Bugfix release

Minor release fixing a very rare bug and with some new features.

Breaking changes

• The random trajectory has been changed slightly to improve handling of ancient sampling events (:pr:782). Thus, simulations for a given random seed will not be identical to previous versions, if ancient samples are used.

New features

• Automated Docker builds (:user:agladstein; :pr:661)
• Add mean coalescence time to DemographyDebugger (:user:petrelharp; :pr:779).
• Improve MassMigration descriptions in DemographyDebugger (:user:marianne-aspbury; :pr:791).

Bug fixes:

• In very, very, very rare cases it was possible to generate a zero waiting time until the next coalescent event, leading to zero branch lengths in the output tree sequence and an error being raised (:user:molpopgen, :user:DL42, :user:jeromekelleher; :issue:783, :pr:785).

DTWF model and population size ground-truth

New features

• Discrete Time Wright-Fisher simulation model (:user:DomNelson).
• SMC/SMC' simulation models (:user:jeromekelleher).
• Mixed simulation models (:user:jeromekelleher).
• Specify end_time to allow early-finish for simulations (:user:jeromekelleher).
• Calculation of historical coalescence rates in the DemographyDebugger (:user:jgallowa07, :user:petrelharp).
• Additional information on population sizes in DemographyDebugger (:user:andrewkern).
• Remove support for Python 2 (:user:hugovk).
• Allow specifying metadata for populations (:user:jeromekelleher).

Bug fixes:

• Various minor bug and doc fixes from :user:hyanwong, :user:petrelharp,
  :user:brianzhang01, :user:mufernando and :user:andrewkern.

Beta release supporting DTWF model

Early release to make the DTWF model available for testing.

Remove tskit from msprime

Separation of tskit from msprime. Msprime is now solely dedicated to simulating the coalescent, and all infrastucture for working with succinct tree sequences is now provided by tskit. To ensure compatability, msprime now imports code from tskit under the old names, which should ensure that all code continues to work without changes.

New features

• Ability to record the full ARG (Jere Koskela; #665)

Bug fixes:

• Fix deprecation warning (#695).

Testing release

Alpha release for testing the tskit/msprime split.

Bugfix release

Minor bugfix release.

New features:

• Add provenance recording option to simplify (#601)
• Minor performance improvement (#598)

Bug fixes:

• Fix performance regression in replication (#608)

Support for completing forwards-time simulations

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.

Forward simulation interoperability release

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().

Bugfix release

This release fixes some OSX bugs in 0.6.0b1.

Preview of kastore and extra tables

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.