Merge branch 'master' into model-methods

R/model.R

@@ -720,6 +720,9 @@ compile <- function(quiet = TRUE,
         error_on_status = FALSE
       )
     }
+
+    writeLines(private$model_methods_env_$hpp_code_,
+               con = wsl_safe_path(private$hpp_file_, revert = TRUE))
   } # End - if(!dry_run)
 
   private$exe_file_ <- exe

R/utils.R

@@ -875,7 +875,7 @@ get_standalone_hpp <- function(stan_file, stancflags) {
       ),
       wsl_compatible_run(
         command = stanc_cmd(),
-        args = c(paste0("--o=", hpp_path), stancflags, stan_file),
+        args = c(paste0("--o=", wsl_safe_path(hpp_path)), stancflags, wsl_safe_path(stan_file)),
         wd = cmdstan_path(),
         error_on_status = FALSE
       )

tests/testthat/test-install.R

@@ -16,7 +16,7 @@ test_that("install_cmdstan() successfully installs cmdstan", {
       install_cmdstan(dir = dir, cores = 2, quiet = FALSE, overwrite = TRUE,
                       release_url = cmdstan_test_tarball_url,
                       wsl = os_is_wsl()),
-      "Compiling, linking C++ code",
+      "Compiling C++ code",
       fixed = TRUE
     ),
     "CmdStan path set",

tests/testthat/test-model-compile.R

@@ -174,15 +174,6 @@ test_that("compile errors are shown", {
   )
 })
 
-test_that("compile suggests using format to fix old syntax", {
-  stan_file <- testing_stan_file("old_array_syntax")
-  expect_error(
-    cmdstan_model(stan_file),
-    "To fix deprecated or removed syntax please see ?cmdstanr::format for an example.",
-    fixed = TRUE
-  )
-})
-
 test_that("dir arg works for cmdstan_model and $compile()", {
   tmp_dir <- tempdir()
   tmp_dir_2 <- tempdir()
@@ -689,16 +680,6 @@ test_that("format() works", {
     fixed = TRUE
   )
 
-  expect_output(
-    mod_1$format(canonicalize = TRUE),
-    "target += normal_lpdf(y | 0, 1);",
-    fixed = TRUE
-  )
-  expect_output(
-    mod_1$format(canonicalize = list("deprecations")),
-    "target += normal_lpdf(y | 0, 1);",
-    fixed = TRUE
-  )
   expect_error(
     mod_1$format(),
     "Syntax error found! See the message above for more information.",
@@ -868,4 +849,3 @@ test_that("STANCFLAGS included from make/local", {
   expect_output(print(out), out_w_flags)
   cmdstan_make_local(cpp_options = make_local_old, append = FALSE)
 })
-

tests/testthat/test-model-laplace.R

@@ -54,7 +54,9 @@ test_that("laplace() runs when all arguments specified validly", {
   expect_equal(fit1$metadata()$draws, as.integer(ok_arg_values$draws))
   expect_equal(fit1$mode()$metadata()$jacobian, as.integer(ok_arg_values$jacobian))
   expect_equal(fit1$mode()$metadata()$init_alpha, ok_arg_values$opt_args$init_alpha)
-  expect_equal(fit1$mode()$metadata()$tol_obj, ok_arg_values$opt_args$tol_obj, tolerance = 0)
+
+  # https://github.com/stan-dev/cmdstan/issues/1242
+  #expect_equal(fit1$mode()$metadata()$tol_obj, ok_arg_values$opt_args$tol_obj, tolerance = 0)
 
   # leaving all at default (except 'data')
   expect_laplace_output(fit2 <- mod$laplace(data = data_list, seed = 123))

tests/testthat/test-model-optimize.R

@@ -129,9 +129,11 @@ test_that("optimize() works with (L-)BFGS tolerances specified", {
   expect_equal(metadata$init_alpha, 0.002)
   expect_equal(metadata$tol_obj, 2e-11)
   expect_equal(metadata$tol_rel_obj, 10001)
-  expect_equal(metadata$tol_grad, 5e-07)
+  # https://github.com/stan-dev/cmdstan/issues/1242
+  # expect_equal(metadata$tol_grad, 5e-07)
   expect_equal(metadata$tol_rel_grad, 10000001)
-  expect_equal(metadata$tol_param, 5e-07)
+  # https://github.com/stan-dev/cmdstan/issues/1242
+  # expect_equal(metadata$tol_param, 5e-07)
   expect_equal(metadata$history_size, 6)
 })