graph-tool December 2013

graph-tool@skewed.de

10 participants
18 discussions

Python install build issue
by Gerry Steele 06 Jan '14

06 Jan '14

I've searched the forum repeatedly and not found anything helpful despite this issue being posted 5 or 6 times sadly. I'm working in an environment where I need to build all dependencies from scratch. I've failed at the first hurdle with: > Could not link test program to Python. Maybe the main Python library has been installed in some non-standard library path. If so, pass it to configure via the LDFLAGS environment variable. Note I have built the python install i need to use myself. So when i try: $ ./configure --prefix=`pwd`/gt-inst LDFLAGS="-L/home/gs/Python-2.7.6/python-2.7.6/lib/python2.7/lib" Or similar i just get the same error. What is different about the python install graph-tool configure expects? Thanks Gerry

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Graph dynamics - layout issues
by Igor Strozzi 26 Dec '13

26 Dec '13

I'm working on a project wherein I need to dynamically refresh my graph layout, getting a image for each step of the layout refresh. The problem is: I can't get the continuity of frames we see in this http://graph-tool.skewed.de/static/doc/demos/animation.html#dynamic-layout. My video seems more like a stopmotion: http://www.mediafire.com/watch/4de67mc7nanu2ox/output4.avi This problem seems to arise from 2 facts: 1) the way I'm refreshing the graph - since I'm simply generating another graph (which is not a bigger problem because the model I'm using is deterministic); 2) max_iter = 2, instead of 1. But EVEN when I set it to 1, I get no continuity from one frame to another. I think it will be useful some parts of the algorithm I'm using, but I don't know how comprehensible it is: #main function: makes graphs and save them as images; also save some useful > data > def graph(a, b, BIN): > global prop, init_foot, ibin, fbin > b=0 > while BIN > fbin: > print 'while' > foot = (init_foot)*(10**a) > BIN = ibin - foot*b > g.clear_edges() > for i in g.vertices(): > xj = abs(prop[i])+abs((BIN-1)*dP) > match = gt.find_vertex_range(g,prop,(abs(prop[i]+0.0000000001), > xj)) > val = np.array([g.vertex_index[i], len(match), prop[i], BIN]) > exv.append(val) > for j in xrange(0,len(match)): > e = g.add_edge(g.vertex_index[i], match[j]) > Rij = (dP - abs(prop[i] - prop[match[j]]))/dP > R[e] = Rij > > posa = g.vp['pos'] > pos = gt.sfdp_layout(g, pos=posa, max_iter=2) > gt.graph_draw(g, pos=pos, > vertex_fill_color=Mag,vertex_size=prop_to_size(Mass, mi=3, ma=9.5, > log=False, power=6), fit_view=True, output = '%03d.png' % b) > #some data I`ll need for analysis > comp, hist = gt.label_components(g, directed=False) > compo = len(set(comp.a)) > components.append(compo) > bins.append(BIN) > numed.append(g.num_edges()) > print g.num_edges(), compo, BIN > diam1, end = gt.pseudo_diameter(g) > diam.append(diam1) > gg = g.copy() > graphs.append(gg) > deg = g.degree_property_map('out', weight=None) > degree.append(deg.a) > lclstr = gt.local_clustering(g, undirected=True) > gclstr = gt.global_clustering(g) > lclust.append(lclstr.a) > gclust.append(gclstr) > #the cases the images start to get too big to compute efficiently > if b > 1 and components[b] < 350: > a += 0.1 > if b > 1 and components[b] < 150: > a += 0.3 > > #pace > b+=1 > #pace variation > a +=0.1 > return components, bins, exv, graphs

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bug + fix in blockmodel.py
by Alan Williams 26 Dec '13

26 Dec '13

Hi there, I'd like to report a bug in blockmodel.py, built from source where __version__ = 2.2.28dev (commit da179ff0, Thu Dec 5 00:41:09 2013 +0100) Line 222 has return self.mrp. self.mrm this line returns a tuple of the two PropertyMaps, the full stop should be a comma :) kind regards, Alan

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Wheezy package is still 2.2.25
by Giuseppe Profiti 16 Dec '13

16 Dec '13

Hello, just wondering if still having 2.2.25 on wheezy is due to an understandable lack of time or wheezy is no longer supported. Thank you, Giuseppe

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Float properties and xml
by Giuseppe Profiti 12 Dec '13

12 Dec '13

Hello, I remember an old discussion about vectors of floats saved using the C99 hexadecimal notation. However, a colleague found out that also a simple float property map is saved using that notation and this is giving him troubles of interoperability. As an example from graph_tool.all import * g = Graph() n = g.add_vertex() n1 = g.add_vertex() e = g.add_edge(n,n1) p = g.new_edge_property('float') p[e]=3.14 g.edge_properties['weight']=p g.save('float-test.xml') float-test.xml then contains: ... <key id="key0" for="edge" attr.name="weight" attr.type="float" /> ... <edge id="e0" source="n0" target="n1"> <data key="key0">0x1.91eb851eb851fp+1</data> </edge> Is this the expected behaviour? Also, there is no difference if we change the type from float to double. Thanks, Giuseppe

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ImportError: no module named graph_tool.all
by Rampo 11 Dec '13

11 Dec '13

Hello, I am new to graph-tool. So, I installed it on Mac OS X using the command sudo port install py-graph-tool. Installation was complete and I went on to run my python code. This is what I got: Traceback (most recent call last): File "SIR.py", line 1, in <module> from graph_tool.all import * ImportError: No module named graph_tool.all The piece of code that created this so called error: from graph_tool.all import * from random import * import smallworld I figured that after installing py-graph-tool, it should work. What I already tried is adding this line to .profile: export PYTHONPATH=/usr/local/lib/python2.7/site-packages/ However, no success. Please, help me out here. Regards -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

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Installing graph-tool to use with Anaconda
by Csernai, Eszter 04 Dec '13

04 Dec '13

Hello, I have successfully installed graph-tool on Ubuntu 1310 using apt-get. So it works with the default python of the system. However, I would like to use it with the python included in the Anaconda distribution. Can anybody please help how to do that? Does it need to be compiled from source in that case? Thanks very much, Eszter

3 5

compiling from source - configure problem with cairomm
by Matthias Ekman 02 Dec '13

02 Dec '13

Hi, I'm trying to install graph-tool-2.2.27 from source (Debian 6.0/python 2.7.5) ./configure --prefix=${HOME}/scratch/temp/gt <snip> checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for CAIROMM... no configure: error: Package requirements (cairomm-1.0) were not met: No package 'cairomm-1.0' found </snip THIS tells me that cairomm-1.0 is not installed. I'm a bit surprised as this is marked as an optional dependency here: http://graph-tool.skewed.de/download However dpkg -L libcairomm-1.0-1 /usr/share/doc /usr/share/doc/libcairomm-1.0-1 /usr/share/doc/libcairomm-1.0-1/README /usr/share/doc/libcairomm-1.0-1/AUTHORS /usr/share/doc/libcairomm-1.0-1/copyright /usr/share/doc/libcairomm-1.0-1/changelog.Debian.gz /usr/share/doc/libcairomm-1.0-1/NEWS.gz /usr/share/doc/libcairomm-1.0-1/changelog.gz /usr/lib /usr/lib/libcairomm-1.0.so.1.4.0 /usr/lib/libcairomm-1.0.so.1 But pkg-config cairomm-1.0-1 --libs ckage cairomm-1.0-1 was not found in the pkg-config search path. Perhaps you should add the directory containing `cairomm-1.0-1.pc' to the PKG_CONFIG_PATH environment variable No package 'cairomm-1.0-1' found I suspect this is a rather simple issue. Could you please tell me how to adjust configure to find my cairomm installation? Much appreciated, Matthias

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graph-tool December 2013