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setup.py
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setup.py
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"""MDTraj: A modern, open library for the analysis of molecular dynamics trajectories
MDTraj is a python library that allows users to manipulate molecular dynamics
(MD) trajectories and perform a variety of analyses, including fast RMSD,
solvent accessible surface area, hydrogen bonding, etc. A highlight of MDTraj
is the wide variety of molecular dynamics trajectory file formats which are
supported, including RCSB pdb, GROMACS xtc, tng, and trr, CHARMM / NAMD dcd, AMBER
binpos, AMBER NetCDF, AMBER mdcrd, TINKER arc and MDTraj HDF5.
"""
from __future__ import print_function, absolute_import
DOCLINES = __doc__.split("\n")
import os
import sys
from glob import glob
from setuptools import setup, Extension, find_packages
sys.path.insert(0, '.')
from basesetup import (write_version_py, build_ext,
StaticLibrary, CompilerDetection)
try:
import numpy
import Cython
if Cython.__version__ < '0.19':
raise ImportError
from Cython.Build import cythonize
except ImportError:
print('-'*80, file=sys.stderr)
print('''Error: building mdtraj requires numpy and cython>=0.19
Try running the command ``pip install numpy cython`` or
``conda install numpy cython``.
or see http://docs.scipy.org/doc/numpy/user/install.html and
http://cython.org/ for more information.
If you're feeling lost, we recommend downloading the (free) Anaconda python
distribution https://www.continuum.io/downloads, because it comes with
these components included.''', file=sys.stderr)
print('-'*80, file=sys.stderr)
sys.exit(1)
try:
# add an optional --disable-openmp to disable OpenMP support
sys.argv.remove('--disable-openmp')
disable_openmp = True
except ValueError:
disable_openmp = False
##########################
VERSION = "1.9.3"
ISRELEASED = False
__version__ = VERSION
##########################
CLASSIFIERS = """\
Development Status :: 5 - Production/Stable
Intended Audience :: Science/Research
Intended Audience :: Developers
License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)
Programming Language :: C
Programming Language :: Python
Programming Language :: Python :: 3
Topic :: Scientific/Engineering :: Bio-Informatics
Topic :: Scientific/Engineering :: Chemistry
Operating System :: Microsoft :: Windows
Operating System :: POSIX
Operating System :: Unix
Operating System :: MacOS
"""
# Global info about compiler
compiler = CompilerDetection(disable_openmp)
compiler.initialize()
extra_cpp_libraries = []
if sys.platform == 'darwin':
extra_cpp_libraries.append('stdc++')
os.environ['CXX'] = 'clang++'
os.environ['CC'] = 'clang'
if sys.platform == 'win32':
extra_cpp_libraries.append('Ws2_32')
# For determining if a path is relative (for dtr)
extra_cpp_libraries.append('Shlwapi')
################################################################################
# Declaration of the compiled extension modules (cython + c)
################################################################################
def format_extensions():
compiler_args = compiler.compiler_args_warn
xtc = Extension('mdtraj.formats.xtc',
sources=['mdtraj/formats/xtc/src/xdrfile.c',
'mdtraj/formats/xtc/src/xdr_seek.c',
'mdtraj/formats/xtc/src/xdrfile_xtc.c',
'mdtraj/formats/xtc/xtc.pyx',
],
include_dirs=['mdtraj/formats/xtc/include/',
'mdtraj/formats/xtc/'],
extra_compile_args=compiler_args)
trr = Extension('mdtraj.formats.trr',
sources=['mdtraj/formats/xtc/src/xdrfile.c',
'mdtraj/formats/xtc/src/xdr_seek.c',
'mdtraj/formats/xtc/src/xdrfile_trr.c',
'mdtraj/formats/xtc/trr.pyx'],
include_dirs=['mdtraj/formats/xtc/include/',
'mdtraj/formats/xtc/'],
extra_compile_args=compiler_args)
zlib_include_dirs = []
zlib_library_dirs = []
if sys.platform == 'win32':
