Upgrading GEMSEO#

This page contains the history of the breaking changes in GEMSEO. The codes using those shall be updated according to the target GEMSEO version.

6.0.0#

The tool bump-gemseo can be used to help converting your code to GEMSEO 6.

MDODiscipline#

The class MDODiscipline has been renamed to Discipline, some of its many attributes and methods have been gathered in sub objects via the attributes .io, .execution_statistics, .execution_status and the method get_process_flow.
The signature of the method __init__ has the following changes:
- The arguments use auto_detect_grammar_files is removed, now use the class attribute auto_detect_grammar_files.
- The arguments input_grammar_file, output_grammar_file are removed, use auto_detect_grammar_files.
- The argument grammar_type is removed, now use the class attribute default_grammar_type.
- The argument cache_type is removed, now use the class attribute default_cache_type.
- The argument cache_file_path is removed, now use the method set_cache.
The method _run now takes input_data as argument and may return the output data, this allow a more natural and clearer implementation of the main business logic of a discipline. Moreover, using the provided input_data and also returning the output data will ensure that a discipline can be used with namespaces. Besides the addition of this new method argument in the signature, the usage of input_data is optional, as well as returning the output data: i.e. the body of _run could be left unchanged. But in that case it is not guaranteed to support the use of namespaces.
The signature of _compute_jacobian is now _compute_jacobian(self, input_names=(), output_names=()).
The attributes have the following changes:
- .residual_variables: now use .io.state_equations_are_solved
- .run_solves_residuals: now use .io.state_equations_are_solved
- .exec_for_lin: is removed
- .activate_counters: now use .execution_statistics.is_enabled
- .activate_input_data_check: now use .validate_input_data
- .activate_output_data_check: now use .validate_output_data
- .activate_cache: is removed, now call .set_cache
- .re_exec_policy: is removed
- .N_CPUS: now use gemseo.utils.constants.N_CPUS
- .linear_relationships: is removed, call io.have_linear_relationships
- .disciplines: is removed and only available for classes that derive from ProcessDiscipline
- .time_stamps: now use .execution_statistics.time_stamps
- .n_calls: now use .execution_statistics.n_calls
- .exec_time: now use .execution_statistics.duration
- .n_calls_linearize: now use .execution_statistics.n_calls_linearize
- .grammar_type: now use .io.grammar_type
- .auto_get_grammar_file: now is a class attribute
- .status: now use .execution_status.value
- .cache_tol: now use .cache.tolerance
- .default_inputs: now use .default_input_data
- .default_outputs: now use .default_output_data
- .is_scenario: is removed
- .data_processor: now use .io.data_processor
- .ReExecutionPolicy: is removed
- .ExecutionStatus: now use .io.execution_status.Status
- .ExecutionStatus.PENDING: is removed
The methods have the following changes:
- .activate_time_stamps: now use .execution_statistics.is_time_stamps_enabled
- .deactivate_time_stamps: now use .execution_statistics.is_time_stamps_enabled
- .set_linear_relationships: now use io.set_linear_relationships
- .set_disciplines_statuses: was removed
- .is_output_existing: now use .output_grammar.names
- .is_all_outputs_existing: now use .output_grammar.names
- .is_all_inputs_existing: now use .input_grammar.names
- .is_input_existing: now use .input_grammar.names
- .reset_statuses_for_run: is removed
- .add_status_observer: now use .execution_status.add_observer
- .remove_status_observer: now use .execution_status.remove_observer
- .notify_status_observers: is removed
- .store_local_data: now use .io.update_output_data
- .check_input_data: now use .input_grammar.validate
- .check_output_data: now use .output_grammar.validate
- .get_outputs_asarray: is removed
- .get_inputs_asarray: is removed
- .get_inputs_by_name: now use .get_input_data
- .get_outputs_by_name: now use .get_output_data
- .get_input_data_names: now use .get_input_data
- .get_output_data_names: now use .get_output_data
- .get_input_output_data_names: now use .local_data
- .get_all_inputs: now use .get_input_data
- .get_all_outputs: now use .get_output_data
- .to_pickle: now use gemseo.to_pickle
- .from_pickle: now use gemseo.from_pickle
- .get_local_data_by_name: nw use .local_data
- .get_data_list_from_dict: is removed

DesignSpace#

DesignSpace and ParameterSpace no longer provide a dictionary-like interface to manipulate its items with square brackets [].
The DesignSpace.add_variables_from method can be used to add variables from existing variable spaces.
The class DesignSpace.DesignVariable no longer exists.
A variable of a DesignSpace can no longer have one type (float or integer) per component, but rather a single type, shared by all its components.
DesignSpace.add_variable no longer accepts a sequence of variable types for its var_type argument.
The values of dictionary DesignSpace.variable_types are no longer NumPy arrays of strings, but simple strings.
The components of a (lower or upper) bound of a DesignSpace variable can no longer be None. Unboundedness shall be encoded with -numpy.inf for lower bounds, and numpy.inf for upper bounds.
DesignSpace.add_variable no longer accepts None for its arguments l_b and u_b. These two arguments now default to -numpy.inf and numpy.inf respectively.
DesignSpace.set_lower_bound and DesignSpace.set_upper_bound no longer accept None arguments, but rather infinities.
The return values of DesignSpace.get_lower_bound and DesignSpace.get_upper_bound can no longer be None, but rather NumPy arrays of infinite values.
Arguments var_type, l_b and u_b are respectively renamed type_, lower_bound and upper_bound.
The method array_to_dict is renamed convert_array_to_dict.
The method dict_to_array is renamed convert_dict_to_array.
The method has_current_value is now a property.
The method has_integer_variables is now a property. #709
DesignSpace.filter_dim renamed to DesignSpace.filter_dimensions, its first argument variable renamed to name, and its second argument keep_dimensions to dimensions. #1218
DesignSpace.get_indexed_var_name is removed. Use DesignSpace.get_indexed_variable_names instead.
DesignSpace.SEP is removed.
The DesignSpace.get_indexed_variable_names method is now based on the function gemseo.utils.string_tools.repr_variable. It is now consistent with other Gemseo methods, by naming a variable "x[i]" instead of "x!i". #1336

OptimizationProblem#

OptimizationProblem's callback_func argument renamed to callback.
OptimizationProblem.change_objective_sign: removed; use OptimizationProblem.minimize_objective instead.
cstr_type in OptimizationProblem.add_constraint: constraint_type
cstr_type in OptimizationProblem.repr_constraint: constraint_type
cstr_func in OptimizationProblem.add_constraint: function
cstr_func in OptimizationProblem.add_eq_constraint: function
cstr_func in OptimizationProblem.add_ineq_constraint: function
obs_func in OptimizationProblem.add_observable: observable
func in OptimizationProblem.repr_constraint: function
callback_func in OptimizationProblem.add_callback: callback
The default value of the value argument of the add_constraint methods is 0 instead of None; this does not change the behavior as None was replaced by 0. #728
OptimizationProblem.get_scalar_constraint_names (method): OptimizationProblem.scalar_constraint_names (property).
OptimizationProblem.is_max_iter_reached (method): OptimizationProblem.is_max_iter_reached (property).
OptimizationProblem.get_eq_constraints: OptimizationProblem.constraints.get_equality_constraints().
OptimizationProblem.get_ineq_constraints: OptimizationProblem.constraints.get_inequality_constraints().
OptimizationProblem.get_ineq_constraints_number: removed; use len(optimization_problem.constraints.get_inequality_constraints()) instead.
OptimizationProblem.get_eq_constraints_number: removed; use len(optimization_problem.constraints.get_equality_constraints()) instead.
OptimizationProblem.get_constraints_number: removed; use len(optimization_problem.constraints) instead.
OptimizationProblem.get_design_variable_names (method): OptimizationProblem.design_variable_names (property).
OptimizationProblem.get_all_function_name (method): OptimizationProblem.function_names (property).
OptimizationProblem.has_eq_constraints: removed; use bool(optimization_problem.constraints.get_equality_constraints()) instead, e.g. if optimization_problem.constraints.get_equality_constraints().
OptimizationProblem.has_ineq_constraints: removed; use bool(optimization_problem.constraints.get_inequality_constraints()) instead, e.g. if optimization_problem.constraints.get_inequality_constraints().
OptimizationProblem.has_constraints: removed; use bool(optimization_problem.constraints) instead, e.g. if optimization_problem.constraints.
OptimizationProblem.has_nonlinear_constraints: removed as it did not check whether the problem had non-linear constraints but constraints.
OptimizationProblem.get_dimension: removed; use OptimizationProblem.dimension instead.
OptimizationProblem.check_format: removed as it was only used internally.
OptimizationProblem.get_eq_cstr_total_dim: removed; use OptimizationProblem.constraints.get_equality_constraints().dimension instead.
OptimizationProblem.get_ineq_cstr_total_dim: removed; use OptimizationProblem.constraints.get_inequality_constraints().dimension instead.
OptimizationProblem.get_optimum (method): OptimizationProblem.optimum (property).
OptimizationProblem.current_names: OptimizationProblem.original_to_current_names.
OptimizationProblem.get_constraint_names: removed; use OptimizationProblem.constraints.get_names instead.
OptimizationProblem.get_objective_name (method): OptimizationProblem.objective_name (property) and OptimizationProblem.standardized_objective_name (property)
OptimizationProblem.nonproc_objective: OptimizationProblem.objective.original.
OptimizationProblem.nonproc_constraints (property): OptimizationProblem.constraints.get_originals (method).
OptimizationProblem.nonproc_observables (property): OptimizationProblem.observables.get_originals (method).
OptimizationProblem.nonproc_new_iter_observables` (property): ``OptimizationProblem.new_iter_observables.get_originals (method).
OptimizationProblem.get_nonproc_objective: removed; use OptimizationProblem.objective.original instead.
OptimizationProblem.get_nonproc_constraints: removed; use OptimizationProblem.constraints.get_originals instead.
OptimizationProblem.get_all_functions: removed; use OptimizationProblem.original_functions and OptimizationProblem.functions instead.
OptimizationProblem.DESIGN_VAR_NAMES: removed as it was no longer used.
OptimizationProblem.DESIGN_VAR_SIZE: removed as it was no longer used.
OptimizationProblem.DESIGN_SPACE_ATTRS: removed as it was no longer used.
OptimizationProblem.FUNCTIONS_ATTRS: removed as it was no longer used.
OptimizationProblem.DESIGN_SPACE_GROUP: removed as it was no longer used.
OptimizationProblem.HDF_NODE_PATH: removed as it was no longer used.
OptimizationProblem.OPT_DESCR_GROUP: removed as it was only used internally.
OptimizationProblem.OBJECTIVE_GROUP: removed as it was only used internally.
OptimizationProblem.SOLUTION_GROUP: removed as it was only used internally.
OptimizationProblem.CONSTRAINTS_GROUP: removed as it was only used internally.
OptimizationProblem.OBSERVABLES_GROUP: removed as it was only used internally.
OptimizationProblem._OPTIM_DESCRIPTION: removed as it was only used internally.
OptimizationProblem.KKT_RESIDUAL_NORM: removed as it was only used internally.
OptimizationProblem.HDF5_FORMAT: removed; use OptimizationProblem.HistoryFileFormat.HDF5 instead.
OptimizationProblem.GGOBI_FORMAT: removed; use OptimizationProblem.HistoryFileFormat.GGOBI instead.
OptimizationProblem.add_eq_constraint: removed; use OptimizationProblem.add_constraint with constraint_type="eq" instead.
OptimizationProblem.add_ineq_constraint: removed; use OptimizationProblem.add_constraint with constraint_type="ineq" instead.
OptimizationProblem.OptimumType: removed; use the namedtuple OptimizationProblem.Solution instead.
OptimizationProblem.ineq_tolerance: removed; use Optimization.tolerances.inequality instead.
OptimizationProblem.eq_tolerance: removed; use Optimization.tolerances.equality instead.
OptimizationProblem.preprocess_options: removed as this dictionary was only used as optimization_problem.preprocess_options.get("is_function_input_normalized", False); use optimization_problem.objective.expects_normalized_inputs instead.
OptimizationProblem.get_active_ineq_constraints: removed; use OptimizationProblem.constraints.get_active instead.
OptimizationProblem.execute_observables_callback: removed; use OptimizationProblem.new_iter_observables.evaluate instead.
OptimizationProblem.aggregate_constraint: removed; use OptimizationProblem.constraints.aggregate instead.
OptimizationProblem.original_to_current_names: removed; use OptimizationProblem.constraints.original_to_current_names instead.
OptimizationProblem.get_observable: removed; use OptimizationProblem.observables.get_from_name instead.
OptimizationProblem.is_point_feasible: removed; use OptimizationProblem.constraints.is_point_feasible instead.
OptimizationProblem.get_feasible_points: removed; use OptimizationProblem.history.feasible_points instead.
OptimizationProblem.check_design_point_is_feasible: removed; use OptimizationProblem.history.check_design_point_is_feasible instead.
OptimizationProblem.get_number_of_unsatisfied_constraints: removed; use OptimizationProblem.constraints.get_number_of_unsatisfied_constraints instead.
OptimizationProblem.get_data_by_names: removed; use OptimizationProblem.history.get_data_by_names instead.
OptimizationProblem.get_last_point: removed; use OptimizationProblem.history.last_point instead.
OptimizationProblem.activate_bound_check renamed to OptimizationProblem.check_bounds.
OptimizationProblem's input_database argument renamed to database.
OptimizationProblem.variable_names removed; use OptimizationProblem.design_space.variable_names instead.
OptimizationProblem.dimension removed; use OptimizationProblem.design_space.dimension instead.
OptimizationProblem.add_callback renamed to OptimizationProblem.add_listener, its each_new_iter argument to at_each_iteration and its each_store argument to at_each_function_call.
OptimizationProblem.evaluate_functions's eval_jac argument renamed to compute_jacobians.
OptimizationProblem.evaluate_functions's eval_observables argument renamed to evaluate_observables.
OptimizationProblem.evaluate_functions's eval_obj argument renamed to evaluate_objective.
OptimizationProblem.evaluate_functions's x_vect argument renamed to design_vector.
OptimizationProblem.evaluate_functions's normalize argument renamed to design_vector_is_normalized.
OptimizationProblem.ProblemType: removed; use a boolean mechanism instead to check if the the problem is linear.
OptimizationProblem.pb_type: removed; use the boolean property is_linear instead.
OptimizationProblem's pb_type: removed; use the boolean argument is_linear instead.
OptimizationProblem.clear_listeners: removed as it was no longer used; use EvaluationProblem.database.clear_listeners instead.
OptimizationProblem's fd_step attribute and argument renamed to differentiation_step.
OptimizationProblem's database argument can no longer be a file path and the hdf_node_path argument has been removed; use Database.from_hdf(file_path, hdf_node_path=hdf_node_path) to pass a Database relying on a HDF5 file.
OptimizationProblem's get_x0_normalized removed; use OptimizationProblem.design_space.get_current_value instead. #1104
OptimizationProblem.get_violation_criteria renamed to OptimizationProblem.check_design_point_is_feasible.

