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Use xarray/netCDF4 throughout the pipeline

Merged Chris Jewell requested to merge add_inferencedata_format into master

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.