31.0.0

These release notes are automatically extracted from the full changelog.

Major Changes

• augur mask --mask, augur tree --exclude-sites: BED files with inconsistent CHROM values (i.e., values in the first column of data lines) will throw an error, as Augur (implicitly) expects to be working on a single piece of DNA (chromosome, segment, etc), and multiple CHROM values in a BED file indicate a violation of this expectation. This is a breaking change. #945 (@genehack)
• filter: Empty values in the metadata id column will result in an error that can only be resolved by editing the metadata file or by specifying a different id column with --metadata-id-columns. #1807 (@joverlee521)

Bug fixes

• augur mask --mask, augur tree --exclude-sites: Providing an empty BED file, or one with only header lines and no data lines, will no longer cause an error to be thrown. #945 (@genehack)
• augur.utils.read_bed_file() was rewritten for increased compliance with the BED file specification. In particular, header line dectection is improved and multiple header lines are now supported. #945 (@genehack)
• export v2: Improved the error message that is displayed when the metadata index column has duplicated values #1791 (@genehack)
• tree: Improved help text for --tree-builder-args to explain some IQ-TREE options won't work because of defline rewriting #875 (@genehack)
• export v2: Automatically rename fields within the filters and colorings configs of the provided auspice config file to match the renamed fields in the exported nodes. #1804 (@joverlee521)
• export v2: Divergence values are now exported with increased precision, showing up to 6 significant digits instead of 3. #1801 (@rneher)