SticsRPacks · plecharpent · Sep 4, 2026 · Apr 11, 2024 · Apr 15, 2024 · Apr 16, 2024
diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
@@ -31,7 +31,7 @@ jobs:
             }
           - {
               os: ubuntu-latest,
-              r: "4.2.0",
+              r: "4.4.0",
               rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest",
             }
 
@@ -52,7 +52,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          pak-version: rc
+          #pak-version: rc
           # about pak-version:
           # Ubuntu doesn't install the proper version of XML see https://github.com/r-lib/actions/issues/559. Remove when fixed.
           # see also: https://stackoverflow.com/questions/73243945/pkgdown-action-failing-at-build-xml

diff --git a/.github/workflows/pr-checks.yaml b/.github/workflows/pr-checks.yaml
@@ -32,7 +32,7 @@ jobs:
             }
           - {
               os: ubuntu-latest,
-              r: "4.2.0",
+              r: "4.4.0",
               rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest",
             }
 

diff --git a/CITATION.cff b/CITATION.cff
@@ -7,15 +7,15 @@ cff-version: 1.2.0
 message: 'To cite package "SticsRFiles" in publications use:'
 type: software
 license: LGPL-3.0-or-later
-title: 'SticsRFiles: Read and Modify ''STICS'' Input/Output Files'
-version: 1.6.0
+title: 'SticsRFiles: Read and Modify STICS Input/Output Files'
+version: 1.7.0
 doi: 10.32614/CRAN.package.SticsRFiles
-abstract: Manipulating input and output files of the 'STICS' crop 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.
+abstract: Manipulating input and output files of the STICS crop 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.
 authors:
 - family-names: Lecharpentier
   given-names: Patrice
@@ -40,7 +40,6 @@ authors:
 repository: https://CRAN.R-project.org/package=SticsRFiles
 repository-code: https://github.com/SticsRPacks/SticsRFiles
 url: https://doi.org/10.5281/zenodo.4443206
-date-released: '2025-06-03'
 contact:
 - family-names: Lecharpentier
   given-names: Patrice

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,6 @@
 Package: SticsRFiles
-Title: Read and Modify 'STICS' Input/Output Files
-Version: 1.6.0
-Date: 2025-06-03
+Title: Read and Modify STICS Input/Output Files
+Version: 1.7.0
 Authors@R: c(
     person("Patrice", "Lecharpentier", , "patrice.lecharpentier@inrae.fr", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-4044-4322")),
@@ -23,13 +22,13 @@ Authors@R: c(
     person("Christine", "Le Bas", role = "rev"),
     person("Joel", "Leonard", role = "rev")
   )
-Description: Manipulating input and output files of the 'STICS' crop
-    model. Files are either 'JavaSTICS' XML files or text files used by
-    the model 'fortran' executable. Most basic functionalities are reading
+Description: Manipulating input and output files of the STICS crop
+    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.
+    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
@@ -85,6 +84,7 @@ Collate:
     'check_java_workspace.R'
     'check_output_files.R'
     'check_param_names.R'
+    'check_upgrade_versions.R'
     'col_names_to_var.R'
     'compute_date_from_day.R'
     'compute_day_number.R'
@@ -192,15 +192,9 @@ Collate:
     'static_help.R'
     'stics_environment.R'
     'stics_files_utils.R'
-    'upgrade_ini_xml.R'
-    'upgrade_param_gen_xml.R'
-    'upgrade_param_newform_xml.R'
-    'upgrade_plt_xml.R'
-    'upgrade_sols_xml.R'
-    'upgrade_sta_xml.R'
-    'upgrade_tec_xml.R'
-    'upgrade_usms_xml.R'
-    'upgrade_workspace_xml.R'
+    'upgrade_v10_v11.R'
+    'upgrade_v9_v10.R'
+    'upgrade_xml_files.R'
     'var_to_col_names.R'
     'xml_document.R'
     'xml_files_functions.R'

