GitLab

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. Introduced default unit traffic flow;
2. Removed old test data from data directory.  This now contains real static data only.
3. Brought README.md up to date.
4. Removed extraneous files from root project directory.

CHANGES:

1. Committed missing `case_data.py` file
2. Moved pipeline specification into `covid.ruffus_pipeline`
3. Moved pipeline initialisation into `covid.pipeline`

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