Remove unreachable checks and improve test coverage

R/args.R

@@ -681,7 +681,6 @@ DiagnoseArgs <- R6::R6Class(
 #' @param self A `CmdStanArgs` object.
 #' @return `TRUE` invisibly unless an error is thrown.
 validate_cmdstan_args <- function(self) {
-  validate_exe_file(self$exe_file)
   assert_dir_exists(self$output_dir, access = "rw")
 
   # at least 1 run id (chain id)
@@ -1073,22 +1072,12 @@ process_init.default <- function(init, ...) {
   return(init)
 }
 
-#' Remove the leftmost dimension if equal to 1
+#' Drop the draw dimension from `draws_of()` of a single draw
 #' @noRd
-#' @param x An array like object
+#' @param x The array `posterior::draws_of()` returns for one draw, whose
+#'   first dimension has length 1.
 .remove_leftmost_dim <- function(x) {
-  dims <- dim(x)
-  if (length(dims) == 1) {
-    return(drop(x))
-  } else if (dims[1] == 1) {
-    new_dims <- dims[-1]
-    # Create a call to subset the array, maintaining all remaining dimensions
-    subset_expr <- as.call(c(as.name("["), list(x), 1, rep(TRUE, length(new_dims)), drop = FALSE))
-    new_x <- eval(subset_expr)
-    return(array(new_x, dim = new_dims))
-  } else {
-    return(x)
-  }
+  array(x, dim = dim(x)[-1])
 }
 
 #' Write initial values to files if provided as posterior `draws` object
@@ -1344,21 +1333,19 @@ process_init_approx <- function(init, num_procs, model_variables = NULL,
 
   # resample_draws() needs num_procs distinct candidates
   if (num_procs > num_candidates) {
-    if (inherits(init, "CmdStanPathfinder")) {
-      algo_name <- " Pathfinder "
-      extra_msg <- " Try running Pathfinder with psis_resample=FALSE."
-    } else if (inherits(init, "CmdStanVB")) {
-      algo_name <- " VB "
-      extra_msg <- ""
-    } else if (inherits(init, "CmdStanLaplace")) {
-      algo_name <- " Laplace "
-      extra_msg <- ""
+    algo_name <- switch(
+      class(init)[1],
+      CmdStanPathfinder = "Pathfinder",
+      CmdStanVB = "VB",
+      CmdStanLaplace = "Laplace"
+    )
+    extra_msg <- if (inherits(init, "CmdStanPathfinder")) {
+      " Try running Pathfinder with psis_resample=FALSE."
     } else {
-      algo_name <- ""
-      extra_msg <- ""
+      ""
     }
-    stop(paste0("Not enough distinct draws (", num_procs, ") in", algo_name ,
-                "fit to create inits.", extra_msg))
+    stop(paste0("Not enough distinct draws (", num_procs, ") in ",
+                algo_name, " fit to create inits.", extra_msg))
   }
 
   # CmdStan PSIS-resamples Pathfinder draws only with multiple paths and lp weights
@@ -1493,20 +1480,6 @@ process_init.CmdStanMLE <- function(init, num_procs, model_variables = NULL,
 
 # Validation helpers ------------------------------------------------------
 
-#' Validate exe file exists
-#' @noRd
-#' @param exe_file Path to executable.
-#' @return Either throws an error or returns `invisible(TRUE)`
-validate_exe_file <- function(exe_file) {
-  if (!length(exe_file) ||
-      !nzchar(exe_file) ||
-      !file.exists(exe_file)) {
-    stop("There is no executable at '", exe_file, "'.", call. = FALSE)
-  }
-  invisible(TRUE)
-}
-
-
 #' Validate initial values
 #'
 #' For CmdStan `init` must be `NULL`, a single real number >= 0, or paths to

