29.0.0

These release notes are automatically extracted from the full changelog.

Major Changes

• Updated default latitudes and longitudes for geography traits that includes location name changes. See the pull request for more details. #1744 (@joverlee521)
• curate apply-geolocation-rules: Augur's standard geolocation rules are used by default and rules provided via --geolocation-rules are considered custom rules that have precedence over the default rules. The --no-default-rules flag can be used to ignore the default rules. See the pull request for more details. #1745 (@joverlee521)
• augur.utils.read_strains has been removed as it's been deprecated since January 2024. The same function is available through the public API as augur.io.read_strains. #1749 (@joverlee521)
• Bumped minimum Python version to 3.9 as support for 3.8 was dropped in Augur v27.0.0. #1763 (@joverlee521)

Features

• refine: Added a --remove-outgroup flag which can be used when rooting a tree on a single taxon. Rooting and removal of outgroup will be performed before any temporal inference, if applicable. #1751 (@jameshadfield)
• Added standard geolocation rules in "augur/data/geolocation_rules.tsv" that can be used with augur curate apply-geolocation-rules. #1744 (@joverlee521)
• [refine, export] Ambiguous dates (e.g. those with "XX" in the date string) are now exported in the Auspice JSON, and all tips now have an additional "inferred" boolean property. These changes only apply to temporal trees. #1760 (@jameshadfield)

Bug fixes

• Certain strain names would be silently renamed by augur tree [--method iqtree]. We now avoid such renaming wherever possible and in cases where there are backslashes or single quotes we now raise a fatal error.
  Note that names with spaces in the FASTA header (description line) continue to be modified such that everything after the first space is not used in the resulting tree. #1750 (@jameshadfield)
• Fixed the error that occurred when running augur curate --help. #1755 (@joverlee521)