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>=0.9.6",
    "cython>=0.29",
]
# 'some-pkg @ git+ssh://git@github.com/someorgname/pkg-repo-name@v1.1#egg=some-pkg',
matplotlib_version = "matplotlib==3.3.4"
install_requirements += ["scipy>=1.3.0,<=1.12.0"]

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",
    python_requires=">=3.9",
    keywords="machine-learning gaussian-processes kernels",
    url="https://sheffieldml.github.io/GPy/",
    download_url="https://github.com/SheffieldML/GPy/archive/refs/heads/devel.zip",
    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",
        ],
        "dev": ["pytest", "matplotlib", "pods"],
    },
    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",
    ],
    project_urls={
        "Source Code": "https://github.com/SheffieldML/GPy",
        "Bug Tracker": "https://github.com/SheffieldML/GPy/issues",
    },
)


# 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))