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.