added option to write units in netCDF files based on comment argument

.buildlibrary

@@ -1,8 +1,7 @@
-ValidationKey: '11447946'
+ValidationKey: '11489376'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'
 AcceptedNotes: unable to verify current time
 AutocreateReadme: yes
-UseGithubActions: yes
 allowLinterWarnings: yes

.github/workflows/lucode2-check.yaml

@@ -0,0 +1,79 @@
+# Run CI for R using https://eddelbuettel.github.io/r-ci/
+
+name: lucode2-check
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+env:
+  USE_BSPM: "true"
+  _R_CHECK_FORCE_SUGGESTS_: "false"
+  NO_BINARY_INSTALL_R_PACKAGES: 'c("madrat", "magclass", "citation", "gms", "goxygen")'
+
+jobs:
+  lucode2-check:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Bootstrap
+        run: |
+          curl -OLs https://eddelbuettel.github.io/r-ci/run.sh
+          chmod 0755 run.sh
+          ./run.sh bootstrap
+
+      - name: Enable r-universe repo, modify bspm integration
+        run: |
+          # install packages from https://pik-piam.r-universe.dev and CRAN
+          echo '
+          options(repos = c(universe = "https://pik-piam.r-universe.dev",
+                            CRAN = "https://cloud.r-project.org"))
+          ' >> .Rprofile
+          cat .Rprofile
+          # modify bspm integration to never install binary builds of PIK CRAN packages
+          sudo sed -i '/bspm::enable()/d' /etc/R/Rprofile.site
+          # need double % because of printf, %s is replaced with "$NO_BINARY_INSTALL_R_PACKAGES" (see "env:" above)
+          printf '
+          local({
+            expr <- quote({
+              if (!is.null(repos)) {
+                noBinaryInstallRPackages <- %s
+                pkgs <- c(bspm::install_sys(pkgs[!pkgs %%in%% noBinaryInstallRPackages]),
+                          pkgs[pkgs %%in%% noBinaryInstallRPackages])
+              }
+            })
+            trace(utils::install.packages, expr, print = FALSE)
+          })
+          ' "$NO_BINARY_INSTALL_R_PACKAGES" | sudo tee --append /etc/R/Rprofile.site >/dev/null
+          cat /etc/R/Rprofile.site
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Install dependencies
+        run: |
+          ./run.sh install_aptget libhdf5-dev
+          ./run.sh install_all
+          ./run.sh install_r lucode2 covr
+
+      - name: Remove bspm integration # to get rid of error when running install.packages
+        run: |
+          sudo sed -i '/  trace(utils::install.packages, expr, print = FALSE)/d' /etc/R/Rprofile.site
+          cat /etc/R/Rprofile.site
+
+      - name: Verify validation key
+        shell: Rscript {0}
+        run: lucode2:::validkey(stopIfInvalid = TRUE)
+
+      - name: Checks
+        shell: Rscript {0}
+        run: |
+          options(crayon.enabled = TRUE)
+          lucode2::check(runLinter = FALSE)
+
+      - name: Test coverage
+        shell: Rscript {0}
+        run: covr::codecov(quiet = FALSE)

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "magclass: Data Class and Tools for Handling Spatial-Temporal Data",
-  "version": "6.0.6",
+  "version": "6.0.8",
   "description": "<p>Data class for increased interoperability working with spatial-\n    temporal data together with corresponding functions and methods (conversions,\n    basic calculations and basic data manipulation). The class distinguishes\n    between spatial, temporal and other dimensions to facilitate the development\n    and interoperability of tools build for it. Additional features are name-based\n    addressing of data and internal consistency checks (e.g. checking for the right\n    data order in calculations).<\/p>",
   "creators": [
     {

