New release 1.2.0 (#61)

* fix: masquing message related to common xml_document class name for xml2 and SticsRFIles.

* upgrade files fix and doc

* tests fixes : no more use of dplyr::all_equal

* fixes for versions management
update JavaStics version in avignette

* update data (examples, templates,...) for new version 10.1.0, some fixes in usms files for version 10.0

* fix: txt example files reference

* updates/fixes about versions meta-data and inputs.csv (10.1.0)

* documentatin updates: description, news, readme, man

* Update CITATION.cff

* little update

* fix: testing if objects are of the xml_document class

* fix: limiting execution time of the example

* trying to reduce examples execution duration following CRAN checks results

* Updates func man, according to execution time of examples (rhub check), DESC.

* Update CITATION.cff

* 1.2.0 submission

* missing is_stics_param in pkgdown yaml

---------

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

.Rbuildignore

@@ -21,3 +21,4 @@ man/figures
 ^\.vscode$
 ^CRAN-SUBMISSION$
 ^LICENSE\.md$
+^revdep$

CITATION.cff

@@ -8,7 +8,7 @@ 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: 1.1.3
+version: 1.2.0
 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
@@ -35,7 +35,7 @@ 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: '2023-07-10'
+date-released: '2024-02-23'
 contact:
 - family-names: Lecharpentier
   given-names: Patrice
@@ -50,7 +50,7 @@ references:
   - name: R Core Team
   location:
     name: Vienna, Austria
-  year: '2023'
+  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
   version: '>= 3.6.0'
@@ -64,7 +64,7 @@ references:
   - family-names: Csárdi
     given-names: Gábor
     email: [email protected]
-  year: '2023'
+  year: '2024'
 - type: software
   title: crayon
   abstract: 'crayon: Colored Terminal Output'
@@ -75,7 +75,7 @@ references:
   - family-names: Csárdi
     given-names: Gábor
     email: [email protected]
-  year: '2023'
+  year: '2024'
 - type: software
   title: curl
   abstract: 'curl: A Modern and Flexible Web Client for R'
@@ -87,7 +87,7 @@ references:
     given-names: Jeroen
     email: [email protected]
     orcid: https://orcid.org/0000-0002-4035-0289
-  year: '2023'
+  year: '2024'
 - type: software
   title: data.table
   abstract: 'data.table: Extension of `data.frame`'
@@ -104,7 +104,14 @@ references:
   - family-names: Srinivasan
     given-names: Arun
     email: [email protected]
-  year: '2023'
+  - family-names: Gorecki
+    given-names: Jan
+  - family-names: Chirico
+    given-names: Michael
+  - family-names: Hocking
+    given-names: Toby
+    orcid: https://orcid.org/0000-0002-3146-0865
+  year: '2024'
 - type: software
   title: dplyr
   abstract: 'dplyr: A Grammar of Data Manipulation'
@@ -128,7 +135,7 @@ references:
     given-names: Davis
     email: [email protected]
     orcid: https://orcid.org/0000-0003-4777-038X
-  year: '2023'
+  year: '2024'
   version: '>= 1.0.0'
 - type: software
   title: lifecycle
@@ -144,7 +151,7 @@ references:
     given-names: Hadley
     email: [email protected]
     orcid: https://orcid.org/0000-0003-4757-117X
-  year: '2023'
+  year: '2024'
 - type: software
   title: lubridate
   abstract: 'lubridate: Make Dealing with Dates a Little Easier'
@@ -159,7 +166,7 @@ references:
     given-names: Garrett
   - family-names: Wickham
     given-names: Hadley
-  year: '2023'
+  year: '2024'
 - type: software
   title: methods
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -168,7 +175,7 @@ references:
   - name: R Core Team
   location:
     name: Vienna, Austria
-  year: '2023'
+  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
 - type: software
@@ -184,7 +191,7 @@ references:
   - family-names: Wickham
     given-names: Hadley
     email: [email protected]
-  year: '2023'
+  year: '2024'
 - type: software
   title: rstudioapi
