Ensembl Web Metadata API

Metadata API for new Ensembl website (https://beta.ensembl.org)

Project is managed with uv. If you don't have it:

pipx install uv
# This should also give you optional dev dependencies
uv sync --locked
cp .env.sample .env
# Look at .env, edit as appropriate
# ensure the metadata DuckDB is copied to ./data/duck_meta.db
uv run uvicorn api.main:app --host 127.0.0.1 --port 8000 --reload

Build and run with Docker/podman

sudo podman build --tag=duck-meta .
cp .env.sample .env
vi .env # add values for redis or database settings as needed
sudo podman run -it --env-file .env --mount type=bind,src=./data,dst=/data -p 8014:8014 duck-meta:latest

The container image installs dependencies at build time and starts uvicorn directly from the built virtual environment. Do not change the container startup command to uv run ..., because that triggers dependency resolution at runtime.

Run together with Redis

vi .env # add values for PORT / enable or disable redis
sudo podman-compose up

Run unit tests:

uv run pytest

Format code

uv run black src/api

Dependency management

# Add/remove project dependency
uv add httpx
uv remove httpx
# Dev dependency
uv add --dev httpx
# Alternative
uv add httpx --group dev
uv remove --dev httpx
# List dependencies
uv tree

# A venv is managed by uv. You don't need an extra one. You don't have to
# activate it. pyproject.toml is updated for you. A uv.lock file is written and
# kept up to date. Changes to uv.lock should be committed to git.