[sage-devel] Re: [sage-forum] sage-2.8.8

[Hamptonio]

I had the following failure from make test,  from devel/sage-main/
sage/numerical/test.py.  I'm guessing its from the convoluted history
of my fortran installs on that machine (a powerpc apple powerbook):

sage -t  devel/sage-main/sage/numerical/test.py
**
File test.py, line 4:
: from cvxopt.base import *
Exception raised:
Traceback (most recent call last):
  File /Users/mh/sage-2.8.4.1/local/lib/python2.5/doctest.py,
line 1212, in __run
compileflags, 1) in test.globs
  File doctest __main__.example_0[0], line 1, in module
from cvxopt.base import *###line 4:
: from cvxopt.base import *
ImportError: dlopen(/Users/mh/sage-2.8.4.1/local/lib/python/site-
packages/cvxopt/base.so, 2): Symbol not found: __g95_ioparm
  Referenced from: /Users/mh/sage-2.8.4.1/local/lib/python/site-
packages/cvxopt/base.so
  Expected in: dynamic lookup

**
File test.py, line 5:
: from cvxopt import umfpack
Exception raised:
Traceback (most recent call last):
  File /Users/mh/sage-2.8.4.1/local/lib/python2.5/doctest.py,
line 1212, in __run
compileflags, 1) in test.globs
  File doctest __main__.example_0[1], line 1, in module
from cvxopt import umfpack###line 5:
: from cvxopt import umfpack
ImportError: dlopen(/Users/mh/sage-2.8.4.1/local/lib/python/site-
packages/cvxopt/umfpack.so, 2): Symbol not found: __g95_st_write_done
  Referenced from: /Users/mh/sage-2.8.4.1/local/lib/python/site-
packages/cvxopt/umfpack.so
  Expected in: dynamic lookup

**
1 items had failures:
   2 of   8 in __main__.example_0
***Test Failed*** 2 failures.

On Oct 21, 3:03 pm, John Cremona [EMAIL PROTECTED] wrote:
 Successfully upgraded to 2.8.8.1 on linux (Kubuntu 7.04):

 sage --testall
 (...)

 All tests passed!
 Total time for all tests: 1978.6 seconds

 John Cremona


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[sage-devel] Re: Fwd: ode_solver

[Hamptonio]

 Perhaps this could be written to use the new rdef function code, to
 make it easier for the user to provide a cdef function to the solver.


That would be great.  As a short term alternative, I think I will
write my own simple 4th-order Runge-Kutta solver in cython, but it
would be nice to be able to exploit the GSL fully.

-Marshall


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[sage-devel] Re: Video of Robert's talk on Cython

[Hamptonio]

I was really enjoying this when it froze at 4:37.  I can't seem to get
past that point.

-Marshall

On Oct 9, 12:27 pm, William Stein [EMAIL PROTECTED] wrote:
 Hello,

 I've posted the video of Robert Bradshaw's Sage Days 5 talk on Cython
 at Google Video:
http://video.google.com/videoplay?docid=8155731528590036456hl=en

 The slides for the talk are here:
http://wiki.sagemath.org/days5/sched?action=AttachFiledo=gettarget=...

 --
 William Stein
 Associate Professor of Mathematics
 University of Washingtonhttp://wstein.org


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[sage-devel] Re: Video of Robert's talk on Cython

[Hamptonio]

It works fine on another computer; my old apple laptop can be funny
with multimedia.

Marshall

On Oct 10, 9:28 am, William Stein [EMAIL PROTECTED] wrote:
 On 10/10/07, Hamptonio [EMAIL PROTECTED] wrote:



  I was really enjoying this when it froze at 4:37.  I can't seem to get
  past that point.

 ???  I have no problem at all viewing any part.  Anyways, it's Google
 Video, so I have nothing to do with serving the video -- it's supposed
 to just work.

 If you continue to have problems (maybe try another computer or
 net connection), I can make the original mpeg2 file available to you.
 Just let me know.

 William





  -Marshall

  On Oct 9, 12:27 pm, William Stein [EMAIL PROTECTED] wrote:
   Hello,

   I've posted the video of Robert Bradshaw's Sage Days 5 talk on Cython
   at Google Video:
  http://video.google.com/videoplay?docid=8155731528590036456hl=en

   The slides for the talk are here:
  
   http://wiki.sagemath.org/days5/sched?action=AttachFiledo=gettarget=...

   --
   William Stein
   Associate Professor of Mathematics
   University of Washingtonhttp://wstein.org

 --
 William Stein
 Associate Professor of Mathematics
 University of Washingtonhttp://wstein.org


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[sage-devel] Re: Minor notebook CSS / HTML changes

[Hamptonio]

Thanks for working on this.  At the moment (on firefox at least) the
toggle function hides the top bar but doesn't increase the size of the
rest of the worksheet.  I am wondering if I should apply your first
patch and then the second?  I applied the toggle.patch on an
unmodified 2.8.5.1 version.  Also, the toggle is reset upon a page
refresh, although I don't know if that is a problem.

Marshall

On Oct 4, 1:04 am, Mike Hansen [EMAIL PROTECTED] wrote:
  I like the idea of having a toggle.

 Preliminary patch for toggle (and another misc. fix) up 
 athttp://www.sagetrac.org/sage_trac/attachment/ticket/643/toggle.patch.
  I went the more conservative route and kept the very top bar visible.

  Wait a minute!  Your changes have made it so the topbar scrolls with the 
  rest of the page.
  I find this to be rather obnoxious, since one needs to scroll to the top to 
  say, restart
  a process which doesn't want to be interrupted and is spitting out a 
  thousand
  lines a second.

 I will take care of this eventually since there should be a nice way
 to handle, but I'll need to do some restructuring.  I'm going to be
 doing that in bits and pieces when I feel like taking a break from
 writing math code :)

 --Mike


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[sage-devel] minor issue: remainders with floats

[Hamptonio]

I am porting some Mathematica code to sage and I ran into a minor
issue.  I was using the Mod command in mathematica with argument types
Mod[float,integer] to create a periodic function.  In sage, the mod
command gives an error on that sort of input.  So I made a simple
function:

def float_mod(x,divisor):
'''An extension of the mod command for floats.'''
return x-floor(float(x)/divisor)*divisor

which does what I want.  Is there something like this already in
sage?  I know the normal python % operation does something similar but
that's taken out by the preparser.


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[sage-devel] Re: minor issue: remainders with floats

[Hamptonio]

Thanks for clearing up my confusion.  I will try to implement this. I
have added it as ticket #825.

Marshall

On Oct 4, 11:48 am, William Stein [EMAIL PROTECTED] wrote:
 On 10/4/07, Hamptonio [EMAIL PROTECTED] wrote:



  I am porting some Mathematica code to sage and I ran into a minor
  issue.  I was using the Mod command in mathematica with argument types
  Mod[float,integer] to create a periodic function.  In sage, the mod
  command gives an error on that sort of input.  So I made a simple
  function:

  def float_mod(x,divisor):
  '''An extension of the mod command for floats.'''
  return x-floor(float(x)/divisor)*divisor

  which does what I want.  Is there something like this already in
  sage?

 Yes, %, e.g.,

 sage: a = float(1.2393); b = int(5)
 sage: a % b
 1.23930001
 sage: a = float(1.2393); b = int(1)
 sage: a % b
 0.23937

 That this doesn't work on Sage types, i.e., Sage real numbers
 and Sage integers is because we didn't think to implement it:

 sage: 1.2394 % 1

 boom because we didn't think to implement.

 Should this be added to Sage?  If somebody thinks so...
 implement it and post a trac ticket.

  I know the normal python % operation does something similar but
  that's taken out by the preparser.

 The Sage preparser doesn't touch %:

 sage: preparse('a % b')
 'a % b'

 William


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[sage-devel] Re: Mathematica and Free Software in Mexico

[Hamptonio]

Nice article.  I'll be at CIMAT next July I think, Jordi if you're
reading this I look forward to meeting you if you'll still be there.

I'll tape an English version of this to my office door.

-Marshall

On Sep 28, 11:35 am, William Stein [EMAIL PROTECTED] wrote:
 Hi,

 If you read Spanish, you might enjoy reading this aritlce that was
 written by a mathematician in Mexico right after Mathematica
 visited his university to make a presentation.  It mentioned Sage
 a lot at the end:

http://sums.math.mcgill.ca/~jordi/rants/mathematica.html

 Here's a Google Translated version to English, which is enough
 to understand most of the article:
  http://www.google.com/translate?u=http%3A%2F%2Fsums.math.mcgill.ca%2F...

