Include more prepare-data options #61
Description
As part of nextstrain/forecasts-ncov#134, I'm comparing the evofr prepare-data command to the forecasts-ncov script prepare-data.py.
TODOs
Add missing config options
There are some options that are missing in the evofr command. They are included in the testing config, but are not used in the prepare-data command:
- location_min_seq
- location_min_seq_days
- clade_min_seq
- clade_min_seq_days
- excluded_locations
Port over latest changes
The --force-include-clades option for the prepare-data.py script has been updated to take a TSV file of clade/variant (see changes in the PR)
Port over additional tests
Current test checks that the output files are created but does not verify the contents of the files. We can port over some version of the Cram tests from forecasts-ncov to ensure the prepare-data command outputs the expected data.