January 2018 - graph-tool - archives.skewed.de

Grouping and drawing
by Mátyás Csongor 07 Feb '18

07 Feb '18

Is there an example that uses multiple groups within the graph and draw it accordingly. I have multiple groups and I would like to draw the graph in a way that all vertices within each group to be close to each other. I could not achieve this with a problem that has a known solution, so I thought maybe it is not possible, or if it is, someone could help me in how I should try doing it. The test problem that I've chosen is to take all amino acids, organize them into groups according to their properties, and to get to this planar grouping: https://www.researchgate.net/publication/11265315/figure/fig1/AS:2812510187… I would like some general help ideas, but if someone would like to join me in this small project, I can share what I've tried until now. Csongor

2 1

Running all_shortest_path on large graph
by Evangelos Petsalis 06 Feb '18

06 Feb '18

Hi, I have a large graph (800K vertices and 6e6 edges) and I am running the all_shortest_paths function with edge weights. The problem is that due to the size of the graph, there are probably millions of paths that qualify and the function fails with a "MemoryError" code. Is there a way to limit the number of shortest paths returned, or even better a version that returns an iterator and compute the paths as needed? Thanks -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

2 5

libpython3.5 error on Ubuntu17.10
by Snehal Shekatkar 25 Jan '18

25 Jan '18

Dear Tiago, I am trying to install graph-tool on ubuntu17.10 and I get the following error: sudo apt-get install python3-graph-tool The following packages have unmet dependencies: python3-graph-tool : Depends: libpython3.5 (>= 3.5.0~b1) but it is not installable E: Unable to correct problems, you have held broken packages. How can I fix this? Thank you Snehal M. Shekatkar Pune India www.snehalshekatkar.com

3 7

libpython3.5 error on Ubuntu17.10
by Snehal Shekatkar 22 Jan '18

22 Jan '18

Dear Tiago, I am trying to install graph-tool on ubuntu17.10 and I get the following error: sudo apt-get install python3-graph-tool The following packages have unmet dependencies: python3-graph-tool : Depends: libpython3.5 (>= 3.5.0~b1) but it is not installable E: Unable to correct problems, you have held broken packages. How can I fix this? Thank you Sent with [ProtonMail](https://protonmail.com) Secure Email.

1 0

APT Key Server Timeout
by Spencer Gardner 20 Jan '18

20 Jan '18

Is the key server currently down? I've tried to add the apt key from computers on two different networks and in both cases I get a keyserver time out. Thanks!

2 1

Return multiple specific vertices from graph.vertex()
by Spencer Gardner 18 Jan '18

18 Jan '18

Is there a way to efficiently return multiple specific vertices? I'm looking for something between graph.vertex(i) and graph.vertices() in which I can pass multiple vertex indices and return the corresponding vertex object. Something like: graph.vertices([i,j,...]) Ultimately, these would be needed to pull out the corresponding values from a PropertyMap on the vertices, so if there's an efficient way to do it that I'm not thinking of I'd love to hear ideas. Thanks!

2 1

Add vertex properties while adding edges via add_edge_list
by Spencer Gardner 17 Jan '18

17 Jan '18

I'm converting a pandas dataframe to a gt graph. I can successfully add edges with accompany attributes from the dataframe, but the network I'm building has its own internal vertex and edge IDs that I need to be able to reference. I can store the edge IDs when adding edges with the eprops= argument. However, it's unclear how I can associate my vertex IDs to the vertices. Is there an established way to do this? The confusion I have is knowing which vertex in the gt graph I should associate back to the vertices in my input data. I suppose I could read through edges and compare the edge ID in the gt graph with my source data and then assign the correct information to the source and target nodes, but that seems inefficient. Is there something I'm missing? My dataframe is in the format fnode,tnode,edgeid 1 3 1 1 4 2 ... 23 15 32 Thanks for any help.

2 2

Re: [graph-tool] Debian (stretch) install ModuleNotFoundError with Py3
by Duccio Aiazzi 14 Jan '18

14 Jan '18

I don’t know about a Debian installation, but I used a Docker image based on Ubuntu to do the same thing. I wrote about it here, maybe it can help: https://towardsdatascience.com/a-working-environment-for-geospatial-analysi… On Fri, 12 Jan 2018, 12:00 , <graph-tool-request(a)skewed.de> wrote: > Send graph-tool mailing list submissions to > graph-tool(a)skewed.de > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.skewed.de/mailman/listinfo/graph-tool > or, via email, send a message with subject or body 'help' to > graph-tool-request(a)skewed.de > > You can reach the person managing the list at > graph-tool-owner(a)skewed.de > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of graph-tool digest..." > Today's Topics: > > 1. Re: Debian (stretch) install ModuleNotFoundError with Py3 > (Kuan Butts) > 2. Re: Debian (stretch) install ModuleNotFoundError with Py3 > (Tiago de Paula Peixoto) > > > > ---------- Forwarded message ---------- > From: Kuan Butts <kuanbutts(a)gmail.com> > To: graph-tool(a)skewed.de > Cc: > Bcc: > Date: Thu, 11 Jan 2018 09:38:07 -0800 > Subject: Re: [graph-tool] Debian (stretch) install ModuleNotFoundError > with Py3 > Yes, it was a bad idea. Sorry I shared it out. > > The image that my works is based off of is the official repository for > Python on Docker Hub (FROM python:3.6-stretch). Link to the Dockerfile to > build my image: > https://github.com/kuanb/peartree/blob/a202d216abb7b1dab77d84602862dcf02bd9… > > As to your question as to if this is a custom Python install - I would > assume not? If it was, then that would have been set within the > instructions for creating that python:3.6-stretch image. It does appear > that Python is aware only of packages in /usr/local. > > Re: my original issue. It turns out the ModuleNotFound error stemmed from > /usr/lib/python3/dist-packages/ having older versions of Numpy and Scipy. > Adding the PYTHONPATH first, then upgrading Numpy and Scipy (numpy==1.14.0 > scipy==1.0.0) allowed me to import graph_tool successfully (and have it be > able to import the various dependencies it was err'ing on before). > > If you have thoughts about the different versions of Python and some > cursory familiarity with the configuration of that Python 3.6 image; I'd be > interested in finding a less awkward solution than what I did to get > graph_tool up and running. Otherwise, I'd label this issue as "resolved." > Thanks. > > -- > *KUAN BUTTS* > kuanbutts.com > > > > ---------- Forwarded message ---------- > From: Tiago de Paula Peixoto <tiago(a)skewed.de> > To: graph-tool(a)skewed.de > Cc: > Bcc: > Date: Thu, 11 Jan 2018 20:57:50 +0100 > Subject: Re: [graph-tool] Debian (stretch) install ModuleNotFoundError > with Py3 > On 11.01.2018 18:38, Kuan Butts wrote: > > Yes, it was a bad idea. Sorry I shared it out. > > > > The image that my works is based off of is the official repository for > > Python on Docker Hub (FROM python:3.6-stretch). Link to the Dockerfile to > > build my > > image: > https://github.com/kuanb/peartree/blob/a202d216abb7b1dab77d84602862dcf02bd9… > > > > As to your question as to if this is a custom Python install - I would > > assume not? If it was, then that would have been set within the > instructions > > for creating that python:3.6-stretch image. It does appear that Python is > > aware only of packages in /usr/local. > > That can't be. The default Debian python install would never look in > /usr/local. It must be a custom install done in the docker image you are > referencing. > > > Re: my original issue. It turns out the ModuleNotFound error stemmed > > from /usr/lib/python3/dist-packages/ having older versions of Numpy and > > Scipy. Adding the PYTHONPATH first, then upgrading Numpy and Scipy > > (numpy==1.14.0 scipy==1.0.0) allowed me to import graph_tool successfully > > (and have it be able to import the various dependencies it was err'ing on > > before). > > I don't see how that would happen, but I'm glad it is working. > > > If you have thoughts about the different versions of Python and some > cursory > > familiarity with the configuration of that Python 3.6 image; I'd be > > interested in finding a less awkward solution than what I did to get > > graph_tool up and running. Otherwise, I'd label this issue as "resolved. > > Just installing from a clean Debian install using the steps explained in > the > graph-tool website should just work. The issues you describe seem to be due > to a custom python install. > > Best, > Tiago > > -- > Tiago de Paula Peixoto <tiago(a)skewed.de> > > _______________________________________________ > graph-tool mailing list > graph-tool(a)skewed.de > https://lists.skewed.de/mailman/listinfo/graph-tool >

1 0

Debian (stretch) install ModuleNotFoundError with Py3
by Kuan Butts 11 Jan '18

11 Jan '18

I am trying to create a Docker image with graph-tool installed along with a number of geospatial C libraries with Debian stretch OS. Everything but graph-tool has been set up, and is available here ( https://hub.docker.com/r/kuanb/peartree/) The Dockerfile to create that image can be viewed here ( https://github.com/kuanb/peartree/blob/ea45bdd0a045c1bb7769f88801b5dab85c3f… ). I attempt to install graph-tool in a container from the above image with the following: sed -i -e '$a\ deb http://downloads.skewed.de/apt/stretch stretch main\ deb-src http://downloads.skewed.de/apt/stretch stretch main' /etc/apt/sources.list && \ apt-get update && \ apt-get install python3-graph-tool This appears to be successful. I then go into a Python3 repl and attempt to import graph_tool which results in a ModuleNotFoundError. I suspect the error has to do with versions of Python3 and where the library (graph-tool) is being placed versus where pip is placing its libraries. Unfortunately, I am not entirely confident navigating this and would be appreciative of any guidance - I suspect I am "almost there" and someone on this list may be more familiar with setting this up and could point me in the right direction. Thanks in advance and happy new year. :) -- *KUAN BUTTS* kuanbutts.com

2 4

Running all_shortest_path on large graph
by Evangelos Petsalis 10 Jan '18

10 Jan '18

-- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

1 0