Feat add option arguments to run()

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: whirl
 Title: Logging package
-Version: 0.1.2
+Version: 0.1.3
 Authors@R: c(
     person("Aksel", "Thomsen", , "[email protected]", role = c("aut", "cre")),
     person("Lovemore", "Gakava", , "[email protected]", role = "aut"),

NEWS.md

@@ -1,3 +1,16 @@
+# whirl 0.1.3 (2024-10-23)
+* Adding additional arguments to `run()` allowing the user to: 
+  - control the verbosity level 
+  - specify whether renv should be checked
+  - specify which files to track
+  - adjust the output format of the log files. 
+
+# whirl 0.1.2 (2024-10-21)
+* Updated package website url and example code
+
+# whirl 0.1.1 (2024-10-07)  
+* Fix enabling rendering of md log formats("gfm", "commonmark", "markua").
+
 # whirl 0.1.0 (2024-10-01)
 * First public release.
 

R/enrich_input.R

@@ -4,10 +4,12 @@
 #' @param input Can be a vector, a list or a whirl config file.
 #' @param steps A filter argument for selecting specific steps that should be
 #'   executed
+#' @inheritParams options_params
 #'
 #' @return A list
 #' @noRd
-enrich_input <- function(input, steps = NULL) {
+enrich_input <- function(input, steps = NULL,
+                         verbosity_level = options::opt("verbosity_level", env = "whirl")) {
 
   # Characterize the input
   is_config_file <- any(grepl("yaml|yml", tools::file_ext(input)))
@@ -19,7 +21,7 @@ enrich_input <- function(input, steps = NULL) {
     config_whirl <- yaml::yaml.load_file(input)
     got <- config_whirl$"steps"
   } else {
-    root_dir = "."
+    root_dir = getwd()
   }
 
   # Convert vector to list
@@ -93,7 +95,8 @@ enrich_input <- function(input, steps = NULL) {
 
   zephyr::msg(message_,
               msg_fun = cli::cli_inform,
-              levels_to_write = "verbose"
+              levels_to_write = "verbose",
+              verbosity_level = verbosity_level
   )
 
   invisible(out)

R/internal_run.R

@@ -10,13 +10,14 @@
 #'   steps listed in the config file will be executed.
 #' @param queue The whirl_r_queue that should execute the scripts
 #' @param level Depth of the recursive config calls. The initial call will have 1
-#'
+#' @inheritParams options_params
 #' @return A tibble containing the execution results for all the scripts.
 #' @noRd
-internal_run <- function(input, steps, queue, level) {
+internal_run <- function(input, steps, queue, level,
+                         verbosity_level = options::opt("verbosity_level", env = "whirl")) {
 
   # Enrich the input with "name" and "path" elements
-  enriched <- enrich_input(input, steps)
+  enriched <- enrich_input(input, steps, verbosity_level)
 
   # Loop over the elements
   for (i in seq_along(enriched)) {
@@ -26,7 +27,10 @@ internal_run <- function(input, steps, queue, level) {
 
     # Messages
     cli_level <- get(paste0("cli_h", min(level, 3)), envir = asNamespace("cli"))
-    zephyr::msg(name, msg_fun = cli_level, levels_to_write = "verbose")
+    zephyr::msg(name,
+                msg_fun = cli_level,
+                levels_to_write = "verbose",
+                verbosity_level = verbosity_level)
 
     # If the step points to a config file then re-initiate internal_run()
     if (any(grepl("yaml|yml", tools::file_ext(files)))) {

R/run.R

@@ -19,7 +19,6 @@
 #' @param summary_file A character string specifying the file path where the
 #'   summary log will be stored.
 #' @inheritParams options_params
-#'
 #' @return A tibble containing the execution results for all the scripts.
 #'
 #'@examplesIf FALSE
@@ -41,22 +40,34 @@
 
 run <- function(input,
                 steps = NULL,
+                summary_file = "summary.html",
                 n_workers = options::opt("n_workers", env = "whirl"),
-                summary_file = "summary.html"
+                check_renv = options::opt("check_renv", env = "whirl"),
+                verbosity_level = options::opt("verbosity_level", env = "whirl"),
+                track_files = options::opt("track_files", env = "whirl"),
+                out_formats = options::opt("out_formats", env = "whirl")
                 ) {
 
+  # Additional Settings
+  track_files_discards = options::opt("track_files_discards", env = "whirl")
+  track_files_keep = options::opt("track_files_keep", env = "whirl")
+  approved_pkgs_folder = options::opt("approved_pkgs_folder", env = "whirl")
+  approved_pkgs_url = options::opt("approved_pkgs_url", env = "whirl")
+
   # Message when initiating
   d <- cli::cli_div(theme = list(rule = list(
     color = "skyblue3", "line-type" = "double"
   )))
 
   zephyr::msg("Executing scripts and generating logs",
-              levels_to_write = "verbose",
+              levels_to_write = c("verbose", "minimal"),
+              verbosity_level = verbosity_level,
               msg_fun = cli::cli_rule)
 
   # Message when ending
   on.exit(zephyr::msg("End of process",
-                      levels_to_write = "verbose",
+                      levels_to_write = c("verbose", "minimal"),
+                      verbosity_level = verbosity_level,
                       msg_fun = cli::cli_rule))
   on.exit(cli::cli_end(d), add = TRUE)
 
@@ -65,19 +76,30 @@ run <- function(input,
 
   zephyr::msg("Executing scripts in parallel using {n_workers} cores\n",
               levels_to_write = "verbose",
+              verbosity_level = verbosity_level,
               msg_fun = cli::cli_inform)
 
   # Initiating the queue
-  queue <- whirl_queue$new(n_workers = n_workers)
+  queue <- whirl_queue$new(n_workers = n_workers,
+                           check_renv = check_renv,
+                           verbosity_level = verbosity_level,
+                           track_files = track_files,
+                           out_formats = out_formats,
+                           track_files_discards = track_files_discards,
+                           track_files_keep = track_files_keep,
+                           approved_pkgs_folder = approved_pkgs_folder,
+                           approved_pkgs_url = approved_pkgs_url)
 
   result <- internal_run(input = input,
                          steps = steps,
                          queue = queue,
-                         level = 1)
+                         level = 1,
+                         verbosity_level = verbosity_level)
 
   # Create the summary log
   summary_tibble <- util_queue_summary(result$queue)
   render_summary(input = summary_tibble, summary_file = summary_file)
 
   invisible(result$queue)
+
 }

R/whirl_queue.R

@@ -12,11 +12,29 @@ whirl_queue <- R6::R6Class(
   classname = "whirl_queue",
   public = list(
 
+    #' @inheritParams options_params
     #' @description Initialize the new whirl_queue
-    #' @param n_workers [numeric] Maximum number of workers to be used simultaneously
     #' @return A [whirl_queue] object
-    initialize = \(n_workers = options::opt("n_workers", env = "whirl")) {
-      wq_initialise(self, private, n_workers)
+    initialize = \(n_workers = options::opt("n_workers", env = "whirl"),
+                   verbosity_level = options::opt("verbosity_level", env = "whirl"),
+                   check_renv = options::opt("check_renv", env = "whirl"),
+                   track_files = options::opt("track_files", env = "whirl"),
+                   out_formats = options::opt("out_formats", env = "whirl"),
+                   track_files_discards = options::opt("track_files_discards", env = "whirl"),
+                   track_files_keep = options::opt("track_files_keep", env = "whirl"),
+                   approved_pkgs_folder = options::opt("approved_pkgs_folder", env = "whirl"),
+                   approved_pkgs_url = options::opt("approved_pkgs_url", env = "whirl")
+                   ) {
+      wq_initialise(self, private,
+                    n_workers,
+                    verbosity_level,
+                    check_renv,
+                    track_files,
+                    out_formats,
+                    track_files_discards,
+                    track_files_keep,
+                    approved_pkgs_folder,
+                    approved_pkgs_url)
     },
 
     #' @description Push scripts to the queue
@@ -96,11 +114,32 @@ whirl_queue <- R6::R6Class(
   private = list(
     .queue = NULL,
     .workers = NULL,
-    .n_workers = NULL
+    .n_workers = NULL,
+    verbosity_level = NULL,
+    check_renv = NULL,
+    track_files = NULL,
+    out_formats = NULL,
+    track_files_discards = NULL,
+    track_files_keep = NULL,
+    approved_pkgs_folder = NULL,
+    approved_pkgs_url = NULL
   )
 )
 
