Merge pull request #9 from A2-ai/workflow_test

Workflow test

.github/workflows/RunChecks.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, workflow_test]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, workflow_test]
 
 name: R-CMD-check
 
@@ -39,34 +39,48 @@ jobs:
         run: |
           mkdir -p /usr/local/bin
           cd /tmp
-          gh release download "sinfo/v0.2.0" -R a2-ai-tech-training/slurm-mocks -p "*Linux_x86_64.tar.gz" -D /usr/local/bin/
+          gh release download "sinfo/v0.2.1" -R a2-ai-tech-training/slurm-mocks -p "*Linux_x86_64.tar.gz" -D /usr/local/bin/
           tar -xvf /usr/local/bin/sinfo_Linux_x86_64.tar.gz
           mv ./sinfo /usr/local/bin/sinfo
-          chmod +x /usr/local/bin/sinfo
+          chmod 755 /usr/local/bin/sinfo
 
           gh release download "sacct/v0.2.0" -R a2-ai-tech-training/slurm-mocks -p "*Linux_x86_64.tar.gz" -D /usr/local/bin/
           tar -xvf /usr/local/bin/sacct_Linux_x86_64.tar.gz
           mv ./sacct /usr/local/bin/sacct
-          chmod +x /usr/local/bin/sacct
+          chmod 755 /usr/local/bin/sacct
+
+          gh release download "squeue/v0.2.0" -R a2-ai-tech-training/slurm-mocks -p "*Linux_x86_64.tar.gz" -D /usr/local/bin/
+          tar -xvf /usr/local/bin/squeue_Linux_x86_64.tar.gz
+          mv ./squeue /usr/local/bin/squeue
+          chmod 755 /usr/local/bin/squeue
+
+          gh release download "sbatch/v0.2.0" -R a2-ai-tech-training/slurm-mocks -p "*Linux_x86_64.tar.gz" -D /usr/local/bin/
+          tar -xvf /usr/local/bin/sbatch_Linux_x86_64.tar.gz
+          mv ./sbatch /usr/local/bin/sbatch
+          chmod 755 /usr/local/bin/sbatch
 
           echo "/usr/local/bin" >> $GITHUB_PATH
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
-      - name: Grab outputs directory from mocked repo
+      - name: Check mocked binaries work in different step
         run: |
-          cd /tmp
-          gh repo clone a2-ai-tech-training/slurm-mocks
-          mv /tmp/slurm-mocks/sinfo/outputs $GITHUB_WORKSPACE/
-          rm -rf /tmp/slurm-mocks
-        env:
-          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          Rscript -e 'if (!requireNamespace("processx", quietly = TRUE)) install.packages("processx"); processx::run("sinfo", args = c("--format", "%P,%c,%m"),)'
+          Rscript -e 'processx::run("sacct", args = "--json")'
+          Rscript -e 'processx::run("squeue", args = "--version")'
+          Rscript -e 'processx::run("squeue", args = "--json")'
+          Rscript -e 'processx::run("sbatch", args = "path_to_file")'
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: |
+            metrumresearchgroup/mrgmisc
+            metrumresearchgroup/nmrec
+            metrumresearchgroup/bbr
+            any::rcmdcheck
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+

.gitignore

@@ -1,5 +1,4 @@
 .Rproj.user
 docs
-inst/doc
 /doc/
 /Meta/

R/get-jobs.R

@@ -45,7 +45,8 @@ parse_jobs_json <- function(.json) {
 #' @param user user filter
 #' @export
 get_slurm_jobs <- function(user = NULL){
-  cmd <- list(cmd = "squeue", args = "--json")
+
+  cmd <- list(cmd = Sys.which("squeue"), args = "--json")
   res <- processx::run(cmd$cmd, args = cmd$args)
   if (res$status != 0) {
     # todo: better handle returning why
@@ -55,7 +56,16 @@ get_slurm_jobs <- function(user = NULL){
   res_df$submit_time <- as.POSIXct(res_df$submit_time, origin = "1970-01-01")
   res_df$start_time <- as.POSIXct(res_df$start_time, origin = "1970-01-01")
   if (!is.null(user)) {
-    return(dplyr::filter(res_df, user_name == user))
+    df <- tryCatch(
+      {
+        dplyr::filter(res_df, user_name == user)
+      },
+      error = function(e) {
+        res_df
+      }
+    )
+  } else {
+    df <- res_df
   }
-  res_df
+  return(df)
 }

