From 377ceaf23ba3b50c6bf90e22ba5f7a9fda45ddfb Mon Sep 17 00:00:00 2001
From: Ben Jeffery <ben.jeffery@bdi.ox.ac.uk>
Date: Fri, 4 Sep 2020 13:43:35 +0100
Subject: [PATCH 1/2] Update changelogs

---
 c/CHANGELOG.rst      | 7 ++++++-
 python/CHANGELOG.rst | 9 ++++++++-
 2 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/c/CHANGELOG.rst b/c/CHANGELOG.rst
index b14569a542..84e1fe37f4 100644
--- a/c/CHANGELOG.rst
+++ b/c/CHANGELOG.rst
@@ -1,7 +1,12 @@
 ---------------------
-[0.99.6] - 2020-XX-XX
+[0.99.6] - 2020-09-04
 ---------------------
 
+**Bugfixes**
+
+- :issue:`823` - Fix mutation time error when using
+  ``tsk_table_collection_simplify`` with ``TSK_KEEP_INPUT_ROOTS``
+  (:user:`petrelharp`, :pr:`823`).
 
 ---------------------
 [0.99.5] - 2020-08-27
diff --git a/python/CHANGELOG.rst b/python/CHANGELOG.rst
index c2c7f3e5e8..1897dd4ea7 100644
--- a/python/CHANGELOG.rst
+++ b/python/CHANGELOG.rst
@@ -1,7 +1,14 @@
 --------------------
-[0.X.X] - 2020-XX-XX
+[0.3.1] - 2020-09-04
 --------------------
 
+**Bugfixes**
+
+- :issue:`823` - Fix mutation time error when using
+  ``simplify(keep_input_roots=True)`` (:user:`petrelharp`, :pr:`823`).
+
+- :issue:`821` - Fix mutation rows with unknown time never being
+  equal (:user:`petrelharp`, :pr:`822`).
 
 --------------------
 [0.3.0] - 2020-08-27

From 710483c57b25f512a33f26953eac6aff4b9651b4 Mon Sep 17 00:00:00 2001
From: Ben Jeffery <ben.jeffery@bdi.ox.ac.uk>
Date: Fri, 4 Sep 2020 13:46:02 +0100
Subject: [PATCH 2/2] Set python version for release

---
 python/tskit/_version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/tskit/_version.py b/python/tskit/_version.py
index 986d1eed12..50949c214a 100644
--- a/python/tskit/_version.py
+++ b/python/tskit/_version.py
@@ -1,4 +1,4 @@
 # Definitive location for the version number.
 # During development, should be x.y.z.devN
 # For beta should be x.y.zbN
-tskit_version = "0.3.1.dev1"
+tskit_version = "0.3.1"