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Forward simulation interoperability release
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@jeromekelleher jeromekelleher released this 20 Jun 08:23
0.6.0
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This release is focused on ensuring interoperability with the forthcoming SLiM 3.0 release, which has support for outputting tree sequences in msprime's .trees format. The release represents a substantial step towards the goal of separating the tskit code from msprime. It removes the troublesome HDF5 dependency in favour of the much simpler kastore library.

The principle new features are the mutate() function which allows us to easily add mutations to any tree
sequence, preliminary support for Individuals and Populations within the data model, and the addition of the new TableCollection object as the central structure in the Tables API.

Breaking changes:

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

New features:

  • The mutate function (#507).

  • Removed HDF5 library dependency. Now use the embedded kastore library for storing data.

  • Numpy and h5py are now install time dependencies, solving some installation headaches.

  • The new TableCollection type gives much tighter integration with the low-level library. Functions like sort_tables and simplify_tables are now methods of this class. The load_tables function has been replaced by TableCollection.tree_sequence. These functions still work, but are deprecated.

  • Preliminary support for Individual and Population types in the Tables
    API and for TreeSequences.

  • Add 'root' argument to SparseTree.newick and support for arbitrary node labels (#510).

  • Larger numbers of alleles now supported via 16-bit genotypes (#466).

  • Substantially improved simplify performance when there is a large number of sites (#453).

Bug fixes:

  • Fix bug in tree drawing with many roots (#486)

  • Fix segfault in accessing trees with zero roots (#515)

  • Fix bug where DemographyDebugger was modifying the input sample sizes (#407)

Deprecated:

  • sort_tables is deprecated in favour of TableCollection.sort().

  • simplify_tables is deprecated in favour of TableCollection.simplify().

  • load_tables is deprecated in favour of TableCollection.tree_sequence().

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