setup.py

#!/usr/bin/env python

# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# MSMTools is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.

"""PyEMMA: Emma's Markov Model Algorithms

PyEMMA is an open source collection of algorithms implemented mostly in
`NumPy <http://www.numpy.org/>`_ and `SciPy <http://www.scipy.org>`_
to analyze trajectories generated from any kind of simulation
(e.g. molecular trajectories) via Markov state models (MSM).
"""

import sys
import os

import versioneer
import warnings
from io import open
import pybind11

from setuptools import setup, Extension, find_packages


if sys.version_info[0] < 3:
    print('PyEMMA requires Python3k')
    sys.exit(2)


DOCLINES = __doc__.split("\n")

CLASSIFIERS = """\
Development Status :: 5 - Production/Stable
Environment :: Console
Environment :: MacOS X
Intended Audience :: Science/Research
License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)
Natural Language :: English
Operating System :: MacOS :: MacOS X
Operating System :: POSIX
Operating System :: Microsoft :: Windows
Programming Language :: Python :: 2.7
Programming Language :: Python :: 3
Topic :: Scientific/Engineering :: Bio-Informatics
Topic :: Scientific/Engineering :: Chemistry
Topic :: Scientific/Engineering :: Mathematics
Topic :: Scientific/Engineering :: Physics

"""
from setup_util import parse_setuppy_commands

try:
    from setuptools import setup, Extension, find_packages
except ImportError as ie:
    print("PyEMMA requires setuptools. Please install it with conda or pip.")
    sys.exit(1)

###############################################################################
# Extensions
###############################################################################
def extensions():
    from Cython.Build import cythonize
    from numpy import get_include as np_get_include
    pybind_inc = pybind11.get_include()
    assert os.path.exists(pybind_inc), 'pybind11 headers not found at %s' % pybind_inc

    from mdtraj import capi as mdtraj_capi
    mdtraj_inc = mdtraj_capi()['include_dir']
    mdtraj_lib = mdtraj_capi()['lib_dir']

    from deeptime import capi_includes
    deeptime_inc = capi_includes(inc_clustering=True)

    lib_prefix = 'lib' if sys.platform.startswith('win') else ''
    common_cflags = ['-O3', ]

    clustering_module = \
        Extension('pyemma.coordinates.clustering._ext',
                  sources=['pyemma/coordinates/clustering/src/clustering_module.cpp'],
                  include_dirs=[
                      mdtraj_inc,
                      pybind_inc,
                  ] + deeptime_inc,
                  language='c++',
                  libraries=[lib_prefix+'theobald'],
                  library_dirs=[mdtraj_lib],
                  extra_compile_args=common_cflags + [''])

    covar_module = \
        Extension('pyemma._ext.variational.estimators.covar_c._covartools',
                  sources=['pyemma/_ext/variational/estimators/covar_c/covartools.cpp'],
                  include_dirs=['pyemma/_ext/variational/estimators/covar_c/',
                                pybind_inc,
                                ],
                  language='c++',
                  extra_compile_args=common_cflags)

    eig_qr_module = \
        Extension('pyemma._ext.variational.solvers.eig_qr.eig_qr',
                  sources=['pyemma/_ext/variational/solvers/eig_qr/eig_qr.pyx'],
                  include_dirs=['pyemma/_ext/variational/solvers/eig_qr/'],
                  extra_compile_args=['-std=c99'] + common_cflags)

    orderedset = \
        Extension('pyemma._ext.orderedset._orderedset',
                  sources=['pyemma/_ext/orderedset/_orderedset.pyx'],
                  extra_compile_args=['-std=c99'] + common_cflags)