R/build_record.R

@@ -127,7 +127,8 @@ assert_record_dependency_entry <- function(value, field) {
 
 #' Check a build record against the format version 1 schema
 #'
-#' Every check of a record's fields is here. `new_build_record()` runs it
+#' Every check of a record's fields except `format_version` is here,
+#' `read_build_record()` checks that first. `new_build_record()` runs it
 #' before a record is written and `read_build_record()` after one is read, so
 #' a record that passes when written passes when read. Fields the schema does
 #' not name are ignored. No feature in `reported_features` is required, since
@@ -141,14 +142,6 @@ assert_record_dependency_entry <- function(value, field) {
 validate_build_record <- function(record) {
   assert_record_shape(record, "object", "record")
 
-  format_version <- record[["format_version"]]
-  if (!checkmate::test_int(format_version, tol = 0) ||
-      format_version != build_record_format_version) {
-    stop_build_record_field(
-      "format_version", paste0("must be ", build_record_format_version)
-    )
-  }
-
   configuration <- assert_record_member(record, "configuration", "object")
   cpp_options <- assert_record_member(
     configuration, "cpp_options", "object", "configuration.cpp_options"

R/fit.R

@@ -41,11 +41,6 @@ CmdStanFit <- R6::R6Class(
       self$runset$num_procs()
     },
     print = function(variables = NULL, ..., digits = 2, max_rows = getOption("cmdstanr_max_rows", 10)) {
-      if (is.null(private$draws_) &&
-          !length(self$output_files(include_failed = FALSE))) {
-        stop("Fitting failed. Unable to print.", call. = FALSE)
-      }
-
       # filter variables before passing to summary to avoid computing anything
       # that won't be printed because of max_rows
       all_variables <- self$metadata()$variables
@@ -302,9 +297,6 @@ draws <- function(variables = NULL, inc_warmup = FALSE, format = getOption("cmds
   } else {
     format <- assert_valid_draws_format(format)
   }
-  if (!length(self$output_files(include_failed = FALSE))) {
-    stop("Fitting failed. Unable to retrieve the draws.", call. = FALSE)
-  }
   if (inc_warmup) {
     warning("`inc_warmup` is ignored except when used with CmdStanMCMC objects.",
             call. = FALSE)
@@ -609,9 +601,7 @@ unconstrain_draws <- function(files = NULL, draws = NULL,
                               format = getOption("cmdstanr_draws_format", "draws_array"),
                               inc_warmup = FALSE) {
   self$init_model_methods()
-  if (!(format %in% valid_draws_formats())) {
-    stop("Invalid draws format requested!", call. = FALSE)
-  }
+  format <- assert_valid_draws_format(format)
   if (!is.null(files) || !is.null(draws)) {
     if (!is.null(files) && !is.null(draws)) {
       stop("Either a list of CSV files or a draws object can be passed, not both",
@@ -1260,9 +1250,6 @@ CmdStanFit$set("public", name = "output", value = output)
 #'
 metadata <- function() {
   if (is.null(private$metadata_)) {
-    if (!length(self$output_files(include_failed = FALSE))) {
-      stop("Fitting failed. Unable to retrieve the metadata.", call. = FALSE)
-    }
     private$read_csv_()
   }
   private$metadata_
@@ -1538,7 +1525,8 @@ CmdStanMCMC <- R6::R6Class(
     inv_metric_ = NULL,
     read_csv_ = function(variables = NULL, sampler_diagnostics = NULL, format = getOption("cmdstanr_draws_format", "draws_array")) {
       if (!length(self$output_files(include_failed = FALSE))) {
-        stop("No chains finished successfully. Unable to retrieve the draws.", call. = FALSE)
+        stop("No chains finished successfully. There is no output to read.",
+             call. = FALSE)
       }
       csv_contents <- read_cmdstan_csv(
         files = self$output_files(include_failed = FALSE),
@@ -1762,10 +1750,6 @@ sampler_diagnostics <- function(inc_warmup = FALSE, format = getOption("cmdstanr
   if (isTRUE(private$metadata_$algorithm == "fixed_param")) {
     stop("There are no sampler diagnostics when fixed_param = TRUE.", call. = FALSE)
   }
-  if (is.null(private$sampler_diagnostics_) &&
-      !length(self$output_files(include_failed = FALSE))) {
