Merge pull request #573 from stan-dev/fix/572-py-typed

Add py.typed and accept os.PathLike objects for paths

Author: mitzimorris

MANIFEST.in

@@ -3,3 +3,4 @@
 
 include requirements*.txt
 include LICENSE.md
+include cmdstanpy/py.typed

cmdstanpy/cmdstan_args.py

@@ -19,6 +19,8 @@
     write_stan_json,
 )
 
+OptionalPath = Union[str, os.PathLike, None]
+
 
 class Method(Enum):
     """Supported CmdStan method names."""
@@ -704,15 +706,15 @@ class CmdStanArgs:
     def __init__(
         self,
         model_name: str,
-        model_exe: Optional[str],
+        model_exe: OptionalPath,
         chain_ids: Optional[List[int]],
         method_args: Union[
             SamplerArgs, OptimizeArgs, GenerateQuantitiesArgs, VariationalArgs
         ],
         data: Union[Mapping[str, Any], str, None] = None,
         seed: Union[int, List[int], None] = None,
         inits: Union[int, float, str, List[str], None] = None,
-        output_dir: Optional[str] = None,
+        output_dir: OptionalPath = None,
         sig_figs: Optional[int] = None,
         save_latent_dynamics: bool = False,
         save_profile: bool = False,

cmdstanpy/compiler_opts.py

@@ -48,6 +48,8 @@
     'version',
 ]
 
+OptionalPath = Union[str, os.PathLike, None]
+
 
 class CompilerOptions:
     """
@@ -64,12 +66,12 @@ def __init__(
         *,
         stanc_options: Optional[Dict[str, Any]] = None,
         cpp_options: Optional[Dict[str, Any]] = None,
-        user_header: Optional[str] = None,
+        user_header: OptionalPath = None,
     ) -> None:
         """Initialize object."""
         self._stanc_options = stanc_options if stanc_options is not None else {}
         self._cpp_options = cpp_options if cpp_options is not None else {}
-        self._user_header = user_header if user_header is not None else ''
+        self._user_header = str(user_header) if user_header is not None else ''
 
     def __repr__(self) -> str:
         return 'stanc_options={}, cpp_options={}'.format(

cmdstanpy/model.py

@@ -49,6 +49,8 @@
 
 from . import progress as progbar
 
+OptionalPath = Union[str, os.PathLike, None]
+
 
 class CmdStanModel:
     # overview, omitted from doc comment in order to improve Sphinx docs.
@@ -91,13 +93,13 @@ class CmdStanModel:
     def __init__(
         self,
         model_name: Optional[str] = None,
-        stan_file: Optional[str] = None,
-        exe_file: Optional[str] = None,
+        stan_file: OptionalPath = None,
+        exe_file: OptionalPath = None,
         # TODO should be Literal['force'] not str
         compile: Union[bool, str] = True,
         stanc_options: Optional[Dict[str, Any]] = None,
         cpp_options: Optional[Dict[str, Any]] = None,
-        user_header: Optional[str] = None,
+        user_header: OptionalPath = None,
     ) -> None:
         """
         Initialize object given constructor args.
@@ -232,12 +234,12 @@ def name(self) -> str:
         return self._name
 
     @property
-    def stan_file(self) -> Optional[str]:
+    def stan_file(self) -> OptionalPath:
         """Full path to Stan program file."""
         return self._stan_file
 
     @property
-    def exe_file(self) -> Optional[str]:
+    def exe_file(self) -> OptionalPath:
         """Full path to Stan exe file."""
         return self._exe_file
 
@@ -253,7 +255,7 @@ def exe_info(self) -> Dict[str, str]:
             return result
         try:
             info = StringIO()
-            do_command(cmd=[self.exe_file, 'info'], fd_out=info)
+            do_command(cmd=[str(self.exe_file), 'info'], fd_out=info)
             lines = info.getvalue().split('\n')
             for line in lines:
                 kv_pair = [x.strip() for x in line.split('=')]
@@ -282,7 +284,7 @@ def src_info(self) -> Dict[str, Any]:
                 + self._compiler_options.compose_stanc()
                 + [
                     '--info',
-                    self.stan_file,
+                    str(self.stan_file),
                 ]
             )
             proc = subprocess.run(
@@ -331,7 +333,7 @@ def format(
                 [os.path.join(cmdstan_path(), 'bin', 'stanc' + EXTENSION)]
                 # handle include-paths, allow-undefined etc
                 + self._compiler_options.compose_stanc()
-                + [self.stan_file]
+                + [str(self.stan_file)]
             )
 
