25.0.0

These release notes are automatically extracted from the full changelog.

Major changes

• curate format-dates: Raises an error if provided date field does not exist in records. #1509 (@joverlee521)
• All curate subcommands: Verifies all input records have the same fields and raises an error if a record does not have matching fields. #1518 (@joverlee521)

Features

• Added a new sub-command augur curate apply-geolocation-rules to apply user curated geolocation rules to the geolocation fields in a metadata file. Previously, this was available as a script within the nextstrain/ingest repo. #1491 (@victorlin)
• Added a default color for the "Asia" region that will be used in augur export is no custom colors are provided. #1490 (@joverlee521)
• Added a new sub-command augur curate apply-record-annotations to apply user curated annotations to existing fields in a metadata file. Previously, this was available as a merge-user-metadata in the nextstrain/ingest repo. #1495 (@joverlee521)
• Added a new sub-command augur curate abbreviate-authors to abbreviate lists of authors to " et al." Previously, this was avaliable as the transform-authors script within the nextstrain/ingest repo. [#1483][] (@genehack)
• Added a new sub-command augur curate parse-genbank-location to parse the geo_loc_name field from GenBank reconds. Previously, this was available as the translate-genbank-location script within the nextstrain/ingest repo. [#1485][] (@genehack)
• curate format-dates: Added defaults to --expected-date-formats so that ISO 8601 dates (%Y-%m-%d) and its various masked forms (e.g. %Y-XX-XX) are automatically parsed by the command. #1501 (@joverlee521)
• Added a new sub-command augur curate transform-strain-name to filter strain names based on matching a regular expression. Previously, this was available as the transform-strain-names script within the nextstrain/ingest repo. #1514 (@genehack)
• Added a new sub-command augur curate rename to rename field / column names. Previously, a similar version was available as the transform-field-names script within the nextstrain/ingest repo however the behaviour is slightly changed here. #1506 (@jameshadfield)

Bug Fixes

• filter: Improve speed of checking duplicates in metadata, especially for large files. #1466 (@victorlin)
• curate: Stop adding double quotes to the metadata TSV output when field values have internal quotes. #1493 (@joverlee521)
• curate format-dates: Mask empty date values as XXXX-XX-XX to represent unknown dates. #1509 (@joverlee521)