# Conda puts the zlib headers in ./Library/... on windows
# If you're not using conda, good luck!
zlib_include_dirs += ["{}/Library/include".format(sys.prefix)]
zlib_library_dirs += ["{}/Library/lib".format(sys.prefix)]
else:
# On linux (and mac(?)) these paths should work for a standard
# install of python+zlib or a conda install of python+zlib
zlib_include_dirs += ["{}/include".format(sys.prefix)]
zlib_library_dirs += ["{}/lib".format(sys.prefix)]
tng = Extension('mdtraj.formats.tng',
sources=glob('mdtraj/formats/tng/src/compression/*.c') +
['mdtraj/formats/tng/src/lib/tng_io.c',
'mdtraj/formats/tng/src/lib/md5.c',
'mdtraj/formats/tng/tng.pyx'],
include_dirs=['mdtraj/formats/tng/include']
+ zlib_include_dirs,
define_macros=[('USE_ZLIB', 1)],
library_dirs=zlib_library_dirs,
libraries=['z'],
)
dcd = Extension('mdtraj.formats.dcd',
sources=['mdtraj/formats/dcd/src/dcdplugin.c',
'mdtraj/formats/dcd/dcd.pyx'],
include_dirs=["mdtraj/formats/dcd/include/",
'mdtraj/formats/dcd/'],
extra_compile_args=compiler_args)
binpos = Extension('mdtraj.formats.binpos',
sources=['mdtraj/formats/binpos/src/binposplugin.c',
'mdtraj/formats/binpos/binpos.pyx'],
include_dirs=['mdtraj/formats/binpos/include/',
'mdtraj/formats/binpos/'],
extra_compile_args=compiler_args)
dtr = Extension('mdtraj.formats.dtr',
sources=['mdtraj/formats/dtr/src/dtrplugin.cxx',
'mdtraj/formats/dtr/dtr.pyx'],
include_dirs=['mdtraj/formats/dtr/include/',
'mdtraj/formats/dtr/'],
define_macros=[('DESRES_READ_TIMESTEP2', 1)],
language='c++',
extra_compile_args=compiler_args,
libraries=extra_cpp_libraries)
return [xtc, trr, tng, dcd, binpos, dtr]
def rmsd_extensions():
compiler_args = (compiler.compiler_args_openmp + compiler.compiler_args_sse2 +
compiler.compiler_args_sse3 + compiler.compiler_args_opt +
compiler.compiler_args_warn)
compiler_libraries = compiler.compiler_libraries_openmp
libtheobald = StaticLibrary(
'mdtraj.core.lib.libtheobald',
sources=[
'mdtraj/rmsd/src/theobald_rmsd.c',
'mdtraj/rmsd/src/center.c'],
include_dirs=[
'mdtraj/rmsd/include'],
export_include=['mdtraj/rmsd/include/theobald_rmsd.h',
'mdtraj/rmsd/include/center.h'],
# don't enable OpenMP
extra_compile_args=(compiler.compiler_args_sse2 +
compiler.compiler_args_sse3 +
compiler.compiler_args_opt))
rmsd = Extension('mdtraj._rmsd',
sources=[
'mdtraj/rmsd/src/theobald_rmsd.c',
'mdtraj/rmsd/src/rotation.c',
'mdtraj/rmsd/src/center.c',
'mdtraj/rmsd/_rmsd.pyx'],
include_dirs=['mdtraj/rmsd/include'],
extra_compile_args=compiler_args,
libraries=compiler_libraries)
lprmsd = Extension('mdtraj._lprmsd',
sources=[
'mdtraj/rmsd/src/theobald_rmsd.c',
'mdtraj/rmsd/src/rotation.c',
'mdtraj/rmsd/src/center.c',
'mdtraj/rmsd/src/fancy_index.cpp',
'mdtraj/rmsd/src/Munkres.cpp',
'mdtraj/rmsd/src/euclidean_permutation.cpp',
'mdtraj/rmsd/_lprmsd.pyx'],
language='c++',
include_dirs=['mdtraj/rmsd/include'],
extra_compile_args=compiler_args,
libraries=compiler_libraries + extra_cpp_libraries)
