Simple documentation fixes

doc/conf.py

@@ -26,7 +26,7 @@ sys.path.append(os.path.abspath('.'))
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest',
               'sphinx.ext.intersphinx', 'mathjax', 'sphinx.ext.autosummary',
-              'sphinxext.numpydoc',
+              'numpydoc',
               'sphinx.ext.extlinks',
               'sphinx.ext.viewcode'
               #'sphinx.ext.linkcode'
@@ -209,15 +209,15 @@ extlinks = {'ticket': ('http://graph-tool.skewed.de/tickets/ticket/%s',
             'arxiv': ('http://arxiv.org/abs/%s', 'arXiv: ')}
 
 
-def process_docstring(app, what, name, obj, options, lines):
-    for i, line in enumerate(lines):
-        if "arg1" in line and "->" in line:
-            lines[i] = ""
-        if "C++ signature :" in line or "graph_tool::Python" in line:
-            lines[i] = ""
+# def process_docstring(app, what, name, obj, options, lines):
+#     for i, line in enumerate(lines):
+#         if "arg1" in line and "->" in line:
+#             lines[i] = ""
+#         if "C++ signature :" in line or "graph_tool::Python" in line:
+#             lines[i] = ""
 
-def setup(app):
-    app.connect('autodoc-process-docstring', process_docstring)
+# def setup(app):
+#     app.connect('autodoc-process-docstring', process_docstring)
 
 # plot directive
 import pyenv
@@ -229,6 +229,7 @@ numpydoc_show_class_members = False
 autodoc_docstring_signature = False
 autodoc_member_order = 'bysource'
 autoclass_content = 'both'
+imported_members = True
 
 def linkcode_resolve(domain, info):
     if domain != 'py':

doc/draw.rst

 .. automodule:: graph_tool.draw
    :no-members:
 
-    Layout algorithms
-    =================
+    .. container:: sec_title
+
+       Layout algorithms
 
     .. autofunction:: sfdp_layout
     .. autofunction:: fruchterman_reingold_layout
@@ -11,9 +12,9 @@
     .. autofunction:: random_layout
 
 
-    Graph drawing
-    =============
+    .. container:: sec_title
 
+       Graph drawing
 
     .. autofunction:: graph_draw
     .. autofunction:: draw_hierarchy
@@ -22,8 +23,9 @@
     .. autofunction:: get_hierarchy_control_points
 
 
-    Low-level graph drawing
-    ^^^^^^^^^^^^^^^^^^^^^^^
+    .. container:: sec_title
+
+       Low-level graph drawing
 
     .. autofunction:: cairo_draw
     .. autofunction:: interactive_window

doc/graph_tool.rst

@@ -182,7 +182,7 @@
    .. autofunction:: group_vector_property
    .. autofunction:: ungroup_vector_property
    .. autofunction:: infect_vertex_property
-   .. autofunction:: edge_difference
+   .. autofunction:: edge_endpoint_property
    .. autofunction:: value_types
    .. autofunction:: show_config
 

src/graph_tool/collection/__init__.py

@@ -33,8 +33,8 @@ This module contains an assortment of useful networks.
     or alternatively in the ``"description"`` graph property which accompanies
     each graph object.
 
-    Examples
-    --------
+Examples
+========
 
     >>> g = gt.collection.data["karate"]
     >>> print(g)

src/graph_tool/community/nested_blockmodel.py

@@ -1434,7 +1434,7 @@ def minimize_nested_blockmodel_dl(g, Bs=None, bs=None, min_B=None,
         entropy will be used to compare different partitions.
     sequential : ``bool`` (optional, default: ``True``)
         If ``True``, the move attempts on the vertices are done in sequential
-        random order. Otherwise a total of `N` moves attempts are made, where
+        random order. Otherwise a total of ``N`` moves attempts are made, where
         `N` is the number of vertices, where each vertex can be selected with
         equal probability.
     checkpoint : function (optional, default: ``None``)
@@ -1448,8 +1448,8 @@ def minimize_nested_blockmodel_dl(g, Bs=None, bs=None, min_B=None,
                 ...
 
         where `state` is either a :class:`~graph_tool.community.NestedBlockState`
-        instance or ``None``, `L` is the current description length, `delta` is
-        the entropy difference in the last MCMC sweep, and `nmoves` is the
+        instance or ``None``, `L` is the current description length, ``delta`` is
+        the entropy difference in the last MCMC sweep, and ``nmoves`` is the
         number of accepted block membership moves. The ``minimize_state``
         argument is a :class:`~graph_tool.community.NestedMinimizeState`
         instance which specifies the current state of the algorithm, which can

src/graph_tool/draw/gtk_draw.py

@@ -171,7 +171,7 @@ class GraphWidget(Gtk.DrawingArea):
             User-supplied callback to be called whenever the positions of the layout
             have changed. It needs to have the following signature:
 
-            .. code-block::
+            .. code-block:: python
 
                def callback(g, picked, pos, vprops, eprops):
                    ...
@@ -185,7 +185,7 @@ class GraphWidget(Gtk.DrawingArea):
             User-supplied callback to be called whenever a key-press event has
             happened. It needs to have the following signature:
 
-            .. code-block::
+            .. code-block:: python
 
                def callback(g, keyval, picked, pos, vprops, eprops):
                    ...