New release 1.2.0 (#20)

* updates: added new JavaStics version/java version, info about how to handle the stics exe generation under MacOS (ref to the JavaStics doc), fixed internal page links.
Fix: mask messages about common names of the SticsRFiles and xml2 xml_document class name.

* Update CITATION.cff

* updates for a new release + little fix about a note about a global variable "."

* Update CITATION.cff

* fix: SticsRFiles in imports

* Update CITATION.cff

* SticsRFiles in suggests

* Update CITATION.cff

* trying to force main install in checks as in CroptimizR

* let SticsRFiles in Imports and Remotes

* Update CITATION.cff

* restoring previous install config for SticsRFiles@main

* SticsRFiles again in Imports

* Update CITATION.cff

* new release 1.2.0

* Update CITATION.cff

---------

Co-authored-by: plecharpent <[email protected]>

Author: plecharpent

CITATION.cff

@@ -8,7 +8,7 @@ message: 'To cite package "SticsOnR" in publications use:'
 type: software
 license: LGPL-3.0-or-later
 title: 'SticsOnR: Manage STICS Simulations Running the Executable or JavaStics,'
-version: 1.1.0
+version: 1.2.0
 abstract: 'Running simulations with the ''STICS'' crop model. Different ways of performing
   simulations are available and based on three use-cases: 1/ Calling ''JavaStics''
   command line to run simulations on given situations. ''JavaStics'' handles text
@@ -37,7 +37,7 @@ authors:
   orcid: https://orcid.org/0000-0002-9310-2377
 repository-code: https://github.com/SticsRPacks/SticsOnR
 url: https://doi.org/10.5281/zenodo.4443130
-date-released: '2023-07-12'
+date-released: '2024-02-22'
 contact:
 - family-names: Lecharpentier
   given-names: Patrice
@@ -52,7 +52,7 @@ references:
   - name: R Core Team
   location:
     name: Vienna, Austria
-  year: '2023'
+  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
   version: '>= 3.6.0'
@@ -66,7 +66,7 @@ references:
   - family-names: Csárdi
     given-names: Gábor
     email: [email protected]
-  year: '2023'
+  year: '2024'
 - type: software
   title: crayon
   abstract: 'crayon: Colored Terminal Output'
@@ -77,7 +77,7 @@ references:
   - family-names: Csárdi
     given-names: Gábor
     email: [email protected]
-  year: '2023'
+  year: '2024'
   version: '>= 1.3.4'
 - type: software
   title: doParallel
@@ -90,7 +90,7 @@ references:
     given-names: Microsoft
   - family-names: Weston
     given-names: Steve
-  year: '2023'
+  year: '2024'
 - type: software
   title: dplyr
   abstract: 'dplyr: A Grammar of Data Manipulation'
@@ -114,7 +114,7 @@ references:
     given-names: Davis
     email: [email protected]
     orcid: https://orcid.org/0000-0003-4777-038X
-  year: '2023'
+  year: '2024'
 - type: software
   title: foreach
   abstract: 'foreach: Provides Foreach Looping Construct'
@@ -125,7 +125,7 @@ references:
   - name: Microsoft
   - family-names: Weston
     given-names: Steve
-  year: '2023'
+  year: '2024'
 - type: software
   title: lifecycle
   abstract: 'lifecycle: Manage the Life Cycle of your Package Functions'
@@ -135,12 +135,12 @@ references:
   authors:
   - family-names: Henry
     given-names: Lionel
-    email: lionel@rstudio.com
+    email: lionel@posit.co
   - family-names: Wickham
     given-names: Hadley
-    email: hadley@rstudio.com
+    email: hadley@posit.co
     orcid: https://orcid.org/0000-0003-4757-117X
-  year: '2023'
+  year: '2024'
 - type: software
   title: magrittr
   abstract: 'magrittr: A Forward-Pipe Operator for R'
@@ -154,7 +154,7 @@ references:
   - family-names: Wickham
