Plecharpent/release/cran (#23)

* news update, date , license file * fix: license * useless * update with latests tests results * fixes: linting, date of release * fix: no man files generation for unexported function using @nord the the functions doc Use of library(SticsRFiles) and SticsRFiles::: in tests removed * fix: some functions doc (internal), removed SticsRFiles::: use in internal functions doc, added SticsRFiles::: in generating XML files vignette * changes: unwrapping examples for exported functions when possible, with minor correction when needed. * unwrapping examples for exported functions for testing them using examples path and tempdir() for outputs * fix: linting issues, examples * fix: examples * examples unwrapped and fixed * donttest replaced by dontrun: checks are failing with github actions ! * added an overwrite argument for forcing to rewrite files types examples folders in tempdir() * Description content and tidy lines * fix: examples for set_param_xml avoiding failing files copy in tempdir(), using directly examples files path. Doc updates. * fix release date * removed getwd() from default arg values in functions, man update * now using message funtion instead of print or cat * fix: linting issues * description and can-comments update * CRAN badge
SticsRPacks · Jul 12, 2023 · 11df844 · 11df844
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: SticsRFiles
 Title: Read and Modify 'STICS' Input/Output Files
 Version: 1.1.3
-Date: 2023-06-29
+Date: 2023-07-10
 Authors@R: c(
     person("Patrice", "Lecharpentier", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-4044-4322")),
@@ -22,14 +22,12 @@ Authors@R: c(
     person("Joel", "Leonard", role = "rev")
   )
 Description: Manipulating input and output files of the 'STICS' crop
-    model.  These files are either standard 'JavaSTICS' XML files or more
-    directly the text files used by the model 'fortran' executable.  The
-    most basic functionality is to read and write parameter names and
-    values through XML queries, or text files ones.  More advanced
-    functionalities include the generation of input XML from XML templates
-    and spreadsheets with as many simulations contexts as needed, or the
-    generation of the input text files from the XML input files for
-    distributed computing.
+    model. Files are either 'JavaSTICS' XML files or text files used by
+    the model 'fortran' executable. Most basic functionalities are reading
+    or writing parameter names and values in both XML or text input files,
+    and getting data from output files.  Advanced functionalities include
+    XML files generation from XML templates and/or spreadsheets, or text
+    files generation from XML files by using 'xslt' transformation.
 License: LGPL (>= 3)
 URL: https://github.com/SticsRPacks/SticsRFiles,
     https://doi.org/10.5281/zenodo.4443206

diff --git a/NAMESPACE b/NAMESPACE
@@ -23,7 +23,6 @@ export(get_obs)
 export(get_param_info)
 export(get_param_txt)
 export(get_param_xml)
-export(get_params_dict)
 export(get_plant_txt)
 export(get_plants_nb)
 export(get_report_results)

diff --git a/NEWS.md b/NEWS.md
@@ -1,8 +1,8 @@
-# SticsRFiles 1.1.3 _2023-06-29_
+# SticsRFiles 1.1.3 _2023-07-10_
 
 * FUNCTIONS
    * New function for generating the new_travail.usm STICS file
-   * New function for generating wheather data file (climat.txt)
+   * New function for generating weather data files (climat.txt)
    * New unit tests added
 
 * FIXES:

