Adjust relocation of on-disk layers

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SeuratObject
 Type: Package
 Title: Data Structures for Single Cell Data
-Version: 5.0.0.9002
+Version: 5.0.0.9003
 Authors@R: c(
   person(given = 'Rahul', family = 'Satija', email = 'rsatija@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0001-9448-8833')),
   person(given = 'Paul', family = 'Hoffman', email = 'seurat@nygenome.org', role = c('aut', 'cre'), comment = c(ORCID = '0000-0002-7693-8957')),

NEWS.md

@@ -2,6 +2,7 @@
 
 ## Changes:
 - Update internal calls to `GetAssayData()` to use `layer` instead of `slot` (#160)
+- Change layer-saving in `SaveSeuratRds()` to move all layers instead of just those in `tempdir()` (#169)
 
 # SeuratObject 5.0.0
 ## Added

R/seurat.R

@@ -610,8 +610,8 @@ RenameAssays <- function(
 #' @param object A \code{\link{Seurat}} object
 #' @param file Path to save \code{object} to; defaults to
 #' \code{file.path(getwd(), paste0(Project(object), ".Rds"))}
-#' @param destdir Destination directory for on-disk layers saved in
-#' \dQuote{\code{\Sexpr[stage=render]{tempdir()}}}
+#' @param move Move on-disk layers into \code(dirname(file))
+#' @param destdir \Sexpr[stage=build,results=rd]{lifecycle::badge("deprecated")}
 #' @param relative Save relative paths instead of absolute ones
 #' @inheritDotParams base::saveRDS
 #'
@@ -685,12 +685,28 @@ RenameAssays <- function(
 SaveSeuratRds <- function(
   object,
   file = NULL,
-  destdir = NULL,
+  move = TRUE,
+  destdir = deprecated(),
   relative = FALSE,
   ...
 ) {
   file <- file %||% file.path(getwd(), paste0(Project(object = object), '.Rds'))
   file <- normalizePath(path = file, winslash = '/', mustWork = FALSE)
+  if (is_present(arg = destdir)) {
+    .Deprecate(
+      when = '5.0.1',
+      what = 'SaveSeuratRds(destdir = )',
+      with = 'SaveSeuratRds(move = )',
+      details = paste(
+        "Specifying a directory to move on-disk layers stored in",
+        sQuote(x = normalizePath(path = tempdir(), winslash = '/', mustWork = FALSE)),
+        "is deprecated; now, specify `move = TRUE` either move all on-disk layers to",
+        sQuote(x = dirname(path = file)),
+        "or `move = FALSE` leave them as-is"
+      )
+    )
+    move <- is_bare_character(x = destdir, n = 1L) || is.null(x = destdir)
+  }
   # Cache v5 assays
   assays <- .FilterObjects(object = object, classes.keep = 'StdAssay')
   p <- progressor(along = assays, auto_finish = TRUE)
@@ -706,13 +722,9 @@ SaveSeuratRds <- function(
   )
   cache <- vector(mode = 'list', length = length(x = assays))
   names(x = cache) <- assays
-  tdir <- normalizePath(path = tempdir(), winslash = '/') # because macOS is weird
-  destdir <- destdir %||% dirname(path = file)
-  if (!is_na(x = destdir) || isTRUE(x = relative)) {
-    check_installed(
-      pkg = 'fs',
-      reason = 'for moving on-disk matrices'
-    )
+  destdir <- dirname(path = file)
+  if (isTRUE(x = move)) {
+    check_installed(pkg = 'fs', reason = 'for moving on-disk matrices')
   }
   for (assay in assays) {
     p(
@@ -746,27 +758,23 @@ SaveSeuratRds <- function(
       p(message = "No on-disk layers found", class = 'sticky', amount = 0)
       next
     }
-    if (!is_na(x = destdir)) {
+    if (isTRUE(x = move)) {
       for (i in seq_len(length.out = nrow(x = df))) {
         pth <- df$path[i]
-        mv <- substr(x = pth, start = 1L, stop = nchar(x = tdir)) == tdir ||
-          isTRUE(x = relative)
-        if (isTRUE(x = mv)) {
-          p(
-            message = paste(
-              "Moving layer",
-              sQuote(x = df$layer[i]),
-              "to",
-              sQuote(x = destdir)
-            ),
-            class = 'sticky',
-            amount = 0
-          )
-          df[i, 'path'] <- as.character(x = .FileMove(
-            path = pth,
-            new_path = destdir
-          ))
-        }
+        p(
+          message = paste(
+            "Moving layer",
+            sQuote(x = df$layer[i]),
+            "to",
+            sQuote(x = destdir)
+          ),
+          class = 'sticky',
+          amount = 0
+        )
+        df[i, 'path'] <- as.character(x = .FileMove(
+          path = pth,
+          new_path = destdir
+        ))
       }
     }
     if (isTRUE(x = relative)) {

R/utils.R

@@ -2276,7 +2276,11 @@ StitchMatrix.matrix <- function(x, y, rowmap, colmap, ...) {
     new_path <- fs::path_expand(path = new_path)
     new_path <- fs::dir_create(path = new_path)
     dest <- tryCatch(
-      expr = fs::dir_copy(path = path, new_path = new_path, overwrite = overwrite),
+      expr = fs::dir_copy(
+        path = path,
+        new_path = new_path,
+        overwrite = overwrite
+      ),
       EEXIST = eexist,
       error = hndlr
     )
@@ -2292,10 +2296,13 @@ StitchMatrix.matrix <- function(x, y, rowmap, colmap, ...) {
     )
   } else {
     abort(
-      message = paste0(
-        "Can't find path: ",
-        sQuote(x = path),
-        "; if path is relative, change working directory."
+      message = paste(
+        strwrap(x = paste0(
+          "Can't find path: ",
+          sQuote(x = path),
+          "; if path is relative, change working directory"
+        )),
+        sep = '\n'
       ),
       call = caller_env(n = 1L + n)
     )