Python simulator.ScipyOdeSimulator类代码示例

def test_integrate_with_expression():
    """Ensure a model with Expressions simulates."""

    Monomer('s1')
    Monomer('s9')
    Monomer('s16')
    Monomer('s20')

    # Parameters should be able to contain s(\d+) without error
    Parameter('ks0',2e-5)
    Parameter('ka20', 1e5)

    Initial(s9(), Parameter('s9_0', 10000))

    Observable('s1_obs', s1())
    Observable('s9_obs', s9())
    Observable('s16_obs', s16())
    Observable('s20_obs', s20())

    Expression('keff', (ks0*ka20)/(ka20+s9_obs))

    Rule('R1', None >> s16(), ks0)
    Rule('R2', None >> s20(), ks0)
    Rule('R3', s16() + s20() >> s16() + s1(), keff)

    time = np.linspace(0, 40)
    sim = ScipyOdeSimulator(model, tspan=time)
    simres = sim.run()
    keff_vals = simres.expressions['keff']
    assert len(keff_vals) == len(time)
    assert np.allclose(keff_vals, 1.8181818181818182e-05)

def test_simres_dataframe():
    """ Test SimulationResult.dataframe() """

    tspan1 = np.linspace(0, 100, 100)
    tspan2 = np.linspace(50, 100, 50)
    tspan3 = np.linspace(100, 150, 100)
    model = tyson_oscillator.model
    sim = ScipyOdeSimulator(model, integrator='lsoda')
    simres1 = sim.run(tspan=tspan1)
    # Check retrieving a single simulation dataframe
    df_single = simres1.dataframe

    # Generate multiple trajectories
    trajectories1 = simres1.species
    trajectories2 = sim.run(tspan=tspan2).species
    trajectories3 = sim.run(tspan=tspan3).species

    # Try a simulation result with two different tspan lengths
    sim = ScipyOdeSimulator(model, param_values={'k6' : [1.,1.]}, integrator='lsoda')
    simres = SimulationResult(sim, [tspan1, tspan2], [trajectories1, trajectories2])
    df = simres.dataframe

    assert df.shape == (len(tspan1) + len(tspan2),
                        len(model.species) + len(model.observables))

    # Next try a simulation result with two identical tspan lengths, stacked
    # into a single 3D array of trajectories
    simres2 = SimulationResult(sim, [tspan1, tspan3],
                               np.stack([trajectories1, trajectories3]))
    df2 = simres2.dataframe

    assert df2.shape == (len(tspan1) + len(tspan3),
                         len(model.species) + len(model.observables))

    def setup(self):
        self.nsims = 100
        self.timer = timeit.default_timer
        self.model = earm_1_0.model
        self.model.reset_equations()
        self.parameter_set = np.repeat(
            [[p.value for p in self.model.parameters]], self.nsims, axis=0)
        integrator_options_common = {
            'model': self.model,
            'tspan': np.linspace(0, 20000, 101),
            'param_values': self.parameter_set
        }

        self.sim_lsoda = ScipyOdeSimulator(
            integrator='lsoda',
            compiler='cython',
            integrator_options={'atol': 1e-6, 'rtol': 1e-6, 'mxstep': 20000},
            **integrator_options_common
        )
        self.sim_lsoda_no_compiler_directives = ScipyOdeSimulator(
            integrator='lsoda',
            compiler='cython',
            cython_directives={},
            integrator_options={'atol': 1e-6, 'rtol': 1e-6, 'mxstep': 20000},
            **integrator_options_common
        )

        self.sim_cupsoda = CupSodaSimulator(
            integrator_options={'atol': 1e-6, 'rtol': 1e-6, 'max_steps': 20000},
            **integrator_options_common
        )

 def test_unicode_obsname_nonascii():
     """Ensure non-ascii unicode observable names error in python 2."""
     t = np.linspace(0, 100)
     rob_copy = copy.deepcopy(robertson.model)
     rob_copy.observables[0].name = u'A_total\u1234'
     sim = ScipyOdeSimulator(rob_copy)
     simres = sim.run(tspan=t)

def test_earm_integration():
    """Ensure earm_1_0 model simulates."""
    t = np.linspace(0, 1e3)
    # Run with or without inline
    sim = ScipyOdeSimulator(earm_1_0.model, tspan=t)
    sim.run()
    if sim._compiler != 'python':
        # Also run without inline
        ScipyOdeSimulator(earm_1_0.model, tspan=t, compiler='python').run()

def test_unicode_obsname_ascii():
    """Ensure ascii-convetible unicode observable names are handled."""
    t = np.linspace(0, 100)
    rob_copy = copy.deepcopy(robertson.model)
    rob_copy.observables[0].name = u'A_total'
    sim = ScipyOdeSimulator(rob_copy)
    simres = sim.run(tspan=t)
    simres.all
    simres.dataframe

def setup_module(module):
    """Doctest fixture for nose."""
    # Distutils' temp directory creation code has a more-or-less unsuppressable
    # print to stdout which will break the doctest which triggers it (via
    # scipy.weave.inline). So here we run an end-to-end test of the inlining
    # system to get that print out of the way at a point where it won't matter.
    # As a bonus, the test harness is suppressing writes to stdout at this time
    # anyway so the message is just swallowed silently.
    ScipyOdeSimulator._test_inline()

 def test_unicode_exprname_nonascii():
     """Ensure non-ascii unicode expression names error in python 2."""
     t = np.linspace(0, 100)
     rob_copy = copy.deepcopy(robertson.model)
     ab = rob_copy.observables['A_total'] + rob_copy.observables['B_total']
     expr = Expression(u'A_plus_B\u1234', ab, _export=False)
     rob_copy.add_component(expr)
     sim = ScipyOdeSimulator(rob_copy)
     simres = sim.run(tspan=t)

