graph-tool 1.0

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graph-tool 1.0

Tiago de Paula Peixoto
Hi.

I'm pleased to announce version 1.0 of graph-tool. This version contains
many new features, improvements and bug fixes. In fact, previous
versions (0.9 namely) are considered deprecated, and should be avoided.
;-) From now on, hopefully, there should be no more radical changes on
how things work between versions, and improvements should be more
incremental.

Notable changes
===============

A lot of things changed since the 0.9 version, including how certain
options work, and lots of new stuff have been added. For a full list of
modifications, see

https://projects.forked.de/graph-tool/log/?action=stop_on_copy&rev=69&stop_rev=28&mode=stop_on_copy&verbose=on

The most important new features are:

 * Community detection support
 * Extended clustering coefficient
 * Line graph generation
 * Minimum spanning tree
 * Sampled distance statistics

Also the documentation on the website has been massively updated and
reorganized. Check it out at:

   https://projects.forked.de/graph-tool/wiki/GraphToolGuide

Download
========

Download information is available on the website:

   https://projects.forked.de/graph-tool/wiki/GraphToolDownload

Enjoy!

Ps. graph-tool has now support for bash command line completion! For how
to enable it, please read http://furius.ca/optcomplete/. I'll post later
some more specific instructions on the wiki.

--
Tiago de Paula Peixoto <[hidden email]>


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Re: graph-tool 1.0

Jens Müller
Tiago de Paula Peixoto schrieb:
> Hi.
>
> I'm pleased to announce version 1.0 of graph-tool. This version contains
> many new features, improvements and bug fixes. In fact, previous
> versions (0.9 namely) are considered deprecated, and should be avoided.
> ;-) From now on, hopefully, there should be no more radical changes on
> how things work between versions, and improvements should be more
> incremental.
>
OK, I'll try it out, tomorrow I'm gonna buy two more gigs of RAM anyway.

Regarding the GraphML reader: Do you think it would make programs faster
to remove this wrapper interface with any and make the reader a template
for MutableGraphs?


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Re: graph-tool 1.0

Tiago de Paula Peixoto
On 02/08/2007 12:58 PM, Jens Müller wrote:
> Regarding the GraphML reader: Do you think it would make programs faster
> to remove this wrapper interface with any and make the reader a template
> for MutableGraphs?

Not much, I think, since most of the function-calling overhead would be
from the expat hook functions anyway. But the idea of the wrapper is to
separate the part that depends from the expat library from the rest, so
it can be compiled separately as a library (like the graphviz reader).

If you're curious you can do some profiling and see how much time it
actually spends with the wrapper...

--
Tiago de Paula Peixoto <[hidden email]>


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Re: graph-tool 1.0

Jens Müller
In reply to this post by Jens Müller
Jens Müller schrieb:

> Tiago de Paula Peixoto schrieb:
>> Hi.
>>
>> I'm pleased to announce version 1.0 of graph-tool. This version contains
>> many new features, improvements and bug fixes. In fact, previous
>> versions (0.9 namely) are considered deprecated, and should be avoided.
>> ;-) From now on, hopefully, there should be no more radical changes on
>> how things work between versions, and improvements should be more
>> incremental.
>>
> OK, I'll try it out, tomorrow I'm gonna buy two more gigs of RAM anyway.

Did it - make; make install.

Now I get:

$ graph-tool
Traceback (most recent call last):
  File "/usr/local/bin/graph-tool", line 22, in ?
    from libgraph_tool import *
ImportError: No module named libgraph_tool

What do I have to do?


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Re: graph-tool 1.0

Tiago de Paula Peixoto
On 02/09/2007 03:32 PM, Jens Müller wrote:

> Jens Müller schrieb:
>> Tiago de Paula Peixoto schrieb:
>>> Hi.
>>>
>>> I'm pleased to announce version 1.0 of graph-tool. This version contains
>>> many new features, improvements and bug fixes. In fact, previous
>>> versions (0.9 namely) are considered deprecated, and should be avoided.
>>> ;-) From now on, hopefully, there should be no more radical changes on
>>> how things work between versions, and improvements should be more
>>> incremental.
>>>
>> OK, I'll try it out, tomorrow I'm gonna buy two more gigs of RAM anyway.
>
> Did it - make; make install.
>
> Now I get:
>
> $ graph-tool
> Traceback (most recent call last):
>   File "/usr/local/bin/graph-tool", line 22, in ?
>     from libgraph_tool import *
> ImportError: No module named libgraph_tool
>
> What do I have to do?
Well, if you did "make install" the libgraph_tool.so module should have
been installed, by default, in a place where python could find it, and
everything should have worked... Are you sure the prefix you used for
the installation is the same where python is installed, and that the
place where libgraph_tool.so ended up is known to the python interpreter
(via the PYTHONPATH variable)?

In any case, if you don't want to install it all, you can just put both
graph-tool and libgraph_tool.so (found in src/graph/.libs after
compilation) in the same directory, and it should work.

--
Tiago de Paula Peixoto <[hidden email]>


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Re: graph-tool 1.0

Jens Müller
Tiago de Paula Peixoto schrieb:

> Well, if you did "make install" the libgraph_tool.so module should have
> been installed, by default, in a place where python could find it, and
> everything should have worked... Are you sure the prefix you used for
> the installation is the same where python is installed, and that the
> place where libgraph_tool.so ended up is known to the python interpreter
> (via the PYTHONPATH variable)?
>
> In any case, if you don't want to install it all, you can just put both
> graph-tool and libgraph_tool.so (found in src/graph/.libs after
> compilation) in the same directory, and it should work.

Yeah, this finds the library at least:


$ PYTHONPATH=/usr/local/lib/python2.4/site-packages/ graph-tool
Traceback (most recent call last):
  File "/usr/local/bin/graph-tool", line 22, in ?
    from libgraph_tool import *
ImportError: /usr/local/lib/python2.4/site-packages/libgraph_tool.so:
undefined symbol: _ZN5boost6python3apineERKNS1_6objectES4_

Of course, the graph-tool file and the libs are both from the same build
 ...

Compiler is still $ g++ --version
g++ (GCC) 4.1.1 (Gentoo 4.1.1-r3) on Gentoo amd64, Boost is Gentoo
packages 1.33.1-r1


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Re: graph-tool 1.0

Tiago de Paula Peixoto
On 02/20/2007 10:16 PM, Jens Müller wrote:

>
> $ PYTHONPATH=/usr/local/lib/python2.4/site-packages/ graph-tool
> Traceback (most recent call last):
>   File "/usr/local/bin/graph-tool", line 22, in ?
>     from libgraph_tool import *
> ImportError: /usr/local/lib/python2.4/site-packages/libgraph_tool.so:
> undefined symbol: _ZN5boost6python3apineERKNS1_6objectES4_
>
> Of course, the graph-tool file and the libs are both from the same build

Strange... How about boost python? Was it also compiled with the same
GCC version?

I'll look at your other problem with the reader soon, I'm a bit out of
time at the moment.

--
Tiago de Paula Peixoto <[hidden email]>





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Re: graph-tool 1.0

Jens Müller
Tiago de Paula Peixoto wrote:

> On 02/20/2007 10:16 PM, Jens Müller wrote:
>
>
>>$ PYTHONPATH=/usr/local/lib/python2.4/site-packages/ graph-tool
>>Traceback (most recent call last):
>>  File "/usr/local/bin/graph-tool", line 22, in ?
>>    from libgraph_tool import *
>>ImportError: /usr/local/lib/python2.4/site-packages/libgraph_tool.so:
>>undefined symbol: _ZN5boost6python3apineERKNS1_6objectES4_
>>
>>Of course, the graph-tool file and the libs are both from the same build
>
>
> Strange... How about boost python? Was it also compiled with the same
> GCC version?

I should think so, gcc 4.1.1 is my system compiler ...

I'm not at home right now, so I can't look at the files right now.

But I'll try to find out if there's a hint in the .so's as to with which
gcc they've been built.


> I'll look at your other problem with the reader soon, I'm a bit out of
> time at the moment.
>

Thanks! Maybe you can send me a GraphML files of yours, it might again
be some issue with the format of my files ...


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Re: graph-tool 1.0

Jens Müller
Jens Müller schrieb:

>> Strange... How about boost python? Was it also compiled with the same
>> GCC version?
>
> I should think so, gcc 4.1.1 is my system compiler ...
>
> I'm not at home right now, so I can't look at the files right now.
>
> But I'll try to find out if there's a hint in the .so's as to with which
> gcc they've been built.

I had a bit of a Boost version chaos here, had a locally modified copy
of the headers in /usr/local/include and other binary libs in
/usr/local/lib64 ...

Now recompiling, I think it should work ...


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Re: graph-tool 1.0

Jens Müller
Jens Müller wrote:

> Now recompiling, I think it should work ...

Sorry, no ...


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Re: graph-tool 1.0

Jens Müller
Jens Müller schrieb:
> Jens Müller wrote:
>
>> Now recompiling, I think it should work ...
>
> Sorry, no ...

OMG ... ldconfig did it ...

Sorry for the bother ...