Distributions#

ComposedDistribution: JointDistribution
OTComposedDistribution: OTJointDistribution
SPComposedDistribution: SPJointDistribution
ParameterSpace.build_composed_distribution: ParameterSpace.build_joint_distribution
Distribution.COMPOSED_DISTRIBUTION_CLASS: Distribution.JOINT_DISTRIBUTION_CLASS
DistributionFactory.create_composed_distribution: DistributionFactory.create_joint_distribution
gemseo.uncertainty.distributions.composed: gemseo.uncertainty.distributions.joint
gemseo.uncertainty.distributions.scipy.composed: gemseo.uncertainty.distributions.scipy.joint
gemseo.uncertainty.distributions.openturns.composed: gemseo.uncertainty.distributions.openturns.joint
gemseo.algos.parameter_space.build_composed_distribution: gemseo.algos.parameter_space.build_joint_distribution #989
The dimension argument of BaseDistribution has been removed as it no longer makes sense for distributions modelling scalar random variables.
Any class deriving from BaseDistribution and ScalarDistributionMixin models a scalar random variable, e.g. OTDistribution and SPDistribution, while the BaseJointDistribution models a random vector.
BaseJointDistribution.plot has been removed; use BaseJointDistribution.marginals[i].plot instead.
BaseDistribution.plot_all: removed; used ScalarDistributionMixin.plot instead.
BaseDistribution.marginals: removed; only BaseJointDistribution has this attribute. #1183
The variable argument of BaseDistribution has been removed as a probability distribution is not defined from a variable name.
The variable_name attribute of BaseDistribution has been removed in connection with the removal of the variable argument. #1184
BaseDistribution.distribution_name has been removed as it was no longer used.
BaseDistribution.parameters has been removed as it was no longer used.
BaseDistribution.standard_parameters has been removed as it was no longer used. #1186
The argument use_asymptotic_distributions is no longer an instantiation argument but an argument of SobolAnalysis.compute_indices. #1189

DOE#

DOELibrary.DIMENSION: removed as it was no longer used.
DOELibrary.LEVEL_KEYWORD: removed as it was no longer used.
DOELibrary.PHIP_CRITERIA: removed as it was no longer used.
DOELibrary.SAMPLES_TAG: removed as it was no longer used.
DOELibrary.DESIGN_ALGO_NAME: removed as it was no longer used.
DOELibraryOutputType: removed; use EvaluationType instead.
DOELibraryOptionType: removed; use DriverLibraryOptionType instead.
DOELibrary.__call__: removed; use BaseDOELibrary.compute_doe instead.
DOELibrary.evaluate_samples: removed; use BaseDOELibrary.execute instead.
DOELibrary.eval_jac: removed as it was no longer used; note, however, that the DOE algorithm option eval_jac is still available.
DOELibrary.export_samples: removed because it simply saved the NumPy array BaseDOELibrary.unit_samples to a text file; use numpy.savetxt(file_path, doe_library.unit_samples, delimiter=",") to obtain the same result.

Disciplines#

AutoPyDiscipline.input_names: removed; use Discipline API instead.
AutoPyDiscipline.output_names: removed; use Discipline API instead.
AutoPyDiscipline.use_arrays: removed as it was no longer used.
gemseo.disciplines.auto_py.to_arrays_dict: removed as it was no longer used.
AnalyticDiscipline's fast_evaluation argument: removed; always use fast evaluation.
SobieskiBase.DTYPE_COMPLEX: removed; use SobieskiBase.DataType.COMPLEX instead.
SobieskiBase.DTYPE_DOUBLE: removed; use SobieskiBase.DataType.FLOAT instead.
SobieskiBase.DTYPE_DEFAULT: removed as it was no longer used.
SobieskiDiscipline.DTYPE_COMPLEX: removed; use SobieskiBase.DataType.COMPLEX instead.
SobieskiDiscipline.DTYPE_DOUBLE: removed; use SobieskiBase.DataType.FLOAT instead.
Boxplot.opacity_level: removed; use the opacity_level option of Boxplot instead.
DiscFromExe's use_shell argument: removed as it was no longer used.
DiscFromExe's executable_command argument renamed to command_line.
DiscFromExe.executable_command renamed to DiscFromExe.command_line.
DiscFromExe's folders_iter argument renamed to directory_naming_method.
DiscFromExe's output_folder_basepath argument renamed to root_directory.
RemappingDiscipline maps the differentiated data names of the underlying discipline and use the same linearization mode. #1197
gemseo.wrappers renamed to gemseo.disciplines.wrappers. #1193
The module scheduler_wrapped_disc.py was renamed to discipline_wrapper.py. #1191

Machine learning#

All functions and MLAlgo's attributes and methods to save and load instances of machine learning algorithms models (namely MLAlgo.FILENAME, MLAlgo.to_pickle, MLAlgo.load_algo, import_mlearning_model, import_regression_model, import_classification_model and import_clustering_model); use the functions to_pickle and from_pickle instead. #540
MLQualityMeasure.evaluate_bootstrap: removed; use BaseMLAlgoQuality.compute_bootstrap_measure instead.
MLQualityMeasure.evaluate_kfolds: removed; use BaseMLAlgoQuality.compute_cross_validation_measure instead.
MLQualityMeasure.evaluate_learn: removed; use BaseMLAlgoQuality.compute_learning_measure instead.
MLQualityMeasure.evaluate_loo: removed; use BaseMLAlgoQuality.compute_leave_one_out_measure instead.
MLQualityMeasure.evaluate_test: removed; use BaseMLAlgoQuality.compute_test_measure instead.
SensitivityAnalysis: BaseSensitivityAnalysis
ToleranceInterval: BaseToleranceInterval
distribution.ToleranceIntervalFactory: factory.ToleranceIntervalFactory
distribution: base_distribution
Distribution: BaseDistribution
MLClassificationAlgo: BaseClassifier
MLClusteringAlgo: BaseClusterer
MLClassificationAlgo: BaseClassifier
MLAlgo: BaseMLAlgo
MLQualityMeasure: BaseMLAlgoQuality
MLErrorMeasure: BaseRegressorQuality
MLClusteringMeasure: BaseClustererQuality
MLPredictiveClusteringMeasure: BasePredictiveClustererQuality
MLRegressionAlgo: BaseRegressor
resampler: base_resampler
Resampler: BaseResampler
transformer: base_transformer
Transformer: BaseTransformer
dimension_reduction: base_dimension_reduction
DimensionReduction: BaseDimensionReduction
gemseo.mlearning.classification:
- the classification algorithms are in gemseo.mlearning.classification.algos
- the quality measures are in gemseo.mlearning.classification.quality
- gemseo.mlearning.classification.classification.MLClassificationAlgo: renamed to BaseClassifier
- ClassificationModelFactory: renamed to ClassifierFactory
gemseo.mlearning.clustering:
- the clustering algorithms are in gemseo.mlearning.clustering.algos
- the quality measures are in gemseo.mlearning.clustering.quality
- gemseo.mlearning.clustering.clustering.MLClusteringAlgo: renamed to BaseClusterer
- ClusteringModelFactory: renamed to ClustererFactory
- MLClusteringMeasure: renamed to BaseClustererQuality
gemseo.mlearning.regression:
- the regression algorithms are in gemseo.mlearning.regression.algos
- the quality measures are in gemseo.mlearning.regression.quality
- gemseo.mlearning.regression.regression.MLRegressionAlgo: renamed to BaseRegressor
- RegressionModelFactory: renamed to RegressorFactory
- MLErrorMeasure: renamed to BaseRegressorQuality
- MLErrorMeasureFactory: renamed to RegressorQualityFactory
gemseo.mlearning.quality_measures: removed; use instead:
- gemseo.mlearning.core.quality.factory.MLAlgoQualityFactory
- gemseo.mlearning.core.quality.quality_measure.BaseMLAlgoQuality
- gemseo.mlearning.classification.quality for quality measures related to classifiers
- gemseo.mlearning.clustering.quality for quality measures related to clusterers
- gemseo.mlearning.regression.quality for quality measures related to regressors
#1174

