Merge pull request #22 from A2-ai/cleanup

Cleanup
A2-ai · Nov 8, 2024 · c2a121b · c2a121b
2 parents 38e1ff4 + 6380e8d
commit c2a121b
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Showing 11 changed files with 15 additions and 15 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: slurmtools
 Title: slurm tooling 
-Version: 0.0.0.9002
+Version: 0.0.0.9003
 Authors@R: c(person("Devin", "Pastoor", , "[email protected]", role = c("aut", "cre")),
     person("Jenna", "Elwing", email = "[email protected]", role = "aut"),
     person("Matthew", "Smith", email = "[email protected]", role = "aut"))

diff --git a/NAMESPACE b/NAMESPACE
@@ -9,7 +9,7 @@ S3method(format_toml,integer)
 S3method(format_toml,list)
 S3method(format_toml,logical)
 S3method(format_toml,name)
-export(cancel_job)
+export(cancel_slurm_job)
 export(generate_nmm_config)
 export(get_slurm_jobs)
 export(get_slurm_partitions)

diff --git a/R/attach.R b/R/attach.R
@@ -14,21 +14,21 @@ slurmtools_options_message <- function() {
   # Check for each used options
   tmpl_path <- getOption('slurmtools.slurm_job_template_path')
   if (is.null(tmpl_path)) {
-    unset_options <- c(unset_options, "option('slurmtools.slurm_job_template_path') is not set.")
+    unset_options <- c(unset_options, "options('slurmtools.slurm_job_template_path') is not set.")
   } else {
     set_options <- c(set_options, paste("slurmtools.slurm_jon_template_path:", tmpl_path))
   }
 
   root <- getOption('slurmtools.submission_root')
   if (is.null(root)) {
-    unset_options <- c(unset_options, "option('slurmtools.submission_root') is not set.")
+    unset_options <- c(unset_options, "options('slurmtools.submission_root') is not set.")
   } else {
     set_options <- c(set_options, paste("slurmtools.submission_root:", root))
   }
 
   bbi_config <- getOption("slurmtools.bbi_config_path")
   if (is.null(bbi_config)) {
-    unset_options <- c(unset_options, "option('slurmtools.bbi_config_path') is not set.")
+    unset_options <- c(unset_options, "options('slurmtools.bbi_config_path') is not set.")
   } else {
     set_options <- c(set_options, paste("slurmtools.bbi_config_path:", bbi_config))
   }

diff --git a/R/cancel-job.R b/R/cancel-job.R
@@ -10,7 +10,7 @@
 #' @examples \dontrun{
 #' cancel_job(243)
 #' }
-cancel_job <- function(job_id, user = NULL) {
+cancel_slurm_job <- function(job_id, user = NULL) {
 
   current_user = if (is.null(Sys.getenv("USER"))) Sys.info()['user'] else Sys.getenv("USER")
 

diff --git a/R/slurmtools.R b/R/slurmtools.R
@@ -18,7 +18,7 @@
 #'
 #' @section cancelling jobs:
 #' \itemize{
-#'  \item \code{\link{cancel_job}}: Cancels the specified job
+#'  \item \code{\link{cancel_slurm_job}}: Cancels the specified job
 #' }
 #'
 #' @section slurm partitions:

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -40,7 +40,7 @@ reference:
   - submit_nonmem_model
   - generate_nmm_config
   - get_slurm_jobs
-  - cancel_job
+  - cancel_slurm_job
   - get_slurm_partitions
   - slurmtools
 

diff --git a/man/cancel_job.Rd → man/cancel_slurm_job.Rd b/man/cancel_job.Rd → man/cancel_slurm_job.Rd
diff --git a/man/slurmtools.Rd b/man/slurmtools.Rd
diff --git a/vignettes/Running-nonmem.Rmd b/vignettes/Running-nonmem.Rmd
@@ -254,7 +254,7 @@ jobs <- get_slurm_jobs(user = "matthews") %>%
   dplyr::pull(job_id)
 
 for (job in jobs) {
-  cancel_job(job)
+  cancel_slurm_job(job)
 }
 
 unlink(file.path(nonmem, "1001"), recursive = TRUE)

diff --git a/vignettes/custom-alerts.Rmd b/vignettes/custom-alerts.Rmd
@@ -237,7 +237,7 @@ jobs <- get_slurm_jobs(user = "matthews") %>%
   dplyr::pull(job_id)
 
 for (job in jobs) {
-  cancel_job(job)
+  cancel_slurm_job(job)
 }
 
 unlink(file.path(nonmem, "1001"), recursive = TRUE)

diff --git a/vignettes/slack-alerts.Rmd b/vignettes/slack-alerts.Rmd
@@ -146,7 +146,7 @@ jobs <- get_slurm_jobs(user = "matthews") %>%
   dplyr::pull(job_id)
 
 for (job in jobs) {
-  cancel_job(job)
+  cancel_slurm_job(job)
 }
 
 unlink(file.path(nonmem, "1001"), recursive = TRUE)