From af2ddf3fcc724fee6ec7700a46ce017daad9a769 Mon Sep 17 00:00:00 2001
From: Nick-Eagles <nick.eagles@libd.org>
Date: Wed, 4 Oct 2023 14:42:06 -0400
Subject: [PATCH] Try another approach

---
 dev/interactive_testing/my_array_job.sh.sh | 36 ++++++++++++++++++++++
 tests/testthat/test-array_submit.R         | 33 ++++++++++++--------
 2 files changed, 57 insertions(+), 12 deletions(-)
 create mode 100644 dev/interactive_testing/my_array_job.sh.sh

diff --git a/dev/interactive_testing/my_array_job.sh.sh b/dev/interactive_testing/my_array_job.sh.sh
new file mode 100644
index 0000000..4be6901
--- /dev/null
+++ b/dev/interactive_testing/my_array_job.sh.sh
@@ -0,0 +1,36 @@
+#!/bin/bash
+#SBATCH -p shared
+#SBATCH --mem-per-cpu=10G
+#SBATCH --job-name=my_array_job.sh
+#SBATCH -c 1
+#SBATCH -o logs/my_array_job.sh.%a.txt
+#SBATCH -e logs/my_array_job.sh.%a.txt
+#SBATCH --mail-type=ALL
+#SBATCH --array=1-10%5
+
+set -e
+
+echo "**** Job starts ****"
+date
+
+echo "**** JHPCE info ****"
+echo "User: ${USER}"
+echo "Job id: ${SLURM_JOB_ID}"
+echo "Job name: ${SLURM_JOB_NAME}"
+echo "Node name: ${SLURMD_NODENAME}"
+echo "Task id: ${SLURM_ARRAY_TASK_ID}"
+
+## Load the R module
+module load conda_R
+
+## List current modules for reproducibility
+module list
+
+## Edit with your job command
+Rscript -e "options(width = 120); sessioninfo::session_info()"
+
+echo "**** Job ends ****"
+date
+
+## This script was made using slurmjobs version 0.99.0
+## available from http://research.libd.org/slurmjobs/
diff --git a/tests/testthat/test-array_submit.R b/tests/testthat/test-array_submit.R
index 1c4fb2d..b30a378 100644
--- a/tests/testthat/test-array_submit.R
+++ b/tests/testthat/test-array_submit.R
@@ -2,24 +2,33 @@ script_name <- "my_array_job.sh"
 
 #   Write a basic shell script with 'job_single()'
 basic_job <- function() {
-    #   Delete the shell script if it exists
-    unlink(script_name)
+    with_wd(
+        tempdir(),
+        {
+            #   Delete the shell script if it exists
+            unlink(script_name)
 
-    job_single(
-        name = script_name,
-        create_shell = TRUE,
-        task_num = 10,
-        tc = 5
-    )
+            job_single(
+                name = script_name,
+                create_shell = TRUE,
+                task_num = 10,
+                tc = 5
+            )
+        }
 }
 
 #   Write a basic shell script but break it by removing the '--array' line
 broken_job <- function() {
-    basic_job()
+    with_wd(
+        tempdir(),
+        {
+            basic_job()
 
-    orig_script <- readLines(script_name)
-    orig_script <- sub("^#SBATCH", "something", orig_script)
-    writeLines(orig_script, script_name)
+            orig_script <- readLines(script_name)
+            orig_script <- sub("^#SBATCH", "something", orig_script)
+            writeLines(orig_script, script_name)
+        }
+    )
 }
 
 #   Create (write) some shell script with the 'shell_creation_fun' function,