R/submit-model.R

@@ -109,6 +109,7 @@ submit_nonmem_model <-
           template_list
         )
       })
+
     script_file_path <-
         file.path(submission_root, sprintf("%s.sh", basename(.mod$absolute_model_path)))
     if (!dry_run) {
@@ -118,7 +119,7 @@ submit_nonmem_model <-
       brio::write_file(template_script, script_file_path)
       fs::file_chmod(script_file_path, "0755")
     }
-    cmd <- list(cmd = "sbatch", args = script_file_path, template_script = template_script, partition = partition)
+    cmd <- list(cmd = Sys.which("sbatch"), args = script_file_path, template_script = template_script, partition = partition)
     if (dry_run) {
       return(cmd)
     }

R/zzz.R

@@ -4,14 +4,23 @@
 }
 
 .onLoad <- function(libname, pkgname) {
-  processx_output <- processx::run("squeue", args = "--version")
-  if (processx_output$status != 0) {
-    warning("squeue not installed correctly")
-  } else {
-    # stdout format is "slurm major.minor.patch/n"
-    version <- strsplit(processx_output$stdout," ")[[1]][[2]] %>%
-      trimws() %>%
-      package_version()
-    options("squeue.version" = version)
+  result <- tryCatch(
+    {processx::run(Sys.which("squeue"), args = "--version")},
+    error = function(e) {
+      warning("'squeue' command not found or failed to run.")
+      return(NULL)
+    }
+  )
+
+  if (!is.null(result)) {
+    if (result$status != 0) {
+      warning("squeue not installed correctly")
+    } else {
+      # stdout format is "slurm major.minor.patch/n"
+      version <- strsplit(result$stdout," ")[[1]][[2]] %>%
+        trimws() %>%
+        package_version()
+      options("squeue.version" = version)
+    }
   }
 }

vignettes/Running-nonmem.Rmd

@@ -250,20 +250,20 @@ To reiterate, this template file is run as a bash shell script so anything you c
 
 ```{r, include = FALSE}
 #cancelling any running nonmem jobs
-state <- slurmtools::get_slurm_jobs(user = "matthews")
-
-if (any(state$job_state %in% c("RUNNING", "CONFIGURING"))) {
-  for (job_id in state %>% dplyr::filter(job_state == "RUNNING") %>% dplyr::pull("job_id")) {
-    processx::run("scancel", args = paste0(job_id))
-  }
-}
-
-#removing generated files from running this vignette
-nonmem <- file.path("model", "nonmem")
-
-unlink(file.path(nonmem, "1001"), recursive = TRUE)
-unlink(file.path(nonmem, "1001.yaml"))
-unlink(file.path(nonmem, "1001.toml"))
-unlink(file.path(nonmem, "submission-log"), recursive = TRUE) 
-unlink(file.path(nonmem, "in_progress"), recursive = TRUE)
+# state <- slurmtools::get_slurm_jobs(user = "matthews")
+# 
+# if (any(state$job_state %in% c("RUNNING", "CONFIGURING"))) {
+#   for (job_id in state %>% dplyr::filter(job_state == "RUNNING") %>% dplyr::pull("job_id")) {
+#     processx::run("scancel", args = paste0(job_id))
+#   }
+# }
+# 
+# #removing generated files from running this vignette
+# nonmem <- file.path("model", "nonmem")
+# 
+# unlink(file.path(nonmem, "1001"), recursive = TRUE)
+# unlink(file.path(nonmem, "1001.yaml"))
+# unlink(file.path(nonmem, "1001.toml"))
+# unlink(file.path(nonmem, "submission-log"), recursive = TRUE) 
+# unlink(file.path(nonmem, "in_progress"), recursive = TRUE)
 ```

