Hello
As we are dealing in Sage with a patch concerning the plotting of
Trees, I wondered why we were not using Graphviz to plot them.. The
answer is the usual one : Graphviz is not GPL-Uncompatible... Even
though, there is in Sage an optional package for Graphviz that can be
installed
Hello everybody !!!
I am trying to make Linear Programming in Sage a bit easier, and I
looked into Sage's features concerning multivariate polynomials...
I first wanted indexed variables, and it seems pretty easy to build :
y = RR['y0, y1, y2'].gens()
and then
y[0]*y[1]
But I have two
I don't see the problem, because *anything* can be stored as value in
a dictionary.
Your answer with a dictionary in which are stored variables is pretty
good, though there's a different with what I had in mind :
You first need to define each cell of the dictionary as a variable,
and you have
Thank you for your answers !! I think I can build something from them
and from William's idea of a .__getitem__ function :-)
On Aug 27, 12:50 am, Simon King simon.k...@nuigalway.ie wrote:
Hi Martin,
On Aug 26, 10:46 pm, Martin Albrecht m...@informatik.uni-bremen.de
wrote:
Hi,
isn't
Good news !!
http://www.mail-archive.com/help-g...@gnu.org/msg01208.html
I'd love to see it work for CBC also :-)
On Aug 27, 8:18 pm, Nathann Cohen nathann.co...@gmail.com wrote:
Working on it :-)
We do not have arbitrary precision linear programming ( perhaps weo do
have it by CVXOPT, I
Working on it :-)
We do not have arbitrary precision linear programming ( perhaps weo do
have it by CVXOPT, I don't know, but not on what I am working on --
the link between Sager and usual LP solvers ) , but I'd be delighted
to work on it...
The thing is that I do not want to give up the usual
Hello everybody !!!
I would like to test the functions I write to learn which instructions take
most of the time, and if possible find a way around.. There may not be some
tool for this in Sage, but perhaps it already exists for Python Do you
know about such a thing ? :-)
Nathann
Hello !!!
I used Sage to compute a few things today, which included at some step the
mean of a list of values :
def mean(l):
return sum(l)/len(l)
At some point I was amazed by the fact I only had integer values, which was
far from probable... The mean command had been defined in a script,
Hello !!!
I remember there is an easy way ( through matrices ) to get the best
approximation of a function by a polynomial of bounded degree ( and not only
the usual approximation by a line ) I looked for such functions in Sage,
but found none... Does it mean there is not already in Sage some
Scipy was the asnwer Thank you very much :-)
Nathann
On Nov 2, 7:15 pm, Jason Grout jason-s...@creativetrax.com wrote:
Robert Bradshaw wrote:
On Nov 2, 2009, at 8:41 AM, Nathann Cohen wrote:
Hello !!!
I remember there is an easy way ( through matrices ) to get the
best
Hello !!!
I have a pretty easy simplification problem When I have a looong
fraction, something like :
1 / ( 1 - 1/ ( 1- 1/ a ))
How can I ask sage to rewrite i as rational value ?
I would like something like : 1 / ( 1 - 1/a ) to give me a / (a-1), and a
similar behaviour for longer
Excellent !! Thank you !!!
I understand that moving the code from rational_simplify to simplify
would mean trouble ? ;-)
Nathann
On Nov 12, 8:46 am, Mike Hansen mhan...@gmail.com wrote:
Hello,
On Thu, Nov 12, 2009 at 2:40 PM, Nathann Cohen nathann.co...@gmail.com
wrote:
Hello !!!
I
Hello !!!
Your problem comes from the fact that the CBC packages got updated
very recently, and is compatible with the brand-new implementation of
the MIP class in Sage... I guess you need to use the last Alpha
version of Sage, or to wait until the next stable version is released.
Sorry for the
A temporary solution is of course to use the FORMER version of the CBC
package.
To do so, please type :
sage -f http://www-sop.inria.fr/members/Nathann.Cohen/cbc-2.3.p0.spkg
But these early versions of MixedIntegerLinearProgram have been
updated much since, so the best way for you is still to
I was a bit worried about it :-)
You will find everything about the current Alpha there :
http://groups.google.com/group/sage-release/browse_thread/thread/0020c82d825abe15/b52579bc51bc9a14?show_docid=b52579bc51bc9a14
Please remember to use the last versions of the spkg in this case --
i.e. the
Hello !!!
