setup.py

"""
GEMCAT GUI - Gene Expression-based Metabolic Context Analysis Tool
Setup configuration for package installation
"""
from setuptools import setup, find_packages
import os

# Read the requirements from requirements.txt
def read_requirements(filename='requirements.txt'):
    """Read requirements from file."""
    req_path = os.path.join(os.path.dirname(__file__), filename)
    if os.path.exists(req_path):
        with open(req_path, 'r') as f:
            return [line.strip() for line in f if line.strip() and not line.startswith('#')]
    return []

# Read the long description from README if it exists
long_description = "GEMCAT GUI - A graphical interface for metabolic context analysis based on gene expression data"
readme_path = os.path.join(os.path.dirname(__file__), 'README.md')
if os.path.exists(readme_path):
    with open(readme_path, 'r', encoding='utf-8') as f:
        long_description = f.read()

setup(
    name='gemcat-gui',
    version='1.4.0',
    author='Molecular Bioinformatics',
    description='Gene Expression-based Metabolic Context Analysis Tool - GUI Application',
    long_description=long_description,
    long_description_content_type='text/markdown',
    url='https://github.com/MolecularBioinformatics/gemcat_gui',
    
    # Package configuration
    packages=find_packages(where='src'),
    package_dir={'': 'src'},
    
    # Include package data (models, styles, etc.)
    include_package_data=True,
    package_data={
        'gemcat_gui': [
            'models/**/*',
            'styles/*.qss',
        ],
    },
    
    # Dependencies
    install_requires=read_requirements('requirements.txt'),
    
    # Python version requirement
    python_requires='>=3.9',
    
    # Entry points for command-line scripts
    entry_points={
        'console_scripts': [
            'gemcat-gui=gemcat_gui.gui.main_window:main',
        ],
    },
    
    # Classifiers
    classifiers=[
        'Development Status :: 4 - Beta',
        'Intended Audience :: Science/Research',
        'Topic :: Scientific/Engineering :: Bio-Informatics',
        'Programming Language :: Python :: 3',
        'Programming Language :: Python :: 3.9',
        'Programming Language :: Python :: 3.10',
        'Programming Language :: Python :: 3.11',
    ],
    
    # Keywords
    keywords='bioinformatics metabolic-modeling gene-expression cobra',
)