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setup.py
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setup.py
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import os
import sys
import platform
from os import sep as dirsep
from os.path import isfile, join
from setuptools import setup
from setuptools import Extension
import shutil
if sys.version_info[:2] < (2, 7):
sys.stderr.write('Python 2.6 and older is not supported\n')
sys.exit()
if sys.version_info[:2] == (2, 7) or sys.version_info[:2] <= (3, 5):
INSTALL_REQUIRES=['numpy>=1.10', 'biopython<=1.76', 'pyparsing', 'scipy']
else:
INSTALL_REQUIRES=['numpy>=1.10,<2', 'biopython', 'pyparsing<=3.1.1', 'scipy', 'setuptools']
if sys.version_info[0] == 3 and sys.version_info[1] < 6:
sys.stderr.write('Python 3.5 and older is not supported\n')
sys.exit()
if os.name == 'java':
sys.stderr.write('JavaOS is not supported\n')
sys.exit()
try:
import numpy
except ImportError:
sys.stderr.write('numpy is not installed, you can find it at: '
'http://www.numpy.org/\n')
sys.exit()
if [int(dgt) for dgt in numpy.__version__.split('.')[:2]] < [1, 10]:
sys.stderr.write('numpy v1.10 or later is required, you can find it at: '
'http://www.numpy.org/\n')
sys.exit()
__version__ = ''
with open('prody/__init__.py') as inp:
for line in inp:
if line.startswith('__version__'):
exec(line.strip())
break
with open('README.rst') as inp:
long_description = inp.read()
PACKAGES = ['prody',
'prody.atomic',
'prody.database',
'prody.dynamics',
'prody.ensemble',
'prody.kdtree',
'prody.measure',
'prody.proteins',
'prody.sequence',
'prody.trajectory',
'prody.chromatin',
'prody.compounds',
'prody.domain_decomposition',
'prody.utilities',
'prody.apps',
'prody.apps.prody_apps',
'prody.apps.evol_apps',
'prody.tests',
'prody.tests.apps',
'prody.tests.atomic',
'prody.tests.datafiles',
'prody.tests.dynamics',
'prody.tests.ensemble',
'prody.tests.kdtree',
'prody.tests.measure',
'prody.tests.proteins',
'prody.tests.sequence',
'prody.tests.trajectory',
'prody.tests.utilities',]
PACKAGE_DATA = {
'prody.utilities': ['datafiles/*.dat'],
'prody.tests': ['datafiles/pdb*.pdb',
'datafiles/*.dat',
'datafiles/*.coo',
'datafiles/dcd*.dcd',
'datafiles/xml*.xml',
'datafiles/msa*',
'datafiles/mmcif*cif',],
'prody.proteins': ['tabulated_energies.txt'],
}
PACKAGE_DIR = {}
for pkg in PACKAGES:
PACKAGE_DIR[pkg] = join(*pkg.split('.'))
from glob import glob
tntDir = join('prody', 'utilities', 'tnt')
hpbSoDir = join('prody', 'proteins', 'hpbmodule',
'hpb_Python{0}.{1}'.format(sys.version_info[0],
sys.version_info[1]))
proteinsDir = join('prody', 'proteins')
try:
shutil.copy(hpbSoDir + "/hpb.so", proteinsDir)
except FileNotFoundError:
pass
EXTENSIONS = [
Extension('prody.dynamics.rtbtools',
glob(join('prody', 'dynamics', 'rtbtools.c')),
include_dirs=[numpy.get_include()]),
Extension('prody.dynamics.smtools',
glob(join('prody', 'dynamics', 'smtools.c')),
include_dirs=[numpy.get_include()]),
# Extension('prody.dynamics.saxstools',
# glob(join('prody', 'dynamics', 'saxstools.c')),
# include_dirs=[numpy.get_include()]),
Extension('prody.sequence.msatools',
[join('prody', 'sequence', 'msatools.c'),],
include_dirs=[numpy.get_include()]),
Extension('prody.sequence.msaio',
[join('prody', 'sequence', 'msaio.c'),],
include_dirs=[numpy.get_include()]),
Extension('prody.sequence.seqtools',
[join('prody', 'sequence', 'seqtools.c'),],
include_dirs=[numpy.get_include()]),
]
# extra arguments for compiling C++ extensions on MacOSX
if platform.system() == 'Darwin':
os_ver = platform.mac_ver()[0]
os.environ['MACOSX_DEPLOYMENT_TARGET'] = os_ver
os.environ['CC'] = 'clang'
os.environ['CXX'] = 'clang++'
#extra_compile_args.append('-stdlib=libc++')
# extra compilation of reg_tet.f (hpb):
# import subprocess
# subprocess.call(['gfortran', '-O3', '-fPIC', '-c',
# join('prody', 'proteins', 'hpbmodule', 'reg_tet.f'),
# '-o', join('prody', 'proteins', 'hpbmodule', 'reg_tet.o')])
CONTRIBUTED = [
Extension('prody.kdtree._CKDTree',
[join('prody', 'kdtree', 'KDTree.c'),
join('prody', 'kdtree', 'KDTreemodule.c')],
include_dirs=[numpy.get_include()]),
Extension('prody.proteins.ccealign',
[join('prody', 'proteins', 'ccealign', 'ccealignmodule.cpp')],
include_dirs=[tntDir], language='c++'),
#Extension('prody.proteins.hpb',
# [join('prody', 'proteins', 'hpbmodule', 'reg_tet.c')],
# include_dirs=[hpbDir], language='c++',
# extra_compile_args=['-O3', '-fPIC'],
# extra_objects=[join(hpbDir, 'libf2c', 'libf2c.a')]
# )
]
for ext in CONTRIBUTED:
if all([isfile(src) for src in ext.sources]):
EXTENSIONS.append(ext)
# SCRIPTS = ['scripts/prody', 'scripts/evol']
# if (platform.system() == 'Windows' or
# len(sys.argv) > 1 and sys.argv[1] not in ('build', 'install')):
# for script in list(SCRIPTS):
# SCRIPTS.append(script + '.bat')
SCRIPTS = ['prody=prody.apps:prody_main', 'evol=prody.apps:evol_main']
setup(
name='ProDy',
version=__version__,
author='James Krieger, Karolina Mikulska-Ruminska, She Zhang, Hongchun Li, Cihan Kaya, Ahmet Bakan, and others',
author_email='[email protected]',
description='A Python Package for Protein Dynamics Analysis',
long_description=long_description,
url='http://www.csb.pitt.edu/ProDy',
packages=PACKAGES,
#package_dir=PACKAGE_DIR,
package_data=PACKAGE_DATA,
ext_modules=EXTENSIONS,
license='MIT License',
keywords=('protein, dynamics, elastic network model, '
'Gaussian network model, anisotropic network model, '
'essential dynamics analysis, principal component analysis, '
'Protein Data Bank, PDB, GNM, ANM, SM, PCA'),
classifiers=[
'Development Status :: 5 - Production/Stable',
'Intended Audience :: Education',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: MIT License',
'Operating System :: MacOS',
'Operating System :: Microsoft :: Windows',
'Operating System :: POSIX',
'Programming Language :: Python',
'Programming Language :: Python :: 2',
'Programming Language :: Python :: 3',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Topic :: Scientific/Engineering :: Chemistry',
],
#scripts=SCRIPTS,
entry_points = {
'console_scripts': SCRIPTS,
},
install_requires=INSTALL_REQUIRES,
#provides=['ProDy ({0:s})'.format(__version__)]
)