[Biopython-dev] flex, setup.py and Bio.PDB.mmCIF (Bug 2619)

Peter Cock p.j.a.cock at googlemail.com
Sat Feb 16 10:42:50 UTC 2013

On Sat, Feb 16, 2013 at 2:46 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> Hi Lenna,
> Maybe we are confusing each other..
> I am looking for a solution that (a) doesn't introduce new dependencies,


> (b) is pure-Python so it can run on Jython,

+1 And on PyPy (which to me is more interesting that Jython) etc.

> and (c) if that is not possible and we do need to use C, then that C code
> should be understandable so that it can be debugged if necessary.
> I was suggesting to clean up lex.yy.c so that we can at least achieve (c).

This does mean we essentially give up on ever regenerating the lex.yy.c
file every again - could that be a problem if Flex itself changes much?

> The alternative is to start from the PLY-based parser and remove the
> dependency on PLY.
> Best,
> -Michiel.


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