removed getwd() from default arg values in functions, man update

SticsRPacks · Jul 7, 2023 · f14eae8 · f14eae8
1 parent 29c9790
commit f14eae8
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Showing 24 changed files with 65 additions and 74 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -27,7 +27,7 @@ Description: Manipulating input and output files of the 'STICS' crop
     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

diff --git a/R/gen_ini_xml.R b/R/gen_ini_xml.R
@@ -63,9 +63,9 @@
 #'
 #' @export
 #'
-gen_ini_xml <- function(param_df = NULL,
+gen_ini_xml <- function(param_df,
                         file = NULL,
-                        out_dir = getwd(),
+                        out_dir,
                         crop_tag = "Crop",
                         stics_version = "latest",
                         ini_in_file = lifecycle::deprecated(),

diff --git a/R/gen_new_travail.R b/R/gen_new_travail.R
@@ -20,23 +20,25 @@
 
 gen_new_travail <- function(workspace,
                             usm,
-                            lai_forcing = 0,
-                            codesuite = 0,
-                            codoptim = 0,
-                            out_dir = getwd()) {
+                            lai_forcing = NULL,
+                            codesuite = NULL,
+                            codoptim = NULL,
+                            out_dir = NULL) {
 
   usm_data <- get_usm_data(workspace,
                            usm,
-                           lai_forcing = 0,
-                           codesuite = 0,
-                           codoptim = 0)
+                           lai_forcing = lai_forcing,
+                           codesuite = codesuite,
+                           codoptim = codoptim)
 
   data_order <- c("codesimul", "codoptim", "codesuite", "nbplantes", "nom",
                   "datedebut", "datefin", "finit", "numsol", "nomsol",
                   "fstation",
                   "fclim1", "fclim2", "nbans", "culturean", "fplt1",
                   "ftec1", "flai1", "fplt2", "ftec2", "flai2")
 
+  if (is.null(out_dir)) out_dir <- workspace
+
   out_file <- file.path(out_dir, "new_travail.usm")
 
   p_table <- vector(mode = "character", length = 2 * length(data_order))
@@ -54,9 +56,9 @@ gen_new_travail <- function(workspace,
 
 get_usm_data <- function(workspace,
                          usm,
-                         lai_forcing = 0,
-                         codesuite = 0,
-                         codoptim = 0) {
+                         lai_forcing = NULL,
+                         codesuite = NULL,
+                         codoptim = NULL) {
 
   data <- list()
 
@@ -65,13 +67,18 @@ get_usm_data <- function(workspace,
                         usm, select = "usm",
                         select_value = usm)$usms.xml
 
-  # codesimul
+  # forcing codesimul
   # 0: culture, 1: feuille, lai forcing
-  data$codesimul <- get_codesimul(lai_forcing)
+  if(!is.null(lai_forcing) & lai_forcing %in% c(0,1))
+    data$codesimul <- get_codesimul(lai_forcing)
 
-  data$codoptim <- codoptim
+  # forcing codoptim
+  if(!is.null(codoptim) & codoptim %in% c(0,1))
+    data$codoptim <- codoptim
 
-  data$codesuite <- codesuite
+  # forcing codesuite
+  if(!is.null(codesuite) & codesuite %in% c(0,1))
+    data$codesuite <- codesuite
 
   # nbplantes
   #data$nbplantes
@@ -110,7 +117,7 @@ get_usm_data <- function(workspace,
   data$nbans <-
     as.numeric(strsplit(x = data$fclim2, split = ".", fixed = TRUE)[[1]][2]) -
     as.numeric(strsplit(x = data$fclim1, split = ".", fixed = TRUE)[[1]][2]) +
-    data$culturean
+    1
 
