unwrapping examples for exported functions for testing them using exa…

…mples path and tempdir() for outputs

R/convert_xml2txt.R

@@ -22,10 +22,11 @@
 #' @return None
 #'
 #' @examples
+#'
 #' \donttest{
 #' 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

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(),

R/gen_ini_xml.R

@@ -51,21 +51,18 @@
 #' @return an invisible xml_document object or a list of
 #'
 #' @examples
-#' \dontrun{
 #' library(readxl)
 #'
-#' xl_path <- "inputs_stics_example.xlsx"
-#' download_usm_xl(file = xl_path)
+#' xl_path <- download_usm_xl(file = "inputs_stics_example.xlsx")
+#'
 #' ini_param_df <- read_excel(xl_path, sheet = "Ini")
 #' gen_ini_xml(
-#'   out_dir = "/path/to/dest/dir",
+#'   out_dir = tempdir(),
 #'   param_table = ini_param_df
 #' )
-#' }
 #'
 #' @export
 #'
-# TODO: refactor with gen_sta_file, gen_tec_file : same code
 gen_ini_xml <- function(param_df = NULL,
                         file = NULL,
                         out_dir = getwd(),

R/gen_sols_xml.R

@@ -52,12 +52,10 @@
 #' @return an invisible xml_document object
 #'
 #' @examples
-#' \dontrun{
 #'
 #' xl_path <- download_usm_xl(file = "inputs_stics_example.xlsx")
 #' sols_param_df <- read_params_table(file = xl_path, sheet_name = "Soils")
 #' gen_sols_xml(file = "sols.xml", param_df = sols_param_df)
-#' }
 #'
 #' @export
 #'

R/gen_usms_xml.R

@@ -53,7 +53,8 @@
 #' @examples
 #' xl_path <- download_usm_xl(file = "inputs_stics_example.xlsx")
 #' usms_param_df <- read_params_table(file = xl_path, sheet_name = "USMs")
-#' gen_usms_xml(usms_out_file = "usms.xml", usms_param = usms_param_df)
+#' gen_usms_xml(file = file.path(tempdir(), "usms.xml"),
+#'  param_df = usms_param_df)
 #'
 #' @export
 #'

R/gen_varmod.R

@@ -25,9 +25,9 @@
 #' @return None
 #'
 #' @examples
-#' gen_varmod(".", c("lai(n)", "hauteur"))
+#' gen_varmod(tempdir(), c("lai(n)", "hauteur"))
 #' # Add a variable to the others:
-#' gen_varmod(".", "masec(n)", append = TRUE)
+#' gen_varmod(tempdir(), "masec(n)", append = TRUE)
 #' # NB: var.mod will have "lai(n)","hauteur" and "masec(n)"
 #'
 #'

R/get_lai_forcing.R

@@ -12,14 +12,12 @@
 #' for each usm
 #'
 #' @examples
-#' \dontrun{
-#'
 #' # Xml case
 #' xml_usms <- file.path(get_examples_path(file_type = "xml"), "usms.xml")
 #' get_lai_forcing(xml_usms)
 #' get_lai_forcing(xml_usms, "wheat")
 #' get_lai_forcing(xml_usms, c("wheat", "intercrop_pea_barley"))
-#' }
+#'
 #'
 #' @export
 #'

R/get_param_xml.R

@@ -22,7 +22,7 @@
 #' @return A list of parameter values for each xml_file (a list of list)
 #'
 #' @examples
-#' \dontrun{
+#'
 #' # Soil file
 #' file <- file.path(get_examples_path(file_type = "xml"), "sols.xml")
 #'
@@ -55,7 +55,7 @@
 #'
 #' # Getting all parameters for a given formalism: "irrigation"
 #' get_param_xml(file, select = "formalisme", select_value = "irrigation")
-#' }
+#'
 #' @export
 get_param_xml <- function(file,
                           param = NULL,

R/upgrade_ini_xml.R

@@ -21,13 +21,15 @@
 #' @details See SticsRFiles::get_stics_versions_compat() for listing versions
 #'
 #' @examples
-#' \dontrun{
+#'
+#' dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")
+#'
 #' upgrade_ini_xml(
-#'   file = "/path/to/_ini.xml",
-#'   out_dir = "/path/to/directory",
-#'   param_gen_file = "/path/to/param_gen.xml"
+#'   file = file.path(dir_path,"file_ini.xml"),
+#'   out_dir = tempdir(),
+#'   param_gen_file = file.path(dir_path, "param_gen.xml")
 #' )
-#' }
+#'
 upgrade_ini_xml <- function(file,
                             out_dir,
                             param_gen_file,

R/upgrade_param_gen_xml.R

@@ -15,15 +15,16 @@
 #'
 #' @export
 #'
-#' @details See SticsRFiles::get_stics_versions_compat() for listing versions
+#' @details See get_stics_versions_compat() for listing versions
 #'
 #' @examples
-#' \dontrun{
+#' dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")
+#'
 #' upgrade_param_gen_xml(
-#'   file = "/path/to/param_gen.xml",
-#'   out_dir = "/path/to/directory"
+#'   file = file.path(dir_path, "param_gen.xml"),
+#'   out_dir = tempdir()
 #' )
-#' }
+
 upgrade_param_gen_xml <- function(file,
                                   out_dir,
                                   stics_version = "V9.2",

