1.3.1

Minor bugfix release

[1.3.1] - 2024-02-09

Bug fixes:

• Change tolerance of polynomial approximation in Beta-coalescent acceptance probabilities ({issue}2256, {pr}2257, {user}JereKoskela)

1.3.0

[1.3.0] - 2022-12-13

New features

• Add a MicrosatMutationModel mutation model class, that
  represents a generalized interface for constructing mutational
  models appropriate to STRs. In addition 3 specific microsat models
  are added SMM, TPM, and EL2. (#2013, @andrewkern).

• Raise an error if log_arg_likelihood is called on a recombinant tree
  sequence that has no recombination nodes (#2123, #2124, @hyanwong)

• Add ability to record specific node types with the additional_nodes
  flag as well as record edges for coalescing nodes along non-coalescing segments. (#2128, #2132, #2162, @GertjanBisschop)

• Enable additional_nodes and coalescing_segments_only flags for DTWF and FIXED_PEDIDGREE models (#2129, #2133, #2167, #2176, @GertjanBisschop)

• Support Python 3.11 (#2177, #2180, @benjeffery)

Bug fixes:

• Fix segfault in case of non-binary merger for log_arg_likelihood (#2107, #2114, @JereKoskela)

Maintenance:

• Update tskit to Python 0.5.2 (#2116, @benjeffery).

• Automatically flush edges whenever an edge with a different parent is added to the edge buffer. (#2182, #2183, @GertjanBisschop)

Breaking changes:

• msprime no longer supports Python 3.7

Simulation through fixed pedigree

New features

• Add the FixedPedigree ancestry model and various infrastructure for importing pedigree information into msprime.

Bug fixes:

• Fix rare assertion trip in the single sweep model caused by numerical jitter. (#1966, #2038, @jeromekelleher, @molpopgen)

• Fix edge case in Demography.from_old_style() (#2047, #2048, @grahamgower)

Maintenance:

• Documentation improvements (#2054, #2033, #2011 @petrelharp, @gregorgorjanc)

Minor bugfix release

Minor bugfix release

Bug fixes:

• Fix (very) rare assertion trip caused by underlying GSL bug. (#1997, #2000, @chriscrsmith, @molpopgen, @andrewkern)

Maintenance:

• Various documentation improvements.

Maintenance release integrating new tskit features

[1.1.0] - 2021-12-14

New features

• Add support for tree sequence time_units field. The time_units will be set to “generations” for the output of sim_ancestry (and simulate), unless the initial_state argument is used. In this case, the time_units value will be inherited from the input. (#1953, #1951, #1877, #1948, @jeromekelleher).

Bug fixes:

• Raise an error if Demography.from_demes() is passed a model with non-zero selfing_rate or cloning_rate values (which msprime does not support). (#1938, #1937, @grahamgower).

• Do not assume Population metadata schemas contain the properties and additionalProperties attributes (#1947, #1954, @jeromekelleher).

• Read the population name from PopulationConfiguration metadata in Demography.from_old_style (#1950, #1954, @jeromekelleher)

Maintenance:

• Update tskit to Python 0.4.0 and C 0.99.15.

Minor maintenance release

New features:

Support for Demes 0.2.0, which introduces a change to how pulse sources and proportions are specified. (#1936, #1930, @apragsdale)

Bugfix release

[1.0.3] - 2021-11-12

This is a bugfix release recommended for all users.

New features:

• Support for running full ARG simulations with gene conversion (#1801, #1773, @JereKoskela).
• Improved performance when running many small simulations (#1909, @jeromekelleher).
• Update to tskit C API 0.99.14 (#1829).

Bug fixes:

• Fix bug in full ARG simulation with missing regions of the genome, where ARG nodes were not correctly returned. (#1893, @jeromekelleher, @hyl317)
• Fix memory leak when running sim_ancestry in a loop (#1904, #1899, @jeromekelleher, @grahamgower).
• Fix printing small values in rate maps (#1906, #1905, @petrelharp).

Minor feature release

Minor feature release with improved Demes support and a few small bugfixes.

New features:

• Support for Demes input and logging in the msp simulate CLI (#1716, @jeromekelleher).
• Add Demography.to_demes method for creating a Demes demographic model from an msprime demography (#1724, @grahamgower).
• Improved mapping of Demes models to Demography objects (#1758, #1757, #1756 @apragsdale).
• Improved numerical algorithms in DemographyDebugger (#1788, @grahamgower, @petrelharp).

Bugfixes:

• Raise an error if running full ARG simulations with gene conversion (#1774).

Minor feature release

Minor feature release with experimental Demes support.

• Change the semantics of Admixture events slightly so that ancestral populations that are inactive, are marked as active (#1662, #1657, @jeromekelleher, @apragsdale)

• Initial support for Demes via the Demography.from_demes method. (#1662, #1675, @jeromekelleher, @apragsdale, @grahamgower)

Initial stable release for 1.0 series

This is a major update recommended for all users. Please see the changelog for details.