Merge branch '4-import-initial-conditions-from-a-result-to-a-new-scenario-variant' into 'main'

Resolve "Import initial conditions from a result to a new scenario/variant"

Closes #4

See merge request !2

DESCRIPTION

@@ -19,4 +19,5 @@ Depends:
 RoxygenNote: 7.1.1
 Roxygen: list(markdown = TRUE)
 Imports: 
+    logger,
     terra

NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
+export(convert_sic_params)
 export(loadConfig)
+export(set_initial_conditions)
 export(sic_run_fortran)

R/convert_sic_params.R

+#' Convert a list of parameters into command line arguments
+#'
+#' @param params a [list] of [character] containing the parameters to send to the fortran program with format `list(param=value, ...)`
+#' @template param_cfg
+#'
+#' @return A [character] with each parameter is converted to `[key param]=[value param]` and each parameter separated by a space character.
+#' @export
+#'
+#' @examples
+#' convert_sic_param(list(SCE = 1, VAR = 1))
+#'
+convert_sic_params <- function(params, cfg = loadConfig()) {
+  if (!"INTERF" %in% names(params)) {
+    params <- c(list(INTERF = cfg$sic$fortran$prms$INTERF), params)
+  }
+  params <- sapply(names(params), function(key) {
+    paste(key, params[[key]], sep= "=")
+  })
+  paste(params, collapse = " ")
+}

R/set_initial_conditions.R

+#' Import initial conditions
+#'
+#' Import initial conditions from a scenario/variant result calculation to a new scenario/variant.
+#'
+#' @param params [numeric], arguments passed to Edisic for importing initial conditions. See details
+#' @template param_cfg
+#'
+#' @details `params` [numeric] vector of length 5. Each number correspond to:
+#'
+#' 1. number of the scenario from which import initial conditions
+#' 1. number of the variant from which import initial conditions (Use "0" for no variant)
+#' 1. Time in seconds of the initial conditions to import (Use "0" for a single permanent simulation with no time steps)
+#' 1. number of the scenario where the initial conditions are exported to
+#' 1. number of the variant where the initial conditions are exported to  (Use "0" for no variant)
+#'
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' # Import initial conditions from the scenario #1 without variant at time 0s
+#' # to the variant #1 in the scenario #1
+#' set_initial_conditions(c(1, 0, 0, 1, 1))
+#' }
+set_initial_conditions <- function(params, cfg = loadConfig()) {
+  if (!is.numeric(params) || length(params) != 5) {
+    stop("`params` should be a numeric of length 5")
+  }
+  sArgs <- paste(params, collapse = " ")
+  cmd_line <- shQuote(
+    paste(
+      file.path(cfg$sic$path, cfg$sic$edisic),
+      shQuote(dirname(cfg$project$path), type = "cmd"),
+      "CI",
+      shQuote(basename(cfg$project$path), type = "cmd"),
+      sArgs
+    ),
+    type = "cmd2"
+  )
+  logger::log_debug(cmd_line)
+  shell(
+    cmd_line,
+    wait = T,
+    translate = T
+  )
+}

R/sic_run_fortran.R

@@ -2,7 +2,7 @@
 #'
 #' @param prog [character], the program to run. Should be one of "talweg"
 #' @param params [list] or [character], see details
-#' @param cfg
+#' @template param_cfg
 #'
 #' @details If argument `params` is a [list], arguments are injected in the command line by taking the items of the list with the conversion
 #' `[key]=[value]`. If argument `params` is a [character]
@@ -18,14 +18,17 @@
 #'}
 sic_run_fortran <- function(prog, params, cfg = loadConfig()) {
   if (is.list(params)) params <- convert_sic_params(params, cfg)
+  cmd_line <- shQuote(
+    paste(
+      file.path(cfg$sic$path, cfg$sic[[prog]]),
+      shQuote(cfg$project$path, type = "cmd"),
+      params
+    ),
+    type = "cmd2"
+  )
+  logger::log_debug(cmd_line)
   shell(
-    shQuote(
-      paste(
-        file.path(cfg$sic$path, cfg$sic[[prog]]),
-        shQuote(cfg$project$path, type = "cmd"),
-        params
-      ),
-      type = "cmd2"),
+    cmd_line,
     wait = T,
     translate = T
   )

man-roxygen/param_cfg.R

+#' @param cfg a [config] object. Configuration to use. See [loadConfig] for details

man/convert_sic_params.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/convert_sic_params.R
+\name{convert_sic_params}
+\alias{convert_sic_params}
+\title{Convert a list of parameters into command line arguments}
+\usage{
+convert_sic_params(params, cfg = loadConfig())
+}
+\arguments{
+\item{params}{a \link{list} of \link{character} containing the parameters to send to the fortran program with format \code{list(param=value, ...)}}
+
+\item{cfg}{a \link{config} object. Configuration to use. See \link{loadConfig} for details}
+}
+\value{
+A \link{character} with each parameter is converted to \verb{[key param]=[value param]} and each parameter separated by a space character.
+}
+\description{
+Convert a list of parameters into command line arguments
+}
+\examples{
+convert_sic_param(list(SCE = 1, VAR = 1))
+
+}

man/set_initial_conditions.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/set_initial_conditions.R
+\name{set_initial_conditions}
+\alias{set_initial_conditions}
+\title{Import initial conditions}
+\usage{
+set_initial_conditions(params, cfg = loadConfig())
+}
+\arguments{
+\item{params}{\link{numeric}, arguments passed to Edisic for importing initial conditions. See details}
+
+\item{cfg}{a \link{config} object. Configuration to use. See \link{loadConfig} for details}
+}
+\description{
+Import initial conditions from a scenario/variant result calculation to a new scenario/variant.
+}
+\details{
+\code{params} \link{numeric} vector of length 5. Each number correspond to:
+\enumerate{
+\item number of the scenario from which import initial conditions
+\item number of the variant from which import initial conditions (Use "0" for no variant)
+\item Time in seconds of the initial conditions to import (Use "0" for a single permanent simulation with no time steps)
+\item number of the scenario where the initial conditions are exported to
+\item number of the variant where the initial conditions are exported to  (Use "0" for no variant)
+}
+}
+\examples{
+\dontrun{
+# Import initial conditions from the scenario #1 without variant at time 0s
+# to the variant #1 in the scenario #1
+set_initial_conditions(c(1, 0, 0, 1, 1))
+}
+}

man/sic_run_fortran.Rd

@@ -11,7 +11,7 @@ sic_run_fortran(prog, params, cfg = loadConfig())
 
 \item{params}{\link{list} or \link{character}, see details}
 
-\item{cfg}{}
+\item{cfg}{a \link{config} object. Configuration to use. See \link{loadConfig} for details}
 }
 \value{
 

tests/testthat/helper-sic_local_config.R

 # Set local configuration for SIC tests
-
-xml_path <- tempfile("sic_project", fileext = ".xml")
-file.copy(system.file("sic_project_test1.xml", package = "rsic2"),
-          xml_path,
-          overwrite = TRUE)
-cfg <- loadConfig(xml_path = xml_path)
+loadLocalConfig <- function() {
+  xml_path <- tempfile("sic_project", fileext = ".xml")
+  file.copy(system.file("sic_project_test1.xml", package = "rsic2"),
+            xml_path,
+            overwrite = TRUE)
+  loadConfig(xml_path = xml_path)
+}

tests/testthat/test-set_initial_conditions.R

+skip_on_ci()
+
+test_that("set_initial_conditions works", {
+  cfg <- loadLocalConfig()
+  sic_run_fortran("fluvia", list(SCE = 1), cfg = cfg)
+  set_initial_conditions(c(1, 0, 0, 1, 1), cfg = cfg)
+  sic_run_fortran("sirene", list(SCE = 1, VAR = 1), cfg = cfg)
+  expect_true(file.exists(gsub("\\.xml", "_1_1.res", cfg$project$path)))
+})

tests/testthat/test-sic_run_fortran.R

+skip_on_ci()
+
 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)))