def test_save_load_observables_expressions():
buff = io.BytesIO()
tspan = np.linspace(0, 100, 100)
sim = ScipyOdeSimulator(tyson_oscillator.model, tspan).run()
sim.save(buff, include_obs_exprs=True)
sim2 = SimulationResult.load(buff)
assert len(sim2.observables) == len(tspan)
# Tyson oscillator doesn't have expressions
assert_raises(ValueError, lambda: sim2.expressions)
def test_save_load():
tspan = np.linspace(0, 100, 101)
model = tyson_oscillator.model
test_unicode_name = u'Hello \u2603 and \U0001f4a9!'
model.name = test_unicode_name
sim = ScipyOdeSimulator(model, integrator='lsoda')
simres = sim.run(tspan=tspan, param_values={'k6': 1.0})
sim_rob = ScipyOdeSimulator(robertson.model, integrator='lsoda')
simres_rob = sim_rob.run(tspan=tspan)
# Reset equations from any previous network generation
robertson.model.reset_equations()
A = robertson.model.monomers['A']
# NFsim without expressions
nfsim1 = BngSimulator(robertson.model)
nfres1 = nfsim1.run(n_runs=2, method='nf', tspan=np.linspace(0, 1))
# Test attribute saving (text, float, list)
nfres1.custom_attrs['note'] = 'NFsim without expressions'
nfres1.custom_attrs['pi'] = 3.14
nfres1.custom_attrs['some_list'] = [1, 2, 3]
# NFsim with expressions
nfsim2 = BngSimulator(expression_observables.model)
nfres2 = nfsim2.run(n_runs=1, method='nf', tspan=np.linspace(0, 100, 11))
with tempfile.NamedTemporaryFile() as tf:
# Cannot have two file handles on Windows
tf.close()
simres.save(tf.name, dataset_name='test', append=True)
# Try to reload when file contains only one dataset and group
SimulationResult.load(tf.name)
simres.save(tf.name, append=True)
# Trying to overwrite an existing dataset gives a ValueError
assert_raises(ValueError, simres.save, tf.name, append=True)
# Trying to write to an existing file without append gives an IOError
assert_raises(IOError, simres.save, tf.name)
# Trying to write a SimulationResult to the same group with a
# different model name results in a ValueError
assert_raises(ValueError, simres_rob.save, tf.name,
dataset_name='robertson', group_name=model.name,
append=True)
simres_rob.save(tf.name, append=True)
# Trying to load from a file with more than one group without
# specifying group_name should raise a ValueError
assert_raises(ValueError, SimulationResult.load, tf.name)
# Trying to load from a group with more than one dataset without
# specifying a dataset_name should raise a ValueError
assert_raises(ValueError, SimulationResult.load, tf.name,
group_name=model.name)
# Load should succeed when specifying group_name and dataset_name
simres_load = SimulationResult.load(tf.name, group_name=model.name,
dataset_name='test')
assert simres_load._model.name == test_unicode_name
# Saving network free results requires include_obs_exprs=True,
# otherwise a warning should be raised
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
nfres1.save(tf.name, dataset_name='nfsim_no_obs', append=True)
assert len(w) == 1
assert issubclass(w[-1].category, UserWarning)
nfres1.save(tf.name, include_obs_exprs=True,
dataset_name='nfsim test', append=True)
# NFsim load
nfres1_load = SimulationResult.load(tf.name,
group_name=nfres1._model.name,
dataset_name='nfsim test')
# NFsim with expression
nfres2.save(tf.name, include_obs_exprs=True, append=True)
nfres2_load = SimulationResult.load(tf.name,
group_name=nfres2._model.name)
_check_resultsets_equal(simres, simres_load)
_check_resultsets_equal(nfres1, nfres1_load)
_check_resultsets_equal(nfres2, nfres2_load)
def test_save_load():
tspan = np.linspace(0, 100, 101)
# Make a copy of model so other tests etc. don't see the changed name.
model = copy.deepcopy(tyson_oscillator.model)
test_unicode_name = u'Hello \u2603 and \U0001f4a9!'
model.name = test_unicode_name
sim = ScipyOdeSimulator(model, integrator='lsoda')
simres = sim.run(tspan=tspan, param_values={'k6': 1.0})
sim_rob = ScipyOdeSimulator(robertson.model, integrator='lsoda')
simres_rob = sim_rob.run(tspan=tspan)
# Reset equations from any previous network generation
robertson.model.reset_equations()
A = robertson.model.monomers['A']
# NFsim without expressions
nfsim1 = BngSimulator(robertson.model)
nfres1 = nfsim1.run(n_runs=2, method='nf', tspan=np.linspace(0, 1))
# Test attribute saving (text, float, list)
nfres1.custom_attrs['note'] = 'NFsim without expressions'
nfres1.custom_attrs['pi'] = 3.14
nfres1.custom_attrs['some_list'] = [1, 2, 3]
# NFsim with expressions
nfsim2 = BngSimulator(expression_observables.model)
nfres2 = nfsim2.run(n_runs=1, method='nf', tspan=np.linspace(0, 100, 11))
with tempfile.NamedTemporaryFile() as tf:
# Cannot have two file handles on Windows
tf.close()
simres.save(tf.name, dataset_name='test', append=True)
# Try to reload when file contains only one dataset and group
SimulationResult.load(tf.name)
simres.save(tf.name, append=True)
# Trying to overwrite an existing dataset gives a ValueError
assert_raises(ValueError, simres.save, tf.name, append=True)
# Trying to write to an existing file without append gives an IOError
assert_raises(IOError, simres.save, tf.name)
# Trying to write a SimulationResult to the same group with a
# different model name results in a ValueError
assert_raises(ValueError, simres_rob.save, tf.name,
dataset_name='robertson', group_name=model.name,
append=True)
simres_rob.save(tf.name, append=True)
# Trying to load from a file with more than one group without
# specifying group_name should raise a ValueError
assert_raises(ValueError, SimulationResult.load, tf.name)
# Trying to load from a group with more than one dataset without
# specifying a dataset_name should raise a ValueError
assert_raises(ValueError, SimulationResult.load, tf.name,
group_name=model.name)
# Load should succeed when specifying group_name and dataset_name
simres_load = SimulationResult.load(tf.name, group_name=model.name,
dataset_name='test')
assert simres_load._model.name == test_unicode_name
# Saving network free results requires include_obs_exprs=True,
# otherwise a warning should be raised
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
nfres1.save(tf.name, dataset_name='nfsim_no_obs', append=True)
assert len(w) == 1
assert issubclass(w[-1].category, UserWarning)
nfres1.save(tf.name, include_obs_exprs=True,
dataset_name='nfsim test', append=True)
# NFsim load
nfres1_load = SimulationResult.load(tf.name,
group_name=nfres1._model.name,
dataset_name='nfsim test')
# NFsim with expression
nfres2.save(tf.name, include_obs_exprs=True, append=True)
nfres2_load = SimulationResult.load(tf.name,
group_name=nfres2._model.name)
_check_resultsets_equal(simres, simres_load)
_check_resultsets_equal(nfres1, nfres1_load)
_check_resultsets_equal(nfres2, nfres2_load)