A simple example of an SEIRS epidemiological model using the FAIR Data Pipeline.
- Create and activate new python 3 virtual environment.
pip install fair-cli.- Install a local registry:
- Install graphviz
fair registry install
- Clone this repository:
git clone https://github.com/FAIRDataPipeline/pySimpleModel.git. - Change directory
cd pySimpleModel. - Install this package
pip install .. - Initialise the registry
fair init
The user configuration script for running the python SEIRS model can be found inside this repo - simpleModel/ext/SEIRSconfig.yaml - and for this self-contained example, it includes all of the information to register the input data that the model needs, so that you don't have to be connected to a registry that already knows about it. The code can be executed by first ensuring that all of the input data is available in the local registry (using fair pull) and then running the code (using fair run). So:
fair pull simpleModel/ext/SEIRSconfig.yaml
fair run simpleModel/ext/SEIRSconfig.yaml- Ensure the local registry is started
fair registry start. - Visit the local registry in your browser (by default at http://localhost:8000), you should see the input and output data recorded in the registry.