Hi Tiago,
sometimes, when delete the graph and create a new one, then plot it, the
plotted graph is shown upside down (in terms of the node text). So how could
we control the orientation of the graph? Or which parameter we should use to
always make node text shown in a correct orientation. Thanks a lot.
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Hi,
I'm suffering from the same issue mentioned in this post:
https://git.skewed.de/count0/graph-tool/issues/174
Namely, I'm trying to draw a graph that includes a lot of self-looping
edges, and my labels are being printed upside down. If I remove the
self-loops the labels are shown the right way up.
Is there a fix for it?
Thanks,
Charlie
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I am curious what is being used to calculate the standard deviation of the
average in gt.vertex_average and gt.edge_average
>>> t2=gt.Graph()
>>> t2.add_vertex(2)
>>> t2.add_edge(t2.vertex(0), t2.vertex(1))
>>> gt.vertex_average(t2, "in")
(0.5, 0.35355339059327373)
Now, shouldn't std be σ(n)=sqrt(((0-0.5)^2+(1-0.5)^2)/2)=0.5 ?
also q(n-1)=sqrt((0.5^2+0.5^2)/(2-1))~=0.70710
0.3535 is sqrt(2)/4 which happens to be σ(n-1)/2, so it seems there is some
relation to that.
A little bigger graph.
>>> t3=gt.Graph()
>>> t3.add_vertex(5)
>>> t3.add_edge(t3.vertex(0), t3.vertex(1))
>>> gt.vertex_average(t3, "in")
(0.2, 0.17888543819998318)
Now, we should have 0,1,0,0,0 series for vertex incoming degree.
So Windows calc gives σ(n)=0.4 and σ(n-1)~=0.44721, so where does 0.1788854
come from ?
Reason, I am asking because, I have a large graph, where the average looks
quite alright but the std makes no sense, as going by the histogram, degree
values are quite a bit more distributed than the std would indicate.
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Hi,
I was wondering if there is any way to assign vertex properties while
adding edges to the graph. for example using "add_edge_list" I can assign
edge properties but later I have to iterate through all vertices again to
assign their properties.
I know this is not a problem when the vertex property is of the type "int"
or "float" because then one can use "vprop.a = values", but in case of
"string" and "object" this method doesn't work
What would be the best/fastest way to handle this situation.
I guess it would be very helpful to extend the "add_edge_list" function to
accept vertex property in some way.
cheers,
--
Mohsen

I'd like to use the "add_edge_list" function to add edges to my graph, and
simultaneously assign a value for an edge property map for each of the added
edges.
When I try the following example (with no edge property map information)
works fine:
elist1 = np.array([[0,1], [1, 2]]) #edge list with no value for edge
property map data (only the source and target for the edges)
g = gt.Graph()
my_eprop = g.new_edge_property('bool')
g.add_edge_list(elist)
But with the following example, I get the error below:
elist2 = np.array([[0,1, 1], [1, 2, 0]]) #edge list with edge property map
value in 3rd column
g = gt.Graph()
my_eprop = g.new_edge_property('bool')
g.add_edge_list(elist2, eprops=my_eprop)
Error:
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-48-6a949ea52c9b> in <module>()
----> 1 g.add_edge_list(elist2, eprops=my_eprop)
/usr/lib/python2.7/dist-packages/graph_tool/__init__.pyc in
add_edge_list(self, edge_list, hashed, string_vals, eprops)
1969 eprops = ()
1970 else:
-> 1971 convert = [_converter(x.value_type()) for x in eprops]
1972 eprops = [_prop("e", self, x) for x in eprops]
1973 if not isinstance(edge_list, numpy.ndarray):
/usr/lib/python2.7/dist-packages/graph_tool/__init__.pyc in
__getitem__(self, k)
534 kt = "Graph"
535 raise ValueError("invalid key '%s' of type '%s',
wanted type: %s"
--> 536 % (str(k), str(type(k)), kt) )
537
538 def __setitem__(self, k, v):
ValueError: invalid key '0' of type '<type 'int'>', wanted type: Edge
---------------------------------------------------------------------------
Please help!
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I tried the following command in Python and ipython prompt (2.7 version)
---------------------------------------------------------------------------
In [1]: from graph_tool.all import *
---------------------------------------------------------------------------
Its giving the following error. How can we solve it?
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-1-100bbe2bc9d9> in <module>()
----> 1 from graph_tool.all import *
/usr/lib/python2.7/dist-packages/graph_tool/__init__.py in <module>()
103
104 from .dl_import import *
--> 105 dl_import("from . import libgraph_tool_core as libcore")
106 __version__ = libcore.mod_info().version
107
/usr/lib/python2.7/dist-packages/graph_tool/dl_import.pyc in dl_import(import_expr)
55
56 try:
---> 57 exec(import_expr, local_dict, global_dict)
58 finally:
59 sys.setdlopenflags(orig_dlopen_flags) # reset it to normal case to
<string> in <module>()
ImportError: /usr/lib/python2.7/dist-packages/graph_tool/libgraph_tool_core.so: undefined symbol: _ZN5boost9iostreams4zlib6finishE
---------------------------------------------------------------------------
Thanks

Dear Dr. Tiago Peixoto,
I have a question regarding weighted graphs. I would like to classify a
network with weighted edges into groups taking into account these weights.
I have used minimize_blockmodel_dl and minimize_nested_blockmodel_dl before
but I don't know exactly how to implement these functions in a weighted
network. I'm not sure if I have to use the layered version, but in this
case I don't know how to get these layers from my network.
Thank you very much and sorry for the basic question,
Andrea

Hi,
I have installed the package python3-graph-tool and when I use
graph_tool.search.dfs_iterator I got the error:
Traceback (most recent call last):
File "/home/steph/bin/superGraph.py", line 160, in <module>
gg.create_revdep(gg.getPackage('umda'))
File "/home/steph/bin/superGraph.py", line 88, in create_revdep
for e in bfs_iterator(self.graph, node):
File "/usr/lib/python3/dist-packages/graph_tool/search/__init__.py", line
345, in bfs_iterator
return libgraph_tool_search.bfs_search_generator(g._Graph__graph,
int(source))
RuntimeError: This functionality is not available because boost::coroutine
was not found at compile-time
Ubuntu: 14.04
python3-graph-tool version 2.12-1 (from deb
http://downloads.skewed.de/apt/trusty trusty universe)
There is a way to install python3-graph-tool binaries compiled with boost ?
Of course I can compile myself graph-tool, but it is not my goal.

I am trying to install graph-tool on a Trusty Ubuntu virtualbox being hosted on a Mac. I've added the requisite lines
deb http://downloads.skewed.de/apt/trusty trusty main
deb-src http://downloads.skewed.de/apt/trusty trusty main
to my /etc/apt/sources.list, but when I run a sudo apt-get update, I get the following errors:
W: Failed to fetch http://downloads.skewed.de/apt/trusty/dists/trusty/Release Unable to find expected entry 'main/source/Sources' in Release file (Wrong sources.list entry or malformed file)
E: Some index files failed to download. They have been ignored, or old ones used instead.
I have the main, universe, and multiverse repositories available. If any one has come across this problem before, please let me know how to fix it. Thanks.
Andy_