diff --git a/R/add_node_to_doc.R b/R/add_node_to_doc.R
@@ -10,35 +10,37 @@
 #' \dontrun{
 #'
 #' tec_xml <- file.path(get_examples_path(file_type = "xml"), "file_tec.xml")
-#' tec_doc <- SticsRFiles:::xmldocument(tec_xml)
+#' tec_doc <- xmldocument(tec_xml)
 #'
 #' # Getting a new irrigation operation node
-#' irrigation_node <- SticsRFiles:::get_xml_base_node("tec", "irrigation")
-#' parent_path <- SticsRFiles:::get_param_type(
+#' irrigation_node <- get_xml_base_node("tec", "irrigation")
+#' parent_path <- get_param_type(
 #'   tec_doc, "ta", "formalisme",
 #'   "irrigation"
 #' )$xpath
 #'
 #' # Adding one irrigation operation
-#' SticsRFiles:::add_node_to_doc(
+#' add_node_to_doc(
 #'   xml_doc = tec_doc, new_node = irrigation_node,
 #'   nodes_nb = 1, parent_path = parent_path
 #' )
 #'
 #' # Checking irrigations operations number
-#' irrigations_nb <- length(SticsRFiles:::get_param_value(
+#' irrigations_nb <- length(get_param_value(
 #'   tec_doc,
 #'   "julapI_or_sum_upvt"
 #' ))
 #' # Fixing it in nb_interventions attribute
-#' SticsRFiles:::set_param_value(
+#' set_param_value(
 #'   tec_doc, "nb_interventions", irrigations_nb,
 #'   "irrigation"
 #' )
 #' }
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 add_node_to_doc <- function(xml_doc, new_node, nodes_nb = 1, parent_path) {
 
   # Checking that parent_path is valid xpath for xml_doc

diff --git a/R/add_stics_nodes.R b/R/add_stics_nodes.R
@@ -9,16 +9,19 @@
 #' \dontrun{
 #'
 #' tec_xml <- file.path(get_examples_path(file_type = "xml"), "file_tec.xml")
-#' tec_doc <- SticsRFiles:::xmldocument(tec_xml)
+#' tec_doc <- xmldocument(tec_xml)
 #'
 #' # Adding one irrigation operation
-#' SticsRFiles:::add_stics_nodes(tec_doc, "irrigation")
+#' add_stics_nodes(tec_doc, "irrigation")
 #'
 #' # Adding three irrigation operations
-#' SticsRFiles:::add_stics_nodes(tec_doc, "irrigation", nodes_nb = 3)
+#' add_stics_nodes(tec_doc, "irrigation", nodes_nb = 3)
 #' }
 #'
 #' @keywords internal
+#'
+#' @noRd
+#'
 add_stics_nodes <- function(xml_doc, formalism_name = NULL, nodes_nb = 1,
                             stics_version = "latest") {
 

diff --git a/R/all_out_var.R b/R/all_out_var.R
@@ -17,6 +17,8 @@
 #' }
 #' @keywords internal
 #'
+#' @noRd
+#'
 all_out_var <- function(stics_version = "latest") {
 
   # Checking and getting the right version
@@ -68,10 +70,9 @@ all_out_var <- function(stics_version = "latest") {
 #' @return A data.frame with information about variable(s) with columns
 #'        `name`, `definition`, `unit`, `type`
 #'
-#' @seealso \code{\link{all_out_var}}
 #'
 #' @examples
-#' \dontrun{
+#'
 #' # Find by variable name (fuzzy search):
 #' SticsRFiles::get_var_info("lai")
 #'
@@ -80,7 +81,7 @@ all_out_var <- function(stics_version = "latest") {
 #'
 #' # Find for a particular version:
 #' SticsRFiles::get_var_info("lai", stics_version = "V9.0")
-#' }
+#'
 #'
 #' @export
 #'
@@ -137,16 +138,15 @@ get_var_info <- function(var = NULL,
 #' @param version `r lifecycle::badge("deprecated")` `version` is no
 #'   longer supported, use `stics_version` instead.
 #'
-#' @return A boolean vector: `TRUE` if the variable exist, `FALSE` if it doesn't
+#' @return A boolean vector: `TRUE` if the variable exist, `FALSE` otherwise
 #'
 #' @seealso `get_var_info()` for interactive use.
 #'
 #' @export
 #'
 #' @examples
-#' \dontrun{
-#' is_stics_var(c("lai(n)", "masec(n)", "truc"))
-#' }
+#' is_stics_var(c("lai(n)", "masec(n)", "unknown"))
+#'
 is_stics_var <- function(var,
                          stics_version = "latest",
                          version = lifecycle::deprecated()) {

