module_setup

Specify all CLI-accessible modules and their configurations, the pipeline to run by default, and define special functions for the config and pipeline CLI option trees.

ModuleConfig

Represents a module's configuration, containing the following attributes:

Attributes:

Name	Type	Description
func		A callable that executes the module's functionality.
add_args		A callable that populates the module's sub-parser arguments.
description		A description of the module's functionality.
help		A help message for the module's command-line interface.
common_parsers		A list of common parsers to add to the module's sub-parser, appending the 'dataset' and 'core' parsers to those passed.

Source code in src/nhssynth/cli/module_setup.py

class ModuleConfig:
    """
    Represents a module's configuration, containing the following attributes:

    Attributes:
        func: A callable that executes the module's functionality.
        add_args: A callable that populates the module's sub-parser arguments.
        description: A description of the module's functionality.
        help: A help message for the module's command-line interface.
        common_parsers: A list of common parsers to add to the module's sub-parser, appending the 'dataset' and 'core' parsers to those passed.
    """

    def __init__(
        self,
        func: Callable[..., argparse.Namespace],
        add_args: Callable[..., None],
        description: str,
        help: str,
        common_parsers: Optional[list[str]] = None,
        no_seed: bool = False,
    ) -> None:
        self.func = func
        self.add_args = add_args
        self.description = description
        self.help = help
        self.common_parsers = ["core", "seed"] if not no_seed else ["core"]
        if common_parsers:
            assert set(common_parsers) <= COMMON_PARSERS.keys(), "Invalid common parser(s) specified."
            # merge the below two assert statements
            assert (
                "core" not in common_parsers and "seed" not in common_parsers
            ), "The 'seed' and 'core' parser groups are automatically added to all modules, remove the from `ModuleConfig`s."
            self.common_parsers += common_parsers

    def __call__(self, args: argparse.Namespace) -> argparse.Namespace:
        return self.func(args)

add_config_args(parser)

Adds arguments to parser relating to configuration file handling and module-specific config overrides.

Source code in src/nhssynth/cli/module_setup.py

def add_config_args(parser: argparse.ArgumentParser) -> None:
    """Adds arguments to `parser` relating to configuration file handling and module-specific config overrides."""
    parser.add_argument(
        "-c",
        "--input-config",
        required=True,
        help="specify the config file name",
    )
    parser.add_argument(
        "-cp",
        "--custom-pipeline",
        action="store_true",
        help="infer a custom pipeline running order of modules from the config",
    )
    for module_name in PIPELINE:
        MODULE_MAP[module_name].add_args(parser, f"{module_name} option overrides", overrides=True)
    for module_name in VALID_MODULES - set(PIPELINE):
        MODULE_MAP[module_name].add_args(parser, f"{module_name} options overrides", overrides=True)

add_pipeline_args(parser)

Adds arguments to parser for each module in the pipeline.

Source code in src/nhssynth/cli/module_setup.py

def add_pipeline_args(parser: argparse.ArgumentParser) -> None:
    """Adds arguments to `parser` for each module in the pipeline."""
    for module_name in PIPELINE:
        MODULE_MAP[module_name].add_args(parser, f"{module_name} options")

add_subparser(subparsers, name, module_config)

Add a subparser to an argparse argument parser.

Parameters:

Name	Type	Description	Default
subparsers	_SubParsersAction	The subparsers action to which the subparser will be added.	required
name	str	The name of the subparser.	required
module_config	ModuleConfig	A ModuleConfig object containing information about the subparser, including a function to execute and a function to add arguments.	required

Returns:

Type	Description
ArgumentParser	The newly created subparser.

Source code in src/nhssynth/cli/module_setup.py

def add_subparser(
    subparsers: argparse._SubParsersAction,
    name: str,
    module_config: ModuleConfig,
) -> argparse.ArgumentParser:
    """
    Add a subparser to an argparse argument parser.

    Args:
        subparsers: The subparsers action to which the subparser will be added.
        name: The name of the subparser.
        module_config: A [`ModuleConfig`][nhssynth.cli.module_setup.ModuleConfig] object containing information about the subparser, including a function to execute and a function to add arguments.

    Returns:
        The newly created subparser.
    """
    parent_parsers = get_parent_parsers(name, module_config.common_parsers)
    parser = subparsers.add_parser(
        name=name,
        description=module_config.description,
        help=module_config.help,
        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
        parents=parent_parsers,
    )
    if name not in {"pipeline", "config"}:
        module_config.add_args(parser, f"{name} options")
    else:
        module_config.add_args(parser)
    parser.set_defaults(func=module_config.func)
    return parser

get_parent_parsers(name, module_parsers)

Get a list of parent parsers for a given module, based on the module's common_parsers attribute.

Source code in src/nhssynth/cli/module_setup.py

def get_parent_parsers(name: str, module_parsers: list[str]) -> list[argparse.ArgumentParser]:
    """Get a list of parent parsers for a given module, based on the module's `common_parsers` attribute."""
    if name in {"pipeline", "config"}:
        return [p(name == "config") for p in COMMON_PARSERS.values()]
    elif name == "dashboard":
        return [COMMON_PARSERS[pn](True) for pn in module_parsers]
    else:
        return [COMMON_PARSERS[pn]() for pn in module_parsers]

run_pipeline(args)

Runs the specified pipeline of modules with the passed configuration args.

Source code in src/nhssynth/cli/module_setup.py

def run_pipeline(args: argparse.Namespace) -> None:
    """Runs the specified pipeline of modules with the passed configuration `args`."""
    print("Running full pipeline...")
    args.modules_to_run = PIPELINE
    for module_name in PIPELINE:
        args = MODULE_MAP[module_name](args)