Release/devel v6.0.3 (#242)

* This version produces the same output as the previous version.
* Update `SOILWAT2` to v7.2.0 which improves error handling and fixes memory leaks on error (close #239; @dschlaep, @N1ckP3rsl3y).
* Code no longer requires (unused) `pcg` header (@dschlaep).

.gitignore

@@ -51,3 +51,5 @@ doc
 vignettes/*.pdf
 vignettes/*.html
 vignettes/*.log
+/doc/
+/Meta/

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rSOILWAT2
-Version: 6.0.2
+Version: 6.0.3
 Title: An Ecohydrological Ecosystem-Scale Water Balance Simulation Model
-Description: Access to the C-based SOILWAT2 v7.1.0 and functionality for
+Description: Access to the C-based SOILWAT2 v7.2.0 and functionality for
   SQLite-database of weather data.
 Authors@R: c(
   person(

NEWS.md

@@ -1,9 +1,18 @@
+# rSOILWAT2 v6.0.3
+* This version produces the same output as the previous version.
+* Update `SOILWAT2` to v7.2.0 which improves error handling and fixes
+  memory leaks on error (#239; @dschlaep, @N1ckP3rsl3y).
+* Code no longer requires (unused) `pcg` header (@dschlaep).
+
+
 # rSOILWAT2 v6.0.2
 * This version produces the same output as the previous version.
 * Update `SOILWAT2` to v7.1.0 which prepares for thread-safety and reentrancy
+  (@N1ckP3rsl3y, @dschlaep).
 * C-side of `rSOILWAT2` gains new globals of the four main abstract types in
   `SOILWAT2` - SW_ALL, SW_OUTPUT_POINTERS, LOG_INFO, and PATH_INFO -
-  to interact with `SOILWAT2`.
+  to interact with `SOILWAT2`(@N1ckP3rsl3y, @dschlaep).
+
 
 # rSOILWAT2 v6.0.1
 

R/Rsw.R

@@ -44,7 +44,7 @@ sw_args <- function(dir, files.in, echo, quiet) {
 #'
 #' @export
 sw_verbosity <- function(verbose = TRUE) {
-  invisible(!.Call(C_sw_quiet, !as.logical(verbose)))
+  invisible(.Call(C_sw_verbose, as.logical(verbose)))
 }
 
 
@@ -243,6 +243,8 @@ sw_exec <- function(
   on.exit(setwd(dir_prev), add = TRUE)
 
   quiet <- as.logical(quiet)
+  prev_verbosity <- sw_verbosity(!quiet)
+  on.exit(sw_verbosity(prev_verbosity), add = TRUE)
 
   input <- sw_args(dir, files.in, echo, quiet)
 
@@ -310,7 +312,7 @@ sw_exec <- function(
 
 
   # Run SOILWAT2
-  res <- .Call(C_start, input, inputData, weatherList, quiet)
+  res <- .Call(C_sw_start, input, inputData, weatherList)
 
   slot(res, "version") <- rSW2_version()
   slot(res, "timestamp") <- rSW2_timestamp()
@@ -380,30 +382,12 @@ sw_inputDataFromFiles <- function(
   on.exit(setwd(dir_prev), add = TRUE)
 
   quiet <- as.logical(quiet)
+  prev_verbosity <- sw_verbosity(!quiet)
+  on.exit(sw_verbosity(prev_verbosity), add = TRUE)
 
   input <- sw_args(dir, files.in, echo = FALSE, quiet = quiet)
 
-  res <- .Call(C_onGetInputDataFromFiles, input, quiet)
-
-  slot(res, "version") <- rSW2_version()
-  slot(res, "timestamp") <- rSW2_timestamp()
-
-  res
-}
-
-
-#' Return output data
-#'
-#' @inheritParams sw_exec
-#'
-#' @return An object of class \code{\linkS4class{swOutput}}.
-#' @export
-sw_outputData <- function(inputData) {
-
-  dir_prev <- getwd()
-  on.exit(setwd(dir_prev), add = TRUE)
-
-  res <- .Call(C_onGetOutput, inputData)
+  res <- .Call(C_onGetInputDataFromFiles, input)
 
   slot(res, "version") <- rSW2_version()
   slot(res, "timestamp") <- rSW2_timestamp()
@@ -439,9 +423,6 @@ sw_outputData <- function(inputData) {
 #'
 #' @export
 sw_inputData <- function() {
-  dir_prev <- getwd()
-  on.exit(setwd(dir_prev), add = TRUE)
-
   tmp <- swInputData() # default values (minus some deleted slots)
   utils::data(package = "rSOILWAT2", "weatherData", envir = environment())
   slot(tmp, "weatherHistory") <- get("weatherData", envir = environment())
@@ -455,7 +436,7 @@ sw_inputData <- function() {
 #' @return A logical value
 #' @export
 has_soilTemp_failed <- function() {
-  .Call(C_tempError)
+  isTRUE(.Call(C_tempError))
 }
 
 

