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

[Peter Cock]

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