Add topological evaluation order

Cluster.cs

@@ -15,41 +15,45 @@ public class Cluster : INucleus {
         set => _name = value;
     }
 
-    public ClusterPrefab storedPrefab;
+    #region Init
+
+    public Cluster(ClusterPrefab prefab, Cluster parent) {
+        this.prefab = prefab;
+        this.name = prefab.name;
 
-    public Cluster(Cluster parent, ClusterPrefab realPrefab) {
-        this.storedPrefab = realPrefab;
         this.parent = parent;
         this.parent?.nuclei.Add(this);
 
         ClonePrefab();
+        this.sortedNuclei = TopologicalSort(this.nuclei);
     }
 
-    public Cluster(ClusterPrefab realPrefab) {
-        this.storedPrefab = realPrefab;
-        this.name = realPrefab.name;
-        this.cluster = null;
-        if (this.cluster != null)
-            this.cluster.nuclei.Add(this);
-
-        ClonePrefab();
-    }
-
-    public Cluster(ClusterPrefab parent, ClusterPrefab realPrefab) {
-        this.storedPrefab = realPrefab;
-        //this.prefab = realPrefab.Clone();
-        this.name = realPrefab.name;
+    public Cluster(ClusterPrefab prefab, ClusterPrefab parent = null) {
+        this.prefab = prefab;
+        this.name = prefab.name;
         this.cluster = parent;
+
         if (this.cluster != null)
             this.cluster.nuclei.Add(this);
 
         ClonePrefab();
+        this.sortedNuclei = TopologicalSort(this.nuclei);
     }
 
+    // public Cluster(ClusterPrefab parent, ClusterPrefab realPrefab) {
+    //     this.prefab = realPrefab;
+    //     this.name = realPrefab.name;
+    //     this.cluster = parent;
+    //     if (this.cluster != null)
+    //         this.cluster.nuclei.Add(this);
+
+    //     ClonePrefab();
+    // }
+
     private void ClonePrefab() {
-        IReceptor[] nucleiArray = this.storedPrefab.nuclei.ToArray();
+        IReceptor[] nucleiArray = this.prefab.nuclei.ToArray();
         // first clone the nuclei without their connections
-        foreach (IReceptor nucleus in this.storedPrefab.nuclei)
+        foreach (IReceptor nucleus in this.prefab.nuclei)
             nucleus.ShallowCloneTo(this);
         IReceptor[] clonedNuclei = this.nuclei.ToArray();
 
@@ -83,6 +87,43 @@ public class Cluster : INucleus {
         }
     }
 
+    // Sort the nuclei in a correct evaluation order
+    private List<IReceptor> TopologicalSort(List<IReceptor> nodes) {
+        Dictionary<IReceptor, int> inDegree = new();
+        foreach (IReceptor node in nodes)
+            inDegree[node] = 0; // Initialize in-degree to zero
+
+        // Calculate in-degrees
+        foreach (IReceptor node in nodes) {
+            foreach (INucleus receiver in node.receivers)
+                inDegree[receiver]++;            
+        }
+
+        Queue<IReceptor> queue = new();
+        foreach (IReceptor node in nodes) {
+            if (inDegree[node] == 0) // Nodes with no dependencies            
+                queue.Enqueue(node);            
+        }
+
+        List<IReceptor> sortedOrder = new();
+        while (queue.Count > 0) {
+            IReceptor current = queue.Dequeue();
+            sortedOrder.Add(current); // Process the node
+
+            foreach (INucleus receiver in current.receivers) {
+                inDegree[receiver]--;
+                if (inDegree[receiver] == 0) // If all dependencies resolved
+                    queue.Enqueue(receiver);
+            }
+        }
+
+        // Check for cycles in the graph
+        if (sortedOrder.Count != nodes.Count)
+            throw new InvalidOperationException("Graph is not a DAG; a cycle exists.");        
+
+        return sortedOrder;
+    }
+
     public virtual IReceptor Clone() {
         Neuron clone = new(this.cluster, this.name) {
             array = this.array,
@@ -99,7 +140,7 @@ public class Cluster : INucleus {
     }
 
     public IReceptor ShallowCloneTo(Cluster parent) {
-        Cluster clone = new(parent, this.storedPrefab) {
+        Cluster clone = new(this.prefab, parent) {
             name = this.name,
         };
         return clone;
@@ -113,11 +154,18 @@ public class Cluster : INucleus {
         return -1;
     }
 
