Added metabolic polytope simplification

.gitignore

@@ -1,4 +1,6 @@
 test/build
+test/bigg/*.json
+!test/bigg/e_coli_core.json
 external/_deps
 examples/build
 .vscode

examples/metabolic_simplification/CMakeLists.txt

@@ -0,0 +1,68 @@
+# VolEsti (volume computation and sampling library)
+
+# Copyright (c) 2012-2026 Vissarion Fisikopoulos
+# Copyright (c) 2018-2026 Apostolos Chalkis
+# Copyright (c) 2026      Dimitrios Pavlou
+
+# Contributed and/or modified by Dimitrios Pavlou, as part of Google Summer of Code 2026 program
+
+# Licensed under GNU LGPL.3, see LICENCE file
+
+project (VolEsti)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 3.11)
+
+set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS true)
+
+if(COMMAND cmake_policy)
+    cmake_policy(SET CMP0003 NEW)
+endif(COMMAND cmake_policy)
+
+add_definitions(-DDISABLE_NLP_ORACLES)
+
+include("../../external/cmake-files/Eigen.cmake")
+GetEigen()
+
+include("../../external/cmake-files/Boost.cmake")
+GetBoost()
+
+include("../../external/cmake-files/Spectra.cmake")
+GetSpectra()
+
+include("../../external/cmake-files/HiGHS.cmake")
+GetHighs()
+
+include("../../external/cmake-files/LPSolve.cmake")
+GetLPSolve()
+
+include("../../external/cmake-files/SuiteSparse.cmake")
+GetSuiteSparse()
+
+include("../../external/cmake-files/JSON.cmake")
+GetJSON()
+
+set(CMAKE_EXPORT_COMPILE_COMMANDS "ON")
+
+include_directories (BEFORE ../../external)
+include_directories (BEFORE ../../include)
+include_directories (BEFORE ../../include/convex_bodies)
+include_directories (BEFORE ../../include/misc)
+include_directories (BEFORE ../../include/preprocess)
+
+# for Eigen
+if (${CMAKE_VERSION} VERSION_LESS "3.12.0")
+    add_compile_options(-D "EIGEN_NO_DEBUG")
+else ()
+    add_compile_definitions("EIGEN_NO_DEBUG")
+endif ()
+
+
+add_definitions(${CMAKE_CXX_FLAGS} "-std=c++17")  # enable C++17 standard
+add_definitions(${CMAKE_CXX_FLAGS} "-O3")  # optimization of the compiler
+add_definitions(${CMAKE_CXX_FLAGS} "-g")
+add_definitions(${CXX_COVERAGE_COMPILE_FLAGS} "-DBOOST_NO_AUTO_PTR")
+
+find_package(LAPACK REQUIRED)
+find_package(BLAS REQUIRED)
+add_executable(metabolic_simplification metabolic_simplification.cpp)
+TARGET_LINK_LIBRARIES(metabolic_simplification highs::highs lp_solve nlohmann_json::nlohmann_json ${SUITESPARSE_LIBRARIES} ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} ${MKL_LINK})