R/upgrade_param_newform_xml.R

@@ -21,13 +21,16 @@
 #' @details See SticsRFiles::get_stics_versions_compat() for listing versions
 #'
 #' @examples
-#' \donttest{
+
+#' dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")
+#'
 #' upgrade_param_newform_xml(
-#'   file = "/path/to/param_newform.xml",
-#'   out_dir = "/path/to/directory",
-#'   param_gen_file = "/path/to/param_gen.xml"
+#'   file = file.path(dir_path,"param_newform.xml"),
+#'   out_dir = tempdir(),
+#'   param_gen_file = file.path(dir_path, "param_gen.xml")
 #' )
-#' }
+#'
+#'
 upgrade_param_newform_xml <- function(file,
                                       out_dir,
                                       param_gen_file,

R/upgrade_plt_xml.R

@@ -23,14 +23,16 @@
 #' @details See get_stics_versions_compat() for listing versions
 #'
 #' @examples
-#' \donttest{
+#'
+#' dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")
+#'
 #' upgrade_plt_xml(
-#'   file = "/path/to/_plt.xml",
-#'   param_gen_file = "/path/to/param_gen.xml",
-#'   param_newform_file = "/path/to/param_newform.xml",
-#'   out_dir = "/path/to/directory"
+#'   file = file.path(dir_path,"file_plt.xml"),
+#'   out_dir = tempdir(),
+#'   param_newform_file = file.path(dir_path, "param_newform.xml"),
+#'   param_gen_file = file.path(dir_path, "param_gen.xml")
 #' )
-#' }
+#'
 upgrade_plt_xml <- function(file,
                             out_dir,
                             param_newform_file,

R/upgrade_sols_xml.R

@@ -20,13 +20,15 @@
 #' @details See SticsRFiles::get_stics_versions_compat() for listing versions
 #'
 #' @examples
-#' \dontrun{
+#'
+#' dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")
+#'
 #' upgrade_sols_xml(
-#'   file = "/path/to/sols.xml",
-#'   param_gen_file = "/path/to/param_gen.xml",
-#'   out_dir = "/path/to/an/output/directory"
+#'   file = file.path(dir_path,"sols.xml" ),
+#'   out_dir = tempdir(),
+#'   param_gen_file = file.path(dir_path, "param_gen.xml")
 #' )
-#' }
+#'
 upgrade_sols_xml <- function(file,
                              out_dir,
                              param_gen_file,

R/upgrade_sta_xml.R

@@ -21,13 +21,15 @@
 #' @details See SticsRFiles::get_stics_versions_compat() for listing versions
 #'
 #' @examples
-#' \donttest{
+#'
+#' dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")
+#'
 #' upgrade_sta_xml(
-#'   file = "/path/to/_sta.xml",
-#'   out_dir = "/path/to/directory",
-#'   param_gen_file = "/path/to/param_gen.xml"
+#'   file = file.path(dir_path,"file_sta.xml" ),
+#'   out_dir = tempdir(),
+#'   param_gen_file = file.path(dir_path, "param_gen.xml")
 #' )
-#' }
+#'
 upgrade_sta_xml <- function(file,
                             out_dir,
                             param_gen_file,

R/upgrade_tec_xml.R

@@ -20,17 +20,20 @@
 #'
 #' @export
 #'
-#' @details See SticsRFiles::get_stics_versions_compat() for listing versions
+#' @details See get_stics_versions_compat() for listing versions
 #'
 #' @examples
-#' \dontrun{
+#'
+#' dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")
+#'
 #' upgrade_tec_xml(
-#'   file = "/path/to/_tec.xml",
-#'   out_dir = "/path/to/directory",
-#'   param_newform_file = "/path/to/param_newform.xml",
-#'   param_gen_file = "/path/to/param_gen.xml"
+#'   file = file.path(dir_path,"file_tec.xml"),
+#'   out_dir = tempdir(),
+#'   param_newform_file = file.path(dir_path, "param_newform.xml"),
+#'   param_gen_file = file.path(dir_path, "param_gen.xml")
 #' )
-#' }
+#'
+#'
 upgrade_tec_xml <- function(file,
                             out_dir,
                             param_newform_file,

R/upgrade_usms_xml.R

@@ -21,14 +21,15 @@
 #' @details See get_stics_versions_compat() for listing versions
 #'
 #' @examples
-#' \donttest{
+#'
+#' dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")
+#'
 #' upgrade_usms_xml(
-#'   file = "/path/to/usms.xml",
-#'   out_dir = "/path/to/directory",
-#'   param_gen_file = "/path/to/param_gen.xml",
-#'   obs_dir = "/path/to/obs/directory"
+#'   file = file.path(dir_path,"usms.xml"),
+#'   out_dir = tempdir(),
+#'   param_gen_file = file.path(dir_path, "param_gen.xml")
 #' )
-#' }
+#'
 upgrade_usms_xml <- function(file,
                              out_dir,
                              param_gen_file,