setup.py

""" BHMM: A toolkit for Bayesian hidden Markov model analysis of single-molecule trajectories.

This project provides tools for estimating the number of metastable states, rate
constants between the states, equilibrium populations, distributions
characterizing the states, and distributions of these quantities from
single-molecule data. This data could be FRET data, single-molecule pulling
data, or any data where one or more observables are recorded as a function of
time. A Hidden Markov Model (HMM) is used to interpret the observed dynamics,
and a distribution of models that fit the data is sampled using Bayesian
inference techniques and Markov chain Monte Carlo (MCMC), allowing for both the
characterization of uncertainties in the model and modeling of the expected
information gain by new experiments.
"""

from __future__ import print_function
import os
import sys
from distutils.version import StrictVersion
from setuptools import setup, Extension, find_packages
import numpy
import glob
from os.path import relpath, join
import subprocess
from Cython.Build import cythonize

DOCLINES = __doc__.split("\n")

########################
VERSION = "0.3.0"
ISRELEASED = False
__version__ = VERSION
########################
CLASSIFIERS = """\
Development Status :: 3 - Alpha
Intended Audience :: Science/Research
Intended Audience :: Developers
License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
Programming Language :: Python
Topic :: Scientific/Engineering :: Bio-Informatics
Topic :: Scientific/Engineering :: Chemistry
Operating System :: Microsoft :: Windows
Operating System :: POSIX
Operating System :: Unix
Operating System :: MacOS
"""

################################################################################
# Writing version control information to the module
################################################################################

def git_version():
    # Return the git revision as a string
    # copied from numpy setup.py
    def _minimal_ext_cmd(cmd):
        # construct minimal environment
        env = {}
        for k in ['SYSTEMROOT', 'PATH']:
            v = os.environ.get(k)
            if v is not None:
                env[k] = v
        # LANGUAGE is used on win32
        env['LANGUAGE'] = 'C'
        env['LANG'] = 'C'
        env['LC_ALL'] = 'C'
        out = subprocess.Popen(
            cmd, stdout=subprocess.PIPE, env=env).communicate()[0]
        return out

    try:
        out = _minimal_ext_cmd(['git', 'rev-parse', 'HEAD'])
        GIT_REVISION = out.strip().decode('ascii')
    except OSError:
        GIT_REVISION = 'Unknown'

    return GIT_REVISION


def write_version_py(filename='bhmm/version.py'):
    cnt = """
# This file is automatically generated by setup.py
short_version = '%(version)s'
version = '%(version)s'
full_version = '%(full_version)s'
git_revision = '%(git_revision)s'
release = %(isrelease)s

if not release:
    version = full_version
"""
    # Adding the git rev number needs to be done inside write_version_py(),
    # otherwise the import of numpy.version messes up the build under Python 3.
    FULLVERSION = VERSION
    if os.path.exists('.git'):
        GIT_REVISION = git_version()
    else:
        GIT_REVISION = 'Unknown'

    if not ISRELEASED:
        FULLVERSION += '.dev-' + GIT_REVISION[:7]

    a = open(filename, 'w')
    try:
        a.write(cnt % {'version': VERSION,
                       'full_version': FULLVERSION,
                       'git_revision': GIT_REVISION,
                       'isrelease': str(ISRELEASED)})
    finally:
        a.close()

################################################################################
# USEFUL SUBROUTINES
################################################################################

def find_package_data(data_root, package_root):
    files = []
    for root, dirnames, filenames in os.walk(data_root):
        for fn in filenames:
            files.append(relpath(join(root, fn), package_root))
    return files


################################################################################
# SETUP
################################################################################

#try:
#    import pyemma
#    print(pyemma.__version__)
#    if not StrictVersion(pyemma.__version__) >= '1.1.2':
#        raise ImportError
#except:
#    print('Bulding and running bhmm requires pyemma >= 1.1.2. Install first.')
#    sys.exit(1)

extensions = [Extension('bhmm.hidden.impl_c.hidden',
                        sources = ['./bhmm/hidden/impl_c/hidden.pyx',
                                   './bhmm/hidden/impl_c/_hidden.c'],
                        include_dirs = ['/bhmm/hidden/impl_c/',numpy.get_include()]),
              Extension('bhmm.output_models.impl_c.gaussian',
                        sources = ['./bhmm/output_models/impl_c/gaussian.pyx',
                                   './bhmm/output_models/impl_c/_gaussian.c'],
                        include_dirs = ['/bhmm/output_models/impl_c/',numpy.get_include()]),
              Extension('bhmm.msm.tmatrix_sampling',
                        sources = ['./bhmm/msm/tmatrix_sampling.pyx'],
                        include_dirs = [numpy.get_include()])]

write_version_py()

setup(
    name='bhmm',
    author='John Chodera and Frank Noe',
    author_email='john.chodera@choderalab.org',
    description=DOCLINES[0],
    long_description="\n".join(DOCLINES[2:]),
    version=__version__,
    license='LGPL',
    url='https://github.com/bhmm/bhmm',
    platforms=['Linux', 'Mac OS-X', 'Unix', 'Windows'],
    classifiers=CLASSIFIERS.splitlines(),
    package_dir={'bhmm': 'bhmm'},
    #packages=['bhmm', "bhmm.tests"] + ['bhmm.%s' % package for package in find_packages('bhmm')],
    packages=['bhmm', 'bhmm.tests', 'bhmm.hmm', 'bhmm.estimators', 'bhmm.msm', 'bhmm.hidden', 'bhmm.init', 'bhmm.msm', 'bhmm.output_models', 'bhmm.output_models.impl_c', 'bhmm.util', 'bhmm.hidden.impl_python', 'bhmm.hidden.impl_c'],
    # + ['bhmm.%s' % package for package in find_packages('bhmm')],
    package_data={'bhmm': find_package_data('examples', 'bhmm') + find_package_data('bhmm/tests/data', 'bhmm')},  # NOTE: examples installs to bhmm.egg/examples/, NOT bhmm.egg/bhmm/examples/.  You need to do utils.get_data_filename("../examples/*/setup/").
    zip_safe=False,
    install_requires=[
        'cython',
        'numpy',
        'scipy',
        'pyemma>=1.2',
        'scikit-learn',
        ],
    ext_modules = cythonize(extensions)
    )