Continue cleaning up deprecations and backwards compat

stan-dev · May 18, 2024 · 16724a3 · 16724a3
1 parent 1e886a0
commit 16724a3
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Showing 23 changed files with 79 additions and 262 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -36,17 +36,14 @@ export(cmdstanr_example)
 export(draws_to_csv)
 export(eng_cmdstan)
 export(install_cmdstan)
-export(num_threads)
 export(print_example_program)
 export(read_cmdstan_csv)
 export(read_sample_csv)
 export(rebuild_cmdstan)
 export(register_knitr_engine)
 export(set_cmdstan_path)
-export(set_num_threads)
 export(write_stan_file)
 export(write_stan_json)
-export(write_stan_tempfile)
 import(R6)
 importFrom(posterior,as_draws)
 importFrom(stats,aggregate)
diff --git a/R/args.R b/R/args.R
@@ -68,8 +68,14 @@ CmdStanArgs <- R6::R6Class(
         self$output_dir <- ifelse(is.null(output_dir),
                                   file.path(wsl_dir_prefix(), wsl_tempdir()),
                                   wsl_safe_path(output_dir))
+      } else if (getRversion() < "3.5.0") {
+        self$output_dir <- output_dir %||% tempdir()
       } else {
-        self$output_dir <- output_dir %||% tempdir(check = TRUE)
+        if (getRversion() < "3.5.0") {
+          self$output_dir <- output_dir %||% tempdir()
+        } else {
+          self$output_dir <- output_dir %||% tempdir(check = TRUE)
+        }
       }
       self$output_dir <- repair_path(self$output_dir)
       self$output_basename <- output_basename
@@ -692,6 +698,9 @@ validate_cmdstan_args <- function(self) {
   checkmate::assert_integerish(self$refresh, lower = 0, null.ok = TRUE)
   checkmate::assert_integerish(self$sig_figs, lower = 1, upper = 18, null.ok = TRUE)
   checkmate::assert_integerish(self$save_cmdstan_config, lower = 0, upper = 1, len = 1, null.ok = TRUE)
+  if (!is.null(self$sig_figs) && cmdstan_version() < "2.25") {
+    warning("The 'sig_figs' argument is only supported with cmdstan 2.25+ and will be ignored!", call. = FALSE)
+  }
   if (!is.null(self$refresh)) {
     self$refresh <- as.integer(self$refresh)
   }
@@ -707,6 +716,9 @@ validate_cmdstan_args <- function(self) {
   validate_init(self$init, num_inits)
   validate_seed(self$seed, num_procs)
   if (!is.null(self$opencl_ids)) {
+    if (cmdstan_version() < "2.26") {
+      stop("Runtime selection of OpenCL devices is only supported with CmdStan version 2.26 or newer.", call. = FALSE)
+    }
     checkmate::assert_vector(self$opencl_ids, len = 2)
   }
   invisible(TRUE)
@@ -824,6 +836,9 @@ validate_optimize_args <- function(self) {
                            choices = c("bfgs", "lbfgs", "newton"))
   checkmate::assert_flag(self$jacobian, null.ok = TRUE)
   if (!is.null(self$jacobian)) {
+    if (cmdstan_version() < "2.32") {
+      warning("The 'jacobian' argument is only supported with cmdstan 2.32+ and will be ignored!", call. = FALSE)
+    }
     self$jacobian <- as.integer(self$jacobian)
   }
 
