Remove unused ScriptingPanel and make jython test-only dependency

ScriptingPanel was commented out of the tree model and unreachable from
the GUI. Remove it along with SCRIPTING_NODE enum, ActiveViewID.scripting,
and the GuiConstants entry. With no main source code using jython, change
jython-standalone to test scope in vcell-math.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: jcschaff

vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/BioModelEditor.java

@@ -95,8 +95,6 @@ public class BioModelEditor extends DocumentEditor {
 	private BioModel bioModel = null;
 
 	private BioModelEditorModelPanel bioModelEditorModelPanel = null;
-	private ScriptingPanel scriptingPanel = null;
-
 	private BioModelEditorTreeCellRenderer bioModelEditorTreeCellRenderer = null;
 	private BioModelEditorTreeModel bioModelEditorTreeModel = null;
 	private BioModelPropertiesPanel bioModelPropertiesPanel = null;	
@@ -909,17 +907,6 @@ protected void setRightBottomPanelOnSelection(Object[] selections) {
 }
 
 
-private ScriptingPanel getScriptingPanel() {
-	if (scriptingPanel == null) {
-		try {
-			scriptingPanel = new ScriptingPanel();
-		} catch (java.lang.Throwable ivjExc) {
-			handleException(ivjExc);
-		}
-	}
-	return scriptingPanel;
-}
-
 @Override
 protected void treeSelectionChanged() {
 	try {
@@ -975,8 +962,6 @@ private void setRightTopPanel(Object selectedObject, SimulationContext simulatio
 			newTopPanel = bioModelEditorApplicationsPanel;
 //		} else if (folderClass == DocumentEditorTreeFolderClass.DATA_NODE) {
 //			newTopPanel = dataSymbolsPanel;
-		} else if (folderClass == DocumentEditorTreeFolderClass.SCRIPTING_NODE) {
-			newTopPanel = getScriptingPanel();
 		} else if (folderClass == DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE
 				|| folderClass == DocumentEditorTreeFolderClass.PROTOCOLS_NODE
 				|| folderClass == DocumentEditorTreeFolderClass.SIMULATIONS_NODE
@@ -1038,7 +1023,6 @@ public void setBioModel(BioModel bioModel) {
 	getSpeciesContextSpecPanel().setBioModel(bioModel);
 	getMolecularStructuresPropertiesPanel().setBioModel(bioModel);
 	getReactionRuleSpecPropertiesPanel().setBioModel(bioModel);
-	getScriptingPanel().setBioModel(bioModel);	
 	getBioModelEditorPathwayPanel().setBioModel(bioModel);
 	getBioModelEditorPathwayDiagramPanel().setBioModel(bioModel);
 	bioModelEditorTreeModel.setBioModel(bioModel);

vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/BioModelEditorTreeModel.java

@@ -50,21 +50,18 @@ enum RunSimulationsNodeID {
 			new DocumentEditorTreeFolderNode(DocumentEditorTreeFolderClass.BIOMODEL_PARAMETERS_NODE, true),
 			new DocumentEditorTreeFolderNode(DocumentEditorTreeFolderClass.PATHWAY_NODE, true),
 //			new DocumentEditorTreeFolderNode(DocumentEditorTreeFolderClass.DATA_NODE, true),
-//			new DocumentEditorTreeFolderNode(DocumentEditorTreeFolderClass.SCRIPTING_NODE, true),
 		};
 	private BioModelNode modelNode = new BioModelNode(bioModelChildFolderNodes[0], true);
 	private BioModelNode applicationsNode = new BioModelNode(bioModelChildFolderNodes[1], true);	
 	private BioModelNode bioModelParametersNode = new BioModelNode(bioModelChildFolderNodes[2], false);
 	private BioModelNode pathwayNode = new BioModelNode(bioModelChildFolderNodes[3], true);
-//	private BioModelNode dataNode = new BioModelNode(bioModelChildFolderNodes[4], false);	
-//	private BioModelNode scriptingNode = new BioModelNode(bioModelChildFolderNodes[4], false);	
+//	private BioModelNode dataNode = new BioModelNode(bioModelChildFolderNodes[4], false);
 	private BioModelNode  bioModelChildNodes[] = {
 			modelNode,
 			applicationsNode,
 			bioModelParametersNode,
 			pathwayNode,
 //			dataNode,
-//			scriptingNode,
 	};
 	@Deprecated
 	List<BioModelNode> annotationNodes = new ArrayList<BioModelNode>();

vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/DocumentEditorTreeModel.java

@@ -68,8 +68,6 @@ public enum DocumentEditorTreeFolderClass {
 		DATA_NODE(					cbit.vcell.client.constants.GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_DATA),	
 		APPLICATIONS_NODE(			cbit.vcell.client.constants.GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_APPLICATIONS),	
 		BIOMODEL_PARAMETERS_NODE(	cbit.vcell.client.constants.GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_BIOMODEL_PARAMETERS),	
-		SCRIPTING_NODE(				cbit.vcell.client.constants.GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_SCRIPTING),
-
 		REACTIONS_NODE(				cbit.vcell.client.constants.GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_REACTIONS),
 		REACTION_DIAGRAM_NODE(		cbit.vcell.client.constants.GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_DIAGRAM),
 		STRUCTURES_NODE(			cbit.vcell.client.constants.GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_STRUCTURES),

vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/ScriptingPanel.java

@@ -28,8 +28,6 @@ public static enum ActiveViewID {
 
 		data,	
 		applications,	
-		scripting,
-
 		reactions,
 		structures,
 		species,

vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/SelectionManager.java

@@ -32,7 +32,6 @@ public class GuiConstants {
 	public final static String DOCUMENT_EDITOR_FOLDERNAME_DATA = "Experimental Data";
 	public final static String DOCUMENT_EDITOR_FOLDERNAME_APPLICATIONS = "Applications";
 	public final static String DOCUMENT_EDITOR_FOLDERNAME_BIOMODEL_PARAMETERS = "Parameters, Functions, Units, etc.";
-	public final static String DOCUMENT_EDITOR_FOLDERNAME_SCRIPTING = "Scripting";
 	public final static String DOCUMENT_EDITOR_FOLDERNAME_REACTIONS = "Reactions";
 	public final static String DOCUMENT_EDITOR_FOLDERNAME_DIAGRAM = "Reaction Diagram";
 	public final static String DOCUMENT_EDITOR_FOLDERNAME_STRUCTURES = "Structures";

vcell-core/src/main/java/cbit/vcell/client/constants/GuiConstants.java

@@ -125,7 +125,7 @@
             <groupId>org.python</groupId>
             <artifactId>jython-standalone</artifactId>
             <version>2.7.4</version>
-            <scope>compile</scope>
+            <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>