setup.py

# MIT License
#
# Copyright (c) 2025 CTLab-ITMO
#
# Authors: Daniil Smutin, Aleksandr Serdiukov, Vitalii Dravgelis, Artem Ivanov,
# Aleksei Zabashta, Sergey Muravyov, and the CTLab-ITMO university team.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.


from setuptools import setup, find_packages
import os

def read_requirements():
    """Read requirements from requirements.txt file."""
    requirements_path = os.path.join(os.path.dirname(__file__), 'requirements.txt')
    with open(requirements_path, 'r') as f:
        requirements = []
        for line in f:
            line = line.strip()
            # Skip empty lines and comments
            if line and not line.startswith('#'):
                requirements.append(line)
        return requirements

def read_readme():
    """Read README.md from project root."""
    readme_path = os.path.join(os.path.dirname(__file__), 'README.md')
    try:
        with open(readme_path, 'r', encoding='utf-8') as f:
            return f.read()
    except:
        return "PROBESt: package for nucleotide probes generation"

# Get src directory
src_dir = os.path.join(os.path.dirname(__file__), 'src')

setup(
    name='PROBESt',
    version='0.2.2',
    packages=find_packages(where=src_dir),
    package_dir={'': src_dir},
    py_modules=['pipeline'],
    python_requires='>=3.12',
    install_requires=read_requirements(),
    author='CTLab',
    author_email='dvsmutin@itmo.ru',
    description='PROBESt: package for nucleotide probes generation',
    long_description=read_readme(),
    long_description_content_type='text/markdown',
    url='https://github.com/CTLab-ITMO/PROBESt',
    classifiers=[
        'Development Status :: 3 - Alpha',
        'Intended Audience :: Science/Research',
        'License :: OSI Approved :: MIT License',
        'Programming Language :: Python :: 3.12',
        'Topic :: Scientific/Engineering :: Bio-Informatics',
    ],
    entry_points={
        'console_scripts': [
            'PROBESt=PROBESt.pipeline_entry:main',
            'probebase=PROBESt.scripts.probebase:main',
            'genome_operations=PROBESt.genome_operations:main',
        ],
    },
)