as_epi_archive doesn't preserve keys from a keyed data.table or epi_df

[kenmawer]

What should be discussed is to what extent as_epi_archive should retain already defined keys in a keyed data.table or epi_df.

[brookslogan]

it looks like we have a few unwanted behaviors:

• keyed data.table + no other_keys arg --> we ignore the current key & replace with default geo time version
• epi_df with other_keys + no other_keys arg --> same deal
• epi_df with additional metadata --> no $additional_metadata

(Some of these may currently be tested for, but unwanted. We should alter+add tests accordingly.)

We should probably aim for something like the following:

• If user provides other_keys arg, just use that as the archive's other keys.
• If user does not provide other_keys arg:
  • If x is an epi_df, set archive other keys as something like c(setdiff(attr(x,"metadata")$other_keys, "version"), "version")
  • If x is a keyed data.table, check that they key includes geo&time value (error if not), then set archive other keys to c(setdiff(key(x), c("geo_value","time_value","version")), "version")
  • If x is an unkeyed data.table, use character(0L) as the archive other keys