[Biopython-dev] [GSoC] Gsoc 2014 aspirant

[Michiel de Hoon]

Hi Nigel,

While compiling Biopython on Windows can be tricky, in my experience it has been easy to compile the C libraries in Biopython on other platforms (Unix/Linux/MacOSX). Have you run into specific problems compiling Biopython? I would think that wrapping 3rd-party libraries or executables is much more error-prone.

Best,
-Michiel.

--------------------------------------------
On Tue, 3/4/14, Nigel Delaney <nigel.delaney at outlook.com> wrote:

 Subject: Re: [Biopython-dev] [GSoC] Gsoc 2014 aspirant
 To: "'Peter Cock'" <p.j.a.cock at googlemail.com>, "'Fields, Christopher J'" <cjfields at illinois.edu>
 Cc: biopython-dev at lists.open-bio.org, "'Harsh Beria'" <harsh.beria93 at gmail.com>
 Date: Tuesday, March 4, 2014, 5:39 PM
 
 As a quick $0.02 from a library user
 on this.  Back in 2006 when I first
 started using biopython I was working with Bio.pairwise2,
 and learned that
 it was too slow for the task at hand, so wound up switching
 to
 passing/parsing files to an aligner on the command line to
 get around this,
 as (on windows back then), I never got the compiled C code
 to work properly.
 Although pypy may be fast enough and has been very
 impressive in my
 experience (plus computers are much faster now), I think
 wrapping a library
 that is cross platform and maintains its own binaries would
 be a great
 option rather than implementing C-code (I think this might
 be what the GSoC
 student did last year for BioPython by wrapping Python).
 
 Mostly though I just wanted to second Peter's wariness about
 adding C-code
 into the library.  I have found over the years that a
 lot of python
 scientific tools that in theory should be cross platform
 (Stampy, IPython,
 Matplotlib, Numpy, GATK, etc.) are really not and can be a
 huge timesuck of
 dealing with installation issues as code moves between
 computers and
 operating systems, usually due to some C code or OS specific
 behavior.
 Since code in python works anywhere python is installed, I
 really appreciate
 the extent that the library can be as much pure python as
 allowable or
 strictly dependent on a particular downloadable binary for a
 specific
 OS/Architecture/Scenario.
 _______________________________________________
 Biopython-dev mailing list
 Biopython-dev at lists.open-bio.org
 http://lists.open-bio.org/mailman/listinfo/biopython-dev