numpy-discussion

[Numpy-discussion] Numpy subversion compatibility with Scipy release?

[Mark H. <ma...@mi...>]

Is there any general sync point with development Numpy from subversion 
and the SciPy releases?  Ive got Numpy 0.9.9.2761 and Scipy 0.4.9 
installed with (I believe several) breakages, in particular:

> In [8]: from scipy import special
...
> /usr/lib/python2.4/site-packages/scipy/linalg/basic.py
>      20      
> conjugate,ravel,r_,mgrid,take,ones,dot,transpose,sqrt,add,real
>      21 import numpy
> ---> 22 from numpy import asarray_chkfinite, outerproduct, 
> concatenate, reshape, single
>      23 from numpy import matrix as Matrix
>      24 import calc_lwork
>
> ImportError: cannot import name outerproduct
I suppose Scipy is not picking up the deprecation of outerproduct.  No 
surprise that bleeding edge Numpy subversion doesn't play with a SciPy 
release; I was just wondering if there generally used/known way to make 
it happen.  Do I need to fall back to a Numpy release? Or move forward 
on SciPy?

Mark

Re: [Numpy-discussion] Numpy subversion compatibility with Scipy release?

[Robert K. <rob...@gm...>]

Mark Heslep wrote:
> Is there any general sync point with development Numpy from subversion 
> and the SciPy releases?  Ive got Numpy 0.9.9.2761 and Scipy 0.4.9 
> installed with (I believe several) breakages, in particular:
> 
>> In [8]: from scipy import special
> ...
>> /usr/lib/python2.4/site-packages/scipy/linalg/basic.py
>>      20      
>> conjugate,ravel,r_,mgrid,take,ones,dot,transpose,sqrt,add,real
>>      21 import numpy
>> ---> 22 from numpy import asarray_chkfinite, outerproduct, 
>> concatenate, reshape, single
>>      23 from numpy import matrix as Matrix
>>      24 import calc_lwork
>>
>> ImportError: cannot import name outerproduct
> I suppose Scipy is not picking up the deprecation of outerproduct.  No 
> surprise that bleeding edge Numpy subversion doesn't play with a SciPy 
> release; I was just wondering if there generally used/known way to make 
> it happen.  Do I need to fall back to a Numpy release? Or move forward 
> on SciPy?

The releases are synched such that the numpy version is "twice" (by an 
idiosyncratic form of arithmetic) that of the scipy version. numpy 0.9.8 <-> 
scipy 0.4.9 .

The latest SVN revisions should match (it's a bug, otherwise). numpy 2761 is 
recent enough that an SVN checkout of scipy will probably be fine.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
  that is made terrible by our own mad attempt to interpret it as though it had
  an underlying truth."
   -- Umberto Eco

Re: [Numpy-discussion] OptimizationDemo [was: Numpy subversion compatibility with Scipy release? ]

[Mark H. <ma...@mi...>]

Robert Kern wrote:
>
> The latest SVN revisions should match (it's a bug, otherwise). numpy 2761 is 
> recent enough that an SVN checkout of scipy will probably be fine.
>   
Yes SVN scipy/numpy fix the problem. Sorry, I missed Travis's post on 
scipy-user here:
http://projects.scipy.org/pipermail/scipy-user/2006-June/008438.html
to that effect.

I should just get specific: I was simply trying to run the basic 
optimization demo on the front page of the wiki as check on SVN 
(http://www.scipy.org/Cookbook/OptimizationDemo1) and it appears SVN 
scipy/numpy breaks matplotlib -0.87.2-1 (fc5) in the demo. Do I need SVN 
matplotlib as well?

