def solver(self, value):
not_valid_interface = SolverNotFound(
'%s is not a valid solver interface. Pick from %s, or specify an '
'optlang interface (e.g. optlang.glpk_interface).' % (
value, list(solvers.keys())))
if isinstance(value, six.string_types):
try:
interface = solvers[interface_to_str(value)]
except KeyError:
raise not_valid_interface
elif isinstance(value, types.ModuleType) and hasattr(value, 'Model'):
interface = value
elif isinstance(value, optlang.interface.Model):
interface = value.interface
else:
raise not_valid_interface
# Do nothing if the solver did not change
if self.problem == interface:
return
self._solver = interface.Model.clone(self._solver)
def __init__(self, appdata: CnaData):
QDialog.__init__(self)
self.setWindowTitle("Configure COBRApy")
self.appdata = appdata
self.layout = QVBoxLayout()
# allow MILP solvers only?
avail_solvers = list(set(solvers.keys()) - {'scipy'}) # SCIPY currently not even usable for FBA
h2 = QHBoxLayout()
label = QLabel("Default solver:\n(set when loading a model)")
h2.addWidget(label)
self.default_solver = QComboBox()
self.default_solver.addItems(avail_solvers)
self.default_solver.setCurrentIndex(avail_solvers.index(interface_to_str(cobra.Configuration().solver)))
h2.addWidget(self.default_solver)
self.layout.addItem(h2)
h9 = QHBoxLayout()
label = QLabel("Solver for current model:")
h9.addWidget(label)
self.current_solver = QComboBox()
self.current_solver.addItems(avail_solvers)
self.current_solver.setCurrentIndex(avail_solvers.index(interface_to_str(appdata.project.cobra_py_model.problem)))
h9.addWidget(self.current_solver)
self.layout.addItem(h9)
h7 = QHBoxLayout()
label = QLabel(
"Number of processes for multiprocessing (e.g. FVA):")
h7.addWidget(label)
self.num_processes = QLineEdit()
self.num_processes.setFixedWidth(100)
self.num_processes.setText(str(cobra.Configuration().processes))
validator = QIntValidator(1, cpu_count(), self)
self.num_processes.setValidator(validator)
h7.addWidget(self.num_processes)
self.layout.addItem(h7)
h8 = QHBoxLayout()
label = QLabel(
"Default tolerance:\n(set when loading a model)")
h8.addWidget(label)
self.default_tolerance = QLineEdit()
self.default_tolerance.setFixedWidth(100)
self.default_tolerance.setText(str(cobra.Configuration().tolerance))
validator = QDoubleValidator(self)
validator.setBottom(1e-9) # probably a reasonable consensus value
self.default_tolerance.setValidator(validator)
h8.addWidget(self.default_tolerance)
self.layout.addItem(h8)
h10 = QHBoxLayout()
label = QLabel(
"Tolerance for current model:")
h10.addWidget(label)
self.current_tolerance = QLineEdit()
self.current_tolerance.setFixedWidth(100)
self.current_tolerance.setText(str(self.appdata.project.cobra_py_model.tolerance))
validator = QDoubleValidator(self)
validator.setBottom(0)
self.current_tolerance.setValidator(validator)
h10.addWidget(self.current_tolerance)
self.layout.addItem(h10)
l2 = QHBoxLayout()
self.button = QPushButton("Apply Changes")
self.cancel = QPushButton("Close")
l2.addWidget(self.button)
l2.addWidget(self.cancel)
self.layout.addItem(l2)
self.setLayout(self.layout)
self.cancel.clicked.connect(self.reject)
self.button.clicked.connect(self.apply)
"""Test optimization functions."""
from .fixtures import community
import cobra
from cobra.util.solver import solvers
import numpy as np
import pytest
from micom.solution import CommunitySolution
stable = ["glpk", "cplex"]
solvers = [s for s in solvers.keys() if s in stable]
def test_community_objective(community):
x = community.optimize()
y = community.optimize(fluxes=True)
assert isinstance(x, CommunitySolution)
assert np.allclose(x.growth_rate, 0.873922)
assert np.allclose(x.members.growth_rate.dropna().sum(), 4 * 0.873922)
assert isinstance(y, CommunitySolution)
assert y.fluxes.shape[0] == 5
def test_individual_objective(community):
growth_rates = community.optimize_all()
assert np.allclose(growth_rates, 4 * 0.873922)
