Merge pull request #6 from caviddhen/main

update for workshop 2024

Author: caviddhen

.buildlibrary

@@ -1,7 +1,8 @@
-ValidationKey: '4105710'
+ValidationKey: '4182653'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'
 AcceptedNotes: ~
 AutocreateReadme: yes
 allowLinterWarnings: yes
+enforceVersionUpdate: no

.github/workflows/check.yaml

@@ -1,5 +1,3 @@
-# Run CI for R using https://eddelbuettel.github.io/r-ci/
-
 name: check
 
 on:
@@ -8,96 +6,53 @@ 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
+      - uses: actions/checkout@v4
 
-      - 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
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Set up Pandoc
-        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@v5
+        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)
 
+      - name: Verify that lucode2::buildLibrary was successful
+        if: github.event_name == 'pull_request'
+        shell: Rscript {0}
+        run: lucode2:::isVersionUpdated()
+
       - name: Checks
         shell: Rscript {0}
         run: |
@@ -106,6 +61,8 @@ jobs:
 
       - name: Test coverage
         shell: Rscript {0}
-        run: covr::codecov(quiet = FALSE)
+        run: |
+          nonDummyTests <- setdiff(list.files("./tests/testthat/"), c("test-dummy.R", "_snaps"))
+          if(length(nonDummyTests) > 0) 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: v4.4.0
+    rev: v4.5.0
     hooks:
     -   id: check-case-conflict
     -   id: check-json
@@ -15,7 +15,7 @@ repos:
     -   id: mixed-line-ending
 
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.3.2.9013
+    rev: v0.4.0
     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: 'mrtutorial: Tutorial Package For Madrat Package Library'
-version: 0.2.10
-date-released: '2023-07-13'
+version: 0.2.11
+date-released: '2024-04-10'
 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: 0.2.10
-Date: 2023-07-13
+Version: 0.2.11
+Date: 2024-04-10
 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

R/downloadTutorialWDI.R

@@ -19,12 +19,13 @@ downloadTutorialWDI<-function(){
                  "NV.AGR.TOTL.CD") # Ag GDP current US$
   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,
               unit          = NULL))
-  
+
 }

R/imports.R

@@ -1,4 +1,4 @@
 # Generated by lucode2: do not edit by hand
 
-#' @import magclass madrat
+#' @import madrat magclass
 NULL

R/readTutorialWDI.R

@@ -22,20 +22,22 @@
 #' @importFrom magclass as.magpie
 #' @importFrom rlang .data
 
-readTutorialWDI<-function(subtype){
+readTutorialWDI<-function(subtype = "SP.POP.TOTL"){
 
   load("WDI.rda")
 
-  #convert the iso2c to iso3c using madrat tool
-  wdi$iso2c <- toolCountry2isocode(wdi$iso2c)
-
+  #clean up: remove other country ids, remove rows with NAs as country,
+             #pivot to long format and convert to magclass object
   wdi <- wdi %>%
-         dplyr::select(!.data$country)  %>%
-         filter(!is.na(.data$iso2c)) %>%
-         pivot_longer(cols=3:6) %>%
+         dplyr::select(!c(.data$country, .data$iso2c))  %>%
+         filter(!is.na(.data$iso3c), .data$iso3c != "") %>%
+         pivot_longer(cols = c("NY.GDP.MKTP.CD", "SP.POP.TOTL",
+                               "SL.AGR.EMPL.ZS", "NV.AGR.TOTL.CD"),
+                      names_to = "variable") %>%
          as.magpie(spatial = 1, temporal = 2, replacement =".")
 
-  wdi <- wdi[,,subtype]
+  #select the subtype
+  wdi <- wdi[, , subtype]
 
   getNames(wdi) <- gsub("\\.", "_", getNames(wdi))
   # Replacement of . with _ in dimension is also done automatically in as.magpie()

README.md

@@ -1,12 +1,14 @@
 # Tutorial Package For Madrat Package Library
 
-R package **mrtutorial**, version **0.2.10**
+R package **mrtutorial**, version **0.2.11**
 
-[![CRAN status](https://www.r-pkg.org/badges/version/mrtutorial)](https://cran.r-project.org/package=mrtutorial)  [![R build status](https://github.com/whitehacker/mrtutorial/workflows/check/badge.svg)](https://github.com/whitehacker/mrtutorial/actions) [![codecov](https://codecov.io/gh/whitehacker/mrtutorial/branch/master/graph/badge.svg)](https://app.codecov.io/gh/whitehacker/mrtutorial) [![r-universe](https://pik-piam.r-universe.dev/badges/mrtutorial)](https://pik-piam.r-universe.dev/builds)
+[![CRAN status](https://www.r-pkg.org/badges/version/mrtutorial)](https://cran.r-project.org/package=mrtutorial)  [![R build status](https://github.com/caviddhen/mrtutorial/workflows/check/badge.svg)](https://github.com/caviddhen/mrtutorial/actions) [![codecov](https://codecov.io/gh/caviddhen/mrtutorial/branch/master/graph/badge.svg)](https://app.codecov.io/gh/caviddhen/mrtutorial) [![r-universe](https://pik-piam.r-universe.dev/badges/mrtutorial)](https://pik-piam.r-universe.dev/builds)
 
 ## Purpose and Functionality
 
-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 .
+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 .
 
 
 ## Installation
@@ -38,15 +40,15 @@ In case of questions / problems please contact David Meng-Chuen Chen <david.chen
 
 To cite package **mrtutorial** in publications use:
 
-Chen D (2023). _mrtutorial: Tutorial Package For Madrat Package Library_. R package version 0.2.10.
+Chen D (2024). _mrtutorial: Tutorial Package For Madrat Package Library_. R package version 0.2.11.
 
 A BibTeX entry for LaTeX users is
 
  ```latex
 @Manual{,
   title = {mrtutorial: Tutorial Package For Madrat Package Library},
   author = {David Meng-Chuen Chen},
-  year = {2023},
-  note = {R package version 0.2.10},
+  year = {2024},
+  note = {R package version 0.2.11},
 }
 ```