envopts: seal_envopts: Update.

R/envopts.R

@@ -89,7 +89,7 @@ seal_envopts <- function(o) {
     if (is.null(o$metfrag$java_bin)) o$metfrag$java_bin=Sys.which("java")
     if (is.null(o$metfrag$jar)) o$metfrag$jar = ""
     if (is.null(o$metfrag$max_proc)) o$metfrag$max_proc = parallel::detectCores()
-    
+    if (is.null(o$no_structure_plots)) o$no_structure_plots = F 
     check_dir_absent(o$projects,what="projects-dir")
     o$projects = norm_path(o$projects)
 

tests/testthat/helper.R

@@ -81,7 +81,7 @@ envopts_from_dirs <- function(dirs) {
 
 trim_tmp_paths_envopts <- function(x) {
     y=list()
-    for (n in setdiff(names(x),"metfrag")) {
+    for (n in setdiff(names(x),c("metfrag","no_structure_plots"))) {
         y[[n]] = basename(x[[n]])
     }
     
@@ -90,6 +90,7 @@ trim_tmp_paths_envopts <- function(x) {
         y$metfrag[[n]]=basename(x$metfrag[[n]])
     }
     y$metfrag$max_proc = x$metfrag$max_proc
+    y$no_structure_plots = y$no_structure_plots
     y
 }
 

tests/testthat/test-api.R

@@ -9,9 +9,10 @@ test_that("Test basic initialisation.",{
              metfrag_jar = file.path(dirs$mfjardir,"metfrag.jar"),
              java_bin = file.path(dirs$mfjardir,"java"),
              metfrag_max_proc=3L,
+             no_structure_plots=F,
              merge=F,
              save=F)
-    
+
     ## Function `gen_test_dirs' creates shinyscreen root structure in
     ## a temp dir. We need to strip the random part for comparison.
     y = trim_tmp_paths_envopts(x)