cclib-devel

[cclib-devel] Numeric --> numpy

[Noel O'B. <bao...@gm...>]

Hello all,

We're going to have to start thinking about transitioning to numpy at
some point this year. Numeric is not available for Python 2.5 on
Windows, for example, and there is a big push for users to move to
numpy.

How are things on Gentoo at this stage?

Regards,
  Noel

Re: [cclib-devel] Numeric --> numpy

[Karol L. <kar...@kn...>]

On Thursday 25 of January 2007 13:17, Noel O'Boyle wrote:
> Hello all,
>
> We're going to have to start thinking about transitioning to numpy at
> some point this year. Numeric is not available for Python 2.5 on
> Windows, for example, and there is a big push for users to move to
> numpy.
>
> How are things on Gentoo at this stage?
>
> Regards,
>   Noel

I was actually going to ask about this soon, and will certainly help when the 
time comes if I'm not loaded with work. I guess you're thinking about making 
the transition quickly?

Karol

-- 
written by Karol Langner
Thu Jan 25 16:23:06 CET 2007

Re: [cclib-devel] Numeric --> numpy

[Adam T. <a-t...@st...>]

I agree that we should move to numpy soon as Numeric is old. Are  
there major differences between the two? Hopefully the conversion  
won't be too difficult or time consuming...

Adam

On Jan 25, 2007, at 7:24 AM, Karol Langner wrote:

> On Thursday 25 of January 2007 13:17, Noel O'Boyle wrote:
>> Hello all,
>>
>> We're going to have to start thinking about transitioning to numpy at
>> some point this year. Numeric is not available for Python 2.5 on
>> Windows, for example, and there is a big push for users to move to
>> numpy.
>>
>> How are things on Gentoo at this stage?
>>
>> Regards,
>>   Noel
>
> I was actually going to ask about this soon, and will certainly  
> help when the
> time comes if I'm not loaded with work. I guess you're thinking  
> about making
> the transition quickly?
>
> Karol
>
> -- 
> written by Karol Langner
> Thu Jan 25 16:23:06 CET 2007
>
> ---------------------------------------------------------------------- 
> ---
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Re: [cclib-devel] Numeric --> numpy

[Noel O'B. <bao...@gm...>]

I don't know much about the differences, but I'd be hoping they are
minor. But it might be a better idea to do this immediately *after*
the next release, rather than before - we have enough to go into it at
the moment. But I recall that one of the original reasons we didn't
move to numpy this time last year was that it didn't compile easily on
Gentoo. Has this situation improved?

On 25/01/07, Adam Tenderholt <a-t...@st...> wrote:
> I agree that we should move to numpy soon as Numeric is old. Are
> there major differences between the two? Hopefully the conversion
> won't be too difficult or time consuming...
>
> Adam
>
> On Jan 25, 2007, at 7:24 AM, Karol Langner wrote:
>
> > On Thursday 25 of January 2007 13:17, Noel O'Boyle wrote:
> >> Hello all,
> >>
> >> We're going to have to start thinking about transitioning to numpy at
> >> some point this year. Numeric is not available for Python 2.5 on
> >> Windows, for example, and there is a big push for users to move to
> >> numpy.
> >>
> >> How are things on Gentoo at this stage?
> >>
> >> Regards,
> >>   Noel
> >
> > I was actually going to ask about this soon, and will certainly
> > help when the
> > time comes if I'm not loaded with work. I guess you're thinking
> > about making
> > the transition quickly?
> >
> > Karol
> >
> > --
> > written by Karol Langner
> > Thu Jan 25 16:23:06 CET 2007
> >
> > ----------------------------------------------------------------------
> > ---
> > Take Surveys. Earn Cash. Influence the Future of IT
> > Join SourceForge.net's Techsay panel and you'll get the chance to
> > share your
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> > page=join.php&p=sourceforge&CID=DEVDEV
> > _______________________________________________
> > cclib-devel mailing list
> > ccl...@li...
> > https://lists.sourceforge.net/lists/listinfo/cclib-devel
>
>
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Re: [cclib-devel] Numeric --> numpy

[Adam T. <a-t...@st...>]

I briefly looked into the conversion from Numeric to numpy, and it  
looks like there is a script that does all of the conversion for you  
since there is an oldnumeric module of numpy. Granted, the script  
probably isn't flawless. Also, it may be that we can detect whether  
numpy is available and if so, import the numpy.oldnumeric interface  
as Numeric (that's actually what the aforementioned script does);  
otherwise, just import Numeric.

I do agree that we should wait until after the next release as this  
release already had numerous changes. I don't know if numpy compiles  
on Gentoo---since I bought my mac, I don't develop on Gentoo much  
these days.

Adam

On Jan 25, 2007, at 11:12 AM, Noel O'Boyle wrote:

> I don't know much about the differences, but I'd be hoping they are
> minor. But it might be a better idea to do this immediately *after*
> the next release, rather than before - we have enough to go into it at
> the moment. But I recall that one of the original reasons we didn't
> move to numpy this time last year was that it didn't compile easily on
> Gentoo. Has this situation improved?
>
> On 25/01/07, Adam Tenderholt <a-t...@st...> wrote:
>> I agree that we should move to numpy soon as Numeric is old. Are
>> there major differences between the two? Hopefully the conversion
>> won't be too difficult or time consuming...
>>
>> Adam
>>
>> On Jan 25, 2007, at 7:24 AM, Karol Langner wrote:
>>
>>> On Thursday 25 of January 2007 13:17, Noel O'Boyle wrote:
>>>> Hello all,
>>>>
>>>> We're going to have to start thinking about transitioning to  
>>>> numpy at
>>>> some point this year. Numeric is not available for Python 2.5 on
>>>> Windows, for example, and there is a big push for users to move to
>>>> numpy.
>>>>
>>>> How are things on Gentoo at this stage?
>>>>
>>>> Regards,
>>>>   Noel
>>>
>>> I was actually going to ask about this soon, and will certainly
>>> help when the
>>> time comes if I'm not loaded with work. I guess you're thinking
>>> about making
>>> the transition quickly?
>>>
>>> Karol
>>>
>>> --
>>> written by Karol Langner
>>> Thu Jan 25 16:23:06 CET 2007
>>>
>>> -------------------------------------------------------------------- 
>>> --
>>> ---
>>> Take Surveys. Earn Cash. Influence the Future of IT
>>> Join SourceForge.net's Techsay panel and you'll get the chance to
>>> share your
>>> opinions on IT & business topics through brief surveys - and earn  
>>> cash
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>>> page=join.php&p=sourceforge&CID=DEVDEV
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>>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>>
>>
>> --------------------------------------------------------------------- 
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>
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Re: [cclib-devel] Numeric --> numpy

[Karol L. <kar...@kn...>]

On Thursday 25 of January 2007 20:25, Adam Tenderholt wrote:
> I briefly looked into the conversion from Numeric to numpy, and it
> looks like there is a script that does all of the conversion for you
> since there is an oldnumeric module of numpy. Granted, the script
> probably isn't flawless. Also, it may be that we can detect whether
> numpy is available and if so, import the numpy.oldnumeric interface
> as Numeric (that's actually what the aforementioned script does);
> otherwise, just import Numeric.

Yes, there is a script, but I've read some people complaining about it (don't 
know if justified).

> I do agree that we should wait until after the next release as this
> release already had numerous changes. I don't know if numpy compiles
> on Gentoo---since I bought my mac, I don't develop on Gentoo much
> these days.

I checked on a machine that runs an up-to-date Gentoo system, and numpy is 
installed system-wide there from portage, version 0.9.8 with python 2.4.3. 
Seems to work fine when played with, but running numpy.test() ends in a 
segmentation fault. That's probably caused by a problem with system 
libraries, becasue I also have a local install of numpy 1.0 with python 2.5 
on that machine, and the tests finish fine in that case - the local 
installation uses my local ATLAS compilation.

Here is a list of attributes cclib uses in Numeric:

['Numeric.matrixmultiply', 'Numeric.resize', 'Numeric.multiply', 
'Numeric.divide', 'Numeric.array', 'Numeric.swapaxes', 
'Numeric.innerproduct', 'Numeric.alltrue', 'Numeric.transpose', 
'Numeric.arange', 'Numeric.add', 'Numeric.__version__', 'Numeric.reshape', 
'Numeric.zeros']

As you can see, it isn't much, so there really shouldn't be much work in this 
regard. There's also the slicing and other references to arrays, but that 
hasn't really changed in numpy.

What has changed in the above functions:
1. matrixmultiply is no more (use numpy.dot)
2. innerproduct is no more (I don't know what to use instead)

Also, there is a new matrix object (matrix multiplication for a*b), but that's 
not too useful for cclib.

