def test_glpk_solver_pickle(self):
self.solver = GlpkSolver()
self.solver.build_problem(self.model)
solver_from_pickle = pickle.loads(pickle.dumps(self.solver))
self.assertEqual(FBA(self.model, solver=self.solver).status,
FBA(self.model, solver=solver_from_pickle).status)
def test_glpk_lazy_loading(self):
self.solver_one = GlpkSolver()
self.solver_one.build_problem(self.model)
sol_one = FBA(self.model, solver=self.solver_one)
self.solver_two = GlpkSolverLazy()
self.solver_two.build_problem(self.model)
sol_two = FBA(self.model, solver=self.solver_two)
self.assertAlmostEqual(sol_one.fobj, sol_two.fobj, places=5)
def test_glpk_against_gurobi(self):
self.solver_one = GurobiSolver()
self.solver_one.build_problem(self.model)
sol_one = FBA(self.model, solver=self.solver_one)
self.solver_two = GlpkSolver()
self.solver_two.build_problem(self.model)
sol_two = FBA(self.model, solver=self.solver_two)
self.assertAlmostEqual(sol_one.fobj, sol_two.fobj, places=5)
class SolverPickleTest(unittest.TestCase):
"""docstring for SolverPickleTest"""
def setUp(self):
self.model = load_sbml_model(SMALL_TEST_MODEL, kind=CONSTRAINT_BASED)
fix_bigg_model(self.model)
def test_gurobi_solver_pickle(self):
self.solver = GurobiSolver()
self.solver.build_problem(self.model)
solver_from_pickle = pickle.loads(pickle.dumps(self.solver))
FBA(self.model, solver=self.solver)
self.assertEqual(FBA(self.model, solver=self.solver).status,
FBA(self.model, solver=solver_from_pickle).status)
def test_glpk_solver_pickle(self):
self.solver = GlpkSolver()
self.solver.build_problem(self.model)
solver_from_pickle = pickle.loads(pickle.dumps(self.solver))
self.assertEqual(FBA(self.model, solver=self.solver).status,
FBA(self.model, solver=solver_from_pickle).status)
def test_remove_constraint(self):
""" This tests works only for the ecoli core model.
"""
constr_id = "M_glu_L_c"
self.solver_one = GlpkSolverLazy()
self.solver_one.build_problem(self.model)
self.solver_one.remove_constraint(constr_id)
sol_one = FBA(self.model, solver=self.solver_one)
self.solver_two = GlpkSolver()
self.solver_two.build_problem(self.model)
nRows_before = glp_get_num_rows(self.solver_two.problem)
self.solver_two.remove_constraint(constr_id)
nRows_after = glp_get_num_rows(self.solver_two.problem)
sol_two = FBA(self.model, solver=self.solver_two)
self.assertEqual(nRows_before, nRows_after + 1)
self.assertAlmostEqual(sol_one.fobj, sol_two.fobj, places=5)
def test_remove_variable(self):
""" This tests works only for the ecoli core model.
"""
var_id = "R_SUCOAS"
self.solver_one = GlpkSolverLazy()
self.solver_one.build_problem(self.model)
self.solver_one.remove_variable(var_id)
sol_one = FBA(self.model, solver=self.solver_one)
self.solver_two = GlpkSolver()
self.solver_two.build_problem(self.model)
nCols_before = glp_get_num_cols(self.solver_two.problem)
self.solver_two.remove_variable(var_id)
nCols_after = glp_get_num_cols(self.solver_two.problem)
sol_two = FBA(self.model, solver=self.solver_two)
self.assertEqual(nCols_before, nCols_after + 1)
self.assertAlmostEqual(sol_one.fobj, sol_two.fobj, places=5)
class SolverGLPKTest(unittest.TestCase):
def setUp(self):
self.model = load_sbml_model(SMALL_TEST_MODEL, kind=CONSTRAINT_BASED)
fix_bigg_model(self.model)
def test_glpk_alone(self):
result = solve_lp_prob_glpk()
self.assertEqual(result[0], 1.25)
self.assertEqual(result[1], 45)
self.assertEqual(result[2], 6.25)
def test_glpk_against_gurobi(self):
self.solver_one = GurobiSolver()
self.solver_one.build_problem(self.model)
sol_one = FBA(self.model, solver=self.solver_one)
self.solver_two = GlpkSolver()
self.solver_two.build_problem(self.model)
sol_two = FBA(self.model, solver=self.solver_two)
self.assertAlmostEqual(sol_one.fobj, sol_two.fobj, places=5)
def test_glpk_milp_alone(self):
# binary variables only
result = solve_milp_bin_prob_glpk()
self.assertEqual(result[0], -14)
self.assertEqual(result[1], 1)
self.assertEqual(result[2], 1)
self.assertEqual(result[3], 0)
self.assertEqual(result[4], 0)
def test_glpk_lazy_loading(self):
self.solver_one = GlpkSolver()
self.solver_one.build_problem(self.model)
sol_one = FBA(self.model, solver=self.solver_one)
self.solver_two = GlpkSolverLazy()
self.solver_two.build_problem(self.model)
sol_two = FBA(self.model, solver=self.solver_two)
self.assertAlmostEqual(sol_one.fobj, sol_two.fobj, places=5)
def test_remove_constraint(self):
""" This tests works only for the ecoli core model.
"""
constr_id = "M_glu_L_c"
self.solver_one = GlpkSolverLazy()
self.solver_one.build_problem(self.model)
self.solver_one.remove_constraint(constr_id)
sol_one = FBA(self.model, solver=self.solver_one)
self.solver_two = GlpkSolver()
self.solver_two.build_problem(self.model)
nRows_before = glp_get_num_rows(self.solver_two.problem)
self.solver_two.remove_constraint(constr_id)
nRows_after = glp_get_num_rows(self.solver_two.problem)
sol_two = FBA(self.model, solver=self.solver_two)
self.assertEqual(nRows_before, nRows_after + 1)
self.assertAlmostEqual(sol_one.fobj, sol_two.fobj, places=5)
def test_remove_variable(self):
""" This tests works only for the ecoli core model.
"""
var_id = "R_SUCOAS"
self.solver_one = GlpkSolverLazy()
self.solver_one.build_problem(self.model)
self.solver_one.remove_variable(var_id)
sol_one = FBA(self.model, solver=self.solver_one)
self.solver_two = GlpkSolver()
self.solver_two.build_problem(self.model)
nCols_before = glp_get_num_cols(self.solver_two.problem)
self.solver_two.remove_variable(var_id)
nCols_after = glp_get_num_cols(self.solver_two.problem)
sol_two = FBA(self.model, solver=self.solver_two)
self.assertEqual(nCols_before, nCols_after + 1)
self.assertAlmostEqual(sol_one.fobj, sol_two.fobj, places=5)