return rmsd, lprmsd, libtheobald
def geometry_extensions():
compiler.initialize()
compiler_args = (
compiler.compiler_args_openmp +
compiler.compiler_args_sse2 + compiler.compiler_args_sse3 +
compiler.compiler_args_opt + compiler.compiler_args_warn)
define_macros = None
compiler_libraries = compiler.compiler_libraries_openmp + extra_cpp_libraries
return [
Extension('mdtraj.geometry._geometry',
sources=['mdtraj/geometry/src/sasa.cpp',
'mdtraj/geometry/src/dssp.cpp',
'mdtraj/geometry/src/geometry.cpp',
'mdtraj/geometry/src/_geometry.pyx',],
include_dirs=['mdtraj/geometry/include',
'mdtraj/geometry/src/kernels'],
depends=['mdtraj/geometry/src/kernels/anglekernels.h',
'mdtraj/geometry/src/kernels/dihedralkernels.h',
'mdtraj/geometry/src/kernels/distancekernels.h'],
define_macros=define_macros,
extra_compile_args=compiler_args,
libraries=compiler_libraries,
language='c++'),
Extension('mdtraj.geometry.drid',
sources=["mdtraj/geometry/drid.pyx",
"mdtraj/geometry/src/dridkernels.cpp",
"mdtraj/geometry/src/moments.cpp"],
include_dirs=["mdtraj/geometry/include"],
define_macros=define_macros,
extra_compile_args=compiler_args,
libraries=compiler_libraries,
language='c++'),
Extension('mdtraj.geometry.neighbors',
sources=["mdtraj/geometry/neighbors.pyx",
"mdtraj/geometry/src/neighbors.cpp"],
include_dirs=["mdtraj/geometry/include",],
define_macros=define_macros,
extra_compile_args=compiler_args,
libraries=compiler_libraries,
language='c++'),
Extension('mdtraj.geometry.neighborlist',
sources=["mdtraj/geometry/neighborlist.pyx",
"mdtraj/geometry/src/neighborlist.cpp"],
include_dirs=["mdtraj/geometry/include",],
define_macros=define_macros,
extra_compile_args=compiler_args,
libraries=compiler_libraries,
language='c++'),
]
extensions = format_extensions()
extensions.extend(rmsd_extensions())
extensions.extend(geometry_extensions())
write_version_py(VERSION, ISRELEASED, 'mdtraj/version.py')
setup(name='mdtraj',
author='Robert McGibbon',
author_email='rmcgibbo@gmail.com',
description=DOCLINES[0],
long_description="\n".join(DOCLINES[2:]),
version=__version__,
license='LGPLv2.1+',
url='http://mdtraj.org',
download_url = "https://github.com/rmcgibbo/mdtraj/releases/latest",
platforms=['Linux', 'Mac OS-X', 'Unix', 'Windows'],
classifiers=CLASSIFIERS.splitlines(),
packages=find_packages(),
cmdclass={'build_ext': build_ext},
ext_modules=cythonize(extensions),
# setup_requires really doesn't work sufficently well with `pip install`
# to use. See https://github.com/mdtraj/mdtraj/issues/984. Also
# setup_requires=['setuptools>=18', 'cython>=0.22', 'numpy>=1.6'],
# Also, install_requires is no better, especially with numpy.
# See http://article.gmane.org/gmane.comp.python.distutils.devel/24218
# install_requires=['numpy>=1.6'],
package_data={'mdtraj.formats.pdb': ['data/*'], },
zip_safe=False,
entry_points={'console_scripts':
['mdconvert = mdtraj.scripts.mdconvert:entry_point',
'mdinspect = mdtraj.scripts.mdinspect:entry_point']},
)