[sage-devel] Re: #16577: enable 0-based row/column permutation of matrices

2014-09-06 Thread Dima Pasechnik
On 2014-09-06, Travis Scrimshaw wrote: > >> >> Yes, I must agree that in Pythonic world >> sage: Permutation((1,2,3)) >> > > > must be equal to >> sage: Permutation([1,2,3]) >> > > > And if you mean the cyclic permutation (1,2,3) this should be >> sage: Permutation([(1,2,3)]) > > > So to

Re: [sage-devel] Re: Tracking Citations; How?

2014-09-06 Thread Bill Hart
On Saturday, 6 September 2014 20:34:56 UTC+2, Robert Bradshaw wrote: > > Note that Cython supports cProfile these days: > http://docs.cython.org/src/tutorial/profiling_tutorial.html However, > that won't help too much as the real missing pieces are the calls from > Cython into the various C li

[sage-devel] Re: Tracking Citations; How?

2014-09-06 Thread Bill Hart
The code for the profiler in the project I mentioned seems to have been custom written for the project. You can see it here: https://github.com/JuliaLang/julia/blob/master/src/profile.c and here: https://github.com/JuliaLang/julia/blob/master/base/profile.jl There looks to be fairly good separ

Re: [sage-devel] Re: Tracking Citations; How?

2014-09-06 Thread Robert Bradshaw
Note that Cython supports cProfile these days: http://docs.cython.org/src/tutorial/profiling_tutorial.html However, that won't help too much as the real missing pieces are the calls from Cython into the various C libraries. I'm also -1 to an approach that slows down all of Sage to track this uncon

[sage-devel] Re: Tracking Citations; How?

2014-09-06 Thread Volker Braun
On Saturday, September 6, 2014 5:44:57 PM UTC+1, Bill Hart wrote: > > It takes samples at regular points during the computation > Thats the aforementioned http://trac.sagemath.org/ticket/16777. See that ticket for technical obstacles of that approach. -- You received this message because you ar

Re: [sage-devel] Re: #16577: enable 0-based row/column permutation of matrices

2014-09-06 Thread Travis Scrimshaw
> > Yes, I must agree that in Pythonic world > sage: Permutation((1,2,3)) > must be equal to > sage: Permutation([1,2,3]) > And if you mean the cyclic permutation (1,2,3) this should be > sage: Permutation([(1,2,3)]) So to be pythonic, because a tuple should be the same as a list by

[sage-devel] Re: Tracking Citations; How?

2014-09-06 Thread Bill Hart
On additional technical point. The profiling approach need not slow Sage down. The same approach is used in another project I'm aware of (not for citation though). It takes samples at regular points during the computation, figures out which function is currently being called and tallies the res

[sage-devel] Re: Tracking Citations; How?

2014-09-06 Thread Bill Hart
I don't have any concrete suggestions, but have some random personal thoughts on the matter. * I personally don't mind Pari being cited if flint actually performs a computation. What I mean is, I'm not sure how important it is to look all the way down the decision tree to see which package actu

Re: [sage-devel] Re: #16577: enable 0-based row/column permutation of matrices

2014-09-06 Thread Nathann Cohen
> > Also, I agree Nathan has a point with the cycle notation. It shouln't be a > single cycle but a list. There is still the problem of backward compatibily. > I don't consider that we have to stay backward-compatible with past bugs. But we can have the usual 1-year 'deprecationwarning' whenever an

Re: [sage-devel] Re: #16577: enable 0-based row/column permutation of matrices

2014-09-06 Thread Viviane Pons
Le 6 sept. 2014 11:41, "Volker Braun" a écrit : > > I'd just write two different classes for permutations. The underlying bit-twiddling is different but various high-level structures can be inherited to both. At the end of the day the permutation should be defined how it acts on an ordered contain

[sage-devel] Re: Tracking Citations; How?

2014-09-06 Thread Volker Braun
I'm also uncomfortable with sprinkling explicit citation management calls everywhere. There are many many places that use external shared library code. Apart from the potential slowdown and difficulty in maintaining the code: You never going to get all of them. The source code for calling a sha

Re: [sage-devel] Re: pyzmq not installing

2014-09-06 Thread Thierry
Hi, On Sat, Sep 06, 2014 at 11:22:04AM +0100, Vincent Delecroix wrote: > I see... but still, it is annoying that > > - there is no a dependency between pyzmq and zmq Sage packages Actually, there is one, but is is not handled automatically by Sage install script: http://git.sagemath.org/sage.gi

[sage-devel] Re: pyzmq not installing

2014-09-06 Thread Dima Pasechnik
On 2014-09-04, Anthony Savagar wrote: > Log file attached. Thanks for any help. I want to be able to do sage > -ipython notebook. I gather pyzmq is a necessary condition. > > > anthony@anthony-VPCZ12V9E:~/Downloads$ sudo sage -i pyzmq-2.1.11.p1.spkg This looks like an old spkg. sudo sage -i pyzmq

Re: [sage-devel] Re: pyzmq not installing

2014-09-06 Thread Vincent Delecroix
014-09-06 11:08 UTC+01:00, Volker Braun : > For starters, did you ask him whether he has administrator permissions on > his machine? I see... but still, it is annoying that - there is no a dependency between pyzmq and zmq Sage packages - the default is to not use the system wide libraries Vincen

Re: [sage-devel] Re: pyzmq not installing

2014-09-06 Thread Volker Braun
For starters, did you ask him whether he has administrator permissions on his machine? On Saturday, September 6, 2014 11:07:24 AM UTC+1, vdelecroix wrote: > > Why not a system wide installation of zeromq? It just works fine on my > computer. > > -- You received this message because you are s

