version 0.1.10

cran · Jun 16, 2023 · 40501eb · 40501eb
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: PaRe
 Type: Package
 Title: A Way to Perform Code Review or QA on Other Packages
-Version: 0.1.9
+Version: 0.1.10
 Language: en-US
 Authors@R: 
     person("Maarten", "van Kessel", email = "m.l.vankessel@erasmusmc.nl",
@@ -20,11 +20,13 @@ Imports: cli (>= 3.6.0), cyclocomp (>= 1.1.0), desc (>= 1.4.2),
         pak (>= 0.2.0), rmarkdown (>= 2.20), rsvg (>= 2.4.0), stringr
         (>= 1.5.0), igraph (>= 1.3.5), utils, R6 (>= 2.5.1), git2r (>=
         0.31.0), checkmate (>= 2.1.0)
-Suggests: ggplot2, plotly, ggraph, DT, magick, withr, cowplot, knitr
+Suggests: ggplot2, plotly, ggraph, DT, magick, withr, cowplot, knitr,
+        testthat (>= 3.0.0)
 VignetteBuilder: knitr
+Config/testthat/edition: 3
 NeedsCompilation: no
-Packaged: 2023-06-12 12:14:34 UTC; mvankessel
+Packaged: 2023-06-16 14:37:21 UTC; mvankessel
 Author: Maarten van Kessel [aut, cre]
 Maintainer: Maarten van Kessel <m.l.vankessel@erasmusmc.nl>
 Repository: CRAN
-Date/Publication: 2023-06-12 12:30:03 UTC
+Date/Publication: 2023-06-16 14:50:02 UTC
diff --git a/MD5 b/MD5
@@ -1,15 +1,16 @@
-e09ddd1580ba2e63d5a05a4322713403 *DESCRIPTION
-1f8872827c5944a4083e3a67e01f02d0 *NAMESPACE
-4f3c2760a56948a8c2890621cade4ece *NEWS.md
+157d493b8ec1ebc52c399ce32ae53725 *DESCRIPTION
+7ce7e89c91aa1cf431f5cecc99b745c9 *NAMESPACE
+4551cba1583b3a5c71f94c1b335e94ab *NEWS.md
 5c8bca3dc5926d17a2a309d1dbc4c7bf *R/PaRe-package.R
 690883c60013852f5e1e67c9e1e20c61 *R/R6-Code.R
 9f0aa369b24fc227f2ed394b6a74331e *R/R6-File.R
-d25793e59157161699a9e85b28d038c3 *R/R6-Function.R
-24f819cfb13f35164527051d1f25ce96 *R/R6-Repository.R
-759240826d491eb327652b7ad6de4c1e *R/callInvestigators.R
-fbc031d8397fe8efb4d64f6cdc05c7c3 *R/checkDependencies.R
+dd0993d10da9e466ba267ffc2a3821fc *R/R6-Function.R
+22fa355e3237367cab984a8fa48d7202 *R/R6-Repository.R
+eae9034b467cf7b59cc740360860b681 *R/addPareArticle.R
+7912f53547507127ab036551abc1472c *R/callInvestigators.R
+7f36ee141ef4ff64d18fe4a920653c7c *R/checkDependencies.R
 52ccf7d4a66821ba4cc94aa1db884cc7 *R/countPackageLines.R
-83cc4f68f21c3bfbf759926af08624c5 *R/getDefaultPermittedPackages.R
+fae4f2918fc0dbdd7fc4875343dd30f2 *R/getDefaultPermittedPackages.R
 e95fbb0329c0e82edd8ffd93e3bc909e *R/getDefinedFunctions.R
 69852b6bfc046756a05a93a2e2d3a023 *R/getFunctionDiagram.R
 4d443a770d57ac467518f85be4908f08 *R/getFunctionUse.R
@@ -23,17 +24,18 @@ cf794928715019cf81bd51d467156178 *R/utils-pipe.R
 b29edef0eaedf18b9a00f64e65c4647c *inst/WORDLIST
 aeb3de472dbf4860bbea20ecd9ab8497 *inst/doc/Documentation.R
 a84e134bd7a35928e8d001467d70c5c2 *inst/doc/Documentation.Rmd
-b3e79e0dccf3f9d3f2ae4d5f5ce394ca *inst/doc/Documentation.html
+e01df61baf190f92a040c28dde1c8f9b *inst/doc/Documentation.html
 d62b3c4c1af50d76ef77784a8cb26bd1 *inst/img/logo.png
-a48bb48401b7f3d9405b85111c0a6262 *inst/rmd/ReportInjectable.Rmd
-70fbd9c5231bc16201c45c9c271d8f2b *inst/rmd/report.Rmd
+ae0c22d8657758a685abc4a70ddffc76 *inst/rmd/ReportInjectable.Rmd
