PYTHON.md

Python Environment Setup for HADDOCK3

This guide provides instructions for setting up Python environments for HADDOCK3 development and usage.

Python Version Requirements

HADDOCK3 requires Python 3.9 or later:

• Recommended: Python 3.14+ for best compatibility
• Supported versions: 3.9-3.14
• Minimum required: Python 3.9

Python Installation

HADDOCK3 requires Python 3.9 or later.

Using uv (Recommended)

uv is a modern Python package manager that provides fast dependency resolution and virtual environment management:

# Install uv
curl -LsSf https://astral.sh/uv/install.sh | sh

# Create and activate a virtual environment
uv venv .venv --python=3.14
source .venv/bin/activate

System Python

Alternatively, use your system's package manager:

Linux (Ubuntu/Debian)

sudo apt-get update
sudo apt-get install python3.14 python3.14-dev python3.14-venv

macOS (Homebrew)

brew install python@3.14

---

python3.14 -m venv .venv
source .venv/bin/activate 

Troubleshooting

Common Issues

Python version conflicts:

# Check which Python is being used
which python
which python3

Virtual environment activation issues:

# Ensure proper shell integration
echo $VIRTUAL_ENV

Permission errors:

# Use --user flag or virtual environment
pip install --user package

Debugging Tools

# Check installed packages
pip list

# Check package locations
pip show package_name

# Verify Python environment
python -c "import sys; print(sys.executable)"