  -- William

 --
 William Stein
 Associate Professor of Mathematics
 University of Washingtonhttp://wstein.org


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[sage-devel] Re: making new infix operators

[Hamptonio]

I would appreciate any tips on how to extend the + operator in this
way, since I would like to implement Minkowski sums of polytopes and
this is natural notation for that.
Marshall

On Sep 25, 10:37 am, Mike Hansen [EMAIL PROTECTED] wrote:
 In SAGE, '+' is used for union of sets.  For example,

 sage: a = Set([1,2])
 sage: b = Set([2,3])
 sage: a+b
 {1, 2, 3}

 Since currently, + is not defined for graphs, it'd be a natural choice.

 --Mike

 On 9/25/07, Jason Grout [EMAIL PROTECTED] wrote:



  I'm thinking more about how to make the Graph class easy to use.  One
  thing that crops up is that the operations that combine graphs only
  combine two graphs at a time (e.g., g.union(h), where g and h are graphs).

  Is there a way to define an infix operator that would allow one to say:

  g union h union i union j union k?

  I could do it with something like:

  reduce(lambda x,y: x.union(y), [g,h,i,j,k])

  But that doesn't seem as clear as the infix things above.

  For reference, Mathematica allows an operator in backticks to be applied
  to its surrounding arguments, so the equivalent operation above would be:

  g `union` h `union` i `union` j `union` k

  And of course, you can set whether the operator is left-associative or
  right-associative.

  Of course, one solution is to use a for loop:

  newgraph=Graph()
  for graph in [g,h,i,j,k]:
   newgraph.union(graph)

  But that seems a lot clunkier than the infix expression above.

  I guess another solution is to return the new graph from the union, so
  that you could do:

  g.union(h).union(i).union(j)

  Thoughts?

  -Jason


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[sage-devel] Re: making new infix operators

[Hamptonio]

Thanks, now I understand what to do.  However, I don't understand your
comment about ...the SAGE coercion model.  What is an example of
that - the sage integers?

-M. Hampton

On Sep 25, 12:10 pm, Mike Hansen [EMAIL PROTECTED] wrote:
 Since I don't think that graphs and polytopes fall under the SAGE
 coercion model, overloading operators is pretty straightforward.  You
 just need to define the __add__ method in your class.  x + y will call
 x.__add__(y).

 sage: class Foo:
 : def __add__(self, y):
 : return 42
 :
 sage: a = Foo()
 sage: b = Foo()
 sage: a + b
 42
 sage: b + a
 42

 Note that you'll want to do some type-checking so that y is what you
 actually think it should be.

 --Mike

 On 9/25/07, Hamptonio [EMAIL PROTECTED] wrote:



  I would appreciate any tips on how to extend the + operator in this
  way, since I would like to implement Minkowski sums of polytopes and
  this is natural notation for that.
  Marshall

  On Sep 25, 10:37 am, Mike Hansen [EMAIL PROTECTED] wrote:
   In SAGE, '+' is used for union of sets.  For example,

   sage: a = Set([1,2])
   sage: b = Set([2,3])
   sage: a+b
   {1, 2, 3}

   Since currently, + is not defined for graphs, it'd be a natural choice.

   --Mike

   On 9/25/07, Jason Grout [EMAIL PROTECTED] wrote:

I'm thinking more about how to make the Graph class easy to use.  One
thing that crops up is that the operations that combine graphs only
combine two graphs at a time (e.g., g.union(h), where g and h are 
graphs).

Is there a way to define an infix operator that would allow one to say:

g union h union i union j union k?

I could do it with something like:

reduce(lambda x,y: x.union(y), [g,h,i,j,k])

But that doesn't seem as clear as the infix things above.

For reference, Mathematica allows an operator in backticks to be applied
to its surrounding arguments, so the equivalent operation above would 
be:

g `union` h `union` i `union` j `union` k

And of course, you can set whether the operator is left-associative or
right-associative.

Of course, one solution is to use a for loop:

newgraph=Graph()
for graph in [g,h,i,j,k]:
 newgraph.union(graph)

But that seems a lot clunkier than the infix expression above.

I guess another solution is to return the new graph from the union, so
that you could do:

g.union(h).union(i).union(j)

Thoughts?

-Jason


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[sage-devel] Re: Fwd: Trac rules

[Hamptonio]

What about an intermediate solution: once someone is a contributor,
you could give them edit access to a wiki page listing contributors,
and then they could keep their entry current.

On Sep 21, 5:53 pm, [EMAIL PROTECTED] wrote:
  Sure.  I should probably move that page to the wiki so people
  can update it themselves.

What do people think about moving the contributors page to
a wiki?
Pro: It's easier to update and more complete
Con: It doesn't hold as much weight to be listed, since just anybody
can list themselves.

 +1

 I don't think the con is valid, these days.  If somebody adds something 
 fishy, contact them / remove it / block their wiki account, depending on 
 severity.


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[sage-devel] Re: Burlington, VT on May 30-31, 2008

[Hamptonio]

I'm interested!

My first thought is I could speak on using sage in bioinformatics/
computational biology courses, although if the organizers had a
particular focus some of my other interests might be more relevant
(polytopes, teaching ODEs and calculus with sage, celestial
mechanics).

Marshall

On Sep 20, 7:59 am, William Stein [EMAIL PROTECTED] wrote:
 Hello,

 If there is a Sage user/developer who is interested in representing
 Sage -- especially for purposes of teaching -- at an MAA, etc., meeting in

   ** Burlington, VT on May 30-31, 2008, **

 please send me an email.Certainly people on the organizing committee
 for that meeting _may_ be interesting in putting together a Sage-related
 component, if there were a speaker or speakers available.

   -- William

 -


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[sage-devel] Re: newbie development questions

[Hamptonio]

Thanks for the blueprint! I knew most of that but it was very helpful
to see it all spelled out in order.
-Marshall

On Sep 20, 2:52 pm, Robert Miller [EMAIL PROTECTED] wrote:
 Maybe I can offer more words of advice. The source revision system
 used by sage is Mercurial:http://www.genunix.org/wiki/index.php/Mercurial
 The commands listed there have their equivalents in sage-land:
 $ hg ci
 becomes
 $ sage -hg ci
 The 'devel' directory contains all the different branches. When you
 are running sage, you are running a single branch. The link 'sage' in
 devel always points to the current branch. If you are running sage in
 a certain branch, the objects hg_sage, hg_doc, hg_extcode and
 hg_scripts correspond to Mercurial repositories for the main sage
 library (including graph.py), the documentation, external files
 (including our graph database ;) ), and scripts related to interfacing
 etc, respectively. I usually only work with hg_sage, which is what you
 want if you're editing graph.py.

 Maybe the easiest way to explain it is to describe a development cycle
 (the answer to your question #1 is at 4b):

 1. Download and install sage ( you may want to read your favorite
 Dickens novel while this is happening ;) )
 2. (Optional) do sage -upgrade if it has been a while since you did
 #1. This will download and install the latest packages, including the
 package for the main sage library. In other words, this will bring you
 up to date with the latest 'official' version. Sometimes this breaks,
 but don't panic-- most likely, you will just need to force some
 package to install again (mail the list at this point, probably).
 3. (Also optional) if you want the latest, bleeding edge, super-
 current code, you can also do hg_sage.pull() while you're running in
 the 'main' branch. I always like to have my main branch as up to date
 as possible, and do coding work on other branches, which brings us to:
 4. Editing and testing code:
 Suppose you have just done 1-3 in order. You are now ready to begin
 hacking! To follow a concrete example, we'll start from the beginning:
 4a. Create a branch you can safely hack in. If you simply run sage,
 you will be in the current branch, which is by dafault sage-main. Do:
 sage: hg_sage.clone('hackbranch')
 This will copy the current branch to a branch called 'hackbranch', as
 well as change the current branch to 'hackbranch'. Once the clone
 command finishes, you will already be in the new branch. You can
 verify this (or check what branch you are in whenever you like) by
 typing hg_sage.status(). This will show you what you have modified, as
 well as identify which branch you are in.
 4b. Switching between branches: Anytime you do
 $ sage -b branch,
 you will build the branch 'branch'. If you aren't editing the files in
 branch, you won't have access to the changes, since this also switches
 the current branch to 'branch'. After doing 4a, you are in the branch
 'hackbranch', so you shouldn't need to switch back and forth at all
 while you are working: the command
 $ sage -br
 will build and run the current branch.
 4c. Writing and testing code: now that you're this far, write some
 functions, doing sage -br to test them out. Once you're happy with the
 way the function works, write some doctests for the function and test
 them, for example:
 $ sage -t devel/sage-hackbranch/sage/graphs/graph.py
 This tells sage to do all the doctests in graph.py and report if any
 fail. Not specifying a file will test every file in sage! Note that
 this is equivalent to
 $ sage -t devel/sage/sage/graphs/graph.py,
 since hackbranch is the current branch, and the symbolic link 'sage'
 points to hackbranch.
 5. Check in your changes, and submit a patch:
 Once you have something that you definitely like, you should check in
 your changes. This is done by
 sage: hg_sage.ci()
 When you do this, you will be shown the changes you have made, so
 simply hit q when you're done looking at them. Then it will take you
 to a vi screen, or something similar. Insert an insightful comment,
 explaining what you have done, and save the file. Upon exit, Mercurial
 will do the rest- it records the change in the repository, so that you
 can share your changes with others, by:
 sage: hg_sage.bundle('blah')
 This creates a file called blah.hg, which contains the information of
 what you changed. You can unbundle a bundle, which applies the changes
 to a branch, via
 sage: hg_sage.apply('blah.hg').

 Note:
 You must check in your changes before any transaction. If you haven't
 checked in, and you try to do something else, Mercurial will
 automatically put you into 'checking-in' mode first.

 As far as the following, are you getting this error when you run the
 main branch of sage, before modification?



   2. Something seems wrong with my mercurial installation.  I can't figure
   out where something might be misconfigured, though.  I get errors about
   hgext/hct when using hg_sage inside of sage, but when running hg 

[sage-devel] Re: Interactive cells, GUIs, javascript, ...

[Hamptonio]

Yes, thanks, that example looks like it will help me a lot.

Btw, before reading William's instructions, I ran it without the -
python option and it seemed fine.  Does the -python option just turn
off the preparser?

Cheers,
Marshall

On Sep 14, 7:52 pm, William Stein [EMAIL PROTECTED] wrote:
 On 9/14/07, alex clemesha [EMAIL PROTECTED] wrote:

  I just posted a cleaned-up example of AJAX-twisted.web2-SAGE here:

 http://sage.math.washington.edu/home/agc/simple_ajax_twisted_sage.py

  just getting your hands dirty by messing with examples is best, then
  go to the books / google and learn about the details of the code.

  The script above pretty much gives you the simplest possible example
  of how to combine the technologies that make up the SAGE notebook.
  There is a tiny README at the top of the file.

 Thanks!  Great simple example.

 For the total newbie, the way to use it is to download
   simple_ajax_twisted_sage.py
 to a file on your computer, then type
 sage -python simple_ajax_twisted_sage.py
 and follow the directions, i.e. open your browser to localhost:8000.

 Make sure you aren't already running a sage notebook on that
 port.

 I'll put this in the SAGE_ROOT/examples directory so it comes with
 future versions of SAGE.

 William


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[sage-devel] Re: Interactive cells, GUIs, javascript, ...

[Hamptonio]

My impression is that recalculates on the fly, but until you stop
(moving a slider for example) it tries to do quick-and-dirty
computations and rendering.  This is pretty clear if you manipulate a
3D graph of a function f(x,y,a) with a the parameter - it doesn't even
draw the mesh until you let go of the slider.

-MH

On Sep 15, 10:51 am, Ted Kosan [EMAIL PROTECTED] wrote:
 Marshall wrote:
  Recently I started using Mathematica 6 in the computer labs of some
  courses I teach, and I cannot help but be impressed.  The new dynamic
  commands such as Manipulate are very impressive, and are perfect for
  teaching.

 I looked at Mathematica's new manipulate command and I am now
 wondering if it calculates the rendering data on-the-fly when the
 sliders are moved or does it precalculate the rendering data and then
 the sliders are used to navigate through this data?

 Ted


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[sage-devel] Interactive cells, GUIs, javascript, ...

[Hamptonio]

Recently I started using Mathematica 6 in the computer labs of some
courses I teach, and I cannot help but be impressed.  The new dynamic
commands such as Manipulate are very impressive, and are perfect for
teaching.  Before seeing how powerful it is, I had hoped to switch
from using mathematica to sage in the fall of 2008.  But now I am not
sure I can justisfy that switch or convince my colleagues it would
make sense.  (As an aside: assume for the sake of argument that my
department gets mathematica for free, which is true in a certain
bureaucratic sense).

For some sense of what mathematica can now do, check out:
http://www.wolfram.com/products/mathematica/newin6/content/DynamicInteractivity/.
I actually think its more impressive in person.

While I would like to help remedy the gap between sage and mathematica/
matlab in this respect, I am not sure how it would be done.  I am
learning a little about wxPython, but I don't think that would work
through the notebook at all, unless a program was created on the
server for download and byte-compilation by the client.  Does anyone
have any ideas? If javascript is a possibility, can someone recommend
a good reference for learning to use it for such complicated
purposes?  Or is java an option?

-Marshall


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[sage-devel] Re: Interactive cells, GUIs, javascript, ...

[Hamptonio]

 Isn't this exactly the sort of thing that javascript/AJAX is good at doing?
 When you move an html control the server is contacted for the updated
 output and it is displayed (by directly manipulating the DOM).  I'm sure
 it won't be as snappy as a purely local GUI (e.g., Mathematica), but it
 will work from anywhere over a web browser, which counts for a lot
 these days.

Well that's why I asked, I am ignorant about javascript/AJAX.  Can you
suggest a good reference?


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[sage-devel] Re: Interactive cells, GUIs, javascript, ...

[Hamptonio]

Yeah, I have used mathematica for 17 years and I've pushed it very
hard at times.  6.0 seems much buggier than previous releases, but
they added and rewrote so much that I am not that surprised.  I still
think its an amazing accomplishment, and for illustrating basic ideas
in calculus I don't think anything matches it.

I have submitted bugs to mathematica and gotten no response, so I know
what you mean there as well.

But I am committed to using and improving sage over the long haul,
don't get me wrong.  I think the superiority of the development model
will win on most fronts eventually.

Cheers,
Marshall

On Sep 14, 5:50 pm, Chris Chiasson [EMAIL PROTECTED] wrote:
 ... wait until you actually start pushing Mathematica, it gets
 sluggish on you, produces wrong results and/or crashes, and you
 receive apathy and blame dodging instead of tech support and bug
 fixing.

 On Sep 14, 3:31 pm, Hamptonio [EMAIL PROTECTED] wrote:

  Recently I started using Mathematica 6 in the computer labs of some
  courses I teach, and I cannot help but be impressed.  The new dynamic
  commands such as Manipulate are very impressive, and are perfect for
  teaching.  Before seeing how powerful it is, I had hoped to switch
  from using mathematica to sage in the fall of 2008.  But now I am not
  sure I can justisfy that switch or convince my colleagues it would
  make sense.  (As an aside: assume for the sake of argument that my
  department gets mathematica for free, which is true in a certain
  bureaucratic sense).

  For some sense of what mathematica can now do, check 
  out:http://www.wolfram.com/products/mathematica/newin6/content/DynamicInt
  I actually think its more impressive in person.

  While I would like to help remedy the gap between sage and mathematica/
  matlab in this respect, I am not sure how it would be done.  I am
  learning a little about wxPython, but I don't think that would work
  through the notebook at all, unless a program was created on the
  server for download and byte-compilation by the client.  Does anyone
  have any ideas? If javascript is a possibility, can someone recommend
  a good reference for learning to use it for such complicated
  purposes?  Or is java an option?

  -Marshall


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[sage-devel] Re: compiling on AIX/PowerPPC

[Hamptonio]

Oops, I am in the middle of giving the gcc-4.2.1 package a try.  I
hope I am using it correctly - I installed it, and then removed
everything from spkg/installed, and now I am recompiliing by using
make.  Will that rebuild with gcc-4.2.1? It looks like it from what
I can see during compilation.

If this doesn't help at all, I will try your suggestion of a local
binutils.

Thanks for the help,
Marshall

On Sep 10, 11:10 pm, mabshoff [EMAIL PROTECTED]
dortmund.de wrote:
 On Sep 10, 8:36 pm, Hamptonio [EMAIL PROTECTED] wrote:

  cat /etc/issue gives:

 Hello Marshall,



  Welcome to SUSE LINUX Enterprise Server 9 (x86_64) - Kernel \r (\l).

  The tail end of the polymake build, when it crashes, has the
  following:

  make[2]: Leaving directory `/home/bc1/hamptonm/sage-2.8.3.6/spkg/build/
  polymake-2.2.p2/build/modules/graph'
  g++   -I/home/bc1/hamptonm/sage-2.8.3.6/local/lib  -I/home/bc1/
  hamptonm/sage-2.8.3.6/local/lib  -o cayley_embedding
  cayley_embedding.o libpolytope.a ../../lib/libpoly.a  -lgmp
  collect2: ld terminated with signal 11 [Segmentation fault]

 Okay, this is not a gcc issue (at least the output makes it very
 unlikely), but that the linker shoots itself. Check with the sysadmin
 if there is a more current ld somewhere in the systems, otherwise
 compile your own binutils locally and make sure that they are in $PATH
 before the systems ld. Try again with that ld and let us know if the
 problem goes away. You should also make sure the polymake doesn't hard
 code the path to ld somewhere in the makefile in case the error
 doesn't go away with the new binutils.

  make[2]: *** [cayley_embedding] Error 1
  make[1]: *** [do_all] Error 2
  make[1]: Leaving directory `/home/bc1/hamptonm/sage-2.8.3.6/spkg/build/
  polymake-2.2.p2/build/apps/polytope'
  make: *** [all] Error 2
  cp: cannot create regular file `/home/bc1/hamptonm/sage-2.8.3.6/local/
  polymake/bin/polymake': No such file or directory
  Do not worry if there is an error message above, as long as the build
  says it worked below.
  Error building and installing polymake

  real6m1.033s
  user5m19.608s
  sys 0m31.232s

 Cheers,

 Michael


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[sage-devel] Python 3000 (aka 3.0)

[Hamptonio]

Many of you are probably already aware of this, but there is an early
alpha release of python 3000 that came out a couple of weeks ago.  I
thought that might be worth pointing out now so folks can take a look
and get used to it early.  The final release is tentatively scheduled
for late 2008:

http://www.python.org/download/releases/3.0/

I would think most of the python in sage is relatively clean code that
won't need a lot of changing, but it will help if we avoid conflicts
now.

-Marshall


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[sage-devel] Re: compiling on AIX/PowerPPC

[Hamptonio]

cat /etc/issue gives:

Welcome to SUSE LINUX Enterprise Server 9 (x86_64) - Kernel \r (\l).

The tail end of the polymake build, when it crashes, has the
following:

make[2]: Leaving directory `/home/bc1/hamptonm/sage-2.8.3.6/spkg/build/
polymake-2.2.p2/build/modules/graph'
g++   -I/home/bc1/hamptonm/sage-2.8.3.6/local/lib  -I/home/bc1/
hamptonm/sage-2.8.3.6/local/lib  -o cayley_embedding
cayley_embedding.o libpolytope.a ../../lib/libpoly.a  -lgmp
collect2: ld terminated with signal 11 [Segmentation fault]
make[2]: *** [cayley_embedding] Error 1
make[1]: *** [do_all] Error 2
make[1]: Leaving directory `/home/bc1/hamptonm/sage-2.8.3.6/spkg/build/
polymake-2.2.p2/build/apps/polytope'
make: *** [all] Error 2
cp: cannot create regular file `/home/bc1/hamptonm/sage-2.8.3.6/local/
polymake/bin/polymake': No such file or directory
Do not worry if there is an error message above, as long as the build
says it worked below.
Error building and installing polymake

real6m1.033s
user5m19.608s
sys 0m31.232s

On Sep 9, 10:35 pm, William Stein [EMAIL PROTECTED] wrote:
 On 9/9/07, Hamptonio [EMAIL PROTECTED] wrote:





  From the MSI webpage, it says the bladecenter is: ...a Linux Cluster
  from IBM. It is a IBM BladeCenter H with 307 LS 21 nodes. Each node
  has two dual-core 2.6 GHz AMD Opteron processors sharing 8 GB of
  memory.

  The interactive node that I can read /proc/cpuinfo on says there are 4
  cores, each with:
  vendor_id   : AuthenticAMD
  cpu family  : 15
  model   : 65
  model name  : Dual-Core AMD Opteron(tm) Processor 2218
  stepping: 2
  cpu MHz : 2600.209
  cache size  : 1024 KB

  uname -a:
  Linux blade288 2.6.5-7.244-smp #1 SMP Mon Dec 12 18:32:25 UTC 2005
  x86_64 x86_64 x86_64 GNU/Linux

 Which linux distribution is it?  Try

   cat /etc/issue

 It's probably SUSE, since that is listed in the gcc output below.

 Also, regarding polymake, maybe you should report what the
 error is when it builds?

 William





  Jobs are scheduled with something called PBS.

  Polymake fails to compile, which is bad news for me - although I
  haven't tried to install polymake on a fresh 2.8.4 install so it might
  be a more pervasive problem.

  One problem is that it looks like an older gcc, is this a problem(?):
  
  GCC Version
  gcc -v
  Reading specs from /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/specs
  Configured with: ../configure --enable-threads=posix --prefix=/usr --
  with-local-prefix=/usr/local --
  infodir=/usr/share/info --mandir=/usr/share/man --enable-languages=c,c+
  +,f77,objc,java,ada --disable
  -checking --libdir=/usr/lib64 --enable-libgcj --with-gxx-include-dir=/
  usr/include/g++ --with-slibdir
  =/lib64 --with-system-zlib --enable-shared --enable-__cxa_atexit
  x86_64-suse-linux
  Thread model: posix
  gcc version 3.3.3 (SuSE Linux)
  

  It would be very cool if I could use this machine for polytope/
  algebraic geometry/groebner basis stuff.  At the moment I am using it
  for pretty routine bioinformatics stuff that I can do without sage if
  necessary.

  -Marshall

 --
 William Stein
 Associate Professor of Mathematics
 University of Washingtonhttp://www.williamstein.org


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[sage-devel] Re: compiling on AIX/PowerPPC

[Hamptonio]

I didn't really try any further with the AIX compilation after
starting on the linux bladecenter.  I could try a bit if it is of
interest.

On the BladeCenter, only one test failed after upgrading to 2.8.4:

sage -t  devel/sage-main/sage/rings/real_rqdf.pyx
**
File real_rqdf.pyx, line 24:
sage: RQDF( 123.2) * RR (.543)
Expected:
66.897600624851281827432114309792736749325567465385058291
Got:
NaN
**
1 items had failures:
   1 of   9 in __main__.example_0
***Test Failed*** 1 failures.
For whitespace errors, see the file .doctest_real_rqdf.pyx



On Sep 8, 10:24 am, mabshoff [EMAIL PROTECTED]
dortmund.de wrote:
 On Sep 8, 4:33 pm, Hamptonio [EMAIL PROTECTED] wrote:

  It turns out that I also have access to a linux-based supercomputer,
  (an IBM BladeCenter with about 300 quad-processor nodes), which should
  be faster than the Power4 system anyway.  So I will give up, for the
  moment, trying to install sage on AIX.

 Ok, how far did you get?

   I have installed sage-2.8.3.6
  on the BladeCenter successfully, with the following make test
  failures:

  sage -t  devel/sage-main/sage/modular/modform/ambient_g1.py
  sage -t  devel/sage-main/sage/modular/modform/
  eisenstein_submodule.py
  sage -t  devel/sage-main/sage/modular/modform/submodule.py
  sage -t  devel/sage-main/sage/rings/real_rqdf.pyx
  Total time for all tests: 2137.4 seconds

  Probably some of those have been fixed in 2.8.4.

 Please do an ./sage -upgrade and then rerun the testsuite. If any of
 those persist we should fix them. There was a last minute 32 bit only
 regression at the very end of 2.8.4. It was so late that William
 respun the tarball ;)

  Now I'll have to learn more about DSage; I am not sure how to exploit
  all those processors the way I usually code.

  Cheers,
  Marshall

 Cheers,

 Michael


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[sage-devel] Re: compiling on AIX/PowerPPC

[Hamptonio]

From the MSI webpage, it says the bladecenter is: ...a Linux Cluster
from IBM. It is a IBM BladeCenter H with 307 LS 21 nodes. Each node
has two dual-core 2.6 GHz AMD Opteron processors sharing 8 GB of
memory.

The interactive node that I can read /proc/cpuinfo on says there are 4
cores, each with:
vendor_id   : AuthenticAMD
cpu family  : 15
model   : 65
model name  : Dual-Core AMD Opteron(tm) Processor 2218
stepping: 2
cpu MHz : 2600.209
cache size  : 1024 KB

uname -a:
Linux blade288 2.6.5-7.244-smp #1 SMP Mon Dec 12 18:32:25 UTC 2005
x86_64 x86_64 x86_64 GNU/Linux

Jobs are scheduled with something called PBS.

Polymake fails to compile, which is bad news for me - although I
haven't tried to install polymake on a fresh 2.8.4 install so it might
be a more pervasive problem.

One problem is that it looks like an older gcc, is this a problem(?):

GCC Version
gcc -v
Reading specs from /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/specs
Configured with: ../configure --enable-threads=posix --prefix=/usr --
with-local-prefix=/usr/local --
infodir=/usr/share/info --mandir=/usr/share/man --enable-languages=c,c+
+,f77,objc,java,ada --disable
-checking --libdir=/usr/lib64 --enable-libgcj --with-gxx-include-dir=/
usr/include/g++ --with-slibdir
=/lib64 --with-system-zlib --enable-shared --enable-__cxa_atexit
x86_64-suse-linux
Thread model: posix
gcc version 3.3.3 (SuSE Linux)


It would be very cool if I could use this machine for polytope/
algebraic geometry/groebner basis stuff.  At the moment I am using it
for pretty routine bioinformatics stuff that I can do without sage if
necessary.

-Marshall

On Sep 9, 10:19 am, William Stein [EMAIL PROTECTED] wrote:
 On 9/9/07, Hamptonio [EMAIL PROTECTED] wrote:



  On the BladeCenter, only one test failed after upgrading to 2.8.4:

  sage -t  devel/sage-main/sage/rings/real_rqdf.pyx
  **
  File real_rqdf.pyx, line 24:
  sage: RQDF( 123.2) * RR (.543)
  Expected:
  66.897600624851281827432114309792736749325567465385058291
  Got:
  NaN
  **
  1 items had failures:
 1 of   9 in __main__.example_0
  ***Test Failed*** 1 failures.
  For whitespace errors, see the file .doctest_real_rqdf.pyx

 What is the BladeCenter hardware-wise exactly?
 Failure of the above test is very weird/curious.

 William


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[sage-devel] Re: compiling on AIX/PowerPPC

[Hamptonio]

It turns out that I also have access to a linux-based supercomputer,
(an IBM BladeCenter with about 300 quad-processor nodes), which should
be faster than the Power4 system anyway.  So I will give up, for the
moment, trying to install sage on AIX.  I have installed sage-2.8.3.6
on the BladeCenter successfully, with the following make test
failures:

sage -t  devel/sage-main/sage/modular/modform/ambient_g1.py
sage -t  devel/sage-main/sage/modular/modform/
eisenstein_submodule.py
sage -t  devel/sage-main/sage/modular/modform/submodule.py
sage -t  devel/sage-main/sage/rings/real_rqdf.pyx
Total time for all tests: 2137.4 seconds

Probably some of those have been fixed in 2.8.4.

Now I'll have to learn more about DSage; I am not sure how to exploit
all those processors the way I usually code.

Cheers,
Marshall

On Sep 7, 1:50 pm, William Stein [EMAIL PROTECTED] wrote:
 On 9/7/07, Hamptonio [EMAIL PROTECTED] wrote:



  Thanks guys.  I can't use the notebook anyway from that machine, I
  would be running pre-written scripts to do heavy calculations.  It got
  far enough that I am hopeful I can get it to where it does what I
  need.

 Please post anything you figure out.  We would be very happy
 to have AIX officially supported one day!!

 William


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[sage-devel] compiling on AIX/PowerPPC

[Hamptonio]

Hi,

I am hoping to use sage on some supercomputers and/or clusters.
Currently I am trying to compile it on the IBM Power4 machine at the
Minnesota Supercomputing Center (see http://www.msi.umn.edu/power4/index.html
for some details on that).   Its about 300 Power4 processors running
AIX.

I just tried compiliing sage-2.8.3.6 on it, and it started off OK but
failed while compiling libgcrypt.  It seems this is often a difficult
package, since it looks like a sticking point on Solaris and cygwin as
well.  Is there a  way to build around that? Would it help to try an
earlier sage version?

Marshall Hampton


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[sage-devel] Re: compiling on AIX/PowerPPC

[Hamptonio]

Thanks guys.  I can't use the notebook anyway from that machine, I
would be running pre-written scripts to do heavy calculations.  It got
far enough that I am hopeful I can get it to where it does what I
need.

Cheers,
Marshall

On Sep 7, 11:10 am, mabshoff [EMAIL PROTECTED]
dortmund.de wrote:
 On Sep 7, 7:00 pm, Hamptonio [EMAIL PROTECTED] wrote:

  Hi,

  I am hoping to use sage on some supercomputers and/or clusters.
  Currently I am trying to compile it on the IBM Power4 machine at the
  Minnesota Supercomputing Center (seehttp://www.msi.umn.edu/power4/index.html
  for some details on that).   Its about 300 Power4 processors running
  AIX.

  I just tried compiliing sage-2.8.3.6 on it, and it started off OK but
  failed while compiling libgcrypt.  It seems this is often a difficult
  package, since it looks like a sticking point on Solaris and cygwin as
  well.  Is there a  way to build around that? Would it help to try an
  earlier sage version?

  Marshall Hampton

 Hey Marshall,

 I believe libgcrypt is only the openssl replacement. So if you have
 an openssl on that box you can probably ignore it. Do a touch in spkg/
 installed/name_of_spkg to skip over it. I also believe to recall that
 all the SLL stuff is only needed for the notebook, so I am fairly
 certain that you won't run your computations that way.

 I am not sure if AIX these days is pure 64 bit or a hyprid 32/64
 userspace. If it is pure 64 bit you shouldn't run into too much
 trouble. Let me know if you have any problems. I anybody has access to
 an AIX box for me I would be willing to get Sage to work on AIX, too -
 I just love UNIX :)

 Cheers,

 Michael


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[sage-devel] Re: Quitting ignored worksheet vs. long computations

[Hamptonio]

I agree.  I think a big selling point for sage is using the notebook
for teaching.  A related thing I would love to have someday is the
ability to control which users can see which worksheets, in a fine-
grained sense.  E.g., I would like to be able to assign students to
small groups, and have each group able to see the worksheets of other
group members but not the rest of the class, and then after some time
let everyone see all the worksheets.  The new notebook betas I have
seen get at least partway there.

On Aug 10, 2:59 pm, Jonathan Bober [EMAIL PROTECTED] wrote:
   Obviously, this option should not exist on servers that serve a wide
   range of users.
   It's really for people doing big computations on their own set of
   computers.

  OK.

 Just a thought - it might be even better to have this option available
 or not on a per-user basis. In fact, though I haven't used the notebook
 much, I imagine that it might be nice in general to have a way to assign
 different privileges to different users. (For example, perhaps user was
 ought to be able to run a computation on the public notebook on
 sage.math that is going use 100% load on 8 processors for 3 weeks,
 whereas user bober, if he exists, shouldn't be able to do that.)


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[sage-devel] Re: SAGE download stats -- how to increase SAGE usage?

[Hamptonio]

Anyone who is an academic using SAGE should try to give a little talk
on it to your department (unneccessary at UW of course).  I did this
and I generated a fair amount of interest from our grad students.  The
faculty weren't overwhelmed, they all wanted particular things that
sage currently lacks - an easy linear programming interface, support
for R, bifurcation analysis, etc.

I think the exhibit at the joint meetings will help a lot.  We should
do similar things at other meetings - I haven't had the time or energy
to do that yet, but after the joint meetings maybe it will be easier
for 1-2 people to set up a table at things like MathFest, SIAM,
Society for Mathematical Biology, local MAA meetings, whatever.

One of my goals is also to do more undergraduate research/development
work with sage.  One can view big unfergrad poster sessions as free
advertising, at least to an academic audience.

I agree with some other posters that eye-candy is crucial.  I think a
lot more could be done with Tachyon that might impress people.  Also,
exporting to PDF is very important I think, and currently seems a
little broken (although maybe I am not doing it right).

-Marshall

On Aug 7, 4:22 pm, William Stein [EMAIL PROTECTED] wrote:
 Hi Sage-Devel,

 The SAGE downloads during the last week are as follows:

 Linux Binary
 42
 OS X Binary
 42
 Source
 91
 VMware (= Windows)
 57

 Total .. 232

 The number of new downloads of SAGE per week have been roughly
 constant during the last 2-3 months.   The growth of SAGE is definitely
 not what I hoped for during my talk at SAGE Days 4.Does anybody
 have any good ideas about how to increase the number of people
 downloading SAGE?   My hope is that this question will spark a relaxed
 but enthusiastic and positive open-ended brainstorming thread in which
 a lot of crazy ideas appear.

 I'm laying a lot of groundwork (e.g., writing books, articles, etc.)
 and I think other people are (esp David Joyner), but there is probably
 much more that could be done.

 Please share your thoughts!

 -- William


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[sage-devel] Re: [Sage-announce] SAGE-2.7.1!

[Hamptonio]

And on a 1.5 Ghz G4 (rev 1.2):

real166m36.901s
user104m24.042s
sys 30m26.661s

-Marshall

On Jul 25, 8:28 pm, Justin C. Walker [EMAIL PROTECTED] wrote:
 On Jul 25, 2007, at 17:38 , William Stein wrote:



  On 7/25/07, Justin C. Walker [EMAIL PROTECTED] wrote:
  For the record: Built and installed on PowerPC/G5, MacBook Pro/Core
  Duo, MacBook Pro/Core 2 Duo.

  'sage -testall' ran to completion on
  G5: 3319 seconds
  Core 2 Duo: 1697 seconds
  Core Duo: 1951 seconds

  How long did each build take?

 G5:
 real101m59.112s
 user63m11.317s
 sys 29m51.753s

 Core 2 Duo:
 real67m0.881s
 user42m10.335s
 sys 18m52.443s

 Core Duo:
 real74m35.586s
 user48m30.320s
 sys 19m2.767s

 This is plain old 'make'.  I'll try it with an increased j
 invariant :-}

 Justin

 --
 Justin C. Walker, Curmudgeon at Large
 Institute for the Absorption of Federal Funds
 ---
 My wife 'n kids 'n dogs are gone,
 I can't get Jesus on the phone,
 But Ol' Milwaukee's Best is my best friend.
 ---


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[sage-devel] Re: SAGE Documentation brainstorming

[Hamptonio]

I would vote for putting that content in the Guided Tour part of the
tutorial.  I think the variety of documentation would be a little too
fragmented otherwise.  In my limited experience so far, new users of
sage can already be confused about where they should look things up.

-Marshall

On Jul 23, 5:51 am, David Joyner [EMAIL PROTECTED] wrote:
 Ted: Very very interesting. Thanks for the great comments and the
 offer to help.

 +++

 On 7/23/07, Ted Kosan [EMAIL PROTECTED] wrote:



  William wrote:

   I think SAGE might potentially greatly benefit from certain types of new
   documentation.  snip

  I have been thinking about the topic of SAGE's documentation for a
  couple of months now and here is what I have come up with so far.

  Before one can determine what SAGE's documentation should look like, I
  think that one must first try to gain an understanding of how the
  technologies that SAGE depends on ( and also technologies in general )
  are going to evolve over the next 20 years.  The most detailed
  projections I currently know of are contained the book The
  Singularity Is Near by Ray Kurzweil and if his projections are even
  partially correct, the world is going to undergo enormous changes over
  the next 20 years that will significantly impact SAGE on a number of
  levels.  I highly recommend that the members of the SAGE documentation
  team read this book ( or an equivalent ) before making a plan for
  SAGE's documentation so that projections about how SAGE is going to
  have to evolve to keep pace with these changes can be made.  My
  thought is that commercial mathematics software companies like Wolfram
  Research are making these kind of projections and I think that this
  should be done for SAGE too.

  Moving to more concrete issues, a weakness I have noticed in the
  documentation for most mathematics software that I have used is that
  it seems like it consists of shorthand explanations for the underlying
  topics that are being covered.  It feels like perhaps 80% of the
  documentation is simply missing.  The documentation is also not well
  organized and it tends to jump from topic to topic in a somewhat
  haphazard way.  I think the way that commercial software like
  Mathematica has overcome this weakness is that numerous people have
  written books and articles about Mathematica which attempt to explain
  it better than its standard documentation does.  Even though the core
  documentation is inefficient, I think that Mathematica has still been
  able to move forward because of the enormous amount of external
  support it receives.  I found Maxima's documentation to be fairly weak
  and TeXmacs' documentation was incomplete and confusing.   SAGE's
  documentation is actually pretty good and the support on its lists is
  excellent.

  My thoughts on making SAGE's documentation even better include
  developing a detailed topic dependency map for SAGE and then having
  the documentation conform to this map.  When a person initially
  encounters SAGE, the first thing I imagine them doing is locating the
  topic on the map that is of interest to them ( Calculus for example )
  and then navigating backwards through the map until they reach a level
  that matches their competency level.  They should then work forward
  through all of the documentation which exists between where their
  competency starts and the topic they are interested in.

  Here is an example of the map I have been using to develop what I have
  referred to in the support list as pre-SAGE educational materials:

 http://206.21.94.60/tkosan/misc/example_paths_map_v1.0.pdf

  This specific map contains some topics that are not directly related
  to SAGE, but hopefully it is still able to illustrate what a SAGE
  topic map might look like.

  As for the topics themselves, instead of being presented in shorthand
  form, I think topic documentation should be more complete with a clear
  explanation of the fundamental principles that underly the topic along
  with how SAGE can be used to work with these principles.  I have just
  begun working on the SAGE Beginner's Tutorial I had talked about on
  the support list and the first topic the tutorial is addressing are
  the fundamental programming skills that are needed to work with SAGE.
  Even in its early draft stage, I think it is able to serve as an
  illustration of what I mean about striving to provide clear
  explanations of the fundamental principles of a topic before
  discussing more advanced issues that are built on top of them:

 http://206.21.94.60/tkosan/misc/sage_tutorial_draft_v.26.pdf

  I also think that the documentation for each topic should have a
  section for more complete examples which include the context they were
  drawn from.  By context, I mean the type of information that is
  typically contained in word problems.  Here is an example from
  calculus:

  Problem xx: An open rectangular tank is to 

[sage-devel] Re: build test help?

[Hamptonio]

Everything built OK on a powerpc laptop running OS X 10.4.10.  The
import scipy.optimize was fine as well apart from some compiler
warnings:

sage: import scipy.optimize
/Users/mh/sage-2.0/local/lib/python2.5/site-packages/numpy/testing/
numpytest.py:634: DeprecationWarning: ScipyTest is now called
NumpyTest; please update your code
  DeprecationWarning)
Overwriting info=function info at 0xa573df0 from scipy.misc (was
function info at 0x9bde870 from numpy.lib.utils)

which I assume are expected.

make test gives the following failures:
sage -t  devel/sage-main/sage/functions/transcendental.py
sage -t  devel/sage-main/sage/matrix/matrix2.pyx
sage -t  devel/sage-main/sage/schemes/elliptic_curves/
ell_rational_field.py
sage -t  devel/sage-main/sage/schemes/elliptic_curves/
padic_lseries.py

-Marshall

On Jul 22, 8:30 pm, William Stein [EMAIL PROTECTED] wrote:
 Hi,

 This weekend Josh Kantor and I redid the new SAGE build system so that
   (1) it uses g95 instead of gfortran, and
   (2) it includes the g95 binaries (instead of downloading them during
 the build).

 It would be incredibly useful to Josh Kantor and I if a few of you
 could download the
 tarball here:

http://sage.math.washington.edu/home/was/sage2.7.1/

 extract it, type make, and let me know what happens.  I.e., does it
 build or not?
 I'm interested mainly in building on 64-bit linux installs, then
 32-bit linux installs,
 then os x (powerpc).   The output of make test, might also be
 interested, though I know
 that 2 or 3 tests will fail.   Another good test that scipy built
 correctly is that

 sage: import scipy.optimize

 doesn't bomb out.  (I know it bombs out on powerpc os x, and haven't figured 
 out
 why -- it should work on everything else).

 Many thanks for any build feedback.  And of course any comments about
 using g95, our whole build approach, etc., would be appreciated (the comments
 last week were very helpful -- there's no weird g2c ar stuff going on
 any more).

  -- William

 --
 William Stein
 Associate Professor of Mathematics
 University of Washingtonhttp://www.williamstein.org


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[sage-devel] sage 2.7 on ppc build problem

[Hamptonio]

Building from scratch on a ppc laptop, I run aground when it gets to
lapack.  I already had a gfortran installed which may be the problem.
Here are the errors I get at the end of the install attempt:

( cd INSTALL; make; ./testlsame; ./testslamch; \
  ./testdlamch; ./testsecond; ./testdsecnd; ./testversion )
gfortran -fPIC  -c lsame.f -o lsame.o
gfortran -fPIC  -c lsametst.f -o lsametst.o
gfortran  -o testlsame lsame.o lsametst.o
/usr/bin/ld: Undefined symbols:
__gfortran_store_exe_path
collect2: ld returned 1 exit status
make[3]: *** [testlsame] Error 1
/bin/sh: line 1: ./testlsame: No such file or directory
/bin/sh: line 1: ./testslamch: cannot execute binary file
/bin/sh: line 1: ./testdlamch: cannot execute binary file
/bin/sh: line 1: ./testsecond: No such file or directory
/bin/sh: line 1: ./testdsecnd: cannot execute binary file
/bin/sh: line 1: ./testversion: cannot execute binary file
make[2]: *** [lapack_install] Error 126
Error compiling lapack.


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[sage-devel] Re: popen3 deadlocks in polymake interface

[Hamptonio]

I have put a patch for this problem as sage-trac ticket 403:

http://sagemath.org:9002/sage_trac/ticket/403

I just used the subprocess module instead of popen3, and it seems to
have fixed the problem.

Similar code appears in three other places, but since I am not
familiar with those modules I did not try to fix them.  Problems with
popen3 seem to occur only if the process takes quite a while to
complete - about 10-15 minutes for the issue with polymake.  There
might also be some similar issues with popen2, which is more heavily
used.  Eventually these should probably all be changed to use
subprocess instead.

Search Source Code: popen3

   1. geometry/lattice_polytope.py
   2. geometry/polytope.py
   3. interfaces/ecm.py
   4. misc/hg.py

-Marshall

On Jul 9, 10:35 pm, Hamptonio [EMAIL PROTECTED] wrote:
 Recently I was doing some middleweight polytope calculations - meaning
 stuff that takes about 15 minutes to compute on a nice machine - and
 the convex_hull call to polymake began to hang at a certain point.
 The faster your machine, the bigger a polytope you need to reproduce
 this, but its a pretty robust bug.

