feat(ingest): Use augur curate to curate country metadata

[anna-parker]

resolves #

preview URL: https://add-country-metadata.loculus.org/

Summary

Prompted by work in #2991, this uses augur curate for formatting.

Screenshot

PR Checklist

• All necessary documentation has been adapted.
• The implemented feature is covered by an appropriate test

micromamba activate pp-integrity
cd tests/regression-testing 
snakemake results/ebola-zaire.meta.format-authors.add-country-metadata.diff 
snakemake results/cchf.meta.format-authors.add-country-metadata.diff 
snakemake results/west-nile.meta.format-authors.add-country-metadata.diff 

[anna-parker]

Sadly with further testing this no longer seems like a good approach:

1. It requires a python downgrade and tedious refactor of our code
2. augur curate splits the geoLocCountry field in NCBI into country: division, location. For samples where this is incorrect it will only curate them if there is an exact match in the config. For example Conneticut/Hartford is curated as Conneticut/Hartford but not Connecticut/xxx unless it is also in the config. It also does not catch cases where the state has been replaced with an abbreviation (unless that exact case is in the config), the division and location field is not clearly split, or the order of division and location has been inverted unless if the exact case is specified in the config, e.g. these states show in the location field: