December 2017 - graph-tool - archives.skewed.de

ImportError: No module named 'scipy._lib.decorator'
by Snehal Shekatkar 22 Dec '17

22 Dec '17

Dear Tiago, I am getting the following error while importing graph-tool. Scipy is installed by default but still this is happening. I am on Ubuntu 16.04. I changed my RAM and this started happening but it looks silly to connect the two things. Any ideas? In [1]: import graph_tool.all as gt --------------------------------------------------------------------------- ImportError Traceback (most recent call last) <ipython-input-1-86968a62f6b1> in <module>() ----> 1 import graph_tool.all as gt /usr/lib/python3/dist-packages/graph_tool/__init__.py in <module>() 105 import numpy.ma 106 import scipy --> 107 import scipy.stats 108 109 /usr/lib/python3/dist-packages/scipy/stats/__init__.py in <module>() 336 from __future__ import division, print_function, absolute_import 337 --> 338 from .stats import * 339 from .distributions import * 340 from .morestats import * /usr/lib/python3/dist-packages/scipy/stats/stats.py in <module>() 181 import scipy.linalg as linalg 182 import numpy as np --> 183 from . import distributions 184 from . import mstats_basic 185 from ._distn_infrastructure import _lazywhere /usr/lib/python3/dist-packages/scipy/stats/distributions.py in <module>() 8 from __future__ import division, print_function, absolute_import 9 ---> 10 from ._distn_infrastructure import (entropy, rv_discrete, rv_continuous, 11 rv_frozen) 12 /usr/lib/python3/dist-packages/scipy/stats/_distn_infrastructure.py in <module>() 22 23 # for root finding for discrete distribution ppf, and max likelihood estimation ---> 24 from scipy import optimize 25 26 # for functions of continuous distributions (e.g. moments, entropy, cdf) /usr/lib/python3/dist-packages/scipy/optimize/__init__.py in <module>() 231 232 from .optimize import * --> 233 from ._minimize import * 234 from ._root import * 235 from .minpack import * /usr/lib/python3/dist-packages/scipy/optimize/_minimize.py in <module>() 28 29 # constrained minimization ---> 30 from .lbfgsb import _minimize_lbfgsb 31 from .tnc import _minimize_tnc 32 from .cobyla import _minimize_cobyla /usr/lib/python3/dist-packages/scipy/optimize/lbfgsb.py in <module>() 42 _check_unknown_options, wrap_function, 43 _approx_fprime_helper) ---> 44 from scipy.sparse.linalg import LinearOperator 45 46 __all__ = ['fmin_l_bfgs_b', 'LbfgsInvHessProduct'] /usr/lib/python3/dist-packages/scipy/sparse/linalg/__init__.py in <module>() 110 from __future__ import division, print_function, absolute_import 111 --> 112 from .isolve import * 113 from .dsolve import * 114 from .interface import * /usr/lib/python3/dist-packages/scipy/sparse/linalg/isolve/__init__.py in <module>() 4 5 #from info import __doc__ ----> 6 from .iterative import * 7 from .minres import minres 8 from .lgmres import lgmres /usr/lib/python3/dist-packages/scipy/sparse/linalg/isolve/iterative.py in <module>() 8 9 from scipy.sparse.linalg.interface import LinearOperator ---> 10 from scipy._lib.decorator import decorator 11 from .utils import make_system 12 from scipy._lib._util import _aligned_zeros ImportError: No module named 'scipy._lib.decorator' Thank you -- Snehal M. Shekatkar Pune India www.snehalshekatkar.com

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centrality measures for multilayer networks
by Rafael Pereira 20 Dec '17

20 Dec '17

Hi all, I am not a physicists nor a mathematician, so I am really just a layman when it comes to the mathematical calculations of network science. Sorry if my question doesn't make sense. However, I've read in a few papers* suggesting that the calculation of centrality measures for multilayer networks are a bit different than for single layer networks. I would like to know if graph-tool incorporates this advances in the literature, does it? * http://www.sciencedirect.com/science/article/pii/S0370157314002105 https://journals.aps.org/prx/abstract/10.1103/PhysRevX.3.041022 https://www.nature.com/articles/ncomms7868 best wishes, Rafael H M Pereira

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Re: [graph-tool] graph-tool Digest, Vol 119, Issue 9
by Duccio Aiazzi 19 Dec '17

19 Dec '17

After another bit of investigation and a careful study of the config.log, I could install it by passing the variable PYTHON_EXTRA_LDFLAGS with the correct location of the Python framework. Ex. ./configure PYTHON_EXTRA_LDFLAGS=“-F/path/to/python/framework” Thank you, Duccio On Mon, 18 Dec 2017 at 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. Installation error: Could not link test program to Python > (Duccio Aiazzi) > 2. Re: Installation error: Could not link test program to Python > (Tiago de Paula Peixoto) > > > > ---------- Forwarded message ---------- > From: Duccio Aiazzi <duccio.aiazzi(a)gmail.com> > To: graph-tool(a)skewed.de > Cc: > Bcc: > Date: Sun, 17 Dec 2017 14:55:27 +0000 > Subject: [graph-tool] Installation error: Could not link test program to > Python > Hello, > I am following the instructions for the installation in a virtual > environment. > I run the command: > ./configure --prefix=/usr/local/Cellar LDFLAGS="-L/usr/local/lib" > I get the error “Could not link test program to Python” with the > suggestion to pass LIBS or LDFLAGS variables. > From the config.log gives the following error: > > clang: error: no such file or directory: > 'Python.framework/Versions/3.6/Python' > > This error occurs in the following line, something to do with > CoreFoundation: > > configure:19079: gcc -o conftest -g -O2 -DNDEBUG > -I/usr/local/Cellar/python3/3.6.3/Frameworks/Python.framework/Versions/3.6/include/python3.6m > -L/usr/local/lib -Wl,-stack_size,1000000 -framework CoreFoundation > Python.framework/Versions/3.6/Python conftest.c > -L/usr/local/opt/python3/Frameworks/Python.framework/Versions/3.6/lib > -lpython3.6m -ldl -framework CoreFoundation -ldl -framework > CoreFoundation >&5 > > I have two questions: > How can I pass the variable for this line? > How can I find out what the right path is? > > Thank you, > Duccio > > > > > ---------- Forwarded message ---------- > From: Tiago de Paula Peixoto <tiago(a)skewed.de> > To: graph-tool(a)skewed.de > Cc: > Bcc: > Date: Sun, 17 Dec 2017 16:01:43 +0100 > Subject: Re: [graph-tool] Installation error: Could not link test program > to Python > On 17.12.2017 15:55, Duccio Aiazzi wrote: > > Hello, > > I am following the instructions for the installation in a virtual > environment. > > I run the command: > > ./configure --prefix=/usr/local/Cellar LDFLAGS="-L/usr/local/lib" > > I get the error “Could not link test program to Python” with the > suggestion > > to pass LIBS or LDFLAGS variables. > > From the config.log gives the following error: > > > > clang: error: no such file or directory: > 'Python.framework/Versions/3.6/Python' > > > > This error occurs in the following line, something to do with > CoreFoundation: > > > > configure:19079: gcc -o conftest -g -O2 -DNDEBUG > > > -I/usr/local/Cellar/python3/3.6.3/Frameworks/Python.framework/Versions/3.6/include/python3.6m > > -L/usr/local/lib -Wl,-stack_size,1000000 -framework CoreFoundation > > Python.framework/Versions/3.6/Python conftest.c > > -L/usr/local/opt/python3/Frameworks/Python.framework/Versions/3.6/lib > > -lpython3.6m -ldl -framework CoreFoundation -ldl -framework > > CoreFoundation >&5 > > > > I have two questions: > > How can I pass the variable for this line? > > How can I find out what the right path is? > > Please post the _complete_ output of configure and config.log, not only > snippets, as they do not tell the whole story. Also, do not forget to tell > us which OS you are using, as well as compiler, Python and boost versions. > > (From the kind of error messages you show, I would venture this is related > to the following homebrew bug: > https://github.com/Homebrew/homebrew-core/issues/21212 ) > > 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 >

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Installation error: Could not link test program to Python
by Duccio Aiazzi 17 Dec '17

17 Dec '17

Hello, I am following the instructions for the installation in a virtual environment. I run the command: ./configure --prefix=/usr/local/Cellar LDFLAGS="-L/usr/local/lib" I get the error “Could not link test program to Python” with the suggestion to pass LIBS or LDFLAGS variables. >From the config.log gives the following error: clang: error: no such file or directory: 'Python.framework/Versions/3.6/Python' This error occurs in the following line, something to do with CoreFoundation: configure:19079: gcc -o conftest -g -O2 -DNDEBUG -I/usr/local/Cellar/python3/3.6.3/Frameworks/Python.framework/Versions/3.6/include/python3.6m -L/usr/local/lib -Wl,-stack_size,1000000 -framework CoreFoundation Python.framework/Versions/3.6/Python conftest.c -L/usr/local/opt/python3/Frameworks/Python.framework/Versions/3.6/lib -lpython3.6m -ldl -framework CoreFoundation -ldl -framework CoreFoundation >&5 I have two questions: How can I pass the variable for this line? How can I find out what the right path is? Thank you, Duccio

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Re: [graph-tool] Multiplex and Graph construction
by Tiago de Paula Peixoto 17 Dec '17

17 Dec '17

On 17.12.2017 01:12, Bernardo Alves Furtado wrote: > Now, all the examples access the vertices by their number of generation. > > I have created a vertex property of names. > > How can I access the vertices by such property (without find_vertex). You must create a dictionary that does the mapping: vertices = dict((name[v], v) for v in g.vertices()) The reason why this is not built-in is because the property map values are not in general unique. -- Tiago de Paula Peixoto <tiago(a)skewed.de>

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Multiplex and Graph construction
by Bernardo Alves Furtado 15 Dec '17

15 Dec '17

Hi all, I use Python, but I am new to graph_tool and I have three simple questions I couldn’t find in the documentation. 1. Is there a MULTI LAYER feature? I have 7 layers of different transport network, nodes and edges and some nodes connect among the layers. Would the layer of the multiplex only be an attribute of the edges? Or is there an explicit configuration I should follow? 1. From the first checking of the documentation, I am assuming I have to build my Graph from the ground up. * Create vertices * Create properties (coordinates, weight of edges, names of nodes, layers) * Generate edges Given this format of lists of nodes and edges is there an automatic way of loading the Graph? edges.head(2) orig orig_layer dest dest_layer weight 0 node_1 Roads node_27306 Roads 0.840336 1 node_1 Roads node_81562 Roads 0.869565 nodes.head(2) nodeID nodeLabel nodeLong nodeLat 0 1 node_1 -43.436771 -22.869942 1 2 node_2 -43.360008 -22.892489 1. Setting the LONG LAT as attributes is enough to later draw the network with the nodes in the correct coordinate position? Thanks a lot. And thanks for the building of the tool. Best,

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Error during installation
by davide 15 Dec '17

15 Dec '17

Hi, After create a make file with this command: /./configure CXX='g++-5' --with-boost-libdir=/usr/lib/i386-linux-gnu/ i'vs start make file and then this is the result (contains an error): / Making install in src make[1]: Entering directory `/home/davide/Downloads/graph-tool-2.26/src' Making install in graph make[2]: Entering directory `/home/davide/Downloads/graph-tool-2.26/src/graph' Making install in centrality make[3]: Entering directory `/home/davide/Downloads/graph-tool-2.26/src/graph/centrality' CXX graph_betweenness.lo CXX graph_closeness.lo CXX graph_eigentrust.lo CXX graph_eigenvector.lo CXX graph_hits.lo CXX graph_katz.lo CXX graph_pagerank.lo CXX graph_trust_transitivity.lo CXXLD libgraph_tool_centrality.la make[4]: Entering directory `/home/davide/Downloads/graph-tool-2.26/src/graph/centrality' make[4]: Nothing to be done for `install-exec-am'. /bin/mkdir -p '/usr/lib/python2.7/dist-packages/graph_tool/centrality' /bin/bash ../../../libtool --mode=install /usr/bin/install -c libgraph_tool_centrality.la '/usr/lib/python2.7/dist-packages/graph_tool/centrality' libtool: install: /usr/bin/install -c .libs/libgraph_tool_centrality.so /usr/lib/python2.7/dist-packages/graph_tool/centrality/libgraph_tool_centrality.so libtool: install: /usr/bin/install -c .libs/libgraph_tool_centrality.lai /usr/lib/python2.7/dist-packages/graph_tool/centrality/libgraph_tool_centrality.la libtool: finish: PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/sbin" ldconfig -n /usr/lib/python2.7/dist-packages/graph_tool/centrality ---------------------------------------------------------------------- Libraries have been installed in: /usr/lib/python2.7/dist-packages/graph_tool/centrality If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the '-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the 'LD_RUN_PATH' environment variable during linking - use the '-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to '/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- /bin/mkdir -p '/usr/lib/python2.7/dist-packages/graph_tool/include/centrality' /usr/bin/install -c -m 644 graph_closeness.hh graph_eigentrust.hh graph_eigenvector.hh graph_pagerank.hh graph_hits.hh graph_katz.hh graph_trust_transitivity.hh minmax.hh '/usr/lib/python2.7/dist-packages/graph_tool/include/centrality' make[4]: Leaving directory `/home/davide/Downloads/graph-tool-2.26/src/graph/centrality' make[3]: Leaving directory `/home/davide/Downloads/graph-tool-2.26/src/graph/centrality' Making install in clustering make[3]: Entering directory `/home/davide/Downloads/graph-tool-2.26/src/graph/clustering' CXX graph_clustering.lo CXX graph_extended_clustering.lo CXX graph_motifs.lo In file included from graph_motifs.cc:26:0: ../../../src/graph/graph_python_interface.hh:85:33: error: ‘asymmetric_coroutine’ in namespace ‘graph_tool::coroutines’ does not name a template type typedef graph_tool::coroutines::asymmetric_coroutine<boost::python::object> ^ ../../../src/graph/graph_python_interface.hh:107:21: error: ‘coro_t’ was not declared in this scope std::shared_ptr<coro_t::pull_type> _coro; ^ ../../../src/graph/graph_python_interface.hh:107:38: error: template argument 1 is invalid std::shared_ptr<coro_t::pull_type> _coro; ^ ../../../src/graph/graph_python_interface.hh:108:5: error: ‘coro_t’ does not name a type coro_t::pull_type::iterator _iter; ^ ../../../src/graph/graph_python_interface.hh:109:5: error: ‘coro_t’ does not name a type coro_t::pull_type::iterator _end; ^ ../../../src/graph/graph_python_interface.hh: In constructor ‘graph_tool::CoroGenerator::CoroGenerator(Dispatch&)’: ../../../src/graph/graph_python_interface.hh:93:27: error: ‘coro_t’ was not declared in this scope : _coro(make_coro<coro_t::pull_type>(dispatch)), ^ ../../../src/graph/graph_python_interface.hh:93:17: error: parse error in template argument list : _coro(make_coro<coro_t::pull_type>(dispatch)), ^ ../../../src/graph/graph_python_interface.hh:94:11: error: class ‘graph_tool::CoroGenerator’ does not have any field named ‘_iter’ _iter(begin(*_coro)), _end(end(*_coro)), _first(true) {} ^ ../../../src/graph/graph_python_interface.hh:94:24: error: invalid type argument of unary ‘*’ (have ‘int’) _iter(begin(*_coro)), _end(end(*_coro)), _first(true) {} ^ ../../../src/graph/graph_python_interface.hh:94:29: error: there are no arguments to ‘begin’ that depend on a template parameter, so a declaration of ‘begin’ must be available [-fpermissive] _iter(begin(*_coro)), _end(end(*_coro)), _first(true) {} ^ ../../../src/graph/graph_python_interface.hh:94:29: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated) ../../../src/graph/graph_python_interface.hh:94:33: error: class ‘graph_tool::CoroGenerator’ does not have any field named ‘_end’ _iter(begin(*_coro)), _end(end(*_coro)), _first(true) {} ^ ../../../src/graph/graph_python_interface.hh:94:43: error: invalid type argument of unary ‘*’ (have ‘int’) _iter(begin(*_coro)), _end(end(*_coro)), _first(true) {} ^ ../../../src/graph/graph_python_interface.hh:94:48: error: there are no arguments to ‘end’ that depend on a template parameter, so a declaration of ‘end’ must be available [-fpermissive] _iter(begin(*_coro)), _end(end(*_coro)), _first(true) {} ^ ../../../src/graph/graph_python_interface.hh: In member function ‘boost::python::api::object graph_tool::CoroGenerator::next()’: ../../../src/graph/graph_python_interface.hh:100:15: error: ‘_iter’ was not declared in this scope ++_iter; ^ ../../../src/graph/graph_python_interface.hh:101:13: error: ‘_iter’ was not declared in this scope if (_iter == _end) ^ ../../../src/graph/graph_python_interface.hh:101:22: error: ‘_end’ was not declared in this scope if (_iter == _end) ^ ../../../src/graph/graph_python_interface.hh:103:37: error: ‘_iter’ was not declared in this scope boost::python::object oe = *_iter; ^ make[3]: *** [graph_motifs.lo] Error 1 make[3]: Leaving directory `/home/davide/Downloads/graph-tool-2.26/src/graph/clustering' make[2]: *** [install-recursive] Error 1 make[2]: Leaving directory `/home/davide/Downloads/graph-tool-2.26/src/graph' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/home/davide/Downloads/graph-tool-2.26/src' make: *** [install-recursive] Error 1 / have a solution? Thanks -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Re: [graph-tool] Vertex text size proportional to the size of the vertex
by Snehal Shekatkar 11 Dec '17

11 Dec '17

Yes I saw this before asking. I am sorry that I don't understand it though. What do I write in front of "vertex_font_weight"? Thank you On Dec 12, 2017 2:28 AM, "Tiago de Paula Peixoto" <tiago(a)skewed.de> wrote: On 11.12.2017 20:19, Snehal Shekatkar wrote: > Worked! How can I make the text bold also? I'm pretty sure all this is in the documentation.... vertex_font_weight=cairo.FONT_WEIGHT_BOLD -- 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

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Vertex text size proportional to the size of the vertex
by Snehal Shekatkar 11 Dec '17

11 Dec '17

Dear all, I am drawing a graph with the names of the vertex on each vertex. I am also specifying that the sizes of vertices should be "proportional" to their degree values (high degree vertices are bigger). Now, I want to do the same for the vertex text also. Something like this: size = g.new_vertex_property('float') text_size = g.new_vertex_property('float') for v in g.vertices(): size[v] = 4 * np.sqrt(v.out_degree()) + 5 text_size = 0.2 * size[v] gt.graph_draw(g, vertex_size = size, vertex_text = names, vertex_font_size = text_size, output = 'test.pdf') However, this doesn't produce the desired result. What happens is that if the vertex name is longer, the size of the vertex gets increased to accommodate the text inside the vertex. I don't want this. I want all the vertices with the same degree to have the same size, and the text size inside the bigger vertex should be bigger. I am okay if the text goes outside the vertex. How can I achieve this? Thank you -- Snehal M. Shekatkar Pune India www.snehalshekatkar.com

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Removing duplicate graph states
by Snehal Shekatkar 03 Dec '17

03 Dec '17

Dear all, I have many different states of the same graph. Every state corresponds to a given set of values on the nodes fixed using 'new_vertex_property.' I want to select unique network states, i.e., I want to remove the duplicate states from the collection. Is there any way in graph-tool to achieve this? If not, what is the solution? Thank you -- Snehal M. Shekatkar Pune India www.snehalshekatkar.com

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