[Biopython-dev] Re: Work towards getting KDTree compiling

Thomas Hamelryck thamelry at binf.ku.dk
Fri May 14 02:58:20 EDT 2004

> o) The source in Bio/PDB/mmCIF/lex.yy.c uses some Unix-specific
> commands from  unistd.h. Microsoft's compiler barfs on these, the
> mingw32 compiler does not. It  may be a good idea anyway to check if
> the mingw32-compiled version actually works.

lex.yy.c is a lex-generated file. I presume it will look different when
generated on a windows system. lex.yy.c is part of the distribution
because (a) not everyone has lex installed and (b) it's not clear to me
how to fire up lex from distutils. I have no objections if you want to
comment this out in setup.py.

> o) Recently I found out that the official Numerical Python version is
> now  numarray. The Numeric module is now unsupported (see
> http://www.pfdubois.com/numpy). We'll need to decide if Biopython is
> going over  to numarray, or whether to stick with Numeric for now. Some
> modifications will  be needed in the Python and C code if we start
> using numarray.

Good point. We should indeed move to numarray, I think, though we might
wait some months until numarray is more widely used.
Cheers & thanks for the C++ related work,

Thomas Hamelryck
Bioinformatik centret
København Universitet
Universitetsparken 15
Bygning 10
DK-2100 København Ø

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