3.0.5.dev1 (26 November 2018)
- translate: Nucleotide ("nuc") annotation for non-bacterial builds starts at 0 again, not 1, fixing a regression.
- Schemas: Correct coordinate system description for genome start/end annotations.
3.0.4.dev1 (26 November 2018)
- validate: Fix regression for gene names containing an asterisk.
- Fix Travis CI tests which were silently not running.
3.0.3.dev1 (26 November 2018)
refine: Add a
traits: Add a
--sampling-bias-correctionoption 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.
filter: Only consider A, T, C, and G when calculating sequence length for the
filter: Allow comments in files passed to
filter: Ignore case when matching trait values against excluded values.
Normalize custom geographic names to lower case for consistent matching.
Fix typo in geographic entry for
Schemas: Reconcile naming patterns used in gene definitions and tree annotations.
Upgrade TreeTime dependency to 0.5.x and at least 0.5.1.
environment.ymlfile for use with
conda env create.
Stop testing under Python 2.7 on Travis CI.
3.0.2.dev1 (27 September 2018)
- translate: Fix broken
3.0.1.dev1 (27 September 2018)
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.
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
auguris run without arguments.
Briefly describe each command in its
--helpoutput and in the global
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.
- Geographic coordinates added for the Netherlands and the Philippines.
releasebranch when rewinding a failed local release process.
Refactor the augur program and command architecture for improved maintainability.
3.0.0.dev3 (4 September 2018)
Use an allowed Topic classifier so we can upload to PyPi
Ignore distribution egg-info build files
3.0.0.dev2 (4 September 2018)
Export: Add safety checks for optional annotations and geo data
Include more lat/longs in the default geo data
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.
- Start versioning augur beginning with 3.0.0. A new
augur versioncommand reports the running version.