CMake Support

.github/workflows/build_binaries_cmake.yml

@@ -0,0 +1,77 @@
+# This starter workflow is for a CMake project running on multiple platforms. There is a different starter workflow if you just want a single platform.
+# See: https://github.com/actions/starter-workflows/blob/main/ci/cmake-single-platform.yml
+name: Build binaries CMake
+
+on:
+  push:
+  pull_request:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      # Set fail-fast to false to ensure that feedback is delivered for all matrix combinations. Consider changing this to true when your workflow is stable.
+      fail-fast: false
+
+      # Set up a matrix to run the following 3 configurations:
+      # 1. <Windows, Release, latest MSVC compiler toolchain on the default runner image, default generator>
+      # 2. <Linux, Release, latest GCC compiler toolchain on the default runner image, default generator>
+      # 3. <Linux, Release, latest Clang compiler toolchain on the default runner image, default generator>
+      #
+      # To add more build types (Release, Debug, RelWithDebInfo, etc.) customize the build_type list.
+      matrix:
+        include:
+          - os: windows-latest
+            c_compiler: cl
+            cpp_compiler: cl
+            build_physiboss: "OFF"
+          - os: ubuntu-latest
+            c_compiler: gcc
+            cpp_compiler: g++
+            build_physiboss: "ON"
+          - os: ubuntu-latest
+            c_compiler: clang
+            cpp_compiler: clang++
+            build_physiboss: "ON"
+          - os: macos-latest
+            c_compiler: gcc-15
+            cpp_compiler: g++-15
+            build_physiboss: "ON"
+          # - os: macos-latest
+          #   c_compiler: cc
+          #   cpp_compiler: c++
+          #   build_physiboss: "ON"
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set reusable strings
+      # Turn repeated input strings (such as the build output directory) into step outputs. These step outputs can be used throughout the workflow file.
+      id: strings
+      shell: bash
+      run: |
+        echo "build-output-dir=${{ github.workspace }}/build" >> "$GITHUB_OUTPUT"
+
+    - name: Install dependencies (Linux)
+      if: matrix.os == 'ubuntu-latest'
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libomp-dev
+
+    - name: Configure CMake
+      # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
+      # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
+      run: >
+        cmake -B ${{ steps.strings.outputs.build-output-dir }}
+        -DCMAKE_CXX_COMPILER=${{ matrix.cpp_compiler }}
+        -DCMAKE_C_COMPILER=${{ matrix.c_compiler }}
+        -DCMAKE_BUILD_TYPE=Release
+        -DPHYSICELL_BUILD_PHYSIBOSS=${{ matrix.build_physiboss }}
+        -S ${{ github.workspace }}
+
+    - name: Build
+      # Build your program with the given configuration. Note that --config is needed because the default Windows generator is a multi-config generator (Visual Studio generator).
+      run: cmake --build ${{ steps.strings.outputs.build-output-dir }} --config Release

