Merge pull request #129 from MaxRobinsonTheGreat/develop

Develop

package-lock.json

@@ -222,9 +222,9 @@
       "dev": true
     },
     "ansi-regex": {
-      "version": "4.1.0",
+      "version": "4.1.1",
-      "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-4.1.0.tgz",
+      "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-4.1.1.tgz",
-      "integrity": "sha512-1apePfXM1UOSqw0o9IiFAovVz9M5S1Dg+4TrDwfMewQ6p/rmMueb7tWZjQ1rx4Loy1ArBggoqGpfqqdI4rondg==",
+      "integrity": "sha512-ILlv4k/3f6vfQ4OoP2AGvirOktlQ98ZEL1k9FaQjxa3L1abBgbuTDAdPOpvbGncC0BTVQrl+OM8xZGK6tWXt7g==",
       "dev": true
     },
     "ansi-styles": {
@@ -1089,24 +1089,24 @@
       }
     },
     "elliptic": {
-      "version": "6.5.3",
+      "version": "6.5.4",
-      "resolved": "https://registry.npmjs.org/elliptic/-/elliptic-6.5.3.tgz",
+      "resolved": "https://registry.npmjs.org/elliptic/-/elliptic-6.5.4.tgz",
-      "integrity": "sha512-IMqzv5wNQf+E6aHeIqATs0tOLeOTwj1QKbRcS3jBbYkl5oLAserA8yJTT7/VyHUYG91PRmPyeQDObKLPpeS4dw==",
+      "integrity": "sha512-iLhC6ULemrljPZb+QutR5TQGB+pdW6KGD5RSegS+8sorOZT+rdQFbsQFJgvN3eRqNALqJer4oQ16YvJHlU8hzQ==",
       "dev": true,
       "requires": {
-        "bn.js": "^4.4.0",
+        "bn.js": "^4.11.9",
-        "brorand": "^1.0.1",
+        "brorand": "^1.1.0",
         "hash.js": "^1.0.0",
-        "hmac-drbg": "^1.0.0",
+        "hmac-drbg": "^1.0.1",
-        "inherits": "^2.0.1",
+        "inherits": "^2.0.4",
-        "minimalistic-assert": "^1.0.0",
+        "minimalistic-assert": "^1.0.1",
-        "minimalistic-crypto-utils": "^1.0.0"
+        "minimalistic-crypto-utils": "^1.0.1"
       },
       "dependencies": {
         "bn.js": {
-          "version": "4.11.9",
+          "version": "4.12.0",
-          "resolved": "https://registry.npmjs.org/bn.js/-/bn.js-4.11.9.tgz",
+          "resolved": "https://registry.npmjs.org/bn.js/-/bn.js-4.12.0.tgz",
-          "integrity": "sha512-E6QoYqCKZfgatHTdHzs1RRKP7ip4vvm+EyRUeE2RF0NblwVvb0p6jSVeNTOFxPn26QXN2o6SMfNxKp6kU8zQaw==",
+          "integrity": "sha512-c98Bf3tPniI+scsdk237ku1Dc3ujXQTSgyiPUDEOe7tRkhrqridvh8klBv0HCEso1OLOYcHuCv/cS6DNxKH+ZA==",
           "dev": true
         }
       }
@@ -1706,9 +1706,9 @@
       "dev": true
     },
     "ini": {
-      "version": "1.3.5",
+      "version": "1.3.8",
-      "resolved": "https://registry.npmjs.org/ini/-/ini-1.3.5.tgz",
+      "resolved": "https://registry.npmjs.org/ini/-/ini-1.3.8.tgz",
-      "integrity": "sha512-RZY5huIKCMRWDUqZlEi72f/lmXKMvuszcMBduliQ3nnWbx9X/ZBQO7DijMEYS9EhHBb2qacRUMtC7svLwe0lcw==",
+      "integrity": "sha512-JV/yugV2uzW5iMRSiZAyDtQd+nxtUnjeLt0acNdw98kKLrvuRVyB80tsREOE7yvGVgalhZ6RNXCmEHkUKBKxew==",
       "dev": true
     },
     "interpret": {
@@ -2934,9 +2934,9 @@
       }
     },
     "ssri": {
-      "version": "6.0.1",
+      "version": "6.0.2",
-      "resolved": "https://registry.npmjs.org/ssri/-/ssri-6.0.1.tgz",
+      "resolved": "https://registry.npmjs.org/ssri/-/ssri-6.0.2.tgz",
-      "integrity": "sha512-3Wge10hNcT1Kur4PDFwEieXSCMCJs/7WvSACcrMYrNp+b8kDL1/0wJch5Ni2WrtwEa2IO8OsVfeKIciKCDx/QA==",
+      "integrity": "sha512-cepbSq/neFK7xB6A50KHN0xHDotYzq58wWCa5LeWqnPrHG8GzfEjO/4O8kpmcGW+oaxkvhEJCWgbgNk4/ZV93Q==",
       "dev": true,
       "requires": {
         "figgy-pudding": "^3.5.1"
@@ -3569,9 +3569,9 @@
       "dev": true
     },
     "y18n": {
-      "version": "4.0.0",
+      "version": "4.0.3",
-      "resolved": "https://registry.npmjs.org/y18n/-/y18n-4.0.0.tgz",
+      "resolved": "https://registry.npmjs.org/y18n/-/y18n-4.0.3.tgz",
-      "integrity": "sha512-r9S/ZyXu/Xu9q1tYlpsLIsa3EeLXXk0VwlxqTcFRfg9EhMW+17kbt9G0NrgCmhGb5vT2hyhJZLfDGx+7+5Uj/w==",
+      "integrity": "sha512-JKhqTOwSrqNA1NY5lSztJ1GrBiUodLMmIZuLiDaMRJ+itFd+ABVE8XBjOvIWL+rSqNDC74LCSFmlb/U4UZ4hJQ==",
       "dev": true
     },
     "yallist": {