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,62 @@
+# SticsRFiles 1.7.0
+* FUNCTIONS
+  * Added new functions for upgrading STICS input files from version 10 to version 11
+  * Management of STICS versions using the 'semver' package (major, minor, patch components)
+  * Removed useless warnings in some functions
+  * Using now get_version_num function for comparing versions (using 'svlist' object from 'semver' package)
+  * new function get_dev_stages for extracting STICS development stages dates from a list
+  of data.frame of simulations outputs
+  * parallelisation mode introduced for STICS inputs text files generation
+  * parallelisation mode introcuced for reading STICS output files
+  * new function for extracting a new xml workspace from a workspace, with possible usm selection (rewriting usms.xml, sols.xml)
+  * new function for calculating an approximate value of vapor pressure
+  * manage branches use in download_data function
+  * Added verbosity use in functions managing Stics variables and replaced warning by message in some cases
+
+* DOCUMENTATION
+  * functions help: added missing examples for exported functions
+  * vignettes update: for STICS files upgrading
+
+* FIXES
+  * Download function for examples csv files 
+  * Function for reading csv or xls examples files
+  * managing text version to version number using 'semver'
+  * Remove `overwrite` argument from set_xml_file_version
+  * rename STICS humirac parameter to code_humirac following fortran code
+  * find general parameters files, .mod files location (either in workspace or in JavaStics config directory)
+  * manage duplicate values or files in gen_climate function
+  * get_xml_files_param_df: for the long format table the "value" column is converted to character for binding data.frame rows,
+  data selection with parameters names, management of empty parameters values when pivot_wider
+  * getting plants names with or without using the usms.xml file, for mixed usms directories (soles crops and intercrops)
+  * set_param_value: converting parameters values to a list if it is not a list when dimensions are compatible
+  * writing errors for weather data files
+  * functions arguments renaming to have more consistency among functions
+  * compute_date_from_day returns NA instead of 999
+  * removed old deprecated arguments management (and 'lifecycle' dependency)
+  * sub-directories detection for reading observation and simulation outputs files, and duplicates
+  * download_data: error management
+  * fixed default values for mandatory parameters in _tec.xml templates files (V10 and V11)
+  * Added checks for calculating weather data years number and added new tests
+
+* DATA
+  * Input STICS files sets: simplification according to versions compatibility
+  * Update examples files for STICS version 11.0.0
+  * adaptation of functions used for data manipulation for new data set of STICS 11.0.0
+
+* REFACTORING
+  * Removed useless code, superfluous arguments and commented code
+  * Checking version function
+  * Functions simplification for upgrading files from STICS version 9 to 10
+  * code style fixes
+
+* TESTS
+  * Checks and integration tests restructured
+  * Use of an automatic action for checking code style and updates
+  * Updates about testhat function used 
+  * Added in workflows a dependabot for checking packages updates (producing pull requests)
+  * Removed from tests useless version number
+
+
 # SticsRFiles 1.6.0 _2025-06-03_
 * FUNCTIONS
   * convert_xml2txt allows to convert sols.xml file to text files

diff --git a/R/add_node_to_doc.R b/R/add_node_to_doc.R
@@ -44,7 +44,7 @@
 add_node_to_doc <- function(xml_doc, new_node, nodes_nb = 1, parent_path) {
   # Checking that parent_path is valid xpath for xml_doc
   if (is.null(get_nodes(xml_doc, parent_path))) {
-    warning(paste("Given xpath is not a valid one:", parent_path))
+    warning("Given xpath is not a valid one:", parent_path)
     return(invisible())
   }
 

diff --git a/R/add_stics_nodes.R b/R/add_stics_nodes.R
@@ -54,7 +54,7 @@ add_stics_nodes <- function(
     form_idx <- which(node_types$form_names[[file_tag]] == formalism_name)
 
     if (!length(form_idx)) {
-      stop(paste("Unkown formalism name", formalism_name))
+      stop("Unkown formalism name", formalism_name)
     }
 
     if (formalism_name == "special techniques") {

diff --git a/R/all_in_par.R b/R/all_in_par.R
@@ -20,11 +20,8 @@
 #'
 all_in_par <- function(stics_version = "latest") {
   # Checking and getting the right version
-  stics_version <- check_version_compat(stics_version = stics_version)
+  stics_version <- check_version(stics_version = stics_version)
 
-  #  if (get_version_num(stics_version = stics_version) < 9.2) {
-  #    cols_idx <- 1:4
-  #  } else {
   cols_idx <- c(1, 4, 7:8, 2, 3, 10)
   #  }
 
@@ -40,7 +37,15 @@ all_in_par <- function(stics_version = "latest") {
     stringsAsFactors = FALSE
   )[, cols_idx]
 
-  names(par_df) <- c("name", "file", "min", "max", "definition", "unit", "cultivar")
+  names(par_df) <- c(
+    "name",
+    "file",
+    "min",
+    "max",
+    "definition",
+    "unit",
+    "cultivar"
+  )
 
   par_df$cultivar <- as.logical(par_df$cultivar)
 
