Msprime

This release fixes an important bug in the legacy ms compatible interface and is therefore strongly recommended of all mspms users.

Bug fixes:

- Fix error in mspms output of tree spans. In previous versions, the length of genome spanned by trees in the newick output was incorrect in certain situations (specifically, when “invisible” recombinations are present so that two or more identical trees are printed out). Thanks to fbaumdicker for spotting the problem. (jeromekelleher, 837, 836)
- Fix assertion tripped when we have very low recombination rates in the DTWF model. Thanks to terhorst for the bug report. (jeromekelleher, 833, 831).
- Fix bug in memory allocation when simulating mutations on a tree sequence that already contains many mutations. Thanks to santaci for the bug report. (jeromekelleher, petrelharp, 838, 806)

New features:

- Add the new Census event, which allows us to place nodes on all extant branches at a given time (gtsambos 799).
- Improved error reporting for input parameters, in particular demographic events (829).

Documentation:

- Improved container documentation (agladstein, 822, 809).
- Improved developer docs for macs (gtsambos, molpopgen, 805).
- Clarify meaning of migration matrix (petrelharp, 830).

**Bug fixes**:

- Support for SMC models coupled with the record_full_arg feature was erroneously removed in a previous version (:issue:`795`). The feature has been resinstated (:pr:`796`).

Minor release fixing a very rare bug and with some new features.

**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`).

**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`.

Early release to make the DTWF model available for testing.

Separation of tskit from msprime. Msprime is now solely dedicated to simulating the coalescent, and all infrastucture for working with succinct tree sequences is now provided by tskit. To ensure compatability, 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 (Jere Koskela; 665)

**Bug fixes**:

- Fix deprecation warning (695).