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Hello Kieran,

>>> from libsbml import *
> runs into the error
>>> Fatal Python error: Interpreter not initialized (version mismatch?)

that error indicates that you are not running with the python interpreter bundled with OSX lion. Which is:

/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python

which is

/System/Library/Frameworks/Python.framework/Versions/Current/bin/python

and on my machine /usr/bin/python.

This is what we created the binaries for. If you want to use a different interpreter you will have to compile the python bindings manually.


> Could this be because libsbml.py and libsbml.pyc aren't in the
> site-packages folder?

No, these files are not needed. They are there in the form of libsbm/__init__.py which will be loaded when importing libsbml with the site-package path set.

I hope this helps
Frank

> k
>
> On 24/12/2011 01:28, Frank T. Bergmann wrote:
>> Hello Kieran …
>>
>> it should be simpler than all that, the DMG installer for lion
>> contains the binaries. They are installed by default into
>>
>> /usr/local/lib/python2.7/site-packages/
>>
>> so running:
>>
>> $ PYTHONPATH=/usr/local/lib/python2.7/site-packages/ python Python
>> 2.7.1 (r271:86832, Jun 16 2011, 16:59:05) [GCC 4.2.1 (Based on Apple
>> Inc. build 5658) (LLVM build 2335.15.00)] on darwin Type "help",
>> "copyright", "credits" or "license" for more information.
>>>>> from libsbml import * print getLibSBMLDottedVersion()
>> 5.3.0
>>>>>
>>
>> would be all that is needed. These binaries are also universal:
>>
>> file python2.7/site-packages/libsbml/_libsbml.so
>> python2.7/site-packages/libsbml/_libsbml.so: Mach-O universal binary
>> with 2 architectures python2.7/site-packages/libsbml/_libsbml.so (for
>> architecture i386): Mach-O bundle i386
>> python2.7/site-packages/libsbml/_libsbml.so (for architecture
>> x86_64): Mach-O 64-bit bundle x86_64
>>
>>
>> so they include the 32 and 64bit bindings. So is the default python
>> on OSX:
>>
>> $ file `which python` /usr/bin/python: Mach-O universal binary with 2
>> architectures /usr/bin/python (for architecture x86_64): Mach-O
>> 64-bit executable x86_64 /usr/bin/python (for architecture i386):
>> Mach-O executable i386
>>
>> So you simply switch it to 64 / 32 bit mode as needed with an
>> environment variable:
>>
>> VERSIONER_PYTHON_PREFER_32_BIT=no
>>
>> to force 64bit mode or yes for 32bit mode.
>>
>> When you want to compile it yourself on osx it is sufficient to
>> compile with:
>>
>> ./configure --with-python --enable-universal-binaries=yes
>>
>> best Frank
>>
>> On Dec 23, 2011, at 5:13 PM, kieran wrote:
>>
>>> Hello all,
>>>
>>> I've decided to give python a go, but have been having real
>>> problems getting it to speak to libSBML. All problems below may
>>> just be my being a python newb, but thought I should ask.
>>>
>>> I installed enthought (on my Mac OSX lion), a 64 bit python
>>> package located by default at
>>> /Library/Frameworks/EPD64.framework/Versions/Current/bin/python
>>>
>>> After installing the stable 5.3.0 binary, I followed the
>>> instructions, changing ~/.bashprofile to include the line export
>>> PYTHONPATH=/usr/local/lib/python2.7/site-packages and the
>>> permissions of all files located there. However, typing
>>>> from libsbml import *
>>> produced
>>>> Fatal Python error: Interpreter not initialized (version
>>>> mismatch?)
>>> Further investigation revealed that the .py and .pyc files were
>>> missing, with __init__.py/c in their place.
>>>
>>> So I decided to try the experimental binary instead. This time the
>>> error was
>>>> ImportError: No module named libsbml
>>> and I saw that the file libsbml.pyc was missing.
>>>
>>> Finally, I decided to try compiling the (stable) source with
>>> ./configure
>>> --with-python=/Library/Frameworks/EPD64.framework/Versions/Current
>>> but I ran into the same problems (error and wrongly named files) as
>>> when using the stable binary.
>>>
>>> Any ideas what I'm doing wrong?
>>>
>>> Cheers, k
>>>
>>> -- kieran smallbone kieran.smallbone@manchester.ac.uk
>>> http://u003f.com/
>>>
>>> manchester centre for integrative systems biology manchester
>>> interdisciplinary biocentre 131 princess street manchester m1 7dn.
>>> uk ____________________________________________________________ To
>>> manage your libsbml-development list subscription, visit
>>> https://utils.its.caltech.edu/mailman/listinfo/libsbml-development
>>>
>>> For a web interface to the libsbml-development mailing list, visit
>>> http://sbml.org/Forums/
>>>
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>>> contact sbml-team@caltech.edu
>>>
>>
>> ____________________________________________________________ To
>> manage your libsbml-development list subscription, visit
>> https://utils.its.caltech.edu/mailman/listinfo/libsbml-development
>>
>> For a web interface to the libsbml-development mailing list, visit
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>>
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>> sbml-team@caltech.edu
>>
>
> --
> kieran smallbone
> kieran.smallbone@manchester.ac.uk
> http://u003f.com/
>
> manchester centre for integrative systems biology
> manchester interdisciplinary biocentre
> 131 princess street
> manchester m1 7dn. uk
> ____________________________________________________________
> To manage your libsbml-development list subscription, visit
> https://utils.its.caltech.edu/mailman/listinfo/libsbml-development
>
> For a web interface to the libsbml-development mailing list, visit
> http://sbml.org/Forums/
>
> For questions or feedback about the libsbml-development list,
> contact sbml-team@caltech.edu
>

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