+bed6ce49704747db142f98cba8638968 *inst/rmd/report.Rmd
 40a1c71111751992f944d14f4c839718 *inst/testScript.R
 1c6f840fc50c6d11fd8c53b2cedbdb65 *inst/whiteList.csv
 4fe9810cdec58eda3bfd93e477573bf0 *man/Code.Rd
-fb1c213c6b9774076e61f655dbb9afc5 *man/File.Rd
-e05e6a2583a3a1d45895a14c200d8487 *man/Function.Rd
-0b662bfc2940703b4776f7eca130e4d9 *man/PaRe-package.Rd
+b77ebe242a5c024c080f6d834e5943fa *man/File.Rd
+9bc04719441eaa99b18a3b8727add56c *man/Function.Rd
+e4a62c4e74f164ac71ff62a6ebf51486 *man/PaRe-package.Rd
 2a106d209f264abd4bb8eba10424d299 *man/Repository.Rd
+902f611637db6d22f6b3be2e1b3ae6f0 *man/addPareArticle.Rd
 9efdbb8f255557ca0e1aed582a822e4a *man/checkDependencies.Rd
 191038bb66a3ca92eb08629a684471fa *man/checkInstalled.Rd
 5d24f00a3b1c79f76e517767facab5d9 *man/countPackageLines.Rd
@@ -67,6 +69,18 @@ d14143c9b0a631d6ee07e9da956d9867 *man/getGraphData.Rd
 5ef87067fec0edf62a0670b70e14c467 *man/pkgDiagram.Rd
 e0db61bd097f0f30c129ec957562e993 *man/printMessage.Rd
 d33e53f5d0121239eb85c6150e326189 *man/whiteList.Rd
+32502e0a19a7dba5b947b24955a39d27 *tests/testthat.R
+fd919324481ccdcd647a679d1de26afd *tests/testthat/setup.R
+b6e151a5e54d5dc34312a481e6c64d7e *tests/testthat/test-addPareArticle.R
+6315cb1b1ea84edf3b8d85233271ec6c *tests/testthat/test-checkDependencies.R
+9f686ad86c212d391877685b38b5204d *tests/testthat/test-getApplyCall.R
+3ced46199bfdc613138a60c3c37cd22f *tests/testthat/test-getApplyFromLines.R
+08c6cbd34629e5ea22a1460ec2836ec5 *tests/testthat/test-getDlplyCall.R
+04aa0d38401fe145668737f6ea7e9d1c *tests/testthat/test-getDlplyCallFromLines.R
+8c63ce7226f879d1a27630df22dc5ebb *tests/testthat/test-getDoCall.R
+c9152ed5f259c127d8becfc40464d48f *tests/testthat/test-getDoCallFromLines.R
+c37e7ffff7ce12875d2ff4374a4932d5 *tests/testthat/test-getFunCall.R
+6670ead09cc590eb2aed1476cb071abd *tests/testthat/test-getMultiLineFun.R
 a84e134bd7a35928e8d001467d70c5c2 *vignettes/Documentation.Rmd
 08d9d6b171b970059f24dabd6c576712 *vignettes/img/glueDiagram.svg
 78c2ea0c0cc50c7ba60892bc9e42e460 *vignettes/img/glueGraph.png
diff --git a/NAMESPACE b/NAMESPACE
@@ -4,6 +4,7 @@ export("%>%")
 export(File)
 export(Function)
 export(Repository)
+export(addPareArticle)
 export(checkDependencies)
 export(countPackageLines)
 export(exportDiagram)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,24 @@
+PaRe 0.1.10
+==========
+1. Fixed issue with pattern matching of files in .gitignore.
+2. Fixed issue with retrieving the correct amount of arguments from a function.
+3. Changed colour highlights for report.
+4. Added addPareArticle function to add a PaRe report as an article.
+5. Added setup for unittesting.
+6. Added unittest for:
+    - getDefaultPermittedPackages
+    - addPareArticle
+    - getApplyCall
+    - getApplyFromLines
+    - getDlplyCall
+    - getDlplyCallFromLines
+    - getDoCall
+    - getDoCallFromLines
+    - getFunCall
+    - getMultiLineFun
+    - checkDependencies
+7. Fixed issue detecting functions called by plyr::dlply
+
 PaRe 0.1.9
 ==========
 1. Added CRAN badge to README

