Merge branch 'master' of github.com:pik-piam/magclass

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '119866320'
+ValidationKey: '120779572'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

.github/workflows/check.yaml

@@ -23,6 +23,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: |
+            gamstransfer=?ignore
             any::lucode2
             any::covr
             any::madrat
@@ -31,9 +32,9 @@ jobs:
             any::gms
             any::goxygen
             any::GDPuc
-          # explicitly installing all piam packages which are also on
-          # CRAN (madrat, magclass, citation, gms, goxygen, GDPuc) to
-          # get newest version instad of outdated binary version from CRAN
+          # piam packages also available on CRAN (madrat, magclass, citation,
+          # gms, goxygen, GDPuc) will usually have an outdated binary version
+          # available; by using extra-packages we get the newest version
 
       - uses: actions/setup-python@v4
         with:
@@ -56,6 +57,8 @@ jobs:
 
       - name: Test coverage
         shell: Rscript {0}
-        run: covr::codecov(quiet = FALSE)
+        run: |
+          nonDummyTests <- setdiff(list.files("./tests/testthat/"), c("test-dummy.R", "_snaps"))
+          if(length(nonDummyTests) > 0) covr::codecov(quiet = FALSE)
         env:
           NOT_CRAN: "true"

.pre-commit-config.yaml

@@ -3,7 +3,7 @@
 exclude: '^tests/testthat/_snaps/.*$'
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
     -   id: check-case-conflict
     -   id: check-json
@@ -15,7 +15,7 @@ repos:
     -   id: mixed-line-ending
 
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.3.2.9019
+    rev: v0.3.2.9025
     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: 6.12.0
-date-released: '2023-08-17'
+version: 6.12.1
+date-released: '2024-01-10'
 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: 6.12.0
-Date: 2023-08-17
+Version: 6.12.1
+Date: 2024-01-10
 Authors@R: c(
     person("Jan Philipp", "Dietrich", , "[email protected]", role = c("aut", "cre")),
     person("Benjamin Leon", "Bodirsky", , "[email protected]", role = "aut"),

NAMESPACE

@@ -120,11 +120,8 @@ importFrom(methods,setGeneric)
 importFrom(methods,setMethod)
 importFrom(methods,signature)
 importFrom(stats,as.formula)
-importFrom(utils,capture.output)
 importFrom(utils,head)
-importFrom(utils,read.csv)
 importFrom(utils,read.table)
 importFrom(utils,tail)
-importFrom(utils,toBibtex)
 importFrom(utils,type.convert)
 importFrom(utils,write.table)

R/mbind.R

@@ -28,7 +28,7 @@
 
 mbind <- function(...) { #nolint
   inputs <- list(...)
-  if (length(inputs) == 1 & is.list(inputs[[1]])) inputs <- inputs[[1]]
+  if (length(inputs) == 1 && is.list(inputs[[1]])) inputs <- inputs[[1]]
   # Remove NULL elements from list
   for (i in rev(seq_along(inputs))) {
     if (is.null(inputs[[i]])) {
@@ -43,6 +43,9 @@ mbind <- function(...) { #nolint
   if (0 == length(inputs))
     return(NULL)
 
+  # store total number of elements to ensure that they remain unchanged
+  nElems <- sum(vapply(inputs, length, integer(1)))
+
   cells <- NULL
   elems <- NULL
   years <- NULL
@@ -63,19 +66,19 @@ mbind <- function(...) { #nolint
     years <- c(years, getYears(inputs[[i]]))
     elems <- c(elems, getNames(inputs[[i]]))
     cells <- c(cells, getCells(inputs[[i]]))
-    if (!diffspat & ncells(inputs[[1]]) > 1) inputs[[i]] <- inputs[[i]][getCells(inputs[[1]]), , ]
-    if (!difftemp & nyears(inputs[[1]]) > 1) inputs[[i]] <- inputs[[i]][, getYears(inputs[[1]]), ]
-    if (!diffdata &  ndata(inputs[[1]]) > 1) inputs[[i]] <- inputs[[i]][, , getNames(inputs[[1]])]
+    if (!diffspat && ncells(inputs[[1]]) > 1) inputs[[i]] <- inputs[[i]][getCells(inputs[[1]]), , ]
+    if (!difftemp && nyears(inputs[[1]]) > 1) inputs[[i]] <- inputs[[i]][, getYears(inputs[[1]]), ]
+    if (!diffdata &&  ndata(inputs[[1]]) > 1) inputs[[i]] <- inputs[[i]][, , getNames(inputs[[1]])]
   }
 
   if (!(length(grep(".", cells, fixed = TRUE)) %in% c(0, length(cells)))) {
     stop("Mixture of regional (no cell numbers) and cellular (with cell numbers)",
          " data objects! Cannot handle this case!")
   }
 