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: magclass
 Type: Package
 Title: Data Class and Tools for Handling Spatial-Temporal Data
-Version: 6.0.6
-Date: 2021-09-21
+Version: 6.0.8
+Date: 2021-09-27
 Authors@R: c(person("Jan Philipp", "Dietrich", email = "[email protected]", role = c("aut","cre")),
              person("Benjamin Leon", "Bodirsky", email = "[email protected]", role = "aut"),
              person("Markus", "Bonsch", role = "aut"),
@@ -51,5 +51,5 @@ BugReports: https://github.com/pik-piam/magclass/issues
 License: LGPL-3 | file LICENSE
 LazyData: true
 Encoding: UTF-8
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 VignetteBuilder: knitr

R/write.magpie.R

@@ -80,7 +80,7 @@
 #' [ sets | Set names with \\n as delimiter | character | 1*nchar_sets Byte] \cr
 #' [ metadata | serialized metadata information (currently not in use) | bytes | 1*nbyte_metadata Byte] \cr
 #'
-#' @author Jan Philipp Dietrich, Stephen Bi
+#' @author Jan Philipp Dietrich, Stephen Bi, Florian Humpenoeder
 #' @seealso \code{"\linkS4class{magpie}"},
 #' \code{\link{read.magpie}},\code{\link{mbind}}
 #' @examples
@@ -197,15 +197,26 @@ write.magpie <- function(x, file_name, file_folder = "", file_type = NULL, appen
       varnames <- getItems(x, dim = 3)
       zunit <- ifelse(all(isYear(getYears(x))), "years", "")
       if (is.null(varnames)) varnames <- "Variable"
+      if (is.null(comment)) {
+       unit <- "not specified"
+      } else {
+        indicators <- substring(text = comment, first = 1, last = regexpr(pattern = ": ", text = comment) - 1)
+        units <- substring(text = comment, first = (regexpr(pattern = ": ", text = comment) + 2))
+        if (!any(indicators == "unit")) {
+          unit <- "not specified"
+        } else {
+          unit <- units[which(indicators == "unit")]
+        }
+      }
       raster::writeRaster(.sub(rx, varnames[1]), filename = filePath, format = "CDF", overwrite = TRUE,
-                          compression = 9, zname = "Time", zunit = zunit, varname = varnames[1], ...)
+                          compression = 9, zname = "Time", zunit = zunit, varname = varnames[1], varunit = unit, ...)
       nc <- ncdf4::nc_open(filePath, write = TRUE)
       if (zunit == "years") {
         ncdf4::ncvar_put(nc, "Time", getYears(x, as.integer = TRUE))
       }
       if (length(varnames) > 1) {
         for (i in varnames[-1]) {
-          nc <- ncdf4::ncvar_add(nc, ncdf4::ncvar_def(i, "", nc$dim, compression = 9))
+          nc <- ncdf4::ncvar_add(nc, ncdf4::ncvar_def(i, unit, nc$dim, compression = 9))
           ncdf4::ncvar_put(nc, i, aperm(as.array(.sub(rx, i)), c(2, 1, 3)))
         }
       }

README.md

@@ -1,8 +1,8 @@
 # Data Class and Tools for Handling Spatial-Temporal Data
 
-R package **magclass**, version **6.0.6**
+R package **magclass**, version **6.0.8**
 
-[![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://codecov.io/gh/pik-piam/magclass) [![r-universe](https://pik-piam.r-universe.dev/badges/magclass)](https://pik-piam.r-universe.dev/ui#builds)
+[![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://codecov.io/gh/pik-piam/magclass) [![r-universe](https://pik-piam.r-universe.dev/badges/magclass)](https://pik-piam.r-universe.dev/ui#builds)
 
 ## Purpose and Functionality
 
@@ -55,7 +55,7 @@ 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 (2021). _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 6.0.6, <URL: https://github.com/pik-piam/magclass>.
+Dietrich J, Bodirsky B, Bonsch M, Humpenoeder F, Bi S, Karstens K, Leip D (2021). _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 6.0.8, <URL: https://github.com/pik-piam/magclass>.
 
 A BibTeX entry for LaTeX users is
 
@@ -64,7 +64,7 @@ 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 = {2021},
-  note = {R package version 6.0.6},
+  note = {R package version 6.0.8},
   doi = {10.5281/zenodo.1158580},
   url = {https://github.com/pik-piam/magclass},
 }