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elif library == 'pyswarm':
optimizer = pypesto.PyswarmOptimizer(options=options)
else:
raise ValueError("This code should not be reached")
optimizer.temp_file = os.path.join('test', 'tmp_{index}.csv')
dim = len(objective.x_ids)
lb = -2 * np.ones((1, dim))
ub = 2 * np.ones((1, dim))
pars = objective.amici_model.getParameters()
problem = pypesto.Problem(objective, lb, ub,
x_fixed_indices=fixed_pars,
x_fixed_vals=[pars[idx] for idx in fixed_pars])
optimize_options = pypesto.OptimizeOptions(
allow_failed_starts=False,
startpoint_resample=True,
)
pypesto.minimize(problem, optimizer, n_starts, options=optimize_options)
def test_error_leastsquares_with_ssigma():
petab_problem = petab.Problem.from_yaml(
folder_base + "Zheng_PNAS2012/Zheng_PNAS2012.yaml")
petab_problem.model_name = "Zheng_PNAS2012"
importer = pypesto.PetabImporter(petab_problem)
obj = importer.create_objective()
problem = importer.create_problem(obj)
optimizer = pypesto.ScipyOptimizer('ls_trf', options={'max_nfev': 50})
with pytest.raises(RuntimeError):
pypesto.minimize(
problem=problem, optimizer=optimizer, n_starts=1,
options=pypesto.OptimizeOptions(allow_failed_starts=False)
)
if library == 'scipy':
optimizer = pypesto.ScipyOptimizer(method=solver,
options=options)
elif library == 'ipopt':
optimizer = pypesto.IpoptOptimizer()
elif library == 'dlib':
optimizer = pypesto.DlibOptimizer(method=solver,
options=options)
elif library == 'pyswarm':
optimizer = pypesto.PyswarmOptimizer(options=options)
lb = 0 * np.ones((1, 2))
ub = 1 * np.ones((1, 2))
problem = pypesto.Problem(objective, lb, ub)
optimize_options = pypesto.OptimizeOptions(
allow_failed_starts=allow_failed_starts)
result = pypesto.minimize(
problem=problem,
optimizer=optimizer,
n_starts=1,
startpoint_method=pypesto.startpoint.uniform,
options=optimize_options
)
assert isinstance(result.optimize_result.list[0]['fval'], float)
def check_history(self):
kwargs = {
'objective': self.obj,
'ub': self.ub,
'lb': self.lb,
}
if self.fix_pars:
kwargs = {**kwargs, **{
'x_fixed_indices': self.x_fixed_indices,
'x_fixed_vals': self.x_fixed_indices
}}
self.problem = pypesto.Problem(**kwargs)
optimize_options = pypesto.OptimizeOptions(
allow_failed_starts=False
)
self.history_options.trace_save_iter = 1
for storage_file in ['tmp/traces/conversion_example_{id}.csv', None]:
self.history_options.storage_file = storage_file
result = pypesto.minimize(
problem=self.problem,
optimizer=self.optimizer,
n_starts=1,
startpoint_method=pypesto.startpoint.uniform,
options=optimize_options,
history_options=self.history_options
)