cmdstanpy 1.3.0__tar.gz → 1.3.1__tar.gz

{cmdstanpy-1.3.0/cmdstanpy.egg-info → cmdstanpy-1.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cmdstanpy
-Version: 1.3.0
+Version: 1.3.1
 Summary: Python interface to CmdStan
 Author: Stan Dev Team
 License: BSD-3-Clause
@@ -34,8 +34,8 @@ Requires-Dist: mypy; extra == "test"
 Requires-Dist: xarray; extra == "test"
 Requires-Dist: polars>=1.8.2; extra == "test"
 Provides-Extra: docs
-Requires-Dist: sphinx<6,>5; extra == "docs"
-Requires-Dist: pydata-sphinx-theme<0.9; extra == "docs"
+Requires-Dist: sphinx<9; extra == "docs"
+Requires-Dist: pydata-sphinx-theme<0.17; extra == "docs"
 Requires-Dist: nbsphinx; extra == "docs"
 Requires-Dist: ipython; extra == "docs"
 Requires-Dist: ipykernel<7; extra == "docs"

cmdstanpy-1.3.1/cmdstanpy/_version.py

@@ -0,0 +1,3 @@
+"""PyPi Version"""
+
+__version__ = '1.3.1'

{cmdstanpy-1.3.0 → cmdstanpy-1.3.1}/cmdstanpy/cmdstan_args.py

@@ -632,7 +632,7 @@ class CmdStanArgs:
     def __init__(
         self,
         model_name: str,
-        model_exe: OptionalPath,
+        model_exe: str,
         chain_ids: Optional[list[int]],
         method_args: Union[
             SamplerArgs,
@@ -692,10 +692,6 @@ class CmdStanArgs:
         * if no seed specified, set random seed.
         * length of per-chain lists equals specified # of chains
         """
-        if self.model_name is None:
-            raise ValueError('no stan model specified')
-        if self.model_exe is None:
-            raise ValueError('model not compiled')
 
         if self.chain_ids is not None:
             for chain_id in self.chain_ids:
@@ -857,10 +853,10 @@ class CmdStanArgs:
                         idx, len(self.chain_ids)
                     )
                 )
-            cmd.append(self.model_exe)  # type: ignore # guaranteed by validate
+            cmd.append(self.model_exe)
             cmd.append(f'id={self.chain_ids[idx]}')
         else:
-            cmd.append(self.model_exe)  # type: ignore # guaranteed by validate
+            cmd.append(self.model_exe)
 
         if self.seed is not None:
             if not isinstance(self.seed, list):

{cmdstanpy-1.3.0 → cmdstanpy-1.3.1}/cmdstanpy/compilation.py

@@ -8,7 +8,6 @@ import os
 import platform
 import shutil
 import subprocess
-from copy import copy
 from datetime import datetime
 from pathlib import Path
 from typing import Any, Iterable, Optional, Union
@@ -37,12 +36,6 @@ STANC_OPTS = [
     'warn-pedantic',
 ]
 
-# TODO(2.0): remove
-STANC_DEPRECATED_OPTS = {
-    'allow_undefined': 'allow-undefined',
-    'include_paths': 'include-paths',
-}
-
 STANC_IGNORE_OPTS = [
     'debug-lex',
     'debug-parse',
@@ -67,7 +60,6 @@ STANC_IGNORE_OPTS = [
 OptionalPath = Union[str, os.PathLike, None]
 
 
-# TODO(2.0): can remove add function and other logic
 class CompilerOptions:
     """
     User-specified flags for stanc and C++ compiler.
@@ -95,26 +87,6 @@ class CompilerOptions:
             self._stanc_options, self._cpp_options
         )
 
-    def __eq__(self, other: Any) -> bool:
-        """Overrides the default implementation"""
-        if self.is_empty() and other is None:  # equiv w/r/t compiler
-            return True
-        if not isinstance(other, CompilerOptions):
-            return False
-        return (
-            self._stanc_options == other.stanc_options
-            and self._cpp_options == other.cpp_options
-            and self._user_header == other.user_header
-        )
-
-    def is_empty(self) -> bool:
-        """True if no options specified."""
-        return (
-            self._stanc_options == {}
-            and self._cpp_options == {}
-            and self._user_header == ''
-        )
-
     @property
     def stanc_options(self) -> dict[str, Union[bool, int, str, Iterable[str]]]:
         """Stanc compiler options."""
@@ -144,31 +116,12 @@ class CompilerOptions:
         Check stanc compiler args and consistency between stanc and C++ options.
         Raise ValueError if bad config is found.
         """
-        # pylint: disable=no-member
         if self._stanc_options is None:
             return
         ignore = []
         paths = None
         has_o_flag = False
 
