Merge branch 'develop' of github.com:HenrikBengtsson/future.batchtools into develop

Author: HenrikBengtsson

NEWS.md

@@ -5,13 +5,14 @@
  * **future.batchtools** now implements the FutureBackend API
    introduced in **future** 1.40.0 (2025-04-10).
 
- * Removed option `future.delete`. To control whether batchtools
-   futures should be deleted from the file system, see future backend
-   argument `delete`, which defaults to `"on-success"`, but can also
-   be set to `"never"` and `"always"`.
-
 ## New Features
 
+ * Batchtools future backends gained argument `delete` for controlling
+   if and when batchtools futures should be deleted from the file
+   system`. Supported values are `"on-success"`, `"never"` and
+   `"always"`. The default value can be set via R option
+   `future.batchtools.delete`.
+
  * Most types of batchtools future can now be interrupted, including
    `batchtools_multicore` and all job-scheduler backends, e.g.
    `batchtools_sge` and `batchtools_slurm`.
@@ -52,6 +53,16 @@
    **future.batchtools** will no longer wait for such files and only
    read their content if they exists when checked.
 
+## Deprecated and Defunct
+
+ * R option `future.delete` is deprecated. Please use new R option
+   `future.batchtools.delete` instead. For backward compatible
+   reasons, if R option `future.delete` sets option
+   `future.batchtools.delete` when the packages is loaded and the
+   latter is not already set. If `future.delete` is FALSE, then
+   `future.batchtools.delete` is set to `"never"`.  If `future.delete`
+   is TRUE, then `future.batchtools.delete` is set to `"on-success"`.
+   
 
 # Version 0.12.2 [2025-06-06]
 
@@ -177,19 +188,16 @@
    `status()`, which were functions that were used for internal
    purposes.
 
-
 ## Documentation
 
  * Document option `future.delete` and clarify option
    `future.cache.path` in `help("future.batchtools.options")`.
 
-
 ## Bug Fixes
 
  * If `run()` was called twice for a BatchtoolsFuture, it would not
    produce a FutureError but only a regular non-classed error.
 
-
 ## Deprecated and Defunct
 
  * Removed S3 generic functions `await()`, `finished()`, and

R/BatchtoolsFutureBackend-class.R

@@ -53,7 +53,7 @@ BatchtoolsFutureBackend <- function(
                              registry = list(),
                              conf.file = findConfFile(),
                              interrupts = TRUE,
-			     delete = "on-success",
+                             delete = getOption("future.batchtools.debug", "on-success"),
                              ...) {
   assert_no_positional_args_but_first()
 
@@ -987,7 +987,7 @@ delete.BatchtoolsFuture <- function(future,
         if (debug) mdebugf("delete(): %s", msg)
         warning(msg)
         return(invisible(FALSE))
-      }	
+      }
     }
   }
 

R/BatchtoolsTemplateFutureBackend-class.R

@@ -47,7 +47,7 @@
 #' @importFrom batchtools makeClusterFunctionsSlurm
 #' @importFrom batchtools makeClusterFunctionsTORQUE
 #' @export
-BatchtoolsTemplateFutureBackend <- function(type, scheduler.latency = 1.0, fs.latency = 65.0, resources = list(), delete = "on-success", template = NULL, makeClusterFunctions = NULL, workers = getOption("future.batchtools.workers", default = 100L), ...) {
+BatchtoolsTemplateFutureBackend <- function(type, scheduler.latency = 1.0, fs.latency = 65.0, resources = list(), delete = getOption("future.batchtools.delete", "on-success"), template = NULL, makeClusterFunctions = NULL, workers = getOption("future.batchtools.workers", default = 100L), ...) {
   assert_no_positional_args_but_first()
   stop_if_not(
     is.character(type),

R/batchtools_bash.R

@@ -76,7 +76,7 @@ BatchtoolsBashFutureBackend <- function(..., template = "bash", fs.latency = 0.0
 #' print(info)
 #' 
 #' @export
-batchtools_bash <- function(..., template = "bash", fs.latency = 0.0, resources = list(), delete = "on-success") {
+batchtools_bash <- function(..., template = "bash", fs.latency = 0.0, resources = list(), delete = getOption("future.batchtools.delete", "on-success")) {
  stop("INTERNAL ERROR: The future.batchtools::batchtools_bash() must never be called directly")
 }
 class(batchtools_bash) <- c(

R/batchtools_interactive.R

@@ -62,7 +62,7 @@ BatchtoolsInteractiveFutureBackend <- function(fs.latency = 0.0, ...) {
 #' @inheritParams BatchtoolsInteractiveFutureBackend
 #'
 #' @export
-batchtools_interactive <- function(..., fs.latency = 0.0, delete = "on-success") {
+batchtools_interactive <- function(..., fs.latency = 0.0, delete = getOption("future.batchtools.delete", "on-success")) {
  stop("INTERNAL ERROR: The future.batchtools::batchtools_interactive() must never be called directly")
 }
 class(batchtools_interactive) <- c(

R/batchtools_local.R

@@ -92,7 +92,7 @@ BatchtoolsLocalFutureBackend <- function(fs.latency = 0.0, ...) {
 #' print(info)
 #' 
 #' @export
-batchtools_local <- function(..., fs.latency = 0.0, delete = "on-success") {
+batchtools_local <- function(..., fs.latency = 0.0, delete = getOption("future.batchtools.delete", "on-success")) {
  stop("INTERNAL ERROR: The future.batchtools::batchtools_local() must never be called directly")
 }
 class(batchtools_local) <- c(

R/batchtools_lsf.R

@@ -59,7 +59,7 @@ BatchtoolsLsfFutureBackend <- function(...) {
 #' * <https://en.wikipedia.org/wiki/IBM_Spectrum_LSF>
 #'
 #' @export
-batchtools_lsf <- function(..., template = "lsf", scheduler.latency = 1.0, fs.latency = 65.0, resources = list(), delete = "on-success", workers = getOption("future.batchtools.workers", default = 100L)) {
+batchtools_lsf <- function(..., template = "lsf", scheduler.latency = 1.0, fs.latency = 65.0, resources = list(), delete = getOption("future.batchtools.delete", "on-success"), workers = getOption("future.batchtools.workers", default = 100L)) {
  stop("INTERNAL ERROR: The future.batchtools::batchtools_lsf() must never be called directly")
 }
 class(batchtools_lsf) <- c(

R/batchtools_multicore.R

@@ -31,7 +31,7 @@
 #' @importFrom parallelly availableCores supportsMulticore
 #' @importFrom tools pskill
 #' @export
-BatchtoolsMulticoreFutureBackend <- function(workers = availableCores(constraints = "multicore"), fs.latency = 0.0, delete = "on-success", ...) {
+BatchtoolsMulticoreFutureBackend <- function(workers = availableCores(constraints = "multicore"), fs.latency = 0.0, delete = getOption("future.batchtools.delete", "on-success"), ...) {
   assert_no_positional_args_but_first()
 
   if (is.function(workers)) workers <- workers()
@@ -103,7 +103,7 @@ BatchtoolsMulticoreFutureBackend <- function(workers = availableCores(constraint
 #' print(info)
 #' 
 #' @export
-batchtools_multicore <- function(..., workers = availableCores(constraints = "multicore"), fs.latency = 0.0, delete = "on-success") {
+batchtools_multicore <- function(..., workers = availableCores(constraints = "multicore"), fs.latency = 0.0, delete = getOption("future.batchtools.delete", "on-success")) {
  stop("INTERNAL ERROR: The future.batchtools::batchtools_multicore() must never be called directly")
 }
 class(batchtools_multicore) <- c(

R/batchtools_openlava.R

@@ -59,7 +59,7 @@ BatchtoolsOpenLavaFutureBackend <- function(...) {
 #' * <https://en.wikipedia.org/wiki/OpenLava>
 #'
 #' @export
-batchtools_openlava <- function(..., template = "openlava", scheduler.latency = 1.0, fs.latency = 65.0, resources = list(), delete = "on-success", workers = getOption("future.batchtools.workers", default = 100L)) {
+batchtools_openlava <- function(..., template = "openlava", scheduler.latency = 1.0, fs.latency = 65.0, resources = list(), delete = getOption("future.batchtools.delete", "on-success"), workers = getOption("future.batchtools.workers", default = 100L)) {
  stop("INTERNAL ERROR: The future.batchtools::batchtools_openlava() must never be called directly")
 }
 class(batchtools_openlava) <- c(

R/batchtools_sge.R

@@ -63,7 +63,7 @@ BatchtoolsSGEFutureBackend <- function(...) {
 #' * <https://en.wikipedia.org/wiki/Oracle_Grid_Engine>
 #'
 #' @export
-batchtools_sge <- function(..., template = "sge", scheduler.latency = 1.0, fs.latency = 65.0, resources = list(), delete = "on-success", workers = getOption("future.batchtools.workers", default = 100L)) {
+batchtools_sge <- function(..., template = "sge", scheduler.latency = 1.0, fs.latency = 65.0, resources = list(), delete = getOption("future.batchtools.delete", "on-success"), workers = getOption("future.batchtools.workers", default = 100L)) {
  stop("INTERNAL ERROR: The future.batchtools::batchtools_sge() must never be called directly")
 }
 class(batchtools_sge) <- c(