diff --git a/R/attributes_list2matrix.R b/R/attributes_list2matrix.R
@@ -10,8 +10,8 @@
 #' \dontrun{
 #'
 #' xml_path <- file.path(get_examples_path(file_type = "xml"), "sols.xml")
-#' sols_doc <- SticsRFiles:::xmldocument(xml_path)
-#' node_set <- SticsRFiles:::get_nodes(sols_doc,
+#' sols_doc <- xmldocument(xml_path)
+#' node_set <- get_nodes(sols_doc,
 #'                                "//*[@nom=\"solcanne\" or @nom=\"mulchbat\"]")
 #' attr_list <- sapply(node_set, function(x) XML::xmlAttrs(x))
 #'
@@ -27,7 +27,7 @@
 #' #> format        max        min        nom
 #' #> "real"      "2.0"      "0.0" "mulchbat"
 #'
-#' SticsRFiles:::attributes_list2matrix(attr_list)
+#' attributes_list2matrix(attr_list)
 #'
 #' #>      nom        format max   min
 #' #> [1,] "solcanne" NA     NA    NA
@@ -37,6 +37,8 @@
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 
 attributes_list2matrix <- function(attr_list) {
   # Getting unique attributes names list

diff --git a/R/check_choice_param.R b/R/check_choice_param.R
@@ -7,6 +7,8 @@
 #' @return invisible NULL
 #' @keywords internal
 #'
+#' @noRd
+#'
 #' @examples
 #' \dontrun{
 #' check_choice_param(xml_doc = xml_doc, param_name = param_name)

diff --git a/R/check_java_path.R b/R/check_java_path.R
@@ -11,7 +11,9 @@
 #' }
 #'
 #' @keywords internal
-
+#'
+#' @noRd
+#'
 check_java_path <- function(javastics) {
   if (!file.exists(javastics)) {
     stop("The JavaStics folder doesn't exist : ", javastics)

diff --git a/R/check_java_workspace.R b/R/check_java_workspace.R
@@ -12,6 +12,7 @@
 #' @return An absolute JavaSTICS workspace path
 #'
 #' @keywords internal
+#' @noRd
 
 check_java_workspace <- function(javastics, workspace = NULL) {
 

diff --git a/R/check_output_files.R b/R/check_output_files.R
@@ -18,6 +18,7 @@
 #' }
 #'
 #' @keywords internal
+#' @noRd
 
 check_output_files <- function(run_dir, usm_name = NULL) {
   if (base::is.null(usm_name)) {

diff --git a/R/check_usms_files.R b/R/check_usms_files.R
@@ -12,6 +12,8 @@
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 #' @examples
 #' \dontrun{
 #'

diff --git a/R/col_names_to_var.R b/R/col_names_to_var.R
@@ -7,9 +7,11 @@
 #'
 #' @examples
 #' col_names <- c("var1", "var2_n", "var3.1.")
-#' valid_names <- SticsRFiles:::col_names_to_var(col_names)
+#' valid_names <- col_names_to_var(col_names)
 #' @keywords internal
 #'
+#' @noRd
+#'
 col_names_to_var <- function(var_list = c()) {
   . <- NULL
 

diff --git a/R/compute_doy_cumul.R b/R/compute_doy_cumul.R
@@ -9,15 +9,17 @@
 #'
 #' @examples
 #' \dontrun{
-#' SticsRFiles:::compute_doy_cumul(c(350, 360, 10, 20, 30), c(
+#' compute_doy_cumul(c(350, 360, 10, 20, 30), c(
 #'   1990, 1990, 1991,
 #'   1991, 1991
 #' ))
 #' }
 #'
-#' #
+#'
 #' @keywords internal
 #'
+#' @noRd
+#'
 compute_doy_cumul <- function(doys_vec, years_vec) {
   if (!all(c(class(doys_vec), class(years_vec)) %in% c("numeric", "integer"))) {
     stop("Vectors are not all numeric/integer ones, aborting !")

