fix indentation

k4rst3ns · Jul 20, 2023 · ccebf7c · ccebf7c
1 parent 88164ef
commit ccebf7c
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Showing 18 changed files with 95 additions and 108 deletions.
diff --git a/.buildlibrary b/.buildlibrary
@@ -1,4 +1,4 @@
-ValidationKey: '8712610'
+ValidationKey: '8742426'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

diff --git a/CITATION.cff b/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: 'lucode2: Code Manipulation and Analysis Tools'
-version: 0.44.6
-date-released: '2023-06-27'
+version: 0.44.7
+date-released: '2023-07-20'
 abstract: A collection of tools which allow to manipulate and analyze code.
 authors:
 - family-names: Dietrich

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: lucode2
 Title: Code Manipulation and Analysis Tools
-Version: 0.44.6
-Date: 2023-06-27
+Version: 0.44.7
+Date: 2023-07-20
 Authors@R: c(
     person("Jan Philipp", "Dietrich", , "[email protected]", role = c("aut", "cre")),
     person("Pascal", "Führlich", role = "aut"),

diff --git a/R/buildLibrary.R b/R/buildLibrary.R
@@ -230,17 +230,17 @@ handleUpdateType <- function(updateType = NULL, title = "Please choose an update
   if (!is.null(updateType)) {
     # convert character updateType parameters to numbers
     updateType <- switch(as.character(updateType),
-                          "major" = 1,
-                          "1" = 1,
-                          "minor" = 2,
-                          "2" = 2,
-                          "patch" = 3,
-                          "3" = 3,
-                          "development" = 4,
-                          "4" = 4,
-                          "none" = 0,
-                          "0" = 0,
-                          handleUpdateType(title = title))
+                         "major" = 1,
+                         "1" = 1,
+                         "minor" = 2,
+                         "2" = 2,
+                         "patch" = 3,
+                         "3" = 3,
+                         "development" = 4,
+                         "4" = 4,
+                         "none" = 0,
+                         "0" = 0,
+                         handleUpdateType(title = title))
     return(updateType)
   }
   updateType <- c("major revision (for major rewrite of the whole package)",

diff --git a/R/checkRepoUpToDate.R b/R/checkRepoUpToDate.R
@@ -23,7 +23,7 @@ checkRepoUpToDate <- function(pathToRepo = ".", autoCheckRepoUpToDate = TRUE) {
   # check whether we are merging
   gitStatus <- system2("git", "status", stdout = TRUE)
   if ("You have unmerged paths." %in% gitStatus ||
-      "All conflicts fixed but you are still merging." %in% gitStatus) {
+        "All conflicts fixed but you are still merging." %in% gitStatus) {
     # gert::git_ahead_behind will say we are behind during merge, so cannot use auto check
     message("Automatic repo up-to-date check does not work during merge.")
     askUpToDate()
@@ -69,7 +69,7 @@ checkRepoUpToDate <- function(pathToRepo = ".", autoCheckRepoUpToDate = TRUE) {
     }
     if (behindUpstream > 0) {
       errorMessage <- paste0(errorMessage, "\nYou are ", behindUpstream, " commits behind upstream. ",
-                              "Please run:\ngit pull upstream ", usethis::git_default_branch())
+                             "Please run:\ngit pull upstream ", usethis::git_default_branch())
     }
     stop(errorMessage)
   } else {

diff --git a/R/citationDoi.R b/R/citationDoi.R
@@ -8,10 +8,8 @@ citationDoi <- function(meta) {
     tmp <- strsplit(cit$note, ",[ \n]*")[[1]]
     urls <- grep("http", tmp, value = TRUE)
     cit$note <- paste0(grep("http", tmp, value = TRUE, invert = TRUE), collapse = ", ")
-    cit$doi <- gsub(
-      "\n", "", gsub(
-        "https://doi.org/", "", grep(
-          "doi.org", urls, fixed = TRUE, value = TRUE), fixed = TRUE))
+    cit$doi <- gsub("\n", "", gsub("https://doi.org/", "",
+                                   grep("doi.org", urls, fixed = TRUE, value = TRUE), fixed = TRUE))
     cit$url <- c(cit$url, grep("doi.org", urls, fixed = TRUE, value = TRUE, invert = TRUE))
     if (cit$note == "") cit$note <- paste("R package version", meta$Version)
     if (!length(cit$url)) cit$url <- NULL

