cellmap_flow.utils.cli_utils

Utility functions for CLI generation and management.

Functions

`get_all_subclasses`(→ Dict[str, Type])	Get all subclasses of a base class and convert their names to CLI-friendly format.
`get_all_model_configs`()	Discover all ModelConfig subclasses using __subclasses__().
`print_available_models`([cli_command_name])	Print a formatted list of all available model configurations.
`parse_type_annotation`(→ Tuple[type, bool])	Parse type annotations to determine the base type and if it's optional.
`parse_comma_separated_values`(→ Any)	Parse comma-separated string into list of target type.
`create_click_option_from_param`(→ Dict[str, Any])	Create a click.option configuration from a parameter.
`process_constructor_args`(→ Dict[str, Any])	Process kwargs to match the constructor signature.

Module Contents

cellmap_flow.utils.cli_utils.get_all_subclasses(base_class: Type) → Dict[str, Type]

Get all subclasses of a base class and convert their names to CLI-friendly format.

Parameters:: base_class – The base class to find subclasses for
Returns:: Dictionary mapping CLI-friendly names to class objects

Example

>>> from cellmap_flow.models.models_config import ModelConfig
>>> configs = get_all_subclasses(ModelConfig)
>>> # Returns: {'dacapo': DaCapoModelConfig, 'script': ScriptModelConfig, ...}

cellmap_flow.utils.cli_utils.get_all_model_configs()

Discover all ModelConfig subclasses using __subclasses__().

Returns:: Dictionary mapping CLI-friendly names to ModelConfig classes

cellmap_flow.utils.cli_utils.print_available_models(cli_command_name: str = 'cellmap_flow')

Print a formatted list of all available model configurations.

Parameters:: cli_command_name – Name of the CLI command for help text

cellmap_flow.utils.cli_utils.parse_type_annotation(annotation) → Tuple[type, bool]

Parse type annotations to determine the base type and if it’s optional.

Parameters:: annotation – The type annotation to parse
Returns:: Tuple of (base_type, is_optional)

Example

>>> parse_type_annotation(str)
(str, False)
>>> parse_type_annotation(Optional[int])
(int, True)
>>> parse_type_annotation(list[str])
(str, False)

cellmap_flow.utils.cli_utils.parse_comma_separated_values(value: str, target_type: type) → Any

Parse comma-separated string into list of target type.

Parameters:

value – Comma-separated string (e.g., “1,2,3” or “a,b,c”)
target_type – Type to convert elements to (str, int, float)

Returns:

List of parsed values

Example

>>> parse_comma_separated_values("1,2,3", int)
[1, 2, 3]
>>> parse_comma_separated_values("a,b,c", str)
['a', 'b', 'c']

cellmap_flow.utils.cli_utils.create_click_option_from_param(param_name: str, param_info: inspect.Parameter, used_short_names: set = None) → Dict[str, Any]

Create a click.option configuration from a parameter.

Parameters:

param_name – Name of the parameter
param_info – Parameter information from inspect.signature
used_short_names – Set of already used short names to avoid duplicates

Returns:

Dictionary with option configuration for click.option, or None if should skip

Example

>>> sig = inspect.signature(MyClass.__init__)
>>> param = sig.parameters['my_param']
>>> config = create_click_option_from_param('my_param', param)
>>> # Returns: {'param_decls': ['-m', '--my-param'], 'required': True, ...}

cellmap_flow.utils.cli_utils.process_constructor_args(config_class: Type, kwargs: Dict[str, Any]) → Dict[str, Any]

Process kwargs to match the constructor signature. Handle list/tuple type conversions from comma-separated strings.

Parameters:

config_class – The class whose constructor to match
kwargs – Dictionary of keyword arguments

Returns:

Processed kwargs with proper type conversions

Example

>>> class MyConfig:
...     def __init__(self, items: list[int], name: str):
...         pass
>>> kwargs = {'items': '1,2,3', 'name': 'test'}
>>> result = process_constructor_args(MyConfig, kwargs)
>>> # Returns: {'items': [1, 2, 3], 'name': 'test'}