[SciPy-user] scipy.optimize.leastsq error estimates

Chiara Caronna chiaracaronna@hotmail....
Wed Feb 14 07:19:49 CST 2007


Ok, I have an odr directory in Lib/scipy and the file setup.py looks ok:

def configuration(parent_package='',top_path=None):
    from numpy.distutils.misc_util import Configuration
    config = Configuration('scipy',parent_package,top_path)
    config.add_subpackage('cluster')
    config.add_subpackage('fftpack')
    config.add_subpackage('integrate')
    config.add_subpackage('interpolate')
    config.add_subpackage('io')
    config.add_subpackage('lib')
    config.add_subpackage('linalg')
    config.add_subpackage('linsolve')
    config.add_subpackage('maxentropy')
    config.add_subpackage('misc')
    config.add_subpackage('odr')
    config.add_subpackage('optimize')
    config.add_subpackage('sandbox')
    config.add_subpackage('signal')
    config.add_subpackage('sparse')
    config.add_subpackage('special')
    config.add_subpackage('stats')
    config.add_subpackage('ndimage')
    config.add_subpackage('stsci')
    config.add_subpackage('weave')
    config.make_svn_version_py()  # installs __svn_version__.py
    config.make_config_py()
    return config

if __name__ == '__main__':
    from numpy.distutils.core import setup
    setup(**configuration(top_path='').todict())

so.... why it doesn't work?!

