fixing bad vector access due to stress symbiont being removed before symdobirth

Author: anyaevostinar

Makefile

@@ -163,6 +163,9 @@ test-debug-sgp:
 test-executable:
 	$(CXX_nat) $(CFLAGS_nat) $(TEST_DIR)/main.cc -o symbulation.test
 
+test-executable-debug:
+	$(CXX_nat) $(CFLAGS_nat_debug) $(TEST_DIR)/main.cc -o symbulation.test
+
 test-all:
 	$(CXX_nat) $(CFLAGS_nat) $(TEST_DIR)/main.cc -o symbulation.test
 	./symbulation.test || { gdb ./symbulation.test --ex="catch throw" --ex="set confirm off" --ex="run" --ex="backtrace" --ex="quit"; exit 1; }

source/sgp_mode/SGPWorld.h

@@ -141,6 +141,10 @@ class SGPWorld : public SymWorld {
   int GetNeighborHost(size_t id, emp::Ptr<Organism> symbiont);
   bool TaskMatchCheck(emp::Ptr<Organism> sym_parent, emp::Ptr<Organism> host_parent);
 
+  // Prototypes for sym transfering
+  emp::WorldPosition SymFindHost(emp::Ptr<Organism> symbiont, emp::WorldPosition cur_pos);
+
+
   // Prototype for graveyard handling method
   void SendToGraveyard(emp::Ptr<Organism> org) override;
 

source/sgp_mode/SGPWorldSetup.cc

@@ -177,4 +177,31 @@ emp::WorldPosition SGPWorld::SymDoBirth(emp::Ptr<Organism> sym_baby, emp::WorldP
       return emp::WorldPosition();
     }
   }
+
+
+ /**
+  * Input: Pointers to a symbiont and the position of the symbiont. 
+  * Note that the position of the symbiont is a WorldPosition with index as 1-index position
+  * in host's syms list and pop_id as host's location in the world
+  *
+  * Output: Returns a WorldPosition pointer, a valid one for succesful 
+  * infection and an invalid for a failed infection
+  *
+  * Purpose: To place a symbiont in a new location or host in the world. 
+  */
+  emp::WorldPosition SGPWorld::SymFindHost(emp::Ptr<Organism> symbiont, emp::WorldPosition cur_pos) {
+   size_t i = cur_pos.GetPopID();
+    int new_host_pos = GetNeighborHost(i, symbiont);
+    if (new_host_pos > -1) { //-1 means no living neighbors
+      int new_index = pop[new_host_pos]->AddSymbiont(symbiont);
+      if(new_index > 0){ //sym successfully infected
+        return emp::WorldPosition(new_index, new_host_pos);
+      } else { //sym got killed trying to infect
+        return emp::WorldPosition();
+      }
+    } else {
+      symbiont.Delete();
+      return emp::WorldPosition();
+    }
+  }
 #endif

source/sgp_mode/StressHost.h

@@ -92,7 +92,7 @@ class StressHost : public SGPHost {
         for (size_t j = 0; j < syms.size(); j++) {
           emp::Ptr<Organism> cur_sym = syms[j];
           RemoveSymbiont(j+1); //RemoveSymbiont uses 1-indexed value
-          my_world->SymDoBirth(cur_sym, emp::WorldPosition(j+1, pos.GetIndex()));
+          my_world->SymFindHost(cur_sym, emp::WorldPosition(j+1, pos.GetIndex()));
         }
         SetDead();
       }

source/test/sgp_mode_test/StressHost.test.cc

@@ -120,6 +120,7 @@ TEST_CASE("Parasites transfer during stress event", "[sgp]") {
   size_t world_size = config.GRID_X() * config.GRID_Y();
   SGPWorld world(random, &config, LogicTasks);
 
+
   WHEN("There are stress parasites with 100% kill rate in the world"){
     config.START_MOI(1);
     double parasite_death_chance = 1.0; 
@@ -145,13 +146,9 @@ TEST_CASE("Parasites transfer during stress event", "[sgp]") {
       world.AddOrgAt(host,i);
     }
 
-
-
     for (size_t i = 0; i < config.EXTINCTION_FREQUENCY() - 1; i++) world.Update();
     REQUIRE(world.GetNumOrgs() == world_size);
-      
     world.Update();
-
     THEN("Half the hosts died but the remaining got infected by fleeing parasites") {        
       REQUIRE(world.GetNumOrgs() == 50);
       int surviving_syms = 0;