Fix AgMIP reporting

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '5824112'
+ValidationKey: '5863988'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

.github/workflows/check.yaml

@@ -1,5 +1,3 @@
-# Run CI for R using https://eddelbuettel.github.io/r-ci/
-
 name: check
 
 on:
@@ -8,92 +6,44 @@ on:
   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", "GDPuc", "roxygen2")'
-
 jobs:
   check:
     runs-on: ubuntu-latest
 
     steps:
       - uses: actions/checkout@v3
 
-      - name: Bootstrap
-        run: |
-          sudo chown runner -R .
-          sudo locale-gen en_US.UTF-8
-          sudo add-apt-repository -y ppa:ubuntugis/ppa
-          curl -OLs https://eddelbuettel.github.io/r-ci/run.sh
-          chmod 0755 run.sh
-          ./run.sh bootstrap
-          rm -f bspm_*.tar.gz
-
-      - 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 "$NO_BINARY_INSTALL_R_PACKAGES" (see "env:" above)
-          printf '
-          local({
-            expr <- quote({
-              if (!is.null(repos)) {
-                noBinaryInstallRPackages <- %s
-                pkgs <- c(bspm::install_sys(pkgs[!pkgs %%in%% noBinaryInstallRPackages]),
-                          pkgs[pkgs %%in%% noBinaryInstallRPackages])
-              }
-              type <- "source"
-            })
-            trace(utils::install.packages, expr, print = FALSE)
-          })
-          ' "$NO_BINARY_INSTALL_R_PACKAGES" | sudo tee --append /etc/R/Rprofile.site >/dev/null
-          cat /etc/R/Rprofile.site
-
-      - name: Set up Pandoc
-        uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v4
+      - uses: r-lib/actions/setup-r@v2
         with:
-          python-version: 3.9
+          use-public-rspm: true
+          extra-repositories: "https://rse.pik-potsdam.de/r/packages"
 
-      - name: Cache R libraries
-        if: ${{ !env.ACT }} # skip when running locally via nektos/act
-        uses: pat-s/always-upload-cache@v3
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: /usr/local/lib/R/
-          key: 3-${{ runner.os }}-usr-local-lib-R-${{ hashFiles('DESCRIPTION') }}
-          restore-keys: |
-            3-${{ runner.os }}-usr-local-lib-R-
-
-      - name: Restore R library permissions
-        run: |
-          sudo chmod 2777 /usr/local/lib/R /usr/local/lib/R/site-library
-
-      - name: Install dependencies
-        run: |
-          ./run.sh install_aptget libhdf5-dev libharfbuzz-dev libfribidi-dev
-          ./run.sh install_all
-          ./run.sh install_r_binary covr rstudioapi
-          ./run.sh install_r lucode2
+          extra-packages: |
+            any::lucode2
+            any::covr
+            any::madrat
+            any::magclass
+            any::citation
+            any::gms
+            any::goxygen
+            any::GDPuc
+          # 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:
+          python-version: 3.9
 
       - name: Install python dependencies if applicable
         run: |
           [ -f requirements.txt ] && python -m pip install --upgrade pip wheel || true
           [ -f requirements.txt ] && pip install -r requirements.txt || true
 
-      - 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)

.pre-commit-config.yaml

@@ -15,7 +15,7 @@ repos:
     -   id: mixed-line-ending
 
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.3.2.9013
+    rev: v0.3.2.9019
     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: 'iamc: IAMC Tools'
-version: 0.29.8
-date-released: '2023-07-06'
+version: 0.29.9
+date-released: '2023-09-12'
 abstract: A collection of R tools provided by the Integrated Assessment Modeling Consortium
   (IAMC) for data analysis and diagnostics.
 authors:

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: iamc
 Type: Package
 Title: IAMC Tools
-Version: 0.29.8
-Date: 2023-07-06
+Version: 0.29.9
+Date: 2023-09-12
 Authors@R: c(person("Jan Philipp", "Dietrich", email = "[email protected]", role = c("aut","cre")),
              person("Cornelia", "Auer", role = "aut"),
              person("Anastasis", "Giannousakis", role = "aut"),

R/write.reportProject.R

@@ -51,8 +51,9 @@
 
 write.reportProject <- function(mif, mapping,
                                 file=NULL, max_file_size=NULL,
-                                format="default", append=FALSE, missing_log=NULL, ...){
-  if(is.character(mif)){
+                                format="default", append=FALSE, missing_log=NULL, ...) {
+
+  if (is.character(mif)) {
     data <- read.report(mif,as.list=TRUE)
   } else if (is.list(mif)){
     data <- mif
@@ -75,10 +76,11 @@ write.reportProject <- function(mif, mapping,
   }
 
   ### Here the actual magic takes place
-  new_data = RenameAndAggregate(data=data,mapping=mapping,missing_log=missing_log)
+  new_data <- RenameAndAggregate(data = data, mapping = mapping, missing_log = missing_log)
 
   ### write the outputs
   if(!is.null(file)){
+
     # save project reporting
     if(!file.exists(file)) append <- FALSE
     if(format == "default") {
@@ -99,16 +101,33 @@ write.reportProject <- function(mif, mapping,
 
