Use xarray/netCDF4 throughout the pipeline (!30) · Merge requests · Chris Jewell / covid19uk · GitLab

This is an archived project. Repository and other project resources are read-only.

GitLab now enforces expiry dates on tokens that originally had no set expiration date. Those tokens were given an expiration date of one year later. Please review your personal access tokens, project access tokens, and group access tokens to ensure you are aware of upcoming expirations. Administrators of GitLab can find more information on how to identify and mitigate interruption in our documentation.

Chris Jewell requested to merge add_inferencedata_format into master Mar 04, 2021

CHANGES

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