reordered arguments in "[" and "[<-" methods to make it compatible wi…

…th most recent R develop

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '13476573'
+ValidationKey: '119151300'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

.pre-commit-config.yaml

@@ -15,7 +15,7 @@ repos:
     -   id: mixed-line-ending
 
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.3.2.9007
+    rev: v0.3.2.9013
     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: 'magclass: Data Class and Tools for Handling Spatial-Temporal Data'
-version: 6.9.1
-date-released: '2023-05-26'
+version: 6.10.0
+date-released: '2023-06-25'
 abstract: Data class for increased interoperability working with spatial-temporal
   data together with corresponding functions and methods (conversions, basic calculations
   and basic data manipulation). The class distinguishes between spatial, temporal

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: magclass
 Title: Data Class and Tools for Handling Spatial-Temporal Data
-Version: 6.9.1
-Date: 2023-05-26
+Version: 6.10.0
+Date: 2023-06-25
 Authors@R: c(
     person("Jan Philipp", "Dietrich", , "[email protected]", role = c("aut", "cre")),
     person("Benjamin Leon", "Bodirsky", , "[email protected]", role = "aut"),

Makefile

@@ -11,8 +11,9 @@ HELP_PARSING = 'm <- readLines("Makefile");\
 help:           ## Show this help.
 	@Rscript -e $(HELP_PARSING)
 
-build:          ## Build the package using lucode2::buildLibrary().
-	Rscript -e 'lucode2::buildLibrary()'
+build:          ## Build the package using lucode2::buildLibrary(). You can pass the
+                ## updateType with 'make build u=3'
+	Rscript -e 'lucode2::buildLibrary(updateType = "$(u)")'
 
 check:          ## Build documentation and vignettes, run testthat tests,
                 ## and check if code etiquette is followed using lucode2::check().

R/magpie-class.R

@@ -117,7 +117,7 @@
 
 setClass("magpie", contains = "array", prototype = array(0, c(0, 0, 0)))
 
-.mselectDF <- function(x, df) { #nolint
+.mselectDF <- function(x, df) { # nolint
   if (is.null(names(dimnames(x)))) stop("Dimnames must have names in order to use mselect!")
 
   dims <- dimCode(names(df), x)
@@ -139,9 +139,9 @@ setClass("magpie", contains = "array", prototype = array(0, c(0, 0, 0)))
     " Mixtures across main dimensions are not allowed!")
 
   sdims <- as.integer(substring(dims, 3))
-  maxdim <- nchar(gsub("[^\\.]", "", names(dimnames(x))[maindim])) + 1 #nolint
+  maxdim <- nchar(gsub("[^\\.]", "", names(dimnames(x))[maindim])) + 1 # nolint
   if (nrow(df) == 1) df[1, ] <- escapeRegex(df[1, ])
-  if (nrow(df) > 1) df <- data.frame(sapply(df, escapeRegex)) #nolint
+  if (nrow(df) > 1) df <- data.frame(sapply(df, escapeRegex)) # nolint
   dmissing <- which(!(1:maxdim %in% sdims))
   sdims <- c(sdims, dmissing)
   for (d in dmissing) df <- cbind(df, "[^\\.]*")
@@ -191,7 +191,7 @@ setClass("magpie", contains = "array", prototype = array(0, c(0, 0, 0)))
   return(x)
 }
 
-.dimextract <- function(x, i, dim, pmatch = FALSE, invert = FALSE) { #nolint
+.dimextract <- function(x, i, dim, pmatch = FALSE, invert = FALSE) { # nolint
 
   if (is.magpie(i) && is.logical(i)) {
     # check whether input is a 1D magpie object
@@ -270,9 +270,12 @@ setClass("magpie", contains = "array", prototype = array(0, c(0, 0, 0)))
 }
 
