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@jeromekelleher jeromekelleher released this 26 Feb 12:07
0.5.0
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This is a major update to the underlying data structures in msprime to generalise the information that can be modelled, and allow for data from external sources to be efficiently processed. The new Tables API enables efficient interchange of tree sequence data using numpy arrays. Many updates have also been made to the tree sequence API to make it more Pythonic and general. Most changes are backwards compatible, however.

Breaking changes:

  • The SparseTree.mutations() and TreeSequence.mutations() iterators no longer support tuple-like access to values. For example, code like

     for x, u, j in ts.mutations():
     print("mutation at position", x, "node = ", u)

    will no longer work. Code using the old Mutation.position and Mutation.index will still work through deprecated aliases, but new code should access these values through Site.position
    and Site.id, respectively.

  • The TreeSequence.diffs() method no longer works. Please use the TreeSequence.edge_diffs() method instead.

  • TreeSequence.get_num_records() no longer works. Any code using this or the records() iterator should be rewritten to work with the edges() iterator and num_edges instead.

  • Files stored in the HDF5 format will need to upgraded using the msp upgrade command.

New features:

  • The API has been made more Pythonic by replacing (e.g.) tree.get_parent(u) with tree.parent(u), and
    tree.get_total_branch_length() with tree.total_branch_length. The old forms have been maintained as deprecated aliases. (#64)

  • Efficient interchange of tree sequence data using the new Tables API. This consists of classes representing the various tables (e.g. NodeTable) and some utility functions (such as load_tables, sort_tables, etc).

  • Support for a much more general class of tree sequence topologies. For example, trees with multiple roots are fully supported.

  • Substantially generalised mutation model. Mutations now occur at specific sites, which can be associated with zero to many mutations. Each site has an ancestral state (any character string) and each mutation a derived state (any character string).

  • Substantially updated documentation to rigorously define the underlying data model and requirements for imported data.

  • The variants() method now returns a list of alleles for each site, and genotypes are indexes into this array. This is both consistent with existing usage and works with the newly generalised mutation model, which allows arbitrary strings of characters as mutational states.

  • Add the formal concept of a sample, and distinguished from 'leaves'. Change tracked_leaves, etc. to tracked_samples (#225). Also rename sample_size to num_samples for consistency (#227).

  • The simplify() method returns subsets of a large tree sequence.

  • TreeSequence.first() returns the first tree in sequence.

  • Windows support. Msprime is now routinely tested on Windows as part of the suite of continuous integration tests.

  • Newick output is not supported for more general trees. (#117)

  • The genotype_matrix method allows efficient access to the full genotype matrix. (#306)

  • The variants iterator no longer uses a single buffer for genotype data, removing a common source of error (#253).

  • Unicode and ASCII output formats for SparseTree.draw().

  • SparseTree.draw() renders tree in the more conventional 'square shoulders' format.

  • SparseTree.draw() by default returns an SVG string, so it can be easily displayed in a Jupyter notebook. (#204)

  • Preliminary support for a broad class of site-based statistics, including Patterson's f-statistics, has been added, through the SiteStatCalculator, and its branch length analog, BranchLengthStatCalculator. The interface is still in development, and is expected may change.

Bug fixes:

  • Duplicate site no longer possible (#159)

  • Fix for incorrect population sizes in DemographyDebugger (#66).

Deprecated:

  • The records iterator has been deprecated, and the underlying data model has moved away from the concept of coalescence records. The structure of a tree sequence is now defined in terms of a set of nodes
    and edges, essentially a normlised version of coalescence records.

  • Changed population_id to population in various DemographicEvent classes for consistency. The old population_id argument is kept as a deprecated alias.

  • Changed destination to dest in MassMigrationEvent. The old destination argument is retained as a deprecated alias.

  • Changed sample_size to num_samples in TreeSequence and SparseTree. The older versions are retained as deprecated aliases.

  • Change get_num_leaves to num_samples in SparseTree. The get_num_leaves method (and other related methods) that have been retained for backwards compatability are semantically incorrect,
    in that they now return the number of samples. This should have no effect on existing code, since samples and leaves were synonymous. New code should use the documented num_samples form.

  • Accessing the position attribute on a Mutation or Variant object is now deprecated, as this is a property of a Site.

  • Accessing the index attribute on a Mutation or Variant object is now deprecated. Please use variant.site.id instead. In general, objects with IDs (i.e., derived from tables) now have an id field.

  • Various get_ methods in TreeSequence and SparseTree have been replaced by more Pythonic alternatives.

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