update the doc and api doc to 1.2b2

Author: XiaohaoYang

Diff for: doc/manual/source/api/diffpy.Structure.Parsers.rst

@@ -1,98 +1,102 @@
-Parsers Package
-===============
+diffpy.Structure.Parsers package
+================================
 
-:mod:`Parsers` Package
-----------------------
+Submodules
+----------
 
-.. automodule:: diffpy.Structure.Parsers
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`P_auto` Module
---------------------
+diffpy.Structure.Parsers.P_auto module
+--------------------------------------
 
 .. automodule:: diffpy.Structure.Parsers.P_auto
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`P_bratoms` Module
------------------------
+diffpy.Structure.Parsers.P_bratoms module
+-----------------------------------------
 
 .. automodule:: diffpy.Structure.Parsers.P_bratoms
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`P_cif` Module
--------------------
+diffpy.Structure.Parsers.P_cif module
+-------------------------------------
 
 .. automodule:: diffpy.Structure.Parsers.P_cif
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`P_discus` Module
-----------------------
+diffpy.Structure.Parsers.P_discus module
+----------------------------------------
 
 .. automodule:: diffpy.Structure.Parsers.P_discus
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`P_pdb` Module
--------------------
+diffpy.Structure.Parsers.P_pdb module
+-------------------------------------
 
 .. automodule:: diffpy.Structure.Parsers.P_pdb
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`P_pdffit` Module
-----------------------
+diffpy.Structure.Parsers.P_pdffit module
+----------------------------------------
 
 .. automodule:: diffpy.Structure.Parsers.P_pdffit
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`P_rawxyz` Module
-----------------------
+diffpy.Structure.Parsers.P_rawxyz module
+----------------------------------------
 
 .. automodule:: diffpy.Structure.Parsers.P_rawxyz
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`P_xcfg` Module
---------------------
+diffpy.Structure.Parsers.P_xcfg module
+--------------------------------------
 
 .. automodule:: diffpy.Structure.Parsers.P_xcfg
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`P_xyz` Module
--------------------
+diffpy.Structure.Parsers.P_xyz module
+-------------------------------------
 
 .. automodule:: diffpy.Structure.Parsers.P_xyz
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`parser_index_mod` Module
-------------------------------
+diffpy.Structure.Parsers.parser_index_mod module
+------------------------------------------------
 
 .. automodule:: diffpy.Structure.Parsers.parser_index_mod
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`structureparser` Module
------------------------------
+diffpy.Structure.Parsers.structureparser module
+-----------------------------------------------
 
 .. automodule:: diffpy.Structure.Parsers.structureparser
     :members:
     :undoc-members:
     :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: diffpy.Structure.Parsers
+    :members:
+    :undoc-members:
+    :show-inheritance:

Diff for: doc/manual/source/api/diffpy.Structure.applications.rst

@@ -1,26 +1,30 @@
-applications Package
-====================
+diffpy.Structure.applications package
+=====================================
 
-:mod:`applications` Package
----------------------------
+Submodules
+----------
 
-.. automodule:: diffpy.Structure.applications
+diffpy.Structure.applications.anyeye module
+-------------------------------------------
+
+.. automodule:: diffpy.Structure.applications.anyeye
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`anyeye` Module
---------------------
+diffpy.Structure.applications.transtru module
+---------------------------------------------
 
-.. automodule:: diffpy.Structure.applications.anyeye
+.. automodule:: diffpy.Structure.applications.transtru
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`transtru` Module
-----------------------
 
-.. automodule:: diffpy.Structure.applications.transtru
+Module contents
+---------------
+
+.. automodule:: diffpy.Structure.applications
     :members:
     :undoc-members:
     :show-inheritance:

Diff for: doc/manual/source/api/diffpy.Structure.expansion.rst

@@ -1,42 +1,46 @@
-expansion Package
-=================
+diffpy.Structure.expansion package
+==================================
 
-:mod:`expansion` Package
-------------------------
+Submodules
+----------
 
-.. automodule:: diffpy.Structure.expansion
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`makeCuboctahedron` Module
--------------------------------
+diffpy.Structure.expansion.makeCuboctahedron module
+---------------------------------------------------
 
 .. automodule:: diffpy.Structure.expansion.makeCuboctahedron
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`makeEllipsoid` Module
----------------------------
+diffpy.Structure.expansion.makeEllipsoid module
+-----------------------------------------------
 
 .. automodule:: diffpy.Structure.expansion.makeEllipsoid
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`shapeUtils` Module
-------------------------
+diffpy.Structure.expansion.shapeUtils module
+--------------------------------------------
 
 .. automodule:: diffpy.Structure.expansion.shapeUtils
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`supercell_mod` Module
----------------------------
+diffpy.Structure.expansion.supercell_mod module
+-----------------------------------------------
 
 .. automodule:: diffpy.Structure.expansion.supercell_mod
     :members:
     :undoc-members:
     :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: diffpy.Structure.expansion
+    :members:
+    :undoc-members:
+    :show-inheritance: