From cournape at gmail.com  Tue Mar  1 07:44:21 2011
From: cournape at gmail.com (David Cournapeau)
Date: Tue, 1 Mar 2011 21:44:21 +0900
Subject: [SciPy-Dev] Initial support for Harwell Boeing sparse matrix
	format
In-Reply-To: <AANLkTik=7o-JArdspPPbvOAYpCsjVitWoGRpWZE_DkbR@mail.gmail.com>
References: <AANLkTinR8yywcVdwxAw6ZEbFx2coSe-_w-RpH7o0FpEx@mail.gmail.com>
	<ik7rk4$qff$1@dough.gmane.org>
	<AANLkTin3+E7L44C10zcnU3mf8kHXy5P5TwWDRRJBTxJc@mail.gmail.com>
	<AANLkTik=7o-JArdspPPbvOAYpCsjVitWoGRpWZE_DkbR@mail.gmail.com>
Message-ID: <AANLkTikfm7ibn1xA1d2zg_ZiHBHAZPw-MsQn=d235Gxs@mail.gmail.com>

On Sun, Feb 27, 2011 at 10:48 AM, Nathan Bell <wnbell at gmail.com> wrote:
> On Sat, Feb 26, 2011 at 2:37 AM, David Cournapeau <cournape at gmail.com>
> wrote:
>>
>> Indeed. I wonder how we want to export this into scipy.io: I think for
>> file format it actually makes sense to say from scipy.io.format_name
>> import function instead of putting everything into scipy.io, but I
>> don't feel strongly about it either.
>>
>> cheers,
>
> +1
>
> Organizing the routines into
> ? scipy.io.harwell_boeing.*
> ? scipy.io.matrix_market.*
> ? ...
> would be clearer and provide a logical home for high-level and low-level
> APIs.

This is a good idea, I have added the code so that it works as follows:

from scipy.io.hb import read, write

> and obtain a semi-standardized result (e.g. dictionary of name->value pairs,
> where the names can be invented if not specified in the format).

This made me realized: some (yet to be supported) cases of the
HarwellBoeing format may return several matrices. Unfortunately, this
is not very well documented, so I don't think I will add the feature
any time soon.

cheers,

David


From charlesr.harris at gmail.com  Tue Mar  1 11:14:08 2011
From: charlesr.harris at gmail.com (Charles R Harris)
Date: Tue, 1 Mar 2011 09:14:08 -0700
Subject: [SciPy-Dev] Initial support for Harwell Boeing sparse matrix
	format
In-Reply-To: <AANLkTikfm7ibn1xA1d2zg_ZiHBHAZPw-MsQn=d235Gxs@mail.gmail.com>
References: <AANLkTinR8yywcVdwxAw6ZEbFx2coSe-_w-RpH7o0FpEx@mail.gmail.com>
	<ik7rk4$qff$1@dough.gmane.org>
	<AANLkTin3+E7L44C10zcnU3mf8kHXy5P5TwWDRRJBTxJc@mail.gmail.com>
	<AANLkTik=7o-JArdspPPbvOAYpCsjVitWoGRpWZE_DkbR@mail.gmail.com>
	<AANLkTikfm7ibn1xA1d2zg_ZiHBHAZPw-MsQn=d235Gxs@mail.gmail.com>
Message-ID: <AANLkTimd720u9sT7f1RUE0HbKuJRf1nLgp06z_n_0xAj@mail.gmail.com>

On Tue, Mar 1, 2011 at 5:44 AM, David Cournapeau <cournape at gmail.com> wrote:

> On Sun, Feb 27, 2011 at 10:48 AM, Nathan Bell <wnbell at gmail.com> wrote:
> > On Sat, Feb 26, 2011 at 2:37 AM, David Cournapeau <cournape at gmail.com>
> > wrote:
> >>
> >> Indeed. I wonder how we want to export this into scipy.io: I think for
> >> file format it actually makes sense to say from scipy.io.format_name
> >> import function instead of putting everything into scipy.io, but I
> >> don't feel strongly about it either.
> >>
> >> cheers,
> >
> > +1
> >
> > Organizing the routines into
> >   scipy.io.harwell_boeing.*
> >   scipy.io.matrix_market.*
> >   ...
> > would be clearer and provide a logical home for high-level and low-level
> > APIs.
>
> This is a good idea, I have added the code so that it works as follows:
>
> from scipy.io.hb import read, write
>
>
I think harwell_boeing would be a more informative name for the module than
hb. The latter is rather cryptic.

> and obtain a semi-standardized result (e.g. dictionary of name->value
> pairs,
> > where the names can be invented if not specified in the format).
>
> This made me realized: some (yet to be supported) cases of the
> HarwellBoeing format may return several matrices. Unfortunately, this
> is not very well documented, so I don't think I will add the feature
> any time soon.
>
>
Chuck
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From fabian.pedregosa at inria.fr  Wed Mar  2 12:20:41 2011
From: fabian.pedregosa at inria.fr (Fabian Pedregosa)
Date: Wed, 2 Mar 2011 18:20:41 +0100
Subject: [SciPy-Dev] ANN: scikits.learn 0.7
Message-ID: <AANLkTi=BtkF1A_dVRkT+S92_Uq=wx5=bGMPv+bvvnR-Y@mail.gmail.com>

I am pleased to announce the availability of scikits.learn 0.7, a
Python module for machine learning.

Documentation: http://scikit-learn.sourceforge.net

Source code repository: http://github.com/scikit-learn/

Mailing list: https://lists.sourceforge.net/lists/listinfo/scikit-learn-general


Installation
---------

Source packages and precompiled windows binaries can be downloaded
from sourceforge:

    https://sourceforge.net/projects/scikit-learn/files/

or installed through pip:

    pip install -U scikits.learn


Examples
-----------

scikits.learn comes with a full set of ready-to-use examples:

    http://scikit-learn.sourceforge.net/auto_examples/


Changelog
----------

A complete changelog for this release can be found here:

    http://scikit-learn.sourceforge.net/whats_new.html


Benchmarks
----------

The team behind scikits.learn cares about performance, and the
benchmarks we use to fine-tune the software are made public at:

    http://fseoane.net/ml-benchmarks/


Best regards,

    Fabian.


From aman.thakral at gmail.com  Fri Mar  4 11:34:45 2011
From: aman.thakral at gmail.com (Aman Thakral)
Date: Fri, 4 Mar 2011 11:34:45 -0500
Subject: [SciPy-Dev] Comparison of PLS algorithms
Message-ID: <AANLkTinonEqZD0b=zR6RfKDayMg5Z=Fj8NEumwS86rAR@mail.gmail.com>

Hi all,

I've provided a summary of the features between the two PLS libraries
submitted.  Please see the table below:

    *Duchesnay* *Aman*  *Inner Loop* Both NIPALS and CCA NIPALS only  *Mean
Centering* Yes Yes  *Scaling to Unit Variance* Yes Yes  *SVD alternative*
Yes No  *Deflation of Y* Using either X or Y scores X scores Only  *Rotations
(W* matrix)* Both X and Y X only  *Raises exceptions for improper sizing of
input matrices* Yes No  *Provide Statistics (SPE, Hotelling's T)* No
Yes  *Provide
Statistical limits* No Yes  *Provide Variable importance to Projection (VIP)
* No Yes

In terms of performance, they should be same since the equations (for the
parts that are found in both) are identical and both use numpy arrays to do
calculations.  I think the best course of action would be to use Duchesnay's
code for the base, then add the missing parts from my code (statistics,
statistical limits, VIP) to help users in their analysis.  I will also get
some examples together that uses duchesnay's code with some of the
visualization functions to help users get a better understanding of PLS.

Also, I was thinking about incorporating some inline weave for the NIPALS
inner loop to improve the performance.  I haven't used it before, so I'll
have figure out the inner workings of weave first.

Please let me know what you think.

Thanks,
Aman
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From aman.thakral at gmail.com  Fri Mar  4 11:39:27 2011
From: aman.thakral at gmail.com (Aman Thakral)
Date: Fri, 4 Mar 2011 11:39:27 -0500
Subject: [SciPy-Dev] Comparison of PLS algorithms
In-Reply-To: <AANLkTinonEqZD0b=zR6RfKDayMg5Z=Fj8NEumwS86rAR@mail.gmail.com>
References: <AANLkTinonEqZD0b=zR6RfKDayMg5Z=Fj8NEumwS86rAR@mail.gmail.com>
Message-ID: <AANLkTimgbTanwtm9CpecuYv1mBrfUMQAtZaVVn8RoXa1@mail.gmail.com>

Whoops,  just realized, this should have gone to scikits-learn.  My mistake.

Sorry about that,
Aman

On Fri, Mar 4, 2011 at 11:34 AM, Aman Thakral <aman.thakral at gmail.com>wrote:

> Hi all,
>
> I've provided a summary of the features between the two PLS libraries
> submitted.  Please see the table below:
>
>     *Duchesnay* *Aman*  *Inner Loop* Both NIPALS and CCA NIPALS only  *Mean
> Centering* Yes Yes  *Scaling to Unit Variance* Yes Yes  *SVD alternative*
> Yes No  *Deflation of Y* Using either X or Y scores X scores Only  *Rotations
> (W* matrix)* Both X and Y X only  *Raises exceptions for improper sizing
> of input matrices* Yes No  *Provide Statistics (SPE, Hotelling's T)* No
> Yes  *Provide Statistical limits* No Yes  *Provide Variable importance to
> Projection (VIP)
> * No Yes
>
> In terms of performance, they should be same since the equations (for the
> parts that are found in both) are identical and both use numpy arrays to do
> calculations.  I think the best course of action would be to use Duchesnay's
> code for the base, then add the missing parts from my code (statistics,
> statistical limits, VIP) to help users in their analysis.  I will also get
> some examples together that uses duchesnay's code with some of the
> visualization functions to help users get a better understanding of PLS.
>
> Also, I was thinking about incorporating some inline weave for the NIPALS
> inner loop to improve the performance.  I haven't used it before, so I'll
> have figure out the inner workings of weave first.
>
> Please let me know what you think.
>
> Thanks,
> Aman
>
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From P.Schellart at astro.ru.nl  Sat Mar  5 03:32:07 2011
From: P.Schellart at astro.ru.nl (Pim Schellart)
Date: Sat, 5 Mar 2011 09:32:07 +0100
Subject: [SciPy-Dev] Move to git?
Message-ID: <8B60165F-1241-4080-BA0B-F0D10730D2FE@gmail.com>

Hi Everyone,

shortly before the release of version 0.9 it was suggested that SciPy development would move to git for 0.10.
If I look at the developers zone I see NumPy has a git repo but SciPy does not.
Is this still planned to happen soon?
I am now pulling from Ralf's branch but would like to pull from the `official' trunk instead at some point.

Regards,

Pim Schellart

From cournape at gmail.com  Sat Mar  5 05:12:59 2011
From: cournape at gmail.com (David Cournapeau)
Date: Sat, 5 Mar 2011 19:12:59 +0900
Subject: [SciPy-Dev] Move to git?
In-Reply-To: <8B60165F-1241-4080-BA0B-F0D10730D2FE@gmail.com>
References: <8B60165F-1241-4080-BA0B-F0D10730D2FE@gmail.com>
Message-ID: <AANLkTi=GkO3ss9+2szpymJ_R13_PxdRXnVBw-3u2NV_-@mail.gmail.com>

On Sat, Mar 5, 2011 at 5:32 PM, Pim Schellart <P.Schellart at astro.ru.nl> wrote:
> Hi Everyone,
>
> shortly before the release of version 0.9 it was suggested that SciPy development would move to git for 0.10.

I think it was more than a suggestion: it seemed to me that most
developers agreed (or did not say anything).

I think Pauli has already everything to convert the svn to git - I
think we just need to decide on a date to do it, block svn for a
couple of hours and publish the git repo.

cheers,

David


From scopatz at gmail.com  Mon Mar  7 14:45:11 2011
From: scopatz at gmail.com (Anthony Scopatz)
Date: Mon, 7 Mar 2011 19:45:11 +0000
Subject: [SciPy-Dev] Move to git?
In-Reply-To: <AANLkTi=GkO3ss9+2szpymJ_R13_PxdRXnVBw-3u2NV_-@mail.gmail.com>
References: <8B60165F-1241-4080-BA0B-F0D10730D2FE@gmail.com>
	<AANLkTi=GkO3ss9+2szpymJ_R13_PxdRXnVBw-3u2NV_-@mail.gmail.com>
Message-ID: <AANLkTi=Kj+h1Y3Bz_7Ovs8EM=E-+L2kW9zkhRq_r0FE3@mail.gmail.com>

On Sat, Mar 5, 2011 at 10:12 AM, David Cournapeau <cournape at gmail.com>wrote:

> On Sat, Mar 5, 2011 at 5:32 PM, Pim Schellart <P.Schellart at astro.ru.nl>
> wrote:
> > Hi Everyone,
> >
> > shortly before the release of version 0.9 it was suggested that SciPy
> development would move to git for 0.10.
>
> I think it was more than a suggestion: it seemed to me that most
> developers agreed (or did not say anything).
>
> I think Pauli has already everything to convert the svn to git - I
> think we just need to decide on a date to do it, block svn for a
> couple of hours and publish the git repo.
>

Yup, I think this is the situation as well.  As far as picking a date, about
a month ago we talked about setting it for right after 0.9 was released.
 That ship sailed.

Personally, I would have no problem with just saying "tomorrow".  However,
realistically, this sort of thing should happen on a Friday, so that we have
the weekend to recover in case something goes seriously wrong.

Now, given that *this* Friday is PyCon, it will probably have to be Friday
March 18th.  Does anyone have any objections to doing the official transfer
then?  If not, we should announce this date on its own thread today or
tomorrow.  (I'll be happy to do so.)

Be Well
Anthony



>
> cheers,
>
> David
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
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From pav at iki.fi  Mon Mar  7 17:19:17 2011
From: pav at iki.fi (Pauli Virtanen)
Date: Mon, 7 Mar 2011 22:19:17 +0000 (UTC)
Subject: [SciPy-Dev] Move to git!
References: <8B60165F-1241-4080-BA0B-F0D10730D2FE@gmail.com>
	<AANLkTi=GkO3ss9+2szpymJ_R13_PxdRXnVBw-3u2NV_-@mail.gmail.com>
	<AANLkTi=Kj+h1Y3Bz_7Ovs8EM=E-+L2kW9zkhRq_r0FE3@mail.gmail.com>
Message-ID: <il3ll5$j1e$1@dough.gmane.org>

On Mon, 07 Mar 2011 19:45:11 +0000, Anthony Scopatz wrote:
[clip]
> Now, given that *this* Friday is PyCon, it will probably have to be
> Friday March 18th.  Does anyone have any objections to doing the
> official transfer then?  If not, we should announce this date on its own
> thread today or tomorrow.  (I'll be happy to do so.)

I will be away the next week, so 18th does not work out for me.

I don't think it necessarily needs to be Friday -- there's not so much 
commit flow into the SVN at the moment. I'd suggest e.g. next Wednesday, 
9th, or, if later, then on 21st.

Converted and verified repo has been available for testing for some time 
now:

https://github.com/scipy/scipy_svn_test5

	Pauli



From scopatz at gmail.com  Mon Mar  7 17:25:02 2011
From: scopatz at gmail.com (Anthony Scopatz)
Date: Mon, 7 Mar 2011 22:25:02 +0000
Subject: [SciPy-Dev] Move to git!
In-Reply-To: <il3ll5$j1e$1@dough.gmane.org>
References: <8B60165F-1241-4080-BA0B-F0D10730D2FE@gmail.com>
	<AANLkTi=GkO3ss9+2szpymJ_R13_PxdRXnVBw-3u2NV_-@mail.gmail.com>
	<AANLkTi=Kj+h1Y3Bz_7Ovs8EM=E-+L2kW9zkhRq_r0FE3@mail.gmail.com>
	<il3ll5$j1e$1@dough.gmane.org>
Message-ID: <AANLkTimhkTPgLcQ6Yfy3qvDiHfyfUqZTYoEW2Jap__=G@mail.gmail.com>

On Mon, Mar 7, 2011 at 10:19 PM, Pauli Virtanen <pav at iki.fi> wrote:

> On Mon, 07 Mar 2011 19:45:11 +0000, Anthony Scopatz wrote:
> [clip]
> > Now, given that *this* Friday is PyCon, it will probably have to be
> > Friday March 18th.  Does anyone have any objections to doing the
> > official transfer then?  If not, we should announce this date on its own
> > thread today or tomorrow.  (I'll be happy to do so.)
>
> I will be away the next week, so 18th does not work out for me.
>
> I don't think it necessarily needs to be Friday -- there's not so much
> commit flow into the SVN at the moment. I'd suggest e.g. next Wednesday,
> 9th, or, if later, then on 21st.
>

As I said before, the sooner the better for me ;).  If you think Wednesday
the 9th (2 days) is acceptable, then I am OK with this too.

