diff --git a/DESCRIPTION b/DESCRIPTION index a9ff841..c5da72f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: sluRm Title: A Lightweight Wrapper for Slurm -Version: 0.1-0 +Version: 0.2-0 Authors@R: c( person("George", "Vega Yon", email = "g.vegayon@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3171-0844")), person("Paul", "Marjoram", email = "pmarjora@usc.edu", role = c("ctb", "ths"), comment = c(ORCID = "0000-0003-0824-7449")), diff --git a/NEWS.md b/NEWS.md index 71f1ce2..2024889 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# sluRm 0.2-0 + +* JOSS review (finalizing). + # sluRm 0.1-0 * Added a `NEWS.md` file to track changes to the package. diff --git a/docs/404.html b/docs/404.html index 4ec9da3..00b5ad9 100644 --- a/docs/404.html +++ b/docs/404.html @@ -66,7 +66,7 @@ sluRm - 0.1.0 + 0.2.0 diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html index 6f83239..9765e85 100644 --- a/docs/CODE_OF_CONDUCT.html +++ b/docs/CODE_OF_CONDUCT.html @@ -66,7 +66,7 @@ sluRm - 0.1.0 + 0.2.0 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index dc6b62a..4ac0273 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -66,7 +66,7 @@ sluRm - 0.1.0 + 0.2.0 diff --git a/docs/LICENSE.html b/docs/LICENSE.html index da39054..efd5029 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -66,7 +66,7 @@ sluRm - 0.1.0 + 0.2.0 diff --git a/docs/articles/getting-started.html b/docs/articles/getting-started.html index 195135b..e1d7e17 100644 --- a/docs/articles/getting-started.html +++ b/docs/articles/getting-started.html @@ -32,7 +32,7 @@ sluRm - 0.1.0 + 0.2.0 diff --git a/docs/articles/index.html b/docs/articles/index.html index 615ffad..98e5106 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -66,7 +66,7 @@ sluRm - 0.1.0 + 0.2.0 diff --git a/docs/authors.html b/docs/authors.html index a7dc65d..5c1a388 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -66,7 +66,7 @@ sluRm - 0.1.0 + 0.2.0 diff --git a/docs/index.html b/docs/index.html index 60a1f95..c089c5f 100644 --- a/docs/index.html +++ b/docs/index.html @@ -34,7 +34,7 @@ sluRm - 0.1.0 + 0.2.0 @@ -125,7 +125,7 @@

We can use the function Slurm_lapply to distribute computations

ans <- Slurm_lapply(x, mean, plan = "none")
 #  Warning: [submit = FALSE] The job hasn't been submitted yet. Use sbatch() to submit the job, or you can submit it via command line using the following:
-#  sbatch --job-name=sluRm-job-76a05785af3b /home/vegayon/Documents/sluRm/sluRm-job-76a05785af3b/01-bash.sh
+#  sbatch --job-name=sluRm-job-64641d9034ee /home/vegayon/Documents/sluRm/sluRm-job-64641d9034ee/01-bash.sh
 Slurm_clean(ans) # Cleaning after you

Notice the plan = "none" option, this tells Slurm_lapply to only create the job object, but do nothing with it, i.e., skip submission. To get more info, we can actually set the verbose mode on

opts_sluRm$verbose_on()
@@ -133,7 +133,7 @@ 

 #  
 #  --------------------------------------------------------------------------------
 #  [VERBOSE MODE ON] The R script that will be used is located at:
-#  /home/vegayon/Documents/sluRm/sluRm-job-76a05785af3b/00-rscript.r
+#  /home/vegayon/Documents/sluRm/sluRm-job-64641d9034ee/00-rscript.r
 #  and has the following contents:
 #  --------------------------------------------------------------------------------
 #  .libPaths(c("/usr/local/lib/R/site-library", "/usr/lib/R/site-library", "/usr/lib/R/library"))
@@ -146,38 +146,38 @@ 

