added from to UUID in CRISPR (#315)

Co-authored-by: Nigel (MacBook) <nigel@laptop>

src/Creature.ts

@@ -1,6 +1,6 @@
-import { yellow } from "https://deno.land/std@0.219.1/fmt/colors.ts";
-import { format } from "https://deno.land/std@0.219.1/fmt/duration.ts";
-import { emptyDirSync } from "https://deno.land/std@0.219.1/fs/empty_dir.ts";
+import { yellow } from "https://deno.land/std@0.220.1/fmt/colors.ts";
+import { format } from "https://deno.land/std@0.220.1/fmt/duration.ts";
+import { emptyDirSync } from "https://deno.land/std@0.220.1/fs/empty_dir.ts";
 import {
   addTag,
   getTag,
@@ -287,7 +287,7 @@ export class Creature implements CreatureInternal {
         pos < compactCreature.neurons.length - compactCreature.output;
         pos++
       ) {
-        const fromList = compactCreature.efferentConnections(pos).filter(
+        const fromList = compactCreature.outwardConnections(pos).filter(
           (c: SynapseInternal) => {
             return c.from !== c.to;
           },
@@ -303,7 +303,7 @@ export class Creature implements CreatureInternal {
             },
           );
           if (toList.length == 1) {
-            const fromList = compactCreature.efferentConnections(pos).filter(
+            const fromList = compactCreature.outwardConnections(pos).filter(
               (c: SynapseInternal) => {
                 return c.from !== c.to;
               },
@@ -552,7 +552,7 @@ export class Creature implements CreatureInternal {
               `Node ${node.ID()} '${node.type}' has squash: ${node.squash}`,
             );
           }
-          const fromList = this.efferentConnections(indx);
+          const fromList = this.outwardConnections(indx);
           if (fromList.length == 0) {
             if (this.DEBUG) {
               this.DEBUG = false;
@@ -581,7 +581,7 @@ export class Creature implements CreatureInternal {
               "NO_INWARD_CONNECTIONS",
             );
           }
-          const fromList = this.efferentConnections(indx);
+          const fromList = this.outwardConnections(indx);
           if (fromList.length == 0) {
             if (this.DEBUG) {
               this.DEBUG = false;
@@ -756,7 +756,7 @@ export class Creature implements CreatureInternal {
    * @param fromIndx the connections from this neuron by index
    * @returns the list of connections from the neuron.
    */
-  efferentConnections(fromIndx: number): Synapse[] {
+  outwardConnections(fromIndx: number): Synapse[] {
     let results = this.cacheFrom.get(fromIndx);
     if (results === undefined) {
       results = [];
@@ -1527,7 +1527,7 @@ export class Creature implements CreatureInternal {
           /** Each neuron must have at least one from/to connection */
           if (
             (
-              this.efferentConnections(conn.from).length > 1 ||
+              this.outwardConnections(conn.from).length > 1 ||
               this.neurons[conn.from].type === "input"
             ) && this.inwardConnections(conn.to).length > 1
           ) {
@@ -1705,7 +1705,7 @@ export class Creature implements CreatureInternal {
           if (this.inFocus(from, focusList)) {
             if (
               (
-                this.efferentConnections(from).length > 1 ||
+                this.outwardConnections(from).length > 1 ||
                 this.neurons[from].type === "input"
               ) && this.inwardConnections(to).length > 1
             ) {
@@ -1907,7 +1907,7 @@ export class Creature implements CreatureInternal {
       ) {
         if (this.neurons[pos].type == "output") continue;
         if (
-          this.efferentConnections(pos).filter((c) => {
+          this.outwardConnections(pos).filter((c) => {
             return c.from !== c.to;
           }).length == 0
         ) {
@@ -1966,7 +1966,7 @@ export class Creature implements CreatureInternal {
     }
 
     for (let i = this.synapses.length; i--;) {
-      const exportJSON = (this.synapses[i] as Synapse).exportJSON(
+      const exportJSON = this.synapses[i].exportJSON(
         uuidMap,
       );
 
@@ -2037,7 +2037,7 @@ export class Creature implements CreatureInternal {
     }
 
     for (let i = this.synapses.length; i--;) {
-      const internalJSON = (this.synapses[i] as Synapse).internalJSON();
+      const internalJSON = this.synapses[i].internalJSON();
 
       json.synapses[i] = internalJSON;
     }
@@ -2124,6 +2124,10 @@ export class Creature implements CreatureInternal {
         synapse.type,
       );
 
