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Python 0.6.1

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@github-actions github-actions released this 31 Mar 15:59
· 35 commits to main since this release

Bugfixes

  • Fix to TreeSequence.pair_coalescence_counts output dimension when
    provided with time windows containing no nodes (@nspope,
    #3046, #3058)

  • Fix to TreeSequence.pair_coalescence_counts to normalise by non-missing
    span if span_normalise=True. This resolves a bug where
    TreeSequence.pair_coalescence_rates would return incorrect values for
    intervals with missing trees. (@natep, #3053, #3059)

  • Fix to TreeSequence.pair_coalescence_rates causing an
    assertion to be triggered by floating point error, when all coalescence events are inside a single time window (@natep, #3035, #3038)

Features

  • Add support for fixed-length arrays in metadata struct codec using the length property.
    (@benjeffery, #3088,#3090)

  • Add a new TreeSequence.pca method that uses randomized linear algebra
    to find the top eigenvectors/values of the genetic relatedness matrix
    (@hanbin973, @petrelharp, #3008)

  • Add methods on TreeSequence to efficiently get table metadata as a
    numpy structured array. (@benjeffery, #3098)

  • Add Python 3.13 support (@benjeffery, #3107)

  • Add a preamble argument to draw_svg() methods to allow adding arbitrary extra
    graphics (e.g. legends) to SVG plots (@hyanwong, issue:3086`, #3121)