Msprime

**Bug fixes**:

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

**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

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

**Bug fixes:**

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

**Maintenance**:

- Various documentation improvements.

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.

New features:

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