Add conda instructions to README.

Finish conversion to RST format.  Advise about DiffPy-CMI.

Author: pavoljuhas

README.rst

@@ -5,79 +5,107 @@
    :target: http://codecov.io/github/diffpy/diffpy.pdffit2?branch=master
 
 
-diffpy.pdffit2 - real space structure refinement to atomic PDF
-
-The diffpy.pdffit2 package enables calculation and refinement of atomic
-Pair Distribution Function (PDF) from crystal structure model.  It is
-used as a computational engine by PDFgui.  All refinements possible
-in PDFgui can be done with diffpy.pdffit2, it is a lower level library
-and requires fair Python knowledge.  The package includes a pdffit2
-command-line application, which tries to mimic the old PDFFIT program.
-The pdffit2 program launches Python interactive session with several
-libraries and functions preloaded for convenience.  The pdffit2 program
-is suitable for interactive use, however refinement scripts should be
-rather written as normal Python; this is more reliable and needs only
-few extra lines of code.
+PDFfit2
+========================================================================
+
+Real space structure refinement to atomic pair distribution function.
+
+The diffpy.pdffit2 package provides functions for calculation and
+refinement of atomic Pair Distribution Function (PDF) from crystal
+structure model.  It is used as a computational engine by PDFgui.  All
+refinements possible in PDFgui can be done with diffpy.pdffit2,
+although less conveniently and with a fair knowledge of Python.
+The package includes an extension for the interactive `IPython
+<http://ipython.org>`__ shell, which tries to mimic the old PDFFIT
+program.  To start IPython with this extension and also with plotting
+functions enabled, use ::
+
+   ipython --ext=diffpy.pdffit2.ipy_ext --pylab
+
+The IPython extension is suitable for interactive use, however
+refinement scripts should be preferably written as a standard
+Python code.  This is more reliable and needs only a few extra
+statements.
 
 To learn more about diffpy.pdffit2 library, see the examples directory
 included in this distribution or the API documentation at
-
-    http://docs.danse.us/diffraction/diffpy.pdffit2
+http://www.diffpy.org/doc/pdffit2.
 
 
 REQUIREMENTS
+------------------------------------------------------------------------
 
-diffpy.pdffit2 requires Python2.5 and the following external software:
-
-    setuptools  -- software distribution tools for Python
-    python-dev  -- header files for interfacing Python with C
-    GSL         -- GNU Scientific Library for C
-    g++         -- GNU C++ compiler
+diffpy.pdffit2 requires Python 2.6 or 2.7 and the following external
+software:
 
-On Ubuntu Linux the required software can be easily installed using
-the system package manager:
+* ``setuptools`` - software distribution tools for Python
+* ``python-dev`` - header files for interfacing Python with C
+* ``GSL`` - GNU Scientific Library for C
+* ``g++`` - GNU C++ compiler
+* ``diffpy.Structure`` - simple storage and manipulation of atomic
+  structures, https://github.com/diffpy/diffpy.Structure
 
-    sudo aptitude install \
-        python-setuptools python-dev libgsl0-dev g++
+We recommend to use `Anaconda Python <https://www.continuum.io/downloads>`_
+as it allows to install all software dependencies together with
+PDFfit2.  For other Python distributions it is necessary to
+install the required software separately.  As an example, on Ubuntu
+Linux some of the required software can be installed using ::
 
-For other Linux distributions use their respective package manager; note
-the packages may have slightly different names.  diffpy.pdffit2 should work on
-other Unix-like operating systems and on Mac as well.  Please, search the web
-for instructions how to install external dependencies on your particular
-system.
+   sudo apt-get install \
+      python-setuptools python-dev libgsl0-dev build-essential
 
 
 INSTALLATION
+------------------------------------------------------------------------
+
+The preferred method is to use Anaconda Python and install from the
+"diffpy" channel of Anaconda packages ::
+
+   conda config --add channels diffpy
+   conda install diffpy.pdffit2
+
+If you don't use Anaconda or prefer to install from sources, make
+sure the required software is in place and run ::
+
+   python setup.py install
+
+By default the files get installed to standard system directories,
+which may require the use of ``sudo`` for write permissions.  If
+administrator (root) access is not available, consult the output from
+``python setup.py install --help`` for options to install as a regular
+user to other locations.  The installation integrity can be
+verified by changing to the HOME directory and running ::
+
+   python -m diffpy.pdffit2.tests.rundeps
+
+Anaconda Python allows to later update PDFfit2 using ::
 
-Once the requirements are satisfied, diffpy.pdffit2 can be installed with
+   conda update diffpy.pdffit2
 
-    python setup.py install
+With other Python distributions use the easy_install program to
+upgraded to the latest version ::
 
-This installs the library and the pdffit2 program to the default system
-directories.  See the usage info "./setup.py install --help" for options
-to install under different locations.  Note that installation to non-standard
-directories you may require adjustment to the PATH and PYTHONPATH environment
-variables.
+   easy_install --upgrade diffpy.pdffit2
 
-The Python setuptools library provides "easy_install" script, which can
-be used to update diffpy.pdffit2 installation or even to perform a new
-install without explicit need to download and unzip the code:
 
-    easy_install -U diffpy.pdffit2
+DEVELOPMENT
+------------------------------------------------------------------------
 
-This checks the package repository at http://www.diffpy.org/packages/
-for any newer releases of diffpy.pdffit2 and if present, it updates the
-installation.  The easy_install can be also used to get in sync with the
-latest development sources in the subversion repository:
+PDFfit2 is not developed anymore and is only maintained due to its
+status of a sole computational engine for PDFgui.  We don't expect any
+major developments to the code beyond simple bug fixes and compatibility
+features.  The source code to PDFfit2 is available in a git repository
+at https://github.com/diffpy/diffpy.pdffit2.
 
-    easy_install -U \
-        svn://[email protected]/diffraction/diffraction/diffpy.pdffit2/trunk
+For an actively developed codes for PDF simulations see the
+DiffPy-CMI framework at http://www.diffpy.org.
 
 
 CONTACTS
+------------------------------------------------------------------------
 
 For more information on diffpy.pdffit2 please visit the project web-page:
 
-    http://www.diffpy.org/
+http://www.diffpy.org/
 
-or email Prof. Simon Billinge at [email protected]
+or email Prof. Simon Billinge at [email protected].