   abstract: 'rstudioapi: Safely Access the RStudio API'
@@ -204,7 +211,7 @@ references:
   - family-names: Ritchie
     given-names: Gary
     email: [email protected]
-  year: '2023'
+  year: '2024'
 - type: software
   title: stringr
   abstract: 'stringr: Simple, Consistent Wrappers for Common String Operations'
@@ -215,7 +222,7 @@ references:
   - family-names: Wickham
     given-names: Hadley
     email: [email protected]
-  year: '2023'
+  year: '2024'
 - type: software
   title: tibble
   abstract: 'tibble: Simple Data Frames'
@@ -230,7 +237,7 @@ references:
   - family-names: Wickham
     given-names: Hadley
     email: [email protected]
-  year: '2023'
+  year: '2024'
 - type: software
   title: tidyr
   abstract: 'tidyr: Tidy Messy Data'
@@ -246,7 +253,7 @@ references:
     email: [email protected]
   - family-names: Girlich
     given-names: Maximilian
-  year: '2023'
+  year: '2024'
 - type: software
   title: tools
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -255,7 +262,7 @@ references:
   - name: R Core Team
   location:
     name: Vienna, Austria
-  year: '2023'
+  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
 - type: software
@@ -266,7 +273,7 @@ references:
   - name: R Core Team
   location:
     name: Vienna, Austria
-  year: '2023'
+  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
 - type: software
@@ -280,7 +287,7 @@ references:
     given-names: Duncan
     email: [email protected]
     orcid: https://orcid.org/0000-0003-0159-1546
-  year: '2023'
+  year: '2024'
 - type: software
   title: xml2
   abstract: 'xml2: Parse XML'
@@ -295,7 +302,7 @@ references:
     given-names: Jim
   - family-names: Ooms
     given-names: Jeroen
-  year: '2023'
+  year: '2024'
 - type: software
   title: xslt
   abstract: 'xslt: Extensible Style-Sheet Language Transformations'
@@ -307,7 +314,7 @@ references:
     given-names: Jeroen
     email: [email protected]
     orcid: https://orcid.org/0000-0002-4035-0289
-  year: '2023'
+  year: '2024'
 - type: software
   title: covr
   abstract: 'covr: Test Coverage for Packages'
@@ -318,7 +325,7 @@ references:
   - family-names: Hester
     given-names: Jim
     email: [email protected]
-  year: '2023'
+  year: '2024'
 - type: software
   title: formatR
   abstract: 'formatR: Format R Code Automatically'
@@ -330,7 +337,7 @@ references:
     given-names: Yihui
     email: [email protected]
     orcid: https://orcid.org/0000-0003-0645-5666
-  year: '2023'
+  year: '2024'
 - type: software
   title: knitr
   abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
@@ -342,7 +349,7 @@ references:
     given-names: Yihui
     email: [email protected]
     orcid: https://orcid.org/0000-0003-0645-5666
-  year: '2023'
+  year: '2024'
 - type: software
   title: learnr
   abstract: 'learnr: Interactive Tutorials for R'
@@ -365,7 +372,7 @@ references:
     given-names: Alexander
     email: [email protected]
     orcid: https://orcid.org/0000-0001-9412-0457
-  year: '2023'
+  year: '2024'
 - type: software
   title: readxl
   abstract: 'readxl: Read Excel Files'
@@ -381,7 +388,7 @@ references:
     given-names: Jennifer
     email: [email protected]
     orcid: https://orcid.org/0000-0002-6983-2759
-  year: '2023'
+  year: '2024'
 - type: software
   title: rmarkdown
   abstract: 'rmarkdown: Dynamic Documents for R'
@@ -424,7 +431,7 @@ 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'
@@ -439,7 +446,7 @@ references:
   - family-names: Hester
     given-names: Jim
     email: [email protected]
-  year: '2023'
+  year: '2024'
 - type: software
   title: testthat
   abstract: 'testthat: Unit Testing for R'
@@ -450,4 +457,4 @@ references:
   - family-names: Wickham
     given-names: Hadley
     email: [email protected]
-  year: '2023'
+  year: '2024'

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 1.2.0
+Date: 2024-02-23 14:29:17 UTC
+SHA: 238104929d9b5fe938aa9d239559eb5979ee6ebc

