Merge pull request #314 from GillesPy2/develop

Release 1.3.2

.codeclimate.yml

@@ -0,0 +1,44 @@
+---
+version: "2"
+plugins:
+  fixme:
+    enabled: true
+    config:
+      strings:
+      - FIXME
+      - BUG
+      - TODO
+  markdownlint:
+    enabled: false
+  pep8:
+    enabled: true
+  radon:
+    enabled: true
+checks:
+  argument-count:
+    enabled: false
+  complex-logic:
+    enabled: true
+  file-lines:
+    enabled: false
+  method-complexity:
+    enabled: true
+  method-count:
+    enabled: false
+  method-lines:
+    enabled: false
+  nested-control-flow:
+    enabled: false
+  return-statements:
+    enabled: true
+  similar-code:
+    enabled: false
+  identical-code:
+    enabled: false
+exclude_patterns:
+  - "**/docs/"
+  - "**/examples/"
+  - "**/test/"
+  - "**/*.ipynb/"
+  - "**/*.sh"
+  - "**/*.bat"

.coveragerc

@@ -1,3 +1,5 @@
 [run]
-omit = */.local/lib/python3.6/site-packages/numpy/*
-	*/.local/lib/python3.6/site-packages/scipy/*
+omit =  */.local/lib/python3.*/site-packages/numpy/*
+	*/.local/lib/python3.*/site-packages/scipy/*
+	*/.local/lib/python3.*/site-packages/Cython/*
+	*/.local/lib/python3.*/site-packages/pyximport/*

.gitignore

@@ -68,3 +68,4 @@ __pycache__
 .ipynb_checkpoints*
 .coverage
 htmlcov
+/build

.travis.yml

@@ -2,12 +2,20 @@ os: linux
 dist: xenial
 language: python
 python: "3.6"
+before_script:
+    - "curl -L https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64 > ./cc-test-reporter"
+    - "chmod +x ./cc-test-reporter"
+    - "./cc-test-reporter before-build"
 install:
-          - pip3 install .
+          - pip3 install -r requirements.txt
           - pip3 install python-libsbml
           - pip3 install cython
+          - pip3 install coverage
 script:
-          python test/run_tests.py -m release
+    - "coverage run --source=gillespy2 --omit=gillespy2/solvers/stochkit/* test/run_tests.py -m develop"
+after_script:
+    - "coverage xml"
+    - "if [[ \"$TRAVIS_TEST_RESULT\" == 0 ]]; then ./cc-test-reporter after-build -t coverage.py --exit-code $TRAVIS_TEST_RESULT; fi"
 deploy:
   # API token stored in env var PYPI_PASSWORD on Travis CI
   provider: pypi

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 |
-|:---------------:|:--------------:|:--------:|
-| [![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) |
+| Master Branch   | Develop Branch | 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) |
 
 License
 -------

gillespy2/__init__.py

@@ -13,4 +13,4 @@
 from gillespy2.core import *
 import gillespy2.sbml
 import gillespy2.solvers
-import gillespy2.example_models
+#import gillespy2.example_models

gillespy2/__version__.py

@@ -5,7 +5,7 @@
 # @website https://github.com/GillesPy2/GillesPy2
 # =============================================================================
 
-__version__      = '1.3.1'
+__version__      = '1.3.2'
 __title__        = 'GillesPy2'
 __description__  = 'Python interface for Gillespie-style biochemical simulations'
 __url__          = 'https://github.com/GillesPy2/GillesPy2'

gillespy2/core/gillespy2.py

@@ -6,6 +6,7 @@
 from __future__ import division
 import signal, os
 import numpy as np
+import uuid
 from contextlib import contextmanager
 from collections import OrderedDict
 from gillespy2.core.results import Results,EnsembleResults
@@ -601,75 +602,42 @@ def run(self, solver=None, timeout=0, **solver_args):
             solver-specific arguments to be passed to solver.run()
         """
 
-        if os.name == 'nt' and timeout > 0:
-            from gillespy2.core import log
-            log.warning('Timeouts are not currently supported in Windows.')
-        @contextmanager
-        def time_out(time):
-            # Register a function to raise a TimeoutError on the signal.
-            signal.signal(signal.SIGALRM, raise_time_out)
-            # Schedule the signal to be sent after ``time``.
-            signal.alarm(time)
-
-            try:
-                yield
-            except TimeoutError:
-                print('GillesPy2 solver simulation exceeded timeout')
-                pass
-            finally:
-                # Unregister the signal so it won't be triggered
-                # if the time_out is not reached.
-                signal.signal(signal.SIGALRM, signal.SIG_IGN)
+        if solver is not None:
+            if ((isinstance(solver, type)
+                    and issubclass(solver, GillesPySolver))) or issubclass(type(solver), GillesPySolver):
+                solver_results, rc = solver.run(model=self, t=self.tspan[-1],
+                            increment=self.tspan[-1] - self.tspan[-2], timeout=timeout, **solver_args)
+            else:
+                raise SimulationError(
+                    "argument 'solver' to run() must be a subclass of GillesPySolver")
+        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)
 
