Merge pull request #595 from mcveanlab/CHANGELOG-0.6.1

CHANGELOG updates for version 0.6.1.

CHANGELOG.rst

@@ -1,18 +1,32 @@
 ********************
-[0.6.1] - 2018-xx-xx
+[0.6.1] - 2018-08-25
 ********************
 
+Significant features for integration with forwards-time simulators plus
+improvements and bugfixes.
+
 **Breaking changes**:
 
 - Change in the semantics of how populations are treated by simplify. By
-  default, populations that are not refenced will now be removed from the
+  default, populations that are not referenced will now be removed from the
   data model. This can be avoided by setting ``filter_populations=False``.
 
 - Simplify now raises an error if called on a set of tables that contain
   one or more migrations.
 
 **New features**:
 
+- The simulate() function now supports a ``from_ts`` argument allowing
+  msprime to complete the ancestry in tree sequences generated by
+  forward simulations (#503, #541, #572, #581).
+
+- Add start_time and end_time parameters to the ``mutate`` function (#508).
+
+- Add ``reduce_to_site_topology`` argument to simplify. This allows us to
+  find the minimal tree sequence that would be visible from a given set
+  of sites, and is also a useful compression method if we are only interested
+  in the observed sequences. (#545, #307).
+
 - Simplify generalised to support individuals, and the ``filter_populations``,
   ``filter_individuals`` and ``filter_sites`` parameters added to allow
   filtering of unreferenced objects from the data model. (#567).
@@ -21,7 +35,16 @@
   a system source of randomness (#534). Random seeds should also be safely generated
   across multiple processes.
 
-- Add start_time and end_time parameters to the ``mutate`` function (#508).
+- Full text I/0 support for Individuals and Populations (#498, #555)
+
+- Substantially improved performance in ``msprime.load`` for large tables
+  and significant refactoring of C code (#559, #567, #569).
+
+- Improved performance of generating genotypes (#580).
+
+- Formal schema for tree sequence provenance (#566, #583).
+
+- Many updates to documentation.
 
 **Bug fixes**: