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.