setup.py

#! /usr/bin/env python
"""Toolbox for Machine Learning using Topological Data Analysis."""

import os
import codecs
import re
import sys
import platform
import subprocess

from pkg_resources.extern.packaging import version
from setuptools import setup, Extension, find_packages
from setuptools.command.build_ext import build_ext


version_file = os.path.join("gtda", "_version.py")
with open(version_file) as f:
    exec(f.read())

with open("requirements.txt") as f:
    requirements = f.read().splitlines()

DISTNAME = "giotto-tda"
DESCRIPTION = "Toolbox for Machine Learning using Topological Data Analysis."
with codecs.open("README.rst", encoding="utf-8-sig") as f:
    LONG_DESCRIPTION = f.read()
LONG_DESCRIPTION_TYPE = "text/x-rst"
MAINTAINER = "Umberto Lupo, Wojciech Reise"
MAINTAINER_EMAIL = "maintainers@giotto.ai"
URL = "https://github.com/giotto-ai/giotto-tda"
LICENSE = "GNU AGPLv3"
VERSION = __version__  # noqa
DOWNLOAD_URL = f"https://github.com/giotto-ai/giotto-tda/tarball/v{VERSION}"
CLASSIFIERS = ["Intended Audience :: Science/Research",
               "Intended Audience :: Developers",
               "License :: OSI Approved",
               "Programming Language :: C++",
               "Programming Language :: Python",
               "Topic :: Software Development",
               "Topic :: Scientific/Engineering",
               "Operating System :: Microsoft :: Windows",
               "Operating System :: POSIX",
               "Operating System :: Unix",
               "Operating System :: MacOS",
               "Programming Language :: Python :: 3.7",
               "Programming Language :: Python :: 3.8",
               "Programming Language :: Python :: 3.9",
               "Programming Language :: Python :: 3.10",
               "Programming Language :: Python :: 3.11",
               "Programming Language :: Python :: 3.12"]
KEYWORDS = "machine learning, topological data analysis, persistent " \
           "homology, persistence diagrams, Mapper"
INSTALL_REQUIRES = requirements
EXTRAS_REQUIRE = {"tests": ["pandas",
                            "pytest",
                            "pytest-cov",
                            "pytest-azurepipelines",
                            "pytest-benchmark",
                            "jupyter_contrib_nbextensions",
                            "flake8",
                            "hypothesis"],
                  "doc": ["openml",
                          "sphinx",
                          "nbconvert",
                          "sphinx-issues",
                          "sphinx_rtd_theme",
                          "numpydoc"],
                  "examples": ["jupyter",
                               "pandas",
                               "openml",
                               "matplotlib",
                               "gensim",
                               "umap-learn"]}


def combine_requirements(base_keys):
    return list(set(k for v in base_keys for k in EXTRAS_REQUIRE[v]))


EXTRAS_REQUIRE["dev"] = combine_requirements(
    [k for k in EXTRAS_REQUIRE if k != "examples"])


class CMakeExtension(Extension):
    def __init__(self, name, sourcedir=""):
        Extension.__init__(self, name, sources=[])
        self.sourcedir = os.path.abspath(sourcedir)


class CMakeBuild(build_ext):
    def run(self):
        try:
            out = subprocess.check_output(["cmake", "--version"])
        except OSError:
            raise RuntimeError(
                f"CMake must be installed to build the following extensions: "
                f"{', '.join(e.name for e in self.extensions)}"
                )

        if platform.system() == "Windows":
            cmake_version = version.parse(re.search(r"version\s*([\d.]+)",
                                                    out.decode()).group(1))
            if cmake_version < version.parse("3.1.0"):
                raise RuntimeError("CMake >= 3.1.0 is required on Windows")

        self.install_dependencies()

        for ext in self.extensions:
            self.build_extension(ext)

    def install_dependencies(self):
        subprocess.check_call(["git", "submodule", "update",
                               "--init", "--recursive"])

    def build_extension(self, ext):
        extdir = os.path.abspath(os.path.join(os.path.dirname(
            self.get_ext_fullpath(ext.name)), "gtda", "externals", "modules"))
        cmake_args = [f"-DCMAKE_LIBRARY_OUTPUT_DIRECTORY={extdir}",
                      f"-DPYTHON_EXECUTABLE={sys.executable}"]

        cfg = "Debug" if self.debug else "Release"
        build_args = ["--config", cfg]

        if platform.system() == "Windows":
            cmake_args += [f"-DCMAKE_LIBRARY_OUTPUT_DIRECTORY_{cfg.upper()}"
                           f"={extdir}"]
            if sys.maxsize > 2**32:
                cmake_args += ["-A", "x64"]
            build_args += ["--", "/m"]
        else:
            cmake_args += [f"-DCMAKE_BUILD_TYPE={cfg}"]
            build_args += ["--", "-j2"]

        if sys.platform.startswith("darwin"):
            # Cross-compile support for macOS - respect ARCHFLAGS if set
            archs = re.findall(r"-arch (\S+)", os.environ.get("ARCHFLAGS", ""))
            if archs:
                cmake_args += \
                    ["-DCMAKE_OSX_ARCHITECTURES={}".format(";".join(archs))]

        env = os.environ.copy()
        env["CXXFLAGS"] = f"{env.get('CXXFLAGS', '')} -DVERSION_INFO="\
                          f"\\'{self.distribution.get_version()}\\'"
        if not os.path.exists(self.build_temp):
            os.makedirs(self.build_temp)
        subprocess.check_call(["cmake", ext.sourcedir] + cmake_args,
                              cwd=self.build_temp, env=env)
        subprocess.check_call(["cmake", "--build", "."] + build_args,
                              cwd=self.build_temp)


setup(name=DISTNAME,
      maintainer=MAINTAINER,
      maintainer_email=MAINTAINER_EMAIL,
      description=DESCRIPTION,
      license=LICENSE,
      url=URL,
      version=VERSION,
      download_url=DOWNLOAD_URL,
      long_description=LONG_DESCRIPTION,
      long_description_content_type=LONG_DESCRIPTION_TYPE,
      zip_safe=False,
      classifiers=CLASSIFIERS,
      packages=find_packages(),
      keywords=KEYWORDS,
      install_requires=INSTALL_REQUIRES,
      extras_require=EXTRAS_REQUIRE,
      ext_modules=[CMakeExtension("gtda")],
      cmdclass=dict(build_ext=CMakeBuild))