>From: Nils Wagner <nwagner@iam.uni-stuttgart.de>
>Reply-To: SciPy Users List <scipy-user@scipy.org>
>To: SciPy Users List <scipy-user@scipy.org>
>Subject: Re: [SciPy-user] scipy.optimize.leastsq error estimates
>Date: Wed, 14 Feb 2007 14:13:38 +0100
>
>Chiara Caronna wrote:
> > Ah. No, there is not an odr directory... :(
> >
> > Here is the output:
> >
> >
> > drwxr-xr-x   28 root     root         4096 2007-02-14 13:46 .
> > drwxr-xr-x   22 root     root         4096 2007-01-17 09:37 ..
> > -rw-r--r--    1 500      1000            0 2006-01-05 04:35 __init__.py
> > drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 ann
> > drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 arpack
> > drwxr-xr-x    3 root     root         4096 2006-12-08 05:05 arraysetops
> > drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 buildgrid
> > drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 constants
> > drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 cow
> > drwxr-xr-x    3 root     root         4096 2006-12-08 05:05 delaunay
> > -rw-r--r--    1 root     root            4 2007-02-14 13:46
> > enabled_packages.txt
> > drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 exmplpackage
> > drwxr-xr-x    5 root     root         4096 2006-12-08 05:05 fdfpack
> > drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 ga
> > drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 gplt
> > drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 image
> > drwxr-xr-x    5 root     root         4096 2006-12-08 05:05 models
> > drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 montecarlo
> > drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 netcdf
> > drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 newoptimize
> > drwxr-xr-x    3 root     root         4096 2006-12-08 05:05 numexpr
> > drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 plt
> > drwxr-xr-x    5 root     root         4096 2006-12-08 05:05 pyem
> > drwxr-xr-x   12 root     root         4096 2006-12-08 05:05 pysparse
> > drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 rkern
> > -rw-r--r--    1 500      1000         2656 2006-12-02 04:24 setup.py
> > -rw-r--r--    1 root     root         1028 2007-01-17 09:37 setup.pyc
> > drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 spline
> > drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 stats
> > drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 svm
> > drwxr-xr-x    3 root     root         4096 2006-12-08 05:05 umfpack
> > drwxr-xr-x    5 root     root         4096 2006-12-08 05:05 xplt
> >
> >
> >
> >> From: Nils Wagner <nwagner@iam.uni-stuttgart.de>
> >> Reply-To: SciPy Users List <scipy-user@scipy.org>
> >> To: SciPy Users List <scipy-user@scipy.org>
> >> Subject: Re: [SciPy-user] scipy.optimize.leastsq error estimates
> >> Date: Wed, 14 Feb 2007 14:01:19 +0100
> >>
> >> Chiara Caronna wrote:
> >>
> >>>
> >>>> If you use 0.5.2
> >>>>
> >>>> look into the directory scipy/Lib/sandbox
> >>>> and create a file called enabled_packages.txt which should contain
> >>>>
> >>>> odr
> >>>>
> >>>> in the first line (a new line for each package)
> >>>>
> >>>>
> >>> I did what you said, but when reinstalling scipy I got this error:
> >>>
> >>>   File "Lib/sandbox/setup.py", line 22, in configuration
> >>>     config.add_subpackage(p)
> >>>   File
> >>> "/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py",
> >>>
> >> line
> >>
> >>> 765, in add_subpackage
> >>>     caller_level = 2)
> >>>   File
> >>> "/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py",
> >>>
> >> line
> >>
> >>> 741, in get_subpackage
> >>>     caller_level = caller_level+1)
> >>>   File
> >>> "/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py",
> >>>
> >> line
> >>
> >>> 541, in __init__
> >>>     raise ValueError("%r is not a directory" % (package_path,))
> >>> ValueError: 'Lib/sandbox/odr' is not a directory
> >>>
> >>>
> >>>
> >>>
> >> What is the output of ls -l  in your sandbox directory
> >> I have
> >> Lib/sandbox> ls -l
> >>  total 17
> >> drwxr-xr-x   5 root root  272 2006-09-03 11:30 ann
> >> drwxr-xr-x   6 root root  376 2006-11-21 08:45 arpack
> >> drwxr-xr-x   4 root root  184 2006-11-06 08:48 arraysetops
> >> drwxr-xr-x   3 root root  232 2006-06-27 08:32 buildgrid
> >> drwxr-xr-x   5 root root  344 2006-12-15 15:35 cdavid
> >> drwxr-xr-x   3 root root  192 2006-06-22 09:18 constants
> >> drwxr-xr-x   3 root root  248 2006-03-15 08:29 cow
> >> drwxr-xr-x   4 root root  544 2006-10-02 08:19 delaunay
> >> -rw-r--r--   1 root root   40 2007-02-08 13:11 enabled_packages.txt
> >> drwxr-xr-x   5 root root  272 2006-03-15 08:29 exmplpackage
> >> drwxr-xr-x   6 root root  280 2006-04-24 08:41 fdfpack
> >> drwxr-xr-x   3 root root  600 2006-09-03 11:30 ga
> >> drwxr-xr-x   3 root root  360 2006-09-03 11:30 gplt
> >> drwxr-xr-x   3 root root  352 2006-09-03 11:30 image
> >> -rw-r--r--   1 root root    0 2006-02-28 08:50 __init__.py
