Start testing

Author: WardBrian

cmdstanpy/model.py

@@ -298,7 +298,11 @@ def src_info(self) -> Dict[str, Any]:
             return result
 
     def format_model(
-        self, save: bool = False, canonicalize: Union[bool, List[str]] = False
+        self,
+        save: bool = False,
+        canonicalize: Union[bool, str, List[str]] = False,
+        *,
+        unsafe: bool = False,
     ) -> None:
         """
         Run stanc's auto-formatter on the model code. Either saves directly
@@ -311,37 +315,43 @@ def format_model(
             the Stan model, removing things like deprecated syntax. Default is
             False. If True, all canonicalizations are run. If it is a list of
             strings, those options are passed to stanc (new in Stan 2.29)
+        :param unsafe: If True, do not create stanfile.bak backups before
+            writing to the file. Only do this if you're sure you have other
+            copies of the file or are using a version control system like Git.
         """
         if self.stan_file is None or not os.path.isfile(self.stan_file):
             raise ValueError("No Stan file found for this module")
         try:
-            # TODO need include paths if they exist.
-            cmd = [
-                os.path.join('.', 'bin', 'stanc' + EXTENSION),
-                '--auto-format',
-            ]
+            cmd = (
+                [os.path.join(cmdstan_path(), 'bin', 'stanc' + EXTENSION)]
+                # handle include-paths, allow-undefined etc
+                + self._compiler_options.compose_stanc()
+                + [self.stan_file]
+            )
+
             if canonicalize:
                 if isinstance(canonicalize, list):
                     cmd.append('--canonicalize=' + ','.join(canonicalize))
+                elif isinstance(canonicalize, str):
+                    cmd.append('--canonicalize=' + canonicalize)
                 else:
                     cmd.append('--print-canonical')
 
-            cmd.append(self.stan_file)
+            if not (cmdstan_version_before(2, 29) and canonicalize):
+                cmd.append('--auto-format')
 
             out = subprocess.run(
-                cmd,
-                cwd=cmdstan_path(),
-                capture_output=True,
-                text=True,
-                check=True,
+                cmd, capture_output=True, text=True, check=True
             )
             if out.stderr:
-                print(out.stderr)
+                get_logger().warning(out.stderr)
             result = out.stdout
             if save:
-                shutil.copyfile(self.stan_file, self.stan_file + '.bak')
-                with (open(self.stan_file, 'w')) as file:
-                    file.write(result)
+                if result:
+                    if not unsafe:
+                        shutil.copyfile(self.stan_file, self.stan_file + '.bak')
+                    with (open(self.stan_file, 'w')) as file:
+                        file.write(result)
             else:
                 print(result)
 

test/data/format_me.stan

@@ -0,0 +1,5 @@
+# pound-sign comment
+generated quantities {
+   int x;
+   x <- (((((3)))));
+}

test/test_model.py

@@ -1,5 +1,7 @@
 """CmdStanModel tests"""
 
+import contextlib
+import io
 import logging
 import os
 import shutil
@@ -10,7 +12,7 @@
 from testfixtures import LogCapture, StringComparison
 
 from cmdstanpy.model import CmdStanModel
-from cmdstanpy.utils import EXTENSION
+from cmdstanpy.utils import EXTENSION, cmdstan_version_before
 
 HERE = os.path.dirname(os.path.abspath(__file__))
 DATAFILES_PATH = os.path.join(HERE, 'data')
@@ -34,6 +36,7 @@
 BERN_BASENAME = 'bernoulli'
 
 
+# pylint: disable=too-many-public-methods
 class CmdStanModelTest(CustomTestCase):
     def test_model_good(self):
         # compile on instantiation, override model name
@@ -374,6 +377,34 @@ def test_model_includes_implicit(self):
         model2 = CmdStanModel(stan_file=stan)
         self.assertPathsEqual(model2.exe_file, exe)
 
+    def test_model_format(self):
+        # deprecations expire in this version
+        if cmdstan_version_before(2, 32):
+            stan = os.path.join(DATAFILES_PATH, 'format_me.stan')
+
+            model = CmdStanModel(stan_file=stan, compile=False)
+
+            sys_stdout = io.StringIO()
+            with contextlib.redirect_stdout(sys_stdout):
+                model.format_model()
+
+            formatted = sys_stdout.getvalue()
+            self.assertIn("//", formatted)
+            self.assertNotIn("#", formatted)
+            self.assertEqual(formatted.count('('), 5)
+
+            sys_stdout = io.StringIO()
+            with contextlib.redirect_stdout(sys_stdout):
+                model.format_model(canonicalize=True)
+
+            formatted = sys_stdout.getvalue()
+            print(formatted)
+            self.assertNotIn("<-", formatted)
+            self.assertEqual(formatted.count('('), 0)
+
+        else:
+            assert False, "Test needs to be updated for Stan 2.32"
+
 
 if __name__ == '__main__':
     unittest.main()