pysparse-developers — pysparse developer talk

Re: [Pysparse-developers] [Pysparse-users] updated pysparse for numpy

[Daniel W. <dan...@ni...>]

Thanks for the help. I implemented everything you suggested. I hadn't  
tested on a system
without Numeric, which was a little silly.

On Feb 1, 2007, at 6:13 PM, Dominique Orban wrote:

> Daniel,
>
> I just installed the latest NumPy 1.0.1 and downloaded PySparse from
> cvs. I don't have the old Numeric installed, and testing PySparse
> caused a number of problems. Here are a few dirty changes to make
> things work. I suspect it would be best to have a config file (a la
> Matplotlib) while users are still transitioning from Numeric to NumPy,
> in order to know which they are currently using.

I changed the setup so that it automatically installs using numpy if  
available otherwise it falls
back on Numeric. I haven't setup a config file, I don't like that  
idea, in a sense the setup.py is
the config file. Probably should just have a numerix.py file in Lib/  
that is overwritten by setup.py
on install. In the tests you would have "from pysparse import  
numerix" and use numerix instead of
numpy or Numeric. Anyway, Numeric will slowly become obsolete so I  
won't bother.


> In the meantime, here
> are the difficulties I came across:
>
> On line 19 of Src/ll_mat.c, there is an #include
> Numeric/array_object.h which breaks things
> when using NumPy and the old Numeric is not installed. I commented it
> out and could compile the everything.

Got it.

> In test_superlu.py, replace
> import Numeric
> with
> import numpy as Numeric
> Of course, it would be better to import the appropriate "numerix"  
> according to
> local settings.

Done.

> In test_sparray.py, there is an error at the top, replace
> from pysparse import sparray
> with
> from pysparse.sparray import sparray
> After that I still get the error:
>
> testgetitem (__main__.test_sparray) ... ERROR
> testinit (__main__.test_sparray) ... ok
> testsetitem (__main__.test_sparray) ... ok
>
> ======================================================================
> ERROR: testgetitem (__main__.test_sparray)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "test_sparray.py", line 30, in testgetitem
>    self.assertEqual(a[:,3], map(float, (1,2,3,4,5)))
>  File "/usr/lib/python2.3/unittest.py", line 301, in failUnlessEqual
>    if not first == second:
> ValueError: The truth value of an array with more than one element is
> ambiguous. Use a.any() or a.all()
>
> ----------------------------------------------------------------------
> Ran 3 tests in 0.027s
>
> FAILED (errors=1)
>
> I am not familiar with the unittest module, but I guess the test  
> class should
> have a custom assertEqual method.

It's using assertEqual, just that unittest is doing a "==" on a numpy  
array and a tuple
of floats, which numpy doesn't like. Anyway, I fixed it, so should be  
good now.

> In test_spmatrix.py, an error occurs from spmatrix_utils.py, saying  
> that
> pysparse_version doesn't exist. Indeed it doesn't. So in  
> spmatrix_utils.py, I
> commented out line 3 (which imports the fictitious module) and  
> replace line 66
> with
>
> comment = 'generated using pysparse-%s\n' % (pysparse__version__, )

Done.

> Next, I changed line 6 of test_spmatrix.py to read
>
> import numpy as Numeric, numpy.oldnumeric.random_array as RandomArray
>
> and line 119 to read
>
> import numpy as Numeric
>
> After that, test_spmatrix.py ran just fine. Sorry if the changes above
> look dirty. This is just to let you know where the current tests
> break.

Done.

Once again, thanks for your feedback.