examples/metabolic_simplification/metabolic_simplification.cpp

@@ -0,0 +1,89 @@
+// VolEsti (volume computation and sampling library)
+
+// Copyright (c) 2012-2026 Vissarion Fisikopoulos
+// Copyright (c) 2018-2026 Apostolos Chalkis
+// Copyright (c) 2026      Dimitrios Pavlou
+
+// Contributed and/or modified by Dimitrios Pavlou, as part of Google Summer of Code 2026 program
+
+// Licensed under GNU LGPL.3, see LICENCE file
+
+//
+// Usage: ./metabolic_simplification <model_id.json>
+//
+
+#include "Eigen/Eigen"
+#include "cartesian_geom/cartesian_kernel.h"
+#include "convex_bodies/hpolytope.h"
+#include "io/bigg_parser.hpp"
+#include "preprocess/metabolic/exhaustive_simplification.hpp"
+#include "preprocess/metabolic/clarkson_simplification.hpp"
+#include "preprocess/metabolic/transformation.hpp"
+#include "random_walks/random_walks.hpp"
+#include "volume/volume_cooling_balls.hpp"
+#include "generators/boost_random_number_generator.hpp"
+#include <iostream>
+#include <string>
+
+typedef double NT;
+typedef Cartesian<NT> Kernel;
+typedef typename Kernel::Point Point;
+typedef MetabolicPolytope<Point> Polytope;
+typedef HPolytope<Point> Hpolytope;
+typedef Eigen::Matrix<NT, Eigen::Dynamic, Eigen::Dynamic> DenseMT;
+typedef typename Polytope::VT VT;
+typedef BoostRandomNumberGenerator<boost::mt19937, NT> RNG;
+
+int main(int argc, char* argv[]) {
+    if (argc != 2) {
+        std::cerr << "usage: " << argv[0] << " <model.json>" << std::endl;
+        return 1;
+    }
+
+    Polytope P = parse_from_json<Point>(argv[1]);
+
+    std::cout << "input polytope" << "\n"
+              << " reactions     : " << P.getDimension() << "\n"
+              << " metabolites   : " << P.getNumEqualities() << "\n"
+              << " finite bounds : " << P.getNumFiniteBounds() << "\n" << std::endl;
+
+    // Simplifies the polytope, removing redundant bounds and fixing pinned variables.
+    clarkson_simplification::Config config;
+    config.fix_dimensions = true; 
+    config.verbosity = clarkson_simplification::VerbosityLevel::Summary;
+
+    auto result = clarkson_simplification::simplify(P, config);
+
+    if (!result.success) {
+        std::cerr << "simplification failed" << std::endl;
+        return 1;
+    }
+
+    std::cout << "\nsimplified polytope" << "\n"
+              << " finite bounds    : " << result.P.getNumFiniteBounds() << "\n"
+              << " bounds relaxed   : " << result.bounds_relaxed << "\n"
+              << " dimensions fixed : " << result.dims_fixed << std::endl;
+
+    // Transforms the simplified polytope, giving a full dimensional H-Polytope
+    // that volume estimation can work with.
+    auto trans_result = transform(result.P);
+    Hpolytope HP = std::get<0>(trans_result);
+    VT shift = std::get<1>(trans_result);
+    DenseMT N = std::get<2>(trans_result);
+
+    std::cout << "\ntransformed polytope\n"
+              << " dimension                   : " << HP.dimension() << "\n"
+              << " constraints (finite bounds) : " << HP.num_of_hyperplanes() << std::endl;
+
+    // Estimates the volume of the original polytope
+    unsigned walk_len = 10+HP.dimension()/10;
+    NT epsilon = 0.1;
+
+    auto volume = volume_cooling_balls<BallWalk, RNG, Hpolytope>(
+        HP, epsilon, walk_len
+    ).second;
+
+    std::cout << "\nvolume\n" << "estimate : " << volume << std::endl;
+
+    return 0;
+}

external/cmake-files/HiGHS.cmake

@@ -0,0 +1,12 @@
+set(HIGHS_CMAKE_DIR ${CMAKE_CURRENT_LIST_DIR})
+function(GetHighs)
+    include(FetchContent)
+    set(FETCHCONTENT_BASE_DIR "${HIGHS_CMAKE_DIR}/../_deps")
+    FetchContent_Declare(
+        highs
+        GIT_REPOSITORY https://github.com/ERGO-Code/HiGHS.git
+        GIT_TAG v1.10.0
+    )
+    message(STATUS "Fetching HiGHS")
+    FetchContent_MakeAvailable(highs)
+endfunction()

external/nlohmann/LICENSE.MIT

@@ -0,0 +1,21 @@
+MIT License 
+
+Copyright (c) 2013-2026 Niels Lohmann
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.