setup.py

#/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
#   Copyright (c) 2011-2016 The plumed team
#   (see the PEOPLE file at the root of the distribution for a list of names)
#
#   See http://www.plumed.org for more information.
#
#   This file is part of plumed, version 2.
#
#   plumed is free software: you can redistribute it and/or modify
#   it under the terms of the GNU Lesser General Public License as published by
#   the Free Software Foundation, either version 3 of the License, or
#   (at your option) any later version.
#
#   plumed is distributed in the hope that it will be useful,
#   but WITHOUT ANY WARRANTY; without even the implied warranty of
#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#   GNU Lesser General Public License for more details.
#
#   You should have received a copy of the GNU Lesser General Public License
#   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#
# This python routine builds an interface between plumed and python using cython
#
from setuptools import setup
from distutils.extension import Extension
import subprocess
import os
import os.path
import sys
from shutil import copyfile

if os.getenv("plumed_macports") is not None:
    copyfile("../VERSION","VERSION")
    copyfile("../src/wrapper/Plumed.h","Plumed.h")

plumedname = os.getenv("plumed_program_name")
if plumedname is None:
    plumedname = "plumed"

plumedversion = os.getenv("plumed_version")
if plumedversion is None:
    plumedversion = subprocess.check_output(['grep','-v','#','./VERSION']).decode("utf-8")

print( "Module name " + plumedname )
print( "Version number " + plumedversion )

extra_compile_args=['-D__PLUMED_HAS_DLOPEN','-D__PLUMED_WRAPPER_LINK_RUNTIME=1','-D__PLUMED_WRAPPER_CXX=1','-D__PLUMED_WRAPPER_IMPLEMENTATION=1','-D__PLUMED_WRAPPER_EXTERN=0','-D__PLUMED_WRAPPER_CXX_DEFAULT_INVALID=1'] 

defaultkernel=os.getenv("plumed_default_kernel")
if defaultkernel is not None:
    extra_compile_args.append("-D__PLUMED_DEFAULT_KERNEL=" + os.path.abspath(defaultkernel))
    print( "Hardcoded PLUMED_KERNEL " + os.path.abspath(defaultkernel))

def readme():
    with open('README.rst') as f:
        return f.read()

try:
    import numpy
except:
    print('Error: building ' + plumedname + ' requires numpy. Please install it first with pip install numpy')
    sys.exit(-1)

include_dirs=[numpy.get_include()]

try:
    include_dirs.append(os.environ["plumed_include_dir"])
except:
    include_dirs.append(".")

# allow one to force using cython with env var plumed_force_cython=yes
USE_CYTHON = False
try:
    if(os.environ["plumed_force_cython"]=="yes"):
        print('plumed_force_cython=yes')
        USE_CYTHON = True
except:
    pass

# if plumed.cpp is available, do not need cython
if not USE_CYTHON:
    if not os.path.isfile("plumed.cpp"):
        print('plumed.cpp not found, cython is needed')
        USE_CYTHON = True

# try to import cython
if USE_CYTHON:
    try:
        print('importing cython')
        from Cython.Build import cythonize
        extension="pyx"
    except:
        print('Error: building ' + plumedname + ' requires cython. Please install it first with pip install cython')
        sys.exit(-1)
else:
    print('using available plumed.cpp file')
    extension="cpp"

ext_modules=[Extension(
     name=plumedname,
     sources=["plumed." + extension],
     language="c++",
     include_dirs=include_dirs,
     extra_compile_args=extra_compile_args
  )]

if USE_CYTHON:
    ext_modules=cythonize(ext_modules)

setup(
  name=plumedname,
  version=plumedversion,
  description='Python interface to PLUMED',
  long_description=readme(),
  classifiers=[
          'Development Status :: 4 - Beta',
          'Intended Audience :: Science/Research',
          'Topic :: Scientific/Engineering :: Bio-Informatics',
          'Topic :: Scientific/Engineering :: Chemistry',
          'Topic :: Scientific/Engineering :: Physics',
          'License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)',
          'Programming Language :: Python :: 2',
          'Programming Language :: Python :: 2.7',
          'Programming Language :: Python :: 3',
          'Programming Language :: Python :: 3.6',
          'Programming Language :: Python :: 3.7',
  ],
  author='Gareth A. Tribello',
  author_email='plumed-users@googlegroups.com',
  url='http://www.plumed.org',
  ext_modules = ext_modules,
  zip_safe=False,
  test_suite='nose.collector'
)