 #' @exportMethod [
-setMethod("[", #nolint
+setMethod("[", # nolint
   signature(x = "magpie"),
-  function(x, i, j, k, drop = FALSE, pmatch = FALSE, invert = FALSE, dim = NULL) {
+  function(x, i, j, k, ..., pmatch = FALSE, invert = FALSE, dim = NULL, drop = FALSE) {
+    if (length(list(...)) > 0) {
+      stop("unknown argument(s) supplied!")
+    }
     if (!is.null(dim)) {
       if (!is.element(dim, 1:3)) stop("Invalid dim selection (allowed: 1, 2 or 3)")
       if (!missing(j) || (!missing(k) && !is.null(k) && k != FALSE)) {
@@ -302,14 +305,7 @@ setMethod("[", #nolint
       j <- .dimextract(x, j, 2, pmatch = pmatch, invert = invert)
     }
     if (!missing(k)) k <- .dimextract(x, k, 3, pmatch = pmatch, invert = invert)
-
-    if (!missing(i) && missing(j) && !missing(k) && .isFALSE(k) &&
-      .isFALSE(drop) && .isFALSE(pmatch) && .isFALSE(invert)) {
-      # there is a weird case in which k is actually missing but is getting the
-      # value of the next argument in line (drop)
-      # this one is catched via .isFALSE(k)
-      # in addition non-default settings for drop, pmatch and invert indicate that object should still be
-      # returned as magpie object (and not as numeric as the following line will do)
+    if (length(sys.call(-1)) == 3) {
       return(x@.Data[i])
     }
     if (!missing(k) && .isFALSE(k)) {
@@ -324,17 +320,17 @@ setMethod("[", #nolint
 )
 
 #' @exportMethod [<-
-setMethod("[<-", #nolint
+setMethod("[<-", # nolint
   signature(x = "magpie"),
-  function(x, i, j, k, value, pmatch = FALSE, dim = NULL) {
+  function(x, i, j, k, ..., pmatch = FALSE, dim = NULL, value) {
+    if (length(list(...)) > 0) {
+      stop("unknown argument(s) supplied!")
+    }
     if (!is.null(dim)) {
       if (!is.element(dim, 1:3)) stop("Invalid dim selection (allowed: 1, 2 or 3)")
       if (!missing(j) || (!missing(k) && !missing(value))) {
         stop("Only single dimension selection allowed when dim is set!")
       }
-      if (missing(value) && !missing(k)) {
-        value <- k
-      }
       if (dim == 1) {
         x[i, , , pmatch = pmatch] <- value
       } else if (dim == 2) {
@@ -365,26 +361,25 @@ setMethod("[<-", #nolint
       if (is.factor(k)) k <- as.character(k)
       if (is.character(k) || is.list(k)) k <- .dimextract(x, k, 3, pmatch = pmatch)
     }
-    if (missing(value)) {
-      x@.Data[i] <- k
-      return(x)
-    } else {
-      if (is.magpie(value)) {
-        if (missing(i)) ii <- seq_len(dim(x)[1]) else ii <- i
-        if (missing(j)) jj <- seq_len(dim(x)[2]) else jj <- j
-        if (missing(k)) kk <- seq_len(dim(x)[3]) else kk <- k
-        value <- magpie_expand(value, x[ii, jj, kk])
-      } else if (length(value) != length(x@.Data[i, j, k]) & length(value) != 1) {
-        # dangerous writing of value as order might be wrong!
-        stop("Replacement does not work! Different replacement length!")
-      } else if (length(value) != 1 && !is.null(getOption("magclass.verbosity")) &&
-                 getOption("magclass.verbosity") > 1) {
-        message("NOTE ([<-): Dangerous replacement! As replacement value is not",
-          " an MAgPIE object name checking is deactivated!\n")
-      }
-      x@.Data[i, j, k] <- value
+    if (length(sys.call(which = -1)) == 4) {
+      x@.Data[i] <- value
       return(x)
     }
+    if (is.magpie(value)) {
+      if (missing(i)) ii <- seq_len(dim(x)[1]) else ii <- i
+      if (missing(j)) jj <- seq_len(dim(x)[2]) else jj <- j
+      if (missing(k)) kk <- seq_len(dim(x)[3]) else kk <- k
+      value <- magpie_expand(value, x[ii, jj, kk])
+    } else if (length(value) != length(x@.Data[i, j, k]) & length(value) != 1) {
+      # dangerous writing of value as order might be wrong!
+      stop("Replacement does not work! Different replacement length!")
+    } else if (length(value) != 1 && !is.null(getOption("magclass.verbosity")) &&
+               getOption("magclass.verbosity") > 1) {
+      message("NOTE ([<-): Dangerous replacement! As replacement value is not",
+        " an MAgPIE object name checking is deactivated!\n")
+    }
+    x@.Data[i, j, k] <- value
+    return(x)
   }
 )
 

