Nextstrain-augur

Bug Fixes

* dependencies: Relax upper bounds on development dependencies. [821][] and [830][] (victorlin, huddlej)
* refine: Inform users when their requested root sequence is not present in the alignment. [816][] (corneliusroemer)
* utils: Fix crash with `read_metadata` when numexpr is installed. [826][] (victorlin)

[816]: https://github.com/nextstrain/augur/pull/816
[821]: https://github.com/nextstrain/augur/pull/821
[826]: https://github.com/nextstrain/augur/pull/826
[830]: https://github.com/nextstrain/augur/pull/830

Features

* schemas: Add "$id" key to Auspice config schemas so we have a way of referring to these. [806][] (tsibley)

Bug Fixes

* filter: Fix groupby with incomplete dates. [808][] (victorlin)

[806]: https://github.com/nextstrain/augur/pull/806
[808]: https://github.com/nextstrain/augur/pull/808

Bug Fixes

* dependencies: Replace deprecated mutable sequence interface for BioPython. [788][] (Carlosbogo)
* dependencies: Fix backward compatibility with BioPython. [801][] (huddlej)
* data: Add latitude and longitude details for "Reunion". [791][] (corneliusroemer)
* filter: Use pandas functions to determine subsample groups. [794][] and [797][] (victorlin)
* filter: Add clarity to help message and output of probabilistic sampling. [792][] (victorlin)

[788]: https://github.com/nextstrain/augur/pull/788
[791]: https://github.com/nextstrain/augur/pull/791
[792]: https://github.com/nextstrain/augur/pull/792
[794]: https://github.com/nextstrain/augur/pull/794
[797]: https://github.com/nextstrain/augur/pull/797
[801]: https://github.com/nextstrain/augur/pull/801

Bug Fixes

* tree: Handle compressed alignment when excluding sites. [786][] (huddlej)
* docs: Fix typos ([ce0834c][]) and clarify exclude sites inputs ([5ad1574][]). (corneliusroemer)

[786]: https://github.com/nextstrain/augur/pull/786
[ce0834c]: https://github.com/nextstrain/augur/commit/ce0834c476abc9ee99785fa930608218b7d78990
[5ad1574]: https://github.com/nextstrain/augur/commit/5ad157485015623883c6b637d247459f906b63cb

Bug Fixes

* dependencies: Support latest versions of BioPython. [777][] (huddlej)
* tree: Allow users to specify arbitrary IQ-TREE models. [776][] (huddlej)

[776]: https://github.com/nextstrain/augur/pull/776
[777]: https://github.com/nextstrain/augur/pull/777

Bug Fixes

* docs: Fix broken link to latitude/longitude documentation. [766][] (victorlin)
* filter: Fix reproducibility of subsampling by using the user-defined random seed in all random function calls and by ordering strain sets as lists prior to adding strains to group-by priority queues. [772][] (huddlej)

[766]: https://github.com/nextstrain/augur/pull/766
[772]: https://github.com/nextstrain/augur/pull/772