Empirical pointers and variable name case updates

source/default_mode/Host.h

@@ -44,7 +44,7 @@ class Host: public Organism {
   /**
     *
     * Purpose: Represents the set of in-progress "reproductive" symbionts belonging to a host. These are symbionts that aren't yet active.
-    * Symbionts can be added with AddReproSymb(). This can be cleared with ClearSyms()
+    * Symbionts can be added with AddReproSym(). This can be cleared with ClearSyms()
     *
   */
   emp::vector<emp::Ptr<Organism>> repro_syms = {};
@@ -401,17 +401,17 @@ class Host: public Organism {
    * steal resources from the host.
    */
   double StealResources(double _intval){
-    double hostIntVal = GetIntVal();
+    double host_int_val = GetIntVal();
     double res_in_process = GetResInProcess();
     //calculate how many resources another organism can steal from this host
-    if (hostIntVal>0){ //cooperative hosts shouldn't be over punished by StealResources
-      hostIntVal = 0;
+    if (host_int_val >0){ //cooperative hosts shouldn't be over punished by StealResources
+        host_int_val = 0;
     }
-    if (_intval < hostIntVal){
+    if (_intval < host_int_val){
       //organism trying to steal can overcome host's defense
-      double stolen = (hostIntVal - _intval) * res_in_process;
-      double remainingResources = res_in_process - stolen;
-      SetResInProcess(remainingResources);
+      double stolen = (host_int_val - _intval) * res_in_process;
+      double remaining_resources = res_in_process - stolen;
+      SetResInProcess(remaining_resources);
       return stolen;
     } else {
       //defense cannot be overcome, no resources are stolen
@@ -477,7 +477,7 @@ class Host: public Organism {
     }
     else{
      int num_syms = syms.size();
-     //essentially imitaties a 1/ 2^n chance, with n = number of symbionts
+     //essentially imitates a 1/ 2^n chance, with n = number of symbionts
      int enter_chance = random->GetUInt((int) pow(2.0, num_syms));
      if(enter_chance == 0) { return true; }
      return false;
@@ -590,7 +590,7 @@ class Host: public Organism {
   } //end DistribResources
 
   /**
-   * Input: The total resources recieved by the host and its location in the world.
+   * Input: The total resources received by the host and its location in the world.
    *
    * Output: The resources remaining after the host maybe does ectosymbiosis.
    *
@@ -660,7 +660,7 @@ class Host: public Organism {
     size_t location = pos.GetIndex();
     //Currently just wrapping to use the existing function
     double desired_resources = my_config->RES_DISTRIBUTE();
-    double world_resources = my_world->PullResources(desired_resources); //recieve resources from the world
+    double world_resources = my_world->PullResources(desired_resources); //receive resources from the world
     double resources = HandleEctosymbiosis(world_resources, location);
     if(resources > 0) DistribResources(resources); //if there are enough resources left, distribute them.
 
@@ -683,21 +683,21 @@ class Host: public Organism {
     if (HasSym()) { //let each sym do whatever they need to do
         emp::vector<emp::Ptr<Organism>>& syms = GetSymbionts();
         for(size_t j = 0; j < syms.size(); j++){
-          emp::Ptr<Organism> curSym = syms[j];
+          emp::Ptr<Organism> cur_sym = syms[j];
           if (GetDead()){
             return; //If previous symbiont killed host, we're done
           }
           //sym position should have host index as id and
           //position in syms list + 1 as index (0 as fls index)
           emp::WorldPosition sym_pos = emp::WorldPosition(j+1, location);
-          if(!curSym->GetDead()){
-            curSym->Process(sym_pos);
+          if(!cur_sym->GetDead()){
+              cur_sym->Process(sym_pos);
           }
-          if(curSym->GetDead()) {
+          if(cur_sym->GetDead()) {
             //if the symbiont dies during their process, remove from syms list
             //UNLESS they died by getting ousted
             syms.erase(syms.begin() + j); 
-            curSym.Delete();
+            cur_sym.Delete();
           }
         } //for each sym in syms
       } //if org has syms

