setup.py

#!/usr/bin/env python
# -----------------------------------------------------------------------------------------------------
# CONDOR
# Simulator for diffractive single-particle imaging experiments with X-ray lasers
# http://xfel.icm.uu.se/condor/
# -----------------------------------------------------------------------------------------------------
# Copyright 2016 Max Hantke, Filipe R.N.C. Maia, Tomas Ekeberg
# Condor is distributed under the terms of the BSD 2-Clause License
# -----------------------------------------------------------------------------------------------------
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
#    list of conditions and the following disclaimer.
# 2. Redistributions in binary form must reproduce the above copyright notice,
#    this list of conditions and the following disclaimer in the documentation
#    and/or other materials provided with the distribution.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# -----------------------------------------------------------------------------------------------------
# General note:
# All variables are in SI units by default. Exceptions explicit by variable name.
# -----------------------------------------------------------------------------------------------------

# Always prefer setuptools over distutils
from setuptools import setup, find_packages, Extension
import setuptools.command.install
import setuptools.command.develop
# To use a consistent encoding
from codecs import open
# Other stuff
import sys, os, fileinput
from textwrap import dedent
import numpy
import re

here = os.path.dirname(os.path.realpath(__file__))

# Enable using threads (requires nfft installation with threads (https://www-user.tu-chemnitz.de/~potts/paper/openmpNFFT.pdf)
ENABLE_THREADS = bool(os.environ.get("CONDOR_ENABLE_THREADS"))
# Specify the include directory of the NFFT library
NFFT_LIBRARY_DIR = os.environ.get("NFFT_LIBRARY_DIR")
# Specify the include directory of the NFFT library
NFFT_INCLUDE_DIR = os.environ.get("NFFT_INCLUDE_DIR")


def get_property(prop):
    result = re.search(
        r'{}\s*=\s*[\'"]([^\'"]*)[\'"]'.format(prop),
        open(os.path.join('condor', '__init__.py')).read()
    )
    return result.group(1)

ADDITIONAL_USER_OPTIONS = [
    ('enable-threads=', None, 'Enable using threads (requires nfft installation with threads (https://www-user.tu-chemnitz.de/~potts/paper/openmpNFFT.pdf). While command line options take precendence this option can also be set using the environment variable CONDOR_ENABLE_THREADS.'),
    ('nfft-include-dir=', None, 'Specify the include directory of the NFFT library. While command line options take precendence this option can also be set using the environment variable NFFT_LIBRARY_DIR.'),
    ('nfft-library-dir=', None, 'Specify the library directory of the NFFT library. While command line options take precendence this option can also be set using the environment variable NFFT_INCLUDE_DIR.'),
]

class _Command:
    def _initialize_options(self):
        self.enable_threads = None
        self.nfft_include_dir = None
        self.nfft_library_dir = None

    def _make_ext_nfft(self):
        if self.enable_threads is not None:
            enable_threads = self.enable_threads
        else:
            enable_threads = ENABLE_THREADS

        library_dirs = []
        if self.nfft_library_dir is not None:
            library_dirs = [self.nfft_library_dir]
        elif NFFT_LIBRARY_DIR is not None:
            library_dirs = [NFFT_LIBRARY_DIR]
        
        libraries = ["nfft3"] if not enable_threads else ["nfft3_threads" ,"fftw3_threads" ,"fftw3"]
        
        include_dirs = [numpy.get_include()]
        if self.nfft_include_dir is not None:
            include_dirs += [self.nfft_include_dir]
        elif NFFT_INCLUDE_DIR is not None:
            include_dirs += [NFFT_INCLUDE_DIR]

        define_macros = [] if not enable_threads else [("ENABLE_THREADS", None)]
        
        runtime_library_dirs = library_dirs

        extra_link_args = []
        if library_dirs:
            extra_link_args = ['-Wl']
            for d in library_dirs:
                extra_link_args[0] += ',-rpath,%s' % d
                extra_link_args[0] += ',-L,%s' % d

        return Extension(
            "condor.utils.nfft",
            sources=[os.path.join('condor', 'utils', 'nfftmodule.c')],
            library_dirs=library_dirs,
            libraries=libraries,
            include_dirs=include_dirs,
            define_macros=define_macros,
            runtime_library_dirs=runtime_library_dirs,
            extra_link_args=extra_link_args,
        )
        
    def _run(self):
        self.distribution.ext_modules.append(self._make_ext_nfft())
        

class InstallCommand(_Command, setuptools.command.install.install):
    user_options = setuptools.command.install.install.user_options + ADDITIONAL_USER_OPTIONS
    