R/data.R

@@ -39,7 +39,8 @@
 #' utils::data(sw_exampleData)
 #' path_demo <- system.file("extdata", "example1", package = "rSOILWAT2")
 #' x <- sw_inputDataFromFiles(dir = path_demo, files.in = "files.in")
-#' identical(x, sw_exampleData) ## TRUE
+#' ## expect differences in slots "timestamp" and possibly "version"
+#' all.equal(x, sw_exampleData)
 "sw_exampleData"
 
 

R/rSOILWAT2_deprecated.R

@@ -1255,3 +1255,28 @@ readNumerics <- function(text,expectedArgs,showWarnings=FALSE) {
   }
   return(tmp)
 }
+
+
+
+#------ Other deprecated functions ------
+
+
+#' Return output data
+#'
+#' @inheritParams sw_exec
+#'
+#' @return An object of class \code{\linkS4class{swOutput}}.
+#' @export
+sw_outputData <- function(inputData) {
+  .Deprecated("Store return value of `rSOILWAT2::sw_exec()`.")
+
+  dir_prev <- getwd()
+  on.exit(setwd(dir_prev), add = TRUE)
+
+  res <- .Call(C_onGetOutputDeprecated, inputData)
+
+  slot(res, "version") <- rSW2_version()
+  slot(res, "timestamp") <- rSW2_timestamp()
+
+  res
+}

src/Makevars

@@ -1,5 +1,5 @@
 target = SOILWAT2
-lib_target = lib$(target).a
+lib_target = libr$(target).a
 path_target = SOILWAT2
 path_lib = $(path_target)/bin
 sw_sources = src/SW_Output_outarray.c
@@ -21,7 +21,7 @@ $(path_lib)/$(lib_target):
 # Note: `-I..` is required for rSOILWAT2 headers that are included by
 # SOILWAT2 headers (such as `#include "rSW_SoilWater.h"`)
 #	-@(cd $(path_target) && $(MAKE) compiler_version)
-	cd $(path_target) && $(MAKE) lib \
+	cd $(path_target) && $(MAKE) libr \
 		CC="$(CC)" CPPFLAGS="$(ALL_CPPFLAGS) -I.." CFLAGS="$(ALL_CFLAGS)" \
 		AR="$(AR)" sw_sources="$(sw_sources)"
 

src/SW_R_init.c

@@ -5,14 +5,14 @@
 
 
 /* .Call calls */
-extern SEXP start(SEXP, SEXP, SEXP, SEXP);
+extern SEXP sw_start(SEXP, SEXP, SEXP);
 extern SEXP tempError(void);
-extern SEXP onGetInputDataFromFiles(SEXP, SEXP);
-extern SEXP onGetOutput(SEXP);
+extern SEXP onGetInputDataFromFiles(SEXP);
+extern SEXP onGetOutputDeprecated(SEXP);
 extern SEXP rSW2_processAllWeather(SEXP, SEXP);
 extern SEXP rSW2_readAllWeatherFromDisk(SEXP, SEXP, SEXP, SEXP, SEXP);
 extern SEXP sw_consts(void);
-extern SEXP sw_quiet(SEXP);
+extern SEXP sw_verbose(SEXP);
 extern SEXP rSW2_SWRC_PTF_estimate_parameters(SEXP, SEXP, SEXP, SEXP, SEXP);
 extern SEXP sw_check_SWRC_vs_PTF(SEXP, SEXP);
 extern SEXP rSW2_SWRC_check_parameters(SEXP, SEXP);
@@ -23,14 +23,14 @@ extern SEXP rSW2_estimate_PotNatVeg_composition(SEXP, SEXP, SEXP, SEXP,SEXP, SEX
 extern SEXP rSW2_calc_SiteClimate(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
 
 static const R_CallMethodDef CallEntries[] = {
-  {"start",                      (DL_FUNC) &start,                      4},
+  {"sw_start",                   (DL_FUNC) &sw_start,                   3},
   {"tempError",                  (DL_FUNC) &tempError,                  0},
-  {"onGetInputDataFromFiles",    (DL_FUNC) &onGetInputDataFromFiles,    2},
-  {"onGetOutput",                (DL_FUNC) &onGetOutput,                1},
+  {"onGetInputDataFromFiles",    (DL_FUNC) &onGetInputDataFromFiles,    1},
+  {"onGetOutputDeprecated",      (DL_FUNC) &onGetOutputDeprecated,      1},
   {"rSW2_processAllWeather",     (DL_FUNC) &rSW2_processAllWeather,     2},
   {"rSW2_readAllWeatherFromDisk",(DL_FUNC) &rSW2_readAllWeatherFromDisk,5},
   {"sw_consts",                  (DL_FUNC) &sw_consts,                  0},
-  {"sw_quiet",                   (DL_FUNC) &sw_quiet,                   1},
+  {"sw_verbose",                 (DL_FUNC) &sw_verbose,                 1},
   {"rSW2_SWRC_PTF_estimate_parameters", (DL_FUNC) &rSW2_SWRC_PTF_estimate_parameters, 5},
   {"sw_check_SWRC_vs_PTF",       (DL_FUNC) &sw_check_SWRC_vs_PTF,       2},
   {"rSW2_SWRC_check_parameters", (DL_FUNC) &rSW2_SWRC_check_parameters, 2},