Ongoing documentation improvement

This modified several docstrings and introduces a quick-start guide.

doc/.templates/layout.html

+{% extends "!layout.html" %}
+{% block rootrellink %}
+    <li><img src="/gfx/graph-icon.png" alt="logo" style="margin-right: 5px; margin-bottom:-2px;" /><a href="/graph-tool/">Project Homepage</a> &raquo;</li>
+    {{ super() }}
+{% endblock %}

doc/Makefile

+all:
+	sphinx-build -E -b html . build
+
+test:
+	OMP_NUM_THREADS=1 sphinx-build -b doctest . build
+
+push:
+	rsync -rEvpLz build/* root@forked.de:/var/www/graph-tool-doc/

doc/centrality.rst

+.. automodule:: graph_tool.centrality
+   :members:

doc/clustering.rst

 .. automodule:: graph_tool.clustering
    :members:
+   :undoc-members:

doc/community.rst

+.. automodule:: graph_tool.community
+   :members:
+   :undoc-members:

doc/conf.py

@@ -16,7 +16,7 @@ import sys, os
 # If your extensions are in another directory, add it here. If the directory
 # is relative to the documentation root, use os.path.abspath to make it
 # absolute, like shown here.
-#sys.path.append(os.path.abspath('.'))
+sys.path.append(os.path.abspath('.'))
 
 # General configuration
 # ---------------------
@@ -43,7 +43,7 @@ master_doc = 'index'
 
 # General information about the project.
 project = u'graph-tool'
-copyright = u'2008, Tiago de Paula Peixoto'
+copyright = u'2009, Tiago de Paula Peixoto <tiago@forked.de>'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -52,7 +52,7 @@ copyright = u'2008, Tiago de Paula Peixoto'
 # The short X.Y version.
 version = '2.0'
 # The full version, including alpha/beta/rc tags.
-release = '2.0'
+release = '2.0beta1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -88,6 +88,13 @@ exclude_trees = ['.build']
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
+# doctest
+
+doctest_global_setup = \
+"""
+import graph_tool.all as gt
+from numpy import array
+"""
 
 # Options for HTML output
 # -----------------------
@@ -111,7 +118,7 @@ html_style = 'default.css'
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-#html_favicon = None
+html_favicon = "graph-icon.ico"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -143,12 +150,12 @@ html_static_path = ['.static']
 #html_split_index = False
 
 # If true, the reST sources are included in the HTML build as _sources/<name>.
-#html_copy_source = True
+html_copy_source = True
 
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the
 # base URL from which the finished HTML is served.
-#html_use_opensearch = ''
+html_use_opensearch = 'http://projects.forked.de/graph-tool/doc/'
 
 # If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
 #html_file_suffix = ''
@@ -192,4 +199,7 @@ latex_documents = [
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'http://docs.python.org/dev': None}
+intersphinx_mapping = {'http://docs.python.org': None,
+                       'http://docs.scipy.org/doc/numpy': None,
+                       'http://docs.scipy.org/doc/scipy/reference': None,
+                       'http://matplotlib.sourceforge.net' : None}

doc/correlations.rst

+.. automodule:: graph_tool.correlations
+   :members:
+   :undoc-members:

doc/draw.rst

+.. automodule:: graph_tool.draw
+   :members:
+   :undoc-members:

doc/generation.rst

+.. automodule:: graph_tool.generation
+   :members:
+   :undoc-members:

doc/graph_tool.rst

@@ -6,4 +6,13 @@ Available subpackages
 
 .. toctree::
 
+   centrality
    clustering
+   community
+   correlations
+   draw
+   generation
+   misc
+   run_action
+   stats
+   util 
\ No newline at end of file

doc/misc.rst

+.. automodule:: graph_tool.misc
+   :members:
+   :undoc-members:

