setup.py

# -*- coding: utf-8 -*-
import pathlib
import sys
from collections import defaultdict

import setuptools

# check for python version
if sys.version_info < (3, 8):
    raise SystemExit('Python 3.8+ is required!')


def get_extra_requirements(path, add_all=True):
    """Parse extra-requirements file."""
    with open(path) as depfile:
        extra_deps = defaultdict(set)
        for line in depfile:
            if not line.startswith('#'):
                if ':' not in line:
                    raise ValueError(
                        f'Dependency in {path} not correct formatted: {line}',
                    )
                dep, tags = line.split(':')
                tags = {tag.strip() for tag in tags.split(',')}
                for tag in tags:
                    extra_deps[tag].add(dep)

        # add tag `all` at the end
        if add_all:
            extra_deps['all'] = {
                tag for tags in extra_deps.values() for tag in tags
            }

    return extra_deps


def remove_gh_dark_mode_only_tags(text, tag='#gh-dark-mode-only'):
    """Remove recursively all """
    idx = text.find(tag)
    if idx < 0:
        return text

    idx_tag_end = text.find('>', idx)
    idx_tag_start = text.rfind('<', 0, idx)
    return remove_gh_dark_mode_only_tags(
        text[:idx_tag_start] + text[idx_tag_end + 1:], tag,
    )


# The directory containing this file
HERE = pathlib.Path(__file__).parent

# The text of the README file
README = remove_gh_dark_mode_only_tags(
    (HERE / 'README.md').read_text(),
)

# This call to setup() does all the work
setuptools.setup(
    name='msmhelper',
    version='1.1.1',
    description='Helper functions for Markov State Models.',
    long_description=README,
    long_description_content_type='text/markdown',
    keywords=[
        'MSM',
        'Markov model',
        'Markov state model',
        'MD analysis',
    ],
    author='braniii',
    url='https://github.com/moldyn/msmhelper',
    license='BSD-3-Clause License',
    classifiers=[
        'License :: OSI Approved :: BSD License',
        'Intended Audience :: Science/Research',
        'Natural Language :: English',
        'Programming Language :: Python :: 3',
        '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',
        'Topic :: Scientific/Engineering :: Physics',
        'Topic :: Scientific/Engineering :: Bio-Informatics',
        'Topic :: Software Development :: Libraries :: Python Modules',
    ],
    project_urls={
        'Documentation': 'https://moldyn.github.io/msmhelper',
        'Source Code': 'https://github.com/moldyn/msmhelper',
        'Changelog': 'https://moldyn.github.io/msmhelper/changelog',
        'Bug Tracker': 'https://github.com/moldyn/msmhelper/issues',
    },
    package_dir={'': 'src'},
    packages=setuptools.find_packages(where='src'),
    include_package_data=True,
    python_requires='>=3.8',
    entry_points={
        'console_scripts': [
            'mosaic = mosaic.__main__:main',
        ],
    },
    install_requires=[
        'numpy>=1.21',
        'numba>=0.57',
        'pandas',
        'decorit',
        'scipy',
        'click',
        'prettypyplot>=0.11',
    ],
    extras_require=get_extra_requirements('extra-requirements.txt'),
)