Tskit

.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 The load_tables function has been replaced
by TableCollection.tree_sequence.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().

**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`.
({issue}`2013`, {user}`andrewkern`).

- Raise an error if `log_arg_likelihood` is called on a recombinant tree
sequence that has no recombination nodes (({issue}`2123`, {pr}`2124`,
{user}`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. ({issue}`2128`, {issue}`2132`, {pr}`2162`,
{user}`GertjanBisschop`)

- Enable `additional_nodes` and `coalescing_segments_only` flags for `DTWF` and `FIXED_PEDIDGREE` models ({issue}`2129`, {issue}`2133`, {issue}`2167`, {pr}`2176`,
{user}`GertjanBisschop`)

**Maintenance**:
- Automatically flush edges whenever an edge with a different parent is added to the edge buffer. ({issue}`2182`, {pr}`2183`, {user}`GertjanBisschop`)

**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.
({issue}`1966`, {pr}`2038`, {user}`jeromekelleher`, {user}`molpopgen`)

- Fix edge case in `Demography.from_old_style()`
({issue}`2047`, {pr}`2048`, {user}`grahamgower`)

**Maintenance**:

- Documentation improvements ({pr}`2054`, {pr}`2033`, {pr}`2011`
{user}`petrelharp`, {user}`gregorgorjanc`)

**Bug fixes**:

- Fix (very) rare assertion trip caused by underlying GSL bug.
({issue}`1997`, {pr}`2000`, {user}`chriscrsmith`, {user}`molpopgen`,
{user}`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.
({pr}`1953`, {issue}`1951`, {issue}`1877`, {issue}`1948`, {user}`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).
({pr}`1938`, {issue}`1937`, {user}`grahamgower`).

- Do not assume Population metadata schemas contain the ``properties``
and ``additionalProperties`` attributes ({issue}`1947`, {pr}`1954`,
{user}`jeromekelleher`).

- Read the population name from PopulationConfiguration ``metadata`` in
``Demography.from_old_style`` ({issue}`1950`, {pr}`1954`,
{user}`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.
({pr}`1936`, {issue}`1930`, {user}`apragsdale`)