verveer at embl.de
Fri Feb 4 16:44:50 CST 2005
On Feb 4, 2005, at 8:19 PM, Travis Oliphant wrote:
> konrad.hinsen at laposte.net wrote:
>> On 04.02.2005, at 05:14, Michiel Jan Laurens de Hoon wrote:
>>> give you an example from my own field (computational biology). I am
>>> one of the maintainers of Biopython, which uses LinearAlgebra and
>>> RandomArray. Many of our users are not very familiar with Python.
>>> Even installing Numerical Python sometimes causes problems, and I'm
>>> sure we have lost users in the past because of that. SciPy, in my
>> My experience with users of MMTK, nMOLDYN, and DomainFinder is
>> exactly the same. Installationproblems are the #1 source for support
>> questions, in particular under Windows and Irix.
> O.K. I can see that there are several out there who belive that
> SciPy is sufficiently hard to install that they are concerned about
> requiring it for their math-using packages (despite the provided
> binary distributions, and the work that continues on making it easier
> to install).
I have in the past tried to install SciPy on OSX and I had big problems
with it. Motivated by the recent discussions on the list I tried again
today, and found it much improved, but still quite involved. It would
still be a pain to distribute software that has a dependency on SciPy
to 'average users' that would have trouble installing SciPy. There does
not seem to be a binary distribution on scipy.org for OS X, which would
solve that problem. This is not unimportant, since I guess OS X is
gaining popularity in scientific computing.
> I'm very glad to hear these comments, as I constantly wonder why
> people seem to be duplicating SciPy's efforts instead of helping
I agree with that, but fact is that the split between Numarray and
Numeric prevented me from contributing to SciPy. I have developed for
numarray (the image processing package nd_image, part of numarray, is
done by me) because I felt numarray was much better then Numeric for
that application, and that also ruled out SciPy. There seems now to be
an effort going to either try to merge the two or to bring Numeric up
to numarray standard. Thats great, and if that works out I will try to
rewrite my package so it works with both. Would be happy to contribute
it to SciPy. But I would make sure it remains a package that can be
installed separately from SciPy if required.
> I really would like to help make SciPy into something that many people
> can use. We have done a lot of work in trying to make SciPy modular,
> just for this reason.
Making SciPy modular is in my opinion a very good approach. Why do I
need to install all of it, if I really only need a few parts? If I
can install only the subset I need, the likelihood that I will have an
easier job doing that will increase. That would make it also possible
to have sub-sets that are free of dependencies such as FORTRAN.
> In sum, I would prefer to see people rally behind SciPy and fix it to
> be a package (or collection of packages) that all can use. If that
> doesn't happen, I certainly won't fight people who want to make
> Numeric Packages instead. It just will not be a high priority for me
> and so won't appear in my workflow.
On the other hand, I would think it would be a good idea to write
software that does not have dependencies on big packages such as SciPy
when possible, but only on Numeric/Numarray. That does not exclude them
from being included in SciPy. It seems to me that it would be a
desirable property if a package can be installed just with Numeric (or
numarray), with an appropriate sub-set of SciPy, or come with the big
SciPy package. I would rather see a "collection of SciPy packages" then
a "SciPy package".
Just my 2 cents, although currently I am using numarray exclusively, I
am glad to see that there is some discussion going on to get the main
python numerical packages to work together.
More information about the Numpy-discussion