Nextstrain-augur

Bug Fixes

* filter: Handle errors from `filter_by_query` [942][] (victorlin)
* translate: output nuc annotation when reading from gff3 gene map [976][] (corneliusroemer)
* CI: Remove step for selecting PyPI instance [974][] (victorlin)
* CI: Add token to use GitHub CLI [958][] (victorlin)

[942]: https://github.com/nextstrain/augur/pull/942
[976]: https://github.com/nextstrain/augur/pull/976
[974]: https://github.com/nextstrain/augur/pull/974
[958]: https://github.com/nextstrain/augur/pull/958

Major Changes

* filter: Error when any group-by column is not found [933][] (victorlin)
* Check your workflows for any new errors that may arise from this.
* parse: Error on duplicates instead of silently passing [918][] (victorlin)
* Check your workflows for any new errors that may arise from this.
* utils: Remove `utils.myopen()` [926][] (victorlin)
* Use `io.open_file()` going forwards.
* Moved the following internal functions [929][], [923][] (victorlin):
* `utils.read_vcf` -> `io.read_vcf`
* `utils.run_shell_command` -> `io.run_shell_command`
* `utils.shquote` -> `io.shquote`
* `utils.ambiguous_date_to_date_range` -> `dates.ambiguous_date_to_date_range`
* `utils.is_date_ambiguous` -> `dates.is_date_ambiguous`
* `utils.get_numerical_date_from_value` -> `dates.get_numerical_date_from_value`
* `utils.get_numerical_dates` -> `dates.get_numerical_dates`
* Drop support for dict type as the first parameter [934][]
* `filter.write_vcf` -> `io.write_vcf`

Features

* Add the measurements subcommand with two sub-subcommands, export and concat [879][] (joverlee521)
* filter: Report min and max date separately [930][] (victorlin)
* export v2: Allow the color scale type to be temporal [969][] (jameshadfield)
* Handle `FileNotFoundError` and unexpected exceptions gracefully [914][] (victorlin)

Bug Fixes

* filter: Properly handle error on duplicates [918][] (victorlin)
* filter: Reorganize Cram test files [943][] (victorlin)
* filter: Reword comment on vcftools [924][] (victorlin)
* io: Split io.py into smaller files under new io/ [949][] (victorlin)
* io: Add tests for `io.open_file()` [926][] (victorlin)
* Move AugurError to new errors.py, replace RuntimeError [921][] (victorlin)
* Remove internal usage of `utils.read_metadata()` [934][], [972][] (victorlin)
* schemas: Add missing display_default properties for Auspice config v2 [916][] (tsibley)
* CI: Split codecov into separate job, combine coverage of all matrix jobs [968][] (tsibley)
* CI: Temporarily disable failing test [962][] (victorlin)
* CI: pip install without editable mode [956][] (victorlin)
* CI: Include functional tests in code coverage [899][] (huddlej)
* CI: Move --quiet flag to accommodate snakemake=7.7.0 behavior [927][] (victorlin)
* CI: Move docker rebuild step to release workflow [912][] (victorlin)
* Update release process [913][] (victorlin)

[968]: https://github.com/nextstrain/augur/pull/968
[949]: https://github.com/nextstrain/augur/pull/949
[879]: https://github.com/nextstrain/augur/pull/879
[962]: https://github.com/nextstrain/augur/pull/962
[956]: https://github.com/nextstrain/augur/pull/956
[921]: https://github.com/nextstrain/augur/pull/921
[943]: https://github.com/nextstrain/augur/pull/943
[929]: https://github.com/nextstrain/augur/pull/929
[934]: https://github.com/nextstrain/augur/pull/934
[930]: https://github.com/nextstrain/augur/pull/930
[926]: https://github.com/nextstrain/augur/pull/926
[933]: https://github.com/nextstrain/augur/pull/933
[899]: https://github.com/nextstrain/augur/pull/899
[923]: https://github.com/nextstrain/augur/pull/923
[914]: https://github.com/nextstrain/augur/pull/914
[913]: https://github.com/nextstrain/augur/pull/913
[927]: https://github.com/nextstrain/augur/pull/927
[924]: https://github.com/nextstrain/augur/pull/924
[916]: https://github.com/nextstrain/augur/pull/916
[918]: https://github.com/nextstrain/augur/pull/918
[912]: https://github.com/nextstrain/augur/pull/912
[969]: https://github.com/nextstrain/augur/pull/969
[972]: https://github.com/nextstrain/augur/pull/972

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, fixing a bug caused when the user's input metadata does not have any valid strain id columns [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

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