Be Well
Anthony



> Converted and verified repo has been available for testing for some time
> now:
>
> https://github.com/scipy/scipy_svn_test5
>
>        Pauli
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
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From charlesr.harris at gmail.com  Mon Mar  7 17:48:54 2011
From: charlesr.harris at gmail.com (Charles R Harris)
Date: Mon, 7 Mar 2011 15:48:54 -0700
Subject: [SciPy-Dev] Move to git!
In-Reply-To: <AANLkTimhkTPgLcQ6Yfy3qvDiHfyfUqZTYoEW2Jap__=G@mail.gmail.com>
References: <8B60165F-1241-4080-BA0B-F0D10730D2FE@gmail.com>
	<AANLkTi=GkO3ss9+2szpymJ_R13_PxdRXnVBw-3u2NV_-@mail.gmail.com>
	<AANLkTi=Kj+h1Y3Bz_7Ovs8EM=E-+L2kW9zkhRq_r0FE3@mail.gmail.com>
	<il3ll5$j1e$1@dough.gmane.org>
	<AANLkTimhkTPgLcQ6Yfy3qvDiHfyfUqZTYoEW2Jap__=G@mail.gmail.com>
Message-ID: <AANLkTi=JbyoJ1hkc7+pP0xnbVykxrRmEnih4JQoMrr=Y@mail.gmail.com>

On Mon, Mar 7, 2011 at 3:25 PM, Anthony Scopatz <scopatz at gmail.com> wrote:

> On Mon, Mar 7, 2011 at 10:19 PM, Pauli Virtanen <pav at iki.fi> wrote:
>
>> On Mon, 07 Mar 2011 19:45:11 +0000, Anthony Scopatz wrote:
>> [clip]
>> > Now, given that *this* Friday is PyCon, it will probably have to be
>> > Friday March 18th.  Does anyone have any objections to doing the
>> > official transfer then?  If not, we should announce this date on its own
>> > thread today or tomorrow.  (I'll be happy to do so.)
>>
>> I will be away the next week, so 18th does not work out for me.
>>
>> I don't think it necessarily needs to be Friday -- there's not so much
>> commit flow into the SVN at the moment. I'd suggest e.g. next Wednesday,
>> 9th, or, if later, then on 21st.
>>
>
> As I said before, the sooner the better for me ;).  If you think Wednesday
> the 9th (2 days) is acceptable, then I am OK with this too.
>
>
If we wait till May we could do it on Friday the 13'th ;)

Chuck
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From ralf.gommers at googlemail.com  Mon Mar  7 19:48:17 2011
From: ralf.gommers at googlemail.com (Ralf Gommers)
Date: Tue, 8 Mar 2011 08:48:17 +0800
Subject: [SciPy-Dev] Move to git!
In-Reply-To: <AANLkTi=JbyoJ1hkc7+pP0xnbVykxrRmEnih4JQoMrr=Y@mail.gmail.com>
References: <8B60165F-1241-4080-BA0B-F0D10730D2FE@gmail.com>
	<AANLkTi=GkO3ss9+2szpymJ_R13_PxdRXnVBw-3u2NV_-@mail.gmail.com>
	<AANLkTi=Kj+h1Y3Bz_7Ovs8EM=E-+L2kW9zkhRq_r0FE3@mail.gmail.com>
	<il3ll5$j1e$1@dough.gmane.org>
	<AANLkTimhkTPgLcQ6Yfy3qvDiHfyfUqZTYoEW2Jap__=G@mail.gmail.com>
	<AANLkTi=JbyoJ1hkc7+pP0xnbVykxrRmEnih4JQoMrr=Y@mail.gmail.com>
Message-ID: <AANLkTinP6e9fjYwPTEUPgw+XCcUhuKj8xV3GBYOFR6_x@mail.gmail.com>

On Tue, Mar 8, 2011 at 6:48 AM, Charles R Harris
<charlesr.harris at gmail.com> wrote:
>
>
> On Mon, Mar 7, 2011 at 3:25 PM, Anthony Scopatz <scopatz at gmail.com> wrote:
>>
>> On Mon, Mar 7, 2011 at 10:19 PM, Pauli Virtanen <pav at iki.fi> wrote:
>>>
>>> On Mon, 07 Mar 2011 19:45:11 +0000, Anthony Scopatz wrote:
>>> [clip]
>>> > Now, given that *this* Friday is PyCon, it will probably have to be
>>> > Friday March 18th. ?Does anyone have any objections to doing the
>>> > official transfer then? ?If not, we should announce this date on its
>>> > own
>>> > thread today or tomorrow. ?(I'll be happy to do so.)
>>>
>>> I will be away the next week, so 18th does not work out for me.
>>>
>>> I don't think it necessarily needs to be Friday -- there's not so much
>>> commit flow into the SVN at the moment. I'd suggest e.g. next Wednesday,
>>> 9th, or, if later, then on 21st.
>>
>> As I said before, the sooner the better for me ;). ?If you think Wednesday
>> the 9th (2 days) is acceptable, then I am OK with this too.

This Wednesday would be good. And thanks for doing this!

Ralf


From joshua.m.grant at gmail.com  Mon Mar  7 22:18:24 2011
From: joshua.m.grant at gmail.com (Joshua Grant)
Date: Mon, 7 Mar 2011 22:18:24 -0500
Subject: [SciPy-Dev] Hello / New Tester
Message-ID: <AANLkTinLoNGe0Xhun0DMwRJALn+oAVcm3=jpZibtg=sc@mail.gmail.com>

Hi everyone. I'd like to get involved in SciPy, and develop my python
skills. I can start with testing, writing some test cases and unit tests for
end functionality in python. I'm open to suggestions. Thanks!

Josh
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From ralf.gommers at googlemail.com  Mon Mar  7 23:38:48 2011
From: ralf.gommers at googlemail.com (Ralf Gommers)
Date: Tue, 8 Mar 2011 12:38:48 +0800
Subject: [SciPy-Dev] Hello / New Tester
In-Reply-To: <AANLkTinLoNGe0Xhun0DMwRJALn+oAVcm3=jpZibtg=sc@mail.gmail.com>
References: <AANLkTinLoNGe0Xhun0DMwRJALn+oAVcm3=jpZibtg=sc@mail.gmail.com>
Message-ID: <AANLkTinggps16obGU-PbGjLJvmR9FvorhtCNG_-5JL3z@mail.gmail.com>

On Tue, Mar 8, 2011 at 11:18 AM, Joshua Grant <joshua.m.grant at gmail.com> wrote:
> Hi everyone. I'd like to get involved in SciPy, and develop my python
> skills. I can start with testing, writing some test cases and unit tests for
> end functionality in python. I'm open to suggestions. Thanks!

Welcome Josh!

There are some tickets in the bug tracker related to (missing) tests,
that could be a good place to start:
http://projects.scipy.org/scipy/ticket/1027
http://projects.scipy.org/scipy/ticket/873
http://projects.scipy.org/scipy/ticket/913
Test guidelines are at
https://github.com/numpy/numpy/blob/master/doc/TESTS.rst.txt

Improving the docs is also a good way to get familiar with Scipy. We
have a wiki where you can make commits (need to create a username and
ask on this list for edit permissions):
http://docs.scipy.org/scipy/Milestones/
It would be good to read this first: http://docs.scipy.org/numpy/Front%20Page/

For working on tests (or any code) I recommend using git. The scipy
repo will move from svn to https://github.com/scipy/ on Wednesday if
things go as planned; you can already find an svn mirror there if you
want to get started before then (but you'd have to re-clone on Wed I
think).

Cheers,
Ralf


From ralf.gommers at googlemail.com  Mon Mar  7 23:43:32 2011
From: ralf.gommers at googlemail.com (Ralf Gommers)
Date: Tue, 8 Mar 2011 12:43:32 +0800
Subject: [SciPy-Dev] deleting old docs on www.scipy.org
Message-ID: <AANLkTinFDA52oY8oM3i6SsJ=WhfjfQKEUqBNGpLx7J7J@mail.gmail.com>

Hi,

Can someone with the right permissions remove all the very outdated
docs at http://www.scipy.org/doc/? After that #1397 can be closed.

Thanks,
Ralf


From millman at berkeley.edu  Tue Mar  8 09:04:22 2011
From: millman at berkeley.edu (Jarrod Millman)
Date: Tue, 8 Mar 2011 06:04:22 -0800
Subject: [SciPy-Dev] Move to git!
In-Reply-To: <AANLkTinP6e9fjYwPTEUPgw+XCcUhuKj8xV3GBYOFR6_x@mail.gmail.com>
References: <8B60165F-1241-4080-BA0B-F0D10730D2FE@gmail.com>
	<AANLkTi=GkO3ss9+2szpymJ_R13_PxdRXnVBw-3u2NV_-@mail.gmail.com>
	<AANLkTi=Kj+h1Y3Bz_7Ovs8EM=E-+L2kW9zkhRq_r0FE3@mail.gmail.com>
	<il3ll5$j1e$1@dough.gmane.org>
	<AANLkTimhkTPgLcQ6Yfy3qvDiHfyfUqZTYoEW2Jap__=G@mail.gmail.com>
	<AANLkTi=JbyoJ1hkc7+pP0xnbVykxrRmEnih4JQoMrr=Y@mail.gmail.com>
	<AANLkTinP6e9fjYwPTEUPgw+XCcUhuKj8xV3GBYOFR6_x@mail.gmail.com>
Message-ID: <AANLkTik1ZSi4FzjrLRq+TBGx134U8XGAKGpN6_n_mmAx@mail.gmail.com>

Hi Pauli,

+1 for this Wednesday (the sooner, the better). Thanks for taking care of
this.

Jarrod
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From hoytak at stat.washington.edu  Tue Mar  8 16:57:33 2011
From: hoytak at stat.washington.edu (Hoyt Koepke)
Date: Tue, 8 Mar 2011 13:57:33 -0800
Subject: [SciPy-Dev] Numpy special methods and NotImplemented vs. TypeError
Message-ID: <AANLkTinBmHiuZOqj0A+AGuc-A--F2FFSj-fM3AFfO3Ws@mail.gmail.com>

Hello,

I've been working on implementing a matrix-like class of symbolic
objects that have to interact seamlessly with numpy arrays.  It's a
wrapper for CPlex's Concert library, which effectively represents
variables in an optimization problem as symbolic C++ objects that can
be used to build the model.  I'm trying to wrap this to work with
numpy -- I'd be happy to share my code when it's done -- and I'm
running into a few problems.

The main issue I'm working against is that when ndarray's special
methods, e.g. __add__, __gt__, etc. encounter a type they don't
understand, they raise a TypeError instead of a NotImplemented
exception.  This is a problem as the corresponding right-operator
methods (__radd__, __le__) are only called under three conditions
(http://docs.python.org/reference/datamodel.html#object.__radd__)

1. When the left object doesn't implement the left operator.
2. When the left object raises a NotImplemented exception.
3. When the right object is a subclass of the left object.  In this
case, the left operator method is never called.

Consider working with A + X, where A is an ndarray and X is an array
representing my symbolic objects, and let's suppose my matrix class
implements __radd__ sensibly.  Obviously, 1. doesn't apply here.  If I
go with 2., a TypeError is raised, which blows things apart.  So the
only solution I have is 3.

However, it isn't possible for me to use the underlying array
machinery by, for example, keeping a numpy array of python objects,
each wrapping a single symbolic variable.  This is due to space /
speed constraints and the fact that what I'm really doing is wrapping
a given CPlex array class of these symbolic objects.  Thus, if I
subclass ndarray, the underlying array is meaningless -- while I do
implement slicing and various other array-like methods, the only
reason I'm subclassing ndarray is (3).  The big problem with this is
that many of the attributes and methods of ndarray don't make sense
for my class, so I have to basically cover them up by overriding them
with methods that simply raise exceptions.  Doable, but far from
ideal.

So my main question is this:  Is there any reason that ndarrays throw
a TypeError in this case instead of NotImplemented?  It seems like the
latter would be more standards compliant.

Thanks!
--Hoyt


++++++++++++++++++++++++++++++++++++++++++++++++
+ Hoyt Koepke
+ University of Washington Department of Statistics
+ http://www.stat.washington.edu/~hoytak/
+ hoytak at gmail.com
++++++++++++++++++++++++++++++++++++++++++


From ralf.gommers at googlemail.com  Wed Mar  9 00:17:58 2011
From: ralf.gommers at googlemail.com (Ralf Gommers)
Date: Wed, 9 Mar 2011 13:17:58 +0800
Subject: [SciPy-Dev] Question about subpackage/submodule API
In-Reply-To: <AANLkTikQ1htvZwp86cAc_W9gCn_ZTZtwD-78xhb3WZ7T@mail.gmail.com>
References: <AANLkTikpCCDceGDnGK43GhxPgNiicpaH8c3+xPG+f3q9@mail.gmail.com>
	<AANLkTi=C1AjX_JWmgd7EPwZJ8v0_Cw+zDoz6gGR3Yjvv@mail.gmail.com>
	<AANLkTinPyjQTQp26+ekinQ5gz0xm7PMcRG1A-LqdF8Kc@mail.gmail.com>
	<C2872D45-E526-47DB-8216-789114F1C5F7@enthought.com>
	<ij6sm1$pqk$1@dough.gmane.org>
	<AANLkTinLNs1=_B_LUWaZwj3NuWdsRVLumj-SmbT4KkT7@mail.gmail.com>
	<AANLkTimWu0pquyam1QkOFp4Fmwrkj4UusSo7w_hhPPvN@mail.gmail.com>
	<AANLkTikQ1htvZwp86cAc_W9gCn_ZTZtwD-78xhb3WZ7T@mail.gmail.com>
Message-ID: <AANLkTi=WxXK8fJfJvBukVeXTu0mOZzv+C8d7HoeeZEVN@mail.gmail.com>

On Sun, Feb 20, 2011 at 3:33 PM, Ralf Gommers
<ralf.gommers at googlemail.com> wrote:
> On Tue, Feb 15, 2011 at 7:53 AM, Warren Weckesser
> <warren.weckesser at enthought.com> wrote:
>>
>>
>> On Sat, Feb 12, 2011 at 7:28 PM, Ralf Gommers <ralf.gommers at googlemail.com>
>> wrote:
>>>
>>>
>>> On Sun, Feb 13, 2011 at 5:05 AM, Pauli Virtanen <pav at iki.fi> wrote:
>>>>
>>>> One wild idea to make this clearer could be to prefix all internal sub-
>>>> package names with the usual '_'. In the long run, it probably wouldn't
>>>> be as bad as it initially sounds like.
>>>>
>>> This is not a wild idea at all, I think it should be done. I considered
>>> all modules without '_' prefix public API.
>>>
>>
>>
>> Agreed (despite what I said in my initial post).
>>
>> To actually do this, we'll need to check which packages have modules that
>> should be private.? These can be renamed in 0.10 to have an underscore,? and
>> new public versions created that contain a deprecation warning and that
>> import everything from the private version.?? The deprecated public modules
>> can be removed in 0.11.
>>
>> Some modules will require almost no changes.? For example, scipy.cluster
>> *only* exposes two modules, vq and hierarchy, so no changes are needed.
>> (Well, there is also the module info.py that all packages have.? That should
>> become _info.py--there's no need for that to be public, is there?)
>
> Agreed, rename to _info.py

This can't actually be done very easily, because the info.py name is
hardcoded in PackageLoader in numpy._import_tools.py. So if desired,
it first has to be done in numpy.


>> Other packages will probably require some discussion about what modules should be
>> public.
>>
>> Consider the above a proposed change for 0.10 and 0.11--what do you think?
>>
> Sounds good. Attached is a file that goes through scipy sub-packages
> and checks their __all__ for modules. Those are public by definition
> (but this doesn't give you the whole API). It's pretty messy, for
> example:
>
> signal
> ======
> bsplines
> filter_design
> fir_filter_design
> integrate
> interpolate
> linalg
> ltisys
> np
> numpy
> optimize
> scipy
> signaltools
> sigtools
> special
> spline
> types
> warnings
> waveforms
> wavelets
> windows
>
> That should be cleaned up. Then there are also public modules that
> don't show up of course (for example odr.models).
>
> How about doing the following? :
> 1. Start a doc, perhaps on the wiki, with a full list of public modules.
> 2. Put that doc at the beginning of the reference guide, as well as
> the relevant part in the docstring for each sub-package.
> 3. Clean up existing __all__, and add __all__ to sub-packages that
> don't have them yet.
> 4. Rename private modules, with suitable deprecation warning.

I've done the uncontroversial part (3):
https://github.com/rgommers/scipy/tree/refactor-private-modules
This cleans up the sub-package namespaces quite a bit, which will also
make for example tab-completion in IPython easier to use. For example,
sp.signal.<TAB> gives now 147 results instead of 262.

There is one thing I wasn't sure about: should
arccos/arccosh/arcsinh/... stay exposed in the scipy.special
namespace, even though they are numpy functions?

Here is a complete list of modules that I think are part (or should be
part) of the public API. I added modules because they are documented
as being public in docs, or contain useful functions/objects that are
not exposed one level up, or because the sub-package namespace is very
large and could benefit from a subdivision.

cluster
=======
vq
hierarchy

constants
=========

fftpack
=======

integrate
=========
vode

interpolate
===========
dfitpack

io
==
arff
idl
matlab
mmio
netcdf
wavfile

linalg
======
calc_lwork
cblas
clapack
fblas
flapack
flinalg
lapack
special_matrices

maxentropy
==========
<deprecate this module>

misc
====
doccer
pilutil

ndimage
=======
filters
fourier
interpolation
io
measurements
morphology

odr
===
models
odrpack

optimize
========

signal
======
bsplines
filter_design
fir_filter_design
ltisys
spectral
spline
waveforms
wavelets
windows

sparse
======

sparse.linalg
=============
umfpack

spatial
=======
distance

special
=======

stats
=====
distributions
mstats
<add more after refactoring, Josef wants to break up module. I agree
it's too large and slow to import.>

weave
=====
<didn't look at weave yet>


Cheers,
Ralf


From scopatz at gmail.com  Wed Mar  9 13:07:29 2011
From: scopatz at gmail.com (Anthony Scopatz)
Date: Wed, 9 Mar 2011 18:07:29 +0000
Subject: [SciPy-Dev] Move to git!
In-Reply-To: <AANLkTik1ZSi4FzjrLRq+TBGx134U8XGAKGpN6_n_mmAx@mail.gmail.com>
References: <8B60165F-1241-4080-BA0B-F0D10730D2FE@gmail.com>
	<AANLkTi=GkO3ss9+2szpymJ_R13_PxdRXnVBw-3u2NV_-@mail.gmail.com>
	<AANLkTi=Kj+h1Y3Bz_7Ovs8EM=E-+L2kW9zkhRq_r0FE3@mail.gmail.com>
	<il3ll5$j1e$1@dough.gmane.org>
	<AANLkTimhkTPgLcQ6Yfy3qvDiHfyfUqZTYoEW2Jap__=G@mail.gmail.com>
	<AANLkTi=JbyoJ1hkc7+pP0xnbVykxrRmEnih4JQoMrr=Y@mail.gmail.com>
	<AANLkTinP6e9fjYwPTEUPgw+XCcUhuKj8xV3GBYOFR6_x@mail.gmail.com>
	<AANLkTik1ZSi4FzjrLRq+TBGx134U8XGAKGpN6_n_mmAx@mail.gmail.com>
Message-ID: <AANLkTinRDbJO6m4sp8neT85WNi5EqYVo8nqanVBD2HnO@mail.gmail.com>

Hello All,

I just wanted to let everyone know that in a couple of hours here (14:00
CST, 20:00 UTC) that I'll go ahead and make the svn repo read-only, if there
are no objections.  Get in those last minute commits ;).

