setup.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-

#===============================================================================
# Copyright (c) 2012 - 2014, GPy authors (see AUTHORS.txt).
# Copyright (c) 2014, James Hensman, Max Zwiessele
# Copyright (c) 2015, Max Zwiessele
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
#   list of conditions and the following disclaimer.
#
# * 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.
#
# * Neither the name of GPy nor the names of its
#   contributors may be used to endorse or promote products derived from
#   this software without specific prior written permission.
#
# 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 HOLDER 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.
#===============================================================================

from __future__ import print_function
import os
import sys
from setuptools import setup, Extension
import codecs

try:
    ModuleNotFoundError
except NameError:
    ModuleNotFoundError = ImportError

def read(fname):
    with codecs.open(fname, 'r', 'latin') as f:
        return f.read()

def read_to_rst(fname):
    try:
        import pypandoc
        rstname = "{}.{}".format(os.path.splitext(fname)[0], 'rst')
        pypandoc.convert(read(fname), 'rst', format='md', outputfile=rstname)
        with open(rstname, 'r') as f:
            rststr = f.read()
        return rststr
        #return read(rstname)
    except ImportError:
        return read(fname)

desc = """

Please refer to the github homepage for detailed instructions on installation and usage.

"""

version_dummy = {}
exec(read('GPy/__version__.py'), version_dummy)
__version__ = version_dummy['__version__']
del version_dummy

#Mac OS X Clang doesn't support OpenMP at the current time.
#This detects if we are building on a Mac
def ismac():
    return sys.platform[:6] == 'darwin'

if ismac():
    compile_flags = [ '-O3', ]
    link_args = []
else:
    compile_flags = [ '-fopenmp', '-O3']
    link_args = ['-lgomp' ]

try:
    # So that we don't need numpy installed to determine it's a dependency.
    import numpy as np

    ext_mods = [Extension(name='GPy.kern.src.stationary_cython',
                          sources=['GPy/kern/src/stationary_cython.pyx',
                                   'GPy/kern/src/stationary_utils.c'],
                          include_dirs=[np.get_include(), '.'],
                          extra_compile_args=compile_flags,
                          extra_link_args=link_args),
                Extension(name='GPy.util.choleskies_cython',
                          sources=['GPy/util/choleskies_cython.pyx'],
                          include_dirs=[np.get_include(), '.'],
                          extra_link_args=link_args,
                          extra_compile_args=compile_flags),
                Extension(name='GPy.util.linalg_cython',
                          sources=['GPy/util/linalg_cython.pyx'],
                          include_dirs=[np.get_include(), '.'],
                          extra_compile_args=compile_flags,
                          extra_link_args=link_args),
                Extension(name='GPy.kern.src.coregionalize_cython',
                          sources=['GPy/kern/src/coregionalize_cython.pyx'],
                          include_dirs=[np.get_include(), '.'],
                          extra_compile_args=compile_flags,
                          extra_link_args=link_args),
                Extension(name='GPy.models.state_space_cython',
                          sources=['GPy/models/state_space_cython.pyx'],
                          include_dirs=[np.get_include(), '.'],
                          extra_compile_args=compile_flags,
                          extra_link_args=link_args)]
except ModuleNotFoundError:
    ext_mods = []

install_requirements = ['numpy>=1.7', 'six', 'paramz>=0.9.0', 'cython>=0.29']
matplotlib_version = 'matplotlib==3.3.4'
if sys.version_info < (3, 6):
    install_requirements += ['scipy>=1.3.0,<1.5.0']
    matplotlib_version = 'matplotlib==3.0.0'
else:
    install_requirements += ['scipy>=1.3.0']

