artifacts flag for RUN, default True. If True the etc folder will be …

…created and all the artifacts produced during compilation will be stored there

R/NPrun.R

@@ -62,6 +62,8 @@
 #' in the first cycle, with a speed-up of approximately 80\% of the number of available cores on your machine, e.g. an 8-core machine
 #' will speed up the first cycle by 0.8 * 8 = 6.4-fold.  Subsequent cycles approach about 50\%, e.g. 4-fold increase on an 8-core
 #' machine.  Overall speed up for a run will therefore depend on the number of cycles run and the number of cores.
+#' @param artifacts Default is \code{TRUE}.  Set to \code{FALSE} to suppress creating the \code{etc} folder. This folder
+#' will contain all the compilation artifacts created during the compilation and run steps.
 #' @param alq For internal developer use only.  Should be set to \code{FALSE}.
 #' @param remote Default is \code{FALSE}.  Set to \code{TRUE} if loading results of an NPAG run on remote server.
 #' @param server_address If missing, will use the default server address returned by getPMoptions().
@@ -98,7 +100,7 @@ NPrun <- function(model = "model.txt", data = "data.csv", run,
                   indpts, icen = "median", aucint,
                   idelta = 12, prior,
                   auto = TRUE, intern = FALSE, quiet = FALSE, overwrite = FALSE, nocheck = FALSE, parallel = NA,
-                  alq = FALSE, remote = FALSE, server_address, report = TRUE) {
+                  alq = FALSE, remote = FALSE, server_address, report = TRUE, artifacts = TRUE) {
   if (missing(run)) run <- NULL
   if (missing(include)) include <- NULL
   if (missing(exclude)) exclude <- NULL

R/PM_fit.R

@@ -149,6 +149,14 @@ PM_fit <- R6::R6Class("PM_fit",
       }
       dir.create(newdir)
       setwd(newdir)
+      ### Move temp folder to ect/PMcore ###
+      # check if temp folder exist, create if not
+      if (arglist$artifacts) {
+        if (!file.exists("etc")) {
+          dir.create("etc")
+        }
+        system(sprintf("cp -R %s etc/PMcore", getPMoptions()$rust_template))
+      }
       # Include or exclude subjects according to
       data_filtered <- self$data$standard_data
       if (!is.symbol(arglist$include)) {
@@ -288,6 +296,7 @@ PM_fit <- R6::R6Class("PM_fit",
         }
       } else {
         system2("./NPcore", args = "&")
+        # TODO: The code to generate the report is missing here
       }
       setwd(cwd)
     },