@@ -1461,7 +1476,11 @@ validate_seed <- function(seed, num_procs) {
   if (is.null(seed)) {
     return(invisible(TRUE))
   }
-  lower_seed <- 1
+  if (cmdstan_version() < "2.26") {
+    lower_seed <- 1
+  } else {
+    lower_seed <- 0
+  }
   checkmate::assert_integerish(seed, lower = lower_seed)
   if (length(seed) > 1 && length(seed) != num_procs) {
     stop("If 'seed' is specified it must be a single integer or one per chain.",

diff --git a/R/install.R b/R/install.R
@@ -104,7 +104,7 @@ install_cmdstan <- function(dir = NULL,
     .cmdstanr$WSL <- FALSE
   }
   if (check_toolchain) {
-    check_cmdstan_toolchain(fix = FALSE, quiet = quiet)
+    check_cmdstan_toolchain(quiet = quiet)
   }
   make_local_msg <- NULL
   if (!is.null(cmdstan_version(error_on_NA = FALSE))) {
@@ -321,7 +321,7 @@ check_cmdstan_toolchain <- function(quiet = FALSE) {
     if (os_is_wsl()) {
       check_wsl_toolchain()
     } else if (R.version$major >= "4") {
-      check_rtools4x_windows_toolchain(fix = fix, quiet = quiet)
+      check_rtools4x_windows_toolchain(quiet = quiet)
     } else {
       stop("CmdStanR requires R version 4.0.0 or later on Windows.",
            "Please update R and try again.", call. = FALSE)
@@ -562,7 +562,7 @@ check_wsl_toolchain <- function() {
   }
 }
 
-check_rtools4x_windows_toolchain <- function(fix = FALSE, quiet = FALSE) {
+check_rtools4x_windows_toolchain <- function(quiet = FALSE) {
   rtools_path <- rtools_home_path()
   rtools_version <- paste0("Rtools", rtools4x_version())
   # If RTOOLS4X_HOME is not set (the env. variable gets set on install)
@@ -636,6 +636,9 @@ check_unix_cpp_compiler <- function() {
 cmdstan_arch_suffix <- function(version = NULL) {
   os_needs_arch <- os_is_linux() || os_is_wsl()
   arch <- NULL
+  if (!os_needs_arch) {
+    return(arch)
+  }
   if (os_is_wsl()) {
     arch <- wsl_compatible_run(command = "uname", args = "-m")$stdout
     arch <- gsub("\n", "", arch, fixed = TRUE)

diff --git a/R/model.R b/R/model.R
@@ -1128,8 +1128,8 @@ sample <- function(data = NULL,
                    show_messages = TRUE,
                    show_exceptions = TRUE,
                    diagnostics = c("divergences", "treedepth", "ebfmi"),
-                   save_metric = TRUE,
-                   save_cmdstan_config = TRUE) {
+                   save_metric = NULL,
+                   save_cmdstan_config = NULL) {
   if (!fixed_param) {
     if (self$has_stan_file() && file.exists(self$stan_file())) {
       if (!is.null(self$variables()) && length(self$variables()$parameters) == 0) {

diff --git a/R/run.R b/R/run.R
@@ -24,10 +24,10 @@ CmdStanRun <- R6::R6Class(
       self$procs <- procs
       private$output_files_ <- self$new_output_files()
       private$profile_files_ <- self$new_profile_files()
-      if (isTRUE(self$args$save_cmdstan_config)) {
+      if (!is.null(self$args$save_cmdstan_config) && as.logical(self$args$save_cmdstan_config)) {
         private$config_files_ <- self$new_config_files()
       }
-      if (isTRUE(self$args$method_args$save_metric)) {
+      if (!is.null(self$args$method_args$save_metric) && as.logical(self$args$method_args$save_metric)) {
         private$metric_files_ <- self$new_metric_files()
       }
       if (self$args$save_latent_dynamics) {
@@ -73,6 +73,9 @@ CmdStanRun <- R6::R6Class(
       paste0(tools::file_path_sans_ext(private$output_files_), "_metric.json")
     },
     config_files = function(include_failed = FALSE) {
+      if (!isTRUE(self$args$save_cmdstan_config)) {
+        return(invisible(NULL))
+      }
       files <- private$config_files_
       files_win_path <- sapply(private$config_files_, wsl_safe_path, revert = TRUE)
       if (!length(files) || !any(file.exists(files_win_path))) {
@@ -90,6 +93,13 @@ CmdStanRun <- R6::R6Class(
       }
     },
     metric_files = function(include_failed = FALSE) {
+      if (!isTRUE(self$args$method_args$save_metric)) {
+        stop(
+          "No metric files found. ",
+          "Set 'save_metric=TRUE' when fitting the model.",
+          call. = FALSE
+        )
+      }
       files <- private$metric_files_
       files_win_path <- sapply(private$metric_files_, wsl_safe_path, revert = TRUE)
       if (!length(files) || !any(file.exists(files_win_path))) {
@@ -400,7 +410,7 @@ CmdStanRun <- R6::R6Class(
             self$latent_dynamics_files(include_failed = TRUE),
           if (!private$profile_files_saved_)
             private$profile_files_,
-          if (isTRUE(self$args$save_cmdstan_config)
+          if (isTRUE(self$args$save_cmdstan_config) &&
               !private$config_files_saved_)
             self$config_files(include_failed = TRUE),
           if (isTRUE(self$args$method_args$save_metric) &&

