Nextstrain-augur

Major Changes

* io: Only `read_metadata` and `read_sequences` are available as part of the Python Public API. Other Python API functions of the `augur.io` module are no longer directly available. This is a breaking change, although we suspect few users to be impacted. If you still need to use other imports in your scripts, they can be imported from the [Developer API](https://docs.nextstrain.org/projects/augur/en/stable/api/developer/index.html) but note that they are no longer part of the [Public API](https://docs.nextstrain.org/projects/augur/en/stable/api/public/index.html). [#1087][] (victorlin)

Bug Fixes

* docs: Update the API documentation to reflect the latest state of things in the codebase. [1087][] (victorlin)
* Fix support for Biopython version 1.80 which deprecated `Bio.Seq.Seq.ungap()`. [1102][] (victorlin)
* export v2: Fixed a bug where colorings for zero values via `--colors` would not get applied to the exported Auspice JSON. [1100][] (joverlee521)
* curate: Fixed a bug where metadata TSVs failed to parse if data within a column included comma separated values [1110][] (joverlee521)

[1087]: https://github.com/nextstrain/augur/pull/1087
[1100]: https://github.com/nextstrain/augur/pull/1100
[1102]: https://github.com/nextstrain/augur/pull/1102
[1110]: https://github.com/nextstrain/augur/pull/1110

Features

* Add the curate subcommand with two sub-subcommands, passthru and normalize-strings. The curate subcommand is intended to be a suite of commands to help users with data curation prior to running Nextstrain analyses. We will continue to add more subcommands as we identify other common data curation tasks. Please see the [usage docs](https://docs.nextstrain.org/projects/augur/en/stable/usage/cli/curate) for details. [#1039][] (joverlee521)

[1039]: https://github.com/nextstrain/augur/pull/1039

Bug Fixes

* traits: Fix trait inference when tips have missing values. [1081][] (huddlej)

[1081]: https://github.com/nextstrain/augur/pull/1081

Bug Fixes

* filter: Fixed a bug where `--group-by week` would fail when all samples in a chunk have been dropped due to ambiguous dates. [1080][] (victorlin)

[1080]: https://github.com/nextstrain/augur/pull/1080

Features

* filter: Add support to group by ISO week (`--group-by week`) during subsampling. [1067][] (victorlin)

Bug Fixes

* filter: Fixed unintended behavior in which grouping by `day` would "work" when used with `month` and/or `year`. Updated so it will be ignored. [1070][] (victorlin)
* filter: Fixed unintended behavior in which grouping by `month` with ambiguous years would "work". Updated so date ambiguity is checked properly for all generated columns. [1072][] (victorlin)

[1067]: https://github.com/nextstrain/augur/pull/1067
[1070]: https://github.com/nextstrain/augur/pull/1070
[1072]: https://github.com/nextstrain/augur/pull/1072

Major Changes

* export: The `--node-data` option may now be given multiple times to provide additional `.json` files. Previously, subsequent occurrences of the option overrode prior occurrences. This is a **breaking change**, although we expect few usages to be impacted. Each occurrence of the option may still specify multiple files at a time. [1010][] (tsibley)

Bug Fixes


* refine: 17.1.0 updated TreeTime to version 0.9.2 and introduced the `refine` flag `--use-fft`. This makes previously costly marginal date inference cheaper. This update adjusts when `refine` runs marginal date inference during its iterative optimization. Without the `use-fft` flag, it will now behave as it did before 17.1.0 (marginal inference only during final iterations). With the `--use-fft` flag, marginal date inference will be used at every step during the iteration if refine is run with `--date-inference marginal` [1034][]. (rneher)
* tree: When using IQtree as tre builder, `--nthreads` now sets the maximum number of threads (IQtree argument `-ntmax`). The actual number of threads to use can be specified by the user through the tree-builder-arg `-nt` which defaults to `-nt AUTO`, causing IQtree to automatically chose the best number of threads to use [1042][] (corneliusroemer)
* Make cvxopt as a required dependency, since it is required for titer models to work [1035][]. (victorlin)
* filter: Fix compatibility with Pandas 1.5.0 which could cause an unexpected `AttributeError` with an invalid `--query` given to `augur filter`. [1050][] (tsibley)
* refine: Add `--verbosity` argument that is passed down to TreeTime to facilitate monitoring and debugging. [1033][] (anna-parker)
* Improve handling of errors from TreeTime. [1033][] (anna-parker)

[1010]: https://github.com/nextstrain/augur/pull/1010
[1033]: https://github.com/nextstrain/augur/pull/1033
[1034]: https://github.com/nextstrain/augur/pull/1034
[1035]: https://github.com/nextstrain/augur/pull/1035
[1042]: https://github.com/nextstrain/augur/pull/1042
[1050]: https://github.com/nextstrain/augur/pull/1050