>
> Dominique
>
>
> On 1/4/07, Daniel Wheeler <dan...@ni...> wrote:
>>
>> On Jan 3, 2007, at 4:37 AM, Roman Geus wrote:
>>
>> > Hello Daniel
>> >
>> > Thanks a lot for your contribution. Judging from the description  
>> your
>> > changes make much sense. I have not been using pysparse myself  
>> for a
>> > long time so cannot be the person to test new versions.
>>
>> Hi Roman,
>>
>> Hope all is well. No problem about testing. We still use it a lot
>> with FiPy.
>> I will release a new version of pysparse ASAP and give it a version
>> number
>> of 1.0 since we have changed the namespace and it has now become
>> dependent
>> on a new array package.
>>
>> Cheers
>>
>> >
>> > Happy new year!
>> > -- Roman
>> >
>> > 2007/1/2, Daniel Wheeler <dan...@ni...>:
>> >>
>> >> The changes for compatibility with numpy have now been merged back
>> >> onto
>> >> HEAD. I will do a new release in the near future.
>> >>
>> >> Cheers
>> >>
>> >>
>> >> On Dec 21, 2006, at 12:36 PM, Daniel Wheeler wrote:
>> >>
>> >> Numeric is dying slowly and being replaced by numpy.
>> >> With this in mind, I have updated pysparse to use the new numpy,
>> >> this is all
>> >> on a branch at the moment.
>> >> It was straightforward matter of changing the imported header
>> >> files from
>> >> Numeric's to numpy's. I am sending this email
>> >> to check to see if everybody is happy with the changes that have
>> >> been made.
>> >> If there are no objections, I can merge back
>> >> onto the trunk and maybe make a new release. Changes  and issues
>> >> are as
>> >> follows:
>> >>
>> >>    - Created a C macro defined from setup.py that either imports
>> >> numpy's or
>> >> Numeric's headers depending
>> >>      on the flag "use_numpy". The C macro was confusing me for
>> >> awhile, but I
>> >> think it works
>> >>      now.
>> >>
>> >>    - I have changed the name space of itsolvers, spmatrix, jdsym
>> >> etc to all
>> >> lie under pysparse. So, instead of
>> >>
>> >>          >>> import spmatrix
>> >>
>> >>       you do
>> >>
>> >>          >>> from pysparse import spmatrix
>> >>
>> >>        This change stops site-packages from being polluted. At the
>> >> moment
>> >> the branch version is using pysparse_numpy
>> >>        or pysparse_Numeric as the pysparse name space for testing
>> >> purposes.
>> >>
>> >>     - The branch can be checked out via:
>> >>
>> >>             $ cvs -d:ext:ui...@py...:/cvsroot/pysparse
>> >> co -r
>> >> branch-numpy pysparse
>> >>
>> >>     - I have updated the Examples and Test directories to  
>> import from
>> >> pysparse. They all seem to work apart from stuff that was broken
>> >> already.
>> >>
>> >>     - I got rid of pysparse_version.py and replaced it with an
>> >> __init__.py
>> >> in Lib, which does the imports and holds a __version__ variable.
>> >>       So you can now do:
>> >>
>> >>              >>> import pysparse_numpy
>> >>              >>> print pysparse_numpy.__version__
>> >>              0.34.032-numpy
>> >>
>> >>     - I think the default flag should be use_numpy=True since most
>> >> users
>> >> will now be getting numpy rather than Numeric. This could
>> >>       be automated with a try and except, which tests for the
>> >> availability
>> >> of numpy or Numeric. What do you think?
>> >>
>> >>     - You can diff from your working copy of pysparse with "cvs
>> >> diff -c -r
>> >> branch-numpy" to check the changes.
>> >>
>> >>     - Is it worth bumping the version number of pysparse to 1.0,
>> >> since we
>> >> will be breaking the name space (interface change)?
>> >>
>> >>     - If you are compiling against numpy, the numpy header files
>> >> don't seem
>> >> to be going into the right place at least on my two computers.
>> >>       I haven't resolved this problem yet. For now, I was just
>> >> copying the
>> >> .h files from .../site-packages/python/numpy/core/include/
>> >> to Include/Lib/numpy
>> >>       in my working copy of pysparse.
>> >>
>> >> Merry Christmas!
>> >>
>> >>
>> >> --
>> >> Daniel Wheeler
>> >>
>> >>  
>> ---------------------------------------------------------------------
>> >> ----
>> >> 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
>> >> http://www.techsay.com/default.php?
>> >>  
>> page=join.php&p=sourceforge&CID=DEVDEV_______________________________
>> >> ________________
>> >> Pysparse-users mailing list
>> >> Pys...@li...
>> >> https://lists.sourceforge.net/lists/listinfo/pysparse-users
>> >>
>> >>
>> >> --
>> >>
>> >> Daniel Wheeler
>> >>
>> >>
>> >>  
>> ---------------------------------------------------------------------
>> >> ----
>> >> 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
>> >> http://www.techsay.com/default.php?
>> >> page=join.php&p=sourceforge&CID=DEVDEV
>> >>
>> >> _______________________________________________
>> >> Pysparse-users mailing list
>> >> Pys...@li...
>> >> https://lists.sourceforge.net/lists/listinfo/pysparse-users
>>
>> --
>> Daniel Wheeler
>>
>>
>>
>>

--
Daniel Wheeler

Re: [Pysparse-developers] [Pysparse-users] updated pysparse for numpy

[Dominique O. <dom...@gm...>]

Daniel,

I just installed the latest NumPy 1.0.1 and downloaded PySparse from
cvs. I don't have the old Numeric installed, and testing PySparse
caused a number of problems. Here are a few dirty changes to make
things work. I suspect it would be best to have a config file (a la
Matplotlib) while users are still transitioning from Numeric to NumPy,
in order to know which they are currently using. In the meantime, here
are the difficulties I came across:

On line 19 of Src/ll_mat.c, there is an #include
Numeric/array_object.h which breaks things
when using NumPy and the old Numeric is not installed. I commented it
out and could compile the everything.

In test_superlu.py, replace
 import Numeric
with
 import numpy as Numeric
Of course, it would be better to import the appropriate "numerix" according to
local settings.

In test_sparray.py, there is an error at the top, replace
 from pysparse import sparray
with
 from pysparse.sparray import sparray
After that I still get the error:

testgetitem (__main__.test_sparray) ... ERROR
testinit (__main__.test_sparray) ... ok
testsetitem (__main__.test_sparray) ... ok

======================================================================
ERROR: testgetitem (__main__.test_sparray)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_sparray.py", line 30, in testgetitem
    self.assertEqual(a[:,3], map(float, (1,2,3,4,5)))
  File "/usr/lib/python2.3/unittest.py", line 301, in failUnlessEqual
    if not first == second:
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()

----------------------------------------------------------------------
Ran 3 tests in 0.027s

FAILED (errors=1)

I am not familiar with the unittest module, but I guess the test class should
have a custom assertEqual method.