README.md

@@ -1,6 +1,6 @@
 # Data Class and Tools for Handling Spatial-Temporal Data
 
-R package **magclass**, version **6.9.1**
+R package **magclass**, version **6.10.0**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/magclass)](https://cran.r-project.org/package=magclass) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1158580.svg)](https://doi.org/10.5281/zenodo.1158580) [![R build status](https://github.com/pik-piam/magclass/workflows/check/badge.svg)](https://github.com/pik-piam/magclass/actions) [![codecov](https://codecov.io/gh/pik-piam/magclass/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/magclass) [![r-universe](https://pik-piam.r-universe.dev/badges/magclass)](https://pik-piam.r-universe.dev/builds)
 
@@ -56,7 +56,7 @@ In case of questions / problems please contact Jan Philipp Dietrich <dietrich@pi
 
 To cite package **magclass** in publications use:
 
-Dietrich J, Bodirsky B, Bonsch M, Humpenoeder F, Bi S, Karstens K, Leip D (2023). _magclass: Data Class and Tools for Handling Spatial-Temporal Data_. doi:10.5281/zenodo.1158580 <https://doi.org/10.5281/zenodo.1158580>, R package version 6.9.1, <https://github.com/pik-piam/magclass>.
+Dietrich J, Bodirsky B, Bonsch M, Humpenoeder F, Bi S, Karstens K, Leip D (2023). _magclass: Data Class and Tools for Handling Spatial-Temporal Data_. doi: 10.5281/zenodo.1158580 (URL: https://doi.org/10.5281/zenodo.1158580), R package version 6.10.0, <URL: https://github.com/pik-piam/magclass>.
 
 A BibTeX entry for LaTeX users is
 
@@ -65,7 +65,7 @@ A BibTeX entry for LaTeX users is
   title = {magclass: Data Class and Tools for Handling Spatial-Temporal Data},
   author = {Jan Philipp Dietrich and Benjamin Leon Bodirsky and Markus Bonsch and Florian Humpenoeder and Stephen Bi and Kristine Karstens and Debbora Leip},
   year = {2023},
-  note = {R package version 6.9.1},
+  note = {R package version 6.10.0},
   doi = {10.5281/zenodo.1158580},
   url = {https://github.com/pik-piam/magclass},
 }

tests/testthat/test-magpie.R

@@ -65,13 +65,16 @@ test_that("boolean subsetting works", {
 })
 
 test_that("error detection works", {
+  expect_error(p[, , , ], "argument is missing, with no default")
+  expect_error(p[, , , blub = 42], "unknown argument\\(s\\) supplied")
+  expect_error(p[, , , blub = 42] <- 42, "unknown argument\\(s\\) supplied")
   expect_error(p[, , "A3"], "out of bounds")
   expect_error(p[, , list("A3")], "out of bounds")
   expect_error(p[, , list(scenario = "A3")], "out of bounds")
   expect_error(p[, , list(blub = "A2")], "subdimension does not exist")
 
   names(dimnames(p)) <- NULL
-  expect_error(p[, , list(scenario = "A2")], "subdimension does not exist \\(missing set names\\)") #nolint
+  expect_error(p[, , list(scenario = "A2")], "subdimension does not exist \\(missing set names\\)") # nolint
 
   dimnames(p)[[3]] <- NULL
   expect_error(p[, , "A2"], "Missing element names")
@@ -152,11 +155,11 @@ test_that("data.frame subsetting works", {
   expect_identical(getItems(a[df[3:2][w, ]], 3), getItems(a, 3)[w])
 
   # Unknown dimensions to be added in output!
-  df$blub <- paste0("bl", 1:dim(df)[1])
+  df$blub <- paste0("bl", seq_len(dim(df)[1]))
   expect_identical(getItems(a[df[w, ]], 3), paste(getItems(a, 3), df$blub, sep = ".")[w])
 
   df2 <- df
-  df2$ble <- paste0("ble", 1:dim(df2)[1])
+  df2$ble <- paste0("ble", seq_len(dim(df2)[1]))
   expect_identical(getItems(a[df2[w, ]], 3), paste(getItems(a, 3), df2$blub, df2$ble, sep = ".")[w])
 
   # subselections work