> >> drwxr-xr-x   4 root root  520 2007-02-12 08:33 maskedarray
> >> drwxr-xr-x   6 root root  688 2007-02-12 08:33 models
> >> drwxr-xr-x   5 root root  232 2006-11-23 08:29 montecarlo
> >> drwxr-xr-x   3 root root  320 2006-07-10 08:09 netcdf
> >> drwxr-xr-x   4 root root  264 2007-01-11 10:57 newoptimize
> >> drwxr-xr-x   4 root root  432 2006-11-17 09:02 numexpr
> >> drwxr-xr-x   3 root root   72 2006-10-05 08:30 oliphant
> >> drwxr-xr-x   3 root root  456 2006-09-03 11:30 plt
> >> drwxr-xr-x   6 root root  904 2006-12-07 09:05 pyem
> >> drwxr-xr-x  13 root root  592 2006-08-16 16:21 pysparse
> >> drwxr-xr-x   4 root root  232 2007-02-08 13:11 rbf
> >> drwxr-xr-x   3 root root  184 2006-09-03 11:30 rkern
> >> -rw-r--r--   1 root root 2732 2007-02-08 13:07 setup.py
> >> -rw-r--r--   1 root root 1028 2007-02-08 13:11 setup.pyc
> >> drwxr-xr-x   5 root root  360 2007-02-09 08:42 spline
> >> drwxr-xr-x   3 root root  192 2006-10-10 08:22 stats
> >> drwxr-xr-x   5 root root  464 2006-09-11 08:44 svm
> >> drwxr-xr-x   9 root root  576 2007-02-13 08:27 timeseries
> >> drwxr-xr-x   3 root root   72 2006-12-07 08:52 wavelet
> >> drwxr-xr-x   6 root root 1864 2007-01-23 08:35 xplt
> >>
> >> Note that I am using the svn version. So odr is not present in the 
>sandbox.
> >> How about 0.5.2 ?
> >> Do you have a directory odr in the sandbox ?
> >>
> >> Nils
> >>
> >>
> >> _______________________________________________
> >> SciPy-user mailing list
> >> SciPy-user@scipy.org
> >> http://projects.scipy.org/mailman/listinfo/scipy-user
> >>
> >
> > _________________________________________________________________
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> >
>And in scipy/Lib ? I have
>
>  drwxr-xr-x   6 root root  280 2007-01-24 13:58 cluster
>drwxr-xr-x   7 root root  536 2007-01-11 09:16 fftpack
>drwxr-xr-x   2 root root   80 2006-03-20 11:42 image
>-rw-r--r--   1 root root 2356 2007-01-11 09:16 __init__.py
>drwxr-xr-x   8 root root  656 2007-02-12 09:54 integrate
>drwxr-xr-x   5 root root  456 2007-02-12 09:54 interpolate
>drwxr-xr-x   6 root root  672 2007-02-12 09:54 io
>drwxr-xr-x   5 root root  232 2007-01-11 09:16 lib
>drwxr-xr-x   6 root root 1024 2007-01-25 09:35 linalg
>drwxr-xr-x   5 root root  552 2007-01-25 09:35 linsolve
>drwxr-xr-x   2 root root   80 2006-01-19 10:27 maxent
>drwxr-xr-x   5 root root  296 2007-01-11 09:16 maxentropy
>drwxr-xr-x   3 root root  392 2007-01-11 09:16 misc
>drwxr-xr-x   2 root root   80 2006-01-19 10:27 montecarlo
>drwxr-xr-x   5 root root  456 2007-02-12 09:54 ndimage
>drwxr-xr-x   2 root root   80 2006-03-17 10:51 nd_image
>drwxr-xr-x   5 root root  360 2007-01-24 14:00 odr
>drwxr-xr-x  10 root root  712 2007-01-29 10:06 optimize
>drwxr-xr-x  35 root root 1032 2007-02-12 09:54 sandbox
>-rw-r--r--   1 root root  679 2005-12-01 10:57 scipy_version.pyc
>-rw-r--r--   1 root root 1126 2006-11-28 16:59 setup.py
>-rw-r--r--   1 root root 1141 2006-11-28 17:02 setup.pyc
>drwxr-xr-x   5 root root  744 2007-01-30 15:29 signal
>drwxr-xr-x   5 root root  272 2007-01-15 09:33 sparse
>drwxr-xr-x  12 root root 1056 2007-01-26 11:21 special
>drwxr-xr-x   5 root root  568 2007-01-11 09:16 stats
>drwxr-xr-x   5 root root  208 2006-08-04 09:02 stsci
>drwxr-xr-x   3 root root  232 2006-10-02 08:38 tests
>-rw-r--r--   1 root root  485 2006-12-08 09:21 version.py
>-rw-r--r--   1 root root  580 2006-12-08 09:23 version.pyc
>drwxr-xr-x   8 root root 1272 2007-01-22 09:42 weave
>
>Also look into your setup.py file in scipy/Lib
>
>def configuration(parent_package='',top_path=None):
>     from numpy.distutils.misc_util import Configuration
>     config = Configuration('scipy',parent_package,top_path)
>     config.add_subpackage('cluster')
>     config.add_subpackage('fftpack')
>     config.add_subpackage('integrate')
>     config.add_subpackage('interpolate')
>     config.add_subpackage('io')
>     config.add_subpackage('lib')
>     config.add_subpackage('linalg')
>     config.add_subpackage('linsolve')
>     config.add_subpackage('maxentropy')
>     config.add_subpackage('misc')
>     config.add_subpackage('odr')   #  This should be enabled !!
>     config.add_subpackage('optimize')
>     config.add_subpackage('sandbox')
>     config.add_subpackage('signal')
>     config.add_subpackage('sparse')
>     config.add_subpackage('special')
>     config.add_subpackage('stats')
>     #config.add_subpackage('ndimage')
>     config.add_subpackage('stsci')
>     config.add_subpackage('weave')
>     config.make_svn_version_py()  # installs __svn_version__.py
>     config.make_config_py()
>     return config
>
>if __name__ == '__main__':
>     from numpy.distutils.core import setup
>     setup(**configuration(top_path='').todict())
>
>Nils
>
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>SciPy-user mailing list
>SciPy-user@scipy.org
>http://projects.scipy.org/mailman/listinfo/scipy-user

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