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levitsky / pyteomics

Pyteomics is a collection of lightweight and handy tools for Python that help to handle various sorts of proteomics data. Pyteomics provides a growing set of modules to facilitate the most common tasks in proteomics data analysis.
http://pyteomics.readthedocs.io
Apache License 2.0
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[mzml] `decode_binary` argument documented but not implemented #104

Closed RalfG closed 1 year ago

RalfG commented 1 year ago

Hi everyone,

In the mzml reader documentation for read, the decode_binary argument is listed, but it does not seem to be implemented. Setting the argument results in a TypeError:

TypeError: read() got an unexpected keyword argument 'decode_binary'

Documentation: https://github.com/levitsky/pyteomics/blob/7c7971d468394a1844059a0af605111e515c25b2/pyteomics/mzml.py#L387-L390

Function definition: https://github.com/levitsky/pyteomics/blob/7c7971d468394a1844059a0af605111e515c25b2/pyteomics/mzml.py#L360

I guess the documentation is a left-over from previous functionality?

Best, Ralf

mobiusklein commented 1 year ago

I think this got copied over from the MzML init itself, which read is just a wrapper for. We can add a pass through, but in the interim just call mzml.MzML if you want to use that functionality?