Be Well
Anthony

On Tue, Mar 8, 2011 at 2:04 PM, Jarrod Millman <millman at berkeley.edu> wrote:

> Hi Pauli,
>
> +1 for this Wednesday (the sooner, the better). Thanks for taking care of
> this.
>
> Jarrod
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
>
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From pav at iki.fi  Wed Mar  9 14:17:46 2011
From: pav at iki.fi (Pauli Virtanen)
Date: Wed, 9 Mar 2011 19:17:46 +0000 (UTC)
Subject: [SciPy-Dev] Git move complete
Message-ID: <il8joq$bsr$1@dough.gmane.org>

Dear all,

The development repository for Scipy from now on resides at

	https://github.com/scipy/scipy

Further development should be based on it. We keep the SVN up, but it is 
read-only starting now.

Let me know if you notice something strange in the converted repo or the 
history. It's pretty unlikely that anything is wrong, though.

    ***

Not all the core developers have push permissions there yet --- so please 
create github accounts (if you don't have them yet), and contact the 
people listed at https://github.com/scipy/ to get them.

All the documentation etc. on the various websites we have isn't yet 
updated, so if you want to give a hand, fix checkout instructions if you 
come across them.

Best,
Pauli



From pav at iki.fi  Wed Mar  9 14:19:48 2011
From: pav at iki.fi (Pauli Virtanen)
Date: Wed, 9 Mar 2011 19:19:48 +0000 (UTC)
Subject: [SciPy-Dev] Move to git!
References: <8B60165F-1241-4080-BA0B-F0D10730D2FE@gmail.com>
	<AANLkTi=GkO3ss9+2szpymJ_R13_PxdRXnVBw-3u2NV_-@mail.gmail.com>
	<AANLkTi=Kj+h1Y3Bz_7Ovs8EM=E-+L2kW9zkhRq_r0FE3@mail.gmail.com>
	<il3ll5$j1e$1@dough.gmane.org>
	<AANLkTimhkTPgLcQ6Yfy3qvDiHfyfUqZTYoEW2Jap__=G@mail.gmail.com>
	<AANLkTi=JbyoJ1hkc7+pP0xnbVykxrRmEnih4JQoMrr=Y@mail.gmail.com>
	<AANLkTinP6e9fjYwPTEUPgw+XCcUhuKj8xV3GBYOFR6_x@mail.gmail.com>
	<AANLkTik1ZSi4FzjrLRq+TBGx134U8XGAKGpN6_n_mmAx@mail.gmail.com>
	<AANLkTinRDbJO6m4sp8neT85WNi5EqYVo8nqanVBD2HnO@mail.gmail.com>
Message-ID: <il8jsj$bsr$2@dough.gmane.org>

On Wed, 09 Mar 2011 18:07:29 +0000, Anthony Scopatz wrote:
> I just wanted to let everyone know that in a couple of hours here (14:00
> CST, 20:00 UTC) that I'll go ahead and make the svn repo read-only, if
> there are no objections.  Get in those last minute commits ;).

The window for commits is closed now, the repo is now read-only.

	Pauli



From scopatz at gmail.com  Wed Mar  9 14:57:29 2011
From: scopatz at gmail.com (Anthony Scopatz)
Date: Wed, 9 Mar 2011 19:57:29 +0000
Subject: [SciPy-Dev] Git move complete
In-Reply-To: <il8joq$bsr$1@dough.gmane.org>
References: <il8joq$bsr$1@dough.gmane.org>
Message-ID: <AANLkTi=2Thpe+dWH=zLpdyAxvZvTb=CCsmXe-1d68ezP@mail.gmail.com>

I believe the quote from Warren was "Wooohooo!"

Thanks a ton Pauli.

Be Well
Anthony

On Wed, Mar 9, 2011 at 7:17 PM, Pauli Virtanen <pav at iki.fi> wrote:

> Dear all,
>
> The development repository for Scipy from now on resides at
>
>        https://github.com/scipy/scipy
>
> Further development should be based on it. We keep the SVN up, but it is
> read-only starting now.
>
> Let me know if you notice something strange in the converted repo or the
> history. It's pretty unlikely that anything is wrong, though.
>
>    ***
>
> Not all the core developers have push permissions there yet --- so please
> create github accounts (if you don't have them yet), and contact the
> people listed at https://github.com/scipy/ to get them.
>
> All the documentation etc. on the various websites we have isn't yet
> updated, so if you want to give a hand, fix checkout instructions if you
> come across them.
>
> Best,
> Pauli
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
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From charlesr.harris at gmail.com  Wed Mar  9 15:04:18 2011
From: charlesr.harris at gmail.com (Charles R Harris)
Date: Wed, 9 Mar 2011 13:04:18 -0700
Subject: [SciPy-Dev] Git move complete
In-Reply-To: <il8joq$bsr$1@dough.gmane.org>
References: <il8joq$bsr$1@dough.gmane.org>
Message-ID: <AANLkTiktc=dX-_aEre_whh3rk5nXS-miyq02o5P52xQ7@mail.gmail.com>

On Wed, Mar 9, 2011 at 12:17 PM, Pauli Virtanen <pav at iki.fi> wrote:

> Dear all,
>
> The development repository for Scipy from now on resides at
>
>        https://github.com/scipy/scipy
>
> Further development should be based on it. We keep the SVN up, but it is
> read-only starting now.
>
> Let me know if you notice something strange in the converted repo or the
> history. It's pretty unlikely that anything is wrong, though.
>
>    ***
>
> Not all the core developers have push permissions there yet --- so please
> create github accounts (if you don't have them yet), and contact the
> people listed at https://github.com/scipy/ to get them.
>
> All the documentation etc. on the various websites we have isn't yet
> updated, so if you want to give a hand, fix checkout instructions if you
> come across them.
>
>
Hi Pauli, could you add charris to the developers list?

Chuck
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From bsouthey at gmail.com  Wed Mar  9 15:12:12 2011
From: bsouthey at gmail.com (Bruce Southey)
Date: Wed, 09 Mar 2011 14:12:12 -0600
Subject: [SciPy-Dev] Git move complete
In-Reply-To: <il8joq$bsr$1@dough.gmane.org>
References: <il8joq$bsr$1@dough.gmane.org>
Message-ID: <4D77DF1C.7090601@gmail.com>

On 03/09/2011 01:17 PM, Pauli Virtanen wrote:
> Dear all,
>
> The development repository for Scipy from now on resides at
>
> 	https://github.com/scipy/scipy
>
> Further development should be based on it. We keep the SVN up, but it is
> read-only starting now.
>
> Let me know if you notice something strange in the converted repo or the
> history. It's pretty unlikely that anything is wrong, though.
>
>      ***
>
> Not all the core developers have push permissions there yet --- so please
> create github accounts (if you don't have them yet), and contact the
> people listed at https://github.com/scipy/ to get them.
>
> All the documentation etc. on the various websites we have isn't yet
> updated, so if you want to give a hand, fix checkout instructions if you
> come across them.
>
> Best,
> Pauli
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
Nice job!
Just to let you know (as expected) that I cloned built and installed the 
new repository. All the tests passed on my Linux system!

Bruce


From vincent at vincentdavis.net  Wed Mar  9 15:18:19 2011
From: vincent at vincentdavis.net (Vincent Davis)
Date: Wed, 9 Mar 2011 13:18:19 -0700
Subject: [SciPy-Dev] Git move complete
In-Reply-To: <4D77DF1C.7090601@gmail.com>
References: <il8joq$bsr$1@dough.gmane.org>
	<4D77DF1C.7090601@gmail.com>
Message-ID: <AANLkTimJ4+nOTyU7is6nHGzxg3_y_35tdd9=1N5h6ULH@mail.gmail.com>

Great!
Vincent

On Wed, Mar 9, 2011 at 1:12 PM, Bruce Southey <bsouthey at gmail.com> wrote:

> On 03/09/2011 01:17 PM, Pauli Virtanen wrote:
> > Dear all,
> >
> > The development repository for Scipy from now on resides at
> >
> >       https://github.com/scipy/scipy
> >
> > Further development should be based on it. We keep the SVN up, but it is
> > read-only starting now.
> >
> > Let me know if you notice something strange in the converted repo or the
> > history. It's pretty unlikely that anything is wrong, though.
> >
> >      ***
> >
> > Not all the core developers have push permissions there yet --- so please
> > create github accounts (if you don't have them yet), and contact the
> > people listed at https://github.com/scipy/ to get them.
> >
> > All the documentation etc. on the various websites we have isn't yet
> > updated, so if you want to give a hand, fix checkout instructions if you
> > come across them.
> >
> > Best,
> > Pauli
> >
> > _______________________________________________
> > SciPy-Dev mailing list
> > SciPy-Dev at scipy.org
> > http://mail.scipy.org/mailman/listinfo/scipy-dev
> Nice job!
> Just to let you know (as expected) that I cloned built and installed the
> new repository. All the tests passed on my Linux system!
>
> Bruce
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>



-- 
Thanks
Vincent Davis
720-301-3003
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From pav at iki.fi  Wed Mar  9 15:24:59 2011
From: pav at iki.fi (Pauli Virtanen)
Date: Wed, 9 Mar 2011 20:24:59 +0000 (UTC)
Subject: [SciPy-Dev] Git move complete
References: <il8joq$bsr$1@dough.gmane.org>
Message-ID: <il8nmr$o60$1@dough.gmane.org>

On Wed, 09 Mar 2011 19:17:46 +0000, Pauli Virtanen wrote:
> The development repository for Scipy from now on resides at
> 
> 	https://github.com/scipy/scipy

Aaagh, and as the first thing I do I push --mirror to it instead of 
pushing to my own fork. Sorry about that.

	Pauli



From joshua.m.grant at gmail.com  Wed Mar  9 16:02:36 2011
From: joshua.m.grant at gmail.com (Joshua Grant)
Date: Wed, 9 Mar 2011 16:02:36 -0500
Subject: [SciPy-Dev] Hello / New Tester
In-Reply-To: <AANLkTinggps16obGU-PbGjLJvmR9FvorhtCNG_-5JL3z@mail.gmail.com>
References: <AANLkTinLoNGe0Xhun0DMwRJALn+oAVcm3=jpZibtg=sc@mail.gmail.com>
	<AANLkTinggps16obGU-PbGjLJvmR9FvorhtCNG_-5JL3z@mail.gmail.com>
Message-ID: <AANLkTi=kLBSUkptCHRQyoD5wqseiz5_t5vbBW9C835XY@mail.gmail.com>

Thanks for the information. I'll probably start right away by
adding/improving some tests, right after I get git all set up.

Josh

On Mon, Mar 7, 2011 at 11:38 PM, Ralf Gommers
<ralf.gommers at googlemail.com>wrote:

> On Tue, Mar 8, 2011 at 11:18 AM, Joshua Grant <joshua.m.grant at gmail.com>
> wrote:
> > Hi everyone. I'd like to get involved in SciPy, and develop my python
> > skills. I can start with testing, writing some test cases and unit tests
> for
> > end functionality in python. I'm open to suggestions. Thanks!
>
> Welcome Josh!
>
> There are some tickets in the bug tracker related to (missing) tests,
> that could be a good place to start:
> http://projects.scipy.org/scipy/ticket/1027
> http://projects.scipy.org/scipy/ticket/873
> http://projects.scipy.org/scipy/ticket/913
> Test guidelines are at
> https://github.com/numpy/numpy/blob/master/doc/TESTS.rst.txt
>
> Improving the docs is also a good way to get familiar with Scipy. We
> have a wiki where you can make commits (need to create a username and
> ask on this list for edit permissions):
> http://docs.scipy.org/scipy/Milestones/
> It would be good to read this first:
> http://docs.scipy.org/numpy/Front%20Page/
>
> For working on tests (or any code) I recommend using git. The scipy
> repo will move from svn to https://github.com/scipy/ on Wednesday if
> things go as planned; you can already find an svn mirror there if you
> want to get started before then (but you'd have to re-clone on Wed I
> think).
>
> Cheers,
> Ralf
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
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From charlesr.harris at gmail.com  Wed Mar  9 16:28:21 2011
From: charlesr.harris at gmail.com (Charles R Harris)
Date: Wed, 9 Mar 2011 14:28:21 -0700
Subject: [SciPy-Dev] Git move complete
In-Reply-To: <il8nmr$o60$1@dough.gmane.org>
References: <il8joq$bsr$1@dough.gmane.org>
	<il8nmr$o60$1@dough.gmane.org>
Message-ID: <AANLkTimwyyMKPtcF6uiX47576jM20Krqc4EN2ozdVXZG@mail.gmail.com>

On Wed, Mar 9, 2011 at 1:24 PM, Pauli Virtanen <pav at iki.fi> wrote:

> On Wed, 09 Mar 2011 19:17:46 +0000, Pauli Virtanen wrote:
> > The development repository for Scipy from now on resides at
> >
> >       https://github.com/scipy/scipy
>
> Aaagh, and as the first thing I do I push --mirror to it instead of
> pushing to my own fork. Sorry about that.
>
>
;) And thanks for adding me to the developers list.

Chuck
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From warren.weckesser at enthought.com  Wed Mar  9 17:02:54 2011
From: warren.weckesser at enthought.com (Warren Weckesser)
Date: Wed, 9 Mar 2011 16:02:54 -0600
Subject: [SciPy-Dev] My first steps with the github workflow -- ticket #1328
Message-ID: <AANLkTi=6U9bdNnwH_gb8C+8E1ufWWFexTbGSdqN0GBVn@mail.gmail.com>

As a test of my understanding of the github workflow, I put a possible fix
for ticket #1328 (http://projects.scipy.org/scipy/ticket/1328) here:

    https://github.com/WarrenWeckesser/scipy/tree/ticket1328

Comments welcome.

Warren
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From josef.pktd at gmail.com  Wed Mar  9 18:34:56 2011
From: josef.pktd at gmail.com (josef.pktd at gmail.com)
Date: Wed, 9 Mar 2011 18:34:56 -0500
Subject: [SciPy-Dev] My first steps with the github workflow -- ticket
	#1328
In-Reply-To: <AANLkTi=6U9bdNnwH_gb8C+8E1ufWWFexTbGSdqN0GBVn@mail.gmail.com>
References: <AANLkTi=6U9bdNnwH_gb8C+8E1ufWWFexTbGSdqN0GBVn@mail.gmail.com>
Message-ID: <AANLkTikONzUoScJtTCPcW-405iX6+P=auYzxLa=D-sPk@mail.gmail.com>

On Wed, Mar 9, 2011 at 5:02 PM, Warren Weckesser
<warren.weckesser at enthought.com> wrote:
> As a test of my understanding of the github workflow, I put a possible fix
> for ticket #1328 (http://projects.scipy.org/scipy/ticket/1328) here:
>
> ??? https://github.com/WarrenWeckesser/scipy/tree/ticket1328
>
> Comments welcome.

I don`t have access to my scipy.org password nor to python right now,
so just a question here

Is there a reason why these functions are not vectorized?
>From the changes it looks like they could also easily take a 2d array
and calculate row- or column-wise distances instead of being raveled.

Josef


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


From warren.weckesser at enthought.com  Wed Mar  9 18:57:00 2011
From: warren.weckesser at enthought.com (Warren Weckesser)
Date: Wed, 9 Mar 2011 17:57:00 -0600
Subject: [SciPy-Dev] My first steps with the github workflow -- ticket
	#1328
In-Reply-To: <AANLkTikONzUoScJtTCPcW-405iX6+P=auYzxLa=D-sPk@mail.gmail.com>
References: <AANLkTi=6U9bdNnwH_gb8C+8E1ufWWFexTbGSdqN0GBVn@mail.gmail.com>
	<AANLkTikONzUoScJtTCPcW-405iX6+P=auYzxLa=D-sPk@mail.gmail.com>
Message-ID: <AANLkTinWNFNkmU6NTXH==xr5wpgj9AkFvWFHcB7hR9Ae@mail.gmail.com>

On Wed, Mar 9, 2011 at 5:34 PM, <josef.pktd at gmail.com> wrote:

> On Wed, Mar 9, 2011 at 5:02 PM, Warren Weckesser
> <warren.weckesser at enthought.com> wrote:
> > As a test of my understanding of the github workflow, I put a possible
> fix
> > for ticket #1328 (http://projects.scipy.org/scipy/ticket/1328) here:
> >
> >     https://github.com/WarrenWeckesser/scipy/tree/ticket1328
> >
> > Comments welcome.
>
> I don`t have access to my scipy.org password nor to python right now,
> so just a question here
>
> Is there a reason why these functions are not vectorized?
>


You'd have to ask the original author--Damian Eads, I think.



> >From the changes it looks like they could also easily take a 2d array
> and calculate row- or column-wise distances instead of being raveled.
>
>

Sure, that's possible.  There could even be an n-d generalization that uses
broadcasting and takes an 'axis' keyword.  Patches--err, github
branches--welcome. :)

That does remind me that if we keep the 'ravel' version, I need to update
the docstrings to explain that.

Warren




> Josef
>
>
> >
> > Warren
> >
> >
> >
> > _______________________________________________
> > 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
>
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From millman at berkeley.edu  Thu Mar 10 15:34:11 2011
From: millman at berkeley.edu (Jarrod Millman)
Date: Thu, 10 Mar 2011 12:34:11 -0800
Subject: [SciPy-Dev] Git move complete
In-Reply-To: <il8joq$bsr$1@dough.gmane.org>
References: <il8joq$bsr$1@dough.gmane.org>
Message-ID: <AANLkTiktwDY-sUOO5HXUDGB7uJ2+NaNbc8k9Y6twPf=i@mail.gmail.com>

On Wed, Mar 9, 2011 at 11:17 AM, Pauli Virtanen wrote:

> The development repository for Scipy from now on resides at
>        https://github.com/scipy/scipy
>

Excellent!  Thanks for taking care of this.
Jarrod
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From warren.weckesser at enthought.com  Thu Mar 10 22:55:02 2011
From: warren.weckesser at enthought.com (Warren Weckesser)
Date: Thu, 10 Mar 2011 21:55:02 -0600
Subject: [SciPy-Dev] Follow revision history back past 2007
Message-ID: <AANLkTi=Y76=n3HF61ezHqtHEacbVAao1QhzSyX8RJ0WC@mail.gmail.com>

On github, how can I follow the history of commits back past the following?

    https://github.com/scipy/scipy/commits/master/scipy/signal?page=6

or


https://github.com/scipy/scipy/commits/c4bdd24a3de2ac9b5fe612bfdbc17e613adbbffa/scipy/signal/filter_design.py

Using the "history" button on github, the history of files or modules seems
to end with a renaming that took place in 2007.  How do I see older commits?

Warren
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From pav at iki.fi  Fri Mar 11 04:46:21 2011
From: pav at iki.fi (Pauli Virtanen)
Date: Fri, 11 Mar 2011 09:46:21 +0000 (UTC)
Subject: [SciPy-Dev] Follow revision history back past 2007
References: <AANLkTi=Y76=n3HF61ezHqtHEacbVAao1QhzSyX8RJ0WC@mail.gmail.com>
Message-ID: <ilcr1d$nrl$1@dough.gmane.org>

Thu, 10 Mar 2011 21:55:02 -0600, Warren Weckesser wrote:
[clip]
> Using the "history" button on github, the history of files or modules
> seems to end with a renaming that took place in 2007.  How do I see
> older commits?

Interesting, this should work:

	git log -M -C filename

but apparently also that fails to follow the history of an individual 
file beyond 2007. However,

	git show -M -C 2224a4b9f2

shows that the rename commit is correctly detected. Similarly, this works:

	git blame -M -C filename

and it correctly shows where each line came from, also pre-2007.

    ***

It seems to me that this is a logic problem in how renames are displayed 
in git-log. The rename detection algorithm itself seems to work (as 
evidenced by git-blame), but something is wrong with how git-log displays 
the results.

This might be worth raising on the Git mailing list.

Our repository data does not need to be changed -- it's correct. This is 
an issue that can be only fixed in Git itself.

	Pauli



From pav at iki.fi  Fri Mar 11 04:47:58 2011
From: pav at iki.fi (Pauli Virtanen)
Date: Fri, 11 Mar 2011 09:47:58 +0000 (UTC)
Subject: [SciPy-Dev] Follow revision history back past 2007
References: <AANLkTi=Y76=n3HF61ezHqtHEacbVAao1QhzSyX8RJ0WC@mail.gmail.com>
	<ilcr1d$nrl$1@dough.gmane.org>
Message-ID: <ilcr4e$nrl$2@dough.gmane.org>

Fri, 11 Mar 2011 09:46:21 +0000, Pauli Virtanen wrote:

> Thu, 10 Mar 2011 21:55:02 -0600, Warren Weckesser wrote: [clip]
>> Using the "history" button on github, the history of files or modules
>> seems to end with a renaming that took place in 2007.  How do I see
>> older commits?
> 
> Interesting, this should work:
> 
> 	git log -M -C filename

Ah crap. On the man page it says to use

	git log --follow filename

and this does work as expected.

Github probably doesn't do this -- one can maybe ask their support 
section if this would be feasible for them to add.

	Pauli



From warren.weckesser at enthought.com  Fri Mar 11 14:56:07 2011
From: warren.weckesser at enthought.com (Warren Weckesser)
Date: Fri, 11 Mar 2011 13:56:07 -0600
Subject: [SciPy-Dev] Follow revision history back past 2007
In-Reply-To: <ilcr4e$nrl$2@dough.gmane.org>
References: <AANLkTi=Y76=n3HF61ezHqtHEacbVAao1QhzSyX8RJ0WC@mail.gmail.com>
	<ilcr1d$nrl$1@dough.gmane.org> <ilcr4e$nrl$2@dough.gmane.org>
Message-ID: <AANLkTi=6K4OOR_qpq2ZwXT1sdosHi7i6YacbA-wXKM2L@mail.gmail.com>

On Fri, Mar 11, 2011 at 3:47 AM, Pauli Virtanen <pav at iki.fi> wrote:

> Fri, 11 Mar 2011 09:46:21 +0000, Pauli Virtanen wrote:
>
> > Thu, 10 Mar 2011 21:55:02 -0600, Warren Weckesser wrote: [clip]
> >> Using the "history" button on github, the history of files or modules
> >> seems to end with a renaming that took place in 2007.  How do I see
> >> older commits?
> >
> > Interesting, this should work:
> >
> >       git log -M -C filename
>
> Ah crap. On the man page it says to use
>
>        git log --follow filename
>
> and this does work as expected.
>


Thanks, Pauli.

Warren



>
> Github probably doesn't do this -- one can maybe ask their support
> section if this would be feasible for them to add.
>
>        Pauli
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
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From millman at berkeley.edu  Sun Mar 13 00:22:09 2011
From: millman at berkeley.edu (Jarrod Millman)
Date: Sat, 12 Mar 2011 21:22:09 -0800
Subject: [SciPy-Dev] Call for GSoC 2011 SciPy mentors
Message-ID: <AANLkTimWorS2U9LzJ1cDEdOx3JPHHGoYhK1rjvkfC+t1@mail.gmail.com>

Hi,

It is time to start preparing for the 2011 Google Summer of Code
(SoC).  As in the past, we will participate in SoC with the Python
Software Foundation (PSF) as our mentoring organization.  The PSF has
requested that every project, which wishes to participate in the SoC,
provide a list of at least *three* potential mentors.

If you are interested and willing to potentially mentor someone this
summer to work on SciPy, please send me the following information by
Monday evening: Name, Email, Phone, Link_ID, and whether you want to
mentor a NumPy or SciPy project.

You can find additional information on the 2011 SoC homepage:
  http://socghop.appspot.com/

Here is the PSF SoC page:
  http://wiki.python.org/moin/SummerOfCode

Please start thinking about potential projects and add them to the SoC
ideas page:
  http://projects.scipy.org/scipy/wiki/SummerofCodeIdeas

Thanks,
Jarrod


From tmp50 at ukr.net  Sun Mar 13 01:58:20 2011
From: tmp50 at ukr.net (Dmitrey)
Date: Sun, 13 Mar 2011 08:58:20 +0200
Subject: [SciPy-Dev] [SciPy-User] Call for GSoC 2011 SciPy mentors
In-Reply-To: <AANLkTimWorS2U9LzJ1cDEdOx3JPHHGoYhK1rjvkfC+t1@mail.gmail.com>
References: <AANLkTimWorS2U9LzJ1cDEdOx3JPHHGoYhK1rjvkfC+t1@mail.gmail.com>
Message-ID: <E1PyfFs-0003pQ-1c@ffe10.ukr.net>

          Hi,
     
     It is time to start preparing for the 2011 Google Summer of Code
     (SoC).  As in the past, we will participate in SoC with the Python
     Software Foundation (PSF) as our mentoring organization.  The PSF has
     requested that every project, which wishes to participate in the SoC,
     provide a list of at least *three* potential mentors.
     
     If you are interested and willing to potentially mentor someone this
     summer to work on SciPy, please send me the following information by
     Monday evening: Name, Email, Phone, Link_ID, and whether you want to
     mentor a NumPy or SciPy project.
     
     You can find additional information on the 2011 SoC homepage:
       

     http://socghop.appspot.com/     
     Here is the PSF SoC page:
            http://wiki.python.org/moin/SummerOfCode     
     Please start thinking about potential projects and add them to the SoC
     ideas page:
            http://projects.scipy.org/scipy/wiki/SummerofCodeIdeas     
        

   That page leads to year 2010 and seems to be read-only. I would
   suggest linking numpy with ACML and make result available from
   easy_install and Linux ap-get / yum. Lots of info about linking ACML
   with CBLAS had been published in internet (e.g.
   http://forums.amd.com/forum/messageview.cfm?catid=217&threadid=89362&enterthread=y),
   but somehow the task (I would declare as highest-priority for numpy)
   is not done yet.
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From warren.weckesser at enthought.com  Mon Mar 14 22:35:54 2011
From: warren.weckesser at enthought.com (Warren Weckesser)
Date: Mon, 14 Mar 2011 21:35:54 -0500
Subject: [SciPy-Dev] git workflow for scipy?
Message-ID: <AANLkTik7v6HEPfteXGeO-iVN0H5OAr8mzOH+LQyb5rAK@mail.gmail.com>

Is there a "gitwash" document set up for scipy?  I'm trying to apply the
workflow outlined for nipy here:


http://nipy.sourceforge.net/nipy/stable/devel/guidelines/gitwash/development_workflow.html

At the moment, I'm updating my master branch.  Here's a transcript:

none:scipy warren$ git branch -a
  master
* ticket1328
  remotes/origin/HEAD -> origin/master
  remotes/origin/maintenance/0.5.2.x
  remotes/origin/maintenance/0.6.x
  remotes/origin/maintenance/0.7.x
  remotes/origin/maintenance/0.8.x
  remotes/origin/maintenance/0.9.x
  remotes/origin/master
  remotes/origin/ticket1328
none:scipy warren$ git checkout master
Switched to branch 'master'
none:scipy warren$ git fetch upstream
remote: Counting objects: 76, done.
remote: Compressing objects: 100% (48/48), done.
remote: Total 48 (delta 40), reused 0 (delta 0)
Unpacking objects: 100% (48/48), done.
>From git://github.com/scipy/scipy
 * [new branch]      maintenance/0.5.2.x -> upstream/maintenance/0.5.2.x
 * [new branch]      maintenance/0.6.x -> upstream/maintenance/0.6.x
 * [new branch]      maintenance/0.7.x -> upstream/maintenance/0.7.x
 * [new branch]      maintenance/0.8.x -> upstream/maintenance/0.8.x
 * [new branch]      maintenance/0.9.x -> upstream/maintenance/0.9.x
 * [new branch]      master     -> upstream/master
none:scipy warren$ git merge upsteam/master
fatal: 'upsteam/master' does not point to a commit

So that last command did not work.  Where did I go wrong?

Warren
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From ralf.gommers at googlemail.com  Mon Mar 14 22:49:48 2011
From: ralf.gommers at googlemail.com (Ralf Gommers)
Date: Tue, 15 Mar 2011 10:49:48 +0800
Subject: [SciPy-Dev] git workflow for scipy?
In-Reply-To: <AANLkTik7v6HEPfteXGeO-iVN0H5OAr8mzOH+LQyb5rAK@mail.gmail.com>
References: <AANLkTik7v6HEPfteXGeO-iVN0H5OAr8mzOH+LQyb5rAK@mail.gmail.com>
Message-ID: <AANLkTimYweWKO97Mqxbmfnsx9MgMUCsoiHvcutR7_AXf@mail.gmail.com>

On Tue, Mar 15, 2011 at 10:35 AM, Warren Weckesser
<warren.weckesser at enthought.com> wrote:
> Is there a "gitwash" document set up for scipy?

http://docs.scipy.org/doc/numpy/dev/
Should be pretty much the same for numpy and scipy.

> I'm trying to apply the
> workflow outlined for nipy here:
>
>
> http://nipy.sourceforge.net/nipy/stable/devel/guidelines/gitwash/development_workflow.html
>
> At the moment, I'm updating my master branch.? Here's a transcript:
>
> none:scipy warren$ git branch -a
> ? master
> * ticket1328
> ? remotes/origin/HEAD -> origin/master
> ? remotes/origin/maintenance/0.5.2.x
> ? remotes/origin/maintenance/0.6.x
> ? remotes/origin/maintenance/0.7.x
> ? remotes/origin/maintenance/0.8.x
> ? remotes/origin/maintenance/0.9.x
> ? remotes/origin/master
> ? remotes/origin/ticket1328
> none:scipy warren$ git checkout master
> Switched to branch 'master'
> none:scipy warren$ git fetch upstream
> remote: Counting objects: 76, done.
> remote: Compressing objects: 100% (48/48), done.
> remote: Total 48 (delta 40), reused 0 (delta 0)
> Unpacking objects: 100% (48/48), done.
> From git://github.com/scipy/scipy
> ?* [new branch]????? maintenance/0.5.2.x -> upstream/maintenance/0.5.2.x
> ?* [new branch]????? maintenance/0.6.x -> upstream/maintenance/0.6.x
> ?* [new branch]????? maintenance/0.7.x -> upstream/maintenance/0.7.x
> ?* [new branch]????? maintenance/0.8.x -> upstream/maintenance/0.8.x
> ?* [new branch]????? maintenance/0.9.x -> upstream/maintenance/0.9.x
> ?* [new branch]????? master???? -> upstream/master
> none:scipy warren$ git merge upsteam/master
> fatal: 'upsteam/master' does not point to a commit
>
> So that last command did not work.? Where did I go wrong?

You spelled upstream as upsteam.

Cheers,
Ralf


From warren.weckesser at enthought.com  Mon Mar 14 22:55:01 2011
From: warren.weckesser at enthought.com (Warren Weckesser)
Date: Mon, 14 Mar 2011 21:55:01 -0500
Subject: [SciPy-Dev] git workflow for scipy?
In-Reply-To: <AANLkTimYweWKO97Mqxbmfnsx9MgMUCsoiHvcutR7_AXf@mail.gmail.com>
References: <AANLkTik7v6HEPfteXGeO-iVN0H5OAr8mzOH+LQyb5rAK@mail.gmail.com>
	<AANLkTimYweWKO97Mqxbmfnsx9MgMUCsoiHvcutR7_AXf@mail.gmail.com>
Message-ID: <AANLkTimmiXYVrV+gnu8+gJqG6y=4naecfAT3SknnsoNA@mail.gmail.com>

On Mon, Mar 14, 2011 at 9:49 PM, Ralf Gommers
<ralf.gommers at googlemail.com>wrote:

> On Tue, Mar 15, 2011 at 10:35 AM, Warren Weckesser
> <warren.weckesser at enthought.com> wrote:
> > Is there a "gitwash" document set up for scipy?
>
> http://docs.scipy.org/doc/numpy/dev/
> Should be pretty much the same for numpy and scipy.
>
> > I'm trying to apply the
> > workflow outlined for nipy here:
> >
> >
> >
> http://nipy.sourceforge.net/nipy/stable/devel/guidelines/gitwash/development_workflow.html
> >
> > At the moment, I'm updating my master branch.  Here's a transcript:
> >
> > none:scipy warren$ git branch -a
> >   master
> > * ticket1328
> >   remotes/origin/HEAD -> origin/master
> >   remotes/origin/maintenance/0.5.2.x
> >   remotes/origin/maintenance/0.6.x
> >   remotes/origin/maintenance/0.7.x
> >   remotes/origin/maintenance/0.8.x
> >   remotes/origin/maintenance/0.9.x
> >   remotes/origin/master
> >   remotes/origin/ticket1328
> > none:scipy warren$ git checkout master
> > Switched to branch 'master'
> > none:scipy warren$ git fetch upstream
> > remote: Counting objects: 76, done.
> > remote: Compressing objects: 100% (48/48), done.
> > remote: Total 48 (delta 40), reused 0 (delta 0)
> > Unpacking objects: 100% (48/48), done.
> > From git://github.com/scipy/scipy
> >  * [new branch]      maintenance/0.5.2.x -> upstream/maintenance/0.5.2.x
> >  * [new branch]      maintenance/0.6.x -> upstream/maintenance/0.6.x
> >  * [new branch]      maintenance/0.7.x -> upstream/maintenance/0.7.x
> >  * [new branch]      maintenance/0.8.x -> upstream/maintenance/0.8.x
> >  * [new branch]      maintenance/0.9.x -> upstream/maintenance/0.9.x
> >  * [new branch]      master     -> upstream/master
> > none:scipy warren$ git merge upsteam/master
> > fatal: 'upsteam/master' does not point to a commit
> >
> > So that last command did not work.  Where did I go wrong?
>
> You spelled upstream as upsteam.
>


Oh, right.

That loud cracking sound you just heard was me giving myself a dope slap.

Sorry for the noise.

Warren



>
> Cheers,
> Ralf
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
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From lists at onerussian.com  Wed Mar 16 14:33:22 2011
From: lists at onerussian.com (Yaroslav Halchenko)
Date: Wed, 16 Mar 2011 14:33:22 -0400
Subject: [SciPy-Dev] binom_test incorrect behavior in the tails
Message-ID: <20110316183322.GA10174@onerussian.com>

I am using scipy 0.7.2 in Debian

could anyone check if following behavior is still in place in the
current master:

$> python -c 'import scipy.stats,numpy; print numpy.array([scipy.stats.binom_test(a, 100) for a in [90, 98, 99, 100]])' 
[  1.53164509e-17   1.60428187e-19   1.66102449e-18   2.16868332e-09]   

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


From lists at onerussian.com  Wed Mar 16 14:50:49 2011
From: lists at onerussian.com (Yaroslav Halchenko)
Date: Wed, 16 Mar 2011 14:50:49 -0400
Subject: [SciPy-Dev] binom_test incorrect behavior in the tails
In-Reply-To: <20110316183322.GA10174@onerussian.com>
References: <20110316183322.GA10174@onerussian.com>
Message-ID: <20110316185049.GB10174@onerussian.com>

probably due to incorrect pmf computation (which should be symmetric for
p=0.5, but it isn't):

In [78]: pmfs = scipy.stats.binom.pmf(numpy.arange(0,101), 100, 0.5); print pmfs; print pmfs - pmfs[::-1]
[  7.88860905e-31   7.88860905e-29   3.90486148e-27   1.27558808e-25
   3.09330110e-24   5.93913812e-23   9.40363535e-22   1.26277389e-20
   1.46797465e-19   1.50059631e-18   1.36554264e-17   1.11726216e-16
   8.28636101e-16   5.60922899e-15   3.48573516e-14   1.99848816e-13
   1.06169683e-12   5.24603142e-12   2.41900338e-11   1.04399093e-10
   4.22816327e-10   1.61072886e-09   5.78398092e-09   1.96152396e-08
   6.29322272e-08   1.91313971e-07   5.51867223e-07   1.51252498e-06
   3.94336870e-06   9.79043264e-06   2.31706906e-05   5.23209142e-05
   1.12816971e-04   2.32471335e-04   4.58105277e-04   8.63855666e-04
   1.55973940e-03   2.69792760e-03   4.47287998e-03   7.11073227e-03
   1.08438667e-02   1.58690732e-02   2.22922695e-02   3.00686426e-02
   3.89525598e-02   4.84742966e-02   5.79583981e-02   6.65905000e-02
   7.35270104e-02   7.80286641e-02   7.95892374e-02   7.80286641e-02
   7.35270104e-02   6.65905000e-02   5.79583981e-02   4.84742966e-02
   3.89525598e-02   3.00686426e-02   2.22922695e-02   1.58690732e-02
   1.08438667e-02   7.11073227e-03   4.47287998e-03   2.69792760e-03
   1.55973940e-03   8.63855666e-04   4.58105277e-04   2.32471335e-04
   1.12816971e-04   5.23209142e-05   2.31706906e-05   9.79043264e-06
   3.94336870e-06   1.51252498e-06   5.51867223e-07   1.91313971e-07
   6.29322272e-08   1.96152397e-08   5.78398085e-09   1.61072888e-09
   4.22816337e-10   1.04399045e-10   2.41900944e-11   5.24602584e-12
   1.06170628e-12   1.99840144e-13   3.48610030e-14   5.55111512e-15
   8.88178420e-16   0.00000000e+00   0.00000000e+00   0.00000000e+00
   0.00000000e+00   0.00000000e+00   0.00000000e+00   0.00000000e+00
   0.00000000e+00   0.00000000e+00   0.00000000e+00   0.00000000e+00
   1.11022302e-16]
[ -1.11022302e-16   7.88860905e-29   3.90486148e-27   1.27558808e-25
   3.09330110e-24   5.93913812e-23   9.40363535e-22   1.26277389e-20
   1.46797465e-19   1.50059631e-18   1.36554264e-17   1.11726216e-16
  -5.95423185e-17   5.81138699e-17  -3.65137385e-18   8.67140393e-18
  -9.44431785e-18   5.57974827e-18  -6.06218405e-17   4.80626902e-17
  -1.07373643e-17  -1.97571409e-17   7.03550182e-17  -1.24116201e-17
  -2.13170664e-17  -2.03950711e-17  -1.61294131e-17   1.02130998e-18
  -1.29934854e-18   4.42998231e-18   2.52619106e-17  -4.68239813e-17
   4.14707331e-17  -2.22261445e-17   6.02816408e-17   1.51788304e-18
  -3.98986399e-17   2.08166817e-17  -3.46944695e-18   1.38777878e-17
  -7.97972799e-17   8.67361738e-17  -4.85722573e-17   2.77555756e-17
   1.38777878e-17  -2.77555756e-17   2.77555756e-17  -8.32667268e-17
   1.11022302e-16  -5.55111512e-17   0.00000000e+00   5.55111512e-17
  -1.11022302e-16   8.32667268e-17  -2.77555756e-17   2.77555756e-17
  -1.38777878e-17  -2.77555756e-17   4.85722573e-17  -8.67361738e-17
   7.97972799e-17  -1.38777878e-17   3.46944695e-18  -2.08166817e-17
   3.98986399e-17  -1.51788304e-18  -6.02816408e-17   2.22261445e-17
  -4.14707331e-17   4.68239813e-17  -2.52619106e-17  -4.42998231e-18
   1.29934854e-18  -1.02130998e-18   1.61294131e-17   2.03950711e-17
   2.13170664e-17   1.24116201e-17  -7.03550182e-17   1.97571409e-17
   1.07373643e-17  -4.80626902e-17   6.06218405e-17  -5.57974827e-18
   9.44431785e-18  -8.67140393e-18   3.65137385e-18  -5.81138699e-17
   5.95423185e-17  -1.11726216e-16  -1.36554264e-17  -1.50059631e-18
  -1.46797465e-19  -1.26277389e-20  -9.40363535e-22  -5.93913812e-23
  -3.09330110e-24  -1.27558808e-25  -3.90486148e-27  -7.88860905e-29
   1.11022302e-16]

On Wed, 16 Mar 2011, Yaroslav Halchenko wrote:

> I am using scipy 0.7.2 in Debian

> could anyone check if following behavior is still in place in the
> current master:

> $> python -c 'import scipy.stats,numpy; print numpy.array([scipy.stats.binom_test(a, 100) for a in [90, 98, 99, 100]])' 
> [  1.53164509e-17   1.60428187e-19   1.66102449e-18   2.16868332e-09]   
-- 
=------------------------------------------------------------------=
Keep in touch                                     www.onerussian.com
Yaroslav Halchenko                 www.ohloh.net/accounts/yarikoptic


From fperez.net at gmail.com  Wed Mar 16 14:51:09 2011
From: fperez.net at gmail.com (Fernando Perez)
Date: Wed, 16 Mar 2011 11:51:09 -0700
Subject: [SciPy-Dev] binom_test incorrect behavior in the tails
In-Reply-To: <20110316183322.GA10174@onerussian.com>
References: <20110316183322.GA10174@onerussian.com>
Message-ID: <AANLkTi=eJC5bZSnqFuWoHu76KHvYBk+qRoczxz8MxVsj@mail.gmail.com>

On Wed, Mar 16, 2011 at 11:33 AM, Yaroslav Halchenko
<lists at onerussian.com> wrote:
>
> could anyone check if following behavior is still in place in the
> current master:
>
> $> python -c 'import scipy.stats,numpy; print numpy.array([scipy.stats.binom_test(a, 100) for a in [90, 98, 99, 100]])'
> [ ?1.53164509e-17 ? 1.60428187e-19 1.66102449e-18 ? 2.16868332e-09]
>

looking much better with master from today:

longs[scipy]> python -c 'import scipy.stats,numpy; print
numpy.array([scipy.stats.binom_test(a, 100) for a in [90, 98, 99,
100]])'
[  3.06329018e-17   7.96907286e-27   1.59349903e-28   1.57772181e-30]


cheers,

f


From fperez.net at gmail.com  Wed Mar 16 14:52:02 2011
From: fperez.net at gmail.com (Fernando Perez)
Date: Wed, 16 Mar 2011 11:52:02 -0700
Subject: [SciPy-Dev] binom_test incorrect behavior in the tails
In-Reply-To: <20110316185049.GB10174@onerussian.com>
References: <20110316183322.GA10174@onerussian.com>
	<20110316185049.GB10174@onerussian.com>
Message-ID: <AANLkTikMi0hoPd5MjtZmx-YHM_MjgO4X+ram3eg1aofa@mail.gmail.com>

On Wed, Mar 16, 2011 at 11:50 AM, Yaroslav Halchenko
<lists at onerussian.com> wrote:
> probably due to incorrect pmf computation (which should be symmetric for
> p=0.5, but it isn't):

and the same thing off master:

In [5]: pmfs = scipy.stats.binom.pmf(numpy.arange(0,101), 100, 0.5);
print pmfs; print pmfs - pmfs[::-1]
[  7.88860905e-31   7.88860905e-29   3.90486148e-27   1.27558808e-25
   3.09330110e-24   5.93913812e-23   9.40363535e-22   1.26277389e-20
   1.46797465e-19   1.50059631e-18   1.36554264e-17   1.11726216e-16
   8.28636101e-16   5.60922899e-15   3.48573516e-14   1.99848816e-13
   1.06169683e-12   5.24603142e-12   2.41900338e-11   1.04399093e-10
   4.22816327e-10   1.61072886e-09   5.78398092e-09   1.96152396e-08
   6.29322272e-08   1.91313971e-07   5.51867223e-07   1.51252498e-06
   3.94336870e-06   9.79043264e-06   2.31706906e-05   5.23209142e-05
   1.12816971e-04   2.32471335e-04   4.58105277e-04   8.63855666e-04
   1.55973940e-03   2.69792760e-03   4.47287998e-03   7.11073227e-03
   1.08438667e-02   1.58690732e-02   2.22922695e-02   3.00686426e-02
   3.89525598e-02   4.84742966e-02   5.79583981e-02   6.65905000e-02
   7.35270104e-02   7.80286641e-02   7.95892374e-02   7.80286641e-02
   7.35270104e-02   6.65905000e-02   5.79583981e-02   4.84742966e-02
   3.89525598e-02   3.00686426e-02   2.22922695e-02   1.58690732e-02
   1.08438667e-02   7.11073227e-03   4.47287998e-03   2.69792760e-03
   1.55973940e-03   8.63855666e-04   4.58105277e-04   2.32471335e-04
   1.12816971e-04   5.23209142e-05   2.31706906e-05   9.79043264e-06
   3.94336870e-06   1.51252498e-06   5.51867223e-07   1.91313971e-07
   6.29322272e-08   1.96152396e-08   5.78398092e-09   1.61072886e-09
   4.22816327e-10   1.04399093e-10   2.41900338e-11   5.24603142e-12
   1.06169683e-12   1.99848816e-13   3.48573516e-14   5.60922899e-15
   8.28636101e-16   1.11726216e-16   1.36554264e-17   1.50059631e-18
   1.46797465e-19   1.26277389e-20   9.40363535e-22   5.93913812e-23
   3.09330110e-24   1.27558808e-25   3.90486148e-27   7.88860905e-29
   7.88860905e-31]
[  0.00000000e+00   0.00000000e+00  -2.72636629e-41   0.00000000e+00
   0.00000000e+00   0.00000000e+00   0.00000000e+00   0.00000000e+00
   0.00000000e+00   0.00000000e+00  -9.70668692e-32   0.00000000e+00
   0.00000000e+00   0.00000000e+00   0.00000000e+00   0.00000000e+00
   0.00000000e+00   0.00000000e+00   0.00000000e+00   0.00000000e+00
   0.00000000e+00   5.79026429e-24   0.00000000e+00   0.00000000e+00
  -2.24993127e-22  -6.88214270e-22   0.00000000e+00   0.00000000e+00
   1.35525272e-20   3.38813179e-20   0.00000000e+00   0.00000000e+00
  -4.06575815e-19   0.00000000e+00   0.00000000e+00   3.03576608e-18
   5.63785130e-18   0.00000000e+00   0.00000000e+00  -2.51534904e-17
  -3.81639165e-17   0.00000000e+00   0.00000000e+00   1.07552856e-16
   1.38777878e-16   0.00000000e+00   0.00000000e+00   0.00000000e+00
   0.00000000e+00   0.00000000e+00   0.00000000e+00   0.00000000e+00
   0.00000000e+00   0.00000000e+00   0.00000000e+00   0.00000000e+00
  -1.38777878e-16  -1.07552856e-16   0.00000000e+00   0.00000000e+00
   3.81639165e-17   2.51534904e-17   0.00000000e+00   0.00000000e+00
  -5.63785130e-18  -3.03576608e-18   0.00000000e+00   0.00000000e+00
   4.06575815e-19   0.00000000e+00   0.00000000e+00  -3.38813179e-20
  -1.35525272e-20   0.00000000e+00   0.00000000e+00   6.88214270e-22
   2.24993127e-22   0.00000000e+00   0.00000000e+00  -5.79026429e-24
   0.00000000e+00   0.00000000e+00   0.00000000e+00   0.00000000e+00
   0.00000000e+00   0.00000000e+00   0.00000000e+00   0.00000000e+00
   0.00000000e+00   0.00000000e+00   9.70668692e-32   0.00000000e+00
   0.00000000e+00   0.00000000e+00   0.00000000e+00   0.00000000e+00
   0.00000000e+00   0.00000000e+00   2.72636629e-41   0.00000000e+00
   0.00000000e+00]

In [6]:


cheers

f


From lists at onerussian.com  Wed Mar 16 14:57:13 2011
From: lists at onerussian.com (Yaroslav Halchenko)
Date: Wed, 16 Mar 2011 14:57:13 -0400
Subject: [SciPy-Dev] binom_test incorrect behavior in the tails
In-Reply-To: <AANLkTikMi0hoPd5MjtZmx-YHM_MjgO4X+ram3eg1aofa@mail.gmail.com>
References: <20110316183322.GA10174@onerussian.com>
	<20110316185049.GB10174@onerussian.com>
	<AANLkTikMi0hoPd5MjtZmx-YHM_MjgO4X+ram3eg1aofa@mail.gmail.com>
Message-ID: <20110316185713.GC10174@onerussian.com>

Thank you Fernando!

On Wed, 16 Mar 2011, Fernando Perez wrote:

> On Wed, Mar 16, 2011 at 11:50 AM, Yaroslav Halchenko
> <lists at onerussian.com> wrote:
> > probably due to incorrect pmf computation (which should be symmetric for
> > p=0.5, but it isn't):

> and the same thing off master:
-- 
=------------------------------------------------------------------=
Keep in touch                                     www.onerussian.com
Yaroslav Halchenko                 www.ohloh.net/accounts/yarikoptic


From nwagner at iam.uni-stuttgart.de  Wed Mar 16 16:14:45 2011
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Wed, 16 Mar 2011 21:14:45 +0100
Subject: [SciPy-Dev] FAIL: test_expon (test_morestats.TestAnderson)
Message-ID: <web-143468257@uni-stuttgart.de>

Is this a known issue ?
>>> scipy.__version__
'0.10.0.dev7179'

======================================================================
FAIL: test_expon (test_morestats.TestAnderson)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/tests/test_morestats.py", 
line 72, in test_expon
     assert_array_less(crit[:-1], A)
   File 
"/home/nwagner/local/lib64/python2.6/site-packages/numpy/testing/utils.py", 
line 869, in assert_array_less
     header='Arrays are not less-ordered')
   File 
"/home/nwagner/local/lib64/python2.6/site-packages/numpy/testing/utils.py", 
line 613, in assert_array_compare
     chk_same_position(x_id, y_id, hasval='inf')
   File 
"/home/nwagner/local/lib64/python2.6/site-packages/numpy/testing/utils.py", 
line 588, in chk_same_position
     raise AssertionError(msg)
AssertionError:
Arrays are not less-ordered

x and y inf location mismatch:
  x: array([ 0.911,  1.065,  1.325,  1.587])
  y: array(inf)




From josef.pktd at gmail.com  Wed Mar 16 18:10:11 2011
From: josef.pktd at gmail.com (josef.pktd at gmail.com)
Date: Wed, 16 Mar 2011 18:10:11 -0400
Subject: [SciPy-Dev] FAIL: test_expon (test_morestats.TestAnderson)
In-Reply-To: <web-143468257@uni-stuttgart.de>
References: <web-143468257@uni-stuttgart.de>
Message-ID: <AANLkTi=J+MhSR3C7YAKLi-OQCND6kdC9BYA_CD4m-SA0@mail.gmail.com>

On Wed, Mar 16, 2011 at 4:14 PM, Nils Wagner
<nwagner at iam.uni-stuttgart.de> wrote:
> Is this a known issue ?
>>>> scipy.__version__
> '0.10.0.dev7179'
>
> ======================================================================
> FAIL: test_expon (test_morestats.TestAnderson)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> ? File
> "/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/tests/test_morestats.py",
> line 72, in test_expon
> ? ? assert_array_less(crit[:-1], A)
> ? File
> "/home/nwagner/local/lib64/python2.6/site-packages/numpy/testing/utils.py",
> line 869, in assert_array_less
> ? ? header='Arrays are not less-ordered')
> ? File
> "/home/nwagner/local/lib64/python2.6/site-packages/numpy/testing/utils.py",
> line 613, in assert_array_compare
> ? ? chk_same_position(x_id, y_id, hasval='inf')
> ? File
> "/home/nwagner/local/lib64/python2.6/site-packages/numpy/testing/utils.py",
> line 588, in chk_same_position
> ? ? raise AssertionError(msg)
> AssertionError:
> Arrays are not less-ordered
>
> x and y inf location mismatch:
> ?x: array([ 0.911, ?1.065, ?1.325, ?1.587])
> ?y: array(inf)

looks suspicious, which numpy are you using?

Maybe this shows up now as a consequence of the assert fixes for inf in numpy
https://github.com/numpy/numpy/commit/45269ee1c906269bc3cd481f7ed94c8100e2b858

anderson is not fully tested, so there is no guarantee it`s not still
a mistake in it

Josef

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


From erik.tollerud at gmail.com  Thu Mar 17 19:10:23 2011
From: erik.tollerud at gmail.com (Erik Tollerud)
Date: Thu, 17 Mar 2011 16:10:23 -0700
Subject: [SciPy-Dev] Documentation fixes with new git repo
Message-ID: <AANLkTik5+2ZORHzysLsXiBiRsAJVKP+5HVL3bNiV+VS1@mail.gmail.com>

Now that the scipy repo is on git, what is the workflow for purely
documentation fixes?

Given all the references on docs.scipy.org talk about SVN, I speculate
it doesn't work -  should I just fork the scipy repo and submit a pull
request via git with changes in the docstrings?

-- 
Erik Tollerud


From josef.pktd at gmail.com  Thu Mar 17 19:26:16 2011
From: josef.pktd at gmail.com (josef.pktd at gmail.com)
Date: Thu, 17 Mar 2011 19:26:16 -0400
Subject: [SciPy-Dev] Documentation fixes with new git repo
In-Reply-To: <AANLkTik5+2ZORHzysLsXiBiRsAJVKP+5HVL3bNiV+VS1@mail.gmail.com>
References: <AANLkTik5+2ZORHzysLsXiBiRsAJVKP+5HVL3bNiV+VS1@mail.gmail.com>
Message-ID: <AANLkTi=r+-voa-2GYXV4stYKdykY4ZNLxVJF=4fSDWjG@mail.gmail.com>

On Thu, Mar 17, 2011 at 7:10 PM, Erik Tollerud <erik.tollerud at gmail.com> wrote:
> Now that the scipy repo is on git, what is the workflow for purely
> documentation fixes?
>
> Given all the references on docs.scipy.org talk about SVN, I speculate
> it doesn't work - ?should I just fork the scipy repo and submit a pull
> request via git with changes in the docstrings?

For most of the documentation the doc editor will still remain the
main way to improve and review the docs, I assume.

http://docs.scipy.org/doc/

Josef


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


From pav at iki.fi  Fri Mar 18 14:30:42 2011
From: pav at iki.fi (Pauli Virtanen)
Date: Fri, 18 Mar 2011 18:30:42 +0000 (UTC)
Subject: [SciPy-Dev] Documentation fixes with new git repo
References: <AANLkTik5+2ZORHzysLsXiBiRsAJVKP+5HVL3bNiV+VS1@mail.gmail.com>
Message-ID: <im08ci$llg$1@dough.gmane.org>

On Thu, 17 Mar 2011 16:10:23 -0700, Erik Tollerud wrote:
> Given all the references on docs.scipy.org talk about SVN, I speculate
> it doesn't work

No, it should work.

-- 
Pauli Virtanen



From amenity at enthought.com  Wed Mar 23 08:56:17 2011
From: amenity at enthought.com (Amenity Applewhite)
Date: Wed, 23 Mar 2011 07:56:17 -0500
Subject: [SciPy-Dev] SciPy 2011 Call for Papers
Message-ID: <AANLkTinDGOb0N64LL=OVZzLqz-z+YHnXZAv5H_vLrrOF@mail.gmail.com>

Hello,

SciPy 2011 <http://conference.scipy.org/scipy2011/index.php>, the 10th
Python in Science conference, will be held July 11 - 16, 2011, in Austin,
TX.

At this conference, novel applications and breakthroughs made in the pursuit
of science using Python are presented. Attended by leading figures from both
academia and industry, it is an excellent opportunity to experience the
cutting edge of scientific software development.

The conference is preceded by two days of tutorials, during which community
experts provide training on several scientific Python packages.

*We'd like to invite you to consider presenting at SciPy 2011.*

The list of topics that are appropriate for the conference includes (but is
not limited to):
     * new Python libraries for science and engineering;
     * applications of Python to the solution of scientific or computational
problems;
     * high performance, parallel and GPU computing with Python;
     * use of Python in science education.

*Specialized Tracks*
This year we also have two specialized tracks. They will be run concurrent
to the main conference.

         *Python in Data Science
         Chair: Peter Wang, Streamitive, Inc.*
   This track focuses on the advantages and challenges of applying Python in
   the emerging field of "data science".  This includes a breadth of
   technologies, from wrangling realtime data streams from the social web,
to
   machine learning and semantic analysis, to workflow and repository
   management for large datasets.

         *Python and Core Technologies
         Chair: Anthony Scopatz, Enthought, Inc.*
   In an effort to broaden the scope of SciPy and to engage the larger
   community of software developers, we are pleased to introduce the _Python
&
   Core Technologies_ track. Talks will cover subjects that are not directly
   related to science and engineering, yet nonetheless affect scientific
   computing. Proposals on the Python language, visualization toolkits, web
   frameworks, education, and other topics are appropriate for this session.

*Talk/Paper Submission*

   We invite you to take part by submitting a talk abstract on the
conference
   website at:
   http://conference.scipy.org/scipy2011/papers.php
   Papers are included in the peer-reviewed conference proceedings, to be
   published online.

*Important dates for authors:*
   Friday, April 15: Tutorial proposals due (remember: stipends will be
provided for Tutorial instructors)

http://conference.scipy.org/scipy2011/tutorials.php
   Sunday, April 24: Paper abstracts due
   Sunday, May 8: Student sponsorship request due
http://conference.scipy.org/scipy2011/student.php
   Tuesday, May 10: Accepted talks announced
   Monday, May 16: Student sponsorships announced
   Monday, May 23: Early Registration ends
   Sunday, June 20: Papers due
   Monday-Tuesday, July 11 - 12: Tutorials
   Wednesday-Thursday, July 13 - July 14: Conference
   Friday-Saturday, July 15 - July 16: Sprints


   The SciPy 2011 Team

  @SciPy2011
  http://twitter.com/SciPy2011

_________________________
Amenity Applewhite
Enthought, Inc. <http://www.enthought.com>
Scientific Computing Solutions
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From ralf.gommers at googlemail.com  Wed Mar 23 12:07:24 2011
From: ralf.gommers at googlemail.com (Ralf Gommers)
Date: Wed, 23 Mar 2011 17:07:24 +0100
Subject: [SciPy-Dev] ANN: Numpy 1.6.0 beta 1
Message-ID: <AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs@mail.gmail.com>

Hi,

I am pleased to announce the availability of the first beta of NumPy
1.6.0. Due to the extensive changes in the Numpy core for this
release, the beta testing phase will last at least one month. Please
test this beta and report any problems on the Numpy mailing list.

Sources and binaries can be found at:
http://sourceforge.net/projects/numpy/files/NumPy/1.6.0b1/
For (preliminary) release notes see below.

Enjoy,
Ralf


=========================
NumPy 1.6.0 Release Notes
=========================

This release includes several new features as well as numerous bug fixes and
improved documentation.  It is backward compatible with the 1.5.0 release, and
supports Python 2.4 - 2.7 and 3.1 - 3.2.


Highlights
==========

* Re-introduction of datetime dtype support to deal with dates in arrays.

* A new 16-bit floating point type.

* A new iterator, which improves performance of many functions.


New features
============

New 16-bit floating point type
------------------------------

This release adds support for the IEEE 754-2008 binary16 format, available as
the data type ``numpy.half``.  Within Python, the type behaves similarly to
`float` or `double`, and C extensions can add support for it with the exposed
half-float API.


New iterator
------------

A new iterator has been added, replacing the functionality of the
existing iterator and multi-iterator with a single object and API.
This iterator works well with general memory layouts different from
C or Fortran contiguous, and handles both standard NumPy and
customized broadcasting. The buffering, automatic data type
conversion, and optional output parameters, offered by
ufuncs but difficult to replicate elsewhere, are now exposed by this
iterator.


Legendre, Laguerre, Hermite, HermiteE polynomials in ``numpy.polynomial``
-------------------------------------------------------------------------

Extend the number of polynomials available in the polynomial package. In
addition, a new ``window`` attribute has been added to the classes in
order to specify the range the ``domain`` maps to. This is mostly useful
for the Laguerre, Hermite, and HermiteE polynomials whose natural domains
are infinite and provides a more intuitive way to get the correct mapping
of values without playing unnatural tricks with the domain.


Fortran assumed shape array and size function support in ``numpy.f2py``
-----------------------------------------------------------------------

F2py now supports wrapping Fortran 90 routines that use assumed shape
arrays.  Before such routines could be called from Python but the
corresponding Fortran routines received assumed shape arrays as zero
length arrays which caused unpredicted results. Thanks to Lorenz
H?depohl for pointing out the correct way to interface routines with
assumed shape arrays.

In addition, f2py interprets Fortran expression ``size(array, dim)``
as ``shape(array, dim-1)`` which makes it possible to automatically
wrap Fortran routines that use two argument ``size`` function in
dimension specifications. Before users were forced to apply this
mapping manually.


Other new functions
-------------------

``numpy.ravel_multi_index`` : Converts a multi-index tuple into
an array of flat indices, applying boundary modes to the indices.

``numpy.einsum`` : Evaluate the Einstein summation convention.  Using the
Einstein summation convention, many common multi-dimensional array operations
can be represented in a simple fashion.  This function provides a way compute
such summations.

``numpy.count_nonzero`` : Counts the number of non-zero elements in an array.

``numpy.result_type`` and ``numpy.min_scalar_type`` : These functions expose
the underlying type promotion used by the ufuncs and other operations to
determine the types of outputs. These improve upon the ``numpy.common_type``
and ``numpy.mintypecode`` which provide similar functionality but do
not match the ufunc implementation.


Changes
=======

Changes and improvements in the numpy core
------------------------------------------




``numpy.distutils``
-------------------

Several new compilers are supported for building Numpy: the Portland Group
Fortran compiler on OS X, the PathScale compiler suite and the 64-bit Intel C
compiler on Linux.


``numpy.testing``
-----------------

The testing framework gained ``numpy.testing.assert_allclose``, which provides
a more convenient way to compare floating point arrays than
`assert_almost_equal`, `assert_approx_equal` and `assert_array_almost_equal`.


``C API``
---------

In addition to the APIs for the new iterator and half data type, a number
of other additions have been made to the C API. The type promotion
mechanism used by ufuncs is exposed via ``PyArray_PromoteTypes``,
``PyArray_ResultType``, and ``PyArray_MinScalarType``. A new enumeration
``NPY_CASTING`` has been added which controls what types of casts are
permitted. This is used by the new functions ``PyArray_CanCastArrayTo``
and ``PyArray_CanCastTypeTo``.  A more flexible way to handle
conversion of arbitrary python objects into arrays is exposed by
``PyArray_GetArrayParamsFromObject``.


Removed features
================

``numpy.fft``
-------------

The functions `refft`, `refft2`, `refftn`, `irefft`, `irefft2`, `irefftn`,
which were aliases for the same functions without the 'e' in the name, were
removed.


``numpy.memmap``
----------------

The `sync()` and `close()` methods of memmap were removed.  Use `flush()` and
"del memmap" instead.


``numpy.lib``
-------------

The deprecated functions ``numpy.unique1d``, ``numpy.setmember1d``,
``numpy.intersect1d_nu`` and ``numpy.lib.ufunclike.log2`` were removed.


``numpy.ma``
------------

Several deprecated items were removed from the ``numpy.ma`` module::

  * ``numpy.ma.MaskedArray`` "raw_data" method
  * ``numpy.ma.MaskedArray`` constructor "flag" keyword
  * ``numpy.ma.make_mask`` "flag" keyword
  * ``numpy.ma.allclose`` "fill_value" keyword


``numpy.distutils``
-------------------

The ``numpy.get_numpy_include`` function was removed, use ``numpy.get_include``
instead.

Checksums
=========

89f52ae0f0ea84cfcb457298190bee14
release/installers/numpy-1.6.0b1-py2.7-python.org.dmg
8dee06b362540b2c8c033399951e5386
release/installers/numpy-1.6.0b1-win32-superpack-python2.5.exe
c1b11bf48037ac8fe025bfd297969840
release/installers/numpy-1.6.0b1-win32-superpack-python2.6.exe
2b005cb359d8123bd5ee3063d9eae3ac
release/installers/numpy-1.6.0b1-win32-superpack-python2.7.exe
45627e8f63fe34011817df66722c39a5
release/installers/numpy-1.6.0b1-win32-superpack-python3.1.exe
1d8b214752b19b51ee747a6436ca1d38
release/installers/numpy-1.6.0b1-win32-superpack-python3.2.exe
aeab5881974aac595b87a848c0c6344a  release/installers/numpy-1.6.0b1.tar.gz
3ffc6e308f9e0614531fa3babcb75544  release/installers/numpy-1.6.0b1.zip


From alan.isaac at gmail.com  Wed Mar 23 13:29:49 2011
From: alan.isaac at gmail.com (Alan G Isaac)
Date: Wed, 23 Mar 2011 13:29:49 -0400
Subject: [SciPy-Dev] ANN: Numpy 1.6.0 beta 1
In-Reply-To: <AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs@mail.gmail.com>
References: <AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs@mail.gmail.com>
Message-ID: <4D8A2E0D.8030709@gmail.com>

On 3/23/2011 12:07 PM, Ralf Gommers wrote:
> Sources and binaries can be found at:
> http://sourceforge.net/projects/numpy/files/NumPy/1.6.0b1/


Well ... I wanted to test it on Python32, but I cannot
get nose to install.  (I tried nose 1.0 and I tried an hg
checkout of the repository.)

Alan Isaac



From derek at astro.physik.uni-goettingen.de  Wed Mar 23 13:47:32 2011
From: derek at astro.physik.uni-goettingen.de (Derek Homeier)
Date: Wed, 23 Mar 2011 18:47:32 +0100
Subject: [SciPy-Dev] ANN: Numpy 1.6.0 beta 1
In-Reply-To: <4D8A2E0D.8030709@gmail.com>
References: <AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs@mail.gmail.com>
	<4D8A2E0D.8030709@gmail.com>
Message-ID: <9E948703-BACF-4816-84E9-8218EDC10E73@astro.physik.uni-goettingen.de>

On 23 Mar 2011, at 18:29, Alan G Isaac wrote:

>> Sources and binaries can be found at:
>> http://sourceforge.net/projects/numpy/files/NumPy/1.6.0b1/
>
>
> Well ... I wanted to test it on Python32, but I cannot
> get nose to install.  (I tried nose 1.0 and I tried an hg
> checkout of the repository.)

I thought the main branch of nose did install on Python3, but is non- 
functional
(tons of "print xxx" statements, e.g.).
The only version known to me to work (for Python3.[12] under MacOS X  
10.[56]
in my case) is this branch:

https://bitbucket.org/toshio

HTH,
						Derek




From ralf.gommers at googlemail.com  Wed Mar 23 14:22:54 2011
From: ralf.gommers at googlemail.com (Ralf Gommers)
Date: Wed, 23 Mar 2011 19:22:54 +0100
Subject: [SciPy-Dev] ANN: Numpy 1.6.0 beta 1
In-Reply-To: <9E948703-BACF-4816-84E9-8218EDC10E73@astro.physik.uni-goettingen.de>
References: <AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs@mail.gmail.com>
	<4D8A2E0D.8030709@gmail.com>
	<9E948703-BACF-4816-84E9-8218EDC10E73@astro.physik.uni-goettingen.de>
Message-ID: <AANLkTinNROEoYCLnUCKQtErV5xLwnqGbdw3QXTo3ByPt@mail.gmail.com>

On Wed, Mar 23, 2011 at 6:47 PM, Derek Homeier
<derek at astro.physik.uni-goettingen.de> wrote:
> On 23 Mar 2011, at 18:29, Alan G Isaac wrote:
>
>>> Sources and binaries can be found at:
>>> http://sourceforge.net/projects/numpy/files/NumPy/1.6.0b1/
>>
>>
>> Well ... I wanted to test it on Python32, but I cannot
>> get nose to install. ?(I tried nose 1.0 and I tried an hg
>> checkout of the repository.)
>
> I thought the main branch of nose did install on Python3, but is non-
> functional
> (tons of "print xxx" statements, e.g.).
> The only version known to me to work (for Python3.[12] under MacOS X
> 10.[56]
> in my case) is this branch:
>
> https://bitbucket.org/toshio

nose 1.0.0 works fine with 3.2 for me on both OS X and Windows. No
particular installation issues either.

Ralf


From derek at astro.physik.uni-goettingen.de  Wed Mar 23 15:00:12 2011
From: derek at astro.physik.uni-goettingen.de (Derek Homeier)
Date: Wed, 23 Mar 2011 20:00:12 +0100
Subject: [SciPy-Dev] ANN: Numpy 1.6.0 beta 1
In-Reply-To: <AANLkTinNROEoYCLnUCKQtErV5xLwnqGbdw3QXTo3ByPt@mail.gmail.com>
References: <AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs@mail.gmail.com>
	<4D8A2E0D.8030709@gmail.com>
	<9E948703-BACF-4816-84E9-8218EDC10E73@astro.physik.uni-goettingen.de>
	<AANLkTinNROEoYCLnUCKQtErV5xLwnqGbdw3QXTo3ByPt@mail.gmail.com>
Message-ID: <7BF7E88F-B15F-40BE-BCB0-D58D27194070@astro.physik.uni-goettingen.de>

Hi Ralf,

>> The only version known to me to work (for Python3.[12] under MacOS X
>> 10.[56]
>> in my case) is this branch:
>>
>> https://bitbucket.org/toshio
>
> nose 1.0.0 works fine with 3.2 for me on both OS X and Windows. No
> particular installation issues either.

thanks, I missed they had switched to a different repository once again
(apparently the fink maintainer did as well), so I was still on 0.11!
Was actually getting a bit concerned since Toshio's branch had not been
updated in 5 months...

