def pysb_example_presimulation_module():
"""PySB example_presimulation model module fixture"""
constant_parameters = ['DRUG_0', 'KIN_0']
pysb.SelfExporter.cleanup() # reset pysb
pysb.SelfExporter.do_export = True
model_path = os.path.join(os.path.dirname(__file__), '..',
'examples', 'example_presimulation')
with amici.add_path(model_path):
if 'createModelPresimulation' in sys.modules:
importlib.reload(sys.modules['createModelPresimulation'])
model_module = sys.modules['createModelPresimulation']
else:
model_module = importlib.import_module('createModelPresimulation')
model = copy.deepcopy(model_module.model)
model.name = 'test_model_presimulation_pysb'
outdir = model.name
pysb2amici(model, outdir, verbose=True,
observables=['pPROT_obs'],
constant_parameters=constant_parameters)
with amici.add_path(outdir):
model_module_pysb = importlib.import_module(outdir)
yield model_module_pysb
shutil.rmtree(outdir, ignore_errors=True)
def test_compare_to_pysb_simulation(example):
pysb = pytest.importorskip("pysb")
atol = 1e-8
rtol = 1e-8
with amici.add_path(os.path.dirname(pysb.examples.__file__)):
with amici.add_path(
os.path.join(os.path.dirname(__file__), '..', 'tests',
'pysb_test_models')):
if example == 'earm_1_3' \
and platform.sys.version_info[0] == 3 \
and platform.sys.version_info[1] < 7:
return
# load example
pysb.SelfExporter.cleanup() # reset pysb
pysb.SelfExporter.do_export = True
module = importlib.import_module(example)
pysb_model = module.model
pysb_model.name = pysb_model.name.replace('pysb.examples.', '')
# avoid naming clash for custom pysb models
pysb_model.name += '_amici'
# pysb part
tspan = np.linspace(0, 100, 101)
sim = ScipyOdeSimulator(pysb_model,
tspan=tspan,
integrator_options={
'rtol': rtol,
'atol': atol
},
compiler='python')
pysb_simres = sim.run()
# amici part
outdir = pysb_model.name
if pysb_model.name in ['move_connected_amici']:
with pytest.raises(Exception):
pysb2amici(pysb_model,
outdir,
verbose=logging.INFO,
compute_conservation_laws=True)
compute_conservation_laws = False
else:
compute_conservation_laws = True
pysb2amici(pysb_model,
outdir,
verbose=logging.INFO,
compute_conservation_laws=compute_conservation_laws)
sys.path.insert(0, outdir)
amici_model_module = importlib.import_module(pysb_model.name)
model_pysb = amici_model_module.getModel()
model_pysb.setTimepoints(tspan)
solver = model_pysb.getSolver()
solver.setMaxSteps(int(1e5))
solver.setAbsoluteTolerance(atol)
solver.setRelativeTolerance(rtol)
rdata = amici.runAmiciSimulation(model_pysb, solver)
# check agreement of species simulation
assert np.isclose(rdata['x'], pysb_simres.species, 1e-4,
1e-4).all()
shutil.rmtree(outdir, ignore_errors=True)
def test_compare_to_pysb_simulation(example):
pysb = pytest.importorskip("pysb")
atol = 1e-8
rtol = 1e-8
with amici.add_path(os.path.dirname(pysb.examples.__file__)):
with amici.add_path(
os.path.join(os.path.dirname(__file__), '..', 'tests',
'pysb_test_models')):
if example == 'earm_1_3' \
and platform.sys.version_info[0] == 3 \
and platform.sys.version_info[1] < 7:
return
# load example
pysb.SelfExporter.cleanup() # reset pysb
pysb.SelfExporter.do_export = True
module = importlib.import_module(example)
pysb_model = module.model
pysb_model.name = pysb_model.name.replace('pysb.examples.', '')
# avoid naming clash for custom pysb models
pysb_model.name += '_amici'
# pysb part
tspan = np.linspace(0, 100, 101)
sim = ScipyOdeSimulator(pysb_model,
tspan=tspan,
integrator_options={
'rtol': rtol,
'atol': atol
},
compiler='python')
pysb_simres = sim.run()
# amici part
outdir = pysb_model.name
if pysb_model.name in ['move_connected_amici']:
with pytest.raises(Exception):
pysb2amici(pysb_model,
outdir,
verbose=logging.INFO,
compute_conservation_laws=True)
compute_conservation_laws = False
else:
compute_conservation_laws = True
pysb2amici(pysb_model,
outdir,
verbose=logging.INFO,
compute_conservation_laws=compute_conservation_laws,
observables=list(pysb_model.observables.keys()))
amici_model_module = amici.import_model_module(
pysb_model.name, outdir)
model_pysb = amici_model_module.getModel()
model_pysb.setTimepoints(tspan)
solver = model_pysb.getSolver()
solver.setMaxSteps(int(1e6))
solver.setAbsoluteTolerance(atol)
solver.setRelativeTolerance(rtol)
rdata = amici.runAmiciSimulation(model_pysb, solver)
# check agreement of species simulation
assert np.isclose(rdata['x'], pysb_simres.species, 1e-4,
1e-4).all()
if example not in [
'fricker_2010_apoptosis', 'fixed_initial',
'bngwiki_egfr_simple_deletemolecules'
]:
if example in [
'tyson_oscillator', 'bax_pore_sequential', 'bax_pore',
'kinase_cascade', 'bngwiki_egfr_simple',
'bngwiki_enzymatic_cycle_mm', 'bngwiki_simple'
]:
solver.setAbsoluteTolerance(1e-14)
solver.setRelativeTolerance(1e-14)
epsilon = 1e-4
else:
solver.setAbsoluteTolerance(1e-10)
solver.setRelativeTolerance(1e-10)
epsilon = 1e-3
model_pysb.setParameterScale(
parameterScalingFromIntVector([
ParameterScaling.log10
if p > 0 else ParameterScaling.none
for p in model_pysb.getParameters()
]))
check_derivatives(model_pysb,
solver,
epsilon=epsilon,
rtol=1e-2,
atol=1e-2,
skip_zero_pars=True)
shutil.rmtree(outdir, ignore_errors=True)
def import_model_pysb(
petab_problem: PysbPetabProblem,
model_output_dir: Optional[str] = None,
verbose: Optional[Union[bool, int]] = True,
**kwargs
) -> None:
"""
Create AMICI model from PySB-PEtab problem
:param petab_problem:
PySB PEtab problem
:param model_output_dir:
Directory to write the model code to. Will be created if doesn't
exist. Defaults to current directory.
