Oh, that works. Thanks,
That is nice to know how to do the Python3, and should be documented
somewhere. I couldn't find it.
The problem with the current cmake approach, though, is that it ignores the
standard python installation mechanism using setuptools. Therefore..
1. At least on my system, the files are put in the wrong place lib
directory, rather than site-packages.
2. Egg installations are not possible.
3. It isn't possible to install the package to a virtual_env
4. It isn't possible to maintain several versions of the package.
5. the standard "pythonic" ways of installing don't work:
python setup.py build install
pip install openbabel
python3 setup.py build install
pip3 install openbabel
easy_install openbabel
The good news is that I think i have an openbabel package that appears to
solve these problems. Does someone with more openbabel build knowledge want
to check it?
S Joshua Swamidass
http://swami.wustl.edu/
On Sat, Jan 4, 2014 at 3:27 AM, David Hall <li...@cowsandmilk.net> wrote:
> I'm not sure what exactly you're tying to accomplish, but Geoff pointed
> out that openbabel has a pkg-config file, which is what most people would
> use. On a typical system install, the file is installed at
> /usr/lib/pkgconfig/openbabel-2.0.pc (or an architecture dependent
> equivalent). Rather than looking for that manually, you would run
> pkg-config like below:
>
> $ pkg-config --variable=libdir openbabel-2.0
> /usr/lib
> $ pkg-config --variable=pkgincludedir openbabel-2.0
> /usr/include/openbabel-2.0
> $ pkg-config --variable=includedir openbabel-2.0
> /usr/include
>
> That should provide the info you are looking for in this case?
>
> On a side note, I wanted to point out that for the current openbabel
> master from github, if you want python3 support, the following still works
> for me:
>
> $ cmake -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON
> -DPYTHON_EXECUTABLE=/usr/bin/python3 ..
> $ make
> $ sudo make install
>
> Obviously not in an official release yet, but should work in future
> releases.
>
> -David
>
>
>
> On Fri, Jan 3, 2014 at 11:31 PM, S Joshua Swamidass
> <swamid...@gmail.com>wrote:
>
>> So looking more closely at the build system. I think I've narrowed the
>> problems down to just a couple manageable issues.
>>
>> 1. Currently, it seems, cmake doesn't even use setup.py to install or
>> build python modules.
>>
>> 2. So, setup.py, is actually not runnable in version 2.3.2, but this
>> isn't obvious because cmake doesn't ever actually use it.
>>
>> 3. Here are the offending lines:
>>
>> if "build" in sys.argv:
>> shutil.copyfile(os.path.join(srcdir, "pybel_py%dx.py" %
>> sys.version_info[0]), "pybel.py")
>> shutil.copyfile(os.path.join(srcdir, "openbabel.py"), "openbabel.py")
>>
>> Which are problemeatic because they look for pybel_py2x.py and
>> pybel_py3x.py, neither of which exist on the file system. The good news is
>> that just deleting these lines seems to work just fine.
>>
>>
>> 4. And here are the lines that make the setup.py not portable/uploadable
>> to pypi. Basically, setup.py assumes that we are in a the src directory
>> tree for openbabel, and uses relative references to link the libraries and
>> includes. This is not the right way to do it. Rather, we should link to the
>> installed libraries here.
>>
>> obExtension = Extension('_openbabel',
>> [os.path.join(srcdir, "openbabel-python.cpp")],
>> include_dirs=[os.path.join(srcdir, "..", "..",
>> "include"),
>> os.path.join("..", "include")],
>> library_dirs=[os.path.join(srcdir, "..", "..", "lib"),
>> os.path.join(srcdir, "..", "..", "lib64"),
>> os.path.join("..", "lib")],
>> libraries=['openbabel']
>> )
>>
>> So here is the question, what is the best way for this python scipt to
>> discover where the openbabel libraries and includes are installed? An
>> environmental variable? An option to setup.py? Or, ideally, something run
>> off the commandline?
>>
>> If we can solve this problem, we are about 90% of the way to a final
>> solution here.
>>
>>
>>
>>
>> S Joshua Swamidass
>> http://swami.wustl.edu/
>>
>>
>> On Fri, Jan 3, 2014 at 6:05 PM, S Joshua Swamidass
>> <swamid...@gmail.com>wrote:
>>
>>> I'm up for helping a bit. I do understand the setup.py system, and have
>>> a few packages already on pypi.
>>>
>>> But I'll need some help figuring out how the current system works. Is
>>> there someone already familiar with this that could help do this?
>>>
>>> S Joshua Swamidass
>>> http://swami.wustl.edu/
>>>
>>>
>>> On Thu, Jan 2, 2014 at 8:27 AM, Geoffrey Hutchison <
>>> geoff.hutchi...@gmail.com> wrote:
>>>
>>>> > 1. Possibly this could be detected by seeing what libraries are
>>>> installed in the openbabel install
>>>>
>>>> Indeed. Many of these things should already be set in the babelconfig.h
>>>> header, which should be trivially parseable by Python. If something is
>>>> missing, let me know and I can change CMake to add the needed info to
>>>> babelconfig.h for this purpose.
>>>>
>>>> Moreover, most of this info should also be accessible in the
>>>> openbabel-2.0.pc for pkg-config, and the CMake module installed for Open
>>>> Babel.
>>>>
>>>> > 2. More reliably, openbabel could install a comand to the install bin
>>>> that (perhaps named openbabel-config) that provides all this information
>>>> (like include dir, lib dir, compile options, etc) as text to stdout. This
>>>> is the mechanism that python uses for its self (with python-config).
>>>>
>>>> Meh. We already install a CMake module and a pkg-config module, plus
>>>> babelconfig.h. It's certainly easy to write such a script, but I guess my
>>>> question is "how many of these things do we need?"
>>>>
>>>> > 3. Have setup.py give clean information about why it fails if it
>>>> can't get info (e.g. need to upgrade openbabel before install, etc.)
>>>>
>>>> This would be an extremely welcome improvement.
>>>>
>>>> > What do you think?
>>>>
>>>> Sounds great. Are you volunteering? ;-)
>>>>
>>>> Cheers,
>>>> -Geoff
>>>>
>>>>
>>>
>>
>>
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