Add argument 'force' to clean(), clean.library(), and clean.software()

NEWS

@@ -9,8 +9,12 @@ icesTAF 3.4-0 (2020-03-27)
 
 * Added function taf.session() to show session information.
 
+* Added argument 'force' to clean(), clean.library(), and clean.software().
+
 * Added argument 'ignore' to cp().
 
+* Improved clean.software() to remove software folder, not just software files.
+
 * Improved download.github() to store GitHub metadata in the DESCRIPTION file,
   if the GitHub resource is an R package. Warn if the tar.gz file looks like an
   R package nested inside a repository.

R/clean.R

@@ -4,6 +4,8 @@
 #' \verb{report}), \verb{bootstrap}, or other directories.
 #'
 #' @param dirs directories to delete.
+#' @param force passed to \code{software} and \code{clean.library} if any of the
+#'        \code{dirs} is \code{"bootstrap"}.
 #'
 #' @note
 #' The purpose of removing the directories is to make sure that subsequent TAF
@@ -17,16 +19,13 @@
 #' \verb{bootstrap/initial} and \verb{*.bib} metadata files from being
 #' accidentally deleted.
 #'
-#' The commands \code{clean("bootstrap/software")} and
-#' \code{clean("bootstrap/library")} remove those directories completely.
-#'
 #' @seealso
-#' \code{\link{clean.library}} selectively removes packages from
-#' \verb{bootstrap/library}.
-#'
 #' \code{\link{clean.software}} selectively removes software from
 #' \verb{bootstrap/software}.
 #'
+#' \code{\link{clean.library}} selectively removes packages from
+#' \verb{bootstrap/library}.
+#'
 #' \code{\link{mkdir}} and \code{\link{rmdir}} create and remove empty
 #' directories.
 #'
@@ -39,7 +38,7 @@
 #'
 #' @export
 
-clean <- function(dirs=c("data", "model", "output", "report"))
+clean <- function(dirs=c("data", "model", "output", "report"), force=FALSE)
 {
   ## Convert "bootstrap/" to "bootstrap", so clean("bootstrap/") doesn't go wild
   dirs <- sub("/$", "", dirs)
@@ -48,8 +47,8 @@ clean <- function(dirs=c("data", "model", "output", "report"))
   {
     ## An odd directory called 'library:' can appear in Linux
     unlink(c("bootstrap/data", "bootstrap/library:"), recursive=TRUE)
-    clean.software("bootstrap/software")
-    clean.library("bootstrap/library")
+    clean.software("bootstrap/software", force=force)
+    clean.library("bootstrap/library", force=force)
     dirs <- dirs[dirs != "bootstrap"]
   }
 

R/clean.library.R

@@ -5,6 +5,8 @@
 #'
 #' @param folder location of local TAF library.
 #' @param quiet whether to suppress messages about removed packages.
+#' @param force whether to remove the local TAF library, regardless of how it
+#'        compares to SOFTWARE.bib entries.
 #'
 #' @note
 #' For each package, the cleaning procedure selects between three cases:
@@ -39,11 +41,11 @@
 #'
 #' @export
 
-clean.library <- function(folder="bootstrap/library", quiet=FALSE)
+clean.library <- function(folder="bootstrap/library", quiet=FALSE, force=FALSE)
 {
   installed <- dir(folder)
 
-  if(!file.exists(file.path(folder, "../SOFTWARE.bib")))
+  if(!file.exists(file.path(folder, "../SOFTWARE.bib")) || force)
   {
     unlink(folder, recursive=TRUE)
   }

R/clean.software.R

@@ -5,6 +5,8 @@
 #'
 #' @param folder location of local TAF software folder.
 #' @param quiet whether to suppress messages about removed software.
+#' @param force whether to remove the local TAF software folder, regardless of
+#'        how it compares to SOFTWARE.bib entries.
 #'
 #' @note
 #' For each file (and subdirectory) in the software folder, the cleaning
@@ -39,11 +41,12 @@
 #'
 #' @export
 
-clean.software <- function(folder="bootstrap/software", quiet=FALSE)
+clean.software <- function(folder="bootstrap/software", quiet=FALSE,
+                           force=FALSE)
 {
   software.files <- dir(folder, full.names=TRUE)
 
-  if(!file.exists(file.path(folder, "../SOFTWARE.bib")))
+  if(!file.exists(file.path(folder, "../SOFTWARE.bib")) || force)
   {
     unlink(folder, recursive=TRUE)
   }
@@ -54,8 +57,8 @@ clean.software <- function(folder="bootstrap/software", quiet=FALSE)
     for(file in software.files)
     {
       ## Read sha.file, the SHA for a software file
-      pkg <- sub(".*/(.*)_.*", "\\1", file)          # path/pkg_sha.tar.gz -> pkg
-      sha.file <- sub(".*_(.*?)\\..*", "\\1", file)  # path/pkg_sha.tar.gz -> sha
+      pkg <- sub(".*/(.*)_.*", "\\1", file)         # path/pkg_sha.tar.gz -> pkg
+      sha.file <- sub(".*_(.*?)\\..*", "\\1", file) # path/pkg_sha.tar.gz -> sha
       ## Read sha.bib, the corresponding SHA from SOFTWARE.bib
       if(pkg %in% names(bib))
       {