Merge pull request #220 from amlalejini/2024-alex-dev

Update complex-syms-clean to use most recent version of Empirical

.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/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
@@ -546,7 +546,7 @@ 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;
     }

source/default_mode/SymWorld.h

@@ -146,7 +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();
     }
@@ -263,7 +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;
   }
@@ -281,7 +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) {
@@ -524,7 +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.
@@ -669,7 +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
@@ -781,7 +781,7 @@ class SymWorld : public emp::World<Organism>{
     if (counts.size() <= result.size()) {
       result.resize(counts.size());
     }
-  
+
     return result;
   }
 

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

@@ -27,8 +27,8 @@ class Bacterium : public Host {
   emp::Ptr<LysisWorld> my_world = NULL;
 
   /**
-    * 
-    * Purpose: Holds all configuration settings and points to same configuration 
+    *
+    * Purpose: Holds all configuration settings and points to same configuration
     * object as my_config from superclass, but with the correct subtype.
     *
   */
@@ -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;
 

source/lysis_mode/Phage.h

@@ -50,7 +50,7 @@ class Phage: public Symbiont {
 
   /**
     *
-    * Purpose: Holds all configuration settings and points to same configuration 
+    * Purpose: Holds all configuration settings and points to same configuration
     * object as my_config from superclass, but with the correct subtype.
     *
   */
@@ -110,7 +110,7 @@ class Phage: public Symbiont {
 
   /**
   * Input: None
-  * 
+  *
   * Output: Name of class as string, Phage
   *
   * Purpose: To know which subclass the object is
@@ -135,7 +135,7 @@ class Phage: public Symbiont {
    *
    * Purpose: To increment a phage's burst timer.
    */
-  void IncBurstTimer() {burst_timer += random->GetRandNormal(1.0, 1.0);}
+  void IncBurstTimer() {burst_timer += random->GetNormal(1.0, 1.0);}
 
 
   /**
@@ -261,17 +261,17 @@ class Phage: public Symbiont {
     if (random->GetDouble(0.0, 1.0) <= local_rate) {
       //mutate chance of lysis/lysogeny, if enabled
       if(lysis_config->MUTATE_LYSIS_CHANCE()){
-        chance_of_lysis += random->GetRandNormal(0.0, local_size);
+        chance_of_lysis += random->GetNormal(0.0, local_size);
         if(chance_of_lysis < 0) chance_of_lysis = 0;
         else if (chance_of_lysis > 1) chance_of_lysis = 1;
       }
       if(lysis_config->MUTATE_INDUCTION_CHANCE()){
-        induction_chance += random->GetRandNormal(0.0, local_size);
+        induction_chance += random->GetNormal(0.0, local_size);
         if(induction_chance < 0) induction_chance = 0;
         else if (induction_chance > 1) induction_chance = 1;
       }
       if(lysis_config->MUTATE_INC_VAL()){
-        incorporation_val += random->GetRandNormal(0.0, local_size);
+        incorporation_val += random->GetNormal(0.0, local_size);
         if(incorporation_val < 0) incorporation_val = 0;
         else if (incorporation_val > 1) incorporation_val = 1;
       }

source/pgg_mode/PGGSymbiont.h

@@ -20,18 +20,18 @@ class PGGSymbiont: public Symbiont {
     *
   */
   emp::Ptr<PGGWorld> my_world = NULL;
-  
+
   /**
     *
-    * Purpose: Holds all configuration settings and points to same configuration 
+    * Purpose: Holds all configuration settings and points to same configuration
     * object as my_config from superclass, but with the correct subtype.
     *
   */
   emp::Ptr<SymConfigPGG> pgg_config = NULL;
 
 public:
   PGGSymbiont(emp::Ptr<emp::Random> _random, emp::Ptr<PGGWorld> _world, emp::Ptr<SymConfigPGG> _config, double _intval = 0.0, double _donation = 0.0, double _points = 0.0) : Symbiont(_random, _world, _config, _intval, _points), PGG_donate(_donation) {
-    pgg_config = _config; 
+    pgg_config = _config;
     my_world = _world;
   }
 
@@ -86,7 +86,7 @@ class PGGSymbiont: public Symbiont {
 
   /**
   * Input: None
-  * 
+  *
   * Output: Name of class as string, PGGSymbiont
   *
   * Purpose: To know which subclass the object is
@@ -127,7 +127,7 @@ class PGGSymbiont: public Symbiont {
   void Mutate(){
     Symbiont::Mutate();
     if (random->GetDouble(0.0, 1.0) <= pgg_config->MUTATION_RATE()) {
-      PGG_donate += random->GetRandNormal(0.0, pgg_config->MUTATION_SIZE());
+      PGG_donate += random->GetNormal(0.0, pgg_config->MUTATION_SIZE());
       if(PGG_donate < 0) PGG_donate = 0;
       else if (PGG_donate > 1) PGG_donate = 1;
     }

source/pgg_mode/PGGWorldSetup.cc

@@ -34,12 +34,12 @@ void PGGWorld::SetupSymbionts(long unsigned int* total_syms) {
 	//If the user wants the symbionts' donation rate to be randomly initialized
 	if (pgg_config->PGG_DONATE_RANDOM()) {
 	  //If the user wants the initialization of the symbionts' donation
-	  //rate to be selected using a normal distribution  
+	  //rate to be selected using a normal distribution
 	  if (pgg_config->PGG_DONATE_NORMAL()) {
 		double mean = pgg_config->PGG_DONATE_NORMAL_MEAN();
 		double std = pgg_config->PGG_DONATE_NORMAL_STD();
 
-		sym_donation = random_ptr->GetRandNormal(mean, std);
+		sym_donation = random_ptr->GetNormal(mean, std);
 
 		//If selected value is out of the initialization range
 		if (sym_donation > pgg_config->PGG_DONATE_MAX()) {

source/sgp_mode/Instructions.h

@@ -105,7 +105,7 @@ INST(PrivateIO, {
   }
   uint32_t next;
   if (state.world->GetConfig()->RANDOM_IO_INPUT()) {
-    next = sgpl::tlrand.Get().GetBits50();
+    next = sgpl::tlrand.Get().GetUInt();
   } else {
     next = 1;
   }
@@ -127,7 +127,7 @@ INST(SharedIO, {
   AddOrganismPoints(state, *a);
   uint32_t next;
   if (state.world->GetConfig()->RANDOM_IO_INPUT()) {
-    next = sgpl::tlrand.Get().GetBits50();
+    next = sgpl::tlrand.Get().GetUInt();
   } else {
     next = 1;
   }