arf parallelization fix

.Rbuildignore

@@ -30,3 +30,4 @@
 ^xplainfi-manual\.tex$
 ^CRAN-SUBMISSION$
 ^codemeta\.json$
+^scratch$

.gitignore

@@ -1,5 +1,6 @@
 .Rprofile
 attic
+scratch
 README.html
 # Created by https://www.toptal.com/developers/gitignore/api/r
 # Edit at https://www.toptal.com/developers/gitignore?templates=r
@@ -55,3 +56,10 @@ lib
 /.quarto/
 TODO.md
 tests/testthat/_problems
+
+# Agent context: track only the shared CLAUDE.md, ignore personal state.
+# First re-include .claude/ because the global ~/.config/git/ignore
+# excludes it; then ignore its contents except CLAUDE.md.
+!.claude/
+.claude/*
+!.claude/CLAUDE.md

DESCRIPTION

@@ -32,6 +32,7 @@ Imports:
 Suggests:
     arf,
     DiagrammeR,
+    doParallel,
     foreach,
     future,
     future.apply,

NEWS.md

@@ -2,6 +2,7 @@
 
 - Fix `$obs_loss()` being erroneously called without `measure` in `PerturbationImportance`, resulting in an error when `measures` was not the task-default.
 - `ConditionalARFSampler$sample()` now errors when `parallel = TRUE` but no parallel backend is registered, e.g. after deserializing a sampler in a new session.
+- `PerturbationImportance` (PFI/CFI/RFI) now registers a `doParallel` backend inside each mirai daemon when the sampler is configured with `parallel = TRUE`. This lets `ConditionalARFSampler` use parallel `arf::forge()` from within mirai workers, which don't inherit the caller's foreach state. Worker count per daemon is controlled by the new `arf_workers` option (default `2L`); see `?xplain_opt`. Requires the `doParallel` package (now in Suggests).
 
 # xplainfi 1.1.0
 

R/PerturbationImportance.R

@@ -229,6 +229,7 @@ PerturbationImportance = R6Class(
 						n_repeats,
 						batch_size,
 						learner_packages,
+						arf_workers,
 						is_sequential = TRUE
 					) {
 						# Load required packages in parallel workers
@@ -239,6 +240,19 @@ PerturbationImportance = R6Class(
 							for (pkg in learner_packages) {
 								library(pkg, character.only = TRUE)
 							}
+							# If sampler is configured for parallel sampling (e.g. arf::forge
+							# with parallel = TRUE), foreach needs a backend registered inside
+							# THIS daemon's R session — mirai daemons are separate processes
+							# and don't inherit the caller's foreach state. arf's sequential
+							# %do% path has bugs at scale, so the only reliable way to use
+							# ARF inside a mirai daemon is to give it a parallel backend.
+							# Tune workers per daemon via `xplain_opt(arf_workers = N)`
+							# in the caller session (value resolved before dispatch).
+							if (isTRUE(sampler$param_set$values$parallel) && arf_workers > 0L) {
+								require_package("doParallel")
+								doParallel::registerDoParallel(cores = arf_workers)
+								on.exit(doParallel::stopImplicitCluster(), add = TRUE)
+							}
 						}
 
 						# Sample feature - sampler handles conditioning appropriately
@@ -275,7 +289,12 @@ PerturbationImportance = R6Class(
 						test_row_ids = test_row_ids,
 						n_repeats = n_repeats,
 						batch_size = batch_size,
-						learner_packages = this_learner$packages
+						learner_packages = this_learner$packages,
+						# Resolved once on caller side — mirai daemons are separate R
+						# sessions and don't inherit options from the caller, so reading
+						# `xplain_opt()` inside the daemon would always see the package
+						# default. Pass the resolved value through `.args` instead.
+						arf_workers = xplain_opt("arf_workers")
 					)
 				)
 

R/utils-opt.R

@@ -21,6 +21,7 @@
 #' | `progress` | `FALSE` | Show progress bars during computation |
 #' | `sequential` | `FALSE` | Force sequential execution (disable parallelization) |
 #' | `debug` | `FALSE` | Enable debug output for development and troubleshooting |
+#' | `arf_workers` | `2L` | doParallel workers registered inside each mirai daemon when the sampler is configured with `parallel = TRUE`. Has no effect on sequential or non-ARF execution. |
 #'
 #' @return
 #' - When **getting** a single option: the option value (logical)
@@ -59,7 +60,8 @@ xplain_opt <- function(...) {
 		verbose = TRUE,
 		progress = FALSE,
 		sequential = FALSE,
-		debug = FALSE
+		debug = FALSE,
+		arf_workers = 2L
 	)
 
 	args <- list(...)
@@ -115,19 +117,33 @@ xplain_opt <- function(...) {
 }
 
 #' Get option value with precedence: R option > env var > default
+#'
+#' Coerces to the default's storage type, so logical options stay
+#' logical and integer options like `arf_workers` stay integer. Anything
+#' that fails to coerce is treated as unset.
+#'
 #' @noRd
 #' @keywords internal
 get_option_value <- function(name, default) {
 	opt <- getOption(paste0("xplain.", tolower(name)), default = NA)
 	envvar <- Sys.getenv(toupper(paste0("xplain_", name)), unset = NA)
 
-	opt <- as.logical(opt)
-	if (is.na(opt)) {
+	coerce <- switch(
+		typeof(default),
+		logical = as.logical,
+		integer = function(x) suppressWarnings(as.integer(x)),
+		double = function(x) suppressWarnings(as.numeric(x)),
+		character = as.character,
+		identity
+	)
+
+	opt <- coerce(opt)
+	if (length(opt) == 0L || is.na(opt)) {
 		opt <- NULL
 	}
 
-	envvar <- as.logical(envvar)
-	if (is.na(envvar)) {
+	envvar <- coerce(envvar)
+	if (length(envvar) == 0L || is.na(envvar)) {
 		envvar <- NULL
 	}
 

tests/testthat/test-RFI.R

@@ -97,6 +97,10 @@ test_that("RFI single feature", {
 # -----------------------------------------------------------------------------
 
 test_that("RFI difference vs ratio relations", {
+	# Seed needed: 33-row holdout + rpart on 2dnormals can yield a zero
+	# baseline classif.ce, which makes the ratio relation 0/0 = NaN.
+	# Flaky under covr where the RNG state differs from R CMD check.
+	withr::local_seed(42)
 	task = tgen("2dnormals")$generate(n = 100)
 
 	test_relation_parameter(