def run(self):
        """Run method that performs all the real work"""
        
        layers = self.iface.mapCanvas().layers()
        layer_list = []
        self.dlg.layerComboBox.clear()
        for layer in layers:
            layer_list.append(layer.name())
        self.dlg.layerComboBox.addItems(layer_list)
        # TODO: Make the active layer the selected item in combo box  aLayer = qgis.utils.iface.activeLayer()
        
        # TODO: Add signal to update toleranceSpinBox.suffix (Degrees) from layerComboBox.crs.mapUnits when layer is selected:
        #my_UnitType = { 0: 'Meters', 1: 'Feet', 2: 'Degrees', 7: 'NauticalMiles', 8: 'Kilometers', 9: 'Yards', 10: 'Miles', 3: 'UnknownUnit'}
        #suffix = my_UnitType[aLayer.crs().mapUnits()]
        
        # show the dialog
        self.dlg.show()
        # Run the dialog event loop
        result = self.dlg.exec_()
        # See if OK was pressed
        if result:
            if self.checkNetworkXModule() < 0:
                return -4
            import networkx as nx
            
            layerName = self.dlg.layerComboBox.currentText()
            try:
                aLayer = QgsProject.instance().mapLayersByName(layerName)[0]
            except:
                self.iface.messageBar().pushMessage("Error", "Failed to load layer!", level=Qgis.Critical)
                return -1

            try:

                previousEditingMode = True
                if not aLayer.isEditable():
                    aLayer.startEditing()
                    #self.iface.messageBar().pushMessage("Info", "Layer " + aLayer.name() + " needs to be in edit mode", level=Qgis.Info)
                    #self.iface.messageBar().pushMessage("Error", "Layer " + aLayer.name() + " needs to be in edit mode", level=Qgis.Critical)
                    #return -2
                    previousEditingMode = False
                     
                attrIdx = self.getAttributeIndex(aLayer)
                if attrIdx < 0:
                    return -3  

                progressMessageBar = self.iface.messageBar().createMessage("Creating network graph...")
                progress = QProgressBar()
                progress.setMaximum(aLayer.featureCount())
                progress.setAlignment(Qt.AlignLeft|Qt.AlignVCenter)
                progressMessageBar.layout().addWidget(progress)
                self.iface.messageBar().pushWidget(progressMessageBar, Qgis.Info)          
                
                G = nx.Graph()

                aLayer.beginEditCommand("Clear group attribute, create graph")
                # construct undirected graph
                tolerance = self.dlg.toleranceSpinBox.value()
                if tolerance == 0:
                    tolerance = 0.000001
                count = 0
                for feat in aLayer.getFeatures():
                    count += 1
                    progress.setValue(count)
                    done = aLayer.changeAttributeValue(feat.id(), attrIdx, -1)
                    geom = feat.geometry()
                    QgsGeometry.convertToSingleType(geom)       # QGIS 3.x seems to load single LineString as MultiLineString??
                    line = geom.asPolyline()
                    
                    for i in range(len(line)-1):
                        G.add_edges_from([((int(line[i][0]/tolerance), int(line[i][1]/tolerance)), (int(line[i+1][0]/tolerance), int(line[i+1][1]/tolerance)), 
                                          {'fid': feat.id()})])     # first scale by tolerance, then convert to int.  Before doing this, there were problems (in NetworkX v1) with floats not equating, thus creating disconnects that weren't there.
                    if count % 100 == 0:
                        QApplication.processEvents()      # keep the UI responsive, every 100 features
                        #TODO: check to see if Esc pressed

                aLayer.endEditCommand()
                
                self.iface.messageBar().pushMessage("Finding connected subgraphs, please wait...",  level=Qgis.Warning)     # WARNING - to highlight the next stage, where we cannot show progress
                QApplication.processEvents()
                connected_components = list(G.subgraph(c) for c in nx.connected_components(G)) # this takes a long time.  TODO: how to show progress?
                self.iface.messageBar().pushMessage("Updating group attribute...",  level=Qgis.Info)
                QApplication.processEvents()
                          
                # gather edges and components to which they belong
                fid_comp = {}
                for i, graph in enumerate(connected_components):
                   for edge in graph.edges(data=True):
                       fid_comp[edge[2].get('fid', None)] = i
                
