Assorted documentation fixes

doc/Makefile

@@ -7,17 +7,18 @@ ORIGIMAGES = ${HUGEIMAGES:.pdf=.pdf-orig}
 PNGCONV = pdftoppm -png -singlefile -r 96 -freetype yes -aa yes -aaVector yes
 PDFCONV = gm convert
 
-all: #$(ORIGIMAGES) $(PNGIMAGES)
+#all: $(ORIGIMAGES) $(PNGIMAGES)
+all:
 	sphinx-build -E -b html . build
 
-%.pdf-orig: %.pdf
-	$(PNGCONV) $< > $@-tmp.png
-	$(PDFCONV) $@-tmp.png $@
-	rm $@-tmp.png
+# %.pdf-orig: %.pdf
+# 	$(PNGCONV) $< > $@-tmp.png
+# 	$(PDFCONV) $@-tmp.png $@
+# 	rm $@-tmp.png
 
-%.png: %.pdf
-	test -d $<-orig && $(PNGCONV) $<-orig > $@ || true
-	test -d $<-orig || $(PNGCONV) $< > $@ || true
+# %.png: %.pdf
+# 	test -d $<-orig && $(PNGCONV) $<-orig > $@ || true
+# 	test -d $<-orig || $(PNGCONV) $< > $@ || true
 
 latex:
 	sphinx-build -E -b latex . build
@@ -25,11 +26,11 @@ latex:
 test:
 	OMP_NUM_THREADS=1 sphinx-build -b doctest . build
 
-push:
-	rsync -rEvpLz build/* root@skewed.de:/var/www/graph-tool-doc/
+#push:
+#	rsync -rEvpLz build/* root@skewed.de:/var/www/graph-tool-doc/
 
-push-dev:
-	rsync -rEvpLz build/* root@skewed.de:/var/www/graph-tool-doc/dev/
+#push-dev:
+#	rsync -rEvpLz build/* root@skewed.de:/var/www/graph-tool-doc/dev/
 
 clean:
 	rm -rf build

doc/conf.py

@@ -159,7 +159,7 @@ 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 = 'http://projects.skewed.de/graph-tool/doc/'
+html_use_opensearch = 'http://graph-tool.skewed.de/doc/'
 
 # If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
 #html_file_suffix = ''
@@ -199,7 +199,7 @@ intersphinx_mapping = {'python': ('http://docs.python.org', None),
                        'matplotlib': ('http://matplotlib.sourceforge.net', None),
                        'cairo': ('http://www.cairographics.org/documentation/pycairo/3/', None)}
 
-extlinks = {'ticket': ('http://projects.skewed.de/graph-tool/ticket/%s',
+extlinks = {'ticket': ('http://graph-tool.skewed.de/tickets/ticket/%s',
                        'ticket '),
             'doi': ('http://dx.doi.org/%s', 'DOI: '),
             'arxiv': ('http://arxiv.org/abs/%s', 'arXiv: ')}

doc/graph_tool.rst

@@ -43,6 +43,9 @@
        .. automethod:: add_edge
        .. automethod:: remove_edge
 
+       .. automethod:: set_fast_edge_removal
+       .. automethod:: get_fast_edge_removal
+
        The following functions allow for easy removal of vertices of
        edges from the graph.
 

doc/price.py

@@ -99,3 +99,4 @@ xlabel("$k_{in}$")
 ylabel("$NP(k_{in})$")
 tight_layout()
 savefig("price-deg-dist.pdf")
+savefig("price-deg-dist.png")

doc/quickstart.rst

@@ -89,14 +89,14 @@ visualize the graph we created so far with the
 .. doctest::
 
    >>> graph_draw(g, vertex_text=g.vertex_index, vertex_font_size=18,
-   ...            output_size=(200, 200), output="two-nodes.pdf")
+   ...            output_size=(200, 200), output="two-nodes.png")
    <...>
 
 .. doctest::
    :hide:
 
    graph_draw(g, vertex_text=g.vertex_index, vertex_font_size=18,
-              output_size=(200, 200), output="two-nodes.png")
+              output_size=(200, 200), output="two-nodes.pdf")
 
 
 .. figure:: two-nodes.*
@@ -157,12 +157,22 @@ Edges and vertices can also be removed at any time with the
    internally stored in a `STL vector <http://en.wikipedia.org/wiki/Vector_%28STL%29>`_,
    so removing an element somewhere in the middle of the list requires
    the shifting of the rest of the list. Thus, fast :math:`O(1)`
-   removals are only possible if one can guarantee that only vertices in
-   the end of the list are removed (the ones last added to the graph).
+   removals are only possible either if one can guarantee that only
+   vertices in the end of the list are removed (the ones last added to
+   the graph), or if the relative vertex ordering is invalidated. This
+   last behavior can be achieved by passing the option ``fast == True``,
+   to :meth:`~graph_tool.Graph.remove_vertex`, which causes vertex
+   being deleted to be 'swapped' with the last vertex (i.e. with the
+   largest index), which will in turn inherit the index of the vertex
+   being deleted.
+
 
    Removing an edge is an :math:`O(k_{s} + k_{t})` operation, where
    :math:`k_{s}` is the out-degree of the source vertex, and
-   :math:`k_{t}` is the in-degree of the target vertex.
+   :math:`k_{t}` is the in-degree of the target vertex. This can be made
+   faster by setting :meth:`~graph_tool.Graph.set_fast_edge_removal` to
+   `True`, in which case it becomes :math:`O(1)`, at the expense of
+   additional data of size :math:`O(E)`.
 
