Installation

Prerequisites

• Python 3.11 or higher

• UV package manager (recommended)

Add to Your Project

# Basic installation
uv add biosample-enricher

# Or with pip
pip install biosample-enricher

# Optional dependencies
uv add biosample-enricher --extra metrics   # Metrics and visualization
uv add biosample-enricher --extra mongodb   # MongoDB support for NMDC/GOLD
uv add biosample-enricher --extra all       # All optional features

From Source (Development)

git clone https://github.com/contextualizer-ai/biosample-enricher.git
cd biosample-enricher
uv sync