For me, nose 1.0.0 built from source and worked with 3.1 and 3.2 as  
well -
Alan, have you got distribute installed for Python3.2?

Cheers,
						Derek




From derek at astro.physik.uni-goettingen.de  Wed Mar 23 17:08:46 2011
From: derek at astro.physik.uni-goettingen.de (Derek Homeier)
Date: Wed, 23 Mar 2011 22:08:46 +0100
Subject: [SciPy-Dev] ANN: Numpy 1.6.0 beta 1
In-Reply-To: <AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs@mail.gmail.com>
References: <AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs@mail.gmail.com>
Message-ID: <90A85509-C029-4684-BE95-91ED9CD45C50@astro.physik.uni-goettingen.de>

Hi,

On 23 Mar 2011, at 17:07, Ralf Gommers wrote:

> I am pleased to announce the availability of the first beta of NumPy
> 1.6.0. Due to the extensive changes in the Numpy core for this
> release, the beta testing phase will last at least one month. Please
> test this beta and report any problems on the Numpy mailing list.

building for Python3.x fails with an import error in the default fink  
build
environment:

RefactoringTool: No changes to /scratch/fink.build/numpy- 
py32-1.6.0b1-1/numpy-1.6.0b1/build/py3k/numpy/compat/py3k.py
RefactoringTool: Refactored /scratch/fink.build/numpy-py32-1.6.0b1-1/ 
numpy-1.6.0b1/build/py3k/numpy/core/defchararray.py
RefactoringTool: Files that were modified:
RefactoringTool: /scratch/fink.build/numpy-py32-1.6.0b1-1/ 
numpy-1.6.0b1/build/py3k/numpy/compat/py3k.py
RefactoringTool: /scratch/fink.build/numpy-py32-1.6.0b1-1/ 
numpy-1.6.0b1/build/py3k/numpy/core/defchararray.py
Traceback (most recent call last):
   File "setup.py", line 201, in <module>
     setup_package()
   File "setup.py", line 178, in setup_package
     from numpy.distutils.core import setup
   File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/ 
distutils/__init__.py", line 22, in <module>
     import numpy.distutils.ccompiler
   File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/ 
distutils/ccompiler.py", line 15, in <module>
     from numpy.distutils.exec_command import exec_command
   File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/ 
distutils/exec_command.py", line 58, in <module>
     from numpy.compat import open_latin1
   File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/ 
compat/__init__.py", line 11, in <module>
     import _inspect
ImportError: No module named _inspect

- I suspect exec_command.py is supposed to import from
%b/build/py3k/numpy/compat instead of
%b/numpy/compat (since the former's __init__.py has "from . import  
_inspect")

I managed work around this by building with
mkdir -p build/py3k/numpy/compat
PYTHONPATH=%b/build/py3k/numpy/compat %p/bin/python%type_raw[python]  
setup.py build

(%b is a placeholder for the fink build directory), but I suspect  
that's not the desired
way to have the build work, and anyway then the build fails soon  
afterwards on

RefactoringTool: /scratch/fink.build/numpy-py32-1.6.0b1-1/ 
numpy-1.6.0b1/build/py3k/numpy/core/defchararray.py
Traceback (most recent call last):
   File "setup.py", line 201, in <module>
     setup_package()
   File "setup.py", line 178, in setup_package
     from numpy.distutils.core import setup
   File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/ 
distutils/core.py", line 25, in <module>
     from numpy.distutils.command import config, config_compiler, \
   File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/ 
distutils/command/build_ext.py", line 16, in <module>
     from numpy.distutils.system_info import combine_paths
   File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/ 
distutils/system_info.py", line 1242
     except Exception, msg: # failed to get version from file -- maybe  
on Windows
                     ^
SyntaxError: invalid syntax

Cheers,
					Derek



From derek at astro.physik.uni-goettingen.de  Wed Mar 23 17:51:04 2011
From: derek at astro.physik.uni-goettingen.de (Derek Homeier)
Date: Wed, 23 Mar 2011 22:51:04 +0100
Subject: [SciPy-Dev] ANN: Numpy 1.6.0 beta 1
In-Reply-To: <90A85509-C029-4684-BE95-91ED9CD45C50@astro.physik.uni-goettingen.de>
References: <AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs@mail.gmail.com>
	<90A85509-C029-4684-BE95-91ED9CD45C50@astro.physik.uni-goettingen.de>
Message-ID: <4426C763-D075-437A-8C65-4219F40DDA18@astro.physik.uni-goettingen.de>

On 23 Mar 2011, at 22:08, Derek Homeier wrote:

> I managed work around this by building with
> mkdir -p build/py3k/numpy/compat
> PYTHONPATH=%b/build/py3k/numpy/compat %p/bin/python%type_raw[python]
> setup.py build
>
> (%b is a placeholder for the fink build directory), but I suspect
> that's not the desired
> way to have the build work, and anyway then the build fails soon
> afterwards on
>
> RefactoringTool: /scratch/fink.build/numpy-py32-1.6.0b1-1/
> numpy-1.6.0b1/build/py3k/numpy/core/defchararray.py
> Traceback (most recent call last):
>   File "setup.py", line 201, in <module>
>     setup_package()
>   File "setup.py", line 178, in setup_package
>     from numpy.distutils.core import setup
>   File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/
> distutils/core.py", line 25, in <module>
>     from numpy.distutils.command import config, config_compiler, \
>   File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/
> distutils/command/build_ext.py", line 16, in <module>
>     from numpy.distutils.system_info import combine_paths
>   File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/
> distutils/system_info.py", line 1242
>     except Exception, msg: # failed to get version from file -- maybe
> on Windows
>                     ^
> SyntaxError: invalid syntax

As an update; since that exception did not use "msg" I decided to  
comment it out to
get past that point, only to fail later on, but I am not sure whether  
the failure now is
due to my tweaking of PYTHONPATH or a refactoring issue (it comes down  
to a
non-refactored "print" of course, but I am wondering about all the  
path warnings)

Cheers,
						Derek

RefactoringTool: /scratch/fink.build/numpy-py32-1.6.0b1-1/ 
numpy-1.6.0b1/build/py3k/numpy/core/defchararray.py
non-existing path in 'numpy/distutils': 'site.cfg'
F2PY Version 2
blas_opt_info:
   FOUND:
     extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
     define_macros = [('NO_ATLAS_INFO', 3)]
     extra_compile_args = ['-msse3', '-I/System/Library/Frameworks/ 
vecLib.framework/Headers']

non-existing path in 'numpy/lib': 'benchmarks'
lapack_opt_info:
/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/distutils/ 
system_info.py:531: UserWarning: Specified path  is invalid.
   warnings.warn('Specified path %s is invalid.' % d)
   FOUND:
     extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
     define_macros = [('NO_ATLAS_INFO', 3)]
     extra_compile_args = ['-msse3']

non-existing path in '': 'doc/cython/'
non-existing path in '': 'doc/pyrex/'
non-existing path in '': 'doc/swig/'
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands -- 
compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands -- 
fcompiler options
running build_src
build_src
building py_modules sources
creating build
creating build/src.macosx-10.5-i386-3.2
creating build/src.macosx-10.5-i386-3.2/numpy
creating build/src.macosx-10.5-i386-3.2/numpy/distutils
building library "npymath" sources
Traceback (most recent call last):
   File "setup.py", line 201, in <module>
     setup_package()
   File "setup.py", line 194, in setup_package
     configuration=configuration )
   File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/ 
distutils/core.py", line 186, in setup
     return old_setup(**new_attr)
   File "/sw/lib/python3.2/distutils/core.py", line 149, in setup
     dist.run_commands()
   File "/sw/lib/python3.2/distutils/dist.py", line 919, in run_commands
     self.run_command(cmd)
   File "/sw/lib/python3.2/distutils/dist.py", line 938, in run_command
     cmd_obj.run()
   File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/ 
distutils/command/build.py", line 37, in run
     old_build.run(self)
   File "/sw/lib/python3.2/distutils/command/build.py", line 128, in run
     self.run_command(cmd_name)
   File "/sw/lib/python3.2/distutils/cmd.py", line 315, in run_command
     self.distribution.run_command(command)
   File "/sw/lib/python3.2/distutils/dist.py", line 938, in run_command
     cmd_obj.run()
   File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/ 
distutils/command/build_src.py", line 152, in run
     self.build_sources()
   File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/ 
distutils/command/build_src.py", line 163, in build_sources
     self.build_library_sources(*libname_info)
   File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/ 
distutils/command/build_src.py", line 298, in build_library_sources
     sources = self.generate_sources(sources, (lib_name, build_info))
   File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/ 
distutils/command/build_src.py", line 385, in generate_sources
     source = func(extension, build_dir)
   File "numpy/core/setup.py", line 694, in get_mathlib_info
     st = config_cmd.try_link('int main(void) { return 0;}')
   File "/sw/lib/python3.2/distutils/command/config.py", line 245, in  
try_link
     self._check_compiler()
   File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/ 
distutils/command/config.py", line 75, in _check_compiler
     c_compiler=self.compiler)
   File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/ 
distutils/fcompiler/__init__.py", line 817, in new_fcompiler
     load_all_fcompiler_classes()
   File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/ 
distutils/fcompiler/__init__.py", line 728, in  
load_all_fcompiler_classes
     __import__ (module_name)
   File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/ 
distutils/fcompiler/pathf95.py", line 36
     print compiler.get_version()
                  ^
SyntaxError: invalid syntax


From bsouthey at gmail.com  Wed Mar 23 17:56:44 2011
From: bsouthey at gmail.com (Bruce Southey)
Date: Wed, 23 Mar 2011 16:56:44 -0500
Subject: [SciPy-Dev] ANN: Numpy 1.6.0 beta 1
In-Reply-To: <4426C763-D075-437A-8C65-4219F40DDA18@astro.physik.uni-goettingen.de>
References: <AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs@mail.gmail.com>	<90A85509-C029-4684-BE95-91ED9CD45C50@astro.physik.uni-goettingen.de>
	<4426C763-D075-437A-8C65-4219F40DDA18@astro.physik.uni-goettingen.de>
Message-ID: <4D8A6C9C.1010005@gmail.com>

On 03/23/2011 04:51 PM, Derek Homeier wrote:
> On 23 Mar 2011, at 22:08, Derek Homeier wrote:
>
>> I managed work around this by building with
>> mkdir -p build/py3k/numpy/compat
>> PYTHONPATH=%b/build/py3k/numpy/compat %p/bin/python%type_raw[python]
>> setup.py build
>>
>> (%b is a placeholder for the fink build directory), but I suspect
>> that's not the desired
>> way to have the build work, and anyway then the build fails soon
>> afterwards on
>>
>> RefactoringTool: /scratch/fink.build/numpy-py32-1.6.0b1-1/
>> numpy-1.6.0b1/build/py3k/numpy/core/defchararray.py
>> Traceback (most recent call last):
>>    File "setup.py", line 201, in<module>
>>      setup_package()
>>    File "setup.py", line 178, in setup_package
>>      from numpy.distutils.core import setup
>>    File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/
>> distutils/core.py", line 25, in<module>
>>      from numpy.distutils.command import config, config_compiler, \
>>    File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/
>> distutils/command/build_ext.py", line 16, in<module>
>>      from numpy.distutils.system_info import combine_paths
>>    File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/
>> distutils/system_info.py", line 1242
>>      except Exception, msg: # failed to get version from file -- maybe
>> on Windows
>>                      ^
>> SyntaxError: invalid syntax
> As an update; since that exception did not use "msg" I decided to
> comment it out to
> get past that point, only to fail later on, but I am not sure whether
> the failure now is
> due to my tweaking of PYTHONPATH or a refactoring issue (it comes down
> to a
> non-refactored "print" of course, but I am wondering about all the
> path warnings)
>
> Cheers,
> 						Derek
>
> RefactoringTool: /scratch/fink.build/numpy-py32-1.6.0b1-1/
> numpy-1.6.0b1/build/py3k/numpy/core/defchararray.py
> non-existing path in 'numpy/distutils': 'site.cfg'
> F2PY Version 2
> blas_opt_info:
>     FOUND:
>       extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
>       define_macros = [('NO_ATLAS_INFO', 3)]
>       extra_compile_args = ['-msse3', '-I/System/Library/Frameworks/
> vecLib.framework/Headers']
>
> non-existing path in 'numpy/lib': 'benchmarks'
> lapack_opt_info:
> /scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/distutils/
> system_info.py:531: UserWarning: Specified path  is invalid.
>     warnings.warn('Specified path %s is invalid.' % d)
>     FOUND:
>       extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
>       define_macros = [('NO_ATLAS_INFO', 3)]
>       extra_compile_args = ['-msse3']
>
> non-existing path in '': 'doc/cython/'
> non-existing path in '': 'doc/pyrex/'
> non-existing path in '': 'doc/swig/'
> running build
> running config_cc
> unifing config_cc, config, build_clib, build_ext, build commands --
> compiler options
> running config_fc
> unifing config_fc, config, build_clib, build_ext, build commands --
> fcompiler options
> running build_src
> build_src
> building py_modules sources
> creating build
> creating build/src.macosx-10.5-i386-3.2
> creating build/src.macosx-10.5-i386-3.2/numpy
> creating build/src.macosx-10.5-i386-3.2/numpy/distutils
> building library "npymath" sources
> Traceback (most recent call last):
>     File "setup.py", line 201, in<module>
>       setup_package()
>     File "setup.py", line 194, in setup_package
>       configuration=configuration )
>     File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/
> distutils/core.py", line 186, in setup
>       return old_setup(**new_attr)
>     File "/sw/lib/python3.2/distutils/core.py", line 149, in setup
>       dist.run_commands()
>     File "/sw/lib/python3.2/distutils/dist.py", line 919, in run_commands
>       self.run_command(cmd)
>     File "/sw/lib/python3.2/distutils/dist.py", line 938, in run_command
>       cmd_obj.run()
>     File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/
> distutils/command/build.py", line 37, in run
>       old_build.run(self)
>     File "/sw/lib/python3.2/distutils/command/build.py", line 128, in run
>       self.run_command(cmd_name)
>     File "/sw/lib/python3.2/distutils/cmd.py", line 315, in run_command
>       self.distribution.run_command(command)
>     File "/sw/lib/python3.2/distutils/dist.py", line 938, in run_command
>       cmd_obj.run()
>     File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/
> distutils/command/build_src.py", line 152, in run
>       self.build_sources()
>     File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/
> distutils/command/build_src.py", line 163, in build_sources
>       self.build_library_sources(*libname_info)
>     File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/
> distutils/command/build_src.py", line 298, in build_library_sources
>       sources = self.generate_sources(sources, (lib_name, build_info))
>     File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/
> distutils/command/build_src.py", line 385, in generate_sources
>       source = func(extension, build_dir)
>     File "numpy/core/setup.py", line 694, in get_mathlib_info
>       st = config_cmd.try_link('int main(void) { return 0;}')
>     File "/sw/lib/python3.2/distutils/command/config.py", line 245, in
> try_link
>       self._check_compiler()
>     File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/
> distutils/command/config.py", line 75, in _check_compiler
>       c_compiler=self.compiler)
>     File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/
> distutils/fcompiler/__init__.py", line 817, in new_fcompiler
>       load_all_fcompiler_classes()
>     File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/
> distutils/fcompiler/__init__.py", line 728, in
> load_all_fcompiler_classes
>       __import__ (module_name)
>     File "/scratch/fink.build/numpy-py32-1.6.0b1-1/numpy-1.6.0b1/numpy/
> distutils/fcompiler/pathf95.py", line 36
>       print compiler.get_version()
>                    ^
> SyntaxError: invalid syntax
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev:
>
> http://mail.scipy.org/pipermail/numpy-discussion/2011-March/055601.html
Sorry as I should I have paid more attention to you first email as I 
raised this on the numpy list. (At least with gmail, the reply is to the 
scipy-dev list rather than the numpy list.)

Based on Pauli's answer I got around it by commenting out a line in the 
setup.py file about the git version:
http://mail.scipy.org/pipermail/numpy-discussion/2011-March/055603.html

Bruce


From derek at astro.physik.uni-goettingen.de  Wed Mar 23 18:43:50 2011
From: derek at astro.physik.uni-goettingen.de (Derek Homeier)
Date: Wed, 23 Mar 2011 23:43:50 +0100
Subject: [SciPy-Dev] ANN: Numpy 1.6.0 beta 1
In-Reply-To: <4D8A6C9C.1010005@gmail.com>
References: <AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs@mail.gmail.com>	<90A85509-C029-4684-BE95-91ED9CD45C50@astro.physik.uni-goettingen.de>
	<4426C763-D075-437A-8C65-4219F40DDA18@astro.physik.uni-goettingen.de>
	<4D8A6C9C.1010005@gmail.com>
Message-ID: <0B87A30E-5EBB-4F8F-847F-B46ABF8397A9@astro.physik.uni-goettingen.de>

Hi Bruce,

> Sorry as I should I have paid more attention to you first email as I
> raised this on the numpy list. (At least with gmail, the reply is to  
> the
> scipy-dev list rather than the numpy list.)
>
> Based on Pauli's answer I got around it by commenting out a line in  
> the
> setup.py file about the git version:
> http://mail.scipy.org/pipermail/numpy-discussion/2011-March/ 
> 055603.html
>
thanks, I was not subscribed to numpy-discussion (I realise I better  
should before
going into major testing...)! This patch

diff -ruN --exclude='*~' numpy-1.6.0b1.orig/setup.py numpy-1.6.0b1/ 
setup.py
--- numpy-1.6.0b1.orig/setup.py	2011-03-23 09:24:00.000000000 +0100
+++ numpy-1.6.0b1/setup.py	2011-03-23 23:03:19.000000000 +0100
@@ -99,9 +99,10 @@
  FULLVERSION = VERSION
  if os.path.exists('.git'):
      GIT_REVISION = git_version()
-elif os.path.exists('numpy/version.py'):
-    # must be a source distribution, use existing version file
-    from numpy.version import git_revision as GIT_REVISION
+# does not work in a clean source distribution:
+#elif os.path.exists('numpy/version.py'):
+#    # must be a source distribution, use existing version file
+#    from numpy.version import git_revision as GIT_REVISION
  else:
      GIT_REVISION = "Unknown"

did the build for Python3.1 and Python3.2.