diff --git a/R/conditionalCopy.R b/R/conditionalCopy.R
@@ -20,8 +20,8 @@ conditionalCopy <- function(relativePath, nameInInstExtdata = basename(relativeP
   dir.create(dirname(relativePath), recursive = TRUE, showWarnings = FALSE)
   if (desc("DESCRIPTION")$get("Package") == "lucode2") {
     if (file.exists(instExtdataPath) && md5sum(relativePath) != md5sum(instExtdataPath) &&
-        (!interactive() || (requireNamespace("testthat", quietly = TRUE) && testthat::is_testing()) ||
-         !askYesNo(paste0("Replace ", instExtdataPath, " with ", relativePath, "?")))) {
+          (!interactive() || (requireNamespace("testthat", quietly = TRUE) && testthat::is_testing()) ||
+             !askYesNo(paste0("Replace ", instExtdataPath, " with ", relativePath, "?")))) {
       stop(relativePath, " != ", instExtdataPath)
     }
     file.copy(relativePath, instExtdataPath, overwrite = TRUE)

diff --git a/R/extract_arguments.R b/R/extract_arguments.R
@@ -33,7 +33,7 @@ extract_arguments <- function(inputArg) {  # nolint
   }
   if (length(strsplit(inputArg, ":")[[1]]) == 2) {
     if (suppressWarnings(is.na(as.integer(strsplit(inputArg, ":")[[1]][1])) |
-                         is.na(as.integer(strsplit(inputArg, ":")[[1]][2])))) {
+                           is.na(as.integer(strsplit(inputArg, ":")[[1]][2])))) {
       extractedArguments <- inputArg
     } else {
       extractedArguments <- as.integer(strsplit(inputArg, ":")[[1]][1]):as.integer(strsplit(inputArg, ":")[[1]][2])

diff --git a/R/manipulateConfig.R b/R/manipulateConfig.R
@@ -40,19 +40,16 @@ manipulateConfig <- function(configFile, ...) {
         rpl <- tmp[[i]]
       }
 
-      m[[paste(i, "_pattern1", sep = "")]][1] <- paste(
-        "(\\$[sS][eE][tT][gG][lL][oO][bB][aA][lL][\\t ]*", i, "[\\t ]).*?( *!!|\\n|$)", sep = "")
-      m[[paste(i, "_pattern1", sep = "")]][2] <- paste(
-        "\\1 ", rpl, "\\2", sep = "")
-      m[[paste(i, "_pattern2", sep = "")]][1] <- paste(
-        "((\\n|^)[\\t ]*(scalar|parameter|set|)s?[\\t ]*", i, "(|\\([^\\)]*\\))(/|[\\t ]+(\"[^\"]*\"|)[^\"/;]*/))[^/]*",
-        sep = "")
-      m[[paste(i, "_pattern2", sep = "")]][2] <- paste(
-        "\\1 ", rpl, " ", sep = "")
-      m[[paste(i, "_pattern3", sep = "")]][1] <- paste(
-        "((^|[\\n\\t ])", i, "[ \\t]*=[ \\t]*[\"\']?)[^\"\';]*", sep = "")
-      m[[paste(i, "_pattern3", sep = "")]][2] <- paste(
-        "\\1", rpl, sep = "")
+      m[[paste(i, "_pattern1", sep = "")]][1] <- paste("(\\$[sS][eE][tT][gG][lL][oO][bB][aA][lL][\\t ]*",
+                                                       i, "[\\t ]).*?( *!!|\\n|$)", sep = "")
+      m[[paste(i, "_pattern1", sep = "")]][2] <- paste("\\1 ", rpl, "\\2", sep = "")
+      m[[paste(i, "_pattern2", sep = "")]][1] <- paste("((\\n|^)[\\t ]*(scalar|parameter|set|)s?[\\t ]*",
+                                                       i, "(|\\([^\\)]*\\))(/|[\\t ]+(\"[^\"]*\"|)[^\"/;]*/))[^/]*",
+                                                       sep = "")
+      m[[paste(i, "_pattern2", sep = "")]][2] <- paste("\\1 ", rpl, " ", sep = "")
+      m[[paste(i, "_pattern3", sep = "")]][1] <- paste("((^|[\\n\\t ])", i, "[ \\t]*=[ \\t]*[\"\']?)[^\"\';]*",
+                                                       sep = "")
+      m[[paste(i, "_pattern3", sep = "")]][2] <- paste("\\1", rpl, sep = "")
     }
   } else if (type %in% c("cfg", "R", "r")) {
     for (i in names(tmp)) {