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SticsRFiles
 Title: Read and Modify 'STICS' Input/Output Files
-Version: 1.1.3
-Date: 2023-07-10
+Version: 1.2.0
+Date: 2024-02-23
 Authors@R: c(
     person("Patrice", "Lecharpentier", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-4044-4322")),
@@ -68,7 +68,7 @@ ByteCompile: true
 Encoding: UTF-8
 Language: en-US
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Collate: 
     'add_node_to_doc.R'
     'add_stics_nodes.R'

NEWS.md

@@ -1,11 +1,32 @@
+# SticsRFiles 1.2.0 _2024-02-21_
+
+* FUNCTIONS
+   * Text files generation from xml files are now done without using JavaStics 
+   command line (the speedup is about 10 times)
+   * Getting parameters information (get_param_info) do not use XML files 
+   exploration anymore, the speed is largely improved
+   * Improvement of XML files manipulations/generation for reducing memory 
+   use/freezing in R when intensive use is performed
+   * tests coverage improvement
+
+* FIXES
+   * update of a bunch of unit tests according to other packages evolutions
+   * STICS versions management and XML files upgrade
+
+* DATA
+   * examples, templates files for different files format added for the latest
+   STICS version 10.1.0
+   * versions meta-data update
+
+
 # SticsRFiles 1.1.3 _2023-07-10_
 
 * FUNCTIONS
    * New function for generating the new_travail.usm STICS file
    * New function for generating weather data files (climat.txt)
    * New unit tests added
 
-* FIXES:
+* FIXES
    * get_param_value: forcing to get a character returned value
    * get_var_info: for variables names vector
    * get_param_txt: removed global variables use, looking for parameters names

R/download_data.R

@@ -19,13 +19,7 @@
 #'
 #' @examples
 #'
-#' # Getting all data
-#' download_data()
-#'
-#  # Getting data for a given example : study_case_1
-#' download_data(example_dirs = "study_case_1")
-#'
-#' # Getting data for a given example : study_case_1 and a given version
+#' # Getting data for a given example : study_case_1 and a given STICS version
 #' download_data(example_dirs = "study_case_1", stics_version = "V9.0")
 #'
 download_data <- function(out_dir = tempdir(), example_dirs = NULL,

R/expand_stics_names.R

@@ -4,7 +4,7 @@
 #'
 #' @param in_csv_file Input csv file path
 #' @param out_csv_file Output csv file path
-#' @param header_vec An optional header vector
+#' @param header A logical TRUE if a header line exists, FALSE otherwise
 #'
 #'
 #' @examples
@@ -20,17 +20,20 @@
 #'
 #' @noRd
 #'
-expand_stics_names <- function(in_csv_file, out_csv_file, header_vec = NULL) {
+expand_stics_names <- function(in_csv_file, out_csv_file, header = FALSE) {
+
+  skip <- as.integer(header)
   in_data <- utils::read.table(in_csv_file,
     sep = ";", stringsAsFactors = FALSE,
-    header = FALSE
+    header = FALSE, skip = skip
   )
-  if (base::is.null(header_vec)) {
+
+  #if (base::is.null(header_vec)) {
     names(in_data) <- c(
       "name", "def", "unit", "param", "dim", "type",
       "min", "max", "optim", "n"
     )
-  }
+  #}
 
   # getting param names to duplicate
   par_to_expand <- in_data[in_data$dim > 1, ]

R/gen_ini_xml.R

@@ -58,7 +58,7 @@
 #' ini_param_df <- read_excel(xl_path, sheet = "Ini")
 #' gen_ini_xml(
 #'   out_dir = tempdir(),
-#'   param_table = ini_param_df
+#'   param_df = ini_param_df[1:2,]
 #' )
 #'
 #' @export
@@ -166,6 +166,6 @@ gen_ini_xml <- function(param_df,
     delete(xml_docs[[f]])
   }
 
-  if (!base::is.null(xml_doc_tmpl) && class(xml_doc_tmpl) == "xml_document")
+  if (!base::is.null(xml_doc_tmpl) && inherits(xml_doc_tmpl, "xml_document"))
     delete(xml_doc_tmpl)
 }