Improved installation and performance

Changes from previous version:

• Installation instructions for Mac on Homebrew
• Improved documentations, removing TODO items.
• Added initial version of msp command line utility
• Added low-level LeafListIterator, improves performance of leaves() method.
• Improved performance of haplotype generation.

This is a pre-release to allow testing of installation on various platforms.

Bugfix release

• Fixes a bug in which dump did not work after an explicit call to set_mutations.
• Adds a get_index function to the SparseTree class that gives the index of the tree within the sequence.

Updated leaf counting

This release adds support for counting a specific subset of the leaves in a tree.

Changes:

• Minor change to the signature for TreeSequence.trees(), which now takes an optional list of tracked leaves.
• Added the SparseTree.get_num_tracked_leaves() method to count the number of these leaves in the subtree rooted at a given node.

Initial stable API release

This is the initial release of the API. Any documented APIs will try to remain stable from this point, and will go through a process of deprecation before change.

Differences from 0.1.2a2:

• Renamed the sparse_trees method to trees.
• Changed the ordering of records_out in the diffs iterator.
• Added documentation for more features in the TreeSequence class.
• Added set_mutations to allow user defined mutations.
• Added get_num_leaves and options to enable constant time implementation.

Initial version of Python API.

This is a minor update to 0.1.2a1 fixing missing files and version number problems.

Initial version of Python API.

This is the initial version of the Python API with draft documentation. This should be considered alpha status, and many details of how the API works may change before it is stabilised.

Initial release

This is the initial release of msprime. The ms-compatible command line interface is ready for use and supports:

• newick tree and haplotype output
• recombination
• exponentially expanding/contracting populations
• past demographic events via the -eG and -eN options

The Python API and tree storage format are not yet finalised or documented.

Final alpha for testing

This is a minor update for distribution testing.

Early alpha release for testing and feedback

This release is a minor update over 0.1.1a1, addressing PyPI issues and various minor portability problems.

Alpha release for testing

This is an early alpha release for testing. Major incompatibilities exist with previous versions.