def test_auto_cli():
tmpdir = nbtmp.InTemporaryDirectory()
config_file = op.join(tmpdir.name, 'test.toml')
arg_dict = afb.func_dict_to_arg_dict()
arg_dict['BIDS']['bids_path']['default'] = tmpdir.name
afb.generate_config(config_file, arg_dict, False)
with pytest.raises(
ValueError,
match="There must be a dataset_description.json in bids_path"):
afb.parse_config_run_afq(config_file, arg_dict, False)
def test_run_using_auto_cli():
tmpdir, bids_path, _ = get_temp_hardi()
config_file = op.join(tmpdir.name, 'test.toml')
arg_dict = afb.func_dict_to_arg_dict()
# set our custom defaults for the toml file
# It is easier to edit them here, than to parse the file and edit them
# after the file is written
arg_dict['BIDS']['bids_path']['default'] = bids_path
arg_dict['BIDS']['dmriprep']['default'] = 'vistasoft'
arg_dict['BUNDLES']['bundle_names']['default'] = ["CST"]
arg_dict['TRACTOGRAPHY']['n_seeds']['default'] = 500
arg_dict['TRACTOGRAPHY']['random_seeds']['default'] = True
afb.generate_config(config_file, arg_dict, False)
afb.parse_config_run_afq(config_file, arg_dict, False)