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Tasklist

FS#23086 - [python-openbabel] iterators do not work with python 3 + one function was not wrapped

Attached to Project: Community Packages
Opened by Hector Mtz-Seara Monne (hseara) - Tuesday, 01 March 2011, 10:01 GMT
Last edited by Thomas Dziedzic (tomd123) - Wednesday, 07 December 2011, 15:02 GMT
Task Type Bug Report
Category Packages
Status Closed
Assigned To Kaiting Chen (kaitocracy)
Architecture All
Severity High
Priority Normal
Reported Version
Due in Version Undecided
Due Date Undecided
Percent Complete 100%
Votes 1
Private No

Details

Description:
a) python-openbabel iterators do not work with python 3. An upstream patch correcting this is added (Applied in openbabel SVN: r4399).
b) One function was not wrapped. They missed (Applied in openbabel SVN: r4400).

Additional info:
* package version(s)
python-openbabel
python2-openbablel

* config and/or log files etc.
configure with cmake options: -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON

After rebuild openbabel python module: make openbabel_
(this will run SWIG, regenerate the bindings and build the module)

Steps to reproduce:
Run the attached OB_iterator.py with python3. You will get the following error:

Traceback (most recent call last):
File "/home/hector/OB_iterator.py", line 5, in <module>
for n, i in enumerate(openbabel.OBMolAtomIter(mol)):
TypeError: iter() returned non-iterator of type 'OBMolAtomIter'
   openbabel-python-2.3.0-py3_it... (0.3 KiB)
   openbabel-python-2.3.0-wrap_O... (0.4 KiB)
   OB_iterator.py (0.2 KiB)
This task depends upon

Closed by  Thomas Dziedzic (tomd123)
Wednesday, 07 December 2011, 15:02 GMT
Reason for closing:  Fixed
Additional comments about closing:  2.3.1
Comment by Thomas Dziedzic (tomd123) - Tuesday, 01 March 2011, 16:21 GMT
maybe we should just pull python-openbabel from svn for now until next release?
Comment by Hector Mtz-Seara Monne (hseara) - Tuesday, 01 March 2011, 20:18 GMT
It is an option
Comment by Hector Mtz-Seara Monne (hseara) - Saturday, 05 March 2011, 16:58 GMT
I just got to know from the mailing list of openbabel that in about a month it is likely that there will be a new openbabel release. Maybe we can close this upstream bug and when the new release appear just update the package.
Comment by Kaiting Chen (kaitocracy) - Saturday, 09 April 2011, 04:41 GMT
Does this actually have anything to do with python2-openbabel? Anyways I think I'll just apply the patches until the next release.
Comment by Fabian Homborg (alfa) - Tuesday, 09 August 2011, 01:07 GMT
Just to clarify, the versions are python-openbabel 2.3.0-3 and python2-openbabel 2.3.0-2 made on 23 feb 2011 and 20 nov 2010, respectively.
Comment by Hector Mtz-Seara Monne (hseara) - Wednesday, 07 December 2011, 14:07 GMT
This problem is corrected in the new version (2.3.1) already in archlinux. This bug should be then closed.

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