Empress 0.2.0: Alpha Release

• Add a --p-filter-extra-samples parameter for use with tandem plots that removes samples present in the table but not in the ordination
  • Added information to the README about selecting tables for use with tandem plots, and the various tradeoffs of this choice
• Enhance Empress / Emperor integration: now, clicking on a tip node in Empress in a tandem plot highlights samples in Emperor containing the corresponding feature (or, for an internal node, clicking on the node highlights samples that contain at least one of the descendant tips)
• Fix styling issues:
  • Add scrollbars when the side panel gets taller than the screen, or when node names get longer than the menu box
  • Clean up the tandem plot interface: remove the scrollbar on the side of the screen and add a clear dividing vertical line
  • Add a maximum width to certain selection elements
• Add a new "Tree Properties" tab in the side panel with:
  • The ability to re-center the camera
  • The ability to toggle node circles on and off
• Replace references to "node ID" with "node name", to be consistent with Newick file / scikit-bio conventions
• Alert user if no unique features can be colored (#239)
• Position node selection menus more intuitively
• Various performance / storage improvements:
  • Encode data for the balanced parentheses structure in a more efficient manner (#228)
  • Compress feature table and sample / feature metadata information to take up less space in the visualization
• Add more comprehensive tests
• Various bug fixes
• Miscellaneous code improvements

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Acknowledgements

This work is supported by IBM Research AI through the AI Horizons Network. For more information visit the IBM AI Horizons Network website.