toil.batchSystems.options

Module Contents

Classes

OptionSetter

Protocol for the setOption function we get to let us set up CLI options for

Functions

set_batchsystem_options(batch_system, set_option)

Call set_option for all the options for the given named batch system, or

add_all_batchsystem_options(parser)

set_batchsystem_config_defaults(config)

Set default and environment-based options for builtin batch systems. This

Attributes

logger

toil.batchSystems.options.logger
class toil.batchSystems.options.OptionSetter[source]

Bases: Protocol

Inheritance diagram of toil.batchSystems.options.OptionSetter

Protocol for the setOption function we get to let us set up CLI options for each batch system.

Actual functionality is defined in the Config class.

OptionType
__call__(option_name, parsing_function=None, check_function=None, default=None, env=None, old_names=None)[source]
Parameters

  • option_name (str) –

  • parsing_function (Optional[Callable[[Any], OptionType]]) –

  • check_function (Optional[Callable[[OptionType], Union[None, bool]]]) –

  • default (Optional[OptionType]) –

  • env (Optional[List[str]]) –

  • old_names (Optional[List[str]]) –

Return type

bool

toil.batchSystems.options.set_batchsystem_options(batch_system, set_option)[source]

Call set_option for all the options for the given named batch system, or all batch systems if no name is provided.

Parameters
Return type

None

toil.batchSystems.options.add_all_batchsystem_options(parser)[source]
Parameters

parser (Union[argparse.ArgumentParser, argparse._ArgumentGroup]) –

Return type

None

toil.batchSystems.options.set_batchsystem_config_defaults(config)[source]

Set default and environment-based options for builtin batch systems. This is required if a Config object is not constructed from an Options object.

Return type

None