Repository files navigation

A simple example of an SEIRS epidemiological model using theFAIR Data Pipeline.

1. Create and activate new python 3 virtual environment.
2. pip install fair-cli.
3. Install a local registry:
   1. Install graphviz
   2. fair registry install
4. Clone this repository:git clone https://github.com/FAIRDataPipeline/pySimpleModel.git.
5. Change directorycd pySimpleModel.
6. Install this packagepip install ..
7. Initialise the registryfair 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 (usingfair pull) and then running the code (usingfair run). So:

fair pull simpleModel/ext/SEIRSconfig.yamlfair run simpleModel/ext/SEIRSconfig.yaml

1. Ensure the local registry is startedfair registry start.
2. Visit the local registry in your browser (by default athttp://localhost:8000), you should see the input and output data recorded in the registry.