Merge pull request #357 from GillesPy2/develop

Release 1.4.1 - MERGE BADGES FIRST

README.md

@@ -147,9 +147,9 @@ New developments happen primarily in the [`develop`](https://github.com/GillesPy
 
 <p align="center">
 
-| Master Branch   | Develop Branch | Coverage | Maintainability |
+| Master Branch   | Develop Branch | Test Coverage | Maintainability |
 |:---------------:|:--------------:|:--------:|:---------------:|
-| [![Build Status](https://travis-ci.org/GillesPy2/GillesPy2.svg?branch=master)](https://travis-ci.org/GillesPy2/GillesPy2) | [![Build Status](https://travis-ci.org/GillesPy2/GillesPy2.svg?branch=develop)](https://travis-ci.org/GillesPy2/GillesPy2) | ![Coverage](https://raw.githubusercontent.com/GillesPy2/GillesPy2/develop/.graphics/coverage.svg?sanitize=true) | [![Maintainability](https://api.codeclimate.com/v1/badges/990ac9d778d681d32eea/maintainability)](https://codeclimate.com/github/GillesPy2/GillesPy2/maintainability) |
+| [![Build Status](https://travis-ci.org/GillesPy2/GillesPy2.svg?branch=master)](https://travis-ci.org/GillesPy2/GillesPy2) | [![Build Status](https://travis-ci.org/GillesPy2/GillesPy2.svg?branch=develop)](https://travis-ci.org/GillesPy2/GillesPy2) | [![Test Coverage](https://api.codeclimate.com/v1/badges/990ac9d778d681d32eea/test_coverage)](https://codeclimate.com/github/GillesPy2/GillesPy2/test_coverage) | [![Maintainability](https://api.codeclimate.com/v1/badges/990ac9d778d681d32eea/maintainability)](https://codeclimate.com/github/GillesPy2/GillesPy2/maintainability) |
 
 License
 -------

gillespy2/__version__.py

@@ -5,7 +5,7 @@
 # @website https://github.com/GillesPy2/GillesPy2
 # =============================================================================
 
-__version__      = '1.4.0'
+__version__      = '1.4.1'
 __title__        = 'GillesPy2'
 __description__  = 'Python interface for Gillespie-style biochemical simulations'
 __url__          = 'https://github.com/GillesPy2/GillesPy2'

gillespy2/core/events.py

@@ -120,6 +120,34 @@ class Event:
         TODO: MORE INFO
     use_values_from_trigger_time: boolean
     """
+    def __eq__(self, other):
+        return str(self)==str(other)
+
+    def __ne__(self, other):
+        return not self.__eq__(other)
+
+    def __gt__(self, other):
+        return not self.__le__(other)
+
+    def __ge__(self, other):
+        return not self.__lt__(other)
+
+    def __lt__(self, other):
+        return str(self) < str(other)
+
+    def __le__(self, other):
+        return str(self) <= str(other)
+
+    def __hash__(self):
+        if hasattr(self, '_hash'):
+            return self._hash
+        if hasattr(self, 'id'):
+            self._hash = hash(self.id)
+        elif hasattr(self, 'name'):
+            self._hash = hash(self.name)
+        else:
+            self._hash = hash(self)
+        return self._hash
 
     def __init__(self, name="", delay = None, assignments = [], priority="0", 
         trigger = None, use_values_from_trigger_time = False):
@@ -171,6 +199,7 @@ def __init__(self, name="", delay = None, assignments = [], priority="0",
         else:
             raise EventError(
                 'use_values_from_trigger_time requires bool')
+
     def __str__(self):
         print_string = self.name
         print_string += '\n\tTrigger: ' + str(self.trigger)

gillespy2/core/gillespy2.py

@@ -66,28 +66,13 @@ def __ge__(self, other):
         return not self.__lt__(other)
 
     def __lt__(self, other):
-        if hasattr(self, 'id') and hasattr(other, 'id'):
-            return self.id.lower() < other.id.lower()
-        elif hasattr(self, 'name') and hasattr(other, 'name'):
-            return self.name.lower() < other.name.lower()
-        else:
-            return repr(self) < repr(other)
+        return str(self) < str(other)
 
     def __le__(self, other):
-        if hasattr(self, 'id') and hasattr(other, 'id'):
-            return self.id.lower() <= other.id.lower()
-        elif hasattr(self, 'name') and hasattr(other, 'name'):
-            return self.name.lower() <= other.name.lower()
-        else:
-            return repr(self) <= repr(other)
+        return str(self) <= str(other)
 
