Nextstrain-augur

Bug Fixes

* traits: Fix crash when inferring traits with a single value. [891][] (huddlej)
* index: Properly handle missing inputs. [900][] (huddlej)
* index: Use standard UNIX-style line endings for output. [900][] (huddlej)

[891]: https://github.com/nextstrain/augur/pull/891
[900]: https://github.com/nextstrain/augur/pull/900

Major Changes

* export: Move extensions block to meta [888][] (corneliusroemer)

Note: this is technically a breaking change, but the misplaced extensions block was added in version 14.1.0 and intended for internal use by Nextclade. We don't expect any users to be impacted by this.

Features

* filter: Support relative dates for `--min-date` and `--max-date` [740][] (benjaminotter, victorlin)
* frequencies: Support relative dates for `--min-date` and `--max-date` [890][] (victorlin, huddlej)
* docs: Add page describing how to use your own tree builder [884][] (jameshadfield, joverlee521)

Bug Fixes

* parse: Fix `--fix-dates` [878][] (huddlej)
* tree: Fix internal comment on excluded sites [880][] (jameshadfield)

[888]: https://github.com/nextstrain/augur/pull/888
[740]: https://github.com/nextstrain/augur/pull/740
[890]: https://github.com/nextstrain/augur/pull/890
[884]: https://github.com/nextstrain/augur/pull/884
[878]: https://github.com/nextstrain/augur/pull/878
[880]: https://github.com/nextstrain/augur/pull/880

Features

* schemas: Extend export v2 schema to support an array of trees [851][] (tsibley)
* schemas: Add JSON schemas for our root-sequence and tip-frequencies sidecars [852][] (tsibley)
* schemas: Add JSON schema for measurements sidecar [859][] (joverlee521)
* filter: Send warnings to stderr to be consistent with other warnings [862][] (victorlin)
* export: Allow an extensions block in auspice config & dataset JSONs [865][] (jameshadfield)
* export: Allow skipping of input/output schema validation [865][] (jameshadfield)
* export: Order keys in dataset for easier reading [868][] (jameshadfield)

Bug Fixes

* parse: Fix typo in internal variable name [850][] (emmahodcroft)

[850]: https://github.com/nextstrain/augur/pull/850
[851]: https://github.com/nextstrain/augur/pull/851
[852]: https://github.com/nextstrain/augur/pull/852
[859]: https://github.com/nextstrain/augur/pull/859
[862]: https://github.com/nextstrain/augur/pull/862
[865]: https://github.com/nextstrain/augur/pull/865
[868]: https://github.com/nextstrain/augur/pull/868

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