source/default_mode/SymWorld.h

@@ -119,7 +119,7 @@ class SymWorld : public emp::World<Organism>{
    *
    * Purpose: To destruct the objects belonging to SymWorld to conserve memory.
    */
-  ~SymWorld() {
+  virtual ~SymWorld() {
     if (data_node_hostintval) data_node_hostintval.Delete();
     if (data_node_symintval) data_node_symintval.Delete();
     if (data_node_freesymintval) data_node_freesymintval.Delete();
@@ -224,7 +224,7 @@ class SymWorld : public emp::World<Organism>{
    * Output: The standard function object that determines which bin organisms
    * should belong to depending on their interaction value
    *
-   * Purpose: To classify organsims based on their interaction value.
+   * Purpose: To classify organisms based on their interaction value.
    */
   fun_calc_info_t GetCalcInfoFun() {
     if (!calc_info_fun) {

source/default_mode/Symbiont.h

@@ -296,7 +296,7 @@ class Symbiont: public Organism {
 
 
   /**
-   * Input: The double representing the points to be set as a symbinot's points
+   * Input: The double representing the points to be set as a symbiont's points
    *
    * Output: None
    *
@@ -306,7 +306,7 @@ class Symbiont: public Organism {
 
 
   /**
-   * Input: The double representing the points to be added to a symbinot's points
+   * Input: The double representing the points to be added to a symbiont's points
    *
    * Output: None
    *
@@ -333,7 +333,7 @@ class Symbiont: public Organism {
   void SetAge(int _in) {age = _in;}
 
   /**
-   * Input: The pointer to an organism that will be set as the symbinot's host
+   * Input: The pointer to an organism that will be set as the symbiont's host
    *
    * Output: None
    *
@@ -353,8 +353,6 @@ class Symbiont: public Organism {
     else infection_chance = _in;
   }
 
-  //void SetResTypes(std::set<int> _in) {res_types = _in;}
-
 
   /**
    * Input: None
@@ -503,7 +501,6 @@ class Symbiont: public Organism {
    * Purpose: To process a symbiont, meaning to check for reproduction, distribute resources,
    * and to allow for movement
    */
-   //size_t rank=-1
   void Process(emp::WorldPosition location) {
     //ID is where they are in the world, INDEX is where they are in the host's symbiont list (or 0 if they're free living)
     if (my_host.IsNull() && my_config->FREE_LIVING_SYMS()) { //free living symbiont

source/pgg_mode/PGGHost.h

@@ -122,8 +122,8 @@ class PGGHost: public Host {
     Host::DistribResources(resources);
 
     for(size_t i=0; i < syms.size(); i++){
-      double hostPool = syms[i]->ProcessPool();
-      this->AddPool(hostPool);
+      double host_pool = syms[i]->ProcessPool();
+      this->AddPool(host_pool);
     }
     if(syms.size()>0){this->DistribPool();}
   } //end DistribResources

source/pgg_mode/PGGSymbiont.h

@@ -140,16 +140,16 @@ class PGGSymbiont: public Symbiont {
    *
    * Output: The double representation of resources to be given to the host.
    *
-   * Purpose: Deteremines the resources that the symbiont is contributing
+   * Purpose: Determines the resources that the symbiont is contributing
    * to the host's resource pool, and decriments them from the symbiont's own
    * own resource collection.
    */
   double ProcessPool(){
-    double symdonation = GetDonation();
-    double symPortion = GetPoints();
-    double hostreturn = symdonation*symPortion;
-    SetPoints(symPortion-hostreturn);
-    return hostreturn;
+    double sym_donation = GetDonation();
+    double sym_portion = GetPoints();
+    double host_return = sym_donation * sym_portion;
+    SetPoints(sym_portion - host_return);
+    return host_return;
   }
 
   /**

source/test/default_mode_test/Host.test.cc

@@ -5,7 +5,7 @@
 
 TEST_CASE("Host Constructor", "[default]") {
 
-    emp::Ptr<emp::Random> random = new emp::Random(-1);
+    emp::Ptr<emp::Random> random = emp::NewPtr<emp::Random>(4);
     SymConfigBase config;
     SymWorld w(*random, &config);
     SymWorld * world = &w;
@@ -56,10 +56,11 @@ TEST_CASE("Host Constructor", "[default]") {
     host1.Delete();
     host2.Delete();
     host3.Delete();
+    random.Delete();
 }
 
