Add tuning history to OptHistory

examples/molecule_search/experiment.py

@@ -109,7 +109,7 @@ def visualize_results(molecules: Iterable[MolGraph],
 
     # Plot pareto front (if multi-objective)
     if objective.is_multi_objective:
-        visualise_pareto(history.archive_history[-1],
+        visualise_pareto(history.evolution_best_archive[-1],
                          objectives_names=objective.metric_names[:2],
                          folder=str(save_path))
 
@@ -193,7 +193,7 @@ def run_experiment(optimizer_setup: Callable,
             result_dir = Path('results') / exp_name
             result_dir.mkdir(parents=True, exist_ok=True)
             history.save(result_dir / f'history_trial_{trial}.json')
-        trial_results.extend(history.final_choices)
+        trial_results.extend(history.evolution_results)
         trial_histories.append(history)
 
     # Compute mean & std for metrics of trials

examples/synthetic_graph_evolution/experiment_setup.py

@@ -66,7 +66,7 @@ def run_experiments(optimizer_setup: Callable,
             found_graph = found_graphs[0] if isinstance(found_graphs, Sequence) else found_graphs
             history = optimizer.history
 
-            trial_results.extend(history.final_choices)
+            trial_results.extend(history.evolution_results)
             found_nx_graph = BaseNetworkxAdapter().restore(found_graph)
 
             duration = datetime.now() - start_time

experiments/experiment_analyzer.py

@@ -104,7 +104,7 @@ def _analyze_convergence(history: OptHistory, metrics_num: int) -> List[float]:
         # find best final metric for each objective
         best_fitness_per_objective = [np.inf] * metrics_num
         for i in range(metrics_num):
-            for ind in history.final_choices.data:
+            for ind in history.evolution_results.data:
                 if ind.fitness.values[i] < best_fitness_per_objective[i]:
                     best_fitness_per_objective[i] = ind.fitness.values[i]
 
@@ -231,7 +231,8 @@ def plot_convergence(self, path_to_save: str, with_confidence: bool = True,
 
     def analyze_statistical_significance(self, data_to_analyze: Dict[str, Dict[str, List[float]]],
                                          stat_tests: List[Callable], path_to_save: Optional[str] = None,
-                                         test_format: Optional[List[str]] = None) -> Dict[str, Dict[str, Dict[str, float]]]:
+                                         test_format: Optional[List[str]] = None
+                                         ) -> Dict[str, Dict[str, Dict[str, float]]]:
         """ Method to perform statistical analysis of data. Metric data obtained with 'analyze_metrics' and
         convergence data obtained with 'analyze_convergence' can be simply analyzed, for example.
         :param data_to_analyze: data to analyze.
@@ -291,7 +292,8 @@ def analyze_structural_complexity(self, path_to_save: str, dir_name: str, class_
             os.makedirs(path_to_save, exist_ok=True)
 
         for setup, dataset, path_to_launch in self._get_path_to_launch():
-            if not self._check_if_file_or_folder_present(path=os.path.join(path_to_launch, dir_name), is_raise=is_raise):
+            if not self._check_if_file_or_folder_present(path=os.path.join(path_to_launch, dir_name),
+                                                         is_raise=is_raise):
                 continue
 
             path_to_json = None
@@ -324,7 +326,7 @@ def analyze_structural_complexity(self, path_to_save: str, dir_name: str, class_
             saved_results = [int(cur_name.split("_")[0]) for cur_name in os.listdir(cur_path_to_save)
                              if cur_name not in self._folders_to_ignore]
             max_saved_num = max(saved_results) if saved_results else 0
-            cur_path_to_save = os.path.join(cur_path_to_save, f'{max_saved_num+1}_result.png')
+            cur_path_to_save = os.path.join(cur_path_to_save, f'{max_saved_num + 1}_result.png')
             result.show(cur_path_to_save, title=title)
             self._log.info(f"Resulting graph was saved to {cur_path_to_save}")
 

experiments/experiment_launcher.py

@@ -133,7 +133,7 @@ def launch(self, optimizer_setup: Callable, **kwargs):
                 found_graph = found_graphs[0] if isinstance(found_graphs, Sequence) else found_graphs
                 history = optimizer.history
 