def test_unicode_exprname_ascii():
    """Ensure ascii-convetible unicode expression names are handled."""
    t = np.linspace(0, 100)
    rob_copy = copy.deepcopy(robertson.model)
    ab = rob_copy.observables['A_total'] + rob_copy.observables['B_total']
    expr = Expression(u'A_plus_B', ab, _export=False)
    rob_copy.add_component(expr)
    sim = ScipyOdeSimulator(rob_copy)
    simres = sim.run(tspan=t)
    simres.all
    simres.dataframe

def test_earm_integration():
    """Ensure earm_1_0 model simulates."""
    t = np.linspace(0, 1e3)
    # Run with or without inline
    sim = ScipyOdeSimulator(earm_1_0.model, tspan=t)
    sim.run()
    if ScipyOdeSimulator._use_inline:
        # Also run without inline
        ScipyOdeSimulator._use_inline = False
        ScipyOdeSimulator(earm_1_0.model, tspan=t).run()
        ScipyOdeSimulator._use_inline = True

def test_robertson_integration():
    """Ensure robertson model simulates."""
    t = np.linspace(0, 100)
    # Run with or without inline
    sim = ScipyOdeSimulator(robertson.model)
    simres = sim.run(tspan=t)
    assert simres.species.shape[0] == t.shape[0]
    if sim._compiler != 'python':
        # Also run without inline
        sim = ScipyOdeSimulator(robertson.model, tspan=t, compiler='python')
        simres = sim.run()
        assert simres.species.shape[0] == t.shape[0]

def test_robertson_integration():
    """Ensure robertson model simulates."""
    t = np.linspace(0, 100)
    # Run with or without inline
    sim = ScipyOdeSimulator(robertson.model)
    simres = sim.run(tspan=t)
    assert simres.species.shape[0] == t.shape[0]
    if ScipyOdeSimulator._use_inline:
        # Also run without inline
        ScipyOdeSimulator._use_inline = False
        sim = ScipyOdeSimulator(robertson.model, tspan=t)
        simres = sim.run()
        assert simres.species.shape[0] == t.shape[0]
        ScipyOdeSimulator._use_inline = True

    def setUp(self):
        Monomer('A', ['a'])
        Monomer('B', ['b'])

        Parameter('ksynthA', 100)
        Parameter('ksynthB', 100)
        Parameter('kbindAB', 100)

        Parameter('A_init', 0)
        Parameter('B_init', 0)

        Initial(A(a=None), A_init)
        Initial(B(b=None), B_init)

        Observable("A_free", A(a=None))
        Observable("B_free", B(b=None))
        Observable("AB_complex", A(a=1) % B(b=1))

        Rule('A_synth', None >> A(a=None), ksynthA)
        Rule('B_synth', None >> B(b=None), ksynthB)
        Rule('AB_bind', A(a=None) + B(b=None) >> A(a=1) % B(b=1), kbindAB)

        self.model = model

        # Convenience shortcut for accessing model monomer objects
        self.mon = lambda m: self.model.monomers[m]

        # This timespan is chosen to be enough to trigger a Jacobian evaluation
        # on the various solvers.
        self.time = np.linspace(0, 1)
        self.sim = ScipyOdeSimulator(self.model, tspan=self.time,
                                     integrator='vode')

    def setup_tropical(self, tspan, type_sign, find_passengers_by):
        """

        :param tspan: time of simulation
        :param type_sign: type of dynamical signature. It can either 'production' or 'consumption
        :param find_passengers_by: Method to find non important species
        :return:
        """
        if tspan is not None:
            self.tspan = tspan
        else:
            raise SimulatorException("'tspan' must be defined.")

        if type_sign not in ['production', 'consumption']:
            raise Exception('Wrong type_sign')

        self.sim = ScipyOdeSimulator(self.model, self.tspan)

        if find_passengers_by is 'imp_nodes':
            self.find_nonimportant_nodes()
            self.equations_to_tropicalize()

        if not self.all_comb:
            self.set_combinations_sm(type_sign=type_sign)

        self.is_setup = True
        return

class TestScipyOdeCompilerTests(TestScipySimulatorBase):
    """Test vode and analytic jacobian with different compiler backends"""
    def setUp(self):
        super(TestScipyOdeCompilerTests, self).setUp()
        self.args = {'model': self.model,
                     'tspan': self.time,
                     'integrator': 'vode',
                     'use_analytic_jacobian': True}

        self.python_sim = ScipyOdeSimulator(compiler='python', **self.args)
        self.python_res = self.python_sim.run()

    def test_cython(self):
        sim = ScipyOdeSimulator(compiler='cython', **self.args)
        simres = sim.run()
        assert simres.species.shape[0] == self.args['tspan'].shape[0]
        assert np.allclose(self.python_res.dataframe, simres.dataframe)

    def test_theano(self):
        sim = ScipyOdeSimulator(compiler='theano', **self.args)
        simres = sim.run()
        assert simres.species.shape[0] == self.args['tspan'].shape[0]
        assert np.allclose(self.python_res.dataframe, simres.dataframe)

    @unittest.skipIf(sys.version_info.major >= 3, 'weave not available for '
                                                  'Python 3')
    def test_weave(self):
        sim = ScipyOdeSimulator(compiler='weave', **self.args)
        simres = sim.run()
        assert simres.species.shape[0] == self.args['tspan'].shape[0]
        assert np.allclose(self.python_res.dataframe, simres.dataframe)