.github/workflows/tests_cmake.yml

@@ -0,0 +1,89 @@
+name: Tests CMake
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  tests:
+    name: Testing ${{ matrix.projects.name }} on ${{ matrix.platform.os }}
+    runs-on: ${{ matrix.platform.os }}
+
+    strategy:
+      # Set fail-fast to false to ensure that feedback is delivered for all matrix combinations. Consider changing this to true when your workflow is stable.
+      fail-fast: false
+
+      # Set up a matrix to run cross-product of projects and OS/compiler combinations
+      matrix:
+        projects: [
+          {"use_physiboss": false, cwd: "build/sample_projects/template", name: "PhysiCell Template", binary: "template", max_time: 120, config: "config/PhysiCell_settings.xml", validation_output_folder: "output_template"},
+          {"use_physiboss": true, cwd: "build/sample_projects_intracellular/boolean/template_BM", name: "PhysiBoSS Template", binary: "template_BM", max_time: 120, config: "config/PhysiCell_settings.xml", validation_output_folder: "output_template_BM"},
+          {"use_physiboss": true, cwd: "build/sample_projects_intracellular/boolean/physiboss_cell_lines", name: "PhysiBoSS Cell Lines", binary: "physiboss_cell_lines", max_time: 120, config: "config/PhysiCell_settings.xml", validation_output_folder: "output_physiboss-cell-lines-sample"},
+          {"use_physiboss": false, cwd: "build/sample_projects/physimess", name: "PhysiMeSS Sample", binary: "physimess", config: "config/Fibre_Degradation/mymodel_matrix_degradation.xml", max_time: 120, validation_output_folder: ""},
+          {"use_physiboss": true, cwd: "build/sample_projects_intracellular/boolean/tutorial", name: "PhysiBoSS Tutorial", binary: "tutorial", config: "config/cell_cycle/PhysiCell_settings.xml", max_time: 300, validation_output_folder: "output_physiboss-tutorial"},
+          {"use_physiboss": false, cwd: "build/sample_projects/worm", name: "PhysiCell worm", binary: "worm", config: "config/PhysiCell_settings.xml", max_time: 120, validation_output_folder: "output_worm-sample"},
+          {"use_physiboss": false, cwd: "build/sample_projects/virus_macrophage", name: "Virus Macrophage", binary: "virus_macrophage", config: "config/PhysiCell_settings.xml", max_time: 120, validation_output_folder: "output_virus-macrophage-sample"},
+          {"use_physiboss": false, cwd: "build/sample_projects/mechano", name: "PhysiCell Mechano", binary: "mechano", config: "config/PhysiCell_settings.xml", max_time: 120, validation_output_folder: "output_mechano-sample"},
+          {"use_physiboss": false, cwd: "build/sample_projects/cancer_biorobots", name: "PhysiCell Cancer Biorobots", binary: "cancer_biorobots", config: "config/PhysiCell_settings.xml", max_time: 120, validation_output_folder: ""},
+          {"use_physiboss": false, cwd: "build/sample_projects/biorobots", name: "PhysiCell Biorobots", binary: "biorobots", config: "config/PhysiCell_settings.xml", max_time: 120, validation_output_folder: ""},
+          {"use_physiboss": false, cwd: "build/sample_projects/celltypes3", name: "PhysiCell Celltypes3", binary: "celltypes3", config: "config/PhysiCell_settings.xml", max_time: 120, validation_output_folder: ""},
+          {"use_physiboss": false, cwd: "build/sample_projects/custom_division", name: "PhysiCell custom division", binary: "custom_division", config: "config/PhysiCell_settings.xml", max_time: 120, validation_output_folder: ""},
+          {"use_physiboss": false, cwd: "build/sample_projects/interactions", name: "PhysiCell interactions", binary: "interactions", config: "config/PhysiCell_settings.xml", max_time: 120, validation_output_folder: ""},
+          {"use_physiboss": false, cwd: "build/sample_projects/pred_prey_farmer", name: "PhysiCell prey predator", binary: "pred_prey_farmer", config: "config/PhysiCell_settings.xml", max_time: 120, validation_output_folder: ""},
+          {"use_physiboss": false, cwd: "build/sample_projects/rules_sample", name: "PhysiCell rules sample", binary: "rules_sample", config: "config/PhysiCell_settings.xml", max_time: 120, validation_output_folder: ""},
+          {"use_physiboss": false, cwd: "build/sample_projects/asymmetric_division", name: "PhysiCell asymmetric division", binary: "asymmetric_division", config: "config/PhysiCell_settings.xml", max_time: 120, validation_output_folder: ""},
+          {"use_physiboss": false, cwd: "build/sample_projects/episode", name: "PhysiCell Episode", binary: "episode", max_time: 120, config: "config/PhysiCell_settings.xml", validation_output_folder: ""},
+        ]
+        platform: [
+          {"os": "windows-latest", "c_compiler": "cl", "cpp_compiler": "cl", "build_physiboss": "OFF"},
+          {"os": "ubuntu-latest", "c_compiler": "gcc", "cpp_compiler": "g++", "build_physiboss": "ON"},
+          {"os": "ubuntu-latest", "c_compiler": "clang", "cpp_compiler": "clang++", "build_physiboss": "ON"},
+          {"os": "macos-latest", "c_compiler": "gcc-15", "cpp_compiler": "g++-15", "build_physiboss": "ON"},
+          # {"os": "macos-latest", "c_compiler": "cc", "cpp_compiler": "c++", "build_physiboss": "ON"},
+        ]
+        exclude:
+          - { projects: { use_physiboss: true }, platform: { build_physiboss: "OFF" } }
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set reusable strings
+      # Turn repeated input strings (such as the build output directory) into step outputs. These step outputs can be used throughout the workflow file.
+      id: strings
+      shell: bash
+      run: |
+        echo "build-output-dir=${{ github.workspace }}/build" >> "$GITHUB_OUTPUT"
+
+    - name: Install dependencies (Linux)
+      if: matrix.platform.os == 'ubuntu-latest'
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libomp-dev
+
+    - name: Configure CMake
+      # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
+      # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
+      run: >
+        cmake -B ${{ steps.strings.outputs.build-output-dir }}
+        -DCMAKE_CXX_COMPILER=${{ matrix.platform.cpp_compiler }}
+        -DCMAKE_C_COMPILER=${{ matrix.platform.c_compiler }}
+        -DCMAKE_BUILD_TYPE=Release
+        -DPHYSICELL_BUILD_PHYSIBOSS=${{ matrix.platform.build_physiboss }}
+        -S ${{ github.workspace }}
+
+    - name: Build
+      # Build your program with the given configuration. Note that --config is needed because the default Windows generator is a multi-config generator (Visual Studio generator).
+      run: cmake --build ${{ steps.strings.outputs.build-output-dir }} --config Release --target ${{ matrix.projects.binary }}
+
+    - name: Run ${{ matrix.projects.name }} project
+      run: |
+        python ${{ github.workspace }}/beta/test_run_sample.py ${{ matrix.platform.os == 'windows-latest' && 'Release/' || '' }}${{ matrix.projects.binary }} ${{ matrix.projects.config }} ${{ matrix.projects.max_time }}
+      working-directory: ${{ matrix.projects.cwd }}
+
+    - name: Check ${{ matrix.projects.name }} project simulation results
+      if: matrix.projects.validation_output_folder != ''
+      run: |
+        python ${{ github.workspace }}/beta/test_diff_svg.py output ${{ github.workspace }}/tests/cases/${{ matrix.projects.validation_output_folder }}
+      working-directory: ${{ matrix.projects.cwd }}
+

