Merge pull request #343 from MathCancer/development

PhysiCell 1.14.1 release

Author: MathCancer

.github/workflows/build_binaries.yml

@@ -4,7 +4,7 @@ on:
   push:
   pull_request:
   release:
-    types: [created]
+    types: [published]
 
 jobs:
 
@@ -124,29 +124,34 @@ jobs:
           {short_name: "interaction", project: "interaction-sample", name: "PhysiCell Interaction", binary: "interaction_demo", extra_run: ""},
        ]
 
-    runs-on: macos-12
+    runs-on: macos-13
 
     steps:
     - uses: actions/checkout@v4
 
     - name: Install dependencies
-      run : brew install gcc@13
+      run : |
+        if ! brew list gcc@13 &>/dev/null; then
+          brew install gcc@13
+        else
+          echo "gcc@13 is already installed."
+        fi
       
     - name: Build ${{ matrix.projects.name }} project
       run: |
-        export MACOSX_DEPLOYMENT_TARGET=12
+        export MACOSX_DEPLOYMENT_TARGET=13
         make ${{ matrix.projects.project }}
         make clean
         ${{ matrix.projects.extra_run }}
         make PHYSICELL_CPP=g++-13 static
-        cp ${{ matrix.projects.binary }} ${{ matrix.projects.binary }}_macos12
+        cp ${{ matrix.projects.binary }} ${{ matrix.projects.binary }}_macos13
 
     - name: Caching produced project binary 
       uses: actions/cache@v4
       with:
         path: |
-          ${{ github.workspace }}/${{ matrix.projects.binary }}_macos12
-        key: ${{ runner.os }}-macos12-${{ github.run_id }}
+          ${{ github.workspace }}/${{ matrix.projects.binary }}_macos13
+        key: ${{ runner.os }}-macos13-${{ github.run_id }}
 
     - name: Look at the generated binary
       run: |
@@ -174,11 +179,16 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Install dependencies
-      run : brew install gcc@13
+      run : |
+        if ! brew list gcc@13 &>/dev/null; then
+          brew install gcc@13
+        else
+          echo "gcc@13 is already installed."
+        fi
       
     - name: Build ${{ matrix.projects.name }} project
       run: |
-        export MACOSX_DEPLOYMENT_TARGET=12
+        export MACOSX_DEPLOYMENT_TARGET=13
         make ${{ matrix.projects.project }}
         make clean
         ${{ matrix.projects.extra_run }}
@@ -212,7 +222,7 @@ jobs:
           {short_name: "interaction", project: "interaction-sample", name: "PhysiCell Interaction", binary: "interaction_demo", extra_run: ""},
         ]
 
-    runs-on: macos-12
+    runs-on: macos-13
     needs: [macos_step0a, macos_step0b]
 
     steps:
@@ -229,12 +239,12 @@ jobs:
       uses: actions/cache@v4
       with:
         path: |
-          ${{ github.workspace }}/${{ matrix.projects.binary }}_macos12
-        key: ${{ runner.os }}-macos12-${{ github.run_id }}
+          ${{ github.workspace }}/${{ matrix.projects.binary }}_macos13
+        key: ${{ runner.os }}-macos13-${{ github.run_id }}
 
     - name: Creating universal binary
       run: | 
-        lipo -create -output ${{ matrix.projects.binary }} ${{ matrix.projects.binary }}_macos12 ${{ matrix.projects.binary }}_macosm1
+        lipo -create -output ${{ matrix.projects.binary }} ${{ matrix.projects.binary }}_macos13 ${{ matrix.projects.binary }}_macosm1
 
     - name: Checking universal binary
       run: |

.github/workflows/tests.yml

@@ -13,7 +13,7 @@ jobs:
       matrix:
         os: [
           {name: "Ubuntu", os: "ubuntu-latest", shell: "bash", compiler: "g++"},
-          {name: "MacOS 12", os: "macos-12", shell: "bash", compiler: "g++-12"},
+          {name: "MacOS 13", os: "macos-13", shell: "bash", compiler: "g++-12"},
           {name: "MacOS 14 (M1)", os: "macos-14", shell: "bash", compiler: "g++-13"},
           {name: "Windows", os: "windows-latest", shell: "msys2", compiler: "g++"},
         ]
@@ -32,6 +32,8 @@ jobs:
           {project: "custom-division-sample", name: "PhysiCell custom division", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
           {project: "interaction-sample", name: "PhysiCell interactions", binary: "interaction_demo", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
           {project: "pred-prey-farmer", name: "PhysiCell prey predator", binary: "pred_prey", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
+          {project: "rules-sample", name: "PhysiCell rules sample", binary: "rules_sample", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
+          {project: "asymmetric-division-sample", name: "PhysiCell asymmetric division", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""}
         ]
 
