Merge branch 'complex-syms-clean' of https://github.com/K-Johnson-Hor…

…rigan/SymbulationEmp into refactor

.github/workflows/CI.yml

@@ -24,16 +24,16 @@ jobs:
       - name: run symbulation
         run: cd SymbulationEmp && make debug-default && ./symbulation_default -GRID_X 5 -GRID_Y 5
 
-      - name: test web build
-        run: cd SymbulationEmp/emsdk && ./emsdk install 1.38.48 && ./emsdk activate 1.38.48 && source ./emsdk_env.sh && cd .. && make web
-
       # Runs a single command using the runners shell
       - name: Make tests
         run: cd SymbulationEmp && make coverage
-
+
+      - name: test web build
+        run: cd SymbulationEmp/emsdk && ./emsdk install 1.38.48 && ./emsdk activate 1.38.48 && source ./emsdk_env.sh && cd .. && make web
+
       - name: Generate coverage
         run: cd SymbulationEmp && gcov -abcfu main.cc
-        
+
       - name: Upload coverage
         uses: codecov/[email protected]
         with:

.gitmodules

@@ -6,4 +6,4 @@
 	url = https://github.com/emscripten-core/emsdk
 [submodule "signalgp-lite"]
 	path = signalgp-lite
-	url = https://github.com/tolziplohu/signalgp-lite
+	url = https://github.com/amlalejini/signalgp-lite

Makefile

@@ -4,7 +4,8 @@ EMP_DIR := Empirical/include
 SGP_DIR := signalgp-lite/include
 
 # Flags to use regardless of compiler
-CFLAGS_all := -Wall -Wno-unused-function -std=c++17 -I$(EMP_DIR)/ -I$(SGP_DIR)/
+VENDORIZE_EMP_FLAGS := -DUIT_VENDORIZE_EMP -DUIT_SUPPRESS_MACRO_INSEEP_WARNINGS
+CFLAGS_all := -Wall -Wno-unused-function -std=c++20 -I$(EMP_DIR)/ -I$(SGP_DIR)/ ${VENDORIZE_EMP_FLAGS}
 
 # Native compiler information
 CXX_nat := g++
@@ -65,27 +66,27 @@ debug:
 	@echo SGP mode: make debug-sgp
 
 debug-default: CFLAGS_nat := $(CFLAGS_nat_debug)
-debug-default: default-mode 
+debug-default: default-mode
 default-debug: debug-default
 
 debug-parasite: CFLAGS_nat := $(CFLAGS_nat_debug)
-debug-parasite: parasite-mode 
+debug-parasite: parasite-mode
 parasite-debug: debug-parasite
 
 debug-efficient: CFLAGS_nat := $(CFLAGS_nat_debug)
-debug-efficient: efficient-mode 
+debug-efficient: efficient-mode
 efficient-debug: debug-efficient
 
 debug-lysis: CFLAGS_nat := $(CFLAGS_nat_debug)
-debug-lysis: lysis-mode 
+debug-lysis: lysis-mode
 lysis-debug: debug-lysis
 
 debug-pgg: CFLAGS_nat := $(CFLAGS_nat_debug)
-debug-pgg: pgg-mode 
+debug-pgg: pgg-mode
 pgg-debug: debug-pgg
 
 debug-sgp: CFLAGS_nat := $(CFLAGS_nat_debug)
-debug-sgp: sgp-mode 
+debug-sgp: sgp-mode
 sgp-debug: debug-sgp
 
 debug-web:	CFLAGS_web := $(CFLAGS_web_debug)
@@ -102,7 +103,7 @@ test:
 	@echo To run only the tests for each mode, use the following:
 	@echo Default mode testing: make test-default
 	@echo Efficient mode testing: make test-efficient
-	@echo Lysis mode testing: make test-lysis 
+	@echo Lysis mode testing: make test-lysis
 	@echo PGG mode testing: make test-pgg
 	@echo SGP mode testing: make test-sgp
 
@@ -112,7 +113,7 @@ test-debug:
 	@echo To debug and test for each mode, use the following:
 	@echo Default mode: make test-debug-default
 	@echo Efficient mode: make test-debug-efficient
-	@echo Lysis mode: make test-debug-lysis 
+	@echo Lysis mode: make test-debug-lysis
 	@echo PGG mode: make test-debug-pgg
 	@echo SGP mode: make test-debug-sgp
 
@@ -146,7 +147,7 @@ test-debug-pgg:
 
 test-sgp:
 	$(CXX_nat) $(CFLAGS_nat) $(TEST_DIR)/main.cc -o symbulation.test
-	./symbulation.test [sgp] 
+	./symbulation.test [sgp]
 test-debug-sgp:
 	$(CXX_nat) $(CFLAGS_nat_debug) $(TEST_DIR)/main.cc -o symbulation.test
 	./symbulation.test [sgp]

source/ConfigSetup.h

@@ -33,6 +33,7 @@ EMP_BUILD_CONFIG(SymConfigBase,
     VALUE(NUM_PHYLO_BINS, size_t, 5, "How many bins should organisms be sepeated into if phylogeny is on?"),
     VALUE(NO_MUT_UPDATES, int, 0, "How many updates should be run after the end of UPDATES with all mutation turned off?"),
     VALUE(PHAGE_EXCLUDE, bool, 0, "Do symbionts have a decreasing chance of getting into the host the more symbionts are already infecting it? (0 for no, 1 for yes)"), // todo: alias phage_exclude, and change name to sym_exclude
+    VALUE(OUSTING, bool, 0, "Should ousting (incoming symbiont kills and replaces existing symbiont) be turned on? (0 for no, 1 for yes)"),
     VALUE(FILE_PATH, std::string, "", "Output file path"),
     VALUE(FILE_NAME, std::string, "_data", "Root output file name"),
     VALUE(DOMINANT_COUNT, size_t, 10, "Number of dominant hosts to select"),

source/default_mode/Host.h

@@ -200,7 +200,7 @@ class Host: public Organism {
 
   /**
   * Input: None
-  * 
+  *
   * Output: Name of class as string, Host
   *
   * Purpose: To know which subclass the object is
@@ -439,7 +439,18 @@ class Host: public Organism {
    * Purpose: To add a symbionts to a host's symbionts
    */
   int AddSymbiont(emp::Ptr<Organism> _in) {
-    if((int)syms.size() < my_config->SYM_LIMIT() && SymAllowedIn()){
+    bool allowed_in = SymAllowedIn();
+    if (my_config->OUSTING() && allowed_in && (int)syms.size() == my_config->SYM_LIMIT()) {
+      // if there's more than one sym, randomly choose one to replace, otherwise replace the one sym
+      const int new_sym_pos = (syms.size() > 1) ? random->GetInt(syms.size()) : 0;
+      emp::Ptr<Organism> old_sym = syms[new_sym_pos];
+      my_world->SendToGraveyard(old_sym);
+      syms[new_sym_pos] = _in;
+      _in->SetHost(this);
+      _in->UponInjection();
+      return new_sym_pos+1;
+    }
+    else if((int)syms.size() < my_config->SYM_LIMIT() && allowed_in){
       syms.push_back(_in);
       _in->SetHost(this);
       _in->UponInjection();
@@ -536,7 +547,7 @@ class Host: public Organism {
     if (mutation_rate == -1) mutation_rate = my_config->MUTATION_RATE();
 
     if(random->GetDouble(0.0, 1.0) <= mutation_rate){
-      interaction_val += random->GetRandNormal(0.0, mutation_size);
+      interaction_val += random->GetNormal(0.0, mutation_size);
       if(interaction_val < -1) interaction_val = -1;
       else if (interaction_val > 1) interaction_val = 1;
     }
@@ -682,8 +693,10 @@ class Host: public Organism {
           if(!curSym->GetDead()){
             curSym->Process(sym_pos);
           }
-          if(curSym->GetDead()){
-            syms.erase(syms.begin() + j); //if the symbiont dies during their process, remove from syms list
+          if(curSym->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();
           }
         } //for each sym in syms

source/default_mode/SymWorld.h

@@ -30,6 +30,15 @@ class SymWorld : public emp::World<Organism>{
   */
   pop_t sym_pop;
 
+  /**
+    *
+    * Purpose: Represents the set of organisms which have been unlinked from 
+    * their standard managing structures and need to be deleted at the end 
+    * of every update.
+    *
+  */
+  emp::vector<emp::Ptr<Organism>> graveyard = {};
+
   /**
     *
     * Purpose: Represents a standard function object which determines which taxon an organism belongs to.
@@ -137,7 +146,7 @@ class SymWorld : public emp::World<Organism>{
     }
 
     if(my_config->PHYLOGENY()){ //host systematic deletion is handled by empirical world destructor
-      Clear(); // delete hosts here so that hosted symbionts get 
+      Clear(); // delete hosts here so that hosted symbionts get
       // deleted and unlinked from the sym_sys
       sym_sys.Delete();
     }
@@ -164,6 +173,14 @@ class SymWorld : public emp::World<Organism>{
    */
   emp::World<Organism>::pop_t GetSymPop() {return sym_pop;}
 
+   /**
+   * Input: None
+   *
+   * Output: A reference to the world graveyard.
+   *
+   * Purpose: To get the world's graveyard.
+   */
+  emp::vector<emp::Ptr<Organism>>& GetGraveyard() { return graveyard; }
 
   /**
    * Input: None
@@ -246,7 +263,7 @@ class SymWorld : public emp::World<Organism>{
    * Purpose: To add a symbiont to the systematic and to set it to track its taxon
    */
   emp::Ptr<emp::Taxon<int>> AddSymToSystematic(emp::Ptr<Organism> sym, emp::Ptr<emp::Taxon<int>> parent_taxon=nullptr){
-    emp::Ptr<emp::Taxon<int>> taxon = sym_sys->AddOrg(*sym, emp::WorldPosition(0,0), parent_taxon, GetUpdate());
+    emp::Ptr<emp::Taxon<int>> taxon = sym_sys->AddOrg(*sym, emp::WorldPosition(0,0), parent_taxon);
     sym->SetTaxon(taxon);
     return taxon;
   }
@@ -264,7 +281,7 @@ class SymWorld : public emp::World<Organism>{
    */
   float PullResources(float desired_resources) {
     // if LIMITED_RES_TOTAL == -1, unlimited, even if limited resources was on before
-    if (total_res == -1 || my_config->LIMITED_RES_TOTAL() == -1) { 
+    if (total_res == -1 || my_config->LIMITED_RES_TOTAL() == -1) {
       return desired_resources;
     } else {
       if (total_res>=desired_resources) {
@@ -312,6 +329,18 @@ class SymWorld : public emp::World<Organism>{
   }
 
 
+  /**
+   * Input: An organism pointer to add to the graveyard
+   *
+   * Output: None
+   *
+   * Purpose: To add organisms to the graveyard
+   */
+  virtual void SendToGraveyard(emp::Ptr<Organism> org) {
+    graveyard.push_back(org);
+  }
+
+
   /**
    * Input: The pointer to the new organism;
    * the world position of the location to add
@@ -495,7 +524,7 @@ class SymWorld : public emp::World<Organism>{
    * Input: The pointer to the symbiont that is moving, the WorldPosition of its
    * current location.
    *
-   * Output: The WorldPosition object describing the symbiont's new location (it describes an 
+   * Output: The WorldPosition object describing the symbiont's new location (it describes an
    * invalid position if the symbiont is deleted during movement)
    *
    * Purpose: To move a symbiont into a new world position.
@@ -640,7 +669,7 @@ class SymWorld : public emp::World<Organism>{
   /**
   * Input: A size_t location to check in the symbiont population vector.
   *
-  * Output: A boolean representing whether the the position is valid and 
+  * Output: A boolean representing whether the the position is valid and
   * occupied by a free living symbiont/
   *
   * Purpose: To determine if a given index is valid and occipied in the symbiont
@@ -752,7 +781,7 @@ class SymWorld : public emp::World<Organism>{
     if (counts.size() <= result.size()) {
       result.resize(counts.size());
     }
-  
+
     return result;
   }
 
@@ -789,6 +818,12 @@ class SymWorld : public emp::World<Organism>{
         else sym_pop[i]->Process(sym_pos); //index 0, since it's freeliving, and id its location in the world
       }
     } // for each cell in schedule
+
+    // clean up the graveyard
+    for (size_t i = 0; i < graveyard.size(); i++) {
+      graveyard[i].Delete();
+    }
+    graveyard.clear();
   } // Update()
 };// SymWorld class
 #endif

source/default_mode/Symbiont.h

@@ -161,12 +161,12 @@ class Symbiont: public Organism {
    * Purpose: To destruct the symbiont and remove the symbiont from the systematic.
    */
   ~Symbiont() {
-    if(my_config->PHYLOGENY() == 1) {my_world->GetSymSys()->RemoveOrg(my_taxon, my_world->GetUpdate());}
+    if(my_config->PHYLOGENY() == 1) {my_world->GetSymSys()->RemoveOrg(my_taxon);}
   }
 
     /**
     * Input: None
-    * 
+    *
     * Output: Name of class as string, Symbiont
     *
     * Purpose: To know which subclass the object is
@@ -396,13 +396,13 @@ class Symbiont: public Organism {
     double local_size = my_config->MUTATION_SIZE();
 
     if (random->GetDouble(0.0, 1.0) <= local_rate) {
-      interaction_val += random->GetRandNormal(0.0, local_size);
+      interaction_val += random->GetNormal(0.0, local_size);
       if(interaction_val < -1) interaction_val = -1;
       else if (interaction_val > 1) interaction_val = 1;
 
       //also modify infection chance, which is between 0 and 1
       if(my_config->FREE_LIVING_SYMS()){
-        infection_chance += random->GetRandNormal(0.0, local_size);
+        infection_chance += random->GetNormal(0.0, local_size);
         if (infection_chance < 0) infection_chance = 0;
         else if (infection_chance > 1) infection_chance = 1;
       }

source/efficient_mode/EfficientSymbiont.h

@@ -109,7 +109,7 @@ class EfficientSymbiont: public Symbiont {
 
   /**
   * Input: None
-  * 
+  *
   * Output: Name of class as string, EfficientSymbiont
   *
   * Purpose: To know which subclass the object is
@@ -189,19 +189,19 @@ class EfficientSymbiont: public Symbiont {
     }
 
     if (random->GetDouble(0.0, 1.0) <= int_rate) {
-      interaction_val += random->GetRandNormal(0.0, local_size);
+      interaction_val += random->GetNormal(0.0, local_size);
       if(interaction_val < -1) interaction_val = -1;
       else if (interaction_val > 1) interaction_val = 1;
 
       //also modify infection chance, which is between 0 and 1
       if(efficient_config->FREE_LIVING_SYMS()){
-        infection_chance += random->GetRandNormal(0.0, local_size);
+        infection_chance += random->GetNormal(0.0, local_size);
         if (infection_chance < 0) infection_chance = 0;
         else if (infection_chance > 1) infection_chance = 1;
       }
     }
     if (random->GetDouble(0.0, 1.0) <= eff_mut_rate) {
-      efficiency += random->GetRandNormal(0.0, local_size);
+      efficiency += random->GetNormal(0.0, local_size);
       if(efficiency < 0) efficiency = 0;
       else if (efficiency > 1) efficiency = 1;
     }
@@ -239,7 +239,7 @@ class EfficientSymbiont: public Symbiont {
     return sym_baby;
   }
   #pragma clang diagnostic pop
-  
+
 
   /**
    * Input: The pointer to the organism that is the new host baby

source/lysis_mode/Bacterium.h

@@ -82,7 +82,7 @@ class Bacterium : public Host {
 
   /**
   * Input: None
-  * 
+  *
   * Output: Name of class as string, Bacterium
   *
   * Purpose: To know which subclass the object is
@@ -139,7 +139,7 @@ class Bacterium : public Host {
 
       //mutate host genome if enabled
       if(lysis_config->MUTATE_INC_VAL()){
-        host_incorporation_val += random->GetRandNormal(0.0, lysis_config->MUTATION_SIZE());
+        host_incorporation_val += random->GetNormal(0.0, lysis_config->MUTATION_SIZE());
 
         if(host_incorporation_val < 0) host_incorporation_val = 0;