improved docs for core.Grid

CHANGELOG

@@ -29,6 +29,7 @@ The rules for this file:
 
   * The new mrc module correctly reorients the coordinate system based
     on mapc, mapr, maps and correctly calculates the origin (issue #76)
+  * documented Grid attributes, including axis convention (issue #69)
 
   Deprecations
 

doc/source/index.rst

@@ -62,13 +62,5 @@ the `GridDataFormats repository on GitHub`_ and submit a pull request. Participa
    installation	      
    gridData/overview
    gridData/basic
-   gridData/formats
    gridData/core
-
-
-.. rubric:: Indices and tables
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
-
+   gridData/formats

gridData/__init__.py

@@ -3,9 +3,9 @@
 # Released under the GNU Lesser General Public License, version 3 or later.
 # See the files COPYING and COPYING.LESSER for details.
 
-"""
-:mod:`gridData` -- Handling grids of data
-=========================================
+r"""
+Handling grids of data --- :mod:`gridData`
+==========================================
 
 Overview
 --------
@@ -18,9 +18,10 @@
 coordinates of the intersections of the grid (mesh) lines on the
 axes. In this way the grid is anchored in space.
 
-The :class:`~gridData.core.Grid` object can be resampled at arbitrary resolution (by
-interpolating the data). Standard algebraic operations are defined for
-grids on a point-wise basis (same as for :class:`numpy.ndarray`).
+The :class:`~gridData.core.Grid` object can be resampled at arbitrary
+resolution (by interpolating the data). Standard algebraic operations
+are defined for grids on a point-wise basis (same as for
+:class:`numpy.ndarray`).
 
 
 Description
@@ -44,25 +45,26 @@
 
 :class:`~gridData.core.Grid` objects have some convenient properties:
 
-* The data is represented as a :class:`numpy.ndarray` and thus shares
-  all the advantages coming with this sophisticated and powerful
-  library.
+* The data is represented as a :class:`numpy.ndarray` in
+  :attr:`Grid.grid<~gridData.core.Grid.grid>` and thus can be directly
+  manipulated with all the tools available in NumPy.
 
-* They can be manipulated arithmetically, e.g. one can simply add or
-  subtract two of them and get another one, or multiply by a
-  constant. Note that all operations are defined point-wise (see the
-  :mod:`numpy` documentation for details) and that only grids defined
-  on the same cell edges can be combined.
+* :class:`Grid` instances can be manipulated arithmetically, e.g. one
+  can simply add or subtract two of them and get another one, or
+  multiply by a constant. Note that all operations are defined
+  point-wise (see the :mod:`numpy` documentation for details) and that
+  only grids defined on the same cell edges can be combined.
 
-* A :class:`~gridData.core.Grid` object can also be created from within python code
-  e.g. from the output of the :func:`numpy.histogramdd` function.
+* A :class:`~gridData.core.Grid` object can also be created from
+  within python code e.g. from the output of the
+  :func:`numpy.histogramdd` function.
 
 * The representation of the data is abstracted from the format that
   the files are saved in. This makes it straightforward to add
   additional readers for new formats.
 
 * The data can be written out again in formats that are understood by
-  other programs such as VMD or PyMOL.
+  other programs such as VMD_, ChimeraX_ or PyMOL_.
 
 
 Reading grid data files
@@ -96,15 +98,21 @@
 For the available file formats see :ref:`supported-file-formats`.
 
 
+.. _VMD: https://www.ks.uiuc.edu/Research/vmd/
+
+.. _PyMOL: https://pymol.org/
+
+.. _ChimeraX: https://www.cgl.ucsf.edu/chimerax/
 
 """
 
 from .core import Grid
 from . import OpenDX
 from . import gOpenMol
-from . import CCP4
+from . import mrc
+from . import CCP4  # remove in 0.8.0
 
-__all__ = ['Grid', 'OpenDX', 'gOpenMol', 'CCP4']
+__all__ = ['Grid', 'OpenDX', 'gOpenMol', 'mrc', 'CCP4']
 
 from ._version import get_versions
 __version__ = get_versions()['version']