     name: Testing ${{ matrix.projects.name }} on ${{ matrix.os.name }}
@@ -53,7 +55,7 @@ jobs:
 
     - name: Build ${{ matrix.projects.name }} project 
       run: |
-        make data-cleanup && make ${{ matrix.projects.project }} && make PHYSICELL_CPP=${{ matrix.os.compiler }}
+        make data-cleanup && make ${{ matrix.projects.project }} && make PHYSICELL_CPP=${{ matrix.os.compiler }} PROGRAM_NAME=${{ matrix.projects.binary }}
         
     - name: Run ${{ matrix.projects.name }} project
       run: |

BioFVM/BioFVM_MultiCellDS.cpp

@@ -515,15 +515,21 @@ void set_save_biofvm_cell_data_as_custom_matlab( bool newvalue )
 
 /* writing parts of BioFVM to a MultiCellDS file */ 
 
+static bool BioFVM_substrates_initialized_in_dom = false;
+
+void reset_BioFVM_substrates_initialized_in_dom( void )
+{
+	BioFVM_substrates_initialized_in_dom = false;
+}
+
+
 void add_BioFVM_substrates_to_open_xml_pugi( pugi::xml_document& xml_dom , std::string filename_base, Microenvironment& M )
 {
 	add_MultiCellDS_main_structure_to_open_xml_pugi( xml_dom ); 
 
 	pugi::xml_node root = biofvm_doc.child( "MultiCellDS" );
 	pugi::xml_node node = root.child( "microenvironment" ); 
 
-	static bool BioFVM_substrates_initialized_in_dom = false; 
-	
 	// if the TME has not yet been initialized in the DOM, create all the 
 	// right data elements, and populate the meshes. 
 	if( !BioFVM_substrates_initialized_in_dom )
@@ -564,36 +570,9 @@ void add_BioFVM_substrates_to_open_xml_pugi( pugi::xml_document& xml_dom , std::
 		// if Cartesian, add the x, y, and z coordinates 
 		if( M.mesh.Cartesian_mesh == true )
 		{
-			char temp [10240];
-			int position = 0; 
-			for( unsigned int k=0 ; k < M.mesh.x_coordinates.size()-1 ; k++ )
-			{ position += sprintf( temp+position, "%f " , M.mesh.x_coordinates[k] ); }
-			sprintf( temp+position , "%f" , M.mesh.x_coordinates[ M.mesh.x_coordinates.size()-1] ); 
-			node = node.append_child( "x_coordinates" ); 
-			node.append_child( pugi::node_pcdata ).set_value( temp ); 
-			attrib = node.append_attribute("delimiter");
-			attrib.set_value( " " ); 
-			
-			node = node.parent();
-			position = 0; 
-			for( unsigned int k=0 ; k < M.mesh.y_coordinates.size()-1 ; k++ )
-			{ position += sprintf( temp+position, "%f " , M.mesh.y_coordinates[k] ); }
-			sprintf( temp+position , "%f" , M.mesh.y_coordinates[ M.mesh.y_coordinates.size()-1] ); 
-			node = node.append_child( "y_coordinates" ); 
-			node.append_child( pugi::node_pcdata ).set_value( temp ); 
-			attrib = node.append_attribute("delimiter");
-			attrib.set_value( " " ); 
-			
-			node = node.parent();
-			position = 0; 
-			for( unsigned int k=0 ; k < M.mesh.z_coordinates.size()-1 ; k++ )
-			{ position += sprintf( temp+position, "%f " , M.mesh.z_coordinates[k] ); }
-			sprintf( temp+position , "%f" , M.mesh.z_coordinates[ M.mesh.z_coordinates.size()-1] ); 
-			node = node.append_child( "z_coordinates" ); 
-			node.append_child( pugi::node_pcdata ).set_value( temp ); 
-			attrib = node.append_attribute("delimiter");
-			attrib.set_value( " " ); 
-			node = node.parent(); 
+			write_coordinates_node(node, M.mesh.x_coordinates, "x_coordinates");
+			write_coordinates_node(node, M.mesh.y_coordinates, "y_coordinates");
+			write_coordinates_node(node, M.mesh.z_coordinates, "z_coordinates");
 		}
 		// write out the voxels -- minimal data, even if redundant for cartesian 
 		if( save_mesh_as_matlab == false )
@@ -744,7 +723,7 @@ void add_BioFVM_substrates_to_open_xml_pugi( pugi::xml_document& xml_dom , std::
 			{ filename_start++; } 
 			strcpy( filename_without_pathing , filename_start ); 
 
