fix tests

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '63234546'
+ValidationKey: '63330315'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'
@@ -7,3 +7,4 @@ AutocreateReadme: yes
 allowLinterWarnings: no
 enforceVersionUpdate: no
 skipCoverage: no
+AutocreateCITATION: yes

.pre-commit-config.yaml

@@ -3,7 +3,7 @@
 exclude: '^tests/testthat/_snaps/.*$'
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: 2c9f875913ee60ca25ce70243dc24d5b6415598c  # frozen: v4.6.0
+    rev: cef0300fd0fc4d2a87a85fa2093c6b283ea36f4b  # frozen: v5.0.0
     hooks:
     -   id: check-case-conflict
     -   id: check-json
@@ -15,7 +15,7 @@ repos:
     -   id: mixed-line-ending
 
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: bae853d82da476eee0e0a57960ee6b741a3b3fb7  # frozen: v0.4.3
+    rev: 3b70240796cdccbe1474b0176560281aaded97e6  # frozen: v0.4.3.9003
     hooks:
     -   id: parsable-R
     -   id: deps-in-desc

CITATION.cff

@@ -2,8 +2,8 @@ cff-version: 1.2.0
 message: If you use this software, please cite it using the metadata from this file.
 type: software
 title: 'madrat: May All Data be Reproducible and Transparent (MADRaT) *'
-version: 3.15.4
-date-released: '2024-11-22'
+version: 3.15.5
+date-released: '2024-12-16'
 abstract: Provides a framework which should improve reproducibility and transparency
   in data processing. It provides functionality such as automatic meta data creation
   and management, rudimentary quality management, data caching, work-flow management

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: madrat
 Title: May All Data be Reproducible and Transparent (MADRaT) *
-Version: 3.15.4
-Date: 2024-11-22
+Version: 3.15.5
+Date: 2024-12-16
 Authors@R: c(
     person("Jan Philipp", "Dietrich", , "[email protected]", role = c("aut", "cre"),
            comment = c(affiliation = "Potsdam Institute for Climate Impact Research", ORCID = "0000-0002-4309-6431")),

R/prepFunctionName.R

@@ -1,11 +1,10 @@
 #' prepFunctionName
-#' 
+#'
 #' Function to prepare a function call for a given type and prefix
-#' 
-#' 
+#'
 #' @aliases prepFunctionName
 #' @param type name of calculation/source
-#' @param prefix Type of calculations. Available options are "download" (source download), 
+#' @param prefix Type of calculations. Available options are "download" (source download),
 #' "read" (source read), "correct" (source corrections), "convert" (source conversion to ISO countries),
 #' "calc" (further calculations), and "full" (collections of calculations)
 #' @param ignore vector of arguments which should be ignored (not be part of the function call)
@@ -14,72 +13,78 @@
 #' @author Jan Philipp Dietrich
 #' @seealso \code{\link{readSource}}, \code{\link{setConfig}}
 #' @examples
-#' 
-#' print(madrat:::prepFunctionName("Tau","read"))
-#' print(madrat:::prepFunctionName("TauTotal","calc"))
-#' print(madrat:::prepFunctionName("EXAMPLE","full"))
+#'
+#' print(madrat:::prepFunctionName("Tau", "read"))
+#' print(madrat:::prepFunctionName("TauTotal", "calc"))
+#' print(madrat:::prepFunctionName("EXAMPLE", "full"))
 #' @importFrom utils tail
 
-prepFunctionName <- function(type, prefix="calc", ignore=NULL, error_on_missing=TRUE) {
+prepFunctionName <- function(type, prefix = "calc", ignore = NULL,
+                             error_on_missing = TRUE) { # nolint: object_name_linter.
   getCalc <- getCalculations(prefix = prefix)
-  if(!(type %in% getCalc$type)) {
-    if(error_on_missing) {
-      stop("Type \"",type, "\" is not a valid output type. Check getCalculations(\"",prefix,"\") for available types!")
+  if (!(type %in% getCalc$type)) {
+    if (error_on_missing) {
+      stop("Type \"", type, "\" is not a valid output type. Check getCalculations(\"",
+           prefix, "\") for available types!")
     } else {
       return(NULL)
     }
   }
   # creates functionname and checks that all arguments
   # expected by the function are actually beeing provided
-  name <- getCalc$call[getCalc$type==type]
-  package <- getCalc$package[getCalc$type==type]
-  if(length(name)>1) {
-    name <- as.character(tail(name,1))
-    package <- as.character(tail(package,1))
-    warning("More than one function found for type \"",type,"\" and prefix \"",prefix,"\". Use last occurrence (package \"",package,"\")")
-    if(package==".GlobalEnv" & type %in% c("TauTotal","Tau")) {
-      stop("Cannot substitute package internal function for type \"",type,"\" and prefix \"",prefix,"\" with function in global environment. Please use other function name instead!")  
-    } 
+  name <- getCalc$call[getCalc$type == type]
+  package <- getCalc$package[getCalc$type == type]
+  if (length(name) > 1) {
+    name <- as.character(tail(name, 1))
+    package <- as.character(tail(package, 1))
+    warning("More than one function found for type \"", type, "\" and prefix \"", prefix,
+            "\". Use last occurrence (package \"", package, "\")")
+    if (package == ".GlobalEnv" && type %in% c("TauTotal", "Tau")) {
+      stop("Cannot substitute package internal function for type \"", type, "\" and prefix \"",
+           prefix, "\" with function in global environment. Please use other function name instead!")
+    }
   }
-  
+
   # extract arguments which agree between the given function and its corresponding wrapper function
   # (because they have to be mentioned specifically in the function call)
-  
-  wrapper <- list(calc     = "calcOutput", 
+
+  wrapper <- list(calc     = "calcOutput",
                   download = "downloadSource",
-                  read     = "readSource", 
+                  read     = "readSource",
                   correct  = "readSource",
                   convert  = "readSource",
                   full     = "retrieveData")
-  
-  if(prefix %in% c("convert", "correct")) {
+
+  if (prefix %in% c("convert", "correct")) {
     add <- "x"
-  } else{
+  } else {
     add <- NULL
   }
-  
+
   fformals <- names(formals(eval(parse(text = name))))
-  wformals <- c(add,names(formals(as.character(wrapper[prefix]))))
+  wformals <- c(add, names(formals(as.character(wrapper[prefix]))))
   formals <- intersect(wformals, fformals)
   fcomplete <- all(fformals %in% formals)
-  formals <- setdiff(formals,"...")
-  
-  if(!fcomplete & !("..." %in% wformals)) {
+  formals <- setdiff(formals, "...")
+
+  if (!fcomplete && !("..." %in% wformals)) {
     warning("Some arguments of function \"", name, "\" cannot be adressed by the wrapper (\"",
-            paste0(fformals[!(fformals %in% formals)], collapse = "\", \""),"\")!")
+            paste0(fformals[!(fformals %in% formals)], collapse = "\", \""), "\")!")
   }
-
-  formals <- setdiff(formals,ignore)
-  args <- paste(formals,formals,sep="=")
-  if("..." %in% wformals & !fcomplete) args <- c(args,"...")
-  out <- paste0(name,'(',paste(args,collapse=", "),')')
-
-  attr(out,"formals") <- formals
-  attr(out,"package") <- package
-  if(package==".GlobalEnv") {
-    attr(out,"pkgcomment") <- ".GlobalEnv"
+
+  formals <- setdiff(formals, ignore)
+  args <- paste(formals, formals, sep = "=")
+  if ("..." %in% wformals && !fcomplete) {
+    args <- c(args, "...")
+  }
+  out <- paste0(name, "(", paste(args, collapse = ", "), ")")
+
+  attr(out, "formals") <- formals
+  attr(out, "package") <- package
+  if (package == ".GlobalEnv") {
+    attr(out, "pkgcomment") <- ".GlobalEnv"
   } else {
-    attr(out,"pkgcomment") <- paste(package, unname(getNamespaceVersion(package)))
+    attr(out, "pkgcomment") <- paste(package, unname(getNamespaceVersion(package)))
   }
   return(out)
 }

R/putMadratMessage.R

@@ -39,6 +39,6 @@ putMadratMessage <- function(name, value, fname = -1, add = FALSE) {
     for (n in name) {
       madratMessage[[name]][[fname]] <- if (add) c(madratMessage[[name]][[fname]], value) else value
     }
-    options(madratMessage = madratMessage) # nolint: undesirable_function_linter
+    options(madratMessage = madratMessage) # nolint: undesirable_function_linter.
   }
 }

R/readSource.R

@@ -49,7 +49,7 @@
 #' }
 #'
 #' @export
-readSource <- function(type, subtype = NULL, subset = NULL, # nolint: cyclocomp_linter
+readSource <- function(type, subtype = NULL, subset = NULL, # nolint: cyclocomp_linter.
                        convert = TRUE, supplementary = FALSE) {
   argumentValues <- as.list(environment())  # capture arguments for logging
 

R/resetMadratMessages.R

@@ -34,5 +34,5 @@ resetMadratMessages <- function(name = NULL, fname = NULL) {
     madratMessage[[name]][[fname]] <- NULL
   }
   if (length(madratMessage) == 0) madratMessage <- NULL
-  options(madratMessage = madratMessage) # nolint: undesirable_function_linter
+  options(madratMessage = madratMessage) # nolint: undesirable_function_linter.
 }

R/robustOrder.R

@@ -15,7 +15,7 @@
 #' @seealso \code{\link[base]{order}}
 #' @author Pascal Sauer
 robustOrder <- function(...,
-                        na.last = TRUE, # nolint: object_name_linter
+                        na.last = TRUE, # nolint: object_name_linter.
                         decreasing = FALSE, method = "radix") {
   args <- list(...)
   if (any(lapply(args, length) == 0)) {

R/visualizeDependencies.R

@@ -20,7 +20,7 @@
 #' @export
 
 
-visualizeDependencies <- function(..., direction = "both", order = 2, filter = NULL, # nolint: cyclocomp_linter
+visualizeDependencies <- function(..., direction = "both", order = 2, filter = NULL, # nolint: cyclocomp_linter.
                                   packages = getConfig("packages"), filename = NULL) {
   # check for required packages
   if (!requireNamespace("graphics", quietly = TRUE)) {

README.md

@@ -1,6 +1,6 @@
 # May All Data be Reproducible and Transparent (MADRaT) *
 
-R package **madrat**, version **3.15.4**
+R package **madrat**, version **3.15.5**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/madrat)](https://cran.r-project.org/package=madrat) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1115490.svg)](https://doi.org/10.5281/zenodo.1115490) [![R build status](https://github.com/pik-piam/madrat/workflows/check/badge.svg)](https://github.com/pik-piam/madrat/actions) [![codecov](https://codecov.io/gh/pik-piam/madrat/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/madrat) [![r-universe](https://pik-piam.r-universe.dev/badges/madrat)](https://pik-piam.r-universe.dev/builds)
 
@@ -55,17 +55,18 @@ In case of questions / problems please contact Jan Philipp Dietrich <dietrich@pi
 
 To cite package **madrat** in publications use:
 
-Dietrich J, Baumstark L, Wirth S, Giannousakis A, Rodrigues R, Bodirsky B, Leip D, Kreidenweis U, Klein D, Sauer P (2024). _madrat: May All Data be Reproducible and Transparent (MADRaT)_. doi:10.5281/zenodo.1115490 <https://doi.org/10.5281/zenodo.1115490>, R package version 3.15.4, <https://github.com/pik-piam/madrat>.
+Dietrich J, Baumstark L, Wirth S, Giannousakis A, Rodrigues R, Bodirsky B, Leip D, Kreidenweis U, Klein D, Sauer P (2024). "madrat: May All Data be Reproducible and Transparent (MADRaT) *." doi:10.5281/zenodo.1115490 <https://doi.org/10.5281/zenodo.1115490>, Version: 3.15.5, <https://github.com/pik-piam/madrat>.
 
 A BibTeX entry for LaTeX users is
 
  ```latex
-@Manual{,
-  title = {madrat: May All Data be Reproducible and Transparent (MADRaT)},
+@Misc{,
+  title = {madrat: May All Data be Reproducible and Transparent (MADRaT) *},
   author = {Jan Philipp Dietrich and Lavinia Baumstark and Stephen Wirth and Anastasis Giannousakis and Renato Rodrigues and Benjamin Leon Bodirsky and Debbora Leip and Ulrich Kreidenweis and David Klein and Pascal Sauer},
+  doi = {10.5281/zenodo.1115490},
+  date = {2024-12-16},
   year = {2024},
-  note = {R package version 3.15.4},
   url = {https://github.com/pik-piam/madrat},
-  doi = {10.5281/zenodo.1115490},
+  note = {Version: 3.15.5},
 }
 ```

tests/testthat/test-toolCountryFill.R

@@ -2,7 +2,7 @@ test_that("toolCountryFill works as expected", {
   x <- new.magpie("DEU", 1994, "bla", 0)
   expect_message(y <- toolCountryFill(x, 99), "toolCountryFill set missing values for IMPORTANT")
   expect_equal(dim(y)[1], 249)
-  expect_true(y["DEU", , ] == 0)
+  expect_true(all(y["DEU", , ] == 0))
   expect_true(all(y["DEU", , , invert = TRUE] == 99))
 
   x2 <- new.magpie(c("DEU", "XYZ"), 1994, "bla", 0)
@@ -19,9 +19,9 @@ test_that("toolCountryFill works as expected", {
 
   x3 <- new.magpie(c("DEU", "FRA"), 1994, "bla", 0)
   x3["FRA", , ] <- 42
-  expect_true(toolCountryFill(x3, 99, FRA = "DEU")["FRA", , ] == 42)
+  expect_true(all(toolCountryFill(x3, 99, FRA = "DEU")["FRA", , ] == 42))
   expect_message(y5 <- toolCountryFill(x3, 99, FRA = "DEU", overwrite = TRUE), "data overwritten")
-  expect_true(y5["FRA", , ] == 0)
+  expect_true(all(y5["FRA", , ] == 0))
 
   empty <- new.magpie(NULL, NULL, c("bla"))
   expect_silent(y6 <- toolCountryFill(empty, verbosity = 3))