Algorithms#

DriverLibrary.get_x0_and_bounds_vects renamed to BaseDriverLibrary.get_x0_and_bounds.
DriverLibOptionType renamed to DriverLibraryOptionType.
CustomDOE.read_file's dimension argument: removed as it was unused.
OptimizationLibrary.algorithm_handles_eqcstr renamed to BaseOptimizationLibrary.check_equality_constraint_support.
OptimizationLibrary.algorithm_handles_ineqcstr renamed to BaseOptimizationLibrary.check_inequality_constraint_support.
OptimizationLibrary.is_algo_requires_positive_cstr renamed to BaseOptimizationLibrary.check_positivity_constraint_requirement.
The attribute BaseDriverLibrary.MAX_DS_SIZE_PRINT no longer exists; it is replaced by the argument max_design_space_dimension_to_log of BaseDriverLibrary.execute. #1163
gemseo.algos.algorithm_library.AlgorithmLibrary: gemseo.algos.base_algorithm_library.BaseAlgorithmLibrary.
gemseo.algos.driver_library.DriverLibrary: gemseo.algos.base_driver_library.BaseDriverLibrary.
gemseo.algos.ode.driver_library.DriverLibrary: gemseo.algos.base_driver_library.BaseDriverLibrary.
gemseo.algos.ode_solver_lib.ODESolverLibrary: gemseo.algos.ode.base_ode_solver_library.BaseODESolverLibrary.
gemseo.algos.doe.doe_library.DOELibrary: gemseo.algos.doe.base_doe_library.BaseDOELibrary.
gemseo.algos.opt.optimization_library.BaseDOELibrary: gemseo.algos.opt.base_optimization_library.BaseOptimizationLibrary.
BaseAlgorithmLibrary.driver_has_option: removed; use name in BaseAlgorithmLibrary._option_grammar instead.
AlgorithmLibrary.init_options_grammar: removed; use BaseAlgorithmLibrary._init_options_grammar instead, which will disappear in the next version.
AlgorithmLibrary.opt_grammar: removed; use BaseAlgorithmLibrary._option_grammar instead, which will disappear in the next version.
AlgorithmLibrary.OPTIONS_DIR: removed; use BaseAlgorithmLibrary._OPTIONS_DIR instead, which will disappear in the next version.
AlgorithmLibrary.OPTIONS_MAP: removed; use BaseAlgorithmLibrary._OPTIONS_MAP instead, which will disappear in the next version.
AlgorithmLibrary.internal_algo_name: removed; use BaseAlgorithmLibrary.description[algo_name].internal_algo_name instead.
AlgorithmLibrary.algorithms: removed; use list(BaseAlgorithmLibrary.descriptions) instead.
AlgorithmLibrary.LIBRARY_NAME: removed as it was no longer used (note that this information is already included in the class names and in the docstrings).
LinearSolverLibrary.solve: removed; use BaseLinearSolverLibrary.execute instead.
LinearSolverLibrary.solution: removed; use problem.solution instead, where problem is the LinearProblem passed to the method BaseLinearSolverLibrary.execute.
LinearSolverLibrary.save_fpath (str | None): BaseLinearSolverLibrary.file_path (Path).
DriverLibrary.get_optimum_from_database: removed; use OptimizationResult.from_optimization_problem instead.
DriverLibrary.ensure_bounds: removed as it was no longer used.
DriverLibrary.requires_gradient: removed; use BaseDriverLibrary.description[algo_name].require_gradient instead.
DriverLibrary.finalize_iter_observer: removed as it was only used once internally, by DriverLibrary.execute.
DriverLibrary.new_iteration_callback: protected because it is not an end-user feature.
DriverLibrary.deactivate_progress_bar: protected because it is not an end-user feature.
DriverLibrary.init_iter_observer: protected because it is not an end-user feature.
DriverLibrary.clear_listeners: protected because it is not an end-user feature.
DriverLibrary.get_x0_and_bounds: removed; use get_value_and_bounds instead.
OptimizationLibrary.check_inequality_constraint_support: removed; use BaseOptimizationLibrary.descriptions[algo_name].handle_inequality_constraints instead.
OptimizationLibrary.check_equality_constraint_support: removed; use BaseOptimizationLibrary.descriptions[algo_name].handle_equality_constraints instead.
OptimizationLibrary.check_positivity_constraint_requirement: removed; use BaseOptimizationLibrary.descriptions[algo_name].positive_constraints instead.
OptimizationLibrary.get_right_sign_constraints: protected because it is not an end-user feature.
ScipyLinalgAlgos.BASE_INFO_MSG: removed as it was used only internally.
ScipyOpt.LIB_COMPUTE_GRAD: removed as it was no longer used.
ScipyMILP.LIB_COMPUTE_GRAD: removed as it was no longer used.
ScipyGlobalOpt.LIB_COMPUTE_GRAD: removed as it was no longer used.
NLopt.LIB_COMPUTE_GRAD: removed as it was no longer used.
ScipyLinprog.LIB_COMPUTE_GRAD: removed as it was no longer used.
ScipyLinalgAlgos.get_default_properties: removed; use ScipyLinalgAlgos.descriptions[algo_name] instead.
NLopt's class attributes defining error messages: removed as it was used only internally.
ScipyGlobalOpt.iter_callback: protected because it is not an end-user feature.
ScipyGlobalOpt.max_func_calls: protected because it is not an end-user feature.
ScipyGlobalOpt.normalize_ds: protected because it is not an end-user feature.
ScipyLinalgAlgos.LGMRES_SPEC_OPTS: protected because it is not an end-user feature.
DriverLibrary.EQ_TOLERANCE: removed as it was used only internally.
DriverLibrary.EVAL_OBS_JAC_OPTION: removed as it was used only internally.
DriverLibrary.INEQ_TOLERANCE: removed as it was used only internally.
DriverLibrary.MAX_TIME: removed as it was used only internally.
DriverLibrary.NORMALIZE_DESIGN_SPACE_OPTION: removed as it was used only internally.
DriverLibrary.ROUND_INTS_OPTION: removed as it was used only internally.
DriverLibrary.USE_DATABASE_OPTION: removed as it was used only internally.
DriverLibrary.USE_ONE_LINE_PROGRESS_BAR: removed as it was used only internally.
DOELibrary.EVAL_JAC: removed as it was used only internally.
DOELibrary.N_PROCESSES: removed as it was used only internally.
DOELibrary.N_SAMPLES: removed as it was used only internally.
DOELibrary.SEED: removed as it was used only internally.
DOELibrary.WAIT_TIME_BETWEEN_SAMPLES: removed as it was used only internally.
OptimizationLibrary.MAX_ITER: removed as it was used only internally.
OptimizationLibrary.F_TOL_REL: removed as it was used only internally.
OptimizationLibrary.F_TOL_ABS: removed as it was used only internally.
OptimizationLibrary.X_TOL_REL: removed as it was used only internally.
OptimizationLibrary.X_TOL_ABS: removed as it was used only internally.
OptimizationLibrary.STOP_CRIT_NX: removed as it was used only internally.
OptimizationLibrary.LS_STEP_SIZE_MAX: removed as it was used only internally.
OptimizationLibrary.LS_STEP_NB_MAX: removed as it was used only internally.
OptimizationLibrary.MAX_FUN_EVAL: removed as it was used only internally.
OptimizationLibrary.PG_TOL: removed as it was used only internally.
OptimizationLibrary.SCALING_THRESHOLD: removed as it was used only internally.
OptimizationLibrary.VERBOSE: removed as it was used only internally.
OptimizationLibrary.descriptions (instance attribute): renamed to OptimizationLibrary.ALGORITHM_INFOS (class attribute).
OptimizationLibrary.algo_name is now a read-only attribute; set the algorithm name at instantiation instead.
OptimizationLibrary.execute's algo_name attribute: removed; set the algorithm name at instantiation instead.
BaseLinearSolverLibrary.SAVE_WHEN_FAIL: removed as it was used only internally.
Nlopt.INNER_MAXEVAL: removed as it was used only internally.
Nlopt.STOPVAL: removed as it was used only internally.
Nlopt.CTOL_ABS: removed as it was used only internally.
Nlopt.INIT_STEP: removed as it was used only internally.
ScipyLinprog.REDUNDANCY_REMOVAL: removed as it was used only internally.
ScipyLinprog.REVISED_SIMPLEX: removed as it was used only internally.
CustomDOE.COMMENTS_KEYWORD: removed as it was used only internally.
CustomDOE.DELIMITER_KEYWORD: removed as it was used only internally.
CustomDOE.DOE_FILE: removed as it was used only internally.
CustomDOE.SAMPLES: removed as it was used only internally.
CustomDOE.SKIPROWS_KEYWORD: removed as it was used only internally.
OpenTURNS.OT_SOBOL: removed as it was used only internally.
OpenTURNS.OT_RANDOM: removed as it was used only internally.
OpenTURNS.OT_HASEL: removed as it was used only internally.
OpenTURNS.OT_REVERSE_HALTON: removed as it was used only internally.
OpenTURNS.OT_HALTON: removed as it was used only internally.
OpenTURNS.OT_FAURE: removed as it was used only internally.
OpenTURNS.OT_MC: removed as it was used only internally.
OpenTURNS.OT_FACTORIAL: removed as it was used only internally.
OpenTURNS.OT_COMPOSITE: removed as it was used only internally.
OpenTURNS.OT_AXIAL: removed as it was used only internally.
OpenTURNS.OT_LHSO: removed as it was used only internally.
OpenTURNS.OT_LHS: removed as it was used only internally.
OpenTURNS.OT_FULLFACT: removed as it was used only internally.
OpenTURNS.OT_SOBOL_INDICES: removed as it was used only internally.
PyDOE's class attributes: removed as it was used only internally.
AlgorithmLibrary.problem: removed as it was used only internally.
is_kkt_residual_norm_reached: moved to gemseo.algos.stop_criteria.
kkt_residual_computation: moved to gemseo.algos.stop_criteria. #1224
BaseAlgorithmLibrary and its derived classes now validate their settings (referred to as options in previous versions of GEMSEO) using a Pydantic model. The Pydantic models replace the JSONGrammar validation used in previous versions of GEMSEO. The aforementioned models have a hierarchical structure, for instance, the BaseDriverSettings shall inherit from BaseAlgorithmSettings in the same way as BaseDriverLibrary inherits from BaseAlgorithmLibrary. Instead of passing the settings one by one, a Pydantic model can be passed using the special argument "settings_model".
The CustomDOE module has been renamed from lib_custom_doe.py to custom_doe.py.
The OpenTURNS module has been renamed from lib_openturns.py to openturns.py.
The PyDOE module has been renamed from lib_pydoe.py to pydoe.py.
The DiagonalDOE module has ben renamed from lib_scalable.py to scalable.py.
The SciPyDOE module has been renamed from lib_scipy.py to scipy_doe.py.
The delimiter setting of the CustomDOE no longer accepts None as a value.
The ScipyODEAlgos module has been renamed from lib_scipy_ode.py to scipy_ode.py.
The ScipyGlobalOpt module has been renamed from lib_scipy_global.py to scipy_global.py.
The ScipyLinprog module has been renamed from lib_scipy_linprog.py to scipy_linprog.py.
The following setting names for ScipyLinprog have been modified:
max_iter is now maxiter,
verbose is now disp,
redundancy removal is now rr,
The ScipyOpt module has been renamed from lib_scipy.py to scipy_local.py.
The following setting names for ScipyOpt have been modified:

max_ls_step_size is now maxls,

max_ls_step_nb is now stepmx,

max_fun_eval is now maxfun,

pg_tol is now gtol,

The ScipyMILP module has been renamed from lib_scipy_milp.py to scipy_local_milp.py.
The following setting names for ScipyMILP has been modified:

max_iter is now node_limit.

The SciPy linear algebra library module has been renamed from lib_scipy_linalg.py to scipy_linalg.py.

The DEFAULT linear solver from ScipyLinalgAlgos has been modified. Now it simply runs the LGMRES algorithm. Before it first attempted to solve using GMRES, the LGMRES in case of failure, then using direct method in case of failure.

The following setting names have been modified:
- max_iter is now maxiter (for all the scipy.linalg algorithms)
- store_outer_av is now store_outer_Av (LGMRES)
The following setting names for MNBI have been modified:
- doe_algo_options is now doe_algo_settings,
- sub_optim_algo_options is now sub_optim_algo_settings.
#1450
sub_solver_algorithm in BaseAugmentedLagragian: sub_algorithm_name.
sub_problem_options in BaseAugmentedLagragian: sub_algorithm_settings. #1318
The following legacy algorithms from the SciPy linear programming library are no longer interfaced:
- Linear interior point method
- Simplex
- Revised Simplex
One should now use the HiGHS algorithms: INTERIOR_POINT or DUAL_SIMPLEX. #1317
A BaseMLAlgo is instantiated from a Dataset and either a BaseMLAlgoSettings instance defining all settings or a few settings; the signature is self, data: Dataset, settings_model: BaseMLAlgoSettings, **settings: Any).
The dictionary BaseMLAlgo.parameters has been replaced by the read-only Pydantic model BaseMLAlgo.settings.
BaseMLAlgo.IDENTITY has been removed; use gemseo.utils.constants.READ_ONLY_EMPTY_DICT instead.
A BaseFormulation is instantiated from a set of disciplines, objective name(s), a DesignSpace and either a BaseFormulation instance defining all settings or a few settings; the signature is self, disciplines: Iterable[Discipline], objective_name: str | Sequence[str], design_space: DesignSpace data: Dataset, settings_model: BaseFormulationSettings, **settings: Any).
maximize_objective is no longer an argument or an option of BaseFormulation; use BaseFormulation.optimization_problem.minimize_objective to minimize or maximize the objective (default: minimize). #1314
The settings of any machine learning algorithm are validated using a Pydantic model, whose class is BaseMLAlgo.Settings and instance is BaseMLAlgo.settings.