In test_spmatrix.py, an error occurs from spmatrix_utils.py, saying that
pysparse_version doesn't exist. Indeed it doesn't. So in spmatrix_utils.py, I
commented out line 3 (which imports the fictitious module) and replace line 66
with

 comment = 'generated using pysparse-%s\n' % (pysparse__version__, )

Next, I changed line 6 of test_spmatrix.py to read

 import numpy as Numeric, numpy.oldnumeric.random_array as RandomArray

and line 119 to read

 import numpy as Numeric

After that, test_spmatrix.py ran just fine. Sorry if the changes above
look dirty. This is just to let you know where the current tests
break.

Dominique


On 1/4/07, Daniel Wheeler <dan...@ni...> wrote:
>
> On Jan 3, 2007, at 4:37 AM, Roman Geus wrote:
>
> > Hello Daniel
> >
> > Thanks a lot for your contribution. Judging from the description your
> > changes make much sense. I have not been using pysparse myself for a
> > long time so cannot be the person to test new versions.
>
> Hi Roman,
>
> Hope all is well. No problem about testing. We still use it a lot
> with FiPy.
> I will release a new version of pysparse ASAP and give it a version
> number
> of 1.0 since we have changed the namespace and it has now become
> dependent
> on a new array package.
>
> Cheers
>
> >
> > Happy new year!
> > -- Roman
> >
> > 2007/1/2, Daniel Wheeler <dan...@ni...>:
> >>
> >> The changes for compatibility with numpy have now been merged back
> >> onto
> >> HEAD. I will do a new release in the near future.
> >>
> >> Cheers
> >>
> >>
> >> On Dec 21, 2006, at 12:36 PM, Daniel Wheeler wrote:
> >>
> >> Numeric is dying slowly and being replaced by numpy.
> >> With this in mind, I have updated pysparse to use the new numpy,
> >> this is all
> >> on a branch at the moment.
> >> It was straightforward matter of changing the imported header
> >> files from
> >> Numeric's to numpy's. I am sending this email
> >> to check to see if everybody is happy with the changes that have
> >> been made.
> >> If there are no objections, I can merge back
> >> onto the trunk and maybe make a new release. Changes  and issues
> >> are as
> >> follows:
> >>
> >>    - Created a C macro defined from setup.py that either imports
> >> numpy's or
> >> Numeric's headers depending
> >>      on the flag "use_numpy". The C macro was confusing me for
> >> awhile, but I
> >> think it works
> >>      now.
> >>
> >>    - I have changed the name space of itsolvers, spmatrix, jdsym
> >> etc to all
> >> lie under pysparse. So, instead of
> >>
> >>          >>> import spmatrix
> >>
> >>       you do
> >>
> >>          >>> from pysparse import spmatrix
> >>
> >>        This change stops site-packages from being polluted. At the
> >> moment
> >> the branch version is using pysparse_numpy
> >>        or pysparse_Numeric as the pysparse name space for testing
> >> purposes.
> >>
> >>     - The branch can be checked out via:
> >>
> >>             $ cvs -d:ext:ui...@py...:/cvsroot/pysparse
> >> co -r
> >> branch-numpy pysparse
> >>
> >>     - I have updated the Examples and Test directories to import from
> >> pysparse. They all seem to work apart from stuff that was broken
> >> already.
> >>
> >>     - I got rid of pysparse_version.py and replaced it with an
> >> __init__.py
> >> in Lib, which does the imports and holds a __version__ variable.
> >>       So you can now do:
> >>
> >>              >>> import pysparse_numpy
> >>              >>> print pysparse_numpy.__version__
> >>              0.34.032-numpy
> >>
> >>     - I think the default flag should be use_numpy=True since most
> >> users
> >> will now be getting numpy rather than Numeric. This could
> >>       be automated with a try and except, which tests for the
> >> availability
> >> of numpy or Numeric. What do you think?
> >>
> >>     - You can diff from your working copy of pysparse with "cvs
> >> diff -c -r
> >> branch-numpy" to check the changes.
> >>
> >>     - Is it worth bumping the version number of pysparse to 1.0,
> >> since we
> >> will be breaking the name space (interface change)?
> >>
> >>     - If you are compiling against numpy, the numpy header files
> >> don't seem
> >> to be going into the right place at least on my two computers.
> >>       I haven't resolved this problem yet. For now, I was just
> >> copying the
> >> .h files from .../site-packages/python/numpy/core/include/
> >> to Include/Lib/numpy
> >>       in my working copy of pysparse.
> >>
> >> Merry Christmas!
> >>
> >>
> >> --
> >> Daniel Wheeler
> >>
> >> ---------------------------------------------------------------------
> >> ----
> >> 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
> >> http://www.techsay.com/default.php?
> >> page=join.php&p=sourceforge&CID=DEVDEV_______________________________
> >> ________________
> >> Pysparse-users mailing list
> >> Pys...@li...
> >> https://lists.sourceforge.net/lists/listinfo/pysparse-users
> >>
> >>
> >> --
> >>
> >> Daniel Wheeler
> >>
> >>
> >> ---------------------------------------------------------------------
> >> ----
> >> 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
> >> http://www.techsay.com/default.php?
> >> page=join.php&p=sourceforge&CID=DEVDEV
> >>
> >> _______________________________________________
> >> Pysparse-users mailing list
> >> Pys...@li...
> >> https://lists.sourceforge.net/lists/listinfo/pysparse-users
>
> --
> Daniel Wheeler
>
>
>
>

Re: [Pysparse-developers] [Pysparse-users] updated pysparse for numpy

[Daniel W. <dan...@ni...>]

On Jan 3, 2007, at 4:37 AM, Roman Geus wrote:

> Hello Daniel
>
> Thanks a lot for your contribution. Judging from the description your
> changes make much sense. I have not been using pysparse myself for a
> long time so cannot be the person to test new versions.