Re: [sage-devel] Re: pyzmq not installing

2014-09-06 Thread Vincent Delecroix
Why not a system wide installation of zeromq? It just works fine on my computer. Vincent 2014-09-06 11:05 UTC+01:00, Volker Braun : > Typo: > > sage -i zeromq > sage -i pyzmq > > > On Saturday, September 6, 2014 11:04:46 AM UTC+1, Volker Braun wrote: >> >> In this order: >> >> sage -i zmq >> sage

[sage-devel] Re: pyzmq not installing

2014-09-06 Thread Volker Braun
Typo: sage -i zeromq sage -i pyzmq On Saturday, September 6, 2014 11:04:46 AM UTC+1, Volker Braun wrote: > > In this order: > > sage -i zmq > sage -i pyzmq > > > On Friday, September 5, 2014 12:29:03 AM UTC+1, Anthony Savagar wrote: >> >> Log file attached. Thanks for any help. I want to be able

[sage-devel] Re: pyzmq not installing

2014-09-06 Thread Volker Braun
In this order: sage -i zmq sage -i pyzmq On Friday, September 5, 2014 12:29:03 AM UTC+1, Anthony Savagar wrote: > > Log file attached. Thanks for any help. I want to be able to do sage > -ipython notebook. I gather pyzmq is a necessary condition. > > > anthony@anthony-VPCZ12V9E:~/Downloads$ sud

Re: [sage-devel] pyzmq not installing

2014-09-06 Thread Vincent Delecroix
>From your log, it seems that zmq is not installed on your computer (http://zeromq.org/). If you are on a debian like OS this is just $ apt-get install libzmq-dev Vincent -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this

[sage-devel] Re: #16577: enable 0-based row/column permutation of matrices

2014-09-06 Thread Dima Pasechnik
On 2014-09-05, Viviane Pons wrote: > The Permutation0 might be a good idea, I don't know... It wouldn't change > the tuple vs. list thing which is used to distinguish between the cycle > notation and the word notation. > > I agree some of the syntax could be improved. But I do think backward > com

Re: [sage-devel] pyzmq not installing

2014-09-06 Thread Vincent Delecroix
Hi, I would rather install it from pip $ sage - i pip $ sage -sh -c "pip install pyzmq" see http://trac.sagemath.org/ticket/16897 for a proposal that just remove pyzmq from the list of packages. Vincent 2014-09-05 0:29 UTC+01:00, Anthony Savagar : > Log file attached. Thanks for any help. I

Re: [sage-devel] Tracking Citations; How?

2014-09-06 Thread Vincent Delecroix
Hallo Martin, I agree that it would be nice to have a proper view on what components of Sage have been used. But for me, anything which would slow down the code is a big -1 (in particular decorators that modifies functions). >From that point of view, I like the implemented approach of Mike which i

Re: [sage-devel] Re: #16577: enable 0-based row/column permutation of matrices

2014-09-06 Thread Volker Braun
I'd just write two different classes for permutations. The underlying bit-twiddling is different but various high-level structures can be inherited to both. At the end of the day the permutation should be defined how it acts on an ordered container, regardless of whether the container is indexe

Re: [sage-devel] Re: #16577: enable 0-based row/column permutation of matrices

2014-09-06 Thread Vincent Delecroix
Hello, In GAP everything is coherent: permutations are based on 1..n and arrays start at 1. Note that, in the background, permutations are stored as a C array of ints on 0..n-1. But the C code is inaccesible from the console and everything is nice from both the programmer and user point of views.

[sage-devel] Tracking Citations; How?

2014-09-06 Thread Martin Raum
Dear Sage-developer, I'm writing to get an impression on the communities opinion on how citation management should be implemented. As a background, I should say that I have taken it into my head to modernize citation management in Sage. I personally find this very important, as it signalized

Re: [sage-devel] Re: #16577: enable 0-based row/column permutation of matrices

2014-09-06 Thread Vincent Delecroix
2014-09-06 10:06 UTC+01:00, Dima Pasechnik : > OK, sorry, perhaps, I am too used to GAP, which allows things like > a:=(1,2)(3,4); > b:=(3,4,5); GAP is very cool to work with permutations. But this is not possible to be as smart in Sage as (1,2,3) is a tuple. > Yes, I must agree that in Pythonic

[sage-devel] Re: #16577: enable 0-based row/column permutation of matrices

2014-09-06 Thread Dima Pasechnik
On 2014-09-06, Nathann Cohen wrote: > Yo ! > >> sage: Permutation([1,2,3]) >> > [1, 2, 3] >> > sage: Permutation((1,2,3)) >> > [2, 3, 1] >> >> this actually makes perfect sense for someone with some >> group theory background. >> (array notation vs cyclic notation) >> > > I will repeat it f

[sage-devel] Re: #16577: enable 0-based row/column permutation of matrices

2014-09-06 Thread Nathann Cohen
Yo ! > sage: Permutation([1,2,3]) > > [1, 2, 3] > > sage: Permutation((1,2,3)) > > [2, 3, 1] > > this actually makes perfect sense for someone with some > group theory background. > (array notation vs cyclic notation) > I will repeat it for as long as people will ignore it, but NO it does

Re: [sage-devel] Re: #16577: enable 0-based row/column permutation of matrices

2014-09-06 Thread Nathann Cohen
> So how about making it explicit, have separate Permutation and Permutation0 > (instead of tuple vs list). They can share most of the backend, its just a > slightly different set that they operate on. In Code, you just call sigma = > Permutation0(sigma) on user input in the beginning to convert