Style code and devtools::document()

NAMESPACE

@@ -5,6 +5,7 @@ export(job_info)
 export(job_loop)
 export(job_report)
 export(job_single)
+export(partition_info)
 export(with_wd)
 import(dplyr)
 import(glue)

R/job_info.R

@@ -7,7 +7,7 @@
 #' @param user A `character(1)` vector specifying the username of the jobs to
 #' query. Set NULL to return info about all users' jobs.
 #' @param partition A `character(1)` vector specifying the partition of the jobs
-#' to query. Set NULL to return info about jobs of all paritions.
+#' to query. Set NULL to return info about jobs of all partitions.
 #'
 #' @return A tibble with job information about currently running jobs.
 #' @export

R/job_loop.R

@@ -31,9 +31,8 @@
 #'     name = "bsp2_test_array"
 #' )
 #'
-job_loop <- function(
-        loops, name, create_shell = FALSE, partition = "shared", memory = "10G",
-        cores = 1L, email = "ALL", logdir = "logs", task_num = NULL, tc = 20) {
+job_loop <- function(loops, name, create_shell = FALSE, partition = "shared", memory = "10G",
+    cores = 1L, email = "ALL", logdir = "logs", task_num = NULL, tc = 20) {
     ## Check that the loops are correctly defined
     if (!is.list(loops)) {
         stop("'loops' should be a named list.", call. = FALSE)

R/job_single.R

@@ -54,10 +54,11 @@
 #' ## 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) {
     ## Remove any spaces
     name <- gsub(" ", "_", name)
 

R/partition_info.R

@@ -24,15 +24,15 @@
 #'     #    Print summary of CPU availability for the 'shared' partition
 #'     print(
 #'         sprintf(
-#'             'The %s partition has %i CPUs free (%.1f%% of total)',
+#'             "The %s partition has %i CPUs free (%.1f%% of total)",
 #'             part_df$partition,
 #'             part_df$free_cpus,
 #'             100 * part_df$prop_free_cpus
 #'         )
 #'     )
 #' }
 partition_info <- function(partition = "shared", all_nodes = FALSE) {
-    command = paste(
+    command <- paste(
         #   Grab info about CPUs and memory with 'sinfo'
         "sinfo -N -O 'PartitionName,NodeList:50,FreeMem,AllocMem,Memory,StateLong,CPUsState'",
         #   Properly delimit columns by "|"
@@ -44,17 +44,17 @@ partition_info <- function(partition = "shared", all_nodes = FALSE) {
         sep = " | "
     )
 
-    part_df = read.csv(text = system(command, intern = TRUE), sep = "|") |>
+    part_df <- read.csv(text = system(command, intern = TRUE), sep = "|") |>
         as_tibble()
-    
+
     #   Subset by partition if not null
-    if(!is.null(partition)) {
-        part_df = part_df |> filter(PARTITION == partition)
+    if (!is.null(partition)) {
+        part_df <- part_df |> filter(PARTITION == partition)
     }
 
-    colnames(part_df) = tolower(colnames(part_df))
+    colnames(part_df) <- tolower(colnames(part_df))
 
-    part_df = part_df |>
+    part_df <- part_df |>
         #   Use more informative and consistent column names
         rename(
             node = nodelist,
@@ -65,27 +65,26 @@ partition_info <- function(partition = "shared", all_nodes = FALSE) {
         mutate(
             state = as.factor(state),
             #   Convert from MB to GB to match other slurmjobs functions
-            across(matches('.*_mem_gb$'), ~ .x / 1000)
+            across(matches(".*_mem_gb$"), ~ .x / 1000)
         )
 
     #   When 'all_nodes' is FALSE, sum across all nodes within a partition to
     #   provide summary statistics
-    if (! all_nodes) {
-        part_df = part_df |>
+    if (!all_nodes) {
+        part_df <- part_df |>
             group_by(partition) |>
             #   Note free resources don't count hypothetically free resources (i.e. CPUs
             #   or memory that aren't being used, but aren't available for use now).
             #   'total*' columns do include these hypothetical resources
             summarize(
-                free_cpus = sum(inactive_cpus[state %in% c('mixed', 'idle')]),
+                free_cpus = sum(inactive_cpus[state %in% c("mixed", "idle")]),
                 total_cpus = sum(total_cpus),
                 prop_free_cpus = free_cpus / total_cpus,
-                free_mem_gb = sum(free_mem_gb[state %in% c('mixed', 'idle')]),
+                free_mem_gb = sum(free_mem_gb[state %in% c("mixed", "idle")]),
                 total_mem_gb = sum(total_mem_gb),
                 prop_free_mem_gb = free_mem_gb / total_mem_gb
             )
     }
 
-    return (part_df)
+    return(part_df)
 }
-

tests/testthat/test-array_submit.R

@@ -41,7 +41,7 @@ run_test <- function(shell_creation_fun, ...) {
             final <- readLines(paste0(script_name, ".sh"))
         }
     )
-    
+
     return(list("original" = original, "final" = final))
 }