 #      y
 #  }
 #  ARRAY_ID         <- as.integer(Slurm_env("SLURM_ARRAY_TASK_ID"))
-#  INDICES          <- readRDS("/home/vegayon/Documents/sluRm/sluRm-job-76a05785af3b/INDICES.rds")
-#  X                <- readRDS(sprintf("/home/vegayon/Documents/sluRm/sluRm-job-76a05785af3b/X_%04d.rds", ARRAY_ID))
-#  FUN              <- readRDS("/home/vegayon/Documents/sluRm/sluRm-job-76a05785af3b/FUN.rds")
-#  mc.cores         <- readRDS("/home/vegayon/Documents/sluRm/sluRm-job-76a05785af3b/mc.cores.rds")
-#  seeds            <- readRDS("/home/vegayon/Documents/sluRm/sluRm-job-76a05785af3b/seeds.rds")
+#  INDICES          <- readRDS("/home/vegayon/Documents/sluRm/sluRm-job-64641d9034ee/INDICES.rds")
+#  X                <- readRDS(sprintf("/home/vegayon/Documents/sluRm/sluRm-job-64641d9034ee/X_%04d.rds", ARRAY_ID))
+#  FUN              <- readRDS("/home/vegayon/Documents/sluRm/sluRm-job-64641d9034ee/FUN.rds")
+#  mc.cores         <- readRDS("/home/vegayon/Documents/sluRm/sluRm-job-64641d9034ee/mc.cores.rds")
+#  seeds            <- readRDS("/home/vegayon/Documents/sluRm/sluRm-job-64641d9034ee/seeds.rds")
 #  set.seed(seeds[ARRAY_ID], kind = NULL, normal.kind = NULL)
 #  ans <- parallel::mclapply(
 #      X                = X,
 #      FUN              = FUN,
 #      mc.cores         = mc.cores
 #  )
-#  saveRDS(ans, sprintf("/home/vegayon/Documents/sluRm/sluRm-job-76a05785af3b/03-answer-%03i.rds", ARRAY_ID), compress = TRUE)
+#  saveRDS(ans, sprintf("/home/vegayon/Documents/sluRm/sluRm-job-64641d9034ee/03-answer-%03i.rds", ARRAY_ID), compress = TRUE)
 #  
 #  --------------------------------------------------------------------------------
 #  The bash file that will be used is located at:
-#  /home/vegayon/Documents/sluRm/sluRm-job-76a05785af3b/01-bash.sh
+#  /home/vegayon/Documents/sluRm/sluRm-job-64641d9034ee/01-bash.sh
 #  and has the following contents:
 #  --------------------------------------------------------------------------------
 #  #!/bin/sh
-#  #SBATCH --job-name=sluRm-job-76a05785af3b
-#  #SBATCH --output=/home/vegayon/Documents/sluRm/sluRm-job-76a05785af3b/02-output-%A-%a.out
+#  #SBATCH --job-name=sluRm-job-64641d9034ee
+#  #SBATCH --output=/home/vegayon/Documents/sluRm/sluRm-job-64641d9034ee/02-output-%A-%a.out
 #  #SBATCH --array=1-2
 #  #SBATCH --ntasks=1
 #  #SBATCH --cpus-per-task=1
 #  export OMP_NUM_THREADS=1
-#  /usr/lib/R/bin/Rscript --vanilla /home/vegayon/Documents/sluRm/sluRm-job-76a05785af3b/00-rscript.r
+#  /usr/lib/R/bin/Rscript --vanilla /home/vegayon/Documents/sluRm/sluRm-job-64641d9034ee/00-rscript.r
 #  
 #  --------------------------------------------------------------------------------
 #  EOF
 #  --------------------------------------------------------------------------------
 #  Warning: [submit = FALSE] The job hasn't been submitted yet. Use sbatch() to submit the job, or you can submit it via command line using the following:
-#  sbatch --job-name=sluRm-job-76a05785af3b /home/vegayon/Documents/sluRm/sluRm-job-76a05785af3b/01-bash.sh
+#  sbatch --job-name=sluRm-job-64641d9034ee /home/vegayon/Documents/sluRm/sluRm-job-64641d9034ee/01-bash.sh
 Slurm_clean(ans) # Cleaning after you
diff --git a/docs/news/index.html b/docs/news/index.html index 9861c96..df44494 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -66,7 +66,7 @@ sluRm - 0.1.0 + 0.2.0
@@ -122,6 +122,13 @@

