[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 Eric Talevich.


Flex takes a .lex file and generates a .c file. The .c file is the important thing to compile, not .lex. Looking at the generated C in lex.yy.c, I'd guess the same thing can be compiled all the platforms we support (though I haven't confirmed). As a short-term solution, can we check in lex.yy.c and include that with the distribution, in order to eliminate the flex dependency?

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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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