CHANGES:

1. The posterior NGM is now not saved, only the sum over all destinations to give $R_{it}$
2. Replace Rt as the dominant eigenvalue of the NGM with weighted average by population size.
3. ngm.nc now contains both $R_{it}$ and $R_t$ posterior predictive values.

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.

Chris Jewell authored Feb 24, 2021 and Chris Jewell committed Feb 24, 2021

Changes:

1. Where xarrays were pickled to disc, we now use xarray.to_netcdf
2. Where xarrays were read from Python pickles, we now use xarray.load_dataset


(cherry picked from commit 63519eb3)

CHANGES:

1. Replaced `read_phe_cases` with `CasesData`
2. Column-name fix in `case_exceedance`
3. Fix column heading in `summarize.infec_incidence`
4. Add Rt_exceed to `summarize.rt`
5. Add layer option to `summary_geopackage`
6. Update `ruffus_pipeline.py` to reflect above changes
7. Update `template_config.yaml` to reflect above changes