+      if (synapse.tags) {
+        connection.tags = synapse.tags.slice();
+      }
+
       if ((synapse as SynapseTrace).trace) {
         const cs = this.state.connection(connection.from, connection.to);
         const trace = (synapse as SynapseTrace).trace;

src/architecture/CreatureUtils.ts

@@ -1,4 +1,4 @@
-import { generate as generateV5 } from "https://deno.land/std@0.219.1/uuid/v5.ts";
+import { generate as generateV5 } from "https://deno.land/std@0.220.1/uuid/v5.ts";
 import { Creature } from "../Creature.ts";
 
 export class CreatureUtil {

src/architecture/ElitismUtils.ts

@@ -5,7 +5,7 @@ import {
   red,
   white,
   yellow,
-} from "https://deno.land/std@0.219.1/fmt/colors.ts";
+} from "https://deno.land/std@0.220.1/fmt/colors.ts";
 import { getTag } from "https://deno.land/x/[email protected]/mod.ts";
 import { Creature } from "../Creature.ts";
 

src/architecture/FineTune.ts

@@ -1,4 +1,4 @@
-import { blue, bold, cyan } from "https://deno.land/std@0.219.1/fmt/colors.ts";
+import { blue, bold, cyan } from "https://deno.land/std@0.220.1/fmt/colors.ts";
 import { addTag, getTag } from "https://deno.land/x/[email protected]/mod.ts";
 import { Creature } from "../Creature.ts";
 import { CreatureUtil } from "./CreatureUtils.ts";

src/architecture/Neat.ts

@@ -1,6 +1,6 @@
-import { blue } from "https://deno.land/std@0.219.1/fmt/colors.ts";
-import { format } from "https://deno.land/std@0.219.1/fmt/duration.ts";
-import { ensureDirSync } from "https://deno.land/std@0.219.1/fs/ensure_dir.ts";
+import { blue } from "https://deno.land/std@0.220.1/fmt/colors.ts";
+import { format } from "https://deno.land/std@0.220.1/fmt/duration.ts";
+import { ensureDirSync } from "https://deno.land/std@0.220.1/fs/ensure_dir.ts";
 import {
   addTag,
   getTag,

src/architecture/Neuron.ts

@@ -124,7 +124,7 @@ export class Neuron implements TagsInterface, NeuronInternal {
     }
 
     if (this.type == "hidden") {
-      const fromList = this.creature.efferentConnections(this.index);
+      const fromList = this.creature.outwardConnections(this.index);
       if (fromList.length == 0) {
         const targetIndx = Math.min(
           1,

src/architecture/Synapse.ts

@@ -1,3 +1,4 @@
+import { TagInterface } from "https://deno.land/x/[email protected]/mod.ts";
 import { SynapseExport, SynapseInternal } from "./SynapseInterfaces.ts";
 
 export class Synapse implements SynapseInternal {
@@ -6,6 +7,8 @@ export class Synapse implements SynapseInternal {
   public type?: "positive" | "negative" | "condition";
   public weight: number;
 
+  public tags?: TagInterface[];
+
   public static randomWeight() {
     return Math.random() * 0.2 - 0.1;
   }
@@ -33,6 +36,7 @@ export class Synapse implements SynapseInternal {
       fromUUID: fromUUID,
       toUUID: toUUID,
       type: this.type,
+      tags: this.tags ? this.tags.slice() : undefined,
     };
 
     return json;
@@ -44,6 +48,7 @@ export class Synapse implements SynapseInternal {
       from: this.from,
       to: this.to,
       type: this.type,
+      tags: this.tags ? this.tags.slice() : undefined,
     };
 
     return json;

src/architecture/SynapseInterfaces.ts

@@ -1,8 +1,11 @@
+import { TagInterface } from "https://deno.land/x/[email protected]/mod.ts";
 import { SynapseState } from "./CreatureState.ts";
 
 interface SynapseCommon {
   weight: number;
   type?: "positive" | "negative" | "condition";
+
+  tags?: TagInterface[];
 }
 
 export interface SynapseInternal extends SynapseCommon {

src/architecture/Training.ts

@@ -1,6 +1,6 @@
-import { blue, yellow } from "https://deno.land/std@0.219.1/fmt/colors.ts";
-import { format } from "https://deno.land/std@0.219.1/fmt/duration.ts";
-import { ensureDirSync } from "https://deno.land/std@0.219.1/fs/ensure_dir.ts";
+import { blue, yellow } from "https://deno.land/std@0.220.1/fmt/colors.ts";
+import { format } from "https://deno.land/std@0.220.1/fmt/duration.ts";
+import { ensureDirSync } from "https://deno.land/std@0.220.1/fs/ensure_dir.ts";
 import { Costs } from "../Costs.ts";
 import { Creature } from "../Creature.ts";
 import { TrainOptions } from "../config/TrainOptions.ts";

src/compact/CompactUnused.ts

@@ -63,7 +63,7 @@ function removeNeuron(uuid: string, creature: Creature, activation: number) {
   const neuron = creature.neurons.find((n) => n.uuid === uuid);
   if (neuron?.index) {
     let useConstant = false;
-    const fromList = creature.efferentConnections(neuron.index);
+    const fromList = creature.outwardConnections(neuron.index);
 
     for (const synapse of fromList) {
       const squash = creature.neurons[synapse.to].findSquash();