added research-archiveCleanedPackage

DESCRIPTION

@@ -23,7 +23,8 @@ Imports:
     Rcpp (>= 1.0.12),
     rlang,
     testthat,
-    usethis
+    usethis,
+    R.utils
 LinkingTo: Rcpp
 Suggests:
     covr,

NAMESPACE

@@ -3,6 +3,7 @@
 S3method(getfirst,default)
 S3method(getlast,default)
 export(add)
+export(archiveCleanedPackage)
 export(bound)
 export(closestWord)
 export(colToRownames)

R/research.R

@@ -0,0 +1,177 @@
+#' @title Archive and clean Package Directory
+#'
+#' @description
+#' `r lifecycle::badge("experimental")`
+#'
+#' This function processes an R package directory, removing irrelevant files
+#' (e.g., `.git`, `.gitignore`-listed files, etc.) and strips parts of lines
+#' matching a specified regex from source code. It then creates a clean folder
+#' or a zipped archive of the package without modifying the original directory.
+#'
+#' MAJOR NOTE this is no where near perfect and the regexes used at the moment
+#' for removing comments are prone to issues such as not detecting whether
+#' the symbols are inside special strings.
+#'
+#' @param packageDir A string specifying the path to the package directory.
+#' @param output A string specifying the name of the output cleaned directory.
+#' If the string ends with .zip, the function will create a zipped archive of
+#' the cleaned directory.
+#' @param removeHidden Logical; if `TRUE`, removes hidden files and folders
+#' (starting with a dot). Default is `TRUE`.
+#' @param removeGitignore Logical; if `TRUE`, removes files listed in the
+#' `.gitignore`. Default is `TRUE`.
+#' @param verbose Logical; if `TRUE`, prints additional information about the
+#' cleaning process. Default is `FALSE`.
+#'
+#' @details
+#' The function cleans the package directory by:
+#' - Removing hidden files and folders like `.git`.
+#' - Excluding files listed in `.gitignore`.
+#' - Stripping out parts of lines matching a regex pattern from source files.
+#'
+#' The output will be either a cleaned directory or a zipped archive of it.
+#'
+#' @return A cleaned directory or a zipped file of the package directory.
+#' @keywords research
+#'
+#' @examples
+#' \dontrun{
+#' # Clean and archive the package directory
+#' archiveCleanedPackage("/path/to/package", "clean_package.zip")
+#'
+#' # Clean package directory without zipping it
+#' archiveCleanedPackage("/path/to/package", NULL)
+#' }
+#' @export
+archiveCleanedPackage <- function(
+    packageDir, output, removeHidden = TRUE,
+    removeGitignore = TRUE, verbose = FALSE
+) {
+
+    assert_that(is.string(packageDir), dir.exists(packageDir))
+    assert_that(is.string(output))
+    assert_that(is.flag(removeHidden))
+    assert_that(is.flag(removeGitignore))
+    assert_that(is.flag(verbose))
+
+    tempDir <- tempfile()
+    dir.create(tempDir)
+
+    gitignorePatterns <-
+        if (removeGitignore)
+            getGitignorePatterns(packageDir)
+        else
+            NULL
+
+    copyCleanedRFiles(
+        packageDir, tempDir, patterns = gitignorePatterns,
+        removeHidden = removeHidden, verbose = verbose
+    )
+
+    if (grepl("*\\.zip$", output)) {
+
+        if (verbose) message("Creating zip archive at: ", output)
+
+        zip(
+            zipfile = output,
+            files = list.files(tempDir, full.names = TRUE),
+            flags = "-r"
+        )
+
+    } else {
+        dir.create(output, showWarnings = FALSE)
+
+        R.utils::copyDirectory(
+            tempDir, output, recursive = TRUE
+        )
+
+        if (verbose)
+            message("Cleaned package directory created at: ", output)
+    }
+
+    unlink(tempDir, recursive = TRUE)
+}
+
+getGitignorePatterns <- function(dir) {
+
+    gitignorePath <- file.path(dir, ".gitignore")
+
+    if (!file.exists(gitignorePath)) return(NULL)
+
+    gitignoreLines <- readLines(gitignorePath)
+
+    patterns <- gitignoreLines[
+        (!grepl("^#", gitignoreLines)) &
+            gitignoreLines != "" &
+            gitignoreLines != "\n"
+    ]
+
+    return(patterns)
+}
+
+stripLinesAfterRegex <- function(lines, regex) {
+    gsub(paste0("\\s*", regex, ".*"), "", lines, perl = TRUE)
+}
+
+stripTrailingWhiteSpace <- function(lines) {
+    gsub("\\s+$", "", lines)
+}
+
+ensureSingleNewLineAtEnd <- function(lines) {
+    lines <- lines[rev(cumsum(rev(lines != "")) > 0)]
+    if (tail(lines, 1) != "") {
+        lines <- c(lines, "")
+    }
+    lines
+}
+
+
+copyCleanedRFiles <- function(
+    from, to, patterns = NULL, removeHidden = TRUE, verbose = FALSE
+) {
+
+    dir.create(to, showWarnings = FALSE, recursive = TRUE)
+
+    files <- list.files(
+        from, all.files = TRUE, recursive = TRUE, full.names = TRUE
+    )
+
+    if (removeHidden) files <- files[!grepl("/\\.", files)]
+
+    if (!is.null(patterns)) {
+        for (pattern in patterns) {
+            files <- files[!grepl(pattern, files, perl = TRUE)]
+        }
+    }
+
+    for (file in files) {
+        relativePath <- sub(paste0("^", from), "", file)
+        destPath <- file.path(to, relativePath)
+
+        if (dir.exists(file)) {
+            dir.create(destPath, showWarnings = FALSE, recursive = TRUE)
+            next
+        }
+
+        if (verbose) message("Processing file: ", file)
+        fileLines <- readLines(file, warn = FALSE)
+
+        # this regex isnt perfect either
+        if (grepl("\\.(R|r|Rmd|rmd|Rnw|rnw|cpp|hpp|c|h|rs)$", file)) {
+
+            # this isnt perfect because this might be in a string
+            cleanedLines <- fileLines %>%
+                stripLinesAfterRegex(" *#+ *(TODO|FIXME|BUG|HACK)") %>%
+                stripTrailingWhiteSpace() %>%
+                ensureSingleNewLineAtEnd()
+
+            if (verbose)
+                message("Stripped lines matching TODO/FIXME from: ", file)
+
+        } else {
+            cleanedLines <- fileLines
+        }
+
+        writeLines(cleanedLines, destPath)
+    }
+}

_pkgdown.yml

@@ -43,6 +43,8 @@ reference:
 - contents: has_keyword("packageDevelopment")
 - title: Package Loading
 - contents: has_keyword("packageLoading")
+- title: Research
+- contents: has_keyword("research")
 - title: Regex
 - contents: has_keyword("regex")
 - title: Spelling