             if canonicalize:
@@ -379,7 +381,7 @@ def format(
                     if backup:
                         shutil.copyfile(
                             self.stan_file,
-                            self.stan_file
+                            str(self.stan_file)
                             + '.bak-'
                             + datetime.now().strftime("%Y%m%d%H%M%S"),
                         )
@@ -426,7 +428,7 @@ def compile(
         force: bool = False,
         stanc_options: Optional[Dict[str, Any]] = None,
         cpp_options: Optional[Dict[str, Any]] = None,
-        user_header: Optional[str] = None,
+        user_header: OptionalPath = None,
         override_options: bool = False,
     ) -> None:
         """
@@ -569,10 +571,10 @@ def compile(
 
     def optimize(
         self,
-        data: Union[Mapping[str, Any], str, None] = None,
+        data: Union[Mapping[str, Any], str, os.PathLike, None] = None,
         seed: Optional[int] = None,
-        inits: Union[Dict[str, float], float, str, None] = None,
-        output_dir: Optional[str] = None,
+        inits: Union[Dict[str, float], float, str, os.PathLike, None] = None,
+        output_dir: OptionalPath = None,
         sig_figs: Optional[int] = None,
         save_profile: bool = False,
         algorithm: Optional[str] = None,
@@ -733,7 +735,7 @@ def optimize(
     # pylint: disable=too-many-arguments
     def sample(
         self,
-        data: Union[Mapping[str, Any], str, None] = None,
+        data: Union[Mapping[str, Any], str, os.PathLike, None] = None,
         chains: Optional[int] = None,
         parallel_chains: Optional[int] = None,
         threads_per_chain: Optional[int] = None,
@@ -755,7 +757,7 @@ def sample(
         adapt_metric_window: Optional[int] = None,
         adapt_step_size: Optional[int] = None,
         fixed_param: bool = False,
-        output_dir: Optional[str] = None,
+        output_dir: OptionalPath = None,
         sig_figs: Optional[int] = None,
         save_latent_dynamics: bool = False,
         save_profile: bool = False,
@@ -1197,10 +1199,10 @@ def sample(
 
     def generate_quantities(
         self,
-        data: Union[Mapping[str, Any], str, None] = None,
+        data: Union[Mapping[str, Any], str, os.PathLike, None] = None,
         mcmc_sample: Union[CmdStanMCMC, List[str], None] = None,
         seed: Optional[int] = None,
-        gq_output_dir: Optional[str] = None,
+        gq_output_dir: OptionalPath = None,
         sig_figs: Optional[int] = None,
         show_console: bool = False,
         refresh: Optional[int] = None,
@@ -1341,10 +1343,10 @@ def generate_quantities(
 
     def variational(
         self,
-        data: Union[Mapping[str, Any], str, None] = None,
+        data: Union[Mapping[str, Any], str, os.PathLike, None] = None,
         seed: Optional[int] = None,
         inits: Optional[float] = None,
-        output_dir: Optional[str] = None,
+        output_dir: OptionalPath = None,
         sig_figs: Optional[int] = None,
         save_latent_dynamics: bool = False,
         save_profile: bool = False,

cmdstanpy/py.typed

@@ -1402,7 +1402,9 @@ class MaybeDictToFilePath:
 
     def __init__(
         self,
-        *objs: Union[str, Mapping[str, Any], List[Any], int, float, None],
+        *objs: Union[
+            str, Mapping[str, Any], List[Any], int, float, os.PathLike, None
+        ],
     ):
         self._unlink = [False] * len(objs)
         self._paths: List[Any] = [''] * len(objs)
@@ -1417,7 +1419,7 @@ def __init__(
                 write_stan_json(data_file, obj)
                 self._paths[i] = data_file
                 self._unlink[i] = True
-            elif isinstance(obj, str):
+            elif isinstance(obj, (str, os.PathLike)):
                 if not os.path.exists(obj):
                     raise ValueError("File doesn't exist {}".format(obj))
                 self._paths[i] = obj

cmdstanpy/utils.py

@@ -72,7 +72,11 @@ def get_version() -> str:
     long_description_content_type="text/markdown",
     author='Stan Dev Team',
     url='https://github.com/stan-dev/cmdstanpy',
+    license_files=['LICENSE.md'],
     packages=['cmdstanpy', 'cmdstanpy.stanfit'],
+    package_data={
+        'cmdstanpy': ['py.typed'],
+    },
     entry_points={
         'console_scripts': [
             'install_cmdstan=cmdstanpy.install_cmdstan:__main__',