update doc and api doc to 1.0a0

Author: XiaohaoYang

doc/manual/source/api/diffpy.rst

@@ -1,13 +1,17 @@
-diffpy Package
+diffpy package
 ==============
 
-:mod:`diffpy` Package
----------------------
-
 Subpackages
 -----------
 
 .. toctree::
 
     diffpy.srreal
 
+Module contents
+---------------
+
+.. automodule:: diffpy
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/manual/source/api/diffpy.srreal.rst

@@ -1,170 +1,166 @@
-srreal Package
-==============
+diffpy.srreal package
+=====================
 
-:mod:`srreal` Package
----------------------
+Submodules
+----------
 
-.. automodule:: diffpy.srreal
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`atomradiitable` Module
-----------------------------
+diffpy.srreal.atomradiitable module
+-----------------------------------
 
 .. automodule:: diffpy.srreal.atomradiitable
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`attributes` Module
-------------------------
+diffpy.srreal.attributes module
+-------------------------------
 
 .. automodule:: diffpy.srreal.attributes
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`bondcalculator` Module
-----------------------------
+diffpy.srreal.bondcalculator module
+-----------------------------------
 
 .. automodule:: diffpy.srreal.bondcalculator
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`bvparameterstable` Module
--------------------------------
+diffpy.srreal.bvparameterstable module
+--------------------------------------
 
 .. automodule:: diffpy.srreal.bvparameterstable
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`bvscalculator` Module
----------------------------
+diffpy.srreal.bvscalculator module
+----------------------------------
 
 .. automodule:: diffpy.srreal.bvscalculator
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`eventticker` Module
--------------------------
+diffpy.srreal.eventticker module
+--------------------------------
 
 .. automodule:: diffpy.srreal.eventticker
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`overlapcalculator` Module
--------------------------------
+diffpy.srreal.overlapcalculator module
+--------------------------------------
 
 .. automodule:: diffpy.srreal.overlapcalculator
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`pairquantity` Module
---------------------------
+diffpy.srreal.pairquantity module
+---------------------------------
 
 .. automodule:: diffpy.srreal.pairquantity
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`parallel` Module
-----------------------
+diffpy.srreal.parallel module
+-----------------------------
 
 .. automodule:: diffpy.srreal.parallel
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`pdfbaseline` Module
--------------------------
+diffpy.srreal.pdfbaseline module
+--------------------------------
 
 .. automodule:: diffpy.srreal.pdfbaseline
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`pdfcalculator` Module
----------------------------
+diffpy.srreal.pdfcalculator module
+----------------------------------
 
 .. automodule:: diffpy.srreal.pdfcalculator
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`pdfenvelope` Module
--------------------------
+diffpy.srreal.pdfenvelope module
+--------------------------------
 
 .. automodule:: diffpy.srreal.pdfenvelope
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`peakprofile` Module
--------------------------
+diffpy.srreal.peakprofile module
+--------------------------------
 
 .. automodule:: diffpy.srreal.peakprofile
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`peakwidthmodel` Module
-----------------------------
+diffpy.srreal.peakwidthmodel module
+-----------------------------------
 
 .. automodule:: diffpy.srreal.peakwidthmodel
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`scatteringfactortable` Module
------------------------------------
+diffpy.srreal.scatteringfactortable module
+------------------------------------------
 
 .. automodule:: diffpy.srreal.scatteringfactortable
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`structureadapter` Module
-------------------------------
+diffpy.srreal.structureadapter module
+-------------------------------------
 
 .. automodule:: diffpy.srreal.structureadapter
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`structureconverters` Module
----------------------------------
+diffpy.srreal.structureconverters module
+----------------------------------------
 
 .. automodule:: diffpy.srreal.structureconverters
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`version` Module
----------------------
+diffpy.srreal.version module
+----------------------------
 
 .. automodule:: diffpy.srreal.version
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`wraputils` Module
------------------------
+diffpy.srreal.wraputils module
+------------------------------
 
 .. automodule:: diffpy.srreal.wraputils
     :members:
     :undoc-members:
     :show-inheritance:
 
-Subpackages
------------
-
-.. toctree::
 
-    diffpy.srreal.tests
+Module contents
+---------------
 
+.. automodule:: diffpy.srreal
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/manual/source/index.rst

@@ -13,6 +13,7 @@ Last updated |today|.
 
 diffpy.srreal - calculators for PDF, bond valence sum and other pair quantities
 
+
 The diffpy.srreal package provides calculators for atomic pair distribution
 function (PDF), bond valence sums (BVS), atom overlaps for a hard-sphere
 model, bond distances and directions up to specified maximum distance.   The
@@ -31,7 +32,7 @@ be done in two modes - either as a real-space summation of peak profiles
 transform of the total scattering structure function (DebyePDFCalculator).
 