src/Controllers/ControlPanel.js

@@ -204,7 +204,6 @@ class ControlPanel {
             if (!env.reset(true, false)) return;
             let center = env.grid_map.getCenter();
             let org = this.editor_controller.env.getCopyOfOrg();
-            this.env_controller.add_new_species = true;
             this.env_controller.dropOrganism(org, center[0], center[1])
         });
         $('#save-env').click( () => {
@@ -464,8 +463,6 @@ class ControlPanel {
 
         if (mode == Modes.Clone) {
             this.env_controller.org_to_clone = this.engine.organism_editor.getCopyOfOrg();
-            this.env_controller.add_new_species = this.editor_controller.new_species;
-            this.editor_controller.new_species = false;
         }
     }
 

src/Controllers/EditorController.js

@@ -3,6 +3,7 @@ const Modes = require("./ControlModes");
 const CellStates = require("../Organism/Cell/CellStates");
 const Directions = require("../Organism/Directions");
 const Hyperparams = require("../Hyperparameters");
+const Species = require("../Stats/Species");
 
 class EditorController extends CanvasController{
     constructor(env, canvas) {
@@ -10,7 +11,6 @@ class EditorController extends CanvasController{
         this.mode = Modes.None;
         this.edit_cell_type = null;
         this.highlight_org = false;
-        this.new_species = false;
         this.defineCellTypeSelection();
         this.defineEditorDetails();
         this.defineSaveLoad();
@@ -46,7 +46,6 @@ class EditorController extends CanvasController{
         else if (this.right_click)
             this.env.removeCellFromOrg(this.mouse_c, this.mouse_r);
 
-        this.new_species = true;
         this.setBrainPanelVisibility();
         this.setMoveRangeVisibility();
         this.updateDetails();
@@ -134,6 +133,9 @@ class EditorController extends CanvasController{
                     this.refreshDetailsPanel();
                     this.env.organism.updateGrid();
                     this.env.renderFull();
+                    this.env.organism.species = new Species(this.env.organism.anatomy, null, 0);
+                    if (org.species_name)
+                        this.env.organism.species.name = org.species_name;
                     if (this.mode === Modes.Clone)
                         $('#drop-org').click();
                     // have to clear the value so change() will be triggered if the same file is uploaded again

src/Controllers/EnvironmentController.js

@@ -12,7 +12,6 @@ class EnvironmentController extends CanvasController{
         super(env, canvas);
         this.mode = Modes.FoodDrop;
         this.org_to_clone = null;
-        this.add_new_species = false;
         this.defineZoomControls();
         this.scale = 1;
     }
@@ -171,15 +170,15 @@ class EnvironmentController extends CanvasController{
         var new_org = new Organism(col, row, this.env, organism);
 
         if (new_org.isClear(col, row)) {
-            if (this.add_new_species){
+            let new_species = !FossilRecord.speciesIsExtant(new_org.species.name);
+            if (new_org.species.extinct) {
+                FossilRecord.resurrect(new_org.species);
+            }
+            else if (new_species) {
                 FossilRecord.addSpeciesObj(new_org.species);
                 new_org.species.start_tick = this.env.total_ticks;
-                this.add_new_species = false;
                 new_org.species.population = 0;
             }
-            else if (this.org_to_clone.species.extinct){
-                FossilRecord.resurrect(this.org_to_clone.species);
-            }
 
             this.env.addOrganism(new_org);
             new_org.species.addPop();

src/Environments/OrganismEditor.js

@@ -72,7 +72,6 @@ class OrganismEditor extends Environment{
         this.organism = new Organism(center[0], center[1], this, orig_org);
         this.organism.updateGrid();
         this.controller.updateDetails();
-        this.controller.new_species = false;
     }
     
     getCopyOfOrg() {
@@ -109,7 +108,6 @@ class OrganismEditor extends Environment{
             newOrganism.species = new Species(newOrganism.anatomy, null, 0);
             var col = Math.floor(size + (Math.random() * (env.grid_map.cols-(size*2)) ) );
             var row = Math.floor(size + (Math.random() * (env.grid_map.rows-(size*2)) ) );
-            env.controller.add_new_species = true;
             env.controller.dropOrganism(newOrganism, col, row);
         }
     }

src/Environments/WorldEnvironment.js

@@ -36,10 +36,10 @@ class WorldEnvironment extends Environment{
                 to_remove.push(i);
             }
         }
+        this.removeOrganisms(to_remove);
         if (Hyperparams.foodDropProb > 0) {
             this.generateFood();
         }
-        this.removeOrganisms(to_remove);
         this.total_ticks ++;
         if (this.total_ticks % this.data_update_rate == 0) {
             FossilRecord.updateData();
@@ -123,6 +123,16 @@ class WorldEnvironment extends Environment{
         this.organisms = [];
     }
     
+    clearDeadOrganisms() {
+        let to_remove = [];
+        for (let i in this.organisms) {
+            let org = this.organisms[i];
+            if (!org.living)
+                to_remove.push(i);
+        }
+        this.removeOrganisms(to_remove);
+    }
+
     generateFood() {
         var num_food = Math.max(Math.floor(this.grid_map.cols*this.grid_map.rows*Hyperparams.foodDropProb/50000), 1)
         var prob = Hyperparams.foodDropProb;
@@ -168,6 +178,7 @@ class WorldEnvironment extends Environment{
     }
 
     serialize() {
+        this.clearDeadOrganisms();
         let env = SerializeHelper.copyNonObjects(this);
         env.grid = this.grid_map.serialize();
         env.organisms = [];
@@ -198,7 +209,7 @@ class WorldEnvironment extends Environment{
             org.loadRaw(orgRaw);
             this.addOrganism(org);
             let s = species[orgRaw.species_name];
-            if (!s){ // ideally, every organisms species should exists, but there is a bug somewhere
+            if (!s){ // ideally, every organisms species should exists, but there is a bug that misses some species sometimes
                 s = new Species(org.anatomy, null, env.total_ticks);
                 species[orgRaw.species_name] = s;
             }

src/Stats/FossilRecord.js

@@ -4,8 +4,8 @@ const Species = require("./Species");
 
 const FossilRecord = {
     init: function(){
-        this.extant_species = [];
+        this.extant_species = {};
-        this.extinct_species = [];
+        this.extinct_species = {};
 
         // if an organism has fewer than this cumulative pop, discard them on extinction
         this.min_discard = 10;
@@ -20,45 +20,44 @@ const FossilRecord = {
 
     addSpecies: function(org, ancestor) {
         var new_species = new Species(org.anatomy, ancestor, this.env.total_ticks);
-        this.extant_species.push(new_species);
+        this.extant_species[new_species.name] = new_species;
         org.species = new_species;
         return new_species;
     },
 
     addSpeciesObj: function(species) {
-        this.extant_species.push(species);
+        if (this.extant_species[species.name]) {
+            console.warn('Tried to add already existing species. Add failed.');
+            return;
+        }
+        this.extant_species[species.name] = species;
         return species;
     },
 
