NEXT

3.0.5.dev1 (26 November 2018)

Bug fixes

• translate: Nucleotide ("nuc") annotation for non-bacterial builds starts at 0 again, not 1, fixing a regression.

Documentation

• Schemas: Correct coordinate system description for genome start/end annotations.

3.0.4.dev1 (26 November 2018)

Bug fixes

• validate: Fix regression for gene names containing an asterisk.

Development

• Fix Travis CI tests which were silently not running.

3.0.3.dev1 (26 November 2018)

Features

• refine: Add a --clock-std-dev option

• traits: Add a --sampling-bias-correction option for mugration model

• validate: Gene names in tree annotations may now contain hyphens. Compatible with Auspice version 1.33.0 and later.

• All JSON is now emitted with sorted keys, making it easier to diff and run other textual comparisons against output.

Bug fixes

• filter: Only consider A, T, C, and G when calculating sequence length for the --min-length option.

• filter: Allow comments in files passed to --exclude.

• filter: Ignore case when matching trait values against excluded values.

• Normalize custom geographic names to lower case for consistent matching.

Data

• Fix typo in geographic entry for netherlands.

• Schemas: Reconcile naming patterns used in gene definitions and tree annotations.

Development

• Upgrade TreeTime dependency to 0.5.x and at least 0.5.1.

• Add an environment.yml file for use with conda env create.

• Stop testing under Python 2.7 on Travis CI.

3.0.2.dev1 (27 September 2018)

Bug fixes

• translate: Fix broken --help message

3.0.1.dev1 (27 September 2018)

Features

• align and tree: The --nthreads option now accepts the special value "auto" to automatically set the number of threads to the number of CPU cores available.

• Alias augur --version to augur version

Bug fixes

• tree: The --nthreads option is now respected. Previously all tree builders were ignoring the value and using either 2 threads (RAxML, IQ-TREE) or as many threads as cores (FastTree, if the OpenMP version).

• translate: Check for and, if necessary pad, nucleotide sequences which aren't a multiple of 3 earlier to avoid errors later.

• export: Optionally write inferred nucleotide and amino acid sequences (or mutations) to a separate file.

• export: Omit genes with no amino acid mutations.

• validate: Allow underscores in gene names.

• refine: Remove unused --nthreads argument.

• ancestral, filter, tree, refine: Exit 1 instead of -1 on error.

• Print the help message, instead of throwing an exception, when augur is run without arguments.

Documentation

• Briefly describe each command in its --help output and in the global augur --help output.

• Revamp README to emphasize new, modular augur and make it suitable for inclusion on PyPi.

• Reconciled conflicting license declarations; augur is AGPLv3 (not MIT) licensed like the rest of Nextstrain.

• Include URLs for bug reports, the change log, and the source on PyPi.

Data

• Geographic coordinates added for the Netherlands and the Philippines.

Development

• Reset the release branch when rewinding a failed local release process.

• Refactor the augur program and command architecture for improved maintainability.

3.0.0.dev3 (4 September 2018)

Development

• Use an allowed Topic classifier so we can upload to PyPi

• Ignore distribution egg-info build files

3.0.0.dev2 (4 September 2018)

Features

• Export: Add safety checks for optional annotations and geo data

• Include more lat/longs in the default geo data

Development

• Add release tooling

• Document the release process and a few development practices

• Travis CI: Switch to rebuilding the Docker image only for new releases

• Remove ebola, lassa, tb, WNV, and zika builds now in their own repos. These builds are now available at URLs like https://github.com/nextstrain/ebola, for example.

3.0.0.dev1 (unreleased)

Development

• Start versioning augur beginning with 3.0.0. A new augur version command reports the running version.