    extra_compile_args = ["-O3", "-std=c99"]
    ext_bar = Extension(
        "pyemma.thermo.extensions.bar",
        sources=["pyemma/thermo/extensions/bar/bar.pyx",
                 "pyemma/thermo/extensions/bar/_bar.c",
                 "pyemma/thermo/extensions/util/_util.c"],
        extra_compile_args=extra_compile_args)
    ext_wham = Extension(
        "pyemma.thermo.extensions.wham",
        sources=["pyemma/thermo/extensions/wham/wham.pyx",
                 "pyemma/thermo/extensions/wham/_wham.c",
                 "pyemma/thermo/extensions/util/_util.c"],
        extra_compile_args=extra_compile_args)
    ext_mbar = Extension(
        "pyemma.thermo.extensions.mbar",
        sources=["pyemma/thermo/extensions/mbar/mbar.pyx",
                 "pyemma/thermo/extensions/mbar/_mbar.c",
                 "pyemma/thermo/extensions/util/_util.c"],
        extra_compile_args=extra_compile_args)
    ext_tram = Extension(
        "pyemma.thermo.extensions.tram",
        sources=["pyemma/thermo/extensions/tram/tram.pyx",
                 "pyemma/thermo/extensions/tram/_tram.c",
                 "pyemma/thermo/extensions/util/_util.c"],
        extra_compile_args=extra_compile_args)
    ext_dtram = Extension(
        "pyemma.thermo.extensions.dtram",
        sources=["pyemma/thermo/extensions/dtram/dtram.pyx",
                 "pyemma/thermo/extensions/dtram/_dtram.c",
                 "pyemma/thermo/extensions/util/_util.c"],
        extra_compile_args=extra_compile_args)
    ext_trammbar = Extension(
        "pyemma.thermo.extensions.trammbar",
        sources=["pyemma/thermo/extensions/trammbar/trammbar.pyx",
                 "pyemma/thermo/extensions/tram/_tram.c",
                 "pyemma/thermo/extensions/util/_util.c"],
        extra_compile_args=extra_compile_args + ["-DTRAMMBAR"])
    ext_mbar_direct = Extension(
        "pyemma.thermo.extensions.mbar_direct",
        sources=["pyemma/thermo/extensions/mbar_direct/mbar_direct.pyx",
                 "pyemma/thermo/extensions/mbar_direct/_mbar_direct.c",
                 "pyemma/thermo/extensions/util/_util.c"],
        extra_compile_args=extra_compile_args)
    ext_tram_direct = Extension(
        "pyemma.thermo.extensions.tram_direct",
        sources=["pyemma/thermo/extensions/tram_direct/tram_direct.pyx",
                 "pyemma/thermo/extensions/tram_direct/_tram_direct.c",
                 "pyemma/thermo/extensions/util/_util.c"],
        extra_compile_args=extra_compile_args)
    ext_trammbar_direct = Extension(
        "pyemma.thermo.extensions.trammbar_direct",
        sources=["pyemma/thermo/extensions/trammbar_direct/trammbar_direct.pyx",
                 "pyemma/thermo/extensions/tram_direct/_tram_direct.c",
                 "pyemma/thermo/extensions/util/_util.c"],
        extra_compile_args=extra_compile_args + ["-DTRAMMBAR"])
    ext_util = Extension(
        "pyemma.thermo.extensions.util",
        sources=["pyemma/thermo/extensions/util/util.pyx",
                 "pyemma/thermo/extensions/util/_util.c"],
        extra_compile_args=extra_compile_args)

    exts_thermo = [
        ext_bar,
        ext_wham,
        ext_mbar,
        ext_tram,
        ext_dtram,
        ext_trammbar,
        ext_mbar_direct,
        ext_tram_direct,
        ext_trammbar_direct,
        ext_util]

    exts = [clustering_module,
            covar_module,
            eig_qr_module,
            orderedset
    ]
    exts += exts_thermo

