setup.py

#!/usr/bin/env python

import os
import sys
from shutil import rmtree
from setuptools import Command, find_packages, setup

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


def get_version():
    init_py_path = os.path.join(os.path.abspath(os.path.dirname(__file__)), "dosma", "__init__.py")
    init_py = open(init_py_path, "r").readlines()
    version_line = [l.strip() for l in init_py if l.startswith("__version__")][0]  # noqa: E741
    version = version_line.split("=")[-1].strip().strip("'\"")

    # The following is used to build release packages.
    # Users should never use it.
    suffix = os.getenv("DOSMA_VERSION_SUFFIX", "")
    version = version + suffix
    if os.getenv("BUILD_NIGHTLY", "0") == "1":
        from datetime import datetime

        date_str = datetime.today().strftime("%y%m%d")
        version = version + ".dev" + date_str

        new_init_py = [l for l in init_py if not l.startswith("__version__")]  # noqa: E741
        new_init_py.append('__version__ = "{}"\n'.format(version))
        with open(init_py_path, "w") as f:
            f.write("".join(new_init_py))
    return version


def get_resources():
    """Get the resources files for dosma. To be used with `package_data`.

    All files under 'dosma/resources/{elastix,templates}'.
    """
    import pathlib

    files = []
    # Elastix files
    for path in pathlib.Path("dosma/resources/elastix/params").rglob("*.*"):
        files.append(str(path))
    for path in pathlib.Path("dosma/resources/templates").rglob("*.*"):
        files.append(str(path))
    return [x.split("/", 1)[1] for x in files]


class UploadCommand(Command):
    """Support setup.py upload.

    Adapted from https://github.com/robustness-gym/meerkat.
    """

    description = "Build and publish the package."
    user_options = []

    @staticmethod
    def status(s):
        """Prints things in bold."""
        print("\033[1m{0}\033[0m".format(s))

    def initialize_options(self):
        pass

    def finalize_options(self):
        pass

    def run(self):
        try:
            self.status("Removing previous builds…")
            rmtree(os.path.join(here, "dist"))
        except OSError:
            pass

        self.status("Building Source and Wheel (universal) distribution…")
        os.system("{0} setup.py sdist bdist_wheel --universal".format(sys.executable))

        self.status("Uploading the package to PyPI via Twine…")
        os.system("twine upload dist/*")

        self.status("Pushing git tags…")
        os.system("git tag v{0}".format(get_version()))
        os.system("git push --tags")

        sys.exit()


# ---------------------------------------------------
# Setup Information
# ---------------------------------------------------

# Required pacakges.
REQUIRED = [
    "matplotlib",
    "numpy",
    "h5py",
    "natsort",
    "nested-lookup",
    "nibabel",
    "nipype",
    "packaging",
    "pandas",
    # TODO Issue #57: Remove pydicom upper bound (https://github.com/ad12/DOSMA/issues/57)
    "pydicom>=1.6.0",
    "scikit-image",
    "scipy",
    "seaborn",
    "openpyxl",
    "Pmw",
    "PyYAML",
    "tabulate",
    "termcolor",
    "tqdm>=4.42.0",
]

# Optional packages.
# TODO Issue #106: Fix to only import tensorflow version with fixed version
# once keras import statements are properly handled.
EXTRAS = {
    "dev": [
        "coverage",
        "flake8",
        "flake8-bugbear",
        "flake8-comprehensions",
        "isort",
        "black==21.4b2",
        "click==8.0.2",
        "simpleitk",
        "sphinx",
        "sphinxcontrib.bibtex",
        "m2r2",
        "tensorflow<=2.4.1",
        "keras<=2.4.3",
        "sigpy",
    ],
    "ai": ["tensorflow<=2.4.1", "keras<=2.4.3"],
    "docs": ["mistune>=0.8.1,<2.0.0", "sphinx", "sphinxcontrib.bibtex", "m2r2"],
}

with open("README.md", "r", encoding="utf-8") as fh:
    long_description = fh.read()


setup(
    name="dosma",
    version=get_version(),
    author="Arjun Desai",
    url="https://github.com/ad12/DOSMA",
    project_urls={"Documentation": "https://dosma.readthedocs.io/"},
    description="An AI-powered open-source medical image analysis toolbox",
    long_description=long_description,
    long_description_content_type="text/markdown",
    packages=find_packages(exclude=("configs", "tests", "tests.*")),
    package_data={"dosma": get_resources()},
    python_requires=">=3.6",
    install_requires=REQUIRED,
    license="GNU",
    classifiers=[
        "Programming Language :: Python :: 3",
        "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
        "Operating System :: OS Independent",
    ],
    extras_require=EXTRAS,
    # $ setup.py publish support.
    cmdclass={
        "upload": UploadCommand,
    },
)