Set up Posit Package Manager integration

manage_renv_environment <- function(
    cran_url,
    bioc_url = NULL,
    bioc_version = NULL,
    packages = NULL
) {
  
  # =================================================================
  # 0. ENSURE FULLY UNATTENDED EXECUTION
  # =================================================================
  # Grant consent for the one-time 'first use' prompt.
  original_consent <- getOption("renv.consent")
  options(renv.consent = TRUE)
  on.exit(options(renv.consent = original_consent), add = TRUE)
  
  # Force non-interactive behavior for all other operations (install, snapshot, etc.)
  original_interactive <- getOption("rlang_interactive", default = TRUE)
  options(rlang_interactive = FALSE)
  on.exit(options(rlang_interactive = original_interactive), add = TRUE)

  # =================================================================
  # HELPER FUNCTION
  # =================================================================
  build_repos_vector <- function(repos_list) {
    if (is.null(repos_list) || length(repos_list) == 0) return(c())
    # Handles both new and old lockfile formats
    if (is.list(repos_list[[1]])) {
      repo_urls <- sapply(repos_list, function(repo) repo$URL)
      repo_names <- sapply(repos_list, function(repo) repo$Name)
      names(repo_urls) <- repo_names
      return(repo_urls)
    } else {
      return(unlist(repos_list))
    }
  }
  
  # =================================================================
  # VALIDATE PARAMETERS
  # =================================================================
  if (missing(cran_url)) {
    stop("FATAL: The 'cran_url' parameter is required.")
  }
  if (!is.null(bioc_url) && is.null(bioc_version)) {
    stop("FATAL: 'bioc_version' is required when 'bioc_url' is provided for a new project.")
  }
  if (!requireNamespace("renv", quietly = TRUE)) {
    stop("FATAL: renv is not installed. Please install it in your user library.")
  }
  
  # Load the renv library to ensure all its components are fully loaded and accessible.
  library(renv)
  
  lockfile_path <- "renv.lock"
  
  # =================================================================
  # CHECK FOR EXISTING LOCKFILE AND EXECUTE CORRECT MODE
  # =================================================================
  
  if (file.exists(lockfile_path)) {
    
    # ----- UPGRADE MODE -----
    message("Existing renv.lock found. Performing a CRAN snapshot upgrade...")
    lockfile <- renv::lockfile_read(lockfile_path)
    
    # Persistently update the project's repository settings.
    message("Updating project settings with new repository URL...")
    current_repos <- build_repos_vector(lockfile$R$Repositories)
    if (!("CRAN" %in% names(current_repos))) stop("Could not find CRAN repository in lockfile.")
    current_repos["CRAN"] <- cran_url
    
    # <<< THE FINAL FIX IS HERE: Remove the 'renv::' prefix >>>
    # Since library(renv) was called, 'settings' is directly available.
    settings$repos <- current_repos
    
    # Now, update the lockfile itself to match the new settings
    message("Updating renv.lock file with new repository URL...")
    repos_list <- lockfile$R$Repositories
    if (is.list(repos_list[[1]])) {
      cran_idx <- which(sapply(repos_list, function(repo) repo$Name == "CRAN"))
      if (length(cran_idx) == 0) stop("Could not find CRAN repository in lockfile.")
      lockfile$R$Repositories[[cran_idx]]$URL <- cran_url
    } else {
      if (!("CRAN" %in% names(repos_list))) stop("Could not find CRAN repository in lockfile.")
      lockfile$R$Repositories[["CRAN"]] <- cran_url
    }
    
    renv::lockfile_write(lockfile, file = lockfile_path)
    message("renv.lock successfully updated.")
    
    message("Synchronizing project library with the new snapshot date...")
    renv::restore(prompt = FALSE)
    
    if (!is.null(packages) && length(packages) > 0) {
      message("Installing newly requested packages (and updating lockfile)...")
      renv::install(packages, prompt = FALSE)
    }

    message("Performing final library synchronization check...")
    renv::restore(prompt = FALSE)
    
  } else {
    
    # ----- INITIALIZATION MODE -----
    message("No renv.lock found. Initializing a new environment in the current directory...")
    
    repos_to_set <- c(CRAN = cran_url)
    if (!is.null(bioc_url)) {
      Sys.setenv(BIOCONDUCTOR_VERSION = bioc_version)
      repos_to_set <- c(repos_to_set, BIOC = bioc_url)
    }
    options(repos = repos_to_set)
    
    renv::init(force = TRUE, bare = TRUE, restart = FALSE)
    
    if (!is.null(packages) && length(packages) > 0) {
      message(paste("Installing", length(packages), "packages into project library..."))
      
      if (!is.null(bioc_url) && !requireNamespace("BiocManager", quietly = TRUE)) {
        renv::install("BiocManager", prompt = FALSE)
      }
      
      if (!is.null(bioc_url)) {
        renv::run(
          code = { BiocManager::install(packages, update = FALSE, ask = FALSE) }
        )
      } else {
        renv::install(packages, prompt = FALSE)
      }
    }
    
    renv::snapshot(prompt = FALSE, type = "all")
  }
  
  # =================================================================
  # ACTIVATE THE PROJECT IN THE CURRENT SESSION
  # =================================================================
  message("Activating the project to apply settings to the current R session...")
  renv::load()
  
  message(paste0("Script finished successfully for project: '", getwd(), "'"))
  message("Your session is now fully synchronized and configured.")
}