MDA#

The method _run is renamed to _execute.
The following properties of BaseMDA has been removed:
- acceleration_method,
- over_relaxation_factor,
- max_mda_iter,
- log_convergence,
- tolerance.
The following properties of MDAChain has been removed:
- max_mda_iter,
- log_convergence,
The following property of MDASequential has been removed:
- log_convergence,
The inner_mda_name argument of MDF and BiLevel formulations has been removed. When relevant, this argument must now be passed via main_mda_settings={"inner_mda_name": "foo"}. #1322
MDA.RESIDUALS_NORM is now MDA.NORMALIZED_RESIDUAL_NORM.
MDAQuasiNewton: the quasi-Newton method names are no longer attributes but names of the enumeration MDAQuasiNewton.QuasiNewtonMethod.
MDANewtonRaphson's relax_factor argument and attributes removed; use over_relaxation_factor instead.
MDAJacobi's SECANT_ACCELERATION and M2D_ACCELERATION attributes removed; use AccelerationMethod instead.
MDAJacobi's acceleration argument and attribute removed; use acceleration_method instead.
MDAJacobi's over_relax_factor argument and attribute removed; use over_relaxation_factor instead.
mda: base_mda
MDA: BaseMDA
gemseo.mda.newton: removed; instead:
- import MDANewtonRaphson from gemseo.mda.newton_raphson
- import MDAQuasiNewton from gemseo.mda.quasi_newton
- import MDARoot from gemseo.mda.root
MDANewtonRaphson no longer has a parallel argument; set the n_processes argument to 1 for serial computation (default: parallel computation using all the CPUs in the system).
MDA classes no longer have execute_all_disciplines and linearize_all_disciplines methods.
MDAJacobi.n_processes: removed.
BaseMDARoot.use_threading: removed.
BaseMDARoot.n_processes: removed.
BaseMDARoot.parallel: removed. #1278
BaseMDA: linear_solver_options is now linear_solver_settings,
MDANewtonRaphson: newton_linear_solver_options is now newton_linear_solver_settings,
MDAChain: inner_mda_options is now inner_mda_settings, mdachain_parallel_options is now mdachain_parallel_settings.
The following BaseMDA attributes names have been modified:
- BaseMDA.linear_solver is now accessed via BaseMDA.settings.linear_solver,
- BaseMDA.linear_solver_options is now accessed via BaseMDA.settings.linear_solver_settings,
- BaseMDA.linear_solver_tolerance is now accessed via BaseMDA.settings.linear_solver_tolerance,
- BaseMDA.max_mda_iter is now accessed via BaseMDA.settings.max_mda_iter,
- BaseMDA.tolerance is now accessed via BaseMDA.settings.tolerance,
- BaseMDA.use_lu_fact is now accessed via BaseMDA.settings.use_lu_fact,
- BaseMDA.warm_start is now accessed via BaseMDA.settings.warm_start.
The inner MDA settings of MDAChain can no longer be passed using **inner_mda_options, and must now be passed either as dictionnary or an instance of MDAChain_Settings.
The signature of MDAGSNewton has been modified. Settings for the MDAGaussSeidel and the MDANewtonRaphson are now respectively passed via the gauss_seidel_settings and the newton_settings arguments, which can be either key/value pairs or the appropriate Pydantic settings model.
The MDA settings for the IDF formulation are now passed via the mda_chain_settings_for_start_at_equilibrium argument which can be either key/value pairs or an MDAChain_Settings instance.

The MDA settings for the MDF and BiLevel formulations are now passed via the main_mda_settings argument which can be either key/value pairs or an appropriate Pydantic settings model.: #1322

The parallel_execution attribute of MDAJacobi is None when n_processes is 1 (serial mode). #1277
The relax_factor argument of MDAGSNewton has been removed; use over_relaxation_factor instead. #1279

MDOFunction#

NormFunction: removed as it was only used internally by OptimizationProblem.preprocess_functions; replaced by ProblemFunction.
NormDBFunction: removed as it was only used internally by OptimizationProblem.preprocess_functions; replaced by ProblemFunction.
MDOFunction.n_calls: removed; only ProblemFunction has this mechanism.
gemseo.core.mdofunctions.func_operations.LinearComposition renamed to gemseo.core.mdofunctions.linear_composite_function.LinearCompositeFunction.
gemseo.core.mdofunctions.func_operations.RestrictedFunction renamed to gemseo.core.mdofunctions.restricted_function.RestrictedFunction.
LinearCompositeFunction.name is "[f o A]" where "f" is the name of the original function.
The MDOFunction subclasses wrapping MDOFunction objects use the func methods of these objects instead of evaluate for the sake of efficiency. #1220
MDOFunction.__call__: removed; use MDOFunction.evaluate instead.
MDOFunction.func is now an alias of the wrapped function MDOFunction._func; use MDOFunction.evaluate to both evaluate _func and increment the number of calls when MDOFunction.activate_counters is True.
MDOFunction's expects_normalized_inputs argument renamed to with_normalized_inputs. #1221

Post processing#

Post-processing classes use Pydantic models instead of JSONGrammar, the models are available via the class attribute Settings.
Renamed the class OptPostProcessor to BasePost.
Removed the method OptPostProcessor.check_options.
Renamed the attribute OptPostProcessor.output_files to BasePost.output_file_paths.
Removed the attribute OptPostProcessor.opt_grammar.
Removed the attribute DEFAULT_FIG_SIZE for all post processing classes, use the fig_size field of the Pydantic model instead.
The arguments of the method OptPostProcessor.execute are all keyword arguments.
The argument opt_problem of the method OptPostProcessor.execute can no longer be a str.
The arguments of the method PostFactory.execute are keyword arguments in addition to the arguments opt_problem, post_name.
Renamed the module scatter_mat.py to scatter_plot_matrix.py.
Renamed the module para_coord.py to parallel_coordinates.py.
Removed the attribute Animation.DEFAULT_OPT_POST_PROCESSOR.
Removed the attributes ConstraintsHistory.cmap, ConstraintsHistory.ineq_cstr_cmap, ConstraintsHistory.eq_cstr_cmap.
Removed the attributes OptHistoryView.cmap, OptHistoryView.ineq_cstr_cmap, OptHistoryView.eq_cstr_cmap.
Removed the attribute QuadApprox.grad_opt.
Removed the attributes SOM.cmap, SOM.som.
Removed the method OptPostProcessor.list_generated_plots. #1091
Following the recommendation of matplotlib, the names ax and pluralized axs have been preferred over axes because for the latter it's not clear if it refers to a single Axes instance or a collection of these. #1306

Uncertainty#

gemseo.uncertainty.use_cases: gemseo.problems.uncertainty #1147
All the arguments of Resampler have default values except model; the arguments predict and output_data_shape have been removed. #1156
gemseo.uncertainty.sensitivity.analysis: gemseo.uncertainty.sensitivity.base_sensitivity_analysis
gemseo.uncertainty.sensitivity.correlation.analysis: gemseo.uncertainty.sensitivity.correlation_analysis
gemseo.uncertainty.sensitivity.hsic.analysis: gemseo.uncertainty.sensitivity.hsic_analysis
gemseo.uncertainty.sensitivity.morris.analysis: gemseo.uncertainty.sensitivity.morris_analysis
gemseo.uncertainty.sensitivity.sobol.analysis: gemseo.uncertainty.sensitivity.sobol_analysis #1205
gemseo.uncertainty.statistics.parametric renamed to gemseo.uncertainty.statistics.parametric_statistics.
gemseo.uncertainty.statistics.empirical renamed to gemseo.uncertainty.statistics.empirical_statistics. #1206

Factories#

gemseo.algos.doe.doe_factory: gemseo.algos.doe.factory
gemseo.linear_solvers.linear_solvers_factory: gemseo.algos.linear_solvers.factory
gemseo.algos.ode.ode_solvers_factory: gemseo.algos.ode.factory
gemseo.algos.opt.opt_factory: gemseo.algos.opt.factory
gemseo.algos.opt.opt_factory: gemseo.algos.opt.factory
gemseo.algos.sequence_transformer.sequence_transformer_factory: gemseo.algos.sequence_transformer.factory
gemseo.caches.cache_factory: gemseo.caches.factory
gemseo.caches.cache_factory: gemseo.caches.factory
gemseo.datasets.dataset_factory: gemseo.datasets.factory
gemseo.formulations.dataset_factory: gemseo.formulations.factory
gemseo.mda.mda_factory: gemseo.mda.factory
gemseo.post.post_factory: gemseo.post.factory
gemseo.post.post_factory: gemseo.post.factory
gemseo.post.dataset.base_plot: gemseo.post.dataset.plots.base_plot
gemseo.post.dataset.plot_factory: gemseo.post.dataset.plots.factory
gemseo.post.dataset.plot_factory_factory: gemseo.post.dataset.plots.factory_factory
gemseo.problems.disciplines_factory: gemseo.problems.factory
gemseo.scenarios.scenario_results.scenario_result_factory: gemseo.scenarios.scenario_results.factory
gemseo.utils.derivatives.gradient_approximator_factory: gemseo.utils.derivatives.factory
gemseo.wrappers.job_schedulers.schedulers_factory: gemseo.wrappers.job_schedulers.factory
BaseFormulationsFactory: FormulationFactory
DisciplinesFactory: MDODisciplineFactory
DOEFactory: DOELibraryFactory
LinearSolversFactory: LinearSolverLibraryFactory
ODESolversFactory: ODESolverLibraryFactory
ODESolverLib: BaseODESolverLibrary
OptimizersFactory: OptimizationLibraryFactory
SchedulersFactory: JobSchedulerDisciplineWrapperFactory #1161
DistributionFactory.available_distributions: removed; use DistributionFactory.class_names instead.
GrammarFactory.grammars: removed; use GrammarFactory.class_names instead.
DatasetPlotFactory.plots: removed; use DatasetPlotFactory.class_names instead.
SensitivityAnalysisFactory.available_sensitivity_analyses: removed; use SensitivityAnalysisFactory.class_names instead.
CacheFactory.caches: removed; use CacheFactory.class_names instead.
MDODisciplineFactory.disciplines: removed; use MDODisciplineFactory.class_names instead.
BaseFormulationFactory.formulations: removed; use BaseFormulationFactory.class_names instead.
MDAFactory.mdas: removed; use MDAFactory.class_names instead.
MLAlgoFactory.models: removed; use MLAlgoFactory.class_names instead.
PostFactory renamed to OptPostProcessorFactory.
OptPostProcessorFactory.posts: removed; use OptPostProcessorFactory.class_names instead.
ScalableModelFactory.scalable_models: removed; use ScalableModelFactory.class_names instead.
GradientApproximatorFactory.gradient_approximators: removed; use GradientApproximatorFactory.class_names instead.
JobSchedulerDisciplineWrapperFactory.scheduler_names: removed; use JobSchedulerDisciplineWrapperFactory.class_names instead. #1240

Problems#

gemseo.problems.analytical: gemseo.problems.optimization
gemseo.problems.aerostructure: gemseo.problems.mdo.aerostructure
gemseo.problems.propane: gemseo.problems.mdo.propane
gemseo.problems.scalable: gemseo.problems.mdo.scalable
gemseo.problems.sellar: gemseo.problems.mdo.sellar
gemseo.problems.sobieski: gemseo.problems.mdo.sobieski
gemseo.problems.analytical.rosenbrock.RosenMF: gemseo.problems.optimization.rosen_mf.RosenMF
gemseo.problems.disciplines_factory: gemseo.disciplines.disciplines_factory
gemseo.problems.topo_opt: gemseo.problems.topology_optimization
gemseo.problems.binh_korn: gemseo.problems.multiobjective_optimization.binh_korn
gemseo.problems.fonseca_fleming: gemseo.problems.multiobjective_optimization.fonseca_fleming
gemseo.problems.poloni: gemseo.problems.multiobjective_optimization.poloni
gemseo.problems.viennet: gemseo.problems.multiobjective_optimization.viennet #1162
The module sellar has been removed from gemseo.problems.sellar; instead of this module, use the modules
- sellar_1 for Sellar1,
- sellar_2 for Sellar2,
- sellar_system for SellarSystem,
- variables for the variable names and
- utils for get_inputs (renamed to get_initial_data) and get_y_opt. #1164

Sensitivity Analysis#

BaseSensitivityAnalysis and its subclasses (MorrisAnalysis, SobolAnalysis, CorrelationAnalysis and HSICAnalysis) no longer compute samples at instantiation but with a specific method, namely compute_samples, whose signature matches that of the previous constructor and which returns samples as an IODataset. One can also instantiate these classes from existing samples and then directly use the method compute_indices.
create_sensitivity_analysis creates a BaseSensitivityAnalysis from samples; if missing, use the method compute_samples of the BaseSensitivityAnalysis.
BaseSensitivityAnalysis.to_pickle and BaseSensitivityAnalysis.from_pickle: removed; instantiate BaseSensitivityAnalysis from an IODataset instead, which could typically be generated by BaseSensitivityAnalysis.compute_samples. #1203
BaseSensitivityAnalysis.indices is now a dataclass to be used as analysis.indices.index_name[output_name][output_component][input_name].
CorrelationAnalysis.kendall: removed; use CorrelationAnalysis.indices.kendall instead.
CorrelationAnalysis.pcc: removed; use CorrelationAnalysis.indices.pcc instead.
CorrelationAnalysis.pearson: removed; use CorrelationAnalysis.indices.pearson instead.
CorrelationAnalysis.prcc: removed; use CorrelationAnalysis.indices.prcc instead.
CorrelationAnalysis.spearman: removed; use CorrelationAnalysis.indices.spearman instead.
CorrelationAnalysis.src: removed; use CorrelationAnalysis.indices.src instead.
CorrelationAnalysis.srrc: removed; use CorrelationAnalysis.indices.srrc instead.
CorrelationAnalysis.ssrc: removed; use CorrelationAnalysis.indices.ssrc instead.
SobolAnalysis.first_order_indices: removed; use SobolAnalysis.indices.first instead.
SobolAnalysis.second_order_indices: removed; use SobolAnalysis.indices.second instead.
SobolAnalysis.total_order_indices: removed; use SobolAnalysis.indices.total instead.
SobolAnalysis.total_order_indices: removed; use SobolAnalysis.indices.total instead.
HSICAnalysis.hsic: removed; use HSICAnalysis.indices.hsic instead.
HSICAnalysis.r2_hsic: removed; use HSICAnalysis.indices.r2_hsic instead.
HSICAnalysis.p_value_permutation: removed; use HSICAnalysis.indices.p_value_permutation instead.
HSICAnalysis.p_value_asymptotic: removed; use HSICAnalysis.indices.p_value_asymptotic instead.
MorrisAnalysis.mu: removed; use MorrisAnalysis.indices.mu instead.
MorrisAnalysis.mu_star: removed; use MorrisAnalysis.indices.mu_star instead.
MorrisAnalysis.sigma: removed; use MorrisAnalysis.indices.sigma instead.
MorrisAnalysis.relative_sigma: removed; use MorrisAnalysis.indices.relative_sigma instead.
MorrisAnalysis.min: removed; use MorrisAnalysis.indices.min instead.
MorrisAnalysis.max: removed; use MorrisAnalysis.indices.max instead. #1211
MorrisAnalysis can now be used with outputs of size greater than 1. #1212
BaseSensitivityAnalysis: the arguments inputs have been renamed to input_names.
BaseSensitivityAnalysis.compute_indices's outputs argument has been renamed to output_names.
BaseSensitivityAnalysis's. sort_parameters method renamed to sort_input_variables. #1242
The SobolAnalysis.output_variances are estimated using twice as many samples, i.e. both A and B batches of the pick-freeze technique instead of A only. #1185
SensitivityAnalysis.outputs renamed to SensitivityAnalysis.output_names.

Miscellaneous#

The MDODisciplineAdapter's linear_candidate argument; this is now deduced at instantiation. #1207
KMeans derived from OptPostProcessor; use KMeans derived from BaseMLAlgo instead, based on a Dataset generated from an OptimizationProblem or a BaseScenario. #1248
API change: gemseo.utils.linear_solver.LinearSolver has been removed; use gemseo.algos.linear_solvers instead. #1260
Removed the n_processes attribute and argument of MDAChain. When the inner MDA class has this argument, it can be set through the **inner_mda_options options of the MDAChain #1295
The public method real_part_obj_fun from ScipyGlobalOpt has been removed.
The ctol setting for Nlopt has been removed. Instead, use the (already existing) settings eq_tolerance and ineq_tolerance.
The solver_options attribute of LinearProblem has been removed.
The methods_map class variable of ScipyLinalgAlgos has been removed. It is replaced by the private class variable __NAMES_TO_FUNCTIONS.
MDOFunction.to_pickle: removed; use the to_pickle function instead.
MDOFunction.from_pickle: removed; use the from_pickle function instead.
BaseSensitivityAnalysis.to_pickle: removed; use the to_pickle function instead.
BaseSensitivityAnalysis.from_pickle: removed; use the from_pickle function instead.
load_sensitivity_analysis: removed; use the from_pickle function instead.
The arguments each_new_iter, each_store, pre_load and generate_opt_plot of BaseScenario.set_optimization_history_backup are renamed to at_each_iteration, at_each_function_call, load and plot respectively. #1187
gemseo.core.base_formulation: gemseo.formulations.base_formulation
gemseo.core.formulation: gemseo.formulations.mdo_formulation
gemseo.formulations.formulations_factory: gemseo.formulations.factory
gemseo.core.base_formulation.BaseFormulationsFactory: gemseo.formulations.base_factory.BaseFormulationFactory
MDOFormulationsFactory: MDOFormulationFactory
gemseo.core.cache: gemseo.caches.base_cache
gemseo.core.cache.AbstractFullCache: gemseo.caches.base_full_cache.BaseFullCache
AbstractCache: BaseCache
AbstractFullCache: BaseFullCache
gemseo.core.cache.CacheEntry: gemseo.caches.cache_entry.CacheEntry
gemseo.core.cache.hash_data_dict: gemseo.caches.utils.hash_data
gemseo.core.cache.to_real: gemseo.caches.utils.to_real
gemseo.caches.hdf5_file_singleton: removed (the namesake class is available in a protected module)
gemseo.core.scenario.Scenario: gemseo.scenarios.base_scenario.BaseScenario
gemseo.core.doe_scenario: gemseo.scenarios.doe_scenario
gemseo.core.mdo_scenario: gemseo.scenarios.mdo_scenario
gemseo.algos.opt_problem renamed to gemseo.algos.optimization_problem.
gemseo.algos.opt_result renamed to gemseo.algos.optimization_result.
gemseo.algos.opt_result renamed to gemseo.algos.multiobjective_optimization_result.
gemseo.algos.pareto renamed to gemseo.algos.pareto.pareto_front.
gemseo.algos.pareto_front split into gemseo.algos.pareto.utils (including compute_pareto_optimal_points and generate_pareto_plots) and gemseo.algos.pareto.pareto_plot_biobjective (including ParetoPlotBiObjective).
OptPostProcessor's opt_grammar argument renamed to option_grammar.
FininiteElementAnalysis renamed to FiniteElementAnalysis.
gemseo.SEED: removed; use gemseo.utils.seeder.SEED instead.
gemseo.algos.progress_bar: removed; replace by the protected package gemseo.algos._progress_bars.
The N_CPUS constants have been replaced by a unique one in gemseo.utils.constants. #928
renamed the argument size of compute_doe to n_samples.
renamed the argument size of BaseDOELibrary.compute_doe to n_samples. #979
gemseo.utils.multiprocessing.get_multi_processing_manager moved to gemseo.utils.multiprocessing.manager.
gemseo.utils.data_conversion.dict_to_array: removed; use `` gemseo.utils.data_conversion .concatenate_dict_of_arrays_to_array`` instead.
gemseo.utils.data_conversion.array_to_dict: removed; use `` gemseo.utils.data_conversion.split_array_to_dict_of_arrays`` instead.
gemseo.utils.data_conversion.update_dict_of_arrays_from_array: removed since it was not used.
Argument observations of methods plot_residuals_vs_observations, plot_residuals_vs_inputs and plot_predictions_vs_observations of class MLRegressorQualityViewer is either a MLRegressorQualityViewer.ReferenceDataset or a Dataset. #1122
gradient_approximator: base_gradient_approximator
GradientApproximator: BaseGradientApproximator #1129
DependencyGraph.write_condensed_graph: DependencyGraph.render_condensed_graph
DependencyGraph.write_full_graph: DependencyGraph.render_full_graph #1341
GaussianMixture's n_components argument renamed to n_clusters; any BaseClusterer has this argument. #1235
The executable deserialize-and-run no longer takes the working directory as its first argument. The working directory, if needed, shall be set before calling it. #1238
MDOCouplingStructure renamed to CouplingStructure. #1267
MDODisciplineAdapter.linear_candidate: MDODisciplineAdapter.is_linear.
ConsistencyCstr: ConsistencyConstraint.
ConsistencyCstr.linear_candidate removed; use ConsistencyConstraint.coupling_function.discipline_adapter.is_linear instead.
ConsistencyCstr.input_dimension removed; use ConsistencyConstraint.coupling_function.discipline_adapter.input_dimension instead.
FunctionFromDiscipline.linear_candidate removed; use FunctionFromDiscipline.discipline_adapter.is_linear instead.
FunctionFromDiscipline.input_dimension removed; use FunctionFromDiscipline.discipline_adapter.input_dimension instead.
LinearCandidateFunction: removed.
FunctionFromDiscipline's differentiable argument: is_differentiable.
MDODisciplineAdapterGenerator.get_function's differentiable argument: is_differentiable. #1223
gemseo.caches._hdf5_file_singleton including HDF5FileSingleton is now a protected module.
BaseMDOFormulation's NAME attribute: removed as it was not longer used.
gemseo.formulations.mdo_formulation.MDOFormulation renamed to gemseo.formulations.base_mdo_formulation.BaseMDOFormulation #1084
BaseGrammmar.update's exclude_names argument renamed to excluded_names.
DirectoryCreator.get_unique_run_folder_path removed; use DirectoryCreator.create instead.
RestrictedFunction's orig_function argument renamed to function.
LinearCompositeFunction's orig_function argument renamed to function.
LinearCompositeFunction's interp_operator argument renamed to matrix.
ScalableDiagonalApproximation's seed argument: removed since it was not used. #1052

5.0.0#

End user API#

The high-level functions defined in gemseo.api have been moved to gemseo.
Features have been extracted from GEMSEO and are now available in the form of plugins:
- gemseo.algos.opt.lib_pdfo has been moved to gemseo-pdfo, a GEMSEO plugin for the PDFO library,
- gemseo.algos.opt.lib_pseven has been moved to gemseo-pseven, a GEMSEO plugin for the pSeven library,
- gemseo.wrappers.matlab has been moved to gemseo-matlab, a GEMSEO plugin for MATLAB,
- gemseo.wrappers.template_grammar_editor has been moved to gemseo-template-editor-gui, a GUI to create input and output file templates for DiscFromExe.