doc/price.py

+#! /usr/bin/env python
+
+# We probably will need some things from several places
+import sys, os
+from pylab import * # for plotting
+from numpy.random import * # for random sampling
+seed(42)
+
+# We need to import the graph_tool module itself
+from graph_tool.all import *
+
+# let's construct a Price network (the one that existed before Barabasi). It is
+# a directed network, with preferential attachment. The algorithm below is a
+# very naive, and a bit slow, but quite simple.
+
+# We start with an empty, directed graph
+g = Graph()
+
+# We want also to keep the age information for each vertex and edge. For that
+# let's create some property maps
+v_age = g.new_vertex_property("int")
+e_age = g.new_edge_property("int")
+
+# The final size of the network
+N = 100000
+
+# We have to start with one vertex
+v = g.add_vertex()
+v_age[v] = 0
+
+# we will keep a list of the vertices. The number of times a vertex is in this
+# list will give the probability of it being selected.
+vlist = [v]
+
+# let's now add the new edges and vertices
+for i in xrange(1, N):
+    # create our new vertex
+    v = g.add_vertex()
+    v_age[v] = i
+
+    # we need to sample a new vertex to be the target, based on its in-degree +
+    # 1. For that, we simply randomly sample it from vlist.
+    i = randint(0, len(vlist))
+    target = vlist[i]
+
+    # add edge
+    e = g.add_edge(v, target)
+    e_age[e] = i
+
+    # put v and target in the list
+    vlist.append(target)
+    vlist.append(v)
+
+# now we have a graph!
+# let's calculate its in-degree distribution and plot it to a file
+
+in_hist = vertex_hist(g, "in")
+
+clf()
+errorbar(in_hist[1], in_hist[0], fmt=".", yerr=sqrt(in_hist[0]))
+gca().set_yscale("log")
+gca().set_xscale("log")
+xlabel("$k_{in}$")
+ylabel("$P(k_{in})$")
+savefig("deg-hist.png")
+
+# let's do a random walk on the graph and print the age of the vertices we find,
+# just for fun.
+
+v = g.vertex(randint(0, g.num_vertices()))
+for i in xrange(0, 100):
+    print "vertex:", v, "in-degree:", v.in_degree(), "out-degree:",\
+          v.out_degree(), "age:", v_age[v]
+
+    if v.out_degree() == 0:
+        print "Nowhere else to go... We found the main hub!"
+        break
+
+    n_list = []
+    for w in v.out_neighbours():
+        n_list.append(w)
+    v = n_list[randint(0, len(n_list))]
+
+# let's save our graph for posterity We want to save the age properties as
+# well... To do this, they must become "internal" properties, as such:
+
+g.vertex_properties["age"] = v_age
+g.edge_properties["age"] = e_age
+
+# now we can save it
+g.save("price.xml.gz")
+

doc/quickstart.rst

 Quick start using `graph-tool`
 ==============================
 
-Testy test test
+The :mod:`graph_tool` module provides a :class:`~graph_tool.Graph` class and
+several algorithms that operate on it. The internals of this class, and of most
+algorithms, are written in C++ for performance.
 
-.. math::
+The module must be of course imported before it can be used. The package is
+subdivided into several sub-modules. To import everything from all of them, one
+can do:
 
