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1 | 1 | -------------------- |
2 | | -[0.1.2] - 2020-XX-XX |
| 2 | +[0.1.2] - 2020-05-29 |
3 | 3 | -------------------- |
4 | 4 |
|
| 5 | +Important bugfix and feature release, recommended for all users. |
| 6 | + |
| 7 | +Significant errors in the HomSap/OutOfAfrica_3G09 and HomSap/OutOfAfrica_2T12 |
| 8 | +models have been fixed. **We recommend repeating any analyses performed using |
| 9 | +these models**. See `here |
| 10 | +<https://github.com/jeromekelleher/msprime-model-errors>`__ for more details on |
| 11 | +the error in the three population Out of Africa model and analysis of the |
| 12 | +differences from the correct model. |
| 13 | + |
| 14 | +The recombination rate for AraTha was also off by a factor of 10. |
| 15 | +**We recommend repeating any analyses performed using this species**. |
5 | 16 |
|
6 | 17 | **Bug fixes**: |
7 | 18 |
|
| 19 | +- Fix error in HomSap/OutOfAfrica_3G09 model, in which migration between |
| 20 | + ancestral African and European populations was allowed to continue in the |
| 21 | + most ancient time period (:user:`apragsdale`, :pr:`496`, :issue:`516`). |
| 22 | + |
| 23 | +- Fix similar error in HomSap/OutOfAfrica_2T12 model |
| 24 | + (:user:`ndukler`, :pr:`520`, :issue:`516`). |
| 25 | + |
| 26 | +- Fix recombination rate estimate for AraTha (:user:`grahamgower`, |
| 27 | + :issue:`537`, :pr:`527`), which was off by a factor of 10. |
| 28 | + |
| 29 | +- Require attrs >=19.10 (:user:`grahamgower`, :pr:`399`, :issue:`394`) |
| 30 | + |
| 31 | +**New species**: |
| 32 | + |
| 33 | +- Canis familiaris (:user:`grahamgower`, :pr:`375`). |
| 34 | + |
| 35 | +- Pongo abelii (:user:`apragsdale`, :pr:`363`). |
| 36 | + |
| 37 | +**New models**: |
| 38 | + |
| 39 | +- HomSap/PapuansOutOfAfrica_10J19 model (:user:`grahamgower`, :pr:`372`). |
| 40 | + QC'd by :user:`noscode`, :pr:`387`. |
| 41 | + |
| 42 | +- HomSap/AshkSub_7G19 model (:user:`agladstein`, :pr:`494`). |
| 43 | + QC'd by :user:`ndukler`, :pr:`536`. |
8 | 44 |
|
9 | 45 | **New features**: |
10 | 46 |
|
| 47 | +- SLiM simulation engine (:user:`grahamgower`, :pr:`409`, plus numerous others. |
| 48 | + See e.g. :issue:`132` and :issue:`133` for background.) |
| 49 | + |
| 50 | +- Support for DTWF, SMC, and SMC' models in msprime engine |
| 51 | + (:user:`grahamgower`, :pr:`398`, :issue:`392`). |
| 52 | + |
| 53 | +- Warnings for users running simulations on non-autosomes |
| 54 | + (:user:`grahamgower`, :pr:`407`). |
| 55 | + |
| 56 | +- Migrate all genetic map data to AWS (:user:`ndukler`, :pr:`514`, :issue:`335`) |
| 57 | + |
| 58 | +- Warnings for users running simulations on non QC'd models |
| 59 | + (:user:`grahamgower`, :pr:`525`). |
| 60 | + |
| 61 | +- Add `generation_time` (default=1) attribute to generic models |
| 62 | + (:user:`grahamgower`, :pr:`477`, :issue:`471`). |
| 63 | + |
| 64 | +- Various documentation and citation improvements. |
| 65 | + |
11 | 66 | **Breaking changes**: |
12 | 67 |
|
13 | 68 | - Move the --quiet/-q command line option to the top-level. Previously |
|
17 | 72 | - The long form ``--verbosity`` argument has been changed to ``--verbose`` |
18 | 73 | (:pr:`547`). |
19 | 74 |
|
| 75 | +- Removed DroMel chrM (:user:`grahamgower`, :pr:`528`, :issue:`405`). |
| 76 | + |
20 | 77 | -------------------- |
21 | 78 | [0.1.1] - 2020-01-02 |
22 | 79 | -------------------- |
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