CHANGES:

1. Implemented log-linear model for weekday effect in I->R hazard;
2. Updated summary.py and within_between.py to match;
3. Implemented linear random walk for new gamma0 parameter.
4. Implemented per-parameter data structure in output HDF5 file.

CHANGES:

1. Updated the model to use the new gemlib library;
2. Removed automatic deletion of results directory by prepare_config.py;
3. Parameterised `gamma` prior parameters and added to template_config.yaml;
4. Updated within_between.py to use global configuration file.

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enqueue_pipeline.sh --> covid_pipeline.sge --> prepare_config.py --> inference.py --> summary.py

enqueue_pipeline.sh identifies the dataset and analysis period, launching 4 SGE jobs [P1, P1+2]\times[specimen_date, report_date]

Each SGE job runs the inference and summary scripts, using information contained in a config.yaml file.

The config.yaml file, together with results outputs, are stored in a results directory specified the config file
and over-ridden in the top-level enqueue_pipeline.sh script.