    def initialize_options(self):
        self._initialize_options()
        try:
            super().initialize_options() # Python 3
        except TypeError:
            setuptools.command.install.install.initialize_options(self) # Python 2
    
    def run(self):
        self._run()
        try:
            super().run() # Python 3
        except TypeError:
            setuptools.command.install.install.run(self) # Python 2



class DevelopCommand(_Command, setuptools.command.develop.develop):
    user_options = setuptools.command.develop.develop.user_options + ADDITIONAL_USER_OPTIONS

    def initialize_options(self):
        self._initialize_options()
        try:
            super().initialize_options() # Python 3
        except TypeError:
            setuptools.command.develop.develop.initialize_options(self) # Python 2
    
    def run(self):
        self._run()
        try:
            super().run() # Python 3
        except TypeError:
            setuptools.command.develop.develop.run(self) # Python 2


# Get the long description from the README file
with open(os.path.join(here, 'README.rst'), encoding='utf-8') as f:
    long_description = f.read()
    
setup(
    cmdclass={
        'install'  : InstallCommand,
        'develop' : DevelopCommand,
    },
    
    name='condor',

    # Versions should comply with PEP440.  For a discussion on single-sourcing
    # the version across setup.py and the project code, see
    # https://packaging.python.org/en/latest/single_source_version.html
    version=get_property('__version__'),

    description='Condor: Simulation of single particle X-ray diffraction patterns',
    long_description=long_description,

    # The project's main homepage.
    url='https://github.com/FXIhub/condor',

    # Author details
    author='Hantke, Max Felix',
    author_email='hantke@xray.bmc.uu.se',

    # Choose your license
    license='BSD',

    # See https://pypi.python.org/pypi?%3Aaction=list_classifiers
    classifiers=[
        # How mature is this project? Common values are
        #   3 - Alpha
        #   4 - Beta
        #   5 - Production/Stable
        'Development Status :: 3 - Alpha',

        # Indicate who your project is intended for
        'Intended Audience :: Science/Research',
        'Topic :: Scientific/Engineering :: Physics',

        # Pick your license as you wish (should match "license" above)
        'License :: OSI Approved :: BSD License',

        # Specify the Python versions you support here. In particular, ensure
        # that you indicate whether you support Python 2, Python 3 or both.
        'Programming Language :: Python :: 2',
        'Programming Language :: Python :: 2.7',
        'Programming Language :: Python :: 3',
        'Programming Language :: Python :: 3.4',
        'Programming Language :: Python :: 3.5',
        'Programming Language :: Python :: 3.6',
        'Programming Language :: Python :: 3.7',
        'Programming Language :: Python :: 3.8',
    ],

    # What does your project relate to?
    keywords='X-ray diffraction single particle',

    # You can just specify the packages manually here if your project is
    # simple. Or you can use find_packages().
    packages = ['condor', 'condor.utils', 'condor.particle', 'condor.scripts', 'condor.data'],
    package_dir = {'condor':'condor'},
    ext_modules = [
        Extension(
            "condor.utils.icosahedron",
            sources=[os.path.join('condor', 'utils' , 'icosahedronmodule.c')],
            include_dirs=[numpy.get_include()],
        )
    ],
    
    # Alternatively, if you want to distribute just a my_module.py, uncomment 
    # this:
    #   py_modules=["my_module"],

    # List run-time dependencies here.  These will be installed by pip when
    # your project is installed. For an analysis of "install_requires" vs pip's
    # requirements files see:
    # https://packaging.python.org/en/latest/requirements.html
    install_requires=['numpy', 'scipy', 'h5py'],

    # List additional groups of dependencies here (e.g. development
    # dependencies). You can install these using the following syntax,
    # for example:
    # $ pip install -e .[dev,test]
    #extras_require={
    #    'dev': ['check-manifest'],
    #    'test': ['coverage'],
    #},

    # If there are data files included in your packages that need to be
    # installed, specify them here.  If using Python 2.6 or less, then these
    # have to be included in MANIFEST.in as well.
    package_data={
        'condor': [
            os.path.join('data', '*.dat'),
        ]
    },

    # Although 'package_data' is the preferred approach, in some case you may
    # need to place data files outside of your packages. See:
    # http://docs.python.org/3.4/distutils/setupscript.html#installing-additional-files # noqa
    # In this case, 'data_file' will be installed into '<sys.prefix>/my_data'
    #data_files=[('my_data', ['data/data_file'])],

    # To provide executable scripts, use entry points in preference to the
    # "scripts" keyword. Entry points provide cross-platform support and allow
    # pip to create the appropriate form of executable for the target platform.
    entry_points={
        'console_scripts': [
            'condor=condor.scripts.condor_script:main',
        ],
    },
)