.gitignore

@@ -1,23 +1,48 @@
 *.asv
 ._.DS_Store
 .DS_Store
-*.exe
 *.o
 addons/libRoadrunner/roadrunner/
 addons/libRoadrunner/roadrunner-win64-vs14-cp35m.zip
 addons/PhysiBoSS/MaBoSS/
 addons/PhysiBoSS/libMaBoSS-*.tar.gz
-biorobots
-cancer_immune_3D
+build/
 config/PhysiCell_settings-backup.xml
-heterogeneity
 initial.svg
-interaction_demo
 Makefile-backup
 pmb_debug.log
-project
 studio_debug.log
 user_projects/*
 !user_projects/empty.txt
 Studio.zip
 /studio
+
+# executables
+/project
+/biorobots
+/cancer_biorobots
+/cancer_immune_3D
+/celltypes3
+/heterogeneity
+/interaction_demo
+/pred_prey
+/virus-sample
+/worm
+/*.exe
+
+# boolean intracellular project executables
+/invasion_model
+/PhysiBoSS_Cell_Lines
+
+# fba intracellular project executables
+/cancer_metabolism
+/ecoli-dfba
+
+# ode intracellular project executables
+/ode_energy
+
+# test project executables
+/time_tests
+/unit_tests
+/test_custom_DCs
+/test_voxel_values

BioFVM/BioFVM_microenvironment.cpp

@@ -272,12 +272,12 @@ void Microenvironment::apply_dirichlet_conditions( void )
 {
 	/*
 	#pragma omp parallel for 
-	for( unsigned int i=0 ; i < dirichlet_indices.size() ; i++ )
+	for( long long i=0 ; i < dirichlet_indices.size() ; i++ )
 	{ density_vector( dirichlet_indices[i] ) = dirichlet_value_vectors[i]; }
 	*/
 
 	// #pragma omp parallel for 
-	for( unsigned int i=0 ; i < mesh.voxels.size() ;i++ )
+	for( long long i=0 ; i < mesh.voxels.size() ;i++ )
 	{
 		/*
 		if( mesh.voxels[i].is_Dirichlet == true )
@@ -740,7 +740,7 @@ void Microenvironment::simulate_bulk_sources_and_sinks( double dt )
 	}
 
 	#pragma omp parallel for
-	for( unsigned int i=0; i < mesh.voxels.size() ; i++ )
+	for( long long i=0; i < mesh.voxels.size() ; i++ )
 	{
 		bulk_supply_rate_function( this,i, &bulk_source_sink_solver_temp1[i] ); // temp1 = S
 		bulk_supply_target_densities_function( this,i, &bulk_source_sink_solver_temp2[i]); // temp2 = T
@@ -762,7 +762,7 @@ void Microenvironment::simulate_bulk_sources_and_sinks( double dt )
 void Microenvironment::simulate_cell_sources_and_sinks( std::vector<Basic_Agent*>& basic_agent_list , double dt )
 {
 	#pragma omp parallel for
-	for( unsigned int i=0 ; i < basic_agent_list.size() ; i++ )
+	for( long long i=0 ; i < basic_agent_list.size() ; i++ )
 	{		
 		basic_agent_list[i]->simulate_secretion_and_uptake( this , dt ); 
 	}
@@ -787,7 +787,7 @@ void Microenvironment::update_rates( void )
 	{ uptake_rates.assign( number_of_voxels() , zero ); }
 
 	#pragma omp parallel for 
-	for( unsigned int i=0 ; i < number_of_voxels() ; i++ )
+	for( long long i=0 ; i < number_of_voxels() ; i++ )
 	{
 		bulk_uptake_rate_function( this,i, &(uptake_rates[i]) ); 		
 		bulk_supply_rate_function( this,i, &(supply_rates[i]) ); 		
@@ -858,7 +858,7 @@ void Microenvironment::compute_all_gradient_vectors( void )
 	}
 
 	#pragma omp parallel for 
-	for( unsigned int k=0; k < mesh.z_coordinates.size() ; k++ )
+	for( long long k=0; k < mesh.z_coordinates.size() ; k++ )
 	{
 		for( unsigned int j=0; j < mesh.y_coordinates.size() ; j++ )
 		{
@@ -904,7 +904,7 @@ void Microenvironment::compute_all_gradient_vectors( void )
 	}
 
 	#pragma omp parallel for 
-	for( unsigned int k=0; k < mesh.z_coordinates.size() ; k++ )
+	for( long long k=0; k < mesh.z_coordinates.size() ; k++ )
 	{
 		for( unsigned int i=0; i < mesh.x_coordinates.size() ; i++ )
 		{
@@ -953,7 +953,7 @@ void Microenvironment::compute_all_gradient_vectors( void )
 	{ return; }
 
 	#pragma omp parallel for 
-	for( unsigned int j=0; j < mesh.y_coordinates.size() ; j++ )
+	for( long long j=0; j < mesh.y_coordinates.size() ; j++ )
 	{
 		for( unsigned int i=0; i < mesh.x_coordinates.size() ; i++ )
 		{