-   (a + b)^2 = a^2 + 2ab + b^2
+.. doctest::
+
+   >>> from graph_tool.all import *
+
+In the following, it will always be assumed that the previous line was run.
+
+Creating and manipulating graphs
+--------------------------------
+
+An empty graph can be created by instantiating a :class:`~graph_tool.Graph`
+class:
+
+.. doctest::
+
+   >>> g = Graph()
+
+By default, newly created graphs are always directed. To construct undirected
+graphs, one must pass the ``directed`` parameter:
+
+.. doctest::
+
+   >>> ug = Graph(directed=False)
+
+A graph can always be switched on-the-fly from directed to undirected (and vice
+versa), with the :meth:`~graph_tool.Graph.set_directed` method. The "directedness" of the
+graph can be queried with the :meth:`~graph_tool.Graph.is_directed` method,
+
+.. doctest::
+
+   >>> ug = Graph()
+   >>> ug.set_directed(False)
+   >>> assert(ug.is_directed() == False)
+
+A graph can also be created from another graph, in which case the entire graph
+(and its internal property maps, see :ref:`sec_property_maps`) is copied:
+
+.. doctest::
+
+   >>> g1 = Graph()
+   >>> # ... populate g1 ...
+   >>> g2 = Graph(g1)                 # g1 and g2 are copies
+
+Once a graph is created, it can be populated with vertices and edges. A vertex
+can be added with the :meth:`~graph_tool.Graph.add_vertex` method,
+
+.. doctest::
+
+   >>> v = g.add_vertex()
+
+which returns an instance of a :class:`~graph_tool.Vertex` class, also called a
+*vertex descriptor*. The :meth:`~graph_tool.Graph.add_vertex` method also
+accepts an optional parameter which specifies the number of vertices to
+create. If this value is greater than 1, it returns a list of vertices:
+
+.. doctest::
+
+   >>> vlist = g.add_vertex(10)
+   >>> print len(vlist)
+   10
+
+Each vertex has an unique index, which is numbered from 0 to N-1, where N is the
+number of vertices. This index can be obtained by using the
+:attr:`~graph_tool.Graph.vertex_index` attribute of the graph (which is a
+*property map*, see :ref:`sec_property_maps`), or by converting the vertex
+descriptor to an int.
+
+.. doctest::
+
+   >>> v = g.add_vertex()
+   >>> print g.vertex_index[v], int(v)
+   11 11
+
+There is no need to keep the vertex descriptor lying around to access them at a
+later point: One can obtain the descriptor of a vertex with a given index using
+the :meth:`~graph_tool.Graph.vertex` method,
+
+.. doctest::
+
+   >>> print g.vertex(8)
+   8
+
+Another option is to iterate through the vertices, as described in section
+:ref:`sec_iteration`.
+
+Once we have some vertices in the graph, we can create some edges between them
+with the :meth:`~graph_tool.Graph.add_edge` method, which returns an edge
+descriptor (an instance of the :class:`~graph_tool.Edge` class).
+
+.. doctest::
+
+   >>> v1 = g.add_vertex()
+   >>> v2 = g.add_vertex()
+   >>> e = g.add_edge(v1, v2)
+
+Edges also have an unique index, which is given by the :attr:`~graph_tool.Graph.edge_index`
+property:
+
+.. doctest::
+
+   >>> print g.edge_index[e]
+   0
+
+Unlike the vertices, edge indexes are not guaranteed to be continuous in any
+range, but they are always unique.
+
+Both vertex and edge descriptors have methods which query associate information,
+such as :meth:`~graph_tool.Vertex.in_degree`,
+:meth:`~graph_tool.Vertex.out_degree`, :meth:`~graph_tool.Edge.source` and
+:meth:`~graph_tool.Edge.target`:
+
+.. doctest::
+
+   >>> v1 = g.add_vertex()
+   >>> v2 = g.add_vertex()
+   >>> e = g.add_edge(v1, v2)
+   >>> print v1.out_degree(), v2.in_degree()
+   1 1
+   >>> assert(e.source() == v1 and e.target() == v2)
+
+Edges and vertices can also be removed at any time with the
+:meth:`~graph_tool.Graph.remove_vertex` and :meth:`~graph_tool.Graph.remove_edge` methods,
+
+.. doctest::
+
+   >>> e = g.add_edge(g.vertex(0), g.vertex(1))
+   >>> g.remove_edge(e)                                      # e no longer exists
+   >>> g.remove_vertex(g.vertex(1))              # the second vertex is also gone
+
+.. _sec_iteration:
+
+Iterating over vertices and edges
++++++++++++++++++++++++++++++++++
+
+Algorithms must often iterate through the vertices, edges, out edge, etc. of the
+graph. The :class:`~graph_tool.Graph` and :class:`~graph_tool.Edge` classes
+provide the necessary iterators for doing so. The iterators always give back
+edge or vertex descriptors.
+
+In order to iterate through the vertices or edges of the graph, the
+:meth:`~graph_tool.Graph.vertices` and :meth:`~graph_tool.Graph.edges` methods should be used, as such:
+
+.. doctest::
+
+   for v in g.vertices():
+       print v
+   for e in e.vertices():
+       print e
+
+The code above will print the vertices and edges of the graph in the order they
+are found.
+
+The out- and in-edges of a vertex, as well as the out- and in-neighbours can be
+iterated through with the :meth:`~graph_tool.Vertex.out_edges`,
+:meth:`~graph_tool.Vertex.in_edges`, :meth:`~graph_tool.Vertex.out_neighbours`
+and :meth:`~graph_tool.Vertex.in_neighbours` respectively.
+
+.. doctest::
+
+   from itertools import izip
+   for v in g.vertices():
+      for e in v.out_edges():
+          print e
+      for e in v.out_neighbours():
+          print e
+
+      # the edge and neighbours order always match
+      for e,w in izip(v.out_edges(), v.out_neighbours()):
+          assert(e.target() == w)
+
+.. warning:
+