-    stop("No chains finished successfully. Unable to retrieve the sampler diagnostics.", call. = FALSE)
-  }
   to_read <- remaining_columns_to_read(
     requested = NULL,
     currently_read = posterior::variables(private$sampler_diagnostics_),
@@ -1928,9 +1912,6 @@ CmdStanMCMC$set("public", name = "diagnostic_summary", value = diagnostic_summar
 #' }
 #'
 inv_metric <- function(matrix = TRUE) {
-  if (!length(self$output_files(include_failed = FALSE))) {
-    stop("No chains finished successfully. Unable to retrieve the inverse metrics.", call. = FALSE)
-  }
   if (is.null(private$inv_metric_)) {
     private$read_csv_(variables = "", sampler_diagnostics = "")
   }
@@ -2058,7 +2039,7 @@ CmdStanMLE <- R6::R6Class(
     # inherits draws_ and metadata_ slots from CmdStanFit
     read_csv_ = function(format = getOption("cmdstanr_draws_format", "draws_matrix")) {
       if (!length(self$output_files(include_failed = FALSE))) {
-        stop("Optimization failed. Unable to retrieve the draws.", call. = FALSE)
+        stop("Optimization failed. There is no output to read.", call. = FALSE)
       }
       csv_contents <- read_cmdstan_csv(self$output_files(), format = format)
       private$draws_ <- csv_contents$point_estimates
@@ -2192,7 +2173,8 @@ CmdStanLaplace <- R6::R6Class(
     # inherits draws_ and metadata_ slots from CmdStanFit
     read_csv_ = function(format = getOption("cmdstanr_draws_format", "draws_matrix")) {
       if (!length(self$output_files(include_failed = FALSE))) {
-        stop("Laplace inference failed. Unable to retrieve the draws.", call. = FALSE)
+        stop("Laplace inference failed. There is no output to read.",
+             call. = FALSE)
       }
       csv_contents <- read_cmdstan_csv(self$output_files(), format = format)
       private$draws_ <- csv_contents$draws
@@ -2309,7 +2291,8 @@ CmdStanVB <- R6::R6Class(
     # inherits draws_ and metadata_ slots from CmdStanFit
     read_csv_ = function(format = getOption("cmdstanr_draws_format", "draws_matrix")) {
       if (!length(self$output_files(include_failed = FALSE))) {
-        stop("Variational inference failed. Unable to retrieve the draws.", call. = FALSE)
+        stop("Variational inference failed. There is no output to read.",
+             call. = FALSE)
       }
       csv_contents <- read_cmdstan_csv(self$output_files(), format = format)
       private$draws_ <- csv_contents$draws
@@ -2404,7 +2387,7 @@ CmdStanPathfinder <- R6::R6Class(
     # inherits draws_ and metadata_ slots from CmdStanFit
     read_csv_ = function(format = getOption("cmdstanr_draws_format", "draws_matrix")) {
       if (!length(self$output_files(include_failed = FALSE))) {
-        stop("Pathfinder failed. Unable to retrieve the draws.", call. = FALSE)
+        stop("Pathfinder failed. There is no output to read.", call. = FALSE)
       }
       csv_contents <- read_cmdstan_csv(self$output_files(), format = format)
       private$draws_ <- csv_contents$draws
@@ -2496,9 +2479,6 @@ CmdStanGQ <- R6::R6Class(
     },
     # override CmdStanFit draws method
     draws = function(variables = NULL, inc_warmup = FALSE, format = getOption("cmdstanr_draws_format", "draws_array")) {
-      if (!length(self$output_files(include_failed = FALSE))) {
-        stop("Generating quantities for all MCMC chains failed. Unable to retrieve the generated quantities.", call. = FALSE)
-      }
       if (inc_warmup) {
         warning("`inc_warmup` is ignored except when used with CmdStanMCMC objects.",
                 call. = FALSE)
@@ -2538,7 +2518,8 @@ CmdStanGQ <- R6::R6Class(
     # inherits draws_ and metadata_ slots from CmdStanFit
     read_csv_ = function(variables = NULL, format = getOption("cmdstanr_draws_format", "draws_array")) {
       if (!length(self$output_files(include_failed = FALSE))) {
-        stop("Generating quantities for all MCMC chains failed. Unable to retrieve the generated quantities.", call. = FALSE)
+        stop("Generating quantities for all MCMC chains failed. ",
+             "There is no output to read.", call. = FALSE)
       }
       csv_contents <- read_cmdstan_csv(
         files = self$output_files(include_failed = FALSE),

