Nextstrain-augur

Bug Fixes

* Fix typo with Python classifiers in setup.py

Major Changes

* Drop support for Python 3.4 and 3.5 [482][]
* Drop support for `--output` flag in augur ancestral, clades, sequence-traits, traits, and translate in favor of `--output-node-data` flag [529][]

Features

* improve testing by
* adding a simple shell script to run tests and improving pytest configuration and output [463][]
* adding code coverage reports ([486][], [491][]) and integration with codecov.io [508][]
* adding unit tests for align ([477][]), filter ([478][], [479][], [487][]), utils ([501][])
* align: reverse complement sequences when necessary using mafft’s autodirection flag [467][]
* align: speed up replacement of gaps with “ambiguous” bases [474][]
* mask: add support for FASTA input files [493][]
* traits: bump TreeTime version to 0.7.4 and increase maximum number of unique traits allowed from 180 to 300 [495][]

Bug Fixes

* align: enable filling gaps in input sequences even if no reference is provided instead of throwing an exception [466][]
* align: detect duplicate sequences by comparing sequence objects instead of (often truncated) string representations of those objects [468][]
* import_beast: use raw strings for regular expressions to avoid syntax errors in future versions of Python [469][]
* scripts: update exception syntax to new style [484][]
* filter: fail loudly when a given priority file is invalid and exit instead of just printing an error [487][]

Documentation

* README: document need for brew tap prior to brew install [471][]
* DEV_DOCS: add a proper section on how to write and run tests [481][]
* README: improve discoverability of core documentation with RTD badge [490][]

[463]: https://github.com/nextstrain/augur/pull/463/
[466]: https://github.com/nextstrain/augur/pull/466
[467]: https://github.com/nextstrain/augur/pull/467
[468]: https://github.com/nextstrain/augur/pull/468
[469]: https://github.com/nextstrain/augur/pull/469
[471]: https://github.com/nextstrain/augur/pull/471
[474]: https://github.com/nextstrain/augur/pull/474
[477]: https://github.com/nextstrain/augur/pull/477
[478]: https://github.com/nextstrain/augur/pull/478
[479]: https://github.com/nextstrain/augur/pull/479
[481]: https://github.com/nextstrain/augur/pull/481
[482]: https://github.com/nextstrain/augur/pull/482
[484]: https://github.com/nextstrain/augur/pull/484
[486]: https://github.com/nextstrain/augur/pull/486
[487]: https://github.com/nextstrain/augur/pull/487
[490]: https://github.com/nextstrain/augur/pull/490
[491]: https://github.com/nextstrain/augur/pull/491
[493]: https://github.com/nextstrain/augur/pull/493
[495]: https://github.com/nextstrain/augur/pull/495
[501]: https://github.com/nextstrain/augur/pull/501
[508]: https://github.com/nextstrain/augur/pull/508
[529]: https://github.com/nextstrain/augur/pull/529

Bug Fixes

* align: Remove reference sequence from alignments even when no gaps exist in
input sequences relative to the reference. Thank you danielsoneg!
[456][]

Documentation

* Reorganize README, improve findability of documentation, and add separate dev
docs.
[461][]

[456]: https://github.com/nextstrain/augur/pull/456
[461]: https://github.com/nextstrain/augur/pull/461

Bug Fixes

* Require Snakemake less than 5.11 to avoid a breaking change. The `--cores`
argument is now required by 5.11, which will affect many existing augur-based
workflows. Reported upstream as
[snakemake/snakemake283](https://github.com/snakemake/snakemake/issues/283).

* align: Run mafft with the `--nomemsave` option. This makes alignments of
sequences over 10k in length run much, much faster in the general case and
shouldn't cause issues for most modern hardware. We may end up needing to
add an off-switch for this mode if it causes issues for other users of augur,
but the hope is that it will make things just magically run faster for most
folks! There is likely more tuning that could be done with mafft, but this
is a huge improvement in our testing.
[458][]

* align: Ignore blank lines in `--include` files. Thanks CameronDevine!
[451][]

* align: Properly quote filenames when invoking mafft. Thanks CameronDevine!
[452][]


[451]: https://github.com/nextstrain/augur/pull/451
[452]: https://github.com/nextstrain/augur/pull/452
[458]: https://github.com/nextstrain/augur/pull/458

Bug Fixes

* export: AA labels are now exported for branches where a clade is also labeled
[See PR 447](https://github.com/nextstrain/augur/pull/447)

* export / validation: a dataset title is no longer required

* release script now works on MacOS & code-signing is optional
[See PR 448](https://github.com/nextstrain/augur/pull/448)

* traits: Missing data is correctly handled

Features

* align: New sequences can now be added to an existing alignment. [422][]

* align: Multiple sequence files can be provided as input. [422][]

* align: Extra debugging files such as `*.pre_aligner.fasta` and
`*.post_aligner.fasta` are no longer produced by default. To request them,
pass the `--debug` flag. [422][]

* align: De-duplicate input sequences, with a warning. [422][]

* export v2: Add support for the `branch_label` property in `display_defaults`,
which was recently added to Auspice. [445][]

Bug fixes

* align: Exits with an error earlier if arguments are invalid instead of only
printing a warning. [422][]

* align: Performs more error checking and clarifies the help and error
messages. [422][]

* export v2: Traits which are filters but not colorings are now exported as
well, instead of being left out. [442][]

* export v2: Exits non-zero when validation fails, instead of masking errors.
[441][]

* validate: In order to improve clarity, messages now include the filenames
involved and distinguish between schema validation and internal consistency
checks. [441][]

[422]: https://github.com/nextstrain/augur/pull/422
[441]: https://github.com/nextstrain/augur/pull/441
[442]: https://github.com/nextstrain/augur/pull/442
[445]: https://github.com/nextstrain/augur/pull/445