Numpy issue and bugfix when installing GRIT v1.1.2

[Fabian Buske]

Hi,

I had some issues installing GRIT v1.1.2 on our HPC cluster, where I have a Python 2.7 version at a custom location.

-bash-4.1$ python setup.py install

running install

running bdist_egg

running egg_info

writing requirements to GRIT.egg-info/requires.txt

writing GRIT.egg-info/PKG-INFO

writing top-level names to GRIT.egg-info/top_level.txt

writing dependency_links to GRIT.egg-info/dependency_links.txt

reading manifest file 'GRIT.egg-info/SOURCES.txt'

reading manifest template 'MANIFEST.in'

writing manifest file 'GRIT.egg-info/SOURCES.txt'

installing library code to build/bdist.linux-x86_64/egg

running install_lib

running build_py

running build_ext

building 'grit.sparsify_support_fns' extension

gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/share/ClusterShare/software/contrib/fabbus/python/2.7.3/include/python2.7 -c grit/sparsify_support_fns.c -o build/temp.linux-x86_64-2.7/grit/sparsify_support_fns.o

grit/sparsify_support_fns.c:346:31: error: numpy/arrayobject.h: No such file or directory

grit/sparsify_support_fns.c:347:31: error: numpy/ufuncobject.h: No such file or directory

grit/sparsify_support_fns.c:602: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘__pyx_t_5numpy_int8_t’

Essentially setup could not locate numpy.

I fixed this by adding two lines to the setup.py, importing numpy and adding the 'include_dirs' directive to the config part:

#from distutils.core import setup

#from distutils.extension import Extension

from setuptools import setup, Extension, find_packages

import numpy

...

config = {

    'include_package_data': True,

...

   'include_dirs': [numpy.get_include()],

...

}

if __name__== '__main__':

    setup(**config)

~

Cheers,

Fabian

[Nathan Boley]

Dear Fabian,

> I fixed this by adding two lines to the setup.py, importing numpy and adding
> the 'include_dirs' directive to the config part:

< snip fix >

Thanks for the report and useful suggestion. I've released 1.1.3 with
this fixed.

Best, Nathan

[Chris Zaleski]

Hello Nathan,

I'm experiencing this exact problem while trying to build version 2.0.4. Should I use the fix originally suggested here, or do you recommend an alternate method?

Thanks,
Chris

[Nathan Boley]

Hi Chris,

I'm experiencing this exact problem while trying to build version 2.0.4. Should I use the fix originally suggested here, or do you recommend an alternate method?

That fix would work - I also just tagged and pushed 2.0.5beta1 (https://github.com/nboley/grit/releases/tag/2.0.5beta1) which includes the fix.

Best, Nathan