update hpc desc

Author: kinh-nguyen

R/hpc.R

@@ -14,7 +14,14 @@ sbatch <- function(file) {
 
 #' Prepare the R script and sh file to submit to HPC managed with SLURM
 #'
-#' adjust SLURM and conda configuration to your case
+#' The workflow is: you're working on a R script, and every lines from the
+#' top of the file (or from `first_line` parameter) to the current line (or the last
+# `last.line` parameter) is working fine. Now you want to
+#' run a full-blown model on the HPC. Then adjust the r script and run this
+#' function after the last line you want to send to the cluster (or outside the
+#' range from `first.line` to `last.line`.).
+#'
+#' Adjust SLURM and conda configuration to your case.
 #'
 #' @export
 slurm <- function(
@@ -31,12 +38,20 @@ slurm <- function(
     submit = FALSE,
     monitor = FALSE,
     user = "knguyen",
-    iteration = 1) {
+    iteration = 1, 
+    first.line = 1,
+    last.line = Inf, 
+    shift.line = 2
+    ) {
+    context <- rstudioapi::getSourceEditorContext()
     r.file <- paste0(working.dir, "/", r.file)
     sh.file <- paste0(working.dir, "/", sh.file)
-    context <- rstudioapi::getSourceEditorContext()
     current_row <- context$selections[[1]]$range$start[[1]]
-    writeLines(context$contents[1:(current_row - 2)], r.file)
+    if (is.infinite(last.line)) {
+        last.line <- current_row
+        shift.line <- 0
+    }
+    writeLines(context$contents[first.line:(last.line - shift.line)], r.file)
     writeLines(
         c(
             "#!/bin/bash",