updates for a new release + little fix about a note about a global va…

…riable "."

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: 2024-02-21
 Authors@R: c(
     person("Patrice", "Lecharpentier", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-4044-4322")),
@@ -48,7 +48,7 @@ Imports:
     stats,
     SticsRFiles (>= 1.1.3),
     tibble,
-	tidyr
+    tidyr
 Suggests:
     covr,
     knitr,
@@ -57,6 +57,8 @@ Suggests:
     testthat
 VignetteBuilder:
     knitr
+Remotes:
+    github::SticsRPacks/SticsRFiles@*release
 ByteCompile: true
 Encoding: UTF-8
 Language: en-US

NEWS.md

@@ -1,3 +1,20 @@
+# SticsOnR 1.2.0 _2024-02-21_
+
+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_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%`
 
   }

README.Rmd

@@ -65,7 +65,7 @@ if (!is.null(try_err) && attr(try_err, "class") == "try-error") {
 
 ```
 
-The R package for the [STICS](https://www6.paca.inrae.fr/stics_eng/) model <img src="man/figures/logo.png" alt="logo" width="150" align="right" />
+The R package for the [STICS](https://eng-stics.paca.hub.inrae.fr/) model <img src="man/figures/logo.png" alt="logo" width="150" align="right" />
 
 <!-- badges: start -->
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
@@ -74,7 +74,7 @@ The R package for the [STICS](https://www6.paca.inrae.fr/stics_eng/) model <img
 [![DOI](https://zenodo.org/badge/166790380.svg)](https://zenodo.org/badge/latestdoi/166790380)
 <!-- badges: end -->
 
-The goal of SticsOnR is to perform simulations of the Stics model, downloadable with its graphical user interface from https://www6.paca.inrae.fr/stics_eng/Download.
+The goal of SticsOnR is to perform simulations of the Stics model, downloadable with its graphical user interface from https://eng-stics.paca.hub.inrae.fr/Download.
 
 If you want to be notified when a new release of this package is made, you can tick the Releases box in the "Watch / Unwatch => Custom" menu at the top right of [this page](https://github.com/SticsRPacks/SticsOnR).
 
@@ -85,7 +85,7 @@ If you want to be notified when a new release of this package is made, you can t
 
 JavaStics must be installed and the minimal version is version 1.41.
 
-The latest distribution version for Stics is downloadable [here](https://www6.paca.inrae.fr/stics_eng/Download).
+The latest distribution version for Stics is downloadable [here](https://eng-stics.paca.hub.inrae.fr/Download).
 
 The installation process only consists of unzipping the JavaStics archive, except for MacOS system  (see MacOS installation [specificities](#under-macos-systems))
 

README.md

@@ -1,7 +1,7 @@
 SticsOnR
 ================
 
-The R package for the [STICS](https://www6.paca.inrae.fr/stics_eng/)
+The R package for the [STICS](https://eng-stics.paca.hub.inrae.fr/)
 model
 <img src="man/figures/logo.png" alt="logo" width="150" align="right" />
 
@@ -19,7 +19,7 @@ coverage](https://codecov.io/gh/SticsRPacks/SticsOnR/branch/main/graph/badge.svg
 
 The goal of SticsOnR is to perform simulations of the Stics model,
 downloadable with its graphical user interface from
-<https://www6.paca.inrae.fr/stics_eng/Download>.
+<https://eng-stics.paca.hub.inrae.fr/Download>.
 
 If you want to be notified when a new release of this package is made,
 you can tick the Releases box in the “Watch / Unwatch =\> Custom” menu
@@ -33,7 +33,7 @@ page](https://github.com/SticsRPacks/SticsOnR).
 JavaStics must be installed and the minimal version is version 1.41.
 
 The latest distribution version for Stics is downloadable
-[here](https://www6.paca.inrae.fr/stics_eng/Download).
+[here](https://eng-stics.paca.hub.inrae.fr/Download).
 
 The installation process only consists of unzipping the JavaStics
 archive, except for MacOS system (see MacOS installation