unstable/shaky layouting within compound nodes when using avoidOverlap

[EyMaddis]

I use the cytoscape adapter with compound nodes. It appears that the node within a compound/group are not stable and switch positions with each frame, as you can see below:

Is there a way to mitigate this jumping? All the examples from the website which have compound nodes seem to animate smoothly.

Layout options:

            name: 'cola',
            maxSimulationTime: 4000,
            padding: 6,
            ungrabifyWhileSimulating: true

The following graph data was used:

{
    "nodes": [
        {
            "data": {
                "id": "test-system123-nodeGroup-1",
                "name": "CoCoMe",
                "systemId": "system123",
                "type": "nodeGroup",
                "label": "CoCoMe"
            }
        },
        {
            "data": {
                "id": "test-system123-node-2",
                "name": "Logicnode",
                "ip": "10.0.0.2",
                "hostname": "host2",
                "nodeGroupId": "test-system123-nodeGroup-1",
                "systemId": "system123",
                "type": "node",
                "label": "Logicnode",
                "parent": "test-system123-nodeGroup-1"
            }
        },
        {
            "data": {
                "id": "test-system123-node-3",
                "name": "Adapter",
                "ip": "10.0.0.2",
                "hostname": "host3",
                "nodeGroupId": "test-system123-nodeGroup-1",
                "systemId": "system123",
                "type": "node",
                "label": "Adapter",
                "parent": "test-system123-nodeGroup-1"
            }
        },
        {
            "data": {
                "id": "test-system123-node-4",
                "name": "Database",
                "ip": "10.0.0.2",
                "hostname": "host4",
                "nodeGroupId": "test-system123-nodeGroup-1",
                "systemId": "system123",
                "type": "node",
                "label": "Database",
                "parent": "test-system123-nodeGroup-1"
            }
        },
        {
            "data": {
                "id": "test-system123-node-1",
                "name": "WebNode",
                "ip": "10.0.0.1",
                "hostname": "test hostname",
                "nodeGroupId": "test-system123-nodeGroup-1",
                "systemId": "system123",
                "type": "node",
                "label": "WebNode",
                "parent": "test-system123-nodeGroup-1"
            }
        },
        {
            "data": {
                "id": "test-system123-serviceInstance-4",
                "name": "Inventory",
                "nodeId": "test-system123-node-2",
                "serviceId": "test-system123-service-4",
                "systemId": "system123",
                "type": "serviceInstance",
                "label": "Inventory",
                "parent": "test-system123-node-2"
            }
        },
        {
            "data": {
                "id": "test-system123-serviceInstance-5",
                "name": "Data",
                "nodeId": "test-system123-node-3",
                "serviceId": "test-system123-service-5",
                "systemId": "system123",
                "type": "serviceInstance",
                "label": "Data",
                "parent": "test-system123-node-3"
            }
        },
        {
            "data": {
                "id": "test-system123-serviceInstance-6",
                "name": "PostgreSQL",
                "nodeId": "test-system123-node-4",
                "serviceId": "test-system123-service-6",
                "systemId": "system123",
                "type": "serviceInstance",
                "label": "PostgreSQL",
                "parent": "test-system123-node-4"
            }
        },
        {
            "data": {
                "id": "test-system123-serviceInstance-1",
                "name": "FrontEnd",
                "nodeId": "test-system123-node-1",
                "serviceId": "test-system123-service-1",
                "systemId": "system123",
                "type": "serviceInstance",
                "label": "FrontEnd",
                "parent": "test-system123-node-1"
            }
        },
        {
            "data": {
                "id": "test-system123-serviceInstance-2",
                "name": "WebService",
                "nodeId": "test-system123-node-2",
                "serviceId": "test-system123-service-2",
                "systemId": "system123",
                "type": "serviceInstance",
                "label": "WebService",
                "parent": "test-system123-node-2"
            }
        },
        {
            "data": {
                "id": "test-system123-serviceInstance-3",
                "name": "CashDesk",
                "nodeId": "test-system123-node-2",
                "serviceId": "test-system123-service-3",
                "systemId": "system123",
                "type": "serviceInstance",
                "label": "CashDesk",
                "parent": "test-system123-node-2"
            }
        }
    ],
    "edges": [
        {
            "data": {
                "id": "test-system123-communicationInstance-1",
                "sourceId": "test-system123-serviceInstance-1",
                "targetId": "test-system123-serviceInstance-2",
                "communicationId": null,
                "systemId": "system123",
                "type": "communicationInstance",
                "source": "test-system123-serviceInstance-1",
                "target": "test-system123-serviceInstance-2"
            }
        },
        {
            "data": {
                "id": "test-system123-communicationInstance-2",
                "sourceId": "test-system123-serviceInstance-2",
                "targetId": "test-system123-serviceInstance-3",
                "communicationId": null,
                "systemId": "system123",
                "type": "communicationInstance",
                "source": "test-system123-serviceInstance-2",
                "target": "test-system123-serviceInstance-3"
            }
        },
        {
            "data": {
                "id": "test-system123-communicationInstance-3",
                "sourceId": "test-system123-serviceInstance-3",
                "targetId": "test-system123-serviceInstance-4",
                "communicationId": null,
                "systemId": "system123",
                "type": "communicationInstance",
                "source": "test-system123-serviceInstance-3",
                "target": "test-system123-serviceInstance-4"
            }
        },
        {
            "data": {
                "id": "test-system123-communicationInstance-4",
                "sourceId": "test-system123-serviceInstance-3",
                "targetId": "test-system123-serviceInstance-5",
                "communicationId": null,
                "systemId": "system123",
                "type": "communicationInstance",
                "source": "test-system123-serviceInstance-3",
                "target": "test-system123-serviceInstance-5"
            }
        },
        {
            "data": {
                "id": "test-system123-communicationInstance-5",
                "sourceId": "test-system123-serviceInstance-4",
                "targetId": "test-system123-serviceInstance-5",
                "communicationId": null,
                "systemId": "system123",
                "type": "communicationInstance",
                "source": "test-system123-serviceInstance-4",
                "target": "test-system123-serviceInstance-5"
            }
        },
        {
            "data": {
                "id": "test-system123-communicationInstance-6",
                "sourceId": "test-system123-serviceInstance-5",
                "targetId": "test-system123-serviceInstance-6",
                "communicationId": null,
                "systemId": "system123",
                "type": "communicationInstance",
                "source": "test-system123-serviceInstance-5",
                "target": "test-system123-serviceInstance-6"
            }
        }
    ]
}

Please note that the graph above if dynamically generated, therefor I cannot set any fixed positions as I don't know how the graph has to look like beforehand.

I would appreciate some help. Thanks

EDIT: I noticed that it only happens when avoidOverlap is set.

[EyMaddis]

I created a jsbin to with the graph model the cytoscape adapter generated from the data above, rendered with D3:

http://jsbin.com/sedezekade/1/edit?html,js,output

Notice that the output has the input data within the HTML file. I also added names and some debugging information (like _sourceName), just to make things easier.
Everything except the data was extracted from the smallgroups example.

[EyMaddis]

I fixed it locally!

It happens because the cytoscape adapter adds all descendants as leaves of a compound node, but I should only add direct children which are leaves.

I will create a PR for the cytoscape adapter!