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Support for completing forwards-time simulations
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@jeromekelleher jeromekelleher released this 25 Aug 14:36
0.6.1
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Significant features for integration with forwards-time simulators plus improvements and bugfixes.

Breaking changes:

  • Change in the semantics of how populations are treated by simplify. By default, populations that are not referenced will now be removed from the data model. This can be avoided by setting filter_populations=False.

  • Simplify now raises an error if called on a set of tables that contain one or more migrations.

New features:

  • The simulate() function now supports a from_ts argument allowing msprime to complete the ancestry in tree sequences generated by forward simulations (#503, #541, #572, #581).

  • Add start_time and end_time parameters to the mutate function (#508).

  • Add reduce_to_site_topology argument to simplify. This allows us to find the minimal tree sequence that would be visible from a given set of sites, and is also a useful compression method if we are only interested in the observed sequences. (#545, #307).

  • Simplify generalised to support individuals, and the filter_populations, filter_individuals and filter_sites parameters added to allow filtering of unreferenced objects from the data model. (#567).

  • Default random seeds are now generated from a sequence initialised by a system source of randomness (#534). Random seeds should also be safely generated across multiple processes.

  • Full text I/0 support for Individuals and Populations (#498, #555)

  • Substantially improved performance in msprime.load for large tables and significant refactoring of C code (#559, #567, #569).

  • Improved performance of generating genotypes (#580).

  • Formal schema for tree sequence provenance (#566, #583).

  • Many updates to documentation.

Bug fixes:

  • Throw a more intelligle error during simulation if a topology is produced where the time of a parent is equal to the time of the child. (#570, #87).

  • Pickle supported in the TableCollection object. (#574, #577).

Deprecated:

  • The filter_zero_mutation_sites parameter for simplify has been deprecated in favour of filter_sites.
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