#9808: Upgrade numpy to 1.5.0 and scipy to 0.8
--------------------------------------------------------------------------------------------------+
Reporter: maldun
| Owner: maldun
Type: task
| Status: needs_work
Priority: major
| Milestone: sage-4.6
Component: packages
| Keywords: numpy, scipy
Author: Stefan Reiterer, Francois Bissey, John Palmieri, David Kirkby,
Karl-Dieter Crisman | Upstream: Fixed upstream, but not in a stable
release.
Reviewer: Karl-Dieter Crisman, David Kirkby, Leif Leonhardy, Francois
Bissey | Merged:
Work_issues:
|
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Old description:
> This ticket updates two packages, which must be updated together,
>
> http://sage.math.washington.edu/home/kcrisman/numpy-1.5.0.spkg
>
> http://boxen.math.washington.edu/home/kirkby/patches/scipy-0.8.spkg
>
> However, these changes have made it necessary to update the scipy_sandbox
> package too (#10092), which now has positive review and is in Sage
> 4.6.alpha3.
>
> http://boxen.math.washington.edu/home/kirkby/patches/scipy_sandbox-20071020.p6.spkg
>
> After installing Numpy, one needs to execute sage -ba, or do
> {{{
> touch $SAGE_LOCAL/lib/python/site-packages/Cython/Includes/numpy.pxd
> }}}
> or else one will get runtime warnings. (Or if someone wants less hassle,
> they can patch sage-4.6.alpha2.spkg before building Sage).
>
> trac_9808_numpy_doctest_change.patch in the attachment has to be applied,
> in order to get all doctests running because some of the output has
> changed.
>
> '''For reviewers:'''
> changes.txt holds a summary of all changes with reference to the diffs,
> and links to other tickets
New description:
This ticket updates two packages, which must be updated together,
http://sage.math.washington.edu/home/kcrisman/numpy-1.5.0.spkg
http://sage.math.washington.edu/home/palmieri/SPKG/scipy-0.8.spkg
If you are applying these to any version before Sage 4.6.alpha3, then you
also have to update the scipy_sandbox package too (#10092). This has been
merged in 4.6.alpha3, though.
http://boxen.math.washington.edu/home/kirkby/patches/scipy_sandbox-20071020.p7.spkg
After installing Numpy, one needs to execute sage -ba, or do
{{{
touch $SAGE_LOCAL/lib/python/site-packages/Cython/Includes/numpy.pxd
}}}
or else one will get runtime warnings. (Or if someone wants less hassle,
they can patch sage-4.6.alpha3.spkg before building Sage).
trac_9808_numpy_doctest_change.patch in the attachment has to be applied,
in order to get all doctests running because some of the output has
changed.
'''For reviewers:'''
changes.txt holds a summary of all changes with reference to the diffs,
and links to other tickets
--
Comment(by jhpalmieri):
Updates: my doctest failure in citation.pyx is a "red herring". In
particular, it's not because of the patches here; it's because of a flaw
in how the function get_systems works. Often when I've been testing the
packages and patches on this ticket, I've created a new version of sage in
a directory called "numpy", and get_systems sees that string in the path
name and adds "numpy" to the systems used by the particular command. If I
rename the directory to something else, then the doctest passes. So let's
not worry about this; at some point, someone can fix get_systems so it
ignores the initial chunk of the path name (ignore the parent of
SAGE_ROOT, for example).
My doctest failure in matrix1.pyx is still there. For some reason, the
"Datetime" type codes are not there on some systems. Any ideas why? I
glanced at the install log for numpy, but I didn't see anything
suspicious, not that I really know what to look for. Here's the log from
my OS X 10.6 machine, which is one place I see this problem:
[http://sage.math.washington.edu/home/palmieri/misc/numpy-1.5.0.log].
Finally, I have a new version of the scipy spkg, which works for me on all
of the machines I've tested on: linux, !OpenSolaris, Solaris on x86, Mac
OS X 10.6. I'm putting the link in the ticket description, and I'm
posting the Mercurial patch -- it's very small.
I'm leaving this as "needs work" because of the matrix1.pyx issue, but I
think that's the only remaining problem. Please test the new scipy spkg
on other systems to make sure, though.
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/9808#comment:287>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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