Pathogen-embed

Features

* pathogen-cluster-mutations: Add this new top-level command to allow users to create a table of mutations that appear in clusters or other previously defined genetic groups ([36][])

[36]: https://github.com/blab/pathogen-embed/pull/36

Major Changes

* pathogen-embed: Use "simplex" encoding by default for PCA ([35][])
* pathogen-cluster: Change default minimum number of samples for a cluster from 5 to 10 ([35][])

[35]: https://github.com/blab/pathogen-embed/pull/35

Features

* pathogen-cluster: Add `--distance-matrix` input argument to support HDBSCAN clustering of genetic distances from `pathogen-distance` ([33][])

[33]: https://github.com/blab/pathogen-embed/pull/33

Bug Fixes

* Do not internally sort embedding inputs by sequence name ([32][])
* Let scikit-learn automatically pick SVD algorithm to use for PCA instead of hardcoding the "full" solver ([31][])

[31]: https://github.com/blab/pathogen-embed/pull/31
[32]: https://github.com/blab/pathogen-embed/pull/32

Features

* admin: Publish to PyPI with GitHub Actions ([30][])

Bug Fixes

* Use inferred types for external embedding parameters ([29][])

[29]: https://github.com/blab/pathogen-embed/pull/29
[30]: https://github.com/blab/pathogen-embed/pull/30

Features

* Add alternate encodings of nucleotide sequences for PCA in `pathogen-embed` ([23][])

[23]: https://github.com/blab/pathogen-embed/pull/23