This initial release establishes minimal feature parity with the internal EpiNow2 Rt modeling pipeline. It adds wrappers to integrate with internal data schemas and ingest pre-estimated model parameters (i.e., generation intervals, right-truncation). It defines an output schema and adds comprehensive logging. The repository also has functionality to set up and deploy to Azure Batch.
Features
- GitHub Actions to build Docker images on PR and merge to main, deploy Azure Batch environments off the built images, and tear down the environment on PR close.
- Comprehensive documentation of pipeline code and validation of input data, parameters, and model run configs
- Set up comprehensive logging of model runs and handle pipeline failures to preserve logs where possible
- Automatically download and upload inputs and outputs from Azure Blob Storage