Merge pull request #553 from mcveanlab/changelog-0.1.2

Changelog for 0.1.2.

Author: jeromekelleher

CHANGELOG.rst

@@ -1,13 +1,68 @@
 --------------------
-[0.1.2] - 2020-XX-XX
+[0.1.2] - 2020-05-29
 --------------------
 
+Important bugfix and feature release, recommended for all users.
+
+Significant errors in the HomSap/OutOfAfrica_3G09 and HomSap/OutOfAfrica_2T12
+models have been fixed. **We recommend repeating any analyses performed using
+these models**. See `here
+<https://github.com/jeromekelleher/msprime-model-errors>`__ for more details on
+the error in the three population Out of Africa model and analysis of the
+differences from the correct model.
+
+The recombination rate for AraTha was also off by a factor of 10.
+**We recommend repeating any analyses performed using this species**.
 
 **Bug fixes**:
 
+- Fix error in HomSap/OutOfAfrica_3G09 model, in which migration between
+  ancestral African and European populations was allowed to continue in the
+  most ancient time period (:user:`apragsdale`, :pr:`496`, :issue:`516`).
+
+- Fix similar error in HomSap/OutOfAfrica_2T12 model
+  (:user:`ndukler`, :pr:`520`, :issue:`516`).
+
+- Fix recombination rate estimate for AraTha (:user:`grahamgower`,
+  :issue:`537`, :pr:`527`), which was off by a factor of 10.
+
+- Require attrs >=19.10 (:user:`grahamgower`, :pr:`399`, :issue:`394`)
+
+**New species**:
+
+- Canis familiaris (:user:`grahamgower`, :pr:`375`).
+
+- Pongo abelii (:user:`apragsdale`, :pr:`363`).
+
+**New models**:
+
+- HomSap/PapuansOutOfAfrica_10J19 model (:user:`grahamgower`, :pr:`372`).
+  QC'd by :user:`noscode`, :pr:`387`.
+
+- HomSap/AshkSub_7G19 model (:user:`agladstein`, :pr:`494`).
+  QC'd by :user:`ndukler`, :pr:`536`.
 
 **New features**:
 
+- SLiM simulation engine (:user:`grahamgower`, :pr:`409`, plus numerous others.
+  See e.g. :issue:`132` and :issue:`133` for background.)
+
+- Support for DTWF, SMC, and SMC' models in msprime engine
+  (:user:`grahamgower`, :pr:`398`, :issue:`392`).
+
+- Warnings for users running simulations on non-autosomes
+  (:user:`grahamgower`, :pr:`407`).
+
+- Migrate all genetic map data to AWS (:user:`ndukler`, :pr:`514`, :issue:`335`)
+
+- Warnings for users running simulations on non QC'd models
+  (:user:`grahamgower`, :pr:`525`).
+
+- Add `generation_time` (default=1) attribute to generic models
+  (:user:`grahamgower`, :pr:`477`, :issue:`471`).
+
+- Various documentation and citation improvements.
+
 **Breaking changes**:
 
 - Move the --quiet/-q command line option to the top-level. Previously
@@ -17,6 +72,8 @@
 - The long form ``--verbosity`` argument has been changed to ``--verbose``
   (:pr:`547`).
 
+- Removed DroMel chrM (:user:`grahamgower`, :pr:`528`, :issue:`405`).
+
 --------------------
 [0.1.1] - 2020-01-02
 --------------------