Hi Roman,

Hope all is well. No problem about testing. We still use it a lot  
with FiPy.
I will release a new version of pysparse ASAP and give it a version  
number
of 1.0 since we have changed the namespace and it has now become  
dependent
on a new array package.

Cheers

>
> Happy new year!
> -- Roman
>
> 2007/1/2, Daniel Wheeler <dan...@ni...>:
>>
>> The changes for compatibility with numpy have now been merged back  
>> onto
>> HEAD. I will do a new release in the near future.
>>
>> Cheers
>>
>>
>> On Dec 21, 2006, at 12:36 PM, Daniel Wheeler wrote:
>>
>> Numeric is dying slowly and being replaced by numpy.
>> With this in mind, I have updated pysparse to use the new numpy,  
>> this is all
>> on a branch at the moment.
>> It was straightforward matter of changing the imported header  
>> files from
>> Numeric's to numpy's. I am sending this email
>> to check to see if everybody is happy with the changes that have  
>> been made.
>> If there are no objections, I can merge back
>> onto the trunk and maybe make a new release. Changes  and issues  
>> are as
>> follows:
>>
>>    - Created a C macro defined from setup.py that either imports  
>> numpy's or
>> Numeric's headers depending
>>      on the flag "use_numpy". The C macro was confusing me for  
>> awhile, but I
>> think it works
>>      now.
>>
>>    - I have changed the name space of itsolvers, spmatrix, jdsym  
>> etc to all
>> lie under pysparse. So, instead of
>>
>>          >>> import spmatrix
>>
>>       you do
>>
>>          >>> from pysparse import spmatrix
>>
>>        This change stops site-packages from being polluted. At the  
>> moment
>> the branch version is using pysparse_numpy
>>        or pysparse_Numeric as the pysparse name space for testing  
>> purposes.
>>
>>     - The branch can be checked out via:
>>
>>             $ cvs -d:ext:ui...@py...:/cvsroot/pysparse  
>> co -r
>> branch-numpy pysparse
>>
>>     - I have updated the Examples and Test directories to import from
>> pysparse. They all seem to work apart from stuff that was broken  
>> already.
>>
>>     - I got rid of pysparse_version.py and replaced it with an  
>> __init__.py
>> in Lib, which does the imports and holds a __version__ variable.
>>       So you can now do:
>>
>>              >>> import pysparse_numpy
>>              >>> print pysparse_numpy.__version__
>>              0.34.032-numpy
>>
>>     - I think the default flag should be use_numpy=True since most  
>> users
>> will now be getting numpy rather than Numeric. This could
>>       be automated with a try and except, which tests for the  
>> availability
>> of numpy or Numeric. What do you think?
>>
>>     - You can diff from your working copy of pysparse with "cvs  
>> diff -c -r
>> branch-numpy" to check the changes.
>>
>>     - Is it worth bumping the version number of pysparse to 1.0,  
>> since we
>> will be breaking the name space (interface change)?
>>
>>     - If you are compiling against numpy, the numpy header files  
>> don't seem
>> to be going into the right place at least on my two computers.
>>       I haven't resolved this problem yet. For now, I was just  
>> copying the
>> .h files from .../site-packages/python/numpy/core/include/
>> to Include/Lib/numpy
>>       in my working copy of pysparse.
>>
>> Merry Christmas!
>>
>>
>> --
>> Daniel Wheeler
>>
>> --------------------------------------------------------------------- 
>> ----
>> 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
>> http://www.techsay.com/default.php? 
>> page=join.php&p=sourceforge&CID=DEVDEV_______________________________ 
>> ________________
>> Pysparse-users mailing list
>> Pys...@li...
>> https://lists.sourceforge.net/lists/listinfo/pysparse-users
>>
>>
>> --
>>
>> Daniel Wheeler
>>
>>
>> --------------------------------------------------------------------- 
>> ----
>> 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
>> http://www.techsay.com/default.php? 
>> page=join.php&p=sourceforge&CID=DEVDEV
>>
>> _______________________________________________
>> Pysparse-users mailing list
>> Pys...@li...
>> https://lists.sourceforge.net/lists/listinfo/pysparse-users

--
Daniel Wheeler

Re: [Pysparse-developers] [Pysparse-users] updated pysparse for numpy

[Daniel W. <dan...@ni...>]

On Jan 2, 2007, at 3:28 PM, Daniel Wheeler wrote:

> The changes for compatibility with numpy have now been merged back  
> onto HEAD. I will do a new release in the near future.

