forked from mdtraj/mdtraj
/
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 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 sys
from setuptools import setup, Extension
sys.path.insert(0, '.')
from basesetup import (find_packages, write_version_py, build_ext,
StaticLibrary, CompilerDetection)
try:
import numpy
except ImportError:
print('Building and running mdtraj requires numpy', file=sys.stderr)
sys.exit(1)
try:
import Cython
if Cython.__version__ < '0.19':
raise ImportError
from Cython.Build import cythonize
except ImportError:
print('Building from source requires cython >= 0.19', file=sys.stderr)
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
try:
# add an optional command line flag --no-install-deps to setup.py
# to turn off setuptools automatic downloading of dependencies
sys.argv.remove('--no-install-deps')
no_install_deps = True
except ValueError:
no_install_deps = False
if sys.version_info[0] == 2:
# required to fix cythoninze() for old versions of setuptools on
# python 2
m = sys.modules['setuptools.extension']
m.Extension.__dict__ = m._Extension.__dict__
##########################
VERSION = "1.4.2"
ISRELEASED = True
__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)
extra_cpp_libraries = []
if sys.platform == 'darwin':
extra_cpp_libraries.append('stdc++')
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)
################################################################################
xtc = Extension('mdtraj.formats.xtc',
sources=['mdtraj/formats/xtc/src/xdrfile.c',
'mdtraj/formats/xtc/src/xdrfile_xtc.c',
'mdtraj/formats/xtc/xtc.pyx'],
include_dirs=['mdtraj/formats/xtc/include/',
'mdtraj/formats/xtc/', numpy.get_include()])
trr = Extension('mdtraj.formats.trr',
sources=['mdtraj/formats/xtc/src/xdrfile.c',
'mdtraj/formats/xtc/src/xdrfile_trr.c',
'mdtraj/formats/xtc/trr.pyx'],
include_dirs=['mdtraj/formats/xtc/include/',
'mdtraj/formats/xtc/', numpy.get_include()])
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/', numpy.get_include()])
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/', numpy.get_include()])
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/', numpy.get_include()],
define_macros = [('DESRES_READ_TIMESTEP2', 1)],
language='c++',
libraries=extra_cpp_libraries)
def rmsd_extensions():
compiler_args = (compiler.compiler_args_openmp + compiler.compiler_args_sse2 +
compiler.compiler_args_sse3 + compiler.compiler_args_opt)
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', numpy.get_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', numpy.get_include()],
extra_compile_args=compiler_args,
libraries=compiler_libraries + extra_cpp_libraries)
return rmsd, lprmsd, libtheobald
def geometry_extensions():
compiler_args = (compiler.compiler_args_sse2 + compiler.compiler_args_sse3 +
compiler.compiler_args_opt)
define_macros = None
return [
Extension('mdtraj.geometry._geometry',
sources=['mdtraj/geometry/src/geometry.c',
'mdtraj/geometry/src/sasa.c',
'mdtraj/geometry/src/dssp.cpp',
'mdtraj/geometry/src/_geometry.pyx'],
include_dirs=['mdtraj/geometry/include',
'mdtraj/geometry/src/kernels',
numpy.get_include()],
define_macros=define_macros,
extra_compile_args=compiler_args,
libraries=extra_cpp_libraries,
language='c++'),
Extension('mdtraj.geometry.drid',
sources=["mdtraj/geometry/drid.pyx",
"mdtraj/geometry/src/dridkernels.c",
"mdtraj/geometry/src/cephes/cbrt.c",
"mdtraj/geometry/src/cephes/isnan.c",
"mdtraj/geometry/src/moments.c"],
include_dirs=["mdtraj/geometry/include",
"mdtraj/geometry/include/cephes",
numpy.get_include()],
define_macros=define_macros,
extra_compile_args=compiler_args),
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,
language='c++'),
]
extensions = [xtc, trr, dcd, binpos, dtr]
extensions.extend(rmsd_extensions())
extensions.extend(geometry_extensions())
write_version_py(VERSION, ISRELEASED)
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),
package_data={'mdtraj.formats.pdb': ['data/*'],
'mdtraj.testing': ['reference/*',
'reference/ala_dipeptide_trj/*',
'reference/ala_dipeptide_trj/not_hashed/*',
'reference/frame0.dtr/*',
'reference/frame0.dtr/not_hashed/*',],
'mdtraj.html': ['static/*']},
exclude_package_data={'mdtraj.testing': ['reference/ala_dipeptide_trj',
'reference/ala_dipeptide_trj/not_hashed',
'reference/frame0.dtr',
'reference/frame0.dtr/not_hashed',]},
zip_safe=False,
entry_points={'console_scripts':
['mdconvert = mdtraj.scripts.mdconvert:entry_point',
'mdinspect = mdtraj.scripts.mdinspect:entry_point']},
)