Merge branch 'development' into make-output-folder

.github/workflows/build_binaries.yml

@@ -4,7 +4,7 @@ on:
   push:
   pull_request:
   release:
-    types: [created]
+    types: [published]
 
 jobs:
 

.github/workflows/tests.yml

@@ -18,21 +18,22 @@ jobs:
           {name: "Windows", os: "windows-latest", shell: "msys2", compiler: "g++"},
         ]
         projects: [
-          {project: "template", name: "PhysiCell Template", binary: "project", max_time: 120, config: "config/PhysiCell_settings.xml", compare_svgs: true, output_folder: "output"},
-          {project: "template_BM", name: "PhysiBoSS Template", binary: "project", max_time: 120, config: "config/PhysiCell_settings.xml", compare_svgs: true, output_folder: "output"},
-          {project: "physiboss-cell-lines-sample", name: "PhysiBoSS Cell Lines", binary: "PhysiBoSS_Cell_Lines", max_time: 120, config: "config/PhysiCell_settings.xml", compare_svgs: true, output_folder: "output"},
-          {project: "physimess-sample", name: "PhysiMeSS Sample", binary: "project", config: "config/Fibre_Degradation/mymodel_matrix_degradation.xml", max_time: 120, compare_svgs: false, output_folder: "output"},
-          {project: "physiboss-tutorial", name: "PhysiBoSS Tutorial", binary: "project", config: "config/cell_cycle/PhysiCell_settings.xml", max_time: 300, compare_svgs: true, output_folder: "output"},
-          {project: "worm-sample", name: "PhysiCell worm", binary: "worm", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: true, output_folder: "output"},
-          {project: "virus-macrophage-sample", name: "Virus Macrophage", binary: "virus-sample", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: true, output_folder: "output"},
-          {project: "mechano-sample", name: "PhysiCell Mechano", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: true, output_folder: "output"},
-          {project: "cancer-biorobots-sample", name: "PhysiCell Cancer Biorobots", binary: "cancer_biorobots", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: false, output_folder: "output"},
-          {project: "biorobots-sample", name: "PhysiCell Biorobots", binary: "biorobots", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: false, output_folder: "output"},
-          {project: "celltypes3-sample", name: "PhysiCell Celltypes3", binary: "celltypes3", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: false, output_folder: "output"},
-          {project: "custom-division-sample", name: "PhysiCell custom division", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: false, output_folder: "output"},
-          {project: "interaction-sample", name: "PhysiCell interactions", binary: "interaction_demo", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: false, output_folder: "output"},
-          {project: "pred-prey-farmer", name: "PhysiCell prey predator", binary: "pred_prey", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: false, output_folder: "output"},
-          {project: "template", name: "PhysiCell Template - make output folder", binary: "project", max_time: 120, config: "config/PhysiCell_settings.xml", compare_svgs: false, "output_folder": "test/create/output/folder"}
+          {project: "template", name: "PhysiCell Template", binary: "project", max_time: 120, config: "config/PhysiCell_settings.xml", output_folder: "output"},
+          {project: "template_BM", name: "PhysiBoSS Template", binary: "project", max_time: 120, config: "config/PhysiCell_settings.xml", output_folder: "output"},
+          {project: "physiboss-cell-lines-sample", name: "PhysiBoSS Cell Lines", binary: "PhysiBoSS_Cell_Lines", max_time: 120, config: "config/PhysiCell_settings.xml", output_folder: "output"},
+          {project: "physimess-sample", name: "PhysiMeSS Sample", binary: "project", config: "config/Fibre_Degradation/mymodel_matrix_degradation.xml", max_time: 120, output_folder: ""},
+          {project: "physiboss-tutorial", name: "PhysiBoSS Tutorial", binary: "project", config: "config/cell_cycle/PhysiCell_settings.xml", max_time: 300, output_folder: "output"},
+          {project: "worm-sample", name: "PhysiCell worm", binary: "worm", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: "output"},
+          {project: "virus-macrophage-sample", name: "Virus Macrophage", binary: "virus-sample", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: "output"},
+          {project: "mechano-sample", name: "PhysiCell Mechano", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: "output"},
+          {project: "cancer-biorobots-sample", name: "PhysiCell Cancer Biorobots", binary: "cancer_biorobots", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
+          {project: "biorobots-sample", name: "PhysiCell Biorobots", binary: "biorobots", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
+          {project: "celltypes3-sample", name: "PhysiCell Celltypes3", binary: "celltypes3", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
+          {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 }}
@@ -54,7 +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: |

