Merge pull request #4 from whitehacker/main

Adjusted the where value in toolGetMapping()

.Rbuildignore

@@ -6,3 +6,7 @@
 ^\.github$
 ^codecov\.yml$
 ^workflow$
+^Makefile$
+^.lintr$
+^tests/.lintr$
+^.*CITATION.cff$

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '552682'
+ValidationKey: '4105710'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

.github/workflows/lucode2-check.yaml → .github/workflows/check.yaml

@@ -1,6 +1,6 @@
 # Run CI for R using https://eddelbuettel.github.io/r-ci/
 
-name: lucode2-check
+name: check
 
 on:
   push:
@@ -11,14 +11,14 @@ 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", "GDPuc", "roxygen2")'
 
 jobs:
-  lucode2-check:
+  check:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Bootstrap
         run: |
@@ -28,6 +28,7 @@ jobs:
           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: |
@@ -48,19 +49,45 @@ jobs:
                 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@v1
+      - name: Set up Pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Cache R libraries
+        if: ${{ !env.ACT }} # skip when running locally via nektos/act
+        uses: pat-s/always-upload-cache@v3
+        with:
+          path: /usr/local/lib/R/
+          key: 3-${{ 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
+          ./run.sh install_aptget libhdf5-dev libharfbuzz-dev libfribidi-dev
           ./run.sh install_all
-          ./run.sh install_r lucode2 covr
+          ./run.sh install_r_binary covr rstudioapi
+          ./run.sh install_r lucode2
+
+      - 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: |

.lintr

@@ -0,0 +1,2 @@
+linters: lucode2::lintrRules()
+encoding: "UTF-8"

.pre-commit-config.yaml

@@ -1,12 +1,28 @@
+# testthat snapshots are machine-generated regression tests that
+# have to be preserved exactly as they are
+exclude: '^tests/testthat/_snaps/.*$'
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v4.4.0
     hooks:
     -   id: check-case-conflict
     -   id: check-json
-    -   id: check-yaml
     -   id: check-merge-conflict
+    -   id: check-yaml
     -   id: fix-byte-order-marker
-    -   id: end-of-file-fixer
+    -   id: check-added-large-files
+        args: ['--maxkb=100']
+    -   id: mixed-line-ending
+
+-   repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.3.2.9013
+    hooks:
+    -   id: parsable-R
+    -   id: deps-in-desc
+        args: [--allow_private_imports]
+    -   id: no-browser-statement
+    -   id: no-debug-statement
+    -   id: readme-rmd-rendered
+    -   id: use-tidy-description
 ci:
     autoupdate_schedule: quarterly

CITATION.cff

@@ -0,0 +1,15 @@
+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'
+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
+  .'
+authors:
+- family-names: Chen
+  given-names: David Meng-Chuen
+  email: [email protected]
+license: GPL-3.0
+

DESCRIPTION

@@ -1,28 +1,30 @@
-Package: mrtutorial
 Type: Package
+Package: mrtutorial
 Title: Tutorial Package For Madrat Package Library
-Date: 2022-03-07
-Version: 0.2.9
+Version: 0.2.10
+Date: 2023-07-13
 Authors@R: 
-    person("David Meng-Chuen",  "Chen", email = "[email protected]", role = c("aut","cre"))
-Description: 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 .
+    person("David Meng-Chuen", "Chen", , "[email protected]", role = c("aut", "cre"))
+Description: 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 .
+License: GPL-3
 Depends:
-    R(>= 2.10.0),
-    magclass(>= 3.17),
-    madrat(>= 2.11.3)
-License: GPL-3 
-Encoding: UTF-8
-LazyData: true
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+    R (>= 2.10.0),
+    madrat (>= 2.11.3),
+    magclass (>= 3.17)
 Imports:
     WDI,
     countrycode,
+    dplyr,
     lucode2,
-    reshape2,
     magpiesets,
-    dplyr,
-    tidyr,
-    rlang
+    reshape2,
+    rlang,
+    tidyr
 Suggests: 
     covr
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3

