Try to fix rest of deprecated tests, add filename-in-msg

Author: WardBrian

cmdstanpy/compiler_opts.py

@@ -275,8 +275,12 @@ def add_include_path(self, path: str) -> None:
         elif path not in self._stanc_options['include-paths']:
             self._stanc_options['include-paths'].append(path)
 
-    def compose_stanc(self) -> List[str]:
+    def compose_stanc(self, filename_in_msg: Optional[str]) -> List[str]:
         opts = []
+
+        if filename_in_msg is not None:
+            opts.append(f'--filename-in-msg={filename_in_msg}')
+
         if self._stanc_options is not None and len(self._stanc_options) > 0:
             for key, val in self._stanc_options.items():
                 if key == 'include-paths':
@@ -295,11 +299,11 @@ def compose_stanc(self) -> List[str]:
                     opts.append(f'--{key}')
         return opts
 
-    def compose(self) -> List[str]:
+    def compose(self, filename_in_msg: Optional[str]) -> List[str]:
         """Format makefile options as list of strings."""
         opts = [
             'STANCFLAGS+=' + flag.replace(" ", "\\ ")
-            for flag in self.compose_stanc()
+            for flag in self.compose_stanc(filename_in_msg)
         ]
         if self._cpp_options is not None and len(self._cpp_options) > 0:
             for key, val in self._cpp_options.items():

cmdstanpy/model.py

@@ -300,7 +300,7 @@ def src_info(self) -> Dict[str, Any]:
         cmd = (
             [os.path.join(cmdstan_path(), 'bin', 'stanc' + EXTENSION)]
             # handle include-paths, allow-undefined etc
-            + self._compiler_options.compose_stanc()
+            + self._compiler_options.compose_stanc(None)
             + ['--info', str(self.stan_file)]
         )
         proc = subprocess.run(cmd, capture_output=True, text=True, check=False)
@@ -343,7 +343,7 @@ def format(
             cmd = (
                 [os.path.join(cmdstan_path(), 'bin', 'stanc' + EXTENSION)]
                 # handle include-paths, allow-undefined etc
-                + self._compiler_options.compose_stanc()
+                + self._compiler_options.compose_stanc(None)
                 + [str(self.stan_file)]
             )
 
@@ -528,7 +528,7 @@ def compile(
             )
             cmd = [make]
             if self._compiler_options is not None:
-                cmd.extend(self._compiler_options.compose())
+                cmd.extend(self._compiler_options.compose(self._stan_file))
             cmd.append(Path(exe_file).as_posix())
 
             sout = io.StringIO()

test/data/bernoulli_include.stan

@@ -3,7 +3,7 @@ functions {
 }
 data {
   int<lower=0> N;
-  int<lower=0,upper=1> y[N];
+  array[N] int<lower=0,upper=1> y;
 }
 parameters {
   real<lower=0,upper=1> theta;

test/data/path with space/bernoulli_path_with_space.stan

@@ -5,9 +5,10 @@ data {
 parameters {
   real<lower=0, upper=1> theta;
 }
+;
 model {
   theta ~ beta(1, 1);
-  for (n in 1 : N) 
+  for (n in 1 : N)
     y[n] ~ bernoulli(theta);
 }