[Numpy-discussion] Future directions for SciPy in light of meeting at Berkeley

Michiel Jan Laurens de Hoon mdehoon at ims.u-tokyo.ac.jp
Wed Mar 9 00:33:07 CST 2005


Travis Oliphant wrote:
> It would seem that while the scipy conference demonstrates a continuing 
> and even increasing use of Python for scientific computing,  not as many 
> of these users are scipy devotees.   Why?
> 
> I think the answers come down to a few issues which I will attempt to 
> answer with proposals.
> 
> 1) Plotting
While plotting is important, I don't think that SciPy needs to offer 
plotting capabilities in order to become successful. Numerical Python 
doesn't include plotting, and it's hugely popular. I would think that 
installing Scipy-lite + (selection of SciPy-lib sub-packages) + (your 
favorite plotting package) separately is acceptable.

> 2) Installation problems
This is the real problem. I'm one of the maintainers of Biopython 
(python and C code for computational biology), which relies on Numerical 
Python. Now that Numerical Python is not being actively maintained, I'd 
love to be able to direct our users to SciPy instead. But as long as 
SciPy doesn't install out of the box with a python setup.py install, 
it's not viable as a replacement for Numerical Python. I'd spend the 
whole day dealing with installation problems from Biopython users.

There are three other reasons why I have not become a SciPy devotee, 
although I use Python for scientific computing all the time:

3) Numerical Python already does the job very well. There are few 
packages in SciPy that I actually need. Special functions would be nice, 
but it's easier to write your own module than to install SciPy.

4) SciPy looks bloated. It seems to try to do too many things, so that 
it becomes impossible to maintain SciPy well.

5) Uncertain future. With Numerical Python, we know what we get. I don't 
know what SciPy will look like in a few years (numarray? Numeric3? 
Numeric2?) and if it still has a trouble-free installation. So it's too 
risky for Biopython to go over to SciPy.

It's really unfortunate, because my impression is that the SciPy 
developers are smart people who write good code, which currently is not 
used as much as it could because of these problems. I hope my comments 
will be helpful.

--Michiel.




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