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One Codex Python Library updated to 0.17.0

The onecodex python library and CLI has been updated with the following changes.
Added
  • Adds
    SampleCollection.beta_diversity_stats()
    to test for significant differences between groups of samples based on their beta diversity distances (global and posthoc pairwise PERMANOVA tests are supported)
  • Adds categorical data palette to
    onecodex
    Altair theme
  • Adds support for passing both
    facet_by
    and
    secondary_haxis
    to
    plot_metadata()
  • Adds filtering and warning if samples are missing abundances in
    plot_metadata()
    ,
    plot_pcoa()
    ,
    plot_mds()
    ,
    plot_pca()
    ,
    alpha_diversity_stats()
    , and
    beta_diversity_stats()
  • Adds docs about Shannon diversity being calculated using log base 2 instead of base
    e
Changed
  • Upgrades Altair to 5.4.1 and replaces
    altair_saver
    with
    vl-convert
  • Upgrades
    notebook
    to 6.5.7
  • Upgrades
    WeasyPrint
    to 63.0
  • Removes
    node
    and
    vega
    npm dependencies
  • Removes
    jupyter-client
    dependency
  • Removes
    selenium
    dependency
  • Removes pinned
    pydyf
    version
Fixed
  • Fixes
    Api()
    call when Altair is not installed
  • Fixes scikit-bio and pandas warnings
  • Improves error message and docstring in
    SampleCollection.to_df(normalize=False)
Deprecated
  • Deprecates
    AlphaDiversityStatsResults.posthoc_df
    in favor of
    AlphaDiversityStatsResults.posthoc.adjusted_pvalues
More details are available in GitHub.