setup.py

"""
CBI Toolbox contains a collection of algorithms used for computational
bioimaging and microscopy.
"""

# Copyright (c) 2020 Idiap Research Institute, http://www.idiap.ch/
# Written by François Marelli <francois.marelli@idiap.ch>
#
# This file is part of CBI Toolbox.
#
# CBI Toolbox is free software: you can redistribute it and/or modify
# it under the terms of the 3-Clause BSD License.
#
# CBI Toolbox is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# 3-Clause BSD License for more details.
#
# You should have received a copy of the 3-Clause BSD License along
# with CBI Toolbox. If not, see https://opensource.org/licenses/BSD-3-Clause.
#
# SPDX-License-Identifier: BSD-3-Clause


from os import path
import os
import platform
import subprocess
import sys
import glob

from setuptools import setup, Extension, find_packages
from setuptools.command.build_ext import build_ext

__version__ = "1.6"

requires = [
    "numpy>=1.17",
    "scipy>=1.6.0",
    "scikit-image>=0.19",
    "poppy",
    "opensimplex>=0.4",
    "numba>=0.57",
    "scs",
    "jax",
    "jaxlib",
    "optax",
    # Posix-specific dependencies
    'pyconcorde @ git+https://github.com/jvkersch/pyconcorde ;platform_system!="Windows"',
]

extras_require = {
    "plots": ["napari>=0.4", "matplotlib"],
    "mpi": ["mpi4py"],
    "docs": ["sphinx>=4", "sphinxcontrib-apidoc", "sphinx_rtd_theme"],
    "ome": [
        "apeer-ometiff-library @ git+https://github.com/FrailHand/apeer-ometiff-library"
    ],
}


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

        sources = glob.glob("pybind11/tools/*")
        sources.extend(glob.glob("pybind11/include/**/*", recursive=True))
        sources.append("pybind11/CMakeLists.txt")
        sources.extend(glob.glob("**/src/*", recursive=True))
        sources.append("CMakeLists.txt")

        Extension.__init__(self, name, sources=sources)


class CMakeBuild(build_ext):
    def run(self):
        try:
            _ = subprocess.check_output(["cmake", "--version"])
        except OSError as exception:
            raise RuntimeError(
                "CMake must be installed to build the following extensions: "
                + ", ".join(e.name for e in self.extensions)
            ) from exception

        for ext in self.extensions:
            if isinstance(ext, CMakeExtension):
                self.build_extension(ext)

    def build_extension(self, ext):
        extdir = os.path.abspath(os.path.dirname(self.get_ext_fullpath(ext.name)))

        if not extdir.endswith(os.path.sep):
            extdir += os.path.sep

        cmake_args = [
            "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=" + extdir,
            "-DPYTHON_EXECUTABLE=" + sys.executable,
        ]

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

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

        env = os.environ.copy()
        env["CXXFLAGS"] = '{} -DVERSION_INFO=\\"{}\\"'.format(
            env.get("CXXFLAGS", ""), self.distribution.get_version()
        )
        if os.path.exists(self.build_temp):
            import shutil

            shutil.rmtree(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
        )


this_directory = path.abspath(path.dirname(__file__))
with open(path.join(this_directory, "README.rst"), encoding="utf-8") as f:
    long_description = f.read()


setup(
    name="cbi_toolbox",
    version=__version__,
    author="François Marelli",
    author_email="francois.marelli@idiap.ch",
    description="A python toolbox for computational bioimaging",
    long_description=long_description,
    long_description_content_type="text/markdown",
    license="BSD-3",
    url="https://github.com/idiap/cbi_toolbox",
    ext_modules=[CMakeExtension("cbi_toolbox.cmake_ext")],
    packages=find_packages(exclude=("tests",)),
    setup_requires=["cython"],
    install_requires=requires,
    python_requires=">=3.7, <3.11",
    extras_require=extras_require,
    cmdclass={"build_ext": CMakeBuild},
    zip_safe=False,
)