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PopPUNK v2.4.0

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@johnlees johnlees released this 23 Mar 17:32
· 1241 commits to master since this release
v2.4.0
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Learn about vigilant mode.

Minimum sketchlib version for this release is v1.7.0

To use --gpu-graph requires cudf and cugraph to be installed from the nvidia conda channel, which is not part of the standard installation)

New features:

  • Adds minimum spanning tree computation and visualisation #141 #148
  • Add two new network scores based on betweenness #146
  • Move boundary code into a C++ extension in this package #146 #158
  • Adds GPU accelerated graphs #87 #148
  • Adds a docker container which is used for web.poppunk.net #151 #162
  • New github actions for testing and building the web API #151
  • Add progress bars in for model assignment #155
  • Parallelise model assignment #155
  • Adds the VLKC terminology, and 'unword' cluster names #161

Bug fixes:

  • Correctly specify thread count with rapidnj #139
  • Regenerate random match changes after --update-db #149
  • Fix issue with label order when using --update-db more than once #152
  • Update some scripts/ to work with newer versions of numpy and scikit-learn #160
  • Keep hyphens in sample names in trees #159
  • Fix a plot name #158
  • Pin some package versions #140 #142
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