-			node.append_child( pugi::node_pcdata ).set_value( filename_without_pathing ); // filename );				
+			node.append_child( pugi::node_pcdata ).set_value( filename_without_pathing ); // filename ); 
 
 			node = node.parent(); 
 		}
@@ -812,6 +791,21 @@ void add_BioFVM_substrates_to_open_xml_pugi( pugi::xml_document& xml_dom , std::
 	return; 
 }
 
+void write_coordinates_node(pugi::xml_node &node, const std::vector<double> &coordinates, std::string name)
+{
+    std::ostringstream oss;
+    for (size_t i = 0; i < coordinates.size(); ++i)
+    {
+        if (i != 0)
+        { oss << " "; }
+        oss << coordinates[i];
+    }
+    pugi::xml_node coord_node = node.append_child(name.c_str());
+    coord_node.append_child(pugi::node_pcdata).set_value(oss.str().c_str());
+    pugi::xml_attribute attrib = coord_node.append_attribute("delimiter");
+    attrib.set_value(" ");
+}
+
 // not yet implemented 
 void add_BioFVM_basic_agent_to_open_xml_pugi( pugi::xml_document& xml_dom, Basic_Agent& BA  ); 
 

BioFVM/BioFVM_MultiCellDS.h

@@ -181,11 +181,14 @@ void set_save_biofvm_cell_data_as_custom_matlab( bool newvalue ); // default: tr
 
 /* writing parts of BioFVM to a MultiCellDS file */ 
 
+void reset_BioFVM_substrates_initialized_in_dom( void );
 void add_BioFVM_substrates_to_open_xml_pugi( pugi::xml_document& xml_dom , std::string filename_base , Microenvironment& M ); 
 void add_BioFVM_basic_agent_to_open_xml_pugi(  pugi::xml_document& xml_dom, Basic_Agent& BA ); // not implemented -- future edition 
 void add_BioFVM_agents_to_open_xml_pugi( pugi::xml_document& xml_dom, std::string filename_base, Microenvironment& M  ); 
 void add_BioFVM_to_open_xml_pugi( pugi::xml_document& xml_dom , std::string filename_base, double current_simulation_time , Microenvironment& M );
 
+void write_coordinates_node(pugi::xml_node &node, const std::vector<double> &coordinates, std::string name);
+
 void save_BioFVM_to_MultiCellDS_xml_pugi( std::string filename_base , Microenvironment& M , double current_simulation_time); 
 
 /* beta in PhysiCell 1.11.0 */

BioFVM/BioFVM_basic_agent.cpp

@@ -54,10 +54,16 @@ namespace BioFVM{
 
 std::vector<Basic_Agent*> all_basic_agents(0); 
 
+static int max_basic_agent_ID = 0;
+
+void reset_max_basic_agent_ID( void )
+{
+	max_basic_agent_ID = 0;
+}
+
 Basic_Agent::Basic_Agent()
 {
 	//give the agent a unique ID  
-	static int max_basic_agent_ID = 0; 
 	ID = max_basic_agent_ID; // 
 	max_basic_agent_ID++; 
 	// initialize position and velocity
@@ -78,7 +84,7 @@ Basic_Agent::Basic_Agent()
 
 	internalized_substrates = new std::vector<double>(0); // 
 	fraction_released_at_death = new std::vector<double>(0); 
-	fraction_transferred_when_ingested = new std::vector<double>(0); 
+	fraction_transferred_when_ingested = new std::vector<double>(1.0); 
 	register_microenvironment( get_default_microenvironment() );
 
