added project_name and project_path to default provided values to tem…

…plate.
A2-ai · Sep 5, 2024 · dc3347c · dc3347c
1 parent a4bd234
commit dc3347c
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Showing 3 changed files with 27 additions and 4 deletions.
diff --git a/R/submit-model.R b/R/submit-model.R
@@ -56,26 +56,45 @@ submit_nonmem_model <-
     }
 
     config_toml_path <- paste0(.mod$absolute_model_path, ".toml")
-    if (!fs::file_exists(config_toml_path)) {
-      rlang::warn(sprintf("config.toml file not found, if submitting the job with nmm this is required. Please run generate_nmm_config()"))
-    }
+    #if (!fs::file_exists(config_toml_path)) {
+    #  rlang::warn(sprintf("config.toml file not found, if submitting the job with nmm this is required. Please run generate_nmm_config()"))
+    #}
 
     if (is.null(slurm_template_opts$nmm_exe_path)) {
       nmm_exe_path <- Sys.which("nmm")
     } else {
       nmm_exe_path <- slurm_template_opts$nmm_exe_path
     }
+
     if (is.null(slurm_template_opts$bbi_exe_path)) {
       bbi_exe_path <- Sys.which("bbi")
     } else {
       bbi_exe_path <- slurm_template_opts$bbi_exe_path
     }
 
+
+    if (is.null(slurm_template_opts$project_path)) {
+      project_path <- rstudioapi::getActiveProject()
+    } else {
+      project_path <- slurm_template_opts$project_path
+    }
+    if (is.null(slurm_template_opts$project_name)) {
+      project_name <- tools::file_path_sans_ext(
+        list.files(
+          path = project_path,
+          pattern = ".Rproj$")
+        )
+    } else {
+      project_name <- slurm_template_opts$project_name
+    }
+
     default_template_list = list(
       partition = partition,
       parallel = parallel,
       ncpu = ncpu,
       job_name = sprintf("%s-nonmem-run", basename(.mod$absolute_model_path)),
+      project_path = project_path,
+      project_name = project_name,
       bbi_exe_path = bbi_exe_path,
       bbi_config_path = bbi_config_path,
       model_path = .mod$absolute_model_path,

diff --git a/vignettes/model/nonmem/slurm-job-nmm.tmpl b/vignettes/model/nonmem/slurm-job-nmm.tmpl
@@ -4,6 +4,9 @@
 #SBATCH --ntasks=1
 #SBATCH --cpus-per-task={{ncpu}}
 #SBATCH --partition={{partition}}
+#SBATCH --account={{project_name}}
+
+#{{project_path}}
 
 unset SLURM_NODELIST
 unset SLURM_JOB_NODELIST

diff --git a/vignettes/slack-alerts.Rmd b/vignettes/slack-alerts.Rmd
@@ -111,7 +111,8 @@ submission_nmm <- slurmtools::submit_nonmem_model(
   overwrite = TRUE,
   slurm_job_template_path = file.path(nonmem, "slurm-job-nmm.tmpl"),
   slurm_template_opts = list(
-    nmm_exe_path = normalizePath("~/.local/bin/nmm"))
+    nmm_exe_path = normalizePath("~/.local/bin/nmm")
+  )
 )
 
 submission_nmm