Merge branch 'main' into add/xml-upgrades/v11

DESCRIPTION

@@ -99,6 +99,7 @@ Collate:
     'find_names.R'
     'force_param_values.R'
     'gen_climate.R'
+    'gen_general_param_xml.R'
     'gen_ini_doc.R'
     'gen_ini_xml.R'
     'gen_new_travail.R'

NAMESPACE

@@ -8,6 +8,7 @@ export(download_data)
 export(download_usm_csv)
 export(download_usm_xl)
 export(force_param_values)
+export(gen_general_param_xml)
 export(gen_ini_xml)
 export(gen_obs)
 export(gen_sols_xml)

R/gen_general_param_xml.R

@@ -0,0 +1,56 @@
+#' @title Generate STICS general parameters xml file(s) from a template
+#' file according to a STICS version
+#'
+# @param param_df A table (df, tibble) containing the values of the parameters
+# to use (see details)
+# @param file Path of a sta xml file to be used as a template. Optional,
+# if not provided, the function will use a standard template depending
+# on the STICS version.
+#' @param out_dir Path of the directory where to generate the file(s).
+#' @param stics_version Name of the STICS version. Optional, the latest one
+#' is used as default
+#' @param overwrite Optional logical, TRUE for overwriting files,
+#' FALSE otherwise (default)
+#'
+#' @details Please see `get_stics_versions_compat()` for the full list of
+#' STICS versions that can be used for the argument `stics_version`.
+#'
+#' @return None
+#'
+#' @examples
+#' gen_general_param_xml(out_dir = tempdir())
+#'
+#' gen_general_param_xml(out_dir = tempdir(),
+#'                       stics_version = "V10.0",
+#'                       overwrite = TRUE)
+#'
+#' @export
+#'
+gen_general_param_xml <- function(out_dir,
+                                  stics_version = "latest",
+                                  overwrite = FALSE) {
+
+
+  # check/get version
+  stics_version <- get_xml_stics_version(
+    stics_version = stics_version
+  )
+
+  # getting dir path of templates
+  files_dir <- get_examples_path(file_type = "xml",
+                                 stics_version = stics_version)
+
+  # Copying files to out_dir
+  files_name <- c("param_gen.xml", "param_newform.xml")
+  xml_files <- file.path(files_dir, files_name)
+
+  copy_status <- file.copy(xml_files, out_dir, overwrite = overwrite)
+
+  if (!all(copy_status))
+    stop("Some error occured while copying files: \n",
+          paste(files_name[!copy_status], collapse = ", \n"),
+          "\nConsider setting overwrite to TRUE as function additional input")
+
+
+
+}

R/get_usms_files.R

@@ -178,8 +178,9 @@ get_usms_files <- function(workspace,
 
     # Keeping usms xml files, except plant files, obs, lai, null
     useless_files_idx <- grep("\\.obs|\\.lai|null", usm_files)
+
     if (length(useless_files_idx) > 0) usm_files <- usm_files[-useless_files_idx]
-    usm_files <- unique(usm_files)
+
     usm_files_path <- file.path(workspace_path, usm_files)
 
 

_pkgdown.yml

@@ -42,6 +42,7 @@ reference:
       - gen_sta_xml
       - gen_tec_xml
       - gen_usms_xml
+      - gen_general_param_xml
 
   - title: "Upgrade JavaStics XML files from version 9.2 or (9.1) to 10.0"
     desc: Functions for upgrading parameter files

tests/testthat/test-gen_general_param_xml.R

@@ -0,0 +1,21 @@
+
+context("Generating xml general parameters files")
+
+gen_general_param_xml(out_dir = tempdir())
+
+files <- c("param_gen.xml", "param_newform.xml")
+
+test_that("latest version", {
+  expect_true(all(file.exists(file.path(tempdir(), files))))
+  expect_error(gen_general_param_xml(out_dir = tempdir()))
+  expect_no_error(gen_general_param_xml(out_dir = tempdir(), overwrite = TRUE))
+})
+
+
+
+test_that("other version", {
+  expect_no_error(gen_general_param_xml(out_dir = tempdir(),
+                                        stics_version = "V10.0",
+                                        overwrite = TRUE))
+  expect_true(all(file.exists(file.path(tempdir(), files))))
+})

vignettes/Generating_Stics_XML_files.Rmd

@@ -54,6 +54,7 @@ There is not at the moment an integrated function which is able to produce all n
 * gen_ini_xml: for generating simulations initialization files (`*_ini.xml`)
 * gen_tec_xml: for generating crop management files (`*_tec.xml`)
 * gen_sta_xml: for generating weather stations files (`*_sta.xml`)
+* gen_general_param_xml: for generating general parameters files (`param_gen.xml and param_newform.xml`)
 
 
 
@@ -450,3 +451,18 @@ Example of a `sta` parameters file content sub-list:
 l <- readLines(con = file.path(workspace_path, "climatex_sta.xml"))
 cat(paste(c(l[1:41], "...", l[length(l) - 1]), collapse = "\n"))
 ```
+
+# Generating general parameters XML files (param_gen.xml and param_newform.xml)
+
+Nothing is to be done for specifying parameters values, the function is to be called with an optional argument for setting the desired version as follows.
+
+<!-- Only for the show -->
+```{r gen_gen_param, eval = FALSE}
+# with the latest version
+gen_general_param_xml(out_dir = workspace_path)
+
+# or with a specific version
+gen_general_param_xml(out_dir = workspace_path, stics_version = "V10.0")
+
+```
+