+   You should never remove vertex or edge descriptors when iterating over them,
+   since this invalidates the iterators. If you plan to remove vertices or edges
+   during iteration, you must first store them somewhere (such as in a list) and
+   remove them only later. Removal during iteration will cause bad things to
+   happen.
+
+.. _sec_property_maps:
+
+Property maps
+-------------
+
+Property maps are a way of associating additional to the vertices, edges or to
+the graph itself. There are thus three types of property maps: vertex, edge and
+graph. All of them are instances of the same class,
+:class:`~graph_tool.PropertyMap`. Each property map has an associated *value
+type*, which must be chosen from the predefined set:
+
+.. tabularcolumns:: |l|l|
+
+.. table::
+
+    =======================     ================
+     Type name                  Aliases
+    =======================     ================
+    ``bool``                    ``uint8_t``
+    ``int32_t``                 ``int``   
+    ``int64_t``                 ``long``  
+    ``double``                  ``float``
+    ``long double``             
+    ``string``                  
+    ``vector<bool>``            ``vector<uint8_t>``
+    ``vector<int32_t>``         ``vector<int>``
+    ``vector<int64_t>``         ``vector<long>``
+    ``vector<double>``          ``vector<float>``
+    ``vector<long double>``
+    ``vector<string>``
+    ``python::object``          ``object`` 
+    =======================     ================
+
+New property maps can be created for a given graph by calling the
+:meth:`~graph_tool.Graph.new_vertex_property`, :meth:`~graph_tool.Graph.new_edge_property`, or
+:meth:`~graph_tool.Graph.new_graph_property`, for each map type. The values are then
+accessed by vertex or edge descriptors, or the graph itself, as such:
+
+.. doctest::
+
+    from itertools import izip
+    from numpy.random import randint
+
+    g = Graph()
+    g.add_vertex(100)
+    # insert some random links
+    for s,t in izip(randint(0, 100, 100), randint(0, 100, 100)):
+        g.add_edge(g.vertex(s), g.vertex(t))
+    
+    vprop_double = g.new_vertex_property("double")
+    vprop_vint = g.new_vertex_property("vector<int>")
+
+    eprop_dict = g.new_edge_property("object")
+
+    gprop_bool = g.new_edge_property("bool")
+
+    vprop_double[g.vertex(10)] = 3.1416
+
+    vprop_vint[g.vertex(40)] = [1, 3, 42, 54]
+    
+    eprop_dict[g.edges().next()] = {"foo":"bar", "gnu":42}
+
+    gprop_bool[g] = True
+
+Property maps with scalar value types can also be accessed as a numpy
+:class:`~numpy.ndarray`, with the :meth:`~graph_tool.PropertyMap.get_array`
+method, i.e.,
+
+.. doctest::
+
+    from numpy.random import random
+
+    # this assigns random values to the properties
+    vprop_double.get_array()[:] = random(g.num_vertices())
+
+Internal property maps
+++++++++++++++++++++++
+
+Any created property map can be made "internal" to the respective graph. This
+means that it will be copied and saved to a file together with the
+graph. Properties are internalized by including them in the graph's
+dictionary-like attributes :attr:`~graph_tool.Graph.vertex_properties`,
+:attr:`~graph_tool.Graph.edge_properties` or
+:attr:`~graph_tool.Graph.graph_properties`. When inserted in the graph, the
+property maps must have an unique name (between those of the same type):
+
+.. doctest::
+
+    >>> eprop = g.new_edge_property("string")
+    >>> g.edge_properties["some name"] = eprop
+    >>> g.list_properties()
+    some name      (edge)    (type: string)
+
+
+Graph I/O
+---------
+
+Graphs can be saved and loaded in two formats: `graphml
+<http://graphml.graphdrawing.org/>`_ and `dot
+<http://www.graphviz.org/doc/info/lang.html>`_. Graphml is the default and
+preferred format. The dot format is also supported, but since it contains no
+type information, all properties are read later as strings, and must be
+converted per hand. Therefore you should always use graphml, except when
+interfacing with another software which expects dot format.
+
+A graph can be saved or loaded to a file with the :attr:`~graph_tool.Graph.save`
+and :attr:`~graph_tool.Graph.load` methods, which take either a file name or a
+file-like object. A graph can also be loaded from disk with the
+:func:`~graph_tool.load_graph` function, as such:
+
+.. doctest::
+
+    g = Graph()
+    #  ... fill the graph ...
+    g.save("my_graph.xml.gz")    
+    g2 = load_graph("my_graph.xml.gz")
+    # g and g2 should be a copy of each other
+
+Graph classes can also be pickled with the :mod:`pickle` module.
+
+
+An Example: Building a Price Network
+------------------------------------
+
+.. literalinclude:: price.py
+   :linenos:
+
+.. testcode::
+   :hide:
+
+   from price import *
+   clf()
+
+.. testoutput::
+
+    vertex: 36063 in-degree: 0 out-degree: 1 age: 36063
+    vertex: 9075 in-degree: 4 out-degree: 1 age: 9075
+    vertex: 5967 in-degree: 3 out-degree: 1 age: 5967
+    vertex: 1113 in-degree: 7 out-degree: 1 age: 1113
+    vertex: 25 in-degree: 84 out-degree: 1 age: 25
+    vertex: 10 in-degree: 541 out-degree: 1 age: 10
+    vertex: 5 in-degree: 140 out-degree: 1 age: 5
+    vertex: 2 in-degree: 459 out-degree: 1 age: 2
+    vertex: 1 in-degree: 520 out-degree: 1 age: 1
+    vertex: 0 in-degree: 210 out-degree: 0 age: 0
+    Nowhere else to go... We found the main hub!
+
+
+.. image:: deg-hist.png
 
