testing and bugfixes

benchmarks/flux_analysis.py

@@ -23,25 +23,39 @@
 fva_setup = """
 from cameo.flux_analysis.analysis import flux_variability_analysis
 from cameo import config
-from cameo.parallel import SequentialView
+from cameo.parallel import SequentialView, MultiprocessingView
+"""
 
-config.default_view = SequentialView()
+sequential_fva_statement = """
+flux_variability_analysis(model, view=SequentialView())
 """
 
-fva_statement = """
-flux_variability_analysis(model)
+#GLPK
+glpk_sequential_fva_benchmark = Benchmark(sequential_fva_statement,
+                               common_setup + fva_setup + glpk_model_setup,
+                               start_date=datetime(2014, 7, 15))
+
+#CPLEX
+cplex_sequential_fva_benchmark = Benchmark(sequential_fva_statement,
+                                common_setup + fva_setup + cplex_model_setup,
+                                start_date=datetime(2014, 7, 15))
+
+
+multiprocessing_fva_statement = """
+flux_variability_analysis(model, view=MultiprocessingView())
 """
 
 #GLPK
-glpk_fva_benchmark = Benchmark(fva_statement,
+glpk_multiprocessing_fva_benchmark = Benchmark(multiprocessing_fva_statement,
                                common_setup + fva_setup + glpk_model_setup,
                                start_date=datetime(2014, 7, 15))
 
 #CPLEX
-cplex_fva_benchmark = Benchmark(fva_statement,
+cplex_multiprocessing_fva_benchmark = Benchmark(multiprocessing_fva_statement,
                                 common_setup + fva_setup + cplex_model_setup,
                                 start_date=datetime(2014, 7, 15))
 
+
 ######################
 # Simulation methods #
 ######################

cameo/parallel.py

@@ -14,9 +14,10 @@
 
 import Queue
 from multiprocessing import Pool, cpu_count
+from cameo.util import Singleton
 
 
-class MultiprocessingView(object):
+class MultiprocessingView(Singleton):
 
     """docstring for Parallel"""
 

cameo/strain_design/heuristic/__init__.py

@@ -105,7 +105,6 @@ def __init__(self, model=None, heuristic_method=inspyred.ec.GA, objective_functi
         self.model = model
         self.termination = termination
         self._objective_function = objective_function
-        self._heuristic_method = heuristic_method
         self.heuristic_method = heuristic_method
         self._generator = None
 
@@ -115,7 +114,7 @@ def objective_function(self):
 
     @objective_function.setter
     def objective_function(self, objective_function):
-        if self._heuristic_method.__module__ == inspyred.ec.__name__ and isinstance(objective_function, list):
+        if self._heuristic_method.__module__ == inspyred.ec.ec.__name__ and isinstance(objective_function, list):
             if len(objective_function) == 1:
                 self._objective_function = objective_function[0]
             else:
@@ -133,7 +132,7 @@ def heuristic_method(self):
     def heuristic_method(self, heuristic_method):
         if heuristic_method.__module__ == inspyred.ec.emo.__name__ and not self.is_mo():
             self._objective_function = [self.objective_function]
-        elif heuristic_method.__module__ == inspyred.ec.__name__ and self.is_mo():
+        elif heuristic_method.__module__ == inspyred.ec.ec.__name__ and self.is_mo():
             if len(self.objective_function) == 1:
                 self._objective_function = self.objective_function[0]
             else:
@@ -269,7 +268,7 @@ def run(self, **kwargs):
         super(KnockoutOptimization, self).run(
             distance_function=set_distance_function,
             representation=self.representation,
-            max_candidate_size=self.max_size,
+            candidate_size=self.max_size,
             variable_candidate_size=self.variable_size,
             **kwargs)
         return KnockoutOptimizationResult(model=self.model,

cameo/strain_design/heuristic/generators.py

@@ -15,8 +15,23 @@
 
 
 def set_generator(random, args):
+    """
+    Generates a list containing non-repeated elements of a discrete or
+    continuous representation.
+
+    :param random: Random()
+    :param args: dict
+        representation: set containing the possible values
+        max_candidate_size: int, default: 9
+        variable_candidate_size: bool, default: True
+
+    :return: candidate
+        A list containing a sample of the elements. If variable_candidate_size is
+        True the list size is up to max_candidate_size, otherwise the candidate
+        size equals candidate_size
+    """
     representation = args.get('representation')
-    max_size = args.get('max_candidate_size', 9)
+    max_size = args.get('candidate_size', 9)
     variable_size = args.get('variable_candidate_size', True)
     if variable_size:
         size = random.randint(1, max_size)
@@ -28,8 +43,28 @@ def set_generator(random, args):
 
 @diversify
 def unique_set_generator(random, args):
+    """
+    Generates a list containing non-repeated elements of a discrete or
+    continuous representation. When this generator is used, the population
+    will contain unique individuals.
+
+    See Also
+    --------
+    inspyred.ec.generators.diversify
+
+    :param random: Random()
+    :param args: dict
+        representation: set containing the possible values
+        max_candidate_size: int, default: 9
+        variable_candidate_size: bool, default: True
+
+    :return: candidate
+        A list containing a sample of the elements. If variable_candidate_size is
+        True the list size is up to max_candidate_size, otherwise the candidate
+        size equals candidate_size
+    """
     representation = args.get('representation')
-    max_size = args.get('max_candidate_size', 9)
+    max_size = args.get('candidate_size', 9)
     variable_size = args.get('variable_candidate_size', True)
     if variable_size:
         size = random.randint(1, max_size)

cameo/strain_design/heuristic/objective_functions.py

@@ -73,7 +73,7 @@ class number_of_knockouts():
 
     def __init__(self, sense='min'):
         self.sense = sense
-        if sense == max:
+        if sense == 'max':
             self.name = "max #knockouts"
         else:
             self.name = "min #knockouts"

cameo/util.py

@@ -19,6 +19,18 @@
 import colorsys
 
 
+class Singleton(object):
+    """
+    Singleton class to be extended
+    """
+    _instance = None
+
+    def __new__(cls, *args, **kwargs):
+        if not cls._instance:
+            cls._instance = super(Singleton, cls).__new__(cls, *args, **kwargs)
+        return cls._instance
+
+
 class AutoVivification(dict):
 
     """Implementation of perl's autovivification feature. Checkout http://stackoverflow.com/a/652284/280182"""