Merge branch '3-export-simulation-results-and-import-them-into-r' into 'main'

Resolve "Export simulation results and import them into R"

Closes #3

See merge request !3

.gitignore

@@ -48,3 +48,4 @@ vignettes/*.pdf
 /tests/testthat/config.yml
 *.INI
 *.ini
+*.log

NAMESPACE

@@ -3,4 +3,5 @@
 export(convert_sic_params)
 export(loadConfig)
 export(set_initial_conditions)
+export(sic_run_export)
 export(sic_run_fortran)

R/file.pathwin.R

+#' file.path for Windows
+#'
+#' Same behavior as [file.path] but remove duplicated slashes and use backslashes as the path separator.
+#'
+#' @param ... Arguments sent to [file.path]
+#'
+file.pathwin <- function(...) {
+  sPath = file.path(...)
+  sPath = gsub("\\\\","/",sPath) # Remplace les antislashes présents (bug avec la command system)
+  sPath = gsub("//","/",sPath) #Suppression des séparateurs en double
+  sPath = gsub("/","\\\\",sPath) #Remplacement des slashs par des anti-slashes
+  return(sPath)
+}

R/loadConfig.R

 #' Read default configuration of the package and complete it with eventual user config
 #'
+#' @param sic_path [character], the path to an installation of SIC (see details)
+#' @param xml_path [character], the path of the XML project file (see details)
 #' @param userFile location of the user config YML file
 #' @param pathDefaultCfg The location of the default configuration (located in "inst/config.yml" of the package by default)
 #'
+#' @details
+#' The path to SIC and to the XML project file can be defined in the user XML file by defining the appropriate items:
+#'
+#' ```yaml
+#' sic:
+#'   path: Path/To/SIC/installation
+#' project:
+#'   path: Path/To/Xml/Project/File.xml
+#' ```
+#'
+#' Moreover, the `sic_path` can be defined with the environment variable "SICPATH". This setting is a default which is overwritten
+#' by the path defined in the user YAML file, which is also overwritten by the one define by the `sic_path` argument.
+#'
 #' @return A configuration as it is returned by [config::get].
 #'
 #' Configuration of RSIC2 as the following structure:
@@ -30,6 +45,10 @@
 #' str(cfg)
 loadConfig <- function(sic_path = NULL, xml_path = NULL, userFile = "config.yml", pathDefaultCfg = system.file("config.yml", package = "rsic2")) {
     cfg <- config::get(file = pathDefaultCfg)
+    if (Sys.getenv("SICPATH") != "" & is.null(sic_path)) {
+      cfg$sic$path <- Sys.getenv("SICPATH")
+      message("`sic_path` defined by environment variable SICPATH=", cfg$sic$path)
+    }
     if (file.exists(userFile)) {
       message("Reading user configuration from ", userFile)
       cfg = config::merge(cfg,config::get(file = userFile))

R/sic_run_export.R

+#' Run SicExport and read the exported file
+#'
+#' @details
+#' `params` parameter is a list representing parameters available in \url{https://sic.g-eau.fr/sicexport-utilitaire-d-exportation} to set the model network location of exported results. The string parameter `/x=n /yy=ii` in the command line is here represented by `list(xxx = nnn, yy = ii)`.
+#'
+#' @param scenario [numeric], the scenario to read
+#' @param variant [numeric], the variant to read
+#' @param params [list] location parameters of the result, see details.
+#' @template param_cfg
+#'
+#' @return [matrix] with the read result
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' params <- list(SCE=1)
+#' sic_run_fortran("fluvia", params)
+#' # For exporting result in sections at time 0
+#' sic_run_export(scenario = 1, params = list(t = 0))
+#' }
+sic_run_export <- function(scenario, variant = 0, params, cfg = loadConfig()) {
+  if (is.list(params)) params <- unlist(params)
+  params <- paste(paste0("/", names(params)), params, sep = "=", collapse = " ")
+
+  file <- tempfile("sicexport", fileext = ".tsv")
+  cmd_line <-
+    paste(
+      shQuote(file.pathwin(cfg$sic$path, cfg$sic$export), type = "cmd"),
+      shQuote(cfg$project$path, type = "cmd"),
+      paste0("/sce=", scenario),
+      paste0("/var=", variant),
+      params,
+      "/quiet=1",
+      paste0("/out=", shQuote(file, type = "cmd"))
+    )
+  logger::log_debug(cmd_line)
+  shell(
+    shQuote(cmd_line, type = "cmd2"),
+    wait = T,
+    translate = F
+  )
+  as.matrix(read.csv(file, sep = "\t"))
+}

man/file.pathwin.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/file.pathwin.R
+\name{file.pathwin}
+\alias{file.pathwin}
+\title{file.path for Windows}
+\usage{
+file.pathwin(...)
+}
+\arguments{
+\item{...}{Arguments sent to \link{file.path}}
+}
+\description{
+Same behavior as \link{file.path} but remove duplicated slashes and use backslashes as the path separator.
+}

man/loadConfig.Rd

@@ -12,6 +12,10 @@ loadConfig(
 )
 }
 \arguments{
+\item{sic_path}{\link{character}, the path to an installation of SIC (see details)}
+
+\item{xml_path}{\link{character}, the path of the XML project file (see details)}
+
 \item{userFile}{location of the user config YML file}
 
 \item{pathDefaultCfg}{The location of the default configuration (located in "inst/config.yml" of the package by default)}
@@ -46,6 +50,16 @@ Configuration of RSIC2 as the following structure:
 \description{
 Read default configuration of the package and complete it with eventual user config
 }
+\details{
+The path to SIC and to the XML project file can be defined in the user XML file by defining the appropriate items:\if{html}{\out{<div class="yaml">}}\preformatted{sic:
+  path: Path/To/SIC/installation
+project:
+  path: Path/To/Xml/Project/File.xml
+}\if{html}{\out{</div>}}
+
+Moreover, the \code{sic_path} can be defined with the environment variable "SICPATH". This setting is a default which is overwritten
+by the path defined in the user YAML file, which is also overwritten by the one define by the \code{sic_path} argument.
+}
 \examples{
 library(rsic2)
 sic_path <- tempdir(check = TRUE)

man/sic_run_export.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/sic_run_export.R
+\name{sic_run_export}
+\alias{sic_run_export}
+\title{Run SicExport and read the exported file}
+\usage{
+sic_run_export(scenario, variant = 0, params, cfg = loadConfig())
+}
+\arguments{
+\item{scenario}{\link{numeric}, the scenario to read}
+
+\item{variant}{\link{numeric}, the variant to read}
+
+\item{params}{\link{list} location parameters of the result, see details.}
+
+\item{cfg}{a \link{config} object. Configuration to use. See \link{loadConfig} for details}
+}
+\value{
+\link{matrix} with the read result
+}
+\description{
+Run SicExport and read the exported file
+}
+\details{
+\code{params} parameter is a list representing parameters available in \url{https://sic.g-eau.fr/sicexport-utilitaire-d-exportation} to set the model network location of exported results. The string parameter \verb{/x=n /yy=ii} in the command line is here represented by \code{list(xxx = nnn, yy = ii)}.
+}
+\examples{
+\dontrun{
+params <- list(SCE=1)
+sic_run_fortran("fluvia", params)
+# For exporting result in sections at time 0
+sic_run_export(scenario = 1, params = list(t = 0))
+}
+}

man/sic_run_fortran.Rd

@@ -4,7 +4,7 @@
 \alias{sic_run_fortran}
 \title{Run Talweg, Fluvia or Sirene}
 \usage{
-sic_run_fortran(prog, params, cfg = loadConfig())
+sic_run_fortran(prog, params = list(), cfg = loadConfig())
 }
 \arguments{
 \item{prog}{\link{character}, the program to run. Should be one of "talweg"}

tests/testthat/test-sic_run_export.R

+skip_on_ci()
+
+cfg <- loadLocalConfig()
+
+test_that("multiplication works", {
+  sic_run_fortran("fluvia", list(SCE = 1), cfg = cfg)
+  m <- sic_run_export(scenario = 1, params = list(t = 0), cfg = cfg)
+  expect_type(m, "double")
+  expect_equal(colnames(m)[1:3], c("Bief", "Section", "Abscisse"))
+})

tests/testthat/test-sic_run_fortran.R

 skip_on_ci()
 
+cfg <- loadLocalConfig()
+
 test_that("fluvia on SCE=1 should create a binary result file", {
-  cfg <- loadLocalConfig()
   sic_run_fortran("fluvia", list(SCE = 1), cfg = cfg)
   expect_true(file.exists(gsub("\\.xml", "_1_0.res", cfg$project$path)))
   expect_true(file.exists(gsub("\\.xml", "_1_0.rci", cfg$project$path)))