py2exe misses many of the obf files so you need to specify them
explicity with the data_files option. The following setup.py works for
me (with "python setup.py py2exe"):

import os
import glob
from distutils.core import setup

import py2exe

data_files=[(".", glob.glob(os.path.join(os.environ["BABEL_DATADIR"],
                                         "*.obf")))]

setup(name="TestScript",
      version="1.0",
      author="Noel O'Boyle",
      author_email="baoille...@users.sf.net",
      console = [{'script':'simple.py'}],
      options = {'py2exe': {'dll_excludes':['MSVCP80.dll', 'MSVCR80.dll'],
                 'excludes': ["Tkconstants","Tkinter","tcl"]}},
      data_files = data_files,
      )

- Noel

On 22 July 2010 15:40, Noel O'Boyle <baoille...@gmail.com> wrote:
> py2exe creates a zip file. Take a look in there. Does it contain all
> of OpenBabel's DLLs and obf files?
>
> If so, then the problem is that OpenBabel cannot find them. Try just
> copying them all into the directory containing the .exe.
>
> If you don't mind me asking, why are you interested in using py2exe?
> If there's general interest in this, I could look into sorting it out.
>
> - Noel
>
> On 18 July 2010 16:26, Fergal Duffy <ferga...@gmail.com> wrote:
>> Hi,
>>
>> I want to create a windows executable based on python scripts, and using the
>> pybel openbabel interface, using py2exe to budle it all up. My application
>> works fine as a script run from the command line, but when I package it up
>> with py2exe, it fails to run, with the following message written to the log
>>
>> Traceback (most recent call last):
>>   File "pepgui.py", line 14, in <module>
>>     import pybel
>>   File "pybel.pyc", line 37, in <module>
>>   File "pybel.pyc", line 33, in _formatstodict
>> ValueError: need more than 1 value to unpack
>>
>>
>> My application is in a scrip file: pepgui.py, and I have written a short
>> setup.py file to bundle it as an .exe:
>>
>> from distutils.core import setup
>> import py2exe
>>
>> opts = {"py2exe": {"dll_excludes": ["MSVCR80.dll","MSVCP80.dll"]}}
>>
>> setup(options=opts, windows=['pepgui.py'])
>>
>> Thanks,
>>
>> Fergal Duffy
>>
>>
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