diff --git a/R/mergestatistics.R b/R/mergestatistics.R
@@ -61,10 +61,10 @@ mergestatistics <- function(dir = ".", file = NULL, renew = FALSE, quickcheck =
     }
     stats$solution <- modelstat
     stats$id <- gsub("\\.[rR]da", "", f)
-    outlist[[stats$id]] <- as.data.table(t(unlist(c(
-      stats[c("user", "date", "version_management", "revision", "revision_date", "solution")],
-      runtime = as.numeric(stats[["runtime"]], units = "hours"),
-      stats$config[!(names(stats$config) %in% removeCols)]))))
+    outlist[[stats$id]] <- as.data.table(t(unlist(c(stats[c("user", "date", "version_management",
+                                                            "revision", "revision_date", "solution")],
+                                                    runtime = as.numeric(stats[["runtime"]], units = "hours"),
+                                                    stats$config[!(names(stats$config) %in% removeCols)]))))
   }
   out <- rbind(out, rbindlist(outlist, fill = TRUE, idcol = TRUE), fill = TRUE)
   out <- as.data.table(lapply(out, function(x) return(type.convert(as.character(x), as.is = TRUE))))

diff --git a/R/package2readme.R b/R/package2readme.R
@@ -135,9 +135,7 @@ package2readme <- function(package = ".", add = NULL, logo = NULL) { # nolint
     if (!is.null(folder)) {
       try({
         projectPath <- normalizePath(folder, mustWork = TRUE, winslash = "/")
-        ci <- citationDoi(packageDescription(
-          basename(projectPath),
-          lib.loc = dirname(projectPath)))
+        ci <- citationDoi(packageDescription(basename(projectPath), lib.loc = dirname(projectPath)))
       })
     }
     # If previous code did not work or folder is not set, get citation from installed package.

diff --git a/R/packageInfo.R b/R/packageInfo.R
@@ -18,9 +18,9 @@ packageInfo <- function(package, repos = c("https://cran.rstudio.com/",
     installed <- "<never>"
   } else {
     version <- as.character(version)
-    installed <- paste(
-      as.integer(difftime(Sys.time(), file.mtime(system.file("DESCRIPTION", package = package)), units = "mins")),
-      "minutes ago")
+    installed <- paste(as.integer(difftime(Sys.time(),
+                                           file.mtime(system.file("DESCRIPTION", package = package)), units = "mins")),
+                       "minutes ago")
   }
 
   cat("\nPackage:", package, "\n")
@@ -31,9 +31,8 @@ packageInfo <- function(package, repos = c("https://cran.rstudio.com/",
     cat("Availability in repositories:\n")
     v <- list()
     for (r in repos) {
-      v$r <- tryCatch(
-        available.packages(file.path(r, "src", "contrib"))[package, "Version"],
-        error = function(e) return("<not available>"))
+      v$r <- tryCatch(available.packages(file.path(r, "src", "contrib"))[package, "Version"],
+                      error = function(e) return("<not available>"))
       cat(v$r, "|", r, "\n")
     }
     cat("\n")

diff --git a/R/readArgs.R b/R/readArgs.R
@@ -56,15 +56,15 @@
 #'
 #' ### function that reads all allowed arguments from command line ###
 readArgs <- function(..., .argv = commandArgs(trailingOnly = TRUE),
-                          .envir = parent.frame(), .flags = NULL, .silent = FALSE) {
+                     .envir = parent.frame(), .flags = NULL, .silent = FALSE) {
   allowedArgs <- c(...)
   # search for strings that look like -i1asrR and transform them into long flags
   oneDashFlags <- unlist(strsplit(paste0(.argv[grepl("^-[a-zA-Z0-9]*$", .argv)], collapse = ""), split = ""))
   twoDashFlags <- .argv[grepl("^--[a-zA-Z0-9]*$", .argv) & .argv %in% .flags]
   knownFlags <- sort(unique(c(twoDashFlags, unlist(.flags[names(.flags) %in% oneDashFlags]))))
-  unknownFlags <- c(sort(paste0("-", oneDashFlags)[! oneDashFlags %in% c(names(.flags), "-")]),
-                    .argv[grepl("^--[a-zA-Z0-9]*$", .argv) & ! .argv %in% .flags])
-  .argv <- .argv[! grepl("^-", .argv)]
+  unknownFlags <- c(sort(paste0("-", oneDashFlags)[!oneDashFlags %in% c(names(.flags), "-")]),
+                    .argv[grepl("^--[a-zA-Z0-9]*$", .argv) & !.argv %in% .flags])
+  .argv <- .argv[!grepl("^-", .argv)]
   if (length(.argv) > 0) {
     ### apply additional command line arguments ###
     for (argnr in seq_along(.argv)) {

diff --git a/R/readRuntime.R b/R/readRuntime.R
@@ -206,9 +206,9 @@ readRuntime <- function(path, plot = FALSE, types = NULL, coupled = FALSE, outfn
     }
 
     pSorted <- ggplot2::ggplot(data = runtime,
-                                ggplot2::aes_string(x = "run",
-                                                    y = "value",
-                                                    fill = ifelse(is.null(types), "NULL", "type"))) +
+                               ggplot2::aes_string(x = "run",
+                                                   y = "value",
+                                                   fill = ifelse(is.null(types), "NULL", "type"))) +
       ggplot2::geom_bar(colour = "black", stat = "identity") +
       ggplot2::coord_flip() +
       ggplot2::ylab(yUnit) +
@@ -225,7 +225,7 @@ readRuntime <- function(path, plot = FALSE, types = NULL, coupled = FALSE, outfn
              section = factor(.data$section, levels = c("total", "prep", "GAMS", "output"), ordered = TRUE))
 
     pTimeline <- ggplot2::ggplot(dat, ggplot2::aes_string(color = ifelse(is.null(types), "NULL", "type"),
-                                                           alpha = "section")) +
+                                                          alpha = "section")) +
       ggplot2::geom_segment(ggplot2::aes_string(x = "start", xend = "end", y = "run", yend = "run"), size = 6) +
       ggplot2::scale_alpha_manual(values = c("total" = 1, "prep" = 0.5, "GAMS" = 1, "output" = 0.5)) +
       ggplot2::scale_color_manual(values = c("rem" = "royalblue3", "mag" = "seagreen")) +

diff --git a/R/updateRepo.R b/R/updateRepo.R
@@ -35,8 +35,8 @@ updateRepo <- function(path = ".", check = TRUE, forceRebuild = FALSE, clean = T
   repoPaths <- list.dirs(path, recursive = FALSE)
   packageNames <- basename(repoPaths)
   repoPaths <- repoPaths[!startsWith(packageNames, ".") &
-                         !(packageNames %in% skipFolders) &
-                         dir.exists(file.path(repoPaths, ".git"))]
+                           !(packageNames %in% skipFolders) &
+                           dir.exists(file.path(repoPaths, ".git"))]
   repoPaths <- repoPaths[order(tolower(repoPaths))]
 
   collectedErrors <- lapply(repoPaths, function(repoPath) {
@@ -87,8 +87,8 @@ updateRepo <- function(path = ".", check = TRUE, forceRebuild = FALSE, clean = T
 
