Nextstrain-augur

Major Changes

* Drop support for Python 3.6, add support for 3.9 and 3.10 [822][] (victorlin)

Features

* refine: Enable bootstrap support by passing confidence values through to Auspice JSONs from `augur refine` node data JSONs [839][] (huddlej)
* tree: Allow users to override default tree builder arguments with a new `--override-default-args` flag [839][] (huddlej)
* clades: Allow descendant clades to be defined by explicitly inheriting from ancestral clade names [846][] (corneliusroemer)

Bug Fixes

* tree: Fix segmentation fault that can occur when user-provided tree builder args conflict hardcoded defaults for IQ-TREE's. The new `--override-default-args` flag allows users to override the defaults that conflict with their values. [839][] (huddlej)
* filter/utils: fix year-only and numeric date handling [841][] (victorlin)
* CI: test earliest supported Biopython versions in matrix, remove redundant installs [843][] (victorlin)

[822]: https://github.com/nextstrain/augur/pull/822
[841]: https://github.com/nextstrain/augur/pull/841
[843]: https://github.com/nextstrain/augur/pull/843
[846]: https://github.com/nextstrain/augur/pull/846
[839]: https://github.com/nextstrain/augur/pull/839

Features

Bug Fixes

* filter: Set default filter priority to negative infinity instead of 0. [835][] (huddlej)
* filter: Cast strains to list when subsetting metadata to prevent pandas FutureWarning. [833][] (victorlin)
* export v2: Allow periods (.) in accession numbers. [832][] (tsibley)

[835]: https://github.com/nextstrain/augur/pull/835
[833]: https://github.com/nextstrain/augur/pull/833
[832]: https://github.com/nextstrain/augur/pull/832

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