setup(name = 'GPy',
      version = __version__,
      author = read_to_rst('AUTHORS.txt'),
      author_email = "gpy.authors@gmail.com",
      description = ("The Gaussian Process Toolbox"),
      long_description = desc,
      license = "BSD 3-clause",
      keywords = "machine-learning gaussian-processes kernels",
      url = "http://sheffieldml.github.com/GPy/",
      download_url='https://github.com/SheffieldML/GPy/',
      ext_modules = ext_mods,
      packages = ["GPy",
                  "GPy.core",
                  "GPy.core.parameterization",
                  "GPy.kern",
                  "GPy.kern.src",
                  "GPy.kern.src.psi_comp",
                  "GPy.models",
                  "GPy.inference",
                  "GPy.inference.optimization",
                  "GPy.inference.mcmc",
                  "GPy.inference.latent_function_inference",
                  "GPy.likelihoods",
                  "GPy.mappings",
                  "GPy.examples",
                  "GPy.testing",
                  "GPy.util",
                  "GPy.plotting",
                  "GPy.plotting.gpy_plot",
                  "GPy.plotting.matplot_dep",
                  "GPy.plotting.matplot_dep.controllers",
                  "GPy.plotting.plotly_dep",
                  ],
      package_dir={'GPy': 'GPy'},
      #package_data = {'GPy': ['defaults.cfg', 'installation.cfg',
      #                        'util/data_resources.json',
      #                        'util/football_teams.json',
      #                        'testing/plotting_tests/baseline/*.png'
      #                        ]},
      #data_files=[('GPy/testing/plotting_tests/baseline', 'testing/plotting_tests/baseline/*.png'),
      #            ('GPy/testing/', 'GPy/testing/pickle_test.pickle'),
      #             ],
      include_package_data = True,
      py_modules = ['GPy.__init__'],
      test_suite = 'GPy.testing',
      setup_requires = ['numpy>=1.7'],
      install_requires = install_requirements,
      extras_require = {'docs':['sphinx'],
                        'optional':['mpi4py',
                                    'ipython>=4.0.0',
                                    ],
                        #matplotlib Version see github issue #955
                        'plotting':[matplotlib_version,
                                    'plotly >= 1.8.6'],
                        'notebook':['jupyter_client >= 4.0.6',
                                    'ipywidgets >= 4.0.3',
                                    'ipykernel >= 4.1.0',
                                    'notebook >= 4.0.5',
                                    ],
                        },
      classifiers=['License :: OSI Approved :: BSD License',
                   'Natural Language :: English',
                   'Operating System :: MacOS :: MacOS X',
                   'Operating System :: Microsoft :: Windows',
                   'Operating System :: POSIX :: Linux',
                   'Programming Language :: Python :: 3.5',
                   'Programming Language :: Python :: 3.6',
                   'Programming Language :: Python :: 3.7',
                   'Programming Language :: Python :: 3.8',
                   'Programming Language :: Python :: 3.9',
                   'Framework :: IPython',
                   'Intended Audience :: Science/Research',
                   'Intended Audience :: Developers',
                   'Topic :: Software Development',
                   'Topic :: Software Development :: Libraries :: Python Modules',

                   ]
      )


# Check config files and settings:
local_file = os.path.abspath(os.path.join(os.path.dirname(__file__), 'GPy', 'installation.cfg'))
home = os.getenv('HOME') or os.getenv('USERPROFILE')
user_file = os.path.join(home,'.config', 'GPy', 'user.cfg')

print("")
try:
    if not os.path.exists(user_file):
        # Does an old config exist?
        old_user_file = os.path.join(home,'.gpy_user.cfg')
        if os.path.exists(old_user_file):
            # Move it to new location:
            print("GPy: Found old config file, moving to new location {}".format(user_file))
            if not os.path.exists(os.path.dirname(user_file)):
                os.makedirs(os.path.dirname(user_file))
            os.rename(old_user_file, user_file)
        else:
            # No config file exists, save informative stub to user config folder:
            print("GPy: Saving user configuration file to {}".format(user_file))
            if not os.path.exists(os.path.dirname(user_file)):
                os.makedirs(os.path.dirname(user_file))
            with open(user_file, 'w') as f:
                with open(local_file, 'r') as l:
                    tmp = l.read()
                    f.write(tmp)
    else:
        print("GPy: User configuration file at location {}".format(user_file))
except:
    print("GPy: Could not write user configuration file {}".format(user_file))