-        for deprecated, replacement in STANC_DEPRECATED_OPTS.items():
-            if deprecated in self._stanc_options:
-                if replacement:
-                    get_logger().warning(
-                        'compiler option "%s" is deprecated, use "%s" instead',
-                        deprecated,
-                        replacement,
-                    )
-                    self._stanc_options[replacement] = copy(
-                        self._stanc_options[deprecated]
-                    )
-                    del self._stanc_options[deprecated]
-                else:
-                    get_logger().warning(
-                        'compiler option "%s" is deprecated and should '
-                        'not be used',
-                        deprecated,
-                    )
         for key, val in self._stanc_options.items():
             if key in STANC_IGNORE_OPTS:
                 get_logger().info('ignoring compiler option: %s', key)
@@ -267,37 +220,6 @@ class CompilerOptions:
 
             self._cpp_options['USER_HEADER'] = self._user_header
 
-    def add(self, new_opts: "CompilerOptions") -> None:  # noqa: disable=Q000
-        """Adds options to existing set of compiler options."""
-        if new_opts.stanc_options is not None:
-            if self._stanc_options is None:
-                self._stanc_options = new_opts.stanc_options
-            else:
-                for key, val in new_opts.stanc_options.items():
-                    if key == 'include-paths':
-                        if isinstance(val, Iterable) and not isinstance(
-                            val, str
-                        ):
-                            for path in val:
-                                self.add_include_path(str(path))
-                        else:
-                            self.add_include_path(str(val))
-                    else:
-                        self._stanc_options[key] = val
-        if new_opts.cpp_options is not None:
-            for key, val in new_opts.cpp_options.items():
-                self._cpp_options[key] = val
-        if new_opts._user_header != '' and self._user_header == '':
-            self._user_header = new_opts._user_header
-
-    def add_include_path(self, path: str) -> None:
-        """Adds include path to existing set of compiler options."""
-        path = os.path.abspath(os.path.expanduser(path))
-        if 'include-paths' not in self._stanc_options:
-            self._stanc_options['include-paths'] = [path]
-        elif path not in self._stanc_options['include-paths']:
-            self._stanc_options['include-paths'].append(path)
-
     def compose_stanc(self, filename_in_msg: Optional[str]) -> list[str]:
         opts = []
 
@@ -343,7 +265,8 @@ class CompilerOptions:
 
 
 def src_info(
-    stan_file: str, compiler_options: CompilerOptions
+    stan_file: str,
+    stanc_options: Optional[dict[str, Any]] = None,
 ) -> dict[str, Any]:
     """
     Get source info for Stan program file.
@@ -354,7 +277,7 @@ def src_info(
     cmd = (
         [stanc_path()]
         # handle include-paths, allow-undefined etc
-        + compiler_options.compose_stanc(None)
+        + CompilerOptions(stanc_options=stanc_options).compose_stanc(None)
         + ['--info', str(stan_file)]
     )
     proc = subprocess.run(cmd, capture_output=True, text=True, check=False)
@@ -407,12 +330,26 @@ def compile_stan_file(
     )
     compiler_options.validate()
 
+    # if program has include directives, record path
+    if '#include' in src.read_text():
+        path = os.fspath(src.parent.resolve())
+        if 'include-paths' not in compiler_options.stanc_options:
+            compiler_options.stanc_options['include-paths'] = [path]
+        else:
+            paths: list[str] = compiler_options.stanc_options[
+                'include-paths'
+            ]  # type: ignore
+            if path not in paths:
+                paths.append(path)
+
     exe_target = src.with_suffix(EXTENSION)
     if exe_target.exists():
         exe_time = os.path.getmtime(exe_target)
         included_files = [src]
         included_files.extend(
-            src_info(str(src), compiler_options).get('included_files', [])
+            src_info(str(src), compiler_options.stanc_options).get(
+                'included_files', []
+            )
         )
         out_of_date = any(
             os.path.getmtime(included_file) > exe_time
@@ -482,7 +419,7 @@ def compile_stan_file(
             raise ValueError(
                 f"Failed to compile Stan model '{src}'. Console:\n{console}"
             )
-        return str(exe_target)
+        return os.fspath(exe_target)
 
 
 def format_stan_file(

{cmdstanpy-1.3.0 → cmdstanpy-1.3.1}/cmdstanpy/install_cxx_toolchain.py

@@ -33,16 +33,14 @@ IS_64BITS = sys.maxsize > 2**32
 
 def usage() -> None:
     """Print usage."""
-    print(
-        """Arguments:
+    print("""Arguments:
         -v (--version) :CmdStan version
         -d (--dir) : install directory
         -s (--silent) : install with /VERYSILENT instead of /SILENT for RTools
         -m (--no-make) : don't install mingw32-make (Windows RTools 4.0 only)
         --progress : flag, when specified show progress bar for RTools download
         -h (--help) : this message
-        """
-    )
+        """)
 
 
 def get_config(dir: str, silent: bool) -> list[str]:
@@ -244,11 +242,11 @@ def get_url(version: str) -> str:
         if version == '4.0':
             # pylint: disable=line-too-long
             if IS_64BITS:
-                url = 'https://cran.r-project.org/bin/windows/Rtools/rtools40-x86_64.exe'  # noqa: disable=E501
+                url = 'https://cran-archive.r-project.org/bin/windows/Rtools/rtools40-x86_64.exe'  # noqa: disable=E501
             else:
-                url = 'https://cran.r-project.org/bin/windows/Rtools/rtools40-i686.exe'  # noqa: disable=E501
+                url = 'https://cran-archive.r-project.org/bin/windows/Rtools/rtools40-i686.exe'  # noqa: disable=E501
         elif version == '3.5':
-            url = 'https://cran.r-project.org/bin/windows/Rtools/Rtools35.exe'
+            url = 'https://cran-archive.r-project.org/bin/windows/Rtools/Rtools35.exe'  # noqa: disable=E501
     return url