October 2019 - graph-tool - archives.skewed.de

Random graph with degree sequence.
by Alvaro Sechinel 07 Nov '19

07 Nov '19

Hi, I'm using graph-tool to try to generate random graphs with a sequence of degrees. For example, in a 3-node graph, I generated a random graph with all nodes with input degrees 1 and output degrees 1. My code: >>> import graph_tool.all as gt>>> def deg_sampler():... return 1,1... >>> g = gt.random_graph(3,deg_sampler,parallel_edges=True, self_loops=False)>>> gt.graph_draw(g) Can I generate a random graph defining the input and output degrees of each node? For example, tree nodes with respectively the input degrees (1, 2, 0) and output degrees (1, 0, 2). Thanks, Alvaro

2 1

graph-tool 2.29 breaks backward compatibility
by Adrien Dulac 01 Nov '19

01 Nov '19

Hello folks, I've discovered, while trying to fix and 'never seen before' bug in my code, after having installed graph-tool 2.29 from an Ubuntu repo, that some new features was not backward compatible. For example, my error came from that fact that now, the function `get_edges` returns by default a `Nx2` matrix, whereas it used to return a `Nx3` matrix in prior version. Another one is that edge property doesn't seem to accept node tuple anymore (e.g. g.ep['weights'][i,j]) After a quick search on the doc, changelog and mailing list, I didn't find mention of these changes, so I am wandering if there is a place to find such information, and if there may be other changes that affect the backward compatibility in new version ? Regards, adrien

2 5

Inverted keyword argument in GraphView
by Gerion Entrup 31 Oct '19

31 Oct '19

Hi, I have a graph with two types of nodes. This is specified via the boolean vertex property `is_typeA`. I currently have code like: ``` typeA_graph = graph_tool.GraphView(my_graph, vfilt=is_typeA) ``` I'd like to create an `typeB_graph` GraphView, too. The condition obviously is that the node is _not_ typeA. However, I don't see an inverted keyword argument like in the `set_vertex_filter()` function. Is there a possibility to get that? Best, Gerion

2 1

Filter in iterators
by Gerion Entrup 31 Oct '19

31 Oct '19

Hi, I often have this pattern in Python: ``` for vertex in mygraph.vertices(): if not mygraph.vp.is_foo[vertex]: continue do_stuff_that_uses_all_vertices() ``` `is_foo` is a boolean property. I know that there a vertex filters and GraphViews but in the loop body I need access to all vertices. Only the iterator should be filtered. Is there a way to specify a vertex filter only in the vertices iterator? Something like: ``` for vertex in mygraph.vertices(vfilt=mygraph.vp.is_foo): do_stuff_that_uses_all_vertices() ``` Of course, this would be nice in all iterators (edges(), out_edges(), ...) ;). Best, Gerion

2 1

C++: Extract internal property maps of an GraphInterface object
by Gerion Entrup 30 Oct '19

30 Oct '19

Hi, when using graph-tool from C++, you can use one or more PropertyMaps. In the documentation they are always given as an extra argument. Since graph-tool has internal PropertyMaps, is it possible to extract internal PropertyMaps out of the GraphInterface object? In pseudo code (like in the documentation): ``` void kcore_bind(GraphInterface& gi) { // Vertex property map of type int32_t typedef typename vprop_map_t<int32_t>::type vprop_t; vprop_t c = boost::any_cast<vprop_t>(gi.get_internal_vertex_property_map("foo")); gt_dispatch<>() ([&](auto& g){ kcore_decomposition(g, c.get_unchecked()); }, all_graph_views()) (gi.get_graph_view()); } ``` Is there a way to simulate the `get_internal_vertex_property_map` method? Gerion

2 2

graph-tool 2.29 breaks backward compatibility
by Adrien Dulac 30 Oct '19

30 Oct '19

Hello folks, I've discovered, while trying to fix and 'never seen before bug', after having installed graph-tool 2.29 from a Ubuntu repo, that some new features was not backward compatible. For example, my error came from that fact that now, the function `get_edges` returns by default a `Nx2` matrix, whereas it used to return a `Nx3` matrix in prior version. After a quick search on the doc, changelog and mailing list, I didn't find mention of these changes, so I am wandering if there is a place to find such information, and if there may be other changes that affect the backward compatibility in new version ? Regards, adrien

1 0

Permission denied of Docker
by 四正（红砖） 28 Oct '19

28 Oct '19

Hello everyone, An error occurred when I want to run jupyter notebooks in a docker container. My OS is CentOS7. The snapshot is as follows: I don't understand. Does it mean the user "user" doesnot have the right? Thanks! Gang Lu

1 0

Permission denied of Docker
by 四正（红砖） 24 Oct '19

24 Oct '19

Hello everyone, An error occurred when I want to run jupyter notebooks in a docker container. My OS is CentOS7. https://git.skewed.de/count0/graph-tool/wikis/Installation-instructions I don't understand. Does it mean the user "user" doesnot have the right?  Thanks! Gang Lu

1 0

Recreating figures from Hric, Peixoto, and Fortunato (2016)
by jsfog 23 Oct '19

23 Oct '19

I am trying to recreate figure 2 from Hric, Peixoto, and Fortunato (2016): https://arxiv.org/abs/1604.00255 and would appreciate some assistance. The data come from the college football network and can be pulled directly from an online repository using graph-tool: g = gt.collection.data["football"] I can recreate figure 2a simply by estimating a nested blockmodel and graphing it as follow: state = minimize_nested_blockmodel_dl(g, deg_corr=True) draw_hierarchy(state, output="./results/test.png") However, I am stuck on figure 2b, which graphs the bipartite network of conferences and teams. Does this figure plot the output of estimating the blockmodel on layered data? If so, how should I extract the metadata, which are stored as the vertex property "label"? Do I need to create a second edge list linking the original vertices to the metadata? And if so, is there a way of doing this without a long loop? Eventually I want to run this code on a much larger network so I would like to write code that is as efficient as possible. Thanks for your help, Jamie -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

1 0

Re: [graph-tool] Accessibility from C++
by Gerion Entrup 22 Oct '19

22 Oct '19

Am Donnerstag, 10. Januar 2019, 23:51:29 CEST schrieb Tiago de Paula Peixoto: > Am 10.01.19 um 13:48 schrieb Gerion Entrup: > > So my question is: Is it possible to get the C++ graph object out of the > > Python graph object? Is it possible to fill the C++ graph object > > directly with nodes and edges? > > This is possible, and not very difficult. However, it's undocumented at the > moment. > > I'm working on some documentation, and I'll release it soon. > > > Another point is that I need to attach a pointer (or shared_ptr) to a > > custom C++ type to some nodes. The pointer does not need to be > > accessible or visible from Python. Is this possible in a simple way? > > (Of course I can workaround with an e.g. map of type (vertex id, > > pointer).) > > You can either use a property map of type int64_t, which is enough to hold > pointers. You can also use type python::object, which will hold whatever you > can express in python, inclusive custom classes. > > I have seen that you wrote some documentation [1]. Thank you! Gerion [1] https://graph-tool.skewed.de/static/doc/demos/cppextensions/cppextensions.h…

1 0