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castcollab / tesserae2

Tesserae2: Fast recombination-aware global and local alignment.
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Comment the main tesserae methods #12

Open winni2k opened 4 years ago

jonn-smith commented 4 years ago

As part of this we should add docstrings to all methods as well ala:

def sum(x, y):
    """
    Add two numbers.

    :param: x: first number to add
    :param: y: second number to add
    :return: The sum of given x and y
    """

This will make code usability and readability much better, as well as enabling us to generate more detailed documentation.

winni2k commented 4 years ago

Yup, I completely agree. It would be good to get sphinx up and running. We can probably borrow the setup from cortexpy

winni2k commented 4 years ago

For the Tesserae model, I think it might make sense to keep the variable names fairly short, and then define them in a document that describes the math using the same variable names. I believe @karljohanw is working on such a document. @karljohanw, any chance you could write the doc in restructured text? Then we could add it to the sphinx documentation. I believe restructured text can be converted to latex fairly easily as well.