testthat

DESCRIPTION

@@ -22,8 +22,13 @@ License: MIT + file LICENSE
 RoxygenNote: 7.2.3
 Encoding: UTF-8
 Imports: rlang, R6, utils, Rdpack
-Suggests: ggplot2, patchwork
+Suggests: 
+    ggplot2,
+    patchwork,
+    testthat (>= 3.0.0)
 Depends: 
     R (>= 2.10)
 RdMacros: Rdpack
 LazyData: true
+Config/testthat/edition: 3
+Config/testthat/start-first: setup, pscan, run

R/environment.R

@@ -71,7 +71,7 @@ ModvegeEnvironment = R6Class(
     #'
     initialize = function(site_name,
                           run_name = "-",
-                          years = "all",
+                          years = NULL,
                           param_file = "-",
                           weather_file = "-",
                           management_file = "-",
@@ -117,9 +117,12 @@ ModvegeEnvironment = R6Class(
       self$parameters = ModvegeParameters$new(file.path(self$input_dir, 
                                                         self$param_file))
       self$weather = WeatherData$new(file.path(self$input_dir,
-                                               self$weather_file))
+                                               self$weather_file), self$years)
       self$management = ManagementData$new(file.path(self$input_dir,
                                                      self$management_file))
+      if (is.null(self$years)) {
+        self$years = self$weather$years
+      }
     },
 
     #' @description Ensure a readable filename for given *run_name*.

R/management.R

@@ -23,6 +23,8 @@ ManagementData = R6Class(
   #-Public-attributes-----------------------------------------------------------
     management_file = NULL,
     is_empty = TRUE,
+    #' @field years List of unique years for which data is available.
+    years = NULL,
     cut_years = NULL,
     cut_DOY = NULL,
     intensity = NULL,
@@ -36,7 +38,7 @@ ManagementData = R6Class(
     #'   extracted.
     #'
     #' @seealso [ManagementData$read_management()]
-    initialize = function(management_file = NULL, years = "all") {
+    initialize = function(management_file = NULL, years = NULL) {
       if (!is.null(management_file)) {
         self$read_management(management_file, years)
       }
@@ -46,23 +48,24 @@ ManagementData = R6Class(
     #'
     #' @param management_file Path to or name of file containing management data.
     #' @param years Years for which the management is to be extracted.  
-    #'   Default is "all" to read in all found years.
+    #'   Default (NULL) is to read in all found years.
     #'
-    read_management = function(management_file, years = "all") {
+    read_management = function(management_file, years = NULL) {
       # Prepare the resulting container
       self[["management_file"]] = management_file
       if (file.exists(management_file)) {
         logger(sprintf("Loading management data from %s.", management_file), 
                level = DEBUG)
         cut_data = read.table(management_file, header = TRUE)
         # Only consider specified years
-        if (years == "all") {
+        if (is.null(years)) {
           selector = TRUE
         } else {
           selector = cut_data$year %in% years
         }
         self$is_empty = FALSE
         self$cut_years = cut_data$year[selector]
+        self$years = unique(self$cut_years)
         self$cut_DOY = cut_data$DOY[selector]
         self$intensity = NA
       } else {

R/parameter_scan.R

@@ -89,7 +89,7 @@ run_parameter_scan = function(environment, param_values, force = FALSE,
   }
   logger("Completed parameter scan.", level = INFO)
   logger(paste0("Time used: ", Sys.time() - start_time), level = INFO)
-  if (length(outfilename) > "") {
+  if (outfilename != "") {
     logger(sprintf("Storing results as `%s`.", outfilename))
     saveRDS(results, outfilename)
   }

R/setup.R

@@ -86,3 +86,13 @@ setup_directory = function(root = ".", include_examples = TRUE) {
   print(sprintf("Copied example files to respective directories."))
 }
 
+dirs = c("input", "output", "data")
+files = c("example_config.txt", "compare.R")
+
+## Used when testing
+clean_up_dir = function() {
+  for (dir in c(dirs, files)) {
+    unlink(dir, recursive = TRUE)
+  }
+}
+

R/weather.R

@@ -80,7 +80,7 @@ WeatherData = R6Class(
     #'   extracted.
     #'
     #' @seealso WeatherData$read_weather()
-    initialize = function(weather_file = NULL, years = "all") {
+    initialize = function(weather_file = NULL, years = NULL) {
       if (!is.null(weather_file)) {
         self$read_weather(weather_file, years)
       }
@@ -90,9 +90,9 @@ WeatherData = R6Class(
     #'
     #' @param weather_file Path to or name of file containing weather data.
     #' @param years Years for which the weather is to be extracted.
-    #'   Default is "all" to read in all found years.
+    #'   Default (NULL) is to read in all found years.
     #'
-    read_weather = function(weather_file, years = "all") {
+    read_weather = function(weather_file, years = NULL) {
       self$years = years
       self$weather_file = weather_file
       # Load weather data
@@ -108,8 +108,10 @@ WeatherData = R6Class(
 
       # Only consider relevant years and omit leap days
       selector = weather$DOY < 366
-      if (years != "all") {
+      if (!is.null(years)) {
         selector = selector & weather$year %in% years
+      } else {
+        self$years = unique(weather$year)
       }
 
       # Warn if no matching data was found

inst/extdata/example_config.txt

@@ -1,7 +1,7 @@
 # site name 	# run name 	# year(s) 	# param file 			# weather data 			# cut dates
 sorens1 	-  	2013:2022   	sorens_parameters.csv	sorens_weather.txt    	sorens_management1.txt
-sorens2 	-  	2013:2022   	sorens_parameters.csv	sorens_weather.txt    	sorens_management2.txt
-sorens2 	autocut  	2013:2022   	sorens_parameters.csv	sorens_weather.txt    	high
-posieux1 	-  	2013:1022   	posieux_parameters.csv	posieux_weather.txt    	posieux_management1.txt
-posieux2 	-  	2013:2022   	posieux_parameters.csv	posieux_weather.txt    	posieux_management2.txt
-posieux2 	autocut  	2013:2022   	posieux_parameters.csv	posieux_weather.txt    	high
+#sorens2 	-  	2013:2022   	sorens_parameters.csv	sorens_weather.txt    	sorens_management2.txt
+#sorens2 	autocut  	2013:2022   	sorens_parameters.csv	sorens_weather.txt    	high
+posieux1 	-  	2013:2022   	posieux_parameters.csv	posieux_weather.txt    	posieux_management1.txt
+#posieux2 	-  	2013:2022   	posieux_parameters.csv	posieux_weather.txt    	posieux_management2.txt
+#posieux2 	autocut  	2013:2022   	posieux_parameters.csv	posieux_weather.txt    	high

tests/testthat.R

@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(rmodvege)
+
+test_check("rmodvege")