@@ -86,6 +91,9 @@ all_in_par <- function(stics_version = "latest") {
 #'
 #' @export
 #'
+#' @examples
+#' get_param_info()
+#'
 get_param_info <- function(
   param = NULL,
   keyword = NULL,
@@ -149,7 +157,7 @@ is_stics_param <- function(param, stics_version = "latest") {
   pars_names_parsed <- var_to_col_names(all_pars$name)
   index_par <- match(par_parsed, pars_names_parsed)
   par_found <- !is.na(index_par)
-  if (any(!par_found)) {
+  if (!all(par_found)) {
     cli::cli_alert_warning(
       paste0(
         "paremeters{?s} {.var {par_parsed[!par_found]}}",

diff --git a/R/all_out_var.R b/R/all_out_var.R
@@ -20,7 +20,7 @@
 #'
 all_out_var <- function(stics_version = "latest") {
   # Checking and getting the right version
-  stics_version <- check_version_compat(stics_version = stics_version)
+  stics_version <- check_version(stics_version = stics_version)
 
   if (get_version_num(stics_version = stics_version) < get_version_num("9.2")) {
     cols_idx <- 1:4
@@ -81,6 +81,10 @@ all_out_var <- function(stics_version = "latest") {
 #'
 #' @export
 #'
+#' @examples
+#'
+#' get_var_info()
+#'
 get_var_info <- function(var = NULL, keyword = NULL, stics_version = "latest") {
   all_vars <- all_out_var(stics_version)
   if (!is.null(var)) {

diff --git a/R/approx_vapour_pressure.R b/R/approx_vapour_pressure.R
@@ -1,12 +1,18 @@
-##' Approximate vapour pressure
-##'
-##' Approximates vapour pressure as the saturated vapour pressure at the daily mean air temperature using relative humidity.
-##' See section 9.3 of the STICS book, as well as M. Launay's explanations on the STICS forum (\href{https://w3.avignon.inrae.fr/forge/boards/26/topics/2237?r=2243#message-2243}{link}).
-##' @param mean_temp numeric vector of daily mean air temperature (in Celsius degrees)
-##' @param rel_humid numeric vector of relative humidity (in percentage)
-##' @return numeric vector
-##' @author Timothee Flutre
-##' @export
+#' Approximate vapour pressure
+#'
+#' @description Approximates vapour pressure as the saturated vapour pressure at the daily
+#' mean air temperature using relative humidity.
+#' See section 9.3 of the STICS book, as well as M. Launay's explanations on the STICS forum
+#' (\href{https://w3.avignon.inrae.fr/forge/boards/26/topics/2237?r=2243#message-2243}{link}).
+#' @param mean_temp numeric vector of daily mean air temperature (in Celsius degrees)
+#' @param rel_humid numeric vector of relative humidity (in percentage)
+#' @return numeric vector
+#' @author Timothee Flutre
+#' @export
+#'
+#' @examples
+#' approx_vapour_pressure(15, 60)
+#'
 approx_vapour_pressure <- function(mean_temp, rel_humid) {
   stopifnot(
     length(mean_temp) == length(rel_humid),

diff --git a/R/check_choice_param.R b/R/check_choice_param.R
@@ -22,7 +22,7 @@ check_choice_param <- function(xml_doc, param_name, stop = FALSE) {
   #--------------------------------------------------------------------#
 
   # Early exiting for other docs than tec ones
-  if (!XML::xmlName(XML::xmlRoot(xml_doc@content)) == "fichiertec") {
+  if (XML::xmlName(XML::xmlRoot(xml_doc@content)) != "fichiertec") {
     return(invisible())
   }
 

diff --git a/R/check_java_workspace.R b/R/check_java_workspace.R
@@ -18,7 +18,7 @@ check_java_workspace <- function(javastics, workspace = NULL) {
   # Ensure that the user working directory is unchanged after
   # the function has run
   current_wd <- getwd()
-  on.exit(setwd(current_wd))
+  on.exit(setwd(current_wd), add = TRUE)
 
   setwd(javastics)
 
@@ -43,11 +43,11 @@ check_java_workspace <- function(javastics, workspace = NULL) {
   }
 
   if (base::is.null(ws) || !dir.exists(ws)) {
-    warning(paste(
+    warning(
       "The given directory does not exist or JavaSTICS working
                   directory is not set :\n",
       ws
-    ))
+    )
     return()
   }