Changelog

Source: NEWS.md +
+

+sluRm 0.2-0

+ +

sluRm 0.1-0

@@ -135,6 +142,7 @@

Contents

diff --git a/docs/reference/Slurm_EvalQ.html b/docs/reference/Slurm_EvalQ.html index 09c37c1..1f4915b 100644 --- a/docs/reference/Slurm_EvalQ.html +++ b/docs/reference/Slurm_EvalQ.html @@ -68,7 +68,7 @@ sluRm - 0.1.0 + 0.2.0

diff --git a/docs/reference/Slurm_clean.html b/docs/reference/Slurm_clean.html index d51213c..1effa0e 100644 --- a/docs/reference/Slurm_clean.html +++ b/docs/reference/Slurm_clean.html @@ -68,7 +68,7 @@ sluRm - 0.1.0 + 0.2.0 diff --git a/docs/reference/Slurm_collect.html b/docs/reference/Slurm_collect.html index 3bd9ae1..07ecc65 100644 --- a/docs/reference/Slurm_collect.html +++ b/docs/reference/Slurm_collect.html @@ -68,7 +68,7 @@ sluRm - 0.1.0 + 0.2.0 diff --git a/docs/reference/Slurm_env.html b/docs/reference/Slurm_env.html index 05255e6..1092495 100644 --- a/docs/reference/Slurm_env.html +++ b/docs/reference/Slurm_env.html @@ -71,7 +71,7 @@ sluRm - 0.1.0 + 0.2.0 diff --git a/docs/reference/Slurm_lapply.html b/docs/reference/Slurm_lapply.html index 722b43a..a5e42d8 100644 --- a/docs/reference/Slurm_lapply.html +++ b/docs/reference/Slurm_lapply.html @@ -68,7 +68,7 @@ sluRm - 0.1.0 + 0.2.0 diff --git a/docs/reference/WhoAmI.html b/docs/reference/WhoAmI.html index b488ffa..3299afe 100644 --- a/docs/reference/WhoAmI.html +++ b/docs/reference/WhoAmI.html @@ -69,7 +69,7 @@ sluRm - 0.1.0 + 0.2.0 diff --git a/docs/reference/index.html b/docs/reference/index.html index 516bb31..a6dd30a 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -66,7 +66,7 @@ sluRm - 0.1.0 + 0.2.0 diff --git a/docs/reference/new_rscript.html b/docs/reference/new_rscript.html index caaaf1f..1dbe7b2 100644 --- a/docs/reference/new_rscript.html +++ b/docs/reference/new_rscript.html @@ -69,7 +69,7 @@ sluRm - 0.1.0 + 0.2.0 diff --git a/docs/reference/opts_sluRm.html b/docs/reference/opts_sluRm.html index 2beb55c..f23a3ec 100644 --- a/docs/reference/opts_sluRm.html +++ b/docs/reference/opts_sluRm.html @@ -70,7 +70,7 @@ sluRm - 0.1.0 + 0.2.0 diff --git a/docs/reference/parse_flags.html b/docs/reference/parse_flags.html index 15135dd..d759cf7 100644 --- a/docs/reference/parse_flags.html +++ b/docs/reference/parse_flags.html @@ -68,7 +68,7 @@ sluRm - 0.1.0 + 0.2.0 diff --git a/docs/reference/sbatch.html b/docs/reference/sbatch.html index 131b4a9..ded6030 100644 --- a/docs/reference/sbatch.html +++ b/docs/reference/sbatch.html @@ -68,7 +68,7 @@ sluRm - 0.1.0 + 0.2.0 diff --git a/docs/reference/sluRm.html b/docs/reference/sluRm.html index 8d48c4f..5ff34bf 100644 --- a/docs/reference/sluRm.html +++ b/docs/reference/sluRm.html @@ -68,7 +68,7 @@ sluRm - 0.1.0 + 0.2.0 diff --git a/docs/reference/slurm_job.html b/docs/reference/slurm_job.html index 3426de6..9a1191f 100644 --- a/docs/reference/slurm_job.html +++ b/docs/reference/slurm_job.html @@ -68,7 +68,7 @@ sluRm - 0.1.0 + 0.2.0 diff --git a/docs/reference/snames.html b/docs/reference/snames.html index 3553eb8..63e223f 100644 --- a/docs/reference/snames.html +++ b/docs/reference/snames.html @@ -70,7 +70,7 @@ sluRm - 0.1.0 + 0.2.0 diff --git a/docs/reference/state.html b/docs/reference/state.html index 58b50fa..4b12246 100644 --- a/docs/reference/state.html +++ b/docs/reference/state.html @@ -68,7 +68,7 @@ sluRm - 0.1.0 + 0.2.0 diff --git a/docs/reference/the_plan.html b/docs/reference/the_plan.html index cfe4ffa..2c4c0bc 100644 --- a/docs/reference/the_plan.html +++ b/docs/reference/the_plan.html @@ -71,7 +71,7 @@ sluRm - 0.1.0 + 0.2.0