[Biopython-dev] Fwd: [biopython] Fix flex library dependency of MMCIFlex; closes 2619 (#31)

[Lenna Peterson]

Just added a minor commit (a header for the generated C).

I'm very close (as in, possibly today) to being able to deploy a pure
Python (PLY) version of this parser for Jython/PyPy etc.

A few questions about that:

1. Should addition of a pure Python parser be a separate pull request
or should I add it to this one?

2. How would I add the PLY dependency to setup.py?

Lenna


On Wed, Mar 21, 2012 at 12:23 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Forwarding for public discussion (here or on github)
>
> P.S. Would anyone object to pull request emails going to the dev list?
>
> Peter
>
> ---------- Forwarded message ----------
> From: Lenna Peterson
> <reply+i-3741005-0709e439ad9856c74e1a778db76b2407a71a7c33-63959 at reply.github.com>
> Date: Wed, Mar 21, 2012 at 6:28 AM
> Subject: [biopython] Fix flex library dependency of MMCIFlex; closes 2619 (#31)
> To: Peter Cock <p.j.a.cock at googlemail.com>
>
>
> (All filenames are relative to Bio/PDB)
>
> A small modification of the flex input (mmCIF/mmcif.lex) allows flex
> to produce generated C (mmCIF/lex.yy.c) that can be compiled without
> the flex header. Flex generated on Debian stable.
>
> This allows the MMCIFlex module to be built on any platform that
> supports C modules. A pure Python implementation is in the works.
>
> Further modifications to mmCIF/mmcif.lex and mmCIF/MMCIFlexmodule.c --
> function prototype corrections to suppress compiler warnings.
>
> MMCIF2Dict was producing an invalid dict, so I've changed it to
> subclass dict and it now functions as expected.
>
> Module tested on Debian stable and Mac OS X 10.6.8 Snow Leopard (both
> Python 2.6.7).
>
>
> You can merge this Pull Request by running:
>
>  git pull https://github.com/lennax/biopython MMCIFlex
>
> Or you can view, comment on it, or merge it online at:
>
>  https://github.com/biopython/biopython/pull/31
>
> -- Commit Summary --
>
> * Remove flex header dependency of CIF parser.
> * Update MMCIFParser call of MMCIF2Dict.
> * Cleaned up import.
> * Subclassed dict.
> * Restored MMCIFParser call to MMCIF2Dict.
> * Removed main() from lex input.
> * Restored newline.
> * Fix C prototype warnings.
>
> -- File Changes --
>
> M Bio/PDB/MMCIF2Dict.py (32)
> M Bio/PDB/mmCIF/MMCIFlexmodule.c (6)
> M Bio/PDB/mmCIF/lex.yy.c (1456)
> M Bio/PDB/mmCIF/mmcif.lex (6)
> M setup.py (12)
>
> -- Patch Links --
>
>  https://github.com/biopython/biopython/pull/31.patch
>  https://github.com/biopython/biopython/pull/31.diff
>
> ---
> Reply to this email directly or view it on GitHub:
> https://github.com/biopython/biopython/pull/31
>
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