Add file argument to get_nml_value

.Rbuildignore

@@ -2,3 +2,5 @@
 ^\.Rproj\.user$
 .travis.yml
 appveyor.yml
+^README\.Rmd$
+^README-.*\.png$

NAMESPACE

@@ -39,9 +39,10 @@ export(validate_sim)
 export(water.temperature)
 export(whole.lake.temperature)
 export(write_nml)
-import(GLMr)
 import(rLakeAnalyzer)
 import(tools)
+importFrom(GLMr,nml_template_path)
+importFrom(GLMr,run_glm)
 importFrom(akima,interp)
 importFrom(grDevices,colorRampPalette)
 importFrom(grDevices,dev.off)

R/get_nml_value.R

@@ -3,19 +3,28 @@
 #'@description This function returns an nml value according to the arg_name nml list for GLM.
 #'@param glm_nml a nml (a list) for GLM config
 #'@param arg_name a string representing a valid field in glm_nml
-#' @param \dots additional arguments passed to \code{get_block}, such as warn=TRUE
+#'@param \dots additional arguments passed to \code{get_block}, such as warn=TRUE
+#'@param nml_file a string with the path to the GLM glm2.nml file or 
+#'\code{'template'} for loading the GLM template nml file with GLMr (default)
 #'@return arg_val value for the valid field in glm_nml specified by \code{arg_name}
 #'@author
 #'Jordan S. Read
 #'@seealso \link{read_nml}, \link{set_nml}
-#'@import GLMr
 #'@examples
 #'# read in default nml template from GLMr
 #'glm_nml <- read_nml()
 #'get_nml_value(glm_nml,arg_name = 'Kw')
 #'@export
-get_nml_value  <-	function(glm_nml, arg_name, ...){
+get_nml_value  <-	function(glm_nml = NA, arg_name, nml_file = 'template', ...){
 
+  if(!all(is.na(glm_nml)) & nml_file != 'template'){
+    stop("Must specify either an nml object via 'glm_nml' or 
+         an nml file path via 'nml_file'")
+  }
+
+  if(all(is.na(glm_nml))){
+    glm_nml <- read_nml(nml_file)
+  }
 
   blck = get_block(glm_nml, arg_name, ...)
   arg_name = get_arg_name(arg_name)

R/nml_helpers.R

@@ -6,12 +6,12 @@ buildVal	<-	function(textLine, lineNum, blckName){
 	# remove all text after comment string
 	textLine	<-	strsplit(textLine,'!')[[1]][1]
 
-	if (!any(grep("=",textLine))){
+	if (!any(grep("=", textLine))){
     stop(c("no hanging lines allowed in .nml, used ",textLine,'.\nSee line number:',lineNum,' in "&',blckName,'" section.'))
 	}
 	params	<-	strsplit(textLine,"=") # break text at "="
-	parNm	<-	params[[1]][1]
-	parVl	<-	params[[1]][2]
+	parNm	  <-	params[[1]][1]
+	parVl	  <-	params[[1]][2]
 	# figure out what parval is...if string, remove quotes and keep as string
 	# ***for boolean text, use "indentical" so that 0!= FALSE
 	# can be: string, number, comma-sep-numbers, or boolean

R/read_nml.R

@@ -13,12 +13,11 @@
 #'@examples 
 #'glm_nml <- read_nml()
 #'print(glm_nml)
-#'@import GLMr
 #'@export
 read_nml  <-	function(nml_file = 'template'){
+
   nml_file <- nml_path_norm(nml_file)
 
-
   if (!ascii_only(nml_file)){
     stop('non-ASCII characters found in nml file on line ', what_ascii(nml_file))
   }
@@ -34,50 +33,53 @@ read_nml  <-	function(nml_file = 'template'){
   fileLines	<-	fileLines[!ignoreLn]
   # find all lines which start with "&" * requires FIRST char to be value
 
-
   lineIdx		<- seq(1,length(lineStart))
   blckOpen	<-	lineIdx[lineStart=="&"]
   blckClse	<-	lineIdx[lineStart=="/"]
 
-
   nml <- list()
-  for (i in 1:length(blckOpen)){
-    blckName	<-	substr(fileLines[blckOpen[i]],2,nchar(fileLines[blckOpen[i]]))
-    blckName <- gsub("\\s", "", blckName) 
-    oldNms	<-	names(nml)
-    nml[[i]]	<-	list()
-    names(nml)	<-	c(oldNms,blckName)
+  for (i in seq_len(length(blckOpen))){
+    blckName   <-	substr(fileLines[blckOpen[i]], 
+                         2, nchar(fileLines[blckOpen[i]]))
+    blckName   <- gsub("\\s", "", blckName) 
+    oldNms	   <-	names(nml)
+    nml[[i]]   <-	list()
+    names(nml) <-	c(oldNms,blckName)
 
-    carryover = ''
+    carryover <- ''
 
     for (j in (blckOpen[i]+1):(blckClse[i]-1)){
 
-      textLine	<-	paste(carryover, gsub("\t","",gsub(" ","",fileLines[j])), sep='')
-      if(substr(textLine,1,1)!='!'){
+      textLine	<-	paste(carryover, 
+                        gsub("\t", "", gsub(" ", "", fileLines[j])), sep = '')
+
+      if(substr(textLine, 1, 1) != '!'){
         # Add a check here, sometimes, if there is a hanging comma, 
         #and only sometimes that means add next row
-        if(substr(textLine,nchar(textLine), nchar(textLine)) == ',' && 
-             j+1 <= length(fileLines) && !any(grep("=",fileLines[j+1])) && !any(grep("/",fileLines[j+1]))){
+        if(substr(textLine, nchar(textLine), nchar(textLine)) == ',' && 
+           j+1 <= length(fileLines) && 
+           !any(grep("=", fileLines[j + 1])) && 
+           !any(grep("/", fileLines[j + 1]))){
 
           carryover = textLine
           next
         }else{
           carryover = ''
         }
         # else, line is commented out
-        lineVal	<-	buildVal(textLine, lineNum=j, blckName)
-        nml[[i]]	<-	c(nml[[i]],lineVal)
+        lineVal	  <-	buildVal(textLine, lineNum = j, blckName)
+        nml[[i]]	<-	c(nml[[i]], lineVal)
       }
     }
   }
   nml <- .nml(nml)
   return(nml)
 }
 
-
+#' @importFrom GLMr nml_template_path
 nml_path_norm <- function(nml_file){
   if (nml_file == "template"){
-    nml_file <- nml_template_path()
+    nml_file <- GLMr::nml_template_path()
   }
   if (!is_nml_file(nml_file)){
     stop(nml_file, ' is not of file type *.nml')

R/run_example_sim.R

@@ -4,6 +4,7 @@
 #'@param verbose should operations and output of GLM be shown
 #'@keywords methods
 #'@seealso \code{\link[GLMr]{run_glm}}
+#'@importFrom GLMr run_glm
 #'@author
 #'Jordan S. Read, Luke A. Winslow
 #'@examples 
@@ -73,7 +74,7 @@ run_example_sim = function(sim_folder, verbose = TRUE){
   if(verbose){cat('writing nml file to ', nml_file,'\n')}
   write_nml(glm_nml = nml, file = nml_file)
 
-  run_glm(sim_folder = sim_folder, verbose = verbose)
+  GLMr::run_glm(sim_folder = sim_folder, verbose = verbose)
 
   if(verbose){cat('simulation complete. \n*.nc output located in ', nc_file,'\n')}
 

tests/testthat/test-nml.R

@@ -28,6 +28,21 @@ test_that("can read in nml with vector for logicals", {
   expect_is(get_nml_value(nml, 'flt_off_sw'), 'logical')
 })
 
+test_that("can read values from an nml file", {
+  nml <- read_nml()
+  nml <- set_nml(nml, "sim_name", "test")
+  temp_nml <- tempfile(fileext = ".nml")
+  write_nml(nml, temp_nml)
+
+  expect_true(get_nml_value(arg_name = "sim_name") == "GLMSimulation")
+  expect_true(
+    get_nml_value(arg_name = "sim_name", nml_file = temp_nml) == "test")
+
+  nml <- read_nml()
+  expect_error(
+    get_nml_value(nml, arg_name = "sim_name", nml_file = temp_nml))
+})
+
 context("reading a bad nml file")
 test_that("file errors out",{
   expect_error(read_nml(system.file('extdata','bad_glm2.nml',package='glmtools')))