Rebase CMA on master

Author: Tanguy Damart

bluepyopt/__init__.py

@@ -33,7 +33,6 @@
 import bluepyopt.stoppingCriteria
 import bluepyopt.deapext.optimisations
 import bluepyopt.deapext.optimisationsCMA
-import bluepyopt.deapext.hype
 
 # Add some backward compatibility for the time when DEAPoptimisation not in
 # deapext yet

bluepyopt/deapext/CMA_SO.py

@@ -135,11 +135,11 @@ def update(self, population):
             (
                 numpy.linalg.norm(self.ps)
                 / sqrt(1.0 - (1.0 - self.cs) **
-                    (2.0 * (self.update_count + 1.0)))
+                (2.0 * (self.update_count + 1.0)))
                 / self.chiN
                 < (1.4 + 2.0 / (self.dim + 1.0))
             )
-        )
+        )  # noqa
 
         self.update_count += 1
 

bluepyopt/deapext/algorithms.py

@@ -112,11 +112,7 @@ def eaAlphaMuPlusLambdaCheckpoint(
         terminator (multiprocessing.Event): exit loop when is set.
             Not taken into account if None.
     """
-<<<<<<< HEAD
 
-=======
-    
->>>>>>> 7e9c3ea (Added rules)
     if cp_filename:
         cp_filename_tmp = cp_filename + '.tmp'
 
@@ -147,13 +143,11 @@ def eaAlphaMuPlusLambdaCheckpoint(
         history = deap.tools.History()
 
         invalid_count = _evaluate_invalid_fitness(toolbox, population)
-        
+
         utils.update_history_and_hof(halloffame, history, population)
-        utils.record_stats(stats,
-                           logbook,
-                           start_gen,
-                           population,
-                           invalid_count)
+        utils.record_stats(
+            stats, logbook, start_gen, population, invalid_count
+        )
 
     stopping_criteria = [MaxNGen(ngen)]
 

bluepyopt/deapext/optimisations.py

@@ -160,14 +160,14 @@ def setup_deap(self):
 
         # Number of parameters
         IND_SIZE = len(self.evaluator.params)
-        
         if IND_SIZE == 0:
             raise Exception(
                 "Length of evaluator.params is zero. At least one "
-                "non-fix parameter is neededto run an optimization."
+                "non-fix parameter is needed to run an optimization."
             )
 
         # Bounds for the parameters
+
         LOWER = []
         UPPER = []
 

bluepyopt/deapext/optimisationsCMA.py

@@ -24,6 +24,8 @@
 import pickle
 import random
 import functools
+import shutil
+import os
 
 import deap.tools
 
@@ -91,11 +93,9 @@ def __init__(
         self.hof = hof
         if self.hof is None:
             self.hof = deap.tools.HallOfFame(10)
-        
-        if offspring_size < 2:
-            raise Exception("offspring_size has to be at least 2.")
+
         self.offspring_size = offspring_size
-        
+
         self.fitness_reduce = fitness_reduce
         self.centroids = centroids
         self.sigma = sigma
@@ -251,6 +251,9 @@ def run(
                 Not taken into account if None.
         """
 
+        if cp_filename:
+            cp_filename_tmp = cp_filename + '.tmp'
+
         stats = self.get_stats()
 
         if continue_cp:
@@ -345,8 +348,10 @@ def run(
                     np_rndstate=numpy.random.get_state(),
                     CMA_es=CMA_es,
                 )
-                pickle.dump(cp, open(cp_filename, "wb"))
-                logger.debug("Wrote checkpoint to %s", cp_filename)
+                pickle.dump(cp, open(cp_filename_tmp, "wb"))
+                if os.path.isfile(cp_filename_tmp):
+                    shutil.copy(cp_filename_tmp, cp_filename)
+                    logger.debug('Wrote checkpoint to %s', cp_filename)
 
                 CMA_es.map_function = temp_mf
 

bluepyopt/deapext/stoppingCriteria.py

@@ -1,7 +1,7 @@
 """StoppingCriteria class"""
 
