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Empress 1.2.0: New features, bug fixes, and other improvements

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@fedarko fedarko released this 20 Jul 22:08
· 11 commits to master since this release
v1.2.0
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New features

  • Add optional "abbreviated" parameters for EMPress' standalone CLI (#481)
  • Add more detailed options for choosing when to show node circles; the new default is showing circles just for internal nodes with exactly one child (#486, #527)
  • Add a new color map, Green-LightOrange-Purple (#483)
  • Add the ability to dynamically shear the tree based on feature metadata (#490, #492, #505)
  • Adjust the way taxonomy feature metadata is handled so that more specific levels of the taxonomy (e.g. c__Bacilli) include all ancestral levels of the taxonomy (e.g. k__Bacteria; p__Firmicutes; c__Bacilli) (#487)
    • This makes it easier to distinguish general metadata values like g__, and matches the behavior in q2-taxa's taxonomy barplots.
  • Automatically adjust the main legend's size when changing tree coloring (#512)
  • Limit the speed of zooming slightly to make navigation easier on certain computers (#516)
  • Use the excellent toastr library to support showing multiple (now color-coded by error, warning, etc.!) toast messages at once (#519)

Documentation

  • Fix some broken image links in the README when viewed on PyPI (#478)
  • Add citation for EMPress' recent publication in mSystems (#493, #494)
  • Add important details to standalone EMPress installation instructions (#495)
  • Adjust the levels of headers used in the README (#507)
  • Update screenshots and README text (#535)

Bug fixes

  • Fix an error that was thrown when creating an EMPire plot using a biplot ordination without providing feature metadata (#485)
  • Fix a bug that occurred when running EMPress outside of QIIME 2 (#495)
  • Fix a bug that was thrown when running tree-plot with the --shear-to-feature-metadata parameter but without passing feature metadata (#525)

Performance improvements

  • Speed up tree coloring (#505)
  • Cache parent nodes to speed up various functionality (#505)

Development improvements

  • Add a new GitHub Actions workflow for specifically testing running EMPress outside of QIIME 2 (#499)
  • Various updates to the GitHub Actions workflows (#498, #502, #523)
  • Simplify iteration over the tree in the code (#492)

🌴 ✂️ 🚖 🍞 🪲 📚

rn4

Acknowledgements

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

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