CHANGES:

1. `thin_samples['init_state']` --> `thin_samples['initial_state']`
2. `thin_samples['events']` --> `thin_samples['seir']`
3. add time dimension to next generation matrix
4. update downstream scripts to changes.

CHANGES

1. Most tasks touched to use netCDF4 inferencedata file.
2. Added netCDF4 metadata copy to covid.util
3. Updated model_spec.py to use xarray
4. Updated covid.ruffus_pipeline to use netCDF4 files, adding pipeline metadata
5. Updated pyproject.toml
6. Removed chunk specification in inference.py.  Defer to automatic chunking for now.

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.