Merge pull request #85 from orichters/smallfix

allow to read empty mif files, but warn; read IIASA xlsx snapshots

.buildlibrary

@@ -1,8 +1,10 @@
-ValidationKey: '618891372'
+ValidationKey: '619755850'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'
-AcceptedNotes: Imports includes .* non-default packages.
+AcceptedNotes:
+- Imports includes .* non-default packages.
+- checking installed package size
 AutocreateReadme: yes
 allowLinterWarnings: yes
 enforceVersionUpdate: no

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: 'quitte: Bits and pieces of code to use with quitte-style data frames'
-version: 0.3128.4
-date-released: '2024-03-01'
+version: 0.3128.5
+date-released: '2024-03-28'
 abstract: A collection of functions for easily dealing with quitte-style data frames,
   doing multi-model comparisons and plots.
 authors:

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: quitte
 Title: Bits and pieces of code to use with quitte-style data frames
-Version: 0.3128.4
-Date: 2024-03-01
+Version: 0.3128.5
+Date: 2024-03-28
 Authors@R: c(
     person("Michaja", "Pehl", , "[email protected]", role = c("aut", "cre")),
     person("Nico", "Bauer", , "[email protected]", role = "aut"),

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(as.quitte,"NULL")
 S3method(as.quitte,character)
 S3method(as.quitte,data.frame)
 S3method(as.quitte,list)

R/as.quitte.R

@@ -17,10 +17,11 @@
 #' @param na.rm if set to TRUE entries with value NA will be removed
 #' @author Jan Philipp Dietrich
 #' @keywords classes
-#' @importFrom dplyr bind_rows relocate
+#' @importFrom dplyr bind_rows filter relocate
 #' @importFrom forcats fct_na_value_to_level
 #' @importFrom magclass clean_magpie getNames getNames<- getSets getSets<-
 #' @importFrom reshape2 melt
+#' @importFrom rlang .data
 #' @importFrom stats setNames
 #' @importFrom tibble as_tibble
 #'
@@ -238,6 +239,12 @@ as.quitte.list <- function(x, periodClass = "integer", addNA = FALSE, na.rm = FA
     return(bind_rows(lapply(x, as.quitte, periodClass = periodClass, addNA = addNA, na.rm = na.rm)))
 }
 
+#' @method as.quitte NULL
+#' @export
+as.quitte.NULL <- function(x, periodClass = "integer", addNA = FALSE, na.rm = FALSE) { # nolint
+    return(filter(as_tibble(as.quitte(data.frame(value = 0), periodClass = periodClass)), .data$value > 1))
+}
+
 qaddNA <- function(x) {
   for (col in colnames(x)) {
     if (is.factor(x[[col]]))

R/read.quitte.R

@@ -103,6 +103,10 @@ read.quitte <- function(file,
 
         if (grepl("\\.xlsx?$", f)) {
             data <- read_excel(path = f, sheet = if ('data' %in% excel_sheets(f)) 'data' else 1, guess_max = 21474836)
+            if (! any(grepl("^[0-9]{4}$", colnames(data)))) {
+                warning("File ", f, " contains no data, returning empty data.frame.")
+                return(as.quitte(NULL))
+            }
             data <- pivot_longer(data, matches("^[0-9]{4}$"), names_to = 'period', values_drop_na = drop.na)
             missing.default.columns <- default.columns[! default.columns %in% tolower(colnames(data))]
             if (length(missing.default.columns) > 0) {
@@ -130,7 +134,9 @@ read.quitte <- function(file,
                  paste(setdiff(default.columns, header[1:5]), collapse = ", "))
 
         if (length(period.columns) == 0) {
-            stop("No column name found that could be understood as a 4-digit year in file ", f, ".")
+            warning("No column name found that could be understood as a 4-digit year in file ", f,
+                    ". Returning empty data.frame.")
+            return(as.quitte(NULL))
         }
 
         if (last(period.columns) != length(header))

R/read.snapshot.R

@@ -33,9 +33,11 @@ read.snapshot <- function(file, keep = list(), filter.function = NULL) {
   joinelements <- function(v, list) return(setNames(list(unique(unname(unlist(list[names(list) == v])))), v))
   keep <- do.call(c, lapply(unique(names(keep)), joinelements, list = keep))
 
+  if (! file.exists(file)) stop("file '", file, "' not found.")
+
   # temporary file
-  tmpfile <- tempfile(pattern = "data", fileext = ".csv")
-  if (length(setdiff(names(keep), "period")) > 0) {
+  tmpfile <- tempfile(pattern = "data", fileext = gsub("^.*\\.", ".", basename(file)))
+  if (length(setdiff(names(keep), "period")) > 0 && ! grepl("\\.xlsx?$", file)) {
     # check whether system commands are supported
     testcommand <- c("grep", "head", "tail")
     notavailable <- Sys.which(testcommand) == ""

R/write.mif.R

@@ -1,7 +1,7 @@
 #' Write .mif file
 #'
-#' A wrapper around [`readr::write_lines] for writing files conforming to the
-#' [`.mif` standard](https://redmine.pik-potsdam.de/projects/mo/wiki/Model_Intercomparison_File_Format_(mif)).
+#' A wrapper around [`readr::write_lines`] for writing files conforming to the
+#' [`.mif` standard](https://gitlab.pik-potsdam.de/rse/rsewiki/-/wikis/Model-Intercomparison-File-Format-(mif)).
 #'
 #' @md
 #' @param x A [`quitte`] data frame.

README.md

@@ -1,6 +1,6 @@
 # Bits and pieces of code to use with quitte-style data frames
 
-R package **quitte**, version **0.3128.4**
+R package **quitte**, version **0.3128.5**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/quitte)](https://cran.r-project.org/package=quitte)  [![R build status](https://github.com/pik-piam/quitte/workflows/check/badge.svg)](https://github.com/pik-piam/quitte/actions) [![codecov](https://codecov.io/gh/pik-piam/quitte/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/quitte) [![r-universe](https://pik-piam.r-universe.dev/badges/quitte)](https://pik-piam.r-universe.dev/builds)
 
@@ -47,7 +47,7 @@ In case of questions / problems please contact Michaja Pehl <michaja.pehl@pik-po
 
 To cite package **quitte** in publications use:
 
-Pehl M, Bauer N, Hilaire J, Levesque A, Luderer G, Schultes A, Dietrich J, Richters O (2024). _quitte: Bits and pieces of code to use with quitte-style data frames_. R package version 0.3128.4, <URL: https://github.com/pik-piam/quitte>.
+Pehl M, Bauer N, Hilaire J, Levesque A, Luderer G, Schultes A, Dietrich J, Richters O (2024). _quitte: Bits and pieces of code to use with quitte-style data frames_. R package version 0.3128.5, <URL: https://github.com/pik-piam/quitte>.
 
 A BibTeX entry for LaTeX users is
 
@@ -56,7 +56,7 @@ A BibTeX entry for LaTeX users is
   title = {quitte: Bits and pieces of code to use with quitte-style data frames},
   author = {Michaja Pehl and Nico Bauer and Jérôme Hilaire and Antoine Levesque and Gunnar Luderer and Anselm Schultes and Jan Philipp Dietrich and Oliver Richters},
   year = {2024},
-  note = {R package version 0.3128.4},
+  note = {R package version 0.3128.5},
   url = {https://github.com/pik-piam/quitte},
 }
 ```