Makefile

@@ -0,0 +1,46 @@
+.PHONY: help build check test lint lint-all format format-all install docs
+.DEFAULT_GOAL = help
+
+# extracts the help text and formats it nicely
+HELP_PARSING = 'm <- readLines("Makefile");\
+				m <- grep("\#\#", m, value=TRUE);\
+				command <- sub("^([^ ]*) *\#\#(.*)", "\\1", m);\
+				help <- sub("^([^ ]*) *\#\#(.*)", "\\2", m);\
+				cat(sprintf("%-8s%s", command, help), sep="\n")'
+
+help:           ## Show this help.
+	@Rscript -e $(HELP_PARSING)
+
+build:          ## Build the package using lucode2::buildLibrary(). You can pass the
+                ## updateType with 'make build u=3'
+	Rscript -e 'lucode2::buildLibrary(updateType = "$(u)")'
+
+check:          ## Build documentation and vignettes, run testthat tests,
+                ## and check if code etiquette is followed using lucode2::check().
+	Rscript -e 'lucode2::check()'
+
+test:           ## Run testthat tests
+	Rscript -e 'devtools::test(show_report = TRUE)'
+
+lint:           ## Check if code etiquette is followed using lucode2::lint().
+                ## Only checks files you changed.
+	Rscript -e 'lucode2::lint()'
+
+lint-all:       ## Check if code etiquette is followed using lucode2::lint().
+                ## Checks all files.
+	Rscript -e 'lucode2::lint(".")'
+
+format:         ## Apply auto-formatting to changed files and lint afterwards.
+	Rscript -e 'lucode2::autoFormat()'
+
+format-all:     ## Apply auto-formatting to all files and lint afterwards.
+	Rscript -e 'lucode2::autoFormat(files=list.files("./R", full.names = TRUE, pattern = "\\.R"))'
+
+install:        ## Install the package locally via devtools::install() after
+                ## generating NAMESPACE and docs (see docs target).
+	Rscript -e 'roxygen2::roxygenize(); devtools::install(upgrade = "never")'
+
+docs:           ## Generate the package documentation (man/*.Rd files) and
+                ## NAMESPACE via roxygen2::roxygenize(), view the generated
+                ## documentation with `?package::function`.
+	Rscript -e 'roxygen2::roxygenize()'

R/mrtutorial-package.R

@@ -0,0 +1,4 @@
+# The package documentation is defined in this file.
+# You can get it via `library(<package>); ?<package>`.
+#' @docType package
+"_PACKAGE"

R/spatialHeader.R

@@ -26,7 +26,7 @@ spatialHeader <- function(mapping) {
   regionscode <- regionscode(map)
   reg <- as.character(map$RegionCode)
   names(reg) <- as.character(map$CountryCode)
-  iso <- toolGetMapping(type = "cell", name = "CountryToCellMapping.csv")$iso
+  iso <- toolGetMapping(type = "cell", name = "CountryToCellMapping.csv", where = "mappingfolder")$iso
   spatialHeader <- paste(reg[iso], seq_along(iso), sep = ".")
   return(spatialHeader)
 }

README.md

@@ -1,8 +1,8 @@
 # Tutorial Package For Madrat Package Library
 
-R package **mrtutorial**, version **0.2.9**
+R package **mrtutorial**, version **0.2.10**
 
-[![CRAN status](https://www.r-pkg.org/badges/version/mrtutorial)](https://cran.r-project.org/package=mrtutorial)  [![R build status](https://github.com/pik-piam/mrtutorial/workflows/check/badge.svg)](https://github.com/pik-piam/mrtutorial/actions) [![codecov](https://codecov.io/gh/pik-piam/mrtutorial/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/mrtutorial) [![r-universe](https://pik-piam.r-universe.dev/badges/mrtutorial)](https://pik-piam.r-universe.dev/ui#builds)
+[![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)
 
 ## Purpose and Functionality
 
@@ -38,15 +38,15 @@ In case of questions / problems please contact David Meng-Chuen Chen <david.chen
 
 To cite package **mrtutorial** in publications use:
 
-Chen D (2022). _mrtutorial: Tutorial Package For Madrat Package Library_. R package version 0.2.9.
+Chen D (2023). _mrtutorial: Tutorial Package For Madrat Package Library_. R package version 0.2.10.
 
 A BibTeX entry for LaTeX users is
 
  ```latex
 @Manual{,
   title = {mrtutorial: Tutorial Package For Madrat Package Library},
   author = {David Meng-Chuen Chen},
-  year = {2022},
-  note = {R package version 0.2.9},
+  year = {2023},
+  note = {R package version 0.2.10},
 }
 ```

tests/.lintr

@@ -0,0 +1,2 @@
+linters: lucode2::lintrRules(allowUndesirable = TRUE)
+encoding: "UTF-8"