Merge pull request #23 from DominikRafacz/release/0.3

release 0.3.0

DESCRIPTION

@@ -1,12 +1,13 @@
 Package: deepdep
 Title: Visualise and Explore the Deep Dependencies of R Packages 
-Version: 0.2.5.4
+Version: 0.3.0
 Authors@R: c(person("Dominik", "Rafacz", email = "[email protected]",
                   role = c("aut", "cre"),
                   comment = c(ORCID = "0000-0003-0925-1909")),
              person("Hubert", "Baniecki", role = c("aut")),
              person("Szymon", "Maksymiuk", role = c("aut")),
-             person("Mateusz", "Bakala", role = c("aut")))
+             person("Laura", "Bakala", role = c("aut")),
+             person("Dirk", "Eddelbuettel", role = c("ctb")))
 Description: Provides tools for exploration of R package dependencies. 
     The main deepdep() function allows to acquire deep dependencies of any package and plot them in an elegant way.
     It also adds some popularity measures for the packages e.g. in the form of download count through the 'cranlogs' package. 

NEWS.md

@@ -1,3 +1,7 @@
+# deepdep 0.3.0
+* adjusted `dependency_type` argument to be consistent with `tools` package (issue #19)
+* added `show_stamp` parameter for plot function (issue #20)
+
 # deepdep 0.2.5
 * wrapped `deepdep` in tests with `tryCatch` in case of R-devel and Bioc-devel versions mismatch
 * marked all non-local examples with "donttest"

R/get_dependencies.R

@@ -9,8 +9,11 @@
 #' @param bioc A \code{logical} value. If \code{TRUE} the Bioconductor dependencies data will be taken from the
 #' Bioconductor repository. For this option to work properly, \code{BiocManager} package needs to be installed.
 #' @param local A \code{logical} value. If \code{TRUE} only data of locally installed packages will be used (without API usage).
-#' @param dependency_type A \code{character} vector. Types of the dependencies that should be sought.
-#' Possibilities are: \code{"Imports", "Depends", "Suggests", "Enhances", "LinkingTo"}. By default it's \code{"Depends", "Imports"}.
+#' @param dependency_type A \code{character} vector. Types of the dependencies that should be sought, a subset of
+#' \code{c("Imports", "Depends", "LinkingTo", "Suggests", "Enhances")}. Other possibilities are: character string
+#' \code{"all"}, a shorthand for the whole vector; character string \code{"most"} for the same vector without \code{"Enhances"};
+#' character string \code{"strong"} (default) for the first three elements of that vector. Works analogously to
+#' \code{\link[tools]{package_dependencies}}.
 #'
 #' @return An object of \code{package_dependencies} class.
 #'
@@ -29,16 +32,12 @@
 #'
 #' @export
 get_dependencies <- function(package, downloads = TRUE, bioc = FALSE, local = FALSE,
-                             dependency_type = c("Depends", "Imports")) {
+                             dependency_type = "strong") {
 
   if (downloads && (local || bioc)) stop("If you use downloads, you cannot use",
                                          " neither bioc nor local")
 
-  possible_types <- c("Depends", "Imports", "Suggests", "Enhances", "LinkingTo")
-
-  dependency_type <- unique(dependency_type)
-  if (!all(dependency_type %in% possible_types) || length(dependency_type) < 1)
-    stop("'dependency_type' should specify which types of dependencies should be included")
+  dependency_type <- match_dependency_type(dependency_type)
 
   l_dependency_type <- tolower(dependency_type)
   names(dependency_type) <- l_dependency_type
@@ -98,3 +97,21 @@ get_dependencies <- function(package, downloads = TRUE, bioc = FALSE, local = FA
 print.package_dependencies <- function(x, ...) {
   print.data.frame(x)
 }
+
+#' Match vector of dependency types
+#'
+#' @inheritParams get_dependencies
+#'
+#' Based on `tools:::.expand_dependency_type_spec`, according to the suggestion of Dirk Eddelbuettel
+#'
+#' @noRd
+match_dependency_type <- function(dependency_type) {
+  possible_types <- c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")
+
+  if (identical(dependency_type, "strong")) possible_types[1:3]
+  else if (identical(dependency_type, "most")) possible_types[1:4]
+  else if (identical(dependency_type, "all")) possible_types
+  else if (!all(dependency_type %in% possible_types) || length(dependency_type) < 1)
+    stop("'dependency_type' should specify which types of dependencies should be included")
+  else dependency_type
+}

