Fixing small bug when parsing flags. @pmarjora is (ctb,ths) now.

USCbiostats · Jun 28, 2019 · ac76c7e · ac76c7e
1 parent ec746cb
commit ac76c7e
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Showing 28 changed files with 55 additions and 50 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -3,7 +3,7 @@ Title: A Lightweight Wrapper for Slurm
 Version: 0.1-0
 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("aut"), comment = c(ORCID = "0000-0003-0824-7449")),
+  person("Paul", "Marjoram", email = "pmarjora@usc.edu", role = c("ctb", "ths"), comment = c(ORCID = "0000-0003-0824-7449")),
   person("National Cancer Institute (NCI)", role = "fnd", comment = "Grant Number 5P01CA196569-02"),
   person("Michael", "Schubert", role = "rev", comment = c(what = "JOSS reviewer", ORCID = "0000-0002-6862-5221")),
   person("Michel", "Lang", role = "rev", comment = c(what = "JOSS reviewer", ORCID = "0000-0001-9754-0393"))

diff --git a/R/utils.R b/R/utils.R
@@ -22,7 +22,7 @@ check_path <- function() {
 #' @param ... Options to be parsed as bash flags.
 #' @examples
 #' cat(parse_flags(a=1, b=TRUE, hola=2, y="I have spaces", ms=2, `cpus-per-task`=4))
-#' # -a=1 -b --hola=2 -y="I have spaces" --ms=2 --cpus-per-task=4
+#' # -a 1 -b --hola=2 -y "I have spaces" --ms=2 --cpus-per-task=4
 #' @export
 #' @family Utility
 parse_flags <- function(...) UseMethod("parse_flags")
@@ -46,23 +46,29 @@ parse_flags.list <- function(x, ...) {
   if (!length(x))
     return("")
 
+  single_char <- nchar(names(x)) == 1
+
   option <- ifelse(
-    nchar(names(x)) > 1,
-    paste0("--", names(x)),
-    paste0("-", names(x))
+    single_char,
+    paste0("-", names(x)),
+    paste0("--", names(x))
   )
 
   vals <- character(length(option))
   for (i in seq_along(x)) {
+
+    # Includes equal
+    equal_sign <- ifelse(single_char[i], " ", "=")
+
     if (is.logical(x[[i]]) && !x[[i]])
       option[i] <- ""
     else if (!is.logical(x[[i]]) && !is.character(x[[i]]))
-      vals[i] <- paste0("=", x[[i]])
+      vals[i] <- paste0(equal_sign, x[[i]])
     else if (is.character(x[[i]])) {
       if (grepl("\\s+", x[[i]]))
-        vals[i] <- sprintf("=\"%s\"", x[[i]])
+        vals[i] <- sprintf("%s\"%s\"", equal_sign, x[[i]])
       else
-        vals[i] <- sprintf("=%s", x[[i]])
+        vals[i] <- sprintf("%s%s", equal_sign, x[[i]])
 
     }
   }

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/getting-started.html b/docs/articles/getting-started.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/reference/Slurm_EvalQ.html b/docs/reference/Slurm_EvalQ.html
diff --git a/docs/reference/Slurm_clean.html b/docs/reference/Slurm_clean.html
diff --git a/docs/reference/Slurm_collect.html b/docs/reference/Slurm_collect.html
diff --git a/docs/reference/Slurm_env.html b/docs/reference/Slurm_env.html
diff --git a/docs/reference/Slurm_lapply.html b/docs/reference/Slurm_lapply.html
diff --git a/docs/reference/WhoAmI.html b/docs/reference/WhoAmI.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/new_rscript.html b/docs/reference/new_rscript.html
diff --git a/docs/reference/opts_sluRm.html b/docs/reference/opts_sluRm.html