Merge branch 'master' into add-cmdstanr-to-gha

Author: jgabry

.github/workflows/test-coverage.yaml

@@ -44,7 +44,7 @@ jobs:
           covr::to_cobertura(cov)
         shell: Rscript {0}
 
-      - uses: codecov/codecov-action@v5
+      - uses: codecov/codecov-action@v6
         with:
           # Fail if error if not on PR, or if on PR and token is given
           fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}

NEWS.md

@@ -1,5 +1,7 @@
 # bayesplot (development version)
 
+* Replace `apply()` with `storage.mode()` for integer-to-numeric matrix conversion in `validate_predictions()`.
+* Fixed `is_chain_list()` to correctly reject empty lists instead of silently returning `TRUE`.
 * Added unit tests for `mcmc_areas_ridges_data()`, `mcmc_parcoord_data()`, and `mcmc_trace_data()`.
 * Added unit tests for `ppc_error_data()` and `ppc_loo_pit_data()` covering output structure, argument handling, and edge cases.
 * Added vignette sections demonstrating `*_data()` companion functions for building custom ggplot2 visualizations (#435)

R/helpers-mcmc.R

@@ -247,6 +247,9 @@ df_with_chain2array <- function(x) {
 #' @param x object to check
 #' @return TRUE or FALSE
 is_chain_list <- function(x) {
+  if (length(x) == 0) {
+    return(FALSE)
+  }
   check1 <- !is.data.frame(x) && is.list(x)
   dims <- try(sapply(x, function(chain) length(dim(chain))), silent=TRUE)
   if (inherits(dims, "try-error")) {

R/helpers-ppc.R

@@ -73,12 +73,7 @@ validate_predictions <- function(predictions, n_obs = NULL) {
   }
 
   if (is.integer(predictions)) {
-    if (nrow(predictions) == 1) {
-      predictions[1, ] <- as.numeric(predictions[1,, drop = FALSE])
-    }
-    else {
-      predictions <- apply(predictions, 2, as.numeric)
-    }
+    storage.mode(predictions) <- "numeric"
   }
 
   if (anyNA(predictions)) {

tests/testthat/test-helpers-mcmc.R

@@ -156,6 +156,7 @@ test_that("is_chain_list works", {
   expect_true(is_chain_list(chainlist))
   expect_true(is_chain_list(chainlist1))
   expect_true(is_chain_list(chainlist1chain))
+  expect_false(is_chain_list(list()))
 })
 
 test_that("validate_chain_list works", {