So the good news is that Noel's suggestions actually does work even if it
is a bit ugly to manually find all the python references in CMakeCache.txt.
What is everyones opinion of fixing setup.py to be standalone and work with
pypi and pip? I still think this would be the best path forward.
S Joshua Swamidass
http://swami.wustl.edu/
On Fri, Dec 27, 2013 at 12:49 PM, S Joshua Swamidass <swamid...@gmail.com>wrote:
> So Noel responded thusly...
>
> "Python 3 support should be working fine. You just need to specify the
> location to the appropriate Python installation when running CMake.
> Use "grep PYTHON CMakeCache.txt" to see the names of the variables if
> it's not in the docs."
>
> I'll have yet to try it but can email back here later this afternoon to
> see if it works.
>
>
> I just got done installing the python 2 wrappers too, and have a couple
> observations about the process.
>
> 1. Greatly improved install system from before. Cmake is a good idea for
> the most part, except one key issue (will explain more in a sec).
>
>
> 2. Still has some challenging warts with compiling python bindings...
>
> a. Compiling for Python should not require Cmake edits, especially with
> the excellent installers that are now available.
>
> b. There are some non-intuitive issues with compiling boost libraries (a
> specific flag is needed) before the python bindings will compile.
>
> c. openbabel.py pybel.py and _openbabel.so are put into the system library
> directory instead of into the python sitepackages directory. This is a
> pretty bad situation actually, because it means you have to (1) recognize
> this and (2) find them and (3) move them to an appropriate location.
> Reading online, it seems that this is a cmake problem. It only knows how to
> install things in one place.
>
>
> 3. 2c is not an easy problem to resolve, because trying to install from
> the scripts/python/setup.py does not work.
>
>
> I don't know how to fix 2.b. other than just documenting this better, but
> 2.a. and 2.c. should be fixed by addressing problem 3. If there was a way
> to create a standalone, source isntall (that just assumed that boost and
> openbabel were already installed), the whole process of making python
> bindings would be much cleaner. Ideally it could even be uploaded to pypi,
> so people could just use pip to install. I looked at the setup.py, but
> there are several issues deep in the build process that make it farm from a
> trivial change for a person unfamilar with cmake like me. Here are some of
> the errors I get:
>
> 1. setup.py can't find pybel_py2.py (builtt by cmake?)
> 2. setup.py can't find pybel_py3.py (built by cmake?)
> 3. setup.py looks for includes based on the __path__ variable, rather than
> looking for installed libraries or providing an option for other behaivior.
> 4. if you add the include direcotry in the source directory, it still
> can't find babelconfig.h (built or different location?)
>
> Basically, setup.py is not configured to work as a standalone package
> installer. It is probably fixable, and would greatly easy the installation.
> What do you guys think?
>
>
>
>
> S Joshua Swamidass
> http://swami.wustl.edu/
>
>
> On Fri, Dec 27, 2013 at 11:41 AM, Geoffrey Hutchison <
> geoff.hutchi...@gmail.com> wrote:
>
>> > Hope you are well. I'm trying to figure out how to install python
>> bindings for Python 3. Is this functional yet?
>>
>> Hi there!
>>
>> Yes, Pybel has been compatible with Python 3 for a while now. What are
>> your problems installing the bindings?
>>
>> Thanks,
>> -Geoff
>>
>>
>
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