Msprime

Latest version: v1.3.1

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0.7.0a1

Alpha release for testing the tskit/msprime split.

0.6.2

Minor bugfix release.

**New features**:
- Add provenance recording option to simplify (601)
- Minor performance improvement (598)

**Bug fixes**:

- Fix performance regression in replication (608)

0.6.1

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``.

0.6.0

This release is focused on ensuring interoperability with the forthcoming SLiM 3.0 release, which has support for outputting tree sequences in msprime's .trees format. The release represents a substantial step towards the goal of separating the ``tskit`` code from ``msprime``. It removes the troublesome HDF5 dependency in favour of the much simpler ``kastore`` library.

The principle new features are the mutate() function which allows us to easily add mutations to any tree
sequence, preliminary support for Individuals and Populations within the data model, and the addition of the new TableCollection object as the central structure in the Tables API.

**Breaking changes**:

- Files stored in the HDF5 format will need to upgraded using the ``msp upgrade`` command.

**New features**:

- The mutate function (507).

- Removed HDF5 library dependency. Now use the embedded kastore library for storing data.

- Numpy and h5py are now install time dependencies, solving some installation headaches.

- The new TableCollection type gives much tighter integration with the low-level library. Functions like sort_tables and simplify_tables are now methods of this class. The load_tables function has been replaced by TableCollection.tree_sequence. These functions still work, but are deprecated.

- Preliminary support for Individual and Population types in the Tables
API and for TreeSequences.

- Add 'root' argument to SparseTree.newick and support for arbitrary node labels (510).

- Larger numbers of alleles now supported via 16-bit genotypes (466).

- Substantially improved simplify performance when there is a large number of sites (453).


**Bug fixes**:

- Fix bug in tree drawing with many roots (486)

- Fix segfault in accessing trees with zero roots (515)

- Fix bug where DemographyDebugger was modifying the input sample sizes (407)


**Deprecated**:

- sort_tables is deprecated in favour of TableCollection.sort().

- simplify_tables is deprecated in favour of TableCollection.simplify().

- load_tables is deprecated in favour of TableCollection.tree_sequence().

0.6.0b2

This release fixes some OSX bugs in 0.6.0b1.

0.6.0b1

This is preview release of the following major changes:

1. Remove HDF5 and use kastore for tree sequence files
2. Add Individual and Population types
3. The mutate() function.

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