test github action fix

.Rbuildignore

@@ -8,3 +8,5 @@ carbon_stored.*
 ^\.buildlibrary$
 ^\.github$
 ^codecov\.yml$
+^\.pre-commit-config\.yaml$
+^workflow$

.buildlibrary

@@ -1,9 +1,10 @@
-ValidationKey: '12547608'
+ValidationKey: '3062864'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'
 AcceptedNotes:
 - unable to verify current time
 - Imports includes .* non-default packages.
+- installed size is .*
 AutocreateReadme: yes
 allowLinterWarnings: yes

.github/workflows/lucode2-check.yaml

@@ -11,7 +11,7 @@ on:
 env:
   USE_BSPM: "true"
   _R_CHECK_FORCE_SUGGESTS_: "false"
-  NO_BINARY_INSTALL_R_PACKAGES: 'c("madrat", "magclass", "citation", "gms", "goxygen")'
+  NO_BINARY_INSTALL_R_PACKAGES: 'c("madrat", "magclass", "citation", "gms", "goxygen", "raster")'
 
 jobs:
   lucode2-check:
@@ -55,7 +55,7 @@ jobs:
 
       - name: Install dependencies
         run: |
-          ./run.sh install_aptget libhdf5-dev
+          ./run.sh install_aptget libgdal-dev
           ./run.sh install_all
           ./run.sh install_r lucode2 covr
 

.pre-commit-config.yaml

@@ -0,0 +1,12 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+    -   id: check-case-conflict
+    -   id: check-json
+    -   id: check-yaml
+    -   id: check-merge-conflict
+    -   id: fix-byte-order-marker
+    -   id: end-of-file-fixer
+ci:
+    autoupdate_schedule: quarterly

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "mrcommons: MadRat commons Input Data Library",
-  "version": "0.66.4",
+  "version": "1.6.1",
   "description": "<p>Provides useful functions and a common structure to all the input data required to run models like MAgPIE\n    and REMIND of model input data.<\/p>",
   "creators": [
     {

