increment version

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '2603874'
+ValidationKey: '2754640'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

.github/workflows/check.yaml

@@ -1,5 +1,3 @@
-# Run CI for R using https://eddelbuettel.github.io/r-ci/
-
 name: check
 
 on:
@@ -8,92 +6,45 @@ 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
 
-      - 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
-
-      - name: Set up Pandoc
-        uses: r-lib/actions/setup-pandoc@v2
+      - 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: |
+            gamstransfer=?ignore
+            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@v4
+        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)
@@ -106,6 +57,8 @@ 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: v0.3.2.9025
     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: 'goxygen: In-Code Documentation for ''GAMS'''
-version: 1.3.3
-date-released: '2023-08-09'
+version: 1.4.0
+date-released: '2023-11-15'
 abstract: A collection of tools which extract a model documentation from 'GAMS' code
   and comments. In order to use the package you need to install 'pandoc' and 'pandoc-citeproc'
   first (<https://pandoc.org/>).

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: goxygen
 Type: Package
 Title: In-Code Documentation for 'GAMS'
-Version: 1.3.3
-Date: 2023-08-09
+Version: 1.4.0
+Date: 2023-11-15
 Authors@R: c(person("Jan Philipp", "Dietrich", email = "[email protected]", role = c("aut","cre")),
              person("Kristine", "Karstens", email = "[email protected]", role = "aut"),
              person("David", "Klein", email = "[email protected]", role = "aut"),

R/helper_functions.R

@@ -8,7 +8,7 @@
 #' @export
 #'
 .empty <- function(zz) {
-  writeLines("",zz)
+  writeLines("", zz)
 }
 
 #' .write
@@ -20,8 +20,8 @@
 #' @author Jan Philipp Dietrich
 #' @seealso \code{\link{goxygen}}, \code{\link{createModulePage}}
 #'
-.write <- function(zz,data) {
-  if(!is.null(data)) writeLines(data,zz)
+.write <- function(zz, data) {
+  if (!is.null(data)) writeLines(data, zz)
   .empty(zz)
 }
 
@@ -36,19 +36,19 @@
 #' @author Jan Philipp Dietrich
 #' @seealso \code{\link{goxygen}}, \code{\link{createModulePage}}
 #'
-.header <- function(zz,title,level,id=NULL) {
-  if(length(title)>1) {
+.header <- function(zz, title, level, id = NULL) {
+  if (length(title) > 1) {
     warning("Multiline entry to title detected. Only first line will be used!")
     title <- title[1]
   }
-  if(!is.null(id)) id <- paste0(" {#id-",id,"}")
-  if(level<3) {
-    writeLines(paste0(title,id),zz)
-    symbol <- ifelse(level==1,"=","-")
-    writeLines(paste(rep(symbol,nchar(title)), collapse=""),zz)
+  if (!is.null(id)) id <- paste0(" {#id-", id, "}")
+  if (level < 3) {
+    writeLines(paste0(title, id), zz)
+    symbol <- ifelse(level == 1, "=", "-")
+    writeLines(paste(rep(symbol, nchar(title)), collapse = ""), zz)
   } else {
-    start <- paste(rep("#",level),collapse="")
-    writeLines(paste(start,title),zz)
+    start <- paste(rep("#", level), collapse = "")
+    writeLines(paste(start, title), zz)
   }
   .empty(zz)
 }
@@ -68,7 +68,7 @@
 #' @seealso \code{\link{goxygen}}, \code{\link{createModulePage}}
 #'
 .section <- function(data, zz, title, level, id = NULL) {
-  if(!is.null(data)){
+  if (!is.null(data)) {
     .header(zz, title, level, id)
     .write(zz, data)
   }
@@ -84,12 +84,12 @@
 #' @author Jan Philipp Dietrich
 #' @seealso \code{\link{goxygen}}, \code{\link{createModulePage}}
 #'
-.interfaceplot <- function(zz,name,docfolder) {
-  file <- paste0("images/interfaces_",sub("^[^_]*_","",name),".png")
-  if(file.exists(paste0(docfolder,"/",file))) {
-    .write(zz,paste0("![Interfaces to other modules](",file,"){ height=50% width=100% }"))
+.interfaceplot <- function(zz, name, docfolder) {
+  file <- paste0("images/interfaces_", sub("^[^_]*_", "", name), ".png")
+  if (file.exists(paste0(docfolder, "/", file))) {
+    .write(zz, paste0("![Interfaces to other modules](", file, "){ height=50% width=100% }"))
   } else {
-    .write(zz,"**Interface plot missing!**")
+    .write(zz, "**Interface plot missing!**")
   }
 }
 