Cheers,
						Derek



From cimrman3 at ntc.zcu.cz  Thu Mar 24 10:02:01 2011
From: cimrman3 at ntc.zcu.cz (Robert Cimrman)
Date: Thu, 24 Mar 2011 15:02:01 +0100 (CET)
Subject: [SciPy-Dev] ANN: SfePy 2011.1
Message-ID: <alpine.DEB.1.10.1103241457551.15008@eryx1.zcu.cz>

I am pleased to announce release 2011.1 of SfePy.

Description
-----------

SfePy (simple finite elements in Python) is a software for solving systems 
of coupled partial differential equations by the finite element method. 
The code is based on NumPy and SciPy packages. It is distributed under the 
new BSD license.

Home page: http://sfepy.org
Mailing lists, issue tracking: http://code.google.com/p/sfepy/
Git (source) repository: http://github.com/sfepy

Documentation: http://docs.sfepy.org/doc

Highlights of this release
--------------------------
- discontinuous approximations
- user-defined material nonlinearities
- improved surface approximations
- speed-up mesh reading
- extensive clean-up - less code

For more information on this release, see
http://sfepy.googlecode.com/svn/web/releases/2011.1_RELEASE_NOTES.txt
(full release notes, rather long and technical).

Best regards,
Robert Cimrman and Contributors (*)

(*) Contributors to this release (alphabetical order):

Vladim?r Luke?, Andre Smit, Logan Sorenson

From thouis at gmail.com  Fri Mar 25 06:53:29 2011
From: thouis at gmail.com (Thouis (Ray) Jones)
Date: Fri, 25 Mar 2011 11:53:29 +0100
Subject: [SciPy-Dev] review request: median in scipy.ndimage.measurements
Message-ID: <AANLkTinjHW8HiNv3hvzYJdX6nJbEfO3NWVtxiZhmPC98@mail.gmail.com>

I was prompted to add median() to the set of per-object measurements
available in scipy.ndimage.measurements.  It was not a difficult
change to add, given the existing structure.  Any comments on the
following?

https://github.com/thouis/scipy/compare/master...ndimage-measurements-median

I was thinking of also adding median_positions(), but I'm not sure
it's that useful.

Thouis Jones


From rowen at uw.edu  Tue Mar 29 18:22:31 2011
From: rowen at uw.edu (Russell E. Owen)
Date: Tue, 29 Mar 2011 15:22:31 -0700
Subject: [SciPy-Dev] ANN: Numpy 1.6.0 beta 1
References: <AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs@mail.gmail.com>
Message-ID: <rowen-3A77F5.15223129032011@news.gmane.org>

In article 
<AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs at mail.gmail.com>,
 Ralf Gommers <ralf.gommers at googlemail.com> wrote:

> Hi,
> 
> I am pleased to announce the availability of the first beta of NumPy
> 1.6.0. Due to the extensive changes in the Numpy core for this
> release, the beta testing phase will last at least one month. Please
> test this beta and report any problems on the Numpy mailing list.
> 
> Sources and binaries can be found at:
> http://sourceforge.net/projects/numpy/files/NumPy/1.6.0b1/
> For (preliminary) release notes see below.

Great!

FYI: it works for me on MacOS X 10.5.8 with python.org python 2.6.6:

python setup.py build --fcompiler=gnu95
python setup.py install
cd ..
python -Wd -c 'import numpy; numpy.test()'

NumPy version 1.6.0b1
NumPy is installed in 
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-pack
ages/numpy
Python version 2.6.6 (r266:84374, Aug 31 2010, 11:00:51) [GCC 4.0.1 
(Apple Inc. build 5493)]
nose version 0.11.4
...
Ran 3399 tests in 25.474s

OK (KNOWNFAIL=3, SKIP=1)

-- Russell



From sbellem at gmail.com  Thu Mar 31 01:27:32 2011
From: sbellem at gmail.com (Sylvain Bellemare)
Date: Wed, 30 Mar 2011 22:27:32 -0700
Subject: [SciPy-Dev] Willing to contribute to SciPy & NumPy ...
Message-ID: <BANLkTikKSLcJuSmL94eG8Q2KmL+EvyCY-A@mail.gmail.com>

Hi,

 I would like to seriously start contributing to NumPy and/or SciPy, as much
as I possibly can.

Because NumPy & SciPy are new to me, I'm not so sure whether I could be of
some help. But if my help is welcomed, and if it makes sense to ask: "What
could I best contribute to?", then perhaps some background information about
myself would be useful ...

*ACADEMICS*
I completed an undergraduate degree in Computer Science, along with some
mathematics and physics courses. For the mathematics, I did some Calculus,
Linear Algebra, Differential Equations, Fourier series, Fourier & Laplace
transform. In Physics, I did up to and including a first course in Quantum
Mechanics.

I also did some undergraduate research work, that involved computational
high energy physics (proton-proton collision). The work was done with some
Mathematica packages (FeynArts <http://www.feynarts.de/>).

*INDUSTRY*
I currently work in the software industry and for the past few months, have
been performing both software development and system administration tasks.
In terms of object-oriented programming, my main experience is with Java.
I'm a beginner with Python. I used Python at work to automate the
reverse-engineering process of some Java programs.

Career-wise, one of my goals is to go into scientific computing, and use
Python as the main programming language, and to perhaps pursue graduate
studies in Computational Physics, hence my current interest for contributing
to NumPy & SciPy.

If you wish to know more about me I have a LinkedIn profile at
http://www.linkedin.com/in/sylvainbellemare.

*DOCUMENTATION*
Documentation-wise, I can use LaTeX. For instance, my resume, which is
attached with this email, was written with LaTeX. It's noteworthy to mention
that I like to work on documentation, as long as it balances with coding
work [?].

If that makes any sense to you and you have ideas on projects that I could
contribute to, please let me know, and I'll be very happy to do my very best
to contribute.

Best regards,
-Sylvain
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From scott.sinclair.za at gmail.com  Thu Mar 31 04:04:58 2011
From: scott.sinclair.za at gmail.com (Scott Sinclair)
Date: Thu, 31 Mar 2011 10:04:58 +0200
Subject: [SciPy-Dev] [Numpy-discussion] Willing to contribute to SciPy &
	NumPy ...
In-Reply-To: <BANLkTikKSLcJuSmL94eG8Q2KmL+EvyCY-A@mail.gmail.com>
References: <BANLkTikKSLcJuSmL94eG8Q2KmL+EvyCY-A@mail.gmail.com>
Message-ID: <AANLkTimTC_th2oq5bBqXs7yd+6gAfTwVy73w01NVpFz4@mail.gmail.com>

On 31 March 2011 07:27, Sylvain Bellemare <sbellem at gmail.com> wrote:
> ?I would like to seriously start contributing to NumPy and/or SciPy, as much as I possibly can.

I'm sure that your help will be welcomed!

A good place to get started is helping out with documentation (see
http://docs.scipy.org/numpy/Front%20Page/). SciPy has plenty of work
required - you'll probably learn your way into the code that way.
Another place to look is http://www.scipy.org/Developer_Zone. It's
worthwhile learning how to work with Git and Github if you want to get
patches accepted more easily.

Cheers,
Scott


From cournape at gmail.com  Thu Mar 31 05:19:39 2011
From: cournape at gmail.com (David Cournapeau)
Date: Thu, 31 Mar 2011 18:19:39 +0900
Subject: [SciPy-Dev] [Numpy-discussion] ANN: Numpy 1.6.0 beta 1
In-Reply-To: <rowen-3A77F5.15223129032011@news.gmane.org>
References: <AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs@mail.gmail.com>
	<rowen-3A77F5.15223129032011@news.gmane.org>
Message-ID: <AANLkTinZprs58RcatxtpA0svTZF3w2ci3gWL-=5eG5vA@mail.gmail.com>

On Wed, Mar 30, 2011 at 7:22 AM, Russell E. Owen <rowen at uw.edu> wrote:
> In article
> <AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs at mail.gmail.com>,
> ?Ralf Gommers <ralf.gommers at googlemail.com> wrote:
>
>> Hi,
>>
>> I am pleased to announce the availability of the first beta of NumPy
>> 1.6.0. Due to the extensive changes in the Numpy core for this
>> release, the beta testing phase will last at least one month. Please
>> test this beta and report any problems on the Numpy mailing list.
>>
>> Sources and binaries can be found at:
>> http://sourceforge.net/projects/numpy/files/NumPy/1.6.0b1/
>> For (preliminary) release notes see below.

I see a segfault on Ubuntu 64 bits for the test
TestAssumedShapeSumExample in numpy/f2py/tests/test_assumed_shape.py.
Am I the only one seeing it ?

David


From pearu.peterson at gmail.com  Thu Mar 31 05:37:24 2011
From: pearu.peterson at gmail.com (Pearu Peterson)
Date: Thu, 31 Mar 2011 12:37:24 +0300
Subject: [SciPy-Dev] [Numpy-discussion] ANN: Numpy 1.6.0 beta 1
In-Reply-To: <AANLkTinZprs58RcatxtpA0svTZF3w2ci3gWL-=5eG5vA@mail.gmail.com>
References: <AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs@mail.gmail.com>
	<rowen-3A77F5.15223129032011@news.gmane.org>
	<AANLkTinZprs58RcatxtpA0svTZF3w2ci3gWL-=5eG5vA@mail.gmail.com>
Message-ID: <AANLkTikiBWtgWFg560c0VC+Vf7o-=TkK9hMJLtG5gxYS@mail.gmail.com>

On Thu, Mar 31, 2011 at 12:19 PM, David Cournapeau <cournape at gmail.com>wrote:

> On Wed, Mar 30, 2011 at 7:22 AM, Russell E. Owen <rowen at uw.edu> wrote:
> > In article
> > <AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs at mail.gmail.com>,
> >  Ralf Gommers <ralf.gommers at googlemail.com> wrote:
> >
> >> Hi,
> >>
> >> I am pleased to announce the availability of the first beta of NumPy
> >> 1.6.0. Due to the extensive changes in the Numpy core for this
> >> release, the beta testing phase will last at least one month. Please
> >> test this beta and report any problems on the Numpy mailing list.
> >>
> >> Sources and binaries can be found at:
> >> http://sourceforge.net/projects/numpy/files/NumPy/1.6.0b1/
> >> For (preliminary) release notes see below.
>
> I see a segfault on Ubuntu 64 bits for the test
> TestAssumedShapeSumExample in numpy/f2py/tests/test_assumed_shape.py.
> Am I the only one seeing it ?
>
>
The test work here ok on Ubuntu 64 with numpy master. Could you try the
maintenance/1.6.x branch where the related bugs are fixed.

Pearu
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From nwagner at iam.uni-stuttgart.de  Thu Mar 31 08:02:21 2011
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Thu, 31 Mar 2011 14:02:21 +0200
Subject: [SciPy-Dev] Harwell Boeing support
Message-ID: <web-143926001@uni-stuttgart.de>

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.

http://projects.scipy.org/scipy/ticket/354

Nils


From scopatz at gmail.com  Thu Mar 31 15:04:47 2011
From: scopatz at gmail.com (Anthony Scopatz)
Date: Thu, 31 Mar 2011 14:04:47 -0500
Subject: [SciPy-Dev] [Numpy-discussion] Willing to contribute to SciPy &
	NumPy ...
In-Reply-To: <AANLkTimTC_th2oq5bBqXs7yd+6gAfTwVy73w01NVpFz4@mail.gmail.com>
References: <BANLkTikKSLcJuSmL94eG8Q2KmL+EvyCY-A@mail.gmail.com>
	<AANLkTimTC_th2oq5bBqXs7yd+6gAfTwVy73w01NVpFz4@mail.gmail.com>
Message-ID: <AANLkTi=r4-PROhomb4DL1wpTc9fovqt5-iKfk3iEsxfA@mail.gmail.com>

On Thu, Mar 31, 2011 at 3:04 AM, Scott Sinclair <scott.sinclair.za at gmail.com
> wrote:

> On 31 March 2011 07:27, Sylvain Bellemare <sbellem at gmail.com> wrote:
> >  I would like to seriously start contributing to NumPy and/or SciPy, as
> much as I possibly can.
>
> I'm sure that your help will be welcomed!
>
> A good place to get started is helping out with documentation (see
> http://docs.scipy.org/numpy/Front%20Page/).


Actually, according to the Jacob Kaplan-Moss's talk at PyCon this year (
http://pycon.blip.tv/file/4881071/)
(with which I am inclined to agree), documentation is probably not the best
way to get started.

Do check out the developer zone, maybe search the the open tickets and see
if there are any bugs you want to tackle.
Maybe write some tests for untested code you find.  If you have questions,
don't hesitate to ask.  And don't forget
to test and document your own code!

Be Well
Anthony


> SciPy has plenty of work
> required - you'll probably learn your way into the code that way.
> Another place to look is http://www.scipy.org/Developer_Zone. It's
> worthwhile learning how to work with Git and Github if you want to get
> patches accepted more easily.
>
> Cheers,
> Scott
> _______________________________________________
> NumPy-Discussion mailing list
> NumPy-Discussion at scipy.org
> http://mail.scipy.org/mailman/listinfo/numpy-discussion
>
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From joshua.m.grant at gmail.com  Thu Mar 31 19:04:34 2011
From: joshua.m.grant at gmail.com (Joshua Grant)
Date: Thu, 31 Mar 2011 19:04:34 -0400
Subject: [SciPy-Dev] Git Push
Message-ID: <AANLkTikwXmwU5Y2utG3DBB58Bh0LhjY8_5D8-ZYEiDiq@mail.gmail.com>

Hello. I've made some commits and would like to push them back into the
repository at github.com/scipy/scipy.git but I'm getting and error of
"error: Cannot access URL https://github.com/scipy/scipy/, return code 22".

Do I have to push to check in changes? And if so, any ideas? Thanks.
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From robert.kern at gmail.com  Thu Mar 31 19:11:28 2011
From: robert.kern at gmail.com (Robert Kern)
Date: Thu, 31 Mar 2011 18:11:28 -0500
Subject: [SciPy-Dev] Git Push
In-Reply-To: <AANLkTikwXmwU5Y2utG3DBB58Bh0LhjY8_5D8-ZYEiDiq@mail.gmail.com>
References: <AANLkTikwXmwU5Y2utG3DBB58Bh0LhjY8_5D8-ZYEiDiq@mail.gmail.com>
Message-ID: <AANLkTimc_KNWWHbzA3b4NbusyH8NLR3ZQzttQekSHCAR@mail.gmail.com>

On Thu, Mar 31, 2011 at 18:04, Joshua Grant <joshua.m.grant at gmail.com> wrote:
> Hello. I've made some commits and would like to push them back into the
> repository at github.com/scipy/scipy.git but I'm getting and error of
> "error: Cannot access URL https://github.com/scipy/scipy/, return code 22".
>
> Do I have to push to check in changes? And if so, any ideas? Thanks.

You should probably clone the SSH repo rather than the HTTPS repo.
Have you been given commit privileges? It would probably be best to
fork scipy to your own github account, make your changes in a branch
there, and then make a pull request so the changes can be reviewed.
You can take a look at IPython's guide to development for an idea of
how to do this (just replace the URLs appropriately):

http://ipython.scipy.org/doc/nightly/html/development/gitwash/git_development.html

-- 
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 joshua.m.grant at gmail.com  Thu Mar 31 21:09:24 2011
From: joshua.m.grant at gmail.com (Joshua Grant)
Date: Thu, 31 Mar 2011 21:09:24 -0400
Subject: [SciPy-Dev] Git Push
In-Reply-To: <AANLkTimc_KNWWHbzA3b4NbusyH8NLR3ZQzttQekSHCAR@mail.gmail.com>
References: <AANLkTikwXmwU5Y2utG3DBB58Bh0LhjY8_5D8-ZYEiDiq@mail.gmail.com>
	<AANLkTimc_KNWWHbzA3b4NbusyH8NLR3ZQzttQekSHCAR@mail.gmail.com>
Message-ID: <AANLkTinFRj3sZpswN_PjNMzLTrcriCwfz3+OKB+UnPkt@mail.gmail.com>

Thanks for the link. That makes a lot more sense now. Thanks again!

Josh

On Thu, Mar 31, 2011 at 7:11 PM, Robert Kern <robert.kern at gmail.com> wrote:

> On Thu, Mar 31, 2011 at 18:04, Joshua Grant <joshua.m.grant at gmail.com>
> wrote:
> > Hello. I've made some commits and would like to push them back into the
> > repository at github.com/scipy/scipy.git but I'm getting and error of
> > "error: Cannot access URL https://github.com/scipy/scipy/, return code
> 22".
> >
> > Do I have to push to check in changes? And if so, any ideas? Thanks.
>
> You should probably clone the SSH repo rather than the HTTPS repo.
> Have you been given commit privileges? It would probably be best to
> fork scipy to your own github account, make your changes in a branch
> there, and then make a pull request so the changes can be reviewed.
> You can take a look at IPython's guide to development for an idea of
> how to do this (just replace the URLs appropriately):
>
>
> http://ipython.scipy.org/doc/nightly/html/development/gitwash/git_development.html
>
> --
> 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
>
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