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: mrcommons
 Type: Package
 Title: MadRat commons Input Data Library
-Version: 0.66.4
-Date: 2021-09-27
+Version: 1.6.1
+Date: 2022-02-01
 Authors@R: c(person("Benjamin Leon", "Bodirsky", email = "[email protected]", role = "aut"),
              person("Kristine", "Karstens", role = "aut"),
              person("Lavinia", "Baumstark", role = "aut"),
@@ -36,17 +36,17 @@ Description: Provides useful functions and a common structure to all the input d
 Depends:
     R(>= 2.10.0),
     magclass(>= 3.17),
-    madrat(>= 2.2.1),
+    madrat(>= 2.5.1),
+    mrdrivers (>= 0.2.1),
     mstools
 Imports:
-    bezier,
     countrycode,
     data.table,
     dplyr,
     hdf5r,
     GDPuc,
-    glue,
     lazyeval,
+    lifecycle,
     lpjclass,
     luscale,
     magpiesets(>= 0.44.2),
@@ -61,10 +61,7 @@ Imports:
     rlang,
     SPEI,
     stringr,
-    tibble,
     tidyr,
-    tidyselect,
-    WDI,
     zoo
 Suggests:
     covr,
@@ -83,3 +80,4 @@ LazyData: no
 Encoding: UTF-8
 RoxygenNote: 7.1.2
 VignetteBuilder: knitr
+Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(calc1stBioenergyPast)
+export(calcAdjustGrassi2021)
 export(calcBodyHeight)
 export(calcConstructionWoodDemand)
 export(calcDemography)
@@ -18,6 +19,7 @@ export(calcPhysicalInactivity)
 export(calcPlantEstablishCalib)
 export(calcTimberDemand)
 export(convertMAgPIE)
+export(readEurostat)
 export(readFAO_FRA2015)
 export(readFRA2020)
 export(readFeedEfficiencyReg)
@@ -27,6 +29,7 @@ export(toolAggregateCell2Country)
 export(toolCalcIEAfromStructureMappingPEFE)
 export(toolCell2isoCell)
 export(toolCoord2Isocell)
+export(toolExtrapolateFodder)
 export(toolFAOcombine)
 export(toolFreezeEffect)
 export(toolGetMappingCoord2Country)
@@ -39,36 +42,33 @@ export(toolSmooth)
 import(countrycode)
 import(madrat)
 import(magclass)
+import(mrdrivers)
+import(mstools)
 importFrom(GDPuc,convertGDP)
 importFrom(SPEI,thornthwaite)
 importFrom(countrycode,countrycode)
 importFrom(data.table,as.data.table)
 importFrom(data.table,fread)
 importFrom(dplyr,"%>%")
-importFrom(dplyr,across)
 importFrom(dplyr,all_of)
 importFrom(dplyr,arrange)
-importFrom(dplyr,arrange_)
-importFrom(dplyr,bind_rows)
+importFrom(dplyr,count)
 importFrom(dplyr,filter)
 importFrom(dplyr,filter_)
 importFrom(dplyr,full_join)
 importFrom(dplyr,group_by)
 importFrom(dplyr,inner_join)
 importFrom(dplyr,intersect)
+importFrom(dplyr,last)
 importFrom(dplyr,left_join)
-importFrom(dplyr,matches)
 importFrom(dplyr,mutate)
-importFrom(dplyr,mutate_)
 importFrom(dplyr,n)
 importFrom(dplyr,rename)
 importFrom(dplyr,right_join)
 importFrom(dplyr,select)
-importFrom(dplyr,select_)
 importFrom(dplyr,summarise)
 importFrom(graphics,plot)
 importFrom(hdf5r,h5file)
-importFrom(lazyeval,interp)
 importFrom(lpjclass,as.lpj)
 importFrom(lpjclass,read.LPJ_input)
 importFrom(lpjclass,readLPJ)
@@ -79,7 +79,6 @@ importFrom(luscale,speed_aggregate)
 importFrom(luscale,superAggregate)
 importFrom(luscale,weighted_mean.groupAggregate)
 importFrom(madrat,calcOutput)
-importFrom(madrat,getConfig)
 importFrom(madrat,metadataGFZ)
 importFrom(madrat,readSource)
 importFrom(madrat,regionscode)
@@ -95,9 +94,7 @@ importFrom(madrat,toolSplitSubtype)
 importFrom(madrat,toolSubtypeSelect)
 importFrom(madrat,toolTimeAverage)
 importFrom(madrat,toolTimeSpline)
-importFrom(madrat,toolXlargest)
 importFrom(madrat,vcat)
-importFrom(magclass,"getCells<-")
 importFrom(magclass,"getNames<-")
 importFrom(magclass,"getRegionList<-")
 importFrom(magclass,"getSets<-")
@@ -124,7 +121,7 @@ importFrom(magclass,hasCoords)
 importFrom(magclass,magpie_expand)
 importFrom(magclass,magpiesort)
 importFrom(magclass,mbind)
-importFrom(magclass,ncells)
+importFrom(magclass,ndim)
 importFrom(magclass,new.magpie)
 importFrom(magclass,nregions)
 importFrom(magclass,nyears)
@@ -151,7 +148,6 @@ importFrom(purrr,map)
 importFrom(purrr,map2)
 importFrom(purrr,pmap)
 importFrom(purrr,walk)
-importFrom(quitte,add_countrycode_)
 importFrom(quitte,as.quitte)
 importFrom(quitte,inline.data.frame)
 importFrom(raster,"extent<-")
@@ -165,13 +161,12 @@ importFrom(raster,extent)
 importFrom(raster,extract)
 importFrom(raster,projectRaster)
 importFrom(raster,raster)
+importFrom(raster,rasterToPoints)
 importFrom(raster,res)
 importFrom(raster,resample)
 importFrom(raster,stack)
 importFrom(raster,subset)
 importFrom(raster,writeRaster)
-importFrom(readr,read_csv2)
-importFrom(readxl,excel_sheets)
 importFrom(readxl,read_excel)
 importFrom(readxl,read_xlsx)
 importFrom(reshape2,acast)
@@ -192,15 +187,12 @@ importFrom(stringr,str_sub)
 importFrom(stringr,str_subset)
 importFrom(stringr,str_trim)
 importFrom(tidyr,expand_grid)
-importFrom(tidyr,gather)
 importFrom(tidyr,pivot_longer)
-importFrom(tidyr,pivot_wider)
 importFrom(tidyr,starts_with)
-importFrom(tidyr,unite)
 importFrom(tidyr,unnest)
-importFrom(tidyselect,starts_with)
 importFrom(tools,file_ext)
 importFrom(tools,file_path_sans_ext)
+importFrom(utils,bibentry)
 importFrom(utils,data)
 importFrom(utils,download.file)
 importFrom(utils,head)
@@ -212,4 +204,3 @@ importFrom(utils,read.table)
 importFrom(utils,tail)
 importFrom(utils,unzip)
 importFrom(utils,write.table)
-importFrom(zoo,na.locf)

