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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