headers
Rob Clewley | 1 Jun 20:26
Picon

ANN: PyDSTool 0.86 released

The latest update to the open-source python dynamical systems modeling
toolbox, PyDSTool 0.86, has been posted on Sourceforge.
Major highlights are:

 * Now compatible with Python 2.5 and Numpy 1.0.4 / Scipy 0.6.0
 * Decreased overhead for simulating hybrid models
 * Improved efficiency of VODE Generator in computing trajectories
 * Interval class now supports discrete valued intervals
 * Improved diagnostic reporting structure in Generator and Model classes
 * Inclusion of intuitive arithmetic operations for Point and Pointset classes
 * Various bug fixes and other API tidying

This is a minor update in preparation for a substantial upgrade at
version 0.90, which will move symbolic expression support over to
SymPy, support much more sophisticated data-driven model inference,
and greatly improve the implementation of C-based ODE integrators.

You can download the latest version from
http://www.sourceforge.net/projects/pydstool/
For installation and setting up, as well as some tutorial information,
see http://pydstool.sourceforge.net
The download contains full API documentation, BSD license information,
and further details of recent code changes.

As ever, all feedback is welcome as we try to find time to improve our
code base.
Permalink | Reply | 0 comments |
headers
Paul Smith | 1 Jun 23:15
Picon
Gravatar

OpenOpt errors with ALGENCAN

Dear All,

I am trying to run the nlp_1.py example of OpenOpt on F9 with ALGENCAN
solver, but getting these errors:

========================
starting solver ALGENCAN (license: GPL)  with problem  unnamed
Traceback (most recent call last):
  File "nlp_1.py", line 109, in <module>
    r = p.solve('ALGENCAN')
  File "/usr/lib/python2.5/site-packages/scikits/openopt/Kernel/
BaseProblem.py", line 230, in solve
    return runProbSolver(self, solvers, *args, **kwargs)
  File "/usr/lib/python2.5/site-packages/scikits/openopt/Kernel/
runProbSolver.py", line 225, in runProbSolver
    solver(p)
  File "/usr/lib/python2.5/site-packages/scikits/openopt/solvers/
BrasilOpt/ALGENCAN_oo.py", line 586, in __solver__

algencan.solvers(evalf,evalg,evalh,evalc,evaljac,evalhc,evalhlp,inip,endp)
TypeError: solvers() takes exactly 12 arguments (9 given)

Any ideas?

Thanks in advance,

Paul
Permalink | Reply | 8 comments |
headers
Paul Smith | 1 Jun 23:25
Picon
Gravatar

Re: OpenOpt errors with ALGENCAN

On Jun 1, 10:15 pm, Paul Smith <phh...@gmail.com> wrote:
> I am trying to run the nlp_1.py example of OpenOpt on F9 with ALGENCAN
> solver, but getting these errors:
>
> ========================
> starting solver ALGENCAN (license: GPL)  with problem  unnamed
> Traceback (most recent call last):
>   File "nlp_1.py", line 109, in <module>
>     r = p.solve('ALGENCAN')
>   File "/usr/lib/python2.5/site-packages/scikits/openopt/Kernel/
> BaseProblem.py", line 230, in solve
>     return runProbSolver(self, solvers, *args, **kwargs)
>   File "/usr/lib/python2.5/site-packages/scikits/openopt/Kernel/
> runProbSolver.py", line 225, in runProbSolver
>     solver(p)
>   File "/usr/lib/python2.5/site-packages/scikits/openopt/solvers/
> BrasilOpt/ALGENCAN_oo.py", line 586, in __solver__
>
> algencan.solvers(evalf,evalg,evalh,evalc,evaljac,evalhc,evalhlp,inip,endp)
> TypeError: solvers() takes exactly 12 arguments (9 given)
>
> Any ideas?

