27.2.0

These release notes are automatically extracted from the full changelog.

Features

• export: Added a new option --warning to display a warning banner in Auspice, supported as of Auspice version 2.62.0. #1722 (@victorlin)

27.1.0

These release notes are automatically extracted from the full changelog.

Features

• ancestral: Add --seed argument to enable deterministic inference of root states by TreeTime. #1690 (@huddlej)

Bug Fixes

• ancestral, refine: Explicitly specify how the root and ambiguous states are handled during sequence reconstruction and mutation counting. #1690 (@rneher)
• titers: Fix type errors in code associated with cross-validation of models. #1688 (@huddlej)
• export: The help text for --lat-longs has been improved with a link to the defaults and specifics around the overriding behavior. #1715 (@victorlin)
• augur.io.read_metadata: Pandas versions <1.4.0 prevented this function from properly setting the index column's data type. Support for those older versions has been dropped. #1716 (@victorlin)
• In version 24.4.0, one of the new features was that all options that take multiple values could be repeated. Unfortunately, it overlooked a few that have been fixed in this version. #1707 (@victorlin)
  • augur curate rename --field-map
  • augur curate transform-strain-name --backup-fields
• augur curate format-dates --expected-date-formats help text has been improved with clarifications regarding how values provided interact with builtin formats and how to match masked date parts. #1707, #1718 (@victorlin)
• parse: Transform strain names the same way in both metadata and sequences instead of only transforming sequences. #1712 (@huddlej)

27.0.0

These release notes are automatically extracted from the full changelog.

Major Changes

• Drop support for Python 3.8. #1693 (@victorlin)
• Drop support for older versions of jsonschema (<4.18.0). #1691 (@victorlin)
• Drop support for xopen <2.0.0. #1692 (@victorlin)

Bug fixes

• export: validation will no longer crash with KeyError: 'tree' when newer versions of jsonschema (≥4.18.0) are installed. #1358 (@victorlin)

26.2.0

These release notes are automatically extracted from the full changelog.

Features

• This is the first version to officially support Python 3.12 and Pandas v2. #1671 #1678 (@corneliusroemer, @victorlin)
• curate: change output metadata to RFC 4180 CSV-like TSVs to match the TSV format output by other Augur subcommands and the Nextstrain ecosystem as discussed in #1566. #1565 (@joverlee521)

26.1.0

These release notes are automatically extracted from the full changelog.

Features

• ancestral, translate: Add --skip-validation as an alias to --validation-mode=skip. #1656 (@victorlin)
• clades: Allow customizing the validation of input node data JSON files with --validation-mode and --skip-validation. #1656 (@victorlin)
• tree: When using iqtree, check for all synonyms of default args when detecting potential conflicts, e.g. --threads-max is equivalent to -ntmax. Previously, we were only checking for the latter. Also use new, preferred IQtree2 option names (e.g. --polytomy instead of -czb etc.). #1547 (@corneliusroemer)

Bug Fixes

• index: Previously specifying a directory that does not exist in the path to --output would result in an incorrect error stating that the input file does not exist. It now shows the correct path responsible for the error. #1644 (@victorlin)
• curate format-dates: Update help docs and improve failure messages to show use of --expected-date-formats. #1653 (@joverlee521)

26.0.0

These release notes are automatically extracted from the full changelog.

Major Changes

• filter: Duplicate header names in the FASTA file (--sequences) will now result in an error. #1613 (@victorlin)
• parse: When both strain and name fields are present, the strain field will now be used as the sequence ID field. #1629 (@victorlin)
• merge: Generated source columns (e.g. __source_metadata_{NAME}) are now omitted by default. They may be explicitly included with --source-columns=TEMPLATE or explicitly omitted with --no-source-columns. This may be a breaking change for any existing uses of augur merge relying on the generated columns, though as augur merge is relatively new we believe usage to be scant if extant at all. #1625 #1632 (@tsibley)

Bug Fixes

• filter: Previously, when --subsample-max-sequences was slightly lower than the number of groups, it was possible to fail with an uncaught AssertionError. Internal calculations have been adjusted to prevent this from happening. #1588 #1598 (@victorlin)

25.4.0

These release notes are automatically extracted from the full changelog.

Features

• merge: Table-specific id columns and delimiters may now be specified, e.g. --metadata-id-columns X=id Y=strain and --metadata-delimiters X=, Y=';', to allow more precise behaviour and avoid ordering issues. #1594 (@tsibley)

Bug Fixes

• filter: Improved warning and error messages in the case of missing columns. #1604 (@victorlin)
• merge: Any user-customized ~/.sqliterc file is now ignored so it doesn't break augur merge's internal use of SQLite. #1608 (@tsibley)
• merge: Non-id columns in metadata inputs that would conflict with the output id column are now forbidden and will cause an error if present. Previously they would overwrite values in the output id column, causing incorrect output. #1593 (@tsibley)
• import: Spaces in BEAST MCC tree annotations (for example, from a discrete state reconstruction) no longer break augur import beast's parsing. #1610 (@watronfire)

25.3.0

These release notes are automatically extracted from the full changelog.

Features

• A new command, augur merge, now allows for generalized merging of two or more metadata tables. #1563 (@tsibley)
• Two new commands, augur read-file and augur write-file, now allow external programs to do i/o like Augur by piping from/to these new commands. They provide handling of compression formats and newlines consistent with the rest of Augur. #1562 (@tsibley)
• A new debugging mode can be enabled by setting the AUGUR_DEBUG environment variable to 1 (or any non-empty value). Currently the only effect is to print more information about handled (i.e. anticipated) errors. For example, stack traces and parent exceptions in an exception chain are normally omitted for handled errors, but setting this env var includes them. Future debugging and troubleshooting features, like verbose operation logging, will likely also condition on this new debugging mode. #1577 (@tsibley)
• filter: Added the ability to use weights in subsampling. See help text of --group-by-weights and the updated Filtering and Subsampling guide for more information. #1454 (@victorlin)

Bug Fixes

• Embedded newlines in quoted field values of metadata files read/written by many commands, annotation files read by augur curate apply-record-annotations, and index files written by augur index are now properly handled. #1561 #1564 (@tsibley)
• Output written to stderr (e.g. informational messages, warnings, errors, etc.) is now always line-buffered regardless of the Python version in use. This helps with interleaved stderr and stdout. Previously, stderr was block-buffered on Python 3.8 and line-buffered on 3.9 and higher. #1563 (@tsibley)

25.2.0

These release notes are automatically extracted from the full changelog.

Features

• export v2: we now limit numerical precision on floats in the JSON. This should not change how a dataset is displayed / interpreted in Auspice but allows the gzipped & minimised JSON filesize to be reduced by around 30% (dataset-dependent). #1512 (@jameshadfield)
• traits, export v2: augur traits now reports all confidence values above 0.1% rather than limiting them to the top 4 results. There is no change in the eventual Auspice dataset as augur export v2 will still only consider the top 4. #1512 (@jameshadfield)
• curate: Excel (.xlsx and .xls) and OpenOffice (.ods) spreadsheet files are now also supported as metadata inputs (--metadata). The first sheet in the workbook is read as tabular data. #1550 (@tsibley)

Bug Fixes

• titers sub: Fixes a bug where antigenic weights were assigned to branches for substitutions in the incorrect order of <derived allele><position><ancestral allele> instead of <ancestral allele><position><derived allele>. #1555 (@huddlej)

25.1.1

These release notes are automatically extracted from the full changelog.

Bug Fixes

• curate parse-genbank-location: Fix a bug where a mix of empty and populated location-field values would result in inconsistent fields in the output NDJSON #1531(@genehack)