doc fixes

- include nhaa_equilibrium in docs...
- minor fixes

Author: orbeckst

MDAnalysisData/base.py

@@ -37,8 +37,10 @@
 from pkg_resources import resource_string
 
 #: Default value for the cache directory. It can be changed by setting
-#: The environment variable :envvar:`MDANALYSIS_DATA`. The current
+#: the environment variable :envvar:`MDANALYSIS_DATA`. The current
 #: value should be queried with :func:`get_data_home`.
+#:
+#: .. SeeAlso:: :ref:`managing-data`.
 DEFAULT_DATADIR = join('~', 'MDAnalysis_data')
 
 class Bunch(dict):
@@ -186,7 +188,7 @@ def _fetch_remote(remote, dirname=None):
 
 
 def _read_description(filename, description_dir='descr'):
-    """Read the description from restructured text file `descr`.
+    """Read the description from restructured text file.
 
     Arguments
     ---------
@@ -196,9 +198,10 @@ def _read_description(filename, description_dir='descr'):
     Note
     ----
     All description files are supposed to be stored in the directory
-    ``description_dir`="descr"` that lives in the same directory as
+    `description_dir` ``="descr"`` that lives in the same directory as
     the :mod:`MDAnalysisData.base` module file. All descriptions are
     assumed to be in restructured text format and in UTF-8 encoding.
+
     """
     # The descr directory should be in the same directory as this file base.py.
     # `resource_string` returns bytes, which we need to decode to UTF-8

MDAnalysisData/descr/nhaa_equilibrium.rst

@@ -3,7 +3,7 @@
 .. _`nhaa-equilibrium-dataset`:
 
 NhaA equilibrium trajectory dataset
-==================================
+===================================
 
 Molecular dynamics (MD) trajectory of the NhaA membrane protein in a
 POPE:POPG 4:1 model membrane. The equilibrium simulation was performed

docs/helpers.rst

@@ -17,7 +17,7 @@ For users
 .. autoclass:: Bunch
    :members:
 
-.. data:: DEFAULT_DATADIR
+.. autodata:: DEFAULT_DATADIR
 
 .. autofunction:: get_data_home
 

docs/index.rst

@@ -87,4 +87,5 @@ of pull requests are very welcome.
    adk_equilibrium
    adk_transitions
    ifabp_water
+   nhaa_equilibrium
    vesicles