 Each vertex in a graph 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

src/graph_tool/__init__.py

@@ -1344,13 +1344,13 @@ class Graph(object):
 
            This operation is normally :math:`O(k_s + k_t)`, where :math:`k_s`
            and :math:`k_s` are the total degrees of the source and target
-           vertices, respectively. However, if :method:`~Graph.set_fast_edge_removal`
+           vertices, respectively. However, if :meth:`~Graph.set_fast_edge_removal`
            is set to `True`, this operation becomes :math:`O(1)`.
 
         .. warning::
 
            The relative ordering of the remaining edges in the graph is kept
-           unchanged, unless :method:`~Graph.set_fast_edge_removal` is set to
+           unchanged, unless :meth:`~Graph.set_fast_edge_removal` is set to
            `True`, in which case it can change.
         """
         self.__check_perms("del_edge")

src/graph_tool/community/__init__.py

@@ -189,10 +189,22 @@ def community_structure(g, n_iter, n_spins, gamma=1.0, corr="erdos",
     ...                                history_file="community-history1")
     >>> gt.graph_draw(g, pos=pos, vertex_fill_color=spins, output_size=(420, 420), output="comm1.pdf")
     <...>
+
+    .. testcode::
+       :hide:
+
+       gt.graph_draw(g, pos=pos, vertex_fill_color=spins, output_size=(420, 420), output="comm1.png")
+
     >>> spins = gt.community_structure(g, 10000, 40, t_range=(5, 0.1),
     ...                                gamma=2.5, history_file="community-history2")
     >>> gt.graph_draw(g, pos=pos, vertex_fill_color=spins, output_size=(420, 420), output="comm2.pdf")
     <...>
+
+    .. testcode::
+       :hide:
+
+       gt.graph_draw(g, pos=pos, vertex_fill_color=spins, output_size=(420, 420), output="comm2.png")
+
     >>> figure(figsize=(6, 4))
     <...>
     >>> xlabel("iterations")
@@ -203,6 +215,12 @@ def community_structure(g, n_iter, n_spins, gamma=1.0, corr="erdos",
     >>> plot(a[0], a[2])
     [...]
     >>> savefig("comm1-hist.pdf")
+
+    .. testcode::
+       :hide:
+
+       savefig("comm1-hist.png")
+
     >>> clf()
     >>> xlabel("iterations")
     <...>
@@ -213,6 +231,11 @@ def community_structure(g, n_iter, n_spins, gamma=1.0, corr="erdos",
     [...]
     >>> savefig("comm2-hist.pdf")
 
+    .. testcode::
+       :hide:
+
+       savefig("comm2-hist.png")
+
 
     The community structure with :math:`\gamma=1`:
 

src/graph_tool/correlations/__init__.py

@@ -393,7 +393,7 @@ def combined_corr_hist(g, deg1, deg2, bins=[[0, 1], [0, 1]], float_count=True):
     .. testcode::
        :hide:
 
-       savefig("combined_corr.pdf")
+       savefig("combined_corr.png")
 
     .. figure:: combined_corr.*
         :align: center

src/graph_tool/generation/__init__.py

@@ -310,7 +310,7 @@ def random_graph(N, deg_sampler, directed=True,
 
     The blockmodel can be generated as follows.
 
-    >>> g, bm = gt.random_graph(5000, lambda: poisson(10), directed=False,
+    >>> g, bm = gt.random_graph(2000, lambda: poisson(10), directed=False,
     ...                         model="blockmodel-traditional",
     ...                         block_membership=lambda: randint(10),
     ...                         vertex_corr=corr)
@@ -1445,12 +1445,12 @@ def price_network(N, m=1, c=None, gamma=1, directed=True, seed_graph=None):
 
        gt.seed_rng(42)
 
-    >>> g = gt.price_network(100000)
+    >>> g = gt.price_network(20000)
     >>> gt.graph_draw(g, pos=gt.sfdp_layout(g, epsilon=1e-2, cooling_step=0.95),
     ...               vertex_fill_color=g.vertex_index, vertex_size=2,
     ...               edge_pen_width=1, output="price-network.png")
     <...>
-    >>> g = gt.price_network(100000, c=0.1)
+    >>> g = gt.price_network(20000, c=0.1)
     >>> gt.graph_draw(g, pos=gt.sfdp_layout(g, epsilon=1e-2, cooling_step=0.95),
     ...               vertex_fill_color=g.vertex_index, vertex_size=2,
     ...               edge_pen_width=1, output="price-network-broader.png")
@@ -1459,13 +1459,13 @@ def price_network(N, m=1, c=None, gamma=1, directed=True, seed_graph=None):
     .. figure:: price-network.png
         :align: center
 
-        Price network with :math:`N=10^5` nodes and :math:`c=1`.  The colors
+        Price network with :math:`N=2\times 10^4` nodes and :math:`c=1`.  The colors
         represent the order in which vertices were added.
 
