Tskit

Bugfix release affecting all users of the Python API. Version 0.2.0 contained a
confusing and inconsistent mix of times and rates being expressed in both
coalescent units and generations. This release changes _all_ times and rates
used when describing demographic models to generations, and also changes
all population sizes to be absolute. In the interest of consistency, the
units of the trees output by msprime are also changed to generations. This
is a major breaking change, and will require updates to all scripts using the
API.

This release also include some performance improvements and additional
functionality.

Mspms users are not affected, other than benefiting from performance
improvements.

Breaking changes:

- Time values are now rescaled into generations when a TreeSequence is
created, and so all times associated with tree nodes are measured in
generations. The time values in any existing HDF5 file will now be
interpreted as being in generations, so stored simulations must be
rerun. To minimise the chance of this happening silently, we have
incremented the file format major version number, so that attempts
to read older versions will fail.
- Growth rate values for the PopulationConfiguration class are now
per generation, and population sizes are absolute. These were in
coalescent units and relative to Ne previously.
- GrowthRateChangeEvents and SizeChangeEvents have been replaced with
a single class, PopulationParametersChange. This new class takes
an initial_size as the absolute population size, and growth_rate
per generation. Since the change in units was a breaking one,
potentially leading to subtle and confusing bugs, we decided that
the name refactoring would at least ensure that users would need
to be aware that the change had been made. This API should now
be stable, and will not be changed again without an excellent
reason.
- MigrationRateChangeEvent has been renamed to MigrationRateChange
and the migration rates are now per-generation.
- MassMigrationEvent has been renamed to MassMigration, and the
values of source and destination swapped, fixing the bug in
issue 14.
- The TreeSequence.records() method now returns an extra value,
potentially breaking client code.

Improvements:

- Added tutorial for demographic events.
- Added DemographyDebugger class to help view the changes in populations
over time.
- Added population tracking for coalescent events. We can now determine
the population associated with every tree node. The relevant information
has been added to the HDF5 file format.
- Improved performance for replication by reusing the same low-level
simulator instance. This leads to significant improvements for large
numbers of replicates of small simulations. Issue 8.
- Changed the TreeSequence.records() method to return named tuples.
- Added get_total_branch_length method. Issue 12.
- Fixed bug in reading Hapmap files. Issue 13.

Major update release, adding significant new functionality to the Python
API and several breaking changes. All code written for the 0.1.x API
will be affected, unfortunately.

Breaking changes:

- Sample IDs are now zero indexed. In previous versions of msprime, the
samples were numbered from 1 to n inclusive, which is not Pythonic.
This change has been made to make the API more usable, but will
cause issues for existing code.
- There is now an Ne parameter to simulate(), and recombination,
mutation and migration rates are now all per-generation. The
keyword arguments have been changed to recombination_rate
and mutation_rate, which should mean that silent errors will
be avoided. All rates in existing code will need to be
divided by 4 as a result of this. This change was made to make
working with recombination maps and per generation recombination
rates easier.
- Msprime now uses continuous values to represent coordinates, and
the num_loci parameter has been replaced with a new length parameter
to simulate(). Internally, a discrete recombination model is still
used, but by default the potential number of discrete sites is
very large and effectively continuous. True discrete recombination
models can still be specified by using the recombination_map
argument to simulate.
- The population_models argument to simulate() has been removed, and
replaced with the population_configuration and demographic_events
parameters. This was necessary to provide the full demographic
model.
- The HDF5 file format has been updated to accommodate the continuous
coordinates, along with other minor changes. As a consequence,
simulation results will be somewhat larger. Stored simulations will
need to be re-run and saved.
- Removed the random_seed key from the provenance JSON strings.
- Removed the simulate_tree() function, as it seemed to offer little
extra value.

New features:

- Simulation of variable recombination rates via arbitrary recombination
maps.
- Full support for population structure and demographic events.
- API support for replication via the num_replicates argument to simulate().
- Fully reworked random generation mechanisms, so that in the nominal
case a single instance of gsl_rng is used throughout the entire
simulation session.
- Addition of several miscellaneous methods to the TreeSequence API.
- Added NULL_NODE constant to make tree traversals more readable.

Bugfix release. Fixes serious issue affecting simulations with small
sample sizes.

<https://github.com/jeromekelleher/msprime/issues/7>

All users of mspms should update immediately and any analyses using
a small sample size (< 10) with mutations should be repeated.

Many thanks to Konrad Lohse for identifying the issue.

Bugfix release. Fixes serious issue affecting random seeds in mspms.

<https://github.com/jeromekelleher/msprime/issues/6>

All users of mspms should update immediately and any analyses using
the `-seeds` option in mspms should be repeated.

Many thanks to Derek Setter for identifying the issue.

Transitional release providing population structure support for the
ms-compatible command line interface. A considerable amount of low-level
plumbing was required to provide the required flexibility. This is currently
not visible from the high-level API, but will shortly be made available in the
forthcoming 0.2.x series.

The current implementation of migration should work well for small numbers of
populations (e.g. < 10), but will not scale well for large numbers of
populations.

Changes

- Added the -I, -m, -ma, -em, -eM, -ema, -eG, -eg, -eN, -en,
-ej and -es options to mspms. These should provide full ms
compatibility, except for the -es option which is currently
limited in scope.
- Added some extra keys to the low-level configuration JSON in
the HDF5 file format to describe the population structure.
This will be documented in a future release.
- Added a {}`get_pairwise_diversity` method to the TreeSequence
class to efficiently calculate the population genetics
statistic pi.