From neyhmor at gmail.com  Fri Apr  1 16:42:11 2011
From: neyhmor at gmail.com (N H)
Date: Fri, 1 Apr 2011 22:42:11 +0200
Subject: [SciPy-Dev] Noob on board :)
Message-ID: <AANLkTinBi5vn-nuV8ptAF=Jgx8UsWQqij=WOzVb1rWdb@mail.gmail.com>

Hallo Friends

My Name is Ney Henrique, Brazilian based in Germany, Chemist and I`m about
to conclude my PhD in Computational Physics.

First of all I would like to thank Mr. Ed Schofield for his nice reply on my
original contact.

As most of you might guess, I?m writing you today to introduce my self and
let you know about my interest in contributing to the Scipy project.

Honestly I?m not an experienced programmer, but I guess that helping you
would be a great chance for both learning and getting into a collaborative
project.

Please let me know how can I help the Project ( Testing, Debugging,
Developping some small tools ... etc ). I?m eager to contribute!

Best Regards

NH
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From ralf.gommers at googlemail.com  Sat Apr  2 06:46:58 2011
From: ralf.gommers at googlemail.com (Ralf Gommers)
Date: Sat, 2 Apr 2011 12:46:58 +0200
Subject: [SciPy-Dev] Noob on board :)
In-Reply-To: <AANLkTinBi5vn-nuV8ptAF=Jgx8UsWQqij=WOzVb1rWdb@mail.gmail.com>
References: <AANLkTinBi5vn-nuV8ptAF=Jgx8UsWQqij=WOzVb1rWdb@mail.gmail.com>
Message-ID: <AANLkTikJSMjz2Obi+wxjx6neLOOLDDh46rt84iqFdPTn@mail.gmail.com>

Hi Ney, welcome!

On Fri, Apr 1, 2011 at 10:42 PM, N H <neyhmor at gmail.com> wrote:
> Hallo Friends
> My Name is Ney Henrique, Brazilian based in Germany, Chemist and I`m about
> to conclude my PhD in Computational Physics.
> First of all I would like to thank Mr. Ed Schofield for his nice reply on my
> original contact.
> As most of you might guess, I?m writing you today to introduce my self and
> let you know about my interest in contributing to the Scipy project.
> Honestly I?m not an experienced programmer, but I guess that helping you
> would be a great chance for both learning and getting into a collaborative
> project.
> Please let me know how can I help the Project ( Testing, Debugging,
> Developping some small tools ... etc ). I?m eager to contribute!

There are many things you could help out with: tests, documentation,
new functionality, addressing reported bugs, reviewing patches on the
bug tracker, ....

Before you start it would be good to read through
http://docs.scipy.org/doc/numpy/dev/index.html, it's the same workflow
for numpy and scipy. You'll probably want to start with just one of
the sub-packages of scipy, just browse the docs and see what interests
you. You can also look at http://projects.scipy.org/scipy/report/1,
sort by "Component", and look at open tickets.

If you want to work on bug fixes, test and doc improvements, you can
just start and then ask for review. For new functionality or
backwards-incompatible changes it's usually better to first discuss on
this mailing list.

Cheers,
Ralf


From cournape at gmail.com  Sun Apr  3 05:20:49 2011
From: cournape at gmail.com (David Cournapeau)
Date: Sun, 3 Apr 2011 18:20:49 +0900
Subject: [SciPy-Dev] Harwell Boeing support
In-Reply-To: <web-143926001@uni-stuttgart.de>
References: <web-143926001@uni-stuttgart.de>
Message-ID: <BANLkTinLLz3prtEWdwMH+hC6ogHMCwQPZA@mail.gmail.com>

On Thu, Mar 31, 2011 at 9:02 PM, Nils Wagner
<nwagner at iam.uni-stuttgart.de> wrote:
> Hi David,
>
> Is there a chance, that the Harwell Boeing format will be
> available in the trunk ?
> I saw that you have started a branch.

I cleaned up the code a bit and put it on top of the new scipy repository:

https://github.com/scipy/scipy/pull/11

cheers,

David


From nwagner at iam.uni-stuttgart.de  Mon Apr  4 06:18:22 2011
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Mon, 04 Apr 2011 12:18:22 +0200
Subject: [SciPy-Dev] Fwd:  Harwell Boeing support
Message-ID: <web-144018429@uni-stuttgart.de>

An embedded message was scrubbed...
From: "Nils Wagner" <nwagner at iam.uni-stuttgart.de>
Subject: Re: [SciPy-Dev] Harwell Boeing support
Date: Mon, 04 Apr 2011 12:16:18 +0200
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From cournape at gmail.com  Tue Apr  5 04:04:15 2011
From: cournape at gmail.com (David Cournapeau)
Date: Tue, 5 Apr 2011 17:04:15 +0900
Subject: [SciPy-Dev] Fwd: Harwell Boeing support
In-Reply-To: <web-144018429@uni-stuttgart.de>
References: <web-144018429@uni-stuttgart.de>
Message-ID: <BANLkTin=bZQk7kS7wxt0acZYFsTUmu6vig@mail.gmail.com>

On Mon, Apr 4, 2011 at 7:18 PM, Nils Wagner
<nwagner at iam.uni-stuttgart.de> wrote:
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
>
> ---------- Forwarded message ----------
> From:?"Nils Wagner" <nwagner at iam.uni-stuttgart.de>
> To:?David Cournapeau <cournape at gmail.com>
> Date:?Mon, 04 Apr 2011 12:16:18 +0200
> Subject:?Re: [SciPy-Dev] Harwell Boeing support
> On Sun, 3 Apr 2011 18:20:49 +0900
> ?David Cournapeau <cournape at gmail.com> wrote:
>>
>> On Thu, Mar 31, 2011 at 9:02 PM, Nils Wagner
>> <nwagner at iam.uni-stuttgart.de> wrote:
>>>
>>> Hi David,
>>>
>>> Is there a chance, that the Harwell Boeing format will be
>>> available in the trunk ?
>>> I saw that you have started a branch.
>>
>> I cleaned up the code a bit and put it on top of the new scipy repository:
>>
>> https://github.com/scipy/scipy/pull/11
>>
>> cheers,
>>
>> David
>
> Hi David,
>
> Thank you. What do you mean by new repository ?
> I have used
>
> git clone https://github.com/scipy/scipy.git

I have done all my scipy developement with git for a long time, using
a git-svn imported repository. Now that scipy itself is on git, I need
to convert all my branches to the new scipy repo.

The HB branch is already there (on
http://github.com/cournape/scipy.git). Note that it does not support
all possible formats (most likely a significant portions of them) -
the format is unfortunately not well documented, and I don't
understand a lot of information I found about it. I am sure it would
be relatively simple to add support for people familiar with the
concerned fields (fluid mechanics or ODE problems for example).

cheers,

David


From nwagner at iam.uni-stuttgart.de  Tue Apr  5 09:04:18 2011
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Tue, 05 Apr 2011 15:04:18 +0200
Subject: [SciPy-Dev] Fwd: Harwell Boeing support
In-Reply-To: <BANLkTin=bZQk7kS7wxt0acZYFsTUmu6vig@mail.gmail.com>
References: <web-144018429@uni-stuttgart.de>
	<BANLkTin=bZQk7kS7wxt0acZYFsTUmu6vig@mail.gmail.com>
Message-ID: <web-144069198@uni-stuttgart.de>

> The HB branch is already there (on
> http://github.com/cournape/scipy.git). Note that it does 
>not support
> all possible formats (most likely a significant portions 
>of them) -
> the format is unfortunately not well documented, and I 
>don't
> understand a lot of information I found about it. I am 
>sure it would
> be relatively simple to add support for people familiar 
>with the
> concerned fields (fluid mechanics or ODE problems for 
>example).
> 
> cheers,
> 
> David

David,

a detailed description of the HB format can be found here

http://people.sc.fsu.edu/~jburkardt/data/hb/hb.html

Cheers,

   Nils



From nwagner at iam.uni-stuttgart.de  Fri Apr  8 04:46:54 2011
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Fri, 08 Apr 2011 10:46:54 +0200
Subject: [SciPy-Dev] Sparse generalized eigenvalue problems
Message-ID: <web-144176146@uni-stuttgart.de>

Hi all,

what is recommended to tackle sparse generalized 
eigenvalue problems in scipy ?

http://docs.scipy.org/doc/scipy/reference/sparse.linalg.html?highlight=sparse#scipy.sparse.linalg

AFAIK, eigs doesn't support generalized eigenvalue 
problems A x = \lambda B x

lobpcg is a way out but it is restricted to real symmetric 
matrices.


Nils




From pav at iki.fi  Fri Apr  8 07:34:58 2011
From: pav at iki.fi (Pauli Virtanen)
Date: Fri, 8 Apr 2011 11:34:58 +0000 (UTC)
Subject: [SciPy-Dev] Sparse generalized eigenvalue problems
References: <web-144176146@uni-stuttgart.de>
Message-ID: <inmrt2$ju3$2@dough.gmane.org>

Fri, 08 Apr 2011 10:46:54 +0200, Nils Wagner wrote:
> what is recommended to tackle sparse generalized eigenvalue problems in
> scipy?

Writing a patch that adds support for generalized eigenvalue problems to 
eigs :)

The necessary low-level ARPACK routines can be found in 
scipy.sparse.linalg.eigen.arpack._arpack -- in principle you can use 
those directly, although they shouldn't be treated as public.

-- 
Pauli Virtanen



From nwagner at iam.uni-stuttgart.de  Fri Apr  8 08:06:10 2011
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Fri, 08 Apr 2011 14:06:10 +0200
Subject: [SciPy-Dev] Sparse generalized eigenvalue problems
In-Reply-To: <inmrt2$ju3$2@dough.gmane.org>
References: <web-144176146@uni-stuttgart.de>
 <inmrt2$ju3$2@dough.gmane.org>
Message-ID: <web-144184954@uni-stuttgart.de>

On Fri, 8 Apr 2011 11:34:58 +0000 (UTC)
  Pauli Virtanen <pav at iki.fi> wrote:
>Fri, 08 Apr 2011 10:46:54 +0200, Nils Wagner wrote:
>> what is recommended to tackle sparse generalized 
>>eigenvalue problems in
>> scipy?
> 
> Writing a patch that adds support for generalized 
>eigenvalue problems to 
> eigs :)
> 
> The necessary low-level ARPACK routines can be found in 
> scipy.sparse.linalg.eigen.arpack._arpack -- in principle 
>you can use 
> those directly, although they shouldn't be treated as 
>public.
> 
> -- 
> Pauli Virtanen
> 

BTW, which version of Arpack is used by scipy ?

I found an interesting comment by Andreas Kl?ckner. See

http://mathema.tician.de/node/373

for details.
  
http://mathema.tician.de/software/arpack

Nils



From nwagner at iam.uni-stuttgart.de  Fri Apr  8 08:17:58 2011
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Fri, 08 Apr 2011 14:17:58 +0200
Subject: [SciPy-Dev] scipy.io.savemat and sparse matrices
Message-ID: <web-144185395@uni-stuttgart.de>

Hi all,

I tried to save a sparse matrix


     savemat('mass.mat',dict(M_sparse))
   File 
"/data/home/nwagner/local/lib/python2.5/site-packages/scipy/sparse/base.py", 
line 109, in __iter__
     yield self[r,:]
TypeError: 'coo_matrix' object is unsubscriptable
  
>>> type(M_sparse)
<class 'scipy.sparse.coo.coo_matrix'>

How can I resolve the problem ?

Nils


From aric.hagberg at gmail.com  Fri Apr  8 10:27:00 2011
From: aric.hagberg at gmail.com (Aric Hagberg)
Date: Fri, 8 Apr 2011 08:27:00 -0600
Subject: [SciPy-Dev] Sparse generalized eigenvalue problems
In-Reply-To: <web-144184954@uni-stuttgart.de>
References: <web-144176146@uni-stuttgart.de> <inmrt2$ju3$2@dough.gmane.org>
	<web-144184954@uni-stuttgart.de>
Message-ID: <BANLkTimbsxpTxzV5ks-_Pi-+mg-omhuSwQ@mail.gmail.com>

On Fri, Apr 8, 2011 at 6:06 AM, Nils Wagner
<nwagner at iam.uni-stuttgart.de> wrote:
> On Fri, 8 Apr 2011 11:34:58 +0000 (UTC)
> ?Pauli Virtanen <pav at iki.fi> wrote:
>>Fri, 08 Apr 2011 10:46:54 +0200, Nils Wagner wrote:
>>> what is recommended to tackle sparse generalized
>>>eigenvalue problems in
>>> scipy?
>>
>> Writing a patch that adds support for generalized
>>eigenvalue problems to
>> eigs :)
>>
>> The necessary low-level ARPACK routines can be found in
>> scipy.sparse.linalg.eigen.arpack._arpack -- in principle
>>you can use
>> those directly, although they shouldn't be treated as
>>public.
>>
>> --
>> Pauli Virtanen
>>
>
> BTW, which version of Arpack is used by scipy ?
>
> I found an interesting comment by Andreas Kl?ckner. See
>
> http://mathema.tician.de/node/373
>
> for details.
>
> http://mathema.tician.de/software/arpack
>

From
https://github.com/scipy/scipy/blob/master/scipy/sparse/linalg/eigen/arpack/README
---
This is the ARPACK package from
http://www.caam.rice.edu/software/ARPACK/

Specifically the files are from
http://www.caam.rice.edu/software/ARPACK/SRC/arpack96.tar.gz
with the patch
http://www.caam.rice.edu/software/ARPACK/SRC/patch.tar.gz
---

So it doesn't include those patches regarding the "second()"
function/subroutine signatures being different in ARPACK v LAPACK.
But I think we avoid that problem since we explicitly include and
build the ARPACK second() subroutine.

Aric


From jsseabold at gmail.com  Fri Apr  8 11:20:30 2011
From: jsseabold at gmail.com (Skipper Seabold)
Date: Fri, 8 Apr 2011 11:20:30 -0400
Subject: [SciPy-Dev] warnings in quadpack.py are printed, patch linked
Message-ID: <BANLkTin0Hr3yvd_G4G8qHFfJJvw+E=tyfw@mail.gmail.com>

The warnings in quadpack are printed. Does this change look ok?

https://github.com/jseabold/scipy/compare/master...quadpack-warn-fix

Skipper


From matthew.brett at gmail.com  Fri Apr  8 14:05:50 2011
From: matthew.brett at gmail.com (Matthew Brett)
Date: Fri, 8 Apr 2011 11:05:50 -0700
Subject: [SciPy-Dev] scipy.io.savemat and sparse matrices
In-Reply-To: <web-144185395@uni-stuttgart.de>
References: <web-144185395@uni-stuttgart.de>
Message-ID: <BANLkTincvrjF50YaAGNAJLbNAOcQ5ZRNKA@mail.gmail.com>

Hi,

On Fri, Apr 8, 2011 at 5:17 AM, Nils Wagner
<nwagner at iam.uni-stuttgart.de> wrote:
> Hi all,
>
> I tried to save a sparse matrix
>
>
> ? ? savemat('mass.mat',dict(M_sparse))
> ? File
> "/data/home/nwagner/local/lib/python2.5/site-packages/scipy/sparse/base.py",
> line 109, in __iter__
> ? ? yield self[r,:]
> TypeError: 'coo_matrix' object is unsubscriptable

I think you'll get the same error from:

dict(M_sparse)

that is - you need to give the input dict a key, with the sparse
matrix as a value, as in

savemat('mass.mat', dict(aname=M_sparse))

Best,

Matthew


From josef.pktd at gmail.com  Sun Apr 10 08:38:50 2011
From: josef.pktd at gmail.com (josef.pktd at gmail.com)
Date: Sun, 10 Apr 2011 08:38:50 -0400
Subject: [SciPy-Dev] OT: bug in matplotlib for py32
Message-ID: <BANLkTik=Z6KPfzRod4ymrptotHRRLpXBeg@mail.gmail.com>

I'm going through py23 conversion for statsmodels, using Goehlke's matplotlib

we have a function that uses squeeze=False, and get an exception

in pyplot.py

def subplots(nrows=1, ncols=1, sharex=False, sharey=False, squeeze=True,
                subplot_kw=None, **fig_kw):

doesn't have a ret defined,
no return value

(Sorry for OT, I'm not setup for reporting matplotlib bugs)

Josef


From josef.pktd at gmail.com  Sun Apr 10 13:18:42 2011
From: josef.pktd at gmail.com (josef.pktd at gmail.com)
Date: Sun, 10 Apr 2011 13:18:42 -0400
Subject: [SciPy-Dev] OT: bug in matplotlib for py32
In-Reply-To: <BANLkTik=Z6KPfzRod4ymrptotHRRLpXBeg@mail.gmail.com>
References: <BANLkTik=Z6KPfzRod4ymrptotHRRLpXBeg@mail.gmail.com>
Message-ID: <BANLkTingLfFCyVqVYty=PuQCpXaTT4ZEOA@mail.gmail.com>

On Sun, Apr 10, 2011 at 8:38 AM,  <josef.pktd at gmail.com> wrote:
> I'm going through py23 conversion for statsmodels, using Goehlke's matplotlib
>
> we have a function that uses squeeze=False, and get an exception
>
> in pyplot.py
>
> def subplots(nrows=1, ncols=1, sharex=False, sharey=False, squeeze=True,
> ? ? ? ? ? ? ? ?subplot_kw=None, **fig_kw):
>
> doesn't have a ret defined,
> no return value
>
> (Sorry for OT, I'm not setup for reporting matplotlib bugs)

adding the else part in

    if squeeze:
        # Reshape the array to have the final desired dimension (nrow,ncol),
        # though discarding unneeded dimensions that equal 1.  If we only have
        # one subplot, just return it instead of a 1-element array.
        if nplots==1:
            ret = fig, axarr[0,0]
        else:
            ret = fig, axarr.squeeze()
    else:
        ret = fig, axarr

fixes it for our test suite, but I don't know whether it is correct

Josef
>
> Josef
>


From josef.pktd at gmail.com  Sun Apr 10 13:22:33 2011
From: josef.pktd at gmail.com (josef.pktd at gmail.com)
Date: Sun, 10 Apr 2011 13:22:33 -0400
Subject: [SciPy-Dev] scipy.factorial in python 3.2
Message-ID: <BANLkTi=P4tS9QHhhwRsq48FfpdMkZVfQyA@mail.gmail.com>

python 3.2 (64 bit version) doesn't have scipy.factorial anymore, with
python 2.7 it's there.

