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Evan Mason wrote:
> Thank you Jeff. Setting LD_LIBRARY_PATH works fine as a quick test, 
> though that leads me to the "ImportError: No module named 
> pkg_resources" problem that the other recent posters had. I'll either 
> try setuptools or wait for 0.9.9 to come out - will it be long?
>
> -Evan
Evan: Sometime next week probably, If you have svn installed, you can 
get the latest version that way.
-Jeff
-- 
Jeffrey S. Whitaker Phone : (303)497-6313
Meteorologist FAX : (303)497-6449
NOAA/OAR/PSD R/PSD1 Email : Jef...@no...
325 Broadway Office : Skaggs Research Cntr 1D-124
Boulder, CO, USA 80303-3328 Web : http://tinyurl.com/5telg

Thank you Jeff. Setting LD_LIBRARY_PATH works fine as a quick test, though
that leads me to the "ImportError: No module named pkg_resources" problem
that the other recent posters had. I'll either try setuptools or wait for
0.9.9 to come out - will it be long?
-Evan

Evan Mason wrote:
> Hi all,
>
> Just updated basemap from 0.9.4 to 0.9.8 on Mandriva Linux 2008. I 
> also installed basemap-data-fullres-0.9.7. I've noticed there's a 
> couple of recent posts about problems (on Macs) with 0.9.8, the 
> solution being to install setuptools until 0.9.9 comes along; the 
> problem I have is similar to the posts but not the same, so I'd like 
> to check here before proceeding with setuptools.
>
> I installed the included geos-2.2.3, then basemap-0.9.8, then 
> basemap-data-fullres-0.9.7 . However when I now import basemap I get:
>
> In [1]: from matplotlib.toolkits.basemap import Basemap
> ---------------------------------------------------------------------------
> <type 'exceptions.ImportError'> Traceback (most recent call 
> last)
>
> /home/emason/python/tools/<ipython console> in <module>()
>
> /usr/lib/python2.5/site-packages/matplotlib/toolkits/basemap/__init__.py 
> in <module>()
> ----> 1 from basemap import __doc__, __version__
> 2 from basemap import *
>
> /usr/lib/python2.5/site-packages/matplotlib/toolkits/basemap/basemap.py 
> in <module>()
> 29 from matplotlib.cbook import is_scalar, dedent
> 30 from shapelib import ShapeFile
> ---> 31 import _geos, pupynere
> 32
> 33 # basemap data files now installed in 
> lib/matplotlib/toolkits/basemap/data
>
> <type 'exceptions.ImportError'>: libgeos_c.so.1: cannot open shared 
> object file: No such file or directory
>
> Yet the file, in fact a link, libgeos_c.so.1, does exist at the 
> location (/usr/local/lib) where it is supposed to be:
>
> [root@msasa lib]# ll
> total 44230
> -rw-r--r-- 1 root root 28107924 2007年12月28日 16:31 libgeos.a
> -rw-r--r-- 1 root root 581806 2007年12月28日 16:31 libgeos_c.a
> -rwxr-xr-x 1 root root 830 2007年12月28日 16:31 libgeos_c.la*
> lrwxrwxrwx 1 root root 18 2007年12月28日 16:31 libgeos_c.so -> 
> libgeos_c.so.1.1.1*
> lrwxrwxrwx 1 root root 18 2007年12月28日 16:31 libgeos_c.so.1 -> 
> libgeos_c.so.1.1.1*
> -rwxr-xr-x 1 root root 452162 2007年12月28日 16:31 libgeos_c.so.1.1.1*
> -rwxr-xr-x 1 root root 790 2007年12月28日 16:31 libgeos.la*
> lrwxrwxrwx 1 root root 16 2007年12月28日 16:31 libgeos.so -> 
> libgeos.so.2.2.3*
> lrwxrwxrwx 1 root root 16 2007年12月28日 16:31 libgeos.so.2 -> 
> libgeos.so.2.2.3*
> -rwxr-xr-x 1 root root 13443604 2007年12月28日 16:31 libgeos.so.2.2.3*
>
> I'd appreciate any help with this.
>
> Thanks, Evan
Evan: I think this is a LD_LIBRARY_PATH problem. There are two 
possible workarounds:
1) set the LD_LIBRARY_PATH environment variable to include 
/usr/local/lib, i.e.
export LD_LIBRARY_PATH="/usr/local/lib:$LD_LIBRARY_PATH"
2) edit setup.py and make the following change
currents_nbp:(basemap_svn)$ svn diff
Index: setup.py
===================================================================
--- setup.py (revision 4791)
+++ setup.py (working copy)
@@ -90,7 +90,11 @@
extensions.append(Extension("matplotlib.toolkits.basemap._geod",deps+['src/_geod.c'],include_dirs 
= ['src'],))
 # for some reason, pickling won't work if this extension is installed
 # as "matplotlib.toolkits.basemap._geos"
-extensions.append(Extension("_geos",['src/_geos.c'],library_dirs=geos_library_dirs,include_dirs=geos_include_dirs,libraries=['geos_c','geos'])) 
+extensions.append(Extension("_geos",['src/_geos.c'],
+ library_dirs=geos_library_dirs,
+ runtime_library_dirs=geos_library_dirs,
+ include_dirs=geos_include_dirs,
+ libraries=['geos_c','geos']))
then rebuild. As Eric Firing pointed out to me, adding 
runtime_library_dirs negates the need to set LD_LIBRARY_PATH manually. 
This is already done in svn, and so 0.9.9 will not require manually 
setting LD_LIBRARY_PATH.
HTH,
-Jeff
-- 
Jeffrey S. Whitaker Phone : (303)497-6313
Meteorologist FAX : (303)497-6449
NOAA/OAR/PSD R/PSD1 Email : Jef...@no...
325 Broadway Office : Skaggs Research Cntr 1D-124
Boulder, CO, USA 80303-3328 Web : http://tinyurl.com/5telg

Hi Johann,
I believe the scipy optimization package gives a variety of 
optimization algorithms but you would have to implement your own 
codes to fix/thaw parameters. That being said, there is a lot there 
and I haven't dug into all of it into detail. I would suggest posting 
a message to the scipy mailing list after the holidays and you may 
get a better response.
Cheers,
Jessica
On Dec 26, 2007, at 3:52 PM, Johann Cohen-Tanugi wrote:
> hi jessica, thanks.... So scipy.optmizer as it stands cannot do 
> that? I gues I should move the issue to the scipy list then. Yes 
> there is mpfit, there is also pyminuit in google.code that is 
> wrapper of the high energy physics standard package MINUIT, etc.... 
> but I would think that fitting data, with fixed/thawed parameters, 
> is a basic feature of a scientific package. As there seems to be a 
> snergy between matplotlib and scipy, I would expect the latter to 
> take care of optimization....
> thanks for the replies,
> Johann
>
> Jessica Lu wrote:
>> Hi Johann,
>>
>> I would recommend using the python mpfit module:
>>
>> http://cars9.uchicago.edu/software/python/mpfit.html
>>
>> Cheers,
>> Jessica
>>
>> On Dec 22, 2007, at 8:57 PM, Johann Cohen-Tanugi wrote:
>>
>>> hi jessica,
>>> This FittingData tutorial is very nice. Could you illustrate how to
>>> fix/thaw parameters?
>>> I did not find any such attribute and when I try some kludges 
>>> they fail
>>> with a msg saying
>>> <type 'exceptions.ValueError'>: shape mismatch: objects cannot be
>>> broadcast to a single shape
>>>
>>>
>>> thanks,
>>> Johann
>>>
>>> -------------------------------------------------------------------- 
>>> -----
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>>
>

Hi all,
Just updated basemap from 0.9.4 to 0.9.8 on Mandriva Linux 2008. I also
installed basemap-data-fullres-0.9.7. I've noticed there's a couple of
recent posts about problems (on Macs) with 0.9.8, the solution being to
install setuptools until 0.9.9 comes along; the problem I have is similar to
the posts but not the same, so I'd like to check here before proceeding with
setuptools.
I installed the included geos-2.2.3, then basemap-0.9.8, then
basemap-data-fullres-0.9.7. However when I now import basemap I get:
In [1]: from matplotlib.toolkits.basemap import Basemap
---------------------------------------------------------------------------
<type 'exceptions.ImportError'> Traceback (most recent call last)
/home/emason/python/tools/<ipython console> in <module>()
/usr/lib/python2.5/site-packages/matplotlib/toolkits/basemap/__init__.py in
<module>()
----> 1 from basemap import __doc__, __version__
 2 from basemap import *
/usr/lib/python2.5/site-packages/matplotlib/toolkits/basemap/basemap.py in
<module>()
 29 from matplotlib.cbook import is_scalar, dedent
 30 from shapelib import ShapeFile
---> 31 import _geos, pupynere
 32
 33 # basemap data files now installed in
lib/matplotlib/toolkits/basemap/data
<type 'exceptions.ImportError'>: libgeos_c.so.1: cannot open shared object
file: No such file or directory
Yet the file, in fact a link, libgeos_c.so.1, does exist at the location
(/usr/local/lib) where it is supposed to be:
[root@msasa lib]# ll
total 44230
-rw-r--r-- 1 root root 28107924 2007年12月28日 16:31 libgeos.a
-rw-r--r-- 1 root root 581806 2007年12月28日 16:31 libgeos_c.a
-rwxr-xr-x 1 root root 830 2007年12月28日 16:31 libgeos_c.la*
lrwxrwxrwx 1 root root 18 2007年12月28日 16:31 libgeos_c.so ->
libgeos_c.so.1.1.1*
lrwxrwxrwx 1 root root 18 2007年12月28日 16:31 libgeos_c.so.1 ->
libgeos_c.so.1.1.1*
-rwxr-xr-x 1 root root 452162 2007年12月28日 16:31 libgeos_c.so.1.1.1*
-rwxr-xr-x 1 root root 790 2007年12月28日 16:31 libgeos.la*
lrwxrwxrwx 1 root root 16 2007年12月28日 16:31 libgeos.so ->
libgeos.so.2.2.3*
lrwxrwxrwx 1 root root 16 2007年12月28日 16:31 libgeos.so.2 ->
libgeos.so.2.2.3*
-rwxr-xr-x 1 root root 13443604 2007年12月28日 16:31 libgeos.so.2.2.3*
I'd appreciate any help with this.
Thanks, Evan