[Biopython-dev] [Biopython - Bug #2619] Bio.PDB.MMCIFParser component MMCIFlex commented out in setup.py

[redmine at redmine.open-bio.org]

Issue #2619 has been updated by Lenna Peterson.


Peter: I've got a github branch going and I'm on the mailing list. 

Eric Talevich wrote:
> PLY is written entirely in Python, and appears to be supported on all the Python versions we support. I haven't used it, but it looks like a good option.
> 
> Not sure if we would need to add PLY as a dependency, or if it generates Python files we could check in to Git and distribute directly.
> 
> (a) Write (or use PLY to generate) a pure-Python version of the module Bio.PDB.mmCIF.MMCIFlex. This is currently compiled as a C extension, but a Python version of it could be imported as a backup if the C version isn't available.

I've got a good start on (a).

It seems like I need to import PLY's lex module. Is the etiquette to include ply/lex.py in the mmCIF module (as far as I can tell, the author/license allow this), or to list PLY as a dependency? The full yacc functionality from PLY is not needed (just the lex-style tokenizing). 
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Bug #2619: Bio.PDB.MMCIFParser component MMCIFlex commented out in setup.py
https://redmine.open-bio.org/issues/2619

Author: Chris Oldfield
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 1.48
URL: 


MMCIFParser is a documented feature of Bio.PDB, but it is broken by default because the MMCIFlex build is commented out in the distribution setup.py.  According to  

http://osdir.com/ml/python.bio.devel/2006-02/msg00038.html

this is because it doesn't compile on Windows.  Though the function is documented, the changes need to enable are not, so this seems like an installation bug to me.

The fix on linux is to uncomment setup.py lines 486 on.  A general work around might be to condition the compile on the os.sys.platform variable. I'd offer a diff, but I'm new to biopython and python in general, so please forgive my ignorance.

Source install of version 1.48, gentoo linux 2008, x86_64.


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