 """
-Copyright (c) 2016-2020, EPFL/Blue Brain Project
+Copyright (c) 2016-2021, EPFL/Blue Brain Project
 
  This file is part of BluePyOpt <https://github.com/BlueBrain/BluePyOpt>
 

bluepyopt/ephys/__init__.py

@@ -37,7 +37,6 @@
 from . import recordings  # NOQA
 from . import objectivescalculators  # NOQA
 from . import stimuli  # NOQA
-from . import rules  # NOQA
 
 # TODO create all the necessary abstract methods
 # TODO check inheritance structure

bluepyopt/ephys/evaluators.py

@@ -116,8 +116,13 @@ def objective_dict(self, objective_array):
     def objective_list(self, objective_dict):
         """Convert objective_dict in objective_list"""
         objective_list = []
+<<<<<<< HEAD
         objective_names = [objective.name for objective in self.fitness_calculator.objectives]
 
+=======
+        objective_names = [objective.name
+                           for objective in self.fitness_calculator.objectives]
+>>>>>>> 923c7e5 (Rebase CMA on master)
         for objective_name in objective_names:
             objective_list.append(objective_dict[objective_name])
 

bluepyopt/ephys/objectives.py

@@ -127,52 +127,3 @@ def calculate_score(self, responses):
             score += weight * feature_score
 
         return score
-
-
-class RuleObjective(bluepyopt.objectives.Objective):
-
-    """Multi rules objective"""
-
-    def __init__(self, name, rules=None):
-        """Constructor
-        Args:
-            name (str): name of this object
-            rules (list): rule used in the Objective
-        """
-
-        super(RuleObjective, self).__init__(name)
-        self.name = name
-        self.rules = rules
-
-    def calculate_scores(self, cell_model):
-        """Calculate the scores for the individual rules"""
-
-        scores = []
-        for rule in self.rules:
-            scores.append(rule.calculate_score(cell_model))
-
-        return scores
-
-
-class SingletonRuleObjective(RuleObjective):
-
-    """Single rule objective"""
-
-    def __init__(self, name, rule):
-        """Constructor
-        Args:
-            name (str): name of this object
-            rule (EFeature): single rule inside this objective
-        """
-
-        super(SingletonRuleObjective, self).__init__(name, [rule])
-
-    def calculate_score(self, cell_model):
-        """Objective score"""
-
-        return self.calculate_scores(cell_model)[0]
-
-    def __str__(self):
-        """String representation"""
-
-        return '( %s )' % self.rule[0]

bluepyopt/ephys/objectivescalculators.py

@@ -19,7 +19,10 @@
  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 """
 
+<<<<<<< HEAD
 from . import objectives
+=======
+>>>>>>> 923c7e5 (Rebase CMA on master)
 
 class ObjectivesCalculator(object):
 
@@ -36,8 +39,9 @@ def __init__(
 
         self.objectives = objectives
 
-    def calculate_scores(self, responses, cell_model=None, param_dict=None):
+    def calculate_scores(self, responses):
         """Calculator the score for every objective"""
+<<<<<<< HEAD
 
         scores = {}
 
@@ -58,6 +62,11 @@ def calculate_scores(self, responses, cell_model=None, param_dict=None):
             cell_model.unfreeze(param_dict.keys())
 
         return scores
+=======
+
+        return {objective.name: objective.calculate_score(responses)
+                for objective in self.objectives}
+>>>>>>> 923c7e5 (Rebase CMA on master)
 
     def calculate_values(self, responses):
         """Calculator the value of each objective"""
@@ -66,7 +75,10 @@ def calculate_values(self, responses):
                 for objective in self.objectives}
 
     def __str__(self):
+<<<<<<< HEAD
 
+=======
+>>>>>>> 923c7e5 (Rebase CMA on master)
         return 'objectives:\n  %s' % '\n  '.join(
             [str(obj) for obj in self.objectives]) \
             if self.objectives is not None else 'objectives:\n'