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"
 	@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 +198,23 @@ 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/
 
 # ---- intracellular projects 
 ode-energy-sample:

addons/PhysiMeSS/PhysiMeSS.cpp

@@ -134,8 +134,7 @@ void physimess_update_cell_velocity( Cell* pCell, Phenotype& phenotype, double d
 
 void physimess_mechanics( double dt ) 
 {    
-    static double dt_tolerance = 0.001 * dt; 
-    if(fabs(((PhysiCell_globals.current_time - last_update_time)) - dt) < dt_tolerance)
+    if ( PhysiCell_globals.current_time >= last_update_time + dt - 0.5 * diffusion_dt) // last_update_time + dt = next update time; - 0.5 * diffusion_dt will give the time step closest to the desired next time (assumign diffusion_dt is the smallest time step)
     {
         last_update_time = PhysiCell_globals.current_time;
 

beta/download_binary.py

@@ -12,10 +12,10 @@
 import stat
 import shutil
 
-physicell_version = "1.14.0"
+physicell_version = "1.14.1"
 repo_physicell = "MathCancer/PhysiCell"
 physiboss_version = "v2.2.3"
-repo_physiboss = "sysbio-curie/PhysiBoSS"
+repo_physiboss = "PhysiBoSS/PhysiBoSS"
 list_models = {
     "physiboss-tutorial": "https://github.com/" + repo_physiboss + "/releases/download/" + physiboss_version + "/", 
     "physiboss-tutorial-invasion": "https://github.com/" + repo_physiboss + "/releases/download/" + physiboss_version + "/", 

config/PhysiCell_settings.xml

@@ -255,7 +255,7 @@
 
     <cell_rules>
         <rulesets>
-            <ruleset protocol="CBHG" version="2.0" format="csv" enabled="true">
+            <ruleset protocol="CBHG" version="3.0" format="csv" enabled="true">
                 <folder>./config</folder>
                 <filename>cell_rules_v2.csv</filename>
             </ruleset>

core/PhysiCell_cell.cpp

@@ -173,6 +173,7 @@ Cell_Definition::Cell_Definition()
 	// 					are appropriately sized. Same on motiltiy. 
 	phenotype.cell_interactions.sync_to_cell_definitions(); 
 	phenotype.cell_transformations.sync_to_cell_definitions(); 
+	phenotype.cycle.asymmetric_division.sync_to_cell_definitions();
 	phenotype.motility.sync_to_current_microenvironment(); 
 	phenotype.mechanics.sync_to_cell_definitions(); 
 
@@ -654,8 +655,8 @@ Cell* Cell::divide( )
 	// child->phenotype.integrity.damage = 0.0; // leave alone - damage is heritable 
 	child->state.total_attack_time = 0.0; 
 
-    if( this->functions.cell_division_function )
-        { this->functions.cell_division_function( this, child); }
+	if( this->functions.cell_division_function )
+	{ this->functions.cell_division_function( this, child); }
 
 	return child;
 }
@@ -1341,7 +1342,6 @@ void Cell::ingest_cell( Cell* pCell_to_eat )
 		pCell_to_eat->functions.update_phenotype = NULL; 
 		pCell_to_eat->functions.contact_function = NULL; 
 		pCell_to_eat->functions.cell_division_function = NULL; 
-
 
 		// should set volume fuction to NULL too! 
 		pCell_to_eat->functions.volume_update_function = NULL; 
@@ -1794,7 +1794,7 @@ void display_cell_definitions( std::ostream& os )
 		os << std::endl;
 		os << "\t\t contact function: "; display_ptr_as_bool( pCF->contact_function , std::cout ); 
 		os << std::endl; 
-        os << "\t\t cell division function: "; display_ptr_as_bool( pCF->cell_division_function , std::cout ); 
+		os << "\t\t cell division function: "; display_ptr_as_bool( pCF->cell_division_function , std::cout ); 
 		os << std::endl; 
 
 		// summarize motility 
@@ -2032,6 +2032,9 @@ Cell_Definition* initialize_cell_definition_from_pugixml( pugi::xml_node cd_node
 
