Merge pull request #8 from pik-piam/patch/minor-coding-style-improvements

Minor stylistic code changes to improve readability throughout the tutorial

Author: codeZeilen

.buildlibrary

@@ -1,8 +1,10 @@
-ValidationKey: '4182653'
+ValidationKey: '4296180'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'
 AcceptedNotes: ~
 AutocreateReadme: yes
 allowLinterWarnings: yes
 enforceVersionUpdate: no
+AutocreateCITATION: yes
+skipCoverage: no

.github/workflows/check.yaml

@@ -23,26 +23,24 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: |
-            any::lucode2
-            any::covr
-            any::madrat
-            any::magclass
-            any::citation
-            any::gms
-            any::goxygen
-            any::GDPuc
+            lucode2
+            covr
+            madrat
+            magclass
+            citation
+            gms
+            goxygen
+            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           # gms, goxygen, GDPuc) will usually have an outdated binary version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@v5
-        with:
-          python-version: 3.9
-
-      - name: Install python dependencies if applicable
+      - name: Run pre-commit checks
+        shell: bash
         run: |
-          [ -f requirements.txt ] && python -m pip install --upgrade pip wheel || true
-          [ -f requirements.txt ] && pip install -r requirements.txt || true
+          python -m pip install pre-commit
+          python -m pip freeze --local
+          pre-commit run --show-diff-on-failure --color=always --all-files
 
       - name: Verify validation key
         shell: Rscript {0}
@@ -63,6 +61,6 @@ jobs:
         shell: Rscript {0}
         run: |
           nonDummyTests <- setdiff(list.files("./tests/testthat/"), c("test-dummy.R", "_snaps"))
-          if(length(nonDummyTests) > 0) covr::codecov(quiet = FALSE)
+          if(length(nonDummyTests) > 0 && !lucode2:::loadBuildLibraryConfig()[["skipCoverage"]]) 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: v4.5.0
+    rev: cef0300fd0fc4d2a87a85fa2093c6b283ea36f4b  # frozen: v5.0.0
     hooks:
     -   id: check-case-conflict
     -   id: check-json
@@ -15,7 +15,7 @@ repos:
     -   id: mixed-line-ending
 
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.0
+    rev: 3b70240796cdccbe1474b0176560281aaded97e6  # frozen: v0.4.3.9003
     hooks:
     -   id: parsable-R
     -   id: deps-in-desc
@@ -25,4 +25,4 @@ repos:
     -   id: readme-rmd-rendered
     -   id: use-tidy-description
 ci:
-    autoupdate_schedule: quarterly
+    autoupdate_schedule: weekly

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: 'mrtutorial: Tutorial Package For Madrat Package Library'
-version: 0.2.11
-date-released: '2024-04-10'
+version: 0.2.12
+date-released: '2025-06-26'
 abstract: 'Example package of mr- world libraries, in conjunction with MAgPIE MADRat
   tutorial. For more information please see: https://github.com/magpiemodel/tutorials/tree/master/madrat
   .'

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: mrtutorial
 Title: Tutorial Package For Madrat Package Library
-Version: 0.2.11
-Date: 2024-04-10
+Version: 0.2.12
+Date: 2025-06-26
 Authors@R: 
     person("David Meng-Chuen", "Chen", , "david.chen@pik-potsdam.de", role = c("aut", "cre"))
 Description: Example package of mr- world libraries, in conjunction with
@@ -26,4 +26,4 @@ Suggests:
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2

R/calcAgGDP.R

@@ -18,7 +18,7 @@ calcAgGDP <- function(){
 
   ag_gdp <- readSource("TutorialWDI", subtype="NV.AGR.TOTL.CD")
 
-  x <- ag_gdp/gdp
+  x <- ag_gdp / gdp
   x <- collapseNames(x)
   getNames(x) <- "Ag_GDP_share"
 

R/calcValidPopulation.R

@@ -8,14 +8,14 @@
 
 calcValidPopulation <- function(datasource="WDI") {
 
-  if(datasource=="WDI"){
-
+  if (datasource == "WDI") {
     out <- readSource("TutorialWDI", "SP.POP.TOTL")
+  } else {
+    stop("No datasource of the given name.")
+  }
 
