %s from %s to >= %s", package, current_version, required_version))
    tryCatch({
      install.packages(package, dependencies = TRUE, quiet = TRUE)
      new_version <- get_package_version(package)
      if (version_meets_requirement(new_version, required_version)) {
        log_message(sprintf("✓ Updated %s to version %s", package, new_version), "SUCCESS")
        return(TRUE)
      } else {
        log_message(sprintf("⚠ %s updated to %s but still below required %s", package, new_version, required_version), "WARNING")
        return(FALSE)
      }
    }, error = function(e) {
      log_message(sprintf("✗ Failed to update %s: %s", package, e$message), "ERROR")
      return(FALSE)
    })
  } else {
    log_message(sprintf("✓ %s version %s meets requirement (>= %s)", package, current_version, required_version))
    return(TRUE)
  }
}

# =============================================================================
# MAIN PACKAGE MANAGEMENT FUNCTIONS
# =============================================================================

#' Initialize renv if not already initialized
initialize_renv <- function() {
  log_message("Checking renv initialization...")
  
  if (!file.exists("renv.lock")) {
    log_message("Initializing renv for the first time...")
    if (!requireNamespace("renv", quietly = TRUE)) {
      log_message("Installing renv...")
      install.packages("renv")
    }
    renv::init()
    log_message("✓ renv initialized", "SUCCESS")
  } else {
    log_message("✓ renv already initialized")
    # Check if renv is already active by looking at the library path
    if (!requireNamespace("renv", quietly = TRUE)) {
      install.packages("renv")
    }
      # Check if we're already using the renv project library
    lib_paths <- .libPaths()
    
    if (!any(grepl("renv", lib_paths))) {
      log_message("Activating renv...")
      renv::activate()
      log_message("✓ renv activated")
    } else {
      log_message("✓ renv already active")
    }
  }
}

#' Check and install all required packages
manage_packages <- function() {
  log_message("=== PACKAGE MANAGEMENT STARTED ===")
  log_message(sprintf("R version: %s", R.version.string))
  
  success_count <- 0
  failure_count <- 0
  
  for (package in names(REQUIRED_PACKAGES)) {
    required_version <- REQUIRED_PACKAGES[[package]]
    
    if (install_or_update_package(package, required_version)) {
      success_count <- success_count + 1
    } else {
      failure_count <- failure_count + 1
    }
  }
  
  log_message(sprintf("Package management complete: %d success, %d failures", success_count, failure_count))
  
  if (failure_count > 0) {
    log_message("Some packages failed to install/update. Check log for details.", "WARNING")
  }
  
  return(failure_count == 0)
}

#' Update renv lockfile with current package versions
update_lockfile <- function() {
  log_message("Updating renv lockfile...")
  tryCatch({
    renv::snapshot(prompt = FALSE)
    log_message("✓ renv lockfile updated", "SUCCESS")
  }, error = function(e) {
    log_message(sprintf("✗ Failed to update lockfile: %s", e$message), "ERROR")
  })
}

#' Generate package report
generate_package_report <- function() {
  log_message("=== PACKAGE REPORT ===")
  
  # Check each required package
  for (package in names(REQUIRED_PACKAGES)) {
    required_version <- REQUIRED_PACKAGES[[package]]
    current_version <- get_package_version(package)
    
    if (is.null(current_version)) {
      status <- "❌ NOT INSTALLED"
    } else if (version_meets_requirement(current_version, required_version)) {
      status <- "✅ OK"
    } else {
      status <- "⚠️  VERSION TOO OLD"
    }
    
    log_message(sprintf("%-20s | Required: >= %-8s | Installed: %-8s | %s", 
                       package, required_version, 
                       ifelse(is.null(current_version), "NONE", current_version), 
                       status))
  }
  
  log_message("=== END PACKAGE REPORT ===")
}

#' Main function to run complete package management
run_package_manager <- function() {
  # Initialize log
  cat("", file = LOG_FILE)  # Clear log file
  log_message("SmartCane Project - Package Manager Started")
  log_message(sprintf("Working directory: %s", getwd()))
  
  # Step 1: Initialize renv
  initialize_renv()
  
  # Step 2: Generate initial report
  log_message("\n=== INITIAL STATE ===")
  generate_package_report()
  
  # Step 3: Manage packages
  log_message("\n=== PACKAGE INSTALLATION/UPDATES ===")
  success <- manage_packages()
  
  # Step 4: Update lockfile if successful
  if (success) {
    update_lockfile()
  }
  
  # Step 5: Generate final report
  log_message("\n=== FINAL STATE ===")
  generate_package_report()
  
  # Summary
  end_time <- Sys.time()
  duration <- round(as.numeric(difftime(end_time, START_TIME, units = "secs")), 2)
  
  log_message(sprintf("Package management completed in %s seconds", duration))
  log_message(sprintf("Log saved to: %s", LOG_FILE))
  
  if (success) {
    log_message("🎉 All packages successfully managed!", "SUCCESS")
    log_message("📋 Next steps:")
    log_message("   1. Test your R scripts to ensure everything works")
    log_message("   2. Commit renv.lock to version control")
    log_message("   3. Share this script with your team")
  } else {
    log_message("⚠️  Some issues occurred. Check the log for details.", "WARNING")
    log_message("💡 You may need to:")
    log_message("   1. Update R to a newer version")
    log_message("   2. Install system dependencies")
    log_message("   3. Check your internet connection")
  }
  
  return(success)
}

# =============================================================================
# EXECUTION
# =============================================================================

# Only run if script is sourced directly (not when loaded as module)
if (!exists("PACKAGE_MANAGER_LOADED")) {
  PACKAGE_MANAGER_LOADED <- TRUE
  
  cat("🚀 SmartCane Package Manager\n")
  cat("============================\n")
  cat("This will check and install/update all required R packages.\n")
  cat("Log file:", LOG_FILE, "\n\n")
  
  # Ask for confirmation
  response <- readline("Continue? (y/N): ")
  if (tolower(substr(response, 1, 1)) == "y") {
    result <- run_package_manager()
    
    if (result) {
      cat("\n✅ Package management completed successfully!\n")
    } else {
      cat("\n❌ Package management completed with errors. Check the log.\n")
    }
  } else {
    cat("❌ Package management cancelled.\n")
  }
}