Fixes

Editor/ClusterInspector.cs

@@ -19,16 +19,15 @@ public class ClusterInspector : Editor {
     public override VisualElement CreateInspectorGUI() {
         ClusterPrefab prefab = target as ClusterPrefab;
 
-        string path = AssetDatabase.GetAssetPath(prefab); // or known path
-        Debug.Log($"{path}");
-        ClusterPrefab currentWrapper = AssetDatabase.LoadAssetAtPath<ClusterPrefab>(path);
-        if (currentWrapper == null)
-            Debug.LogError("CreateInspectorGUI: Cluster Prefab is not found on disk");
+        // string path = AssetDatabase.GetAssetPath(prefab); // or known path
+        // Debug.Log($"{path}");
+        // ClusterPrefab currentWrapper = AssetDatabase.LoadAssetAtPath<ClusterPrefab>(path);
+        // if (currentWrapper == null)
+        //     Debug.LogError("CreateInspectorGUI: Cluster Prefab is not found on disk");
 
         if (prefab != null)
             prefab.EnsureInitialization();
 
-
         serializedObject.Update();
 
         VisualElement root = new();
@@ -176,20 +175,13 @@ public class ClusterInspector : Editor {
                 return;
             }
 
-            // if (currentWrapper != null)
-            //     DestroyImmediate(currentWrapper);
-            // currentWrapper = CreateInstance<ClusterWrapper>().Init(this.currentNucleus, prefab);
-
             string path = AssetDatabase.GetAssetPath(this.prefab); // or known path
             this.prefabAsset = AssetDatabase.LoadAssetAtPath<ClusterPrefab>(path);
             if (this.prefabAsset == null) {
-                // create and save if it doesn't exist
+                // create in memory save if it doesn't exist
                 this.prefabAsset = CreateInstance<ClusterPrefab>();
-                // AssetDatabase.CreateAsset(currentWrapper, "Assets/ClusterPrefab.asset");
-                // AssetDatabase.SaveAssets();
                 Debug.LogError("Cluster Prefab is not found on disk");
             }
-            //currentWrapper.Init(this.currentNucleus, prefab);
             DrawInspector(inspectorContainer);
         }
 
@@ -579,7 +571,7 @@ public class ClusterInspector : Editor {
             showSynapses = EditorGUILayout.BeginFoldoutHeaderGroup(showSynapses, "Synapses");
             if (showSynapses) {
 
-                ConnectNucleus(this.prefab, this.currentNucleus);
+                anythingChanged = ConnectNucleus(this.prefab, this.currentNucleus);
                 AddSynapse(this.prefab, this.currentNucleus);
                 EditorGUILayout.Space();
 
@@ -809,9 +801,9 @@ public class ClusterInspector : Editor {
         }
 
         // Connect to another nucleus in the same cluster
-        protected virtual void ConnectNucleus(ClusterPrefab cluster, Nucleus nucleus) {
+        protected virtual bool ConnectNucleus(ClusterPrefab cluster, Nucleus nucleus) {
             if (cluster == null)
-                return;
+                return false;
 
             IEnumerable<Nucleus> synapseNuclei = this.currentNucleus.synapses
                 .Where(synapse => synapse.nucleus != null)
@@ -824,10 +816,12 @@ public class ClusterInspector : Editor {
             string[] names = nucleiNames.ToArray();
             int selectedIndex = -1;
             selectedIndex = EditorGUILayout.Popup("Connect", selectedIndex, names);
-            if (selectedIndex >= 0) {
+            if (selectedIndex < 0)
+                return false;
+
             Nucleus receptor = nuclei.ElementAt(selectedIndex);
             receptor.AddReceiver(this.currentNucleus);
-            }
+            return true;
         }
 
         protected virtual void AddSynapse(ClusterPrefab cluster, Nucleus nucleus) {
@@ -865,29 +859,3 @@ public class NeuroidLayer {
     public int ix = 0;
     public List<Nucleus> neuroids = new();
 }
-
-// public class ClusterWrapper : ScriptableObject {
-//     // expose fields that map to GraphNode
-//     //public string title;
-//     public Vector2 position;
-//     Nucleus node;
-//     ClusterPrefab graph; // needed to write back and mark dirty
-
-//     public ClusterWrapper Init(Nucleus node, ClusterPrefab graphAsset) {
-//         this.node = node;
-//         this.graph = graphAsset;
-//         //this.title = " A " + node.name;
-//         //position = node.position;
-//         return this;
-//     }
-//     void OnValidate() {
-//         if (node != null) {
-//             //node.name = title;
-//             //node.position = position;
-// #if UNITY_EDITOR
-//             if (graph != null)
-//                 UnityEditor.EditorUtility.SetDirty(graph);
-// #endif
-//         }
-//     }
-// }

Neuron.cs

@@ -17,11 +17,10 @@ public class Neuron : Nucleus {
     public Neuron(ClusterPrefab parent, string name) {
         this.cluster = parent;
         this.name = name;
-        if (this.cluster != null) {
+        if (this.cluster != null)
             this.cluster.nuclei.Add(this);        
-        }
-        // else
-        //     Debug.LogError("No neuroid network");
+        else
+            Debug.LogError("No prefab when adding neuron to prefab");
     }
 
     #region Serialization

NucleusArray.cs

@@ -13,19 +13,19 @@ public class NucleusArray {
             return _nuclei;
         }
     }
-    public string name;
+    //public string name;
 
     public NucleusArray(Nucleus nucleus) {
-        this.name = nucleus.name;
+        //this.name = nucleus.name;
         this._nuclei = new Nucleus[1];
         this._nuclei[0] = nucleus;
     }
     public NucleusArray(ClusterPrefab cluster) {
-        this.name = cluster.name;
+        //this.name = cluster.name;
         this._nuclei = new Nucleus[0];
     }
     public NucleusArray(int size, string name) {
-        this.name = name;
+        //this.name = name;
         this._nuclei = new Nucleus[size];
     }