+    numExtantSpecies() {return Object.values(this.extant_species).length},
+    numExtinctSpecies() {return Object.values(this.extinct_species).length},
+    speciesIsExtant(species_name) {return !!this.extant_species[species_name]},
+
     fossilize: function(species) {
-        species.end_tick = this.env.total_ticks;
+        if (!this.extant_species[species.name]) {
-        for (i in this.extant_species) {
+            console.warn('Tried to fossilize non existing species.');
-            var s = this.extant_species[i];
+            return false;
-            if (s == species) {
-                this.extant_species.splice(i, 1);
-                species.ancestor = undefined; // garbage collect dead species
-                // if (species.ancestor)
-                //     species.ancestor.ancestor = undefined;
-                if (species.cumulative_pop < this.min_pop) {
-                    return false;
-                }
-                // disabled for now, causes memory problems on long runs
-                // this.extinct_species.push(s);
-                return true;
-            }
         }
+        species.end_tick = this.env.total_ticks;
+        species.ancestor = undefined; // garbage collect ancestors
+        delete this.extant_species[species.name];
+        if (species.cumulative_pop >= this.min_discard) {
+            // TODO: store as extinct species
+            return true;
+        }
+        return false;
     },
 
     resurrect: function(species) {
         if (species.extinct) {
-            for (i in this.extinct_species) {
+            species.extinct = false;
-                var s = this.extinct_species[i];
+            this.extant_species[species.name] = species;
-                if (s == species) {
+            delete this.extinct_species[species.name];
-                    this.extinct_species.splice(i, 1);
-                    this.extant_species.push(species);
-                    species.extinct = false;
-                }
-            }
         }
     },
 
@@ -77,7 +76,7 @@ const FossilRecord = {
         var tick = this.env.total_ticks;
         this.tick_record.push(tick);
         this.pop_counts.push(this.env.organisms.length);
-        this.species_counts.push(this.extant_species.length);
+        this.species_counts.push(this.numExtantSpecies());
         this.av_mut_rates.push(this.env.averageMutability());
         this.calcCellCountAverages();
         while (this.tick_record.length > this.record_size_limit) {
@@ -97,8 +96,8 @@ const FossilRecord = {
             cell_counts[c.name] = 0;
         }
         var first=true;
-        for (let s of this.extant_species) {
+        for (let s of Object.values(this.extant_species)) {
-            if (s.cumulative_pop < this.min_discard && !first){
+            if (!first && this.numExtantSpecies() > 10 && s.cumulative_pop < this.min_discard){
                 continue;
             }
             for (let name in s.cell_counts) {
@@ -107,8 +106,11 @@ const FossilRecord = {
             total_org += s.population;
             first=false;
         }
-        if (total_org == 0)
+        if (total_org == 0) {
-            return cell_counts;
+            this.av_cells.push(0);
+            this.av_cell_counts.push(cell_counts);
+            return;
+        }
 
         var total_cells = 0;
         for (let c in cell_counts) {
@@ -137,7 +139,7 @@ const FossilRecord = {
             av_cell_counts:this.av_cell_counts,
         };
         let species = {};
-        for (let s of this.extant_species) {
+        for (let s of Object.values(this.extant_species)) {
             species[s.name] = SerializeHelper.copyNonObjects(s);
             delete species[s.name].name; // the name will be used as the key, so remove it from the value
         }

src/Stats/StatsPanel.js

@@ -50,7 +50,7 @@ class StatsPanel {
     updateDetails() {
         var org_count = this.env.organisms.length;
         $('#org-count').text("Total Population: " + org_count);
-        $('#species-count').text("Number of Species: " + FossilRecord.extant_species.length);
+        $('#species-count').text("Number of Species: " + FossilRecord.numExtantSpecies());
         $('#largest-org').text("Largest Organism Ever: " + this.env.largest_cell_count + " cells");
         $('#avg-mut').text("Average Mutation Rate: " + Math.round(this.env.averageMutability() * 100) / 100);