Installation

Prerequisites

Python 3.11 or higher
UV package manager (recommended)

Add to Your Project (Recommended)

# Basic installation - all 8 enrichment services
uv add biosample-enricher

# With 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 schema    # Schema analysis tools
uv add biosample-enricher --extra all       # All optional features

From Source (Development)

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

# With optional extras
uv sync --extra mongodb    # MongoDB support
uv sync --extra metrics    # Metrics and visualization
uv sync --extra schema     # Schema analysis tools
uv sync --extra all        # Everything