Provide "shortcuts" to kwb.utils' functions

and use new function get_github_token()

NAMESPACE

@@ -50,7 +50,9 @@ importFrom(kwb.pkgstatus,get_github_repos)
 importFrom(kwb.pkgstatus,get_non_r_packages)
 importFrom(kwb.utils,catAndRun)
 importFrom(kwb.utils,multiSubstitute)
+importFrom(kwb.utils,selectColumns)
 importFrom(kwb.utils,selectElements)
+importFrom(kwb.utils,stringList)
 importFrom(lubridate,as_datetime)
 importFrom(magrittr,"%>%")
 importFrom(plotly,ggplotly)

R/create_pkg_codemeta.R

@@ -15,14 +15,14 @@ create_pkg_codemeta <- function(
     dbg = TRUE
 )
 {
-  cat_and_run <- function(msg, expr) {
-    kwb.utils::catAndRun(msg, expr, dbg = dbg, newLine = 3L)
+  run <- function(msg, expr) {
+    cat_and_run(msg, expr, dbg = dbg, newLine = 3L)
   }
 
   # Get package names from input data frame
-  packages <- kwb.utils::selectColumns(pkgs, "name")
+  packages <- select_columns(pkgs, "name")
 
-  cat_and_run("Creating codemeta object", {
+  run("Creating codemeta object", {
 
     withr::with_libpaths(libpath, {
 
@@ -37,12 +37,12 @@ create_pkg_codemeta <- function(
           n,
           ifelse(n > 1L, "packages are", "package is"),
           libpath,
-          kwb.utils::stringList(sort(packages[!is_installed]))
+          string_list(sort(packages[!is_installed]))
         ))
       }
 
       lapply(packages[is_installed], function(package) {
-        cat_and_run(
+        run(
           sprintf("Writing codemeta for R package %s", package),
           try(codemetar::create_codemeta(file.path(libpath, package)))
         )

R/create_universe_pkgs_json.R

@@ -16,7 +16,7 @@ create_universe_pkgs_json <- function(
     group = "KWB-R",
     ignore_pkgs = NULL,
     non_r_packages = kwb.pkgstatus::get_non_r_packages(),
-    github_token = Sys.getenv("GITHUB_PAT")
+    github_token = get_github_token()
 )
 {
   get_github_packages(

R/download_github.R

@@ -9,8 +9,8 @@
 #' @param use_zip should files be downloades as .tar.gz (use_zip=FALSE) or as
 #' .zip files (use_zip=TRUE); default: FALSE
 #' @param quiet print messages (default: TRUE)
-#' @param auth_token auth_token (needed to download "private" repos), default:
-#' Sys.getenv("GITHUB_PAT")
+#' @param auth_token auth_token (needed to download "private" repos).
+#'   Default: pkgmeta:::get_github_token()
 #' @return downloaded repo in dest. folder
 #' @export
 #' @import remotes
@@ -22,7 +22,7 @@ download_github <- function(
     dest_dir = tempdir(),
     use_zip = FALSE,
     quiet = FALSE,
-    auth_token = Sys.getenv("GITHUB_PAT")
+    auth_token = get_github_token()
 )
 {
   repo_sep <- as.vector(

R/get_gh_ratelimit.R

@@ -1,18 +1,18 @@
 #' Get GitHub rate limit
 #'
-#' @param github_token token passed to \link[gh]{gh} (default:
-#' Sys.getenv("GITHUB_PAT")
+#' @param github_token token passed to \link[gh]{gh}.
+#'   Default: pkgmeta:::get_github_token()
 #' @return overview of rate limit
 #' @export
 #' @importFrom dplyr bind_rows
 #' @importFrom gh gh
 #' @importFrom kwb.utils selectElements
 #' @examples
 #' get_gh_ratelimit()
-get_gh_ratelimit <- function(github_token = Sys.getenv("GITHUB_PAT"))
+get_gh_ratelimit <- function(github_token = get_github_token())
 {
   "https://api.github.com/rate_limit" %>%
     gh::gh(.token = github_token) %>%
-    kwb.utils::selectElements("resources") %>%
+    select_elements("resources") %>%
     dplyr::bind_rows(.id = "id")
 }

R/get_github_packages.R

@@ -6,7 +6,7 @@
 #' @param non_r_packages vector with repos that are not R packages (default:
 #' kwb.pkgstatus::get_non_r_packages())
 #' @param github_token optionally a Github token in order to access private
-#' repositories (default: Sys.getenv("GITHUB_PAT"))
+#'   repositories. Default: pkgmeta:::get_github_token()
 #' @return data frame with R packages on Github
 #' @export
 #' @importFrom kwb.pkgstatus get_github_repos get_non_r_packages
@@ -20,7 +20,7 @@ get_github_packages <- function(
     group = "KWB-R",
     ignore_pkgs = NULL,
     non_r_packages = kwb.pkgstatus::get_non_r_packages(),
-    github_token = Sys.getenv("GITHUB_PAT")
+    github_token = get_github_token()
 )
 {
   repos <- kwb.pkgstatus::get_github_repos(group, github_token)

R/get_pkg_dependencies.R

@@ -86,7 +86,7 @@ get_pkg_dependencies_impl <- function(
 
   pkgs_installed %>%
     lapply(function(pkg) {
-      kwb.utils::catAndRun(
+      cat_and_run(
         sprintf(
           "Getting %s dependencies for '%s'",
           ifelse(recursive, "recursive", "non-recursive"),

R/github_commits.R

@@ -2,7 +2,7 @@
 #' Get Github Commits for One Repo
 #'
 #' @param repo full name of Github repo ("owner/repo_name", e.g. "kwb-r/kwb.utils")
-#' @param github_token default: Sys.getenv("GITHUB_PAT")
+#' @param github_token Default: pkgmeta:::get_github_token()
 #'
 #' @return data frame
 #' @export
@@ -17,7 +17,7 @@
 #'}
 get_github_commits <- function(
     repo,
-    github_token = Sys.getenv("GITHUB_PAT")
+    github_token = get_github_token()
 )
 {
   get_commits <- function(repo, per_page = 100L) {
@@ -77,27 +77,28 @@ get_github_commits <- function(
 #'
 #' @param repos vector with full names of Github repos ("owner/repo_name",
 #' e.g. c("kwb-r/kwb.utils", "kwb-r/kwb.ml", "kwb-r/aquanes.report"))
-#' @param github_token default: Sys.getenv("GITHUB_PAT")
+#' @param github_token Default: pkgmeta:::get_github_token()
 #' @return data frame for all repos with releases
 #' @export
 #' @importFrom kwb.utils catAndRun multiSubstitute
 #' @importFrom dplyr bind_rows if_else mutate
 #' @importFrom tidyr separate
 #' @examples
 #' \dontrun{
-#' #repos <- kwb.pkgstatus::get_github_repos(github_token = Sys.getenv("GITHUB_PAT"))
+#' #token <- Sys.getenv("GITHUB_PAT")
+#' #repos <- kwb.pkgstatus::get_github_repos(github_token = token)
 #' #repos <- repos$full_name
 #' repos <- paste0("kwb-r/", c("aquanes.report", "kwb.ml", "kwb.utils"))
 #' pkgs_commits <- pkgmeta::get_github_commits_repos(repos)
 #' head(pkgs_commits)
 #' }
 get_github_commits_repos <- function(
     repos,
-    github_token = Sys.getenv("GITHUB_PAT")
+    github_token = get_github_token()
 )
 {
   pkg_commit_list <- lapply(repos, function(repo) {
-    kwb.utils::catAndRun(
+    cat_and_run(
       sprintf("Repo: %s", repo),
       try(get_github_commits(repo, github_token = github_token))
     )
@@ -115,7 +116,7 @@ get_github_commits_repos <- function(
       )
     ) %>%
     dplyr::mutate(
-      author_login = kwb.utils::multiSubstitute(.data$author_login, list(
+      author_login = multi_substitute(.data$author_login, list(
         "Andreas Matzinger" = "amatzi",
         "Hauke Sonnenberg" = "hsonne",
         "Mathias Riechel" = "mriech",

R/github_package_versions.R

@@ -2,7 +2,7 @@
 #' Get Github Versions for One Repo
 #'
 #' @param repo full name of Github repo ("owner/repo_name", e.g. "kwb-r/kwb.utils")
-#' @param github_token default: Sys.getenv("GITHUB_PAT")
+#' @param github_token Default: pkgmeta:::get_github_token()
 #'
 #' @return data frame
 #' @export
@@ -17,7 +17,7 @@
 #'}
 github_package_versions <- function(
     repo,
-    github_token = Sys.getenv("GITHUB_PAT")
+    github_token = get_github_token()
 )
 {
   releases <- "https://api.github.com/repos/%s/releases" %>%
@@ -31,8 +31,8 @@ github_package_versions <- function(
   data.frame(
     owner = owner_repo[1L],
     repo = owner_repo[2L],
-    tag = sapply(releases, kwb.utils::selectElements, "tag_name"),
-    date = as.Date(sapply(releases, kwb.utils::selectElements, "published_at")),
+    tag = sapply(releases, select_elements, "tag_name"),
+    date = as.Date(sapply(releases, select_elements, "published_at")),
     author_id = purrr::map_chr(purrr::map(releases, "author"), "login")
   )
 }
@@ -41,7 +41,7 @@ github_package_versions <- function(
 #'
 #' @param repos vector with full names of Github repos ("owner/repo_name",
 #' e.g. c("kwb-r/kwb.utils", "kwb-r/kwb.ml", "kwb-r/aquanes.report"))
-#' @param github_token default: Sys.getenv("GITHUB_PAT")
+#' @param github_token Default: pkgmeta:::get_github_token()
 #' @return data frame for all repos with releases
 #' @export
 #' @importFrom kwb.utils catAndRun
@@ -54,11 +54,11 @@ github_package_versions <- function(
 #' }
 github_packages_versions <- function(
     repos,
-    github_token = Sys.getenv("GITHUB_PAT")
+    github_token = pkgmeta:::get_github_token()
 )
 {
   versions <- lapply(repos, function(repo) {
-    kwb.utils::catAndRun(
+    cat_and_run(
       sprintf("Repo: %s", repo),
       expr = try(
         github_package_versions(repo, github_token = github_token),

R/plot_commits_github.R

@@ -12,7 +12,8 @@
 #' @importFrom magrittr %>%
 #' @examples
 #' \dontrun{
-#' repos <- kwb.pkgstatus::get_github_repos(github_token = Sys.getenv("GITHUB_PAT")
+#' token <- Sys.getenv("GITHUB_PAT")
+#' repos <- kwb.pkgstatus::get_github_repos(github_token = token)
 #' repos_commits <- pkgmeta::github_commits_repos(repos$full_name)
 #' pkgmeta::plot_commits_github(repos_commits)
 #' }

R/utils.R

@@ -0,0 +1,20 @@
+#' @importFrom kwb.utils catAndRun
+cat_and_run <- kwb.utils::catAndRun
+
+# get_github_token -------------------------------------------------------------
+get_github_token <- function()
+{
+  Sys.getenv("GITHUB_PAT")
+}
+
+#' @importFrom kwb.utils multiSubstitute
+multi_substitute <- kwb.utils::multiSubstitute
+
+#' @importFrom kwb.utils selectColumns
+select_columns <- kwb.utils::selectColumns
+
+#' @importFrom kwb.utils selectElements
+select_elements <- kwb.utils::selectElements
+
+#' @importFrom kwb.utils stringList
+string_list <- kwb.utils::stringList

R/write_github_repos_json.R

@@ -52,20 +52,20 @@ get_github_full_names <- function(github_repos = get_github_repos())
 #' Helper function: Get Github Metadata For Repos
 #'
 #' @param group organisation (default: "KWB-R")
-#' @param github_token default: Sys.getenv("GITHUB_PAT")
+#' @param github_token Default: pkgmeta:::get_github_token()
 #' @param dbg should debug messages be printed? (default: TRUE)
 #' @param ... additional arguments passed to gh:::gh_build_request(), see
 #' https://developer.github.com/v3/ (e.g. type = "public")
 #' @importFrom gh gh
 #' @export
 get_github_repos <- function (
     group = "KWB-R",
-    github_token = Sys.getenv("GITHUB_PAT"),
+    github_token = get_github_token(),
     dbg = TRUE,
     ...
 )
 {
-  kwb.utils::catAndRun(
+  cat_and_run(
     messageText = sprintf(
       "\nFetching Github metadata for repos of organisation '%s' at '%s'",
       group,
@@ -104,7 +104,7 @@ write_github_repos_json <- function(
   repo_html_url <- fetch_sorted(what = "html_url")
   repo_names <- fetch_sorted(what = "name")
 
-  kwb.utils::catAndRun(
+  cat_and_run(
     sprintf(
       "Writting '%s' file for %d repos:\n%s",
       file,

R/write_pkg_codemeta_json.R

@@ -15,7 +15,7 @@ write_pkg_codemeta_json <- function(
     dbg = TRUE
 )
 {
-  kwb.utils::catAndRun(
+  cat_and_run(
     sprintf("Writting codemeta to '%s'", file),
     dbg = dbg,
     expr = jsonlite::write_json(