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Nils Wagner | 7 Feb 20:22
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FAIL: Minimize, method=TNC, 1b (approx gradient) version 0.11.0.dev-a4cd737

FAIL: Minimize, method=TNC, 1b (approx gradient)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/home/nwagner/local/lib64/python2.7/site-packages/scipy/optimize/tests/test_optimize.py", 
line 623, in test_minimize_tnc1b
     assert_allclose(self.f1(x), self.f1(xopt), atol=1e-6)
   File 
"/home/nwagner/local/lib64/python2.7/site-packages/numpy/testing/utils.py", 
line 1213, in assert_allclose
     verbose=verbose, header=header)
   File 
"/home/nwagner/local/lib64/python2.7/site-packages/numpy/testing/utils.py", 
line 677, in assert_array_compare
     raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=1e-07, atol=1e-06

(mismatch 100.0%)
  x: array(6.811012399502852e-06)
  y: array(0.0)
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Matt Terry | 7 Feb 19:27
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slices of sparse matrixes

Do scipy sparse matrixes have the same slicing semantics as numpy
arrays?  I would expect the same slice of a numpy array and a scipy
array to have the same shape.  In this simple test, they do not.  I'm
using scipy 0.10.

>>> d = numpy.zeros( (4,3) )
>>> s = scipy.sparse.lil_matrix(d)
>>> d[:,0].shape == s[:,0].shape
False

Bug or feature?

-matt
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Thomas Kluyver | 6 Feb 22:47
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new.scipy.org

I've found that searches can turn up pages from new.scipy.org, a subdomain which was seemingly last updated in 2009, and now has out of date info - e.g. references to SVN (http://new.scipy.org/download.html) and FAQ about Python 3 support (http://new.scipy.org/faq.html#python-version-support). I can't see any details of who maintains the website, but I think leaving out of date information around is liable to cause confusion - can it be taken down or brought up to date?

Thanks,
Thomas 

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Denis Laxalde | 6 Feb 22:23
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numpydoc installation and path

Hi,

While trying to build scipy's documentation, I had to install numpydoc
(python setup.py --install --user). This apparently generates an
'easy-install.pth' file which contains:

 import sys; sys.__plen = len(sys.path)
 ./numpydoc-0.4-py2.6.egg
 /usr/lib/pymodules/python2.6
 import sys; new=sys.path[sys.__plen:]; del sys.path[sys.__plen:];
p=getattr(sys,'__egginsert',0); sys.path[p:p]=new; sys.__egginsert = p+len(new)

This happens to break the python path prepending
/usr/lib/pymodules/python2.6 and numpydoc-0.4-py2.6.egg.

What is the purpose of this? Is that intended?

Thanks.

--

-- 
Denis
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Ralf Gommers | 6 Feb 20:02
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Re: updating optimize tutorial & doc questions



On Mon, Feb 6, 2012 at 7:11 PM, <josef.pktd <at> gmail.com> wrote:
On Mon, Feb 6, 2012 at 1:05 PM, Denis Laxalde <denis.laxalde <at> mcgill.ca> wrote:
> josef.pktd <at> gmail.com wrote:
>> >  - How is it actually updated?
>>
>> either edit the source in git or use the online editor, e.g.
>> http://docs.scipy.org/scipy/docs/scipy-docs/tutorial/optimize.rst/
>> I like the editor because it provides an immediate check on the
>> correctness of the rst.
>>
>> The pages edited on the online documentation editor get merged into
>> the source (ir)regularly
>
> Once merged in git source, how is the website updated? Is there any
> build bot or is this done manually?

Pauli had it set up so it gets automatically updated, I think it
usually took 2 to 4 days. I assume it's still the same.

Still the same, development docs get built automatically, for a release they have to be built and uploaded by hand.

Ralf
 

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Denis Laxalde | 6 Feb 17:30
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updating optimize tutorial & doc questions

Hi,

I've completed the minimize function which provides a common interface
to both unconstrained an constrained minimizers of multivariate
functions. Now I wonder if the optimize tutorial should be updated
in order to put this forward. I think new users should be pointed to
this interface instead of individual functions and that it should be
clearer in the tutorial. What do others think?

Besides, a couple of questions about the documentation on
<http://docs.scipy.org/>:

 - How is it actually updated?
 - The content of reference pages (e.g.
   <http://docs.scipy.org/doc/scipy/reference/sparse.html>) appears to
   be generated using automodule. There is also some bits in packages'
   __init__.py file but this is not consistent with the latter. So
   what's the documentation in __init__.py?

Thanks.

--

-- 
Denis
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josef.pktd | 6 Feb 00:07
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doc edit: discrete ppf

based on http://projects.scipy.org/scipy/ticket/1421#comment:8

I added an explanation to the stats tutorial for the ppf of discrete
distributions, but I don't quite know how to create a link.

http://docs.scipy.org/scipy/docs/scipy-docs/tutorial/stats.rst

anyone for review and fixing some rst?

Thanks,

Josef
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Ralf Gommers | 5 Feb 12:59
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Trac performance?

Hi,

Is there an end in sight for the troubles with Trac? It's driving me completely crazy. So if not, I'm willing to invest some time in moving all the relevant content on the Trac wikis somewhere else (suggestions welcome). I'm thinking about things like development plans, GSOC info, list of maintainers per module, etc.

Ralf

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Ralf Gommers | 5 Feb 11:17
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anyone want to fix Mann-Whitney test?

Hi,

There's a bug report and a number of new tests for mannwhitneyu at http://projects.scipy.org/scipy/ticket/1593. These plus a fix were contributed by Sebastian Pölsterl, unfortunately he based his initial fix on GPL'ed R code. Therefore I think we can't use that, even after he modified it. I looked at the GPL code too; I think we need someone who didn't do that to implement a new fix based only on the tests and bug report.

Any takers?

Ralf

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Ralf Gommers | 4 Feb 22:52
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scipy 0.10.1 release

Hi all,

A 0.10.1 bugfix release soon is starting to look like a good idea. The two fixes that are most needed are the single-precision Arpack problems and the fix to remain compatible with the macro changes in numpy that Charles made. While we're at it, we may as well backport some other bug and doc fixes. I'll have a look at recent commits for that, suggestions welcome. An RC within a week, and release the week after seems feasible.

Thoughts, comments?

Ralf

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Jeffrey Armstrong | 3 Feb 16:41
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Interest in a "controls" scikit?

After seeing the discussion started by the scikit-signal proposal on the 
list, I wanted to see if there would be interest in a scikit related to 
controls.  While I wouldn't purport to be an expert, I have managed to 
author some control design equation solvers, notably algebraic Riccati and 
Lyapunov equation solvers, and I have a pythonic wrapper for LAPACK's 
Sylvester equation solver.  Combined with much of the LTI code in 
scipy.signal, I think there's a good start here towards providing some 
control system design tools.

I wanted to see if others would be interested in helping out and whether 
the scikit path is the right choice (I admit I was a little confused by 
the outcome of the scikit-signal discussion).  Thanks for any input!

-Jeff

Jeff Armstrong - jba <at> sdf.lonestar.org
SDF Public Access UNIX System - http://sdf.lonestar.org
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Gmane