added project_name and path to default template list. Updated vignette.

R/submit-model.R

@@ -72,18 +72,13 @@ submit_nonmem_model <-
       bbi_exe_path <- slurm_template_opts$bbi_exe_path
     }
 
-
     if (is.null(slurm_template_opts$project_path)) {
-      project_path <- rstudioapi::getActiveProject()
+      project_path <- here::here()
     } else {
       project_path <- slurm_template_opts$project_path
     }
     if (is.null(slurm_template_opts$project_name)) {
-      project_name <- tools::file_path_sans_ext(
-        list.files(
-          path = project_path,
-          pattern = ".Rproj$")
-        )
+      project_name <- here::here() %>% basename()
     } else {
       project_name <- slurm_template_opts$project_name
     }

vignettes/Running-nonmem.Rmd

@@ -53,11 +53,13 @@ This function uses the inputs to populate a template Bash shell script that subm
 By default these values are provided to the slurm template file:
 
 ``` r
-list(
+default_template_list = list(
   partition = partition,
   parallel = parallel,
   ncpu = ncpu,
   job_name = sprintf("%s-nonmem-run", basename(.mod$absolute_model_path)),
+  project_path = project_path,
+  project_name = project_name,
   bbi_exe_path = Sys.which("bbi"),
   bbi_config_path = bbi_config_path,
   model_path = .mod$absolute_model_path,
@@ -99,6 +101,7 @@ Here is an example of a template file that will call `bbi`:
 #SBATCH --ntasks=1
 #SBATCH --cpus-per-task={{ncpu}}
 #SBATCH --partition={{partition}}
+#SBATCH --account={{project_name}}
 
 # submit_nonmem_model uses the whisker package to populate template files
 # https://github.com/edwindj/whisker
@@ -154,7 +157,7 @@ submission <- slurmtools::submit_nonmem_model(
 submission
 ```
 
-Notice we get a Warning about a config.toml file not being found. I'll expand on that later, but for now we see a `status` with an exit code of 0 suggesting a successful command, and the `stdout` gives us the batch job number. We can use `slurmtools::get_slurm_jobs()` to monitor the status of the job. Here, we can supply the user = "matthews" argument to filter to just the jobs I've submitted.
+We see a `status` with an exit code of 0 suggesting a successful command, and the `stdout` gives us the batch job number. We can use `slurmtools::get_slurm_jobs()` to monitor the status of the job. Here, we can supply the user = "matthews" argument to filter to just the jobs I've submitted.
 
 ```{r}
 slurmtools::get_slurm_jobs(user = 'matthews')
@@ -181,6 +184,7 @@ Here is a modified template file that adds a `JOBID=$SLURM_JOBID` and some ntfy
 #SBATCH --ntasks=1
 #SBATCH --cpus-per-task={{ncpu}}
 #SBATCH --partition={{partition}}
+#SBATCH --account={{project_name}}
 
 JOBID=$SLURM_JOBID
 
@@ -231,6 +235,7 @@ Note that the run number will match the run specified in `submission$stdout`. We
 #SBATCH --ntasks=1
 #SBATCH --cpus-per-task=1
 #SBATCH --partition=cpu2mem4gb
+#SBATCH --account=slurmtools
 
 JOBID=$SLURM_JOBID
 

vignettes/custom-alerts.Rmd

@@ -67,8 +67,7 @@ not give you the path to the nmm binary if it is on your path or not. We
 can inject the `nmm_exe_path` like we did with `bbi_exe_path` and assume
 it's not on our path.
 
-Remember that error about the `config.toml` file not existing? Well this
-is the reason. This file controls what `nmm` will monitor and where to
+The `config.toml` file controls what `nmm` will monitor and where to
 look for files and how to alert you. We'll use `generate_nmm_config()`
 to create this file. First we can look at the documentation to see what
 type of information we should pass to this function.![documentation for

vignettes/model/nonmem/slurm-job-bbi-ntfy.tmpl

@@ -4,6 +4,7 @@
 #SBATCH --ntasks=1
 #SBATCH --cpus-per-task={{ncpu}}
 #SBATCH --partition={{partition}}
+#SBATCH --account={{project_name}}
 
 JOBID=$SLURM_JOBID
 

vignettes/model/nonmem/slurm-job-bbi.tmpl

@@ -4,7 +4,8 @@
 #SBATCH --ntasks=1
 #SBATCH --cpus-per-task={{ncpu}}
 #SBATCH --partition={{partition}}
-
+#SBATCH --account={{project_name}}
+#{{project_path}}
 unset SLURM_NODELIST
 unset SLURM_JOB_NODELIST
 unset SLURM_JOB_USER