Mark

 From the Opt. Demo:
> In [1]: from scipy import arange, special, optimize
> In [2]: x = arange(0,10,0.01)
> In [4]: for k in arange(0.5,5.5):
> ...: y = special.jv(k,x)
> ...: plot(x,y)
> ...:
> ---------------------------------------------------------------------------
> exceptions.ZeroDivisionError Traceback (most recent call
... ...
> /usr/lib/python2.4/site-packages/matplotlib/ticker.py in 
> bin_boundaries(self, vmin, vmax)
> 766 def bin_boundaries(self, vmin, vmax):
> 767 nbins = self._nbins
> --> 768 scale, offset = scale_range(vmin, vmax, nbins)
> 769 vmin -= offset
> 770 vmax -= offset
>
> /usr/lib/python2.4/site-packages/matplotlib/ticker.py in 
> scale_range(vmin, vmax, n, threshold)
> 731 dv = abs(vmax - vmin)
> 732 meanv = 0.5*(vmax+vmin)
> --> 733 var = dv/max(abs(vmin), abs(vmax))
> 734 if var < 1e-12:
> 735 return 1.0, 0.0
>
> ZeroDivisionError: float division

Re: [Numpy-discussion] OptimizationDemo [was: Numpy subversion compatibility with Scipy release? ]

[Robert K. <rob...@gm...>]

Mark Heslep wrote:
> Robert Kern wrote:
>> The latest SVN revisions should match (it's a bug, otherwise). numpy 2761 is 
>> recent enough that an SVN checkout of scipy will probably be fine.
>>   
> Yes SVN scipy/numpy fix the problem. Sorry, I missed Travis's post on 
> scipy-user here:
> http://projects.scipy.org/pipermail/scipy-user/2006-June/008438.html
> to that effect.
> 
> I should just get specific: I was simply trying to run the basic 
> optimization demo on the front page of the wiki as check on SVN 
> (http://www.scipy.org/Cookbook/OptimizationDemo1) and it appears SVN 
> scipy/numpy breaks matplotlib -0.87.2-1 (fc5) in the demo. Do I need SVN 
> matplotlib as well?

Yes, you do, thanks to the removal of the Numeric typecodes (Int32, etc.). 
However, the error you get looks to be unrelated.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
  that is made terrible by our own mad attempt to interpret it as though it had
  an underlying truth."
   -- Umberto Eco

Re: [Numpy-discussion] OptimizationDemo [was: Numpy subversion compatibility with Scipy release? ] RESOLVED

[Mark H. <ma...@mi...>]

The problem was matplotlib-0.87.2-1; it is broken wrt to the Demo. The 
lastest matplotlib .3 works. In summary, to run the demo, the following 
versions were required:

Released Packages, all built from tar balls:
------------------------------------------------------
matplotlib-0.87.3 , ie, the current package .2 in Fedora extras fails, 
meaning I needed to chase down the matplotlib dependencies myself (eg 
tk.h in tk-devel)
Numpy 0.9.8 (latest Fedora package is 0.9.5 which is too old)
Scipy 0.4.9

And, at least as of now, svn check outs from the numpy, scipy, and 
matplotlib subversion repos also work together for Demo1.

Mark

Robert Kern wrote:
> Mark Heslep wrote:
>   
>> Robert Kern wrote:
>>     
>>> The latest SVN revisions should match (it's a bug, otherwise). numpy 2761 is 
>>> recent enough that an SVN checkout of scipy will probably be fine.
>>>   
>>>       
>> Yes SVN scipy/numpy fix the problem. Sorry, I missed Travis's post on 
>> scipy-user here:
>> http://projects.scipy.org/pipermail/scipy-user/2006-June/008438.html
>> to that effect.
>>
>> I should just get specific: I was simply trying to run the basic 
>> optimization demo on the front page of the wiki as check on SVN 
>> (http://www.scipy.org/Cookbook/OptimizationDemo1) and it appears SVN 
>> scipy/numpy breaks matplotlib -0.87.2-1 (fc5) in the demo. Do I need SVN 
>> matplotlib as well?
>>     
>
> Yes, you do, thanks to the removal of the Numeric typecodes (Int32, etc.). 
> However, the error you get looks to be unrelated.
>
>