@@ -104,14 +104,14 @@
 #' @author Jan Philipp Dietrich
 #' @seealso \code{\link{goxygen}}, \code{\link{createModulePage}}
 #'
-.limitations <- function(zz,limitations, emptyIfNULL=FALSE) {
-  if(is.null(limitations)) {
-    if(emptyIfNULL) return()
+.limitations <- function(zz, limitations, emptyIfNULL = FALSE) {
+  if (is.null(limitations)) {
+    if (emptyIfNULL) return()
     limitations <- "There are no known limitations."
   }
-  limitations <- c("**Limitations**",limitations)
-  limitations <- paste(">",limitations)
-  .write(zz,limitations)
+  limitations <- c("**Limitations**", limitations)
+  limitations <- paste(">", limitations)
+  .write(zz, limitations)
 }
 
 
@@ -124,8 +124,6 @@
 #' @author Jan Philipp Dietrich
 #' @seealso \code{\link{goxygen}}, \code{\link{createModulePage}}
 #'
-.updateImagePaths <- function(x){
-  return(gsub("\\(([^/]*\\.(png|jpg))\\)","(images/\\1)",x))
+.updateImagePaths <- function(x) {
+  return(gsub("\\(([^/]*\\.(png|jpg))\\)", "(images/\\1)", x))
 }
-
-

README.md

@@ -1,6 +1,6 @@
 # In-Code Documentation for 'GAMS'
 
-R package **goxygen**, version **1.3.3**
+R package **goxygen**, version **1.4.0**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/goxygen)](https://cran.r-project.org/package=goxygen) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1411404.svg)](https://doi.org/10.5281/zenodo.1411404) [![R build status](https://github.com/pik-piam/goxygen/workflows/check/badge.svg)](https://github.com/pik-piam/goxygen/actions) [![codecov](https://codecov.io/gh/pik-piam/goxygen/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/goxygen) [![r-universe](https://pik-piam.r-universe.dev/badges/goxygen)](https://pik-piam.r-universe.dev/builds)
 
@@ -48,7 +48,7 @@ In case of questions / problems please contact Jan Philipp Dietrich <dietrich@pi
 
 To cite package **goxygen** in publications use:
 
-Dietrich J, Karstens K, Klein D, Baumstark L (2023). _goxygen: In-Code Documentation for 'GAMS'_. doi:10.5281/zenodo.1411404 <https://doi.org/10.5281/zenodo.1411404>, R package version 1.3.3, <https://github.com/pik-piam/goxygen>.
+Dietrich J, Karstens K, Klein D, Baumstark L (2023). _goxygen: In-Code Documentation for 'GAMS'_. doi:10.5281/zenodo.1411404 <https://doi.org/10.5281/zenodo.1411404>, R package version 1.4.0, <https://github.com/pik-piam/goxygen>.
 
 A BibTeX entry for LaTeX users is
 
@@ -57,7 +57,7 @@ A BibTeX entry for LaTeX users is
   title = {goxygen: In-Code Documentation for 'GAMS'},
   author = {Jan Philipp Dietrich and Kristine Karstens and David Klein and Lavinia Baumstark},
   year = {2023},
-  note = {R package version 1.3.3},
+  note = {R package version 1.4.0},
   doi = {10.5281/zenodo.1411404},
   url = {https://github.com/pik-piam/goxygen},
 }

vignettes/goxygen.Rmd

@@ -37,8 +37,8 @@ setwd(tempdir())
 We take the GAMS code example from this package and save it to `dummymodel-plain`:
 
 ```{r eval=FALSE}
-# copy the folder containing a simple dummy model with goxygen comments 
-file.copy(from = system.file("dummymodel-plain",package="goxygen"), to = ".", recursive = TRUE)
+# copy the folder containing a simple dummy model with goxygen comments
+file.copy(from = system.file("dummymodel-plain", package = "goxygen"), to = ".", recursive = TRUE)
 ```
 
 and execute `goxygen` on this GAMS file to produce the documentation in HTML as well as PDF format.
@@ -108,7 +108,7 @@ Goxygen is tailored to extract the documentation from this modular structure and
 
 ```{r eval=FALSE}
 # copy all files and folders containing the modular dummy model
-file.copy(from = system.file("dummymodel",package="gms"), to = ".", recursive = TRUE)
+file.copy(from = system.file("dummymodel", package = "gms"), to = ".", recursive = TRUE)
 ```
 
 Now execute `goxygen` on the modular GAMS model: