[sage-devel] Matrix kernel with PARI algorithm - bug fix?

2009-02-28 Thread Rob Beezer
I was creating a doctest for kernels of integer matrices when requesting the algorithm from PARI and consistently get the following behavior. sage: a = matrix(ZZ, [[1,2],[2,4]]) sage: a.kernel(algorithm='pari') --- AttributeE

[sage-devel] Re: trouble installing optional spkg gap_packages-4.4.10_6 in sage-3.3

2009-02-28 Thread mabshoff
On Feb 28, 9:17 pm, Alex Ghitza wrote: > Hi, Hi Alex, > I was trying to install gap_packages-4.4.10_6 in sage-3.3, but got an error > after the download.  It turns out that this optional package hardcodes that > it wants gap-4.4.10, and meanwhile we had upgraded to gap-4.4.12.  This was > eas

[sage-devel] trouble installing optional spkg gap_packages-4.4.10_6 in sage-3.3

2009-02-28 Thread Alex Ghitza
Hi, I was trying to install gap_packages-4.4.10_6 in sage-3.3, but got an error after the download. It turns out that this optional package hardcodes that it wants gap-4.4.10, and meanwhile we had upgraded to gap-4.4.12. This was easy enough to fix even for my very limited spkg-kungfu skills (bu

[sage-devel] Re: Interested in collaborating

2009-02-28 Thread mabshoff
On Feb 28, 6:26 pm, Minh Nguyen wrote: Hi Minh, > > I would not do that. There is very little of networkX left in Sage - > > at least for all performance critical things and Sage's graph code has > > been moving further and further away from it. There should be a lot of > > the graph theory

[sage-devel] Re: Interested in collaborating

2009-02-28 Thread Minh Nguyen
Hi Michael, On Sun, Mar 1, 2009 at 2:02 AM, mabshoff wrote: > >> Because you want to enhance the graph-theoretic component of Sage, I >> think you should start by going through the library files in the >> directory tree sage/graph. Please note also that for much of the >> graph-theoretic calc

[sage-devel] Re: non-english chars causing run-time errors in a clone

2009-02-28 Thread mabshoff
On Feb 28, 6:07 pm, Minh Nguyen wrote: > Hi Michael, Hi Minh, > A number of the library files under sage/combinat has French texts > scattered around them. Some has English texts, followed by their > French translation. Yes, I have complained about that a while ago to the words people and

[sage-devel] Re: non-english chars causing run-time errors in a clone

2009-02-28 Thread Minh Nguyen
Hi Michael, On Sun, Mar 1, 2009 at 1:39 AM, mabshoff wrote: > > > > On Feb 28, 5:27 pm, Ronan Paixão wrote: >> Personally I'd vote for making all files utf-8 encoded. That would >> increase accuracy in names and would also enable easier translations for >> "all languages under the sky". >> >> R

[sage-devel] Re: Interested in collaborating

2009-02-28 Thread mabshoff
On Feb 28, 5:54 pm, Minh Nguyen wrote: > Hi Fidel, > > On Sat, Feb 28, 2009 at 5:30 PM, Fidel wrote: > > > Hello, > > I'm interested in collaborating to develop sage. I'm mainly interested > > in doing things for the graph theoretic component of sage. I know a > > bit of C++ and Python program

[sage-devel] Re: Interested in collaborating

2009-02-28 Thread Minh Nguyen
Hi Fidel, On Sat, Feb 28, 2009 at 5:30 PM, Fidel wrote: > > Hello, > I'm interested in collaborating to develop sage. I'm mainly interested > in doing things for the graph theoretic component of sage. I know a > bit of C++ and Python programming. > I would really appreciate if someone could tell

[sage-devel] Re: non-english chars causing run-time errors in a clone

2009-02-28 Thread mabshoff
On Feb 28, 5:27 pm, Ronan Paixão wrote: > Personally I'd vote for making all files utf-8 encoded. That would > increase accuracy in names and would also enable easier translations for > "all languages under the sky". > > Ronan No, we already agreed on not doing that, i.e. I am not looking forw

[sage-devel] Re: non-english chars causing run-time errors in a clone

2009-02-28 Thread mabshoff
On Feb 28, 5:25 pm, Rob Beezer wrote: > I've had the same problem in a clone of 3.4.alpha0. > > Seems to perhaps just be  Grobner in singular.py, and Mobius in > sloane_functions.py, since I ran a computation successfully after > editing those two files. > > Would a patch editing these two inst

[sage-devel] Re: sage for biology

2009-02-28 Thread Minh Nguyen
Hi folks, On Sat, Feb 28, 2009 at 4:24 PM, Marshall Hampton wrote: > > Its unfortunate they chose that name - its already difficult for us in > biology since most bio people hear "sage" and think "serial analysis > of gene expression", a common technique for cheap mRNA expression > studies. Thi

[sage-devel] Re: non-english chars causing run-time errors in a clone

2009-02-28 Thread Ronan Paixão
Personally I'd vote for making all files utf-8 encoded. That would increase accuracy in names and would also enable easier translations for "all languages under the sky". Ronan Em Sex, 2009-02-27 às 13:57 -0800, mabshoff escreveu: > > > On Feb 27, 1:44 pm, John Cremona wrote: > > Hi John, >

[sage-devel] Re: non-english chars causing run-time errors in a clone

2009-02-28 Thread Rob Beezer
I've had the same problem in a clone of 3.4.alpha0. Seems to perhaps just be Grobner in singular.py, and Mobius in sloane_functions.py, since I ran a computation successfully after editing those two files. Would a patch editing these two instances be welcome as a quick fix for rc0? Rob On Feb

[sage-devel] Re: sage for biology

2009-02-28 Thread rjf
1. Imagine if Merck had called their biology database "Mathematica". 2. Maybe this Sage should provide access to that Sage. 3. For people who like to grouse about sage, perhaps there should be a hold on the url 's involving centrocercus .. Try googling. RJF --~--~-~--~~--

[sage-devel] Re: Idea solicitation for semester-long algebra project

2009-02-28 Thread Francisco Veach
Thanks very much for this article. The implementation of this algorithm is a good candidate for the semester project, and the other recommendations look like excellent mini-projects to acquaint myself with the system. I'm of course still interested in hearing more suggestions, and I appreciate the

[sage-devel] Re: Naming convention again...

2009-02-28 Thread Ronan Paixão
> Given such a set S, the "position" of an element in the enumeration is called > it's rank. So that S.unrank(n) returns the n-th element of S and S.rank(el) > returns it's rank in S. I know nothing of combinatorics, but shouldn't accessing a set's n-th element be more understandable using S[n]

[sage-devel] Re: Naming convention again...

2009-02-28 Thread Carl Witty
On Sat, Feb 28, 2009 at 1:19 PM, Florent Hivert wrote: > We have a good occasion to change this name in the short run, with our > abstract class CombinatorialClass which will become a category. Suggestions of > name for this category are VERY welcome! > >        IterableSets ? >        Combinator

[sage-devel] Re: srange is slow, even with python floats

2009-02-28 Thread Robert Bradshaw
On Feb 28, 2009, at 11:17 AM, Jason Grout wrote: > How come srange is so slow compared to numpy arange? Because no one has ever optimized this case yet. I bet all the additions are being done as Python floats in srange, but as c doubles in numpy. Note that even (on my machine) sage: %timeit

[sage-devel] Naming convention again...

2009-02-28 Thread Florent Hivert
Dear all, The big cleanup of combinat is moving forward. I'd like again to have a wide vote about some names... One of our central concept in combinatorics is: finite or countable set together with a canonical enumeration of its elements; the related operations are: cardinality, __it

[sage-devel] Re: Determinant is very slow for sparse matrices

2009-02-28 Thread Jason Bandlow
William Stein wrote: > On Sat, Feb 28, 2009 at 2:49 PM, Jason Bandlow wrote: >> This seems like a bug to me: >> >>sage: dd = {(0,0):1} >>sage: %timeit matrix(8,dd).det() >>10 loops, best of 3: 213 ms per loop >>sage: %timeit matrix(8,dd,sparse = False).det() >>

[sage-devel] Re: spacey ReST

2009-02-28 Thread Mike Hansen
On Sat, Feb 28, 2009 at 12:07 PM, William Stein wrote: > > On Sat, Feb 28, 2009 at 3:00 PM, Mike Hansen wrot >> Not quite.  The following will work though: > > Why is there only one colon after INPUT but two after EXAMPLES? The two colons denote a verbatim block (which gets syntax highlighted).