         # add metadata such as remote url to DESCRIPTION e.g. for renv
         remoteUrl <- sub("git@github\\.com:(.+)\\.git",
-                          "https://github.com/\\1",
-                          gert::git_remote_info(repo = repoPath)$url)
+                         "https://github.com/\\1",
+                         gert::git_remote_info(repo = repoPath)$url)
         cat("Repository: ", repoUrl, "\n",
             "RemoteUrl: ", remoteUrl, "\n",
             "RemoteRef: HEAD\n",
@@ -125,7 +125,7 @@ updateRepo <- function(path = ".", check = TRUE, forceRebuild = FALSE, clean = T
         if (cranversion > currentVersion && cranversion > newVersion) {
           message(" .::WARNING! CRAN: ", availablePackagesOnCran[packageName, "Version"], " !WARNING::.")
           stop("Package version of package \"", packageName, "\" is newer on CRAN (", cranversion,
-                ") compared to PIK-CRAN (", currentVersion, ")! Check version on CRAN immediatly!")
+               ") compared to PIK-CRAN (", currentVersion, ")! Check version on CRAN immediatly!")
         } else {
           message(" .::CRAN: ", availablePackagesOnCran[packageName, "Version"], "::.")
         }

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # Code Manipulation and Analysis Tools
 
-R package **lucode2**, version **0.44.6**
+R package **lucode2**, version **0.44.7**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/lucode2)](https://cran.r-project.org/package=lucode2) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4389418.svg)](https://doi.org/10.5281/zenodo.4389418) [![R build status](https://github.com/pik-piam/lucode2/workflows/check/badge.svg)](https://github.com/pik-piam/lucode2/actions) [![codecov](https://codecov.io/gh/pik-piam/lucode2/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/lucode2) [![r-universe](https://pik-piam.r-universe.dev/badges/lucode2)](https://pik-piam.r-universe.dev/builds)
 
@@ -39,7 +39,7 @@ In case of questions / problems please contact Jan Philipp Dietrich <dietrich@pi
 
 To cite package **lucode2** in publications use:
 
-Dietrich J, Führlich P, Klein D, Giannousakis A, Bonsch M, Bodirsky B, Baumstark L, Richters O, Pflüger M (2023). _lucode2: Code Manipulation and Analysis Tools_. doi:10.5281/zenodo.4389418 <https://doi.org/10.5281/zenodo.4389418>, R package version 0.44.6, <https://github.com/pik-piam/lucode2>.
+Dietrich J, Führlich P, Klein D, Giannousakis A, Bonsch M, Bodirsky B, Baumstark L, Richters O, Pflüger M (2023). _lucode2: Code Manipulation and Analysis Tools_. doi:10.5281/zenodo.4389418 <https://doi.org/10.5281/zenodo.4389418>, R package version 0.44.7, <https://github.com/pik-piam/lucode2>.
 
 A BibTeX entry for LaTeX users is
 
@@ -48,7 +48,7 @@ A BibTeX entry for LaTeX users is
   title = {lucode2: Code Manipulation and Analysis Tools},
   author = {Jan Philipp Dietrich and Pascal Führlich and David Klein and Anastasis Giannousakis and Markus Bonsch and Benjamin Leon Bodirsky and Lavinia Baumstark and Oliver Richters and Mika Pflüger},
   year = {2023},
-  note = {R package version 0.44.6},
+  note = {R package version 0.44.7},
   doi = {10.5281/zenodo.4389418},
   url = {https://github.com/pik-piam/lucode2},
 }