[graph-tool] Re: Fwd: Adding label to vertices

* Data: seg., 21 de fev. de 2022 às 11:35 Assunto: Re: [graph-tool] Adding label to vertices Para: Alexandre Hannud Abdo Ok, I managed to use the data/key nodes. Thanks a lot. However, how can I access them after loading the grapheme file? See the graphml example: http://graphml.gr

Re: [graph-tool] Description length of consensus partition

Ni! Hi Haiko, Do you mean the nested description length as in: NestedBlockState(h, c_nested).entropy() ? .~´ On Fri, Apr 9, 2021 at 4:41 PM Lietz, Haiko wrote: > Dear Tiago, all, > > > > I’m happy to have discovered the new partition overlap functionality. It > works very nicely. But is it

Re: [graph-tool] numpy not found when run ./configure

Ni! Hi, That is the good version. It seems the configure script wasn't updated to require python3 until later. I'm going to stress this again: please, first try using a prepackaged build. Only in case none of the prepackaged options serve you, then: 0. Make sure you've read and understood the

Re: [graph-tool] numpy not found when run ./configure

Ni! Your check says you've got numpy installed for python3.6 ... and yet your configure output tells us you're compiling for python-2.7. Which version of graph-tool are you even compiling ? Recent versions require python 3. Old versions are not supported and not recommended. Also, make sure you

Re: [graph-tool] graph-tool memory usage

Yes. And you can entirely avoid compilation if you install from binary packages such as those available for Debian, Ubuntu, Conda, and Homebrew, or if you use a Docker container. From what I can tell of your current level of understanding, I strongly advise you to do that. Please see <

Re: [graph-tool] graph-tool memory usage

Ni! The algorithms in graph-tool are written in C++, just like the algorithms in igraph are writen in C. In both cases, the C++/C code gets compiled before installation. Graph-tool's python library, like the higher level libraries for igraph, are only interfaces to the underlying compiled code.

Re: [graph-tool] graph-tool memory usage

Ni! Hi Nikhrao, Please note that the phrase you've extracted contains the words «during compilation» while you seem to be talking about runtime memory usage. Runtime memory usage will depend on the algorithm you'll be running and choices of the implementation, as there's often a tradeoff between

Re: [graph-tool] efficent way to assign values to vector property map

Ni! Hello Bleak, I trust two possible solutions to your question stand in plain sight in the sections of the documentation pertaining to property maps. https://graph-tool.skewed.de/static/doc/graph_tool.html#graph_tool.Graph.new_vertex_property

Re: [graph-tool] working with hypergraphs - node_x_edge input

0 0 0 0 0 0 > > to be an adjacency matrix ? > Thanks, > > > On Tue, Mar 3, 2020 at 5:32 PM Alexandre Hannud Abdo > wrote: > >> Ni! >> >> Incidence matrices can be trated as a subset of an adjacency matrix (and >> in this sense hypergraphs as a speci

Re: [graph-tool] working with hypergraphs - node_x_edge input

work with > adjacency matrices. Therefore, I wonder what are the possibilities to > work-around this problem. > > Br > > > On Mon, Mar 2, 2020 at 9:35 PM Alexandre Hannud Abdo > wrote: > >> Ni! Hi Alireza, >> >> One way to work with hypergraphs is to us

Re: [graph-tool] working with hypergraphs - node_x_edge input

Ni! Hi Alireza, One way to work with hypergraphs is to use the incidence graph representation of the hypergraph. Abraços, ale .~´ On Mon, Mar 2, 2020 at 5:28 PM Alireza Kashani < alireza.kashanip...@gmail.com> wrote: > Hi, > > I wonder how one can

Re: [graph-tool] Random graph with degree sequence.

Ni! Hi Alvaro, this is explained in the documentation for the graph_tool.generation.random_graph function concerning the `deg_sampler`: > Optionally, you can also pass a function which receives one or two

Re: [graph-tool] Problem extracting hierarchical blocks

Ni! Hi James, see below. On Thu, Aug 29, 2019 at 4:59 PM James Ruffle wrote: > > r = levels[0].get_blocks()[idx] # group membership of node idx in > level 0 > vertexblocksdf.ix[idx, 'level0'] = r > > r = levels[0].get_blocks()[r] # group membership of node idx in > level 1 >

Re: [graph-tool] Graph views via property maps

Ni! Hi Haiko, GraphView can simultaneously take `vfilt` and `efilt` parameters, if that is what you wanna know. So, g_filter = GraphView(g, vfilt=vp_filter, efilt=ep_filter) should work just fine. Regarding your code snippet, the 'elegance' issues are kinda unrelated to graph_tool. For

Re: [graph-tool] Fwd: Can I use graph-tool for analyzing temporal network?

Ni! Hey Sara, The short answer is yes, you can do a lot with graph-tool for these kinds of networks. Did you take a look at the documentation, and did you not find something you were expecting? Any answer longer than this requires you to be way more specific about what kind of analysis you plan

Re: [graph-tool] Edge property map for int type

Well... The first maps each vertex to a vector of ints, i.e. `v => [4, 9, -2, 1]`, the second maps each vertex to a single int, i.e. `v => 4`. .~´ On Fri, Jan 11, 2019 at 2:36 PM ashutosh wrote: > can you also tell me the difference between the two > > 'vector' and 'int' property types ? > > >

Re: [graph-tool] Edge property map for int type

Hi Ashuein, You're trying to push `int` values into a `vector` type. You should use a `int` for the property map instead. .~' On Friday, January 11, 2019, ashutosh wrote: > > pdat = > pd.DataFrame({'source':['A','B','C'],'target':['p','q','r'],'weight':[1,-1,2]}) > > graph =

Re: [graph-tool] Slow filling graph

Ni! Hi elastica, In graph-tool you can efficiently add edges with properties using the `add_edge_list` function: https://graph-tool.skewed.de/static/doc/graph_tool.html#graph_tool.Graph.add_edge_list I'd also suggest that you benchmark python code with the `cProfile` module, it is much easier

Re: [graph-tool] make[3]: *** [graph_triangulation.lo] Error 1

Ni! Hi Zahra, This last error seems to be a consequence of boost being compiled with a different compiler version than graph_tool. I encourage you to follow Tiago's request and open a bug with the homebrew issue tracker. Only this will properly fix things for you and others in the long run.

Re: [graph-tool] TypeError while using add_edge_list

Tiny typo, the first argument is `hashed=True`. On Wed, Jul 18, 2018 at 1:18 PM, Alexandre Hannud Abdo wrote: > Ni! Hi ashu, > > Please, always try to *read errors carefully* and consult the > documentation. Not to mention, provide self-contained examples. > > Python is thr

Re: [graph-tool] TypeError while using add_edge_list

Ni! Hi ashu, Please, always try to *read errors carefully* and consult the documentation. Not to mention, provide self-contained examples. Python is throwing a "TypeError" and telling you it expects an integer ('unsigned long', the C++ type for vertex indices) while you are passing it a string

Re: [graph-tool] CGAL library not found (though installed)

e: WARNING: No usable boost::coroutine > found! Some functionality will be disabled in the library.” > > And then when I run make, it fails. > > I have attached the new config.log and the output of the make. > > > > Any guidance is much appreciated > > > >

Re: [graph-tool] CGAL library not found (though installed)

, Jun 21, 2018 at 5:18 PM, Srinivasamoorthy, Ganesh (CDC/OID/NCEZID) (CTR) wrote: > Hi Ale > > > > Attached is the copy of the log > > > > *From:* graph-tool *On Behalf Of *Alexandre > Hannud Abdo > *Sent:* Thursday, June 21, 2018 10:56 AM > *To:* Main discus

Re: [graph-tool] CGAL library not found (though installed)

Ni! Hi Ganesh, `./configure` generates a file called "config.log" when run, that is the file you want to transmit when asking for help. A copy/paste of your terminal is not nearly as useful. Meanwhile, I assume you passed the parameter " --with-cgal=/usr/local/" to `./configure`, is that right ?

Re: [graph-tool] Most efficient way to access all nodes in a block

Ni! Hi Philipp, Yes, there are more straightforward paths to the same information: # get some graph and model it import graph_tool.all as gt g = gt.collection.data["celegansneural"] s = gt.minimize_nested_blockmodel_dl(g) # get your groups of vertices in a dictionary l0 = s.levels[0]

Re: [graph-tool] libpython3.5 error on Ubuntu17.10

; > Snehal > > > Sent with ProtonMail <https://protonmail.com> Secure Email. > > Original Message ---- > On January 25, 2018 12:31 AM, Alexandre Hannud Abdo <a...@member.fsf.org> > wrote: > > Hi Snehal, > > I checked the release notes for 17.10 an

Re: [graph-tool] libpython3.5 error on Ubuntu17.10

:amd64.shlibs > /var/lib/dpkg/info/libpython3.6:amd64.symbols > /var/lib/dpkg/info/libpython3.6:amd64.triggers > > Thus, the version 3.6 seems to be installed and I guess I need 3.5. Is > that right? > > > Sent with ProtonMail <https://protonmail.com> Secure Email. > >

Re: [graph-tool] libpython3.5 error on Ubuntu17.10

t; > Original Message > On January 24, 2018 11:48 AM, Alexandre Hannud Abdo <a...@member.fsf.org> > wrote: > > Ni! Hi Snehal, > > Do you mean you tried this command on a new clean install of Ubuntu, > nothing else been done previously to it? - oth

[graph-tool] libpython3.5 error on Ubuntu17.10

Ni! Hi Snehal, Do you mean you tried this command on a new clean install of Ubuntu, nothing else been done previously to it? - other than enabling he PPA and updating the system, I'd guess. Otherwise, this may not be related to graph-tool at all, you just need to figure out why libpython is not

Re: [graph-tool] Displaying Overlapping Communities for Networks Without Clustering with SBMs

You're probably just passing the wrong type to vertex_pie_fractions, but we have no way to know that as we're missing the minimal self-contained example. .~´ On Thu, Oct 5, 2017 at 11:54 AM, isukritgupta wrote: > Hi, I am trying to generate plots for communities

Re: [graph-tool] How to effectively get the nested blockmodel block memberships of each of the nodes in your graph

Ni! What you're looking for is the 'project_level' method of NestedBlockState: some_level = 2 blocks = state.project_level( some_level ).get_blocks() block_for_v_at_level = blocks[ some_vertex ] Hope this helps, ale .~´ On Sat, Aug 5, 2017 at 5:29 PM, lenail wrote: > Hello

Re: [graph-tool] Unable to use subplots with mplfig

Funny thing, messing around with your example I find that graph_draw seems to be drawing onto the wrong axis: when you pass axis 3 it draws inside aixs 1, passing axis 4 draws inside axis 2, and what you pass as axes 1 and 2 is likely being drawn outside the canvas. Also, if you exapnd to 8 axes,

Re: [graph-tool] Can't compile graph-tool on Solus, not enough RAM

Ni! Hi Padraig, Some things which might help us help you: a) gcc version you're using b) graph-tool version you're compiling c) how much ram do you actually have available when you start your compilation d) the actual error message coming out of gcc cheers, ale .~´ On Wed, Jun 28, 2017 at

Re: [graph-tool] Takes enormous memory and then eventually gets terminated.

Hi Isuki, No, that is not expected. We'll need more information to help you, can you provide at least: 1. graph-tool version you're using 3. the graph, exported by graph-tool 2. a minimal script that reproduces the issue Cheers, ale .~´ Le mardi 30 mai 2017 à 02:13 -0700, isukritgupta a écrit 

Re: [graph-tool] Correlation Histogram

Well, yes. Though you can configure your shell and make it permanent. Software Carpentry has some good tutorials on using the shell, for example: http://swcarpentry.github.io/shell-extras/08-environment-variables.html You can also modify the environment from within Python, using the "os.environ"

[graph-tool] general "did not match C++ signature" error

Ni ! The import working means that Python can find the Python component of graph tool. The error you get has to do with boost Python not finding, for a call internal to the Python component, a corresponding function in the C++ component that matches it's argument types. Thus, this happens if

Re: [graph-tool] Average neighbour-neighbour correlation

Ni! avg_neighbour_corr considers as neighbours of v the targets of edges for which v is source. The documentation on the website already states this correlation in terms of 'source' and 'target', and in any case it is pretty straightforward to check what it is doing... but if you want to dig it

Re: [graph-tool] Installation of graph-tool-2.19 fails on RedHat 6.5

Le mardi 06 décembre 2016 à 06:16 -0700, Amihai a écrit : > ./configure CPPFLAGS="-I/usr/include/cairomm-1.0/cairomm/" > > graph_cairo_draw.cc:38:29: fatal error: cairomm/context.h: No such > file or directory Hm, did you try passing CPPFLAGS="-I/usr/include/cairomm-1.0/" ? The code seems to be

Re: [graph-tool] Eigenvector centrality runtime/complexity

Hi Philipp, Not with the sample you provided. Trying here, time decreases below that for the original graph. (I had to change the sample to increase n and sample size, otherwise it was just too fast to capture) In [1]: %paste import random import graph_tool.all as gt n=10 g =

Re: [graph-tool] Eigenvector centrality runtime/complexity

HI Philipp, Can you provide minimal sample code that demonstrates your observations? That usually improves tenfold the chance that anyone will be able to help. Cheers, ale On Wed, Jul 27, 2016 at 3:14 PM, Philipp Singer wrote: > Hi all, > > I have run into a

Re: [graph-tool] Extract a neighborhood of a randomly selected node

Hi jimmy/gogurt, The predecessor graph, returned by predecessor_tree, contains all the nodes from the original graph, and edges representing the predecessor relationships given by the map. In any case, understand that normally you should not have to create an intermediate graph in order to

Re: [graph-tool] First question - Planarity

Cool! Hey, the link to the boost reference in the documentation doesn't work, I think the correct link would be: http://www.boost.org/doc/libs/release/libs/graph/doc/straight_line_drawing.html Ni! ale On Sun, Apr 24, 2016 at 9:48 PM, Tiago de Paula Peixoto wrote: > On

Re: [graph-tool] Installation under Ubuntu 14

https://graph-tool.skewed.de/download#debian On Wed, Apr 13, 2016 at 7:43 PM, Yannis Haralambous wrote: >> An internal compiler error is always a compiler bug, it is not >> graph-tool's fault. >> > It was a memory problem, by allowing 2 GB of RAM I had much more *.lo files

Re: [graph-tool] Most efficient way to model an epidemic?

Hi gogurt, It seems you can keep the state of vertices in a boolean property map and queue the vertices whose neighbors you gotta visit in a python list. []s ale On Thu, Aug 20, 2015 at 3:40 PM, gogurt gog...@gmail.com wrote: Hi all, So I've scoured the documentation for this but I've been

Re: [graph-tool] Animations with graph-tool

On 01/04/2013 08:53 AM, Tiago de Paula Peixoto wrote: I've just included a section in the documentation on how to do animations with graph-tool: http://projects.skewed.de/graph-tool/doc/dev/demos/animation.html terrific! []s ale ___

Re: [graph-tool] Problems installing

Ni! Hi Hugo, Your config.log very likely has a more useful description of the issue. Take a look and share it here. Good luck, q. On 15-11-2012 10:40, Hugo Leeney wrote: Oh sorry, I have a bunch of log outputs on my terminal - I just picked the wrong one. I have been permutating versions

Re: [graph-tool] Welcome to the graph-tool mailing list

On 17-10-2012 18:13, Ronnie Ghose wrote: Sorry i'm new here. Is the code hosted on github? Hi Ronnie, and welcome. Yes, there is a github repository mirroring the main repository which is located at skewed.de. Take a look at the last section in