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Fix codestyle
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@noscode
noscode committed Feb 4, 2024
1 parent e53ca83 commit 49dbca0
Showing 1 changed file with 53 additions and 48 deletions.
101 changes: 53 additions & 48 deletions gadma/cli/settings_storage.py
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Original file line number Diff line number Diff line change
Expand Up @@ -189,60 +189,60 @@ class SettingsStorage(object):
"""

_int_attrs = ['stuck_generation_number', 'verbose',
'print_models_code_every_n_iteration', 'n_elitism',
'draw_models_every_n_iteration', 'size_of_generation',
'number_of_repeats', 'number_of_processes',
'number_of_populations', 'global_maxiter',
'global_maxeval', 'local_maxiter', 'local_maxeval',
'num_init_const', "region_len", 'fixed_ancestral_size']
'print_models_code_every_n_iteration', 'n_elitism',
'draw_models_every_n_iteration', 'size_of_generation',
'number_of_repeats', 'number_of_processes',
'number_of_populations', 'global_maxiter',
'global_maxeval', 'local_maxiter', 'local_maxeval',
'num_init_const', "region_len", 'fixed_ancestral_size']
_float_attrs = ['theta0', 'time_for_generation', 'eps',
'const_of_time_in_drawing', 'vmin', 'min_n', 'max_n',
'min_t', 'max_t', 'min_m', 'max_m',
'upper_bound_of_first_split',
'upper_bound_of_second_split',
'const_for_mutation_strength',
'const_for_mutation_rate',
'mutation_rate', 'recombination_rate',
'time_to_print_summary']
'const_of_time_in_drawing', 'vmin', 'min_n', 'max_n',
'min_t', 'max_t', 'min_m', 'max_m',
'upper_bound_of_first_split',
'upper_bound_of_second_split',
'const_for_mutation_strength',
'const_for_mutation_rate',
'mutation_rate', 'recombination_rate',
'time_to_print_summary']
_probs_attrs = ['mean_mutation_strength', 'mean_mutation_rate',
'p_mutation', 'p_crossover', 'p_random']
'p_mutation', 'p_crossover', 'p_random']
_bool_attrs = ['outgroup', 'linked_snp_s', 'only_sudden',
'no_migrations', 'silence', 'test', 'random_n_a',
'relative_parameters', 'only_models',
'symmetric_migrations', 'split_fractions',
'generate_x_transform', 'global_log_transform',
'local_log_transform', 'inbreeding', 'selection',
'dominance', 'ancestral_size_as_parameter']
'no_migrations', 'silence', 'test', 'random_n_a',
'relative_parameters', 'only_models',
'symmetric_migrations', 'split_fractions',
'generate_x_transform', 'global_log_transform',
'local_log_transform', 'inbreeding', 'selection',
'dominance', 'ancestral_size_as_parameter']
_int_list_attrs = ['pts', 'initial_structure', 'final_structure',
'projections']
'projections']
_float_list_attrs = ['lower_bound', 'upper_bound']
_probs_list_attrs = ['fractions']
_attrs_with_equal_len = ['initial_structure', 'final_structure',
'population_labels', 'projections']
'population_labels', 'projections']
_special_attrs = ['const_for_mutation_strength',
'const_for_mutation_rate', 'vmin',
'parameter_identifiers', 'migration_masks']
'const_for_mutation_rate', 'vmin',
'parameter_identifiers', 'migration_masks']
_exist_file_attrs = ['input_data', 'custom_filename',
'bed_file', "preprocessed_data"]
'bed_file', "preprocessed_data"]
_exist_dir_attrs = ['directory_with_bootstrap',
'resume_from', 'recombination_maps']
'resume_from', 'recombination_maps']
_empty_dir_attrs = ['output_directory']
_data_holder_attrs = ['projections', 'outgroup',
'population_labels', 'sequence_length',
"preprocessed_data", "recombination_maps",
'bed_files_dir', 'non_ascertained_pops']
'population_labels', 'sequence_length',
"preprocessed_data", "recombination_maps",
'bed_files_dir', 'non_ascertained_pops']
_bounds_attrs = ['min_n', 'max_n', 'min_t', 'max_t', 'min_m', 'max_m',
'dynamics']
'dynamics']
_bounds_lists = ['lower_bound', 'upper_bound', 'parameter_identifiers']
_missed_attrs = ['engine', 'global_optimizer', 'local_optimizer',
'_inner_data', '_bootstrap_data', 'X_init', 'Y_init',
'model_func', 'get_engine_args', 'data_holder',
'units_of_time_in_drawing', 'resume_from_settings',
'dadi_available', 'moments_available',
'model_plot_engine', 'demes_available',
'demesdraw_available',
'kernel', 'acquisition_function', 'sequence_length',
'dadi_extrapolation']
'_inner_data', '_bootstrap_data', 'X_init', 'Y_init',
'model_func', 'get_engine_args', 'data_holder',
'units_of_time_in_drawing', 'resume_from_settings',
'dadi_available', 'moments_available',
'model_plot_engine', 'demes_available',
'demesdraw_available',
'kernel', 'acquisition_function', 'sequence_length',
'dadi_extrapolation']
_dict_attrs = ['ld_kwargs']

def __setattr__(self, name, value):
Expand All @@ -262,15 +262,18 @@ def __setattr__(self, name, value):
except AttributeError:
super_hasattr = False
if (name not in self._int_attrs and name not in self._float_attrs and
name not in self._probs_attrs and name not in self._bool_attrs and
name not in self._probs_attrs and
name not in self._bool_attrs and
name not in self._attrs_with_equal_len and
name not in self._int_list_attrs and
name not in self._probs_list_attrs and name not in self._special_attrs and
name not in self._probs_list_attrs and
name not in self._special_attrs and
name not in self._exist_file_attrs and
name not in self._exist_dir_attrs and
name not in self._empty_dir_attrs and
name not in self._data_holder_attrs and
name not in self._bounds_attrs and name not in self._missed_attrs and
name not in self._bounds_attrs and
name not in self._missed_attrs and
name not in self._bounds_lists and not super_hasattr and
name not in self._dict_attrs):
raise ValueError(f"Setting {name} should be checked.")
Expand Down Expand Up @@ -328,7 +331,8 @@ def __setattr__(self, name, value):
if value < 0:
raise ValueError(f"Setting {name} ({value}) must be positive.")
# 1.2 Check is float and probability
if (name in self._float_attrs or name in self._probs_attrs) and we_check:
if (name in self._float_attrs or name in self._probs_attrs) and
we_check:
if (not isinstance(value, numbers.Real) or
isinstance(value, bool)):
raise ValueError(f"Setting {name} ({value}) must be float.")
Expand Down Expand Up @@ -357,8 +361,8 @@ def __setattr__(self, name, value):
raise ValueError(f"Setting {name} ({value}) have positive"
" elements.")
# 1.5 Check is the list of floats and probabilities
if ((name in self._probs_list_attrs or name in self._float_list_attrs) and
we_check):
if ((name in self._probs_list_attrs or
name in self._float_list_attrs) and we_check):
if name in self._probs_list_attrs:
error = ValueError(f"Setting {name} ({value}) must be list of"
" probabilities.")
Expand Down Expand Up @@ -387,8 +391,8 @@ def __setattr__(self, name, value):
attrs_list = self._attrs_with_equal_len
elif name in self._bounds_lists:
attrs_list = self._bounds_lists
if ((name in self._attrs_with_equal_len or name in self._bounds_lists) and
we_check):
if ((name in self._attrs_with_equal_len or
name in self._bounds_lists) and we_check):
if (name not in self._bounds_lists and
hasattr(self, 'number_of_populations') and
len(value) != self.number_of_populations):
Expand Down Expand Up @@ -435,7 +439,8 @@ def __setattr__(self, name, value):
# 1.8.0 expand path of files:
if (value is not None and
(name in self._empty_dir_attrs or
name in self._exist_file_attrs or name in self._exist_dir_attrs)):
name in self._exist_file_attrs or
name in self._exist_dir_attrs)):
abspath_value = []
for val in value.split(","):
abspath_value.append(abspath(val.strip()))
Expand Down

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