Is this intentional?
It's easy to work around, I just import it from scipy.misc

Python 3.2 (r32:88445, Feb 20 2011, 21:30:00) [MSC v.1500 64 bit
(AMD64)] on win32
Type "copyright", "credits" or "license()" for more information.
==== No Subprocess ====
>>> import scipy
>>> scipy.factorial
Traceback (most recent call last):
  File "<pyshell#1>", line 1, in <module>
    scipy.factorial
AttributeError: 'module' object has no attribute 'factorial'

>>> import scipy.misc
>>> scipy.misc.factorial
<function factorial at 0x0000000005475CC8>


Josef


From robert.kern at gmail.com  Sun Apr 10 16:14:18 2011
From: robert.kern at gmail.com (Robert Kern)
Date: Sun, 10 Apr 2011 15:14:18 -0500
Subject: [SciPy-Dev] scipy.factorial in python 3.2
In-Reply-To: <BANLkTi=P4tS9QHhhwRsq48FfpdMkZVfQyA@mail.gmail.com>
References: <BANLkTi=P4tS9QHhhwRsq48FfpdMkZVfQyA@mail.gmail.com>
Message-ID: <BANLkTi=W8nb95sqTtJBZ0Vmn=7uFzqkTqA@mail.gmail.com>

On Sun, Apr 10, 2011 at 12:22,  <josef.pktd at gmail.com> wrote:
> python 3.2 (64 bit version) doesn't have scipy.factorial anymore, with
> python 2.7 it's there.
>
> Is this intentional?

Yes. We stopped using the pkgload() mechanism (the key difference is
numpy/scipy versions, not Python versions). We have been trying to
discourage the use of the scipy.* namespace for some time now. Use the
subpackages.

-- 
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


From josef.pktd at gmail.com  Sun Apr 10 16:26:55 2011
From: josef.pktd at gmail.com (josef.pktd at gmail.com)
Date: Sun, 10 Apr 2011 16:26:55 -0400
Subject: [SciPy-Dev] scipy.factorial in python 3.2
In-Reply-To: <BANLkTi=W8nb95sqTtJBZ0Vmn=7uFzqkTqA@mail.gmail.com>
References: <BANLkTi=P4tS9QHhhwRsq48FfpdMkZVfQyA@mail.gmail.com>
	<BANLkTi=W8nb95sqTtJBZ0Vmn=7uFzqkTqA@mail.gmail.com>
Message-ID: <BANLkTi=FBjggHaC8u819sfOPOEH==iUoSQ@mail.gmail.com>

On Sun, Apr 10, 2011 at 4:14 PM, Robert Kern <robert.kern at gmail.com> wrote:
> On Sun, Apr 10, 2011 at 12:22, ?<josef.pktd at gmail.com> wrote:
>> python 3.2 (64 bit version) doesn't have scipy.factorial anymore, with
>> python 2.7 it's there.
>>
>> Is this intentional?
>
> Yes. We stopped using the pkgload() mechanism (the key difference is
> numpy/scipy versions, not Python versions). We have been trying to
> discourage the use of the scipy.* namespace for some time now. Use the
> subpackages.

I have scipy 0.9.0 on python 2.6,  2.7 and on 3.2

>>> import scipy
>>> scipy.__version__
'0.9.0'

On 2.6 and 2.7 factorial is still in the scipy. namespace, but not in 3.2

I thought some scipy.misc function where still an exception to the
load the subpackage rule

>>> import sys
>>> sys.version
'2.7.1 (r271:86832, Nov 27 2010, 18:30:46) [MSC v.1500 32 bit (Intel)]'
>>> import scipy
>>> scipy.__version__
'0.9.0'
>>> set(dir(scipy)) & set(dir(scipy.misc))
set(['info', 'lena', 'comb', 'pade', '__all__', 'Tester', 'factorial',
'factorialk', '__file__', 'who', '__builtins__',
'central_diff_weights', '__package__', '__path__', 'source',
'__name__', 'test', 'derivative', 'factorial2', '__doc__'])
>>>


>>> import sys
>>> sys.version
'3.2 (r32:88445, Feb 20 2011, 21:30:00) [MSC v.1500 64 bit (AMD64)]'
>>> import scipy
>>> scipy.__version__
'0.9.0'
>>> set(dir(scipy)) & set(dir(scipy.misc))
{'__cached__', 'info', '__all__', 'Tester', '__builtins__',
'__file__', 'who', '__package__', '__path__', 'source', 'test',
'__name__', '__doc__'}


I'm fine loading from misc, I was just surprised

Josef




>
> --
> 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
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>


From sturla at molden.no  Sun Apr 10 21:36:11 2011
From: sturla at molden.no (Sturla Molden)
Date: Mon, 11 Apr 2011 03:36:11 +0200
Subject: [SciPy-Dev] [SciPy-User]  What "Array" means
In-Reply-To: <BANLkTik7x+aeNax+S506W+=SdO7Khs8GDQ@mail.gmail.com>
References: <BANLkTik7x+aeNax+S506W+=SdO7Khs8GDQ@mail.gmail.com>
Message-ID: <4DA25B0B.40901@molden.no>

Den 08.04.2011 12:14, skrev Timothy Wu:
>
> File "/usr/lib/python2.6/dist-packages/scipy/stats/mstats_basic.py", 
> line 1546, in kurtosistest
>     n = a.count(axis=axis).astype(float)
> AttributeError: 'int' object has no attribute 'astype'
>
> I'm not familiar with numpy nor scipy. What exactly should I put in there?

I find multiple cases of code like this:

a, axis = _chk_asarray(a, axis)
n = a.count(axis)

a, axis = _chk_asarray(a, axis)
n = a.count(axis=axis)

a, axis = _chk_asarray(a, axis)
n = a.count(axis)

a, axis = _chk_asarray(a, axis)
n = a.count(axis=axis).astype(float)


All of them are bugs:

_chk_asarray sometimes returns an ndarray (due to np.ma.ravel), which 
does not have a count attribute.

Sometimes count returns an int, which does not have an asfloat attribute.


Sturla




From nwagner at iam.uni-stuttgart.de  Tue Apr 12 03:32:57 2011
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Tue, 12 Apr 2011 09:32:57 +0200
Subject: [SciPy-Dev] Possibly bug in fmin_ncg
Message-ID: <web-144269070@uni-stuttgart.de>

Hi all,


fmin_cg works fine

x_opt, f_opt, func_calls, grad_calls, warnflag, allvecs = 
fmin_cg(func, x0, fprime=fprime, args=(), 
gtol=1.0000000000000001e-05, norm=inf,
         epsilon=1.4901161193847656e-08, maxiter=None, 
full_output=1, disp=1, retall=1, callback=None)


while fmin_ncg fails with

x_opt, f_opt, fcalls, gcalls,hcalls,warnflag 
=fmin_ncg(func, x0, fprime=fprime, fhess_p=None, 
fhess=None, args=(), avextol=1.0000000000000001e-05,
          epsilon=1.4901161193847656e-08, maxiter=None, 
full_output=1, disp=1, retall=1, callback=None)

   File 
"/data/home/nwagner/local/lib/python2.5/site-packages/scipy/optimize/optimize.py", 
line 811, in fmin_ncg
     maggrad = numpy.add.reduce(abs(b))
TypeError: cannot reduce on a scalar

Is it possible to replace numpy.add.reduce by numpy.sum ?

>>> numpy.add.reduce(abs(numpy.array(([1.,2.]))))
3.0
>>> numpy.sum(abs(numpy.array(([1.,2.]))))
3.0
>>> numpy.add.reduce(abs(1.))
Traceback (most recent call last):
   File "<stdin>", line 1, in <module>
TypeError: cannot reduce on a scalar
>>> numpy.sum(abs(1.))
1.0

Nils


From unclejamil at gmail.com  Tue Apr 12 14:39:59 2011
From: unclejamil at gmail.com (jamil egdemir)
Date: Tue, 12 Apr 2011 14:39:59 -0400
Subject: [SciPy-Dev] tzinfo and scikits.timeseries
In-Reply-To: <mailman.2126.1302631244.1781.scipy-dev@scipy.org>
References: <mailman.2126.1302631244.1781.scipy-dev@scipy.org>
Message-ID: <BANLkTinE97qrRXT-O08o=JyrRqpKn1zBwg@mail.gmail.com>

Hi,

When using scikits.timeseries I'm running into an issue with timezone
information. ?When using a datetime.datetime in the constructor for a
scikits.timeseries.Date, the tzinfo
is getting dropped. ?Here's the output I'm getting when working from
inside ipython (on windows):

In [2]: import datetime

In [3]: from pytz import timezone

In [4]: eastern = timezone('US/Eastern')

In [5]: eastern
Out[5]: <DstTzInfo 'US/Eastern' EST-1 day, 19:00:00 STD>

In [6]: testing = eastern.localize(datetime.datetime(year = 2010,
month = 1, day = 1))

In [7]: testing
Out[7]: datetime.datetime(2010, 1, 1, 0, 0, tzinfo=<DstTzInfo
'US/Eastern' EST-1 day, 19:00:00 STD>)

In [8]: type(testing)
Out[8]: <type 'datetime.datetime'>

In [9]: import scikits.timeseries as TS

In [10]: aDate = TS.Date('D', datetime = testing)

In [11]: aDate
Out[11]: <D : 01-Jan-2010>

In [13]: after = aDate.datetime

In [14]: after
Out[14]: datetime.datetime(2010, 1, 1, 0, 0)

In [15]: after.tzinfo

In [16]: type(after.tzinfo)
Out[16]: <type 'NoneType'>

What's the best way to deal with this situation? ?Is there a way to
keep hold of the tzinfo while still using scikits.timeseries.Date?

--
-j

-------------------------------------------------------------
Jamil Egdemir
unclejamil at gmail.com
AIM: unclejamil
YahooMessenger: uncle_jamil
http://grad.physics.sunysb.edu/~jamil
(631) 338-3170?(cell)
-------------------------------------------------------------


From pgmdevlist at gmail.com  Wed Apr 13 06:46:55 2011
From: pgmdevlist at gmail.com (Pierre GM)
Date: Wed, 13 Apr 2011 12:46:55 +0200
Subject: [SciPy-Dev] tzinfo and scikits.timeseries
In-Reply-To: <BANLkTinE97qrRXT-O08o=JyrRqpKn1zBwg@mail.gmail.com>
References: <mailman.2126.1302631244.1781.scipy-dev@scipy.org>
	<BANLkTinE97qrRXT-O08o=JyrRqpKn1zBwg@mail.gmail.com>
Message-ID: <4AD584A4-C578-48EC-8B68-839CF6C3FFAF@gmail.com>


On Apr 12, 2011, at 8:39 PM, jamil egdemir wrote:
> 
> What's the best way to deal with this situation?  Is there a way to
> keep hold of the tzinfo while still using scikits.timeseries.Date?

Currently, no. We never had to use this kind of info, so nothing is coded about it. But that's an excellent idea. The best would be to open a ticket and we'll try to address it as soon as we can (but that's probably be later than you think).
If you really need the tzinfo and your series has the same TZ, you could try to save it as attribute.

From lists at onerussian.com  Wed Apr 13 10:34:35 2011
From: lists at onerussian.com (Yaroslav Halchenko)
Date: Wed, 13 Apr 2011 10:34:35 -0400
Subject: [SciPy-Dev] distributions.ncf.fit -- never converges?
Message-ID: <20110413143435.GD7764@onerussian.com>

Since 0.9.0 (not present in 0.7.2), distributions.ncf.fit seems to never
converge.  could anyone check in development tree if the below call ever
returns (I was waiting for minutes... with 0.7.2 it was taking just a moment):

  python -c 'import scipy.stats.distributions as ssd, numpy as np; d=ssd.ncf; d.fit(np.array([-0.03756533,  0.18115522,  0.06605958, -0.09195276,  0.06162608, 0.07139736, -0.1570828 , -0.11967677, -0.19186652,  0.29411319]));' 

Thanks in advance!

-- 
=------------------------------------------------------------------=
Keep in touch                                     www.onerussian.com
Yaroslav Halchenko                 www.ohloh.net/accounts/yarikoptic


From josef.pktd at gmail.com  Wed Apr 13 12:53:54 2011
From: josef.pktd at gmail.com (josef.pktd at gmail.com)
Date: Wed, 13 Apr 2011 12:53:54 -0400
Subject: [SciPy-Dev] distributions.ncf.fit -- never converges?
In-Reply-To: <20110413143435.GD7764@onerussian.com>
References: <20110413143435.GD7764@onerussian.com>
Message-ID: <BANLkTikBJDuYcfOMNesp+P_MogjUcmFcfg@mail.gmail.com>

On Wed, Apr 13, 2011 at 10:34 AM, Yaroslav Halchenko
<lists at onerussian.com> wrote:
> Since 0.9.0 (not present in 0.7.2), distributions.ncf.fit seems to never
> converge. ?could anyone check in development tree if the below call ever
> returns (I was waiting for minutes... with 0.7.2 it was taking just a moment):
>
> ?python -c 'import scipy.stats.distributions as ssd, numpy as np; d=ssd.ncf; d.fit(np.array([-0.03756533, ?0.18115522, ?0.06605958, -0.09195276, ?0.06162608, 0.07139736, -0.1570828 , -0.11967677, -0.19186652, ?0.29411319]));'

I only have 0.9.0, I forgot to kill the process and 1 hour 22 minutes
of cpu time later it still hadn't returned.
At least a maximum iteration or maximum function evaluation should
have stopped it.

