graph-tool June 2011

graph-tool@skewed.de

5 participants
14 discussions

graph-tool with macports
by Sebastian Weber 11 Jun '11

11 Jun '11

He there! Has someone graph-tool running from within macports? I just tried the git version and found there are some serious issues here: 1. graph-tool installs into a wrong directory its libraries, i.e. /opt/local/lib/python2.7/site-packages, but libs for macports python should go into /opt/local/Library/Frameworks/... https://trac.macports.org/wiki/Python has some info on it, i.e. there are some scripts which one should use to install things, when I got it right in order to comply to the conventions of macports 2. dl.so is not present in macports python. I suppose one ought to use a different loading mechnism of the modules. ctypes/macholib seems to contain files which one is supposed to use instead. I guess, when these issues are solved, in particular the second, then graph-tool will be much easier to install for all the mac users here. Cheers, -- Sebastian Weber Group of Cell Communication and Control Freiburg Institute for Advanced Studies - FRIAS School of Life Sciences - LIFENET Albert-Ludwigs-Universität Freiburg Albertstr. 19 79104 Freiburg T.: +49-761-203-97237 Fax:+49-761-203-97334

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Property map from graph xml
by Håvard Wahl Kongsgård 03 Jun '11

03 Jun '11

Hi, I have quickly explored the documentation. So I am sorry if I have overlooked something essential. I use a graph file exported from gephi (xml file(graphml)) </node> <node id="672712520"> <data key="label">672712520</data> <data key="size">10.0</data> <data key="r">153</data> <data key="g">153</data> <data key="b">153</data> <data key="x">25781.25</data> <data key="y">14798.744</data> </node> However, the the node id object is not listed as a property map (in my case it's not the same as the label for all nodes) Is it possible to access this value? Second, what is the optimal method to find the vertice number for a known property value(ID or label)? Thanks, Håvard -- 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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Error with numpy
by Håvard Wahl Kongsgård 01 Jun '11

01 Jun '11

Hi, with ./configure I get this error checking python2.7 module: numpy... yes checking for /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h... no configure: error: Numpy extension header not found Use latest numpy built from source -- 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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Bug in Graph pruning?
by Sebastian Weber 01 Jun '11

01 Jun '11

Hi! I just discovered a quite strange behavior of graph-tool. I want to keep only the largest component of my network and the following code comp = label_largest_component(G) lc = comp.a == 1 Gv = Graph(GraphView(G, vfilt=lc), prune=True) simply gives wrong results. It deletes vertices which are in the LC and have comp[v]==1 !!! Instead, the much slower G.remove_vertex_if(lambda v: comp[v] == 0) call works just fine. The version of graph-tool is something close to 2.2.12, but I haven't seen any changes on git which seems to relate to this issue. It is quite scary that vertex deletion is somewhat unpredictable or I am doing something wrong here. Any help would be great here. Cheers, -- Sebastian Weber Group of Cell Communication and Control Freiburg Institute for Advanced Studies - FRIAS School of Life Sciences - LIFENET Albert-Ludwigs-Universität Freiburg Albertstr. 19 79104 Freiburg T.: +49-761-203-97237 Fax:+49-761-203-97334

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graph-tool June 2011