R/run.R

@@ -807,9 +807,6 @@ CmdStanProcs <- R6::R6Class(
     show_stdout_messages = function () {
       private$show_stdout_messages_
     },
-    show_stderr_messages = function () {
-      private$show_stderr_messages_
-    },
     num_procs = function() {
       private$num_procs_
     },

R/utils.R

@@ -406,8 +406,6 @@ as_draws_format_fun <- function(draws_format) {
     f <- posterior::as_draws_matrix
   } else if (draws_format %in% c("draws_list", "list")) {
     f <- posterior::as_draws_list
-  } else if (draws_format %in% c("draws_rvars", "rvars")) {
-    f <- posterior::as_draws_rvars
   }
   f
 }
@@ -448,9 +446,7 @@ maybe_convert_draws_format <- function(draws, format, ...) {
     "df" = posterior::as_draws_df(draws, ...),
     "data.frame" = posterior::as_draws_df(draws, ...),
     "list" = posterior::as_draws_list(draws, ...),
-    "matrix" = posterior::as_draws_matrix(draws, ...),
-    "rvars" = posterior::as_draws_rvars(draws, ...),
-    stop("Invalid draws format.", call. = FALSE)
+    "matrix" = posterior::as_draws_matrix(draws, ...)
   )
 }
 
@@ -462,9 +458,7 @@ create_draws_format <- function(format, ...) {
     "df" = posterior::draws_df(...),
     "data.frame" = posterior::draws_df(...),
     "list" = posterior::draws_list(...),
-    "matrix" = posterior::draws_matrix(...),
-    "rvars" = posterior::draws_rvars(...),
-    stop("Invalid draws format.", call. = FALSE)
+    "matrix" = posterior::draws_matrix(...)
   )
 }
 

tests/testthat/test-build-record.R

@@ -233,6 +233,12 @@ test_that("the validator names the field that fails", {
     rebuild(repeated_option), "`configuration.cpp_options`", fixed = TRUE
   )
 
+  odd_name <- base
+  odd_name$configuration$cpp_options <- list(`1THREADS` = "true")
+  expect_error(
+    rebuild(odd_name), "`configuration.cpp_options.1THREADS`", fixed = TRUE
+  )
+
   unknown_kind <- base
   unknown_kind$untracked_dependencies <- list(
     list(kind = "mystery", detected_in = "make/local")

tests/testthat/test-csv.R

@@ -976,6 +976,8 @@ test_that("as_cmdstan_fit creates fitted model objects from csv", {
     error = TRUE,
     fits$laplace$mode()
   )
+
+  expect_length(fits$mcmc$inv_metric(), fit_logistic_thin_1$num_chains())
 })
 
 test_that("as_cmdstan_fit can check MCMC diagnostics", {

tests/testthat/test-data.R

@@ -223,7 +223,9 @@ test_that("process_fitted_params() works with draws_array", {
 
