List view
### Bug Fixes * filter: Move `register_arguments` to the top of the module for better readability [#995][]. (@victorlin) * filter: Fix a regression introduced in 16.0.2 that caused grouping with subsampled max sequences and force-included strains to fail in a data-specific way [#1000][]. (@huddlej) [#995]: https://github.com/nextstrain/augur/pull/995 [#1000]: https://github.com/nextstrain/augur/pull/1000
No due date•2/2 issues closed- No due date•6/6 issues closed
- No due date•7/7 issues closed
https://github.com/nextstrain/augur/pull/959
No due date•23/23 issues closed## Bug Fixes * docs: Fix API documentation rendering and add page for `io` module [#896][] (@joverlee521) * CI: Use GitHub Actions for release process [#904][] (@victorlin) * utils: Fix branch length annotations in `json_to_tree` function [#908][] (@huddlej) * export v2: Use io.read_metadata during export [#909][] (@huddlej) * CI: Call new GitHub Actions workflow to rebuild images [#910][] (@victorlin) [#910]: https://github.com/nextstrain/augur/pull/910 [#909]: https://github.com/nextstrain/augur/pull/909 [#908]: https://github.com/nextstrain/augur/pull/908 [#904]: https://github.com/nextstrain/augur/pull/904 [#896]: https://github.com/nextstrain/augur/pull/896
No due date•5/5 issues closed### 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
No due date•2/2 issues closed### 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
No due date•7/7 issues closed### Major Changes * Drop support for Python 3.6, add support for 3.9 and 3.10 [#822][] ### Features * refine: Enable bootstrap support by passing confidence values through to Auspice JSONs from `augur refine` node data JSONs [#839][] * tree: Allow users to override default tree builder arguments with a new `--override-default-args` flag [#839][] * clades: Allow descendant clades to be defined by explicitly inheriting from ancestral clade names [#846][] ### 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][] * filter/utils: fix year-only and numeric date handling [#841][] * CI: test earliest supported Biopython versions in matrix, remove redundant installs [#843][] [#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
No due date•5/5 issues closed- No due date•3/3 issues closed
- No due date•4/4 issues closed
- No due date•2/2 issues closed
- No due date•6/6 issues closed
- No due date•1/1 issues closed
- No due date•2/2 issues closed
- No due date•2/2 issues closed
- No due date•1/1 issues closed
- No due date•2/2 issues closed
### 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
No due date•6/6 issues closed- No due date•10/10 issues closed
- No due date•6/6 issues closed
- No due date•6/6 issues closed
- No due date•5/5 issues closed
- No due date•1/1 issues closed
- No due date•3/3 issues closed
- No due date•5/5 issues closed
- No due date•1/1 issues closed
- No due date•4/4 issues closed
- Due by November 16, 2020•1/1 issues closed
- No due date•3/3 issues closed
- No due date•3/3 issues closed
- Due by November 6, 2020•2/2 issues closed
- Due by October 26, 2020•2/2 issues closed
Bug fix release for BioPython dependencies.
No due date•1/1 issues closedPatch release with bug fixes
Due by August 28, 2020•1/1 issues closedIssues and PRs to be released as part of version 10.0.0.
Due by August 14, 2020•11/11 issues closed