graph-tool January 2021

graph-tool@skewed.de

7 participants
9 discussions

How to control the orientation of the graph topology
by Xun Xiao 26 Feb '22

26 Feb '22

Hi Tiago, sometimes, when delete the graph and create a new one, then plot it, the plotted graph is shown upside down (in terms of the node text). So how could we control the orientation of the graph? Or which parameter we should use to always make node text shown in a correct orientation. Thanks a lot. -- 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.

3 5

Upside down labels
by charlie 26 Feb '22

26 Feb '22

Hi, I'm suffering from the same issue mentioned in this post: https://git.skewed.de/count0/graph-tool/issues/174 Namely, I'm trying to draw a graph that includes a lot of self-looping edges, and my labels are being printed upside down. If I remove the self-loops the labels are shown the right way up. Is there a fix for it? Thanks, Charlie -- 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.

3 3

random graph
by JM 01 Sep '21

01 Sep '21

Dear Tiago, I have a directed graph of about half a million nodes and approximately a million edges following scale free behaviour and a power law degree distribution. To test some of my hypothesis, I would like to generate random smaller graphs (about 50 up to 200 nodes) representative of the big one. When I used a sample function that samples straight away from the real distribution of the big network, I have following problems: - I generate unconnected nodes with both 0 in AND out degree. - I generate small sub parts of a few nodes that are not connected to the main graph. - If only sampling from nodes with at least 1 degree, the generated graph is coherent, but not representative anymore as I need a big portion of nodes with either only one in or one out degree. Here is the part of my script I used for that, where samples are drawn from dictionaries of the degrees: def sample_in(): a=np.random.randint(num) k_in = in_degrees[a] return k_in def sample_out(): if sample_in()==0: b=np.random.randint(num_out) k_out=out_zero_zeros.values()[b] return k_out else: b=np.random.randint(num) k_out=out_degrees[b] return k_out N=200 g=gt.random_graph(N, lambda:(sample_in(), sample_out()), model="constrained-configuration", directed=True) I also tried sampling from a list of tuples as you have mentioned before in the forum, but I didn't receive any results, as the tuples randomly drawn from my list might not be combinable. degs=[(7,1),(4,3),(5,6),(2,4),(6,8),(2,0),(3,5),(0,3),(2,7),(2,1)] g = gt.random_graph(4, lambda i: degs[i], directed=True) - Is there any option I could active that would help me in those cases I described above? - Is there a better way how to create representative small networks? Any help on that issue will be much appreciated. Best wishes, Jana -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

3 5

get_hierarchy_control_points return values
by Davide Cittaro 20 Apr '21

20 Apr '21

Hi again, I'm writing a small package that builds on graph-tool, but not on its graphics capabilities (also because I have to represent other things rather than the graph itself). Still I could use some of the functions "under the hood" for my purposes. I have a question about gt.draw.get_hierarchy_control_points(): the function returns the Bézier spline control points for edges in a given graph, but I'm having difficulties in understanding how this information is encoded. For a single edge in graph, I have dozens of values as control points (half dozens + 2), hence I suspect all splines going from node A to the root of a hierarchy and back to node B are encoded there, and control points should be taken 6 by 6 (3x2 by 3x2 coordinates?). How (x,y) for control points are encoded then: (x, x, x, y, y, y) or (x, y, x, y, x, y)? What are the 2 additiona values I have for each vector? Also, are values absolute or relative to one node in particular (A, B or root...)? Thanks d

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Segmentation fault in MeasuredBlockState copy method
by h-lima 01 Feb '21

01 Feb '21

Hi, I am using graph_tool version 2.37 (commit 1d377b3e) on a server with Debian 10 Buster. Whenever I try to copy a MeasuredBlockState object I get segmentation fault. This does not happen with Uncertain or MixedMeasured object though. ``` from graph_tool.all import * g = collection.data["lesmis"].copy() n = g.new_ep("int", 2) x = g.new_ep("int", 2) state = MeasuredBlockState(g, n = n, x = x, n_default = 0, x_default = 0) st = state.copy() ``` The stack trace using gdb and calling the script above is as follows: ================================== Starting program: /usr/bin/python3 script.py [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1". [New Thread 0x7ffff4ddd700 (LWP 19803)] [New Thread 0x7ffff45dc700 (LWP 19804)] [New Thread 0x7ffff1ddb700 (LWP 19805)] [New Thread 0x7fffef5da700 (LWP 19806)] [New Thread 0x7fffecdd9700 (LWP 19807)] [New Thread 0x7fffe85d8700 (LWP 19808)] [New Thread 0x7fffe7dd7700 (LWP 19809)] [New Thread 0x7fffe35d6700 (LWP 19810)] [New Thread 0x7fffe0dd5700 (LWP 19811)] [New Thread 0x7fffde5d4700 (LWP 19812)] [New Thread 0x7fffdbdd3700 (LWP 19813)] [New Thread 0x7fffd95d2700 (LWP 19814)] [New Thread 0x7fffd6dd1700 (LWP 19815)] [New Thread 0x7fffd45d0700 (LWP 19816)] [New Thread 0x7fffd3dcf700 (LWP 19817)] [New Thread 0x7fffcf5ce700 (LWP 19818)] [New Thread 0x7fffccdcd700 (LWP 19819)] [New Thread 0x7fffca5cc700 (LWP 19820)] [New Thread 0x7fffc7dcb700 (LWP 19821)] [New Thread 0x7fffc55ca700 (LWP 19822)] [New Thread 0x7fffc2dc9700 (LWP 19823)] [New Thread 0x7fffc05c8700 (LWP 19824)] [New Thread 0x7fffbfdc7700 (LWP 19825)] [New Thread 0x7fffbd5c6700 (LWP 19826)] [New Thread 0x7fffbadc5700 (LWP 19827)] [New Thread 0x7fffb65c4700 (LWP 19828)] [New Thread 0x7fffb3dc3700 (LWP 19829)] [New Thread 0x7fffb15c2700 (LWP 19830)] [New Thread 0x7fffaedc1700 (LWP 19831)] [New Thread 0x7fffac5c0700 (LWP 19832)] [New Thread 0x7fffa9dbf700 (LWP 19833)] [Thread 0x7fffac5c0700 (LWP 19832) exited] [Thread 0x7fffaedc1700 (LWP 19831) exited] [Thread 0x7fffa9dbf700 (LWP 19833) exited] [Thread 0x7fffb15c2700 (LWP 19830) exited] [Thread 0x7fffb3dc3700 (LWP 19829) exited] [Thread 0x7fffb65c4700 (LWP 19828) exited] [Thread 0x7fffbadc5700 (LWP 19827) exited] [Thread 0x7fffbd5c6700 (LWP 19826) exited] [Thread 0x7fffbfdc7700 (LWP 19825) exited] [Thread 0x7fffc05c8700 (LWP 19824) exited] [Thread 0x7fffc2dc9700 (LWP 19823) exited] [Thread 0x7fffc55ca700 (LWP 19822) exited] [Thread 0x7fffc7dcb700 (LWP 19821) exited] [Thread 0x7fffca5cc700 (LWP 19820) exited] [Thread 0x7fffccdcd700 (LWP 19819) exited] [Thread 0x7fffcf5ce700 (LWP 19818) exited] [Thread 0x7fffd3dcf700 (LWP 19817) exited] [Thread 0x7fffd45d0700 (LWP 19816) exited] [Thread 0x7fffd6dd1700 (LWP 19815) exited] [Thread 0x7fffd95d2700 (LWP 19814) exited] [Thread 0x7fffdbdd3700 (LWP 19813) exited] [Thread 0x7fffde5d4700 (LWP 19812) exited] [Thread 0x7fffe0dd5700 (LWP 19811) exited] [Thread 0x7fffe35d6700 (LWP 19810) exited] [Thread 0x7fffe7dd7700 (LWP 19809) exited] [Thread 0x7fffe85d8700 (LWP 19808) exited] [Thread 0x7fffecdd9700 (LWP 19807) exited] [Thread 0x7fffef5da700 (LWP 19806) exited] [Thread 0x7ffff1ddb700 (LWP 19805) exited] [Thread 0x7ffff45dc700 (LWP 19804) exited] [Thread 0x7ffff4ddd700 (LWP 19803) exited] [Detaching after fork from child process 19834] [Detaching after fork from child process 19835] Thread 1 "python3" received signal SIGSEGV, Segmentation fault. 0x00007fff8e1a5ba5 in ?? () from /usr/lib/python3/dist-packages/graph_tool/inference/libgraph_tool_inference.so ================================================== I tried to replicate the issue in my laptop using graph tool version 2.36dev (commit 15a33b72) in Arch Linux, but the issue does not happen, so it seems to be related to recent releases. Thanks in advance, Herlander -- Sent from: https://nabble.skewed.de/

2 3

Drawing local clustering vertices with graph_draw ?
by Binon 31 Jan '21

31 Jan '21

I am working to draw the vertices included in the local clustering algorithm. But, in the documentation only coefficient values are shown. Please help! -- Sent from: https://nabble.skewed.de/

2 1

Compiling graph-tool for pypy?
by Matteo Dell'Amico 26 Jan '21

26 Jan '21

Hi! Thanks for graph-tool, really a great piece of software! I've been experimenting with graph-tool and pypy3 (by making $PYTHON point to the pypy interpreter), and I couldn't manage to successfully run configure, even while setting --with-python-module-path. I don't know if there's a correct value to put for LIBS here--maybe the directory structures for lib directories of cpython and pypy are different? Do you think there's a way to make these two pieces of software cooperate? thanks a lot! Here, the error that I get: configure: error: 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 LIBS environment variable. Example: ./configure LIBS="-L/usr/non-standard-path/python/lib" ============================================================================ ERROR! You probably have to install the development version of the Python package for your distribution. The exact name of this package varies among them. ============================================================================ -- matteo

3 4

Reingold Tilford
by rjalex 14 Jan '21

14 Jan '21

Hello everyone, I need to plot a 5K node/edges tree (a company directory) and after many experiments have seen that the Reingold Tilford (RT) layouting gives the best results. I have tried using iGraph which has this algo but cannot manage to get nice visual results. Also tried exporting the iGraph layout to GraphML and opening it with Gephi but also this does not work well. Is there a way to get a RT (linear or circular) graph layout with graph-tool? Thank you VERY much. Keep safe! Robert -- Sent from: https://nabble.skewed.de/

2 1

Issue with signature for bionic repository
by Tanguy Fardet 08 Jan '21

08 Jan '21

Dear Tiago, trying to install graph-tool on a ubuntu machine, I got the following error: W: GPG error: https://downloads.skewed.de/apt bionic InRelease: The following signatures were invalid: EXPKEYSIG 7A80C8ED4FCCBE09 Tiago de Paula Peixoto <tiago(a)skewed.de> E: The repository 'https://downloads.skewed.de/apt bionic InRelease' is not signed. I suppose this relates to the PGP key at the end of https://downloads.skewed.de/apt/dists/bionic/InRelease <https://downloads.skewed.de/apt/dists/bionic/InRelease>. Could you let me know if the key is indeed expired or if it is an issue on my side? Otherwise the initial addition of the repository seems to work since I get: deb https://downloads.skewed.de/apt bionic mainWarning: Permanently added '[localhost]:22291' (ECDSA) to the list of known hosts. deb-src https://downloads.skewed.de/apt bionic mainWarning: Permanently added '[localhost]:22291' (ECDSA) to the list of known hosts. Thanks in advance for your help. Best. -- Tanguy Fardet Postdoctoral researcher, University of Tübingen, Max Planck Institute for Biological Cybernetics. Website: http://www.msc.univ-paris-diderot.fr/~fardet <http://www.msc.univ-paris-diderot.fr/~fardet> Member of Labos 1point5 <https://labos1point5.org> (mastodon: @labos1point5 <https://botsin.space/@labos1point5>, twitter: @labos1point5 <https://twitter.com/labos1point5>). Member of the Max Planck Sustainability Network <https://www.nachhaltigkeitsnetzwerk.mpg.de/> (twitter: sustainable_mpg <https://twitter.com/sustainable_mpg>)

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graph-tool January 2021