Write up changelog for 0.2.0

Author: jeromekelleher

docs/tutorial.rst

@@ -829,7 +829,7 @@ Computing statistics
 
 Tskit provides an extensive and flexible interface for computing population
 genetic statistics, which is documented in detail in the :ref:`general statistics
-<sec_general_stats>` section. This tutorial aims to give a quick overview of
+<sec_stats>` section. This tutorial aims to give a quick overview of
 how the APIs work how to use them effectively.
 
 First, lets simulate a tree sequence to work with which has roughly human
@@ -859,7 +859,7 @@ is computed using the :meth:`.TreeSequence.diversity` method::
 
 This tells the average diversity across the whole sequence and returns a single
 number. We'll usually want to compute statistics in
-:ref:`windows <sec_general_stats_windowing>` along the genome and we
+:ref:`windows <sec_stats_windows>` along the genome and we
 use the ``windows`` argument to do this::
 
     windows = np.linspace(0, ts.sequence_length, num=5)
@@ -877,7 +877,7 @@ along the genome. Here, we use numpy to create four equally spaced windows
 of size 2.5 megabases (the windows array contains k + 1 elements to define
 k windows). Because we have asked for values in windows, tskit now returns
 a numpy array rather than a single value. (See
-:ref:`sec_general_stats_output_dimensions` for a full description of how the output
+:ref:`sec_stats_output_dimensions` for a full description of how the output
 dimensions of statistics are determined by the ``windows`` argument.)
 
 Suppose we wanted to compute diversity within a specific subset of samples.
@@ -911,7 +911,7 @@ Because we've computed multiple statistics concurrently, tskit returns a numpy a
 of these statistics. We have asked for diversity within three different sample sets,
 and tskit therefore returns an array with three values. (In general, the
 dimensions of the input determines the dimensions of the output: see
-:ref:`sec_general_stats_output_dimensions` for a detailed description of the rules.)
+:ref:`sec_stats_output_dimensions` for a detailed description of the rules.)
 
 We can also compute multiple statistics in multiple windows::
 
@@ -1020,7 +1020,7 @@ output as an array with one value if we wish::
 
     [0.00039765]
 
-Please see :ref:`sec_general_stats_sample_sets` for a
+Please see :ref:`sec_stats_sample_sets` for a
 full description of the ``sample_sets`` and ``indexes`` arguments.
 
 .. _sec_tutorial_afs:

python/CHANGELOG.rst

@@ -13,15 +13,82 @@ In development.
   from numpy "u8" to "i8". This should not affect client code in any way
   unless it specifically depends on the type of the returned numpy array.
 
+- The VCF written by the ``write_vcf`` is no longer compatible with previous
+  versions, which had significant shortcomings. Position values are now rounded
+  to the nearest integer by default, REF and ALT values are derived from the
+  actual allelic states (rather than always being A and T). Sample names
+  are now of the form ``tsk_j`` for sample ID j. Most of the legacy behaviour
+  can be recovered with new options, however.
+
 - The positional parameter ``reference_sets`` in ``genealogical_nearest_neighbours``
   and ``mean_descendants`` TreeSequence methods has been renamed to
   ``sample_sets``.
 
 **New features**
 
+- Support for general windowed statistics. Implementations of diversity,
+  divergence, segregating sites, Tajima's D, Fst, Patterson's F statistics,
+  Y statistics, trait correlations and covariance, and k-dimensional allele
+  frequency specra (:user:`petrelharp`, :user:`jeromekelleher`, :user:`molpopgen`).
+
 - Add the ``keep_unary`` option to simplify (:user:`gtsambos`). See :issue:`1`
   and :pr:`143`.
 
+- Add the ``map_ancestors`` method to TableCollection (user:`gtsambos`). See :pr:`175`.
+
+- Add the ``squash`` method to EdgeTable (:user:`gtsambos`). See :issue:`59` and
+  :pr:`285`.
+
+- Add support for individuals to VCF output, and fix major issues with output
+  format (:user:`jeromekelleher`). Position values are transformed in a much
+  more straightforward manner and output has been generalised substantially.
+  Adds ``individual_names`` and ``position_transform`` arguments.
+  See :pr:`286`, and issues :issue:`2`, :issue:`30` and :issue:`73`.
+
+- Control height scale in SVG trees using 'tree_height_scale' and 'max_tree_height'
+  (:user:`hyanwong`, :user:`jeromekelleher`). See :issue:`167`, :pr:`168`.
+  Various other improvements to tree drawing (:pr:`235`, :pr:`241`, :pr:`242`,
+  :pr:`252`, :pr:`259`).
+
+- Add ``Tree.max_root_time`` property (:user:`hyanwong`, :user:`jeromekelleher`).
+  See :pr:`170`.
+
+- Improved input checking on various methods taking numpy arrays as parameters
+  (:user:`hyanwong`). See :issue:`8` and :pr:`185`.
+
+- Define the branch length over roots in trees to be zero (previously raise
+  an error; :user:`jeromekelleher`). See :issue:`188` and :pr:`191`.
+
+- Implementation of the genealogical nearest neighbours statistic
+  (:user:`hyanwong`, :user:`jeromekelleher`).
+
+- New ``delete_intervals`` and ``keep_intervals`` method for the TableCollection
+  to allow slicing out of topology from specific intervals (:user:`hyanwong`,
+  :user:`andrewkern`, :user:`petrelharp`, :user:`jeromekelleher`). See
+  :pr:`225` and :pr:`261`.
+
+- Support for missing data via a topological definition (:user:`jeromekelleher`).
+  See :issue:`270` and :pr:`272`.
+
+- Add ability to set columns directly in the Tables API (:user:`jeromekelleher`).
+  See :issue:`12` and :pr:`307`.
+
+- Various documentation improvements from :user:`brianzhang`, :user:`hyanwong`,
+  :user:`petrelharp` and :user:`jeromekelleher`.
+
+**Deprecated**
+
+- Deprecate ``Tree.length`` in favour of ``Tree.span`` (:user:`hyanwong`).
+  See :pr:`169`.
+
+- Deprecate ``TreeSequence.pairwise_diversity`` in favour of the new
+  ``diversity`` method. See :issue:`215`, :pr:`312`.
+
+**Bugfixes**
+
+- Catch NaN and infinity values within tables (:user:`hyanwong`).
+  See :issue:`293` and :pr:`294`.
+
 --------------------
 [0.1.5] - 2019-03-27
 --------------------
@@ -45,10 +112,12 @@ new ``tskit`` command line interface.
 
 - Fixes to the low-level C API (:issue:`132` and :issue:`157`)
 
+
 --------------------
 [0.1.4] - 2019-02-01
 --------------------
 
+
 Minor feature update. Using the C API 0.99.1.
 
 **New features**