27.1.0

These release notes are automatically extracted from the full changelog.

Features

• ancestral: Add --seed argument to enable deterministic inference of root states by TreeTime. #1690 (@huddlej)

Bug Fixes

• ancestral, refine: Explicitly specify how the root and ambiguous states are handled during sequence reconstruction and mutation counting. #1690 (@rneher)
• titers: Fix type errors in code associated with cross-validation of models. #1688 (@huddlej)
• export: The help text for --lat-longs has been improved with a link to the defaults and specifics around the overriding behavior. #1715 (@victorlin)
• augur.io.read_metadata: Pandas versions <1.4.0 prevented this function from properly setting the index column's data type. Support for those older versions has been dropped. #1716 (@victorlin)
• In version 24.4.0, one of the new features was that all options that take multiple values could be repeated. Unfortunately, it overlooked a few that have been fixed in this version. #1707 (@victorlin)
  • augur curate rename --field-map
  • augur curate transform-strain-name --backup-fields
• augur curate format-dates --expected-date-formats help text has been improved with clarifications regarding how values provided interact with builtin formats and how to match masked date parts. #1707, #1718 (@victorlin)
• parse: Transform strain names the same way in both metadata and sequences instead of only transforming sequences. #1712 (@huddlej)