From 3ba5dd37857bda05e9bc25f7a74e144216e59c97 Mon Sep 17 00:00:00 2001
From: Nick-Eagles <nick.eagles@libd.org>
Date: Tue, 28 Nov 2023 16:08:21 -0500
Subject: [PATCH] Add documentation for a missing parameter; fix reference to
 'parse_file_or_name' in example

---
 R/job_loop.R              | 5 ++---
 R/job_single.R            | 9 ++++-----
 R/utils.R                 | 3 ++-
 man/parse_file_or_name.Rd | 4 +++-
 4 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/R/job_loop.R b/R/job_loop.R
index f3b8e28..c125ca9 100644
--- a/R/job_loop.R
+++ b/R/job_loop.R
@@ -25,9 +25,8 @@
 #'     cores = 2
 #' )
 #'
-job_loop <- function(
-        loops, name, create_shell = FALSE, partition = "shared", memory = "10G",
-        cores = 1L, tc = 20, email = "ALL", logdir = "logs") {
+job_loop <- function(loops, name, create_shell = FALSE, partition = "shared", memory = "10G",
+    cores = 1L, tc = 20, email = "ALL", logdir = "logs") {
     ## Check that the loops are correctly defined
     if (!is.list(loops)) {
         stop("'loops' should be a named list.", call. = FALSE)
diff --git a/R/job_single.R b/R/job_single.R
index f7406cb..5974ee0 100644
--- a/R/job_single.R
+++ b/R/job_single.R
@@ -56,11 +56,10 @@
 #' ## An array job
 #' job_single("jhpce_job_array", task_num = 20, create_logdir = FALSE)
 #'
-job_single <- function(
-        name, create_shell = FALSE, partition = "shared", memory = "10G",
-        cores = 1L, email = "ALL", logdir = "logs", task_num = NULL, tc = 20,
-        command = 'Rscript -e "options(width = 120); sessioninfo::session_info()"',
-        create_logdir = TRUE) {
+job_single <- function(name, create_shell = FALSE, partition = "shared", memory = "10G",
+    cores = 1L, email = "ALL", logdir = "logs", task_num = NULL, tc = 20,
+    command = 'Rscript -e "options(width = 120); sessioninfo::session_info()"',
+    create_logdir = TRUE) {
     #   Grab the path to the shell script, and the shell script's name,
     #   respectively
     sh_file <- parse_file_or_name(name, should_exist = FALSE, r_ok = FALSE)
diff --git a/R/utils.R b/R/utils.R
index 3d0f131..a754607 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -167,6 +167,7 @@ parse_slurm_time <- function(tim) {
 #' (relative or absolute) to the shell or R script to create
 #' @param should_exist A \code{logical(1)} vector. If TRUE, the specified script
 #' must already exist; if FALSE, it must not exist
+#' @param r_ok A \code{logical(1)} vector. If TRUE, \code{name} may end in '.R'
 #'
 #' @return A \code{character(1)} giving the absolute or relative path to the
 #' shell script
@@ -185,7 +186,7 @@ parse_slurm_time <- function(tim) {
 #'     "my_script"
 #' )
 #' returned_scripts <- sapply(
-#'     acceptable_names, parse_file_or_name,
+#'     acceptable_names, slurmjobs:::parse_file_or_name,
 #'     should_exist = FALSE
 #' )
 #' print(returned_scripts)
diff --git a/man/parse_file_or_name.Rd b/man/parse_file_or_name.Rd
index 1690be7..69dd365 100644
--- a/man/parse_file_or_name.Rd
+++ b/man/parse_file_or_name.Rd
@@ -12,6 +12,8 @@ parse_file_or_name(name, should_exist, r_ok)
 
 \item{should_exist}{A \code{logical(1)} vector. If TRUE, the specified script
 must already exist; if FALSE, it must not exist}
+
+\item{r_ok}{A \code{logical(1)} vector. If TRUE, \code{name} may end in '.R'}
 }
 \value{
 A \code{character(1)} giving the absolute or relative path to the
@@ -34,7 +36,7 @@ acceptable_names <- c(
     "my_script"
 )
 returned_scripts <- sapply(
-    acceptable_names, parse_file_or_name,
+    acceptable_names, slurmjobs:::parse_file_or_name,
     should_exist = FALSE
 )
 print(returned_scripts)