-        def raise_time_out(signum, frame):
+        if rc == 33:
             from gillespy2.core import log
-            import sys
-            def excepthook(type, value, traceback):
-                pass
-            sys.excepthook = excepthook
             log.warning('GillesPy2 simulation exceeded timeout.')
-            raise SimulationTimeoutError()
-
-
-        with time_out(timeout):
-            if solver is not None:
-                if ((isinstance(solver, type)
-                        and issubclass(solver, GillesPySolver))) or issubclass(type(solver), GillesPySolver):
-                    if solver.name == 'SSACSolver':
-                        signal.signal(signal.SIGALRM, signal.SIG_IGN)
-                        solver_args['timeout'] = timeout
-                    solver_results, rc = solver.run(model=self, t=self.tspan[-1], increment=self.tspan[-1] - self.tspan[-2], **solver_args)
-                else:
-                    raise SimulationError(
-                        "argument 'solver' to run() must be a subclass of GillesPySolver")
-            else:
-                from gillespy2.solvers.auto import SSASolver
-                solver = SSASolver
-                if solver.name == 'SSACSolver':
-                    signal.signal(signal.SIGALRM, signal.SIG_IGN)
-                    solver_args['timeout'] = timeout
-                solver_results, rc = SSASolver.run(model=self, t=self.tspan[-1],
-                                          increment=self.tspan[-1] - self.tspan[-2], **solver_args)
-
-            if rc == 33:
-                from gillespy2.core import log
-                log.warning('GillesPy2 simulation exceeded timeout.')
-
-            if isinstance(solver_results[0], (np.ndarray)):
-                return solver_results
-
-            if len(solver_results) is 1:
-                return Results(data=solver_results[0], model=self,
-                    solver_name=solver.name, rc=rc)
-
-            if len(solver_results) > 1:
-                results_list = []
-                for i in range(0,solver_args.get('number_of_trajectories')):
-                    results_list.append(Results(data=solver_results[i],model=self,solver_name=solver.name,
-                        rc=rc))
-                return EnsembleResults(results_list)
-            else:
-                raise ValueError("number_of_trajectories must be non-negative and non-zero")
+
+        if isinstance(solver_results[0], (np.ndarray)):
+            return solver_results
+        if len(solver_results) == 1:
+            return Results(data=solver_results[0], model=self,
+                solver_name=solver.name, rc=rc)
+
+        elif len(solver_results) > 1:
+            results_list = []
+            for i in range(0,solver_args.get('number_of_trajectories')):
+                results_list.append(Results(data=solver_results[i],model=self,solver_name=solver.name,
+                    rc=rc))
+            return EnsembleResults(results_list)
+        elif isinstance(solver_results, (np.ndarray)):
+            return solver_results
+
+        else:
+            raise ValueError("number_of_trajectories must be non-negative and non-zero")
 
 
 class Species(SortableObject):
@@ -734,7 +702,8 @@ def __init__(self, name="", initial_value=0, constant=False,
         if mode == 'continuous':
             self.initial_value = np.float(initial_value)
         else:
-            if not isinstance(initial_value, int): raise ValueError('Discrete values must be of type int.')
+            if np.int(initial_value) != initial_value:
+                raise ValueError("'initial_value' for Species with mode='discrete' must be an integer value. Change to mode='continuous' to use floating point values.")
             self.initial_value = np.int(initial_value)
         if not allow_negative_populations:
             if self.initial_value < 0: raise ValueError('A species initial value must be \
@@ -932,7 +901,7 @@ class Reaction(SortableObject):
     Attributes
     ----------
     name : str
-        The name by which the reaction is called.
+        The name by which the reaction is called (optional).
     reactants : dict
         The reactants that are consumed in the reaction, with stoichiometry. An
         example would be {R1 : 1, R2 : 2} if the reaction consumes two of R1 and
@@ -968,7 +937,10 @@ def __init__(self, name="", reactants={}, products={},
         """
 
         # Metadata
-        self.name = name
+        if name == "" or name is None:
+            self.name = 'rxn' + str(uuid.uuid4()).replace('-', '_')
+        else:
+            self.name = name
         self.annotation = ""
 
         # We might use this flag in the future to automatically generate

gillespy2/solvers/cpp/__init__.py

@@ -2,7 +2,7 @@
 from gillespy2.core import log
 
 def check_cpp_support():
-    from gillespy2.example_models import Example
+    from gillespy2.solvers.cpp.example_models import Example
     try:
         model = Example()
         results = model.run(solver=SSACSolver)

gillespy2/solvers/cpp/example_models.py

@@ -0,0 +1,26 @@
+from gillespy2.core import Model, Species, Reaction, Parameter
+import numpy as np
+
+
+class Example(Model):
+    """
+    This is a simple example for mass-action degradation of species S.
+    """
+
+    def __init__(self, parameter_values=None):
+        # Initialize the model.
+        Model.__init__(self, name="Example")
+        # Species
+        S = Species(name='Sp', initial_value=100)
+        self.add_species([S])
+        # Parameters
+        k1 = Parameter(name='k1', expression=3.0)
+        self.add_parameter([k1])
+        # Reactions
+        rxn1 = Reaction(name='S degradation', reactants={S: 1}, products={}, rate=k1)
+        self.add_reaction([rxn1])
+        self.timespan(np.linspace(0, 20, 101))
+
+
+__all__ = ['Trichloroethylene', 'LacOperon', 'Schlogl', 'MichaelisMenten',
+           'ToggleSwitch', 'Example', 'Tyson2StateOscillator', 'Oregonator']

gillespy2/solvers/numpy/basic_ode_solver.py

@@ -1,6 +1,6 @@
 """GillesPy2 Solver for ODE solutions."""
 
-import signal
+from threading import Thread, Event
 from scipy.integrate import ode
 from scipy.integrate import odeint
 from collections import OrderedDict
@@ -13,13 +13,15 @@ class BasicODESolver(GillesPySolver):
     This Solver produces the deterministic continuous solution via ODE.
     """
     name = "BasicODESolver"
-    interrupted = False
     rc = 0
+    stop_event = None
+    result = None
 
     def __init__(self):
         name = "BasicODESolver"
-        interrupted = False
         rc = 0
+        stop_event = None
+        result = None
 
     @staticmethod
     def __f(t, y, curr_state, model, c_prop):
@@ -49,7 +51,8 @@ def __f(t, y, curr_state, model, c_prop):
 
     @classmethod
     def run(self, model, t=20, number_of_trajectories=1, increment=0.05, 
-            show_labels=True, integrator='lsoda', integrator_options={}, **kwargs):
+            show_labels=True, integrator='lsoda', integrator_options={}, 
+            timeout=None, **kwargs):
         """
 
         :param model: gillespy2.model class object
@@ -66,18 +69,26 @@ def run(self, model, t=20, number_of_trajectories=1, increment=0.05,
         """
         if not isinstance(self, BasicODESolver):
             self = BasicODESolver()
+        self.stop_event = Event()
+        if timeout is not None and timeout <=0: timeout = None
         if len(kwargs) > 0:
             for key in kwargs:
                 log.warning('Unsupported keyword argument to {0} solver: {1}'.format(self.name, key))
         if number_of_trajectories > 1:
             log.warning("Generating duplicate trajectories for model with ODE Solver. Consider running with only 1 trajectory.")
+        sim_thread = Thread(target=self.__run, args=(model,), kwargs={'t':t,
+                                        'number_of_trajectories':number_of_trajectories,
+                                        'increment':increment, 'show_labels':show_labels, 
+                                        'timeout':timeout})
+        sim_thread.start()
+        sim_thread.join(timeout=timeout)
+        self.stop_event.set()
+        while self.result is None: pass
+        return self.result, self.rc
+
+    def __run(self, model, t=20, number_of_trajectories=1, increment=0.05, timeout=None,
+            show_labels=True, integrator='lsoda', integrator_options={}, **kwargs):
 
-
-        def timed_out(signum, frame):
-            self.rc = 33
-            self.interrupted = True
-
-        signal.signal(signal.SIGALRM, timed_out)
         start_state = [model.listOfSpecies[species].initial_value for species in model.listOfSpecies]
 
         # create mapping of species dictionary to array indices
@@ -119,7 +130,9 @@ def timed_out(signum, frame):
         rhs.set_initial_value(y0, curr_time).set_f_params(curr_state, model, c_prop)
 
         while entry_count < timeline.size - 1:
-            if self.interrupted: break
+            if self.stop_event.is_set():
+                self.rc = 33
+                break
             int_time = curr_time + increment
             entry_count += 1
             y0 = rhs.integrate(int_time)
@@ -137,5 +150,5 @@ def timed_out(signum, frame):
             results = [results_as_dict] * number_of_trajectories
         else:
             results = np.stack([result] * number_of_trajectories, axis=0)
-
+        self.result = results
         return results, self.rc