Josef


>
> Thanks in advance!
>
> --
> =------------------------------------------------------------------=
> Keep in touch ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? www.onerussian.com
> Yaroslav Halchenko ? ? ? ? ? ? ? ? www.ohloh.net/accounts/yarikoptic
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>


From lists at onerussian.com  Wed Apr 13 13:08:45 2011
From: lists at onerussian.com (Yaroslav Halchenko)
Date: Wed, 13 Apr 2011 13:08:45 -0400
Subject: [SciPy-Dev] distributions.ncf.fit -- never converges?
In-Reply-To: <BANLkTikBJDuYcfOMNesp+P_MogjUcmFcfg@mail.gmail.com>
References: <20110413143435.GD7764@onerussian.com>
	<BANLkTikBJDuYcfOMNesp+P_MogjUcmFcfg@mail.gmail.com>
Message-ID: <20110413170845.GE7764@onerussian.com>

Thanks Josef for the confirmation and making your computer sweat ;)

I have built current master

*In [3]: scipy.__version__
Out[3]: '0.10.0.dev'

the same story.

apparently it is known to some degree -- ncf is skipped the unittesting:

$> git grep -A 10 'TestFitMethod'
scipy/stats/tests/test_distributions.py:class TestFitMethod(TestCase):
scipy/stats/tests/test_distributions.py-    skip = ['ncf']
scipy/stats/tests/test_distributions.py-
scipy/stats/tests/test_distributions.py-    @dec.slow
scipy/stats/tests/test_distributions.py-    def test_fit(self):
scipy/stats/tests/test_distributions.py-        for func, dist, args, alpha in test_all_distributions():
scipy/stats/tests/test_distributions.py-            if dist in self.skip:
scipy/stats/tests/test_distributions.py-                continue

$> git show ba349771
commit ba349771afebb1473a961139570da770ada59032
Author: Travis Oliphant <oliphant at enthought.com>
Date:   Tue Jun 1 07:59:20 2010 +0000

    Add tests for fit method including fixing input parameters.


;-) :-/

On Wed, 13 Apr 2011, josef.pktd at gmail.com wrote:

> > ?python -c 'import scipy.stats.distributions as ssd, numpy as np; d=ssd.ncf; d.fit(np.array([-0.03756533, ?0.18115522, ?0.06605958, -0.09195276, ?0.06162608, 0.07139736, -0.1570828 , -0.11967677, -0.19186652, ?0.29411319]));'

> I only have 0.9.0, I forgot to kill the process and 1 hour 22 minutes
> of cpu time later it still hadn't returned.
> At least a maximum iteration or maximum function evaluation should
> have stopped it.

> Josef
-- 
=------------------------------------------------------------------=
Keep in touch                                     www.onerussian.com
Yaroslav Halchenko                 www.ohloh.net/accounts/yarikoptic


From lists at onerussian.com  Wed Apr 13 13:25:00 2011
From: lists at onerussian.com (Yaroslav Halchenko)
Date: Wed, 13 Apr 2011 13:25:00 -0400
Subject: [SciPy-Dev] distributions.ncf.fit -- never converges?
In-Reply-To: <20110413170845.GE7764@onerussian.com>
References: <20110413143435.GD7764@onerussian.com>
	<BANLkTikBJDuYcfOMNesp+P_MogjUcmFcfg@mail.gmail.com>
	<20110413170845.GE7764@onerussian.com>
Message-ID: <20110413172500.GF7764@onerussian.com>

just in case it would come useful in troubleshooting -- gets stuck in cumfnc_
(not modified since 2007) and blunt guess could be that reason is could
be related to

cdffnc1_wrap (dfn=-nan(0x8000000000000), dfd=-nan(0x8000000000000), ...

?

*(gdb) bt full 10
#0  0x00007f69103a44eb in cumfnc_ () from /home/yoh/proj/scipy/install/lib/python2.6/site-packages/scipy/special/_cephes.so
No symbol table info available.
#1  0x00007f691039fab0 in cdffnc_ () from /home/yoh/proj/scipy/install/lib/python2.6/site-packages/scipy/special/_cephes.so
No symbol table info available.
#2  0x00007f6910363b84 in cdffnc1_wrap (dfn=-nan(0x8000000000000), dfd=-nan(0x8000000000000), nc=1, f=0.5) at scipy/special/cdf_wrappers.c:254
        which = 1
        q = 8.4886169591766247e-317
        p = <value optimized out>
        bound = <value optimized out>
        status = 6
#3  0x00007f69103668fe in PyUFunc_dddd_d (args=0x7f691067a750, dimensions=<value optimized out>, steps=0x7ff80000, func=<value optimized out>) at scipy/special/ufunc_extras.c:510
        i = 1
        ip1 = 0xf6e2c0 ""
        ip2 = 0x19df1e0 ""
        ip3 = 0x19ee0c0 ""
        ip4 = 0x190c7b0 ""
        op = 0x17dedf0 "\b\357\374\023i\177"
        n = 10
#4  0x00007f6913257209 in ?? () from /usr/lib/pymodules/python2.6/numpy/core/umath.so
No symbol table info available.
#5  0x00007f6913257d13 in ?? () from /usr/lib/pymodules/python2.6/numpy/core/umath.so
No symbol table info available.
#6  0x000000000041ef47 in PyObject_Call (func=<numpy.ufunc at remote 0x14dba50>, arg=<unknown at remote 0x43680000>, kw=<unknown at remote 0x7ff80000>) at ../Objects/abstract.c:2492
        result = < at remote 0xedd180>
        call = 0x7f6913257cb0
#7  0x00000000004a72b8 in do_call (f=
    Frame 0x19e4b60, for file /home/yoh/proj/scipy/install/lib/python2.6/site-packages/scipy/stats/distributions.py, line 4241, in _cdf (self=<ncf_gen(a=<float at remote 0x15f1a88>, moment_type=1, b=<float at remote 0xefa5d0>, vecfunc=<vectorize(nin=4, nin_wo_defaults=1, thefunc=<instancemethod at remote 0x1890640>, otypes='d', lastcallargs=0, ufunc=None, __doc__=None, nout=None) at remote 0x1891f50>, name='ncf', xb=<float at remote 0x1589d58>, xa=<float at remote 0x1589d70>, m=<float at remote 0x1589d28>, vecentropy=<vectorize(nin=4, nin_wo_defaults=None, thefunc=<instancemethod at remote 0x18906e0>, otypes='d', lastcallargs=0, ufunc=None, __doc__=None, nout=None) at remote 0x1891fd0>, numargs=3, generic_moment=<vectorize(nin=4, nin_wo_defaults=1, thefunc=<instancemethod at remote 0x1890fa0>, otypes='d', lastcallargs=0, ufunc=None, __doc__=None, nout=None) at remote 0x1893090>, veccdf=<vectorize(nin=4, nin_wo_defaults=1, thefunc=<instancemethod at remote 0x1890e10>, otypes='d', lastcallargs=0, ufunc=None, __doc_...(truncated), throwflag=<value optimized out>) at ../Python/ceval.c:3968
        callargs = (<numpy.float64 at remote 0x1643710>, <numpy.float64 at remote 0x1553990>, <numpy.float64 at remote 0x18d1b80>, <numpy.ndarray at remote 0x19f4590>)
        kwdict = 0x0
#8  call_function (f=
    Frame 0x19e4b60, for file /home/yoh/proj/scipy/install/lib/python2.6/site-packages/scipy/stats/distributions.py, line 4241, in _cdf (self=<ncf_gen(a=<float at remote 0x15f1a88>, moment_type=1, b=<float at remote 0xefa5d0>, vecfunc=<vectorize(nin=4, nin_wo_defaults=1, thefunc=<instancemethod at remote 0x1890640>, otypes='d', lastcallargs=0, ufunc=None, __doc__=None, nout=None) at remote 0x1891f50>, name='ncf', xb=<float at remote 0x1589d58>, xa=<float at remote 0x1589d70>, m=<float at remote 0x1589d28>, vecentropy=<vectorize(nin=4, nin_wo_defaults=None, thefunc=<instancemethod at remote 0x18906e0>, otypes='d', lastcallargs=0, ufunc=None, __doc__=None, nout=None) at remote 0x1891fd0>, numargs=3, generic_moment=<vectorize(nin=4, nin_wo_defaults=1, thefunc=<instancemethod at remote 0x1890fa0>, otypes='d', lastcallargs=0, ufunc=None, __doc__=None, nout=None) at remote 0x1893090>, veccdf=<vectorize(nin=4, nin_wo_defaults=1, thefunc=<instancemethod at remote 0x1890e10>, otypes='d', lastcallargs=0, ufunc=None, __doc_...(truncated), throwflag=<value optimized out>) at ../Python/ceval.c:3773
        func = <numpy.ufunc at remote 0x14dba50>
        w = <value optimized out>
        nk = <value optimized out>
        n = <value optimized out>
        pfunc = 0x19e4d00
#9  PyEval_EvalFrameEx (f=
    Frame 0x19e4b60, for file /home/yoh/proj/scipy/install/lib/python2.6/site-packages/scipy/stats/distributions.py, line 4241, in _cdf (self=<ncf_gen(a=<float at remote 0x15f1a88>, moment_type=1, b=<float at remote 0xefa5d0>, vecfunc=<vectorize(nin=4, nin_wo_defaults=1, thefunc=<instancemethod at remote 0x1890640>, otypes='d', lastcallargs=0, ufunc=None, __doc__=None, nout=None) at remote 0x1891f50>, name='ncf', xb=<float at remote 0x1589d58>, xa=<float at remote 0x1589d70>, m=<float at remote 0x1589d28>, vecentropy=<vectorize(nin=4, nin_wo_defaults=None, thefunc=<instancemethod at remote 0x18906e0>, otypes='d', lastcallargs=0, ufunc=None, __doc__=None, nout=None) at remote 0x1891fd0>, numargs=3, generic_moment=<vectorize(nin=4, nin_wo_defaults=1, thefunc=<instancemethod at remote 0x1890fa0>, otypes='d', lastcallargs=0, ufunc=None, __doc__=None, nout=None) at remote 0x1893090>, veccdf=<vectorize(nin=4, nin_wo_defaults=1, thefunc=<instancemethod at remote 0x1890e10>, otypes='d', lastcallargs=0, ufunc=None, __doc_...(truncated), throwflag=<value optimized out>) at ../Python/ceval.c:2412
        sp = 0x19e4d08
        stack_pointer = <value optimized out>
        next_instr = 0x1615229 "S"
        opcode = <value optimized out>
        oparg = <value optimized out>
        why = <value optimized out>
        err = <value optimized out>
        x = <value optimized out>
        v = <value optimized out>
        w = <value optimized out>
        u = <value optimized out>
        t = <value optimized out>
        stream = <value optimized out>
        freevars = 0x19e4d00
        retval = 0x0
        tstate = 0xedd180
        co = 0x1614828
        instr_ub = -1
        instr_lb = 0
        instr_prev = -1
        first_instr = 0x1615214 "t"
        names = ('special', 'ncfdtr')
        consts = (None,)
(More stack frames follow...)

-- 
=------------------------------------------------------------------=
Keep in touch                                     www.onerussian.com
Yaroslav Halchenko                 www.ohloh.net/accounts/yarikoptic


From josef.pktd at gmail.com  Wed Apr 13 13:33:56 2011
From: josef.pktd at gmail.com (josef.pktd at gmail.com)
Date: Wed, 13 Apr 2011 13:33:56 -0400
Subject: [SciPy-Dev] distributions.ncf.fit -- never converges?
In-Reply-To: <20110413170845.GE7764@onerussian.com>
References: <20110413143435.GD7764@onerussian.com>
	<BANLkTikBJDuYcfOMNesp+P_MogjUcmFcfg@mail.gmail.com>
	<20110413170845.GE7764@onerussian.com>
Message-ID: <BANLkTinh45dJCN6rvbSqSJfxXPgA92XdAw@mail.gmail.com>

2011/4/13 Yaroslav Halchenko <lists at onerussian.com>:
> Thanks Josef for the confirmation and making your computer sweat ;)
>
> I have built current master
>
> *In [3]: scipy.__version__
> Out[3]: '0.10.0.dev'
>
> the same story.

The default starting parameters have changed. If your example worked
before, then it's possible that it works with explicit starting
parameters.

(I haven't figured out yet how to make my new computer sweat.)

Josef


>
> apparently it is known to some degree -- ncf is skipped the unittesting:
>
> $> git grep -A 10 'TestFitMethod'
> scipy/stats/tests/test_distributions.py:class TestFitMethod(TestCase):
> scipy/stats/tests/test_distributions.py- ? ?skip = ['ncf']
> scipy/stats/tests/test_distributions.py-
> scipy/stats/tests/test_distributions.py- ? ?@dec.slow
> scipy/stats/tests/test_distributions.py- ? ?def test_fit(self):
> scipy/stats/tests/test_distributions.py- ? ? ? ?for func, dist, args, alpha in test_all_distributions():
> scipy/stats/tests/test_distributions.py- ? ? ? ? ? ?if dist in self.skip:
> scipy/stats/tests/test_distributions.py- ? ? ? ? ? ? ? ?continue
>
> $> git show ba349771
> commit ba349771afebb1473a961139570da770ada59032
> Author: Travis Oliphant <oliphant at enthought.com>
> Date: ? Tue Jun 1 07:59:20 2010 +0000
>
> ? ?Add tests for fit method including fixing input parameters.
>
>
> ;-) :-/
>
> On Wed, 13 Apr 2011, josef.pktd at gmail.com wrote:
>
>> > ?python -c 'import scipy.stats.distributions as ssd, numpy as np; d=ssd.ncf; d.fit(np.array([-0.03756533, ?0.18115522, ?0.06605958, -0.09195276, ?0.06162608, 0.07139736, -0.1570828 , -0.11967677, -0.19186652, ?0.29411319]));'
>
>> I only have 0.9.0, I forgot to kill the process and 1 hour 22 minutes
>> of cpu time later it still hadn't returned.
>> At least a maximum iteration or maximum function evaluation should
>> have stopped it.
>
>> Josef
> --
> =------------------------------------------------------------------=
> Keep in touch ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? www.onerussian.com
> Yaroslav Halchenko ? ? ? ? ? ? ? ? www.ohloh.net/accounts/yarikoptic
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>


From bsouthey at gmail.com  Wed Apr 13 13:58:24 2011
From: bsouthey at gmail.com (Bruce Southey)
Date: Wed, 13 Apr 2011 12:58:24 -0500
Subject: [SciPy-Dev] distributions.ncf.fit -- never converges?
In-Reply-To: <BANLkTinh45dJCN6rvbSqSJfxXPgA92XdAw@mail.gmail.com>
References: <20110413143435.GD7764@onerussian.com>	<BANLkTikBJDuYcfOMNesp+P_MogjUcmFcfg@mail.gmail.com>	<20110413170845.GE7764@onerussian.com>
	<BANLkTinh45dJCN6rvbSqSJfxXPgA92XdAw@mail.gmail.com>
Message-ID: <4DA5E440.2060803@gmail.com>

On 04/13/2011 12:33 PM, josef.pktd at gmail.com wrote:
> 2011/4/13 Yaroslav Halchenko<lists at onerussian.com>:
>> Thanks Josef for the confirmation and making your computer sweat ;)
>>
>> I have built current master
>>
>> *In [3]: scipy.__version__
>> Out[3]: '0.10.0.dev'
>>
>> the same story.
> The default starting parameters have changed. If your example worked
> before, then it's possible that it works with explicit starting
> parameters.
>
> (I haven't figured out yet how to make my new computer sweat.)
>
> Josef
>
>
>> apparently it is known to some degree -- ncf is skipped the unittesting:
>>
>> $>  git grep -A 10 'TestFitMethod'
>> scipy/stats/tests/test_distributions.py:class TestFitMethod(TestCase):
>> scipy/stats/tests/test_distributions.py-    skip = ['ncf']
>> scipy/stats/tests/test_distributions.py-
>> scipy/stats/tests/test_distributions.py-    @dec.slow
>> scipy/stats/tests/test_distributions.py-    def test_fit(self):
>> scipy/stats/tests/test_distributions.py-        for func, dist, args, alpha in test_all_distributions():
>> scipy/stats/tests/test_distributions.py-            if dist in self.skip:
>> scipy/stats/tests/test_distributions.py-                continue
>>
>> $>  git show ba349771
>> commit ba349771afebb1473a961139570da770ada59032
>> Author: Travis Oliphant<oliphant at enthought.com>
>> Date:   Tue Jun 1 07:59:20 2010 +0000
>>
>>     Add tests for fit method including fixing input parameters.
>>
>>
>> ;-) :-/
>>
>> On Wed, 13 Apr 2011, josef.pktd at gmail.com wrote:
>>
>>>>   python -c 'import scipy.stats.distributions as ssd, numpy as np; d=ssd.ncf; d.fit(np.array([-0.03756533,  0.18115522,  0.06605958, -0.09195276,  0.06162608, 0.07139736, -0.1570828 , -0.11967677, -0.19186652,  0.29411319]));'
>>> I only have 0.9.0, I forgot to kill the process and 1 hour 22 minutes
>>> of cpu time later it still hadn't returned.
>>> At least a maximum iteration or maximum function evaluation should
>>> have stopped it.
>>> Josef
>> --
>> =------------------------------------------------------------------=
>> Keep in touch                                     www.onerussian.com
>> Yaroslav Halchenko                 www.ohloh.net/accounts/yarikoptic
>> _______________________________________________
>> SciPy-Dev mailing list
>> SciPy-Dev at scipy.org
>> http://mail.scipy.org/mailman/listinfo/scipy-dev
>>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
I did not run it very long because I saw this message:
/usr/lib64/python2.7/site-packages/scipy/stats/distributions.py:1882: 
RuntimeWarning: invalid value encountered in double_scalars
   Lhat = muhat - Shat*mu

It seems that  line 1874 (mu, mu2 = 
self.stats(*args,**{'moments':'mv'})) give mu and mu2 as inf's. So Lhat 
is nan and there are better uses for that cpu power than spinning around 
infinities ...

Bruce






From lists at onerussian.com  Wed Apr 13 15:02:26 2011
From: lists at onerussian.com (Yaroslav Halchenko)
Date: Wed, 13 Apr 2011 15:02:26 -0400
Subject: [SciPy-Dev] distributions.ncf.fit -- never converges?
In-Reply-To: <4DA5E440.2060803@gmail.com>
References: <20110413143435.GD7764@onerussian.com>
	<BANLkTikBJDuYcfOMNesp+P_MogjUcmFcfg@mail.gmail.com>
	<20110413170845.GE7764@onerussian.com>
	<BANLkTinh45dJCN6rvbSqSJfxXPgA92XdAw@mail.gmail.com>
	<4DA5E440.2060803@gmail.com>
Message-ID: <20110413190226.GG7764@onerussian.com>


On Wed, 13 Apr 2011, Bruce Southey wrote:
> I did not run it very long because I saw this message:
> /usr/lib64/python2.7/site-packages/scipy/stats/distributions.py:1882: 
> RuntimeWarning: invalid value encountered in double_scalars
>    Lhat = muhat - Shat*mu

> It seems that  line 1874 (mu, mu2 = 
> self.stats(*args,**{'moments':'mv'})) give mu and mu2 as inf's. So Lhat 
> is nan and there are better uses for that cpu power than spinning around 
> infinities ...

lucky you -- I got none of that warning.  Although I must confess, scipy
0.9.0 is really "talkative" without any way to shut it really up:

$> dpkg -L python-scipy | grep '\.py' | xargs grep -i "print.*warn" | head 
/usr/share/pyshared/scipy/signal/signaltools.py:        print "Warning: imaginary part of x ignored."
/usr/share/pyshared/scipy/signal/signaltools.py:        print "Warning: imaginary part of x ignored."
...
$> dpkg -L python-scipy | grep '\.py' | xargs grep -i "print.*warn" | wc -l
132

great to see that future 0.9.1 will be saner:

$> git describe --tags
v0.4.3-4868-g9b5db2c

$> git grep -i 'print[^f].*war' | wc -l
47


-- 
=------------------------------------------------------------------=
Keep in touch                                     www.onerussian.com
Yaroslav Halchenko                 www.ohloh.net/accounts/yarikoptic


From josh.k.lawrence at gmail.com  Wed Apr 13 15:10:59 2011
From: josh.k.lawrence at gmail.com (Josh Lawrence)
Date: Wed, 13 Apr 2011 15:10:59 -0400
Subject: [SciPy-Dev] calc_lwork.f different from Lapack?
Message-ID: <4DA5F543.8020104@gmail.com>

Hello,

After receiving an error in using linalg.lstsq, I started some 
investigating. I found that scipy/linalg/src/calc_lwork.f is essentially 
a stripped down version of the appropriate functions in Lapack (for 
linalg.lstsq using double precision complex numbers, it is ZGELSS). It 
seems that the portions for gelss in calc_lwork.f do not match the 
current version of lapack. I believe this is the source of my error (it 
doesn't occur if I use linalg.pinv2 for least squares instead). Is there 
a particular rationale for these being different or perhaps an incorrect 
copy and paste? The relevant portions are shown below (a line of % 
characters are prepended before the codes from the two locations).

For example, the first calculation of MAXWRK under Path 1 uses 3*N in 
calc_lwork and 2*N in lapack. If things were just being over-estimated, 
I wouldn't really care, but I was able to isolate down that the variable 
LWORK (calculated from MINWRK) is too small, which if I read the rest of 
the code right means that some work arrays are not long enough.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
calc_lwork.f (from scipy trunk on github, lines 191-261):

       IF( M.GE.N .AND. M.GE.MNTHR ) THEN
*
*     Path 1a - overdetermined, with many more rows than columns
*
          MM = N
          MAXWRK = MAX( MAXWRK, N+N*ILAENV( 1, prefix //  'GEQRF', ' ',
      $        M, N, -1, -1 ) )
          MAXWRK = MAX( MAXWRK, N+NRHS*
      $        ILAENV( 1, prefix //  'ORMQR', 'LT', M, NRHS, N, -1 ) )
       END IF
       IF( M.GE.N ) THEN
*
*     Path 1 - overdetermined or exactly determined
*
*     Compute workspace neede for BDSQR
*
          BDSPAC = MAX( 1, 5*N )
          MAXWRK = MAX( MAXWRK, 3*N+( MM+N )*
      $        ILAENV( 1, prefix // 'GEBRD', ' ', MM, N, -1, -1 ) )
          MAXWRK = MAX( MAXWRK, 3*N+NRHS*
      $        ILAENV( 1, prefix // 'ORMBR', 'QLT', MM, NRHS, N, -1 ) )
          MAXWRK = MAX( MAXWRK, 3*N+( N-1 )*
      $        ILAENV( 1, prefix // 'ORGBR', 'P', N, N, N, -1 ) )
          MAXWRK = MAX( MAXWRK, BDSPAC )
          MAXWRK = MAX( MAXWRK, N*NRHS )
          MINWRK = MAX( 3*N+MM, 3*N+NRHS, BDSPAC )
          MAXWRK = MAX( MINWRK, MAXWRK )
       END IF

       IF( N.GT.M ) THEN
*
*     Compute workspace neede for DBDSQR
*
          BDSPAC = MAX( 1, 5*M )
          MINWRK = MAX( 3*M+NRHS, 3*M+N, BDSPAC )
          IF( N.GE.MNTHR ) THEN
*
*     Path 2a - underdetermined, with many more columns
*     than rows
*
             MAXWRK = M + M*ILAENV( 1, prefix // 'GELQF', ' ',
      $           M, N, -1, -1 )
             MAXWRK = MAX( MAXWRK, M*M+4*M+2*M*
      $           ILAENV( 1, prefix //  'GEBRD', ' ', M, M, -1, -1 ) )
             MAXWRK = MAX( MAXWRK, M*M+4*M+NRHS*
      $           ILAENV( 1, prefix // 'ORMBR', 'QLT', M, NRHS, M, -1 ))
             MAXWRK = MAX( MAXWRK, M*M+4*M+( M-1 )*
      $           ILAENV( 1, prefix // 'ORGBR', 'P', M, M, M, -1 ) )
             MAXWRK = MAX( MAXWRK, M*M+M+BDSPAC )
             IF( NRHS.GT.1 ) THEN
                MAXWRK = MAX( MAXWRK, M*M+M+M*NRHS )
             ELSE
                MAXWRK = MAX( MAXWRK, M*M+2*M )
             END IF
             MAXWRK = MAX( MAXWRK, M+NRHS*
      $           ILAENV( 1, prefix // 'ORMLQ', 'LT', N, NRHS, M, -1 ) )

          ELSE
*
*     Path 2 - underdetermined
*
             MAXWRK = 3*M + ( N+M )*ILAENV( 1, prefix // 'GEBRD', ' ',
      $           M, N, -1, -1 )
             MAXWRK = MAX( MAXWRK, 3*M+NRHS*
      $           ILAENV( 1, prefix // 'ORMBR', 'QLT', M, NRHS, M, -1 ) )
             MAXWRK = MAX( MAXWRK, 3*M+M*
      $           ILAENV( 1, prefix // 'ORGBR', 'P', M, N, M, -1 ) )
             MAXWRK = MAX( MAXWRK, BDSPAC )
             MAXWRK = MAX( MAXWRK, N*NRHS )
          END IF
       END IF

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
ZGELSS.F (from LAPACK on netlib, lines 165-236):

       IF( INFO.EQ.0 ) THEN
          MINWRK = 1
          MAXWRK = 1
          IF( MINMN.GT.0 ) THEN
             MM = M
             MNTHR = ILAENV( 6, 'ZGELSS', ' ', M, N, NRHS, -1 )
             IF( M.GE.N .AND. M.GE.MNTHR ) THEN
*
*              Path 1a - overdetermined, with many more rows than
*                        columns
*
                MM = N
                MAXWRK = MAX( MAXWRK, N + N*ILAENV( 1, 'ZGEQRF', ' ', M,
      $                       N, -1, -1 ) )
                MAXWRK = MAX( MAXWRK, N + NRHS*ILAENV( 1, 'ZUNMQR', 'LC',
      $                       M, NRHS, N, -1 ) )
             END IF
             IF( M.GE.N ) THEN
*
*              Path 1 - overdetermined or exactly determined
*
                MAXWRK = MAX( MAXWRK, 2*N + ( MM + N )*ILAENV( 1,
      $                       'ZGEBRD', ' ', MM, N, -1, -1 ) )
                MAXWRK = MAX( MAXWRK, 2*N + NRHS*ILAENV( 1, 'ZUNMBR',
      $                       'QLC', MM, NRHS, N, -1 ) )
                MAXWRK = MAX( MAXWRK, 2*N + ( N - 1 )*ILAENV( 1,
      $                       'ZUNGBR', 'P', N, N, N, -1 ) )
                MAXWRK = MAX( MAXWRK, N*NRHS )
                MINWRK = 2*N + MAX( NRHS, M )
             END IF
             IF( N.GT.M ) THEN
                MINWRK = 2*M + MAX( NRHS, N )
                IF( N.GE.MNTHR ) THEN
*
*                 Path 2a - underdetermined, with many more columns
*                 than rows
*
                   MAXWRK = M + M*ILAENV( 1, 'ZGELQF', ' ', M, N, -1,
      $                     -1 )
                   MAXWRK = MAX( MAXWRK, 3*M + M*M + 2*M*ILAENV( 1,
      $                          'ZGEBRD', ' ', M, M, -1, -1 ) )
                   MAXWRK = MAX( MAXWRK, 3*M + M*M + NRHS*ILAENV( 1,
      $                          'ZUNMBR', 'QLC', M, NRHS, M, -1 ) )
                   MAXWRK = MAX( MAXWRK, 3*M + M*M + ( M - 1 )*ILAENV( 1,
      $                          'ZUNGBR', 'P', M, M, M, -1 ) )
                   IF( NRHS.GT.1 ) THEN
                      MAXWRK = MAX( MAXWRK, M*M + M + M*NRHS )
                   ELSE
                      MAXWRK = MAX( MAXWRK, M*M + 2*M )
                   END IF
                   MAXWRK = MAX( MAXWRK, M + NRHS*ILAENV( 1, 'ZUNMLQ',
      $                          'LC', N, NRHS, M, -1 ) )
                ELSE
*
*                 Path 2 - underdetermined
*
                   MAXWRK = 2*M + ( N + M )*ILAENV( 1, 'ZGEBRD', ' ', M,
      $                     N, -1, -1 )
                   MAXWRK = MAX( MAXWRK, 2*M + NRHS*ILAENV( 1, 'ZUNMBR',
      $                          'QLC', M, NRHS, M, -1 ) )
                   MAXWRK = MAX( MAXWRK, 2*M + M*ILAENV( 1, 'ZUNGBR',
      $                          'P', M, N, M, -1 ) )
                   MAXWRK = MAX( MAXWRK, N*NRHS )
                END IF
             END IF
             MAXWRK = MAX( MINWRK, MAXWRK )
          END IF
          WORK( 1 ) = MAXWRK
*
          IF( LWORK.LT.MINWRK .AND. .NOT.LQUERY )
      $      INFO = -12
       END IF




From josef.pktd at gmail.com  Fri Apr 15 10:42:36 2011
From: josef.pktd at gmail.com (josef.pktd at gmail.com)
Date: Fri, 15 Apr 2011 10:42:36 -0400
Subject: [SciPy-Dev] distributions.ncf.fit -- never converges?
In-Reply-To: <4DA5E440.2060803@gmail.com>
References: <20110413143435.GD7764@onerussian.com>
	<BANLkTikBJDuYcfOMNesp+P_MogjUcmFcfg@mail.gmail.com>
	<20110413170845.GE7764@onerussian.com>
	<BANLkTinh45dJCN6rvbSqSJfxXPgA92XdAw@mail.gmail.com>
	<4DA5E440.2060803@gmail.com>
Message-ID: <BANLkTi=n+NMH7zgm+-G_MpuZbdUaLUcOZw@mail.gmail.com>

On Wed, Apr 13, 2011 at 1:58 PM, Bruce Southey <bsouthey at gmail.com> wrote:
> On 04/13/2011 12:33 PM, josef.pktd at gmail.com wrote:
>> 2011/4/13 Yaroslav Halchenko<lists at onerussian.com>:
>>> Thanks Josef for the confirmation and making your computer sweat ;)
>>>
>>> I have built current master
>>>
>>> *In [3]: scipy.__version__
>>> Out[3]: '0.10.0.dev'
>>>
>>> the same story.
>> The default starting parameters have changed. If your example worked
>> before, then it's possible that it works with explicit starting
>> parameters.
>>
>> (I haven't figured out yet how to make my new computer sweat.)
>>
>> Josef
>>
>>
>>> apparently it is known to some degree -- ncf is skipped the unittesting:
>>>
>>> $> ?git grep -A 10 'TestFitMethod'
>>> scipy/stats/tests/test_distributions.py:class TestFitMethod(TestCase):
>>> scipy/stats/tests/test_distributions.py- ? ?skip = ['ncf']
>>> scipy/stats/tests/test_distributions.py-
>>> scipy/stats/tests/test_distributions.py- ? ?@dec.slow
>>> scipy/stats/tests/test_distributions.py- ? ?def test_fit(self):
>>> scipy/stats/tests/test_distributions.py- ? ? ? ?for func, dist, args, alpha in test_all_distributions():
>>> scipy/stats/tests/test_distributions.py- ? ? ? ? ? ?if dist in self.skip:
>>> scipy/stats/tests/test_distributions.py- ? ? ? ? ? ? ? ?continue
>>>
>>> $> ?git show ba349771
>>> commit ba349771afebb1473a961139570da770ada59032
>>> Author: Travis Oliphant<oliphant at enthought.com>
>>> Date: ? Tue Jun 1 07:59:20 2010 +0000
>>>
>>> ? ? Add tests for fit method including fixing input parameters.
>>>
>>>
>>> ;-) :-/
>>>
>>> On Wed, 13 Apr 2011, josef.pktd at gmail.com wrote:
>>>
>>>>> ? python -c 'import scipy.stats.distributions as ssd, numpy as np; d=ssd.ncf; d.fit(np.array([-0.03756533, ?0.18115522, ?0.06605958, -0.09195276, ?0.06162608, 0.07139736, -0.1570828 , -0.11967677, -0.19186652, ?0.29411319]));'
>>>> I only have 0.9.0, I forgot to kill the process and 1 hour 22 minutes
>>>> of cpu time later it still hadn't returned.
>>>> At least a maximum iteration or maximum function evaluation should
>>>> have stopped it.
>>>> Josef
>>> --
>>> =------------------------------------------------------------------=
>>> Keep in touch ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? www.onerussian.com
>>> Yaroslav Halchenko ? ? ? ? ? ? ? ? www.ohloh.net/accounts/yarikoptic
>>> _______________________________________________
>>> SciPy-Dev mailing list
>>> SciPy-Dev at scipy.org
>>> http://mail.scipy.org/mailman/listinfo/scipy-dev
>>>
>> _______________________________________________
>> SciPy-Dev mailing list
>> SciPy-Dev at scipy.org
>> http://mail.scipy.org/mailman/listinfo/scipy-dev
> I did not run it very long because I saw this message:
> /usr/lib64/python2.7/site-packages/scipy/stats/distributions.py:1882:
> RuntimeWarning: invalid value encountered in double_scalars
> ? Lhat = muhat - Shat*mu
>
> It seems that ?line 1874 (mu, mu2 =
> self.stats(*args,**{'moments':'mv'})) give mu and mu2 as inf's. So Lhat
> is nan and there are better uses for that cpu power than spinning around
> infinities ...

"To infinity and the nans beyond."

It looks like mean and variance are only finite if the degrees of
freedom for the ncf, dfn, dfd, are large enough, so I guess the
starting values should be large.

I think _fitstart could default back to loc=0, scale=1 if
np.any(~np.isfinite(self.fit_loc_scale(data, *args)))

This would remove at least one source of infs and nans.

Yaroslav,
Did you ever get a good estimate in your example with older versions?
With numpy 1.3, scipy 0.72 and with fully specified starting values in
scipy 0.9, the estimation results are the same as the starting values.
So the estimation doesn't move and does not produce any useful
results. (I don't have scipy 0.8 right now.)

Also as a note: ncf doesn't have the pdf defined. I removed it a long
time ago because it was buggy, and didn't figure out how to fix it. So
any maximum likelihood estimation has to work with the generic pdf.

Josef



>
> Bruce
>
>
>
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>


From xperroni at gmail.com  Sun Apr 17 09:37:19 2011
From: xperroni at gmail.com (Helio Perroni Filho)
Date: Sun, 17 Apr 2011 10:37:19 -0300
Subject: [SciPy-Dev] The state of weave.accelerate?
Message-ID: <BANLkTikGROdx0SX5+QahgpX2zyF3Megc+g@mail.gmail.com>

Dera all,

I have been looking for ways to speed up some portions of Python code
in my current scipy project. The ideal solution would allow me to keep
writing all my code in Python 2.7 ? even if the "accelerated" parts
had to written in a subset of the language, as in PyPy's Restricted
Python ? and be easily turned off for debugging.

When I learned of scipy.weave.inline, my first thought was "now if
only there was a Python-to-C++ translator I could hook up to this!" I
was intrigued when I found that cryptic reference about
sicpy.weave.accelerate providing "automatic acceleration of Python
code"; all the more after searching for more information on it, and
finding none.

So I decided to take a look at the code. The API seemed simple enough
(just a decorator for top-level functions), so I tried it on some toy
scripts I keep around. After hacking around a couple simple bugs (two
incorrect assertions in bytecodecompiler, a typo defining the
one-argument form of the range function and the need to add weave's
directory to the compiler include-path in accelerate_tools) I got
stuck on the many not-yet-implemented instructions in
bytecodecompiler: it seems even basic arithmetic is still to be
included.

I find this frustrating. From the tests I've run it seems accelerate()
already does an adequate work of generating the necessary C++
boilerplate code, compiling it to an extension and then wiring the
result back to the executing script. The only thing missing is getting
the C++ translation to work ? not trivial, I know, but not very hard
either, considering what's already in place.

Is a lack of manpower holding accelerate() back? If that's the case, I
volunteer to work on bytecodecompiler, and get it to at least an
RPython-level of functionality. I have read the documentation on the
Developer Zone, but didn't find how do I create a Trac account. And
besides that, is there anything else not on that page that I should
know?

-- 
Ja ne,
Helio Perroni Filho
http://machineawakening.blogspot.com/


From ralf.gommers at googlemail.com  Sun Apr 17 16:30:02 2011
From: ralf.gommers at googlemail.com (Ralf Gommers)
Date: Sun, 17 Apr 2011 22:30:02 +0200
Subject: [SciPy-Dev] The state of weave.accelerate?
In-Reply-To: <BANLkTikGROdx0SX5+QahgpX2zyF3Megc+g@mail.gmail.com>
References: <BANLkTikGROdx0SX5+QahgpX2zyF3Megc+g@mail.gmail.com>
Message-ID: <BANLkTiks5P-xAxU0MJVB-HvjVXQrres1ZA@mail.gmail.com>

On Sun, Apr 17, 2011 at 3:37 PM, Helio Perroni Filho <xperroni at gmail.com> wrote:
> Dera all,
>
> I have been looking for ways to speed up some portions of Python code
> in my current scipy project. The ideal solution would allow me to keep
> writing all my code in Python 2.7 ? even if the "accelerated" parts
> had to written in a subset of the language, as in PyPy's Restricted
> Python ? and be easily turned off for debugging.
>
> When I learned of scipy.weave.inline, my first thought was "now if
> only there was a Python-to-C++ translator I could hook up to this!" I
> was intrigued when I found that cryptic reference about
> sicpy.weave.accelerate providing "automatic acceleration of Python
> code"; all the more after searching for more information on it, and
> finding none.
>
> So I decided to take a look at the code. The API seemed simple enough
> (just a decorator for top-level functions), so I tried it on some toy
> scripts I keep around. After hacking around a couple simple bugs (two
> incorrect assertions in bytecodecompiler, a typo defining the
> one-argument form of the range function and the need to add weave's
> directory to the compiler include-path in accelerate_tools) I got
> stuck on the many not-yet-implemented instructions in
> bytecodecompiler: it seems even basic arithmetic is still to be
> included.
>
> I find this frustrating. From the tests I've run it seems accelerate()
> already does an adequate work of generating the necessary C++
> boilerplate code, compiling it to an extension and then wiring the
> result back to the executing script. The only thing missing is getting
> the C++ translation to work ? not trivial, I know, but not very hard
> either, considering what's already in place.
>
> Is a lack of manpower holding accelerate() back? If that's the case, I
> volunteer to work on bytecodecompiler, and get it to at least an
> RPython-level of functionality.

Unfortunately all of scipy.weave is not actively developed (only some
basic maintenance the last few years). It is also the only scipy
module that does not (yet?) work with Python 3. It's my impression
that it does its job for legacy code, but for new development people
tend to prefer Cython. Maybe someone who knows more about the weave
history and current state will answer you in more detail.

If you would be willing to work on it that would be great. As you have
already experienced already though, it may be quite some work to fix
the small bugs and modernize the code a bit. I also don't know how the
functionality compares to what's in Shedskin and Nuitka, which are
both (not inline I think) Python to C++ compilers.

> I have read the documentation on the
> Developer Zone, but didn't find how do I create a Trac account. And
> besides that, is there anything else not on that page that I should
> know?

You can create a Trac account at http://projects.scipy.org/scipy/register
Development has moved to git and github, and sending a pull request
there is generally more effective than adding patches in Trac. The
process is described here: http://docs.scipy.org/doc/numpy/dev/

Cheers,
Ralf


From millman at berkeley.edu  Mon Apr 18 21:16:23 2011
From: millman at berkeley.edu (Jarrod Millman)
Date: Mon, 18 Apr 2011 18:16:23 -0700
Subject: [SciPy-Dev] The state of weave.accelerate?
In-Reply-To: <BANLkTikGROdx0SX5+QahgpX2zyF3Megc+g@mail.gmail.com>
References: <BANLkTikGROdx0SX5+QahgpX2zyF3Megc+g@mail.gmail.com>
Message-ID: <BANLkTi=SU=evCperiFF-M8aqwOYFzXsCUA@mail.gmail.com>

Hi,

As Ralf already mentioned, you should probably take a look at Cython:
  http://cython.org/

Cython is very widely used and is improving rapidly.  The Cython
developers added functionality similar to weave.inline last December:
  http://wiki.cython.org/enhancements/inline

There is a nice tutorial for using Cython with NumPy here:
  http://wiki.cython.org/tutorials/numpy

Native support for C++ was added in 0.13:
  http://docs.cython.org/src/userguide/wrapping_CPlusPlus.html

Currently, support for Fortran is provided by fwrap:
  http://fwrap.github.com

You may also be interested in the Cython article in the recent special
issue of CiSE on scientific computing with Python:
http://www.computer.org/portal/web/csdl/abs/mags/cs/2011/02/mcs201102toc.htm

Best,
Jarrod


From zw4131 at gmail.com  Fri Apr 22 13:32:08 2011
From: zw4131 at gmail.com (=?GB2312?B?va20886w?=)
Date: Sat, 23 Apr 2011 01:32:08 +0800
Subject: [SciPy-Dev] I want to do some traslation about the SciPy Reference
	Guide
Message-ID: <BANLkTi=qMBELc5MxWOwzSfR=hPoXV_3rGg@mail.gmail.com>

Hi guys

I am a Chinese postgraduate student in the Australian National University.
And I am using SciPy to develop some machine learning algorithms. But I
found I could not use classes and functions smoothly, because I often
encountered many technical and mathematical words which I could understand
in Chinese but couldn?t in English. So I was often interrupted when I was
thinking, which was quite annoying.

So I guess it is absolutely a major stumbling block for other Chinese
students to use SciPy. You can?t expect them to learn English well as well
as mathematics.

So I want to translate the SciPy Reference Guide into Chinese.

Is it ok? Can you give me some advice or some help?
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From zw4131 at gmail.com  Fri Apr 22 13:38:04 2011
From: zw4131 at gmail.com (=?GB2312?B?va20886w?=)
Date: Sat, 23 Apr 2011 01:38:04 +0800
Subject: [SciPy-Dev] I want to do some translation about the SciPy Reference
	Guide
Message-ID: <BANLkTim0=2vfxpf7hZoCo87bXdgVAPXUAw@mail.gmail.com>

Hi guys
I am a Chinese postgraduate student in the Australian National University.
And I am using SciPy to develop some machine learning algorithms. But I
found I could not use classes and functions smoothly, because I often
encountered many technical and mathematical words which I could understand
in Chinese but couldn?t in English. So I was often interrupted when I was
thinking, which was quite annoying.
So I guess it is absolutely a major stumbling block for other Chinese
students to use SciPy. You can?t expect them to learn English well as well
as mathematics.
So I want to translate the SciPy Reference Guide into Chinese.
Is it ok? Can you give me some advice or some help?
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From zw4131 at gmail.com  Fri Apr 22 17:39:25 2011
From: zw4131 at gmail.com (=?GB2312?B?va20886w?=)
Date: Sat, 23 Apr 2011 05:39:25 +0800
Subject: [SciPy-Dev] possible bug in register
Message-ID: <BANLkTikq8OfwsRnyow4Jk-YYtur3qNEJ2Q@mail.gmail.com>

Dear all


When I tried to registered an new account in the  SciPy dev wiki(
http://projects.scipy.org/scipy/register), the webpage always said incorrect
captcha input but I could not find where the captcha was.

What happened?



cheers

David
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From josef.pktd at gmail.com  Fri Apr 22 18:43:53 2011
From: josef.pktd at gmail.com (josef.pktd at gmail.com)
Date: Fri, 22 Apr 2011 18:43:53 -0400
Subject: [SciPy-Dev] possible bug in register
In-Reply-To: <BANLkTikq8OfwsRnyow4Jk-YYtur3qNEJ2Q@mail.gmail.com>
References: <BANLkTikq8OfwsRnyow4Jk-YYtur3qNEJ2Q@mail.gmail.com>
Message-ID: <BANLkTik=MU2TEcVriPTdTquBbTD=o-i4gg@mail.gmail.com>

2011/4/22 ??? <zw4131 at gmail.com>:
> Dear all
>
>
> When I tried to registered an new account in the  SciPy dev
> wiki(http://projects.scipy.org/scipy/register), the webpage always said
> incorrect captcha input but I could not find where the captcha was.
>
> What happened?

I see the (re)captcha insert just above the "Create account" button.
Maybe your browser filters it out ?

Josef


>
>
>
> cheers
>
> David
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
>


From fabian.pedregosa at inria.fr  Sat Apr 23 03:56:44 2011
From: fabian.pedregosa at inria.fr (Fabian Pedregosa)
Date: Sat, 23 Apr 2011 09:56:44 +0200
Subject: [SciPy-Dev] calc_lwork.f different from Lapack?
In-Reply-To: <1198903824.2028545.1302721868001.JavaMail.root@zmbs3.inria.fr>
References: <1198903824.2028545.1302721868001.JavaMail.root@zmbs3.inria.fr>
Message-ID: <BANLkTi=3ws5BNZ+5yrjO5oDhyqFy7jB1-Q@mail.gmail.com>

On Wed, Apr 13, 2011 at 9:11 PM, Josh Lawrence
<josh.k.lawrence at gmail.com> wrote:
> Hello,
>
> After receiving an error in using linalg.lstsq, I started some
> investigating. I found that scipy/linalg/src/calc_lwork.f is essentially
> a stripped down version of the appropriate functions in Lapack (for
> linalg.lstsq using double precision complex numbers, it is ZGELSS). It
> seems that the portions for gelss in calc_lwork.f do not match the
> current version of lapack. I believe this is the source of my error (it
> doesn't occur if I use linalg.pinv2 for least squares instead). Is there
> a particular rationale for these being different or perhaps an incorrect
> copy and paste? The relevant portions are shown below (a line of %
> characters are prepended before the codes from the two locations).


Hi Josh!

I think we could avoid some of these problems by using the LAPACK
workspace query mechanism instead of calc_lwork. I submitted a patch
for this:

https://github.com/scipy/scipy/pull/13

It would be great if you could comment on it and confirm that it
solves the problem.

Best,

Fabian


From ralf.gommers at googlemail.com  Sat Apr 23 06:04:14 2011
From: ralf.gommers at googlemail.com (Ralf Gommers)
Date: Sat, 23 Apr 2011 12:04:14 +0200
Subject: [SciPy-Dev] I want to do some translation about the SciPy
 Reference Guide
In-Reply-To: <BANLkTim0=2vfxpf7hZoCo87bXdgVAPXUAw@mail.gmail.com>
References: <BANLkTim0=2vfxpf7hZoCo87bXdgVAPXUAw@mail.gmail.com>
Message-ID: <BANLkTim9SzzUyFcVpo+fQg6BuungmN3uMA@mail.gmail.com>

Hi,

On Fri, Apr 22, 2011 at 7:38 PM, ??? <zw4131 at gmail.com> wrote:
> Hi guys
> I am a Chinese postgraduate student in the Australian National University.
> And I am using SciPy to develop some machine learning algorithms. But I
> found I could not use classes and functions smoothly, because I often
> encountered many technical and mathematical words which I could understand
> in Chinese but couldn?t in English. So I was often interrupted when I was
> thinking, which was quite annoying.
> So I guess it is absolutely a major stumbling block for other Chinese
> students to use SciPy. You can?t expect them to learn English well as well
> as mathematics.
> So I want to translate the SciPy Reference Guide into Chinese.
> Is it ok? Can you give me some advice or some help?

It would be great to have more accessible documentation for Chinese
speakers. I would suggest a translation of the first part of the Scipy
Reference Guide, the tutorial
(http://docs.scipy.org/doc/scipy/reference/tutorial/index.html). The
rest of the Reference Guide is autogenerated from docstrings, which I
don't think is feasible to translate for several reasons (no toolchain
support, not maintainable, too much work). We could distribute the
tutorial separately from the rest of the reference guide, this is done
for Numpy too.

You can find the sources for the tutorial under doc/source/tutorial/.
If you think this is the right way to go, it should be easy to jump
in.

Cheers,
Ralf


From charlesr.harris at gmail.com  Sat Apr 23 10:26:02 2011
From: charlesr.harris at gmail.com (Charles R Harris)
Date: Sat, 23 Apr 2011 08:26:02 -0600
Subject: [SciPy-Dev] I want to do some translation about the SciPy
 Reference Guide
In-Reply-To: <BANLkTim9SzzUyFcVpo+fQg6BuungmN3uMA@mail.gmail.com>
References: <BANLkTim0=2vfxpf7hZoCo87bXdgVAPXUAw@mail.gmail.com>
	<BANLkTim9SzzUyFcVpo+fQg6BuungmN3uMA@mail.gmail.com>
Message-ID: <BANLkTi=LTck16+RTNNomOqe078cndr8x-A@mail.gmail.com>

On Sat, Apr 23, 2011 at 4:04 AM, Ralf Gommers
<ralf.gommers at googlemail.com>wrote:

> Hi,
>
> On Fri, Apr 22, 2011 at 7:38 PM, ??? <zw4131 at gmail.com> wrote:
> > Hi guys
> > I am a Chinese postgraduate student in the Australian National
> University.
> > And I am using SciPy to develop some machine learning algorithms. But I
> > found I could not use classes and functions smoothly, because I often
> > encountered many technical and mathematical words which I could
> understand
> > in Chinese but couldn?t in English. So I was often interrupted when I was
> > thinking, which was quite annoying.
> > So I guess it is absolutely a major stumbling block for other Chinese
> > students to use SciPy. You can?t expect them to learn English well as
> well
> > as mathematics.
> > So I want to translate the SciPy Reference Guide into Chinese.
> > Is it ok? Can you give me some advice or some help?
>
> It would be great to have more accessible documentation for Chinese
> speakers. I would suggest a translation of the first part of the Scipy
> Reference Guide, the tutorial
> (http://docs.scipy.org/doc/scipy/reference/tutorial/index.html). The
> rest of the Reference Guide is autogenerated from docstrings, which I
> don't think is feasible to translate for several reasons (no toolchain
> support, not maintainable, too much work). We could distribute the
> tutorial separately from the rest of the reference guide, this is done
> for Numpy too.
>
> You can find the sources for the tutorial under doc/source/tutorial/.
> If you think this is the right way to go, it should be easy to jump
> in.
>
>
Is the documentation copyrighted? If not, should it be?

Chuck
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From ralf.gommers at googlemail.com  Sat Apr 23 14:39:50 2011
From: ralf.gommers at googlemail.com (Ralf Gommers)
Date: Sat, 23 Apr 2011 20:39:50 +0200
Subject: [SciPy-Dev] I want to do some translation about the SciPy
 Reference Guide
In-Reply-To: <BANLkTi=LTck16+RTNNomOqe078cndr8x-A@mail.gmail.com>
References: <BANLkTim0=2vfxpf7hZoCo87bXdgVAPXUAw@mail.gmail.com>
	<BANLkTim9SzzUyFcVpo+fQg6BuungmN3uMA@mail.gmail.com>
	<BANLkTi=LTck16+RTNNomOqe078cndr8x-A@mail.gmail.com>
Message-ID: <BANLkTi=2RuciO4+NV847+XU++04y+gSQkg@mail.gmail.com>

On Sat, Apr 23, 2011 at 4:26 PM, Charles R Harris
<charlesr.harris at gmail.com> wrote:
>
>
> On Sat, Apr 23, 2011 at 4:04 AM, Ralf Gommers <ralf.gommers at googlemail.com>
> wrote:
>>
>> Hi,
>>
>> On Fri, Apr 22, 2011 at 7:38 PM, ??? <zw4131 at gmail.com> wrote:
>> > Hi guys
>> > I am a Chinese postgraduate student in the Australian National
>> > University.
>> > And I am using SciPy to develop some machine learning algorithms. But I
>> > found I could not use classes and functions smoothly, because I often
>> > encountered many technical and mathematical words which I could
>> > understand
>> > in Chinese but couldn?t in English. So I was often interrupted when I
>> > was
>> > thinking, which was quite annoying.
>> > So I guess it is absolutely a major stumbling block for other Chinese
>> > students to use SciPy. You can?t expect them to learn English well as
>> > well
>> > as mathematics.
>> > So I want to translate the SciPy Reference Guide into Chinese.
>> > Is it ok? Can you give me some advice or some help?
>>
>> It would be great to have more accessible documentation for Chinese
>> speakers. I would suggest a translation of the first part of the Scipy
>> Reference Guide, the tutorial
>> (http://docs.scipy.org/doc/scipy/reference/tutorial/index.html). The
>> rest of the Reference Guide is autogenerated from docstrings, which I
>> don't think is feasible to translate for several reasons (no toolchain
>> support, not maintainable, too much work). We could distribute the
>> tutorial separately from the rest of the reference guide, this is done
>> for Numpy too.
>>
>> You can find the sources for the tutorial under doc/source/tutorial/.
>> If you think this is the right way to go, it should be easy to jump
>> in.
>>
>
> Is the documentation copyrighted? If not, should it be?

For the BSD license that's not very clear, at least I can't find a
clear explanation anywhere. Several other license include
documentation explicitly, for example the MIT license starts:
"Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software")".

I'd guess the docs in the source tree are covered by the BSD license, but IANAL.

Ralf


From robert.kern at gmail.com  Sat Apr 23 15:27:24 2011
From: robert.kern at gmail.com (Robert Kern)
Date: Sat, 23 Apr 2011 14:27:24 -0500
Subject: [SciPy-Dev] I want to do some translation about the SciPy
 Reference Guide
In-Reply-To: <BANLkTi=LTck16+RTNNomOqe078cndr8x-A@mail.gmail.com>
References: <BANLkTim0=2vfxpf7hZoCo87bXdgVAPXUAw@mail.gmail.com>
	<BANLkTim9SzzUyFcVpo+fQg6BuungmN3uMA@mail.gmail.com>
	<BANLkTi=LTck16+RTNNomOqe078cndr8x-A@mail.gmail.com>
Message-ID: <BANLkTimCYgmBUMYFVaB0A+WMaTWwaakZqA@mail.gmail.com>

On Sat, Apr 23, 2011 at 09:26, Charles R Harris
<charlesr.harris at gmail.com> wrote:
>
> On Sat, Apr 23, 2011 at 4:04 AM, Ralf Gommers <ralf.gommers at googlemail.com>
> wrote:
>>
>> Hi,
>>
>> On Fri, Apr 22, 2011 at 7:38 PM, ??? <zw4131 at gmail.com> wrote:
>> > Hi guys
>> > I am a Chinese postgraduate student in the Australian National
>> > University.
>> > And I am using SciPy to develop some machine learning algorithms. But I
>> > found I could not use classes and functions smoothly, because I often
>> > encountered many technical and mathematical words which I could
>> > understand
>> > in Chinese but couldn?t in English. So I was often interrupted when I
>> > was
>> > thinking, which was quite annoying.
>> > So I guess it is absolutely a major stumbling block for other Chinese
>> > students to use SciPy. You can?t expect them to learn English well as
>> > well
>> > as mathematics.
>> > So I want to translate the SciPy Reference Guide into Chinese.
>> > Is it ok? Can you give me some advice or some help?
>>
>> It would be great to have more accessible documentation for Chinese
>> speakers. I would suggest a translation of the first part of the Scipy
>> Reference Guide, the tutorial
>> (http://docs.scipy.org/doc/scipy/reference/tutorial/index.html). The
>> rest of the Reference Guide is autogenerated from docstrings, which I
>> don't think is feasible to translate for several reasons (no toolchain
>> support, not maintainable, too much work). We could distribute the
>> tutorial separately from the rest of the reference guide, this is done
>> for Numpy too.
>>
>> You can find the sources for the tutorial under doc/source/tutorial/.
>> If you think this is the right way to go, it should be easy to jump
>> in.
>
> Is the documentation copyrighted? If not, should it be?

Everything is copyrighted, by the Berne Convention. Everything in the
numpy distribution, source code and documentation alike (not least
because most of it is *in* the code), is under the BSD license except
for certain exceptions noted in individual files.

-- 
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


From josef.pktd at gmail.com  Sat Apr 23 15:41:24 2011
From: josef.pktd at gmail.com (josef.pktd at gmail.com)
Date: Sat, 23 Apr 2011 15:41:24 -0400
Subject: [SciPy-Dev] I want to do some translation about the SciPy
 Reference Guide
In-Reply-To: <BANLkTimCYgmBUMYFVaB0A+WMaTWwaakZqA@mail.gmail.com>
References: <BANLkTim0=2vfxpf7hZoCo87bXdgVAPXUAw@mail.gmail.com>
	<BANLkTim9SzzUyFcVpo+fQg6BuungmN3uMA@mail.gmail.com>
	<BANLkTi=LTck16+RTNNomOqe078cndr8x-A@mail.gmail.com>
	<BANLkTimCYgmBUMYFVaB0A+WMaTWwaakZqA@mail.gmail.com>
Message-ID: <BANLkTinWSEf9uSG+Bw6NhZW1svou2n_Osg@mail.gmail.com>

On Sat, Apr 23, 2011 at 3:27 PM, Robert Kern <robert.kern at gmail.com> wrote:
> On Sat, Apr 23, 2011 at 09:26, Charles R Harris
> <charlesr.harris at gmail.com> wrote:
>>
>> On Sat, Apr 23, 2011 at 4:04 AM, Ralf Gommers <ralf.gommers at googlemail.com>
>> wrote:
>>>
>>> Hi,
>>>
>>> On Fri, Apr 22, 2011 at 7:38 PM, ??? <zw4131 at gmail.com> wrote:
>>> > Hi guys
>>> > I am a Chinese postgraduate student in the Australian National
>>> > University.
>>> > And I am using SciPy to develop some machine learning algorithms. But I
>>> > found I could not use classes and functions smoothly, because I often
>>> > encountered many technical and mathematical words which I could
>>> > understand
>>> > in Chinese but couldn?t in English. So I was often interrupted when I
>>> > was
>>> > thinking, which was quite annoying.
>>> > So I guess it is absolutely a major stumbling block for other Chinese
>>> > students to use SciPy. You can?t expect them to learn English well as
>>> > well
>>> > as mathematics.
>>> > So I want to translate the SciPy Reference Guide into Chinese.
>>> > Is it ok? Can you give me some advice or some help?
>>>
>>> It would be great to have more accessible documentation for Chinese
>>> speakers. I would suggest a translation of the first part of the Scipy
>>> Reference Guide, the tutorial
>>> (http://docs.scipy.org/doc/scipy/reference/tutorial/index.html). The
>>> rest of the Reference Guide is autogenerated from docstrings, which I
>>> don't think is feasible to translate for several reasons (no toolchain
>>> support, not maintainable, too much work). We could distribute the
>>> tutorial separately from the rest of the reference guide, this is done
>>> for Numpy too.
>>>
>>> You can find the sources for the tutorial under doc/source/tutorial/.
>>> If you think this is the right way to go, it should be easy to jump
>>> in.
>>
>> Is the documentation copyrighted? If not, should it be?
>
> Everything is copyrighted, by the Berne Convention. Everything in the
> numpy distribution, source code and documentation alike (not least
> because most of it is *in* the code), is under the BSD license except
> for certain exceptions noted in individual files.

To follow Ralf's look at the details of BSD

"Redistribution and use in source and binary forms"  does not include
printed form, nor other processed sphinx docs (html, pdf, ...)

So it's not clear (to me) what usage the BSD license allows for the
documentation, i.e. processed rst files and sphinx docs.

Josef

>
> --
> 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
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>


From robert.kern at gmail.com  Sat Apr 23 15:49:19 2011
From: robert.kern at gmail.com (Robert Kern)
Date: Sat, 23 Apr 2011 14:49:19 -0500
Subject: [SciPy-Dev] I want to do some translation about the SciPy
 Reference Guide
In-Reply-To: <BANLkTinWSEf9uSG+Bw6NhZW1svou2n_Osg@mail.gmail.com>
References: <BANLkTim0=2vfxpf7hZoCo87bXdgVAPXUAw@mail.gmail.com>
	<BANLkTim9SzzUyFcVpo+fQg6BuungmN3uMA@mail.gmail.com>
	<BANLkTi=LTck16+RTNNomOqe078cndr8x-A@mail.gmail.com>
	<BANLkTimCYgmBUMYFVaB0A+WMaTWwaakZqA@mail.gmail.com>
	<BANLkTinWSEf9uSG+Bw6NhZW1svou2n_Osg@mail.gmail.com>
Message-ID: <BANLkTim6iY7kirZt1biTuJtE1zmovU1WQA@mail.gmail.com>

On Sat, Apr 23, 2011 at 14:41,  <josef.pktd at gmail.com> wrote:
> On Sat, Apr 23, 2011 at 3:27 PM, Robert Kern <robert.kern at gmail.com> wrote:
>> On Sat, Apr 23, 2011 at 09:26, Charles R Harris
>> <charlesr.harris at gmail.com> wrote:
>>>
>>> On Sat, Apr 23, 2011 at 4:04 AM, Ralf Gommers <ralf.gommers at googlemail.com>
>>> wrote:
>>>>
>>>> Hi,
>>>>
>>>> On Fri, Apr 22, 2011 at 7:38 PM, ??? <zw4131 at gmail.com> wrote:
>>>> > Hi guys
>>>> > I am a Chinese postgraduate student in the Australian National
>>>> > University.
>>>> > And I am using SciPy to develop some machine learning algorithms. But I
>>>> > found I could not use classes and functions smoothly, because I often
>>>> > encountered many technical and mathematical words which I could
>>>> > understand
>>>> > in Chinese but couldn?t in English. So I was often interrupted when I
>>>> > was
>>>> > thinking, which was quite annoying.
>>>> > So I guess it is absolutely a major stumbling block for other Chinese
>>>> > students to use SciPy. You can?t expect them to learn English well as
>>>> > well
>>>> > as mathematics.
>>>> > So I want to translate the SciPy Reference Guide into Chinese.
>>>> > Is it ok? Can you give me some advice or some help?
>>>>
>>>> It would be great to have more accessible documentation for Chinese
>>>> speakers. I would suggest a translation of the first part of the Scipy
>>>> Reference Guide, the tutorial
>>>> (http://docs.scipy.org/doc/scipy/reference/tutorial/index.html). The
>>>> rest of the Reference Guide is autogenerated from docstrings, which I
>>>> don't think is feasible to translate for several reasons (no toolchain
>>>> support, not maintainable, too much work). We could distribute the
>>>> tutorial separately from the rest of the reference guide, this is done
>>>> for Numpy too.
>>>>
>>>> You can find the sources for the tutorial under doc/source/tutorial/.
>>>> If you think this is the right way to go, it should be easy to jump
>>>> in.
>>>
>>> Is the documentation copyrighted? If not, should it be?
>>
>> Everything is copyrighted, by the Berne Convention. Everything in the
>> numpy distribution, source code and documentation alike (not least
>> because most of it is *in* the code), is under the BSD license except
>> for certain exceptions noted in individual files.
>
> To follow Ralf's look at the details of BSD
>
> "Redistribution and use in source and binary forms" ?does not include
> printed form, nor other processed sphinx docs (html, pdf, ...)

Yes, it does. No, it's not as explicit as it could be, but it does.

-- 
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


From jba at SDF.LONESTAR.ORG  Tue Apr 26 08:40:06 2011
From: jba at SDF.LONESTAR.ORG (Jeffrey Armstrong)
Date: Tue, 26 Apr 2011 12:40:06 +0000 (UTC)
Subject: [SciPy-Dev] Discrete-time additions to scipy.signal
Message-ID: <Pine.NEB.4.64.1104261238080.24144@sdf.lonestar.org>

Hi folks, I've been working on some additions to the scipy.signal module. 
A significant portion of my work involves dealing with linear systems in 
the discrete-time domain, but I found that most of the functionality I 
would need in scipy is implemented only in the continuous domain.  I've 
therefore added some code to handle the discrete time cases.  My fork is 
visible at:

https://github.com/ArmstrongJ/scipy

Additionally, I presented at PyCon 2011, and I briefly discussed a 
discrete algebraic Riccati equation solver I had implemented in Python. 
I've included that code into scipy.signal along with a continuous 
implementation.

I'd appreciate some comments and review of the code.  Everything seems to 
be working for me at this point, but any constructive criticism is greatly 
appreciated.

-Jeff

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


From ralf.gommers at googlemail.com  Tue Apr 26 16:28:54 2011
From: ralf.gommers at googlemail.com (Ralf Gommers)
Date: Tue, 26 Apr 2011 22:28:54 +0200
Subject: [SciPy-Dev] Discrete-time additions to scipy.signal
In-Reply-To: <Pine.NEB.4.64.1104261238080.24144@sdf.lonestar.org>
References: <Pine.NEB.4.64.1104261238080.24144@sdf.lonestar.org>
Message-ID: <BANLkTik3cEjj2Mz3CSS+pLPdQr8vxxO0hQ@mail.gmail.com>

Hi Jeffrey,

On Tue, Apr 26, 2011 at 2:40 PM, Jeffrey Armstrong <jba at sdf.lonestar.org> wrote:
> Hi folks, I've been working on some additions to the scipy.signal module.
> A significant portion of my work involves dealing with linear systems in
> the discrete-time domain, but I found that most of the functionality I
> would need in scipy is implemented only in the continuous domain. ?I've
> therefore added some code to handle the discrete time cases. ?My fork is
> visible at:
>
> https://github.com/ArmstrongJ/scipy
>
> Additionally, I presented at PyCon 2011, and I briefly discussed a
> discrete algebraic Riccati equation solver I had implemented in Python.
> I've included that code into scipy.signal along with a continuous
> implementation.
>
> I'd appreciate some comments and review of the code. ?Everything seems to
> be working for me at this point, but any constructive criticism is greatly
> appreciated.

I looked through your changes and at first glance it looks pretty good
to me. It's not so easy to review however, because it's all in your
master branch, it's a lot of code, and there is quite some code added
that is later deleted again. It would be easier if you would create
separate branches for separate features (not your master branch, keep
that a clean mirror of the numpy master branch). There are at least
two, the discrete versions of features already present for the
continuous domain, and your additions of Riccati, Lyapunov and
Sylvester solvers. Perhaps the sort kw for decomp_schur is a third.

The current names of modules are not very descriptive. They could be
changed to something like:
c2d -> cont2discrete
care+dare -> riccati
lyap+dlyap -> lyapunov
Or maybe put it in a "control" module.

Can you explain the relation to pydare a bit? Is this code all from
pydare and are you relicensing it as BSD and proposing it for
inclusion, or is part of this new code?

Cheers,
Ralf


From jba at SDF.LONESTAR.ORG  Wed Apr 27 07:28:21 2011
From: jba at SDF.LONESTAR.ORG (Jeffrey Armstrong)
Date: Wed, 27 Apr 2011 11:28:21 +0000 (UTC)
Subject: [SciPy-Dev] Discrete-time additions to scipy.signal
In-Reply-To: <BANLkTik3cEjj2Mz3CSS+pLPdQr8vxxO0hQ@mail.gmail.com>
References: <Pine.NEB.4.64.1104261238080.24144@sdf.lonestar.org>
	<BANLkTik3cEjj2Mz3CSS+pLPdQr8vxxO0hQ@mail.gmail.com>
Message-ID: <Pine.NEB.4.64.1104271112500.29054@sdf.lonestar.org>

On Tue, 26 Apr 2011, Ralf Gommers wrote:

> Hi Jeffrey,
>
> I looked through your changes and at first glance it looks pretty good
> to me. It's not so easy to review however, because it's all in your
> master branch, it's a lot of code, and there is quite some code added
> that is later deleted again. It would be easier if you would create
> separate branches for separate features (not your master branch, keep
> that a clean mirror of the numpy master branch). There are at least
> two, the discrete versions of features already present for the
> continuous domain, and your additions of Riccati, Lyapunov and
> Sylvester solvers. Perhaps the sort kw for decomp_schur is a third.

Ralf,

I apologize for the lack of branches.  I must confess that this is my 
first large-scale experience in a git environment so I'm still getting the 
hang of it.  You've summarized the changes pretty well:

1. Duplicating most of the continuous functionality in the discrete domain 
(dltisys.py, c2d.py)

2. Adding Lyapunov and algebraic Riccati equation solvers (lyap.py, 
dlyap.py, dare.py, care.py, decomp_schur.py, trsyl flapack wrapper).

The sort kw in decomp_schur is necessary to properly solve the algebraic 
Riccati equation.

>
> The current names of modules are not very descriptive. They could be
> changed to something like:
> c2d -> cont2discrete
> care+dare -> riccati
> lyap+dlyap -> lyapunov
> Or maybe put it in a "control" module.

The module names could be more descriptive, I agree.  While I think the 
addition of a "control" module in scipy would perhaps be a good idea, I 
didn't have the audacity to make such a suggestion from the start.

>
> Can you explain the relation to pydare a bit? Is this code all from
> pydare and are you relicensing it as BSD and proposing it for
> inclusion, or is part of this new code?
>

The pydare package (http://code.google.com/p/pydare/) is a small package 
providing discrete algebraic Riccati and Lyapunov equation solvers, and I 
am the sole author.  The code was originally licensed under GPLv3 because 
the discrete Lyapunov equation solver utilized code that had been directly 
translated from some Octave code into Python, which was also GPL.  The 
pydare package can also exploit SLICOT, another GPL'd package.

To contribute the code to SciPy, I do indeed relicense the entirety of my 
code as BSD-licensed, and I'll assign copyright or whatever as necessary. 
The GPL-based code in the discrete Lyapunov equation solver has been 
redacted in its entirety, replaced by original code that relies on the 
solution of a Sylvester equation instead (requiring an inversion, which is 
less than ideal).  All references to SLICOT have also been removed, and 
there is not any code present any longer that is not original.

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


From josef.pktd at gmail.com  Wed Apr 27 10:56:43 2011
From: josef.pktd at gmail.com (josef.pktd at gmail.com)
Date: Wed, 27 Apr 2011 10:56:43 -0400
Subject: [SciPy-Dev] replace print by custom Warnings
Message-ID: <BANLkTik5yqEUcEfMudgv5_eRfXGrvNY5Ow@mail.gmail.com>

should scipy get additional custom warnings instead of print statements ?

eg. InterpolationWarning, OptimizationWarning, ....

Josef

---------- Forwarded message ----------
From: Yaroslav Halchenko <debian at onerussian.com>
Date: Wed, Apr 27, 2011 at 10:45 AM
Subject: Re: [pymvpa] minor bug ?
To: pkg-exppsy-pymvpa at lists.alioth.debian.org


On Wed, 27 Apr 2011, josef.pktd at gmail.com wrote:
> You can just temporarily turn off the warnings in the test, if you add
> test for corner cases.
> That's how Ralf silenced the scipy test suite.

and we silence our tests ;-) but apparently not externals checks

> If there are print statements, then it would be a bug in scipy, but
> these look like "Warnings" where you have control over what happens to
> them.

Ha -- poking in my eyes works at times! ?Thanks Josef!

Apparently it is indeed numpy warnings so np.seterr(all="ignore") was
effective!

BUT scipy does use straight printouts of warnings, and that is what made me
believe that it was one of them:


$> dpkg -L python-scipy | grep '\.py' | xargs grep -i "print.*warn" | head
/usr/share/pyshared/scipy/signal/signaltools.py: ? ? ? ?print
"Warning: imaginary part of x ignored."
/usr/share/pyshared/scipy/signal/signaltools.py: ? ? ? ?print
"Warning: imaginary part of x ignored."
/usr/share/pyshared/scipy/signal/filter_design.py: ? ? ? ?print
"Warning, order is zero...check input parametegstop."
/usr/share/pyshared/scipy/interpolate/fitpack.py: ? ? ? ? ? ? ? ?if
quiet<2:print 'Warning: Setting x[%d][%d]=x[%d][0]'%(i,m,i)
/usr/share/pyshared/scipy/interpolate/fitpack.py: ? ? ? ? ? ?print
"Warning: "+_iermess[ier][0]
/usr/share/pyshared/scipy/interpolate/fitpack.py: ? ? ? ? ? ?print
"Warning: "+_iermess[ier][0]
/usr/share/pyshared/scipy/interpolate/fitpack.py: ? ? ? ? ? ?print
"Warning: the number of zeros exceeds mest"
/usr/share/pyshared/scipy/interpolate/fitpack.py: ? ? ? ? ? ?print
"Warning: "+_iermess2[ierm][0]
/usr/share/pyshared/scipy/integrate/quadpack.py: ? ? ? ? ? ?print
"Warning: " + msg
/usr/share/pyshared/scipy/maxentropy/maxentutils.py:# ? ?print
"Warning: could not load the fast FORTRAN library for logsumexp()."


(git)novo:~/proj/scipy[tags/v0.9.0]git
$> git grep -i 'print .*Warning:'
scipy/integrate/quadpack.py: ? ? ? ? ? ?print "Warning: " + msg
scipy/interpolate/fitpack.py: ? ? ? ? ? ? ? ?if quiet<2:print
'Warning: Setting x[%d][%d]=x[%d][0]'%(i,m,i)
scipy/interpolate/fitpack.py: ? ? ? ? ? ?print "Warning: "+_iermess[ier][0]
scipy/interpolate/fitpack.py: ? ? ? ? ? ?print "Warning: "+_iermess[ier][0]
scipy/interpolate/fitpack.py: ? ? ? ? ? ?print "Warning: the number of
zeros exceeds mest"
scipy/interpolate/fitpack.py: ? ? ? ? ? ?print "Warning: "+_iermess2[ierm][0]
scipy/maxentropy/maxentutils.py:# ? ?print "Warning: could not load
the fast FORTRAN library for logsumexp()."
scipy/maxentropy/maxentutils.py: ? ? ? ?print "Warning: OverflowError
using numpy.exp(). Using slower Python"\
scipy/optimize/anneal.py: ? ? ? ? ? ? ? ?print "Warning: Cooled to %f
at %s but this is not" \
scipy/optimize/anneal.py: ? ? ? ? ? ?print "Warning: Maximum number of
iterations exceeded."
scipy/optimize/optimize.py: ? ? ? ? ? ?print "Warning: Maximum number
of function evaluations has "\
scipy/optimize/optimize.py: ? ? ? ? ? ?print "Warning: Maximum number
of iterations has been exceeded"
scipy/optimize/optimize.py: ? ? ? ? ? ?print "Warning: Desired error
not necessarily achieved" \
scipy/optimize/optimize.py: ? ? ? ? ? ?print "Warning: Maximum number
of iterations has been exceeded"
scipy/optimize/optimize.py: ? ? ? ? ? ?print "Warning: Desired error
not necessarily achieved due to precision loss"
scipy/optimize/optimize.py: ? ? ? ? ? ?print "Warning: Maximum number
of iterations has been exceeded"
scipy/optimize/optimize.py: ? ? ? ? ? ?print "Warning: Maximum number
of iterations has been exceeded"
scipy/optimize/optimize.py: ? ? ? ? ? ?print "Warning: Maximum number
of function evaluations has "\
scipy/optimize/optimize.py: ? ? ? ? ? ?print "Warning: Maximum number
of iterations has been exceeded"
scipy/optimize/optimize.py: ? ? ? ? ? ?print "Warning: Final
optimization did not succeed"
scipy/signal/signaltools.py: ? ? ? ?print "Warning: imaginary part of
x ignored."
scipy/signal/signaltools.py: ? ? ? ?print "Warning: imaginary part of
x ignored."
scipy/sparse/linalg/dsolve/umfpack/umfpack.py:
print 'warning: singular matrix'
scipy/sparse/linalg/dsolve/umfpack/umfpack.py:
print 'warning: recomputing symbolic'
scipy/sparse/linalg/dsolve/umfpack/umfpack.py: ? ? ? ? ? ?print
'warning: (almost) singular matrix! '\
scipy/weave/blitz_tools.py: ? ? ? ? ? ?print 'warning: compilation
failed. Executing as python code'
scipy/weave/build_tools.py: ? ? ? ?#print "warning: build directory
was not part of python path."\
scipy/weave/build_tools.py: ? ? ? ?print "warning: specified temp_dir
'%s' does not exist " \
scipy/weave/build_tools.py: ? ? ? ? ? ?print "warning:, neither the
module's directory nor the "\
scipy/weave/build_tools.py: ? ? ? ? ? ?print 'WARNING: failed to build
import library for gcc. Linking will fail.'
scipy/weave/catalog.py: ? ? ? ?print 'warning: default directory is
not write accessible.'
scipy/weave/catalog.py: ? ? ? ?print 'warning: default directory is
not write accessible.'
scipy/weave/catalog.py: ? ? ? ? ? ?print 'warning: unable to repair
catalog entry\n %s\n in\n %s' % \
scipy/weave/swig2_spec.py: ? ? ? ? ? ?print "WARNING: Multiple SWIG
versions detected. ?No version was"



--
=------------------------------------------------------------------=
Keep in touch ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? www.onerussian.com
Yaroslav Halchenko ? ? ? ? ? ? ? ? www.ohloh.net/accounts/yarikoptic

_______________________________________________
Pkg-ExpPsy-PyMVPA mailing list
Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa


From robert.kern at gmail.com  Wed Apr 27 14:05:18 2011
From: robert.kern at gmail.com (Robert Kern)
Date: Wed, 27 Apr 2011 13:05:18 -0500
Subject: [SciPy-Dev] replace print by custom Warnings
In-Reply-To: <BANLkTik5yqEUcEfMudgv5_eRfXGrvNY5Ow@mail.gmail.com>
References: <BANLkTik5yqEUcEfMudgv5_eRfXGrvNY5Ow@mail.gmail.com>
Message-ID: <BANLkTikoKGBswgnfR0Mxk6UcTA=UeGmZHA@mail.gmail.com>

On Wed, Apr 27, 2011 at 09:56,  <josef.pktd at gmail.com> wrote:
> should scipy get additional custom warnings instead of print statements ?
>
> eg. InterpolationWarning, OptimizationWarning, ....

Is that a volunteer I smell?  :-)

Yes, these print statements should become warnings wherever possible.

-- 
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


From gaston.fiore at gmail.com  Wed Apr 27 15:37:38 2011
From: gaston.fiore at gmail.com (Gaston Fiore)
Date: Wed, 27 Apr 2011 15:37:38 -0400
Subject: [SciPy-Dev] Editing NumPy User Guide
Message-ID: <BANLkTik_YRq74nmj2WhBFEgoseWayevj+w@mail.gmail.com>

Hello,

I've just started learning NumPy and I'm reading the Numpy User Guide.
While reading, I've noticed a few minor typos that I'd be happy to
fix. As such, I was wondering whether I could get edit permissions so
I can start slowly contributing to the project.

Thanks,

-Gaston


From pav at iki.fi  Wed Apr 27 16:02:28 2011
From: pav at iki.fi (Pauli Virtanen)
Date: Wed, 27 Apr 2011 20:02:28 +0000 (UTC)
Subject: [SciPy-Dev] Editing NumPy User Guide
References: <BANLkTik_YRq74nmj2WhBFEgoseWayevj+w@mail.gmail.com>
Message-ID: <ip9sok$dmf$1@dough.gmane.org>

Hi,

On Wed, 27 Apr 2011 15:37:38 -0400, Gaston Fiore wrote:
> I've just started learning NumPy and I'm reading the Numpy User Guide.
> While reading, I've noticed a few minor typos that I'd be happy to fix.
> As such, I was wondering whether I could get edit permissions so I can
> start slowly contributing to the project.

Sure, granted.

