31.4.0

These release notes are automatically extracted from the full changelog.

Features

• schema: Allow parentheses (()) in gene names. #1819 (@kimandrews)
• geolocation rules: Add rules to define region per country to ensure that regions are labelled for all countries. This is especially useful for data sources that do not include region in the metadata. #1844 (@joverlee521)
• support numpy v2 in addition to v1. #1855 (@corneliusroemer)
• support for Python 3.13. #1857 (@corneliusroemer)
• tree: Prefer iqtree3 binary over iqtree2 and iqtree when available. #1875 (@joverlee521)
• export v2: URLs encoded in metadata (both TSV and node-data JSONs) will be associated with the value in the exported JSON. Given a column/key <X> then a valid URL in a column/key named <X>__url will be automatically used. This allows values to be a clickable link when viewed in Auspice. #1852 (@jameshadfield)

Bug fixes

• filter: Improved speed of using --group-by month on large datasets. #1845 (@victorlin)
• merge: Added validation to require at least two sequence inputs for merging, consistent with metadata merging behavior. #1865 (@victorlin)
• validate: Send all log messages to stderr. #1869 (@victorlin)
• validate: only print the entire merged Auspice config to stderr when there's a validation error. #1878(@joverlee521)