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import os
import shutil
import sys
import versioneer
import struct
import warnings
if sys.version_info < (3, 6):
sys.exit('You must have at least Python 3.6 for ParmEd to work correctly.')
from setuptools import setup, Extension
kws = {"entry_points" : {"console_scripts" : ["parmed = parmed.scripts:clapp"]}}
from distutils.command.clean import clean as Clean
def prepare_env_for_osx():
""" Prepares the environment for OS X building """
darwin_major_to_osx_map = {
'11': '10.7',
'12': '10.8',
'13': '10.9',
'14': '10.10',
'15': '10.11',
'16': '10.12',
'17': '10.13',
'18': '10.14',
'19': '10.15',
'20': '11.5',
}
os.environ['CXX'] = 'clang++'
os.environ['CC'] = 'clang'
darwin_major = os.uname()[2].split('.')[0]
if darwin_major in darwin_major_to_osx_map:
os.environ['MACOSX_DEPLOYMENT_TARGET'] = darwin_major_to_osx_map[darwin_major]
else:
import subprocess
warnings.warn("darwin_major_to_osx_map needs to be updated! Report this issue if build fails.")
swvers = subprocess.run("sw_vers -productVersion".split(), capture_output=True)
os.environ["MACOSX_DEPLOYMENT_TARGET"] = ".".join(swvers.stdout.decode("utf-8").strip().split(".")[:2])
class CleanCommand(Clean):
"""python setup.py clean """
# lightly adapted from scikit-learn package
description = "Remove build artifacts from the source tree"
def _clean(self, folder):
for dirpath, dirnames, filenames in os.walk(folder):
for filename in filenames:
if (filename.endswith('.so') or filename.endswith('.pyd')
or filename.endswith('.dll')
or filename.endswith('.pyc')):
os.unlink(os.path.join(dirpath, filename))
for dirname in dirnames:
if dirname == '__pycache__':
shutil.rmtree(os.path.join(dirpath, dirname))
def run(self):
Clean.run(self)
if os.path.exists('build'):
shutil.rmtree('build')
self._clean('./')
is_pypy = '__pypy__' in sys.builtin_module_names
if sys.platform == 'darwin' and not is_pypy:
# You *need* to use clang and clang++ for ParmEd extensions on a Mac;
# Anaconda does annoying stuff that breaks this, since their distutils
# automatically tries to use "gcc", which would conflict with the MacPorts
# gcc... sigh.
prepare_env_for_osx()
elif os.environ.get('CC', '').endswith('pgcc'):
# PGI compilers don't play nicely with Python extensions. So force GCC
sys.stderr.write('PGI compilers do not work with Python extensions generally. '
'Using GCC instead.\n')
os.environ['CC'] = 'gcc'
os.environ['CXX'] = 'g++'
# parmed package and all its subpackages
packages = ['parmed', 'parmed.amber', 'parmed.modeller',
'parmed.tinker', 'parmed.unit', 'parmed.amber.mdin',
'parmed.charmm', 'parmed.formats.pdbx', 'parmed.rosetta', 'parmed.rdkit',
'parmed.formats', 'parmed.utils.fortranformat', 'parmed.openmm',
'parmed.utils', 'parmed.gromacs', 'parmed.tools', 'parmed.namd',
'parmed.tools.simulations', 'parmed.entos', 'parmed.dlpoly']
# Optimized readparm
sources = [os.path.join('src', '_rdparm.cpp'),
os.path.join('src', 'readparm.cpp')]
depends = [os.path.join('src', 'CompatabilityMacros.h'),
os.path.join('src', 'readparm.h')]
include_dirs = [os.path.join(os.path.abspath('.'), 'src')]
definitions = []
#if using 64 bit python interpreter on Windows, add the MS_WIN64 flag for 64 bit pointers
if sys.platform == 'win32' and (struct.calcsize("P") == 8):
definitions.append(('MS_WIN64', None))
definitions.append(('_hypot', 'hypot')) #fix MinGW build -- see http://stackoverflow.com/questions/10660524/error-building-boost-1-49-0-with-gcc-4-7-0/12124708#12124708
extensions = [Extension('parmed.amber._rdparm',
sources=sources,
include_dirs=include_dirs,
depends=depends,
define_macros=definitions)
]
if __name__ == '__main__':
# See if we have the Python development headers. If not, don't build the
# optimized prmtop parser extension
from distutils import sysconfig
if not is_pypy and not os.path.exists(os.path.join(sysconfig.get_config_vars()['INCLUDEPY'], 'Python.h')):
extensions = []
cmdclass = dict(clean=CleanCommand)
cmdclass.update(versioneer.get_cmdclass())
setup(name='ParmEd',
version=versioneer.get_version(),
description='Inter-package toolkit for molecular mechanical simulations',
author='Jason Swails',
author_email='jason.swails@gmail.com',
url='https://parmed.github.io/ParmEd/html/index.html',
license='LGPL',
packages=packages,
ext_modules=extensions,
cmdclass=cmdclass,
package_data={'parmed.modeller': ['data/*.lib', 'data/*.json', 'data/*.json.gz']},
python_requires='>=3.8',
**kws
)
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