-- 
Pauli Virtanen



From josef.pktd at gmail.com  Thu Apr 28 14:52:27 2011
From: josef.pktd at gmail.com (josef.pktd at gmail.com)
Date: Thu, 28 Apr 2011 14:52:27 -0400
Subject: [SciPy-Dev] replace print by custom Warnings
In-Reply-To: <BANLkTikoKGBswgnfR0Mxk6UcTA=UeGmZHA@mail.gmail.com>
References: <BANLkTik5yqEUcEfMudgv5_eRfXGrvNY5Ow@mail.gmail.com>
	<BANLkTikoKGBswgnfR0Mxk6UcTA=UeGmZHA@mail.gmail.com>
Message-ID: <BANLkTimwai7gYtPbH-_o2oZ48PGM72hd2A@mail.gmail.com>

On Wed, Apr 27, 2011 at 2:05 PM, Robert Kern <robert.kern at gmail.com> wrote:
> On Wed, Apr 27, 2011 at 09:56, ?<josef.pktd at gmail.com> wrote:
>> should scipy get additional custom warnings instead of print statements ?
>>
>> eg. InterpolationWarning, OptimizationWarning, ....
>
> Is that a volunteer I smell? ?:-)

I'm currently not smelly enough :), but I created
http://projects.scipy.org/scipy/ticket/1428

(
However, after trying for a few hours yesterday, I managed to
authenticate with github so I can push something there.
git(gui) is kind of fun, at least for bugfixes.
)

Josef

>
> Yes, these print statements should become warnings wherever possible.
>
> --
> 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
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>


From ralf.gommers at googlemail.com  Thu Apr 28 17:24:50 2011
From: ralf.gommers at googlemail.com (Ralf Gommers)
Date: Thu, 28 Apr 2011 23:24:50 +0200
Subject: [SciPy-Dev] Discrete-time additions to scipy.signal
In-Reply-To: <Pine.NEB.4.64.1104271112500.29054@sdf.lonestar.org>
References: <Pine.NEB.4.64.1104261238080.24144@sdf.lonestar.org>
	<BANLkTik3cEjj2Mz3CSS+pLPdQr8vxxO0hQ@mail.gmail.com>
	<Pine.NEB.4.64.1104271112500.29054@sdf.lonestar.org>
Message-ID: <BANLkTi=GL6jbdDnbndTtfjQkeGSdReRO3g@mail.gmail.com>

On Wed, Apr 27, 2011 at 1:28 PM, Jeffrey Armstrong <jba at sdf.lonestar.org> wrote:
> On Tue, 26 Apr 2011, Ralf Gommers wrote:
>
>> Hi Jeffrey,
>>
>> I looked through your changes and at first glance it looks pretty good
>> to me. It's not so easy to review however, because it's all in your
>> master branch, it's a lot of code, and there is quite some code added
>> that is later deleted again. It would be easier if you would create
>> separate branches for separate features (not your master branch, keep
>> that a clean mirror of the numpy master branch). There are at least
>> two, the discrete versions of features already present for the
>> continuous domain, and your additions of Riccati, Lyapunov and
>> Sylvester solvers. Perhaps the sort kw for decomp_schur is a third.
>
> Ralf,
>
> I apologize for the lack of branches. ?I must confess that this is my
> first large-scale experience in a git environment so I'm still getting the
> hang of it.

Are you trying to do this? If you need any help let me know (offline perhaps).

>?You've summarized the changes pretty well:
>
> 1. Duplicating most of the continuous functionality in the discrete domain
> (dltisys.py, c2d.py)

> 2. Adding Lyapunov and algebraic Riccati equation solvers (lyap.py,
> dlyap.py, dare.py, care.py, decomp_schur.py, trsyl flapack wrapper).
>
> The sort kw in decomp_schur is necessary to properly solve the algebraic
> Riccati equation.

(1) looks like a good addition, and fits in well in scipy.signal.
(2) could use some discussion, if and where it belongs in scipy. It
looks like these equations are fairly widely used in control theory
(which I don't know all that much about), but they're a bit more
exotic/inaccessible than your average scipy function.

Cheers,
Ralf


>>
>> The current names of modules are not very descriptive. They could be
>> changed to something like:
>> c2d -> cont2discrete
>> care+dare -> riccati
>> lyap+dlyap -> lyapunov
>> Or maybe put it in a "control" module.
>
> The module names could be more descriptive, I agree. ?While I think the
> addition of a "control" module in scipy would perhaps be a good idea, I
> didn't have the audacity to make such a suggestion from the start.
>
>>
>> Can you explain the relation to pydare a bit? Is this code all from
>> pydare and are you relicensing it as BSD and proposing it for
>> inclusion, or is part of this new code?
>>
>
> The pydare package (http://code.google.com/p/pydare/) is a small package
> providing discrete algebraic Riccati and Lyapunov equation solvers, and I
> am the sole author. ?The code was originally licensed under GPLv3 because
> the discrete Lyapunov equation solver utilized code that had been directly
> translated from some Octave code into Python, which was also GPL. ?The
> pydare package can also exploit SLICOT, another GPL'd package.
>
> To contribute the code to SciPy, I do indeed relicense the entirety of my
> code as BSD-licensed, and I'll assign copyright or whatever as necessary.
> The GPL-based code in the discrete Lyapunov equation solver has been
> redacted in its entirety, replaced by original code that relies on the
> solution of a Sylvester equation instead (requiring an inversion, which is
> less than ideal). ?All references to SLICOT have also been removed, and
> there is not any code present any longer that is not original.
>
> Jeff Armstrong - jba at sdf.lonestar.org
> SDF Public Access UNIX System - http://sdf.lonestar.org
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>


From jba at SDF.LONESTAR.ORG  Fri Apr 29 08:39:19 2011
From: jba at SDF.LONESTAR.ORG (Jeffrey Armstrong)
Date: Fri, 29 Apr 2011 12:39:19 +0000 (UTC)
Subject: [SciPy-Dev] Discrete-time additions to scipy.signal
In-Reply-To: <BANLkTi=GL6jbdDnbndTtfjQkeGSdReRO3g@mail.gmail.com>
References: <Pine.NEB.4.64.1104261238080.24144@sdf.lonestar.org>
	<BANLkTik3cEjj2Mz3CSS+pLPdQr8vxxO0hQ@mail.gmail.com>
	<Pine.NEB.4.64.1104271112500.29054@sdf.lonestar.org>
	<BANLkTi=GL6jbdDnbndTtfjQkeGSdReRO3g@mail.gmail.com>
Message-ID: <Pine.NEB.4.64.1104291227170.5418@sdf.lonestar.org>

On Thu, 28 Apr 2011, Ralf Gommers wrote:

> Are you trying to do this? If you need any help let me know (offline perhaps).

I think I've successfully split the changes into two branches:

discrete time additions: 
https://github.com/ArmstrongJ/scipy/tree/discrete-time-signal

Lyapunov and algebraic Riccati solvers: 
https://github.com/ArmstrongJ/scipy/tree/riccati-lyapunov

There could possibly be some minor mess with re-committing __init__.py in 
scipy.signal, but the final product is ok.  Git has taken a bit of time 
to understand.

> (1) looks like a good addition, and fits in well in scipy.signal.

Great!  I'm glad to hear it.

> (2) could use some discussion, if and where it belongs in scipy. It
> looks like these equations are fairly widely used in control theory
> (which I don't know all that much about), but they're a bit more
> exotic/inaccessible than your average scipy function.

A controls module might indeed be a good place for these to live.  Octave 
(and MATLAB for that matter) keeps them in a controls toolbox, but the 
linear system functionality in scipy.signal is also present in these 
toolboxes.  Maybe these solvers along with the scipy.signal functionality 
could provide an interesting place to start on a controls module 
(scipy.control).

I do, however, think that my change introducing the 'sort' keyword to 
scipy.linalg.schur is a valuable addition.  Being able to sort the 
eigenvalues in some manner is quite useful in a number of situations. 
This change is present in my riccati-lyapunov branch.

-Jeff

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


From josef.pktd at gmail.com  Fri Apr 29 09:10:42 2011
From: josef.pktd at gmail.com (josef.pktd at gmail.com)
Date: Fri, 29 Apr 2011 09:10:42 -0400
Subject: [SciPy-Dev] Discrete-time additions to scipy.signal
In-Reply-To: <Pine.NEB.4.64.1104291227170.5418@sdf.lonestar.org>
References: <Pine.NEB.4.64.1104261238080.24144@sdf.lonestar.org>
	<BANLkTik3cEjj2Mz3CSS+pLPdQr8vxxO0hQ@mail.gmail.com>
	<Pine.NEB.4.64.1104271112500.29054@sdf.lonestar.org>
	<BANLkTi=GL6jbdDnbndTtfjQkeGSdReRO3g@mail.gmail.com>
	<Pine.NEB.4.64.1104291227170.5418@sdf.lonestar.org>
Message-ID: <BANLkTim7zmte3NN-nmJ9P6bk++iq5wksmw@mail.gmail.com>

On Fri, Apr 29, 2011 at 8:39 AM, Jeffrey Armstrong <jba at sdf.lonestar.org> wrote:
> On Thu, 28 Apr 2011, Ralf Gommers wrote:
>
>> Are you trying to do this? If you need any help let me know (offline perhaps).
>
> I think I've successfully split the changes into two branches:
>
> discrete time additions:
> https://github.com/ArmstrongJ/scipy/tree/discrete-time-signal
>
> Lyapunov and algebraic Riccati solvers:
> https://github.com/ArmstrongJ/scipy/tree/riccati-lyapunov
>
> There could possibly be some minor mess with re-committing __init__.py in
> scipy.signal, but the final product is ok. ?Git has taken a bit of time
> to understand.
>
>> (1) looks like a good addition, and fits in well in scipy.signal.
>
> Great! ?I'm glad to hear it.
>
>> (2) could use some discussion, if and where it belongs in scipy. It
>> looks like these equations are fairly widely used in control theory
>> (which I don't know all that much about), but they're a bit more
>> exotic/inaccessible than your average scipy function.
>
> A controls module might indeed be a good place for these to live. ?Octave
> (and MATLAB for that matter) keeps them in a controls toolbox, but the
> linear system functionality in scipy.signal is also present in these
> toolboxes. ?Maybe these solvers along with the scipy.signal functionality
> could provide an interesting place to start on a controls module
> (scipy.control).
>
> I do, however, think that my change introducing the 'sort' keyword to
> scipy.linalg.schur is a valuable addition. ?Being able to sort the
> eigenvalues in some manner is quite useful in a number of situations.
> This change is present in my riccati-lyapunov branch.

I browsed the source a bit but haven't tried it.

a few comments:

pep8 : space after comma in function arguments,
class CareSolver:   should subclass object for python 2.4, 2.5 compatibility

Is mixing arrays and matrices a good idea? In general it's confusing.
>From reading the code CareSolver uses matrices, but I didn't see
whether it also uses arrays. The continuous and discrete system should
use the same matrix/array pattern, and as far as I remember ltisys
uses arrays only.


Since this has been a wished for feature on the mailing list for a
long time, it is nice to see a concrete proposal to enhance scipy.

Josef

>
> -Jeff
>
> Jeff Armstrong - jba at sdf.lonestar.org
> SDF Public Access UNIX System - http://sdf.lonestar.org
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>


From thouis at gmail.com  Fri Apr 29 09:45:19 2011
From: thouis at gmail.com (Thouis (Ray) Jones)
Date: Fri, 29 Apr 2011 15:45:19 +0200
Subject: [SciPy-Dev] Possible funding opportunity for numpy and scipy
	development
Message-ID: <BANLkTiniEh_zO6A_S-kT8RGpOA=jHA+3VQ@mail.gmail.com>

(Posted for a friend)

This NSF opportunity just renewed last week and might interest the
NumPy/SciPy community:
NSF Software Infrastructure for Sustained Innovation  (SI2)
http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503489

It sounds like it's not suited for end-user software in a particular
domain but is intended to be more software infrastructure oriented.


From josef.pktd at gmail.com  Sat Apr 30 10:15:45 2011
From: josef.pktd at gmail.com (josef.pktd at gmail.com)
Date: Sat, 30 Apr 2011 10:15:45 -0400
Subject: [SciPy-Dev] replace print by custom Warnings
In-Reply-To: <BANLkTimwai7gYtPbH-_o2oZ48PGM72hd2A@mail.gmail.com>
References: <BANLkTik5yqEUcEfMudgv5_eRfXGrvNY5Ow@mail.gmail.com>
	<BANLkTikoKGBswgnfR0Mxk6UcTA=UeGmZHA@mail.gmail.com>
	<BANLkTimwai7gYtPbH-_o2oZ48PGM72hd2A@mail.gmail.com>
Message-ID: <BANLkTinBCjOpGikissKsXwQqbQCm==cftg@mail.gmail.com>

On Thu, Apr 28, 2011 at 2:52 PM,  <josef.pktd at gmail.com> wrote:
> On Wed, Apr 27, 2011 at 2:05 PM, Robert Kern <robert.kern at gmail.com> wrote:
>> On Wed, Apr 27, 2011 at 09:56, ?<josef.pktd at gmail.com> wrote:
>>> should scipy get additional custom warnings instead of print statements ?
>>>
>>> eg. InterpolationWarning, OptimizationWarning, ....
>>
>> Is that a volunteer I smell? ?:-)
>
> I'm currently not smelly enough :), but I created
> http://projects.scipy.org/scipy/ticket/1428
>
> (
> However, after trying for a few hours yesterday, I managed to
> authenticate with github so I can push something there.
> git(gui) is kind of fun, at least for bugfixes.
> )
>
> Josef
>
>>
>> Yes, these print statements should become warnings wherever possible.

A first attempt, just to get started

https://github.com/josef-pkt/scipy/commit/548a8925c36c2627f0acb8102a835393deeefe26

in optimization, do we drop the disp option for warnings and the
associated prints ? there still remains the final print for success.

Is there a way to set the default warning level for the UserWarning to
"always" ?

Still needs tests, examples that raise the warnings.

(I'm only partially familiar with the internal details of
scipy.optimize, interpolate, ... )

Josef



>>
>> --
>> 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
>> _______________________________________________
>> SciPy-Dev mailing list
>> SciPy-Dev at scipy.org
>> http://mail.scipy.org/mailman/listinfo/scipy-dev
>>
>


From ralf.gommers at googlemail.com  Sat Apr 30 12:13:25 2011
From: ralf.gommers at googlemail.com (Ralf Gommers)
Date: Sat, 30 Apr 2011 18:13:25 +0200
Subject: [SciPy-Dev] Discrete-time additions to scipy.signal
In-Reply-To: <Pine.NEB.4.64.1104291227170.5418@sdf.lonestar.org>
References: <Pine.NEB.4.64.1104261238080.24144@sdf.lonestar.org>
	<BANLkTik3cEjj2Mz3CSS+pLPdQr8vxxO0hQ@mail.gmail.com>
	<Pine.NEB.4.64.1104271112500.29054@sdf.lonestar.org>
	<BANLkTi=GL6jbdDnbndTtfjQkeGSdReRO3g@mail.gmail.com>
	<Pine.NEB.4.64.1104291227170.5418@sdf.lonestar.org>
Message-ID: <BANLkTi=UALnLFhUirsDQ=DDA-A3Oa8K-Tg@mail.gmail.com>

On Fri, Apr 29, 2011 at 2:39 PM, Jeffrey Armstrong <jba at sdf.lonestar.org> wrote:
> On Thu, 28 Apr 2011, Ralf Gommers wrote:
>
>> Are you trying to do this? If you need any help let me know (offline perhaps).
>
> I think I've successfully split the changes into two branches:
>
> discrete time additions:
> https://github.com/ArmstrongJ/scipy/tree/discrete-time-signal
>
> Lyapunov and algebraic Riccati solvers:
> https://github.com/ArmstrongJ/scipy/tree/riccati-lyapunov
>
> There could possibly be some minor mess with re-committing __init__.py in
> scipy.signal, but the final product is ok. ?Git has taken a bit of time
> to understand.

That was a good start. I've taken your discrete-time-signal branch,
and did some more reorganizing to only have a few commits with no
renames and deletions:
https://github.com/rgommers/scipy/tree/armstrong-discrete. I then did
some cleanups of cont2discrete in the last commit, to make the code
cleaner.

Some comments on your code:
- function signatures with *args and **kwargs are usually a bad idea,
it is better to have separate functions or some other way to make
clear what the expected inputs are. (this is why I split up your
cont2discrete function).
- like Josef said, it should conform to PEP8.
- I also agree with him that it's better to not mix arrays and
matrices, and preferably avoid matrices completely.
- the standard numpy/scipy conventions for imports, docstrings etc.
should be followed, like "import numpy as np".  See also
https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt
- the permissions of your test files was wrong, they were executable.
Nose will ignore such files, so your tests were never executed.
- the caps in the test files are a little jarring to read. They can be
lowercase, and moved into the test class. Only the continuous
constants are reused, the discrete ones can be in the actual test
functions where they are used.

In the cont2discrete file, it would also be helpful if you added some
comments (or references) to the least transparent parts. For example,
I can't tell what the like with all the multiple vstack/hstack's is
doing.

I propose you pull my branch of your work and make changes to that.
Later the commits can be rewritten again to keep it easy to review.

Cheers,
Ralf