Installation

omop-emb supports backend-specific optional dependencies so users can install only what they need.

Core only

pip install omop-emb

This installs the shared core package only. It does not guarantee that any particular embedding backend is available.

It also does not remove the need for a database backend. omop-emb still requires database-backed OMOP access and model registration.

PostgreSQL backend

pip install "omop-emb[pgvector]"

Use this when you want the current pgvector/PostgreSQL-backed embedding store and CLI flow.

FAISS backend

pip install "omop-emb[faiss]"

Use this when you want the FAISS backend dependencies available.

Even in this case, a database backend is still required for OMOP concept metadata access.

Everything

pip install "omop-emb[all]"

This is the most convenient choice for development, testing, and mixed environments where you want both backend stacks available.

Recommended runtime pattern

For clarity, backend selection should be explicit at runtime as well as install-time.

Examples:

export OMOP_EMB_BACKEND=pgvector
export OMOP_EMB_BACKEND=faiss
export OMOP_EMB_BASE_STORAGE_DIR=$PWD/.omop_emb

That avoids silent fallback between backend implementations.

OMOP_EMB_BASE_STORAGE_DIR controls where omop-emb stores local metadata (metadata.db) and file-based backend artifacts (such as FAISS files). If it is not set, omop-emb defaults to ./.omop_emb in the current working directory. If a provided path includes ~, it is expanded automatically.