Merge pull request #109 from marrink-lab/sphinx1.8

Update sphinx to 1.8.0

doc/source/conf.py

@@ -17,7 +17,7 @@
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
 # Do not generate APIdocs for members missing docstrings (undoc-members)
-os.environ['APIDOC_OPTIONS'] = 'members,show-inheritence'
+os.environ['APIDOC_OPTIONS'] = 'members,show-inheritence,inherited-members'
 
 # Set APIDOC options
 #os.environ['SPHINX_APIDOC_OPTIONS'] = 'members,undoc-members,show-inheritance,special-members'
@@ -180,7 +180,9 @@
 apidoc_excluded_paths = ['tests', 'redistributed']
 
 autoclass_content = 'both'
-autodoc_default_flags = ['members', 'undoc-members', 'show-inheritance']
+autodoc_default_options = {'members': None,
+                           'undoc-members': None,
+                           'show-inheritance': None}
 
 # -- Options for intersphinx extension ---------------------------------------
 # Example configuration for intersphinx: refer to the Python standard library.

requirements-docs.txt

@@ -1,4 +1,4 @@
-sphinx
+sphinx >= 1.8.0
 sphinxcontrib-apidoc
 pbr
 setuptools >= 30.3.0

vermouth/molecule.py

@@ -158,6 +158,12 @@ class attribute to the number of required keys. If the
     instance will be validated against that number; else, the user can pass an
     arbitrary number of keys without validation.
 
+    Attributes
+    ----------
+    n_keys_asked: int
+        Class attribute describing the number of keys required.
+
+
     .. automethod:: __call__
     .. automethod:: _apply
     """
@@ -660,7 +666,7 @@ class Block(Molecule):
     ----------
     name: str or None
         The name of the residue. Set to `None` if undefined.
-    atoms: iterator of dict
+    atoms: collections.abc.Iterator[dict]
         The atoms in the residue. Each atom is a dict with *a minima* a key
         'name' for the name of the atom, and a key 'atype' for the atom type.
         An atom can also have a key 'charge', 'charge_group', 'comment', or any