Surrogate models#

The high-level functions defined in gemseo.mlearning.api have been moved to gemseo.mlearning.
stieltjes and strategy are no longer arguments of PCERegressor.
Rename MLAlgo.save to MLAlgo.to_pickle.
The name of the method to evaluate the quality measure is passed to MLAlgoAssessor with the argument measure_evaluation_method; any of ["LEARN", "TEST", "LOO", "KFOLDS", "BOOTSTRAP"].
The name of the method to evaluate the quality measure is passed to MLAlgoSelection with the argument measure_evaluation_method; any of ["LEARN", "TEST", "LOO", "KFOLDS", "BOOTSTRAP"].
The name of the method to evaluate the quality measure is passed to MLAlgoCalibration with the argument measure_evaluation_method; any of ["LEARN", "TEST", "LOO", "KFOLDS", "BOOTSTRAP"].
The names of the methods to evaluate a quality measure can be accessed with MLAlgoQualityMeasure.EvaluationMethod. #464
Rename gemseo.mlearning.qual_measure to gemseo.mlearning.quality_measures.
Rename gemseo.mlearning.qual_measure.silhouette to gemseo.mlearning.quality_measures.silhouette_measure.
Rename gemseo.mlearning.cluster to gemseo.mlearning.clustering.
Rename gemseo.mlearning.cluster.cluster to gemseo.mlearning.clustering.clustering.
Rename gemseo.mlearning.transform to gemseo.mlearning.transformers. #701
The enumeration RBFRegressor.Function replaced the constants:
- RBFRegressor.MULTIQUADRIC
- RBFRegressor.INVERSE_MULTIQUADRIC
- RBFRegressor.GAUSSIAN
- RBFRegressor.LINEAR
- RBFRegressor.CUBIC
- RBFRegressor.QUINTIC
- RBFRegressor.THIN_PLATE
- RBFRegressor.AVAILABLE_FUNCTIONS

Post processing#

The visualization Lines uses a specific tuple (color, style, marker, name) per line by default. #677
YvsX no longer has the arguments x_comp and y_comp; the components have to be passed as x=("variable_name", variable_component).
Scatter no longer has the arguments x_comp and y_comp; the components have to be passed as x=("variable_name", variable_component).
ZvsXY no longer has the arguments x_comp, y_comp and z_comp; the components have to be passed as x=("variable_name", variable_component). #722
RobustnessQuantifier.compute_approximation uses None as default value for at_most_niter.
HessianApproximation.get_x_grad_history uses None as default value for last_iter and at_most_niter.
HessianApproximation.build_approximation uses None as default value for at_most_niter.
HessianApproximation.build_inverse_approximation uses None as default value for at_most_niter.
LSTSQApprox.build_approximation uses None as default value for at_most_niter. #750
PostFactory.create uses class_name, then opt_problem and **options as arguments. #752
Dataset.plot no longer refers to specific dataset plots, as ScatterMatrix, lines, curves... Dataset.plot now refers to the standard pandas plot method. To retrieve ready-to-use plots, please check in gemseo.post.dataset. #257

MDO processes#

Renamed InvalidDataException to InvalidDataError. #23
Moved the MatlabDiscipline to the plugin gemseo-matlab.
Rename MakeFunction to MDODisciplineAdapter.
In MDODisciplineAdapter, replace the argument mdo_function of type MDODisciplineAdapterGenerator by the argument discipline of type MDODiscipline.
Rename MDOFunctionGenerator to MDODisciplineAdapterGenerator. #412
Rename AbstractCache.export_to_dataset to AbstractCache.to_dataset.
Rename AbstractCache.export_to_ggobi to AbstractCache.to_ggobi.
Rename Scenario.export_to_dataset to Scenario.to_dataset.
Rename MDODiscipline._default_inputs to MDODiscipline.default_inputs.
Rename MDODiscipline.serialize to MDODiscipline.to_pickle.
Rename MDODiscipline.deserialize to MDODiscipline.from_pickle which is a static method.
Rename ScalabilityResult.save to ScalabilityResult.to_pickle.
Rename BaseGrammar.convert_to_simple_grammar to BaseGrammar.to_simple_grammar.
Removed the method _update_grammar_input from Scenario, Scenario._update_input_grammar shall be used instead. #558
Scenario.xdsmize
- Rename latex_output to save_pdf.
- Rename html_output to save_html.
- Rename json_output to save_json.
- Rename open_browser to show_html.
- Rename outfilename to file_name and do not use suffix.
- Rename outdir to directory_path.
XDSMizer
- Rename latex_output to save_pdf.
- Rename open_browser to show_html.
- Rename output_dir to directory_path.
- Rename XDSMizer.outdir to XDSMizer.directory_path.
- Rename XDSMizer.outfilename to XDSMizer.json_file_name.
- Rename XDSMizer.latex_output to XDSMizer.save_pdf.
XDSMizer.monitor
- Rename latex_output to save_pdf.
- Rename outfilename to file_name and do not use suffix.
- Rename outdir to directory_path.
XDSMizer.run
- Rename latex_output to save_pdf.
- Rename html_output to save_html.
- Rename json_output to save_json.
- Rename open_browser to show_html.
- Rename outfilename to file_name and do not use suffix.
- Rename outdir to directory_path and use "." as default value.
StudyAnalysis.generate_xdsm
- Rename latex_output to save_pdf.
- Rename open_browser to show_html.
- Rename output_dir to directory_path.
CouplingStructure.plot_n2_chart: rename open_browser to show_html.
N2HTML: rename open_browser to show_html.
generate_n2_plot rename open_browser to show_html.
Scenario.xdsmize: rename print_statuses to log_workflow_status.
XDSMizer.monitor: rename print_statuses to log_workflow_status.
Rename XDSMizer.print_statuses to XDSMizer.log_workflow_status.
The CLI of the StudyAnalysis uses the shortcut -p for the option --save_pdf. #564
Replace the argument force_no_exec by execute in MDODiscipline.linearize and JacobianAssembly.total_derivatives.
Rename the argument force_all to compute_all_jacobians in MDODiscipline.linearize. #644
The names of the algorithms proposed by CorrelationAnalysis must be written in capital letters; see CorrelationAnalysis.Method. #654 #464
DOEScenario no longer has a seed attribute. #621
Remove AutoPyDiscipline.get_return_spec_fromstr. #661
Remove Scenario.get_optimum; use Scenario.optimization_result instead. #770
Rename AutoPyDiscipline.in_names to AutoPyDiscipline.input_names.
Rename AutoPyDiscipline.out_names to AutoPyDiscipline.output_names. #661
Replaced the module parallel_execution.py by the package parallel_execution.
Renamed the class ParallelExecution to CallableParallelExecution.
Renamed the function worker to execute_workers.
Renamed the argument input_values to inputs.
Removed the ParallelExecution methods:
- _update_local_objects
- _run_task
- _is_worker
- _filter_ordered_outputs
- _run_task_by_index
ParallelExecution and its derive classes always take a collection of workers and no longer a single worker. #668
Removed the property penultimate_entry from SimpleCache. #480
Rename GSNewtonMDA to MDAGSNewton. #703
The enumeration MDODiscipline.ExecutionStatus replaced the constants:
- MDODiscipline.STATUS_VIRTUAL
- MDODiscipline.STATUS_PENDING
- MDODiscipline.STATUS_DONE
- MDODiscipline.STATUS_RUNNING
- MDODiscipline.STATUS_FAILED
- MDODiscipline.STATUS_LINEARIZE
- MDODiscipline.AVAILABLE_STATUSES
The enumeration MDODiscipline.GrammarType replaced the constants:
- MDODiscipline.JSON_GRAMMAR_TYPE
- MDODiscipline.SIMPLE_GRAMMAR_TYPE
The enumeration MDODiscipline.CacheType replaced the constants:
- MDODiscipline.SIMPLE_CACHE
- MDODiscipline.HDF5_CACHE
- MDODiscipline.MEMORY_FULL_CACHE
- The value None indicating no cache is replaced by MDODiscipline.CacheType.NONE
The enumeration MDODiscipline.ReExecutionPolicy replaced the constants:
- MDODiscipline.RE_EXECUTE_DONE_POLICY
- MDODiscipline.RE_EXECUTE_NEVER_POLICY
The enumeration derivation_modes.ApproximationMode replaced the constants:
- derivation_modes.FINITE_DIFFERENCES
- derivation_modes.COMPLEX_STEP
- derivation_modes.AVAILABLE_APPROX_MODES
The enumeration derivation_modes.DerivationMode replaced the constants:
- derivation_modes.DIRECT_MODE
- derivation_modes.REVERSE_MODE
- derivation_modes.ADJOINT_MODE
- derivation_modes.AUTO_MODE
- derivation_modes.AVAILABLE_MODES
The enumeration JacobianAssembly.DerivationMode replaced the constants:
- JacobianAssembly.DIRECT_MODE
- JacobianAssembly.REVERSE_MODE
- JacobianAssembly.ADJOINT_MODE
- JacobianAssembly.AUTO_MODE
- JacobianAssembly.AVAILABLE_MODES
The enumeration MDODiscipline.ApproximationMode replaced the constants:
- MDODiscipline.FINITE_DIFFERENCES
- MDODiscipline.COMPLEX_STEP
- MDODiscipline.APPROX_MODES
The enumeration MDODiscipline.LinearizationMode replaced the constants:
- MDODiscipline.FINITE_DIFFERENCE
- MDODiscipline.COMPLEX_STEP
- MDODiscipline.AVAILABLE_APPROX_MODES
The high-level functions defined in gemseo.problems.mdo.scalable.data_driven.api have been moved to gemseo.problems.mdo.scalable.data_driven. #707
Removed StudyAnalysis.AVAILABLE_DISTRIBUTED_FORMULATIONS.
The enumeration DiscFromExe.Parser replaced the constants:
- DiscFromExe.Parsers
- DiscFromExe.Parsers.KEY_VALUE_PARSER
- DiscFromExe.Parsers.TEMPLATE_PARSER
The enumeration MatlabEngine.ParallelType replaced:
- matlab_engine.ParallelType
#710
MDOFunciton.check_grad argument method was renamed to approximation_mode and now expects to be passed an ApproximationMode.
For GradientApproximator and its derived classes:
Renamed the class attribute ALIAS to _APPROXIMATION_MODE,
Renamed the instance attribute _par_args to _parallel_args,
Renamed GradientApproximationFactory to GradientApproximatorFactory and moved it to the module gradient_approximator_factory.py,
Moved the duplicated functions to error_estimators.py:
- finite_differences.comp_best_step
- finite_differences.compute_truncature_error
- finite_differences.compute_cancellation_error
- finite_differences.approx_hess
- derivatives_approx.comp_best_step
- derivatives_approx.compute_truncature_error
- derivatives_approx.compute_cancellation_error
- derivatives_approx.approx_hess
- comp_best_step was renamed to compute_best_step
- approx_hess was renamed to compute_hessian_approximation
#735
To update a grammar from data names that shall be validated against Numpy arrays, the update method is now replaced by the method update_from_names.
To update a JSONGrammar from a JSON schema, the update method is now replaced by the method update_from_schema.
Renamed JSONGrammar.write to JSONGrammar.to_file.
Renamed the argument schema_path to file_path for the JSONGrammar constructor.
To update a SimpleGrammar or a JSONGrammar from a names and types, the update method is now replaced by the method update_from_types. #741
Renamed HDF5Cache.hdf_node_name to HDF5Cache.hdf_node_path.
tolerance and name are the first instantiation arguments of HDF5Cache, for consistency with other caches.
Added the arguments newton_linear_solver and newton_linear_solver_options to the constructor of MDANewtonRaphson. These arguments are passed to the linear solver of the Newton solver used to solve the MDA coupling. #715
MDA: Remove the method set_residuals_scaling_options. #780
MDA: Remove the attributes _scale_residuals_with_coupling_size and _scale_residuals_with_first_norm and add the scaling and _scaling_data attributes.
The module gemseo.problems.mdo.scalable.parametric.study has been removed. #717

