Rules upgrade and extensions

Makefile

@@ -42,7 +42,7 @@ BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_contai
 
 PhysiCell_core_OBJECTS := PhysiCell_phenotype.o PhysiCell_cell_container.o PhysiCell_standard_models.o \
 PhysiCell_cell.o PhysiCell_custom.o PhysiCell_utilities.o PhysiCell_constants.o PhysiCell_basic_signaling.o \
-PhysiCell_signal_behavior.o PhysiCell_rules.o
+PhysiCell_signal_behavior.o PhysiCell_rules_extended.o
 
 PhysiCell_module_OBJECTS := PhysiCell_SVG.o PhysiCell_pathology.o PhysiCell_MultiCellDS.o PhysiCell_various_outputs.o \
 PhysiCell_pugixml.o PhysiCell_settings.o PhysiCell_geometry.o
@@ -74,7 +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 "					asymmetric-division-sample template-xml-rules template-xml-rules-extended"
 	@echo ""
 	@echo "Sample intracellular projects: template_BM ode-energy-sample physiboss-cell-lines-sample"
 	@echo "                 cancer-metabolism-sample physiboss-tutorial physiboss-tutorial-invasion"
@@ -87,7 +87,25 @@ template:
 	cp Makefile Makefile-backup
 	cp ./sample_projects/template/Makefile .
 	cp -r ./sample_projects/template/config/* ./config 
-
+
+template-xml-rules:
+	cp -r ./sample_projects/template_xml_rules/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/template_xml_rules/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/template_xml_rules/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp -r ./sample_projects/template_xml_rules/config/* ./config/
+
+template-xml-rules-extended:
+	cp -r ./sample_projects/template_xml_rules_extended/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/template_xml_rules_extended/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/template_xml_rules_extended/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp -r ./sample_projects/template_xml_rules_extended/config/* ./config/
+
 # sample projects 
 
 # ---- non-intracellular projects 
@@ -339,8 +357,8 @@ PhysiCell_constants.o: ./core/PhysiCell_constants.cpp
 PhysiCell_signal_behavior.o: ./core/PhysiCell_signal_behavior.cpp
 	$(COMPILE_COMMAND) -c ./core/PhysiCell_signal_behavior.cpp 
 
-PhysiCell_rules.o: ./core/PhysiCell_rules.cpp
-	$(COMPILE_COMMAND) -c ./core/PhysiCell_rules.cpp 
+PhysiCell_rules_extended.o: ./core/PhysiCell_rules_extended.cpp
+	$(COMPILE_COMMAND) -c ./core/PhysiCell_rules_extended.cpp 
 
 # BioFVM core components (needed by PhysiCell)
 

core/PhysiCell.h

@@ -86,6 +86,6 @@ static std::string PhysiCell_DOI = "10.1371/journal.pcbi.1005991";
 #include "PhysiCell_utilities.h"
 #include "PhysiCell_constants.h"
 
-#include "PhysiCell_rules.h"
+#include "PhysiCell_rules_extended.h"
 
 #endif

core/PhysiCell_cell.cpp

@@ -321,7 +321,7 @@ void Cell::advance_bundled_phenotype_functions( double dt_ )
 	// New March 2023 in Version 1.12.0 
 	// call the rules-based code to update the phenotype 
 	if( PhysiCell_settings.rules_enabled )
-	{ apply_ruleset( this ); }
+	{ apply_behavior_ruleset( this ); }
 	if( get_single_signal(this,"necrotic") > 0.5 )
 	{
 		double rupture = this->phenotype.volume.rupture_volume; 
@@ -1697,7 +1697,7 @@ void prebuild_cell_definition_index_maps( void )
 		node = node.next_sibling( "cell_definition" ); 
 		n++; 
 	}	
-	
+
 	return; 
 }
 

core/PhysiCell_cell.h

@@ -78,7 +78,7 @@
 #include "../modules/PhysiCell_settings.h" 
 
 #include "./PhysiCell_standard_models.h" 
-#include "./PhysiCell_rules.h"
+#include "./PhysiCell_rules_extended.h"
 
 using namespace BioFVM;