+    #endregion Init
+
+    public ClusterPrefab prefab;
+
     public ClusterPrefab cluster { get; set; }
     public Cluster parent { get; set; }
 
     [SerializeReference]
     public List<IReceptor> nuclei = new();
+    // the nuclei sorted using topological sorting
+    // to ensure that the cluster is computer in the right order
+    public List<IReceptor> sortedNuclei;
 
     public List<INucleus> _inputs = null;
     public virtual List<INucleus> inputs {

MemoryCell.cs

@@ -29,10 +29,6 @@ public class MemoryCell : Neuron {
 
         //Applying the weight factgors
         foreach (Synapse synapse in this.synapses) {
-            if (synapse.nucleus == this) {
-                float deltaTime = Time.time - this.lastTime;
-                synapse.weight = deltaTime;
-            }
             result += synapse.weight * synapse.nucleus.outputValue;
             if (lengthsq(synapse.nucleus.outputValue) != 0)
                 n++;

Neuron.cs

@@ -154,7 +154,6 @@ public class Neuron : INucleus {
     // private bool _isSleeping = false;
     // public bool isSleeping => _isSleeping;
     public bool isSleeping => lengthsq(this.outputValue) == 0;
-    public float lastTime { get; private set; }
 
     public void UpdateNuclei() {
         this.stale++;
@@ -292,10 +291,6 @@ public class Neuron : INucleus {
 
         //Applying the weight factgors
         foreach (Synapse synapse in this.synapses) {
-            if (synapse.nucleus == this) {
-                float deltaTime = Time.time - this.lastTime;
-                synapse.weight = deltaTime;
-            }
             sum += synapse.weight * synapse.nucleus.outputValue;
 
             // Perhaps synapses should be removed when the output value goes to 0....
@@ -340,7 +335,6 @@ public class Neuron : INucleus {
             Debug.Log($"{this.parent.name}.{this.name}: {this.outputValue}");
         }
 
-        this.lastTime = Time.time;
         foreach (INucleus receiver in this.receivers)
             receiver.UpdateState();
 

VisualEditor/Editor/ClusterInspector.cs

@@ -621,7 +621,7 @@ public class ClusterInspector : Editor {
         }
 
         private void OnClusterPicked(INucleus nucleus, ClusterPrefab prefab) {
-            Cluster subclusterInstance = new(this.cluster, prefab);
+            Cluster subclusterInstance = new(prefab, this.cluster);
             subclusterInstance.AddReceiver(nucleus);
             // This does not work somehow
             // this.currentNucleus = subclusterInstance;
@@ -630,9 +630,9 @@ public class ClusterInspector : Editor {
 
         private void EditCluster(Cluster subCluster) {
             // May be used with storedPrefab...
-            Selection.activeObject = subCluster.storedPrefab;
-            EditorGUIUtility.PingObject(subCluster.storedPrefab);
-            var editor = Editor.CreateEditor(subCluster.storedPrefab);
+            Selection.activeObject = subCluster.prefab;
+            EditorGUIUtility.PingObject(subCluster.prefab);
+            var editor = Editor.CreateEditor(subCluster.prefab);
         }
 
         // Connect to another nucleus in the same cluster

VisualEditor/Editor/NanoBrainComponent_Editor.cs

@@ -79,7 +79,7 @@ public class NanoBrainComponent_Editor : Editor {
         });
 
         if (brain != null && board != null)
-            board.SetGraph(component.gameObject, brain.storedPrefab, brain.output, inspectorContainer);
+            board.SetGraph(component.gameObject, brain.prefab, brain.output, inspectorContainer);
         // else
         //     Debug.LogWarning(" No brain!");