diff --git a/R/R6-Function.R b/R/R6-Function.R
@@ -107,11 +107,11 @@ Function <- R6::R6Class(
       return(invisible(self))
     },
     getNArgs = function() {
-      nArgs <- private$lines[1] %>%
-        stringr::str_remove_all(pattern = "\\s") %>%
-        stringr::str_split_i(pattern = "function\\(", i = 2) %>%
-        stringr::str_split_i(pattern = "\\)\\{", i = 1) %>%
-        stringr::str_remove_all(pattern = "\\w+\\(.+\\)") %>%
+      nArgs <- getMultiLineFun(line = 1, lines = private$lines) %>%
+        stringr::str_replace_all(pattern = "[ ]?=.+", replacement = ",") %>%
+        paste0(collapse = "") %>%
+        stringr::str_split_i(pattern = "function\\(", 2) %>%
+        stringr::str_split_i(pattern = "\\)[ ]?\\{", 1) %>%
         stringr::str_split(pattern = ",") %>%
         unlist() %>%
         length()

diff --git a/R/R6-Repository.R b/R/R6-Repository.R
@@ -58,7 +58,7 @@ Repository <- R6::R6Class(
       private$git <- git2r::in_repository(private$path)
       private$description <- desc::description$new(private$path)
       private$functionUse <- NULL
-      private$gitIgnore <- readLines(file.path(private$path, ".gitignore"), warn = FALSE)
+      private$gitIgnore <- private$setupGitIgnore()
       private$validate()
 
       private$fetchRFiles()
@@ -207,8 +207,6 @@ Repository <- R6::R6Class(
     description = NULL,
     functionUse = NULL,
     gitIgnore = c(),
-
-
     validate = function() {
       errorMessages <- checkmate::makeAssertCollection()
       # .rproj file
@@ -225,15 +223,22 @@ Repository <- R6::R6Class(
       }
       return(invisible(self))
     },
-
-
+    setupGitIgnore = function() {
+      ignorePath <- file.path(private$path, ".gitignore")
+      if (file.exists(ignorePath)) {
+        gitIgnore <- readLines(ignorePath, warn = FALSE)
+        gitIgnore <- gitIgnore[!startsWith(x = gitIgnore, prefix = "#")]
+        gitIgnore <- gitIgnore[!gitIgnore == ""]
+        gitIgnore <- stringr::str_replace_all(string = gitIgnore, pattern = "\\*", replacement = ".")
+        private$gitIgnore <- gitIgnore
+      }
+    },
     filterIgnored = function(paths) {
       for (pat in private$gitIgnore) {
         paths <- paths[!grepl(pattern = pat, x = paths)]
       }
       return(paths)
     },
-
     fetchRFiles = function() {
       paths <- list.files(file.path(private$path, "R"), recursive = TRUE) %>%
         private$filterIgnored()
@@ -243,13 +248,12 @@ Repository <- R6::R6Class(
       }))
       return(invisible(self))
     },
-
-
     fetchCppFiles = function() {
       paths <- list.files(
         path = private$path,
         pattern = "\\.(cpp|O|h)$",
-        recursive = TRUE) %>%
+        recursive = TRUE
+      ) %>%
         private$filterIgnored()
 
