Nextstrain-augur

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

Bug Fixes

* dependencies: Require the most recent minor versions of TreeTime (0.8.X) to fix numpy matrix errors [633][]

[633]: https://github.com/nextstrain/augur/pull/633

Features

* docs: Migrate non-reference documentation to docs.nextstrain.org [620][]
* filter: Add `--exclude-ambiguous-dates-by` flag to enable exclusion of samples with ambiguous dates [623][] and [631][]

[620]: https://github.com/nextstrain/augur/pull/620
[623]: https://github.com/nextstrain/augur/pull/623
[631]: https://github.com/nextstrain/augur/pull/631

Bug Fixes

* tree: Use a more generic approach to escape special characters from alignment sequence names prior to running IQ-TREE [625][]
* filter: Reduce memory usage by not reading sequences into memory [627][]

[625]: https://github.com/nextstrain/augur/pull/625
[627]: https://github.com/nextstrain/augur/pull/627

Bug Fixes

* refine: Report divergence by number of mutations as an integer instead of a floating point value [618][]
* validate: Allow internal nodes with a single child and do not allow duplicate node names [621][]

[618]: https://github.com/nextstrain/augur/pull/618
[621]: https://github.com/nextstrain/augur/pull/621