Tskit

Latest version: v0.5.6

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0.7.2

**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`).

0.7.1

**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`.

0.7.1b1

Early release making DTWF code available to beta testers.

0.7.0

Separation of tskit from msprime. Msprime is now solely dedicated to simulating
the coalescent, and all infrastructure for working with succinct tree sequences
is now provided by tskit. To ensure compatibility, 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 ({user}`jerekoskela`; {issue}`665`)

**Bug fixes**:

- Fix deprecation warning ({issue}`695`).

0.7.0a1

Alpha release for testing the tskit/msprime split.

0.6.2

Minor bugfix release.

**New features**:

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

**Bug fixes**:

- Fix performance regression in replication (608)

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