Let me add that I have

$ echo $PYTHONPATH
/home/psmith/algencan-2.0-beta/bin/py
$

and therein:
(Continue reading)

Permalink | Reply | 7 comments |
headers
dmitrey | 2 Jun 08:51
Favicon

Re: OpenOpt errors with ALGENCAN

OpenOpt has no connection to ALGENCAN 2.0 beta yet, as it is mentioned 
in http://scipy.org/scipy/scikits/wiki/OpenOptTODO

AFAIK 2.0 beta has no Python API. So currently you should use 1.0 
instead. If this one is already unavailable I could attach tarball with 
1.0 to an openopt webpage.
D.

Paul Smith wrote:
> On Jun 1, 10:15 pm, Paul Smith <phh...@gmail.com> wrote:
>   
>> I am trying to run the nlp_1.py example of OpenOpt on F9 with ALGENCAN
>> solver, but getting these errors:
>>
>> ========================
>> starting solver ALGENCAN (license: GPL)  with problem  unnamed
>> Traceback (most recent call last):
>>   File "nlp_1.py", line 109, in <module>
>>     r = p.solve('ALGENCAN')
>>   File "/usr/lib/python2.5/site-packages/scikits/openopt/Kernel/
>> BaseProblem.py", line 230, in solve
>>     return runProbSolver(self, solvers, *args, **kwargs)
>>   File "/usr/lib/python2.5/site-packages/scikits/openopt/Kernel/
>> runProbSolver.py", line 225, in runProbSolver
>>     solver(p)
>>   File "/usr/lib/python2.5/site-packages/scikits/openopt/solvers/
>> BrasilOpt/ALGENCAN_oo.py", line 586, in __solver__
>>
>> algencan.solvers(evalf,evalg,evalh,evalc,evaljac,evalhc,evalhlp,inip,endp)
>> TypeError: solvers() takes exactly 12 arguments (9 given)
(Continue reading)

Permalink | Reply | 6 comments |
headers
Paul Smith | 2 Jun 10:47
Picon
Gravatar

Re: OpenOpt errors with ALGENCAN

On Mon, Jun 2, 2008 at 7:51 AM, dmitrey <dmitrey.kroshko <at> scipy.org> wrote:
> OpenOpt has no connection to ALGENCAN 2.0 beta yet, as it is mentioned
> in http://scipy.org/scipy/scikits/wiki/OpenOptTODO
>
> AFAIK 2.0 beta has no Python API. So currently you should use 1.0
> instead. If this one is already unavailable I could attach tarball with
> 1.0 to an openopt webpage.

Thanks, Dmitrey. I think it is no longer exact what you claim: there
is now a Python interface for Algencan 2.0 beta (update: May 20th,
2008). Could you please confirm this?

Paul
Permalink | Reply | 5 comments |
headers
dmitrey | 2 Jun 11:54
Favicon

Re: OpenOpt errors with ALGENCAN

I have read README file from algencan2.0beta.tgz. Python binding refers to

$(ALGENCAN)/sources/interfaces/py/runalgencan.py and
$(ALGENCAN)/sources/interfaces/py/toyprob.py

but these files are absent (after all required steps before already done)
the only one py-file is algencan.py.

I had informed algencan developers of the issue.
W/O up-to-date toyprob.py I cannot connect algencan2.0 beta, because I 
don't know those new 12 arguments instead of old-style 9.
Regards, D.

Paul Smith wrote:
> On Mon, Jun 2, 2008 at 7:51 AM, dmitrey <dmitrey.kroshko <at> scipy.org> wrote:
>   
>> OpenOpt has no connection to ALGENCAN 2.0 beta yet, as it is mentioned
>> in http://scipy.org/scipy/scikits/wiki/OpenOptTODO
>>
>> AFAIK 2.0 beta has no Python API. So currently you should use 1.0
>> instead. If this one is already unavailable I could attach tarball with
>> 1.0 to an openopt webpage.
>>     
>
> Thanks, Dmitrey. I think it is no longer exact what you claim: there
> is now a Python interface for Algencan 2.0 beta (update: May 20th,
> 2008). Could you please confirm this?
>
> Paul
> _______________________________________________
(Continue reading)

