I think it works!

changes.md

@@ -5,15 +5,41 @@
 * 1.14.0 : ?? June 2024
 
 changes: 
-* Add `Integrity` to `Phenotype`
+* Add `Cell_Integrity` to `Phenotype`
 * rename `Phenotype.Interactions.damage_rate` to `Phenotype.Interactions.attack_damage_rate`
-* move `Cell.Cell_State.damage` to `Phenotype.Integrity.damage` 
-* added standardized (self-)damage and self repair to `Phenotype.Integrity` as part of built-in phenotype 
+* move `Cell.Cell_State.damage` to `Phenotype.Cell_Integrity.damage` 
+* added standardized (self-)damage and self repair to `Phenotype.Cell_Integrity` as part of built-in phenotype 
 
 
 updating ... phagocytosis models 
 updating .. effector atack models 
 
+* new (or modified) signals: 
+damage (now in cell integrity)
+damage delivered 
+attacking (as a boolean)
+
+* deprecated signals: 
+
+* new (or modified) behaviors: 
+phagocytose apoptotic cells
+phagocytose necrotic cells
+phagocytose other dead cells
+attack damage rate (renamed)
+damage rate (moved)
+damage repair rate 
+
+attack duration
+
+* deprecated behaviors: 
+phagocytose dead cells 
+
+rules: 
+give a warning on dead cell phago rules?
+
+
+
+
 to do: 
 * How to communicate to attacking cells that their target is dead. Fix for now: 
 

config/cell_rules.csv

@@ -1,32 +1,5 @@
-// malignant epithelial cells
-malignant epithelial cell,oxygen,decreases,necrosis,0,3.75,8,0
-malignant epithelial cell,oxygen,increases,cycle entry,0.003333,21.5,4,0
-malignant epithelial cell,pressure,decreases,cycle entry,0,1,4,0
-malignant epithelial cell,apoptotic,increases,apoptotic debris secretion,0.017,0.1,10,1
-malignant epithelial cell,necrotic,increases,necrotic debris secretion,0.017,0.1,10,1
-malignant epithelial cell,oxygen,decreases,migration speed,0,5,4,0
-malignant epithelial cell,damage,increases,apoptosis,0.1,5,8,0
-// 
-// M0 macrophages
-M0 macrophage,necrotic debris,increases,transform to M1 macrophage,0.05,0.005,4,0
-M0 macrophage,apoptotic debris,decreases,migration speed,0.1,0.005,4,0
-M0 macrophage,necrotic debris,decreases,migration speed,0.1,0.005,4,0
-M0 macrophage,volume,decreases,phagocytose dead cell,0,6000,4,0
-// M1 macrophages 
-// M1 macrophage,oxygen,decreases,transform to M2 macrophage,0.0,5,8,0
-M1 macrophage,oxygen,decreases,transform to M2 macrophage,0.0001,5,8,0
-M1 macrophage,apoptotic debris,decreases,migration speed,0.1,0.005,4,0
-M1 macrophage,necrotic debris,decreases,migration speed,0.1,0.005,4,0
-M1 macrophage,volume,decreases,phagocytose dead cell,0.0,6000,4,0
-// M2 macrophages
-M2 macrophage,apoptotic debris,decreases,migration speed,0.1,0.005,4,0
-M2 macrophage,necrotic debris,decreases,migration speed,0.1,0.005,4,0
-M2 macrophage,volume,decreases,phagocytose dead cell,0.0,6000,4,0
-// effector cells 
-effector T cell,pro-inflammatory factor,increases,attack malignant epithelial cell,0.01,1,4,0
-effector T cell,contact with malignant epithelial cell,decreases,migration speed,0.01,0.1,10,0
-effector T cell,pro-inflammatory factor,increases,migration speed,1,0.01,4,0
-effector T cell,anti-inflammatory factor,increases,transform to exhausted T cell,0.001,0.5,4,0
-// exhausted cells 
-exhausted T cell,anti-inflammatory factor,decreases,migration speed,0.001,0.5,4,0
-exhausted T cell,contact with malignant epithelial cell,decreases,migration speed,0.01,0.1,10,0
+// comment line 
+//
+// 0          1       2          3         4                   5         6           7           
+// Cell type, signal, direction, behavior, max response value, half-max, Hill power, applies to dead?  
+tumor cell,damage,increases,apoptosis,9e9,30,100,0

core/PhysiCell_cell.cpp

@@ -1410,8 +1410,12 @@ void Cell::attack_cell( Cell* pCell_to_attack , double dt )
 	{ 
 		// std::cout << this->type_name << " attacks " << pCell_to_attack->type_name << std::endl;
 		// 
-		pCell_to_attack->phenotype.cell_integrity.damage += phenotype.cell_interactions.attack_damage_rate * dt; 
+		double new_damage = phenotype.cell_interactions.attack_damage_rate * dt; 
+
+		pCell_to_attack->phenotype.cell_integrity.damage += new_damage; 
 		pCell_to_attack->state.total_attack_time += dt; 
+
+		phenotype.cell_interactions.total_damage_delivered += new_damage; 
 	}
 	return; 
 }