Release v6.1.0 (#245)

* This version produces the same output as the previous version. * `SOILWAT2` updated to v8.0.0 which now includes a simulation domain; however, this has no impact on `rSOILWAT2`. ## New features * SOILWAT2 gained spin-up functionality (@niteflyunicorns, @dschlaep). A user-requested sequence of (random) years is simulated (without output) before the actual simulation run to provide better starting values (e.g., soil moisture, soil temperature).
DrylandEcology · Jul 15, 2024 · f008e89 · f008e89
2 parents 233217a + 14b88c4
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -5,34 +5,29 @@
 ^backup$
 ^data-raw$
 \.git*
-^\.travis\.yml$
-^appveyor\.yml$
-^\.appveyor\.yml$
-^\.appveyor_clear_cache\.txt$
-^codecov\.yml$
 ^\.lintr$
 ^\.github$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^cran-comments\.md$
 ^NEWS\.md$
+^tests/
 tests/rSOILWAT_IntegrationTestOutput
 src/SOILWAT2/\.git
 src/SOILWAT2/\.github
 src/SOILWAT2/doc
 src/SOILWAT2/build
 src/SOILWAT2/external/googletest
 src/SOILWAT2/tests
-src/SOILWAT2/\.travis\.yml
-src/SOILWAT2/appveyor\.yml
 src/SOILWAT2/codecov\.yml
 src/SOILWAT2/Doxyfile
 src/SOILWAT2/README\.md
 src/SOILWAT2/NEWS\.md
 src/SOILWAT2/tools
 src/SOILWAT2/\.LSAN_suppr\.txt
 src/SOILWAT2/src/SW_Main\.c
-src/SOILWAT2/src/SW_Output_mock\.c
+src/SOILWAT2/.clang-format
+src/SOILWAT2/external/.clang-format
 src/*\.o
 src/*\.so
 src/*\.dll

diff --git a/.gitmodules b/.gitmodules
@@ -1,4 +1,4 @@
 [submodule "src/SOILWAT2"]
 	path = src/SOILWAT2
 	url = https://github.com/DrylandEcology/SOILWAT2
-	branch = master
+	branch = master
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: rSOILWAT2
-Version: 6.0.4
+Version: 6.1.0
 Title: An Ecohydrological Ecosystem-Scale Water Balance Simulation Model
-Description: Access to the C-based SOILWAT2 v7.2.0 and functionality for
+Description: Access to the C-based SOILWAT2 v8.0.0 and functionality for
   SQLite-database of weather data.
 Authors@R: c(
   person(
@@ -41,13 +41,13 @@ Remotes:
     github::DrylandEcology/rSW2data,
     github::DrylandEcology/rSW2exter
 NeedsCompilation: yes
-SystemRequirements: GNU make
+SystemRequirements: USE_C11, GNU make
 License: GPL-3
 URL: https://github.com/DrylandEcology/rSOILWAT2
 BugReports: https://github.com/DrylandEcology/rSOILWAT2/issues
 Encoding: UTF-8
 Config/testthat/edition: 3
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 LazyData: true
 Language: en-US
 VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
@@ -109,6 +109,7 @@ export(set_swProd)
 export(set_swSWC)
 export(set_swSite)
 export(set_swSoils)
+export(set_swSpinup)
 export(set_swWeather)
 export(set_swWeatherData)
 export(set_swYears)
@@ -133,6 +134,7 @@ export(swSWC)
 export(swSWC_hist)
 export(swSite)
 export(swSoils)
+export(swSpinup)
 export(swWeather)
 export(swWeatherData)
 export(swYears)
@@ -177,6 +179,7 @@ exportClasses(swSWC)
 exportClasses(swSWC_hist)
 exportClasses(swSite)
 exportClasses(swSoils)
+exportClasses(swSpinup)
 exportClasses(swWeather)
 exportClasses(swWeatherData)
 exportClasses(swYears)
@@ -194,6 +197,7 @@ exportMethods("set_swProd<-")
 exportMethods("set_swSWC<-")
 exportMethods("set_swSite<-")
 exportMethods("set_swSoils<-")
+exportMethods("set_swSpinup<-")
 exportMethods("set_swWeather<-")
 exportMethods("set_swWeatherData<-")
 exportMethods("set_swYears<-")
@@ -272,6 +276,11 @@ exportMethods("swSite_TranspirationRegions<-")
 exportMethods("swSite_hasSWRCp<-")
 exportMethods("swSoils_Layers<-")
 exportMethods("swSoils_SWRCp<-")
+exportMethods("swSpinup_SpinupActive<-")
+exportMethods("swSpinup_SpinupDuration<-")
+exportMethods("swSpinup_SpinupMode<-")
+exportMethods("swSpinup_SpinupScope<-")
+exportMethods("swSpinup_SpinupSeed<-")
 exportMethods("swWeather_DaysRunningAverage<-")
 exportMethods("swWeather_FirstYearHistorical<-")
 exportMethods("swWeather_MonScalingParams<-")
@@ -297,6 +306,7 @@ exportMethods(get_swProd)
 exportMethods(get_swSWC)
 exportMethods(get_swSite)
 exportMethods(get_swSoils)
+exportMethods(get_swSpinup)
 exportMethods(get_swWeather)
 exportMethods(get_swWeatherData)
 exportMethods(get_swYears)
@@ -374,6 +384,11 @@ exportMethods(swSite_TranspirationRegions)
 exportMethods(swSite_hasSWRCp)
 exportMethods(swSoils_Layers)
 exportMethods(swSoils_SWRCp)
+exportMethods(swSpinup_SpinupActive)
+exportMethods(swSpinup_SpinupDuration)
+exportMethods(swSpinup_SpinupMode)
+exportMethods(swSpinup_SpinupScope)
+exportMethods(swSpinup_SpinupSeed)
 exportMethods(swWeather_DaysRunningAverage)
 exportMethods(swWeather_FirstYearHistorical)
 exportMethods(swWeather_MonScalingParams)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,15 @@
+# rSOILWAT2 v6.1.0-9000
+* This version produces the same output as the previous version.
+* `SOILWAT2` updated to v8.0.0 which now includes a simulation domain;
+  however, this has no impact on `rSOILWAT2`.
+
+## New features
+* SOILWAT2 gained spin-up functionality (@niteflyunicorns, @dschlaep).
+  A user-requested sequence of (random) years is simulated (without output)
+  before the actual simulation run to provide better starting values
+  (e.g., soil moisture, soil temperature).
+
+
 # rSOILWAT2 v6.0.4
 * This version produces the same output as the previous version.
 

diff --git a/R/A_swGenericMethods.R b/R/A_swGenericMethods.R
@@ -62,7 +62,7 @@ setMethod(
     tmp <- try(inherits(object, "numeric_version"), silent = TRUE)
     if (inherits(tmp, "try-error") || !isTRUE(tmp)) {
       tmp <- try(object@version, silent = TRUE)
-      if (inherits(tmp, "try-error")) {
+      if (length(tmp) == 0L || inherits(tmp, "try-error")) {
         NA_character_
       } else {
         as.character(as.numeric_version(tmp))
@@ -105,7 +105,7 @@ check_version <- function(
 ) {
   has <- get_version(object)
 
-  if (is.na(has) || is.na(expected_version)) {
+  if (length(has) == 0L || is.na(has) || is.na(expected_version)) {
     FALSE
 
   } else {
@@ -208,6 +208,10 @@ format_timestamp <- function(object) {
 #'
 #' @section Details:
 #' List of changes:
+#'   * Changes with `v6.1.0`:
+#'       * class [`swInputData-class`]:
+#'         new slot `"spinup"` of new class [`swSpinup-class`]
+#'       * class [`swFiles-class`]: new total of 27 input files
 #'   * Changes with `v6.0.0`:
 #'       * class [`swSite-class`]:
 #'         new slots `"swrc_flags"`, `"has_swrcp"`, and
@@ -747,6 +751,134 @@ setGeneric(
 )
 ########################
 
+#########DOMAIN#########
+#' \code{get_swSpinup}
+#' @param object An object of class \code{\linkS4class{swSpinup}} or
+#'   \code{\linkS4class{swInputData}}.
+#' @seealso \code{\linkS4class{swSpinup}} and \code{\linkS4class{swInputData}}
+setGeneric(
+  "get_swSpinup",
+  function(object) standardGeneric("get_swSpinup")
+)
+
+#' \code{swSpinup_SpinupMode}
+#' @param object An object of class \code{\linkS4class{swSpinup}} or
+#'   \code{\linkS4class{swInputData}}.
+#' @seealso \code{\linkS4class{swSpinup}} and \code{\linkS4class{swInputData}}
+setGeneric(
+  "swSpinup_SpinupActive",
+  function(object) standardGeneric("swSpinup_SpinupActive")
+)
+
+#' \code{swSpinup_SpinupMode}
+#' @param object An object of class \code{\linkS4class{swSpinup}} or
+#'   \code{\linkS4class{swInputData}}.
+#' @seealso \code{\linkS4class{swSpinup}} and \code{\linkS4class{swInputData}}
+setGeneric(
+  "swSpinup_SpinupMode",
+  function(object) standardGeneric("swSpinup_SpinupMode")
+)
+
+#' \code{swSpinup_SpinupScope}
+#' @param object An object of class \code{\linkS4class{swSpinup}} or
+#'   \code{\linkS4class{swInputData}}.
+#' @seealso \code{\linkS4class{swSpinup}} and \code{\linkS4class{swInputData}}
+setGeneric(
+  "swSpinup_SpinupScope",
+  function(object) standardGeneric("swSpinup_SpinupScope")
+)
+
+#' \code{swSpinup_SpinupDuration}
+#' @param object An object of class \code{\linkS4class{swSpinup}} or
+#'   \code{\linkS4class{swInputData}}.
+#' @seealso \code{\linkS4class{swSpinup}} and \code{\linkS4class{swInputData}}
+setGeneric(
+  "swSpinup_SpinupDuration",
+  function(object) standardGeneric("swSpinup_SpinupDuration")
+)
+
+#' \code{swSpinup_SpinupSeed}
+#' @param object An object of class \code{\linkS4class{swSpinup}} or
+#'   \code{\linkS4class{swInputData}}.
+#' @seealso \code{\linkS4class{swSpinup}} and \code{\linkS4class{swInputData}}
+setGeneric(
+  "swSpinup_SpinupSeed",
+  function(object) standardGeneric("swSpinup_SpinupSeed")
+)
+
+# Need to define and export this generic method -- otherwise,
+# \code{\link{set_swSpinup<-}} doesn't work.
+#' \code{set_swSpinup}
+#'
+#' @param object An object of class \code{\linkS4class{swSpinup}} or
+#'   \code{\linkS4class{swInputData}}.
+#' @param value A value to assign to a specific slot of the \code{object}.
+#'
+#' @export
+setGeneric(
+  "set_swSpinup",
+  function(object, value) standardGeneric("set_swSpinup")
+)
+
+#' \code{set_swSpinup<-}
+#' @inheritParams set_swSpinup
+#' @seealso \code{\linkS4class{swSpinup}} and \code{\linkS4class{swInputData}}
+setGeneric(
+  "set_swSpinup<-",
+  function(object, value) standardGeneric("set_swSpinup<-")
+)
+
+#' \code{swSpinup_SpinupActive<-}
+#' @param object An object of class \code{\linkS4class{swSpinup}} or
+#'   \code{\linkS4class{swInputData}}.
+#' @param value A value to assign to a specific slot of the \code{object}.
+#' @seealso \code{\linkS4class{swSpinup}} and \code{\linkS4class{swInputData}}
+setGeneric(
+  "swSpinup_SpinupActive<-",
+  function(object, value) standardGeneric("swSpinup_SpinupActive<-")
+)
+
+#' \code{swSpinup_SpinupMode<-}
+#' @param object An object of class \code{\linkS4class{swSpinup}} or
+#'   \code{\linkS4class{swInputData}}.
+#' @param value A value to assign to a specific slot of the \code{object}.
+#' @seealso \code{\linkS4class{swSpinup}} and \code{\linkS4class{swInputData}}
+setGeneric(
+  "swSpinup_SpinupMode<-",
+  function(object, value) standardGeneric("swSpinup_SpinupMode<-")
+)
+
+#' \code{swSpinup_SpinupScope<-}
+#' @param object An object of class \code{\linkS4class{swSpinup}} or
+#'   \code{\linkS4class{swInputData}}.
+#' @param value A value to assign to a specific slot of the \code{object}.
+#' @seealso \code{\linkS4class{swSpinup}} and \code{\linkS4class{swInputData}}
+setGeneric(
+  "swSpinup_SpinupScope<-",
+  function(object, value) standardGeneric("swSpinup_SpinupScope<-")
+)
+
+#' \code{swSpinup_SpinupDuration<-}
+#' @param object An object of class \code{\linkS4class{swSpinup}} or
+#'   \code{\linkS4class{swInputData}}.
+#' @param value A value to assign to a specific slot of the \code{object}.
+#' @seealso \code{\linkS4class{swSpinup}} and \code{\linkS4class{swInputData}}
+setGeneric(
+  "swSpinup_SpinupDuration<-",
+  function(object, value) standardGeneric("swSpinup_SpinupDuration<-")
+)
+
+#' \code{swSpinup_SpinupSeed<-}
+#' @param object An object of class \code{\linkS4class{swSpinup}} or
+#'   \code{\linkS4class{swInputData}}.
+#' @param value A value to assign to a specific slot of the \code{object}.
+#' @seealso \code{\linkS4class{swSpinup}} and \code{\linkS4class{swInputData}}
+setGeneric(
+  "swSpinup_SpinupSeed<-",
+  function(object, value) standardGeneric("swSpinup_SpinupSeed<-")
+)
+########################
+
 ########WEATHER#########
 #' \code{get_swWeather}
 #' @param object An object of class \code{\linkS4class{swWeather}} or