[Biopython-dev] Future plans for Numerical Python

[Michiel Jan Laurens de Hoon]

Hi folks,

On the Numerical Python mailing list I read the less-than-brilliant idea
to remove LinearAlgebra, FFT, and RandomArray from Numerical
Python 30.0. LinearAlgebra and RandomArray are used in various parts in
Biopython. The numpy developer (who is also a SciPy developer) suggests
that people use the corresponding functions in SciPy. However, in my
experience SciPy is much harder to install than Numerical Python, so
this would result in a major hurdle for Biopython users. Hell, I'm
pretty good with Python now, but I haven't been able to figure out how
to get SciPy installed. So if you are as concerned about this as I am,
please let your voice be heard on the numpy mailing list:

numpy-discussion at lists.sourceforge.net

Several users have already complained about these plans, but so far the
developer has not caved in. Below is the original message.

--Michiel.

Travis Oliphant wrote:
> 
> I've gotten Numeric3 (equivalent to Numeric 30.0) into a state where
> multiarray compiles.
> 
> It is far from production ready.  Several sections of the code still
> need to be cleaned up to avoid segfaults.  But, the general outline
> is there.   As this is very alpha code (though based on a very mature
> code-base) it is named Numeric3 so it does not clobber your current
> Numeric installation just in case you accidentally do an install.
> You will have to make sure the correct multiarray is being loaded
> through your sys.path list (or just point your sys.path to the build
> location of Numeric3) if you want to play with it. No array_number
> methods have been loaded yet (there is an interface to load your own
> if you like).   I expect to have ufuncs working with the new
> arrayobject by the end of the month.  Until then, arrayobjects are
> purely structural beasts.
> 
> If anybody would like to comment on the design or direction of
> Numeric 30.0, your comments are welcome.  If you would like to
> checkout the code through CVS you may do that using
> 
> cvs -d:pserver:anonymous at cvs.sourceforge.net:/cvsroot/numpy login
> 
> press <Enter> when prompted for a password.
> 
> cvs -z3 -d:pserver:anonymous at cvs.sourceforge.net:/cvsroot/numpy co -P
> /Numeric3/
> 
> A rough design document is available by following the link at
> http://www.scipy.org/wikis/numdesign/num3news
> 
> The major goal is:
> 
> Numeric 30.0 will have all the important new features of numarray as
> well as maintain or improve on the speed of Numeric for all array
> types.
> 
> Besides this, Numeric 30.0 will not include any FFT's, LinearAlgebra,
> or Random Numbers (these are all provided much more proficiently by
> SciPy).  Masked Arrays, and Matrices will be provided as standard
> subclasses in Python.   Ideally, RecordArrays will be provided in the
> same way.
> 
> I will not re-invent code that I can borrow from past versions of
> Numeric and or numarray.
> 
> Best wishes,
> 
> -Travis Oliphant
> 
> 
> 
> 
> 
> 
> 
> ------------------------------------------------------- This SF.Net
> email is sponsored by: IntelliVIEW -- Interactive Reporting Tool for
> open source databases. Create drag-&-drop reports. Save time by over
> 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. 
> Download a FREE copy at http://www.intelliview.com/go/osdn_nl 
> _______________________________________________ Numpy-discussion
> mailing list Numpy-discussion at lists.sourceforge.net 
> https://lists.sourceforge.net/lists/listinfo/numpy-discussion
> 
>