To open a ticket on the TRAC server ( http://trac.sagemath.org/sage_trac
) you must first have an account.
* If you do not, the first page of this website advises you to send a
email to William Stein to request one : wstein at gmail.com
* When you have one, you can go to
Hello
Sorry for intruding into your discussion, but I have been working on a
class MixedIntegerLinearProgram in Sage recently (http://bit.ly/7rRmrp
to see what it does)... It is not meant to cover the same areas as
CVXOPT, but I just wondered which kind of things you intended to use
CVXOPT
Hello Tyler !!!
Minh, as is his custom, gave you the perfect answer. I also received
several emails about it, and I am still trying to design an acceptable
answer. For the moment, I only added a line about it at the end of a
tutorial on LP using Sage, which may interest you too :
Hello
Could you be by any chance trying to compute the convex hull of a set
of points ?
http://en.wikipedia.org/wiki/Convex_hull
Nathann
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The fix was done as part of Sage Bug Days 2 a couple of weeks ago and
has already been merged into 4.3.2. Please try that version (just
released a day or two ago).
GREAT ! :-)
Nathann
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Hello everybody
I just learnt about the rsolve function from Maple, which seems to
give the formula of sequences defined by recurrence.. Is there a
similar function in Sage ?
For example, how could I have Sage give me the general formula of
fibonacci's sequence ? :-)
Thank you very much
sage: f = y(n+2) - y(n+1) - y(n)
sage: rsolve(f, y(n), { y(0):1, y(1):1 })
(1/2 + 5**(1/2)/2)**n/2 + (1/2 - 5**(1/2)/2)**n/2 - 5**(1/2)*(1/2 -
5**(1/2)/2)**n/10 + 5**(1/2)*(1/2 + 5**(1/2)/2)**n/10
That's perfect !! Thank you very much !! :-)
Their interface is a bit clumsy though, I admit... It
... :-)
On Feb 10, 10:13 am, Nathann Cohen nathann.co...@gmail.com wrote:
Their interface is a bit clumsy though, I admit... It could be good to
be able to do it directly in Sage :-)
But how would a better interface look like?
I mean, you define a recurrence relation f, involving a function y
I mentionned having to import simpy.*, which included classes like
Symbol or Function, and having to use those types. I wouldn't
personally mind if I had to import rsolve from some Sage class... Why
should it necessarily imported by default (namespace kept clean)?
Nathann
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Should we create a ticket for this ? I'd have done it if not for my
doubt on the section I should pick for this... :-)
Nathann
On Feb 10, 1:42 pm, Harald Schilly harald.schi...@gmail.com wrote:
On Feb 10, 11:16 am, Simon King simon.k...@nuigalway.ie wrote:
sage: f = y(n+2) - y(n+1) - y(n)
Hello !!!
I just wanted to add one line about this very short patch :
http://trac.sagemath.org/sage_trac/ticket/7637
It enables one to define unique variables instead of dictionaries,
which is sometimes useful, for exemple in this case :
Instead of
soldiers =
This would make a very nice, simple, easy example in the docs!
Not to mention the only non-graph-theoretical one ! :-)
Nathann
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For
Hello
By the fundamental circuits, do you mean a base of the Cycle space ?
If so, I have to admit I do not know how to do it...
If you want to compute a shortest cycle in a graph, though, I do not
think the girth function can do it at the moment, but I agree it would
be useful to have for
Well, we still have a generator for binary trees :
http://www.sagemath.org/doc/reference/sage/graphs/graph_generators.html#sage.graphs.graph_generators.GraphGenerators.BalancedTree
And if you want to test whether a graph is a binary tree ( all the
internal vertices have degree 3, except the root
I'm sure of the best way. You could just write your own
little function that checks the conditions for each
(i,j) in a big rectangle. Also, you might be able to use Sage's
MixedIntegerLinearProgram functionality.
