From 363d56043fe0eb3bb9dfde3bfd86341996424f59 Mon Sep 17 00:00:00 2001 From: KeShih Date: Sat, 6 Jul 2024 22:00:16 +0800 Subject: [PATCH 1/2] Add pyoptInterface_based_impl.py and integrate it --- dingo/MetabolicNetwork.py | 66 +- dingo/PolytopeSampler.py | 108 +- dingo/__init__.py | 33 +- .../redundant_facet_removal_experiment.py | 306 --- dingo/fba.py | 67 - dingo/fva.py | 117 - dingo/gurobi_based_implementations.py | 698 ------ dingo/inner_ball.py | 65 - dingo/parser.py | 4 +- dingo/pyoptInterface_based_impl.py | 499 +++++ dingo/volestipy.pyx | 69 +- poetry.lock | 1888 ++++++++++------- pyproject.toml | 1 + tests/fast_implementation_test.py | 75 - tests/fba.py | 10 +- tests/full_dimensional.py | 39 +- tests/max_ball.py | 9 +- tests/rounding.py | 7 +- tests/sampling.py | 6 + tests/sampling_no_multiphase.py | 6 + tests/scaling.py | 5 + 21 files changed, 1734 insertions(+), 2344 deletions(-) delete mode 100644 dingo/experimental_gurobi_functions/redundant_facet_removal_experiment.py delete mode 100644 dingo/fba.py delete mode 100644 dingo/fva.py delete mode 100644 dingo/gurobi_based_implementations.py delete mode 100644 dingo/inner_ball.py create mode 100644 dingo/pyoptInterface_based_impl.py delete mode 100644 tests/fast_implementation_test.py diff --git a/dingo/MetabolicNetwork.py b/dingo/MetabolicNetwork.py index 518f2f5b..8d0dcd6f 100644 --- a/dingo/MetabolicNetwork.py +++ b/dingo/MetabolicNetwork.py @@ -3,6 +3,7 @@ # Copyright (c) 2021 Apostolos Chalkis # Copyright (c) 2021 Vissarion Fisikopoulos +# Copyright (c) 2024 Ke Shi # Licensed under GNU LGPL.3, see LICENCE file @@ -11,15 +12,7 @@ from typing import Dict import cobra from dingo.loading_models import read_json_file, read_mat_file, read_sbml_file, parse_cobra_model -from dingo.fva import slow_fva -from dingo.fba import slow_fba - -try: - import gurobipy - from dingo.gurobi_based_implementations import fast_fba, fast_fva, fast_inner_ball -except ImportError as e: - pass - +from dingo.pyoptInterface_based_impl import fba,fva,inner_ball,remove_redundant_facets class MetabolicNetwork: def __init__(self, tuple_args): @@ -28,13 +21,7 @@ def __init__(self, tuple_args): self._parameters["opt_percentage"] = 100 self._parameters["distribution"] = "uniform" self._parameters["nullspace_method"] = "sparseQR" - - try: - import gurobipy - - self._parameters["fast_computations"] = True - except ImportError as e: - self._parameters["fast_computations"] = False + self._parameters["solver"] = None if len(tuple_args) != 10: raise Exception( @@ -107,30 +94,18 @@ def from_cobra_model(cls, arg): def fva(self): """A member function to apply the FVA method on the metabolic network.""" - if self._parameters["fast_computations"]: - return fast_fva( - self._lb, - self._ub, - self._S, - self._objective_function, - self._parameters["opt_percentage"], - ) - else: - return slow_fva( - self._lb, - self._ub, - self._S, - self._objective_function, - self._parameters["opt_percentage"], - ) + return fva( + self._lb, + self._ub, + self._S, + self._objective_function, + self._parameters["opt_percentage"], + self._parameters["solver"] + ) def fba(self): """A member function to apply the FBA method on the metabolic network.""" - - if self._parameters["fast_computations"]: - return fast_fba(self._lb, self._ub, self._S, self._objective_function) - else: - return slow_fba(self._lb, self._ub, self._S, self._objective_function) + return fba(self._lb, self._ub, self._S, self._objective_function, self._parameters["solver"]) @property def lb(self): @@ -286,20 +261,9 @@ def set_active_bound(reaction: str, reac_index: int, bound: float) -> None: set_active_bound( rxn_id, reac_index, min(0.0, -self._lb[reac_index] if is_export else self._ub[reac_index]) ) - - def set_fast_mode(self): - - try: - import gurobipy - - self._parameters["fast_computations"] = True - except ImportError as e: - print("You have to install gurobi to use the fast computations.") - self._parameters["fast_computations"] = False - - def set_slow_mode(self): - - self._parameters["fast_computations"] = False + + def set_solver(self, solver: str): + self._parameters["solver"] = solver def set_nullspace_method(self, value): diff --git a/dingo/PolytopeSampler.py b/dingo/PolytopeSampler.py index 54f30050..e6576382 100644 --- a/dingo/PolytopeSampler.py +++ b/dingo/PolytopeSampler.py @@ -2,6 +2,7 @@ # dingo is part of GeomScale project # Copyright (c) 2021 Apostolos Chalkis +# Copyright (c) 2024 Ke Shi # Licensed under GNU LGPL.3, see LICENCE file @@ -10,23 +11,13 @@ import warnings import math from dingo.MetabolicNetwork import MetabolicNetwork -from dingo.fva import slow_fva from dingo.utils import ( map_samples_to_steady_states, get_matrices_of_low_dim_polytope, get_matrices_of_full_dim_polytope, ) -try: - import gurobipy - from dingo.gurobi_based_implementations import ( - fast_fba, - fast_fva, - fast_inner_ball, - fast_remove_redundant_facets, - ) -except ImportError as e: - pass +from dingo.pyoptInterface_based_impl import fba,fva,inner_ball,remove_redundant_facets from volestipy import HPolytope @@ -53,14 +44,8 @@ def __init__(self, metabol_net): self._parameters["first_run_of_mmcs"] = True self._parameters["remove_redundant_facets"] = True - try: - import gurobipy - - self._parameters["fast_computations"] = True - self._parameters["tol"] = 1e-06 - except ImportError as e: - self._parameters["fast_computations"] = False - self._parameters["tol"] = 1e-03 + self._parameters["tol"] = 1e-06 + self._parameters["solver"] = None def get_polytope(self): """A member function to derive the corresponding full dimensional polytope @@ -82,24 +67,18 @@ def get_polytope(self): ) = self._metabolic_network.fba() if ( - self._parameters["fast_computations"] - and self._parameters["remove_redundant_facets"] + self._parameters["remove_redundant_facets"] ): - A, b, Aeq, beq = fast_remove_redundant_facets( + A, b, Aeq, beq = remove_redundant_facets( self._metabolic_network.lb, self._metabolic_network.ub, self._metabolic_network.S, self._metabolic_network.objective_function, self._parameters["opt_percentage"], + self._parameters["solver"], ) else: - if (not self._parameters["fast_computations"]) and self._parameters[ - "remove_redundant_facets" - ]: - warnings.warn( - "We continue without redundancy removal (slow mode is ON)" - ) ( min_fluxes, @@ -162,14 +141,9 @@ def generate_steady_states( P = HPolytope(self._A, self._b) - if self._parameters["fast_computations"]: - self._A, self._b, Tr, Tr_shift, samples = P.fast_mmcs( - ess, psrf, parallel_mmcs, num_threads - ) - else: - self._A, self._b, Tr, Tr_shift, samples = P.slow_mmcs( - ess, psrf, parallel_mmcs, num_threads - ) + self._A, self._b, Tr, Tr_shift, samples = P.mmcs( + ess, psrf, parallel_mmcs, num_threads, self._parameters["solver"] + ) if self._parameters["first_run_of_mmcs"]: steady_states = map_samples_to_steady_states( @@ -207,7 +181,7 @@ def generate_steady_states_no_multiphase( else: bias_vector = bias_vector.astype('float64') - samples = P.generate_samples(method, n, burn_in, thinning, self._parameters["fast_computations"], variance, bias_vector) + samples = P.generate_samples(method, n, burn_in, thinning, variance, bias_vector, self._parameters["solver"]) samples_T = samples.T steady_states = map_samples_to_steady_states( @@ -218,7 +192,7 @@ def generate_steady_states_no_multiphase( @staticmethod def sample_from_polytope( - A, b, ess=1000, psrf=False, parallel_mmcs=False, num_threads=1 + A, b, ess=1000, psrf=False, parallel_mmcs=False, num_threads=1, solver=None ): """A static function to sample from a full dimensional polytope. @@ -233,22 +207,16 @@ def sample_from_polytope( P = HPolytope(A, b) - try: - import gurobipy + A, b, Tr, Tr_shift, samples = P.mmcs( + ess, psrf, parallel_mmcs, num_threads, solver + ) - A, b, Tr, Tr_shift, samples = P.fast_mmcs( - ess, psrf, parallel_mmcs, num_threads - ) - except ImportError as e: - A, b, Tr, Tr_shift, samples = P.slow_mmcs( - ess, psrf, parallel_mmcs, num_threads - ) return samples @staticmethod def sample_from_polytope_no_multiphase( - A, b, method = 'billiard_walk', n=1000, burn_in=0, thinning=1, variance=1.0, bias_vector=None + A, b, method = 'billiard_walk', n=1000, burn_in=0, thinning=1, variance=1.0, bias_vector=None, solver=None ): """A static function to sample from a full dimensional polytope with an MCMC method. @@ -267,25 +235,17 @@ def sample_from_polytope_no_multiphase( P = HPolytope(A, b) - try: - import gurobipy - samples = P.generate_samples(method, n, burn_in, thinning, True, variance, bias_vector) - except ImportError as e: - samples = P.generate_samples(method, n, burn_in, thinning, False, variance, bias_vector) + samples = P.generate_samples(method, n, burn_in, thinning, variance, bias_vector, solver) samples_T = samples.T return samples_T @staticmethod def round_polytope( - A, b, method = "john_position" + A, b, method = "john_position", solver = None ): P = HPolytope(A, b) - try: - import gurobipy - A, b, Tr, Tr_shift, round_value = P.rounding(method, True) - except ImportError as e: - A, b, Tr, Tr_shift, round_value = P.rounding(method, False) + A, b, Tr, Tr_shift, round_value = P.rounding(method, solver) return A, b, Tr, Tr_shift @@ -301,6 +261,7 @@ def sample_from_fva_output( psrf=False, parallel_mmcs=False, num_threads=1, + solver = None ): """A static function to sample steady states when the output of FVA is given. @@ -335,16 +296,9 @@ def sample_from_fva_output( P = HPolytope(A, b) - try: - import gurobipy - - A, b, Tr, Tr_shift, samples = P.fast_mmcs( - ess, psrf, parallel_mmcs, num_threads - ) - except ImportError as e: - A, b, Tr, Tr_shift, samples = P.slow_mmcs( - ess, psrf, parallel_mmcs, num_threads - ) + A, b, Tr, Tr_shift, samples = P.mmcs( + ess, psrf, parallel_mmcs, num_threads, solver + ) steady_states = map_samples_to_steady_states(samples, N, N_shift) @@ -381,20 +335,8 @@ def metabolic_network(self): def facet_redundancy_removal(self, value): self._parameters["remove_redundant_facets"] = value - if (not self._parameters["fast_computations"]) and value: - warnings.warn( - "Since you are in slow mode the redundancy removal step is skipped (dingo does not currently support this functionality in slow mode)" - ) - - def set_fast_mode(self): - - self._parameters["fast_computations"] = True - self._parameters["tol"] = 1e-06 - - def set_slow_mode(self): - - self._parameters["fast_computations"] = False - self._parameters["tol"] = 1e-03 + def set_solver(self, solver): + self._parameters["solver"] = solver def set_distribution(self, value): diff --git a/dingo/__init__.py b/dingo/__init__.py index 49f7d043..b1395666 100644 --- a/dingo/__init__.py +++ b/dingo/__init__.py @@ -9,10 +9,7 @@ import sys import os import pickle -from dingo.fva import slow_fva -from dingo.fba import slow_fba from dingo.loading_models import read_json_file -from dingo.inner_ball import slow_inner_ball from dingo.nullspace import nullspace_dense, nullspace_sparse from dingo.scaling import gmscale from dingo.utils import ( @@ -30,11 +27,7 @@ from dingo.MetabolicNetwork import MetabolicNetwork from dingo.PolytopeSampler import PolytopeSampler -try: - import gurobipy - from dingo.gurobi_based_implementations import fast_fba, fast_fva, fast_inner_ball -except ImportError as e: - pass +from dingo.pyoptInterface_based_impl import fba, fva, inner_ball, remove_redundant_facets, set_default_solver from volestipy import HPolytope @@ -82,6 +75,8 @@ def dingo_main(): # Move to the output directory os.chdir(output_path_dir) + + set_default_solver(args.solver) if args.model_name is None: if args.metabolic_network is not None: @@ -130,15 +125,6 @@ def dingo_main(): elif args.fva: - if args.solver == "gurobi": - try: - import gurobipy - except ImportError as error: - raise error.with_traceback(sys.exc_info()[2]) - - if args.solver != "gurobi" and args.solver != "scipy": - raise Exception("An unknown solver requested.") - if args.metabolic_network[-4:] == "json": model = MetabolicNetwork.fom_json(args.metabolic_network) elif args.metabolic_network[-3:] == "mat": @@ -146,6 +132,8 @@ def dingo_main(): else: raise Exception("An unknown format file given.") + model.set_solver(args.solver) + result_obj = model.fva() with open("dingo_fva_" + name + ".pckl", "wb") as dingo_fva_file: @@ -153,21 +141,14 @@ def dingo_main(): elif args.fba: - if args.solver == "gurobi": - try: - import gurobipy - except ImportError as error: - raise error.with_traceback(sys.exc_info()[2]) - - if args.solver != "gurobi" and args.solver != "scipy": - raise Exception("An unknown solver requested.") - if args.metabolic_network[-4:] == "json": model = MetabolicNetwork.fom_json(args.metabolic_network) elif args.metabolic_network[-3:] == "mat": model = MetabolicNetwork.fom_mat(args.metabolic_network) else: raise Exception("An unknown format file given.") + + model.set_solver(args.solver) result_obj = model.fba() diff --git a/dingo/experimental_gurobi_functions/redundant_facet_removal_experiment.py b/dingo/experimental_gurobi_functions/redundant_facet_removal_experiment.py deleted file mode 100644 index 6c26c349..00000000 --- a/dingo/experimental_gurobi_functions/redundant_facet_removal_experiment.py +++ /dev/null @@ -1,306 +0,0 @@ -# dingo : a python library for metabolic networks sampling and analysis -# dingo is part of GeomScale project - -# Copyright (c) 2021 Apostolos Chalkis - -# Licensed under GNU LGPL.3, see LICENCE file - -import sys -import numpy as np -import scipy.sparse as sp -import gurobipy as gp -from gurobipy import GRB -import math - -def update_model_constraints_and_bounds(model, Aeq_sparse=None, beq=None, A_sparse=None, b=None, - new_lower_bounds=None, new_upper_bounds=None): - if Aeq_sparse is not None and beq is not None: - # Remove the old equality constraints - model.remove("c") - - # Add new equality constraints - model.addMConstr(sp.csr_matrix(Aeq_sparse), model.getVars(), "=", np.array(beq), name="c") - - if A_sparse is not None and b is not None: - # Remove the old inequality constraints - model.remove("d") - - # Add new inequality constraints - model.addMConstr(sp.csr_matrix(A_sparse), model.getVars(), "<", np.array(b), name="d") - - if new_lower_bounds is not None or new_upper_bounds is not None: - # Retrieve the variable objects - x_vars = model.getVars() - - # Update variable bounds if specified - if new_lower_bounds is not None: - for i, x_var in enumerate(x_vars): - x_var.lb = new_lower_bounds[i] - - if new_upper_bounds is not None: - for i, x_var in enumerate(x_vars): - x_var.ub = new_upper_bounds[i] - - # Update the model to apply the changes - model.update() - -# Usage example: -# Assuming you have a Gurobi model 'model' and new constraint matrices/vectors and bounds -# Call the function to update the model -# update_model_constraints_and_bounds(model, Aeq_sparse_new, beq_new, A_sparse_new, b_new, new_lower_bounds, new_upper_bounds) - - -def solve_lp_with_different_objectives(model, new_objective_coeffs): - """ - Solve a linear program with a different objective function. - - Parameters: - model (gurobipy.Model): The Gurobi model with the original constraints. - new_objective_coeffs (list or numpy.ndarray): List or array of new objective coefficients for the variables. - - Returns: - gurobipy.Model: The updated Gurobi model with the new objective function. - """ - # Clear the existing objective function - model.setObjective(0, clear=True) - - # TODO: Optimization opportunity - You could pass a numpy array here (instead of a list of coefficients) - # and update the objective in one call without a for loop. - # For example, you can use: - # model.setObjective(new_objective_coeffs, GRB.MINIMIZE) - - # Update the objective function with the new coefficients - for i, var in enumerate(model.getVars()): - var.setAttr(GRB.Attr.Obj, new_objective_coeffs[i]) - - # Optimize the updated model - model.optimize() - - return model - - -def fast_remove_redundant_facets(lb, ub, S, c, opt_percentage=100): - if lb.size != S.shape[1] or ub.size != S.shape[1]: - raise Exception( - "The number of reactions must be equal to the number of given flux bounds." - ) - - redundant_facet_tol = 1e-07 - tol = 1e-06 - - m = S.shape[0] - n = S.shape[1] - beq = np.zeros(m) - Aeq_res = S - - A = np.zeros((2 * n, n), dtype="float") - A[0:n] = np.eye(n) - A[n:] -= np.eye(n, n, dtype="float") - - b = np.concatenate((ub, -lb), axis=0) - b = np.asarray(b, dtype="float") - b = np.ascontiguousarray(b, dtype="float") - - max_biomass_flux_vector, max_biomass_objective = fast_fba(lb, ub, S, c) - val = -np.floor(max_biomass_objective / tol) * tol * opt_percentage / 100 - - b_res = [] - A_res = np.empty((0, n), float) - beq_res = np.array(beq) - - try: - with gp.Env(empty=True) as env: - env.setParam("OutputFlag", 0) - env.start() - - with gp.Model(env=env) as model: - x = model.addMVar( - shape=n, - vtype=GRB.CONTINUOUS, - name="x", - lb=lb, - ub=ub, - ) - - Aeq_sparse = sp.csr_matrix(S) - A_sparse = sp.csr_matrix(np.array(-c)) - b_sparse = np.array(val) - - b = np.array(b) - beq = np.array(beq) - - model.addMConstr(Aeq_sparse, x, "=", beq, name="c") - model.update() - model.addMConstr(A_sparse, x, "<", [val], name="d") - model.update() - - model_iter = model.copy() - - indices_iter = range(n) - removed = 1 - offset = 1 - facet_left_removed = np.zeros((1, n), dtype=bool) - facet_right_removed = np.zeros((1, n), dtype=bool) - - while removed > 0 or offset > 0: - removed = 0 - offset = 0 - indices = indices_iter - indices_iter = [] - - Aeq_sparse = sp.csr_matrix(Aeq_res) - beq = np.array(beq_res) - - b_res = [] - A_res = np.empty((0, n), float) - - update_model_constraints_and_bounds(model_iter, Aeq_sparse, beq, A_sparse, [val], lb, ub) - - - for i in indices: - objective_function = A[i] - - redundant_facet_right = True - redundant_facet_left = True - - objective_function_max = np.asarray( - [-x for x in objective_function] - ) - - model_iter = solve_lp_with_different_objectives( - model_iter.copy(), objective_function_max - ) - - - status = model_iter.status - if status == GRB.OPTIMAL: - max_objective = -model_iter.objVal - else: - max_objective = ub[i] - - if not facet_right_removed[0, i]: - ub_iter = ub.copy() - ub_iter[i] = ub_iter[i] + 1 - - # Call solve_lp_with_different_objectives to solve LP - model_iter = solve_lp_with_different_objectives( - model_iter.copy(), objective_function - ) - - status = model_iter.status - if status == GRB.OPTIMAL: - max_objective2 = -model_iter.objVal - if ( - np.abs(max_objective2 - max_objective) - > redundant_facet_tol - ): - redundant_facet_right = False - else: - removed += 1 - facet_right_removed[0, i] = True - - model_iter.reset() - x = model_iter.getVars() - for j in range(n): - x[j].LB = lb[j] - x[j].UB = ub[j] - x[j].obj = objective_function[j] - - model_iter.optimize() - - status = model_iter.status - if status == GRB.OPTIMAL: - min_objective = model_iter.objVal - else: - min_objective = lb[i] - - if not facet_left_removed[0, i]: - lb_iter = lb.copy() - lb_iter[i] = lb_iter[i] - 1 - - # Call solve_lp_with_different_objectives to solve LP - model_iter = solve_lp_with_different_objectives( - model_iter.copy(), objective_function - ) - - - status = model_iter.status - if status == GRB.OPTIMAL: - min_objective2 = model_iter.objVal - if ( - np.abs(min_objective2 - min_objective) - > redundant_facet_tol - ): - redundant_facet_left = False - else: - removed += 1 - facet_left_removed[0, i] = True - - if (not redundant_facet_left) or (not redundant_facet_right): - width = abs(max_objective - min_objective) - - if width < redundant_facet_tol: - offset += 1 - Aeq_res = np.vstack( - ( - Aeq_res, - A[ - i, - ], - ) - ) - beq_res = np.append( - beq_res, min(max_objective, min_objective) - ) - ub[i] = sys.float_info.max - lb[i] = -sys.float_info.max - else: - indices_iter.append(i) - - if not redundant_facet_left: - A_res = np.append( - A_res, - np.array( - [ - A[ - n + i, - ] - ] - ), - axis=0, - ) - b_res.append(b[n + i]) - else: - lb[i] = -sys.float_info.max - - if not redundant_facet_right: - A_res = np.append( - A_res, - np.array( - [ - A[ - i, - ] - ] - ), - axis=0, - ) - b_res.append(b[i]) - else: - ub[i] = sys.float_info.max - else: - ub[i] = sys.float_info.max - lb[i] = -sys.float_info.max - - b_res = np.asarray(b_res) - A_res = np.asarray(A_res, dtype="float") - A_res = np.ascontiguousarray(A_res, dtype="float") - - return A_res, b_res, Aeq_res, beq_res - - except gp.GurobiError as e: - print("Error code " + str(e.errno) + ": " + str(e)) - except AttributeError: - print("Gurobi solver failed.") - - diff --git a/dingo/fba.py b/dingo/fba.py deleted file mode 100644 index cba061f0..00000000 --- a/dingo/fba.py +++ /dev/null @@ -1,67 +0,0 @@ -# dingo : a python library for metabolic networks sampling and analysis -# dingo is part of GeomScale project - -# Copyright (c) 2021 Apostolos Chalkis - -# Licensed under GNU LGPL.3, see LICENCE file - -import numpy as np -from scipy.optimize import linprog -import scipy.sparse as sp - - -def slow_fba(lb, ub, S, c): - """A Python function to perform fba using scipy.optimize LP solver `linprog` - Returns an optimal solution and its value for the following linear program: - max c*v, subject to, - Sv = 0, lb <= v <= ub - - Keyword arguments: - lb -- lower bounds for the fluxes, i.e., a n-dimensional vector - ub -- upper bounds for the fluxes, i.e., a n-dimensional vector - S -- the mxn stoichiometric matrix, s.t. Sv = 0 - c -- the linear objective function, i.e., a n-dimensional vector - """ - - if lb.size != S.shape[1] or ub.size != S.shape[1]: - raise Exception( - "The number of reactions must be equal to the number of given flux bounds." - ) - if c.size != S.shape[1]: - raise Exception( - "The length of the lineart objective function must be equal to the number of reactions." - ) - - m = S.shape[0] - n = S.shape[1] - optimum_value = 0 - optimum_sol = np.zeros(n) - - A = np.zeros((2 * n, n), dtype="float") - A[0:n] = np.eye(n) - A[n:] -= np.eye(n, n, dtype="float") - - b = np.concatenate((ub, -lb), axis=0) - b = np.asarray(b, dtype="float") - b = np.ascontiguousarray(b, dtype="float") - - beq = np.zeros(m) - - try: - - objective_function = np.asarray(c) - objective_function = np.asarray([-x for x in c]) - - res = linprog( - objective_function, A_ub=A, b_ub=b, A_eq=S, b_eq=beq, bounds=(None, None) - ) - - # If optimized - if res.success: - optimum_value = -res.fun - optimum_sol = np.asarray(res.x) - - return optimum_sol, optimum_value - - except AttributeError: - print("scipy.optimize.linprog failed.") diff --git a/dingo/fva.py b/dingo/fva.py deleted file mode 100644 index 0fb73dd5..00000000 --- a/dingo/fva.py +++ /dev/null @@ -1,117 +0,0 @@ -# dingo : a python library for metabolic networks sampling and analysis -# dingo is part of GeomScale project - -# Copyright (c) 2021 Apostolos Chalkis - -# Licensed under GNU LGPL.3, see LICENCE file - -import numpy as np -from scipy.optimize import linprog -from .fba import slow_fba -import math - - -def slow_fva(lb, ub, S, c, opt_percentage=100): - """A Python function to perform fva using scipy.optimize LP solver `linprog` - Returns the value of the optimal solution for all the following linear programs: - min/max v_i, for all coordinates i=1,...,n, subject to, - Sv = 0, lb <= v <= ub - - Keyword arguments: - lb -- lower bounds for the fluxes, i.e., a n-dimensional vector - ub -- upper bounds for the fluxes, i.e., a n-dimensional vector - S -- the mxn stoichiometric matrix, s.t. Sv = 0 - c -- the objective function to maximize - opt_percentage -- consider solutions that give you at least a certain - percentage of the optimal solution (default is to consider - optimal solutions only) - """ - - if lb.size != S.shape[1] or ub.size != S.shape[1]: - raise Exception( - "The number of reactions must be equal to the number of given flux bounds." - ) - - # declare the tolerance that linprog works properly (we found it experimentally) - tol = 1e-03 - - m = S.shape[0] - n = S.shape[1] - - A = np.zeros((2 * n, n), dtype="float") - A[0:n] = np.eye(n) - A[n:] -= np.eye(n, n, dtype="float") - - b = np.concatenate((ub, -lb), axis=0) - b = np.asarray(b, dtype="float") - b = np.ascontiguousarray(b, dtype="float") - beq = np.zeros(m) - - # call fba to obtain an optimal solution - max_biomass_flux_vector, max_biomass_objective = slow_fba(lb, ub, S, c) - - # add an additional constraint to impose solutions with at least `opt_percentage` of the optimal solution - A = np.vstack((A, -c)) - - b = np.append( - b, -(opt_percentage / 100) * tol * math.floor(max_biomass_objective / tol) - ) - - min_fluxes = [] - max_fluxes = [] - - try: - - for i in range(n): - - # Set the ith row of the A matrix as the objective function - objective_function = A[ - i, - ] - res = linprog( - objective_function, - A_ub=A, - b_ub=b, - A_eq=S, - b_eq=beq, - bounds=(None, None), - ) - - # If optimized - if res.success: - min_objective = res.fun - min_fluxes.append(min_objective) - else: - min_fluxes.append(lb[i]) - - # Set the minus of the ith row of the A matrix as the objective function - objective_function = np.asarray([-x for x in objective_function]) - res = linprog( - objective_function, - A_ub=A, - b_ub=b, - A_eq=S, - b_eq=beq, - bounds=(None, None), - ) - - # If optimized - if res.success: - max_objective = -res.fun - max_fluxes.append(max_objective) - else: - max_fluxes.append(ub[i]) - - # Make lists of fluxes numpy arrays - min_fluxes = np.asarray(min_fluxes) - max_fluxes = np.asarray(max_fluxes) - - return ( - min_fluxes, - max_fluxes, - max_biomass_flux_vector, - max_biomass_objective, - ) - - except AttributeError: - print("scipy.optimize.linprog failed.") diff --git a/dingo/gurobi_based_implementations.py b/dingo/gurobi_based_implementations.py deleted file mode 100644 index 42300128..00000000 --- a/dingo/gurobi_based_implementations.py +++ /dev/null @@ -1,698 +0,0 @@ -# dingo : a python library for metabolic networks sampling and analysis -# dingo is part of GeomScale project - -# Copyright (c) 2021 Apostolos Chalkis - -# Licensed under GNU LGPL.3, see LICENCE file - -import sys -import numpy as np -import scipy.sparse as sp -import gurobipy as gp -from gurobipy import GRB -import math - - -def fast_fba(lb, ub, S, c): - """A Python function to perform fba using gurobi LP solver - Returns an optimal solution and its value for the following linear program: - max c*v, subject to, - Sv = 0, lb <= v <= ub - - Keyword arguments: - lb -- lower bounds for the fluxes, i.e., a n-dimensional vector - ub -- upper bounds for the fluxes, i.e., a n-dimensional vector - S -- the mxn stoichiometric matrix, s.t. Sv = 0 - c -- the linear objective function, i.e., a n-dimensional vector - """ - - if lb.size != S.shape[1] or ub.size != S.shape[1]: - raise Exception( - "The number of reactions must be equal to the number of given flux bounds." - ) - if c.size != S.shape[1]: - raise Exception( - "The length of the lineart objective function must be equal to the number of reactions." - ) - tol = 1e-06 - - m = S.shape[0] - n = S.shape[1] - optimum_value = 0 - optimum_sol = [] - - beq = np.zeros(m) - - A = np.zeros((2 * n, n), dtype="float") - A[0:n] = np.eye(n) - A[n:] -= np.eye(n, n, dtype="float") - - b = np.concatenate((ub, -lb), axis=0) - b = np.asarray(b, dtype="float") - b = np.ascontiguousarray(b, dtype="float") - - try: - - # To avoid printint the output of the optimize() function of Gurobi, we need to set an environment like this - with gp.Env(empty=True) as env: - env.setParam("OutputFlag", 0) - env.start() - - with gp.Model(env=env) as model: - - # Create variables - x = model.addMVar( - shape=n, - vtype=GRB.CONTINUOUS, - name="x", - lb=-GRB.INFINITY, - ub=GRB.INFINITY, - ) - - # Make sparse Aeq - Aeq_sparse = sp.csr_matrix(S) - - # Make A sparse - A_sparse = sp.csr_matrix(A) - - # Set the b and beq vectors as numpy vectors - b = np.array(b) - beq = np.array(beq) - - # Add constraints - model.addMConstr(Aeq_sparse, x, "=", beq, name="c") - - # Update the model to include the constraints added - model.update() - - # Add constraints for the uneqalities of A - model.addMConstr(A_sparse, x, "<", b, name="d") - - # Update the model with the extra constraints and then print it - model.update() - - objective_function = np.asarray([-x for x in c]) - - # Set the objective function in the model - model.setMObjective( - None, objective_function, 0.0, None, None, x, GRB.MINIMIZE - ) - model.update() - - # Optimize model - model.optimize() - - # If optimized - status = model.status - if status == GRB.OPTIMAL: - optimum_value = -model.getObjective().getValue() - v = model.getVars() - optimum_sol = model.getAttr("X", v) - - optimum_sol = np.asarray(optimum_sol) - - return optimum_sol, optimum_value - - # Print error messages - except gp.GurobiError as e: - print("Error code " + str(e.errno) + ": " + str(e)) - except AttributeError: - print("Gurobi failed.") - - -def fast_fva(lb, ub, S, c, opt_percentage=100): - """A Python function to perform fva using gurobi LP solver - Returns the value of the optimal solution for all the following linear programs: - min/max v_i, for all coordinates i=1,...,n, subject to, - Sv = 0, lb <= v <= ub - - Keyword arguments: - lb -- lower bounds for the fluxes, i.e., a n-dimensional vector - ub -- upper bounds for the fluxes, i.e., a n-dimensional vector - S -- the mxn stoichiometric matrix, s.t. Sv = 0 - c -- the objective function to maximize - opt_percentage -- consider solutions that give you at least a certain - percentage of the optimal solution (default is to consider - optimal solutions only) - """ - - if lb.size != S.shape[1] or ub.size != S.shape[1]: - raise Exception( - "The number of reactions must be equal to the number of given flux bounds." - ) - - # declare the tolerance that gurobi works properly (we found it experimentally) - tol = 1e-06 - - m = S.shape[0] - n = S.shape[1] - beq = np.zeros(m) - - A = np.zeros((2 * n, n), dtype="float") - A[0:n] = np.eye(n) - A[n:] -= np.eye(n, n, dtype="float") - - b = np.concatenate((ub, -lb), axis=0) - b = np.asarray(b, dtype="float") - b = np.ascontiguousarray(b, dtype="float") - - # call fba to obtain an optimal solution - max_biomass_flux_vector, max_biomass_objective = fast_fba(lb, ub, S, c) - - # add an additional constraint to impose solutions with at least `opt_percentage` of the optimal solution - A = np.vstack((A, -c)) - - b = np.append( - b, -(opt_percentage / 100) * tol * math.floor(max_biomass_objective / tol) - ) - - min_fluxes = [] - max_fluxes = [] - - try: - - # To avoid printint the output of the optimize() function of Gurobi, we need to set an environment like this - with gp.Env(empty=True) as env: - env.setParam("OutputFlag", 0) - env.start() - - with gp.Model(env=env) as model: - - # Create variables - x = model.addMVar( - shape=n, - vtype=GRB.CONTINUOUS, - name="x", - lb=-GRB.INFINITY, - ub=GRB.INFINITY, - ) - - # Make sparse Aeq - Aeq_sparse = sp.csr_matrix(S) - - # Make A sparse - A_sparse = sp.csr_matrix(A) - - # Set the b and beq vectors as numpy vectors - b = np.array(b) - beq = np.array(beq) - - # Add constraints - model.addMConstr(Aeq_sparse, x, "=", beq, name="c") - - # Update the model to include the constraints added - model.update() - - # Add constraints for the uneqalities of A - model.addMConstr(A_sparse, x, "<", b, name="d") - - # Update the model with the extra constraints and then print it - model.update() - - # Loop through the lines of the A matrix, set objective function for each and run the model - for i in range(n): - - # Set the ith row of the A matrix as the objective function - objective_function = A[ - i, - ] - - # Set the objective function in the model - model.setMObjective( - None, objective_function, 0.0, None, None, x, GRB.MINIMIZE - ) - model.update() - - # Optimize model - model.optimize() - - # If optimized - status = model.status - if status == GRB.OPTIMAL: - - # Get the min objective value - min_objective = model.getObjective().getValue() - min_fluxes.append(min_objective) - else: - min_fluxes.append(lb[i]) - - # Likewise, for the maximum - objective_function = np.asarray([-x for x in objective_function]) - model.setMObjective( - None, objective_function, 0.0, None, None, x, GRB.MINIMIZE - ) - model.update() - model.optimize() - - # Again if optimized - status = model.status - if status == GRB.OPTIMAL: - - # Get the max objective value - max_objective = -model.getObjective().getValue() - max_fluxes.append(max_objective) - else: - max_fluxes.append(ub[i]) - - # Make lists of fluxes numpy arrays - min_fluxes = np.asarray(min_fluxes) - max_fluxes = np.asarray(max_fluxes) - - return ( - min_fluxes, - max_fluxes, - max_biomass_flux_vector, - max_biomass_objective, - ) - - # Print error messages - except gp.GurobiError as e: - print("Error code " + str(e.errno) + ": " + str(e)) - except AttributeError: - print("Gurobi solver failed.") - - -def update_model(model, n, Aeq_sparse, beq, lb, ub, A_sparse, b, objective_function): - """A function to update a gurobi model that solves a linear program - Keyword arguments: - model -- gurobi model - n -- the dimension - Aeq_sparse -- a sparse matrix s.t. Aeq_sparse x = beq - beq -- a vector s.t. Aeq_sparse x = beq - lb -- lower bounds for the variables, i.e., a n-dimensional vector - ub -- upper bounds for the variables, i.e., a n-dimensional vector - A_sparse -- a sparse matrix s.t. A_sparse x <= b - b -- a vector matrix s.t. A_sparse x <= b - objective_function -- the objective function, i.e., a n-dimensional vector - """ - model.remove(model.getVars()) - model.update() - model.remove(model.getConstrs()) - model.update() - x = model.addMVar( - shape=n, - vtype=GRB.CONTINUOUS, - name="x", - lb=lb, - ub=ub, - ) - model.update() - model.addMConstr(Aeq_sparse, x, "=", beq, name="c") - model.update() - model.addMConstr(A_sparse, x, "<", b, name="d") - model.update() - model.setMObjective(None, objective_function, 0.0, None, None, x, GRB.MINIMIZE) - model.update() - - return model - - -def fast_remove_redundant_facets(lb, ub, S, c, opt_percentage=100): - """A function to find and remove the redundant facets and to find - the facets with very small offset and to set them as equalities - - Keyword arguments: - lb -- lower bounds for the fluxes, i.e., a n-dimensional vector - ub -- upper bounds for the fluxes, i.e., a n-dimensional vector - S -- the mxn stoichiometric matrix, s.t. Sv = 0 - c -- the objective function to maximize - opt_percentage -- consider solutions that give you at least a certain - percentage of the optimal solution (default is to consider - optimal solutions only) - """ - - if lb.size != S.shape[1] or ub.size != S.shape[1]: - raise Exception( - "The number of reactions must be equal to the number of given flux bounds." - ) - - # declare the tolerance that gurobi works properly (we found it experimentally) - redundant_facet_tol = 1e-07 - tol = 1e-06 - - m = S.shape[0] - n = S.shape[1] - beq = np.zeros(m) - Aeq_res = S - - A = np.zeros((2 * n, n), dtype="float") - A[0:n] = np.eye(n) - A[n:] -= np.eye(n, n, dtype="float") - - b = np.concatenate((ub, -lb), axis=0) - b = np.asarray(b, dtype="float") - b = np.ascontiguousarray(b, dtype="float") - - # call fba to obtain an optimal solution - max_biomass_flux_vector, max_biomass_objective = fast_fba(lb, ub, S, c) - val = -np.floor(max_biomass_objective / tol) * tol * opt_percentage / 100 - - b_res = [] - A_res = np.empty((0, n), float) - beq_res = np.array(beq) - - try: - - # To avoid printint the output of the optimize() function of Gurobi, we need to set an environment like this - with gp.Env(empty=True) as env: - env.setParam("OutputFlag", 0) - env.start() - - with gp.Model(env=env) as model: - - # Create variables - x = model.addMVar( - shape=n, - vtype=GRB.CONTINUOUS, - name="x", - lb=lb, - ub=ub, - ) - - # Make sparse Aeq - Aeq_sparse = sp.csr_matrix(S) - - # Make A sparse - A_sparse = sp.csr_matrix(np.array(-c)) - b_sparse = np.array(val) - - # Set the b and beq vectors as numpy vectors - b = np.array(b) - beq = np.array(beq) - - # Add constraints - model.addMConstr(Aeq_sparse, x, "=", beq, name="c") - - # Update the model to include the constraints added - model.update() - - # Add constraints for the uneqalities of A - model.addMConstr(A_sparse, x, "<", [val], name="d") - - # Update the model with the extra constraints and then print it - model.update() - - model_iter = model.copy() - - # initialize - indices_iter = range(n) - removed = 1 - offset = 1 - facet_left_removed = np.zeros((1, n), dtype=bool) - facet_right_removed = np.zeros((1, n), dtype=bool) - - # Loop until nor redundant facets are found - while removed > 0 or offset > 0: - - removed = 0 - offset = 0 - indices = indices_iter - indices_iter = [] - - Aeq_sparse = sp.csr_matrix(Aeq_res) - beq = np.array(beq_res) - - b_res = [] - A_res = np.empty((0, n), float) - for i in indices: - - # Set the ith row of the A matrix as the objective function - objective_function = A[ - i, - ] - - redundant_facet_right = True - redundant_facet_left = True - - # for the maximum - objective_function_max = np.asarray( - [-x for x in objective_function] - ) - model_iter = update_model( - model_iter, - n, - Aeq_sparse, - beq, - lb, - ub, - A_sparse, - [val], - objective_function_max, - ) - model_iter.optimize() - - # Again if optimized - status = model_iter.status - if status == GRB.OPTIMAL: - # Get the max objective value - max_objective = -model_iter.getObjective().getValue() - else: - max_objective = ub[i] - - # if this facet was not removed in a previous iteration - if not facet_right_removed[0, i]: - ub_iter = ub.copy() - ub_iter[i] = ub_iter[i] + 1 - model_iter = update_model( - model_iter, - n, - Aeq_sparse, - beq, - lb, - ub_iter, - A_sparse, - [val], - objective_function_max, - ) - model_iter.optimize() - - status = model_iter.status - if status == GRB.OPTIMAL: - # Get the max objective value with relaxed inequality - max_objective2 = -model_iter.getObjective().getValue() - if ( - np.abs(max_objective2 - max_objective) - > redundant_facet_tol - ): - redundant_facet_right = False - else: - removed += 1 - facet_right_removed[0, i] = True - - model_iter = update_model( - model_iter, - n, - Aeq_sparse, - beq, - lb, - ub, - A_sparse, - [val], - objective_function, - ) - model_iter.optimize() - - # If optimized - status = model_iter.status - if status == GRB.OPTIMAL: - # Get the min objective value - min_objective = model_iter.getObjective().getValue() - else: - min_objective = lb[i] - - # if this facet was not removed in a previous iteration - if not facet_left_removed[0, i]: - lb_iter = lb.copy() - lb_iter[i] = lb_iter[i] - 1 - model_iter = update_model( - model_iter, - n, - Aeq_sparse, - beq, - lb_iter, - ub, - A_sparse, - [val], - objective_function, - ) - model_iter.optimize() - - status = model_iter.status - if status == GRB.OPTIMAL: - # Get the min objective value with relaxed inequality - min_objective2 = model_iter.getObjective().getValue() - if ( - np.abs(min_objective2 - min_objective) - > redundant_facet_tol - ): - redundant_facet_left = False - else: - removed += 1 - facet_left_removed[0, i] = True - - if (not redundant_facet_left) or (not redundant_facet_right): - width = abs(max_objective - min_objective) - - # Check whether the offset in this dimension is small (and set an equality) - if width < redundant_facet_tol: - offset += 1 - Aeq_res = np.vstack( - ( - Aeq_res, - A[ - i, - ], - ) - ) - beq_res = np.append( - beq_res, min(max_objective, min_objective) - ) - # Remove the bounds on this dimension - ub[i] = sys.float_info.max - lb[i] = -sys.float_info.max - else: - # store this dimension - indices_iter.append(i) - - if not redundant_facet_left: - # Not a redundant inequality - A_res = np.append( - A_res, - np.array( - [ - A[ - n + i, - ] - ] - ), - axis=0, - ) - b_res.append(b[n + i]) - else: - lb[i] = -sys.float_info.max - - if not redundant_facet_right: - # Not a redundant inequality - A_res = np.append( - A_res, - np.array( - [ - A[ - i, - ] - ] - ), - axis=0, - ) - b_res.append(b[i]) - else: - ub[i] = sys.float_info.max - else: - # Remove the bounds on this dimension - ub[i] = sys.float_info.max - lb[i] = -sys.float_info.max - - b_res = np.asarray(b_res) - A_res = np.asarray(A_res, dtype="float") - A_res = np.ascontiguousarray(A_res, dtype="float") - - return ( - A_res, - b_res, - Aeq_res, - beq_res, - ) - - # Print error messages - except gp.GurobiError as e: - print("Error code " + str(e.errno) + ": " + str(e)) - except AttributeError: - print("Gurobi solver failed.") - - -def fast_inner_ball(A, b): - """A Python function to compute the maximum inscribed ball in the given polytope using gurobi LP solver - Returns the optimal solution for the following linear program: - max r, subject to, - a_ix + r||a_i|| <= b, i=1,...,n - - Keyword arguments: - A -- an mxn matrix that contains the normal vectors of the facets of the polytope row-wise - b -- a m-dimensional vector - """ - - extra_column = [] - - m = A.shape[0] - n = A.shape[1] - - for i in range(A.shape[0]): - entry = np.linalg.norm( - A[ - i, - ] - ) - extra_column.append(entry) - - column = np.asarray(extra_column) - A_expand = np.c_[A, column] - - with gp.Env(empty=True) as env: - env.setParam("OutputFlag", 0) - env.start() - - d = A_expand.shape[1] - - with gp.Model(env=env) as model: - - # Create variable - x = model.addMVar( - shape=d, - vtype=GRB.CONTINUOUS, - name="x", - lb=-GRB.INFINITY, - ub=GRB.INFINITY, - ) - model.update() - - # Make A_full_dim sparse - A_expand_sparse = sp.csr_matrix(A_expand.astype("float")) - - # Add constraints - model.addMConstr(A_expand_sparse, x, "<", b, name="c") - model.update() - - # Set the ith row of the A matrix as the objective function - a = np.ones((1, n + 1)) - azero = np.zeros((1, n)) - a[:, :-1] = azero - objective_function = a[0] - - # Set the objective function in the model - model.setMObjective( - None, objective_function, 0.0, None, None, x, GRB.MAXIMIZE - ) - model.update() - - # Optimize model - model.optimize() - - # Get the solution returned - varss = model.getVars() - - # Get the center point and the radius of max ball from the solution of LP; its last element is the radius - point = [] - for i in range(len(varss)): - if i == len(varss) - 1: - r = varss[i].x - else: - value = varss[i].x - point.append(value) - - # And check whether the computed radius is negative - if r < 0: - print( - "The radius calculated has negative value. The polytope is infeasible or something went wrong with the solver" - ) - else: - return point, r diff --git a/dingo/inner_ball.py b/dingo/inner_ball.py deleted file mode 100644 index ac44e579..00000000 --- a/dingo/inner_ball.py +++ /dev/null @@ -1,65 +0,0 @@ -# dingo : a python library for metabolic networks sampling and analysis -# dingo is part of GeomScale project - -# Copyright (c) 2021 Apostolos Chalkis - -# Licensed under GNU LGPL.3, see LICENCE file - -import numpy as np -from scipy.optimize import linprog -import scipy.sparse as sp - - -# This is a function to get the maximum ball inscribed in the polytope using scipy.optimize LP solver `linprog` -def slow_inner_ball(A, b): - """A Python function to compute the maximum inscribed ball in the given polytope using scipy.optimize LP solver `linprog` - Returns the optimal solution for the following linear program: - max r, subject to, - a_ix + r||a_i|| <= b, i=1,...,n - - Keyword arguments: - A -- an mxn matrix that contains the normal vectors of the facets of the polytope row-wise - b -- a m-dimensional vector - """ - - extra_column = [] - - m = A.shape[0] - n = A.shape[1] - - for i in range(A.shape[0]): - entry = np.linalg.norm( - A[ - i, - ] - ) - extra_column.append(entry) - - column = np.asarray(extra_column) - A_expand = np.c_[A, column] - - a = -np.ones((1, n + 1)) - azero = np.zeros((1, n)) - a[:, :-1] = azero - objective_function = a[0] - - res = linprog(objective_function, A_ub=A_expand, b_ub=b, bounds=(None, None)) - - sol = res.x - - # Get the center point and the radius of max ball from the solution of LP; its last element is the radius - point = [] - for i in range(len(sol)): - if i == len(sol) - 1: - r = sol[i] - else: - value = sol[i] - point.append(value) - - # And check whether the computed radius is negative - if r < 0: - raise Exception( - "The full dimensional polytope is infeasible or the solver failed to compute the maximum inscribed ball." - ) - else: - return point, r diff --git a/dingo/parser.py b/dingo/parser.py index 610d9bac..6736d3cb 100644 --- a/dingo/parser.py +++ b/dingo/parser.py @@ -212,9 +212,9 @@ def dingo_args(): optional.add_argument( "--solver", "-s", - help="the solver to use for the linear programs. Choose between `scipy` and `gurobi` (faster computations --- it needs a licence). The default value is `scipy`.", + help="the solver to use for the linear programs. Choose between `highs` and `gurobi` (faster computations --- it needs a licence). The default value is `highs`.", required=False, - default="scipy", + default="highs", metavar="", ) diff --git a/dingo/pyoptInterface_based_impl.py b/dingo/pyoptInterface_based_impl.py new file mode 100644 index 00000000..c3b3fc40 --- /dev/null +++ b/dingo/pyoptInterface_based_impl.py @@ -0,0 +1,499 @@ +import pyoptinterface as poi +from pyoptinterface import highs, gurobi, copt, mosek +import numpy as np +import sys + +default_solver = "highs" + +def set_default_solver(solver_name): + global default_solver + default_solver = solver_name + +def get_solver(solver_name): + solvers = {"highs": highs, "gurobi": gurobi, "copt": copt, "mosek": mosek} + if solver_name in solvers: + return solvers[solver_name] + else: + raise Exception("An unknown solver {solver_name} is requested.") + +def dot(c, x): + return poi.quicksum(c[i] * x[i] for i in range(len(x)) if abs(c[i]) > 1e-12) + + +def fba(lb, ub, S, c, solver_name=None): + """A Python function to perform fba using PyOptInterface LP modeler + Returns an optimal solution and its value for the following linear program: + max c*v, subject to, + Sv = 0, lb <= v <= ub + + Keyword arguments: + lb -- lower bounds for the fluxes, i.e., a n-dimensional vector + ub -- upper bounds for the fluxes, i.e., a n-dimensional vector + S -- the mxn stoichiometric matrix, s.t. Sv = 0 + c -- the linear objective function, i.e., a n-dimensional vector + solver_name -- the solver to use, i.e., a string of the solver name (if None, the default solver is used) + """ + + if lb.size != S.shape[1] or ub.size != S.shape[1]: + raise Exception( + "The number of reactions must be equal to the number of given flux bounds." + ) + if c.size != S.shape[1]: + raise Exception( + "The length of the linear objective function must be equal to the number of reactions." + ) + + m = S.shape[0] + n = S.shape[1] + optimum_value = 0 + optimum_sol = np.zeros(n) + try: + if solver_name is None: + solver_name = default_solver + SOLVER = get_solver(solver_name) + # Create a model + model = SOLVER.Model() + model.set_model_attribute(poi.ModelAttribute.Silent, True) + + # Create variables and set lb <= v <= ub + v = np.empty(n, dtype=object) + for i in range(n): + v[i] = model.add_variable(lb=lb[i], ub=ub[i]) + + # Add the constraints Sv = 0 + for i in range(m): + model.add_linear_constraint(dot(S[i], v), poi.Eq, 0) + + # Set the objective function + obj = dot(c, v) + model.set_objective(obj, sense=poi.ObjectiveSense.Maximize) + + # Optimize model + model.optimize() + + # If optimized + status = model.get_model_attribute(poi.ModelAttribute.TerminationStatus) + if status == poi.TerminationStatusCode.OPTIMAL: + optimum_value = model.get_value(obj) + for i in range(n): + optimum_sol[i] = model.get_value(v[i]) + return optimum_sol, optimum_value + + except poi.TerminationStatusCode.NUMERICAL_ERROR as e: + print(f"A numerical error occurred: {e}") + except poi.TerminationStatusCode.OTHER_ERROR as e: + print(f"An error occurred: {e}") + except Exception as e: + print(f"An unexpected error occurred: {e}") + + +def fva(lb, ub, S, c, opt_percentage=100, solver_name=None): + """A Python function to perform fva using PyOptInterface LP modeler + Returns the value of the optimal solution for all the following linear programs: + min/max v_i, for all coordinates i=1,...,n, subject to, + Sv = 0, lb <= v <= ub + + Keyword arguments: + lb -- lower bounds for the fluxes, i.e., a n-dimensional vector + ub -- upper bounds for the fluxes, i.e., a n-dimensional vector + S -- the mxn stoichiometric matrix, s.t. Sv = 0 + c -- the objective function to maximize + opt_percentage -- consider solutions that give you at least a certain + percentage of the optimal solution (default is to consider + optimal solutions only) + solver_name -- the solver to use, i.e., a string of the solver name (if None, the default solver is used) + """ + + if lb.size != S.shape[1] or ub.size != S.shape[1]: + raise Exception( + "The number of reactions must be equal to the number of given flux bounds." + ) + + # declare the tolerance that highs and gurobi work properly (we found it experimentally) + tol = 1e-06 + + m = S.shape[0] + n = S.shape[1] + + max_biomass_flux_vector, max_biomass_objective = fba(lb, ub, S, c, solver_name) + + min_fluxes = [] + max_fluxes = [] + + adjusted_opt_threshold = ( + (opt_percentage / 100) * tol * np.floor(max_biomass_objective / tol) + ) + + try: + if solver_name is None: + solver_name = default_solver + SOLVER = get_solver(solver_name) + # Create a model + model = SOLVER.Model() + model.set_model_attribute(poi.ModelAttribute.Silent, True) + + # Create variables and set lb <= v <= ub + v = np.empty(n, dtype=object) + for i in range(n): + v[i] = model.add_variable(lb=lb[i], ub=ub[i]) + + # Add the constraints Sv = 0 + for i in range(m): + model.add_linear_constraint(dot(S[i], v), poi.Eq, 0) + + # add an additional constraint to impose solutions with at least `opt_percentage` of the optimal solution + model.add_linear_constraint(dot(c, v), poi.Geq, adjusted_opt_threshold) + + for i in range(n): + # Set the objective function + obj = poi.ExprBuilder(v[i]) + + model.set_objective(obj, sense=poi.ObjectiveSense.Minimize) + + # Optimize model + model.optimize() + + # If optimized + status = model.get_model_attribute(poi.ModelAttribute.TerminationStatus) + if status == poi.TerminationStatusCode.OPTIMAL: + # Get the min objective value + min_objective = model.get_value(v[i]) + min_fluxes.append(min_objective) + else: + min_fluxes.append(lb[i]) + + # Likewise, for the maximum, optimize model + model.set_objective(obj, sense=poi.ObjectiveSense.Maximize) + + # Again if optimized + model.optimize() + status = model.get_model_attribute(poi.ModelAttribute.TerminationStatus) + if status == poi.TerminationStatusCode.OPTIMAL: + # Get the max objective value + max_objective = model.get_value(v[i]) + max_fluxes.append(max_objective) + else: + max_fluxes.append(ub[i]) + + # Make lists of fluxes numpy arrays + min_fluxes = np.asarray(min_fluxes) + max_fluxes = np.asarray(max_fluxes) + + return ( + min_fluxes, + max_fluxes, + max_biomass_flux_vector, + max_biomass_objective, + ) + + except poi.TerminationStatusCode.NUMERICAL_ERROR as e: + print(f"A numerical error occurred: {e}") + except poi.TerminationStatusCode.OTHER_ERROR as e: + print(f"An error occurred: {e}") + except Exception as e: + print(f"An unexpected error occurred: {e}") + + +def inner_ball(A, b, solver_name=None): + """A Python