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

5.4.0

5.4.0 (7 November 2019)

Features

• frequencies: Include --minimal-clade-size-to-estimate command line option.
  See PR 383
• lbi: Include --no-normalization command line option.
  See PR 380

Compatibility fixes

• export: Include v1 subcommand to allow forwards compatibiliy with Augur v6 builds.
  See PR 398

Bug fixes

• export: Include warning if using a mismatched v6 translate file.
  See PR 392
• frequencies: Fix determination of interval for clipping of non-informative pivots

5.3.0

5.3.0 (9 September 2019)

Features

• export: Improve printing of error messages with missing or conflicting author
  data. See issue 274
• filter: Improve printing of dropped strains to include reasons why strains were
  dropped. See PR 367
• refine: Add support for command line flag --keep-polytomies to not resolve
  polytomies when producing a time tree.
  See PR 345

Bug fixes

• Catch and throw error when there are duplicate strain names.
  See PR 356
• Fix missing annotation of "parent" attribute for the root node
• Run shell commands with more robust error checking.
  See PR 350
• Better handling of rerooting options for trees without temporal information.
  See issue 348

Data

• Small fixes in geographic coordinate file

5.2.1

5.2.1 (4 August 2019)

Bug fixes

• Print more useful error message if Python recursion limit is reached.
  See issue 328
• Print more useful error message if vcftools if missing.
  See PR 312

Development

• Significantly relax version requirements specified in setup.py for biopython,
  pandas, etc... Additionally, move lesser used packages (cvxopt, matplotlib,
  seaborn) into an "extras_require" field. This should reduce conflicts with
  other pip installed packages.
  See PR 323

Data

• Include additional country lat/longs in base data

5.2.0

5.2.0 (23 July 2019)

Features

• ancestral: Adds a new flag --output-sequences and logic to support saving
  ancestral sequences and leaves from the given tree to a FASTA file. Also adds a
  redundant, more specific flag --output-node-data that will replace the current
  --output flag in the next major version release of augur. For now, we issue a
  deprecation warning when the --output flag is used. Note that FASTA output is
  only allowed for FASTA inputs and not for VCFs. We don't allow FASTA output for
  VCFs anywhere else and, if we did here, the output files would be very large.
  See PR 293

• frequencies: Allow --method kde flag to compute frequencies via KDE kernels.
  This complements existing method of --method diffusion. Generally, KDE
  frequencies should be more robust and faster to run, but will not project as
  well when forecasting frequencies into the future.
  See PR 271

Bug fixes

• ancestral, traits, translate: Print warning if supplied tree is missing internal
  node names (normally provided by running augur refine).
  See PR 283

• Include pip in Conda enviroment file.
  See PR 309

Documentation

• Document environment variables respected by Augur

Development

• Remove matplotlib and seaborn from setup.py install. These are still called a
  few places in augur (like titers.validate()), but it was deemed rare enough
  that remove this from setup.py would ease general install for most users.
  Additionally, the ipdb debugger has been moved to dev dependencies.
  See PR 291

• Refactor logic to read trees from multiple formats into a function. Adds a new
  function read_tree to the utils module that tries to safely handle reading
  trees in multiple input formats.
  See PR 310

5.1.1

5.1.1 (1 July 2019)

Features

• tree: Add support for the GTR+R10 substitution model.
• tree: Support parentheses in node names when using IQ-TREE.

Bug fixes

• Use the center of the UK for its coordinates instead of London.
• filter: Mark --output required, which it always was but wasn't marked.
• filter: Avoid error when no excluded strains file is provided.
• export: Fix for preliminary version 2 schema support.
• refine: Correct error handling when the tree file is missing or empty.

Documentation

• Add examples of Augur usage in the wild.
• Rename and reorganize CLI and Python API pages a little bit to make "where do
  I start learning to use Augur?" clearer to non-devs.

Development

• Relax version requirements of pandas and seaborn. The hope is this will make
  installation smoother (particularly alongside other packages which require
  newer pandas versions) while not encountering breaking changes in newer
  versions ourselves.

5.1.0

5.1.0 (29 May 2019)

Documentation

• Documentation is now available online for the augur CLI and Python API via
  Read The Docs: https://nextstrain-augur.readthedocs.io. The latest
  version on RTD points to the git master branch, and the stable version to
  the most recent tagged release. Instructions for building the docs locally
  are in the README.

5.0.0

5.0.0 (26 May 2019)

Features

• ancestral: New option to --keep-ambiguous, which will not infer nucleotides at
  ambiguous (N) sites on tip sequences and instead leave as 'N'
  See PR 280.
• ancestral: New option to --keep-overhangs, which will not infer nucleotides for
  gaps on either side of the alignment and instead leave as '-'.
  See PR 286.
• clades: This module has been reconfigured to identify clade defining mutations on
  top of a reference rather than identifying mutations along the tree. The command
  line arguments are the same except for the addition of --reference, which
  explicitly passes in a reference sequence. If --reference is not defined, then
  reference will be drawn from the root node of the phylogeny by looking for
  sequence attribute attached to root node of --tree.
  See PR 288.
• refine: Revise rooting behavior. Previously --root took 'best', 'residual', 'rsq'
  and 'min_dev' as options. In this update --root takes 'best', least-squares',
  'min_dev' and 'oldest' as rooting options. This eliminates 'residual' and 'rsq'
  as options. This is a backwards-incompatible change. This requires updating
  TreeTime to version 0.5.4 or above.
  See PR 263.
• refine: Add --keep-root option that overrides --root specification to preserve
  tree rooting.
  See PR 263.
• refine: Add --covariance and --no-covariance options that specify TreeTime
  behavior.
  See PR 263.
• titers: This command now throws an InsufficientDataException if there are not
  sufficient titers to infer a model. This is paired with a new --allow-empty-model
  flag that proceeds past the InsufficientDataException and writes out a model
  JSON corresponding to an 'empty' model.
  See PR 281.
• By default JSONs are written with index=1 to give a pretty-printed JSON. However,
  this adds significant file size to large tree JSONs. If the environment variable
  AUGUR_MINIFY_JSON is set then minified JSONs are printed instead. This mirror the
  explicit --minify-json argument available to augur export.
  See PR 278.

Bug fixes

• export: Cast numeric values to strings for export.
  See issue 287.
• export: Legend order preserves ordering passed in by user for traits that have
  default colorings ('country' and 'region').
  See PR 284.
• refine: Previously, the --root argument was silently ignored when no timetree
  was inferred. Re-rooting with an outgroup is sensible even without a timetree.
  See PR 282.

4.0.0

4.0.0 (24 April 2019)

Features

• distance: New interface for specifying distances between sequences. This is
  a backwards-incompatible change. Refer to augur distance --help for
  all the details.

• export: Add a --minify-json flag to omit indentation in Auspice JSONs.

Bug fixes

• frequencies: Emit one-based coordinates (instead of zero-based) for KDE-based
  mutation frequencies

Data

• Include additional country lat/longs in base data