Identify the minimum requirements for automating IQTree2

[khiron]

Identify the simplest possible IQTree2 workflow that provides proof of automation that can be implemented as a first step to complete automation.

This will be the first step in building IQTree2 into a library that can be automated by python

[khiron]

Calculating the distance between two trees appears to be simple, 2 strings containing filenames and no reliance on any general options (other than threads and memory constraints). Return result is STDout text from iqtree

def rf_distance(tree1_file: str, tree2_file: str, general_options: GeneralOptions):
    """
    Compute RF distance using the specified tree files and general options.

    Parameters
    ----------
    tree1_file : str
        Path to the first tree file.
    tree2_file : str
        Path to the second tree file.
    general_options : GeneralOptions
        An instance of GeneralOptions class containing all the general options.

    Returns
    -------
    str
        The output text to stdout.
    """
    # TODO: Implement the function using the parameters and general options
    pass