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@jeromekelleher jeromekelleher released this 31 May 11:14
0.3.0
274343a

Bugfix release affecting all users of the Python API. Version 0.2.0 contained a
confusing and inconsistent mix of times and rates being expressed in both
coalescent units and generations. This release changes all times and rates
used when describing demographic models to generations, and also changes
all population sizes to be absolute. In the interest of consistency, the
units of the trees output by msprime are also changed to generations. This
is a major breaking change, and will require updates to all scripts using the
API.

This release also include some performance improvements and additional
functionality.

Mspms users are not affected, other than benefiting from performance
improvements.

Breaking changes:

  • Time values are now rescaled into generations when a TreeSequence is
    created, and so all times associated with tree nodes are measured in
    generations. The time values in any existing HDF5 file will now be
    interpreted as being in generations, so stored simulations must be
    rerun. To minimise the chance of this happening silently, we have
    incremented the file format major version number, so that attempts
    to read older versions will fail.
  • Growth rate values for the PopulationConfiguration class are now
    per generation, and population sizes are absolute. These were in
    coalescent units and relative to Ne previously.
  • GrowthRateChangeEvents and SizeChangeEvents have been replaced with
    a single class, PopulationParametersChange. This new class takes
    an initial_size as the absolute population size, and growth_rate
    per generation. Since the change in units was a breaking one,
    potentially leading to subtle and confusing bugs, we decided that
    the name refactoring would at least ensure that users would need
    to be aware that the change had been made. This API should now
    be stable, and will not be changed again without an excellent
    reason.
  • MigrationRateChangeEvent has been renamed to MigrationRateChange
    and the migration rates are now per-generation.
  • MassMigrationEvent has been renamed to MassMigration, and the
    values of source and destination swapped, fixing the bug in
    issue #14.
  • The TreeSequence.records() method now returns an extra value,
    potentially breaking client code.

Improvements:

  • Added tutorial for demographic events.
  • Added DemographyDebugger class to help view the changes in populations
    over time.
  • Added population tracking for coalescent events. We can now determine
    the population associated with every tree node. The relevant information
    has been added to the HDF5 file format.
  • Improved performance for replication by reusing the same low-level
    simulator instance. This leads to significant improvements for large
    numbers of replicates of small simulations. Issue #8.
  • Changed the TreeSequence.records() method to return named tuples.
  • Added get_total_branch_length method. Issue #12.
  • Fixed bug in reading Hapmap files. Issue #13.
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