 The diffpy.srreal package is a Python binding to the C++ library libdiffpy
-(https://github.com/diffpy/libdiffpy/).  Calculators are created as
+(https://github.com/diffpy/libdiffpy).  Calculators are created as
 objects of a given calculator type and so multiple instances of the same
 calculator type can exist with different configurations.  Calculators are
 composed of other objects that perform lower-level tasks, such as calculating
@@ -47,7 +48,7 @@ pairs, by defining only the function that processes atom-pair contributions.
 Disclaimer
 ===================
 
-.. include:: ../../../LICENSE.txt
+.. literalinclude:: ../../../LICENSE.txt
 
 ================
 Acknowledgments

doc/manual/source/install.rst

@@ -8,74 +8,72 @@ Requirements
 
 The diffpy.srreal requires Python 2.6 or 2.7 and the following software:
 
-* `setuptools`   - tools for installing Python packages
-* `NumPy`        - library for scientific computing with Python
-* `scons`        - software constructions tool (1.0 or later)
-* `python-dev`   - header files for interfacing Python with C
-* `libboost-dev` - Boost C++ libraries development files (1.43 or later)
-* `libdiffpy`    - C++ library for PDF, bond valence sum and other pair
-                    quantity calculators https://github.com/diffpy/libdiffpy/
-* `diffpy.Structure` - simple storage and manipulation of atomic structures
-                    https://github.com/diffpy/diffpy.Structure/
+* ``setuptools`` - tools for installing Python packages
+* ``NumPy`` - library for scientific computing with Python
+* ``scons`` - software constructions tool (1.0 or later)
+* ``python-dev`` - header files for interfacing Python with C
+* ``libboost-dev`` - Boost C++ libraries development files (1.43 or later)
+* ``libdiffpy`` - C++ library for PDF, bond valence sum and other pair
+  quantity calculators https://github.com/diffpy/libdiffpy
+* ``diffpy.Structure`` - simple storage and manipulation of atomic structures
+  https://github.com/diffpy/diffpy.Structure
 
 Recommended software:
 
-* `periodictable` - periodic table of elements in Python
-                    http://www.reflectometry.org/danse/elements.html
-* `pyobjcryst`    - Python bindings to ObjCryst++, the Object Oriented
-                    Crystallographic library for C++
-                    https://github.com/diffpy/pyobjcryst/
+* ``periodictable`` - periodic table of elements in Python
+  http://www.reflectometry.org/danse/elements.html
+* ``pyobjcryst`` - Python bindings to ObjCryst++, the Object Oriented
+  Crystallographic library for C++, https://github.com/diffpy/pyobjcryst.
 
 Some of the required software may be available in the system package manager,
 for example, on Ubuntu Linux the dependencies can be installed as::
 
-    sudo apt-get install \
-        python-setuptools python-numpy scons \
-        build-essential python-dev libboost-dev
+   sudo apt-get install \
+      python-setuptools python-numpy scons \
+      build-essential python-dev libboost-dev
 
-For Mac OS X machine with the MacPorts package manager one could do::
+For Mac OS X machine with the MacPorts package manager one could do ::
 
-    sudo port install \
-        python27 py27-setuptools py27-numpy scons boost
+   sudo port install \
+      python27 py27-setuptools py27-numpy scons boost
 
 When installing with MacPorts, make sure the MacPorts bin directory is the
-first in the system PATH and that python27 is selected as the default::
-Python version in MacPorts:
+first in the system PATH and that python27 is selected as the default
+Python version in MacPorts::
 
-    sudo port select --set python python27
+   sudo port select --set python python27
 
 For other required packages see their respective web pages for installation
 instructions.
 
-
 .. index:: Installation
 
 Installation
 ------------------------------------------------------------------------
 
 The easiest option is to use the latest DiffPy-CMI release bundle from
-http://www.diffpy.org/, which comes with diffpy.srreal and all other
+http://www.diffpy.org, which comes with diffpy.srreal and all other
 dependencies included.
 
 If you prefer to install from sources, make sure all required software
-packages are in place and then run::
+packages are in place and then run ::
 
-    sudo python setup.py install
+   sudo python setup.py install
 
 This installs diffpy.srreal for all users in the default system location.
 If administrator (root) access is not available, see the usage info from
-"python setup.py install --help" for options to install to a user-writable
+``python setup.py install --help`` for options to install to a user-writable
 location.  The installation integrity can be verified by changing to
-the HOME directory and running::
+the HOME directory and running ::
 
-    python -m diffpy.srreal.tests.run
+   python -m diffpy.srreal.tests.run
 
-An alternative way of installing diffpy.srreal is to use the scons tool,
+An alternative way of installing diffpy.srreal is to use the SCons tool,
 which can speed up the process by compiling the C++ files in parallel (-j4)::
 
-    sudo scons -j4 install
+   sudo scons -j4 install
 
-See "scons -h" for build parameters and options to install to a user-writable
+See ``scons -h`` for build parameters and options to install to a user-writable
 directory.
 
 
@@ -85,16 +83,15 @@ Development
 diffpy.srreal is an open-source software developed as a part of the
 DiffPy-CMI complex modeling initiative at the Brookhaven National
 Laboratory.  The diffpy.srreal sources are hosted at
-
-    https://github.com/diffpy/diffpy.srreal
+https://github.com/diffpy/diffpy.srreal.
 
 Feel free to fork the project and contribute.  To install diffpy.srreal
 in a development mode, where the sources are directly used by Python
-rather than copied to a system directory, use::
+rather than copied to a system directory, use ::
 
-    python setup.py develop --user
+   python setup.py develop --user
 
 To rebuild the C++ extension module and then optionally test the code
-integrity, use::
+integrity, use ::
 
-    scons -j4 build=debug develop [test]
+   scons -j4 build=debug develop [test]