Nextstrain-augur

Major Changes

* measurements export: Supports exporting multiple thresholds per collection via the measurements config and the `--thresholds` option. This change is backwards compatible with previous uses of the `--threshold` option. However, due to the updates to the JSON schema, users will need to update to Auspice v2.43.0 for thresholds to be displayed properly in the measurements panel. [1148][] (joverlee521)

Features

* export v2: Add `--validation-mode={error,warn,skip}` option for more nuanced control of validation. The new "warn" mode performs validation and emits messages about potential problems, but it does not cause the export command to fail even if there are problems. [1135][] (tsibley)

Bug Fixes

* filter, frequencies, refine, parse: Properly handle invalid date errors and output the bad date. [1140][] (victorlin)
* export, validate: Validation errors are now much more human-readable and actually pinpoint the problems. [1134][] (tsibley)

[1134]: https://github.com/nextstrain/augur/pull/1134
[1135]: https://github.com/nextstrain/augur/pull/1135
[1140]: https://github.com/nextstrain/augur/pull/1140
[1148]: https://github.com/nextstrain/augur/pull/1148

Major Changes

* frequencies: Changes the logic for calculating the time points when frequencies are estimated to ensure that the user-provided "end date" is always included. This change in the behavior of the frequencies command fixes a bug where large intervals between time points (e.g., 3 months) could cause recent data to be omitted from frequency calculations. See the pull request for more details included the scientific implications of this bug. [1121][] (huddlej)

[1121]: https://github.com/nextstrain/augur/pull/1121

Features

* titers: Support parsing of thresholded values (e.g., "<80" or ">2560"). [1118][] (huddlej)
* tree: Support bootstrapped trees generated with RAxML via user-provided `--tree-builder-args`. [1127][] (tsibley)

Bug Fixes

* utils: Serialize common numpy data types in `write_json`. [1119][] (victorlin)
* filter: Standardize exit codes from internal error handling. [931][] (victorlin)
* tree: Suppress the `Cannot specify --substitution-model unless using IQTree` warning when `--substitution-model` is left at its default. [1127][] (tsibley)
* tree: Print the underlying error message when tree building fails. [1127][] (tsibley)
* Previously, `numpy` and `scipy` were installed as dependencies of dependencies. Mark them as direct dependencies since they are used directly within Augur. [1120][] (victorlin)

[931]: https://github.com/nextstrain/augur/pull/931
[1118]: https://github.com/nextstrain/augur/pull/1118
[1119]: https://github.com/nextstrain/augur/pull/1119
[1120]: https://github.com/nextstrain/augur/pull/1120
[1127]: https://github.com/nextstrain/augur/pull/1127

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