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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
AMBER NetCDF, AMBER mdcrd, TINKER arc and MDTraj HDF5.
"""
import sys
import versioneer
from setuptools import Extension, find_packages, setup
from basesetup import (
CompilerDetection,
StaticLibrary,
build_ext,
parse_setuppy_commands,
)
DOCLINES = __doc__.split("\n")
sys.path.insert(0, ".")
try:
# add an optional --disable-openmp to disable OpenMP support
sys.argv.remove("--disable-openmp")
disable_openmp = True
except ValueError:
disable_openmp = False
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 == "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 += [f"{sys.prefix}/Library/include"]
zlib_library_dirs += [f"{sys.prefix}/Library/lib"]
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 += [f"{sys.prefix}/include"]
zlib_library_dirs += [f"{sys.prefix}/lib"]
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,
)
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, dcd, 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
define_macros = [("__NO_INTRINSICS", 1)] if compiler.disable_intrinsics else None
libtheobald = StaticLibrary(
"mdtraj.core.lib.libtheobald",
sources=[
"mdtraj/rmsd/src/theobald_rmsd.cpp",
"mdtraj/rmsd/src/center.cpp",
],
include_dirs=[
"mdtraj/rmsd/include",
],
export_include=[
"mdtraj/rmsd/include/theobald_rmsd.h",
"mdtraj/rmsd/include/center.h",
],
language="c++",
# 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.cpp",
"mdtraj/rmsd/src/rotation.cpp",
"mdtraj/rmsd/src/center.cpp",
"mdtraj/rmsd/_rmsd.pyx",
],
include_dirs=["mdtraj/rmsd/include"],
define_macros=define_macros,
extra_compile_args=compiler_args,
libraries=compiler_libraries,
language="c++",
)
lprmsd = Extension(
"mdtraj._lprmsd",
sources=[
"mdtraj/rmsd/src/theobald_rmsd.cpp",
"mdtraj/rmsd/src/rotation.cpp",
"mdtraj/rmsd/src/center.cpp",
"mdtraj/rmsd/src/fancy_index.cpp",
"mdtraj/rmsd/src/Munkres.cpp",
"mdtraj/rmsd/src/euclidean_permutation.cpp",
"mdtraj/rmsd/_lprmsd.pyx",
],
language="c++",
define_macros=define_macros,
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 = [("__NO_INTRINSICS", 1)] if compiler.disable_intrinsics else 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++",
),
]
EXTRAS_REQUIRE = {
"tests": [
"pytest",
"pytest-rerunfailures",
"pytest-xdist",
],
"optional": [
"tables",
"networkx",
"netCDF4",
"pandas",
],
}
metadata = dict(
name="mdtraj",
author="Robert McGibbon",
author_email="rmcgibbo@gmail.com",
description=DOCLINES[0],
long_description="\n".join(DOCLINES[2:]),
version=versioneer.get_version(),
license="LGPLv2.1+",
url="http://mdtraj.org",
download_url="https://github.com/rmcgibbo/mdtraj/releases/latest",
platforms=["Linux", "Mac OS-X", "Unix", "Windows"],
python_requires=">=3.11",
classifiers=CLASSIFIERS.splitlines(),
packages=find_packages(),
cmdclass={**versioneer.get_cmdclass(), "build_ext": build_ext},
install_requires=[
"numpy>=1.25.0,<3",
"scipy",
"pyparsing",
"packaging",
],
extras_require={
"tests": EXTRAS_REQUIRE["tests"],
"optional": EXTRAS_REQUIRE["optional"],
"all": EXTRAS_REQUIRE["tests"] + EXTRAS_REQUIRE["optional"],
},
package_data={"mdtraj.formats.pdb": ["data/*"]},
zip_safe=False,
entry_points={
"console_scripts": [
"mdconvert-mdtraj = mdtraj.scripts.mdconvert:entry_point",
"mdinspect = mdtraj.scripts.mdinspect:entry_point",
],
},
)
if __name__ == "__main__":
# Don't use numpy if we are just - non-build actions are required to succeed
# without NumPy for example when pip is used to install Scipy when
# NumPy is not yet present in the system.
run_build = parse_setuppy_commands()
if run_build:
extensions = format_extensions()
extensions.extend(rmsd_extensions())
extensions.extend(geometry_extensions())
# most extensions use numpy, add headers for it.
try:
import Cython as _c
from Cython.Build import cythonize
if _c.__version__ < "0.29":
raise ImportError("Too old")
except ImportError as e:
print(
"mdtrajs setup depends on Cython (>=0.29). Install it prior invoking setup.py",
)
print(e)
sys.exit(1)
try:
import numpy as np
except ImportError:
print("mdtrajs setup depends on NumPy. Install it prior invoking setup.py")
sys.exit(1)
for e in extensions:
e.include_dirs.append(np.get_include())
metadata["ext_modules"] = cythonize(
extensions,
language_level=sys.version_info[0],
force=True,
)
setup(**metadata)
|
