Fix test tutorial + styling modifications in tests

tests/testthat/test-estim_param.R

@@ -157,6 +157,14 @@ xfun::gsub_file(file=vignette_rmd,
                 pattern="stics_version = \"V9.0\"",
                 replacement=paste0("stics_version = \"",stics_version,"\""),fixed=TRUE)
 
+## Fixing cores number for CI context on Github
+if (Sys.getenv("CI") != "") {
+  xfun::gsub_file(file = vignette_rmd,
+                  "parallel = TRUE","parallel = TRUE, cores = 2",
+                  fixed = TRUE)
+}
+
+
 ## generate the R script
 knitr::purl(input=vignette_rmd,
             output=file.path(tmpdir,"Parameter_estimation_Specific_and_Varietal.R"), documentation = 2)
@@ -519,6 +527,13 @@ xfun::gsub_file(file=vignette_rmd,
                 pattern="stics_version = \"V9.0\"",
                 replacement=paste0("stics_version = \"",stics_version,"\""),fixed=TRUE)
 
+## Fixing cores number for CI context on Github
+if (Sys.getenv("CI") != "") {
+  xfun::gsub_file(file = vignette_rmd,
+                  "parallel = TRUE, cores = 4","parallel = TRUE, cores = 2",
+                  fixed = TRUE)
+}
+
 ## generate the R script
 knitr::purl(input=vignette_rmd,
             output=file.path(tmpdir,"AgMIP_Calibration_Phenology_protocol.R"), documentation = 2)

tests/testthat/test-stics-wrapper.R

@@ -1,6 +1,15 @@
 
 context("Stics Wrapper")
 stics_version <- "V10.0"
+
+# fixing the number of cores in the context of Github CI
+if (Sys.getenv("CI") != "") {
+  cores <- 2
+} else {
+  cores <- NA
+}
+
+
 # Define path to JavaStics and download data
 path_to_JavaStics=system.file("stics", package = "SticsRTests")
 javastics_path=file.path(path_to_JavaStics,stics_version)
@@ -14,7 +23,7 @@ SticsRFiles::gen_usms_xml2txt(javastics = javastics_path, workspace = javastics_
                               out_dir = stics_inputs_path, verbose = TRUE)
 
 # Set options for Stics wrapper
-model_options=SticsOnR::stics_wrapper_options(javastics=javastics_path,workspace = stics_inputs_path, parallel=FALSE)
+model_options=SticsOnR::stics_wrapper_options(javastics=javastics_path,workspace = stics_inputs_path, parallel = FALSE)
 
 # Standard wrapper tests
 param_names=c("dlaimax","durvieF")
@@ -33,7 +42,7 @@ test_that("Stics Wrapper succeed test_wrapper tests", {
 
 # Test forcing of parameter per situation works
 param_values <- data.frame(situation="bo96iN+",dlaimax=0.0005,durvieF=50)
-model_options=SticsOnR::stics_wrapper_options(javastics=javastics_path, workspace = stics_inputs_path, parallel=FALSE)
+model_options=SticsOnR::stics_wrapper_options(javastics=javastics_path, workspace = stics_inputs_path, parallel = FALSE)
 
 var_name="lai_n"
 sim_without_forcing <- SticsOnR::stics_wrapper(model_options = model_options, var="lai_n", situation = c("bo96iN+", "bou99t1"))
@@ -139,13 +148,13 @@ SticsRFiles::gen_usms_xml2txt(javastics = javastics_path, workspace = javastics_
                               out_dir = stics_inputs_path,
                               usm = c("demo_BareSoil2","demo_Wheat1","banana","demo_maize3"), verbose = TRUE)
 
-model_options= SticsOnR::stics_wrapper_options(javastics=javastics_path, workspace = stics_inputs_path, parallel=TRUE)
+model_options= SticsOnR::stics_wrapper_options(javastics=javastics_path, workspace = stics_inputs_path, parallel = TRUE, cores = cores)
 sim_without_successive=SticsOnR::stics_wrapper(model_options=model_options)
 
-model_options= SticsOnR::stics_wrapper_options(javastics=javastics_path, workspace = stics_inputs_path, successive = list(c("demo_Wheat1","demo_BareSoil2","demo_maize3")), parallel=TRUE)
+model_options= SticsOnR::stics_wrapper_options(javastics=javastics_path, workspace = stics_inputs_path, successive = list(c("demo_Wheat1","demo_BareSoil2","demo_maize3")), parallel = TRUE, cores = cores)
 sim_with_successive=SticsOnR::stics_wrapper(model_options=model_options)
 
-model_options= SticsOnR::stics_wrapper_options(javastics=javastics_path, workspace = stics_inputs_path, successive = list(c("demo_Wheat1","demo_BareSoil2","demo_maize3")), parallel=TRUE)
+model_options= SticsOnR::stics_wrapper_options(javastics=javastics_path, workspace = stics_inputs_path, successive = list(c("demo_Wheat1","demo_BareSoil2","demo_maize3")), parallel = TRUE, cores = cores)
 sim_with_successive_restricted_results=SticsOnR::stics_wrapper(model_options=model_options, situation=c("banana","demo_maize3"))
 
 maize_succ_res <- file(file.path(stics_inputs_path,"demo_maize3","mod_bdemo_maize3.sti"), "rb")

tests/testthat/test-tutorial.R

@@ -1,23 +1,31 @@
 
 #Download and transform Tutorial .RMD to .R
 tmpdir <- normalizePath(tempdir(), winslash = "/", mustWork = FALSE)
-tutorial_rmd <-file.path(tmpdir,"SticsRpacks.Rmd")
+tutorial_rmd <- file.path(tmpdir, "SticsRpacks.Rmd")
 download.file("https://raw.githubusercontent.com/SticsRPacks/SticsRPacks/main/inst/tutorials/SticsRpacks/SticsRpacks.Rmd",
               tutorial_rmd)
-xfun::gsub_file(file=tutorial_rmd,
-                "eval=FALSE","eval=TRUE",fixed=TRUE)
+xfun::gsub_file(file = tutorial_rmd,
+                "eval=FALSE","eval=TRUE",
+                fixed = TRUE)
 
-xfun::gsub_file(file=tutorial_rmd,
+xfun::gsub_file(file = tutorial_rmd,
                 "optim_options = list(nb_rep = 3, out_dir = workspace_path)",
-                "optim_options = list(nb_rep = 3, out_dir = workspace_path, maxeval=3)",fixed=TRUE)
+                "optim_options = list(nb_rep = 3, out_dir = workspace_path, maxeval = 3)",
+                fixed = TRUE)
 
+if (Sys.getenv("CI") != "") {
+  xfun::gsub_file(file = tutorial_rmd,
+                  "parallel = TRUE","parallel = TRUE, cores = 2",
+                  fixed = TRUE)
+}
 
-tutorial_r <-file.path(tmpdir,"tutorial.R")
-knitr::purl(input=tutorial_rmd,
-            output=tutorial_r, documentation = 2)
+tutorial_r <-file.path(tmpdir, "tutorial.R")
+knitr::purl(input = tutorial_rmd,
+            output = tutorial_r,
+            documentation = 2)
 
 
-# Test Tutor=ial
+# Test Tutorial
 test_tuto <- function() {
   source(tutorial_r)
   return (TRUE)