R/originize_file.R

In origin: Explicitly Qualifying Namespaces by Automatically Adding 'pkg::' to Functions

#' Originize a specific file
#'
#' @template file
#' @template pkgs
#' @template overwrite
#' @template ask_before_applying_changes
#' @template check_conflicts
#' @template check_base_conflicts
#' @template check_local_conflicts
#' @template path_to_local_functions
#' @template add_base_packages
#' @template excluded_functions
#' @template verbose
#' @template use_markers
#'
#' @details 
#' Currently supported filetypes are .R, .RMD, and .QMD (Quarto) files.
#' `check_conflicts` checks whether multiple packages listed in pkgs
#' export
#' functions with the same name, e.g. `lag()` is both part of the dplyr and
#' data.table namespace. If there are any conflicts actually present
#' in any considered script, these conflicts are shown including how origin
#' would solve them. User input is required to proceed. The order in pkgs
#' determines the precedence, while those listed first have higher precedence
#' than those listed later in the vector. This is consistent with function
#' masking in R.
#'
#' `check_base_conflicts` checks whether functions listed in pkgs mask R 
#'. functions of R core packages (base, utils, stats, methods, graphics, 
#'  grDevices, datasets). Even tough the user might not include those functions
#'  in the pkg::fct logic, potential conflicts require careful evaluation.
#'
#'
#' @return No return value, called for side effects
#'
#' @export
#'
#' @examples
#' \dontrun{
#' originize_file(file = "originize_me.R",
#'                pkgs = c("dplyr", "data.table"),
#'                overwrite = TRUE,
#'                ask_before_applying_changes = TRUE,
#'                excluded_functions = list(dplyr = c("%>%", "tibble"),
#'                                          data.table = c(":=", "%like%"),
#'                                          # generally exclude
#'                                          c("last", "first")),
#'                verbose = TRUE)
#' }
originize_file <-
  function(
    file,
    pkgs = getOption("origin.pkgs", .packages()),
    overwrite = getOption("origin.overwrite", TRUE),
    ask_before_applying_changes =
      getOption("origin.ask_before_applying_changes", TRUE),
    check_conflicts = getOption("origin.check_conflicts", TRUE),
    check_base_conflicts = getOption("origin.check_base_conflicts", TRUE),
    add_base_packages = getOption("origin.add_base_packages", FALSE),
    excluded_functions = getOption("origin.excluded_functions", list()),
    verbose = getOption("origin.verbose", FALSE),
    use_markers = getOption("origin.use_markers_for_logging", TRUE),
    path_to_local_functions = getOption("origin.path_to_local_functions", NULL),
    check_local_conflicts = getOption("origin.check_local_conflicts", TRUE)
  ) {
    
    if (!file.exists(file)) {
      stop("No file in this path\n", file)
    }
    
    # check filetype -----------------------------------------------------------
    # currently supported filetypes
    supported_filetypes <- c("R", "RMD", "QMD")
    # R becomes \\.R$
    supported_filetypes_pattern <- paste("\\.", supported_filetypes, "$",
                                         sep = "",
                                         collapse = "|")
    
    if (!grepl(x = file,
               pattern = supported_filetypes_pattern,
               ignore.case = TRUE)) {
      stop("Only ",
           paste(".", supported_filetypes,
                 sep = "", collapse = ", "),
           " files are supported\n", 
           file)
    }
    
    
    # read file ----------------------------------------------------------------
    script <- suppressWarnings(readLines(file))
    script_clean <- if (is_rmd_file(file)) {
      extract_r_chunks(script)
    } else {
      script
    }
    
    
    # originize ----------------------------------------------------------------
    originize_wrap(scripts = list(script),
                   scripts_clean = list(script_clean),
                   files = file,
                   type = "writeLines",
                   pkgs = pkgs,
                   overwrite = overwrite,
                   ask_before_applying_changes = ask_before_applying_changes,
                   check_conflicts = check_conflicts,
                   check_base_conflicts = check_base_conflicts,
                   add_base_packages = add_base_packages,
                   excluded_functions = excluded_functions,
                   verbose = verbose,
                   use_markers = use_markers,
                   path_to_local_functions = path_to_local_functions,
                   check_local_conflicts = check_local_conflicts)
    
    return(invisible(NULL))
    
  }