       cpp <- paths[endsWith(paths, ".cpp")]
@@ -268,8 +272,6 @@ Repository <- R6::R6Class(
         File$new(repoPath = private$path, filePath = path)
       })
     },
-
-
     fetchJavaFiles = function() {
       paths <- list.files(path = private$path, pattern = "\\.java$", recursive = TRUE)
       paths <- paths[endsWith(paths, ".java")] %>%
@@ -279,13 +281,12 @@ Repository <- R6::R6Class(
         File$new(repoPath = private$path, filePath = path)
       })
     },
-
-
     fetchSqlFiles = function() {
       paths <- list.files(
         path = private$path,
         pattern = "\\.sql$",
-        recursive = TRUE) %>%
+        recursive = TRUE
+      ) %>%
         private$filterIgnored()
 
       private$sqlFiles <- lapply(paths, function(path) {

diff --git a/R/addPareArticle.R b/R/addPareArticle.R
@@ -0,0 +1,69 @@
+#' addPareArticle
+#'
+#' Writes an Rmd-file to `./vignettes/articles/PaReReport.Rmd`. The relative
+#' path is dictated by the specified path in the \link[PaRe]{Repository} object.
+#'
+#' @param repo (\link[PaRe]{Repository})
+#' Repository object.
+#'
+#' @return `NULL`
+#' Writes Rmd-file to ./vignettes/articles/PaReReport.Rmd
+#'
+#' @export
+#'
+#' @examples
+#' fetchedRepo <- tryCatch(
+#'   {
+#'     # Set dir to clone repository to.
+#'     tempDir <- tempdir()
+#'     pathToRepo <- file.path(tempDir, "glue")
+#'
+#'     # Clone repo
+#'     git2r::clone(
+#'       url = "https://github.com/darwin-eu/IncidencePrevalence.git",
+#'       local_path = pathToRepo
+#'     )
+#'
+#'     # Create instance of Repository object.
+#'     repo <- PaRe::Repository$new(path = pathToRepo)
+#'
+#'     # Set fetchedRepo to TRUE if all goes well.
+#'     TRUE
+#'   },
+#'   error = function(e) {
+#'     # Set fetchedRepo to FALSE if an error is encountered.
+#'     FALSE
+#'   },
+#'   warning = function(w) {
+#'     # Set fetchedRepo to FALSE if a warning is encountered.
+#'     FALSE
+#'   }
+#' )
+#'
+#' if (fetchedRepo) {
+#'   # Run makeReport on the Repository object.
+#'   addPaReArticle(repo)
+#' }
+addPareArticle <- function(repo) {
+  injected <- readLines(
+    con = system.file(package = "PaRe", "rmd", "ReportInjectable.Rmd")
+  ) %>%
+    gsub(
+      pattern = "#!P_TITLE",
+      replacement = glue::glue("{repo$getName()} [{repo$getDescription()$get_version()}]")
+    ) %>%
+    gsub(
+      pattern = "#!P_PATH",
+      replacement = repo$getPath()
+    )
+
+  dir.create(file.path(repo$getPath(), "vignettes", "articles"))
+
+  writeLines(
+    text = injected,
+    con = file.path(
+      repo$getPath(), "vignettes", "articles", "PareReport.Rmd"
+    )
+  )
+  return(invisible(NULL))
+}
diff --git a/R/callInvestigators.R b/R/callInvestigators.R
@@ -44,8 +44,8 @@ getDlplyCallFromLines <- function(lines) {
     funCall %>%
       stringr::str_remove_all("\\s") %>%
       stringr::str_split_i(pattern = "dlply\\(", i = 2) %>%
-      stringr::str_split_i(pattern = ",", i = 4) %>%
-      stringr::str_extract(pattern = "\\=\\w+") %>%
+      stringr::str_split_i(pattern = ",", i = 3) %>%
+      stringr::str_extract(pattern = "[\\=]?\\w+") %>%
       stringr::str_extract(pattern = "\\w+")
   })
 }
@@ -80,18 +80,18 @@ getDlplyCall <- function(fun, defFuns) {
 #'
 #' @return (\link[base]{character})
 getApplyFromLines <- function(lines) {
-  pattern <- "[\\w+]?[Aa]pply\\("
+  pattern <- "[\\w+]?[Aa]pply(LB)?\\("
   indices <- grep(pattern, lines)
   unlist(lapply(indices, function(index) {
     funCall <- paste0(getMultiLineFun(index, lines), collapse = " ")
     if (!stringr::str_detect(string = funCall, pattern = "function[ ]?\\(")) {
       funCall <- funCall %>%
         stringr::str_remove_all(pattern = "(\\s)")
 