diff --git a/R/utils.R b/R/utils.R
@@ -809,12 +809,8 @@ prep_fun_cpp <- function(fun_start, fun_end, model_lines) {
   fun_body <- paste(model_lines[fun_start:fun_end], collapse = " ")
   fun_body <- gsub("// [[stan::function]]", "// [[Rcpp::export]]\n", fun_body, fixed = TRUE)
   fun_body <- gsub("std::ostream\\*\\s*pstream__\\s*=\\s*nullptr", "", fun_body)
-  if (grepl("(stan::rng_t|boost::ecuyer1988)", fun_body)) {
-    if (cmdstan_version() < "2.35.0") {
-      fun_body <- gsub("boost::ecuyer1988&\\s*base_rng__", "SEXP base_rng_ptr, SEXP seed", fun_body)
-    } else {
-      fun_body <- gsub("stan::rng_t&\\s*base_rng__", "SEXP base_rng_ptr, SEXP seed", fun_body)
-    }
+  if (grepl("stan::rng_t", fun_body)) {
+    fun_body <- gsub("stan::rng_t&\\s*base_rng__", "SEXP base_rng_ptr, SEXP seed", fun_body)
     rng_seed <- "Rcpp::XPtr<stan::rng_t> base_rng(base_rng_ptr);base_rng->seed(Rcpp::as<int>(seed));"
     fun_body <- gsub("return", paste(rng_seed, "return"), fun_body)
     fun_body <- gsub("base_rng__,", "*(base_rng.get()),", fun_body, fixed = TRUE)

diff --git a/man/install_cmdstan.Rd b/man/install_cmdstan.Rd
diff --git a/man/model-method-compile.Rd b/man/model-method-compile.Rd
diff --git a/man/model-method-laplace.Rd b/man/model-method-laplace.Rd
diff --git a/man/model-method-optimize.Rd b/man/model-method-optimize.Rd
diff --git a/man/model-method-pathfinder.Rd b/man/model-method-pathfinder.Rd
diff --git a/man/model-method-sample.Rd b/man/model-method-sample.Rd
diff --git a/man/model-method-sample_mpi.Rd b/man/model-method-sample_mpi.Rd
diff --git a/man/model-method-variational.Rd b/man/model-method-variational.Rd
diff --git a/man/stan_threads.Rd b/man/stan_threads.Rd
diff --git a/man/write_stan_tempfile.Rd b/man/write_stan_tempfile.Rd
diff --git a/tests/testthat/test-example.R b/tests/testthat/test-example.R
@@ -100,10 +100,6 @@ test_that("write_stan_file by default creates the same file for the same Stan mo
   try(file.remove(f1, f2, f4), silent = TRUE)
 })
 
-test_that("write_stan_tempfile is deprecated", {
-  expect_warning(write_stan_tempfile(stan_program), "deprecated")
-})
-
 test_that("cmdstanr_write_stan_file_dir option works", {
   base_dir <- tempdir()
   test_dir <- file.path(base_dir, "option_test")