-wq_initialise <- function(self, private, n_workers) {
+wq_initialise <- function(self, private, n_workers,
+                          verbosity_level, check_renv, track_files, out_formats,
+                          track_files_discards, track_files_keep,
+                          approved_pkgs_folder, approved_pkgs_url) {
+
+  private$check_renv <- check_renv
+  private$verbosity_level <- verbosity_level
+  private$track_files <- track_files
+  private$out_formats <- out_formats
+  private$track_files_discards <- track_files_discards
+  private$track_files_keep <- track_files_keep
+  private$approved_pkgs_folder <- approved_pkgs_folder
+  private$approved_pkgs_url <- approved_pkgs_url
+
   private$.queue <- tibble::tibble(
     id = numeric(),
     tag = character(),
@@ -138,14 +177,27 @@ wq_skip <- function(self, private, scripts, tag) {
   wq_add_queue(self, private, scripts, tag, status = "skipped")
 }
 
-wq_poll <- function(self, private, timeout) {
+wq_poll <- function(self, private, timeout,
+                    check_renv, verbosity_level, track_files, out_formats,
+                    track_files_discards, track_files_keep,
+                    approved_pkgs_folder, approved_pkgs_url) {
 
   # Start new sessions if there are available workers and waiting scripts in the queue
 
   if (length(self$next_ids)) {
     nid <- self$next_ids
     wid <- self$next_workers
-    private$.workers[["session"]][wid] <- replicate(n = length(wid), expr = whirl_r_session$new(), simplify = FALSE)
+    private$.workers[["session"]][wid] <- replicate(
+      n = length(wid),
+      expr = whirl_r_session$new(check_renv = private$check_renv,
+                                 verbosity_level = private$verbosity_level,
+                                 track_files = private$track_files,
+                                 out_formats = private$out_formats,
+                                 track_files_discards = private$track_files_discards,
+                                 track_files_keep = private$track_files_keep,
+                                 approved_pkgs_folder = private$approved_pkgs_folder,
+                                 approved_pkgs_url = private$approved_pkgs_url),
+      simplify = FALSE)
     private$.workers[wid, "id_script"] <- nid
     private$.workers[wid, "active"] <- TRUE
     private$.queue[nid, "status"] <- "running"
@@ -200,7 +252,7 @@ wq_next_step <- function(self, private, wid) {
             purrr::pluck(private$.queue, "result", id_script) <- session$
               log_finish()$
               create_outputs(out_dir = dirname(purrr::pluck(private$.queue, "script", id_script)),
-                             format = options::opt("out_formats", env = "whirl"))
+                             format = private$out_formats)
 
             purrr::pluck(private$.queue, "status", id_script) <-
               purrr::pluck(private$.queue, "result", id_script, "status", "status")

R/whirl_r_session.R

@@ -10,27 +10,27 @@ whirl_r_session <- R6::R6Class(
   public = list(
 
     #' @description Initialize the new whirl R session
-    #' @param verbose [logical] Should the progress be printed to the console?
-    #' @param check_renv [logical] Should renv be checked?
-    #' @param track_files [logical] Should the files be tracked?
-    #' @param track_files_discards [character] Files to discard from tracking
-    #' @param track_files_keep [character] Files to keep from tracking
-    #' @param approved_pkgs_folder [character] Folder with approved packages
-    #' @param approved_pkgs_url [character] URL with approved packages
+    #' @inheritParams options_params
     #' @return A [whirl_r_session] object
-    initialize = \(
-      verbose = options::opt("verbosity_level", env = "whirl"),
-      check_renv = options::opt("check_renv", env = "whirl"),
-      track_files = options::opt("track_files", env = "whirl"),
-      track_files_discards = options::opt("track_files_discards", env = "whirl"),
-      track_files_keep = options::opt("track_files_keep", env = "whirl"),
-      approved_pkgs_folder = options::opt("approved_pkgs_folder", env = "whirl"),
-      approved_pkgs_url = options::opt("approved_pkgs_url", env = "whirl")
-      ) {
-
-        wrs_initialize(verbose, check_renv, track_files, track_files_discards, track_files_keep, approved_pkgs_folder, approved_pkgs_url, self, private, super)
-      }
-    ,
+    initialize = \(verbosity_level = options::opt("verbosity_level", env = "whirl"),
+                   check_renv = options::opt("check_renv", env = "whirl"),
+                   track_files = options::opt("track_files", env = "whirl"),
+                   out_formats = options::opt("out_formats", env = "whirl"),
+                   track_files_discards = options::opt("track_files_discards", env = "whirl"),
+                   track_files_keep = options::opt("track_files_keep", env = "whirl"),
+                   approved_pkgs_folder = options::opt("approved_pkgs_folder", env = "whirl"),
+                   approved_pkgs_url = options::opt("approved_pkgs_url", env = "whirl")
+                   ) {
+        wrs_initialize(verbosity_level,
+                       check_renv,
+                       track_files,
+                       out_formats,
+                       track_files_discards,
+                       track_files_keep,
+                       approved_pkgs_folder,
+                       approved_pkgs_url,
+                       self, private, super)
+    },
 
