Command line interface (cli package)¶
Argument parsing¶
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class
gadma.cli.arg_parser.
ArgParser
(prog=None, usage=None, description=None, epilog=None, parents=[], formatter_class=<class 'argparse.HelpFormatter'>, prefix_chars='-', fromfile_prefix_chars=None, argument_default=None, conflict_handler='error', add_help=True, allow_abbrev=True)¶ Bases:
argparse.ArgumentParser
Overrided class for argument parser.
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gadma.cli.arg_parser.
get_settings
()¶ Parse args from command line and store them in options_storage.
- Returns
tuple of parsed arguments and settings storage.
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gadma.cli.arg_parser.
test_args
()¶ Put default args for test case.
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gadma.cli.arg_parser.
usage
()¶ Returns usage of tool.
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gadma.cli.arg_parser.
version
()¶ Returns string with current version.
SettingsStorage¶
-
class
gadma.cli.settings_storage.
SettingsStorage
¶ Bases:
object
Class to hold all settings of GADMA run. All default values of settings are defined in
gadma.cli.settings
.-
property
bootstrap_data
¶
-
property
fractions
¶
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static
from_file
(param_file, extra_param_file=None)¶ Creates new object with settings from files.
- Parameters
param_file – File with base parameters.
extra_param_file – File with extra parameters.
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get_engine_args
(engine_id=None)¶ Returns args of
engine.evaluate()
function.
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get_global_optimizer
()¶ Return object of global optimizer for optimization according to current settings.
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get_linear_constrain_for_model
(model)¶ Returns linear constrain for model based of setted upper bound of splits. NOT WORKING.
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get_local_optimizer
()¶ Return object of local optimizer for optimization according to current settings.
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get_model
()¶ Returns demographic model to use according to current settings.
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get_optimizers_init_kwargs
()¶ Returns kwargs for first run of optimization. (X_init and Y_init).
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get_optimizers_kwargs
()¶ Returns kwargs for optimizations. (args and verbose).
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property
inner_data
¶
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read_bootstrap_data
(return_filenames=False)¶ Reads all data in the directory self.bootstrap_data.
- Parameters
return_filenames – If True then each data is a tuple of corresponding filename and data.
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read_data
()¶ Reads data with engine. Attribute of`engine` and data_holder should be set.
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to_files
(params_file, extra_params_file)¶ Saves current options to files.
- Parameters
params_file – File with base parameters.
extra_param_file – File with extra parameters.
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update_from_file
(param_file, extra_param_file=None)¶ Updates settings by reading new from files.
- Parameters
param_file – File with base parameters.
extra_param_file – File with extra parameters.
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property