       } else
         write.report(new_data,file=file,append=append,...)
+
     } else if (format == "IAMC") {
+
       a <- write.report(new_data,file=NULL,...)
       a <- do.call(rbind,do.call(rbind,a))
       write.table(a,file,quote=FALSE,sep=",",row.names=FALSE,col.names=!append,append=append,eol="\n")
+
     } else if (format == "AgMIP") {
-      a <- write.report(new_data,file=NULL,extracols = "Item",...)
-      a <- do.call(rbind,do.call(rbind,a))
-      b<-melt(a,id.vars = c("Model","Scenario","Region","Item","Variable","Unit"),variable.name = "Year",value.name="Value")
-      b<-b[c("Model","Scenario","Region","Item","Variable","Year","Unit","Value")]
-      write.table(b,file,quote=FALSE,sep=",",row.names=FALSE,col.names=!append,append=append,eol="\n")
+
+      if (is.list(new_data)) {
+        a <- NULL
+        for (i in seq_along(new_data)) {
+          model    <- names(new_data[[i]])
+          scenario <- names(new_data)[i]
+          tmp <- write.report(new_data[[i]][[model]], file = NULL,
+                              model = model, scenario = scenario,
+                              extracols = "Item")
+          a <- rbind(a, tmp)
+        }
+      } else {
+        a <- write.report(new_data, file = NULL, extracols = "Item",...)
+      }
+      b <- reshape2::melt(a, id.vars = c("Model", "Scenario", "Region", "Item", "Variable", "Unit"),
+                variable.name = "Year", value.name = "Value")
+      b <- b[c("Model", "Scenario", "Region", "Item", "Variable", "Year", "Unit", "Value")]
+      write.table(b, file, quote = FALSE, sep = ",",
+                  row.names = FALSE, col.names = !append, append = append, eol = "\n")
     }
 
     if (!is.null(max_file_size)) {
@@ -143,14 +162,31 @@ write.reportProject <- function(mif, mapping,
             a <- write.report(tmp,file=NULL,...)
             a <- do.call(rbind,do.call(rbind,a))
             write.csv(a,file=file,row.names = FALSE,quote = FALSE)
+
           } else if (format == "AgMIP") {
-            a <- write.report(tmp,file=NULL,extracols = "Item",...)
-            a <- do.call(rbind,do.call(rbind,a))
-            b<-melt(a,id.vars = c("Model","Scenario","Region","Item","Variable","Unit"),variable.name = "Year",value.name="Value")
-            b<-b[c("Model","Scenario","Region","Item","Variable","Year","Unit","Value")]
-            write.csv(b,file=paste0(file_name[1:last-1],"_part",f,".",file_name[last]),row.names = FALSE,quote = FALSE)
+
+            if (is.list(tmp)) {
+              a <- NULL
+              for (i in seq_along(tmp)) {
+                model    <- names(tmp[[i]])
+                scenario <- names(tmp)[i]
+                b <- write.report(tmp[[i]][[model]], file = NULL,
+                                  model = model, scenario = scenario,
+                                  extracols = "Item")
+                a <- rbind(a, b)
+              }
+            } else {
+              a <- write.report(tmp, file = NULL, extracols = "Item",...)
+            }
+
+            a <- do.call(rbind, do.call(rbind, a))
+            b <- reshape2::melt(a, id.vars = c("Model", "Scenario", "Region", "Item", "Variable", "Unit"),
+                                variable.name = "Year", value.name = "Value")
+            b <- b[c("Model", "Scenario", "Region", "Item", "Variable", "Year", "Unit", "Value")]
+            write.csv(b, file = paste0(file_name[1:last-1], "_part", f, ".", file_name[last]),
+                      row.names = FALSE, quote = FALSE)
           }
-          #set counter for next loop
+          # set counter for next loop
           first_scen <- first_scen+scen_per_file
         }
       }

README.md

@@ -1,8 +1,8 @@
 # IAMC Tools
 
-R package **iamc**, version **0.29.8**
+R package **iamc**, version **0.29.9**
 
-[![CRAN status](https://www.r-pkg.org/badges/version/iamc)](https://cran.r-project.org/package=iamc)  [![R build status](https://github.com/giannou/iamc/workflows/check/badge.svg)](https://github.com/giannou/iamc/actions) [![codecov](https://codecov.io/gh/giannou/iamc/branch/master/graph/badge.svg)](https://app.codecov.io/gh/giannou/iamc) [![r-universe](https://pik-piam.r-universe.dev/badges/iamc)](https://pik-piam.r-universe.dev/builds)
+[![CRAN status](https://www.r-pkg.org/badges/version/iamc)](https://cran.r-project.org/package=iamc)  [![R build status](https://github.com/FelicitasBeier/iamc/workflows/check/badge.svg)](https://github.com/FelicitasBeier/iamc/actions) [![codecov](https://codecov.io/gh/FelicitasBeier/iamc/branch/master/graph/badge.svg)](https://app.codecov.io/gh/FelicitasBeier/iamc) [![r-universe](https://pik-piam.r-universe.dev/badges/iamc)](https://pik-piam.r-universe.dev/builds)
 
 ## Purpose and Functionality
 
@@ -46,7 +46,7 @@ In case of questions / problems please contact Jan Philipp Dietrich <dietrich@pi
 
 To cite package **iamc** in publications use:
 
-Dietrich J, Auer C, Giannousakis A, Bertram C, Benke F, Humpenoeder F, Baumstark L (2023). _iamc: IAMC Tools_. R package version 0.29.8.
+Dietrich J, Auer C, Giannousakis A, Bertram C, Benke F, Humpenoeder F, Baumstark L (2023). _iamc: IAMC Tools_. R package version 0.29.9.
 
 A BibTeX entry for LaTeX users is
 
@@ -55,6 +55,6 @@ A BibTeX entry for LaTeX users is
   title = {iamc: IAMC Tools},
   author = {Jan Philipp Dietrich and Cornelia Auer and Anastasis Giannousakis and Christoph Bertram and Falk Benke and Florian Humpenoeder and Lavinia Baumstark},
   year = {2023},
-  note = {R package version 0.29.8},
+  note = {R package version 0.29.9},
 }
 ```