vignettes/custom-alerts.Rmd

@@ -247,21 +247,21 @@ This gives us the notifications in a much more digestible format
 ![nmm ntfy.sh alerts](data/images/nmm_ntfy_alerts.png)
 
 ```{r, include = FALSE}
-#cancelling any running nonmem jobs
-state <- slurmtools::get_slurm_jobs(user = "matthews")
-
-if (any(state$job_state %in% c("RUNNING", "CONFIGURING"))) {
-  for (job_id in state %>% dplyr::filter(job_state == "RUNNING") %>% dplyr::pull("job_id")) {
-    processx::run("scancel", args = paste0(job_id))
-  }
-}
-
-#removing generated files from running this vignette
-nonmem <- file.path("model", "nonmem")
-
-unlink(file.path(nonmem, "1001"), recursive = TRUE)
-unlink(file.path(nonmem, "1001.yaml"))
-unlink(file.path(nonmem, "1001.toml"))
-unlink(file.path(nonmem, "submission-log"), recursive = TRUE) 
-unlink(file.path(nonmem, "in_progress"), recursive = TRUE)
+# #cancelling any running nonmem jobs
+# state <- slurmtools::get_slurm_jobs(user = "matthews")
+# 
+# if (any(state$job_state %in% c("RUNNING", "CONFIGURING"))) {
+#   for (job_id in state %>% dplyr::filter(job_state == "RUNNING") %>% dplyr::pull("job_id")) {
+#     processx::run("scancel", args = paste0(job_id))
+#   }
+# }
+# 
+# #removing generated files from running this vignette
+# nonmem <- file.path("model", "nonmem")
+# 
+# unlink(file.path(nonmem, "1001"), recursive = TRUE)
+# unlink(file.path(nonmem, "1001.yaml"))
+# unlink(file.path(nonmem, "1001.toml"))
+# unlink(file.path(nonmem, "submission-log"), recursive = TRUE) 
+# unlink(file.path(nonmem, "in_progress"), recursive = TRUE)
 ```

vignettes/slack-alerts.Rmd

@@ -62,7 +62,7 @@ Sys.which("slack_notifier")
 
 slack_notifier requires an additional `slack_notifier/config.yaml` file
 that contains the slack bot OAuth token which is found from
-[[[https://api.slack.com/apps/\\\\](https://api.slack.com/apps/\\){.uri}]([https://api.slack.com/apps/\\](https://api.slack.com/apps/\){.uri}){.uri}\<YOUR
+[[[https://api.slack.com/apps/\\\\](https://api.slack.com/apps/){.uri}](%5Bhttps://api.slack.com/apps/%5D(https://api.slack.com/apps/)%7B.uri%7D){.uri}\<YOUR
 APP ID\> /oauth?].
 
 ``` slack_notifier/config.yaml
@@ -125,21 +125,21 @@ slurmtools::get_slurm_jobs()
 ![nmm slack alerts](data/images/nmm_slack_notifications.png)
 
 ```{r, include = FALSE}
-#cancelling any running nonmem jobs
-state <- slurmtools::get_slurm_jobs(user = "matthews")
-
-if (any(state$job_state %in% c("RUNNING", "CONFIGURING"))) {
-  for (job_id in state %>% dplyr::filter(job_state == "RUNNING") %>% dplyr::pull("job_id")) {
-    processx::run("scancel", args = paste0(job_id))
-  }
-}
-
-#removing generated files from running this vignette
-nonmem <- file.path("model", "nonmem")
-
-unlink(file.path(nonmem, "1001"), recursive = TRUE)
-unlink(file.path(nonmem, "1001.yaml"))
-unlink(file.path(nonmem, "1001.toml"))
-unlink(file.path(nonmem, "submission-log"), recursive = TRUE) 
-unlink(file.path(nonmem, "in_progress"), recursive = TRUE)
+# #cancelling any running nonmem jobs
+# state <- slurmtools::get_slurm_jobs(user = "matthews")
+# 
+# if (any(state$job_state %in% c("RUNNING", "CONFIGURING"))) {
+#   for (job_id in state %>% dplyr::filter(job_state == "RUNNING") %>% dplyr::pull("job_id")) {
+#     processx::run("scancel", args = paste0(job_id))
+#   }
+# }
+# 
+# #removing generated files from running this vignette
+# nonmem <- file.path("model", "nonmem")
+# 
+# unlink(file.path(nonmem, "1001"), recursive = TRUE)
+# unlink(file.path(nonmem, "1001.yaml"))
+# unlink(file.path(nonmem, "1001.toml"))
+# unlink(file.path(nonmem, "submission-log"), recursive = TRUE) 
+# unlink(file.path(nonmem, "in_progress"), recursive = TRUE)
 ```