I *strongly* recommend contacting the openbabel mailing list rather than me
personally. My e-mail box is horrendous.
In this case, I suspect you either have multiple versions of Python installed,
or the active python is not able to load the _openbabel.so correctly.
I usually see this sort of error when you run one Python binary, but
_openbabel.so is linked against a different libpython.
Others may have other suggestions.
Hope that helps,
-Geoff
> On Feb 26, 2015, at 12:10 PM, Damir Herman <damir.her...@gmail.com> wrote:
>
> Geoff,
>
> I saw you are an active contributor to openbabel so I wanted to ask you a
> question about installation and running of python openbabel bindings on a
> mac.
> <Screen Shot 2015-02-26 at 9.08.01 AM.png>
> I pulled openbabel from repo (details below). When I start python, here is
> what I run into. I googled around, but noone reported this issue so far. Do
> you think you can have a look?
>
> Thanks,
>
> --Damir
>
> Python 2.7.9 (default, Jan 7 2015, 11:49:12)
> [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import openbabel
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File "/usr/local/lib/python2.7/site-packages/openbabel.py", line 1727
> def OBPlugin_List(PluginID, param=None, os):
> SyntaxError: non-default argument follows default argument
> >>>
>
> In /usr/local/lib/python2.7/site-packages/openbabel.py, line 1727 I have
>
> 1726
> 1727 def OBPlugin_List(PluginID, param=None, os):
> 1728 return _openbabel.OBPlugin_List(PluginID, param, os)
> 1729 OBPlugin_List = _openbabel.OBPlugin_List
> 1730
>
> If I replace the line 1727 with
>
> def OBPlugin_List(PluginID, os, param=None):
>
> when I import openbabel I get:
>
> >>> import openbabel
> Fatal Python error: PyThreadState_Get: no current thread
> Abort trap: 6
>
>
> =================
> tl;dr
>
>
> cd var
> git clone https://github.com/openbabel/openbabel.git
> <https://github.com/openbabel/openbabel.git>
> mkdir build
> cd build
> cmake -DBUILD_GUI=ON -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON ../openbabel
> output of cmake in cmake.out
> make -j8
> make.out and make.err attached
> sudo make install
> install.out attached
>
> Openbabel command line utilities installed:
>
> obabel -V
> Open Babel 2.3.90 -- Feb 26 2015 -- 08:58:33
>
>
> <cmake.out><make.out><make.err><install.out>
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