 			// transformation 
 			pCD->phenotype.cell_transformations.transformation_rates.assign(number_of_cell_defs,0.0); 
+
+			// asymmetric division
+			pCD->phenotype.cycle.asymmetric_division.asymmetric_division_probabilities.assign(number_of_cell_defs,0.0);
 		}
 		else 
 		{
@@ -2070,6 +2073,7 @@ Cell_Definition* initialize_cell_definition_from_pugixml( pugi::xml_node cd_node
 	// this requires that prebuild_cell_definition_index_maps was already run 
 	pCD->phenotype.cell_interactions.sync_to_cell_definitions(); 
 	pCD->phenotype.cell_transformations.sync_to_cell_definitions(); 
+	pCD->phenotype.cycle.asymmetric_division.sync_to_cell_definitions();
 	pCD->phenotype.mechanics.sync_to_cell_definitions(); 
 
 	// set the reference phenotype 
@@ -2218,11 +2222,49 @@ Cell_Definition* initialize_cell_definition_from_pugixml( pugi::xml_node cd_node
 
 				node = node.next_sibling( "duration" ); 
 			}
-
 		}
 
-
-
+		node = cd_node.child( "phenotype" );
+		node = node.child( "cycle" );
+		node = node.child( "standard_asymmetric_division" );
+		if( node && node.attribute("enabled").as_bool() )
+		{
+			Asymmetric_Division *pAD = &(pCD->phenotype.cycle.asymmetric_division);
+
+			// asymmetric division rates
+			pugi::xml_node node_adp = node.child( "asymmetric_division_probability");
+			while (node_adp)
+			{
+				// get the name of the target cell type
+				std::string target_name = node_adp.attribute("name").value();
+				// now find its index
+				auto search = cell_definition_indices_by_name.find(target_name);
+				// safety first!
+				if( search != cell_definition_indices_by_name.end() )
+				{
+					// if the target is found, set the appropriate rate
+					int target_index = search->second;
+
+					double asymmetric_division_probability = xml_get_my_double_value(node_adp);
+					pAD->asymmetric_division_probabilities[target_index] = asymmetric_division_probability;
+				}
+				else
+				{
+					std::cout << "Error: When processing the " << pCD->name << " cell definition: " << std::endl
+						<< "\tCould not find cell type " << target_name << " for asymmetric division." << std::endl
+						<< "\tRemove this cell type from the asymmetric division probabilities!" << std::endl << std::endl;
+					exit(-1);
+				}
+				node_adp = node_adp.next_sibling("asymmetric_division_probability");
+			}
+			std::cout << "Asymmetric division probabilities for " << pCD->name << ": ";
+			for (int i = 0; i < pAD->asymmetric_division_probabilities.size(); i++)
+			{
+				std::cout << pAD->asymmetric_division_probabilities[i] << " ";
+			}
+			std::cout << std::endl;
+			pCD->functions.cell_division_function = standard_asymmetric_division_function;
+		}
 	}
 
 	// here's what it ***should*** do: 
@@ -2438,45 +2480,11 @@ Cell_Definition* initialize_cell_definition_from_pugixml( pugi::xml_node cd_node
 					node = node.next_sibling( "duration" ); 
 				}
 
-
-/*
-		if( node.child( "phase_durations" ) )
-		{ node = node.child( "phase_durations" ); }
-		if( node )
-		{
-			node = node.child( "duration");
-			while( node )
-			{
-				// which duration? 
-				int start = node.attribute("index").as_int(); 
-				// fixed duration? 
-				bool fixed = false; 
-				if( node.attribute( "fixed_duration" ) )
-				{ fixed = node.attribute("fixed_duration").as_bool(); }
-				// actual value of the duration 
-				double value = xml_get_my_double_value( node ); 
-				
-				// set the transition rate 
-				pCD->phenotype.cycle.data.exit_rate(start) = 1.0 / (value+1e-16); 
-				// set it to fixed / non-fixed 
-				pCD->phenotype.cycle.model().phase_links[start][0].fixed_duration = fixed; 
-				
-				node = node.next_sibling( "duration" ); 
-			}
-			
-		}
-
-*/				
-
-
 				node = node.parent(); // phase_durations 
 				node = node.parent(); // model 
 			}				
 
