[cctbxbb] Boost Import Error

[Magnus Andersson]

Hi again,

It seems as I'm stuck with using the wrapper cctbx.python.

Only one module complains now = Pymol

  File "PyWAXS.py", line 8, in <module>
    import pymol
ImportError: No module named pymol

I have found a fix to the problem in the ccp4 mailing list:

modifying the pymol startup script to source the cctbx setpaths.sh

but I'm not sure how to implement this solution.

Here's what I've tried:

In the macports pymol startup script I've added the line:

source /Users/magnus/Downloads/cctbx_build/setpaths.sh

but I get the same error....

Suggestions?

Magnus
 
On 03 Jun 2014, at 20:55, Magnus Andersson <magnus.andersson at scilifelab.se> wrote:

> Hi Luc,
> 
> The problem is I have a macports python build that contains all the rest of the modules that I import in this script. Because cctbx is not included in macports I have a separate build for this. Hence I need to call my script as:
> 
> /opt/local/bin/python2.7 script.py
> 
> I have set the PYTHONPATH in the bash shell:
> 
> export PYTHONPATH=/Users/magnus/Downloads/cctbx_sources:/opt/local
> 
> But, it's not working. Any suggestions how to deal with this?
> 
> Thanks,
> 
> Magnus
> 
> 
> On 03 Jun 2014, at 20:47, Luc Bourhis <luc_j_bourhis at mac.com> wrote:
> 
>> Hi Magnus,
>> 
>> you need to use the wrappers cctbx.python instead of python as it sets PYTHONPATH correctly so as to add that cctbx_sources/boost.
>> 
>> Best wishes,
>> 
>> Luc
>> 
>> On 3 Jun 2014, at 20:33, Magnus Andersson <magnus.andersson at scilifelab.se> wrote:
>> 
>>> Hi,
>>> 
>>> I've installed the cctbx package from the selfextracting file found in http://cci.lbl.gov/cctbx_build/ 
>>> 
>>> but I run into problems when importing cctbx in my python script:
>>> 
>>>     import iotbx.pdb
>>>   File "/Users/magnus/Downloads/cctbx_sources/iotbx/pdb/__init__.py", line 2, in <module>
>>>     from cctbx.array_family import flex
>>>   File "/Users/magnus/Downloads/cctbx_sources/cctbx/array_family/flex.py", line 2, in <module>
>>>     import scitbx.array_family.flex
>>>   File "/Users/magnus/Downloads/cctbx_sources/scitbx/array_family/flex.py", line 2, in <module>
>>>     import boost.optional # import dependency
>>> ImportError: No module named boost.optional
>>> 
>>> It is flex.py that wants to import boost.optional and does not find it. 
>>> 
>>> However, I find these three files:
>>> 
>>> optional.hpp		optional_fwd.hpp	optional_io.hpp
>>> 
>>> in the following directory:
>>> 
>>> /Users/magnus/Downloads/cctbx_sources/boost/boost/optional
>>> 
>>> which suggests that it's present. What am I missing here? I'm using Mac OS X Version 10.9.3 and Python2.7.
>>> 
>>> Cheers,
>>> 
>>> Magnus
>>> 
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>>> cctbxbb mailing list
>>> cctbxbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>> 
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