Nextstrain-augur

Major Changes

* Updated default latitudes and longitudes for geography traits that includes location name changes. See the pull request for more details. [1744][] (joverlee521)
* curate apply-geolocation-rules: Augur's standard geolocation rules are used by default and rules provided via `--geolocation-rules` are considered custom rules that have precedence over the default rules. The `--no-default-rules` flag can be used to ignore the default rules. See the pull request for more details. [1745][] (joverlee521)
* `augur.utils.read_strains` has been removed as it's been deprecated since January 2024. The same function is available through the public API as `augur.io.read_strains`. [1749][] (joverlee521)
* Bumped minimum Python version to 3.9 as support for 3.8 was dropped in Augur v27.0.0. [1763][] (joverlee521)

Features

* refine: Added a `--remove-outgroup` flag which can be used when rooting a tree on a single taxon. Rooting and removal of outgroup will be performed before any temporal inference, if applicable. [1751][] (jameshadfield)
* Added standard geolocation rules in "augur/data/geolocation_rules.tsv" that can be used with `augur curate apply-geolocation-rules`. [1744][] (joverlee521)
* [refine, export] Ambiguous dates (e.g. those with "XX" in the date string) are now exported in the Auspice JSON, and all tips now have an additional "inferred" boolean property. These changes only apply to temporal trees. [1760][] (jameshadfield)

Bug fixes

* Certain strain names would be silently renamed by `augur tree [--method iqtree]`. We now avoid such renaming wherever possible and in cases where there are backslashes or single quotes we now raise a fatal error.
Note that names with spaces in the FASTA header (description line) continue to be modified such that everything after the first space is not used in the resulting tree. [1750][] (jameshadfield)
* Fixed the error that occurred when running `augur curate --help`. [1755][] (joverlee521)

[1744]: https://github.com/nextstrain/augur/pull/1744
[1745]: https://github.com/nextstrain/augur/pull/1745
[1749]: https://github.com/nextstrain/augur/pull/1749
[1750]: https://github.com/nextstrain/augur/pull/1750
[1751]: https://github.com/nextstrain/augur/pull/1751
[1755]: https://github.com/nextstrain/augur/pull/1755
[1760]: https://github.com/nextstrain/augur/pull/1760
[1763]: https://github.com/nextstrain/augur/pull/1763

Bug Fixes

* schema: document node property values support `url`. This feature has been supported in Auspice since v2.25.0. [1743][] (joverlee521)
* augur.io.read_metadata: Ensure that the index column's dtype is always "string" so that numeric ids don't get converted to numeric dtypes. [1746][] (joverlee521)

[1743]: https://github.com/nextstrain/augur/pull/1743
[1746]: https://github.com/nextstrain/augur/pull/1746
[1751]: https://github.com/nextstrain/augur/pull/1751

Major Changes

* export v2: The string "none" is now an invalid value for `--color-by-metadata` and `--metadata-columns` options and will be ignored to prevent clashes with Auspice's internal use of "none". [1113][] (joverlee521)
* schema: The string "none" is now an invalid branch label, node_attr key, and coloring key. [1113][] (joverlee521)
* curate apply-geolocation-rules: The geolocation rule matching has been updated to be case-insensitive. Use the new `--case-sensitive` flag if you want to revert to the previous behavior of case-sensitive matching. [1740][], [1741][] (joverlee521)
* `augur.io.read_sequences`: Only accept the values `"fasta"` and `"genbank"` for format, instead of allowing any value supported by Biopython. [1731][] (victorlin)
* This also applies to `augur.io.sequences.read_single_sequence`, which is not in the public API.

Features

* All commands: Support compressed formats for input sequence files. This was already the case for most commands. Internal standardization extends the support to all other commands. [1730][] (victorlin)

Bug Fixes

* When using >=Biopython 1.85: properly detect `augur ancestral --root-sequence` file format and, for all commands, support FASTA files with comments. [1731][] (victorlin)

Internal changes

* Added a new function `augur.io.sequences.read_single_sequence` as a wrapper around `Bio.SeqIO.read` with support for compressed formats, similar to the `augur.io.sequences.read_sequences` wrapper around `Bio.SeqIO.parse`. [1730][] (victorlin)

[1113]: https://github.com/nextstrain/augur/pull/1113
[1730]: https://github.com/nextstrain/augur/pull/1730
[1731]: https://github.com/nextstrain/augur/pull/1731
[1740]: https://github.com/nextstrain/augur/pull/1740
[1741]: https://github.com/nextstrain/augur/pull/1741

Features

* export: Added a new option `--warning` to display a warning banner in Auspice, supported as of Auspice version 2.62.0. [1722][] (victorlin)

[1722]: https://github.com/nextstrain/augur/issues/1722

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)

[1688]: https://github.com/nextstrain/augur/pull/1688
[1690]: https://github.com/nextstrain/augur/pull/1690
[1707]: https://github.com/nextstrain/augur/issues/1707
[1712]: https://github.com/nextstrain/augur/pull/1712
[1715]: https://github.com/nextstrain/augur/pull/1715
[1716]: https://github.com/nextstrain/augur/pull/1716
[1718]: https://github.com/nextstrain/augur/pull/1718

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)

[1358]: https://github.com/nextstrain/augur/issues/1358
[1691]: https://github.com/nextstrain/augur/pull/1691
[1692]: https://github.com/nextstrain/augur/pull/1692
[1693]: https://github.com/nextstrain/augur/pull/1693