Merge pull request #19 from giannou/master

version bump after bugfix ff2706e

.Rbuildignore

@@ -10,3 +10,4 @@
 ^codecov\.yml$
 ^\.github$
 ^Makefile$
+^.*CITATION.cff$

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '5743683'
+ValidationKey: '5824112'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

.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:
@@ -14,11 +14,11 @@ env:
   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: |
@@ -48,17 +49,18 @@ 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
 
       - name: Set up Pandoc
-        uses: r-lib/actions/setup-pandoc@v1
+        uses: r-lib/actions/setup-pandoc@v2
 
       - name: Set up Python 3.9
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.9
 
@@ -67,9 +69,9 @@ jobs:
         uses: pat-s/always-upload-cache@v3
         with:
           path: /usr/local/lib/R/
-          key: 2-${{ runner.os }}-usr-local-lib-R-${{ hashFiles('DESCRIPTION') }}
+          key: 3-${{ runner.os }}-usr-local-lib-R-${{ hashFiles('DESCRIPTION') }}
           restore-keys: |
-            2-${{ runner.os }}-usr-local-lib-R-
+            3-${{ runner.os }}-usr-local-lib-R-
 
       - name: Restore R library permissions
         run: |

.pre-commit-config.yaml

@@ -15,7 +15,7 @@ repos:
     -   id: mixed-line-ending
 
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.3.2.9003
+    rev: v0.3.2.9013
     hooks:
     -   id: parsable-R
     -   id: deps-in-desc

CITATION.cff

@@ -0,0 +1,26 @@
+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'
+abstract: A collection of R tools provided by the Integrated Assessment Modeling Consortium
+  (IAMC) for data analysis and diagnostics.
+authors:
+- family-names: Dietrich
+  given-names: Jan Philipp
+  email: dietrich@pik-potsdam.de
+- family-names: Auer
+  given-names: Cornelia
+- family-names: Giannousakis
+  given-names: Anastasis
+- family-names: Bertram
+  given-names: Christoph
+- family-names: Benke
+  given-names: Falk
+- family-names: Humpenoeder
+  given-names: Florian
+- family-names: Baumstark
+  given-names: Lavinia
+license: MIT
+

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: iamc
 Type: Package
 Title: IAMC Tools
-Version: 0.29.7
-Date: 2022-12-13
+Version: 0.29.8
+Date: 2023-07-06
 Authors@R: c(person("Jan Philipp", "Dietrich", email = "dietrich@pik-potsdam.de", role = c("aut","cre")),
              person("Cornelia", "Auer", role = "aut"),
              person("Anastasis", "Giannousakis", role = "aut"),
@@ -26,7 +26,7 @@ Imports: quitte(>= 0.3066),
          writexl
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.3
 Suggests: 
     covr,
     knitr,

Makefile

@@ -1,4 +1,4 @@
-.PHONY: help build check test lint format
+.PHONY: help build check test lint lint-all format format-all install docs
 .DEFAULT_GOAL = help
 
 # extracts the help text and formats it nicely
@@ -11,18 +11,36 @@ HELP_PARSING = 'm <- readLines("Makefile");\
 help:           ## Show this help.
 	@Rscript -e $(HELP_PARSING)
 
-build:          ## Build the package using lucode2::buildLibrary()
-	Rscript -e 'lucode2::buildLibrary()'
+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()
+                ## 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()
+lint:           ## Check if code etiquette is followed using lucode2::lint().
+                ## Only checks files you changed.
 	Rscript -e 'lucode2::lint()'
 
-format:         ## Apply auto-formatting to changed files and lint afterwards
+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()'

README.md

@@ -1,8 +1,8 @@
 # IAMC Tools
 
-R package **iamc**, version **0.29.7**
+R package **iamc**, version **0.29.8**
 
-[![CRAN status](https://www.r-pkg.org/badges/version/iamc)](https://cran.r-project.org/package=iamc)  [![R build status](https://github.com/orichters/iamc/workflows/check/badge.svg)](https://github.com/orichters/iamc/actions) [![codecov](https://codecov.io/gh/orichters/iamc/branch/master/graph/badge.svg)](https://app.codecov.io/gh/orichters/iamc) [![r-universe](https://pik-piam.r-universe.dev/badges/iamc)](https://pik-piam.r-universe.dev/ui#builds)
+[![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)
 
 ## Purpose and Functionality
 
@@ -46,15 +46,15 @@ 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 (2022). _iamc: IAMC Tools_. R package version 0.29.7.
+Dietrich J, Auer C, Giannousakis A, Bertram C, Benke F, Humpenoeder F, Baumstark L (2023). _iamc: IAMC Tools_. R package version 0.29.8.
 
 A BibTeX entry for LaTeX users is
 
  ```latex
 @Manual{,
   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 = {2022},
-  note = {R package version 0.29.7},
+  year = {2023},
+  note = {R package version 0.29.8},
 }
 ```