-   (a - b)^2 = a^2 - 2ab + b^2

doc/run_action.rst

+.. automodule:: graph_tool.run_action
+   :members:
+   :undoc-members:

doc/stats.rst

+.. automodule:: graph_tool.stats
+   :members:
+   :undoc-members:

doc/util.rst

+.. automodule:: graph_tool.util
+   :members:
+   :undoc-members:

src/graph_tool/__init__.py

@@ -66,7 +66,7 @@ misc
 stats
    vertex and edge statistics
 util
-   assorted untilities
+   assorted utilities
 
 Utilities
 ---------
@@ -77,6 +77,9 @@ show_config
 __version__
    ``graph_tool`` version string
 
+Classes
+-------
+
 """
 
 __author__="Tiago de Paula Peixoto <tiago@forked.de>"

src/graph_tool/centrality/__init__.py

@@ -17,8 +17,8 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 """
-Centrality
-==========
+``graph_tool.centrality`` - Centrality measures
+-----------------------------------------------
 
 This module includes centrality-related algorithms.
 """
@@ -55,7 +55,7 @@ def pagerank(g, damping=0.8, prop=None, epslon=1e-6, max_iter=None,
 
     Returns
     -------
-    A vertex property map containing the PageRank values.
+    pagerank : A vertex property map containing the PageRank values.
 
     See Also
     --------
@@ -65,12 +65,13 @@ def pagerank(g, damping=0.8, prop=None, epslon=1e-6, max_iter=None,
 
     Notes
     -----
-    The value of PageRank of vertex v :math:`PR(v)` is given interactively by
-    the relation:
+    The value of PageRank [pagerank_wikipedia]_ of vertex v :math:`PR(v)` is
+    given interactively by the relation:
+
+    .. math::
 
-    .. math:
         PR(v) = \frac{1-d}{N} + d \sum_{w \in \Gamma^{-}(v)}
-                \frac{PR (w)}{d^{+}(w)}</math>
+                \frac{PR (w)}{d^{+}(w)}
 
     where :math:`\Gamma^{-}(v)` are the in-neighbours of v, :math:`d^{+}(w)` is
     the out-degree of w, and d is a damping factor.
@@ -83,33 +84,34 @@ def pagerank(g, damping=0.8, prop=None, epslon=1e-6, max_iter=None,
 
     Examples
     --------
-    >>> from numpy.random import poisson
+    >>> from numpy.random import poisson, seed
+    >>> seed(42)
     >>> g = gt.random_graph(100, lambda: (poisson(3), poisson(3)), seed=42)
     >>> pr = gt.pagerank(g)
     >>> print pr.get_array()
-    [ 1.23631405  1.26200483  1.96751522  0.64733031  0.70919769  0.30955985
-