 TEST_CASE("Host SetIntVal, GetIntVal", "[default]") {
-    emp::Ptr<emp::Random> random = new emp::Random(-1);
+    emp::Ptr<emp::Random> random = emp::NewPtr<emp::Random>(4);
     SymConfigBase config;
     SymWorld world(*random, &config);
     double int_val = 1;
@@ -86,10 +87,11 @@ TEST_CASE("Host SetIntVal, GetIntVal", "[default]") {
 
     host1.Delete();
     host2.Delete();
+    random.Delete();
 }
 
 TEST_CASE("SetPoints, AddPoints, GetPoints", "[default]") {
-    emp::Ptr<emp::Random> random = new emp::Random(-1);
+    emp::Ptr<emp::Random> random = emp::NewPtr<emp::Random>(4);
     SymConfigBase config;
     SymWorld world(*random, &config);
     double int_val = 1;
@@ -107,10 +109,11 @@ TEST_CASE("SetPoints, AddPoints, GetPoints", "[default]") {
     REQUIRE(host->GetPoints() == expected_points);
 
     host.Delete();
+    random.Delete();
 }
 
 TEST_CASE("HasSym", "[default]") {
-    emp::Ptr<emp::Random> random = new emp::Random(-1);
+    emp::Ptr<emp::Random> random = emp::NewPtr<emp::Random>(4);
     SymConfigBase config;
     SymWorld world(*random, &config);
     double int_val = 1;
@@ -131,11 +134,12 @@ TEST_CASE("HasSym", "[default]") {
         }
     }
     host.Delete();
+    random.Delete();
 }
 
 TEST_CASE("Host Mutate", "[default]") {
     //TODO: put in tests for mutation size and mutation rate separately
-    emp::Ptr<emp::Random> random = new emp::Random(3);
+    emp::Ptr<emp::Random> random = emp::NewPtr<emp::Random>(3);
     SymConfigBase config;
     SymWorld world(*random, &config);
     double int_val = -0.31;
@@ -200,10 +204,11 @@ TEST_CASE("Host Mutate", "[default]") {
         host.Delete();
       }
     }
+    random.Delete();
 }
 
 TEST_CASE("DistributeResources", "[default]") {
-    emp::Ptr<emp::Random> random = new emp::Random(-1);
+    emp::Ptr<emp::Random> random = emp::NewPtr<emp::Random>(5);
     SymConfigBase config;
     SymWorld world(*random, &config);
 
@@ -268,10 +273,11 @@ TEST_CASE("DistributeResources", "[default]") {
 
         host.Delete();
     }
+    random.Delete();
 }
 
 TEST_CASE("SetResInProcess, GetResInProcess", "[default]") {
-  emp::Ptr<emp::Random> random = new emp::Random(-1);
+  emp::Ptr<emp::Random> random = emp::NewPtr<emp::Random>(3);
   SymConfigBase config;
   SymWorld world(*random, &config);
   double int_val = 1;
@@ -286,10 +292,11 @@ TEST_CASE("SetResInProcess, GetResInProcess", "[default]") {
   REQUIRE(host->GetResInProcess() == expected_res_in_process);
 
   host.Delete();
+  random.Delete();
 }
 
 TEST_CASE("Steal resources unit test", "[default]"){
-    emp::Ptr<emp::Random> random = new emp::Random(-1);
+    emp::Ptr<emp::Random> random = emp::NewPtr<emp::Random>(3);
     SymConfigBase config;
     SymWorld world(*random, &config);
 
@@ -342,11 +349,12 @@ TEST_CASE("Steal resources unit test", "[default]"){
         }
         host.Delete();
     }
+    random.Delete();
 }
 
 TEST_CASE("GetDoEctosymbiosis", "[default]"){
   GIVEN("A world"){
-    emp::Ptr<emp::Random> random = new emp::Random(17);
+    emp::Ptr<emp::Random> random = emp::NewPtr<emp::Random>(17);
     SymConfigBase config;
     SymWorld world(*random, &config);
     world.Resize(2,2);
@@ -425,11 +433,12 @@ TEST_CASE("GetDoEctosymbiosis", "[default]"){
         REQUIRE(host->GetDoEctosymbiosis(host_pos) == true);
       }
     }
+    random.Delete();
   }
 }
 
