Add basic Population constructor, Population.speciate tests, fix seve…

…ral reference bugs

src/architecture/population.js

@@ -1,5 +1,6 @@
 const _ = require('lodash');
 const Network = require('./network');
+const Species = require('./species')
 const methods = require('../methods/methods');
 const config = require('../config');
 
@@ -69,22 +70,25 @@ const Population = function(options) {
    * @function getPopulation
    * @memberof Population
    *
+   * @param {Object} config A configuration object to control function behavior
+   * @param {number} size The number of networks to place in the returned array
+   * 
    * @return {Network[]} Returns an array of networks. Must be assigned to Population.members if replacing current population.
    * 
    * @todo Add template network functionality
    * @todo Add option to have identical population networks
    */
-  self.getPopulation = function create_networks(options={}) {
+  self.getPopulation = function create_networks(config={}) {
     const population = []
-    for (let i = 0; i < size; i++) {
+    for (let i = 0; i < config.size; i++) {
       population.push(new Network(self.inputs, self.outputs, { connIds: self.connIds, nodeIds: self.nodeIds }));
     }
 
     return population
   };
 
   // Fill the members array on population construction
-  self.members = self.getPopulation(self.size);
+  self.members = self.getPopulation({ size: self.size });
 
   /**
    * Applies the mutation-scheme dictated by Neat to the provided network.

src/architecture/species.js

@@ -1,7 +1,7 @@
-const Network = require('./architecture/network');
-const methods = require('./methods/methods');
-const config = require('./config');
-const _ = require('../util/util')
+const Network = require('./network');
+const methods = require('../methods/methods');
+const config = require('../config');
+const _ = require('../util/utils')
 
 /**
 * Creates a new Species
@@ -10,9 +10,7 @@ const _ = require('../util/util')
 *
 * @param { Network } genome The first network to add to the species' members array
 * @param {object} options
-* @param {number} options.excessCoeff
-* @param {number} options.disjointCoeff
-* @param {number} options.weightsCoeff
+* @param {number[]} options.weights An array of weights for calculating compatability (distance) with the species. From NEAT paper.
 *
 * @prop { Network[] } members An array of species member networks / genomes
 * @prop { Network } bestGenome The best network, by fitness, in the species
@@ -34,7 +32,7 @@ const _ = require('../util/util')
 *
 * console.log(mySpecies.members) // [ myNetwork ]
 */
-const Species = function(genome, options) {
+const Species = function(genome, options={}) {
   const self = this;
 
   // NEAT designated props
@@ -45,7 +43,7 @@ const Species = function(genome, options) {
   self.stagnation = 0; // Generation count without improvement
 
   // Adjustable props - compatibility
-  self.coefficient = options.coefficient || [1,1,0.4];
+  self.weights = options.weights || [1,1,0.4];
   self.threshold = 3; // Threshold for determining whether or not a genome is compatible with the species
 
   // Species metadata

src/carrot.js

@@ -11,6 +11,7 @@ const Carrot = {
   Node: require('./architecture/node'),
   Neat: require('./neat'),
   Population: require('./architecture/population'),
+  Species: require('./architecture/species'),
   GAN: require('./gan'),
   multi: require('./multithreading/multi'),
 };

test/units/architecture/network.1.test.js

@@ -2,7 +2,7 @@ const _ = require('lodash');
 const chai = require('chai');
 const { assert, expect } = chai;
 const should = chai.should();
-chai.use(require('chai-things')); // support for array tests using should
+chai.use(require('chai-things')); // support for array-based assertions
 const {
   Network,
   methods,

test/units/architecture/population.test.js

@@ -1,7 +1,26 @@
-const { assert, expect } = require('chai');
-const should = require('chai').should();
+const chai = require('chai');
+const { assert, expect } = chai;
+const should = chai.should();
+chai.use(require('chai-things')); // support for array-based assertions
 const chalk = require('chalk');
 
-const { Population, Network, methods } = require('../../../src/carrot');
+const { Population, Species, Network, methods } = require('../../../src/carrot');
 
-describe("Population", () => {})
+describe("Population", () => {
+    describe("new Population()", function () {
+        it("new Population() => {Network}", function () {
+            const population = new Population();
+
+            expect(population).instanceOf(Population);
+        })
+    })
+
+    describe(".speciate()", function () {
+        it("(pop.members, pop.species) => {Species[]}", function () {
+            const population = new Population();
+
+            // ".all" checks an assertion against all members of an array
+            expect(population.speciate(population.members, population.species)).all.instanceOf(Species)
+        })
+    })
+})