From 2c784c63404e353dc9042f07c5407fbb1dd5e362 Mon Sep 17 00:00:00 2001
From: philchalmers <rphilip.chalmers@gmail.com>
Date: Tue, 3 Dec 2024 21:31:57 -0500
Subject: [PATCH] add verbose flag for non-interactive use (see #43)

---
 R/runArraySimulation.R    | 11 ++++++++---
 man/runArraySimulation.Rd |  8 +++++++-
 2 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/R/runArraySimulation.R b/R/runArraySimulation.R
index 17ac7027..931a89bd 100644
--- a/R/runArraySimulation.R
+++ b/R/runArraySimulation.R
@@ -111,6 +111,11 @@
 #'
 #' @param ... additional arguments to be passed to \code{\link{runSimulation}}
 #'
+#' @param verbose logical; pass a verbose flag to \code{\link{runSimulation}}.
+#'   Unlike \code{\link{runSimulation}} this is set to FALSE during interactive
+#'   sessions, though set to TRUE when non-interactive and information about the
+#'   session itself should be stored (e.g., in SLURM \code{.out} files)
+#'
 #' @export
 #'
 #' @author Phil Chalmers \email{rphilip.chalmers@@gmail.com}
@@ -289,8 +294,8 @@ runArraySimulation <- function(design, ..., replications,
                                addArrayInfo = TRUE,
                                parallel = FALSE, cl = NULL,
                                ncores = parallelly::availableCores(omit = 1L),
-                               save_details = list(),
-                               control = list()){
+                               save_details = list(), control = list(),
+                               verbose = ifelse(interactive(), FALSE, TRUE)){
     dots <- list(...)
     if(parallel && ncores == 1L) parallel <- FALSE
     if(!is.null(dots$save_results) && isTRUE(dots$save_results))
@@ -339,7 +344,7 @@ runArraySimulation <- function(design, ..., replications,
         dsub <- design[row, , drop=FALSE]
         attr(dsub, 'Design.ID') <- attr(design, 'Design.ID')[row]
         ret <- runSimulation(design=dsub, replications=replications, seed=seed,
-                             verbose=FALSE, save_details=save_details,
+                             verbose=verbose, save_details=save_details,
                              parallel=parallel, cl=cl,
                              control=control, save=FALSE, ...)
         attr(ret, 'extra_info')$number_of_conditions <- nrow(design)
diff --git a/man/runArraySimulation.Rd b/man/runArraySimulation.Rd
index bcdab522..99d8dba2 100644
--- a/man/runArraySimulation.Rd
+++ b/man/runArraySimulation.Rd
@@ -18,7 +18,8 @@ runArraySimulation(
   cl = NULL,
   ncores = parallelly::availableCores(omit = 1L),
   save_details = list(),
-  control = list()
+  control = list(),
+  verbose = ifelse(interactive(), FALSE, TRUE)
 )
 }
 \arguments{
@@ -101,6 +102,11 @@ See \code{\link{runSimulation}}}
   Useful for larger HPC cluster jobs with RAM constraints that could terminate abruptly.
   As a rule of thumb this should be set to around 90% of the maximum possible storage
   available. Default applies no memory limit}
+
+\item{verbose}{logical; pass a verbose flag to \code{\link{runSimulation}}.
+Unlike \code{\link{runSimulation}} this is set to FALSE during interactive
+sessions, though set to TRUE when non-interactive and information about the
+session itself should be stored (e.g., in SLURM \code{.out} files)}
 }
 \description{
 This function has the same purpose as \code{\link{runSimulation}}, however