Contributing

We welcome contributions from the community.

Development setup

Clone the repository:

git clone https://github.com/refgenie/refgenie1.git
cd refgenie1

Install in development mode:

pip install -e ".[dev,server,dash]"

Verify the installation:

refgenie --help

Running tests

Unit tests

Unit tests use in-memory SQLite and require no external dependencies. They run in about 7 seconds:

pytest tests/ --ignore=tests/integration

Integration tests

Integration tests require Docker (for PostgreSQL) and take about 110 seconds. Use the provided script, which manages the PostgreSQL container lifecycle, HTTP data channel, and bulker crate activation:

./tests/scripts/test-integration.sh

Do not run pytest tests/integration/ directly — all tests will skip because the required environment variable and services will not be set up.

For debugging individual integration tests:

./tests/scripts/services.sh start
RUN_INTEGRATION_TESTS=true pytest tests/integration/ -k "test_name"
./tests/scripts/services.sh stop

New assets

We are interested in working with groups who want to add assets into the refgenie system. Refgenie now uses a flexible asset class and recipe system — you can define custom asset types and build recipes via YAML files without modifying refgenie’s source code. See Flexible asset types and Data channels for details.

Project structure

Directory	Contents
`refgenie/`	Core library code
`refgenie/cli/`	CLI command definitions, handlers, and argument models
`refgenie/server/`	Built-in server (FastAPI routers, templates)
`refgenie/dash/`	Dashboard web UI
`refgenie/db/`	Database models (SQLModel)
`refgenie/managers/`	Asset, configuration, and genome managers
`refgenie/config/`	Configuration and database backend setup
`tests/`	Unit tests
`tests/integration/`	Integration tests (require Docker)

Suggestions and feedback

Please open an issue on the GitHub issue tracker with suggestions, bug reports, or other feedback.