smartem-decisions 0.1.0

A proof of concept for a decision engine to automate CryoEM workflows for structural biology

smartem-decisions

Smart data collection system for cryo-electron microscopy at Diamond Light Source.

Installation

SmartEM Agent (data collection)

pip install smartem-decisions[agent]

Windows executable: Download the latest smartem-agent-windows-vX.Y.Z.exe from GitHub Releases.

SmartEM Backend (API server)

pip install smartem-decisions[backend]

All components

pip install smartem-decisions[all]

Usage

Agent

Watch a directory for EPU output and send data to the backend:

# Basic usage
smartem-agent watch /path/to/epu/output --api-url http://localhost:8000

# Dry run (no API calls)
smartem-agent watch /path/to/epu/output --dry-run

# Verbose output
smartem-agent watch /path/to/epu/output -vv

Parse EPU data without watching:

smartem-agent parse dir /path/to/epu/output
smartem-agent parse session /path/to/EpuSession.dm
smartem-agent parse atlas /path/to/Atlas.dm

Backend

Start the API server and message consumer:

# HTTP API server
python -m smartem_backend.api_server

# Message queue consumer
python -m smartem_backend.consumer -v

Components

Package	Description
smartem_agent	Data collection agent that monitors EPU output
smartem_backend	Core backend with HTTP API and message queue processing
smartem_common	Shared schemas, types, and utilities

Installation Extras

Extra	Description
[agent]	Agent dependencies (watchdog, lxml)
[backend]	Backend dependencies (FastAPI, SQLAlchemy, Pika)
[common]	Core schemas only (Pydantic)
[images]	Image processing (Pillow, mrcfile, tifffile)
[dev]	Development tools (pytest, ruff, pyright)
[all]	All dependencies

Development

# Install with dev dependencies
pip install -e ".[dev]"

# Run tests
pytest

# Lint
ruff check src/
ruff format --check src/

# Type check
pyright

Documentation

• Backend API Server
• Agent Deployment
• Kubernetes Deployment

Links

• PyPI: https://pypi.org/project/smartem-decisions/
• Repository: https://github.com/DiamondLightSource/smartem-decisions
• Issues: https://github.com/DiamondLightSource/smartem-decisions/issues
• Changelog: GitHub Releases

License

Apache-2.0