 test_that("process_fitted_params() works with draws_array without lp__", {
   fit <- testing_fit("logistic", method = "sample", seed = 123)
-  fit_params_files <- process_fitted_params(posterior::subset_draws(fit$draws(), variables = c("alpha", "beta[1]", "beta[2]", "beta[3]")))
+  fit_params_files <- process_fitted_params(posterior::subset_draws(
+    fit$draws(), variable = c("alpha", "beta[1]", "beta[2]", "beta[3]")
+  ))
   expect_true(all(file.exists(fit_params_files)))
   chain <- 1
   for(file in fit_params_files) {

tests/testthat/test-failed-chains.R

@@ -121,15 +121,23 @@ test_that("$save_* methods save all files regardless of chain failure", {
 })
 
 test_that("errors when using draws after all chains fail", {
-  expect_error(fit_all_fail$summary(), "No chains finished successfully")
-  expect_error(fit_all_fail$draws(), "No chains finished successfully")
-  expect_error(fit_all_fail$sampler_diagnostics(), "No chains finished successfully")
+  no_output <- "No chains finished successfully"
+  expect_error(fit_all_fail$summary(), no_output)
+  expect_error(fit_all_fail$draws(), no_output)
+  expect_error(fit_all_fail$sampler_diagnostics(), no_output)
   expect_error(fit_all_fail$cmdstan_summary(), "Unable to run bin/stansummary")
   expect_error(fit_all_fail$cmdstan_diagnose(), "Unable to run bin/diagnose")
-  expect_error(fit_all_fail$print(), "Fitting failed. Unable to print")
-  expect_error(fit_all_fail$inv_metric(), "No chains finished successfully")
-  expect_error(fit_all_fail$metadata(), "Fitting failed. Unable to retrieve the metadata")
-  expect_error(fit_all_fail$inv_metric(), "No chains finished successfully")
+  expect_error(fit_all_fail$print(), no_output)
+  expect_error(fit_all_fail$inv_metric(), no_output)
+  expect_error(fit_all_fail$metadata(), no_output)
+})
+
+test_that("a fit whose chains all failed cannot be used as init", {
+  expect_error(
+    mod$sample(data = list(pr_fail = 0), chains = 1, refresh = 0,
+               init = fit_all_fail),
+    "unable to create initial values from a model with no samples"
+  )
 })
 
 test_that("can use draws after some chains fail", {
@@ -166,12 +174,12 @@ test_that("errors when using draws after variational fais", {
     ),
     "Fitting finished unexpectedly!"
   )
-  expect_error(fit$print(), "Fitting failed. Unable to print.")
-  expect_error(fit$summary(), "Fitting failed. Unable to retrieve the draws.")
-  expect_error(fit$draws(), "Fitting failed. Unable to retrieve the draws.")
+  expect_error(fit$print(), "Variational inference failed")
+  expect_error(fit$summary(), "Variational inference failed")
+  expect_error(fit$draws(), "Variational inference failed")
   expect_error(fit$cmdstan_summary(), "Unable to run bin/stansummary")
   expect_error(fit$cmdstan_diagnose(), "Unable to run bin/diagnose")
-  expect_error(fit$metadata(), "Fitting failed. Unable to retrieve the metadata.")
+  expect_error(fit$metadata(), "Variational inference failed")
 })
 
 test_that("gq chains error on wrong input CSV", {
@@ -197,15 +205,15 @@ test_that("gq chains error on wrong input CSV", {
 
   expect_error(
     fit$draws(),
-    "Generating quantities for all MCMC chains failed. Unable to retrieve the generated quantities."
+    "Generating quantities for all MCMC chains failed"
   )
   expect_error(
     fit$metadata(),
-    "Fitting failed. Unable to retrieve the metadata."
+    "Generating quantities for all MCMC chains failed"
   )
   expect_error(
     fit$print(),
-    "Fitting failed. Unable to print."
+    "Generating quantities for all MCMC chains failed"
   )
   expect_warning(
     utils::capture.output(