M2 docstring #2
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M2 docstring #2
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Also add some napoleon config. Setting preprocess_types to True might (have been) a good idea, but will currently cause about 200 warnings, since that will break with e.g. `list[str]`. Instead we'd need to change it to e.g. `list of str`, and IMHO it results in less pretty html
Split argument parsing and argument processing in different functions.
Bash command martinize2 is now a function in vermouth.martinize2. The bash command directly refers to it, so only one function needs to be modified. One issue for the lazy or forgetful: arguments and their documentation now need to be modified two times (in the CLI and the python API). This should however make martinize2 more easily testable. Type hints could be added to the martinize2 function.
Plus implement two esthetic suggestions by pckroon.
Adapt the martinize2 docstring so that sphinx/napoleon can work with it. In essence, wrap lists of options and defaults in backticks. Remove a lot of defaults from the docstring, since they are the same as in the signature. Also remove the parameter subsections. It /is/ possible to add those to napoleon (napoleon_custom_sections in conf.py), but they're not as pretty as the normal parameters section, plus, it bloats the conf.py
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I rebased on marrink-lab#407, and adapted the docstring of the martinize2 function so that sphinx accepts it.