     given-names: Hadley
     email: [email protected]
-  year: '2023'
+  year: '2024'
 - type: software
   title: parallel
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -163,7 +163,7 @@ references:
   - name: R Core Team
   location:
     name: Vienna, Austria
-  year: '2023'
+  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
 - type: software
@@ -185,7 +185,7 @@ references:
   - family-names: Ritchie
     given-names: Gary
     email: [email protected]
-  year: '2023'
+  year: '2024'
 - type: software
   title: stats
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -194,9 +194,40 @@ references:
   - name: R Core Team
   location:
     name: Vienna, Austria
-  year: '2023'
+  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
+- type: software
+  title: tibble
+  abstract: 'tibble: Simple Data Frames'
+  notes: Imports
+  url: https://tibble.tidyverse.org/
+  repository: https://CRAN.R-project.org/package=tibble
+  authors:
+  - family-names: Müller
+    given-names: Kirill
+    email: [email protected]
+    orcid: https://orcid.org/0000-0002-1416-3412
+  - family-names: Wickham
+    given-names: Hadley
+    email: [email protected]
+  year: '2024'
+- type: software
+  title: tidyr
+  abstract: 'tidyr: Tidy Messy Data'
+  notes: Imports
+  url: https://tidyr.tidyverse.org
+  repository: https://CRAN.R-project.org/package=tidyr
+  authors:
+  - family-names: Wickham
+    given-names: Hadley
+    email: [email protected]
+  - family-names: Vaughan
+    given-names: Davis
+    email: [email protected]
+  - family-names: Girlich
+    given-names: Maximilian
+  year: '2024'
 - type: software
   title: SticsRFiles
   abstract: 'SticsRFiles: Read and Modify ''STICS'' Input/Output Files'
@@ -220,23 +251,8 @@ references:
     given-names: Michel
     email: [email protected]
     orcid: https://orcid.org/0000-0002-9310-2377
-  year: '2023'
+  year: '2024'
   version: '>= 1.1.3'
-- type: software
-  title: tibble
-  abstract: 'tibble: Simple Data Frames'
-  notes: Imports
-  url: https://tibble.tidyverse.org/
-  repository: https://CRAN.R-project.org/package=tibble
-  authors:
-  - family-names: Müller
-    given-names: Kirill
-    email: [email protected]
-    orcid: https://orcid.org/0000-0002-1416-3412
-  - family-names: Wickham
-    given-names: Hadley
-    email: [email protected]
-  year: '2023'
 - type: software
   title: covr
   abstract: 'covr: Test Coverage for Packages'
@@ -247,7 +263,7 @@ references:
   - family-names: Hester
     given-names: Jim
     email: [email protected]
-  year: '2023'
+  year: '2024'
 - type: software
   title: knitr
   abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
@@ -259,7 +275,7 @@ references:
     given-names: Yihui
     email: [email protected]
     orcid: https://orcid.org/0000-0003-0645-5666
-  year: '2023'
+  year: '2024'
 - type: software
   title: rmarkdown
   abstract: 'rmarkdown: Dynamic Documents for R'
@@ -302,7 +318,7 @@ references:
     given-names: Richard
     email: [email protected]
     orcid: https://orcid.org/0000-0003-3925-190X
-  year: '2023'
+  year: '2024'
 - type: software
   title: spelling
   abstract: 'spelling: Tools for Spell Checking in R'
@@ -317,7 +333,7 @@ references:
   - family-names: Hester
     given-names: Jim
     email: [email protected]
-  year: '2023'
+  year: '2024'
 - type: software
   title: testthat
   abstract: 'testthat: Unit Testing for R'
@@ -328,4 +344,4 @@ references:
   - family-names: Wickham
     given-names: Hadley
     email: [email protected]
-  year: '2023'
+  year: '2024'

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: SticsOnR
 Title: Manage STICS Simulations Running the Executable or JavaStics,
-Version: 1.1.0
-Date: 2023-07-12
+Version: 1.2.0
+Date: 2024-02-22
 Authors@R: c(
     person("Patrice", "Lecharpentier", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-4044-4322")),
@@ -46,9 +46,9 @@ Imports:
     parallel,
     rstudioapi,
     stats,
-    SticsRFiles (>= 1.1.3),
     tibble,
-	tidyr
+    tidyr,
+    SticsRFiles (>= 1.1.3)
 Suggests:
     covr,
     knitr,
@@ -61,4 +61,4 @@ ByteCompile: true
 Encoding: UTF-8
 Language: en-US
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.3.1

NAMESPACE

@@ -5,6 +5,7 @@ export(run_stics)
 export(stics_wrapper)
 export(stics_wrapper_options)
 importFrom(doParallel,registerDoParallel)
+importFrom(foreach,"%do%")
 importFrom(foreach,"%dopar%")
 importFrom(magrittr,"%>%")
 importFrom(parallel,clusterCall)

NEWS.md

@@ -1,3 +1,20 @@
+# SticsOnR 1.2.0 _2024-02-22_
+
+MAIN CHANGES:
+  * paralellization in the wrapper is now optional (cluster deactivation)
+  * README update with latest JavaStics/STICS versions and information     
+  about executable installation on MacOS systems 
+
+
+FIXES:
+  * tidyr package was missing in imports
+  * checking if the JavaStics folder is given when forcing parameters values
+    in the wrapper
+  * for several years simulations, the wrapper now is returning specific values
+    for stages for each year, not the same one for all the years
+  * limitation of sub-dirs discovering (recursivity deactivated) in the 
+    workspace for the run_system function
+
 # SticsOnR 1.1.0 _2023-07-12_
 
 MAIN CHANGES:

R/global.R

@@ -0,0 +1 @@
+utils::globalVariables(".")

R/stics_exe_utilities.R

@@ -163,8 +163,7 @@ set_stics_exe <- function(javastics,
   # saving a previous version
   file.copy(xml_path, xml_path_prev)
 
-
-  xml_pref <- SticsRFiles:::xmldocument(xml_path)
+  xml_pref <- get_xml_doc(xml_path)
 
 
   # Getting the existing list in pref file
@@ -214,7 +213,9 @@ set_stics_exe <- function(javastics,
     names(stics_exe_list$stics_list),
     stics_exe_list$stics_list
   ), collapse = "")
-  xml_pref <- SticsRFiles:::xmldocument(xml_path)
+
+  xml_pref <- get_xml_doc(xml_path)
+
   SticsRFiles:::set_values(
     xml_pref,
     '//entry[@key="model.last"]', new_stics_name
@@ -274,7 +275,9 @@ list_stics_exe <- function(javastics) {
   } else {
     # If the preferences is availabble, control that it is complete
     # (it is not on at install)
-    xml_pref <- SticsRFiles:::xmldocument(config_pref)
+
+    xml_pref <- get_xml_doc(config_pref)
+
     current_stics <- SticsRFiles:::get_values(
       xml_pref,
       '//entry[@key="model.last"]'
@@ -286,7 +289,8 @@ list_stics_exe <- function(javastics) {
     }
   }
 
-  xml_pref <- SticsRFiles:::xmldocument(config_pref)
+  xml_pref <- get_xml_doc(config_pref)
+
   current_stics <- SticsRFiles:::get_values(
     xml_pref,
     '//entry[@key="model.last"]'
@@ -447,7 +451,8 @@ select_stics_exe <- function(javastics, stics_exe = "stics_modulo") {
   # saving a previous version
   file.copy(xml_path, xml_path_prev)
 
-  xml_pref <- SticsRFiles:::xmldocument(xml_path)
+  xml_pref <- get_xml_doc(xml_path)
+
   current_model <- SticsRFiles:::get_values(
     xml_pref,
     '//entry[@key="model.last"]'
@@ -555,7 +560,7 @@ remove_stics_exe <- function(javastics, stics_exe) {
     stics_exe_list$stics_list
   ), collapse = "")
 
-  xml_pref <- SticsRFiles:::xmldocument(xml_path)
+  xml_pref <- get_xml_doc(xml_path)
 
   # removing model from last if needed
   if (stics_exe_list$current == stics_exe) {
@@ -576,3 +581,18 @@ remove_stics_exe <- function(javastics, stics_exe) {
   # writing file
   SticsRFiles:::save_xml_doc(xml_pref, xml_path)
 }
+
+
+#' Getting a xml_document from an XML file
+#'
+#' @param file
+#'
+#' @return a SticsRFiles xml_document object
+#' @keywords internal
+#'
+#' @noRd
+
+get_xml_doc <- function(file) {
+  suppressMessages(doc <- SticsRFiles:::xmldocument(file))
+  doc
+}

R/stics_wrapper.R

@@ -114,6 +114,7 @@ stics_wrapper <- function(model_options,
   #   + handle the case when simulations does not reach the asked stages ...)
   #
 
+
   if (lifecycle::is_present(sit_names)) {
     lifecycle::deprecate_warn(
       "1.0.0", "stics_wrapper(sit_names)",
@@ -181,10 +182,8 @@ stics_wrapper <- function(model_options,
     registerDoParallel(cl)
     clusterCall(cl, function(x) .libPaths(x), .libPaths())
 
-    #`%doparornot%` <- `%dopar%`
     `%do_par_or_not%` <- foreach::`%dopar%`
   } else {
-    #`%doparornot%` <- `%do%`
     `%do_par_or_not%` <- foreach::`%do%`
 
   }