I forgot to notify about two things. Firstly, you will need version  
1.0 of numpy. Version 0.9.8 didn't have the correct header files
for backwards compatibility with old Numeric modules. Secondly, at  
the current time, at least for me, the numpy header files do
not seem to be going in the right place with the numpy install (same  
thing has happend on my mac and linux).
You'll have to copy or link the header files from python2.4/site- 
packages/numpy/core/include to include/numpy in the base pysparse
directory from where you are building.

Cheers




>
> Cheers
>
> On Dec 21, 2006, at 12:36 PM, Daniel Wheeler wrote:
>
>> Numeric is dying slowly and being replaced by numpy.
>> With this in mind, I have updated pysparse to use the new numpy,  
>> this is all on a branch at the moment.
>> It was straightforward matter of changing the imported header  
>> files from Numeric's to numpy's. I am sending this email
>> to check to see if everybody is happy with the changes that have  
>> been made. If there are no objections, I can merge back
>> onto the trunk and maybe make a new release. Changes  and issues  
>> are as follows:
>>
>>    - Created a C macro defined from setup.py that either imports  
>> numpy's or Numeric's headers depending
>>      on the flag "use_numpy". The C macro was confusing me for  
>> awhile, but I think it works
>>      now.
>>
>>    - I have changed the name space of itsolvers, spmatrix, jdsym  
>> etc to all lie under pysparse. So, instead of
>>
>>          >>> import spmatrix
>>
>>       you do
>>
>>          >>> from pysparse import spmatrix
>>
>>        This change stops site-packages from being polluted. At the  
>> moment the branch version is using pysparse_numpy
>>        or pysparse_Numeric as the pysparse name space for testing  
>> purposes.
>>
>>     - The branch can be checked out via:
>>
>>             $ cvs -d:ext:ui...@py...:/cvsroot/pysparse  
>> co -r branch-numpy pysparse
>>
>>     - I have updated the Examples and Test directories to import  
>> from pysparse. They all seem to work apart from stuff that was  
>> broken already.
>>
>>     - I got rid of pysparse_version.py and replaced it with an  
>> __init__.py in Lib, which does the imports and holds a __version__  
>> variable.
>>       So you can now do:
>>
>>              >>> import pysparse_numpy
>>              >>> print pysparse_numpy.__version__
>>              0.34.032-numpy
>>
>>     - I think the default flag should be use_numpy=True since most  
>> users will now be getting numpy rather than Numeric. This could
>>       be automated with a try and except, which tests for the  
>> availability of numpy or Numeric. What do you think?
>>
>>     - You can diff from your working copy of pysparse with "cvs  
>> diff -c -r branch-numpy" to check the changes.
>>
>>     - Is it worth bumping the version number of pysparse to 1.0,  
>> since we will be breaking the name space (interface change)?
>>
>>     - If you are compiling against numpy, the numpy header files  
>> don't seem to be going into the right place at least on my two  
>> computers.
>>       I haven't resolved this problem yet. For now, I was just  
>> copying the .h files from .../site-packages/python/numpy/core/ 
>> include/ to Include/Lib/numpy
>>       in my working copy of pysparse.
>>
>> Merry Christmas!
>>
>> --
>> Daniel Wheeler
>>
>>
>> --------------------------------------------------------------------- 
>> ----
>> 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
>> http://www.techsay.com/default.php? 
>> page=join.php&p=sourceforge&CID=DEVDEV_______________________________ 
>> ________________
>> Pysparse-users mailing list
>> Pys...@li...
>> https://lists.sourceforge.net/lists/listinfo/pysparse-users
>
> --
> Daniel Wheeler
>
>
> ---------------------------------------------------------------------- 
> ---
> 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
> http://www.techsay.com/default.php? 
> page=join.php&p=sourceforge&CID=DEVDEV________________________________ 
> _______________
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> Pys...@li...
> https://lists.sourceforge.net/lists/listinfo/pysparse-users

--
Daniel Wheeler

Re: [Pysparse-developers] [Pysparse-users] updated pysparse for numpy

[Roman G. <rom...@gm...>]

Hello Daniel

Thanks a lot for your contribution. Judging from the description your
changes make much sense. I have not been using pysparse myself for a
long time so cannot be the person to test new versions.