R/calc1stBioDem.R

@@ -7,13 +7,12 @@
 #' @param subtype all per default. ethanol_oils for selecting 1st gen crop types relevant for REMIND input.
 #' @author Xiaoxi Wang, David Klein
 #' @seealso
-#' \code{\link{calc1stBioenergyPast}}
+#' [calc1stBioenergyPast()]
 #' @examples
 #' 
 #' \dontrun{ 
 #' calcOutput("1stBioDem")
 #' }
-#' @importFrom magclass getNames<- as.magpie
 #' @importFrom magpiesets findset
 
 calc1stBioDem<- function(subtype="all"){

R/calc1stBioenergyPast.R

@@ -1,33 +1,28 @@
 #' @title calc1stBioenergyPast
-#' @description 
-#' Calculates first generation biofuels production, imports, exports for biogas, bioethanol and biodiesel from IEA database. 
-#' The unit is Petajoule. 
+#' @description
+#' Calculates first generation biofuels production, imports, exports for biogas, bioethanol and biodiesel
+#' from IEA database. The unit is Petajoule.
 #'
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
 #' @author Xiaoxi Wang, Isabelle Weindl
-#' @seealso
-#' \code{\link{setConfig}}
 #' @examples
-#' 
-#' \dontrun{ 
+#' \dontrun{
 #' calcOutput("1stBioenergyPast")
 #' }
-#' @importFrom magclass getNames<- as.magpie
-#' @importFrom madrat toolGetMapping
 #' @export
 
-calc1stBioenergyPast <- function(){
+calc1stBioenergyPast <- function() {
   df <- toolCalcIEAfromStructureMappingPEFE(
-    readSource("IEA",subtype="EnergyBalances"),
+    readSource("IEA", subtype = "EnergyBalances"),
     toolGetMapping(type = "sectoral", name = "structuremappingPE.csv", returnPathOnly = TRUE),
-    subtype="magpie")
-  
-  #Unit conversion from ktoe to PJ
-  df <- df[,,c("biogas","ethanol","oils","woodfuel")]*0.041868
-  
-  return(list(x=df,
-              weight=NULL,
-              unit="PJ",
-              description="1st generation bionegy demand")
+    subtype = "magpie")
+
+  # Unit conversion from ktoe to PJ
+  df <- df[, , c("biogas", "ethanol", "oils", "woodfuel")] * 0.041868
+
+  return(list(x = df,
+              weight = NULL,
+              unit = "PJ",
+              description = "1st generation bionegy demand")
   )
 }

R/calcACCMIP.R

@@ -4,7 +4,7 @@
 #' @param glo_incl_oceans if true, a global value will be returned that also includes deposition on oceans and should be equivalent to total emissions.
 #' @author Benjamin Leon Bodirsky
 #' @seealso
-#' \code{\link{calcAtmosphericDeposition}}
+#' [calcAtmosphericDeposition()]
 #' @examples
 #' 
 #' \dontrun{ 
@@ -80,4 +80,4 @@ calcACCMIP<-function(glo_incl_oceans=FALSE){
     min=0,
     max=200,
     description="Atmospheric deposition by cell"))
-}
+}

R/calcAWMSconfShr.R

@@ -4,15 +4,13 @@
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
 #' @author Benjamin Leon Bodirsky. Modifications by Edna J. Molina Bacca
 #' @seealso
-#' \code{\link{calcAWMSconfShrPast}}
+#' [calcAWMSconfShrPast()]
 #' @examples
 #'
 #' \dontrun{
 #' calcOutput("AWMSconfShr")
 #' }
 #' @importFrom magpiesets findset
-#' @importFrom magclass collapseNames add_columns add_dimension getNames<- setYears
-
 
 calcAWMSconfShr<-function(rev=0.1){
 

R/calcAWMSconfShrPast.R

@@ -5,19 +5,14 @@
 #'
 #' @return List of magpie object with results on country level, weight on country level, unit and description.
 #' @seealso
-#' \code{\link{calcAWMSconfShr}},
-#' \code{\link{calcExcretionIPCC}}
+#' [calcAWMSconfShr()],
+#' [calcExcretionIPCC()]
 #' @author Benjamin Leon Bodirsky
 #' @examples
 #' 
 #' \dontrun{ 
 #' calcOutput("AWMSconfShrPast")
 #' }
-#' @importFrom magclass collapseNames where
-#' @importFrom madrat toolXlargest
-
-
-
 
 calcAWMSconfShrPast<-function(products="magpie"){
   excretion<-calcOutput("ExcretionIPCC",products=products,aggregate = FALSE)