17.1.0

Features

• refine: Upgrade TreeTime from 0.8.6 to >= 0.9.2 which enables a speedup of timetree inference in marginal mode due to the use of Fast Fourier Transforms #1018. (@rneher and @anna-parker)

Bug Fixes

• refine, export v1: Use pandas.DataFrame.at instead of .loc for single values #979. (@victorlin)
• refine: Gracefully handle all exceptions from TreeTime #1023. (@anna-parker)
• refine: Document branch length units treetime expects #1024. (@anna-parker)
• dates: Raise an error when metadata to get_numerical_dates() is not a pandas DataFrame #1026. (@victorlin)

17.0.0

17.0.0 (9 August 2022)

Major Changes

• Moved the following modules to subpackages #1002. (@joverlee521)
  These are technically breaking changes for the API, but they do not change the Augur CLI commands.
  • import.py -> import_/__init__.py
  • import_beast.py -> import_/beast.py
  • measurements.py -> measurements/__init__.py + measurements/concat.py + measurements/export.py
• Move the following internal functions/classes #1002. (@joverlee521)
  • augur.add_default_command -> argparse_.add_default_command
  • utils.HideAsFalseAction -> argparse_.HideAsFalseAction
• Subcommands must include a register_parser function to add their own parser instead of a register_arguments function #1002. (@joverlee521)
• utils: Remove internal function utils.read_metadata() #978. (@victorlin)
  • Use io.read_metadata() going forwards.
  • To switch to using metadata as a pandas DataFrame (recommended):
    • Iterate through strains: metadata.items() -> metadata.iterrows()
    • Check strain presence: strain in metadata -> strain in metadata.index
    • Check field presence: field in metadata[strain] -> field in metadata.columns
    • Get metadata for a strain: metadata[strain] -> metadata.loc[strain]
    • Get field for a strain: metadata[strain][field] -> metadata.at[strain, field]
  • To keep using metadata in a dictionary:

    metadata = read_metadata(args.metadata)
    metadata.insert(0, "strain", metadata.index.values)
    columns = metadata.columns
    metadata = metadata.to_dict(orient="index")

Features

• export: --skip-validation now also skips version compatibility checks #902. (@corneliusroemer)
• filter: Report names of duplicate strains found during metadata parsing #1008 (@huddlej)
• translate: Add support for Nextclade gene map GFFs #1017 (@huddlej)

Bug Fixes

• filter: Rename internal force inclusion filtering functions #1006 (@victorlin)

16.0.3

16.0.3 (6 July 2022)

Bug Fixes

• filter: Move register_arguments to the top of the module for better readability #995. (@victorlin)
• filter: Fix a regression introduced in 16.0.2 that caused grouping with subsampled max sequences and force-included strains to fail in a data-specific way #1000. (@huddlej)

16.0.2

16.0.2 (30 June 2022)

Bug Fixes

• The entropy panel was unavailable if mutations were not translated #881. This has been fixed by creating an additional annotations block in augur ancestral containing (nucleotide) genome annotations in the node-data #961 (@jameshadfield)
• ancestral: WARNINGs to stdout have been updated to print to stderr #961 (@jameshadfield)
• filter: Explicitly drop date/year/month columns from metadata during grouping. #967 (@victorlin)
  • This fixes a bug #871 where augur filter would crash with a cryptic ValueError if year and/or month is a custom column in the input metadata and also included in --group-by.
• filter: Fix duplicates that may appear in metadata when using --include/--include-where with subsampling #986 (@victorlin)

6.3.0

Features

• Augur refine, ancestral and traits now use the
  upgraded TreeTime v0.7
  This should have a number of under-the-hood improvements.
  See PR 431
• ancestral: New options to either --keep-ambiguous or --infer-ambiguous. If using
  --infer-ambiguous the previous behavior will be maintained in which tips with N will have
  their nucleotide state inferred. If using --keep-ambiguous, these tips will be left as N.
  With this upgrade, we are still defaulting to --infer-ambiguous, however, we plan to swap
  default to --keep-ambiguous in the future. If this distintion matters to you, we would suggest
  that you explicitly record --keep-ambiguous / --infer-ambiguous in your build process.
  Also part of PR 431
• traits: Allow input of --weights which references a .tsv file in the following format:

  division	Hubei	10.0
  division	Jiangxi	1.0
  division	Chongqing	1.0
  

  where these weights represent equilibrium frequencies in the CTMC transition model. We imagine the
  primary use of user-specified weights to correct for strong sampling biases in available data.
  See PR 443

Bug fixes

• Improvements to make shell scripts run more easily on Windows.
  See PR 437

6.2.0

Features

• refine: Include --divergence-units option to distinguish between mutations
  and mutations-per-site. Keep mutations-per-site as default behavior.
  See PR 435

Bug fixes

• utils: Support v2 auspice JSONs in json_to_tree utility function.
  See PR 432

6.1.1 (17 December 2019)

Bug fixes

• frequencies: Fix bug in string matching for weighted frequencies introduced in
  v6.1.0. See PR 426.

6.1.1

6.1.1 (17 December 2019)

Bug fixes

• frequencies: Fix bug in string matching for weighted frequencies introduced in
  v6.1.0. See PR 426.

6.1.0

6.1.0 (13 December 2019)

Features

• export: Include --description option to pass in a Markdown file with dataset
  description. This is displays in Auspice in the footer. For rationale,
  see Auspice issue 707 and
  for Augur changes see PR 423.

Bug fixes

• frequencies: Fix weighted frequencies when weight keys are unrepresented.
  See PR 420.

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

5.4.1

5.4.1 (12 November 2019)

Bug fixes

• export v1: Include --minify-json option that was mistakenly not included in PR 398.
  See PR 409