     .. figure:: price-network-broader.png
         :align: center
 
-        Price network with :math:`N=10^5` nodes and :math:`c=0.1`.  The colors
+        Price network with :math:`N=2\times 10^4` nodes and :math:`c=0.1`.  The colors
         represent the order in which vertices were added.
 
 

src/graph_tool/search/__init__.py

@@ -1396,6 +1396,13 @@ def astar_search(g, source, weight, visitor=AStarVisitor(),
     ...               edge_pen_width=ewidth, output="astar-delaunay.pdf")
     <...>
 
+    .. testcode::
+       :hide:
+
+       gt.graph_draw(g, pos=pos, output_size=(300, 300), vertex_fill_color=touch_v,
+                     vcmap=matplotlib.cm.binary, edge_color=ecolor,
+                     edge_pen_width=ewidth, output="astar-delaunay.png")
+
     .. figure:: astar-delaunay.*
        :align: center
 

src/graph_tool/topology/__init__.py

@@ -261,6 +261,14 @@ def subgraph_isomorphism(sub, g, max_n=0, vertex_label=None, edge_label=None,
     >>> gt.graph_draw(sub, output_size=(200, 200), output="subgraph-iso.pdf")
     <...>
 
+    .. testcode::
+       :hide:
+
+       gt.graph_draw(g, vertex_fill_color=vmask, edge_color=emask,
+                     edge_pen_width=ewidth, output_size=(200, 200),
+                     output="subgraph-iso-embed.png")
+       gt.graph_draw(sub, output_size=(200, 200), output="subgraph-iso.png")
+
     .. image:: subgraph-iso.*
     .. image:: subgraph-iso-embed.*
 
@@ -383,6 +391,11 @@ def min_spanning_tree(g, weights=None, root=None, tree_map=None):
     >>> gt.graph_draw(g, pos=pos, output="triang_min_span_tree.pdf")
     <...>
 
+    .. testcode::
+       :hide:
+
+       gt.graph_draw(g, pos=pos, output="triang_orig.png")
+       gt.graph_draw(g, pos=pos, output="triang_min_span_tree.png")
 
     .. image:: triang_orig.*
         :width: 400px
@@ -469,6 +482,11 @@ def random_spanning_tree(g, weights=None, root=None, tree_map=None):
     >>> gt.graph_draw(g, pos=pos, output="triang_random_span_tree.pdf")
     <...>
 
+    .. testcode::
+       :hide:
+
+       gt.graph_draw(g, pos=pos, output="rtriang_orig.png")
+       gt.graph_draw(g, pos=pos, output="triang_random_span_tree.png")
 
     .. image:: rtriang_orig.*
         :width: 400px
@@ -1408,6 +1426,11 @@ def is_bipartite(g, partition=False):
     >>> gt.graph_draw(g, vertex_fill_color=part, output_size=(300, 300), output="bipartite.pdf")
     <...>
 
+    .. testcode::
+       :hide:
+
+       gt.graph_draw(g, vertex_fill_color=part, output_size=(300, 300), output="bipartite.png")
+
     .. figure:: bipartite.*
         :align: center
 
@@ -1491,6 +1514,11 @@ def is_planar(g, embedding=False, kuratowski=False):
     >>> gt.graph_draw(g, output_size=(300, 300), output="kuratowski.pdf")
     <...>
 
+    .. testcode::
+       :hide:
+
+       gt.graph_draw(g, output_size=(300, 300), output="kuratowski.png")
+
     .. figure:: kuratowski.*
         :align: center
 
@@ -1564,6 +1592,11 @@ def make_maximal_planar(g, unfilter=False):
     >>> gt.graph_draw(g, output_size=(300, 300), output="maximal_planar.pdf")
     <...>
 
+    .. testcode::
+       :hide:
+
+       gt.graph_draw(g, output_size=(300, 300), output="maximal_planar.png")
+
     .. figure:: maximal_planar.*
         :align: center
 
@@ -1677,6 +1710,12 @@ def max_cardinality_matching(g, heuristic=False, weight=None, minimize=True,
     ...               output="max_card_match.pdf")
     <...>
 
+    .. testcode::
+       :hide:
+
+       gt.graph_draw(g, edge_color=res[0], edge_pen_width=w, vertex_fill_color="grey",
+                     output="max_card_match.png")
+
     .. figure:: max_card_match.*
         :align: center
 
@@ -1749,6 +1788,11 @@ def max_independent_vertex_set(g, high_deg=False, mivs=None):
     >>> gt.graph_draw(g, vertex_fill_color=res, output="mivs.pdf")
     <...>
 
+    .. testcode::
+       :hide:
+
+       gt.graph_draw(g, vertex_fill_color=res, output="mivs.png")
+
     .. figure:: mivs.*
         :align: center