6.0.0

6.0.0 (10 December 2019)

Overview

Version 6 is a major release of augur affecting many augur commands. The format
of the exported JSON (v2) has changed and now merges the previously separate
files containing tree and meta information. To maintain backward compatibility,
the export command was split into export v1 (old) and export v2 (new).
Detailed release notes are provided in the augur documentation on
read-the-docs.
For a migration guide, consult
migrating-v5-v6.

Major features / changes

• export: Swap from a separate _tree.json and _meta.json to a single
  "unified" dataset.json output file
• export: Include additional command line options to alleviate need for Auspice
  config
• export: Include option for reference sequence output
• export: Move to GFF-style annotations
• export: Validate exported JSONs against schema
• ancestral: Allow output of FASTA and JSON files
• import: Include import beast command to import labeled BEAST MCC tree
• parse: Include --prettify-fields option to cleanup metadata fields
• Documentation improvements

Minor features / changes

• colors.tsv: Allow whitespace, but insist on tab delimiting
• lat_longs.tsv: Allow whitespace, but insist on tab delimiting
• Remove code for old "non-modular" augur, old "non-modular" builds and Python
  tests
• Improve test builds
• filter: More interpretable output of how many sequences have been filtered
• filter: Additional flag --subsample-seed to seed the random number generator
  and thereby make subsampling reproducible
• sequence-traits: Numerical output as originally intended, but required an
  Auspice bugfix
• traits: Explanation of what is considered missing data & how it is interpreted
• traits: GTR models are exported in the output JSON for better accountability &
  reproducibility