28.0.0

These release notes are automatically extracted from the full changelog.

Major Changes

• export v2: The string "none" is now an invalid value for --color-by-metadata and --metadata-columns options and will be ignored to prevent clashes with Auspice's internal use of "none". #1113 (@joverlee521)
• schema: The string "none" is now an invalid branch label, node_attr key, and coloring key. #1113 (@joverlee521)
• curate apply-geolocation-rules: The geolocation rule matching has been updated to be case-insensitive. Use the new --case-sensitive flag if you want to revert to the previous behavior of case-sensitive matching. #1740, #1741 (@joverlee521)
• augur.io.read_sequences: Only accept the values "fasta" and "genbank" for format, instead of allowing any value supported by Biopython. #1731 (@victorlin)
  • This also applies to augur.io.sequences.read_single_sequence, which is not in the public API.

Features

• All commands: Support compressed formats for input sequence files. This was already the case for most commands. Internal standardization extends the support to all other commands. #1730 (@victorlin)

Bug Fixes

• When using >=Biopython 1.85: properly detect augur ancestral --root-sequence file format and, for all commands, support FASTA files with comments. #1731 (@victorlin)

Internal changes

• Added a new function augur.io.sequences.read_single_sequence as a wrapper around Bio.SeqIO.read with support for compressed formats, similar to the augur.io.sequences.read_sequences wrapper around Bio.SeqIO.parse. #1730 (@victorlin)