     def __cmp__(self, other):
-        if hasattr(self, 'id') and hasattr(other, 'id'):
-            return cmp(self.id.lower(), other.id.lower())
-        elif hasattr(self, 'name') and hasattr(other, 'name'):
-            return cmp(self.name.lower(), other.name.lower())
-        else:
-            return cmp(repr(self), repr(other))
+        return cmp(str(self), str(other))
 
     def __hash__(self):
         if hasattr(self, '_hash'):
@@ -276,7 +261,6 @@ def add_species(self, obj):
         obj : Species, or list of Species
             The species or list of species to be added to the model object.
         """
-
         if isinstance(obj, list):
             for S in sorted(obj):
                 self.add_species(S)
@@ -790,38 +774,48 @@ def run(self, solver=None, timeout=0, **solver_args):
 
         if solver is not None:
             try:
-                solver_results, rc = solver.run(model=self, t=self.tspan[-1],
-                            increment=self.tspan[-1] - self.tspan[-2], timeout=timeout, **solver_args)
+                solver_results, rc = solver.run(model=self, t=self.tspan[-1], increment=self.tspan[-1] - self.tspan[-2],
+                                                timeout=timeout, **solver_args)
             except Exception as e:
                 raise SimulationError(
                     "argument 'solver={}' to run() failed.  Reason Given: {}".format(solver, e))
         else:
-            from gillespy2.solvers.auto import SSASolver
-            solver = SSASolver
-            solver_results, rc = SSASolver.run(model=self, t=self.tspan[-1],
-                                      increment=self.tspan[-1] -
-                                      self.tspan[-2], timeout=timeout, **solver_args)
+            if len(self.get_all_assignment_rules()) > 0 or len(self.get_all_rate_rules()) > 0 \
+                    or len(self.get_all_function_definitions()) > 0 or len(self.get_all_events()) > 0:
+                        from gillespy2.solvers.numpy import can_use_numpy
+                        if can_use_numpy:
+                            from gillespy2.solvers.numpy.basic_tau_hybrid_solver import BasicTauHybridSolver
+                            solver = BasicTauHybridSolver
+                        else:
+                            raise ModelError('BasicTauHybridSolver is the only solver currently that supports '
+                                             'AssignmentRules, RateRules, FunctionDefinitions, or Events. '
+                                             'Please install Numpy.')
+            else:
+                from gillespy2.solvers.auto import SSASolver
+                solver = SSASolver
+
+            solver_results, rc = solver.run(model=self, t=self.tspan[-1], increment=self.tspan[-1] - self.tspan[-2],
+                                            timeout=timeout, **solver_args)
 
         if rc == 33:
             from gillespy2.core import log
             log.warning('GillesPy2 simulation exceeded timeout.')
 
         if hasattr(solver_results[0], 'shape'):
             return solver_results
+
         if len(solver_results) is 1:
-            results_list = []
-            results_list.append(Trajectory(data=solver_results[0], model=self,
-                solver_name=solver.name, rc=rc))
+            results_list = [Trajectory(data=solver_results[0], model=self,
+                                       solver_name=solver.name, rc=rc)]
             return Results(results_list)
 
         if len(solver_results) > 1:
             results_list = []
             for i in range(0,solver_args.get('number_of_trajectories')):
-                results_list.append(Trajectory(data=solver_results[i],model=self,solver_name=solver.name,
-                    rc=rc))
+                results_list.append(Trajectory(data=solver_results[i], model=self, solver_name=solver.name,
+                    rc = rc))
             return Results(results_list)
 
-
         else:
             raise ValueError("number_of_trajectories must be non-negative and non-zero")
 
@@ -907,6 +901,20 @@ def __str__(self):
         '''
         return print_string
 
+    def set_initial_value(self,num):
+        """
+        Setter method for initial_value of a population
+        :param num: Integer to set initial species population
+        :raises SpeciesError: If num is non-negative or a decimal number
+        """
+        print(num)
+        print(self.mode)
+        if isinstance(num,float) and (self.mode != 'dynamic' or self.mode != 'continuous'):
+            raise SpeciesError("Mode set to discrete, species must be an integer number.")
+        if num < 0 and self.allow_negative_populations == False:
+            raise SpeciesError("Species population must be non-negative, or allow_negative_populations "
+                               "must be set to True")
+        self.initial_value = num
 
 class Parameter(SortableObject):
     """