+      pat <- ",(?=[FUN=]?\\w+?\\w+)"
+
       if (grepl(pattern = "cluster", x = funCall)) {
         pat <- ",(?=[FUN=]?\\w+?\\w+\\))"
-      } else {
-        pat <- ",(?=[FUN=]?\\w+?\\w+)"
       }
 
       funCall <- funCall %>%

diff --git a/R/checkDependencies.R b/R/checkDependencies.R
@@ -144,9 +144,7 @@ checkDependencies <- function(
 
   dependencies <- description$get_deps() %>%
     dplyr::filter(.data$type %in% dependencyType) %>%
-    dplyr::select("package", "version")
-
-  dependencies <- dependencies %>%
+    dplyr::select("package", "version") %>%
     dplyr::filter(.data$package != "R")
 
   dependencies$version <- stringr::str_remove(

diff --git a/R/getDefaultPermittedPackages.R b/R/getDefaultPermittedPackages.R
@@ -18,26 +18,26 @@
 #'
 #' @examples
 #' \donttest{
-#'   # Set cache
-#'   withr::local_envvar(
-#'     R_USER_CACHE_DIR = tempfile()
-#'   )
+#' # Set cache
+#' withr::local_envvar(
+#'   R_USER_CACHE_DIR = tempfile()
+#' )
 #'
-#'   if (interactive()) {
-#'     getDefaultPermittedPackages()
-#'   }
+#' if (interactive()) {
+#'   getDefaultPermittedPackages()
+#' }
 #' }
 getDefaultPermittedPackages <- function(base = TRUE) {
   # Custom list
   tryCatch(
     {
-      customWhiteList <- dplyr::bind_rows(lapply(seq_len(nrow(whiteList)), function(i) {
+      customWhiteList <- dplyr::bind_rows(lapply(seq_len(nrow(PaRe::whiteList)), function(i) {
         pkgs <- utils::read.table(
-          file = unlist(whiteList[i, ]["link"]),
+          file = unlist(PaRe::whiteList[i, ]["link"]),
           sep = ",",
           header = TRUE
         ) %>%
-          select(unlist(whiteList[i, ]["package"]), unlist(whiteList[i, ]["version"]))
+          select(unlist(PaRe::whiteList[i, ]["package"]), unlist(PaRe::whiteList[i, ]["version"]))
       }))
 
       basePackages <- NULL
@@ -76,7 +76,6 @@ getDefaultPermittedPackages <- function(base = TRUE) {
       permittedPackages
     },
     error = function(e) {
-      print(e)
       message(e)
       NULL
     },