diff --git a/R/convert_xml2txt.R b/R/convert_xml2txt.R
@@ -22,10 +22,11 @@
 #' @return None
 #'
 #' @examples
+#'
 #' \dontrun{
 #' xml_path <- "/path/to/corn_plt.xml"
 #' javastics_path <- "/path/to/JavaSTICS/folder"
-#' convert_xml2txt(xml_file = xml_path, java_dir = javastics_path)
+#' convert_xml2txt(file = xml_path, javastics = javastics_path)
 #' }
 #'
 #' @export

diff --git a/R/convert_xml2txt_int.R b/R/convert_xml2txt_int.R
@@ -16,11 +16,13 @@
 #' xsl_file <-
 #'    "/path/to/JavaSTICS/folder/bin/resources/xml/stylesheet/xml2txt.xsl"
 #'
-#' SticsRFiles:::convert_xml2txt_int(xml_file = xml_plt, style_file = xsl_file)
+#' convert_xml2txt_int(xml_file = xml_plt, style_file = xsl_file)
 #' }
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 convert_xml2txt_int <- function(xml_file, style_file, out_file = NULL) {
 
   f_names <- c(xml_file, style_file)

diff --git a/R/download_data.R b/R/download_data.R
@@ -18,7 +18,6 @@
 #' @export
 #'
 #' @examples
-#' \dontrun{
 #'
 #' # Getting all data
 #' download_data()
@@ -28,7 +27,7 @@
 #'
 #' # Getting data for a given example : study_case_1 and a given version
 #' download_data(example_dirs = "study_case_1", stics_version = "V9.0")
-#' }
+#'
 download_data <- function(out_dir = tempdir(), example_dirs = NULL,
                           stics_version = "latest",
                           dir = lifecycle::deprecated(),
@@ -108,18 +107,20 @@ download_data <- function(out_dir = tempdir(), example_dirs = NULL,
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 #' @examples
 #' \dontrun{
 #' # Getting all available dirs from the data repos
-#' SticsRFiles:::get_referenced_dirs()
+#' get_referenced_dirs()
 #'
 #' # Getting dirs for a use case
-#' SticsRFiles:::get_referenced_dirs("study_case_1")
+#' get_referenced_dirs("study_case_1")
 #'
 #' # Getting dirs for a use case and a version
-#' SticsRFiles:::get_referenced_dirs("study_case_1", "V9.0")
+#' get_referenced_dirs("study_case_1", "V9.0")
 #'
-#' SticsRFiles:::get_referenced_dirs(c("study_case_1", "study_case_2"), "V9.0")
+#' get_referenced_dirs(c("study_case_1", "study_case_2"), "V9.0")
 #' }
 #'
 get_referenced_dirs <- function(dirs = NULL, stics_version = NULL) {

diff --git a/R/download_usm_xl.R b/R/download_usm_xl.R
@@ -27,10 +27,9 @@
 #' @return A vector of copied files path.
 #'
 #' @examples
-#' \dontrun{
+#'
 #' download_usm_xl()
-#' download_usm_xl(out_dir = "/path/to/destination/dir")
-#' }
+#'
 #'
 #' @export
 #'
@@ -66,12 +65,6 @@ download_usm_xl <- function(file = NULL,
     dest_dir <- out_dir # to remove when we update inside the function
   }
 
-  oldw <- getOption("warn")
-  if (!verbose) {
-    options(warn = -1)
-  } else {
-    options(warn = 0)
-  }
 
   args <- list(...)
 
@@ -115,7 +108,7 @@ download_usm_xl <- function(file = NULL,
 
   if (any(success)) {
     if (verbose)
-      print(paste(files_list[success],
+      message(paste(files_list[success],
                   " has been copied in directory ",
                   dest_dir))
     dest_list <- dest_list[success]
@@ -125,7 +118,6 @@ download_usm_xl <- function(file = NULL,
     warning("Error copying files:\n", paste(src_list[!success],
                                             collapse = "\n"))
 
-  options(warn = oldw)
 
   return(invisible(dest_list))
 }
@@ -155,9 +147,7 @@ download_usm_xl <- function(file = NULL,
 #' @return A vector of copied files path.
 #'
 #' @examples
-#' \dontrun{
-#' download_usm_csv(out_dir = "/path/to/destination/dir")
-#' }
+#' download_usm_csv(out_dir = tempdir())
 #'
 #' @export
 #'