Merge pull request #208 from emilydolson/update-empirical

Update to latest version of Empirical (and better version of Emscripten)
anyaevostinar · Apr 10, 2024 · b4d5cd3 · b4d5cd3
2 parents 833411c + 4bbc83c
commit b4d5cd3
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Showing 13 changed files with 25 additions and 25 deletions.
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -16,7 +16,7 @@ jobs:
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Checkout Symbulation
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           path: SymbulationEmp
           submodules: "recursive"
@@ -25,7 +25,7 @@ jobs:
         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
+        run: cd SymbulationEmp/emsdk && ./emsdk install 3.1.18 && ./emsdk activate 3.1.18 && source ./emsdk_env.sh && cd .. && make web
 
       # Runs a single command using the runners shell
       - name: Make tests
@@ -35,6 +35,6 @@ jobs:
         run: cd SymbulationEmp && gcov -abcfu main.cc
 
       - name: Upload coverage
-        uses: codecov/codecov-action@v1.5.2
+        uses: codecov/codecov-action@v3
         with:
           root_dir: SymbulationEmp
diff --git a/Empirical b/Empirical
diff --git a/Makefile b/Makefile
@@ -3,7 +3,7 @@ TEST_DIR := source/catch
 EMP_DIR := Empirical/include
 
 # Flags to use regardless of compiler
-CFLAGS_all := -Wall -Wno-unused-function -std=c++17 -I$(EMP_DIR)/
+CFLAGS_all := -Wall -Wno-unused-function -std=c++20 -I$(EMP_DIR)/
 
 # Native compiler information
 CXX_nat := g++

diff --git a/docs/QuickStartGuides/4-CreatingAMode.md b/docs/QuickStartGuides/4-CreatingAMode.md
@@ -232,7 +232,7 @@ void Mutate() {
     //Repeat the below for each new trait that needs mutating
     if (random->GetDouble(0.0, 1.0) <= local_rate) {
       //mutate trait, assuming it should be between 0 and 1
-      trait += random->GetRandNormal(0.0, local_size);
+      trait += random->GetNormal(0.0, local_size);
       if(trait < 0) trait = 0;
       else if (trait > 1) trait = 1;
     }
@@ -248,17 +248,17 @@ The `Phage` class has three new traits and has configuration settings for turnin
     if (random->GetDouble(0.0, 1.0) <= local_rate) {
       //mutate chance of lysis/lysogeny, if enabled
       if(my_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(my_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(my_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;
       }

diff --git a/emsdk b/emsdk
diff --git a/source/default_mode/Host.h b/source/default_mode/Host.h
@@ -537,7 +537,7 @@ 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;
     }

diff --git a/source/default_mode/SymWorld.h b/source/default_mode/SymWorld.h
@@ -233,7 +233,7 @@ 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;
   }

diff --git a/source/default_mode/Symbiont.h b/source/default_mode/Symbiont.h
@@ -161,7 +161,7 @@ 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);}
   }
 
     /**
@@ -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;
       }

diff --git a/source/efficient_mode/EfficientSymbiont.h b/source/efficient_mode/EfficientSymbiont.h
@@ -180,19 +180,19 @@ 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(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;
       }
     }
     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;
     }

diff --git a/source/lysis_mode/Bacterium.h b/source/lysis_mode/Bacterium.h
@@ -130,7 +130,7 @@ class Bacterium : public Host {
 
       //mutate host genome if enabled
       if(my_config->MUTATE_INC_VAL()){
-        host_incorporation_val += random->GetRandNormal(0.0, my_config->MUTATION_SIZE());
+        host_incorporation_val += random->GetNormal(0.0, my_config->MUTATION_SIZE());
 
         if(host_incorporation_val < 0) host_incorporation_val = 0;
 

diff --git a/source/lysis_mode/Phage.h b/source/lysis_mode/Phage.h
@@ -126,7 +126,7 @@ 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);}
 
 
   /**
@@ -252,17 +252,17 @@ class Phage: public Symbiont {
     if (random->GetDouble(0.0, 1.0) <= local_rate) {
       //mutate chance of lysis/lysogeny, if enabled
       if(my_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(my_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(my_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;
       }

diff --git a/source/pgg_mode/PGGSymbiont.h b/source/pgg_mode/PGGSymbiont.h
@@ -118,7 +118,7 @@ class PGGSymbiont: public Symbiont {
   void Mutate(){
     Symbiont::Mutate();
     if (random->GetDouble(0.0, 1.0) <= my_config->MUTATION_RATE()) {
-      PGG_donate += random->GetRandNormal(0.0, my_config->MUTATION_SIZE());
+      PGG_donate += random->GetNormal(0.0, my_config->MUTATION_SIZE());
       if(PGG_donate < 0) PGG_donate = 0;
       else if (PGG_donate > 1) PGG_donate = 1;
     }

diff --git a/source/pgg_mode/PGGWorldSetup.cc b/source/pgg_mode/PGGWorldSetup.cc
@@ -39,7 +39,7 @@ void PGGWorld::SetupSymbionts(long unsigned int* total_syms) {
 		double mean = my_config->PGG_DONATE_NORMAL_MEAN();
 		double std = my_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 > my_config->PGG_DONATE_MAX()) {