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@benjeffery benjeffery released this 27 Nov 13:11
· 1493 commits to main since this release
0.3.3
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Learn about vigilant mode.

Minor feature release

Features

  • Add TreeSequence.genetic_relatedness for calculating genetic relatedness between
    pairs of sets of nodes (@brieuclehmann, #1021, #1023, #974, #973, #898).

  • Expose TreeSequence.coiterate() method to allow iteration over 2 sequences
    simultaneously, aiding comparison of trees from two sequences
    (@jeromekelleher, @hyanwong, #1021, #1022).

  • tskit is now supported on, and has wheels for, python3.9
    (@benjeffery, #982, #907).

  • Tree.newick() now has extra option include_branch_lengths to allow branch
    lengths to be omitted (@hyanwong, #931).

  • Added Tree.generate_star static method to create star-topologies (@hyanwong,
    #934).

  • Added Tree.generate_comb and Tree.generate_balanced methods to create
    example trees. (@jeromekelleher, #1026).

  • Added equals method to TreeSequence, TableCollection and each of the tables which
    provides more flexible equality comparisons, for example, allowing
    users to ignore metadata or provenance in the comparison
    (@mufernando, @jeromekelleher, #896, #897,
    #913, #917).

  • Added __eq__ to TreeSequence
    (@benjeffery, #1011, #1020).

  • ts.dump and tskit.load now support reading and writing file objects such as
    FIFOs and sockets (@benjeffery, #657, #909).

  • Added tskit.write_ms for writing to MS format
    (@saurabhbelsare, #727, #854).

  • Added TableCollection.indexes for access to the edge insertion/removal order indexes
    (@benjeffery, #4, #916).

  • The dictionary representation of a TableCollection now contains its index
    (@benjeffery, #870, #921).

  • Added TreeSequence._repr_html_ for use in jupyter notebooks
    (@benjeffery, #872, #923).

  • Added TreeSequence.__str__ to display a summary for terminal usage
    (@benjeffery, #938, #985).

  • Added TableCollection.dump and TableCollection.load. This allows table
    collections that are not valid tree sequences to be manipulated
    (@benjeffery, #14, #986).

  • Added nbytes method to tables, TableCollection and TreeSequence which
    reports the size in bytes of those objects
    (@jeromekelleher, @benjeffery, #54, #871).

  • Added TableCollection.clear to clear data table rows and optionally
    provenances, table schemas and tree-sequence level metadata and schema
    (@benjeffery, #929, #1001).

Bugfixes

  • LightWeightTableCollection.asdict and TableCollection.asdict now return copies
    of arrays (@benjeffery, #1025, #1029).

  • The map_mutations method previously used the Fitch parsimony method, but this
    does not produce parsimonious results on non-binary trees. We now now use the
    Hartigan parsimony algorithm, which does (@jeromekelleher,
    #987, #1030).

  • The flag argument to tables' add_row was treating the value as signed
    (@benjeffery, #1027, #1031).

Breaking changes

  • The argument to ts.dump and tskit.load has been renamed file from path.
  • All arguments to Tree.newick() except precision are now keyword-only.
  • Renamed ts.trait_regression to ts.trait_linear_model.
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