Optimisation & DOE#

Moved the library of optimization algorithms PSevenOpt to the plugin gemseo-pseven.
Moved the PDFO wrapper to the plugin gemseo-pdfo.
Removed the useless exception NloptRoundOffException.
Rename MDOFunction.serialize to MDOFunction.to_pickle.
Rename MDOFunction.deserialize to MDOFunction.from_pickle which is a static method.
DesignSpace has a class method DesignSpace.from_file and an instance method DesignSpace.to_file.
read_design_space can read an HDF file.
Rename DesignSpace.export_hdf to DesignSpace.to_hdf.
Rename DesignSpace.import_hdf to DesignSpace.from_hdf which is a class method.
Rename DesignSpace.export_to_txt to DesignSpace.to_csv.
Rename DesignSpace.read_from_txt to DesignSpace.from_csv which is a class method.
Rename Database.export_hdf to Database.to_hdf.
Replace Database.import_hdf by the class method Database.from_hdf and the instance method Database.update_from_hdf.
Rename Database.export_to_ggobi to Database.to_ggobi.
Rename Database.import_from_opendace to Database.update_from_opendace.
Database no longer has the argument input_hdf_file; use database = Database.from_hdf(file_path) instead.
Rename OptimizationProblem.export_hdf to OptimizationProblem.to_hdf.
Rename OptimizationProblem.import_hdf to OptimizationProblem.from_hdf which is a class method.
Rename OptimizationProblem.export_to_dataset to OptimizationProblem.to_dataset.
The argument export_hdf of write_design_space has been removed.
Rename export_design_space to write_design_space.
DesignSpace no longer has file_path as argument; use design_space = DesignSpace.from_file(file_path) instead. #450
Rename iks_agg to compute_iks_agg
Rename iks_agg_jac_v to compute_total_iks_agg_jac
Rename ks_agg to compute_ks_agg
Rename ks_agg_jac_v to compute_total_ks_agg_jac
Rename max_agg to compute_max_agg
Rename max_agg_jac_v to compute_max_agg_jac
Rename sum_square_agg to compute_sum_square_agg
Rename sum_square_agg_jac_v to compute_total_sum_square_agg_jac
Rename the first positional argument constr_data_names of ConstraintAggregation to constraint_names.
Rename the second positional argument method_name of ConstraintAggregation to aggregation_function.
Rename the first position argument constr_id of OptimizationProblem.aggregate_constraint to constraint_index.
Rename the aggregation methods "pos_sum", "sum" and "max" to "POS_SUM", "SUM" and "MAX".
Rename gemseo.algos.driver_lib to gemseo.algos.driver_library.
Rename DriverLib to DriverLibrary.
Rename gemseo.algos.algo_lib to gemseo.algos.algorithm_library.
Rename AlgoLib to AlgorithmLibrary.
Rename gemseo.algos.doe.doe_lib to gemseo.algos.doe.doe_library.
Rename gemseo.algos.linear_solvers.linear_solver_lib to gemseo.algos.linear_solvers.linear_solver_library.
Rename LinearSolverLib to LinearSolverLibrary.
Rename gemseo.algos.opt.opt_lib to gemseo.algos.opt.optimization_library. #702
The enumeration DriverLib.DifferentiationMethod replaced the constants:
- DriverLib.USER_DEFINED_GRADIENT
- DriverLib.DIFFERENTIATION_METHODS
The enumeration DriverLib.ApproximationMode replaced the constants:
- DriverLib.COMPLEX_STEP_METHOD
- DriverLib.FINITE_DIFF_METHOD
The enumeration OptProblem.ApproximationMode replaced the constants:
- OptProblem.USER_DEFINED_GRADIENT
- OptProblem.DIFFERENTIATION_METHODS
- OptProblem.NO_DERIVATIVES
- OptProblem.COMPLEX_STEP_METHOD
- OptProblem.FINITE_DIFF_METHOD
The method Scenario.set_differentiation_method no longer accepts None for the argument method.
The enumeration OptProblem.ProblemType replaced the constants:
- OptProblem.LINEAR_PB
- OptProblem.NON_LINEAR_PB
- OptProblem.AVAILABLE_PB_TYPES
The enumeration DesignSpace.DesignVariableType replaced the constants:
- DesignSpace.FLOAT
- DesignSpace.INTEGER
- DesignSpace.AVAILABLE_TYPES
The namedtuple DesignSpace.DesignVariable replaced:
- design_space.DesignVariable
The enumeration MDOFunction.ConstraintType replaced the constants:
- MDOFunction.TYPE_EQ
- MDOFunction.TYPE_INEQ
The enumeration MDOFunction.FunctionType replaced the constants:
- MDOFunction.TYPE_EQ
- MDOFunction.TYPE_INEQ
- MDOFunction.TYPE_OBJ
- MDOFunction.TYPE_OBS
- The value "" indicating no function type is replaced by MDOFunction.FunctionType.NONE
The enumeration LinearSolver.Solver replaced the constants:
- LinearSolver.LGMRES
- LinearSolver.AVAILABLE_SOLVERS
The enumeration ConstrAggregationDisc.EvaluationFunction replaced:
- constraint_aggregation.EvaluationFunction
Use True as default value of eval_observables in OptimizationProblem.evaluate_functions.
Rename outvars to output_names and args to input_names in MDOFunction and its subclasses (names of arguments, attributes and methods).
MDOFunction.has_jac is a property.
Remove MDOFunction.has_dim.
Remove MDOFunction.has_outvars.
Remove MDOFunction.has_expr.
Remove MDOFunction.has_args.
Remove MDOFunction.has_f_type.
Rename DriverLib.is_algo_requires_grad to DriverLibrary.requires_gradient.
Rename ConstrAggegationDisc to ConstraintAggregation. #713
Remove Database.KEYSSEPARATOR.
Remove Database._format_design_variable_names.
Remove Database.get_value; use output_value = database[x_vect] instead of output_value = database.get_value(x_vect).
Remove Database.contains_x; use x_vect in database instead of database.contains_x(x_vect).
Remove Database.contains_dataname; use output_name in database.output_names instead of database.contains_dataname(output_name).
Remove Database.set_dv_names; use database.input_names to access the input names.
Remove Database.is_func_grad_history_empty; use database.check_output_history_is_empty instead with any output name.
Rename Database.get_hashed_key to Database.get_hashable_ndarray.
Rename Database.get_all_data_names to Database.get_function_names.
Rename Database.missing_value_tag to Database.MISSING_VALUE_TAG.
Rename Database.get_x_by_iter to Database.get_x_vect.
Rename Database.clean_from_iterate to Database.clear_from_iteration.
Rename Database.get_max_iteration to Database.n_iterations.
Rename Database.notify_newiter_listeners to Database.notify_new_iter_listeners.
Rename Database.get_func_history to Database.get_function_history.
Rename Database.get_func_grad_history to Database.get_gradient_history.
Rename Database.get_x_history to Database.get_x_vect_history.
Rename Database.get_last_n_x to Database.get_last_n_x_vect.
Rename Database.get_x_at_iteration to Database.get_x_vect.
Rename Database.get_index_of to Database.get_iteration.
Rename Database.get_f_of_x to Database.get_function_value.
Rename the argument all_function_names to function_names in Database.to_ggobi.
Rename the argument design_variable_names to input_names in Database.to_ggobi.
Rename the argument add_dv to with_x_vect in Database.get_history_array.
Rename the argument values_dict to output_value in Database.store.
Rename the argument x_vect to input_value.
Rename the argument listener_func to function.
Rename the arguments funcname, fname and data_name to function_name.
Rename the arguments functions and names to function_names.
Rename the argument names to output_names in Database.filter.
Rename the argument x_hist to add_x_vect_history in Database.get_function_history and Database.get_gradient_history.
Database.get_x_vect starts counting the iterations at 1.
Database.clear_from_iteration starts counting the iterations at 1.
RadarChart, TopologyView and GradientSensitivity starts counting the iterations at 1.
The input history returned by Database.get_gradient_history and Database.get_function_history is now a 2D NumPy array.
Remove Database.n_new_iteration.
Remove Database.reset_n_new_iteration.
Remove the argument reset_iteration_counter in Database.clear.
The Database no longer uses the tag "Iter".
The Database no longer uses the notion of stacked_data. #753
Remove MDOFunction.concatenate; please use Concatenate.
Remove MDOFunction.convex_linear_approx; please use ConvexLinearApprox.
Remove MDOFunction.linear_approximation; please use compute_linear_approximation.
Remove MDOFunction.quadratic_approx; please use compute_quadratic_approximation.
Remove MDOFunction.restrict; please use FunctionRestriction.
Remove DOELibrary.compute_phip_criteria; please use compute_phip_criterion.

UQ#

The high-level functions defined in gemseo.uncertainty.api have been moved to gemseo.uncertainty.
Rename BaseSensitivityAnalysis.export_to_dataset to BaseSensitivityAnalysis.to_dataset.
Rename BaseSensitivityAnalysis.save to BaseSensitivityAnalysis.to_pickle.
Rename BaseSensitivityAnalysis.load to BaseSensitivityAnalysis.from_pickle which is a class method.
ComposedDistribution uses None as value for independent copula.
ParameterSpace no longer uses a copula passed at instantiation but to ParameterSpace.build_composed_distribution.
SPComposedDistribution raises an error when set up with a copula different from None. #655
The enumeration RobustnessQuantifier.Approximation replaced the constant:
- RobustnessQuantifier.AVAILABLE_APPROXIMATIONS
The enumeration OTDistributionFitter.DistributionName replaced the constants:
- OTDistributionFitter.AVAILABLE_DISTRIBUTIONS
- OTDistributionFitter._AVAILABLE_DISTRIBUTIONS
The enumeration OTDistributionFitter.FittingCriterion replaced the constants:
- OTDistributionFitter.AVAILABLE_FITTING_TESTS
- OTDistributionFitter._AVAILABLE_FITTING_TESTS
The enumeration OTDistributionFitter.SignificanceTest replaced the constant:
- OTDistributionFitter.SIGNIFICANCE_TESTS
The enumeration ParametricStatistics.DistributionName replaced the constant:
- ParametricStatistics.AVAILABLE_DISTRIBUTIONS
The enumeration ParametricStatistics.FittingCriterion replaced the constant:
- ParametricStatistics.AVAILABLE_FITTING_TESTS
The enumeration ParametricStatistics.SignificanceTest replaced the constant:
- ParametricStatistics.SIGNIFICANCE_TESTS
The enumeration SobolAnalysis.Algorithm replaced the constant:
- SobolAnalysis.Algorithm.Saltelli by SobolAnalysis.Algorithm.SALTELLI
- SobolAnalysis.Algorithm.Jansen by SobolAnalysis.Algorithm.JANSEN
- SobolAnalysis.Algorithm.MauntzKucherenko by SobolAnalysis.Algorithm.MAUNTZ_KUCHERENKO
- SobolAnalysis.Algorithm.Martinez by SobolAnalysis.Algorithm.MARTINEZ
The enumeration SobolAnalysis.Method replaced the constant:
- SobolAnalysis.Method.first by SobolAnalysis.Method.FIRST
- SobolAnalysis.Method.total by SobolAnalysis.Method.TOTAL
The enumeration ToleranceInterval.ToleranceIntervalSide replaced:
- distribution.ToleranceIntervalSide
The namedtuple ToleranceInterval.Bounds replaced:
- distribution.Bounds
Remove n_legend_cols in ParametricStatistics.plot_criteria.
Rename variables_names, variables_sizes and variables_types to variable_names, variable_sizes and variable_types.
Rename inputs_names and outputs_names to input_names and output_names.
Rename constraints_names to constraint_names.
Rename functions_names to function_names.
Rename inputs_sizes and outputs_sizes to input_sizes and output_sizes.
Rename disciplines_names to discipline_names.
Rename jacobians_names to jacobian_names.
Rename observables_names to observable_names.
Rename columns_names to column_names.
Rename distributions_names to distribution_names.
Rename options_values to option_values.
Rename constraints_values to constraint_values.
Rename jacobians_values to jacobian_values.
SobolAnalysis.AVAILABLE_ALGOS no longer exists; use the enum SobolAnalysis.Algorithm instead.
MLQualityMeasure.evaluate no longer exists; please use either MLQualityMeasure.evaluate_learn, MLQualityMeasure.evaluate_test, MLQualityMeasure.evaluate_kfolds, MLQualityMeasure.evaluate_loo and MLQualityMeasure.evaluate_bootstrap.
Remove OTComposedDistribution.AVAILABLE_COPULA_MODELS; please use OTComposedDistribution.CopulaModel.
Remove ComposedDistribution.AVAILABLE_COPULA_MODELS; please use ComposedDistribution.CopulaModel.
Remove SPComposedDistribution.AVAILABLE_COPULA_MODELS; please use SPComposedDistribution.CopulaModel.
Remove ComposedDistribution.INDEPENDENT_COPULA; please use ComposedDistribution.INDEPENDENT_COPULA.
Remove SobolAnalysis.AVAILABLE_ALGOS; please use SobolAnalysis.Algorithm.