And here is how :
p = MixedIntegerLinearProgram()
x = p.new_variable()
that ! :-)
Nathann
On 7 May 2010 17:41, Robert Bradshaw rober...@math.washington.edu wrote:
Try doing
x in RR
- Robert
On May 7, 2010, at 2:38 PM, Nathann Cohen wrote:
Hello everybody !!!
I am trying to find out how to check whether some Sage variable is
numerical (let's say real, as opposed to None
Hello !
* As a language, Python is vastly superior to R. Python has good
support for object oriented programming, a very wide selection of
existing programs and libraries, and supports threads for handling
realtime data. I recently read a paper about massive contortions
somebody went
You can do this with numpy arrays:
White flag ;-)
Nathann
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Hello everybody
I have been willing for some time to implement a recognition algorithm
for Interval Graphs [1], and I ended up forgetting to sleep one
evening to have it done in the morning. :-)
What I now have is an algorithm which uses PQ-Trees [2] and is able to
tell, given a graph,
It's an error of mine, sorry for garbage. I was considering the third
element of the tuple in sage graph's edges as a dictionary (as networkx
does), but it's only a label! Everithing's ok now and sage is great for
linear programming :).
I was just taking a look at your code ! :-D
By the way,
Hm... If you are just looking for a trick, perhaps the following
line will suit your taste :-)
sage: m = Matrix([[1,2,3],[4,5,6]])
sage: m
[1 2 3]
[4 5 6]
sage: m2 = Matrix(map(list,map(reversed,m.rows(
sage: m2
[3 2 1]
[6 5 4]
I hope there is another solution though, as this requires to
Hello everybody !!!
I would like to write some graph-theoretical function which involves
large polynomials. Actually, what I have is the following : to each
vertex of my graph is associated a variable, and I want to compute the
product over all the edges u,v of (X_u - X_v). I am then just
Hello !
Have you tried using the default polynomials in Sage (which use libsingular)?
Actually not. It felt natural to wonder which existing tools to
manipulate polynomials efficiently were already available, but my
problem is very specific as I am only interested in one coefficient,
of a very
Hello everybody
I have a small Linear Algebra question for you... I am pretty sure it
has a well-known answer, but this is where I feel how far my linear
algebra is... :-)
Actually, it is a simple one. I have one matrix M defined over Z^n,
whose kernel K is of interest to me. I would then
anyway, It was still a
good occasion to work with Sage's matrices ! :-)
Nathann
On Jul 17, 12:17 am, Nathann Cohen nathann.co...@gmail.com wrote:
Hello everybody
I have a small Linear Algebra question for you... I am pretty sure it
has a well-known answer, but this is where I feel how far my
:-D
It's true than when I re-read my question, I am plainly asking how to
solve an binary program :-D
There should be some constraint to add to my question to make it less
powerful than SAT... Sorry for that ^^;
Nathann
On 17 July 2010 01:42, Nathann Cohen nathann.co...@gmail.com wrote:
If I
White Flag !!!
Please forget what I said earlier about addition of digraphs... It
works fine for graphs, but that's all...
At 3am, it's better for me to sleep than to ask questions... sorry
again, and thank you for your answer :-)
Nathann
On 17 July 2010 01:44, Nathann Cohen nathann.co
Hello everybody !!!
I began to use Sage's attach and load functions not so long ago, and I
stopped very soon to resume using the good old execfile. My problem is
that when a script loaded with attach or load fails because of a
mistake in the code, I see no information, while an external code
Hello !!
I am trying to solve this simple linear programming prob using
MixedIntegerLinearProgram and it gives an AttributeError:
LinearFunction instance has no attribute '__float__' exception
This is mainly my fault, and the reason is that min/max arguments do
not like to get something
This is now patch #9579, which is waiting for review :-)
Nathann
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Hello everybody
I have a small problems with graphs = I would like to be able to talk
about a Z/2Z vector space defined over its edges (any set of edges is
independent)
Of course I can just create a Z/2Z vector space of dimension G.size()
(number of edges), but this would later mean that I
It sounds like you are just wanting an order on the edges. If you can
easily compute the index of an edge, you're set (that's the coordinate of
the edge). However, if your problem does not lend itself to that, it sounds
like the easiest thing to do is to maintain dicts to map between an edge
Hello !!