R/plot_deepdep.R

@@ -15,6 +15,8 @@
 #' displayed below package name. Defaults to \code{FALSE}.
 #' @param show_downloads A \code{logical}. If \code{TRUE} total number of downloads of packages
 #' will be displayed below package names. Defaults to \code{FALSE}.
+#' @param show_stamp A \code{logical}. If \code{TRUE} (the default) the package version and
+#' plot creation time will be added
 #' @param ... Other arguments passed to the \code{deepdep} function.
 #'
 #' @return A \code{ggplot2, gg, ggraph, deepdep_plot} class object.
@@ -48,32 +50,36 @@
 #' @rdname plot_deepdep
 #' @export
 plot_dependencies <- function(x, type = "circular", same_level = FALSE, reverse = FALSE,
-                              label_percentage = 1, show_version = FALSE, show_downloads = FALSE, ...) {
+                              label_percentage = 1, show_version = FALSE, show_downloads = FALSE,
+                              show_stamp = TRUE, ...) {
   UseMethod("plot_dependencies")
 }
 
 #' @rdname plot_deepdep
 #' @export
 plot_dependencies.default <- function(x, type = "circular", same_level = FALSE, reverse = FALSE,
-                                      label_percentage = 1, show_version = FALSE, show_downloads = FALSE, ...) {
+                                      label_percentage = 1, show_version = FALSE, show_downloads = FALSE,
+                                      show_stamp = TRUE, ...) {
   stop("This type of object does not have implemented method for 'plot_dependencies'")
 }
 
 #' @rdname plot_deepdep
 #' @export
 plot_dependencies.character <- function(x, type = "circular", same_level = FALSE, reverse = FALSE,
-                                      label_percentage = 1, show_version = FALSE, show_downloads = FALSE, ...) {
+                                        label_percentage = 1, show_version = FALSE, show_downloads = FALSE,
+                                        show_stamp = TRUE, ...) {
   package_name <- NULL
   if (show_downloads == TRUE || label_percentage < 1)
     dd <- deepdep(x, downloads = TRUE, ...)
   else dd <- deepdep(x, ...)
-  plot_dependencies(dd, type, same_level, reverse, label_percentage, show_version, show_downloads)
+  plot_dependencies(dd, type, same_level, reverse, label_percentage, show_version, show_downloads, show_stamp)
 }
 
 #' @rdname plot_deepdep
 #' @export
 plot_dependencies.deepdep <- function(x, type = "circular", same_level = FALSE, reverse = FALSE,
-                                      label_percentage = 1, show_version = FALSE, show_downloads = FALSE, ...) {
+                                      label_percentage = 1, show_version = FALSE, show_downloads = FALSE,
+                                      show_stamp = TRUE, ...) {
   # Due to NSE inside of the function, we have to declare "labeled" as NULL to prevent check fail
   labeled <- NULL
   node1.name <- NULL
@@ -144,11 +150,11 @@ plot_dependencies.deepdep <- function(x, type = "circular", same_level = FALSE,
                     aes(label = name, fill = factor(layer)),
                     show.legend = FALSE,
                     label.padding = unit(0.28, "lines")) +
-    default_nodefill_scale(length(levels(factor(V(G)$layer)))) +
-    labs(caption = paste0("Plot made with deepdep v",
-                          packageVersion("deepdep"),
-                          " on ", format(Sys.time(), usetz = FALSE))
-)
+      default_nodefill_scale(length(levels(factor(V(G)$layer))))
+  if (show_stamp)
+    g <- g + labs(caption = paste0("Plot made with deepdep v",
+                                   packageVersion("deepdep"),
+                                   " on ", format(Sys.time(), usetz = FALSE)))
 
   class(g) <- c(class(g), "deepdep_plot")
   g

README.md

@@ -88,9 +88,9 @@ head(dd_xgboost)
 ```
 
     ##    origin       name  version    type last_day last_week last_month last_quarter last_half grand_total origin_level dest_level
-    ## 1 xgboost     Matrix >= 1.1-0 Imports     1861     29118     116069       314379    715420     6726824            0          1
-    ## 2 xgboost data.table >= 1.9.6 Imports    18594    205828     890362      2556360   4586475    30727748            0          1
-    ## 3 xgboost   jsonlite   >= 1.0 Imports    21610    234767     990987      3494965   6879236    50867651            0          1
+    ## 1 xgboost     Matrix >= 1.1-0 Imports     4454     24384     120814       335932    676904     6818520            0          1
+    ## 2 xgboost data.table >= 1.9.6 Imports    35829    203788     847404      2665713   4659980    31369324            0          1
+    ## 3 xgboost   jsonlite   >= 1.0 Imports    36025    246923    1005752      3362575   6707399    51638636            0          1
 
 ``` r
 plot_downloads(dd_xgboost)

inst/WORDLIST

@@ -1,34 +1,20 @@
-andrie
-api
 AppVeyor
-behaviour
-bioconductor
-Cheatsheet
+Bioc
 CircleCI
 Codecov
-cran
-crandb
+DependenciesGraphs
+Github
+Lifecycle
+RCurl
+andrie
+api
 cranlogs
 datastorm
 dep
-deepdep
-DependenciesGraphs
-github
-http
-https
+donttest
 igraph
-interactively
-iteratively
-Lifecycle
-LinkingTo
 md
 miniCRAN
-org
-pkg
 pkgDepTools
 pkgnet
-RCurl
-README
-rstudio
-RStudio
 vactor