Nextstrain-augur

Bug Fixes

* index: Remove call to deprecated BioPython SeqIO.close method [684][]

[684]: https://github.com/nextstrain/augur/pull/684

Bug Fixes

* filter: Retry probabilistic subsampling when it doesn't select any samples [676][]
* titers: Skip infinite log titer values caused by zero-valued raw titers [677][]
* setup: Include license file with distribution artifacts instead of Python installation root [678][]

[676]: https://github.com/nextstrain/augur/pull/676
[677]: https://github.com/nextstrain/augur/pull/677
[678]: https://github.com/nextstrain/augur/pull/678

Bug Fixes

* align/utils: Improve external command errors [638][]
* filter: Fix parsing of priorities files to allow spaces in sequence IDs [668][]
* utils: Ensure columns `strain` and `name` in metadata get parsed as strings [669][]

Features

* index/filter: Add new `index` subcommand and optional `--sequence-index` argument for `filter` command to enable filtering without inspecting sequences [651][]
* titers: Bump supported cvxopt version to latest 1.* release [671][]

[638]: https://github.com/nextstrain/augur/pull/638
[651]: https://github.com/nextstrain/augur/pull/651
[668]: https://github.com/nextstrain/augur/pull/668
[669]: https://github.com/nextstrain/augur/pull/669
[671]: https://github.com/nextstrain/augur/pull/671

Major Changes

* filter: Use probabilistic sampling by default when requesting a maximum number of sequences to subsample with `--subsample-max-sequences`. Adds `--no-probabilistic-sampling` flag to disable this default behavior and prevent users from requesting fewer maximum sequences than there are subsampling groups. [659][]

[659]: https://github.com/nextstrain/augur/pull/659

Bug Fixes

* scripts: Fix typo in `verify_meta_json.py` [656][] (felixonmars)
* CI: Use the expected Python version in conda environments [658][]
* CI: Minimize codecov feedback [661][]

Features

* frequencies: Add `--pivot-interval-units` argument with support for weekly pivots [660][]
* frequencies: Add support for ISO dates for `--min-date` and `--max-date` arguments [660][]

[656]: https://github.com/nextstrain/augur/pull/656
[658]: https://github.com/nextstrain/augur/pull/658
[660]: https://github.com/nextstrain/augur/pull/660
[661]: https://github.com/nextstrain/augur/pull/661

Features

* filter: Add `--probablistic-sampling` flag to allow subsampling with `--subsample-max-sequences` when the number of groups exceeds the requested number of samples [629][]
* scripts: Add script to identify emerging clades from existing Nextstrain build JSONs [653][]
* docs: Add instructions to update conda installations prior to installing Augur [655][]

[629]: https://github.com/nextstrain/augur/pull/629
[653]: https://github.com/nextstrain/augur/pull/653
[655]: https://github.com/nextstrain/augur/pull/655