2026-06-25

Installing somop

Prerequisites

Python 3.9+
Docker 24+ (required for somop load and somop run)

Install

Clone the repo (it lives alongside the other services) and install in editable mode:

pip install -e path/to/somop

If you are working in a virtual environment (recommended):

python -m venv venv
source venv/bin/activate
pip install -e path/to/somop

Verify

somop --help

Expected output:

Usage: somop [OPTIONS] COMMAND [ARGS]...

Options:
  --help  Show this message and exit.

Commands:
  generate  Generate synthetic OMOP CDM CSV files from a YAML config.
  load      Load generated CSV files into a PostgreSQL database.
  multi     Multi-dataset generate and run.
  run       Generate data + start full stack (Postgres + BUNNY).

Docker

somop load and somop run spin up Docker containers. Ensure Docker Desktop (or Docker Engine) is running before using these commands.

The Docker images used are:

Image	Purpose
`postgres:16`	OMOP CDM database
`ghcr.io/health-informatics-uon/omop-lite:latest`	Schema creation and data loading
`ghcr.io/health-informatics-uon/hutch/bunny:edge`	BUNNY task resolver (or a local build)

These images are pulled automatically on first use.

Using a local BUNNY build

If you are developing BUNNY locally, pass --bunny-build path/to/hutch-bunny to somop run to build the BUNNY image from your local source instead of pulling from the registry.