-			// node = node.parent(); 
-
 			model_node = model_node.next_sibling( "model" ); 
-//			death_model_index++; 
 		}
 
 	}
@@ -2821,7 +2829,7 @@ Cell_Definition* initialize_cell_definition_from_pugixml( pugi::xml_node cd_node
 			}
 			std::cout << std::endl; 
 		}		
-	}	
+	}
 
 	// secretion
 
@@ -2972,6 +2980,10 @@ Cell_Definition* initialize_cell_definition_from_pugixml( pugi::xml_node cd_node
 		pugi::xml_node node_dr = node.child("attack_damage_rate");
 		pCI->attack_damage_rate = xml_get_my_double_value(node_dr); 
 
+		// attack_duration
+		pugi::xml_node node_ad = node.child("attack_duration");
+		pCI->attack_duration = xml_get_my_double_value(node_ad);
+
 		// fusion_rates 
 		pugi::xml_node node_fr = node.child( "fusion_rates");
 		if( node_fr )
@@ -3063,7 +3075,9 @@ Cell_Definition* initialize_cell_definition_from_pugixml( pugi::xml_node cd_node
 		{ pCI->damage_repair_rate = xml_get_my_double_value( node_drr ); }
 	}
 
-    	// intracellular
+	node = cd_node.child( "phenotype" );
+
+		// intracellular
 	node = cd_node.child( "phenotype" );
 	node = node.child( "intracellular" ); 
 	if( node )

core/PhysiCell_cell.h

@@ -188,7 +188,7 @@ class Cell : public Basic_Agent
 
 	bool is_out_of_domain;
 	bool is_movable;
-	
+
 	void flag_for_division( void ); // done 
 	void flag_for_removal( void ); // done 
 

core/PhysiCell_cell_container.cpp

@@ -159,7 +159,7 @@ void Cell_Container::update_all_cells(double t, double phenotype_dt_ , double me
 		}
 	}
 
-	if( fabs(time_since_last_cycle-phenotype_dt_ ) < phenotype_dt_tolerance || !initialzed)
+	if( time_since_last_cycle > phenotype_dt_ - 0.5 * diffusion_dt_ || !initialzed )
 	{
 		// Reset the max_radius in each voxel. It will be filled in set_total_volume
 		// It might be better if we calculate it before mechanics each time 
@@ -201,7 +201,7 @@ void Cell_Container::update_all_cells(double t, double phenotype_dt_ , double me
 	double time_since_last_mechanics= t- last_mechanics_time;
 
 	// if( time_since_last_mechanics>= mechanics_dt || !initialzed)
-	if( fabs(time_since_last_mechanics - mechanics_dt_) < mechanics_dt_tolerance || !initialzed)
+	if( time_since_last_mechanics > mechanics_dt_ - 0.5 * diffusion_dt_ || !initialzed )
 	{
 		if(!initialzed)
 		{

core/PhysiCell_phenotype.cpp

@@ -1358,6 +1358,38 @@ double& Cell_Transformations::transformation_rate( std::string type_name )
 	return transformation_rates[n]; 
 }
 
+Asymmetric_Division::Asymmetric_Division()
+{
+	asymmetric_division_probabilities = {0.0};
+}
+
+void Asymmetric_Division::sync_to_cell_definitions()
+{
+	extern std::unordered_map<std::string,int> cell_definition_indices_by_name; 
+	int number_of_cell_defs = cell_definition_indices_by_name.size(); 
+
+	if( asymmetric_division_probabilities.size() != number_of_cell_defs )
+	{ asymmetric_division_probabilities.resize( number_of_cell_defs, 0.0); }
+
+	return; 
+}
+
+double Asymmetric_Division::probabilities_total( void )
+{
+	double total = 0.0; 
+	for( int i=0; i < asymmetric_division_probabilities.size(); i++ )
+	{ total += asymmetric_division_probabilities[i]; }
+	return total; 
+}
+
+// ease of access
+double& Asymmetric_Division::asymmetric_division_probability( std::string type_name )
+{
+	extern std::unordered_map<std::string,int> cell_definition_indices_by_name; 
+	int n = cell_definition_indices_by_name[type_name]; 
+	return asymmetric_division_probabilities[n]; 
+}
+
 // beta functionality in 1.10.3 
 Cell_Integrity::Cell_Integrity()
 {