Nextstrain-augur

Features

* titers: Allow users to specify a custom prefix for attributes in the JSON output (e.g., `cTiter` can be changed to `custom_prefix_cTiter`). [1106][] (huddlej)

[1106]: https://github.com/nextstrain/augur/pull/1106

Features

* io: Add `open_file` and `write_sequences` to the Python Pubic API. [1114][] (joverlee521)

[1114]: https://github.com/nextstrain/augur/pull/1114

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