 	// these are done in register_microenvironment
@@ -190,7 +196,7 @@ void Basic_Agent::register_microenvironment( Microenvironment* microenvironment_
 	total_extracellular_substrate_change.resize( microenvironment->density_vector(0).size() , 1.0 );
 
 	fraction_released_at_death->resize( microenvironment->density_vector(0).size() , 0.0 ); 
-	fraction_transferred_when_ingested->resize( microenvironment->density_vector(0).size() , 0.0 ); 
+	fraction_transferred_when_ingested->resize( microenvironment->density_vector(0).size() , 1.0 ); 
 
 	return; 
 }
@@ -341,4 +347,4 @@ void Basic_Agent::simulate_secretion_and_uptake( Microenvironment* pS, double dt
 	return; 
 }
 
-};
+};

BioFVM/BioFVM_basic_agent.h

@@ -55,7 +55,9 @@
 #include "BioFVM_vector.h"
 
 namespace BioFVM{
-	
+
+void reset_max_basic_agent_ID( void );
+
 class Basic_Agent
 {
  private:

CITATION.txt

@@ -1,7 +1,7 @@
 If you use PhysiCell in your project, please cite PhysiCell and the version 
 number, such as below:                                                      
 
-We implemented and solved the model using PhysiCell (Version 1.14.0) [1].    
+We implemented and solved the model using PhysiCell (Version 1.14.1) [1].    
 
 [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, 
     PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu-  
@@ -11,7 +11,7 @@ We implemented and solved the model using PhysiCell (Version 1.14.0) [1].
 Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM  
     as below:                                                               
 
-We implemented and solved the model using PhysiCell (Version 1.14.0) [1],    
+We implemented and solved the model using PhysiCell (Version 1.14.1) [1],    
 with BioFVM [2] to solve the transport equations.                           
 
 [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, 
@@ -25,7 +25,7 @@ with BioFVM [2] to solve the transport equations.
 
 If you use PhysiBoSS, please cite as below:
 
-We implemented and solved the model using PhysiCell (Version 1.14.0) [1],    
+We implemented and solved the model using PhysiCell (Version 1.14.1) [1],    
 with PhysiBoSS[2,3] to simulate the intracellular mechanisms.                           
 
 [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, 

Makefile

@@ -74,6 +74,7 @@ list-projects:
 	@echo "Sample projects: template biorobots-sample cancer-biorobots-sample cancer-immune-sample"
 	@echo "                 celltypes3-sample heterogeneity-sample pred-prey-farmer virus-macrophage-sample"
 	@echo "                 worm-sample interaction-sample mechano-sample rules-sample physimess-sample custom-division-sample"
+	@echo "					asymmetric-division-sample immune-function-sample"
 	@echo ""
 	@echo "Sample intracellular projects: template_BM ode-energy-sample physiboss-cell-lines-sample"
 	@echo "                 cancer-metabolism-sample physiboss-tutorial physiboss-tutorial-invasion"
@@ -197,15 +198,32 @@ physimess-sample:
 	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
 	cp -r ./sample_projects/physimess/config/* ./config/
 
-
 custom-division-sample:
-	cp ./sample_projects/custom_division/custom_modules/* ./custom_modules/
+	cp -r ./sample_projects/custom_division/custom_modules/* ./custom_modules/
 	touch main.cpp && cp main.cpp main-backup.cpp
 	cp ./sample_projects/custom_division/main.cpp ./main.cpp 
 	cp Makefile Makefile-backup
 	cp ./sample_projects/custom_division/Makefile .
 	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
-	cp ./sample_projects/custom_division/config/* ./config/
+	cp -r ./sample_projects/custom_division/config/* ./config/
+
+asymmetric-division-sample:
+	cp -r ./sample_projects/asymmetric_division/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/asymmetric_division/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/asymmetric_division/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp -r ./sample_projects/asymmetric_division/config/* ./config/
+
+immune-function-sample:
+	cp -r ./sample_projects/immune_function/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/immune_function/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/immune_function/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp -r ./sample_projects/immune_function/config/* ./config/
 
 # ---- intracellular projects 
 ode-energy-sample: