From b2b42734b537903bc8f7781a0abe44e41baf8f05 Mon Sep 17 00:00:00 2001 From: KeShih Date: Sat, 6 Jul 2024 22:00:16 +0800 Subject: [PATCH] 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 | 0 dingo/{ => archive}/fba.py | 0 dingo/{ => archive}/fva.py | 0 .../gurobi_based_implementations.py | 0 dingo/{ => archive}/inner_ball.py | 0 dingo/parser.py | 4 +- dingo/pyoptInterface_based_impl.py | 497 +++++ dingo/volestipy.pyx | 69 +- poetry.lock | 1888 ++++++++++------- pyproject.toml | 1 + .../{ => archive}/fast_implementation_test.py | 0 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, 1732 insertions(+), 1016 deletions(-) rename dingo/{ => archive}/experimental_gurobi_functions/redundant_facet_removal_experiment.py (100%) rename dingo/{ => archive}/fba.py (100%) rename dingo/{ => archive}/fva.py (100%) rename dingo/{ => archive}/gurobi_based_implementations.py (100%) rename dingo/{ => archive}/inner_ball.py (100%) create mode 100644 dingo/pyoptInterface_based_impl.py rename tests/{ => archive}/fast_implementation_test.py (100%) 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/archive/experimental_gurobi_functions/redundant_facet_removal_experiment.py similarity index 100% rename from dingo/experimental_gurobi_functions/redundant_facet_removal_experiment.py rename to dingo/archive/experimental_gurobi_functions/redundant_facet_removal_experiment.py diff --git a/dingo/fba.py b/dingo/archive/fba.py similarity index 100% rename from dingo/fba.py rename to dingo/archive/fba.py diff --git a/dingo/fva.py b/dingo/archive/fva.py similarity index 100% rename from dingo/fva.py rename to dingo/archive/fva.py diff --git a/dingo/gurobi_based_implementations.py b/dingo/archive/gurobi_based_implementations.py similarity index 100% rename from dingo/gurobi_based_implementations.py rename to dingo/archive/gurobi_based_implementations.py diff --git a/dingo/inner_ball.py b/dingo/archive/inner_ball.py similarity index 100% rename from dingo/inner_ball.py rename to dingo/archive/inner_ball.py 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..c6e109a3 --- /dev/null +++ b/dingo/pyoptInterface_based_impl.py @@ -0,0 +1,497 @@ +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, 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 = model.add_variables(range(n)) + + # 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) + import time + + # 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, Aeq, beq, np.array([-c]), [val], solver_name) + + for i in indices: + + redundant_facet_right = True + redundant_facet_left = True + + for j in range(n): + model_iter.set_variable_attribute( + v[j], poi.VariableAttribute.LowerBound, lb[j] + ) + model_iter.set_variable_attribute( + v[j], poi.VariableAttribute.UpperBound, ub[j] + ) + + # 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) - - self.polytope_cpp.mmcs_initialize(n_variables, ess, check_psrf, parallel, num_threads) - - # Get max inscribed ball for the initial polytope - 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) while True: @@ -269,7 +220,7 @@ cdef class HPolytope: break self.polytope_cpp.get_polytope_as_matrices(&new_A[0,0], &new_b[0]) - new_temp_c, radius = slow_inner_ball(np.asarray(new_A), np.asarray(new_b)) + new_temp_c, radius = inner_ball(np.asarray(new_A), np.asarray(new_b), solver) inner_point_for_c = np.asarray(new_temp_c) cdef double[:,::1] samples = np.zeros((n_variables, N_samples), dtype=np.float64, order="C") diff --git a/poetry.lock b/poetry.lock index 598593c5..683e537b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,24 +2,26 @@ [[package]] name = "anyio" -version = "3.6.2" +version = "4.4.0" description = "High level compatibility layer for multiple 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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/archive/fast_implementation_test.py similarity index 100% rename from tests/fast_implementation_test.py rename to tests/archive/fast_implementation_test.py 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()