Add commens

Author: byzheng

DESCRIPTION

@@ -11,7 +11,7 @@ Description: Implements a task queue system for asynchronous parallel computing
     Dynamically distributes tasks to workers, handles uneven load balancing, and 
     allows new workers to join at any time. Particularly useful for running large 
     numbers of independent tasks on high-performance computing (HPC) clusters with 
-    'SLURM' job schedulers.
+    'SLURM' <https://slurm.schedmd.com/> job schedulers.
 URL: https://taskqueue.bangyou.me/,
     https://github.com/byzheng/taskqueue
 BugReports: https://github.com/byzheng/taskqueue/issues

NAMESPACE

@@ -21,7 +21,6 @@ export(resource_add)
 export(resource_get)
 export(resource_list)
 export(shiny_app)
-export(slurm_deploy)
 export(task_add)
 export(task_clean)
 export(task_get)

R/apply.R

@@ -62,6 +62,7 @@
 #'
 #' @examples
 #' \dontrun{
+#' # Not run:
 #' # Simple example
 #' my_simulation <- function(i, param) {
 #'   out_file <- sprintf("results/sim_%04d.Rds", i)

R/db.R

@@ -28,6 +28,7 @@
 #'
 #' @examples
 #' \dontrun{
+#' # Not run:
 #' # Create a new connection
 #' con <- db_connect()
 #'
@@ -75,6 +76,7 @@ db_connect <- function(con = NULL) {
 #'
 #' @examples
 #' \dontrun{
+#' # Not run:
 #' # Connect and disconnect
 #' con <- db_connect()
 #' # ... perform database operations ...
@@ -116,6 +118,7 @@ db_disconnect <- function(con) {
 #'
 #' @examples
 #' \dontrun{
+#' # Not run:
 #' # Initialize database (run once)
 #' db_init()
 #'
@@ -162,6 +165,7 @@ db_init <- function() {
 #'
 #' @examples
 #' \dontrun{
+#' # Not run:
 #' # Clean entire database (destructive!)
 #' db_clean()
 #'
@@ -268,6 +272,7 @@ table_exist <- function(table, con = NULL) {
 #'
 #' @examples
 #' \dontrun{
+#' # Not run:
 #' # Test connection
 #' if (is_db_connect()) {
 #'   message("Database is accessible")

R/deploy.R

@@ -42,7 +42,6 @@ TASKQUEUE_OPTIONS <- settings::options_manager(
 #' @seealso \code{\link{taskqueue_reset}}, \code{\link{db_connect}}
 #'
 #' @examples
-#' \dontrun{
 #' # View all current options
 #' taskqueue_options()
 #'
@@ -54,7 +53,6 @@ TASKQUEUE_OPTIONS <- settings::options_manager(
 #'
 #' # Reset to environment variable values
 #' taskqueue_reset()
-#' }
 #' @export
 taskqueue_options <- function(...){
     # protect against the use of reserved words.
@@ -83,13 +81,11 @@ taskqueue_options <- function(...){
 #' @seealso \code{\link{taskqueue_options}}
 #'
 #' @examples
-#' \dontrun{
 #' # Override options temporarily
 #' taskqueue_options(host = "test.server.com")
 #'
 #' # Reset to environment variable values
 #' taskqueue_reset()
-#' }
 #' @export
 taskqueue_reset <- function() {
     settings::reset(TASKQUEUE_OPTIONS)

R/options.R

@@ -66,6 +66,7 @@
 #'
 #' @examples
 #' \dontrun{
+#' # Not run:
 #' # Create a project with default memory
 #' project_add("simulation_study")
 #'
@@ -148,6 +149,7 @@ project_add <- function(project, memory = 10) {
 #'
 #' @examples
 #' \dontrun{
+#' # Not run:
 #' # Start project to enable workers
 #' project_start("simulation_study")
 #'
@@ -188,6 +190,7 @@ project_start <- function(project, con = NULL) {
 #'
 #' @examples
 #' \dontrun{
+#' # Not run:
 #' # Stop project and cancel all jobs
 #' project_stop("simulation_study")
 #'
@@ -261,6 +264,7 @@ project_stop <- function(project) {
 #'
 #' @examples
 #' \dontrun{
+#' # Not run:
 #' # Reset project and clean logs
 #' project_reset("simulation_study")
 #'
@@ -320,6 +324,7 @@ project_reset <- function(project, log_clean = TRUE) {
 #'
 #' @examples
 #' \dontrun{
+#' # Not run:
 #' # Get project details
 #' info <- project_get("simulation_study")
 #' print(info$status)  # Check if running
@@ -379,6 +384,7 @@ project_resource_get <- function(project, resource = NULL, con = NULL) {
 #'
 #' @examples
 #' \dontrun{
+#' # Not run:
 #' # List all projects
 #' projects <- project_list()
 #' print(projects)
@@ -426,6 +432,7 @@ project_list <- function(con = NULL) {
 #'
 #' @examples
 #' \dontrun{
+#' # Not run:
 #' # Delete a completed project
 #' project_delete("old_simulation")
 #'
@@ -485,6 +492,7 @@ project_delete <- function(project, con = NULL) {
 #'
 #' @examples
 #' \dontrun{
+#' # Not run:
 #' # Check project status
 #' project_status("simulation_study")
 #' }

R/project.R

@@ -78,6 +78,7 @@
 #'
 #' @examples
 #' \dontrun{
+#' # Not run:
 #' # Assign resource to project with basic settings
 #' project_resource_add(
 #'   project = "simulation_study",
@@ -191,6 +192,7 @@ project_resource_add <- function(project,
 #'
 #' @examples
 #' \dontrun{
+#' # Not run:
 #' # Delete logs for specific project-resource
 #' project_resource_log_delete("simulation_study", "hpc")
 #' }
@@ -250,6 +252,7 @@ project_resource_log_delete <- function(project,
 #'
 #' @examples
 #' \dontrun{
+#' # Not run:
 #' # Add a job (typically done automatically by worker_slurm)
 #' project_resource_add_jobs("simulation_study", "hpc", "job_12345")
 #'

R/project_resource.R

@@ -41,6 +41,7 @@
 #'
 #' @examples
 #' \dontrun{
+#' # Not run:
 #' # List all resources
 #' resources <- resource_list()
 #' print(resources)
@@ -76,6 +77,7 @@ resource_list <- function() {
 #'
 #' @examples
 #' \dontrun{
+#' # Not run:
 #' # Get specific resource
 #' hpc_info <- resource_get("hpc")
 #' print(hpc_info$workers)  # Maximum workers
@@ -134,6 +136,7 @@ resource_get <- function(resource, con = NULL) {
 #'
 #' @examples
 #' \dontrun{
+#' # Not run:
 #' # Add a SLURM cluster resource
 #' resource_add(
 #'   name = "hpc",

R/resource.R

@@ -20,6 +20,7 @@
 #'
 #' @examples
 #' \dontrun{
+#' # Not run:
 #' # Launch monitoring app
 #' shiny_app()
 #' }