Permalink | Reply | 4 comments |
headers
Paul Smith | 2 Jun 12:06
Picon
Gravatar

Re: OpenOpt errors with ALGENCAN

On Mon, Jun 2, 2008 at 10:54 AM, dmitrey <dmitrey.kroshko <at> scipy.org> wrote:
> I have read README file from algencan2.0beta.tgz. Python binding refers to
>
> $(ALGENCAN)/sources/interfaces/py/runalgencan.py and
> $(ALGENCAN)/sources/interfaces/py/toyprob.py
>
> but these files are absent (after all required steps before already done)
> the only one py-file is algencan.py.
>
> I had informed algencan developers of the issue.
> W/O up-to-date toyprob.py I cannot connect algencan2.0 beta, because I
> don't know those new 12 arguments instead of old-style 9.

Thanks again, Dmitrey. I had also noticed yesterday the problem that
you describe: none of the two files (runalgencan.py and toyprob.py)
are created. I sent an e-mail to one of the developers, telling him
about the issue, but I have not received any reply so far.

Paul
Permalink | Reply | 3 comments |
headers
Paul Smith | 2 Jun 16:33
Picon
Gravatar

Re: OpenOpt errors with ALGENCAN

On Mon, Jun 2, 2008 at 11:06 AM, Paul Smith <phhs80 <at> gmail.com> wrote:
>> I have read README file from algencan2.0beta.tgz. Python binding refers to
>>
>> $(ALGENCAN)/sources/interfaces/py/runalgencan.py and
>> $(ALGENCAN)/sources/interfaces/py/toyprob.py
>>
>> but these files are absent (after all required steps before already done)
>> the only one py-file is algencan.py.
>>
>> I had informed algencan developers of the issue.
>> W/O up-to-date toyprob.py I cannot connect algencan2.0 beta, because I
>> don't know those new 12 arguments instead of old-style 9.
>
> Thanks again, Dmitrey. I had also noticed yesterday the problem that
> you describe: none of the two files (runalgencan.py and toyprob.py)
> are created. I sent an e-mail to one of the developers, telling him
> about the issue, but I have not received any reply so far.

Ernest Birgin has just written to me telling me that there is now
available a new version of Algencan with the missing files. The
problem is solved now.

Paul
Permalink | Reply | 2 comments |
headers
Fabrice Silva | 2 Jun 16:35
Picon
Favicon

OdrPack and complex model

Hi, 
I would like to use odr to fit a complex model on reference values as
causality issues occur when trying to adjust separately modulus and
argument.
Is it possible with odr ?

Fabricio
Permalink | Reply | 1 comment |
headers
Tim Michelsen | 2 Jun 19:35
Picon

building and installing timeseries fails on Windows

Hello,
following the (updated) instructions at:
http://www.scipy.org/Cookbook/CompilingExtensionsOnWindowsWithMinGW

I tried to build a windows installer package and install the timeseries scikit
on a Windows XP computer with a recent MinGW.

It fails with the following message:
Microsoft Windows XP [Version 5.1.2600]
(C) Copyright 1985-2001 Microsoft Corp.

C:temp\SVNcheckouts\timeseries>python setup.py bdist_wininst
running bdist_wininst
running build
running scons
Traceback (most recent call last):
  File "setup.py", line 42, in <module>
    setup_package()
  File "setup.py", line 36, in setup_package
    configuration = configuration,
  File "C:\python\Lib\site-packages\numpy\distutils\core.py", line 184, in setup
    return old_setup(**new_attr)
  File "C:\python\lib\distutils\core.py", line 151, in setup
    dist.run_commands()
  File "C:\python\lib\distutils\dist.py", line 974, in run_commands
    self.run_command(cmd)
  File "C:\python\lib\distutils\dist.py", line 994, in run_command
    cmd_obj.run()
  File "C:\python\lib\site-packages\setuptools\command\bdist_wininst.py", line
37, in run
(Continue reading)

Permalink | Reply | 1 comment |

Gmane