 TEST_CASE("Host GrowOlder", "[default]"){
-    emp::Ptr<emp::Random> random = new emp::Random(-1);
+    emp::Ptr<emp::Random> random = emp::NewPtr<emp::Random>(4);
     SymConfigBase config;
     SymWorld world(*random, &config);
     config.HOST_AGE_MAX(2);
@@ -449,10 +458,11 @@ TEST_CASE("Host GrowOlder", "[default]"){
         REQUIRE(world.GetNumOrgs() == 0);
       }
     }
+    random.Delete();
 }
 
 TEST_CASE("Host MakeNew", "[default]"){
-    emp::Ptr<emp::Random> random = new emp::Random(-1);
+    emp::Ptr<emp::Random> random = emp::NewPtr<emp::Random>(4);
     SymConfigBase config;
     SymWorld world(*random, &config);
 
@@ -469,10 +479,11 @@ TEST_CASE("Host MakeNew", "[default]"){
 
     host1.Delete();
     host2.Delete();
+    random.Delete();
 }
 
 TEST_CASE("Host Reproduce", "[default]"){
-    emp::Ptr<emp::Random> random = new emp::Random(-1);
+    emp::Ptr<emp::Random> random = emp::NewPtr<emp::Random>(4);
     SymConfigBase config;
     SymWorld world(*random, &config);
 
@@ -488,10 +499,11 @@ TEST_CASE("Host Reproduce", "[default]"){
 
     host1.Delete();
     host2.Delete();
+    random.Delete();
 }
 
 TEST_CASE("AddSymbiont", "[default]"){
-  emp::Ptr<emp::Random> random = new emp::Random(-1);
+  emp::Ptr<emp::Random> random = emp::NewPtr<emp::Random>(4);
   SymConfigBase config;
   SymWorld world(*random, &config);
   double int_val = 0;
@@ -542,6 +554,7 @@ TEST_CASE("AddSymbiont", "[default]"){
       REQUIRE(world.GetGraveyard().size() == 0);
     }
   }
+  random.Delete();
 }
 
 TEST_CASE("SymAllowedIn", "[default]") {
@@ -554,7 +567,7 @@ TEST_CASE("SymAllowedIn", "[default]") {
   WHEN("Symbiont exclude is set to false") {
     config.PHAGE_EXCLUDE(0);
     THEN("Symbionts are added without issue") {
-      emp::Ptr<emp::Random> random = new emp::Random(3);
+      emp::Ptr<emp::Random> random = emp::NewPtr<emp::Random>(3);
       SymWorld world(*random, &config);
       emp::Ptr<Host> host = emp::NewPtr<Host>(random, &world, &config, int_val);
       for (int i = 0; i < sym_limit; i++) {
@@ -563,6 +576,7 @@ TEST_CASE("SymAllowedIn", "[default]") {
       int num_syms = (host->GetSymbionts()).size();
       REQUIRE(num_syms == sym_limit);
       host.Delete();
+      random.Delete();
     }
   }
 
@@ -571,7 +585,7 @@ TEST_CASE("SymAllowedIn", "[default]") {
     THEN("Symbionts have a decreasing change of entering the host") {
       int goal_num_syms[] = { 3,3,3,3 };
       for (int i = 0; i < 4; i++) {
-        emp::Ptr<emp::Random> random = new emp::Random(i + 1);
+        emp::Ptr<emp::Random> random = emp::NewPtr<emp::Random>(i + 1);
         SymWorld world(*random, &config);
         emp::Ptr<Host> host = emp::NewPtr<Host>(random, &world, &config, int_val);
 
@@ -581,6 +595,7 @@ TEST_CASE("SymAllowedIn", "[default]") {
         int host_num_syms = (host->GetSymbionts()).size();
         REQUIRE(goal_num_syms[i] == host_num_syms);
         host.Delete();
+        random.Delete();
       }
     }
   }