R Under development (unstable) (2024-08-17 r87027 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ## Testing the edit function with a variety of files
> require(apsimx)
Loading required package: apsimx
APSIM(X) not found.
                        If APSIM(X) is installed in an alternative location,
                        set paths manually using 'apsimx_options' or 'apsim_options'.
                        You can still try as the package will look into the registry (under Windows)
> packageVersion("apsimx")
[1] '2.8.0'
> apsimx_options(warn.versions = FALSE)
> 
> extd.dir <- system.file("extdata", package = "apsimx")
> 
> run.apsimx.edit <- get(".run.local.tests", envir = apsimx.options)
> 
> tmp.dir <- tempdir()
> 
> if(run.apsimx.edit){
+   
+   ## Inspect manager, Let's look at fertiliser first
+   inspect_apsimx("maize-manager.apsimx", src.dir = extd.dir, 
+                  node = "Manager", parm = list("SowingFert", NA))
+   ## Inspect the fertilizer
+   inspect_apsimx("maize-manager.apsimx", src.dir = extd.dir, 
+                  node = "Manager", parm = list("SowingFert", 1))
+   ## Generate the path
+   pp <- inspect_apsimx("maize-manager.apsimx", src.dir = extd.dir, 
+                        node = "Manager", parm = list("SowingFert",1),
+                        print.path = TRUE)
+   ## Edit by moving the file to the current directory
+   edit_apsimx("maize-manager.apsimx", src.dir = extd.dir, 
+               wrt.dir = tmp.dir, overwrite = TRUE,
+               node = "Manager", manager.child = "SowingFertiliser",
+               parm = "Amount", value = 150)
+   ## Inspect the new file to make sure it worked
+   inspect_apsimx("maize-manager.apsimx", src.dir = tmp.dir, 
+                  node = "Manager", parm = list("SowingFert", 1))
+   
+   ## Test the maize manager folder
+   edit_apsimx("maize-manager-folder.apsimx", src.dir = extd.dir, 
+               wrt.dir = tmp.dir, overwrite = TRUE,
+               node = "Manager", manager.child = "SowingFertiliser",
+               parm = "Amount", value = 150)
+   
+ }
> 
> run.apsim.edit.millet <- get(".run.local.tests", envir = apsimx.options)
> 
> if(run.apsim.edit.millet){
+   
+   ## Inspect
+   pp <- inspect_apsim("Millet.apsim", src.dir = extd.dir, node = "Manager",
+                   parm = list("Sow on a fixed date",5), print.path = TRUE)
+   ## Edit
+   edit_apsim("Millet.apsim", src.dir = extd.dir, 
+              node = "Other", wrt.dir = tmp.dir,
+              overwrite = TRUE,
+              parm.path = pp,
+              value = 8)
+   
+   ## Try using manager.child
+   inspect_apsim("Millet.apsim", src.dir = extd.dir, node = "Manager")
+   ## This prints available manager childs
+   inspect_apsim("Millet.apsim", src.dir = extd.dir, node = "Manager",
+                 parm = list("Sow on a fixed date",NA))
+   
+   edit_apsim("Millet.apsim", src.dir = extd.dir, 
+               wrt.dir = tmp.dir, node = "Manager",
+              manager.child = "Sow on a fixed date",
+              edit.tag = "-smurf",
+              parm = "cultivar",
+              value = "smurfs")
+   
+   ## Testing with Maize factorial
+   pmf <- inspect_apsim("maize-factorial.apsim", src.dir = extd.dir, 
+                        root = "IA-CC_Canisteo_Cover",
+                        node = "Weather", print.path = TRUE)
+ 
+   ## Testing with the maize-factorial.apsim file
+   inspect_apsim("maize-factorial.apsim", src.dir = extd.dir, 
+                 node = "Weather",
+                 root = "IA-CC_Canisteo_Cover")
+ 
+   inspect_apsim("maize-factorial.apsim", src.dir = extd.dir, 
+                 node = "Weather",
+                 root = "IA-CC_Canisteo_No-Cover")
+ 
+   edit_apsim("maize-factorial.apsim", 
+              src.dir = extd.dir,
+              wrt.dir = tmp.dir,
+              node = "Weather", 
+              root = "IA-CC_Canisteo_Cover",
+              value = "Ames.met")
+   
+   inspect_apsim("maize-factorial-edited.apsim", 
+                 src.dir = tmp.dir, 
+                 node = "Weather",
+                 root = "IA-CC_Canisteo_Cover")
+   
+   edit_apsim("maize-factorial-edited.apsim", 
+              src.dir = tmp.dir,
+              overwrite = TRUE,
+              node = "Weather", 
+              root = "IA-CC_Canisteo_No-Cover",
+              value = "Boone.met")
+   
+   inspect_apsim("maize-factorial-edited.apsim", 
+                 src.dir = tmp.dir, 
+                 node = "Weather",
+                 root = "IA-CC_Canisteo_No-Cover")
+ }
> 
> run.apsimx.edit.maize.soil <- get(".run.local.tests", envir = apsimx.options)
> 
> if(run.apsimx.edit.maize.soil){
+   
+   inspect_apsimx("Wheat.apsimx", src.dir = extd.dir, 
+                  node = "Soil", parm = "Site", print.path = TRUE)
+   
+   edit_apsimx("Wheat.apsimx", 
+               src.dir = extd.dir, wrt.dir = tmp.dir,
+               node = "Soil", soil.child = "Metadata", 
+               parm = "Site", value = "Ames")
+   
+   inspect_apsimx("Wheat-edited.apsimx", src.dir = tmp.dir, 
+                  node = "Soil")
+   
+ }
> 
> run.apsimx.edit.soil.soilwat <- get(".run.local.tests", envir = apsimx.options)
> 
> if(run.apsimx.edit.soil.soilwat){
+ 
+   inspect_apsimx("Wheat.apsimx", src.dir = extd.dir, 
+                  node = "Soil", soil.child = "SoilWater", 
+                  parm = "SummerCona")
+     
+   edit_apsimx("Wheat.apsimx", 
+               src.dir = extd.dir, wrt.dir = tmp.dir,
+               node = "Soil", soil.child = "SoilWater", 
+               parm = "SummerCona", value = 6)
+   
+   inspect_apsimx("Wheat-edited.apsimx", src.dir = tmp.dir, 
+                  node = "Soil", soil.child = "SoilWater", 
+                  parm = "SummerCona")
+ 
+   pp <- inspect_apsimx("Wheat-edited.apsimx", src.dir = tmp.dir,
+                        node = "Soil", soil.child = "SoilWater",
+                        parm = "SummerCona", print.path = TRUE)  
+   
+   edit_apsimx("Wheat-edited.apsimx", 
+               src.dir = tmp.dir, wrt.dir = tmp.dir,
+               node = "Other", parm.path = pp, value = 7,
+               overwrite = TRUE)
+   
+   inspect_apsimx("Wheat-edited.apsimx", src.dir = tmp.dir, 
+                  node = "Soil", soil.child = "SoilWater", 
+                  parm = "SummerCona")
+   
+ }
> 
> ## Testing Report feature
> if(run.apsimx.edit){
+   
+  ex.dir <- auto_detect_apsimx_examples()
+  
+  inspect_apsimx("Wheat.apsimx", src.dir = ex.dir, node = "Report")
+  
+  edit_apsimx("Wheat.apsimx", src.dir = ex.dir,
+              node = "Report", wrt.dir = tmp.dir,
+              parm = "VariableNames",
+              value = "[Soil].esw")
+  
+  inspect_apsimx("Wheat-edited.apsimx", src.dir = tmp.dir, node = "Report")
+  
+  edit_apsimx("Wheat.apsimx", src.dir = ex.dir,
+              node = "Report", wrt.dir = tmp.dir,
+              parm = "EventNames",
+              value = "[Wheat].EndOfDay")
+  
+  inspect_apsimx("Wheat-edited.apsimx", src.dir = tmp.dir, node = "Report")
+  
+  ## Running soil carbon
+  edit_apsimx("Wheat.apsimx", src.dir = ex.dir,
+              node = "Report", wrt.dir = tmp.dir,
+              parm = "VariableNames",
+              value = "[Soil].Nutrient.Organic.C",
+              edit.tag = "-carbon")
+  
+  inspect_apsimx("Wheat-carbon.apsimx", src.dir = tmp.dir, node = "Report")
+  
+  sim.o <- apsimx("Wheat-carbon.apsimx", src.dir = tmp.dir)
+  
+  edit_apsimx("Soybean.apsimx", src.dir = ex.dir,
+              node = "Report", wrt.dir = tmp.dir,
+              parm = "VariableNames",
+              value = "[Soil].Nutrient.Organic.C",
+              edit.tag = "-carbon")
+  
+  inspect_apsimx("Soybean-carbon.apsimx", src.dir = tmp.dir, node = "Report")
+  
+  sim.o <- apsimx("Soybean-carbon.apsimx", src.dir = tmp.dir)
+   
+ }
> 
> #### Testing edit when node = "Other" ----
> 
> if(run.apsimx.edit){
+   
+   extd.dir <- system.file("extdata", package = "apsimx")
+   
+   pp <- inspect_apsimx("Wheat.apsimx", src.dir = extd.dir, node = "Manager",
+                        parm = list("Fert", NA))
+   
+   edit_apsimx("Wheat.apsimx", node = "Other",
+               src.dir = extd.dir, wrt.dir = tmp.dir,
+               parm.path = pp, parm = "Amount", value = 5,
+               overwrite = TRUE)
+ 
+   inspect_apsimx("Wheat.apsimx", src.dir = tmp.dir, node = "Manager",
+                  parm = list("Fert", NA))  
+   
+   file.copy(file.path(tmp.dir, "Wheat.apsimx"), ".")
+   
+   #### Testing edit when node == "Other" and there are multiple simulations
+   ex.dir <- auto_detect_apsimx_examples()
+   file.copy(file.path(ex.dir, "AgPasture.apsimx"), tmp.dir)
+   
+   inspect_apsimx("AgPasture.apsimx", src.dir = tmp.dir, node = "Other")
+   inspect_apsimx("AgPasture.apsimx", src.dir = tmp.dir, node = "Other", parm = 2)
+   
+   edit_apsimx("AgPasture.apsimx", src.dir = tmp.dir, 
+               node = "Other",
+               parm.path = ".Simulations.AgPastureExample.Clock.Start",
+               value = "2024-12-31T00:00:00")
+   
+   inspect_apsimx("AgPasture-edited.apsimx", src.dir = tmp.dir, 
+                  root = list("AgPastureExample"))
+   ### It might have worked?
+   file.remove(file.path(tmp.dir, "AgPasture-edited.apsimx"))
+   
+   
+ }
> 
> ## Testing changing variables in the outputfile
> if(run.apsimx.edit){
+  
+   extd.dir <- system.file("extdata", package = "apsimx")
+   file.copy(file.path(extd.dir, "Millet.apsim"), tmp.dir)
+   
+   inspect_apsim("Millet.apsim", src.dir = tmp.dir, node = "Outputfile", parm = "title")
+ 
+   edit_apsim("Millet.apsim", src.dir = tmp.dir,
+              node = "Outputfile", parm = "variables", 
+              value = "surfaceom_wt")
+     
+   edit_apsim("Millet.apsim", src.dir = tmp.dir,
+              node = "Outputfile",
+              parm = "variables", value = "surfaceom_wt")
+   
+   inspect_apsim("Millet-edited.apsim", src.dir = tmp.dir, 
+                 node = "Outputfile", parm = "variables")
+   
+ }
> 
> #### Testing editing of solute ----
> 
> if(run.apsimx.edit){
+   
+   ex.dir <- auto_detect_apsimx_examples()
+   
+   ex.to.test <- dir(ex.dir, pattern = "apsimx$")
+   
+   ex2test <- ex.to.test[c(2, 16, 18, 30)]
+   
+   for(i in ex2test){
+     
+     cat("Example:", i, "\n")
+ 
+     if(!file.exists(file.path(tmp.dir, i)))
+       file.copy(file.path(ex.dir, i), tmp.dir)
+     
+     inspect_apsimx(i, src.dir = tmp.dir, node = "Soil",
+                    soil.child = "Solute")
+     
+     edf.solute <- extract_data_apsimx(i, src.dir = tmp.dir, node = "Soil",
+                    soil.child = "Solute")
+     
+     initialvalues.length <- nrow(edf.solute$NO3$first)
+     
+     edit_apsimx(i, src.dir = tmp.dir, wrt.dir = tmp.dir,
+                 node = "Soil", soil.child = "NO3",
+                 parm = "InitialValues", 
+                 value = rep(2, initialvalues.length))
+     
+     ii <- paste0(tools::file_path_sans_ext(i), "-edited.apsimx")
+     inspect_apsimx(ii, src.dir = tmp.dir, node = "Soil",
+                    soil.child = "Solute", parm = "NO3")
+     
+     ### The parameters in the second table cannot be edited ATM
+     # edit_apsimx(i, src.dir = tmp.dir, wrt.dir = tmp.dir,
+     #             node = "Soil", soil.child = "NO3",
+     #             parm = "DepthConstant", 
+     #             value = 1,
+     #             edit.tag = "-DepthConstant")
+   }
+ }
> 
> #### Testing edit.tag feature ----
> 
> if(run.apsimx.edit){
+   
+   ex.dir <- auto_detect_apsimx_examples()
+   
+   ex.to.test <- dir(ex.dir, pattern = "apsimx$")
+   
+   ex2test <- ex.to.test[c(2, 16, 18, 30, 34)]
+   
+   for(i in ex2test){
+     
+     cat("Example:", i, "\n")
+     
+     if(!file.exists(file.path(tmp.dir, i)))
+       file.copy(file.path(ex.dir, i), tmp.dir)   
+     
+     edit_apsimx(i, src.dir = tmp.dir, wrt.dir = tmp.dir,
+                 node = "Weather",
+                 value = "temp.met",
+                 edit.tag = "-tempmet")
+   }
+ }
> 
> proc.time()
   user  system elapsed 
   0.46    0.15    0.60