   # culturean
   # data$culturean

diff --git a/R/gen_obs.R b/R/gen_obs.R
@@ -41,7 +41,7 @@
 #' @export
 #'
 gen_obs <- function(df,
-                    out_dir = getwd(),
+                    out_dir,
                     usms_list = NULL,
                     obs_table = lifecycle::deprecated(),
                     out_path = lifecycle::deprecated()) {

diff --git a/R/gen_sols_xml.R b/R/gen_sols_xml.R
@@ -63,8 +63,8 @@
 #'
 #'
 #'
-gen_sols_xml <- function(file = file.path(getwd(), "sols.xml"),
-                         param_df = NULL,
+gen_sols_xml <- function(file,
+                         param_df,
                          template = NULL,
                          stics_version = "latest",
                          sols_in_file = lifecycle::deprecated(),
@@ -111,11 +111,6 @@ gen_sols_xml <- function(file = file.path(getwd(), "sols.xml"),
 
   xml_doc <- NULL
 
-  # Fix : default output file path if not provided
-  if (base::is.null(sols_out_file)) {
-    sols_out_file <- file.path(getwd(), "sols.xml")
-  }
-
   if (!base::is.null(sols_in_file)) {
     xml_doc <- xmldocument(sols_in_file)
   }

diff --git a/R/gen_sta_xml.R b/R/gen_sta_xml.R
@@ -46,9 +46,9 @@
 #' @export
 #'
 # TODO: refactor with gen_tec_file, gen_ini_file : same code
-gen_sta_xml <- function(param_df = NULL,
+gen_sta_xml <- function(param_df,
                         file = NULL,
-                        out_dir = getwd(),
+                        out_dir,
                         stics_version = "latest",
                         param_table = lifecycle::deprecated(),
                         sta_in_file = lifecycle::deprecated(),

diff --git a/R/gen_tec_xml.R b/R/gen_tec_xml.R
@@ -59,7 +59,7 @@
 
 gen_tec_xml <- function(param_df = NULL,
                         file = NULL,
-                        out_dir = getwd(),
+                        out_dir,
                         stics_version = "latest",
                         na_values = NA,
                         param_table = lifecycle::deprecated(),

diff --git a/R/gen_usms_xml.R b/R/gen_usms_xml.R
@@ -1,7 +1,6 @@
 #' @title Generate STICS usms xml file from a template or an input file
 #'
-#' @param file Path (including name) of the usms file to generate. Optional,
-#' set to `file.path(getwd(), "usms.xml")`by default.
+#' @param file Path (including name) of the usms file to generate.
 #' @param param_df A table (df, tibble) containing the values of the parameters
 #' to use (see details)
 #' @param template Path of an USM xml file to be used as a template.
@@ -59,7 +58,7 @@
 #' @export
 #'
 
-gen_usms_xml <- function(file = file.path(getwd(), "usms.xml"),
+gen_usms_xml <- function(file,
                          param_df = NULL,
                          template = NULL,
                          stics_version = "latest",
@@ -99,11 +98,6 @@ gen_usms_xml <- function(file = file.path(getwd(), "usms.xml"),
 
   xml_doc <- NULL
 
-  # Fix : default output file path if not provided
-  if (base::is.null(usms_out_file)) {
-    usms_out_file <- file.path(getwd(), "usms.xml")
-  }
-
   # If a template file is provided
   if (!base::is.null(usms_in_file)) {
     xml_doc <- xmldocument(usms_in_file)

diff --git a/R/get_climate_txt.R b/R/get_climate_txt.R
@@ -28,7 +28,7 @@
 #'
 #' @export
 #'
-get_climate_txt <- function(workspace = getwd(),
+get_climate_txt <- function(workspace,
                             file_name = "climat.txt",
                             preserve = TRUE,
                             dirpath = lifecycle::deprecated(),

diff --git a/R/get_file.R b/R/get_file.R
@@ -117,7 +117,7 @@ get_file <- function(workspace,
 #'
 #' @noRd
 #'
-get_file_ <- function(workspace = getwd(),
+get_file_ <- function(workspace,
                       usm_name = NULL,
                       usms_filepath = NULL,
                       var_list = NULL,

diff --git a/R/get_obs_txt.R b/R/get_obs_txt.R
@@ -36,7 +36,9 @@
 #'
 #' @noRd
 #'
-get_obs_txt <- function(dirpath = getwd(), filename = NULL, mixed = NULL) {
+get_obs_txt <- function(dirpath,
+                        filename = NULL,
+                        mixed = NULL) {
   . <- NULL # to avoid CRAN note for pipe
   if (is.null(mixed)) {
     if (file.exists(file.path(dirpath, "new_travail.usm"))) {

diff --git a/R/get_param_txt.R b/R/get_param_txt.R
@@ -58,7 +58,7 @@
 #'
 #'
 #' @export
-get_param_txt <- function(workspace = getwd(),
+get_param_txt <- function(workspace,
                           param = NULL,
                           variety = NULL,
                           exact = FALSE,

diff --git a/R/set_param_txt.R b/R/set_param_txt.R
@@ -72,7 +72,7 @@
 #'              param = "cailloux", layer = 2, value = 1)
 #'
 #'
-set_param_txt <- function(workspace = getwd(),
+set_param_txt <- function(workspace,
                           param,
                           value,
                           append = FALSE,

diff --git a/R/static_help.R b/R/static_help.R
@@ -23,7 +23,7 @@
 static_help <- function(pkg,
                         links_level = 0,
                         topic = NULL,
-                        out_dir = getwd(),
+                        out_dir,
                         overwrite = TRUE) {
   if (!dir.exists(out_dir)) dir.create(out_dir)
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,9 +1,9 @@
 ── SticsRFiles 1.1.3: NOTE
 
-  Build ID:   SticsRFiles_1.1.3.tar.gz-c4b9e5e1c0f0486ab292c73748a6ed2a
+  Build ID:   SticsRFiles_1.1.3.tar.gz-77acad5161384a8e90d3b0461507f39e
   Platform:   Windows Server 2022, R-devel, 64 bit
-  Submitted:  1h 9m 54.9s ago
-  Build time: 7m 41.8s
+  Submitted:  1h 41m 5.2s ago
+  Build time: 6m 34.7s
 
 ❯ checking CRAN incoming feasibility ... [17s] NOTE
   Maintainer: 'Patrice Lecharpentier <patrice.lecharpentier@inrae.fr>'
@@ -22,12 +22,12 @@
 
 ── SticsRFiles 1.1.3: NOTE
 
-  Build ID:   SticsRFiles_1.1.3.tar.gz-200502a17eab4563a2972360a9407d88
+  Build ID:   SticsRFiles_1.1.3.tar.gz-7a811a73d6964b13ad859b175e690f20
   Platform:   Ubuntu Linux 20.04.1 LTS, R-release, GCC
-  Submitted:  1h 9m 54.9s ago
-  Build time: 57m 29.5s
+  Submitted:  1h 41m 5.2s ago
+  Build time: 33m 20.1s
 
-❯ checking CRAN incoming feasibility ... [7s/26s] NOTE
+❯ checking CRAN incoming feasibility ... [7s/25s] NOTE
   Maintainer: ‘Patrice Lecharpentier <patrice.lecharpentier@inrae.fr>’
 
   New submission
@@ -39,12 +39,12 @@
 
 ── SticsRFiles 1.1.3: NOTE
 
-  Build ID:   SticsRFiles_1.1.3.tar.gz-16096564b3744da893ed5ebd16c3c81f
+  Build ID:   SticsRFiles_1.1.3.tar.gz-c83b92714ee64a8b967a641231cec721
   Platform:   Fedora Linux, R-devel, clang, gfortran
-  Submitted:  1h 9m 54.9s ago
-  Build time: 54m 54.4s
+  Submitted:  1h 41m 5.2s ago
+  Build time: 31m 6.5s
 
-❯ checking CRAN incoming feasibility ... [9s/33s] NOTE
+❯ checking CRAN incoming feasibility ... [8s/29s] NOTE
   Maintainer: ‘Patrice Lecharpentier <patrice.lecharpentier@inrae.fr>’
 
   New submission
@@ -53,9 +53,3 @@
   Skipping checking HTML validation: no command 'tidy' found
 
 0 errors ✔ | 0 warnings ✔ | 2 notes ✖
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diff --git a/man/gen_ini_xml.Rd b/man/gen_ini_xml.Rd
diff --git a/man/gen_obs.Rd b/man/gen_obs.Rd
diff --git a/man/gen_sols_xml.Rd b/man/gen_sols_xml.Rd
diff --git a/man/gen_sta_xml.Rd b/man/gen_sta_xml.Rd
diff --git a/man/gen_tec_xml.Rd b/man/gen_tec_xml.Rd
diff --git a/man/gen_usms_xml.Rd b/man/gen_usms_xml.Rd
diff --git a/man/get_climate_txt.Rd b/man/get_climate_txt.Rd
diff --git a/man/get_param_txt.Rd b/man/get_param_txt.Rd
diff --git a/man/set_param_txt.Rd b/man/set_param_txt.Rd