-  if (diffspat & difftemp) stop("Cannot handle objects! Spatial as well as temporal dimensions differ!")
-  if (difftemp & diffdata) stop("Cannot handle objects! Data as well as temporal dimensions differ!")
-  if (diffdata & diffspat) stop("Cannot handle objects! Data as well as spatial dimensions differ!")
+  if (diffspat && difftemp) stop("Cannot handle objects! Spatial as well as temporal dimensions differ!")
+  if (difftemp && diffdata) stop("Cannot handle objects! Data as well as temporal dimensions differ!")
+  if (diffdata && diffspat) stop("Cannot handle objects! Data as well as spatial dimensions differ!")
   if (difftemp) {
     if (length(years) != length(unique(years))) stop("Some years occur more than once!",
                                                      " Cannot handle this case!")
@@ -98,5 +101,8 @@ mbind <- function(...) { #nolint
   }
   names(dimnames(output)) <- names(dimnames(inputs[[1]]))
 
+  if (length(output) != nElems) {
+    stop("Invalid object (number of values changed during mbind). Does the data contain duplicates?")
+  }
   return(output)
 }

R/write.report.R

@@ -47,6 +47,16 @@ write.report <- function(x, file = NULL, model = NULL, scenario = NULL, unit = N
     }
   } else {
     if (!is.magpie(x)) stop("Input is not a MAgPIE object!")
+
+    if (all(is.na(x)) && isTRUE(skipempty)) {
+      msg <- "magclass object contains only NAs, returning empty data table."
+      if (!is.null(file)) {
+        msg <- paste0(msg, " No file was written.")
+      }
+      message(msg)
+      return(data.table::data.table())
+    }
+
     x <- prepareData(x, model = model, scenario = scenario, unit = unit, skipempty = skipempty,
                      ndigit = ndigit, extracols = extracols)
     if (is.null(file)) return(x)
@@ -82,6 +92,7 @@ write.report <- function(x, file = NULL, model = NULL, scenario = NULL, unit = N
 
 prepareData <- function(x, model = NULL, scenario = NULL, unit = NULL, skipempty = FALSE,
                         ndigit = 4, extracols = NULL) {
+
   sep <- "."
   # clean data
   x <- round(clean_magpie(x, what = "sets"), digits = ndigit)

README.md

@@ -1,6 +1,6 @@
 # Data Class and Tools for Handling Spatial-Temporal Data
 
-R package **magclass**, version **6.12.0**
+R package **magclass**, version **6.12.1**
 
 [![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)
 
@@ -56,17 +56,17 @@ 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 6.12.0, <https://github.com/pik-piam/magclass>.
+Dietrich J, Bodirsky B, Bonsch M, Humpenoeder F, Bi S, Karstens K, Leip D (2024). _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 6.12.1, <https://github.com/pik-piam/magclass>.
 
 A BibTeX entry for LaTeX users is
 
  ```latex
 @Manual{,
   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 6.12.0},
-  doi = {10.5281/zenodo.1158580},
+  year = {2024},
+  note = {R package version 6.12.1},
   url = {https://github.com/pik-piam/magclass},
+  doi = {10.5281/zenodo.1158580},
 }
 ```

tests/testthat/test-mbind.R

@@ -1,7 +1,7 @@
 
 a  <- maxample("animal")
 p  <- maxample("pop")
-attr(p, "Metadata") <- NULL
+attr(p, "Metadata") <- NULL # nolint: object_name_linter
 
 test_that("mbind works", {
   expect_identical(mbind(p, p), p[, , c(1:2, 1:2)])
@@ -19,6 +19,7 @@ test_that("mbind works", {
   expect_error(mbind(p[1:3, 2:4, ], p), "Cannot handle")
   expect_error(mbind(p[, 1:3, 1], p), "Cannot handle")
   expect_error(mbind(p[1:3, , 1], p), "Cannot handle")
+  expect_error(suppressWarnings(mbind(p[, , c(1, 1)])), "Invalid object")
 
   for (i in 1:3) {
     p0 <- p[1, dim = i]

tests/testthat/test-readwritereport.R

@@ -112,3 +112,13 @@ test_that("read/write report works with braces", {
   df <- read.csv(f, sep = ";", stringsAsFactors = FALSE)
   expect_identical(df$Unit, "Mt CO2/yr")
 })
+
+test_that("write report does not crash with only NAs", {
+  f <- tempfile()
+  foo <- new.magpie("DEU", c(2015, 2020),
+                    "Emissions|CO2|Energy|Demand|Transportation (w/ bunkers) (Mt CO2/yr)",
+                    fill = NA)
+  expect_identical(write.report(foo, f), data.table::data.table())
+  expect_message(write.report(foo, f),
+                 "magclass object contains only NAs, returning empty data table. No file was written.")
+})