docs: cleaned up member presentation

- fixed: classes littered the sidebar doc menu
- removed :member: on .. automodule:: and explicitly document classes in core and formats

Author: orbeckst

doc/source/gridData/core.rst

@@ -1,2 +1,2 @@
 .. automodule:: gridData.core
-   :members:
+

doc/source/gridData/formats.rst

@@ -27,7 +27,7 @@ small number of file formats is directly supported.
    ============================ ==========  =========  =====  =====  =========================================
    :mod:`~gridData.OpenDX`      OpenDX_     dx         x      x      subset of OpenDX implemented
    :mod:`~gridData.gOpenMol`    gOpenMol_   plt        x
-   :mod:`~gridData.mrc`         CCP4_       ccp4,mrc   x             subset implemented
+   :mod:`~gridData.mrc`         CCP4_       ccp4,mrc   x      x      subset implemented
    :class:`~gridData.core.Grid` pickle      pickle     x      x      standard Python pickle of the Grid class
    ============================ ==========  =========  =====  =====  =========================================
 

doc/source/gridData/formats/OpenDX.rst

@@ -1,3 +1,3 @@
 .. automodule:: gridData.OpenDX
-   :members:
+
 

doc/source/gridData/formats/gOpenMol.rst

@@ -1,2 +1,2 @@
 .. automodule:: gridData.gOpenMol
-   :members:
+

doc/source/gridData/formats/mrc.rst

@@ -1,2 +1,2 @@
 .. automodule:: gridData.mrc
-   :members:
+

doc/source/index.rst

@@ -49,7 +49,7 @@ GridDataFormats is open source and welcomes your contributions. Fork the `GridDa
 .. Contents (sidebar)
 
 .. toctree::
-   :maxdepth: 4
+   :maxdepth: 3
    :hidden:
 
    installation	      

gridData/OpenDX.py

@@ -160,8 +160,46 @@
    https://web.archive.org/web/20080808140524/http://opendx.sdsc.edu/docs/html/pages/usrgu068.htm
 .. http://opendx.sdsc.edu/docs/html/pages/usrgu068.htm#HDREDF
 
-Classes and functions
----------------------
+Classes
+-------
+
+DX field class
+~~~~~~~~~~~~~~
+
+The primary class is :class:`field`, which is a container for the other classes.
+It contains the following classes:
+
+* :class:`gridpositions`
+* :class:`gridconnections`
+* :class:`array`
+
+The :class:`gridpositions` class contains the position of the grid cells.
+The :class:`gridconnections` class contains the connections between the grid cells.
+The :class:`array` class contains the data on the grid.
+
+.. autoclass:: field
+   :members:
+
+DX components
+~~~~~~~~~~~~~
+
+The :class:`field` class contains the following components:
+
+.. autoclass:: gridpositions
+   :members:
+
+.. autoclass:: gridconnections
+   :members:
+
+.. autoclass:: array
+   :members:
+
+DX parser
+~~~~~~~~~~
+The :class:`DXParser` class is used to parse the DX file and construct the :class:`field` object.
+
+.. autoclass:: DXParser
+   :members:
 
 """
 import numpy

gridData/core.py

@@ -2,8 +2,8 @@
 # Copyright (c) 2009-2014 Oliver Beckstein <orbeckst@gmail.com>
 # Released under the GNU Lesser General Public License, version 3 or later.
 r"""
-Core functionality for storing n-D grids --- :mod:`gridData.core`
-=================================================================
+Core functionality for storing n-D grids
+========================================
 
 The :mod:`core` module contains classes and functions that are
 independent of the grid data format. In particular this module
@@ -19,10 +19,20 @@
  g.load(filename)             # populate with data from filename
 
 
-Classes and functions
----------------------
+Classes
+-------
 
+.. autoclass:: Grid
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Functions
+---------
+
+.. autofunction:: ndmeshgrid
 """
+
 import os
 import errno
 import pickle

gridData/gOpenMol.py

@@ -126,6 +126,9 @@
 Classes
 -------
 
+.. autoclass:: Plt
+   :members:
+
 """
 import warnings
 import struct

gridData/mrc.py

@@ -28,6 +28,10 @@
 Classes
 -------
 
+.. autoclass:: MRC
+   :members:
+
+
 """
 import numpy as np
 import mrcfile
@@ -176,6 +180,7 @@ def write(self, filename):
         header information (including mapc, mapr, maps ordering) is preserved.
         Otherwise, standard ordering (mapc=1, mapr=2, maps=3) is used.
         
+        
         .. versionadded:: 1.1.0
         """
         if filename is not None: