Background

CF-Random is a tool for predicting alternative conformations and fold-switching proteins using AlphaFold. Previously, the project was structured as a collection of Python scripts that required manual setup and path management. This PR converts CF-Random into a properly structured Python package that can be installed via pip, making it more accessible to the scientific community and easier to integrate into workflows.

Why

• Easier installation: Users can now install CF-Random with a single pip install . command instead of manual setup
• Better distribution: The package structure enables future PyPI publishing for pip install cf-random installation
• Improved import capability: Scientists can now use CF-Random as a Python library in their own scripts via import cf_random
• Standard Python practices: Follows PEP 517/518 standards for Python packaging with pyproject.toml and setup.py
• Dependency management: Centralizes all dependencies in configuration files for reproducibility
• CLI integration: Provides a cf-random command-line tool with proper argument parsing

What Was Changed

New Files Created:

• pyproject.toml - Modern Python package configuration (PEP 517/518 compliant)

  • Package metadata, dependencies, and entry points
  • Build system configuration

• setup.py - Setup script for backward compatibility

• MANIFEST.in - Package manifest for including non-Python files

• cf_random/ package directory with:

  • __init__.py - Package initialization and version info
  • main.py - Wrapper module for the original code
  • cli.py - Command-line interface entry point

• INSTALL.md - Installation guide for users

• DEVELOP.md - Development and contribution guidelines

• .gitignore - Python and project-specific ignore patterns

Validation

CLI Testing

# Verify CLI help works
cf-random --help

# Expected output: Shows all available command-line options