Merge branch 'develop' into deprecations/rename-to-inv_metric

Author: WardBrian

.github/workflows/main.yml

@@ -44,7 +44,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:

cmdstanpy/__init__.py

@@ -37,13 +37,13 @@ def _cleanup_tmpdir() -> None:
 from .utils import (
     cmdstan_path,
     cmdstan_version,
+    disable_logging,
+    enable_logging,
     install_cmdstan,
     set_cmdstan_path,
     set_make_env,
     show_versions,
     write_stan_json,
-    enable_logging,
-    disable_logging,
 )
 
 __all__ = [

cmdstanpy/cmdstan_args.py

@@ -5,7 +5,7 @@
 import os
 from enum import Enum, auto
 from time import time
-from typing import Any, List, Mapping, Optional, Union
+from typing import Any, Mapping, Optional, Union
 
 import numpy as np
 from numpy.random import default_rng
@@ -58,8 +58,8 @@ def __init__(
         thin: Optional[int] = None,
         max_treedepth: Optional[int] = None,
         metric_type: Optional[str] = None,
-        metric_file: Union[str, List[str], None] = None,
-        step_size: Union[float, List[float], None] = None,
+        metric_file: Union[str, list[str], None] = None,
+        step_size: Union[float, list[float], None] = None,
         adapt_engaged: bool = True,
         adapt_delta: Optional[float] = None,
         adapt_init_phase: Optional[int] = None,
@@ -75,7 +75,7 @@ def __init__(
         self.thin = thin
         self.max_treedepth = max_treedepth
         self.metric_type: Optional[str] = metric_type
-        self.metric_file: Union[str, List[str], None] = metric_file
+        self.metric_file: Union[str, list[str], None] = metric_file
         self.step_size = step_size
         self.adapt_engaged = adapt_engaged
         self.adapt_delta = adapt_delta
@@ -152,8 +152,9 @@ def validate(self, chains: Optional[int]) -> None:
             ):
                 if self.step_size <= 0:
                     raise ValueError(
-                        'Argument "step_size" must be > 0, '
-                        'found {}.'.format(self.step_size)
+                        'Argument "step_size" must be > 0, found {}.'.format(
+                            self.step_size
+                        )
                     )
             else:
                 if len(self.step_size) != chains:
@@ -226,7 +227,7 @@ def validate(self, chains: Optional[int]) -> None:
                 'When fixed_param=True, cannot specify adaptation parameters.'
             )
 
-    def compose(self, idx: int, cmd: List[str]) -> List[str]:
+    def compose(self, idx: int, cmd: list[str]) -> list[str]:
         """
         Compose CmdStan command for method-specific non-default arguments.
         """
@@ -350,7 +351,7 @@ def validate(self, _chains: Optional[int] = None) -> None:
         positive_float(self.tol_param, 'tol_param')
         positive_int(self.history_size, 'history_size')
 
-    def compose(self, _idx: int, cmd: List[str]) -> List[str]:
+    def compose(self, _idx: int, cmd: list[str]) -> list[str]:
         """compose command string for CmdStan for non-default arg values."""
         cmd.append('method=optimize')
         if self.algorithm:
@@ -394,7 +395,7 @@ def validate(self, _chains: Optional[int] = None) -> None:
             raise ValueError(f'Invalid path for mode file: {self.mode}')
         positive_int(self.draws, 'draws')
 
-    def compose(self, _idx: int, cmd: List[str]) -> List[str]:
+    def compose(self, _idx: int, cmd: list[str]) -> list[str]:
         """compose command string for CmdStan for non-default arg values."""
         cmd.append('method=laplace')
         cmd.append(f'mode={self.mode}')
@@ -462,7 +463,7 @@ def validate(self, _chains: Optional[int] = None) -> None:
         positive_int(self.num_draws, 'num_draws')
         positive_int(self.num_elbo_draws, 'num_elbo_draws')
 
-    def compose(self, _idx: int, cmd: List[str]) -> List[str]:
+    def compose(self, _idx: int, cmd: list[str]) -> list[str]:
         """compose command string for CmdStan for non-default arg values."""
         cmd.append('method=pathfinder')
 
@@ -507,12 +508,13 @@ def compose(self, _idx: int, cmd: List[str]) -> List[str]:
 class GenerateQuantitiesArgs:
     """Arguments needed for generate_quantities method."""
 
-    def __init__(self, csv_files: List[str]) -> None:
+    def __init__(self, csv_files: list[str]) -> None:
         """Initialize object."""
         self.sample_csv_files = csv_files
 
     def validate(
-        self, chains: Optional[int] = None  # pylint: disable=unused-argument
+        self,
+        chains: Optional[int] = None,  # pylint: disable=unused-argument
     ) -> None:
         """
         Check arguments correctness and consistency.
@@ -525,7 +527,7 @@ def validate(
                     'Invalid path for sample csv file: {}'.format(csv)
                 )
 
-    def compose(self, idx: int, cmd: List[str]) -> List[str]:
+    def compose(self, idx: int, cmd: list[str]) -> list[str]:
         """
         Compose CmdStan command for method-specific non-default arguments.
         """
@@ -564,7 +566,8 @@ def __init__(
         self.output_samples = output_samples
 
     def validate(
-        self, chains: Optional[int] = None  # pylint: disable=unused-argument
+        self,
+        chains: Optional[int] = None,  # pylint: disable=unused-argument
     ) -> None:
         """
         Check arguments correctness and consistency.
@@ -588,7 +591,7 @@ def validate(
         positive_int(self.output_samples, 'output_samples')
 
     # pylint: disable=unused-argument
-    def compose(self, idx: int, cmd: List[str]) -> List[str]:
+    def compose(self, idx: int, cmd: list[str]) -> list[str]:
         """
         Compose CmdStan command for method-specific non-default arguments.
         """
@@ -630,7 +633,7 @@ def __init__(
         self,
         model_name: str,
         model_exe: OptionalPath,
-        chain_ids: Optional[List[int]],
+        chain_ids: Optional[list[int]],
         method_args: Union[
             SamplerArgs,
             OptimizeArgs,
@@ -640,8 +643,8 @@ def __init__(
             PathfinderArgs,
         ],
         data: Union[Mapping[str, Any], str, None] = None,
-        seed: Union[int, List[int], None] = None,
-        inits: Union[int, float, str, List[str], None] = None,
+        seed: Union[int, list[int], None] = None,
+        inits: Union[int, float, str, list[str], None] = None,
         output_dir: OptionalPath = None,
         sig_figs: Optional[int] = None,
         save_latent_dynamics: bool = False,
@@ -842,11 +845,11 @@ def compose_command(
         *,
         diagnostic_file: Optional[str] = None,
         profile_file: Optional[str] = None,
-    ) -> List[str]:
+    ) -> list[str]:
         """
         Compose CmdStan command for non-default arguments.
         """
-        cmd: List[str] = []
+        cmd: list[str] = []
         if idx is not None and self.chain_ids is not None:
             if idx < 0 or idx > len(self.chain_ids) - 1:
                 raise ValueError(

cmdstanpy/compilation.py

@@ -11,7 +11,7 @@
 from copy import copy
 from datetime import datetime
 from pathlib import Path
-from typing import Any, Dict, Iterable, List, Optional, Union
+from typing import Any, Iterable, Optional, Union
 
 from cmdstanpy.utils import get_logger
 from cmdstanpy.utils.cmdstan import (
@@ -81,8 +81,8 @@ class CompilerOptions:
     def __init__(
         self,
         *,
-        stanc_options: Optional[Dict[str, Any]] = None,
-        cpp_options: Optional[Dict[str, Any]] = None,
+        stanc_options: Optional[dict[str, Any]] = None,
+        cpp_options: Optional[dict[str, Any]] = None,
         user_header: OptionalPath = None,
     ) -> None:
         """Initialize object."""
@@ -116,12 +116,12 @@ def is_empty(self) -> bool:
         )
 
     @property
-    def stanc_options(self) -> Dict[str, Union[bool, int, str, Iterable[str]]]:
+    def stanc_options(self) -> dict[str, Union[bool, int, str, Iterable[str]]]:
         """Stanc compiler options."""
         return self._stanc_options
 
     @property
-    def cpp_options(self) -> Dict[str, Union[bool, int]]:
+    def cpp_options(self) -> dict[str, Union[bool, int]]:
         """C++ compiler options."""
         return self._cpp_options
 
@@ -165,8 +165,8 @@ def validate_stanc_opts(self) -> None:
                     del self._stanc_options[deprecated]
                 else:
                     get_logger().warning(
-                        'compiler option "%s" is deprecated and '
-                        'should not be used',
+                        'compiler option "%s" is deprecated and should '
+                        'not be used',
                         deprecated,
                     )
         for key, val in self._stanc_options.items():
@@ -225,8 +225,8 @@ def validate_cpp_opts(self) -> None:
                 val = self._cpp_options[key]
                 if not isinstance(val, int) or val < 0:
                     raise ValueError(
-                        f'{key} must be a non-negative integer value,'
-                        f' found {val}.'
+                        f'{key} must be a non-negative integer '
+                        f'value, found {val}.'
                     )
 
     def validate_user_header(self) -> None:
@@ -298,7 +298,7 @@ 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, filename_in_msg: Optional[str]) -> List[str]:
+    def compose_stanc(self, filename_in_msg: Optional[str]) -> list[str]:
         opts = []
 
         if filename_in_msg is not None:
@@ -322,7 +322,7 @@ def compose_stanc(self, filename_in_msg: Optional[str]) -> List[str]:
                     opts.append(f'--{key}')
         return opts
 
-    def compose(self, filename_in_msg: Optional[str] = None) -> List[str]:
+    def compose(self, filename_in_msg: Optional[str] = None) -> list[str]:
         """
         Format makefile options as list of strings.
 
