[pymvpa] issue with pymvpa tutorial on neurodebian VM

Yaroslav Halchenko debian at onerussian.com
Fri Apr 6 14:54:31 UTC 2012


Thanks to Tiziano's dedication to work on holidays -- there is an
updated snapshot package of MDP available from #NeuroDebian (for a
subset of Debian/Ubuntu releases) fixing PyMVPA import issues.

Enjoy!

On Thu, 05 Apr 2012, Yaroslav Halchenko wrote:

> d'oh -- I thought that we finally uploaded mdp which fixes this issue...
> I guess I was wrong (upload is coming though...)

> meanwhile -- a configurational workaround is to disable MDP bindings
> (they aren't used in the tutorial anyways) -- just edit your ~/.pymvpa2.cfg and
> add

> [externals]
> have mdp = no

> that should prevent it from check if MDP is available etc

> On Thu, 05 Apr 2012, Emanuele Olivetti wrote:
> > >  File "<string>", line 1, in <module>
> > >  File "/usr/lib/pymodules/python2.6/mdp/__init__.py", line 166, in <module>
> > >    import nodes
> > >  File "/usr/lib/pymodules/python2.6/mdp/nodes/__init__.py", line 54, in <module>
> > >    del convolution_nodes
> > >NameError: name 'convolution_nodes' is not defined

> > >-----
> > >As far as I understand, besides the warning on the scikits->sklearn renaming, there is
> > >an issue with MDP. I am digging it but in case you already know that I am
> > >sending this message immediately.



> > After a little digging I found out that the package python-mdp has some other
> > bigger issues: even "import mdp" fails. This is quite unexpected...

> > This tiny change in MDP seems to solve the issue of my previous message though.

> > -------------------------------------------
> > --- __init__.py.original    2012-04-05 07:46:13.000000000 -0400
> > +++ __init__.py    2012-04-05 07:48:40.000000000 -0400
> > @@ -51,17 +51,17 @@
> >  if numx_description == 'scipy':
> >      from convolution_nodes import Convolution2DNode
> >      __all__ += ['Convolution2DNode']
> > -    del convolution_nodes
> > +    # del convolution_nodes

> >  if config.has_shogun:
> >      from shogun_svm_classifier import ShogunSVMClassifier
> >      __all__ += ['ShogunSVMClassifier']
> > -    del shogun_svm_classifier
> > +    # del shogun_svm_classifier

> >  if config.has_libsvm:
> >      from libsvm_classifier import LibSVMClassifier
> >      __all__ += ['LibSVMClassifier']
> > -    del libsvm_classifier
> > +    # del libsvm_classifier

> >  if config.has_scikits:
> >      import scikits_nodes
> > --------------------------------------------

> > Best,

> > Emanuele


> > _______________________________________________
> > Pkg-ExpPsy-PyMVPA mailing list
> > Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
> > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa
-- 
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Yaroslav Halchenko                 www.ohloh.net/accounts/yarikoptic



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