[sage-devel] Re: spacey ReST

2009-02-28 Thread William Stein
On Sat, Feb 28, 2009 at 3:00 PM, Mike Hansen wrot > Not quite.  The following will work though: Why is there only one colon after INPUT but two after EXAMPLES? Why is the newline necessarily after INPUT? > > def QuaternionAlgebra(K, a, b, names=['i','j','k'], denom=1): >    """ >    Return the

[sage-devel] Re: Determinant is very slow for sparse matrices

2009-02-28 Thread William Stein
On Sat, Feb 28, 2009 at 2:49 PM, Jason Bandlow wrote: > > This seems like a bug to me: > >        sage: dd = {(0,0):1} >        sage: %timeit matrix(8,dd).det() >        10 loops, best of 3: 213 ms per loop >        sage: %timeit matrix(8,dd,sparse = False).det() >        100 loops, best of 3: 62

[sage-devel] Re: spacey ReST

2009-02-28 Thread Mike Hansen
On Sat, Feb 28, 2009 at 11:48 AM, William Stein wrote: > So just to be clear, I can change the above to the following and it will work. > > def QuaternionAlgebra(K, a, b, names=['i','j','k'], denom=1): >    """ >    Return the quaternion algebra over `K` generated by >    `i`, `j`, and `k` such t

[sage-devel] Determinant is very slow for sparse matrices

2009-02-28 Thread Jason Bandlow
This seems like a bug to me: sage: dd = {(0,0):1} sage: %timeit matrix(8,dd).det() 10 loops, best of 3: 213 ms per loop sage: %timeit matrix(8,dd,sparse = False).det() 100 loops, best of 3: 629 µs per loop Should I open a ticket? Cheers, Jason --~--~---

[sage-devel] Re: spacey ReST

2009-02-28 Thread William Stein
On Sat, Feb 28, 2009 at 2:42 PM, Mike Hansen wrote: > > On Sat, Feb 28, 2009 at 11:33 AM, William Stein wrote: >> I was just looking at some post-rest docstrings and they look like >> this (see below).   Is all that whitespace really necessary??? >> >> def QuaternionAlgebra(K, a, b, names=['i','

[sage-devel] Re: spkg dependencies

2009-02-28 Thread William Stein
On Sat, Feb 28, 2009 at 2:29 PM, mabshoff wrote: > > > > On Feb 28, 11:27 am, William Stein wrote: >> On Sat, Feb 28, 2009 at 3:09 AM, Simon King >> wrote: >> >> > Hi William, >> >> > On 28 Feb., 04:49, William Stein wrote: >> >> You should use Sage in such cases.  Type >> >>  sage: email? >>

[sage-devel] Re: spacey ReST

2009-02-28 Thread Mike Hansen
On Sat, Feb 28, 2009 at 11:33 AM, William Stein wrote: > I was just looking at some post-rest docstrings and they look like > this (see below).   Is all that whitespace really necessary??? > > def QuaternionAlgebra(K, a, b, names=['i','j','k'], denom=1): >    """ >    Return the quaternion algebr

[sage-devel] Re: spkg dependencies

2009-02-28 Thread Michael Abshoff
On Sat, Feb 28, 2009 at 9:48 AM, Ondrej Certik wrote: > Hi Ondrej, >> If building openmx really benefits from "make -j" you might consider >> putting something clever in spkg-install to detect "available cores" and >> maybe build using them... > > Yes, but I need this for all packages, so I t

[sage-devel] Re: spacey ReST

2009-02-28 Thread Jason Grout
William Stein wrote: > Hi, > > I was just looking at some post-rest docstrings and they look like > this (see below). Is all that whitespace really necessary??? > > def QuaternionAlgebra(K, a, b, names=['i','j','k'], denom=1): > """ > Return the quaternion algebra over `K` generated by

[sage-devel] spacey ReST

2009-02-28 Thread William Stein
Hi, I was just looking at some post-rest docstrings and they look like this (see below). Is all that whitespace really necessary??? def QuaternionAlgebra(K, a, b, names=['i','j','k'], denom=1): """ Return the quaternion algebra over `K` generated by `i`, `j`, and `k` such that

[sage-devel] Re: spkg dependencies

2009-02-28 Thread mabshoff
On Feb 28, 11:27 am, William Stein wrote: > On Sat, Feb 28, 2009 at 3:09 AM, Simon King > wrote: > > > Hi William, > > > On 28 Feb., 04:49, William Stein wrote: > >> You should use Sage in such cases.  Type > >>  sage: email? > >> for more details.   That uses Twisted behind the scenes. > >