@@ -344,7 +344,7 @@ def compose(self, filename_in_msg: Optional[str] = None) -> List[str]:
 
 def src_info(
     stan_file: str, compiler_options: CompilerOptions
-) -> Dict[str, Any]:
+) -> dict[str, Any]:
     """
     Get source info for Stan program file.
 
@@ -363,15 +363,15 @@ def src_info(
             f"Failed to get source info for Stan model "
             f"'{stan_file}'. Console:\n{proc.stderr}"
         )
-    result: Dict[str, Any] = json.loads(proc.stdout)
+    result: dict[str, Any] = json.loads(proc.stdout)
     return result
 
 
 def compile_stan_file(
     src: Union[str, Path],
     force: bool = False,
-    stanc_options: Optional[Dict[str, Any]] = None,
-    cpp_options: Optional[Dict[str, Any]] = None,
+    stanc_options: Optional[dict[str, Any]] = None,
+    cpp_options: Optional[dict[str, Any]] = None,
     user_header: OptionalPath = None,
 ) -> str:
     """
@@ -480,7 +480,7 @@ def compile_stan_file(
                     "If the issue persists please open a bug report"
                 )
             raise ValueError(
-                f"Failed to compile Stan model '{src}'. " f"Console:\n{console}"
+                f"Failed to compile Stan model '{src}'. Console:\n{console}"
             )
         return str(exe_target)
 
@@ -492,7 +492,7 @@ def format_stan_file(
     canonicalize: Union[bool, str, Iterable[str]] = False,
     max_line_length: int = 78,
     backup: bool = True,
-    stanc_options: Optional[Dict[str, Any]] = None,
+    stanc_options: Optional[dict[str, Any]] = None,
 ) -> None:
     """
     Run stanc's auto-formatter on the model code. Either saves directly

cmdstanpy/install_cmdstan.py

@@ -17,6 +17,7 @@
    --cores: int, number of cores to use when building, defaults to 1
    -c, --compiler : flag, add C++ compiler to path (Windows only)
 """
+
 import argparse
 import json
 import os
@@ -30,7 +31,7 @@
 from collections import OrderedDict
 from pathlib import Path
 from time import sleep
-from typing import TYPE_CHECKING, Any, Callable, Dict, Optional, Union
+from typing import TYPE_CHECKING, Any, Callable, Optional, Union
 
 from tqdm.auto import tqdm
 
@@ -85,7 +86,7 @@ def is_windows() -> bool:
 EXTENSION = '.exe' if is_windows() else ''
 
 
-def get_headers() -> Dict[str, str]:
+def get_headers() -> dict[str, str]:
     """Create headers dictionary."""
     headers = {}
     GITHUB_PAT = os.environ.get("GITHUB_PAT")  # pylint:disable=invalid-name
@@ -287,13 +288,13 @@ def build(verbose: bool = False, progress: bool = True, cores: int = 1) -> None:
         raise CmdStanInstallError(f'Command "make build" failed\n{str(e)}')
     if not os.path.exists(os.path.join('bin', 'stansummary' + EXTENSION)):
         raise CmdStanInstallError(
-            f'bin/stansummary{EXTENSION} not found'
-            ', please rebuild or report a bug!'
+            f'bin/stansummary{EXTENSION} not found, please rebuild or '
+            'report a bug!'
         )
     if not os.path.exists(os.path.join('bin', 'diagnose' + EXTENSION)):
         raise CmdStanInstallError(
-            f'bin/stansummary{EXTENSION} not found'
-            ', please rebuild or report a bug!'
+            f'bin/stansummary{EXTENSION} not found, please rebuild or '
+            'report a bug!'
         )
 
     if is_windows():
@@ -417,8 +418,8 @@ def install_version(
         )
         if overwrite and os.path.exists('.'):
             print(
-                'Overwrite requested, remove existing build of version '
-                '{}'.format(cmdstan_version)
+                'Overwrite requested, remove existing build '
+                'of version {}'.format(cmdstan_version)
             )
             clean_all(verbose)
             print('Rebuilding version {}'.format(cmdstan_version))
@@ -496,10 +497,8 @@ def retrieve_version(version: str, progress: bool = True) -> None:
             break
         except urllib.error.HTTPError as e:
             raise CmdStanRetrieveError(
-                'HTTPError: {}\n'
-                'Version {} not available from github.com.'.format(
-                    e.code, version
-                )
+                'HTTPError: {}\nVersion {} not available from '
+                'github.com.'.format(e.code, version)
             ) from e
         except urllib.error.URLError as e:
             print(
@@ -645,7 +644,7 @@ def run_install(args: Union[InteractiveSettings, InstallationSettings]) -> None:
             compile_example(args.verbose)
 
 
-def parse_cmdline_args() -> Dict[str, Any]:
+def parse_cmdline_args() -> dict[str, Any]:
     parser = argparse.ArgumentParser("install_cmdstan")
     parser.add_argument(
         '--interactive',