batchtools_custom() and BatchtoolsFuture gained argument 'conf.file' [#10]

Author: HenrikBengtsson

NAMESPACE

@@ -30,6 +30,7 @@ export(status)
 importFrom(batchtools,batchExport)
 importFrom(batchtools,batchMap)
 importFrom(batchtools,clearRegistry)
+importFrom(batchtools,findConfFile)
 importFrom(batchtools,findTemplateFile)
 importFrom(batchtools,getErrorMessages)
 importFrom(batchtools,getLog)

NEWS

@@ -36,6 +36,8 @@ NEW FEATURES:
  * The default location of the '.future' folder can be controlled by R option
    'future.cache.path' or environment variable 'R_FUTURE_CACHE_PATH'.
 
+ * batchtools_custom() and BatchtoolsFuture gained argument 'conf.file'.
+
 DOCUMENTATION:
 
  * Add help("future.batchtools.options") which descriptions R options and

R/BatchtoolsFuture-class.R

@@ -19,14 +19,6 @@
 #' @param label (optional) Label of the future (where applicable, becomes the
 #' job name for most job schedulers).
 #'
-#' @param conf A batchtools configuration environment.
-#'
-#' @param cluster.functions A batchtools
-#' [ClusterFunctions][batchtools::ClusterFunctions] object.
-#'
-#' @param registry (optional) A named list of settings to control the setup
-#' of the batchtools registry.
-#'
 #' @param resources (optional) A named list passed to the batchtools template
 #' (available as variable `resources`).
 #'
@@ -42,6 +34,14 @@
 #' @param finalize If TRUE, any underlying registries are
 #' deleted when this object is garbage collected, otherwise not.
 #'
+#' @param conf.file (optional) A batchtools configuration file.
+#'
+#' @param cluster.functions (optional) A batchtools
+#' [ClusterFunctions][batchtools::ClusterFunctions] object.
+#'
+#' @param registry (optional) A named list of settings to control the setup
+#' of the batchtools registry.
+#'
 #' @param \ldots Additional arguments passed to [future::Future()].
 #'
 #' @return A BatchtoolsFuture object
@@ -53,19 +53,32 @@
 BatchtoolsFuture <- function(expr = NULL, envir = parent.frame(),
                              substitute = TRUE,
                              globals = TRUE, packages = NULL,
-                             label = NULL, cluster.functions = NULL,
-                             registry = list(),
-                             resources = list(), workers = NULL,
+                             label = NULL,
+                             resources = list(),
+                             workers = NULL,
                              finalize = getOption("future.finalize", TRUE),
+                             conf.file = findConfFile(),
+                             cluster.functions = NULL,
+                             registry = list(),
                              ...) {
   if (substitute) expr <- substitute(expr)
 
   if (!is.null(label)) label <- as.character(label)
 
   if (!is.null(cluster.functions)) {
     stop_if_not(is.list(cluster.functions))
+    stop_if_not(inherits(cluster.functions, "ClusterFunctions"))
+  } else if (missing(conf.file)) {
+    ## BACKWARD COMPATILITY: Only when calling BatchtoolsFuture() directly
+    cluster.functions <- makeClusterFunctionsInteractive(external = FALSE)
+  } else {
+    ## If 'cluster.functions' is not specified, then 'conf.file' must
+    ## exist
+    if (!file_test("-f", conf.file)) {
+      stop("No such batchtools configuration file: ", sQuote(conf.file))
+    }
   }
-
+  
   if (is.function(workers)) workers <- workers()
   if (!is.null(workers)) {
     stop_if_not(length(workers) >= 1)
@@ -96,10 +109,12 @@ BatchtoolsFuture <- function(expr = NULL, envir = parent.frame(),
   future$packages <- unique(c(packages, gp$packages))
 
   ## Create batchtools registry
-  reg <- temp_registry(label = future$label, config = registry)
-  if (!is.null(cluster.functions)) {    ### FIXME
-    reg$cluster.functions <- cluster.functions
-  }
+  reg <- temp_registry(
+    label = future$label,
+    conf.file = conf.file,
+    cluster.functions = cluster.functions,
+    config = registry
+  )
   debug <- getOption("future.debug", FALSE)
   if (debug) mprint(reg)
 

R/batchtools_custom.R

@@ -2,6 +2,9 @@
 #'
 #' @inheritParams BatchtoolsFuture
 #'
+#' @param conf.file (character) A batchtools configuration file as for
+#' instance returned by [batchtools::findConfFile()].
+#'
 #' @param cluster.functions A
 #' [ClusterFunctions][batchtools::ClusterFunctions] object.
 #'
@@ -12,20 +15,25 @@
 #' @example incl/batchtools_custom.R
 #'
 #' @export
+#' @importFrom batchtools findConfFile
 #' @importFrom utils file_test
 batchtools_custom <- function(expr, envir = parent.frame(), substitute = TRUE,
-                              globals = TRUE, label = NULL,
-                              cluster.functions,
-                              resources = list(), workers = NULL,
-                              registry = list(), ...) {
+                              globals = TRUE,
+                              label = NULL,
+                              resources = list(),
+                              workers = NULL,
+                              conf.file = findConfFile(),
+                              cluster.functions = NULL,
+                              registry = list(),
+                              ...) {
   if (substitute) expr <- substitute(expr)
-  stop_if_not(inherits(cluster.functions, "ClusterFunctions"))
 
   future <- BatchtoolsFuture(expr = expr, envir = envir, substitute = FALSE,
                             globals = globals,
                             label = label,
-                            cluster.functions = cluster.functions,
                             resources = resources,
+                            conf.file = conf.file,
+                            cluster.functions = cluster.functions,
                             workers = workers,
                             registry = registry,
                             ...)

R/temp_registry.R

@@ -3,8 +3,8 @@ temp_registry <- local({
   ## All known batchtools registries
   regs <- new.env()
 
-  make_registry <- function(config = list(), ...) {
-      ## Temporarily disable batchtools output?
+  make_registry <- function(cluster.functions = NULL, config = list(), ...) {
+    ## Temporarily disable batchtools output?
     ## (i.e. messages and progress bars)
     debug <- getOption("future.debug", FALSE)
     batchtools_output <- getOption("future.batchtools.output", debug)
@@ -20,6 +20,10 @@ temp_registry <- local({
 
     reg <- makeRegistry(work.dir = work.dir, ...)
 
+    if (!is.null(cluster.functions)) {    ### FIXME
+      reg$cluster.functions <- cluster.functions
+    }
+
     ## Post-tweak the batchtools registry?
     ## This avoids having to set up a custom batchtools 'conf.file' etc.
     if (length(config) > 0L) {