GitLab

The check for parallel edges was cleaned up and abstracted into a
function, and other minor things were changed. Code comments were added
to places where it might have been hard to understand.

Improve formatting of src/graph/graph_rewiring.cc (line breaks at column
80, typedefs, trailing whitespace removal, etc)

Conflicts:

	src/graph-tool
	src/graph/graph_bind.cc

Property maps can now be obtained as such:

         weight = g.edge_properties['weight']
         print weight[v] # v is a Vertex object
         weight[v] = 2.0
         # and so on...

The list of properties is obtained from g.vertex_properties,
g.edge_properties and g.graph_properties, which can be read as
dictionaries. The last can be set also, as such:

         g.graph_properties = {foo:"bar", baz:42}

Functions to add and remove vertices or adges were also added
(add_{vertex|edge}, remove_{vertex|edgge}).

Vertex and Edge types can also now be printed for convenience, as such:

       for v in g.vertices():
           print v
       for e in g.edges():
           print e

which results, for example, in:
0
1
2
3
4
5
6
(0,1)
(1,2)
(2,6)
(3,4)
(4,5)
(4,2)
(5,6)
(6,1)

(this also adds the forgotten graph_tool.py file, which was previously
on .gitignore)

Major changes to both correlated and uncorrelated rewiring code.
Both cases are now functional and use iterative shuffling.
Uncorrelated picks edges to rewire directly, correlated picks
vertices in order to choose edges.

Vertices and edges can be accessed from the graph class, as such:

    import graph_tool
    g = graph_tool.Graph()
    for v in g.vertices():
        for e in v.out_edges():
           # do something...

Additionally, the --edit-{vertex|edge|graph}-property was ported to the
new interface, and is working again, as it used to.

The Vertex and Edge class no longer have the 'get_property' and
'set_property' method. They'll be replaced by a new method of accessing
property maps.

The program was split in two parts:

    1. A python module, graph_tool.py, which encapsulates the graph
       manipulation under a Graph class. Now the following can be done:

              import graph_tool
              g1 = graph_tool.Graph()
              g2 = graph_tool.Graph()
              g1.load("foo.xml")
              g2.load("bar.xml")
              print g1.number_of_vertices(), g2.number_of_vertices()

    2. A standalone command line tool, graph-tool, which imports
       graph_tool.py, and exposes the Graph methods as command line
       options.

The whole command line engine was thus (once again) entirely
rewritten. It is now Crack-Free™, and simply mirrors the methods of the
Graph class as command line options, using, for this, the beauty of
function decorators. It classifies now, I believe, as Pythonic™.

This fixes a bug where properties with 'long long' types were not handled
properly through the python interface.

Several changes in the random rewiring code, making it fully
functional for the correlated case.
The reshuffling operations lag in efficiency, even though already
the algorithm runs in little time.

Conflicts:

	src/graph/graph_extended_clustering.cc

Merge branch 'master' of git://finn.forked.de/~count0/stuff/workspace/graph-tool into rewiring-merge

Line breaks at column 80 were added, and all trailing whitespace was deleted. Code
comments were modified and some more were added.

It should be 'size_t' instead of 'long'.

bool entries in option random-rewire were stated as string,
causing graph-tool to crash before loading.

This fixes the same problem as commit 6663be71, but which arises
when a filter range boundary is -inf (such as "<=100").

A comma (,) was missing before the rewiring option in src/graph-tool

    
When only one of vertex or edge filtering was disabled, the allowed
range of the disabled filter was set to
]numeric_limits<double>::min(), numeric_limits<double>::max()[, and
the selected filtering property was the respective index. But
according to the STL documentation from GCC,
numeric_limits<>::min() returns:
    
   "The minimum finite value, or for floating types with
    denormalization, the minimum positive normalized value."
    
which is always positive for double (!), thus introducing a weird
regression, where the first vertex (index 0) is always filtered out if
only the edge filter is active, and vice-versa.

and now we have a good consistent branch where the removal of rewiring
has been properly reverted before new work is added, so it can be
easily merged with the master branch in the future.

Conflicts:

	src/graph-tool

It's still buggy (of course), but now we'll try to fix it in it's own
 branch.

This reverts commit 1cdbdeef.

The Histogram type 'hist_t' should have a 'double' value, so that
counts of 1/2 can be added when it's known things are going to be
counted twice.

(and I don't know what that 'double_t' thing was doing there)

Implements extended_clustering for directed graphs, based on the fraction of possible directed cycles (out-in edges combination).
The old behavior is still present since it was equivalent to treating the directed graph as undirected (use --undirected option).

    
Filtered vertices and edges can be permanently removed from the graph
with --purge-vertices and --purge-edges, respectively. The edge or
vertex filter is automatically removed, afterwards. This is useful if
maximum speed is necessary, and saving and reloading the graph without
filtering is not desired.
    
(this commit also removes some trailing whitespaces)

This will increase memory usage, but guarantees, across different
platforms, that 'long' will always hold larger values than 'int'.