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

Nils Wagner nwagner@iam.uni-stuttgart...
Wed Feb 14 07:13:38 CST 2007


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
>>
>>
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>>     
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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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