Merge pull request #453 from stan-dev/minor_fixes

Fix issue with reading in CSV for models with spaces in name

Author: bbbales2

NEWS.md

@@ -2,6 +2,8 @@
 
 ### Bug fixes
 
+* Fixed issue with retrieving draws with models with spaces in their names. (#453)
+
 ### New features
 
 * New function `as_cmdstan_fit()` that creates CmdStanMCMC/MLE/VB objects

R/csv.R

@@ -223,9 +223,9 @@ read_cmdstan_csv <- function(files,
     if (length(col_select) > 0) {
       if (os_is_windows()) {
         grep_path <- repair_path(Sys.which("grep.exe"))
-        fread_cmd <- paste0(grep_path, " -v '^#' --color=never ", output_file)
+        fread_cmd <- paste0(grep_path, " -v '^#' --color=never '", output_file, "'")
       } else {
-        fread_cmd <- paste0("grep -v '^#' --color=never ", output_file)
+        fread_cmd <- paste0("grep -v '^#' --color=never '", output_file, "'")
       }
       suppressWarnings(
       draws <- data.table::fread(
@@ -512,9 +512,9 @@ read_csv_metadata <- function(csv_file) {
   total_time <- 0
   if (os_is_windows()) {
     grep_path <- repair_path(Sys.which("grep.exe"))
-    fread_cmd <- paste0(grep_path, " '^[#a-zA-Z]' --color=never ", csv_file)
+    fread_cmd <- paste0(grep_path, " '^[#a-zA-Z]' --color=never '", csv_file, "'")
   } else {
-    fread_cmd <- paste0("grep '^[#a-zA-Z]' --color=never ", csv_file)
+    fread_cmd <- paste0("grep '^[#a-zA-Z]' --color=never '", csv_file, "'")
   }
   suppressWarnings(
     metadata <- data.table::fread(

tests/testthat/test-fit-shared.R

@@ -399,3 +399,38 @@ test_that("sig_figs works with all methods", {
     c(0.12, 0.12345, 0.123456789)
   )
 })
+
+test_that("draws are returned for model with spaces", {
+  skip_on_cran()
+  m <- "
+  parameters {
+    real y;
+  }
+  model {
+    y ~ std_normal();
+  }
+  generated quantities {
+    real two_y = 2 * y;
+  }
+  "
+  f <- write_stan_file(m, basename = "file with spaces")
+  expect_equal(basename(f), "file with spaces.stan")
+  mod <- cmdstan_model(f)
+  utils::capture.output(
+    fit_sample <- mod$sample(seed = 123, iter_sampling = 1000, chains = 1)
+  )
+  expect_equal(dim(fit_sample$draws()), c(1000, 1, 3))
+  utils::capture.output(
+    fit <- mod$variational(seed = 123, output_samples = 1000)
+  )
+  expect_equal(dim(fit$draws()), c(1000, 4))
+  utils::capture.output(
+    fit <- mod$optimize(seed = 123)
+  )
+  expect_equal(length(fit$mle()), 2)
+
+  utils::capture.output(
+    fit <- mod$generate_quantities(fitted_params = fit_sample, seed = 123)
+  )
+  expect_equal(dim(fit$draws()), c(1000, 1, 1))
+})

tests/testthat/test-model-compile.R

@@ -6,7 +6,6 @@ if (not_on_cran()) {
   mod <- cmdstan_model(stan_file = stan_program, compile = FALSE)
 }
 
-
 test_that("object initialized correctly", {
   skip_on_cran()
   expect_equal(mod$stan_file(), stan_program)
@@ -399,4 +398,25 @@ test_that("check_syntax() works with include_paths", {
 
 })
 
+test_that("check_syntax() works with pedantic=TRUE", {
+  skip_on_cran()
+  model_code <- "
+  transformed data {
+    real a;
+    a <- 3;
+  }
+  "
+  stan_file <- write_stan_file(model_code)
+  mod_dep_warning <- cmdstan_model(stan_file, compile = FALSE)
+  expect_message(
+    mod_dep_warning$compile(),
+    "Warning: deprecated language construct used in",
+    fixed = TRUE
+  )
+  expect_message(
+    mod_dep_warning$check_syntax(),
+    "Warning: deprecated language construct used in",
+    fixed = TRUE
+  )
+})