From c87879ad32b7acae136214ffca1bc0bad8433240 Mon Sep 17 00:00:00 2001
From: Malte Kyhos <mkyhos@protonmail.com>
Date: Fri, 29 Jul 2022 00:58:25 +0200
Subject: [PATCH 1/2] Initial fix

---
 R/model.R                             | 12 +++++++++-
 tests/testthat/test-model-variables.R | 33 +++++++++++++++++++++++++++
 2 files changed, 44 insertions(+), 1 deletion(-)

diff --git a/R/model.R b/R/model.R
index 5d73ae383..dd26d1d43 100644
--- a/R/model.R
+++ b/R/model.R
@@ -653,7 +653,17 @@ variables <- function() {
   }
   assert_stan_file_exists(self$stan_file())
   if (is.null(private$variables_) && file.exists(self$stan_file())) {
-    private$variables_ <- model_variables(self$stan_file(), self$include_paths(), allow_undefined = private$using_user_header_)
+    private$variables_ <- model_variables(
+      stan_file = self$stan_file(),
+      include_paths = {
+        if (length(self$exe_file()) > 0 && file.exists(self$exe_file())) {
+          self$include_paths()
+        } else {
+          private$precompile_include_paths_
+        }
+      },
+      allow_undefined = private$using_user_header_
+    )
   }
   private$variables_
 }
diff --git a/tests/testthat/test-model-variables.R b/tests/testthat/test-model-variables.R
index 889bd3337..680bb7cdb 100644
--- a/tests/testthat/test-model-variables.R
+++ b/tests/testthat/test-model-variables.R
@@ -108,3 +108,36 @@ test_that("$variables() errors on no stan_file", {
     fixed = TRUE
   )
 })
+
+test_that("$variables() works with #includes, both pre and post compilation.", {
+  
+  data_code <- "
+    data {
+      int N;
+    }
+  "
+  model_code <- "
+    #include data.stan
+    parameters {
+      vector[N] y;
+    }
+    model {
+      y ~ std_normal();
+    }
+  "
+
+  model_file <- write_stan_file(code = model_code)
+  data_file <- write_stan_file(code = data_code, basename = "data.stan")
+
+  mod <- cmdstan_model(
+    stan_file = model_file,
+    include_paths = dirname(data_file),
+    compile = FALSE
+  )
+
+  vars_pre <- mod$variables()
+  mod$compile()
+  vars_post <- mod$variables()
+
+  expect_equal(vars_pre, vars_post)
+})

From 86557d88919b3642e465bd6df8ec7659a1ec5c70 Mon Sep 17 00:00:00 2001
From: Malte Kyhos <mkyhos@protonmail.com>
Date: Fri, 29 Jul 2022 01:12:03 +0200
Subject: [PATCH 2/2] Move logic in () query method

---
 R/model.R | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/R/model.R b/R/model.R
index dd26d1d43..67d4bffe7 100644
--- a/R/model.R
+++ b/R/model.R
@@ -265,7 +265,11 @@ CmdStanModel <- R6::R6Class(
       invisible(self)
     },
     include_paths = function() {
-      private$include_paths_
+      if (length(self$exe_file()) > 0 && file.exists(self$exe_file())) {
+        return(private$include_paths_)
+      } else {
+        return(private$precompile_include_paths_)
+      }
     },
     code = function() {
       if (length(private$stan_code_) == 0) {
@@ -655,13 +659,7 @@ variables <- function() {
   if (is.null(private$variables_) && file.exists(self$stan_file())) {
     private$variables_ <- model_variables(
       stan_file = self$stan_file(),
-      include_paths = {
-        if (length(self$exe_file()) > 0 && file.exists(self$exe_file())) {
-          self$include_paths()
-        } else {
-          private$precompile_include_paths_
-        }
-      },
+      include_paths = self$include_paths(),
       allow_undefined = private$using_user_header_
     )
   }