:param verbose:
Print/log extra information.
:param kwargs:
Additional keyword arguments to be passed to
:meth:`amici.pysb_import.pysb2amici`.
"""
set_log_level(logger, verbose)
logger.info(f"Importing model ...")
observable_table = petab_problem.observable_df
pysb_model = petab_problem.pysb_model
# For pysb, we only allow parameters in the condition table
# those must be pysb model parameters (either natively, or output
# parameters from measurement or condition table that have been added in
# PysbPetabProblem
model_parameters = [p.name for p in pysb_model.parameters]
for x in petab_problem.condition_df.columns:
if x == CONDITION_NAME:
continue
if x not in model_parameters:
raise NotImplementedError(
"For PySB PEtab import, only model parameters, but no states "
"or compartments are allowed in the condition table."
f"Offending column: {x}"
)
constant_parameters = petab_import.get_fixed_parameters(
petab_problem.sbml_model, petab_problem.condition_df)
if observable_table is None:
observables = None
sigmas = None
else:
observables = [expr.name for expr in pysb_model.expressions
if expr.name in observable_table.index]
sigmas = {obs_id: f"{obs_id}_sigma" for obs_id in observables}
from amici.pysb_import import pysb2amici
pysb2amici(pysb_model, model_output_dir, verbose=True,
observables=observables,
sigmas=sigmas,
constant_parameters=constant_parameters,
**kwargs)
def __init__(self,
model,
tspan=None,
initials=None,
param_values=None,
verbose=False,
**kwargs):
if amici is None:
raise ImportError('AmiciSimulator requires a working installation'
'of amici. You can install amici via `pip '
'install amici`.')
super(AmiciSimulator, self).__init__(model,
tspan=tspan,
initials=initials,
param_values=param_values,
verbose=verbose,
**kwargs)
self.modeldir_is_temp = 'modeldir' not in kwargs
self.modeldir = kwargs.pop('modeldir',
mkdtemp(prefix=f'pysbamici_{model.name}_'))
force_recompile = kwargs.pop('force_recompile', False)
if kwargs:
raise ValueError('Unknown keyword argument(s): {}'.format(
', '.join(kwargs.keys())))
# Generate the equations for the model
if force_recompile or not os.path.exists(
os.path.join(self.modeldir, model.name, '__init__.py')):
if not force_recompile and not self.modeldir_is_temp and \
os.path.exists(os.path.join(self.modeldir)):
raise RuntimeError('Model directory already exists. Stopping '
'to prevent data loss. To ignore this '
'warning, pass `force_recompile=True`')
pysb2amici(model,
self.modeldir,
verbose=False,
observables=[],
constant_parameters=[],
compute_conservation_laws=True)
mode = 'compilation'
help = 'file an issue at https://github.com/ICB-DCM/AMICI/issues.'
else:
pysb.bng.generate_equations(model)
mode = 'loading'
help = 'try recompiling the model by passing ' \
'`force_recompile=True`.'
# Load the generated model package
sys.path.insert(0, self.modeldir)
try:
modelModulePYSB = importlib.import_module(model.name)
except Exception as e:
raise RuntimeError(f'Model {mode} failed. Please {help}')
self._model = model
self.amici_model = modelModulePYSB.getModel()
self.amici_solver = self.amici_model.getSolver()
self.amici_model.setTimepoints(tspan if tspan is not None else [])
'sim': sim
}).timeit(number=N_REPEATS) / N_REPEATS
simulation_times[example]['pysb'] = time_pysb
print(f'PySB average simulation time {example}: {time_pysb}')
# amici part
outdir = pysb_model.name
if pysb_model.name in ['move_connected_amici']:
compute_conservation_laws = False
else:
compute_conservation_laws = True
pysb2amici(pysb_model,
outdir,
compute_conservation_laws=compute_conservation_laws,
observables=list(pysb_model.observables.keys()))
amici_model_module = amici.import_model_module(
pysb_model.name, outdir)
model_pysb = amici_model_module.getModel()
model_pysb.setTimepoints(tspan)
solver = model_pysb.getSolver()
solver.setMaxSteps(int(1e6))
solver.setAbsoluteTolerance(atol)
solver.setRelativeTolerance(rtol)
time_amici = timeit.Timer(
'rdata = amici.runAmiciSimulation(model, solver)',
