DOC: move API descriptions to the package document

Author: pavoljuhas

doc/manual/source/index.rst

@@ -55,46 +55,6 @@ by citing the following paper in your publication:
    *Acta Crystallogr. A* **71**, 562-568 (2015).
 
 
-Package contents
-========================================================================
-
-.. module:: diffpy.structure
-
-The top-level diffpy.structure module provides the following objects.
-
-
-Functions
----------
-
-.. autofunction:: loadStructure
-
-
-Classes
--------
-
-:py:class:`~atom.Atom`
-   describes one atom site in the structure - its type, position,
-   displacement parameters and so forth.
-
-:py:class:`~lattice.Lattice`
-   depicts general coordinate system and associated operations.
-
-:py:class:`~structure.Structure`
-   collection of :class:`!Atom` objects that form the structure together
-   with associated :py:class:`!Lattice`.
-
-
-Exceptions
-----------
-
-.. autoclass:: StructureFormatError
-
-.. autoclass:: LatticeError
-
-.. autoclass:: SymmetryError
-
-
-
 Table of contents
 ========================================================================
 

doc/manual/source/package.rst

@@ -1,99 +1,140 @@
-diffpy.structure package
-========================
+:tocdepth: 2
+
+diffpy.structure API
+####################
+
 
 Subpackages
------------
+===========
 
 .. toctree::
+    :titlesonly:
 
     diffpy.structure.parsers
     diffpy.structure.applications
     diffpy.structure.expansion
 
-Submodules
+
+diffpy.structure
+================
+
+.. module:: diffpy.structure
+
+The top-level diffpy.structure module provides the following objects.
+
+
+Functions
+---------
+
+.. autofunction:: loadStructure
+
+
+Classes
+-------
+
+:py:class:`~atom.Atom`
+   describes one atom site in the structure - its type, position,
+   displacement parameters and so forth.
+
+:py:class:`~lattice.Lattice`
+   depicts general coordinate system and associated operations.
+
+:py:class:`~structure.Structure`
+   collection of :class:`!Atom` objects that form the structure together
+   with associated :py:class:`!Lattice`.
+
+
+Exceptions
 ----------
 
-diffpy.structure.spacegroups module
------------------------------------
+.. autoclass:: StructureFormatError
+
+.. autoclass:: LatticeError
+
+.. autoclass:: SymmetryError
+
+
+diffpy.structure.spacegroups
+============================
 
 .. automodule:: diffpy.structure.spacegroups
     :members:
     :undoc-members:
     :show-inheritance:
 
-diffpy.structure.structureerrors module
----------------------------------------
+diffpy.structure.structureerrors
+================================
 
 .. automodule:: diffpy.structure.structureerrors
     :members:
     :undoc-members:
     :show-inheritance:
 
-diffpy.structure.symmetryutilities module
------------------------------------------
+diffpy.structure.symmetryutilities
+==================================
 
 .. automodule:: diffpy.structure.symmetryutilities
     :members:
     :undoc-members:
     :show-inheritance:
 
-diffpy.structure.atom module
-----------------------------
+diffpy.structure.atom
+=====================
 
 .. automodule:: diffpy.structure.atom
     :members:
     :show-inheritance:
 
-diffpy.structure.mmlibspacegroups module
-----------------------------------------
+diffpy.structure.mmlibspacegroups
+=================================
 
 .. automodule:: diffpy.structure.mmlibspacegroups
     :members:
     :undoc-members:
     :show-inheritance:
 
-diffpy.structure.pdffitstructure module
----------------------------------------
+diffpy.structure.pdffitstructure
+================================
 
 .. automodule:: diffpy.structure.pdffitstructure
     :members:
     :undoc-members:
     :show-inheritance:
 
-diffpy.structure.sgtbxspacegroups module
-----------------------------------------
+diffpy.structure.sgtbxspacegroups
+=================================
 
 .. automodule:: diffpy.structure.sgtbxspacegroups
     :members:
     :undoc-members:
     :show-inheritance:
 
-diffpy.structure.spacegroupmod module
--------------------------------------
+diffpy.structure.spacegroupmod
+==============================
 
 .. automodule:: diffpy.structure.spacegroupmod
     :members:
     :undoc-members:
     :special-members: __call__, __eq__
 
-diffpy.structure.structure module
----------------------------------
+diffpy.structure.structure
+==========================
 
 .. automodule:: diffpy.structure.structure
     :members:
     :undoc-members:
     :show-inheritance:
 
-diffpy.structure.utils module
------------------------------
+diffpy.structure.utils
+======================
 
 .. automodule:: diffpy.structure.utils
     :members:
     :undoc-members:
     :show-inheritance:
 
-diffpy.structure.version module
--------------------------------
+diffpy.structure.version
+========================
 
 .. automodule:: diffpy.structure.version
     :members: