obtained by "simmetrization" of a previously directed
> one, by using g.set_directed(False).
Could you please give us an example that shows the problem?
Best,
Tiago
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ink the most straightforward thing
for you to consider is to actually draw the nodes with circle shapes of
the appropriate size, with the same color as the edges. This should
remove a large portion of the raggedness...
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egfault, by giving us a
minimal script that reproduces it, there is nothing we can say.
Note that your gdb backtrace points to functions deep inside python,
that have nothing to do with graph-tool...
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Tiago
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parts of my code in the
> attachment.
It seems to me this is just matplotlib being slow... I'm not sure what
can be done about it from graph-tool's side.
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On 27.01.2016 22:35, kevinc wrote:
> My question is what g.vp["pos"] does?
It retrieves an internal vertex property map named "pos". Please read
the documentation:
https://graph-tool.skewed.de/static/doc/quickstart.html#internal-property-maps
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;
> Would anybody have some hints on the reason of this intermittent error ?
This is most likely a bug, but it cannot have anything to do with the
function you sent, since it does not activate or deactivate graph
filtering.
Please provide a minimal but _complete_ script where the problem can be
e,
since it often very outdated.
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hpad.net/ubuntu/+source/boost-defaults/+bug/1529289
Unfortunately, nobody seems to care about it. You can vote for the bug
or leave a comment, if you want to help it being fixed.
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ool. Some documentation
on this will be added soon; stay tuned.
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On 28.12.2015 01:08, Yannis Haralambous wrote:
> Thanks for the quick reply but it didn't worked.
>
>> Le 27 déc. 2015 à 23:55, Tiago de Paula Peixoto a écrit :
>>
>> Alternatively, you may use "ungroup_vector_property()":
>>
>>eco
g.ep["typee"][e][1]
graphviz_draw(g, ecolor=ecolor)
Alternatively, you may use "ungroup_vector_property()":
ecolor = ungroup_vector_property(g.ep["typee"], [1])[0]
graphviz_draw(g, ecolor=ecolor)
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etc. This would help me getting around to it when time
permits.
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ertex mask
incorrectly. Note that when you do mask.a, it returns an array pointing
to all vertices, even those that are currently being masked. If you want
to obtain an array only for the unmasked nodes, you should use mask.fa.
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Tiago
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Descr
tu-tool chain-r/test'
Thanks, I've fixed it.
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d.de/static/doc/graph_tool.html#graph_tool.PropertyMap
What you want is the PropertyMap.value_type() method.
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On 16.11.2015 00:57, Yannis Haralambous wrote:
> OK, sorry. I didn’t understood that the adjacency function was already
> available.
> It would be nice to include it in the documentation!
But I just **sent you** the link to the documentation!
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e so that I can calculate the adjacency
> matrix?
I don't get what you are trying to accomplish.
If you call the function adjacency(g), it will return you the adjacency
matrix of graph g. Isn't that what you want? Why do you want to copy and
past the function's implementation?
Best,
ferenced
in the centrality documentation purely for convenience of notation.
You can get a copy of the graph as a sparse adjacency matrix via the
function:
https://graph-tool.skewed.de/static/doc/spectral.html#graph_tool.spectral.adjacency
Best,
Tiago
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ory, and type "make test; make". You will need
to have sphinx installed: http://sphinx-doc.org/
Otherwise you can just use wget to download it in html from the website.
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Tiago
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use GTK3Cairo.
Please, since his has nothing to do with graph-tool, this is totally
off-topic for this list. You should contact the matplotlib community.
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ckend
together with graph-tool.
You should bring this to the matplotlib mailing list/issue tracker
instead.
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ax.hist(x,numBins,color='green',alpha=0.8)
>
> Any ideas what is going on? Can it be that Gtk and pyplot don't work well
> together?
I'm not sure what this hast to do with graph-tool. Do things work as
expected when you do not import graph-tool?
Best,
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written in parallel, since the vertices must be
followed in a specific order.
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hon than the one you are using.
If I'm not mistaken, in fedora you need to add the option:
--with-boost-python=boost_python3
when running ./configure. You may also need to install the package
boost-python3-devel beforehand.
Best,
Tiago
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y show up in the internal
dictionary. Here it should be simply:
mylabel = g.new_vertex_property("string")
for v in g.vertices():
mylabel[v] = str(g.vp['labelv'][v])+" ("+str(g.vertex_index[v])+")"
or alternatively, you should store the pro
o figure out from the
context. I will fix it.
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usr/local/lib/python2.7/site-packages/graph_tool/__init__.py", line
> 254, in convert
> return vtype(val)
> UnicodeEncodeError: 'ascii' codec can't encode character u'\u2208' in
> position 3: ordinal not in range(128)
The function does not expect un
start your script with:
#!/usr/bin/env python
# -*- coding: utf-8 -*-
example = u'abcdé'
(I'm assuming you are using python 2. With python 3 it is simpler,
since it accepts utf-8 by default.)
Best,
Tiago
Ps. Note that graph_draw() *does not* use graphviz!
I use graph-tool in a Unicode-compliant way?
It should work out of the box. You just need to use a font family that
has the necessary glyphs. For instance, for me the following works:
graph_draw(g, vertex_text="∈", vertex_font_family="Bitstream Vera Sans")
Best,
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chieve what you want. Sorry, but the
documentation is still a bit scarce in this part, so you will need to
wad through the source code.
Best,
Tiago
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order=g.vp.size.
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On 27.10.2015 01:06, soumajyoti wrote:
> I tried building graph tool from source and it gave me an error after
> running configure. I have attached the log file.
I don't see any errors. Can you be more specific?
Best,
Tiago
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Descripti
ph_tool.Graph.edge
If you pass "all_edges=True" this will give you a list of all the
existing parallel edges incident on two nodes. You can then iterate
through them and check if one of them has the correct property value. If
not, you create a new edge.
Best,
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, you have to compute the
positions once, and pass them every time as the "pos" parameter.
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one, the similarity() function could be used to push
the innermost loop into C++:
https://graph-tool.skewed.de/static/doc/topology.html#graph_tool.topology.similarity
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``-1``, the vertex size will be automatically
increased to accommodate the text. The special
value ``"centered"`` positions the texts rotated
radially around the center of mass.
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nder it. You can still see the full documentation in
the docstring, i.e.
help(graph_draw)
I'll fix it in the website.
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y beginning of the documentation.
https://graph-tool.skewed.de/static/doc/graph_tool.html#how-to-use-the-documentation
In short:
The docstring examples assume that graph_tool.all has been imported as gt:
>>> import graph_tool.all as gt
Best,
Tiago
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t is not a bug. The "vsize" property belongs to the original graph, and
hence will have a different number of elements. You need to do:
vsize = gv.own_property(vsize)
before calling graph_draw(). Note that, like GraphView, this does not
duplicate the property map; it is only a "view".
heck to test if two vertices are unreachable is:
shortest_distance(g, u, v) >= g.num_vertices()
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On 30.09.2015 19:03, Santiago Videla wrote:
> Hi,
>
> I updated graph-tool to 2.9 and I got an exception from
> find_vertex_range method (see below). Can you confirm this is a bug?
Yes it is. I've just fixed it in git.
Thanks for spotting this.
Best,
Tiago
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On 28.09.2015 15:31, François Kawala wrote:
> I'm wondering when should I expect for the new release to be available ?
It already is.
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are removes old versions
automatically. But you can download and install older packages by hand
from here:
http://downloads.skewed.de/graph-tool/packages/
Best,
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On 25.09.2015 17:29, Alexandre Hannud Abdo wrote:
> Ni! Woudn't simply:
>
> u.get_vertex_filter()[0][v]
>
> work?
Yes, of course. And it would also be much faster! :-)
Thanks!
Tiago
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Invalid vertex index: 1
Hence you could do:
def vertex_belongs(v, g):
try:
g.vertex(int(v))
return True
except ValueError:
return False
Best,
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hen you run the script under gdb:
gdb python
(gdb) set args ./script.py
(gdb) run
when the segfault occurs you type
(gdb) bt
and post the _entire_ result.
Best,
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ples.
Also, I'm not sure what you mean with "another GTK backend". TKAgg is
not a GTK backend, it is a matplotlib backend.
Best,
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On 18.09.2015 11:15, Tiago de Paula Peixoto wrote:
> On 18.09.2015 11:13, Christopher Morris wrote:
>> Hi,
>>
>> given a graph G, I want to traverse G in some way, e.g., a random walk of
>> length k, resulting in a set S of vertices or edges. What is the fastest way
&g
tter way than using a property map and then GraphView?
You either use a GraphView, or you build the subgraph by hand while
traversing the graph. I see not other option.
Best,
Tiago
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llow this issue:
https://git.skewed.de/count0/graph-tool/issues/196
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;.
>
> Any ideas?
This has already been fixed in the new version, 2.5.
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tices in g and then applies a filter? This is
> rather inefficient, especially when then graph is huge...
You can set "max_dist" in shortest_distance() to limit the search.
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riation of BFS or DFS. Is
> it possible do use graph_tool.search.bfs_search in some way for this?
Just do:
dist = shortest_distance(g, source=v)
k_disk = GraphView(g, vfilt=dist.fa <= k)
Best,
Tiago
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how could this be achieved?
Just use the "vertex_surface" option in graph_draw(). It should be
either a cairo surface, or the file name of an image.
See here for a concrete example:
https://graph-tool.skewed.de/static/doc/_downloads/animation_zombies.py
Best,
Tiago
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etween 0 and the highest occurring index in my
> dataset. Is there any way to avoid all these unnecessary vertices?
This is possible, but only in the version in git. You would do simply
g.add_edge_list(edges, hashed=True).
In the current version, you have to do the mapping yourself.
Best,
Tiag
is no algorithm that will find
them in any reasonable time.
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ot;vertex_text" property in graph_draw(). If you want
to control the position relative to the vertex, you should use the
"vertex_text_position" property.
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e the program is run.
If you want to modify the number of threads during the program, you can
use the the function graph_tool.openmp_set_num_threads().
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new_infected.append(u)
infected_set.extend(new_infected)
I hope this helps.
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error backtrace, and a specific example, it is a hard to say
what may be going on.
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paste. If you do print(array), it is not a good
idea, since one would need to parse it by hand. Instead do
print(repr(array)).
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ou can lookup t.vertex(v) in time O(1), where t is the predecessor
tree.
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course, it is hard to
guarantee exactness with a decimal representation, hence I still think
it is justifiable to keep the hex format as default.
I'll implement this soon. (If there is any urgency with this, please
open an issue in the website.)
Best,
Tiago
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>> graph-tool mailing list
>> graph-tool@skewed.de
>> http://lists.skewed.de/mailman/listinfo/graph-tool
>
>
>
> _______________
> graph-tool mailing list
> graph-tool@skewed.d
g because I'm finding it difficult to
> track down exactly which edges are missing, but I'm pretty sure something's
> wrong because I'm not getting the number of edges I expect.)
It is difficult to say anything without a specific example of the
problem. Please post a smal
raph-tool I wanted to keep some of
the versatility, so I compile several different instantiations that are
chosen at run time. This improves performance, but adds complexity.
(There is also an unmaintained, deprecated but "official" python
bindings for BGL: https://github.com/erwinvaneijk/
ble of developing two
alternative versions of your code, just so that someone down the line
can avoid the terms of the GPL, i.e. turn it into proprietary code. Why
would you do that?
But it is up to you, of course.
Best,
Tiago
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si
n licence, using anything else means
you don't care about further restrictions being imposed.
The LGPL makes an exception for just linking (importing) the library,
which can make strategic sense in some cases, but I judged it not to be
the case for graph-tool.
Best,
Tiago
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On 23.07.2015 08:36, Flavien Lambert wrote:
> Hi,
> could you tell me how to cite the project in a scientific paper? A
> bibTeX entry would be awesome!
You find this in the documentation:
https://graph-tool.skewed.de/static/doc/faq.html#how-do-i-cite-graph-tool
Best,
Tiago
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a mismatch between the python version you are using,
and the one used to compile boost::python and graph-tool.
For example, you might be using the system's python, whereas
graph-tool/python were compiled with a version installed via homebrew.
If you are still having trouble, open an issue
On 15.07.2015 13:59, François wrote:
> The warning causes "apt-get update" to return a non-zero code. This
> sitaution is problematic to me, would it be possible to fix this
> problem ?
This should be fixed now.
Best,
Tiago
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D
__init__.py#L1368
> seems to examine each and any edge when the weight parameter is provided.
>
> What is the point of this behavior ? what do I miss ?
There might be parallel edges with different weights.
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Tiago
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Des
tyMap.__getitem__(VertexPropertyMap,
> numpy.int64)
> did not match C++ signature:
>
> __getitem__(graph_tool::PythonPropertyMap boost::typed_identity_property_map > > {lvalue},
> graph_tool::PythonVertex)
>
>
>
> How could i circumvent that issue ?
W: Failed to fetch
> http://downloads.skewed.de/apt/stretch/dists/stretch/main/binary-amd64/Packages
> 404 Not Found
These are just warnings; it should not affect the installation of the
package.
Best,
Tiago
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.
This should be fixed now!
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> of nodes). I have tried to make it faster by using g.add_edge_list, but this
> works only for unweighted graphs. Any suggestion how to make it faster?
Yes, use g.add_edge_list() for the edges, and put the weights separately
via the array interface for property maps:
e_weight.a = weight_
l/boost/stage/lib"
> $ make
> $ sudo make install
The boost version is not hard coded into the configure script, so you
must be doing something wrong somewhere. Check which version is actually
linked to the graph-tool binaries with ldd, and also check the output
The specific bug above has been fixed a long time ago. Whatever you are
experiencing, is unrelated to it.
Note that if you want to do this type of visualization, it can be done
most easily now with the draw_hierarchy() function:
https://graph-tool.skewed.de/static/doc/draw.html#graph_tool.dr
t; undefined symbol: PyClass_Type
As you can see from the shared library name, the boost::python that is
being used was compiled with python 2.7, while graph-tool was compiled
with 3.4. Do you have a python 3 version of boost::python installed? If
yes, try passing the correct suffix value to --with-b
be installed. Tiago, do I need to
> move to unstable?
Hm, it seems that it is a mistake on my part: I've built packages for
testing, which is now called 'stretch', not 'jessie'. I'll fix this in
the repository.
Best,
Tiago
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odules must
explicitly include libgraph_tool_core.a (which is redundant and wasteful
in e.g. GNU/Linux).
There was a thread about this a little while ago (but without Cygwin):
http://lists.skewed.de/pipermail/graph-tool/2015-May/001972.html
The build process needs be significantly mod
boost::python, and cannot compile a
boost::graph example. In the latter case, the compiler complains of
missing symbols, which is very strange.
What boost version are you using? Did you compile with the same GCC you
are using for graph-tool? Did you enable boost::python and compile it
against anac
On 27.05.2015 22:31, Tiago de Paula Peixoto wrote:
> On 19.05.2015 07:46, Ryan Compton wrote:
>> I'm having trouble with my vertex text running off the edge of the canvas.
>>
>> For an example see:
>> http://ryancompton.net/assets/darknet-market-basket-analysis
On 07.06.2015 04:18, Артём Демьянов wrote:
> Nothing special, but I found probably copy-paste misprint in documentation:
> https://graph-tool.skewed.de/static/doc/draw.html#graph_tool.draw.graph_draw
I've fixed this now in git. Thanks!
Best,
Tiago
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install.
You cannot install graph-tool via pip.
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Tiago
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graph.
Well, I've never encountered this problem before, and I don't know what
may be causing it. Without a concrete example, I cannot investigate.
Best,
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o
> always make node text shown in a correct orientation. Thanks a lot.
I'm not sure I understand. Can you provide an example?
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d of *out_neighbours*
This is trivial, just compute the avg_neighbour_corr with the reversed
graph:
avg_neighbour_corr(GraphView(g, reversed=True), "in", "out")
Best,
Tiago
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with my own network.
Thanks for this. I have now fixed the bug in git.
I'll make a new release soon with this fix.
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but crashes when I run the
> following command:
>
>>>> state_w = gt.minimize_blockmodel_dl(g,
> eweight=g.edge_properties["weight"], multigraph = True)
This looks like a bug. Can you please also change the network which you
are using, so I can debug it?
Thanks!
Be
that the documentation of the other
spectral functions were inconsistent with this definition. I have fixed
it now:
https://graph-tool.skewed.de/static/doc/dev/spectral.html#graph_tool.spectral.adjacency
Best,
Tiago
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since it can be
more convenient mathematically. See for instance Mark Newman's book.
In any case, this an unimportant issue. A matrix transpose can be
obtained trivially in numpy.
Best,
Tiago
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Tiago de Paula Peixoto
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segfault?
Best,
Tiago
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2D array from a string property map. The value type
must be a "vector<...>".
Best,
Taigo
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On 29.05.2015 17:28, Smith, Steven - 1004 - MITLL wrote:
> This is python 2.7 and graph-tool 2.2.38_0
This has already been fixed. Please update to the latest version.
Best,
Tiago
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0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0
fit_view" with a float would scale things
> properly but it does not seem to change anything.
Indeed there seems to be a bug with the fit_view option. I'll provide a fix.
In the meantime, the best approach would be to set fit_view=False, and
scale your vertex positions accordingly.
ilt=comp)
Both of these approaches should be much faster than bfs_search().
(Note that both these functions use BFS internally, but without
Python interference.)
Best,
Tiago
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