-                trial_results.extend(history.final_choices)
+                trial_results.extend(history.evolution_results)
                 found_nx_graph = BaseNetworkxAdapter().restore(found_graph)
 
                 duration = datetime.now() - start_time

golem/core/optimisers/adaptive/experience_buffer.py

@@ -57,7 +57,7 @@ def unroll_trajectories(history: OptHistory) -> List[GraphTrajectory]:
         """Iterates through history and find continuous sequences of applied operator actions."""
         trajectories = []
         seen_uids = set()
-        for terminal_individual in history.final_choices:
+        for terminal_individual in history.evolution_results:
             trajectory = []
             next_ind = terminal_individual
             while True:

golem/core/optimisers/genetic/gp_optimizer.py

@@ -1,6 +1,6 @@
 from copy import deepcopy
 from random import choice
-from typing import Sequence, Union, Any
+from typing import Any, Sequence, Union
 
 from golem.core.constants import MAX_GRAPH_GEN_ATTEMPTS
 from golem.core.dag.graph import Graph
@@ -9,15 +9,17 @@
 from golem.core.optimisers.genetic.operators.elitism import Elitism
 from golem.core.optimisers.genetic.operators.inheritance import Inheritance
 from golem.core.optimisers.genetic.operators.mutation import Mutation
-from golem.core.optimisers.genetic.operators.operator import PopulationT, EvaluationOperator
+from golem.core.optimisers.genetic.operators.operator import EvaluationOperator, PopulationT
 from golem.core.optimisers.genetic.operators.regularization import Regularization
 from golem.core.optimisers.genetic.operators.reproduction import ReproductionController
 from golem.core.optimisers.genetic.operators.selection import Selection
 from golem.core.optimisers.genetic.parameters.graph_depth import AdaptiveGraphDepth
 from golem.core.optimisers.genetic.parameters.operators_prob import init_adaptive_operators_prob
-from golem.core.optimisers.genetic.parameters.population_size import init_adaptive_pop_size, PopulationSize
+from golem.core.optimisers.genetic.parameters.population_size import PopulationSize, init_adaptive_pop_size
 from golem.core.optimisers.objective.objective import Objective
 from golem.core.optimisers.opt_history_objects.individual import Individual
+from golem.core.optimisers.opt_history_objects.opt_history import EXTENDED_INITIAL_ASSUMPTIONS_LABEL, \
+    INITIAL_ASSUMPTIONS_LABEL
 from golem.core.optimisers.optimization_parameters import GraphRequirements
 from golem.core.optimisers.optimizer import GraphGenerationParams
 from golem.core.optimisers.populational_optimizer import PopulationalOptimizer
@@ -64,13 +66,13 @@ def __init__(self,
     def _initial_population(self, evaluator: EvaluationOperator):
         """ Initializes the initial population """
         # Adding of initial assumptions to history as zero generation
-        self._update_population(evaluator(self.initial_individuals), 'initial_assumptions')
+        self._update_population(evaluator(self.initial_individuals), INITIAL_ASSUMPTIONS_LABEL)
         pop_size = self.graph_optimizer_params.pop_size
 
         if len(self.initial_individuals) < pop_size:
             self.initial_individuals = self._extend_population(self.initial_individuals, pop_size)
             # Adding of extended population to history
-            self._update_population(evaluator(self.initial_individuals), 'extended_initial_assumptions')
+            self._update_population(evaluator(self.initial_individuals), EXTENDED_INITIAL_ASSUMPTIONS_LABEL)
 
     def _extend_population(self, pop: PopulationT, target_pop_size: int) -> PopulationT:
         verifier = self.graph_generation_params.verifier

golem/core/optimisers/meta/surrogate_optimizer.py

@@ -6,6 +6,7 @@
 from golem.core.optimisers.meta.surrogate_evaluator import SurrogateDispatcher
 from golem.core.optimisers.meta.surrogate_model import RandomValuesSurrogateModel
 from golem.core.optimisers.objective import Objective, ObjectiveFunction
+from golem.core.optimisers.opt_history_objects.opt_history import EVOLUTION_RESULTS_LABEL
 from golem.core.optimisers.optimization_parameters import GraphRequirements
 from golem.core.optimisers.optimizer import GraphGenerationParams
 from golem.core.optimisers.populational_optimizer import EvaluationAttemptsError, _try_unfit_graph
@@ -17,6 +18,7 @@ class SurrogateEachNgenOptimizer(EvoGraphOptimizer):
 
