updated readme and added r cmd check badge

A2-ai · Nov 1, 2024 · 44eec44 · 44eec44
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diff --git a/.github/workflows/RunChecks.yaml b/.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, workflow_test, vignette_update]
+    branches: [main]
   pull_request:
-    branches: [main, master, workflow_test]
+    branches: [main]
 
 name: R-CMD-check
 

diff --git a/R/slurmtools-package.R b/R/slurmtools-package.R
@@ -30,7 +30,6 @@
 #' @importFrom rlang dots_list
 #' @importFrom rlang is_atomic
 #' @importFrom rlang is_missing
-#' @importFrom rlang map2_chr
 #' @importFrom rlang names2
 #' @importFrom stringi stri_replace_all_regex
 #' @importFrom tibble tibble

diff --git a/README.Rmd b/README.Rmd
@@ -16,6 +16,7 @@ knitr::opts_chunk$set(
 # slurmtools
 
 <!-- badges: start -->
+[![R-CMD-check](https://github.com/A2-ai/slurmtools/actions/workflows/RunChecks.yaml/badge.svg)](https://github.com/A2-ai/slurmtools/actions/workflows/RunChecks.yaml)
 <!-- badges: end -->
 
 `slurmtools` is a collection of utility functions suitable for interacting with slurm and submitting nonmem jobs.

diff --git a/README.md b/README.md
@@ -4,6 +4,8 @@
 # slurmtools
 
 <!-- badges: start -->
+
+[![R-CMD-check](https://github.com/A2-ai/slurmtools/actions/workflows/RunChecks.yaml/badge.svg)](https://github.com/A2-ai/slurmtools/actions/workflows/RunChecks.yaml)
 <!-- badges: end -->
 