BioFVM/BioFVM_solvers.cpp

@@ -195,7 +195,7 @@ void diffusion_decay_solver__constant_coefficients_LOD_3D( Microenvironment& M,
 
 	M.apply_dirichlet_conditions();
 	#pragma omp parallel for 
-	for( unsigned int k=0; k < M.mesh.z_coordinates.size() ; k++ )
+	for( long long k=0; k < M.mesh.z_coordinates.size() ; k++ )
 	{
 		for( unsigned int j=0; j < M.mesh.y_coordinates.size() ; j++ )
 		{
@@ -225,7 +225,7 @@ void diffusion_decay_solver__constant_coefficients_LOD_3D( Microenvironment& M,
 
 	M.apply_dirichlet_conditions();
 	#pragma omp parallel for 
-	for( unsigned int k=0; k < M.mesh.z_coordinates.size() ; k++ )
+	for( long long k=0; k < M.mesh.z_coordinates.size() ; k++ )
 	{
 		for( unsigned int i=0; i < M.mesh.x_coordinates.size() ; i++ )
 		{
@@ -259,7 +259,7 @@ void diffusion_decay_solver__constant_coefficients_LOD_3D( Microenvironment& M,
 
 	M.apply_dirichlet_conditions();
  #pragma omp parallel for 
- for( unsigned int j=0; j < M.mesh.y_coordinates.size() ; j++ )
+ for( long long j=0; j < M.mesh.y_coordinates.size() ; j++ )
  {
 
   for( unsigned int i=0; i < M.mesh.x_coordinates.size() ; i++ )
@@ -386,7 +386,7 @@ void diffusion_decay_solver__constant_coefficients_LOD_2D( Microenvironment& M,
 
 	// x-diffusion 
 	#pragma omp parallel for 
-	for( unsigned int j=0; j < M.mesh.y_coordinates.size() ; j++ )
+	for( long long j=0; j < M.mesh.y_coordinates.size() ; j++ )
 	{
 		// Thomas solver, x-direction
 
@@ -416,7 +416,7 @@ void diffusion_decay_solver__constant_coefficients_LOD_2D( Microenvironment& M,
 
 	M.apply_dirichlet_conditions();
 	#pragma omp parallel for 
-	for( unsigned int i=0; i < M.mesh.x_coordinates.size() ; i++ )
+	for( long long i=0; i < M.mesh.x_coordinates.size() ; i++ )
 	{
 		// Thomas solver, y-direction
 
@@ -497,7 +497,7 @@ void diffusion_decay_explicit_uniform_rates( Microenvironment& M, double dt )
 	static vector<double> constant4 = M.one - dt * M.decay_rates;
 
 	#pragma omp parallel for
-	for( unsigned int i=0; i < (*(M.p_density_vectors)).size() ; i++ )
+	for( long long i=0; i < (*(M.p_density_vectors)).size() ; i++ )
 	{
 		unsigned int number_of_neighbors = M.mesh.connected_voxel_indices[i].size(); 
 
@@ -591,7 +591,7 @@ void diffusion_decay_solver__constant_coefficients_LOD_1D( Microenvironment& M,
 
 	// x-diffusion 
 	#pragma omp parallel for 
-	for( unsigned int j=0; j < M.mesh.y_coordinates.size() ; j++ )
+	for( long long j=0; j < M.mesh.y_coordinates.size() ; j++ )
 	{
 		// Thomas solver, x-direction
 

BioFVM/CMakeLists.txt

@@ -0,0 +1,7 @@
+add_library(BioFVM OBJECT)
+
+file(GLOB SOURCES "*.cpp")
+target_sources(BioFVM PRIVATE ${SOURCES})
+
+find_package(OpenMP REQUIRED)
+target_link_libraries(BioFVM PUBLIC OpenMP::OpenMP_CXX)