                # write output to csv file
                #with open('C:/Tmp/Components.csv', 'wb') as f:
                #    w = csv.DictWriter(f, fieldnames=['fid', 'group'])
                #    w.writeheader()
                #    for (fid, group) in fid_comp.items():
                #        w.writerow({'fid': fid, 'group': group})
                
                aLayer.beginEditCommand("Update group attribute")
                for (fid, group) in fid_comp.items():
                    done = aLayer.changeAttributeValue(fid, attrIdx, group)
                aLayer.endEditCommand()
                
                groups = list(set(fid_comp.values()))            
                if self.dlg.stylingCheckBox.isChecked():
                    aLayer.beginEditCommand("Update layer styling")
                    categories = []
                    firstCat = True
                    for cat in groups:
                        symbol = QgsSymbol.defaultSymbol(aLayer.geometryType())
                        symbol.setColor(QColor(randint(0,255), randint(0,255), randint(0,255)))
                        if firstCat:
                            firstCat = False
                        else:
                            symbol.setWidth(symbol.width()*5)
                        category = QgsRendererCategory(cat, symbol, "%d" % cat)
                        categories.append(category)

                    field = self.dlg.attributeNameEditBox.text()
                    renderer = QgsCategorizedSymbolRenderer(field, categories)
                    aLayer.setRenderer(renderer)

#                    if self.iface.mapCanvas().isCachingEnabled():
#                        aLayer.setCacheImage(None)
#                    else:
#                        self.iface.mapCanvas().refresh()
                    aLayer.triggerRepaint()
                    aLayer.endEditCommand()            
                   
                self.iface.messageBar().clearWidgets()   
                self.iface.messageBar().pushMessage("Found main network and %d disconnected islands in layer %s" % (len(groups)-1, aLayer.name()),  level=Qgis.Success)

                aLayer.commitChanges()
#                if not previousEditingMode: 
    
            except Exception as e:
                self.iface.messageBar().pushMessage("Error", "Exception caught: %s.  Please report an issue to the author of the plugin." % repr(e), level=Qgis.Critical)
                
    def run(self):
        """Run method that performs all the real work"""
        
        layers = self.iface.mapCanvas().layers()
        layer_list = []
        self.dlg.layerComboBox.clear()
        for layer in layers:
            layer_list.append(layer.name())
        self.dlg.layerComboBox.addItems(layer_list)
        # TODO: Make the active layer the selected item in combo box  aLayer = qgis.utils.iface.activeLayer()
        
        # TODO: Add signal to update toleranceSpinBox.suffix (Degrees) from layerComboBox.crs.mapUnits when layer is selected:
        #my_UnitType = { 0: 'Meters', 1: 'Feet', 2: 'Degrees', 7: 'NauticalMiles', 8: 'Kilometers', 9: 'Yards', 10: 'Miles', 3: 'UnknownUnit'}
        #suffix = my_UnitType[aLayer.crs().mapUnits()]
        
        # show the dialog
        self.dlg.show()
        # Run the dialog event loop
        result = self.dlg.exec_()
        # See if OK was pressed
        if result:
            if self.checkNetworkXModule() < 0:
                return -4
            import networkx as nx
            
            layerName = self.dlg.layerComboBox.currentText()
            try:
                aLayer = QgsProject.instance().mapLayersByName(layerName)[0]
            except:
                self.iface.messageBar().pushMessage("Error", "Failed to load layer!", level=Qgis.Critical)
                return -1

            try:

                previousEditingMode = True
                if not aLayer.isEditable():
                    aLayer.startEditing()
                    #self.iface.messageBar().pushMessage("Info", "Layer " + aLayer.name() + " needs to be in edit mode", level=Qgis.Info)
                    #self.iface.messageBar().pushMessage("Error", "Layer " + aLayer.name() + " needs to be in edit mode", level=Qgis.Critical)
                    #return -2
                    previousEditingMode = False
                     
                attrIdx = self.getAttributeIndex(aLayer)
                if attrIdx < 0:
                    return -3  

                progressMessageBar = self.iface.messageBar().createMessage("Creating network graph...")
                progress = QProgressBar()
                progress.setMaximum(aLayer.featureCount())
                progress.setAlignment(Qt.AlignLeft|Qt.AlignVCenter)
                progressMessageBar.layout().addWidget(progress)
                self.iface.messageBar().pushWidget(progressMessageBar, Qgis.Info)          
                