 `slurmtools` is a collection of utility functions suitable for
@@ -33,6 +35,15 @@ library(slurmtools)
 knitr::kable(get_slurm_jobs())
 ```
 
-| job_id | job_state | cpus | partition | standard_input | standard_output | submit_time | start_time | end_time | user_name | current_working_directory |
-|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|
-|  |  |  |  |  |  |  |  |  |  |  |
+| job_id | partition | user_name | job_state | time | cpus | standard_input | standard_output | submit_time | start_time | end_time | current_working_directory |
+|---:|:---|:---|:---|:---|---:|:---|:---|:---|:---|:---|:---|
+| 87 | cpu2mem4gb | matthews | FAILED | 2 secs | 1 | /dev/null | /tmp/Rtmpci7qIE/Rbuild1941e339490588/slurmtools/vignettes/model/nonmem/submission-log/slurm-87.out | 2024-11-01 15:20:24 | 2024-11-01 15:20:24 | 2024-11-01 15:20:26 | /tmp/Rtmpci7qIE/Rbuild1941e339490588/slurmtools/vignettes/model/nonmem/submission-log |
+| 88 | cpu2mem4gb | matthews | COMPLETED | 1 secs | 1 | /dev/null | /tmp/Rtmpci7qIE/Rbuild1941e339490588/slurmtools/vignettes/model/nonmem/submission-log/slurm-88.out | 2024-11-01 15:20:24 | 2024-11-01 15:20:25 | 2024-11-01 15:20:26 | /tmp/Rtmpci7qIE/Rbuild1941e339490588/slurmtools/vignettes/model/nonmem/submission-log |
+| 89 | cpu2mem4gb | matthews | FAILED | 0 secs | 1 | /dev/null | /tmp/Rtmpci7qIE/Rbuild1941e339490588/slurmtools/vignettes/model/nonmem/submission-log/slurm-89.out | 2024-11-01 15:20:25 | 2024-11-01 15:20:26 | 2024-11-01 15:20:26 | /tmp/Rtmpci7qIE/Rbuild1941e339490588/slurmtools/vignettes/model/nonmem/submission-log |
+| 90 | cpu2mem4gb | matthews | FAILED | 0 secs | 1 | /dev/null | /tmp/Rtmpci7qIE/Rbuild1941e339490588/slurmtools/vignettes/model/nonmem/submission-log/slurm-90.out | 2024-11-01 15:20:25 | 2024-11-01 15:24:06 | 2024-11-01 15:24:06 | /tmp/Rtmpci7qIE/Rbuild1941e339490588/slurmtools/vignettes/model/nonmem/submission-log |
+| 91 | cpu2mem4gb | matthews | FAILED | 0 secs | 1 | /dev/null | /tmp/Rtmpci7qIE/Rbuild1941e339490588/slurmtools/vignettes/model/nonmem/submission-log/slurm-91.out | 2024-11-01 15:20:26 | 2024-11-01 15:20:26 | 2024-11-01 15:20:26 | /tmp/Rtmpci7qIE/Rbuild1941e339490588/slurmtools/vignettes/model/nonmem/submission-log |
+| 92 | cpu2mem4gb | matthews | FAILED | 1 secs | 1 | /dev/null | /tmp/Rtmp5NSlzS/file187f0067bd515b/slurmtools.Rcheck/vign_test/slurmtools/vignettes/model/nonmem/submission-log/slurm-92.out | 2024-11-01 15:20:49 | 2024-11-01 15:24:06 | 2024-11-01 15:24:07 | /tmp/Rtmp5NSlzS/file187f0067bd515b/slurmtools.Rcheck/vign_test/slurmtools/vignettes/model/nonmem/submission-log |
+| 93 | cpu2mem4gb | matthews | COMPLETED | 0 secs | 1 | /dev/null | /tmp/Rtmp5NSlzS/file187f0067bd515b/slurmtools.Rcheck/vign_test/slurmtools/vignettes/model/nonmem/submission-log/slurm-93.out | 2024-11-01 15:20:50 | 2024-11-01 15:20:52 | 2024-11-01 15:20:52 | /tmp/Rtmp5NSlzS/file187f0067bd515b/slurmtools.Rcheck/vign_test/slurmtools/vignettes/model/nonmem/submission-log |
+| 94 | cpu2mem4gb | matthews | FAILED | 0 secs | 1 | /dev/null | /tmp/Rtmp5NSlzS/file187f0067bd515b/slurmtools.Rcheck/vign_test/slurmtools/vignettes/model/nonmem/submission-log/slurm-94.out | 2024-11-01 15:20:51 | 2024-11-01 15:20:52 | 2024-11-01 15:20:52 | /tmp/Rtmp5NSlzS/file187f0067bd515b/slurmtools.Rcheck/vign_test/slurmtools/vignettes/model/nonmem/submission-log |
+| 95 | cpu2mem4gb | matthews | FAILED | 0 secs | 1 | /dev/null | /tmp/Rtmp5NSlzS/file187f0067bd515b/slurmtools.Rcheck/vign_test/slurmtools/vignettes/model/nonmem/submission-log/slurm-95.out | 2024-11-01 15:20:52 | 2024-11-01 15:20:52 | 2024-11-01 15:20:52 | /tmp/Rtmp5NSlzS/file187f0067bd515b/slurmtools.Rcheck/vign_test/slurmtools/vignettes/model/nonmem/submission-log |
+| 96 | cpu2mem4gb | matthews | FAILED | 0 secs | 1 | /dev/null | /tmp/Rtmp5NSlzS/file187f0067bd515b/slurmtools.Rcheck/vign_test/slurmtools/vignettes/model/nonmem/submission-log/slurm-96.out | 2024-11-01 15:20:54 | 2024-11-01 15:20:55 | 2024-11-01 15:20:55 | /tmp/Rtmp5NSlzS/file187f0067bd515b/slurmtools.Rcheck/vign_test/slurmtools/vignettes/model/nonmem/submission-log |
diff --git a/man/get_slurm_jobs.Rd b/man/get_slurm_jobs.Rd
diff --git a/vignettes/slack-alerts.Rmd b/vignettes/slack-alerts.Rmd
@@ -74,10 +74,10 @@ notifications. If we look at the `snt` help message we see that it
 should be called via
 `snt slack -c config_file -k decryption_key -a token -f tokenFile -e email -m message -t timestamp`
 
-the config_file can contain the key, and token file so you don't need to
-repeatedly use that information. I've saved the tokenFile location and
-key in a config file in `~/.local/bin/slack_notifier_settings.yaml` and
-will use the -c flag to point to that.
+the config_file can contain the key (if not using the default snt key), and 
+token file so you don't need to repeatedly use that information. I've saved the tokenFile location in a config file in 
+`~/.local/bin/slack_notifier_settings.yaml` and will use the -c flag to point
+to that.
 
 With this our call to `snt` would look like:
 
@@ -98,7 +98,7 @@ slurmtools::generate_nmm_config(
   watched_dir = "/cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem",
   output_dir = "/cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/in_progress",
   alerter_opts = list(
-    alerter = Sys.which('snt'), #binary location of nmm,
+    alerter = normalizePath('~/.local/bin/snt'), #binary location of nmm,
     command = "slack",
     message_flag = "m", #This is the default so we don't need to specify it
     use_stdout = TRUE, #captures output of snt -- which will include --timestamp aksfl;ajklajl;