    # Note, that we add numpy include to every extension after declaration.
    np_inc = np_get_include()
    for e in exts:
        e.include_dirs.append(np_inc)

    exts = cythonize(exts, language_level=sys.version_info[0])

    return exts


def get_cmdclass():
    versioneer_cmds = versioneer.get_cmdclass()

    from setuptools.command.build_ext import build_ext
    # taken from https://github.com/pybind/python_example/blob/master/setup.py
    class BuildExt(build_ext):
        """A custom build extension for adding compiler-specific options."""
        c_opts = {
            'msvc': ['/EHsc'],
            'unix': [],
        }

        def build_extensions(self):
            from setup_util import cpp_flag, has_flag, detect_openmp
            # enable these options only for clang, OSX
            if sys.platform == 'darwin':
                import sysconfig
                compiler = os.path.basename(sysconfig.get_config_var("CC"))
                if 'clang' in str(compiler):
                    self.c_opts['unix'] += ['-stdlib=libc++', '-mmacosx-version-min=10.7']

            ct = self.compiler.compiler_type
            opts = self.c_opts.get(ct, [])
            if ct == 'unix':
                opts.append('-DVERSION_INFO="%s"' % self.distribution.get_version())
                opts.append(cpp_flag(self.compiler))
                if has_flag(self.compiler, '-fvisibility=hidden'):
                    opts.append('-fvisibility=hidden')
            elif ct == 'msvc':
                opts.append('/std:c++17')
                opts.append('/bigobj')
                opts.append('/DVERSION_INFO=\\"%s\\"' % self.distribution.get_version())

            # setup OpenMP support
            openmp_enabled, additional_libs = detect_openmp(self.compiler)
            if openmp_enabled:
                warnings.warn('enabled openmp')
                if sys.platform == 'darwin':
                    omp_compiler_args = ['-fopenmp=libiomp5']
                else:
                    omp_compiler_args = ['-fopenmp']
                omp_libraries = ['-l%s' % l for l in additional_libs]
                omp_defines = [('USE_OPENMP', None)]
            # debug
            if self.debug:
                dbg_flag = ['-g']
            else:
                dbg_flag = ['-g0', '-DNDEBUG']

            for ext in self.extensions:
                if ext.language == 'c++':
                    ext.extra_compile_args = opts + dbg_flag
                elif ext.language is None:  # C
                    ext.extra_compile_args += dbg_flag
                if openmp_enabled:
                    ext.extra_compile_args += omp_compiler_args
                    ext.extra_link_args += omp_libraries
                    ext.define_macros += omp_defines

            build_ext.build_extensions(self)

    versioneer_cmds['build_ext'] = BuildExt

    return versioneer_cmds


metadata = dict(
    name='pyEMMA',
    maintainer='Martin K. Scherer',
    maintainer_email='m.scherer@fu-berlin.de',
    author='The Emma team',
    author_email='info@emma-project.org',
    url='http://github.com/markovmodel/PyEMMA',
    license='LGPLv3+',
    description=DOCLINES[0],
    long_description=open('README.rst', encoding='utf8').read(),
    version=versioneer.get_version(),
    platforms=["Windows", "Linux", "Solaris", "Mac OS-X", "Unix"],
    classifiers=[c for c in CLASSIFIERS.split('\n') if c],
    keywords='Markov State Model Algorithms',
    cmdclass=get_cmdclass(),
    tests_require=['pytest'],
    # runtime dependencies
    install_requires=[
        'decorator>=4.0.0',
        'h5py>=2.7.1',
        'matplotlib',
        'mdtraj>=1.9.2',
        'numpy>=1.8.0',
        'pathos',
        'psutil>=3.1.1',
        'pyyaml',
        'scipy>=0.11',
        'tqdm>=4.23',
        'deeptime>=0.4.2'
    ],
    zip_safe=False,
    entry_points={
        'console_scripts': ['pyemma_list_models=pyemma._base.serialization.cli:main']
    },
    package_data={
        'pyemma': ['pyemma.cfg', 'logging.yml'],
        'pyemma.coordinates.tests': ['data/*'],
        'pyemma.msm.tests': ['data/*'],
        'pyemma.datasets': ['*.npz'],
        'pyemma.util.tests': ['data/*'],
    },
    # packages are found if their folder contains an __init__.py,
    packages=find_packages(),
)


if __name__ == '__main__':
    if parse_setuppy_commands():
        # now build extension list.
        metadata['ext_modules'] = extensions()

    setup(**metadata)