Karol

-- 
written by Karol Langner
Fri Jan 26 07:51:39 CET 2007

Re: [cclib-devel] Numeric --> numpy

[Noel O'B. <bao...@gm...>]

Both myself and Adam are also thinking of our own programs, which will
also need to be adjusted. They will already have to be changed
slightly to deal with the redefinition of mocoeffs and a couple of
other attributes.

What this adds up to is that if nobody disagrees, this will be the
first thing we'll do after the next release.

Noel

On 26/01/07, Karol Langner <kar...@kn...> wrote:
> On Thursday 25 of January 2007 20:25, Adam Tenderholt wrote:
> > I briefly looked into the conversion from Numeric to numpy, and it
> > looks like there is a script that does all of the conversion for you
> > since there is an oldnumeric module of numpy. Granted, the script
> > probably isn't flawless. Also, it may be that we can detect whether
> > numpy is available and if so, import the numpy.oldnumeric interface
> > as Numeric (that's actually what the aforementioned script does);
> > otherwise, just import Numeric.
>
> Yes, there is a script, but I've read some people complaining about it (don't
> know if justified).
>
> > I do agree that we should wait until after the next release as this
> > release already had numerous changes. I don't know if numpy compiles
> > on Gentoo---since I bought my mac, I don't develop on Gentoo much
> > these days.
>
> I checked on a machine that runs an up-to-date Gentoo system, and numpy is
> installed system-wide there from portage, version 0.9.8 with python 2.4.3.
> Seems to work fine when played with, but running numpy.test() ends in a
> segmentation fault. That's probably caused by a problem with system
> libraries, becasue I also have a local install of numpy 1.0 with python 2.5
> on that machine, and the tests finish fine in that case - the local
> installation uses my local ATLAS compilation.
>
> Here is a list of attributes cclib uses in Numeric:
>
> ['Numeric.matrixmultiply', 'Numeric.resize', 'Numeric.multiply',
> 'Numeric.divide', 'Numeric.array', 'Numeric.swapaxes',
> 'Numeric.innerproduct', 'Numeric.alltrue', 'Numeric.transpose',
> 'Numeric.arange', 'Numeric.add', 'Numeric.__version__', 'Numeric.reshape',
> 'Numeric.zeros']
>
> As you can see, it isn't much, so there really shouldn't be much work in this
> regard. There's also the slicing and other references to arrays, but that
> hasn't really changed in numpy.
>
> What has changed in the above functions:
> 1. matrixmultiply is no more (use numpy.dot)
> 2. innerproduct is no more (I don't know what to use instead)
>
> Also, there is a new matrix object (matrix multiplication for a*b), but that's
> not too useful for cclib.
>
> Karol
>
> --
> written by Karol Langner
> Fri Jan 26 07:51:39 CET 2007
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
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Re: [cclib-devel] Numeric --> numpy

[Karol L. <kar...@kn...>]

On Friday 26 of January 2007 09:00, Noel O'Boyle wrote:
> Both myself and Adam are also thinking of our own programs, which will
> also need to be adjusted. They will already have to be changed
> slightly to deal with the redefinition of mocoeffs and a couple of
> other attributes.

Didn't think about that.

> What this adds up to is that if nobody disagrees, this will be the
> first thing we'll do after the next release.

Incidentally, is there a planned release date?

Karol

-- 
written by Karol Langner
Fri Jan 26 13:35:42 CET 2007

Re: [cclib-devel] Numeric --> numpy

[Karol L. <kar...@kn...>]

On Friday 26 of January 2007 09:00, Noel O'Boyle wrote:
> Both myself and Adam are also thinking of our own programs, which will
> also need to be adjusted. They will already have to be changed
> slightly to deal with the redefinition of mocoeffs and a couple of
> other attributes.
>
> What this adds up to is that if nobody disagrees, this will be the
> first thing we'll do after the next release.
>
> Noel

One more thing: from Numeric 24.2 onwards, there generally is supposed to be 
no major problems with passing numpy arrays to Numeric. There was a thread 
about this a couple of days ago on the Numpy-discussion mailing list.

I'm not pushing for the conversion to be sooner, just wanted to make sure you 
know that your cclib-dependent programs will probably still work fine after a 
cclib upgrade if they are not upgraded themselves.

Karol

-- 
written by Karol Langner
Wed Jan 31 17:01:12 CET 2007