class StaticHelpers():
data_single = [Measurement(name='y0', timepoints=[1, 2, 3], values=[10, 10 ,10], errors=[0.1, 0.2, 0.3])]
data_multi = [
Measurement(name='y0', timepoints=[1, 2, 3], values=[10, 10 ,10], errors=[0.1, 0.2, 0.3], replicate_id='1st'),
Measurement(name='y0', timepoints=[1, 5, 10], values=[10, 10 ,10], errors=[0.1, 0.2, 0.3], replicate_id='2nd'),
]
many_time_series_1 = [
[TimeSeries(name='T1', timepoints=[1, 2, 3, 4], values=[10, 10, 10, 10], replicate_id='1st')],
[TimeSeries(name='T1', timepoints=[1, 2, 3], values=[10, 10, 10], replicate_id='1st')],
]
unknowns = ['y00', 'y10']
bounds = [(-100, 100), (-100, 100)]
def test_init_datatypes_masking_non_numeric(self, input_vector, masked_vector):
"""
Non-numeric values implicitly define a mask, which is in turn applied to all vectors of the corresponding datatypes.
"""
_timeseries = TimeSeries(name=StaticHelpers.name, timepoints=input_vector, values=StaticHelpers.values)
assert all(_timeseries.timepoints) == all(masked_vector)
assert _timeseries.length == len(masked_vector)
_timeseries = TimeSeries(name=StaticHelpers.name, timepoints=StaticHelpers.timepoints, values=input_vector)
assert all(_timeseries.timepoints) == all(masked_vector)
assert _timeseries.length == len(masked_vector)
_measurement = Measurement(name=StaticHelpers.name, timepoints=StaticHelpers.timepoints, values=StaticHelpers.values, errors=input_vector)
assert all(_measurement.timepoints) == all(masked_vector)
assert _measurement.length == len(masked_vector)
class StaticData():
measurements_wo_errors = Measurement(name='M1',
timepoints=[1, 2, 3],
values=[10, 20, 30],
replicate_id='1st')
measurements_w_errors = Measurement(name='M2',
timepoints=[2, 3, 4],
values=[20, 30, 40],
errors=[1 / 20, 1 / 30, 1 / 40],
replicate_id='1st')
time_series_1 = TimeSeries(name='TS1',
timepoints=[1, 2],
values=[10, 20],
replicate_id='1st')
time_series_2 = TimeSeries(name='TS2',
timepoints=[2, 3],
values=[20, 30],
replicate_id='2nd')
def test_init_datatypes(self, values, errors, info, replicate_id):
"""
To test typical instantiations of datatypes.
"""
# Standard instatiations
TimeSeries(name=StaticHelpers.name, timepoints=StaticHelpers.timepoints, values=values, info=info, replicate_id=replicate_id)
ModelState(name=StaticHelpers.name, timepoints=StaticHelpers.timepoints, values=values, info=info, replicate_id=replicate_id)
Measurement(name=StaticHelpers.name, timepoints=StaticHelpers.timepoints, values=values, errors=errors, info=info, replicate_id=replicate_id)
Observation(name=StaticHelpers.name, timepoints=StaticHelpers.timepoints, values=values, observed_state='y1', replicate_id=replicate_id)
Sensitivity(timepoints=StaticHelpers.timepoints, values=values, response='y1', parameter='p1', replicate_id=replicate_id)
Sensitivity(timepoints=StaticHelpers.timepoints, values=values, response='y1', parameter='p1', h=1e-8, replicate_id=replicate_id)
# Must provide timepoints
with pytest.raises(ValueError):
TimeSeries(name=StaticHelpers.name, timepoints=None, values=values)
# Must provide values
with pytest.raises(ValueError):
TimeSeries(name=StaticHelpers.name, timepoints=StaticHelpers.timepoints, values=None)
# Measurements can be created with error_models
Measurement(
name=StaticHelpers.name,
timepoints=StaticHelpers.timepoints,
values=values,
error_model=StaticErrorModelHelpers.constant_error_model,
error_model_parameters=StaticErrorModelHelpers.constant_error_model_parameters,
)
# Must provide a subclass of rvs.continous as p.d.f.
with pytest.raises(ValueError):
Measurement(name=StaticHelpers.name, timepoints=StaticHelpers.timepoints, values=values, error_distribution=scipy.stats.bernoulli)
# Error values must be >0
with pytest.raises(ValueError):
Measurement(name=StaticHelpers.name, timepoints=StaticHelpers.timepoints, values=values, errors=[0]*len(StaticHelpers.values))
with pytest.raises(ValueError):
Measurement(name=StaticHelpers.name, timepoints=StaticHelpers.timepoints, values=values, errors=[-1]*len(StaticHelpers.values))
class StaticDatatypes():
timeseries = TimeSeries(
name=StaticHelpers.name,
timepoints=StaticHelpers.timepoints,
values=StaticHelpers.values,
replicate_id=StaticHelpers.replicate_id
)
modelstate = ModelState(
name=StaticHelpers.name,
timepoints=StaticHelpers.timepoints,
values=StaticHelpers.values,
replicate_id=StaticHelpers.replicate_id
)
measurement_wo_errs = Measurement(
name=StaticHelpers.name,
timepoints=StaticHelpers.timepoints,
values=StaticHelpers.values,
replicate_id=StaticHelpers.replicate_id
)
measurement_w_errs = Measurement(
name=StaticHelpers.name,
timepoints=StaticHelpers.timepoints,
values=StaticHelpers.values,
errors=StaticHelpers.errors,
replicate_id=StaticHelpers.replicate_id
)
observation = Observation(
name=StaticHelpers.name,
timepoints=StaticHelpers.timepoints,
values=StaticHelpers.values,
observed_state=StaticHelpers.state,
replicate_id=StaticHelpers.replicate_id
)
sensitivity = Sensitivity(
timepoints=StaticHelpers.timepoints,
values=StaticHelpers.values,
response=StaticHelpers.state,
parameter=StaticHelpers.parameter,
replicate_id=StaticHelpers.replicate_id
)