Bug: Mira Model Edit Fix rename state and possibly rename transition

[Tom-Szendrey]

The mira code being called in rename state and potentially rename transition doesnt work as intended.
Start with SIR
Add state A
Rename to state S

Expected result:

{
    "id": "S",
    "name": "Susceptible",
    "grounding": {
        "identifiers": {
            "ido": "0000514"
        },
        "modifiers": {}
    },
    "units": {
        "expression": "person",
        "expression_mathml": "<ci>person</ci>"
    }
}

Actual result:

{
    "id": "S",
    "name": "Susceptible",
    "grounding": {
        "identifiers": {
            "ido": "0000514"
        },
        "modifiers": {}
    },
    "units": {
        "expression": "person",
        "expression_mathml": "<ci>person</ci>"
    }
},
{
    "id": "S",
    "name": "S",
    "grounding": {
        "identifiers": {},
        "modifiers": {}
    }
},

[liunelson]

Here's a replacement rename function: https://github.com/liunelson/mira/blob/nliu/experiment/notebooks/nliu/rename_state.py#L109

I hate to have such a long-winded code snippet but it seems necessary to handle all the cases (whether or not the old or new name exists):

    """
    Given a TemplateModel model and the old & new name of a state/concept therein, 
    1. if the old name doesn't exist, do nothing
    2. if the new name is unused, replace the name of that state/concept
    3. if the new name is used, replace the old-name concept by the new-name concept
    
    Apply same replacement to the rate laws, observable expressions, and initials.
    """

[liunelson]

Do we need similar troubleshooting with the transition rename function?