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Major update for Python API
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@jeromekelleher jeromekelleher released this 05 May 15:27
0.2.0
6f7cde1

Major update release, adding significant new functionality to the Python
API and several breaking changes. All code written for the 0.1.x API
will be affected, unfortunately.

Breaking changes:

  • Sample IDs are now zero indexed. In previous versions of msprime, the
    samples were numbered from 1 to n inclusive, which is not Pythonic.
    This change has been made to make the API more usable, but will
    cause issues for existing code.
  • There is now an Ne parameter to simulate(), and recombination,
    mutation and migration rates are now all per-generation. The
    keyword arguments have been changed to recombination_rate
    and mutation_rate, which should mean that silent errors will
    be avoided. All rates in existing code will need to be
    divided by 4 as a result of this. This change was made to make
    working with recombination maps and per generation recombination
    rates easier.
  • Msprime now uses continuous values to represent coordinates, and
    the num_loci parameter has been replaced with a new length parameter
    to simulate(). Internally, a discrete recombination model is still
    used, but by default the potential number of discrete sites is
    very large and effectively continuous. True discrete recombination
    models can still be specified by using the recombination_map
    argument to simulate.
  • The population_models argument to simulate() has been removed, and
    replaced with the population_configuration and demographic_events
    parameters. This was necessary to provide the full demographic
    model.
  • The HDF5 file format has been updated to accommodate the continuous
    coordinates, along with other minor changes. As a consequence,
    simulation results will be somewhat larger. Stored simulations will
    need to be re-run and saved.
  • Removed the random_seed key from the provenance JSON strings.
  • Removed the simulate_tree() function, as it seemed to offer little
    extra value.

New features:

  • Simulation of variable recombination rates via arbitrary recombination
    maps.
  • Full support for population structure and demographic events.
  • API support for replication via the num_replicates argument to simulate().
  • Fully reworked random generation mechanisms, so that in the nominal
    case a single instance of gsl_rng is used throughout the entire
    simulation session.
  • Addition of several miscellaneous methods to the TreeSequence API.
  • Added NULL_NODE constant to make tree traversals more readable.
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