def test_bounds():
"""Test changing bounds."""
config = Configuration()
config.bounds = 100.0, 10000.0
assert config.bounds == (100.0, 10000.0)
# Restore default values.
config.bounds = -1000.0, 1000.0
def test_toy_model_tolerance_with_different_default():
"""Verify that different default tolerance is respected by Model."""
config = Configuration()
config.tolerance = 1e-05
toy_model = Model(name="toy model")
assert toy_model.tolerance == 1e-05
def test_default_tolerance(model):
"""Verify the default solver tolerance."""
config = Configuration()
config.solver = "glpk"
assert config.tolerance == 1e-07
# Test the consistency between cobra.core.Configuration.tolerance and
# cobra.core.Model.tolerance
assert config.tolerance == model.tolerance
def test_solver():
"""Test assignment of different solvers."""
config = Configuration()
config.solver = "glpk"
assert interface_to_str(config.solver) == "glpk"
config.solver = "glpk_exact"
assert interface_to_str(config.solver) == "glpk_exact"
# Restore default solver.
config.solver = "glpk"
def test_default_bounds():
"""Verify the default bounds."""
config = Configuration()
assert config.bounds == (-1000.0, 1000.0)
import libsbml
except ImportError:
libsbml = None
else:
from cobra.io.sbml import create_cobra_model_from_sbml_file as read_sbml2
from cobra.io.sbml import write_cobra_model_to_sbml_file as write_sbml2
try:
from optlang.symbolics import Basic
except ImportError:
class Basic:
pass
CONFIGURATION = Configuration()
# deal with namespaces
namespaces = {
"fbc": "http://www.sbml.org/sbml/level3/version1/fbc/version2",
"sbml": "http://www.sbml.org/sbml/level3/version1/core",
"rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"bqbiol": "http://biomodels.net/biology-qualifiers/"
}
for key in namespaces:
register_namespace(key, namespaces[key])
def ns(query):
"""replace prefixes with namespace"""
for prefix, uri in iteritems(namespaces):
from warnings import warn
from numpy import zeros
from optlang.symbolics import Zero
from pandas import DataFrame
from cobra.core import Configuration, get_solution
from cobra.flux_analysis.deletion import single_gene_deletion, single_reaction_deletion
from cobra.flux_analysis.helpers import normalize_cutoff
from cobra.flux_analysis.loopless import loopless_fva_iter
from cobra.flux_analysis.parsimonious import add_pfba
from cobra.util import ProcessPool
from cobra.util import solver as sutil
logger = logging.getLogger(__name__)
configuration = Configuration()
def _init_worker(model, loopless, sense):
"""Initialize a global model object for multiprocessing."""
global _model
global _loopless
_model = model
_model.solver.objective.direction = sense
_loopless = loopless
def _fva_step(reaction_id):
global _model
global _loopless
rxn = _model.reactions.get_by_id(reaction_id)
"""Test functions of cobra.core.reaction ."""
import warnings
from typing import Iterable
import numpy as np
import pytest
from cobra.core import Configuration, Metabolite, Model, Reaction
config = Configuration()
stable_optlang = ["glpk", "cplex", "gurobi"]
def test_gpr() -> None:
"""Test GPR evaluation."""
model = Model()
reaction = Reaction("test")
# Set GPR to a reaction not in a model
reaction.gene_reaction_rule = "(g1 or g2) and g3"
assert reaction.gene_reaction_rule == "(g1 or g2) and g3"
assert len(reaction.genes) == 3
# Adding reaction with a GPR propagates to the model
model.add_reactions([reaction])
assert len(model.genes) == 3
# Ensure the gene objects are the same in the model and reaction
reaction_gene = list(reaction.genes)[0]
model_gene = model.genes.get_by_id(reaction_gene.id)