Updated docs + version bump.

README.txt

@@ -3,23 +3,19 @@ msprime
 =======
 
 Msprime is a reimplementation of Hudson's classical ms program for modern
-datasets. It is under heavy development at the moment, and the present
-code should be considered beta quality. Bugs may be present,
-and the API might change considerably. We provide an ms-compatible
-command line interface ``mspms``, which should be useful to fit into
-existing workflows. However, the Python API is the recommended way to
-use msprime to gain full advantage of its internal structures.
-
-Full documentation is forthcoming.
+datasets. The Python API and storage format are currently under development
+and are not fully documented, but the command line interface ``mspms`` is
+reliable and ready for use. This program provides a fully ``ms`` compatible
+interface, and can be used as a drop-in replacement in existing workflows.
 
 *************
 Requirements
 *************
 
 Msprime requires Python 2.7+ (Python 3 versions are fully supported from
-3.1 onwards), the `GNU Scientific Library <http://www.gnu.org/software/gsl/>`_
-and `HDF5 <https://www.hdfgroup.org/HDF5/>`_ version 1.8 or later,
-which are available for all major platforms. For example, to install on
+3.1 onwards), the `GNU Scientific Library <http://www.gnu.org/software/gsl/>`_,
+and `HDF5 <https://www.hdfgroup.org/HDF5/>`_ version 1.8 or later. These
+packages are available for all major platforms. For example, to install on
 Debian/Ubuntu use::
 
     # apt-get install python-dev libgsl0-dev libhdf5-serial-dev pkg-config
@@ -38,7 +34,7 @@ TODO
 FreeBSD 10.0
 ------------
 
-To install on FreeBSD, install the gsl and hdf5-18 packages as 
+To install on FreeBSD, install the gsl and hdf5-18 packages as
 follows::
 
     # pkg install gsl hdf5-18

docs/api.rst

@@ -4,12 +4,4 @@
 API Documentation
 =================
 
-.. automodule:: msprime
-    :members:
-
-.. autofunction:: simulate
-.. autofunction:: load
-
-.. autoclass:: TreeSequence
-
-.. autoclass:: SparseTree
+*Under construction*

docs/index.rst

@@ -6,6 +6,12 @@
 Welcome to msprime's documentation!
 ===================================
 
+This is the documentation for ``msprime``, a reimplementation of Hudson's
+classical :command:`ms` simulator. For the initial beta release, only the
+:command:`ms` compatible :ref:`command line interface <sec-cli>` is supported.
+However, full documentation for the Python API and tree storage file format
+are under development, and will be completed soon.
+
 Contents:
 
 .. toctree::

msprime/__init__.py

@@ -28,4 +28,4 @@
 
 from msprime.trees import *  # NOQA
 
-__version__ = '0.1.1a4'
+__version__ = '0.1.1a5'