BjornFJohansson / pydna

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.
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Cannot pass `max_nodes` to `Assembly` #312

Open dgruano opened 1 month ago

dgruano commented 1 month ago

Running: asm = Assembly((pdonr_plasmid, insert), limit=6, max_nodes=10) gives me: TypeError: Assembly.__init__() got an unexpected keyword argument 'max_nodes' Is this intended, or should we be able to pass max_nodes when instanciating a new Assembly object?

manulera commented 1 month ago

This should probably be removed from the Assembly class docstring, since you actually use it in assemble_linear instead (check the assemble_linear docstring). This is probably some remnant of how it used to be before

BjornFJohansson commented 1 month ago

Absolutely! max_nodes is passed in the assemble methods. It is a parameter that I rarely used and perhaps something that might not be needed once we have manuels new assembly code.