Repository: Project-MONAI/MONAI
File: monai/bundle/workflows.py (Python)

Code before:
            for _config_file in _config_files:
                _config_file = Path(_config_file)
                if _config_file.parent != config_root_path:
                    logger.warn(
                        f"Not all config files are in {config_root_path}. If logging_file and meta_file are"
                        f"not specified, {config_root_path} will be used as the default config root directory."
                    )
                if not _config_file.is_file():
                    raise FileNotFoundError(f"Cannot find the config file: {_config_file}.")
        else:
            config_root_path = Path("configs")
        meta_file = str(config_root_path / "metadata.json") if meta_file is None else meta_file
        super().__init__(workflow_type=workflow_type, meta_file=meta_file, properties_path=properties_path)
        self.config_root_path = config_root_path
        logging_file = str(self.config_root_path / "logging.conf") if logging_file is None else logging_file
        if not logging_file:
            logger.warn(f"Logging file is set to {logging_file}, skipping logging.")
        elif logging_file is not None:
            if not os.path.isfile(logging_file):
                if logging_file == str(self.config_root_path / "logging.conf"):
                    logger.warn(f"Default logging file in {logging_file} does not exist, skipping logging.")
                else:
                    raise FileNotFoundError(f"Cannot find the logging config file: {logging_file}.")
            else:
                logger.info(f"Setting logging properties based on config: {logging_file}.")
                fileConfig(logging_file, disable_existing_loggers=False)  # type: ignore[arg-type]

        self.parser = ConfigParser()
        self.parser.read_config(f=config_file)
        if self.meta_file is not None:
            self.parser.read_meta(f=self.meta_file)

        # the rest key-values in the _args are to override config content
        self.parser.update(pairs=override)
        self.init_id = init_id
        self.run_id = run_id
        self.final_id = final_id
        # set tracking configs for experiment management
        if tracking is not None:
            if isinstance(tracking, str) and tracking in DEFAULT_EXP_MGMT_SETTINGS:
                settings_ = DEFAULT_EXP_MGMT_SETTINGS[tracking]
            else:
                settings_ = ConfigParser.load_config_files(tracking)
            self.patch_bundle_tracking(parser=self.parser, settings=settings_)
        self._is_initialized: bool = False

    def initialize(self) -> Any:
        """
        Initialize the bundle workflow before running.

        """

Review comment (suggestion):
```suggestion
                fileConfig(str(logging_file), disable_existing_loggers=False)
```

This might fix the type check issue.

Code after:
            for _config_file in _config_files:
                _config_file = Path(_config_file)
                if _config_file.parent != config_root_path:
                    logger.warn(
                        f"Not all config files are in {config_root_path}. If logging_file and meta_file are"
                        f"not specified, {config_root_path} will be used as the default config root directory."
                    )
                if not _config_file.is_file():
                    raise FileNotFoundError(f"Cannot find the config file: {_config_file}.")
        else:
            config_root_path = Path("configs")
        meta_file = str(config_root_path / "metadata.json") if meta_file is None else meta_file
        super().__init__(workflow_type=workflow_type, meta_file=meta_file, properties_path=properties_path)
        self.config_root_path = config_root_path
        logging_file = str(self.config_root_path / "logging.conf") if logging_file is None else logging_file
        if logging_file is False:
            logger.warn(f"Logging file is set to {logging_file}, skipping logging.")
        else:
            if not os.path.isfile(logging_file):
                if logging_file == str(self.config_root_path / "logging.conf"):
                    logger.warn(f"Default logging file in {logging_file} does not exist, skipping logging.")
                else:
                    raise FileNotFoundError(f"Cannot find the logging config file: {logging_file}.")
            else:
                logger.info(f"Setting logging properties based on config: {logging_file}.")
                fileConfig(str(logging_file), disable_existing_loggers=False)

        self.parser = ConfigParser()
        self.parser.read_config(f=config_file)
        if self.meta_file is not None:
            self.parser.read_meta(f=self.meta_file)

        # the rest key-values in the _args are to override config content
        self.parser.update(pairs=override)
        self.init_id = init_id
        self.run_id = run_id
        self.final_id = final_id
        # set tracking configs for experiment management
        if tracking is not None:
            if isinstance(tracking, str) and tracking in DEFAULT_EXP_MGMT_SETTINGS:
                settings_ = DEFAULT_EXP_MGMT_SETTINGS[tracking]
            else:
                settings_ = ConfigParser.load_config_files(tracking)
            self.patch_bundle_tracking(parser=self.parser, settings=settings_)
        self._is_initialized: bool = False

    def initialize(self) -> Any:
        """
        Initialize the bundle workflow before running.

        """