def apply(self, configuration, schema, args):
        """
        Apply the plugin to the configuration.

        Inheriting plugins should implement this method to add additional functionality.

        Parameters
        ----------
        configuration : dict
            configuration
        schema : dict
            JSON schema
        args : argparse.NameSpace
            parsed command line arguments

        Returns
        -------
        configuration : dict
            updated configuration after applying the plugin
        """
        # Set values from the command line
        for name, path in self.arguments.items():
            value = getattr(args, name.replace('-', '_'))
            if value is not None:
                util.set_value(configuration, path, value)

        return configuration
Apply the plugin to the configuration.

        Inheriting plugins should implement this method to add additional functionality.

        Parameters
        ----------
        configuration : dict
            configuration
        schema : dict
            JSON schema
        args : argparse.NameSpace
            parsed command line arguments

        Returns
        -------
        configuration : dict
            updated configuration after applying the plugin