Nextstrain-augur

Bug Fixes

* Fix Python 3.11 installation for Conda environments. [1334][] (victorlin)
* Bump `pyfastx` dependency to major versions 1 and 2. [1335][] (victorlin)

[1334]: https://github.com/nextstrain/augur/issues/1334
[1335]: https://github.com/nextstrain/augur/pull/1335

Features

* Support treetime 0.11.* [1310][] (corneliusroemer)
* export: Allow minimal export using only a (newick) tree in `augur export v2`. [1299][] (jameshadfield)
* A number of schema updates and improvements [1299][] (jameshadfield)
* We now require all nodes to have `node_attrs` on them with one of `div` or `num_date` present
* Some never-used properties are removed from the schemas, including a pattern for defining nucleotide INDELs which was never used by augur or auspice.
* Tip label defaults are now settable within the auspice-config JSON
* Empty colorings definitions are allowed (the tree will be grey in Auspice)

Bug fixes

* ancestral: Export amino acid sequences inferred for the root node of the tree in the node data JSON output for compatibility with `augur translate` output. [1317][] (huddlej)

[1299]: https://github.com/nextstrain/augur/pull/1299
[1310]: https://github.com/nextstrain/augur/pull/1310
[1317]: https://github.com/nextstrain/augur/pull/1317

Major Changes

* Drop support for Python 3.7. [1296][] (victorlin)

Features

* export v2: Allow the root-sequence data to be included (inlined) in the main dataset JSON file, avoiding the need for a sidecar `_root-sequence.json` file. [1295][] (jameshadfield)

[1295]: https://github.com/nextstrain/augur/pull/1295
[1296]: https://github.com/nextstrain/augur/pull/1296

Features

* refine: Export covariance matrix and standard deviation for clock rate regression in the node data JSON output when these values are calculated by TreeTime. These new values appear in the `clock` data structure of the JSON output as `cov` and `rate_std` keys, respectively. [1284][] (huddlej)

Bug fixes

* clades: Fix outputs for genes named `NA` (previously the value was replaced by `nan`). [1293][] (rneher)
* distance: Improve documentation by describing how gaps get treated as indels and how users can ignore specific characters in distance calculations. [1285][] (huddlej)
* Fix help output compatibility with non-Unicode streams. [1290][] (victorlin)

[1284]: https://github.com/nextstrain/augur/pull/1284
[1285]: https://github.com/nextstrain/augur/pull/1285
[1290]: https://github.com/nextstrain/augur/pull/1290
[1293]: https://github.com/nextstrain/augur/pull/1293

Features

* ancestral: add functionality to reconstruct ancestral amino acid sequences and add inferred mutations to the `node_data_json` with output equivalent to `augur translate`. `ancestral` now takes an annotation (`--annotation`), a list of genes (`--genes`), and a file name pattern for amino acid alignments (`--translations`). Mutations for each of these genes will be inferred and added to the output JSON to each node as a list at `['aa_muts'][gene]`. The annotations will be added to the `annotation` field in the output JSON. Inferred amino acids sequences can be saved with the new `--output-translations` argument. [1258][] (rneher, huddlej)
* ancestral: add the ability to report mutations relative to a sequence other than the inferred root of the tree. This sequence can be specified via `--root-sequence` and difference between this sequence and the inferred root of the tree will be added as mutations to the root node for nucleotides and amino acids. All differences between the specified `root-sequence` and the inferred sequence of the root node of the tree will be added as mutations to the root node. This was previously already possible for `vcf` input via `--vcf-reference`. [1258][] (rneher)
* refine: add `mid_point` as rooting option to `refine`. [1257][] (rneher)

Bug fixes

* filter: In version 22.2.0, `--query` would fail when the `.str` accessor was used on a column. This has been fixed. [1277][] (victorlin)

[1257]: https://github.com/nextstrain/augur/pull/1257
[1258]: https://github.com/nextstrain/augur/pull/1258
[1277]: https://github.com/nextstrain/augur/issues/1277

Features

* Adds a new sub-command augur curate titlecase. The titlecase command is intended to apply titlecase to string fields in a metadata record (e.g. BRAINE-LE-COMTE, FRANCE -> Braine-le-Comte, France). Previously, this was available in the transform-string-fields script within the monkeypox repo.
[1197][] (j23414 and joverlee521)

[1197]: https://github.com/nextstrain/augur/pull/1197

Bug fixes

* export v2: Previously, when `strain` was not used as the metadata ID column, node attributes might have gone missing from the final Auspice JSON. This has been fixed. [1260][], [1262][] (victorlin, joverlee521)
* export v1: Added a deprecation warning for this command. [1265][] (victorlin)
* export v1: The recently introduced flag `--metadata-id-columns` did not work properly due to the same `export v2` bug that was fixed in this release. Instead of fixing it in `export v1`, drop the broken feature since this command is no longer being maintained. [1265][] (victorlin)
* filter: Expose internal Pandas errors from `--query` which may be useful to users. [1267][] (victorlin)
* filter: Previously, `--query` would fail when numerical comparisons were used on columns with missing values. This has been fixed. [1269][] (victorlin)

[1260]: https://github.com/nextstrain/augur/issues/1260
[1262]: https://github.com/nextstrain/augur/issues/1262
[1265]: https://github.com/nextstrain/augur/pull/1265
[1267]: https://github.com/nextstrain/augur/pull/1267
[1269]: https://github.com/nextstrain/augur/issues/1269