Happy new year!
-- Roman

2007/1/2, Daniel Wheeler <dan...@ni...>:
>
> The changes for compatibility with numpy have now been merged back onto
> HEAD. I will do a new release in the near future.
>
> Cheers
>
>
> On Dec 21, 2006, at 12:36 PM, Daniel Wheeler wrote:
>
> Numeric is dying slowly and being replaced by numpy.
> With this in mind, I have updated pysparse to use the new numpy, this is all
> on a branch at the moment.
> It was straightforward matter of changing the imported header files from
> Numeric's to numpy's. I am sending this email
> to check to see if everybody is happy with the changes that have been made.
> If there are no objections, I can merge back
> onto the trunk and maybe make a new release. Changes  and issues are as
> follows:
>
>    - Created a C macro defined from setup.py that either imports numpy's or
> Numeric's headers depending
>      on the flag "use_numpy". The C macro was confusing me for awhile, but I
> think it works
>      now.
>
>    - I have changed the name space of itsolvers, spmatrix, jdsym etc to all
> lie under pysparse. So, instead of
>
>          >>> import spmatrix
>
>       you do
>
>          >>> from pysparse import spmatrix
>
>        This change stops site-packages from being polluted. At the moment
> the branch version is using pysparse_numpy
>        or pysparse_Numeric as the pysparse name space for testing purposes.
>
>     - The branch can be checked out via:
>
>             $ cvs -d:ext:ui...@py...:/cvsroot/pysparse co -r
> branch-numpy pysparse
>
>     - I have updated the Examples and Test directories to import from
> pysparse. They all seem to work apart from stuff that was broken already.
>
>     - I got rid of pysparse_version.py and replaced it with an __init__.py
> in Lib, which does the imports and holds a __version__ variable.
>       So you can now do:
>
>              >>> import pysparse_numpy
>              >>> print pysparse_numpy.__version__
>              0.34.032-numpy
>
>     - I think the default flag should be use_numpy=True since most users
> will now be getting numpy rather than Numeric. This could
>       be automated with a try and except, which tests for the availability
> of numpy or Numeric. What do you think?
>
>     - You can diff from your working copy of pysparse with "cvs diff -c -r
> branch-numpy" to check the changes.
>
>     - Is it worth bumping the version number of pysparse to 1.0, since we
> will be breaking the name space (interface change)?
>
>     - If you are compiling against numpy, the numpy header files don't seem
> to be going into the right place at least on my two computers.
>       I haven't resolved this problem yet. For now, I was just copying the
> .h files from .../site-packages/python/numpy/core/include/
> to Include/Lib/numpy
>       in my working copy of pysparse.
>
> Merry Christmas!
>
>
> --
> Daniel Wheeler
>
> -------------------------------------------------------------------------
> 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
> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV_______________________________________________
> Pysparse-users mailing list
> Pys...@li...
> https://lists.sourceforge.net/lists/listinfo/pysparse-users
>
>
> --
>
> Daniel Wheeler
>
>
> -------------------------------------------------------------------------
> 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
> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
>
> _______________________________________________
> Pysparse-users mailing list
> Pys...@li...
> https://lists.sourceforge.net/lists/listinfo/pysparse-users

Re: [Pysparse-developers] [Pysparse-users] updated pysparse for numpy

[Daniel W. <dan...@ni...>]

The changes for compatibility with numpy have now been merged back  
onto HEAD. I will do a new release in the near future.

Cheers

On Dec 21, 2006, at 12:36 PM, Daniel Wheeler wrote:

> Numeric is dying slowly and being replaced by numpy.
> With this in mind, I have updated pysparse to use the new numpy,  
> this is all on a branch at the moment.
> It was straightforward matter of changing the imported header files  
> from Numeric's to numpy's. I am sending this email
> to check to see if everybody is happy with the changes that have  
> been made. If there are no objections, I can merge back
> onto the trunk and maybe make a new release. Changes  and issues  
> are as follows:
>
>    - Created a C macro defined from setup.py that either imports  
> numpy's or Numeric's headers depending
>      on the flag "use_numpy". The C macro was confusing me for  
> awhile, but I think it works
>      now.
>
>    - I have changed the name space of itsolvers, spmatrix, jdsym  
> etc to all lie under pysparse. So, instead of
>
>          >>> import spmatrix
>
>       you do
>
>          >>> from pysparse import spmatrix
>
>        This change stops site-packages from being polluted. At the  
> moment the branch version is using pysparse_numpy
>        or pysparse_Numeric as the pysparse name space for testing  
> purposes.
>
>     - The branch can be checked out via:
>
>             $ cvs -d:ext:ui...@py...:/cvsroot/pysparse  
> co -r branch-numpy pysparse
>
>     - I have updated the Examples and Test directories to import  
> from pysparse. They all seem to work apart from stuff that was  
> broken already.
>
>     - I got rid of pysparse_version.py and replaced it with an  
> __init__.py in Lib, which does the imports and holds a __version__  
> variable.
>       So you can now do:
>
>              >>> import pysparse_numpy
>              >>> print pysparse_numpy.__version__
>              0.34.032-numpy
>
>     - I think the default flag should be use_numpy=True since most  
> users will now be getting numpy rather than Numeric. This could
>       be automated with a try and except, which tests for the  
> availability of numpy or Numeric. What do you think?
>
>     - You can diff from your working copy of pysparse with "cvs  
> diff -c -r branch-numpy" to check the changes.
>
>     - Is it worth bumping the version number of pysparse to 1.0,  
> since we will be breaking the name space (interface change)?
>
>     - If you are compiling against numpy, the numpy header files  
> don't seem to be going into the right place at least on my two  
> computers.
>       I haven't resolved this problem yet. For now, I was just  
> copying the .h files from .../site-packages/python/numpy/core/ 
> include/ to Include/Lib/numpy
>       in my working copy of pysparse.
>
> Merry Christmas!
>
> --
> Daniel Wheeler
>
>
> ---------------------------------------------------------------------- 
> ---
> 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
> http://www.techsay.com/default.php? 
> page=join.php&p=sourceforge&CID=DEVDEV________________________________ 
> _______________
> Pysparse-users mailing list
> Pys...@li...
> https://lists.sourceforge.net/lists/listinfo/pysparse-users

--
Daniel Wheeler

[Pysparse-developers] Fwd: updated pysparse for numpy

[Daniel W. <dan...@ni...>]

Begin forwarded message:

> From: Daniel Wheeler <dan...@ni...>
> Date: December 21, 2006 12:36:09 PM EST
> To: pys...@li...
> Cc: Jon Guyer <gu...@ni...>, ro...@ge..., Roman Geus  
> <rom...@ps...>
> Subject: updated pysparse for numpy
>
> Numeric is dying slowly and being replaced by numpy.
> With this in mind, I have updated pysparse to use the new numpy,  
> this is all on a branch at the moment.
> It was straightforward matter of changing the imported header files  
> from Numeric's to numpy's. I am sending this email
> to check to see if everybody is happy with the changes that have  
> been made. If there are no objections, I can merge back
> onto the trunk and maybe make a new release. Changes  and issues  
> are as follows:
>
>    - Created a C macro defined from setup.py that either imports  
> numpy's or Numeric's headers depending
>      on the flag "use_numpy". The C macro was confusing me for  
> awhile, but I think it works
>      now.
>
>    - I have changed the name space of itsolvers, spmatrix, jdsym  
> etc to all lie under pysparse. So, instead of
>
>          >>> import spmatrix
>
>       you do
>
>          >>> from pysparse import spmatrix
>
>        This change stops site-packages from being polluted. At the  
> moment the branch version is using pysparse_numpy
>        or pysparse_Numeric as the pysparse name space for testing  
> purposes.
>
>     - The branch can be checked out via:
>
>             $ cvs -d:ext:ui...@py...:/cvsroot/pysparse  
> co -r branch-numpy pysparse
>
>     - I have updated the Examples and Test directories to import  
> from pysparse. They all seem to work apart from stuff that was  
> broken already.
>
>     - I got rid of pysparse_version.py and replaced it with an  
> __init__.py in Lib, which does the imports and holds a __version__  
> variable.
>       So you can now do:
>
>              >>> import pysparse_numpy
>              >>> print pysparse_numpy.__version__
>              0.34.032-numpy
>
>     - I think the default flag should be use_numpy=True since most  
> users will now be getting numpy rather than Numeric. This could
>       be automated with a try and except, which tests for the  
> availability of numpy or Numeric. What do you think?
>
>     - You can diff from your working copy of pysparse with "cvs  
> diff -c -r branch-numpy" to check the changes.
>
>     - Is it worth bumping the version number of pysparse to 1.0,  
> since we will be breaking the name space (interface change)?
>
>     - If you are compiling against numpy, the numpy header files  
> don't seem to be going into the right place at least on my two  
> computers.
>       I haven't resolved this problem yet. For now, I was just  
> copying the .h files from .../site-packages/python/numpy/core/ 
> include/ to Include/Lib/numpy
>       in my working copy of pysparse.
>
> Merry Christmas!
>
> --
> Daniel Wheeler
>
>

--
Daniel Wheeler

[Pysparse-developers] A Mac OS X patch

[Jonathan G. <gu...@ni...>]

A couple of months ago, I submitted a tiny patch to setup.py that  
permits PySparse to build against the fink installation of Python on  
Mac OS X.

<http://sourceforge.net/tracker/index.php? 
func=detail&aid=1089837&group_id=101403&atid=629638>

This is just a correction of a typo in our original submission of OS X  
support. Since Daniel Wheeler has developer permissions, we're happy to  
check the patch into CVS ourselves, but wanted to check with Roman that  
it was OK to do so.

- Jon Guyer for the FiPy team


P.S. We know how easy it is for SourceForge Trackers to fall through  
the cracks, since you have to keep checking your SF page to see them,  
and who does that? In the event that you're unaware of it, something  
that we find useful is to have the Trackers send email to our mailing  
list whenever new ones are filed or changes are made. You can have all  
Trackers mail to the same place by selecting Tracker > Admin and  
filling in "Send email on new submission to address" and "Send email on  
all changes".  You have each Tracker type send mail to a different  
place by selecting Tracker > Admin > (Bugs | Support Requests | etc.) >  
Update preferences and then filling in the same.

Re: [Pysparse-developers] ll_mat not garbage collected

[Roman G. <rom...@gm...>]

Hi

The leak in ll_mat.keys() should be fixed now. A new version of
pysparse has been released.

Thanks again for reporting
-- Roman

On 6/21/05, cc...@cs... <cc...@cs...> wrote:
> no problemo, pysparse is pretty good all round.
>=20
> cheers
>=20
> Quoting Roman Geus <rom...@gm...>:
>=20
> > Hi
> >
> > The keys() method is a fairly new 3rd party contribution. I'll look
> > into this. Thanks for pointing this out.
> >
> > -- Roman
> >
> > On 6/21/05, cc...@cs... <cc...@cs...> wrote:
> > > hi Roman,
> > >
> > > sorry about the false alarm, it's actually the keys() function that i=
s
> > > leaking.
> > >
> > > for example
> > >
> > > import spmatrix
> > >
> > > dim =3D 10000000
> > >
> > > c =3D spmatrix.ll_mat(dim,dim)
> > >
> > > for i in xrange(dim):
> > >     for j in range(3):
> > >         c[i,j] =3D 23.33
> > >
> > >
> > > for x in xrange(dim):
> > >     for k in c.keys():
> > >         sum +=3D c[i,j]
> > >
> > > c chui
> > >
> > > Quoting Roman Geus <rom...@gm...>:
> > >
> > > > Hi
> > > >
> > > > None of the pysparse extension types implement weak referencing.
> > > > However I was not aware of any reference counting bugs in these
> > > > extension types, that would prevent deallocation of unreferenced
> > > > objects. Do you have a small example that illustrates the problem?
> > > >
> > > > -- Roman
> > > >
> > > > On 6/19/05, cc...@cs... <cc...@cs...> wrote:
> > > > > hi,
> > > > >
> > > > > while using pysparse i found that each ll_mat objects created are
> > not
> > > > > garbage even when there are no reference for it anymore.
> > > > >
> > > > > This will result in excessive memory usage, when I did a slice of
> > the
> > > > full
> > > > > matrix.
> > > > >
> > > > > Do you think it might have something to do with ll_mat haven't
> > > > implemented
> > > > > weak referenced yet?
> > > > >
> > > > > http://docs.python.org/lib/weakref-extension.html
> > > > >
> > > > > Please advice.
> > > > >
> > > > > Thanks!
> > > > > c chui
> > > > >
> > > > > ----------------------------------------------------------------
> > > > > This message was sent using IMP, the Internet Messaging Program.
> > > > >
> > > > >
> > > > > -------------------------------------------------------
> > > > > SF.Net email is sponsored by: Discover Easy Linux Migration
> > Strategies
> > > > > from IBM. Find simple to follow Roadmaps, straightforward
> > articles,
> > > > > informative Webcasts and more! Get everything you need to get up
> > to
> > > > > speed, fast.
> > http://ads.osdn.com/?ad_id=3D7477&alloc_id=3D16492&op=3Dclick
> > > > > _______________________________________________
> > > > > Pysparse-developers mailing list
> > > > > Pys...@li...
> > > > > https://lists.sourceforge.net/lists/listinfo/pysparse-developers
> > > > >
> > > >
> > >
> > >
> > >
> > >
> > > ----------------------------------------------------------------
> > > This message was sent using IMP, the Internet Messaging Program.
> > >
> >
>=20
>=20
>=20
>=20
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>

[Pysparse-developers] ll_mat not garbage collected

[<cc...@cs...>]

hi,

while using pysparse i found that each ll_mat objects created are not
garbage even when there are no reference for it anymore.

This will result in excessive memory usage, when I did a slice of the full
matrix.

Do you think it might have something to do with ll_mat haven't implemented
weak referenced yet?

http://docs.python.org/lib/weakref-extension.html

Please advice.

Thanks!
c chui

----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.

[Pysparse-developers] Addition to pysparse

[Roman G. <rom...@gm...>]

Hi all

I just received word from Ed Schofield, that he commited some nice
additions to CVS:

----------------------------
I've just committed some changes to ll_mat.c to support operations
iterating over non-zeros elements.  Here's the changelog:

revision 1.3
date: 2005/04/28 11:50:31;  author: edschofield;  state: Exp;  lines:
+202 -0
Added routines for ll_mat objects:
    (1) scaling by a constant ("scale")
    (2) getting the indices of all non-zero elements ("keys")
    (3) getting all non-zero elements ("values")
    (4) getting a list of (index, value) pairs of non-zero elements
("items")

These routines currently only support non-symmetric matrices.
----------------------------

-- Roman

[Pysparse-developers] PySparse Windows installer

[Daniel W. <dan...@ni...>]

Roman,

The PySparse Windows installers have been added to the download page.

Thus far, I have only tested them on one Windows machine.

-------------------------------------
Daniel Wheeler
Telephone: (301) 975-8358

[Pysparse-developers] FASD project: Online survey launched

[<ben...@id...>]

Dear Open Source developer

I am doing a research project on "Fun and Software Development" in which I kindly invite you to participate.
You will find the online survey under http://fasd.ethz.ch/qsf/. The questionnaire consists of 53 questions and you will need about 15 minutes to complete it.

With the FASD project (Fun and Software Development) we want to define the motivational significance of fun when software developers decide to engage in Open Source projects. What is special about our research project is that a similar survey is planned with software developers in commercial firms. This procedure allows the immediate comparison between the involved individuals and the conditions of production of these two development models. Thus we hope to obtain substantial new insights to the phenomenon of Open Source Development.


With many thanks for your participation,
Benno Luthiger


PS:
The results of the survey will be published under http://www.isu.unizh.ch/fuehrung/blprojects/FASD/.
We have set up the mailing list fa...@we... for this study. Please see http://fasd.ethz.ch/qsf/mailinglist_en.html for registration to this mailing list.

_______________________________________________________________________

Benno Luthiger
Swiss Federal Institute of Technology Zurich
8092 Zurich

Mail: benno.luthiger(at)id.ethz.ch
_______________________________________________________________________

[Pysparse-developers] Test message

[Roman G. <rom...@ps...>]

-- 
Roman Geus  | Paul Scherrer Institut  | phone   +41 56 310 32 74
             | CH-5232 Villigen        | mailto:rom...@ps...
----------------------------------------------------------------