You may also like this :
http://www-sop.inria.fr/members/Nathann.Cohen/tut/LP/
Writing documentation for both graphhs and LP has been responsble for
many of my last sleepless nights, though this documentation is in
french. The next ones will be for the english version :-)
Nathann
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Hello Everybody !!
I just had to write a doctest saying If this bipartite graph is not a
forest, then is has an even cycle
This can of course be written (not g.is_forest() and g.has_even_cycle())
I would have like to have some implication operator, to be able to write :
( not g.is_forest() =
This can of course be written (not g.is_forest() and g.has_even_cycle())
Ok, ok, I know... Let's make it g.is_forest() or g.has_even_cycle()
^^;
Nathann
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Yes, one could create an infix operator, but I think the above is much
more clear than having to learn yet more notation.
Explicit is better than implicit.
Simple is better than complex.
Indeed, but I often use the trick sum( some_list_of_booleans ) to
count the number of True. I was afraid
Hello !!!
I can't seem to figure out how to alter where an edge
goes in sage, specifically wanting it to not go in a straight line.
Is this easily accomplished?
I do not think it can be easily done through the usual methods... If
this kind of thing is easy to do, it will still involve
Clarification: Sage's plot code does not interact with the GPL
incompatible graphviz library in any way.
?.. So we have a graphviz spkg and absolutely no interface between the two ? O_o
Nathann
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Hello !
Making bug-fix releases is an essential part of professional software
development. Jeff is right - it is the professional thing to do.
Unfortunately,
most Sage developers do not have a background in software engineering, so do
not
appreciate that.
I know I am just handing the
Btw, I observed that converting to undirected graph gives the same
edge_cut, 31. Does edge_cut assume implicitly that the graph is
undirected?
No, it has two behaviours depending on the type of Graph.
I am trying to find out where it comes from, but for the moment I am a
bit stuck O_o
What I
I'll post a followup to this thread when I will have found the
cause :-)
I re-read thirty times the code and even tried to debug the LP solver
themselves. It went easier when I had the smart idea to read what was
written and not what I intended to write. The line :
Hello everybody !!!
I am trying to use Valgrind in Sage, and I guess I did not do anything
wrong as I obediently followed
http://wiki.sagemath.org/ValgrindingSage
which just amounted to define a variable, but when I type sage
-valgrind the only thing I get is a message valgrind is being used,
Hello !!
how do i create a graph where i have a label for each vertex and each
edge? Precisely I need to labels for each vertex (like a name and a value).
You can deal with labeled vertices using the set_vertex/get_vertex
methods.
Nathann
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thnx, but that's not excatly what I'm looking for, because te label
does not appear in the picture created by
graph.show()
Can't help on that one :-/
Nathann
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Harald is right. This is a typical English flaw made by Germans.
(I knew I would like to learn German... :-D)
Thank you very much for fixing it ! :-)
Nathann
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how can i add a new edge (a-b) to a given graph G (n.n. connected),
just in the case that there is no path (a - ... - b) before?
From your question, I can not infer whether you are dealing with directed or
undirected graphs. So just in case :
- If your graph is undirected and there are no
Of course finding the shortest path may be (almost) as expensive as
finding all of them... If you're doing this for a lot of edges you
might want to break it up into components, then the test would be
easy. It would be cool if all_paths were an iterator and you could
just ask for the first
Hello !!!
Among the wealth of tricky options one can use in plot/show, you will find :
g.plot(layout='tree')
:-)
Nathann
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Sage is not very happy to draw graphs.
:-/
Though... right :-/
Nathann
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I have written a function which takes a long time to be run. How can I
make it faster?
That's an easy one :-)
First, you create very *BIG* objects, and you create them twice each,
because you convert to a list something which is already a list (which
actually copies it).
Why do you do
Hello everybody !
I want to enumerate the k different translations of [0,1,2] in Z/kZ. I
thought there should exist in Sage something like that (don't try it
it does not work) :
g = CyclicGroup(k)
S = g([1,2,3])
for i in g:
print S+i
Is that possible ? It looks like the CyclicGroup is Sage
I am interested too :-)
https://groups.google.com/d/topic/sage-support/TQt4iQcKCvg/discussion
Nathann
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Hello Jan !
I just wrote a patch for that. What they do in this paper is exactly the
same, except that of course they compute the shortest path in the graph
without the neighbors of v, short of the two we are interested in :-)
http://trac.sagemath.org/sage_trac/ticket/11735
The patch is now
Hello Jan !!!
I am sorry for my vry slow answers, I am on vacation right now, with
very very bad WiFi connections when I get some. If you think you would sleep
better with copying the implementation given in the paper, then the best is
probably to write a patch for this. I like mine better,
Hello !
I'm finally back to the civilisation if you want us to deal with this patch :-)
Nathann
On 29 August 2011 15:46, Nathann Cohen nathann.co...@gmail.com wrote:
Hello Jan !!!
I am sorry for my vry slow answers, I am on vacation right now, with
very very bad WiFi connections when I
Hellooo Jan !
It is 20:20, it is almost dark outside and I am getting home by bike.
Worst of all, I am being assaulted by hungry mosquitoes. I re-read it
the following enough times to be sure that if I miswrote v instead
of x somewhere, reading it again wouldn't have changed anything.
When v
Consider: g = graph({1:[2,3,4,5],2:[3,5],4:[3,5]}).
Hahahahhahaaha ! Dead right :-)
And the code works anyway because the tree it returns actually is *NOT* a
BFS tree :-)
sage: g.lex_BFS(tree = True)[1].edges()
[(2, 1, None), (3, 2, None), (4, 5, None), (5, 2, None)]
Two (obvious) black
Hello Jan !
Quick update :
I just reviewed #11738 which touched some code related to chordality.
http://trac.sagemath.org/sage_trac/ticket/11738
I also updated my patch at #11735 that implements my (still unproved)
version of the algorithm, because it is formally better than the current
one, and
Hello Jan !
I am trying to write the patch corresponding to your modifications,
but the file has changed much since and I have some trouble dealing
with your diff file... Could you copy/paste the totality of the code ?
:-)
Thaanks !
Nathann
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This happens no matter if I use solver=GLPK or solver=coin (cbc is
installed), so it does not seem to be a problem of the underlying milp-
solver.
Pompompom That's probably my fault :-D
I will try to deal with it today. I'll keep this thread updated :-)
Nathann
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Hello again !!!
This happens no matter if I use solver=GLPK or solver=coin (cbc is
installed), so it does not seem to be a problem of the underlying milp-
solver.
This was a mistake ! I actually forgot to free some memory in both of these
backends ! ;-)
The bug is fixed, though. It is
Hellooo again !!!
I finally wrote this patch, available there :
http://trac.sagemath.org/sage_trac/ticket/11961
Though the two algorithms are very similar, I thought it better to
split it into two different parts, so that one can understand better
how each of them works without having
Hello !!
Thanks for fixing it! :) I forgot the issue so my reply is late.
Well, it took me a month to write it ;-)
I looked at the patch you produced.
I think it's fine except for that I would prefer the algorithm
keyword-argument to be placed at the end of the argument list for
backward
Hello everybody !!!
I almost never use the sloane_find function, but it seems to be in a
very bad mood :
sage: sloane_find([1,1,2,3,5,8,13,21])
Searching Sloane's online database...
[]
Perhaps it is just tired of saying it's Fibonacci's sequence and you
should know it each time it is fed with
Hello everybody !!!
Would anyone know if it is possible in a module's docstring to
interrupt the documentation ?
I would like to write something like that :
This module deals with []. Here is the first block of functions
def function():
rthe function's documentation
And here is the
Hello !!
Nonono, I want the docstring to be seen by sphinx, only it is not and I
would like it to be otherwise ! When I add this And here is the second
one in the middle of the document, it just does not appear in the HTML
documentation ! :-/
Nathann
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No, it's not possible since the second string doesn't get saved
anywhere. Sphinx doesn't parse the module, it just reads the Python
created docstrings, and only the first is saved under module.__doc__.
If you want more control over the resulting documentation, just create
a .rst file in the
Hello Jesse !
Well, for a start it wouldn't be very fair to compare graph libraries if
you do not use our graph methods and recode your own ! You seem to have
rewritten your version of strongly connected components to test the
libraries, and such low-level methods are in Sage written in
Hell !