Technical improvements#

Moved gemseo.utils.testing.compare_dict_of_arrays to gemseo.utils.comparisons.compare_dict_of_arrays.
Moved gemseo.utils.testing.image_comparison to gemseo.utils.testing.helpers.image_comparison.
Moved gemseo.utils.pytest_conftest to gemseo.utils.testing.pytest_conftest.
Moved gemseo.utils.testing.pytest_conftest.concretize_classes to gemseo.utils.testing.helpers.concretize_classes. #173
Dataset inherits from DataFrame and uses multi-indexing columns. Some methods have been added to improve the use of multi-index; Dataset.transform_variable has been renamed to Dataset.transform_data. Two derived classes (IODataset and OptimizationDataset) can be considered for specific usages.
Dataset can be imported from gemseo.datasets.dataset.
The default group of Dataset is parameters.
Dataset no longer has the get_data_by_group, get_all_data and get_data_by_names methods. Use Dataset.get_view` instead. It returns a sliced Dataset, to focus on some parts. Different formats can be used to extract data using pandas default methods. For instance, get_data_by_names can be replaced by get_view(variable_names=var_name).to_numpy().
In a Dataset, a variable is identified by a tuple (group_name, variable_name). This tuple called variable identifier is unique, contrary to a variable name as it can be used in several groups. The size of a variable corresponds to its number of components. dataset.variable_names_to_n_components[variable_name]`` returns the size of all the variables named variable_name while len(dataset.get_variable_components(group_name, variable_name)) returns the size of the variable named variable_name and belonging to group_name.
The methods to_dataset no longer have an argument by_group as the Dataset no longer stores the data by group (the previous Dataset stored the data in a dictionary indexed by either variable names or group names).
Dataset no longer has the export_to_dataframe method, since it is a DataFrame itself.
Dataset no longer has the length; use len(dataset) instead.
Dataset no longer has the is_empty method. Use pandas attribute empty instead.
Dataset no longer has the export_to_cache method.
Dataset no longer has the row_names attribute. Use index instead.
Dataset.add_variable no longer has the group argument. Use group_name instead.
Dataset.add_variable no longer has the name argument. Use variable_name instead.
Dataset.add_variable no longer has the cache_as_input argument.
Dataset.add_group no longer has the group argument. Use group_name instead.
Dataset.add_group no longer has the variables argument. Use variable_names instead.
Dataset.add_group no longer has the sizes argument. Use variable_names_to_n_components instead.
Dataset.add_group no longer has the cache_as_input and pattern arguments.
Renamed Dataset.set_from_array to Dataset.from_array.
Renamed Dataset.get_names to Dataset.get_variable_names.
Renamed Dataset.set_metadata to Dataset.misc.
Removed Dataset.n_samples in favor of len().
gemseo.load_dataset is renamed: gemseo.create_benchmark_dataset. Can be used to create a Burgers, Iris or Rosenbrock dataset.
BurgerDataset no longer exists. Create a Burger dataset with create_burgers_dataset.
IrisDataset no longer exists. Create an Iris dataset with create_iris_dataset.
RosenbrockDataset no longer exists. Create a Rosenbrock dataset with create_rosenbrock_dataset.
problems.dataset.factory no longer exists.
Scenario.to_dataset no longer has the by_group argument.
AbstractCache.to_dataset no longer has the by_group and name arguments. #257
Rename MDOObjScenarioAdapter to MDOObjectiveScenarioAdapter.
The scenario adapters MDOScenarioAdapter and MDOObjectiveScenarioAdapter are now located in the package gemseo.disciplines.scenario_adapters. #407
Moved gemseo.core.factory.Factory to gemseo.core.base_factory.BaseFactory
Removed the attribute factory of the factories.
Removed Factory._GEMS_PATH.
Moved singleton._Multiton to factory._FactoryMultitonMeta
Renamed Factory.cache_clear to Factory.clear_cache.
Renamed Factory.classes to Factory.class_names.
Renamed Factory to BaseFactory.
Renamed DriverFactory to BaseAlgoFactory. #522
The way non-serializable attributes of an MDODiscipline are treated has changed. From now on, instead of defining the attributes to serialize with the class variable _ATTR_TO_SERIALIZE, MDODiscipline and its child classes shall define the attributes not to serialize with the class variable _ATTR_NOT_TO_SERIALIZE. When a new attribute that is not serializable is added to the list, the methods __setstate__ and __getstate__ shall be modified to handle its creation properly. #699
utils.python_compatibility was moved and renamed to utils.compatibility.python. #689
The enumeration FilePathManager.FileType replaced the constant:
- file_type_manager.FileType
Rename Factory.classes to Factory.class_names.
Move ProgressBar and TqdmToLogger to gemseo.algos.progress_bar.
Move HashableNdarray to gemseo.algos.hashable_ndarray.
Move the HDF methods of Database to HDFDatabase.
Remove BaseEnum.get_member_from_name; please use BaseEnum.__getitem__.
StudyAnalysis.disciplines_descr has been removed; use MDOStudyAnalysis.study.disciplines instead.
StudyAnalysis.scenarios_descr has been removed; use MDOStudyAnalysis.study.scenarios instead.
StudyAnalysis.xls_study_path has been removed; use CouplingStudyAnalysis.study.xls_study_path instead.
gemseo.utils.study_analysis.StudyAnalysis has been moved to gemseo.utils.study_analyses.mdo_study_analysis and renamed to MDOStudyAnalysis.
gemseo.utils.study_analysis.XLSStudyParser has been moved to gemseo.utils.study_analyses.xls_study_parser.
gemseo.utils.study_analysis_cli has been moved to gemseo.utils.study_analyses.
MDOStudyAnalysis.generate_xdsm no longer returns a MDOScenario but an XDSM.
The option fig_size of the gemseo-study has been replaced by the options height and width.
The CLI gemseo-study can be used for MDO studies with gemseo-study xls_file_path and coupling studies with gemseo-study xls_file_path -t coupling.

Removed#

Removed the gemseo.core.jacobian_assembly module that is now in gemseo.core.derivatives.jacobian_assembly.
Removed the obsolete snopt wrapper.
Removed Python 3.7 support.

4.0.0#

API changes that impact user scripts code#

In post-processing, fig_size is the unique name to identify the size of a figure and the occurrences of figsize, figsize_x and figsize_y have been replaced by fig_size, fig_size_x and fig_size_y.
The argument parallel_exec in IDF.__init__() has been renamed to n_processes.
The argument quantile of VariableInfluence has been renamed to level.
BasicHistory: data_list has been renamed to variable_names.
MDAChain.sub_mda_list has been renamed to MDAChain.inner_mdas.
RadarChart: constraints_list has been renamed to constraint_names.
ScatterPlotMatrix: variables_list has been renamed to variable_names.
All MDA algos now count their iterations starting from 0.
The MDA.residual_history is now a list of normed residuals.
The argument figsize in MDA.plot_residual_history() was renamed to fig_size to be consistent with OptPostProcessor algos.
ConstraintsHistory: constraints_list has been renamed to constraint_names.
The MDAChain now takes inner_mda_name as argument instead of sub_mda_class.
The MDF formulation now takes main_mda_name as argument instead of main_mda_class and inner_mda_name instead of - sub_mda_class.
The BiLevel formulation now takes main_mda_name as argument instead of mda_name. It is now possible to explicitly define an inner_mda_name as well.
In DesignSpace:
- get_current_x has been renamed to get_current_value().
- has_current_x has been renamed to has_current_value().
- set_current_x has been renamed to set_current_value().
- Remove get_current_x_normalized and get_current_x_dict.
The short names of some machine learning algorithms have been replaced by conventional acronyms.
MatlabDiscipline.__init__(): input_data_list and output_data_list has been renamed to input_names and output_names.
save_matlab_file(): dict_to_save has been renamed to data.
The classes of the regression algorithms are renamed as {Prefix}Regressor.
The class ConcatenationDiscipline has been renamed to Concatenater.
In Caches:
- input_names has been renamed to input_names.
- get_all_data() has been replaced by [cache_entry for cache_entry in cache].
- get_data has been removed.
- get_length() has been replaced by len(cache).
- get_outputs(input_data) has been replaced by cache[input_data].outputs.
- {INPUTS,JACOBIAN,OUTPUTS,SAMPLE}_GROUP have been removed.
- get_last_cached_inputs() has been replaced by cache.last_entry.inputs.
- get_last_cached_outputs() has been replaced by cache.last_entry.outputs.
- max_length has been removed.
- merge has been renamed to update().
- output_names has been renamed to output_names.
- varsizes has been renamed to names_to_sizes.
- samples_indices has been removed.

API changes that impact discipline wrappers#

In Grammar:
- update_from has been renamed to update().
- remove_item(name) has been replaced by del grammar[name].
- get_data_names has been renamed to keys().
- initialize_from_data_names has been renamed to update().
- initialize_from_base_dict has been renamed to update_from_data().
- update_from_if_not_in has been renamed to now use update() with exclude_names.
- set_item_value has been removed.
- remove_required(name) has been replaced by required_names.remove(name).
- data_names has been renamed to keys().
- data_types has been renamed to values().
- update_elements has been renamed to update().
- update_required_elements has been removed.
- init_from_schema_file has been renamed to update_from_file().

API changes that affect plugin or features developers#

AlgoLib.lib_dict has been renamed to AlgoLib.descriptions.
gemseo.utils.data_conversion.FLAT_JAC_SEP has been renamed to STRING_SEPARATOR.
In gemseo.utils.data_conversion:
- DataConversion.dict_to_array has been renamed to concatenate_dict_of_arrays_to_array().
- DataConversion.list_of_dict_to_array removed.
- DataConversion.array_to_dict has been renamed to split_array_to_dict_of_arrays().
- DataConversion.jac_2dmat_to_dict has been renamed to split_array_to_dict_of_arrays().
- DataConversion.jac_3dmat_to_dict has been renamed to split_array_to_dict_of_arrays().
- DataConversion.dict_jac_to_2dmat removed.
- DataConversion.dict_jac_to_dict has been renamed to flatten_nested_dict().
- DataConversion.flat_jac_name removed.
- DataConversion.dict_to_jac_dict has been renamed to nest_flat_bilevel_dict().
- DataConversion.update_dict_from_array has been renamed to update_dict_of_arrays_from_array().
- DataConversion.deepcopy_datadict has been renamed to deepcopy_dict_of_arrays().
- DataConversion.get_all_inputs has been renamed to get_all_inputs().
- DataConversion.get_all_outputs has been renamed to get_all_outputs().
DesignSpace.get_current_value can now return a dictionary of NumPy arrays or normalized design values.
The method MDOFormulation.check_disciplines has been removed.
The class variable MLAlgo.ABBR has been renamed to MLAlgo.SHORT_ALGO_NAME.
For OptResult and MDOFunction: get_data_dict_repr has been renamed to to_dict.
Remove plugin detection for packages with gemseo_ prefix.
MDODisciplineAdapterGenerator.get_function: input_names_list and output_names_list has been renamed to output_names and output_names.
MDOScenarioAdapter.__init__: inputs_list and outputs_list has been renamed to input_names and output_names.
OptPostProcessor.out_data_dict has been renamed to OptPostProcessor.materials_for_plotting.
In ParallelExecution:
- input_data_list has been renamed to input_values.
- worker_list has been renamed to workers.
In Grammar, is_type_array has been renamed to is_array().

Internal changes that rarely or not affect users#

In Grammar:
- load_data has been renamed to validate().
- is_data_name_existing(name) has been renamed to name in grammar.
- is_all_data_names_existing(names) has been replaced by set(names) <= set(keys()).
- to_simple_grammar has been renamed to convert_to_simple_grammar().
- is_required(name) has been renamed to name in required_names.
- write_schema has been renamed to write().
- schema_dict has been renamed to schema.
- JSONGrammar class attributes removed has been renamed to PROPERTIES_FIELD, REQUIRED_FIELD, TYPE_FIELD, OBJECT_FIELD, TYPES_MAP.
- AbstractGrammar has been renamed to BaseGrammar.
AnalyticDiscipline.expr_symbols_dict has been renamed to AnalyticDiscipline.output_names_to_symbols.
AtomicExecSequence.get_state_dict has been renamed to AtomicExecSequence.get_statuses().
In CompositeExecSequence:
- CompositeExecSequence.get_state_dict has been renamed to CompositeExecSequence.get_statuses().
- CompositeExecSequence.sequence_list has been renamed to CompositeExecSequence.sequences.
Remove gemseo.utils.multi_processing.

3.0.0#

As GEMS has been renamed to GEMSEO, upgrading from version 2 to version 3 requires to change all the import statements of your code from

import gems
from gems.x.y import z

to

import gemseo
from gemseo.x.y import z

2.0.0#

The API of GEMS 2 has been slightly modified with respect to GEMS 1. In particular, for all the supported Python versions, the strings shall to be encoded in unicode while they were previously encoded in ASCII.

That kind of error:

ERROR - 17:11:09 : Invalid data in : MDOScenario_input
', error : data.algo must be string
Traceback (most recent call last):
  File "plot_mdo_scenario.py", line 85, in <module>
    scenario.execute(algo_name="L-BFGS-B", "max_iter": 100)
  File "/home/distracted_user/workspace/gemseo/src/gemseo/core/discipline.py", line 586, in execute
    self.check_input_data(input_data)
  File "/home/distracted_user/workspace/gemseo/src/gemseo/core/discipline.py", line 1243, in check_input_data
    raise InvalidDataException("Invalid input data for: " + self.name)
gemseo.core.grammar.InvalidDataException: Invalid input data for: MDOScenario

is most likely due to the fact that you have not migrated your code to be compliant with GEMSEO 2. To migrate your code, add the following import at the beginning of all your modules defining literal strings:

from __future__ import unicode_literals