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 _can_import_model(model_name: str, model_output_dir: str) -> bool:
"""
Check whether a module of that name can already be imported.
"""
# try to import (in particular checks version)
try:
with amici.add_path(model_output_dir):
model_module = importlib.import_module(model_name)
except ModuleNotFoundError:
return False
# no need to (re-)compile
return hasattr(model_module, "getModel")
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)
from pysb.simulator import ScipyOdeSimulator
sys.path.insert(0, os.path.join('..', 'tests'))
from test_pysb import pysb_models
simulation_times = dict()
N_REPEATS = 100
atol = 1e-8
rtol = 1e-8
for example in pysb_models:
simulation_times[example] = dict()
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')):
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)