     #' @description Finalize the whirl R session
     finalize = \() {
@@ -105,9 +105,10 @@ whirl_r_session <- R6::R6Class(
     }
   ),
   private = list(
-    verbose = NULL,
+    verbosity_level = NULL,
     wd = NULL,
     track_files = NULL,
+    out_formats = NULL,
     track_files_discards = NULL,
     track_files_keep = NULL,
     approved_pkgs_folder = NULL,
@@ -119,23 +120,27 @@ whirl_r_session <- R6::R6Class(
   inherit = callr::r_session
 )
 
-wrs_initialize <- function(verbose, check_renv, track_files, track_files_discards, track_files_keep, approved_pkgs_folder, approved_pkgs_url,
+wrs_initialize <- function(verbosity_level, check_renv, track_files,
+                           out_formats, track_files_discards, track_files_keep,
+                           approved_pkgs_folder, approved_pkgs_url,
                            self, private, super) {
+
   super$initialize() # uses callr::r_session$initialize()
 
   # TODO: Is there a way to use `.local_envir` to avoid having to clean up the temp dir in finalize?
   private$wd <- withr::local_tempdir(clean = FALSE)
-  private$verbose <- verbose
+  private$verbosity_level <- verbosity_level
   private$check_renv <- check_renv
   private$track_files <- track_files
+  private$out_formats <- out_formats
   private$track_files_discards <- track_files_discards
   private$track_files_keep <- track_files_keep
   private$approved_pkgs_folder <- approved_pkgs_folder
   private$approved_pkgs_url <- approved_pkgs_url
 
   # If the stream does not support dynamic tty, which is needed for progress bars to update in place, the verbosity is downgraded.
-  if (private$verbose == "verbose" && !cli::is_dynamic_tty()) {
-    private$verbose <- "minimal"
+  if (private$verbosity_level == "verbose" && !cli::is_dynamic_tty()) {
+    private$verbosity_level <- "minimal"
   }
 
   super$run(func = setwd, args = list(dir = private$wd))
@@ -168,7 +173,7 @@ wrs_print <- function(self, private, super) {
   msg <- c(
     utils::capture.output(super$print()),
     "Working Directory: {private$wd}",
-    "Verbose: {private$verbose}"
+    "Verbose: {private$verbosity_level}"
   )
 
   cli::cli_bullets(
@@ -221,10 +226,10 @@ wrs_check_status <- function(self, private, super) {
 wrs_log_script <- function(script, self, private, super) {
   private$current_script <- script
 
-  if (private$verbose != "quiet") {
+  if (private$verbosity_level != "quiet") {
     private$pb <- pb_script$new(
       script = private$current_script,
-      use_progress = private$verbose == "verbose"
+      use_progress = private$verbosity_level == "verbose"
       )
   }
 
@@ -363,7 +368,7 @@ wrs_create_outputs <- function(out_dir, format, self, private, super) {
         out_dir,
         gsub(
           pattern = "\\.[^\\.]*$",
-          replacement = ".json",
+          replacement = "_log.json",
           x = basename(private$current_script)
         )
       )