[sage-devel] Re: spkg dependencies

2009-02-28 Thread William Stein
On Sat, Feb 28, 2009 at 3:09 AM, Simon King wrote: > > Hi William, > > On 28 Feb., 04:49, William Stein wrote: >> You should use Sage in such cases.  Type >>  sage: email? >> for more details.   That uses Twisted behind the scenes. > > Very cool -- was my first reaction. But wouldn't this allow

[sage-devel] srange is slow, even with python floats

2009-02-28 Thread Jason Grout
How come srange is so slow compared to numpy arange? -- | Sage Version 3.4.alpha0, Release Date: 2009-02-24 | | Type notebook() for the GUI, and license() for information.| ---

[sage-devel] Re: Interested in collaborating

2009-02-28 Thread William Stein
On Sat, Feb 28, 2009 at 12:30 PM, Fidel wrote: > > Hello, > I'm interested in collaborating to develop sage. I'm mainly interested > in doing things for the graph theoretic component of sage. I know a > bit of C++ and Python programming. > I would really appreciate if someone could tell me what I

[sage-devel] Interested in collaborating

2009-02-28 Thread Fidel
Hello, I'm interested in collaborating to develop sage. I'm mainly interested in doing things for the graph theoretic component of sage. I know a bit of C++ and Python programming. I would really appreciate if someone could tell me what I need to do to get started or where to start. Are there any

[sage-devel] Re: spkg dependencies

2009-02-28 Thread Ondrej Certik
On Fri, Feb 27, 2009 at 7:49 PM, William Stein wrote: > > On Fri, Feb 27, 2009 at 4:24 PM, Ondrej Certik wrote: >> Another thing --- I'd like to create some repository with my packages, so that people can just "sage -i" install them, without having to first wget all the spkg and i

[sage-devel] Re: sage for biology

2009-02-28 Thread Marshall Hampton
Its unfortunate they chose that name - its already difficult for us in biology since most bio people hear "sage" and think "serial analysis of gene expression", a common technique for cheap mRNA expression studies. -Marshall On Feb 28, 10:16 am, William Stein wrote: > On Sat, Feb 28, 2009 at 11

[sage-devel] Re: sage for biology

2009-02-28 Thread William Stein
On Sat, Feb 28, 2009 at 11:10 AM, rjf wrote: > > see > http://scienceblogs.com/commonknowledge/2009/02/sage_-_open_access_data_from_m.php > > > sorry you will have to patch the url above.  or use google to > search for { sage merck} > > RJF The above has nothing to do with the Sage math software

[sage-devel] sage for biology

2009-02-28 Thread rjf
see http://scienceblogs.com/commonknowledge/2009/02/sage_-_open_access_data_from_m.php sorry you will have to patch the url above. or use google to search for { sage merck} RJF --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.c

[sage-devel] Re: matrix exponential

2009-02-28 Thread Jason Grout
Jason Grout wrote: > John Cremona wrote: >> 2009/2/27 Jason Grout : >>> John Cremona wrote: I have just been to a colloquium talk by numerical analyst Nick Higham (Manchester) called "How to compute and not to compute a matrix exponential". He has new methods which are now in mathe

[sage-devel] Re: Sage 3.4.alpha0 released - ReST patch update

2009-02-28 Thread mabshoff
On Feb 28, 3:26 am, "Georg S. Weber" wrote: > Hi Michael, > > it seems that the "libgcrypt-1.4.3.p0.spkg" in the sage-3.4.alpha0.tar > I had downloaded is gzip'ed, not bz2'ed ... Yep, we noticed too and corrected it two days ago. Ironically the problem only happens on OSX 10.4 since I build 3.

[sage-devel] Re: I cannot compile 3.3 in gentoo

2009-02-28 Thread François Bissey
OK latest version of gentoo notes for 3.4. Francois --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at h

[sage-devel] Re: Sage 3.4.alpha0 released - ReST patch update

2009-02-28 Thread Georg S. Weber
Hi Michael, it seems that the "libgcrypt-1.4.3.p0.spkg" in the sage-3.4.alpha0.tar I had downloaded is gzip'ed, not bz2'ed ... Cheers, gsw --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send e

[sage-devel] Re: spkg dependencies

2009-02-28 Thread Simon King
Hi William, On 28 Feb., 04:49, William Stein wrote: > You should use Sage in such cases.  Type >  sage: email? > for more details.   That uses Twisted behind the scenes. Very cool -- was my first reaction. But wouldn't this allow to turn a public notebook into a spam-bot? Is there a security fe