Merge pull request #897 from stan-dev/show_messages-methods

Add show_messages and show_exceptions arguments to all methods

R/model.R

@@ -1495,10 +1495,13 @@ optimize <- function(data = NULL,
                      tol_grad = NULL,
                      tol_rel_grad = NULL,
                      tol_param = NULL,
-                     history_size = NULL) {
+                     history_size = NULL,
+                     show_messages = TRUE,
+                     show_exceptions = TRUE) {
   procs <- CmdStanProcs$new(
     num_procs = 1,
-    show_stdout_messages = (is.null(refresh) || refresh != 0),
+    show_stderr_messages = show_exceptions,
+    show_stdout_messages = show_messages,
     threads_per_proc = assert_valid_threads(threads, self$cpp_options())
   )
   model_variables <- NULL
@@ -1624,7 +1627,9 @@ laplace <- function(data = NULL,
                     mode = NULL,
                     opt_args = NULL,
                     jacobian = TRUE, # different default than for optimize!
-                    draws = NULL) {
+                    draws = NULL,
+                    show_messages = TRUE,
+                    show_exceptions = TRUE) {
   if (cmdstan_version() < "2.32") {
     stop("This method is only available in cmdstan >= 2.32", call. = FALSE)
   }
@@ -1633,7 +1638,8 @@ laplace <- function(data = NULL,
   }
   procs <- CmdStanProcs$new(
     num_procs = 1,
-    show_stdout_messages = (is.null(refresh) || refresh != 0),
+    show_stderr_messages = show_exceptions,
+    show_stdout_messages = show_messages,
     threads_per_proc = assert_valid_threads(threads, self$cpp_options())
   )
   model_variables <- NULL
@@ -1775,10 +1781,13 @@ variational <- function(data = NULL,
                         tol_rel_obj = NULL,
                         eval_elbo = NULL,
                         output_samples = NULL,
-                        draws = NULL) {
+                        draws = NULL,
+                        show_messages = TRUE,
+                        show_exceptions = TRUE) {
   procs <- CmdStanProcs$new(
     num_procs = 1,
-    show_stdout_messages = (is.null(refresh) || refresh != 0),
+    show_stderr_messages = show_exceptions,
+    show_stdout_messages = show_messages,
     threads_per_proc = assert_valid_threads(threads, self$cpp_options())
   )
   model_variables <- NULL
@@ -1902,10 +1911,13 @@ pathfinder <- function(data = NULL,
                        num_paths = NULL,
                        max_lbfgs_iters = NULL,
                        num_elbo_draws = NULL,
-                       save_single_paths = NULL) {
+                       save_single_paths = NULL,
+                       show_messages = TRUE,
+                       show_exceptions = TRUE) {
   procs <- CmdStanProcs$new(
     num_procs = 1,
-    show_stdout_messages = (is.null(refresh) || refresh != 0),
+    show_stderr_messages = show_exceptions,
+    show_stdout_messages = show_messages,
     threads_per_proc = assert_valid_threads(num_threads, self$cpp_options())
   )
   model_variables <- NULL

R/run.R

@@ -844,7 +844,8 @@ CmdStanProcs <- R6::R6Class(
     report_time = function(id = NULL) {
       if (self$proc_state(id) == 7) {
         warning("Fitting finished unexpectedly! Use the $output() method for more information.\n", immediate. = TRUE, call. = FALSE)
-      } else {
+      }
+      if (private$show_stdout_messages_) {
         cat("Finished in ",
             base::format(round(self$total_time(), 1), nsmall = 1),
             "seconds.\n")

man-roxygen/model-common-args.R

@@ -85,3 +85,16 @@
 #'   be compiled with `cpp_options = list(stan_opencl = TRUE)` for this
 #'   argument to have an effect.
 #'
+#' @param show_messages (logical) When `TRUE` (the default), prints all
+#'   output during the execution process, such as iteration numbers and elapsed times.
+#'   If the output is silenced then the [`$output()`][fit-method-output] method of
+#'   the resulting fit object can be used to display the silenced messages.
+#'
+#' @param show_exceptions (logical) When `TRUE` (the default), prints all
+#'   informational messages, for example rejection of the current proposal.
+#'   Disable if you wish to silence these messages, but this is not usually
+#'   recommended unless you are very confident that the model is correct up to
+#'   numerical error. If the messages are silenced then the
+#'   [`$output()`][fit-method-output] method of the resulting fit object can be
+#'   used to display the silenced messages.
+#'

man-roxygen/model-sample-args.R

@@ -74,17 +74,6 @@
 #'   quantities block. If the parameters block is empty then using
 #'   `fixed_param=TRUE` is mandatory. When `fixed_param=TRUE` the `chains` and
 #'   `parallel_chains` arguments will be set to `1`.
-#' @param show_messages (logical) When `TRUE` (the default), prints all
-#'   output during the sampling process, such as iteration numbers and elapsed times.
-#'   If the output is silenced then the [`$output()`][fit-method-output] method of
-#'   the resulting fit object can be used to display the silenced messages.
-#' @param show_exceptions (logical) When `TRUE` (the default), prints all
-#'   informational messages, for example rejection of the current proposal.
-#'   Disable if you wish to silence these messages, but this is not usually
-#'   recommended unless you are very confident that the model is correct up to
-#'   numerical error. If the messages are silenced then the
-#'   [`$output()`][fit-method-output] method of the resulting fit object can be
-#'   used to display the silenced messages.
 #' @param diagnostics (character vector) The diagnostics to automatically check
 #'   and warn about after sampling. Setting this to an empty string `""` or
 #'   `NULL` can be used to prevent CmdStanR from automatically reading in the

tests/testthat/test-fit-shared.R

@@ -288,7 +288,7 @@ test_that("CmdStanArgs erorrs if idx is out of proc_ids range", {
   )
 })
 
-test_that("no output with refresh = 0", {
+test_that("no output with show_messages = FALSE", {
   mod <- testing_model("logistic")
   data_list <- testing_data("logistic")
   output <- utils::capture.output(tmp <- mod$variational(data = data_list, seed = 123))
@@ -298,12 +298,12 @@ test_that("no output with refresh = 0", {
   output <- utils::capture.output(tmp <- mod$sample(data = data_list, chains = 1, seed = 123))
   expect_gt(length(output), 1)
 
-  output <- utils::capture.output(tmp <- mod$variational(data = data_list, refresh = 0, seed = 123))
-  expect_equal(length(output), 1)
-  output <- utils::capture.output(tmp <- mod$optimize(data = data_list, refresh = 0, seed = 123))
-  expect_equal(length(output), 1)
-  output <- utils::capture.output(tmp <- mod$sample(data = data_list, refresh = 0, chains = 1, seed = 123))
-  expect_equal(length(output), 3)
+  output <- utils::capture.output(tmp <- mod$variational(data = data_list, show_messages = FALSE, seed = 123))
+  expect_equal(length(output), 0)
+  output <- utils::capture.output(tmp <- mod$optimize(data = data_list, show_messages = FALSE, seed = 123))
+  expect_equal(length(output), 0)
+  output <- utils::capture.output(tmp <- mod$sample(data = data_list, show_messages = FALSE, chains = 1, seed = 123))
+  expect_equal(length(output), 0)
 })
 
 test_that("sig_figs works with all methods", {