updated config file generating function removed the call from submit-…

…model. Swapped around messages about setting slurmtools options.

DESCRIPTION

@@ -21,7 +21,6 @@ Imports:
     utils,
     whisker,
     withr,
-    configr,
     rextendr,
     here
 Suggests: 

NAMESPACE

@@ -4,7 +4,6 @@ export(generate_watcher_config)
 export(get_slurm_jobs)
 export(get_slurm_partitions)
 export(submit_nonmem_model)
-export(validate_toml)
 importFrom(brio,read_file)
 importFrom(brio,write_file)
 importFrom(dplyr,"%>%")

R/nmm-config.R

@@ -0,0 +1,61 @@
+#' Creates a default watcher configuration file
+#'
+#' @param .mod a bbi nonmem model object
+#' @param model_number a string of model number e.g. 101a15. Default is pulled from .mod
+#' @param files_to_track a vector of file extensions. Default is c("lst", "ext", "grd")
+#' @param tmp_dir a temporary directory location to run nonmem. Default is /tmp
+#' @param watched_dir the directory where nonmem will output. Default is ./model/nonmem
+#' @param output_dir the directory where watcher will place log and any output files default is ./model/nonmem/in_progress
+#' @param poll_duration the amount of time in seconds between the watchers polling
+#' @param alert Where to send alerts if any. Default is None, available options are None or Slack
+#' @param level What level to log at. Default is info. Available options are Trace, Debug, Info, Warn, Fatal
+#' @param email if alert is set to Slack, this should be the email associated with slack to get messages sent directly to you.
+#' @param threads number of threads if running a parallel job. Default is 1
+#'
+#' @return none
+#' @keywords internal
+#' @export
+#'
+#' @examples \dontrun{
+#'   generate_watcher_config(.mod)
+#' }
+generate_watcher_config <- function(
+    .mod,
+    model_number = "",
+    files_to_track = c("lst", "ext", "grd"),
+    tmp_dir = "/tmp",
+    watched_dir = file.path("model", "nonmem"),
+    output_dir = file.path(watched_dir, "in_progress"),
+    poll_duration = 1,
+    alert = "None",
+    level = "Debug",
+    email = "",
+    threads = 1
+) {
+  if (model_number == "") {
+    model_number <- basename(.mod$absolute_model_path)
+  }
+
+  alert <- paste0(toupper(substring(alert, 1, 1)), substring(alert, 2))
+  level <- paste0(toupper(substring(level, 1, 1)), substring(level, 2))
+
+  if (alert == "Slack" && email == "") {
+    rlang::abort("If you want slack notifications you must also supply an email.")
+  }
+
+  toml <- list(
+    model_number = model_number,
+    files_to_track = files_to_track,
+    tmp_dir = tmp_dir,
+    watched_dir = file.path(here::here(), watched_dir),
+    output_dir = file.path(here::here(), output_dir),
+    poll_duration = poll_duration,
+    alert = alert,
+    level = level,
+    email = email,
+    threads = threads
+  )
+
+  config_toml_path <- paste0(.mod$absolute_model_path, ".toml")
+  write_file(rextendr::to_toml(toml), config_toml_path)
+}

R/submit-model.R

@@ -55,35 +55,22 @@ submit_nonmem_model <-
 
     config_toml_path <- paste0(.mod$absolute_model_path, ".toml")
     if (!fs::file_exists(config_toml_path)) {
-      generate_watcher_config(.mod, slurm_template_opts$watch_opts)
+      rlang::abort(sprintf("config.toml file not found, please run generate_config()"))
     }
 
-    config <- configr::read.config(config_toml_path)
-    config$output_dir <- file.path(here::here(), config$output_dir)
-    config$watched_dir <-file.path(here::here(), config$watched_dir)
-
-    new_config_toml_path <-
-      file.path(
-        here::here(), "model", "nonmem", "submission-log",
-        paste0(config$model_number, ".toml")
-      )
-
-    write_file(rextendr::to_toml(config), new_config_toml_path)
-
     default_template_list = list(
       partition = partition,
       parallel = parallel,
       ncpu = ncpu,
-      job_name = sprintf("nonmem-run-%s", basename(.mod$absolute_model_path)),
+      job_name = sprintf("%s-nonmem-run", basename(.mod$absolute_model_path)),
       model_path = .mod$absolute_model_path,
-      config_toml_path = new_config_toml_path,
+      config_toml_path = config_toml_path,
       nmm_exe_path = Sys.which("nmm")
     )
 
     template_list = c(
       default_template_list,
-      slurm_template_opts$alert_opts,
-      slurm_template_opts$watch_opts$log_level)
+      slurm_template_opts)
 
     template_script <-
       withr::with_dir(dirname(.mod$absolute_model_path), {

R/zzz.R

@@ -1,11 +1,13 @@
-.onLoad <- function(libname, pkgname) {
+.onAttach <- function(libname, pkgname) {
   if (is.null(getOption('slurmtools.slurm_job_template_path'))) {
-    rlang::warn(
-      "option('slurmtools.slurm_job_template_path') is not set. Please set it for job submission defaults to work."
-    )
+    # rlang::warn(
+    #   "option('slurmtools.slurm_job_template_path') is not set. Please set it for job submission defaults to work."
+    # )
+    packageStartupMessage("option('slurmtools.slurm_job_template_path') is not set. Please set it for job submission defaults to work.")
   }
 
   if (is.null(getOption('slurmtools.submission_root'))) {
-    rlang::warn("option('slurmtools.submission_root') is not set. Please set it for  job submission defaults to work.")
+    #rlang::warn("option('slurmtools.submission_root') is not set. Please set it for  job submission defaults to work.")
+    packageStartupMessage("option('slurmtools.submission_root') is not set. Please set it for  job submission defaults to work.")
   }
 }