-  } else { stop("No datasource of the given name.") }
-
-  getNames(out)                   <- "Population (million people)"
-  getSets(out,fulldim = FALSE)[3] <- "variable"
+  getNames(out)                    <- "Population (million people)"
+  getSets(out, fulldim = FALSE)[3] <- "variable"
 
   out <- add_dimension(out, dim=3.1, add="scenario", nm = "historical")
   out <- add_dimension(out, dim=3.2, add="model",    nm = datasource)

R/convertTutorialWDI.R

@@ -17,28 +17,25 @@
 #' @importFrom madrat toolCountryFill
 
 
-convertTutorialWDI<-function(x, subtype){
+convertTutorialWDI <- function(x, subtype) {
 
   # change scale of absolute indicators, MAgPIE runs in Million scale for Pop and GDP drivers
-if (subtype %in% c("NY.GDP.MKTP.CD",
+  if (subtype %in% c("NY.GDP.MKTP.CD",
                      "SP.POP.TOTL",
-                     "NV.AGR.TOTL.CD")){
-
-       out <- x/1e6 } else
-
- if (subtype == "SL.AGR.EMPL.ZS"){
-        # don't change for percentage of ag employment
-
-      out <- x } else{
-
-      stop("subtype does not exist in the dataset!")}
+                     "NV.AGR.TOTL.CD")) {
+    out <- x/1e6
+  } else if (subtype == "SL.AGR.EMPL.ZS") {
+    # don't change for percentage of ag employment
+    out <- x
+  } else {
+    stop("subtype does not exist in the dataset!")
+  }
 
   # toolCountryFill fills in missing countries - 249 required for aggregation
+  x <- toolCountryFill(out, fill = 0)
 
-  x<-toolCountryFill(out,fill = 0)
-
-  x[is.na(x)] <- 0  #remove NAs
-
+  #remove NAs
+  x[is.na(x)] <- 0
 
   return(x)
 }

R/downloadTutorialWDI.R

@@ -3,7 +3,7 @@
 #' Download WDI (World development indicators) data .rda file.
 #'
 #' @author  David Chen
-#' @seealso  \code{\link{downloadSource}} \code{\link{WDI}}
+#' @seealso  \code{\link[madrat]{downloadSource}} \code{\link[WDI]{WDI}}
 #' @examples
 #'
 #' \dontrun{ a <- downloadSource(type="TutorialWDI")
@@ -12,20 +12,20 @@
 #' @importFrom WDI WDI WDIcache WDIsearch
 
 
-downloadTutorialWDI<-function(){
+downloadTutorialWDI <- function() {
   indicator <- c("NY.GDP.MKTP.CD", # gdp PPP current US$
-                 "SP.POP.TOTL", # Total population
-                 "SL.AGR.EMPL.ZS", #Employment in agriculture as % of total employment
+                 "SP.POP.TOTL",    # Total population
+                 "SL.AGR.EMPL.ZS", # Employment in agriculture as % of total employment
                  "NV.AGR.TOTL.CD") # Ag GDP current US$
-  wdi <- WDI(indicator = indicator,start= 1960, end = 2018)
-  save(wdi,file = paste("WDI","rda",sep="."))
+  wdi <- WDI(indicator = indicator, start = 1960, end = 2018)
+  save(wdi, file = paste("WDI", "rda", sep = "."))
 
   return(list(url           = "https://data.worldbank.org/indicator/",
               doi           = NULL,
               title         = "World Bank Development Indicators",
               description   = "GDP and Population indicators",
               author        = NULL,
-              license      = NULL,
+              license       = NULL,
               unit          = NULL))
 
 }

R/fullTUTORIAL.R

@@ -8,7 +8,7 @@
 #' @param extra extra text to insert
 #' @author David M Chen
 #' @seealso
-#' \code{\link{readSource}}, \code{\link{getCalculations}}, \code{\link{calcOutput}}
+#' \code{\link[madrat]{readSource}}, \code{\link[madrat]{getCalculations}}, \code{\link[madrat]{calcOutput}}
 #' @examples
 #' \dontrun{
 #' retrieveData("tutorial", rev = numeric_version("12"),