[Biopython-dev] [Biopython] Getting involved

Peter biopython at maubp.freeserve.co.uk
Mon Oct 25 21:28:24 UTC 2010

On Mon, Oct 25, 2010 at 9:32 PM, Dragoslav Zaric wrote:
> Dear Peter,
> I think that this:
> "Can you program in C and are you familiar with the C/Python
> API? We will need to look at porting our C code from Python 2
> to Python 3, and this is quite complicated."
> is best idea for start. I can code in C, and have experience
> both with python 2.7 and 3. Will read tomorrow about C/Python
> API.
> Kind regards

Hi Dragoslav,

I'm glad you sound enthusiastic, and I hope you can make
some progress...

Our plan (following what the NumPy project are doing) is
to have a single code base targeting Python 2.x.

All the Python code is automatically converted using the
2to3 script into Python 3. There are a few special cases,
but that work is mostly done now.

All the C code will need to use #ifdef statements to make
the same C file work on both Python 2 and Python 3. The
bad news is that the basic API for writing C extension
modules for Python has changed.

What I suggest you do first, is make sure you can get
the latest Biopython source code from git, compile it
under Python 2, and run the unit tests. Then try 2to3
and running the tests under Python 3 (see the README

Next I would trying updating one of the smaller C
modules in Biopython to work on Python 3. You'll
need to edit our setup.py to compile what you are
working on (currently we compile none of the C
code on Python 3). I don't yet have a feel for how
much work this will be.

Please sign up to the biopython-dev mailing list where
we can discuss things in more detail. The main list is
more for user support and general discussion.

Thanks, and good luck!


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