function to compute the maximum inscribed ball in the given polytope using PyOptInterface LP modeler + Returns the optimal solution for the following linear program: + max r, subject to, + a_ix + r||a_i|| <= b, i=1,...,n + + Keyword arguments: + A -- an mxn matrix that contains the normal vectors of the facets of the polytope row-wise + b -- a m-dimensional vector + solver_name -- the solver to use, i.e., a string of the solver name (if None, the default solver is used) + """ + + extra_column = [] + + m = A.shape[0] + n = A.shape[1] + + for i in range(A.shape[0]): + entry = np.linalg.norm(A[i]) + extra_column.append(entry) + + column = np.asarray(extra_column) + A_expand = np.c_[A, column] + + if solver_name is None: + solver_name = default_solver + SOLVER = get_solver(solver_name) + model = SOLVER.Model() + model.set_model_attribute(poi.ModelAttribute.Silent, True) + + # Create variables where x[n] is the radius + x = np.empty(n + 1, dtype=object) + for i in range(n + 1): + x[i] = model.add_variable() + + # Add the constraints a_ix + r||a_i|| <= b + for i in range(m): + model.add_linear_constraint(dot(A_expand[i], x), poi.Leq, b[i]) + + # Set the objective function + obj = poi.ExprBuilder(x[n]) + model.set_objective(obj, sense=poi.ObjectiveSense.Maximize) + + # Optimize model + model.optimize() + + # Get the center point and the radius of max ball from the solution of LP + point = [model.get_value(x[i]) for i in range(n)] + + # Get radius + r = model.get_value(obj) + + # And check whether the computed radius is negative + if r < 0: + print( + "The radius calculated has negative value. The polytope is infeasible or something went wrong with the solver" + ) + else: + return point, r + + +def set_model(n, lb, ub, Aeq, beq, A, b, solver_name=None): + """ + A helper function of remove_redundant_facets function + Create a PyOptInterface model with given PyOptInterface variables, equality constraints, inequality constraints and solver name + but without an objective function. + """ + # Create a model + if solver_name is None: + solver_name = default_solver + SOLVER = get_solver(solver_name) + model = SOLVER.Model() + model.set_model_attribute(poi.ModelAttribute.Silent, True) + + # Create variables + x = np.empty(n, dtype=object) + for i in range(n): + x[i] = model.add_variable(lb=lb[i], ub=ub[i]) + + # Add the equality constraints + for i in range(Aeq.shape[0]): + model.add_linear_constraint(dot(Aeq[i], x), poi.Eq, beq[i]) + + # Add the inequality constraints + for i in range(A.shape[0]): + model.add_linear_constraint(dot(A[i], x), poi.Leq, b[i]) + + return model, x + + +def remove_redundant_facets(lb, ub, S, c, opt_percentage=100, solver_name=None): + """A function to find and remove the redundant facets and to find + the facets with very small offset and to set them as equalities + + Keyword arguments: + lb -- lower bounds for the fluxes, i.e., a n-dimensional vector + ub -- upper bounds for the fluxes, i.e., a n-dimensional vector + S -- the mxn stoichiometric matrix, s.t. Sv = 0 + c -- the objective function to maximize + opt_percentage -- consider solutions that give you at least a certain + percentage of the optimal solution (default is to consider + optimal solutions only) + solver_name -- the solver to use, i.e., a string of the solver name (if None, the default solver is used) + """ + + if lb.size != S.shape[1] or ub.size != S.shape[1]: + raise Exception( + "The number of reactions must be equal to the number of given flux bounds." + ) + + # declare the tolerance that highs and gurobi work properly (we found it experimentally) + redundant_facet_tol = 1e-07 + tol = 1e-06 + + m = S.shape[0] + n = S.shape[1] + + # [v,-v] <= [ub,-lb] + A = np.zeros((2 * n, n), dtype="float") + A[0:n] = np.eye(n) + A[n:] -= np.eye(n, n, dtype="float") + + b = np.concatenate((ub, -lb), axis=0) + b = np.ascontiguousarray(b, dtype="float") + + beq = np.zeros(m) + + Aeq_res = S + beq_res = np.array(beq) + b_res = [] + A_res = np.empty((0, n), float) + + max_biomass_flux_vector, max_biomass_objective = fba(lb, ub, S, c, solver_name) + val = -np.floor(max_biomass_objective / tol) * tol * opt_percentage / 100 + + start = np.zeros(n) + + try: + + # initialize + indices_iter = range(n) + removed = 1 + offset = 1 + facet_left_removed = np.zeros(n, dtype=bool) + facet_right_removed = np.zeros(n, dtype=bool) + + # Loop until no redundant facets are found + while removed > 0 or offset > 0: + removed = 0 + offset = 0 + indices = indices_iter + indices_iter = [] + + Aeq = np.array(Aeq_res) + beq = np.array(beq_res) + + A_res = np.empty((0, n), dtype=float) + b_res = [] + + model_iter, v = set_model(n, lb, ub, Aeq, beq, np.array([-c]), [val], solver_name) + + for cnt, i in enumerate(indices): + + redundant_facet_right = True + redundant_facet_left = True + + if cnt > 0: + last_idx = indices[cnt-1] + model_iter.set_variable_attribute( + v[last_idx], poi.VariableAttribute.LowerBound, lb[last_idx] + ) + model_iter.set_variable_attribute( + v[last_idx], poi.VariableAttribute.UpperBound, ub[last_idx] + ) + + # objective function + obj = poi.ExprBuilder(v[i]) + + # maximize v_i (right) + model_iter.set_objective(obj, sense=poi.ObjectiveSense.Maximize) + model_iter.optimize() + + # if optimized + status = model_iter.get_model_attribute( + poi.ModelAttribute.TerminationStatus + ) + if status == poi.TerminationStatusCode.OPTIMAL: + # get the maximum objective value + max_objective = model_iter.get_value(obj) + else: + max_objective = ub[i] + + # if this facet was not removed in a previous iteration + if not facet_right_removed[i]: + # Relax the inequality + model_iter.set_variable_attribute( + v[i], poi.VariableAttribute.UpperBound, ub[i] + 1 + ) + + # Solve the model + model_iter.optimize() + + status = model_iter.get_model_attribute( + poi.ModelAttribute.TerminationStatus + ) + if status == poi.TerminationStatusCode.OPTIMAL: + # Get the max objective value with relaxed inequality + + max_objective2 = model_iter.get_value(obj) + if np.abs(max_objective2 - max_objective) > redundant_facet_tol: + redundant_facet_right = False + else: + removed += 1 + facet_right_removed[i] = True + + # Reset the inequality + model_iter.set_variable_attribute( + v[i], poi.VariableAttribute.UpperBound, ub[i] + ) + + # minimum v_i (left) + model_iter.set_objective(obj, sense=poi.ObjectiveSense.Minimize) + model_iter.optimize() + + # If optimized + status = model_iter.get_model_attribute( + poi.ModelAttribute.TerminationStatus + ) + if status == poi.TerminationStatusCode.OPTIMAL: + # Get the min objective value + min_objective = model_iter.get_value(obj) + else: + min_objective = lb[i] + + # if this facet was not removed in a previous iteration + if not facet_left_removed[i]: + # Relax the inequality + model_iter.set_variable_attribute( + v[i], poi.VariableAttribute.LowerBound, lb[i] - 1 + ) + + # Solve the model + model_iter.optimize() + + status = model_iter.get_model_attribute( + poi.ModelAttribute.TerminationStatus + ) + if status == poi.TerminationStatusCode.OPTIMAL: + # Get the min objective value with relaxed inequality + min_objective2 = model_iter.get_value(obj) + if np.abs(min_objective2 - min_objective) > redundant_facet_tol: + redundant_facet_left = False + else: + removed += 1 + facet_left_removed[i] = True + + # Reset the inequality + # model_iter.set_variable_attribute(v[i], poi.VariableAttribute.LowerBound, lb[i]) + + if (not redundant_facet_left) or (not redundant_facet_right): + width = abs(max_objective - min_objective) + + # Check whether the offset in this dimension is small (and set an equality) + if width < redundant_facet_tol: + offset += 1 + Aeq_res = np.vstack((Aeq_res, A[i])) + beq_res = np.append(beq_res, min(max_objective, min_objective)) + # Remove the bounds on this dimension + ub[i] = sys.float_info.max + lb[i] = -sys.float_info.max + else: + # store this dimension + indices_iter.append(i) + + if not redundant_facet_left: + # Not a redundant inequality + A_res = np.append(A_res, np.array([A[n + i]]), axis=0) + b_res.append(b[n + i]) + else: + lb[i] = -sys.float_info.max + + if not redundant_facet_right: + # Not a redundant inequality + A_res = np.append(A_res, np.array([A[i]]), axis=0) + b_res.append(b[i]) + else: + ub[i] = sys.float_info.max + else: + # Remove the bounds on this dimension + ub[i] = sys.float_info.max + lb[i] = -sys.float_info.max + + b_res = np.asarray(b_res, dtype="float") + A_res = np.asarray(A_res, dtype="float") + A_res = np.ascontiguousarray(A_res, dtype="float") + return A_res, b_res, Aeq_res, beq_res + + except poi.TerminationStatusCode.NUMERICAL_ERROR as e: + print(f"A numerical error occurred: {e}") + except poi.TerminationStatusCode.OTHER_ERROR as e: + print(f"An error occurred: {e}") + except Exception as e: + print(f"An unexpected error occurred: {e}") diff --git a/dingo/volestipy.pyx b/dingo/volestipy.pyx index 2a8db3f8..4b31377c 100644 --- a/dingo/volestipy.pyx +++ b/dingo/volestipy.pyx @@ -5,6 +5,7 @@ # Copyright (c) 2018-2021 Apostolos Chalkis # Copyright (c) 2020-2021 Pedro Zuidberg Dos Martires # Copyright (c) 2020-2021 Haris Zafeiropoulos +# Copyright (c) 2024 Ke Shi # Licensed under GNU LGPL.3, see LICENCE file @@ -25,13 +26,7 @@ import json import scipy.io # ---------------------------------------------------------------------------------- -from dingo.inner_ball import slow_inner_ball -try: - import gurobipy - from dingo.gurobi_based_implementations import fast_inner_ball -except ImportError as e: - pass - +from dingo.pyoptInterface_based_impl import inner_ball # Set the time def get_time_seed(): @@ -122,16 +117,13 @@ cdef class HPolytope: raise Exception('"{}" is not implemented to compute volume. Available methods are: {}'.format(vol_method, volume_methods)) # Likewise, the generate_samples() function - def generate_samples(self, method, number_of_points, number_of_points_to_burn, walk_len, fast_mode, variance_value, bias_vector): + def generate_samples(self, method, number_of_points, number_of_points_to_burn, walk_len, variance_value, bias_vector, solver = None): n_variables = self._A.shape[1] cdef double[:,::1] samples = np.zeros((number_of_points, n_variables), dtype = np.float64, order = "C") # Get max inscribed ball for the initial polytope - if fast_mode: - temp_center, radius = fast_inner_ball(self._A, self._b) - else: - temp_center, radius = slow_inner_ball(self._A, self._b) + temp_center, radius = inner_ball(self._A, self._b, solver) cdef double[::1] inner_point_for_c = np.asarray(temp_center) @@ -168,7 +160,7 @@ cdef class HPolytope: # The rounding() function; as in compute_volume, more than one method is available for this step - def rounding(self, rounding_method = 'john_position', fast_mode = False): + def rounding(self, rounding_method = 'john_position', solver = None): # Get the dimensions of the items about to build n_hyperplanes, n_variables = self._A.shape[0], self._A.shape[1] @@ -182,10 +174,7 @@ cdef class HPolytope: cdef double round_value # Get max inscribed ball for the initial polytope - if fast_mode: - center, radius = fast_inner_ball(self._A, self._b) - else: - center, radius = slow_inner_ball(self._A, self._b) + center, radius = inner_ball(self._A, self._b, solver) cdef double[::1] inner_point_for_c = np.asarray(center) @@ -203,8 +192,8 @@ cdef class HPolytope: return np.asarray(new_A),np.asarray(new_b),np.asarray(T_matrix),np.asarray(shift),np.asarray(round_value) - # The fast version of (m)ultiphase (m)onte (c)arlo (s)ampling algorithm to generate steady states of a metabolic network - def fast_mmcs(self, ess = 1000, psrf_check = True, parallelism = False, num_threads = 2): + # (m)ultiphase (m)onte (c)arlo (s)ampling algorithm to generate steady states of a metabolic network + def mmcs(self, ess = 1000, psrf_check = True, parallelism = False, num_threads = 2, solver = None): n_hyperplanes, n_variables = self._A.shape[0], self._A.shape[1] @@ -220,45 +209,7 @@ cdef class HPolytope: self.polytope_cpp.mmcs_initialize(n_variables, ess, check_psrf, parallel, num_threads) # Get max inscribed ball for the initial polytope - temp_center, radius = fast_inner_ball(self._A, self._b) - cdef double[::1] inner_point_for_c = np.asarray(temp_center) - - while True: - - check = self.polytope_cpp.mmcs_step(&inner_point_for_c[0], radius, N_samples) - - if check > 1.0 and check < 2.0: - break - - self.polytope_cpp.get_polytope_as_matrices(&new_A[0,0], &new_b[0]) - new_temp_c, radius = fast_inner_ball(np.asarray(new_A), np.asarray(new_b)) - inner_point_for_c = np.asarray(new_temp_c) - - cdef double[:,::1] samples = np.zeros((n_variables, N_samples), dtype=np.float64, order="C") - self.polytope_cpp.get_mmcs_samples(&T_matrix[0,0], &T_shift[0], &samples[0,0]) - self.polytope_cpp.get_polytope_as_matrices(&new_A[0,0], &new_b[0]) - - return np.asarray(new_A), np.asarray(new_b), np.asarray(T_matrix), np.asarray(T_shift), np.asarray(samples) - - - # The slow version of (m)ultiphase (m)onte (c)arlo (s)ampling algorithm to generate steady states of a metabolic network - def slow_mmcs(self, ess = 1000, psrf_check = True, parallelism = False, num_threads = 2): - - n_hyperplanes, n_variables = self._A.shape[0], self._A.shape[1] - - cdef double[:,::1] new_A = np.zeros((n_hyperplanes, n_variables), dtype=np.float64, order="C") - cdef double[::1] new_b = np.zeros(n_hyperplanes, dtype=np.float64, order="C") - cdef double[:,::1] T_matrix = np.zeros((n_variables, n_variables), dtype=np.float64, order="C") - cdef double[::1] T_shift = np.zeros((n_variables), dtype=np.float64, order="C") - cdef int N_samples - cdef int N_ess = ess - cdef bint check_psrf = bool(psrf_check) - cdef bint parallel = bool(parallelism) - - 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"sphinx (>=3.5)", "sphinx-lint"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [metadata] lock-version = "2.0" python-versions = "^3.8" -content-hash = "6c3c9de7f7300952d2553972b8595129b073e6210aeda83cdcbb256b743e2867" +content-hash = "39d92730e306a8be6d5c7e13d037893c020efae8f2669fe94d74d2a04831fafb" diff --git a/pyproject.toml b/pyproject.toml index 2e83c04e..e9584d06 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,6 +17,7 @@ matplotlib = "^3.4.1" cobra = "^0.26.0" plotly = "^5.11.0" kaleido = "0.2.1" +pyoptinterface = {version = "^0.2.7", extras = ["highs"]} [tool.poetry.dev-dependencies] diff --git a/tests/fast_implementation_test.py b/tests/fast_implementation_test.py deleted file mode 100644 index a4b1995f..00000000 --- a/tests/fast_implementation_test.py +++ /dev/null @@ -1,75 +0,0 @@ -# dingo : a python library for metabolic networks sampling and analysis -# dingo is part of GeomScale project - -# Copyright (c) 2021 Apostolos Chalkis - -# Licensed under GNU LGPL.3, see LICENCE file - -import unittest -import os -import numpy as np -from dingo import MetabolicNetwork, PolytopeSampler -from dingo.gurobi_based_implementations import fast_inner_ball - -class TestFastMethods(unittest.TestCase): - def test_fast_max_bal_computation(self): - - m = 2 - n = 5 - - A = np.zeros((2 * n, n), dtype="float") - A[0:n] = np.eye(n) - A[n:] -= np.eye(n, n, dtype="float") - b = np.ones(2 * n, dtype="float") - - max_ball = fast_inner_ball(A, b) - - self.assertTrue(abs(max_ball[1] - 1) < 1e-08) - - def test_fast_fva(self): - - current_directory = os.getcwd() - input_file_json = current_directory + "/ext_data/e_coli_core.json" - - model = MetabolicNetwork.from_json(input_file_json) - model.set_fast_mode() - - res = model.fva() - - self.assertTrue(abs(res[3] - 0.8739215069684305) < 1e-08) - self.assertEqual(res[0].size, 95) - self.assertEqual(res[1].size, 95) - - def test_ecoli_to_full_dimensional_polytope(self): - - current_directory = os.getcwd() - input_file_json = current_directory + "/ext_data/e_coli_core.json" - - model = MetabolicNetwork.from_json(input_file_json) - model.set_fast_mode() - - sampler = PolytopeSampler(model) - sampler.set_fast_mode() - - steady_states = sampler.generate_steady_states() - - self.assertEqual(sampler.A.shape[0], 26) - self.assertEqual(sampler.A.shape[1], 24) - - self.assertEqual(steady_states.shape[0], 95) - - def test_fast_fba(self): - - current_directory = os.getcwd() - input_file_json = current_directory + "/ext_data/e_coli_core.json" - - model = MetabolicNetwork.from_json(input_file_json) - model.set_fast_mode() - - res = model.fba() - - self.assertTrue(abs(res[1] - 0.8739215069684305) < 1e-08) - - -if __name__ == "__main__": - unittest.main() diff --git a/tests/fba.py b/tests/fba.py index 94dc5b6f..5628abae 100644 --- a/tests/fba.py +++ b/tests/fba.py @@ -2,12 +2,15 @@ # dingo is part of GeomScale project # Copyright (c) 2021 Apostolos Chalkis +# Copyright (c) 2024 Ke Shi # Licensed under GNU LGPL.3, see LICENCE file import unittest import os +import sys from dingo import MetabolicNetwork +from dingo.pyoptInterface_based_impl import set_default_solver class TestFba(unittest.TestCase): @@ -15,7 +18,6 @@ def test_fba_json(self): input_file_json = os.getcwd() + "/ext_data/e_coli_core.json" model = MetabolicNetwork.from_json(input_file_json) - model.set_slow_mode() res = model.fba() self.assertTrue(abs(res[1] - 0.8739215067486387) < 1e-03) @@ -24,7 +26,6 @@ def test_fba_mat(self): input_file_mat = os.getcwd() + "/ext_data/e_coli_core.mat" model = MetabolicNetwork.from_mat(input_file_mat) - model.set_slow_mode() res = model.fba() @@ -34,7 +35,6 @@ def test_fba_sbml(self): input_file_sbml = os.getcwd() + "/ext_data/e_coli_core.xml" model = MetabolicNetwork.from_sbml(input_file_sbml) - model.set_slow_mode() res = model.fba() @@ -44,7 +44,6 @@ def test_modify_medium(self): input_file_sbml = os.getcwd() + "/ext_data/e_coli_core.xml" model = MetabolicNetwork.from_sbml(input_file_sbml) - model.set_slow_mode() initial_medium = model.medium initial_fba = model.fba()[-1] @@ -81,4 +80,7 @@ def test_modify_medium(self): if __name__ == "__main__": + if len(sys.argv) > 1: + set_default_solver(sys.argv[1]) + sys.argv.pop(1) unittest.main() diff --git a/tests/full_dimensional.py b/tests/full_dimensional.py index a2b1b15d..c8ffec87 100644 --- a/tests/full_dimensional.py +++ b/tests/full_dimensional.py @@ -3,12 +3,15 @@ # Copyright (c) 2021 Apostolos Chalkis # Copyright (c) 2021 Vissarion Fisikopoulos +# Copyright (c) 2024 Ke Shi # Licensed under GNU LGPL.3, see LICENCE file import unittest import os +import sys from dingo import MetabolicNetwork, PolytopeSampler +from dingo.pyoptInterface_based_impl import set_default_solver class TestFullDim(unittest.TestCase): @@ -17,39 +20,63 @@ def test_get_full_dim_json(self): input_file_json = os.getcwd() + "/ext_data/e_coli_core.json" model = MetabolicNetwork.from_json( input_file_json ) - sampler = self.get_polytope_from_model(model) + sampler = self.get_polytope_from_model_without_redundancy_removal(model) self.assertEqual(sampler.A.shape[0], 175) self.assertEqual(sampler.A.shape[1], 24) + + sampler = self.get_polytope_from_model_with_redundancy_removal(model) + + self.assertEqual(sampler.A.shape[0], 26) + self.assertEqual(sampler.A.shape[1], 24) def test_get_full_dim_sbml(self): input_file_sbml = os.getcwd() + "/ext_data/e_coli_core.xml" model = MetabolicNetwork.from_sbml( input_file_sbml ) - sampler = self.get_polytope_from_model( model ) + sampler = self.get_polytope_from_model_without_redundancy_removal( model ) self.assertEqual(sampler.A.shape[0], 175) self.assertEqual(sampler.A.shape[1], 24) + sampler = self.get_polytope_from_model_with_redundancy_removal(model) + + self.assertEqual(sampler.A.shape[0], 26) + self.assertEqual(sampler.A.shape[1], 24) def test_get_full_dim_mat(self): input_file_mat = os.getcwd() + "/ext_data/e_coli_core.mat" model = MetabolicNetwork.from_mat( input_file_mat ) - sampler = self.get_polytope_from_model( model ) + sampler = self.get_polytope_from_model_without_redundancy_removal( model ) self.assertEqual(sampler.A.shape[0], 175) self.assertEqual(sampler.A.shape[1], 24) + + sampler = self.get_polytope_from_model_with_redundancy_removal(model) + + self.assertEqual(sampler.A.shape[0], 26) + self.assertEqual(sampler.A.shape[1], 24) @staticmethod - def get_polytope_from_model (met_model): + def get_polytope_from_model_without_redundancy_removal (met_model): + + sampler = PolytopeSampler(met_model) + sampler.facet_redundancy_removal(False) + sampler.get_polytope() + + return sampler + + @staticmethod + def get_polytope_from_model_with_redundancy_removal (met_model): - met_model.set_slow_mode() sampler = PolytopeSampler(met_model) - sampler.set_slow_mode() sampler.get_polytope() return sampler if __name__ == "__main__": + if len(sys.argv) > 1: + set_default_solver(sys.argv[1]) + sys.argv.pop(1) unittest.main() diff --git a/tests/max_ball.py b/tests/max_ball.py index cd403e2f..a7d80344 100644 --- a/tests/max_ball.py +++ b/tests/max_ball.py @@ -3,15 +3,17 @@ # Copyright (c) 2021 Apostolos Chalkis # Copyright (c) 2021 Vissarion Fisikopoulos +# Copyright (c) 2024 Ke Shi # Licensed under GNU LGPL.3, see LICENCE file import unittest import os +import sys import scipy import numpy as np from dingo import MetabolicNetwork, PolytopeSampler -from dingo.inner_ball import slow_inner_ball +from dingo.pyoptInterface_based_impl import inner_ball, set_default_solver from dingo.scaling import gmscale @@ -25,9 +27,12 @@ def test_simple(self): A[n:] -= np.eye(n, n, dtype="float") b = np.ones(2 * n, dtype="float") - max_ball = slow_inner_ball(A, b) + max_ball = inner_ball(A, b) self.assertTrue(abs(max_ball[1] - 1) < 1e-04) if __name__ == "__main__": + if len(sys.argv) > 1: + set_default_solver(sys.argv[1]) + sys.argv.pop(1) unittest.main() diff --git a/tests/rounding.py b/tests/rounding.py index dcf4cedb..64a55f5f 100644 --- a/tests/rounding.py +++ b/tests/rounding.py @@ -4,14 +4,16 @@ # Copyright (c) 2022 Apostolos Chalkis # Copyright (c) 2022-2024 Vissarion Fisikopoulos # Copyright (c) 2022 Haris Zafeiropoulos +# Copyright (c) 2024 Ke Shi # Licensed under GNU LGPL.3, see LICENCE file import unittest import os +import sys import numpy as np from dingo import MetabolicNetwork, PolytopeSampler -from dingo.gurobi_based_implementations import fast_inner_ball +from dingo.pyoptInterface_based_impl import set_default_solver def test_rounding(self, method_str): @@ -63,4 +65,7 @@ def test_rounding_john_position(self): test_rounding(self, "john_position") if __name__ == "__main__": + if len(sys.argv) > 1: + set_default_solver(sys.argv[1]) + sys.argv.pop(1) unittest.main() \ No newline at end of file diff --git a/tests/sampling.py b/tests/sampling.py index bf731715..665e2517 100644 --- a/tests/sampling.py +++ b/tests/sampling.py @@ -4,12 +4,15 @@ # Copyright (c) 2022 Apostolos Chalkis # Copyright (c) 2022 Vissarion Fisikopoulos # Copyright (c) 2022 Haris Zafeiropoulos +# Copyright (c) 2024 Ke Shi # Licensed under GNU LGPL.3, see LICENCE file import unittest import os +import sys from dingo import MetabolicNetwork, PolytopeSampler +from dingo.pyoptInterface_based_impl import set_default_solver class TestSampling(unittest.TestCase): @@ -52,4 +55,7 @@ def test_sample_sbml(self): if __name__ == "__main__": + if len(sys.argv) > 1: + set_default_solver(sys.argv[1]) + sys.argv.pop(1) unittest.main() diff --git a/tests/sampling_no_multiphase.py b/tests/sampling_no_multiphase.py index 14e8b2b3..f6020eee 100644 --- a/tests/sampling_no_multiphase.py +++ b/tests/sampling_no_multiphase.py @@ -4,12 +4,15 @@ # Copyright (c) 2022 Apostolos Chalkis # Copyright (c) 2022 Vissarion Fisikopoulos # Copyright (c) 2022 Haris Zafeiropoulos +# Copyright (c) 2024 Ke Shi # Licensed under GNU LGPL.3, see LICENCE file import unittest import os +import sys from dingo import MetabolicNetwork, PolytopeSampler +from dingo.pyoptInterface_based_impl import set_default_solver class TestSampling(unittest.TestCase): @@ -117,4 +120,7 @@ def test_sample_sbml(self): if __name__ == "__main__": + if len(sys.argv) > 1: + set_default_solver(sys.argv[1]) + sys.argv.pop(1) unittest.main() diff --git a/tests/scaling.py b/tests/scaling.py index b4de9ce0..d573afb0 100644 --- a/tests/scaling.py +++ b/tests/scaling.py @@ -8,10 +8,12 @@ import unittest import os +import sys import scipy import numpy as np from dingo import MetabolicNetwork from dingo.scaling import gmscale +from dingo.pyoptInterface_based_impl import set_default_solver class TestScaling(unittest.TestCase): @@ -51,4 +53,7 @@ def test_scale_sbml(self): if __name__ == "__main__": + if len(sys.argv) > 1: + set_default_solver(sys.argv[1]) + sys.argv.pop(1) unittest.main() From aba3f19ccb92a3ae846cb9ae01b6d205d99859aa Mon Sep 17 00:00:00 2001 From: KeShih Date: Tue, 20 Aug 2024 20:40:16 +0800 Subject: [PATCH 2/2] Rename and improve pyoptinterface_based_impl.py --- dingo/MetabolicNetwork.py | 2 +- dingo/PolytopeSampler.py | 2 +- dingo/__init__.py | 2 +- ...tInterface_based_impl.py => pyoptinterface_based_impl.py} | 5 +---- dingo/volestipy.pyx | 2 +- tests/fba.py | 2 +- tests/full_dimensional.py | 2 +- tests/max_ball.py | 2 +- tests/rounding.py | 2 +- tests/sampling.py | 2 +- tests/sampling_no_multiphase.py | 2 +- tests/scaling.py | 2 +- 12 files changed, 12 insertions(+), 15 deletions(-) rename dingo/{pyoptInterface_based_impl.py => pyoptinterface_based_impl.py} (99%) diff --git a/dingo/MetabolicNetwork.py b/dingo/MetabolicNetwork.py index 8d0dcd6f..7be66c0a 100644 --- a/dingo/MetabolicNetwork.py +++ b/dingo/MetabolicNetwork.py @@ -12,7 +12,7 @@ from typing import Dict import cobra from dingo.loading_models import read_json_file, read_mat_file, read_sbml_file, parse_cobra_model -from dingo.pyoptInterface_based_impl import fba,fva,inner_ball,remove_redundant_facets +from dingo.pyoptinterface_based_impl import fba,fva,inner_ball,remove_redundant_facets class MetabolicNetwork: def __init__(self, tuple_args): diff --git a/dingo/PolytopeSampler.py b/dingo/PolytopeSampler.py index e6576382..f003a486 100644 --- a/dingo/PolytopeSampler.py +++ b/dingo/PolytopeSampler.py @@ -17,7 +17,7 @@ get_matrices_of_full_dim_polytope, ) -from dingo.pyoptInterface_based_impl import fba,fva,inner_ball,remove_redundant_facets +from dingo.pyoptinterface_based_impl import fba,fva,inner_ball,remove_redundant_facets from volestipy import HPolytope diff --git a/dingo/__init__.py b/dingo/__init__.py index b1395666..067c8b98 100644 --- a/dingo/__init__.py +++ b/dingo/__init__.py @@ -27,7 +27,7 @@ from dingo.MetabolicNetwork import MetabolicNetwork from dingo.PolytopeSampler import PolytopeSampler -from dingo.pyoptInterface_based_impl import fba, fva, inner_ball, remove_redundant_facets, set_default_solver +from dingo.pyoptinterface_based_impl import fba, fva, inner_ball, remove_redundant_facets, set_default_solver from volestipy import HPolytope diff --git a/dingo/pyoptInterface_based_impl.py b/dingo/pyoptinterface_based_impl.py similarity index 99% rename from dingo/pyoptInterface_based_impl.py rename to dingo/pyoptinterface_based_impl.py index c3b3fc40..6c83bf76 100644 --- a/dingo/pyoptInterface_based_impl.py +++ b/dingo/pyoptinterface_based_impl.py @@ -248,7 +248,7 @@ def inner_ball(A, b, solver_name=None): # And check whether the computed radius is negative if r < 0: - print( + raise Exception( "The radius calculated has negative value. The polytope is infeasible or something went wrong with the solver" ) else: @@ -450,9 +450,6 @@ def remove_redundant_facets(lb, ub, S, c, opt_percentage=100, solver_name=None): removed += 1 facet_left_removed[i] = True - # Reset the inequality - # model_iter.set_variable_attribute(v[i], poi.VariableAttribute.LowerBound, lb[i]) - if (not redundant_facet_left) or (not redundant_facet_right): width = abs(max_objective - min_objective) diff --git a/dingo/volestipy.pyx b/dingo/volestipy.pyx index 4b31377c..300f0842 100644 --- a/dingo/volestipy.pyx +++ b/dingo/volestipy.pyx @@ -26,7 +26,7 @@ import json import scipy.io # ---------------------------------------------------------------------------------- -from dingo.pyoptInterface_based_impl import inner_ball +from dingo.pyoptinterface_based_impl import inner_ball # Set the time def get_time_seed(): diff --git a/tests/fba.py b/tests/fba.py index 5628abae..f5716435 100644 --- a/tests/fba.py +++ b/tests/fba.py @@ -10,7 +10,7 @@ import os import sys from dingo import MetabolicNetwork -from dingo.pyoptInterface_based_impl import set_default_solver +from dingo.pyoptinterface_based_impl import set_default_solver class TestFba(unittest.TestCase): diff --git a/tests/full_dimensional.py b/tests/full_dimensional.py index c8ffec87..4af2f12a 100644 --- a/tests/full_dimensional.py +++ b/tests/full_dimensional.py @@ -11,7 +11,7 @@ import os import sys from dingo import MetabolicNetwork, PolytopeSampler -from dingo.pyoptInterface_based_impl import set_default_solver +from dingo.pyoptinterface_based_impl import set_default_solver class TestFullDim(unittest.TestCase): diff --git a/tests/max_ball.py b/tests/max_ball.py index a7d80344..8189f664 100644 --- a/tests/max_ball.py +++ b/tests/max_ball.py @@ -13,7 +13,7 @@ import scipy import numpy as np from dingo import MetabolicNetwork, PolytopeSampler -from dingo.pyoptInterface_based_impl import inner_ball, set_default_solver +from dingo.pyoptinterface_based_impl import inner_ball, set_default_solver from dingo.scaling import gmscale diff --git a/tests/rounding.py b/tests/rounding.py index 64a55f5f..e3d97c62 100644 --- a/tests/rounding.py +++ b/tests/rounding.py @@ -13,7 +13,7 @@ import sys import numpy as np from dingo import MetabolicNetwork, PolytopeSampler -from dingo.pyoptInterface_based_impl import set_default_solver +from dingo.pyoptinterface_based_impl import set_default_solver def test_rounding(self, method_str): diff --git a/tests/sampling.py b/tests/sampling.py index 665e2517..a0827d68 100644 --- a/tests/sampling.py +++ b/tests/sampling.py @@ -12,7 +12,7 @@ import os import sys from dingo import MetabolicNetwork, PolytopeSampler -from dingo.pyoptInterface_based_impl import set_default_solver +from dingo.pyoptinterface_based_impl import set_default_solver class TestSampling(unittest.TestCase): diff --git a/tests/sampling_no_multiphase.py b/tests/sampling_no_multiphase.py index f6020eee..4f074504 100644 --- a/tests/sampling_no_multiphase.py +++ b/tests/sampling_no_multiphase.py @@ -12,7 +12,7 @@ import os import sys from dingo import MetabolicNetwork, PolytopeSampler -from dingo.pyoptInterface_based_impl import set_default_solver +from dingo.pyoptinterface_based_impl import set_default_solver class TestSampling(unittest.TestCase): diff --git a/tests/scaling.py b/tests/scaling.py index d573afb0..525a9498 100644 --- a/tests/scaling.py +++ b/tests/scaling.py @@ -13,7 +13,7 @@ import numpy as np from dingo import MetabolicNetwork from dingo.scaling import gmscale -from dingo.pyoptInterface_based_impl import set_default_solver +from dingo.pyoptinterface_based_impl import set_default_solver class TestScaling(unittest.TestCase):