     Additionally, we need to pass surrogate_model object
     """
+
     def __init__(self,
                  objective: Objective,
                  initial_graphs: Sequence[OptGraph],
@@ -54,5 +56,5 @@ def optimise(self, objective: ObjectiveFunction) -> Sequence[OptGraph]:
                     break
                 # Adding of new population to history
                 self._update_population(new_population)
-        self._update_population(self.best_individuals, 'final_choices')
+        self._update_population(self.best_individuals, EVOLUTION_RESULTS_LABEL)
         return [ind.graph for ind in self.best_individuals]

golem/core/optimisers/opt_history_objects/opt_history.py

@@ -6,20 +6,24 @@
 import os
 import shutil
 from pathlib import Path
-from typing import Any, Dict, List, Optional, Sequence, Union, TYPE_CHECKING
+from typing import Any, Dict, List, Optional, Sequence, TYPE_CHECKING, Union
 
 from golem.core.log import default_log
 from golem.core.optimisers.objective.objective import ObjectiveInfo
 from golem.core.optimisers.opt_history_objects.generation import Generation
-
 from golem.core.paths import default_data_dir
 from golem.serializers.serializer import default_load, default_save
 from golem.visualisation.opt_viz import OptHistoryVisualizer
 
 if TYPE_CHECKING:
-    from golem.core.dag.graph import Graph
     from golem.core.optimisers.opt_history_objects.individual import Individual
 
+INITIAL_ASSUMPTIONS_LABEL = 'initial_assumptions'
+EXTENDED_INITIAL_ASSUMPTIONS_LABEL = 'extended_initial_assumptions'
+EVOLUTION_RESULTS_LABEL = 'evolution_results'
+TUNING_START_LABEL = 'tuning_start'
+TUNING_RESULT_LABEL = 'tuning_result'
+
 
 class OptHistory:
     """
@@ -36,8 +40,7 @@ def __init__(self,
                  default_save_dir: Optional[os.PathLike] = None):
         self._objective = objective or ObjectiveInfo()
         self._generations: List[Generation] = []
-        self.archive_history: List[List[Individual]] = []
-        self._tuning_result: Optional[Graph] = None
+        self.evolution_best_archive: List[List[Individual]] = []
 
         # init default save directory
         if default_save_dir:
@@ -61,8 +64,8 @@ def add_to_history(self, individuals: Sequence[Individual], generation_label: Op
         generation = Generation(individuals, self.generations_count, generation_label, generation_metadata)
         self.generations.append(generation)
 
-    def add_to_archive_history(self, individuals: Sequence[Individual]):
-        self.archive_history.append(list(individuals))
+    def add_to_evolution_best_archive(self, individuals: Sequence[Individual]):
+        self.evolution_best_archive.append(list(individuals))
 
     def to_csv(self, save_dir: Optional[os.PathLike] = None, file: os.PathLike = 'history.csv'):
         save_dir = save_dir or self._default_save_dir
@@ -215,31 +218,36 @@ def initial_assumptions(self) -> Optional[Generation]:
         if not self.generations:
             return None
         for gen in self.generations:
-            if gen.label == 'initial_assumptions':
+            if gen.label == INITIAL_ASSUMPTIONS_LABEL:
                 return gen
 
     @property
-    def final_choices(self) -> Optional[Generation]:
+    def generations_count(self) -> int:
+        return len(self.generations)
+
+    @property
+    def evolution_results(self) -> Optional[Generation]:
         if not self.generations:
             return None
         for gen in reversed(self.generations):
-            if gen.label == 'final_choices':
+            if gen.label == EVOLUTION_RESULTS_LABEL:
                 return gen
 
     @property
-    def generations_count(self) -> int:
-        return len(self.generations)
+    def tuning_start(self) -> Optional[Generation]:
+        if not self.generations:
+            return None
+        for gen in reversed(self.generations):
+            if gen.label == TUNING_START_LABEL:
+                return gen
 
     @property
-    def tuning_result(self):
-        if hasattr(self, '_tuning_result'):
-            return self._tuning_result
-        else:
+    def tuning_result(self) -> Optional[Generation]:
+        if not self.generations:
             return None
-
-    @tuning_result.setter
-    def tuning_result(self, val):
-        self._tuning_result = val
+        for gen in reversed(self.generations):
+            if gen.label == TUNING_RESULT_LABEL:
+                return gen
 
     @property
     def generations(self):
@@ -270,8 +278,7 @@ def lighten_history(history: OptHistory) -> OptHistory:
     without excessive memory usage. """
     light_history = OptHistory()
     light_history._generations = \
-        [Generation(iterable=gen, generation_num=i) for i, gen in enumerate(history.archive_history)]
-    light_history.archive_history = history.archive_history
+        [Generation(iterable=gen, generation_num=i) for i, gen in enumerate(history.evolution_best_archive)]
+    light_history.evolution_best_archive = history.evolution_best_archive
     light_history._objective = history.objective
-    light_history._tuning_result = history.tuning_result
     return light_history

golem/core/optimisers/populational_optimizer.py

@@ -1,17 +1,18 @@
 from abc import abstractmethod
 from random import choice
-from typing import Any, Optional, Sequence, Dict
+from typing import Any, Dict, Optional, Sequence
 
 from golem.core.constants import MIN_POP_SIZE
 from golem.core.dag.graph import Graph
 from golem.core.optimisers.archive import GenerationKeeper
 from golem.core.optimisers.genetic.evaluation import MultiprocessingDispatcher, SequentialDispatcher
-from golem.core.optimisers.genetic.operators.operator import PopulationT, EvaluationOperator
+from golem.core.optimisers.genetic.operators.operator import EvaluationOperator, PopulationT
 from golem.core.optimisers.objective import GraphFunction, ObjectiveFunction
 from golem.core.optimisers.objective.objective import Objective
 from golem.core.optimisers.opt_history_objects.individual import Individual
+from golem.core.optimisers.opt_history_objects.opt_history import EVOLUTION_RESULTS_LABEL
 from golem.core.optimisers.optimization_parameters import GraphRequirements
-from golem.core.optimisers.optimizer import GraphGenerationParams, GraphOptimizer, AlgorithmParameters
+from golem.core.optimisers.optimizer import AlgorithmParameters, GraphGenerationParams, GraphOptimizer
 from golem.core.optimisers.timer import OptimisationTimer
 from golem.core.utilities.grouped_condition import GroupedCondition
 
@@ -105,7 +106,7 @@ def optimise(self, objective: ObjectiveFunction) -> Sequence[Graph]:
                 # Adding of new population to history
                 self._update_population(new_population)
         pbar.close()
-        self._update_population(self.best_individuals, 'final_choices')
+        self._update_population(self.best_individuals, EVOLUTION_RESULTS_LABEL)
         return [ind.graph for ind in self.best_individuals]
 
     @property
@@ -146,7 +147,7 @@ def _update_population(self, next_population: PopulationT, label: Optional[str]
     def _log_to_history(self, population: PopulationT, label: Optional[str] = None,
                         metadata: Optional[Dict[str, Any]] = None):
         self.history.add_to_history(population, label, metadata)
-        self.history.add_to_archive_history(self.generations.best_individuals)
+        self.history.add_to_evolution_best_archive(self.generations.best_individuals)
         if self.requirements.history_dir:
             self.history.save_current_results(self.requirements.history_dir)
 

golem/core/optimisers/random/random_mutation_optimizer.py

@@ -1,11 +1,13 @@
-from typing import Union, Optional, Sequence
+from typing import Optional, Sequence, Union
 
 from golem.core.dag.graph import Graph
 from golem.core.optimisers.genetic.gp_params import GPAlgorithmParameters
 from golem.core.optimisers.genetic.operators.mutation import Mutation
 from golem.core.optimisers.genetic.operators.operator import EvaluationOperator, PopulationT
 from golem.core.optimisers.objective import Objective
 from golem.core.optimisers.opt_history_objects.individual import Individual
+from golem.core.optimisers.opt_history_objects.opt_history import EXTENDED_INITIAL_ASSUMPTIONS_LABEL, \
+    INITIAL_ASSUMPTIONS_LABEL
 from golem.core.optimisers.optimization_parameters import GraphRequirements
 from golem.core.optimisers.optimizer import GraphGenerationParams
 from golem.core.optimisers.populational_optimizer import PopulationalOptimizer
@@ -38,13 +40,13 @@ def _evolve_population(self, evaluator: EvaluationOperator) -> PopulationT:
         return new_population
 
     def _initial_population(self, evaluator: EvaluationOperator):
-        self._update_population(evaluator(self.initial_individuals), 'initial_assumptions')
+        self._update_population(evaluator(self.initial_individuals), INITIAL_ASSUMPTIONS_LABEL)
         pop_size = self.graph_optimizer_params.pop_size
 
         if len(self.initial_individuals) < pop_size:
             self.initial_individuals = self._extend_population(self.initial_individuals, pop_size)
             # Adding of extended population to history
-            self._update_population(evaluator(self.initial_individuals), 'extended_initial_assumptions')
+            self._update_population(evaluator(self.initial_individuals), EXTENDED_INITIAL_ASSUMPTIONS_LABEL)
 
 
 class RandomMutationOptimizer(RandomSearchOptimizer):