Thanks for looking into this. I believe that I stayed within Sage's
library when I wrote my test code.
You did ! My mistake ! But you actually call
strongly_connected_components_digraph instead of
strongly_connected_components, which mean the function is spending most of
its
Oh yes, and something else about your benchmark : try to avoid using rand
methods when you are doing one, especially when you test such low-level
methods, because often the rand() method represents an important part of
the time.
The best would be to compute all the random number you need in a
Hell !!!
and still much faster than the c_graph implementation.
Well... I spent *quite* some time over this problem, wrote a LOT of code
and documentation , to find out later that this could be solved in a *very
small* patch. I hope all the work I did could be used later on
Hello !!!
I'll try to test it asap. Having some patch application issues. :-|
Just in case you're familiar with this, I'll throw it out there. But
this is probably a job for google:
Oh, not really. This problem comes from the fact that I am using a more
recent version of Sage than you
Heloo Yann !!!
Hmmm, like Karl said, what your error tells us is that something went wrong
when CPLEX was installed.
Sage detects that you want to install CPLEX by checking that there is a
file named libcplex.a in SAGE_ROOT/local/lib/ and a file cplex.h in
SAGE_ROOT/local/include/. It
Oh and by the way, I would be very glad to know what you are doing with
Sage and with LP ! Just being curious :-)
Nathann
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Helloo !!
New versions of CPLEX need one more symbolic link. See
http://trac.sagemath.org/sage_trac/ticket/11958 for the ticket from a couple
of months ago.
Arggg !! I had totally forgotten this ticket !
I just updated the patch :-)
Yann, could you add this link Jason mentionned, then
Unfortunately, I had already made the symbolic link to cpxconst.h
before requesting for help on this forum (I did found this ticket you
mentioned by googling) So the bug comes from elsewhere... I'm a
bit desperate :-(
Hello !!!
To be honest I have no idea what is going on. It
Yes, I checked local/include and local/lib. CPLEX runs fine also as a
64 bit standalone.
I recompiled everything with ./sage -ba, and now
MixedIntegerLinearProgram(solver=CPLEX) triggers a new error
message
I put the log below:
Hmmm... Well, I am sorry but I really have no idea what is
Sage has a class name 'Mixed integer linear programming' for modeling
MIPs and class for LP Solver backends like Co-in, CPLEX, GLPK and Gurobi.
At the moment I haven't know any sage class only for vehicle routing
problem.
Yep ! There's a short tutorial about its use there
:
If I wanted to change the last constraint to be w[0]-w[1]-w[2]=1 can I do
this without resetting the whole p?
Not for the moment, but this can be added with a small patch. We just need
to expose the functions from the solver's API :-)
Nathann
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Hello !!!
Thanks! I spent some time with the graph and milp support today, and it's
exactly what I was looking for.
Glad to hear it ! :-)
Do you have an idea of how the current
implementations scale with the size of the graph?
Oh. Well, I do not use LP to solve
Hell Chris !!!
I found that when installing cbc I had to add #include cstdlib to
CbcEventHandler.cpp, otherwise I got compilation errors about NULL not
being defined.
Arg... Well, this interface is being rewritte anyway. I had a lot of
things to do during the previous week (job
Hello everybody !!!
I would like to solve a set of equations with a very easy shape. My
equations are defined on variables p1_x, p1_y, p2_x, p2_y, ..., and I
would like to obtain values for them satisfying constraints like :
|p1 - p2| 1, i.e. (p1_x - p2_x)^2 + (p1_y - p2_y)^2 1
or something
Couldn't you use SCIP for this?
O probably !!
I will take a look at its documentation :-)
Nathann
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Hello !!!
Do you mean to say that you have complex numbers p_j and your inequalities
are of the form
|p_j-p_k|=C and |p_j-p_k|=D, and that you also have
some equations on Re(p_j) and Im(p_j) ?
Oh, well, if you have something like that it would of course solve my
problem too :-)
I was going to suggest exactly the same thing in response to the same
personal email you sent me. It would be much better if you posted such
questions to sage-support, rather than emailing developers personally.
I received it too -_-
Nathann
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