a few more cases

Author: jgabry

tests/testthat/test-fit-laplace.R

@@ -1,4 +1,4 @@
-context("fitted-vb")
+context("fitted-laplace")
 
 set_cmdstan_path()
 fit_laplace <- testing_fit("logistic", method = "laplace", seed = 100)

tests/testthat/test-fit-shared.R

@@ -462,7 +462,7 @@ test_that("sampling with inits works with include_paths", {
                                  include_paths = test_path("resources", "stan"))
 
   data_list <- list(N = 10, y = c(0,1,0,0,0,0,0,0,0,1))
-  expect_no_error(
+  expect_no_error(utils::capture.output(
     fit <- mod_w_include$sample(
       data = data_list,
       seed = 123,
@@ -474,7 +474,7 @@ test_that("sampling with inits works with include_paths", {
                   list(theta = 0.25),
                   list(theta = 0.25))
     )
-  )
+  ))
 })
 
 test_that("CmdStanModel created with exe_file works", {

tests/testthat/test-model-compile.R

@@ -837,7 +837,7 @@ test_that("dirname of stan_file is used as include path if no other paths suppli
 
   mod_tmp <- cmdstan_model(stan_file, compile = FALSE)
   expect_true(mod_tmp$check_syntax())
-  expect_true(mod_tmp$format())
+  utils::capture.output(expect_true(mod_tmp$format()))
   expect_s3_class(mod_tmp$compile(), "CmdStanModel")
 })
 

tests/testthat/test-model-laplace.R

@@ -36,7 +36,9 @@ test_that("laplace() method errors for any invalid argument before calling cmdst
   for (nm in names(bad_arg_values)) {
     args <- ok_arg_values
     args[[nm]] <- bad_arg_values[[nm]]
-    expect_error(do.call(mod$laplace, args), regexp = nm, info = nm)
+    utils::capture.output(
+      expect_error(do.call(mod$laplace, args), regexp = nm, info = nm)
+    )
   }
   args <- ok_arg_values
   args$opt_args <- list(iter = "NOT_A_NUMBER")
@@ -129,14 +131,15 @@ test_that("laplace() errors with bad combinations of arguments", {
 
 test_that("laplace() errors if optimize() fails", {
   mod_schools <- testing_model("schools")
-  expect_error(
-    expect_warning(
-      expect_message(
-        mod_schools$laplace(data = testing_data("schools"), refresh = 0),
-        "Line search failed to achieve a sufficient decrease"
+  utils::capture.output(
+    expect_error(
+      expect_warning(
+        expect_message(
+          mod_schools$laplace(data = testing_data("schools"), refresh = 0),
+          "Line search failed to achieve a sufficient decrease"
+        ),
+        "Fitting finished unexpectedly"
       ),
-      "Fitting finished unexpectedly"
-    ),
-    "Optimization failed"
-  )
+      "Optimization failed"
+    ))
 })

tests/testthat/test-model-pathfinder.R

@@ -11,7 +11,7 @@ data_list <- testing_data("bernoulli")
 data_file_r <- test_path("resources", "data", "bernoulli.data.R")
 data_file_json <- test_path("resources", "data", "bernoulli.data.json")
 
-# these are all valid for sample()
+# these are all valid for pathfinder()
 ok_arg_values <- list(
   data = data_list,
   output_dir = tempdir(),
@@ -32,9 +32,10 @@ ok_arg_values <- list(
   max_lbfgs_iters = 100,
   save_single_paths = FALSE,
   calculate_lp = TRUE,
-  psis_resample=TRUE)
+  psis_resample=TRUE
+)
 
-# using any one of these should cause sample() to error
+# using any one of these should cause pathfinder() to error
 bad_arg_values <- list(
   data = "NOT_A_FILE",
   output_dir = "NOT_A_DIRECTORY",

tests/testthat/test-threads.R

@@ -172,9 +172,13 @@ test_that("correct output when stan_threads not TRUE", {
     fixed = TRUE
   )
   mod <- cmdstan_model(stan_program, cpp_options = list(stan_threads = FALSE), force_recompile = TRUE)
-  expect_warning(
-    mod$sample(data = data_file_json, threads_per_chain = 4),
-    "'threads_per_chain' is set but the model was not compiled with 'cpp_options = list(stan_threads = TRUE)' so 'threads_per_chain' will have no effect!",
+  expect_output(
+    expect_warning(
+      mod$sample(data = data_file_json, threads_per_chain = 4),
+      "'threads_per_chain' is set but the model was not compiled with 'cpp_options = list(stan_threads = TRUE)' so 'threads_per_chain' will have no effect!",
+      fixed = TRUE
+    ),
+    "Running MCMC with 4 sequential chains",
     fixed = TRUE
   )
 })