Convert List/Tuple/Dict typing to generics

Author: amas0

cmdstanpy/cmdstan_args.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 +165,7 @@ 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 +224,7 @@ 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 value, found {val}.'
                     )
 
     def validate_user_header(self) -> None:
@@ -236,8 +234,7 @@ def validate_user_header(self) -> None:
         """
         if self._user_header != "":
             if not (
-                os.path.exists(self._user_header)
-                and os.path.isfile(self._user_header)
+                os.path.exists(self._user_header) and os.path.isfile(self._user_header)
             ):
                 raise ValueError(
                     f"User header file {self._user_header} cannot be found"
@@ -275,9 +272,7 @@ def add(self, new_opts: "CompilerOptions") -> None:  # noqa: disable=Q000
             else:
                 for key, val in new_opts.stanc_options.items():
                     if key == 'include-paths':
-                        if isinstance(val, Iterable) and not isinstance(
-                            val, str
-                        ):
+                        if isinstance(val, Iterable) and not isinstance(val, str):
                             for path in val:
                                 self.add_include_path(str(path))
                         else:
@@ -298,7 +293,7 @@ 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 +317,7 @@ 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.
 
@@ -342,9 +337,7 @@ def compose(self, filename_in_msg: Optional[str] = None) -> List[str]:
         return opts
 
 
-def src_info(
-    stan_file: str, compiler_options: CompilerOptions
-) -> Dict[str, Any]:
+def src_info(stan_file: str, compiler_options: CompilerOptions) -> dict[str, Any]:
     """
     Get source info for Stan program file.
 
@@ -363,15 +356,15 @@ 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 +473,7 @@ 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 +485,7 @@ 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
@@ -532,9 +525,7 @@ def format_stan_file(
                 else:
                     raise ValueError(
                         "Invalid arguments passed for current CmdStan"
-                        + " version({})\n".format(
-                            cmdstan_version() or "Unknown"
-                        )
+                        + " version({})\n".format(cmdstan_version() or "Unknown")
                         + "--canonicalize requires 2.29 or higher"
                     )
             else:

cmdstanpy/compilation.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
@@ -109,9 +110,7 @@ def latest_version() -> str:
                 print('retry ({}/5)'.format(i + 1))
                 sleep(1)
                 continue
-            raise CmdStanRetrieveError(
-                'Cannot connect to CmdStan github repo.'
-            ) from e
+            raise CmdStanRetrieveError('Cannot connect to CmdStan github repo.') from e
     content = json.loads(response.decode('utf-8'))
     tag = content['tag_name']
     match = re.search(r'v?(.+)', tag)
@@ -287,26 +286,18 @@ 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():
         # Add tbb to the $PATH on Windows
-        libtbb = os.path.join(
-            os.getcwd(), 'stan', 'lib', 'stan_math', 'lib', 'tbb'
-        )
+        libtbb = os.path.join(os.getcwd(), 'stan', 'lib', 'stan_math', 'lib', 'tbb')
         os.environ['PATH'] = ';'.join(
-            list(
-                OrderedDict.fromkeys(
-                    [libtbb] + os.environ.get('PATH', '').split(';')
-                )
-            )
+            list(OrderedDict.fromkeys([libtbb] + os.environ.get('PATH', '').split(';')))
         )
 
 
@@ -417,8 +408,9 @@ 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))
@@ -485,9 +477,9 @@ def retrieve_version(version: str, progress: bool = True) -> None:
     for i in range(6):  # always retry to allow for transient URLErrors
         try:
             if progress and progbar.allow_show_progress():
-                progress_hook: Optional[
-                    Callable[[int, int, int], None]
-                ] = wrap_url_progress_hook()
+                progress_hook: Optional[Callable[[int, int, int], None]] = (
+                    wrap_url_progress_hook()
+                )
             else:
                 progress_hook = None
             file_tmp, _ = urllib.request.urlretrieve(
@@ -496,16 +488,13 @@ 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(
+                'HTTPError: {}\nVersion {} not available from github.com.'.format(
                     e.code, version
                 )
             ) from e
         except urllib.error.URLError as e:
             print(
-                'Failed to download CmdStan version {} from github.com'.format(
-                    version
-                )
+                'Failed to download CmdStan version {} from github.com'.format(version)
             )
             print(e)
             if i < 5:
@@ -645,14 +634,13 @@ 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',
         '-i',
         action='store_true',
-        help="Ignore other arguments and run the installation in "
-        + "interactive mode",
+        help="Ignore other arguments and run the installation in " + "interactive mode",
     )
     parser.add_argument(
         '--version',

cmdstanpy/install_cmdstan.py

@@ -12,6 +12,7 @@
    -m --no-make : don't install mingw32-make (Windows RTools 4.0 only)
    --progress : flag, when specified show progress bar for RTools download
 """
+
 import argparse
 import os
 import platform
@@ -21,7 +22,7 @@
 import urllib.request
 from collections import OrderedDict
 from time import sleep
-from typing import Any, Dict, List
+from typing import Any
 
 from cmdstanpy import _DOT_CMDSTAN
 from cmdstanpy.utils import pushd, validate_dir, wrap_url_progress_hook
@@ -44,7 +45,7 @@ def usage() -> None:
     )
 
 
-def get_config(dir: str, silent: bool) -> List[str]:
+def get_config(dir: str, silent: bool) -> list[str]:
     """Assemble config info."""
     config = []
     if platform.system() == 'Windows':
@@ -243,7 +244,9 @@ 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.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
         elif version == '3.5':
@@ -260,7 +263,7 @@ def get_toolchain_version(name: str, version: str) -> str:
     return toolchain_folder
 
 
-def run_rtools_install(args: Dict[str, Any]) -> None:
+def run_rtools_install(args: dict[str, Any]) -> None:
     """Main."""
     if platform.system() not in {'Windows'}:
         raise NotImplementedError(
@@ -308,9 +311,7 @@ def run_rtools_install(args: Dict[str, Any]) -> None:
         else:
             if os.path.exists(toolchain_folder):
                 shutil.rmtree(toolchain_folder, ignore_errors=False)
-            retrieve_toolchain(
-                toolchain_folder + EXTENSION, url, progress=progress
-            )
+            retrieve_toolchain(toolchain_folder + EXTENSION, url, progress=progress)
             install_version(
                 toolchain_folder,
                 toolchain_folder + EXTENSION,
@@ -324,16 +325,14 @@ def run_rtools_install(args: Dict[str, Any]) -> None:
             and (version in ('4.0', '4', '40'))
         ):
             if os.path.exists(
-                os.path.join(
-                    toolchain_folder, 'mingw64', 'bin', 'mingw32-make.exe'
-                )
+                os.path.join(toolchain_folder, 'mingw64', 'bin', 'mingw32-make.exe')
             ):
                 print('mingw32-make.exe already installed')
             else:
                 install_mingw32_make(toolchain_folder, verbose)
 
 
-def parse_cmdline_args() -> Dict[str, Any]:
+def parse_cmdline_args() -> dict[str, Any]:
     parser = argparse.ArgumentParser()
     parser.add_argument('--version', '-v', help="version, defaults to latest")
     parser.add_argument(