                G = nx.Graph()

                aLayer.beginEditCommand("Clear group attribute, create graph")
                # construct undirected graph
                tolerance = self.dlg.toleranceSpinBox.value()
                if tolerance == 0:
                    tolerance = 0.000001
                count = 0
                for feat in aLayer.getFeatures():
                    count += 1
                    progress.setValue(count)
                    done = aLayer.changeAttributeValue(feat.id(), attrIdx, -1)
                    geom = feat.geometry()
                    QgsGeometry.convertToSingleType(geom)       # QGIS 3.x seems to load single LineString as MultiLineString??
                    line = geom.asPolyline()
                    
                    for i in range(len(line)-1):
                        G.add_edges_from([((int(line[i][0]/tolerance), int(line[i][1]/tolerance)), (int(line[i+1][0]/tolerance), int(line[i+1][1]/tolerance)), 
                                          {'fid': feat.id()})])     # first scale by tolerance, then convert to int.  Before doing this, there were problems (in NetworkX v1) with floats not equating, thus creating disconnects that weren't there.
                    if count % 100 == 0:
                        QApplication.processEvents()      # keep the UI responsive, every 100 features
                        #TODO: check to see if Esc pressed

                aLayer.endEditCommand()
                
                self.iface.messageBar().pushMessage("Finding connected subgraphs, please wait...",  level=Qgis.Warning)     # WARNING - to highlight the next stage, where we cannot show progress
                QApplication.processEvents()
                connected_components = list(nx.connected_component_subgraphs(G))    # this takes a long time.  TODO: how to show progress?
                self.iface.messageBar().pushMessage("Updating group attribute...",  level=Qgis.Info)
                QApplication.processEvents()
                          
                # gather edges and components to which they belong
                fid_comp = {}
                for i, graph in enumerate(connected_components):
                   for edge in graph.edges(data=True):
                       fid_comp[edge[2].get('fid', None)] = i
                
                # write output to csv file
                #with open('C:/Tmp/Components.csv', 'wb') as f:
                #    w = csv.DictWriter(f, fieldnames=['fid', 'group'])
                #    w.writeheader()
                #    for (fid, group) in fid_comp.items():
                #        w.writerow({'fid': fid, 'group': group})
                
                aLayer.beginEditCommand("Update group attribute")
                for (fid, group) in fid_comp.items():
                    done = aLayer.changeAttributeValue(fid, attrIdx, group)
                aLayer.endEditCommand()
                
                groups = list(set(fid_comp.values()))            
                if self.dlg.stylingCheckBox.isChecked():
                    aLayer.beginEditCommand("Update layer styling")
                    categories = []
                    firstCat = True
                    for cat in groups:
                        symbol = QgsSymbol.defaultSymbol(aLayer.geometryType())
                        symbol.setColor(QColor(randint(0,255), randint(0,255), randint(0,255)))
                        if firstCat:
                            firstCat = False
                        else:
                            symbol.setWidth(symbol.width()*5)
                        category = QgsRendererCategory(cat, symbol, "%d" % cat)
                        categories.append(category)

                    field = self.dlg.attributeNameEditBox.text()
                    renderer = QgsCategorizedSymbolRenderer(field, categories)
                    aLayer.setRenderer(renderer)

#                    if self.iface.mapCanvas().isCachingEnabled():
#                        aLayer.setCacheImage(None)
#                    else:
#                        self.iface.mapCanvas().refresh()
                    aLayer.triggerRepaint()
                    aLayer.endEditCommand()            
                   
                self.iface.messageBar().clearWidgets()   
                self.iface.messageBar().pushMessage("Found main network and %d disconnected islands in layer %s" % (len(groups)-1, aLayer.name()),  level=Qgis.Success)

                aLayer.commitChanges()
#                if not previousEditingMode: 
    
            except Exception as e:
                self.iface.messageBar().pushMessage("Error", "Exception caught: %s.  Please report an issue to the author of the plugin." % repr(e), level=Qgis.Critical)