 The problem seems to lie in some sort of deadlock with the popen3 call
 in the cmd method of the Polytope class in polytope.py.  I can fix
 this by simply deleting the error-checking code and moving the
 stdin.close() command - i.e. at the end of the cmd definition I have

 stdin, stdout, stderr = os.popen3(c)
 #stdin.close()
 #err = stderr.read()
 #if len(err)  0:
 #raise RuntimeError, err
 ans = stdout.read()
 if len(ans) == 0:
 raise ValueError, %s\nError executing polymake command
 %s%(
 err,cmd)
 stdin.close()
 self.__data = open(F).read()
 return ans

 and it seems to work fine on my bigger polytopes.  In searching the
 source, I noticed that there are similar constructions elsewhere, and
 so this may be a pervasive problem.

 I have become confused trying to understand the finer points of popen,
 popen2, popen3, popen4, and popen2.Popen3, subprocess,
 os.system, python seems to have a bewildering array of such
 functions.  I would be interested in any opinions.  Doug Hellman seems
 to have some clearly written thoughts up at

 http://blog.doughellmann.com/2007/07/pymotw-subprocess.html

 on subprocess.

 If I can get a little help and insight on this I will try to write a
 patch.

 -Marshall


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[sage-devel] Re: predefined symbolic variable names

[Hamptonio]

I would be willing to chip in some effort on the mathematica.sage
file, although not in the very near future.  I plan to begin migrating
my undergraduate courses to sage from mathematica for fall semester
2008.  I hope to convince other faculty do to the same, but it won't
be easy.  I am mainly interested in the mathematica.sage effort as a
way to make it easier for my colleagues to port their labs to sage.

-Marshall

On Jul 11, 1:32 pm, William Stein [EMAIL PROTECTED] wrote:
 On 7/11/07, Joel B. Mohler [EMAIL PROTECTED] wrote:



  I think the init file idea needs to be pushed harder.  I already do this 
  and the
  flexibility is absolutely critical to my happiness.  I even have my init 
  file
  call another file in the current directory so I can have different things
  defined depending on which project I'm working on (Of course, that idea 
  doesn't
  have much merit from the notebook).

  We could publish init files for various CAS's.  I realize we can't match
  semantics, but for myself I don't think the semantics are the hard part -- 
  the
  hard part is remembering the new function name.

  We could also publish init files for various branches of mathematics -- 
  applied,
  number theory, etc.

  I realize this could lead to support questions when people do dumb things in
  their init file, but I think it is easily worth to publish this huge amount 
  of
  flexibility.

 I think this is definitely worth a try, and will probably be pretty fun to do.
 It may or may not be successful (e.g., if you type foo? the examples could
 easily fail because of how you customized your session -- this could be
 very bad).  It would make sense to do something like this at least
 for the following systems, in order of priority:
1. mathematica
2. matlab
3. maple
4. magma
5. pari
6. gap

 For some of these, it is hard to think of where to begin, since there are
 thousands of commands (e.g., matlab has over 8000 commands).
 One could begin by creating a mathematica.sage that defines common
 commands like
Integrate
Sin
Cos
Derivative (?)
N

 etc., with the case conventions of mathematica.  This file could look
 like:

Integrate = integrate
Sin = sin
Cos = cos
...
N = RDF# or something more sophisticated?? I.e., take number of
 digits as input...
...

 Thoughts?   Volunteers?

 William


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[sage-devel] Re: predefined symbolic variable names

[Hamptonio]

Well the biggest reason is just inertia: my department has been using
mathematica for years, and everyone has a full set of computer labs
and handouts and demos already done in mathematica.  Why learn a new
system and have to port everything over?  We don't even directly pay
for the license as a department, as far as I know, so there just isn't
much motivation to change.  My biggest selling points for sage are
that the students can get it for their own computers for free, and I
can set up a server so they can access it online.
So realistically, I expect no one else will want to use sage in fall
2008. But if I get good feedback from students, and offer to help port
mathematica labs to sage, maybe I can win some folks over.
Incidentally, this is one reason I think it is crucial to get an R
interface for sage ASAP.  I think I could convince our stats faculty
to give sage a try if it had R, and then I could argue that we should
use sage for consistency across the department; it would also start
exposing our grad students to sage.
-Marshall

On Jul 11, 2:38 pm, William Stein [EMAIL PROTECTED] wrote:
 On 7/11/07, Hamptonio [EMAIL PROTECTED] wrote:



  I would be willing to chip in some effort on the mathematica.sage
  file, although not in the very near future.  I plan to begin migrating
  my undergraduate courses to sage from mathematica for fall semester
  2008.  I hope to convince other faculty do to the same, but it won't
  be easy.  I am mainly interested in the mathematica.sage effort as a
  way to make it easier for my colleagues to port their labs to sage.

 Thanks!  Let me know what happens.  And definitely feel free to
 post a list of the reasons migrating from Mathematica to SAGE
 definitely won't be easy.  Obviously, bad 3d graphics support
 is one reason, but I would love to hear about any and all other
 reasons as they arise.  I want to be as aware as possible about them,
 so we have some hope of addressing as soon as possible.

  -- William


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[sage-devel] Re: predefined symbolic variable names

[Hamptonio]

I agree that RR(expr) works well as an N(expr) replacement.  It would
be nice for mathematica migrators to actually have N() defined,
although that does clutter up the namespace more.

I hadn't realized that mathematica was so unusual in its behavior in
this regard.  However, there's another environment that behaves that
way - python itself!  If you multiply 1.0*1, the answer is a float.

-Marshall

On Jul 10, 1:39 am, Nick Alexander [EMAIL PROTECTED] wrote:
 Ted Kosan [EMAIL PROTECTED] writes:
  In SAGE, I have ended up using the numerical_approx() method as an
  equivalent to N[] and //N in Mathematica, but I have found it not to
  be as quick and easy to use.

 I use RR(expr) and find it at least as usable as the N[expr] notation
 of Mathematica.

 Nick


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[sage-devel] Re: predefined symbolic variable names

[Hamptonio]

Perhaps it would help to start with a fairly clean namespace and then
have some modules which would imitate various environments.  So for
example, there might be a simple command like:

set_style('mathematica')

which would define the N() function, and some other favorite
mathematica functions.  Conceivably it would even change the behavior
of symbolic objects so that 1.0*sin(1) would evaluate to a numerical
answer, although that seems like more of a pain to implement.

-Marshall

On Jul 10, 10:58 am, [EMAIL PROTECTED] wrote:
 -1 to single-letter functions in the namespace.

 Also note that RDF(expr) works too, and is marginally to extremely faster, 
 depending on the precision that RR is using.

 On Tue, 10 Jul 2007, Hamptonio wrote:

  I agree that RR(expr) works well as an N(expr) replacement.  It would
  be nice for mathematica migrators to actually have N() defined,
  although that does clutter up the namespace more.

  I hadn't realized that mathematica was so unusual in its behavior in
  this regard.  However, there's another environment that behaves that
  way - python itself!  If you multiply 1.0*1, the answer is a float.

  -Marshall

  On Jul 10, 1:39 am, Nick Alexander [EMAIL PROTECTED] wrote:
  Ted Kosan [EMAIL PROTECTED] writes:
  In SAGE, I have ended up using the numerical_approx() method as an
  equivalent to N[] and //N in Mathematica, but I have found it not to
  be as quick and easy to use.

  I use RR(expr) and find it at least as usable as the N[expr] notation
  of Mathematica.

  Nick


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[sage-devel] new version of phcpack interface (phc.py)

[Hamptonio]

I have heavily altered the PHCpack interface for sage, and posted the
relevant files as sage-trac 399:

http://www.sagemath.org:9002/sage_trac/ticket/399

Comments are very welcome.

In order to get it working, I have temporarily removed some potential
functionality - the ability to pass in arbitrary command lists to
phc.  On the positive side, what is there works, and I have added some
parsing of the raw phc output to get at the final complex solutions of
the system.  Here is part of the Examples section to give an idea of
how it works:

EXAMPLES:
sage: from sage.interfaces.phc import phc
sage: R.x,y = PolynomialRing(QQ,2)
sage: testsys = [x^2 + 1, x*y - 1]
sage: v = phc.blackbox(testsys, R)
sage: v.solutions()
[[1.00*I, -1.00*I], [-1.00*I,
1.00*I]]
sage: v.solution_dicts()
[{y: 1.00*I, x: -1.00*I}, {y:
-1.00*I, x: 1.00*I}]
sage: residuals = [[test_equation.subs(sol) for test_equation in
testsys] for sol in v.solution_dicts()]
sage: residuals
[[0, 0], [0, 0]]

-Marshall Hampton


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[sage-devel] Re: Implementing the Tropical Semiring

[Hamptonio]

I have some interest in such an implementation, although more as a
user of it than an architect/developer.  I would encourage you to do
it in sage and not GAP.

I can at least commit to help testing any code you work on.

There might be some helpful overlap with Anders Jensen's gfan program,
which already has a partial interface to sage written.  Gfan is
capable of some tropical computations, although I am not sure exactly
what is externally callable.  If you are unfamiliar with gfan, perhaps
a good place to start is:
http://arxiv.org/abs/math/0507563

Cheers,
Marshall Hampton

On Jul 2, 10:06 am, [EMAIL PROTECTED] wrote:
 I am in need of free software that will work with polynomials over the
 Tropical semiring.  I was unable to find anything suitable, so I
 thought I would take a stab at implementing them in sage.  I have just
 barely found sage though, so I don't yet understand it entirely.  This
 list seemed very friendly so I thought I would ask a few questions:

 1. Is this already implemented under a different name (it's also
 called min-plus algebra), or someplace that I overlooked?

 2. Is it reasonable to implement in sage?  In particular one thing
 that I think may be difficult is that the polynomial 'x+3' is really
 '0*x+3' since 0 is the multiplicative identity (infinity is the
 additive identity).

 3. Where is the best place to go to find out how to develop a sage
 package etc.  Also good tutorials for python would be appreciated,
 since I have never done any python development.  I do have experience
 in a variety of other languages.

 4. Would this be better to implement in something like GAP (so that
 GAP users can take advantage of it as well) and then access it through
 sage?

 Thanks for your comments,
 Ivan Andrus

 --
 MacMail - the Webmail service especially for Mac users 
 worldwidehttp://www.macmail.com


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[sage-devel] Re: Teach a man to fish

[Hamptonio]

I have put some candidate code up on the sage-trac site.  I had some
funny errors trying to upload a patch for the calculus all.py, so I
gave up.  It just needs a line like

from desolvers import desolve, desolve_laplacian, desolve_system

I got somewhat hung up on thinking about how to change these functions
so that they give better output - easier to read at least, but I have
shelved that for now.  I want to focus on rewriting the PHCpack
interface, and then I plan on returning to desolvers and the
plot_vector_field command.  All I did for now was get the tests to
pass.

The trac ticket is 398:
http://www.sagemath.org:9002/sage_trac/ticket/398

-Marshall

On May 9, 7:08 am, David Joyner [EMAIL PROTECTED] wrote:
 Since you asked:-)

 A small project would be to look at the DE-related code
 in the *.sage files contained in SAGEHOME/examples/calculus
 and create a SAGE/Python module from them. They may be fine
 as is or may need some changes (I wrote them but would very
 much appreciate another person's perspective and criticism).

 As far as creating a hg patch, the 
 sectionhttp://www.sagemath.org/doc/html/prog/node68.html
 says it all. Basic steps:

 1) create a clone
 2) do your work
 3) run doc tests on each file (sage -t fullpath/filename.py )
 4) if you prefer emacs to vi, type export EDITOR=emacs
 (assuming you use bash)
 5) hg_sage.add([filenames]) to add new files to your repository
 6) hg_sage.commit()
 7) hg_sage.bundle('mybundle') (this creates the patch mybundle.hg
 in SAGEHOME or SAGEHOME/devel, I forget which)

 On 5/9/07, Hamptonio [EMAIL PROTECTED] wrote:



  Hi,

  Now that my semester is winding down, I would like to learn to
  contribute more actively to SAGE.  I do need a little hand-holding
  when it comes to hg and submitting patches.  I think it would be best
  if I started with a very small project to learn the mechanics of
  contributing, and then I will get more ambitious.

  Perhaps someone can suggest a little project?  Currently I am most
  interested and/or competent in the following areas:

  1) Integrating polymake/cddlib.  I do a lot of heavy-duty exact convex
  hull computations.  I would like some sort of linear programming
  capability in SAGE - cddlib supplies that but I am not sure it is a
  great package for that.

  2) Integrating PHCpack.  I have already done a crude rewrite of
  phcparser.py so that it works in blackbox mode (the '-b' option).  It
  would be nice to add some graphical functions as in PHCmaple -
 http://www.ima.umn.edu/~leykin/PHCmaple/.

  3) Integrating/maintaining the biopython package.  Probably no one
  else here cares about that but I'll toss it out just in case.  I teach
  a bioinformatics course and I want to use SAGE for my course next
  spring.

  4) Differential equations.  I teach ODEs and linear algebra a lot, and
  I would like to someday incorporate SAGE into my teaching.

  Cheers,
  Marshall Hampton
  University of Minnesota Duluth


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[sage-devel] flatten list command

[Hamptonio]

I often want to flatten nested lists, and such a command (like
Mathematica's Flatten) does not seem to be present in sage.  I propose
adding such a command into the misc.py.  I am appending some candidate
code below, and I will also put it on sage-trac (http://
www.sagemath.org:9002/sage_trac/ticket/395)

Here's my function:

def flatten(in_list, ltypes=(list, tuple)):

Flattens a nested list.

INPUT:
in_list -- a list or tuple
ltypes -- optional list of particular types to flatten

OUTPUT:
a flat list of the entries of in_list

EXAMPLES:
sage: flatten([[1,1],[1],2])
[1, 1, 1, 2]
sage: flatten((['Hi',2,vector(QQ,[1,2,3])],(4,5,6)))
['Hi', 2, (1, 2, 3), 4, 5, 6]
sage: flatten((['Hi',2,vector(QQ,[1,2,3])],
(4,5,6)),ltypes=(list, tuple,
sage.modules.vector_rational_dense.Vector_rational_dense))
['Hi', 2, 1, 2, 3, 4, 5, 6]

index = 0
new_list = [x for x in in_list]
while index  len(new_list):
if not new_list[index]:
new_list.pop(index)
continue
while isinstance(new_list[index], ltypes):
new_list[index : index + 1] = list(new_list[index])
index += 1
return new_list


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[sage-devel] Re: flatten list command

[Hamptonio]

To be honest I didn't give it much thought.  This is modified from the
simplest code I could find that did the job.

flatten(GF(5)) does return [0,1,2,3,4], while flatten([GF(5)]) returns
[Finite Field of size 5].  However, you can do:

flatten([GF(5)],ltypes = (list, tuple,
sage.rings.finite_field.FiniteField_prime_modn))

which returns [0,1,2,3,4].

Since I did a fair amount of python programming before using sage, I
guess I tend to favor code that is purely pythonic, which might be
against the grain of most sage development.

-Marshall

On Jun 28, 10:23 am, Nick Alexander [EMAIL PROTECTED] wrote:
  def flatten(in_list, ltypes=(list, tuple)):
  ...
  ltypes -- optional list of particular types to flatten

 Could you elaborate on the decisions made around iterators here?  I
 can see that flatten([GF(5)]) could be tricky -- is it [GF(5)] or [0,
 1, 2, 3, 4]?

 Nick


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[sage-devel] Re: flatten list command

[Hamptonio]

Interesting.  I think I originally ripped mine off from one of the
comments at:

http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/363051

although I've tried to make mine more readable.

The thread you linked to has the apparent winner of Ron Adams:

def flatten(seq):
 s = []
 while seq:
 while isinstance(seq[0],list):
 seq = seq[0]+seq[1:]
 s.append(seq.pop(0))
 return s

But that modifies the input, which I consider to be very undesirable.
The version I'm using does avoid recursive function calls.  Its not
clear to me at the moment how to speed it up significantly while
avoiding the input modification.

-Marshall

On Jun 28, 3:15 pm, [EMAIL PROTECTED] wrote:
 There's a good discussion on the python mailing list regarding flatten:

 http://mail.python.org/pipermail/python-list/2005-July/330367.html

 particularly, it's got a number of different implementations, and benchmarks.

 On Thu, 28 Jun 2007, Hamptonio wrote:

  I often want to flatten nested lists, and such a command (like
  Mathematica's Flatten) does not seem to be present in sage.  I propose
  adding such a command into the misc.py.  I am appending some candidate
  code below, and I will also put it on sage-trac (http://
 www.sagemath.org:9002/sage_trac/ticket/395)

  Here's my function:

  def flatten(in_list, ltypes=(list, tuple)):
 
 Flattens a nested list.

 INPUT:
 in_list -- a list or tuple
 ltypes -- optional list of particular types to flatten

 OUTPUT:
 a flat list of the entries of in_list

 EXAMPLES:
 sage: flatten([[1,1],[1],2])
 [1, 1, 1, 2]
 sage: flatten((['Hi',2,vector(QQ,[1,2,3])],(4,5,6)))
 ['Hi', 2, (1, 2, 3), 4, 5, 6]
 sage: flatten((['Hi',2,vector(QQ,[1,2,3])],
  (4,5,6)),ltypes=(list, tuple,
  sage.modules.vector_rational_dense.Vector_rational_dense))
 ['Hi', 2, 1, 2, 3, 4, 5, 6]
 
 index = 0
 new_list = [x for x in in_list]
 while index  len(new_list):
 if not new_list[index]:
 new_list.pop(index)
 continue
 while isinstance(new_list[index], ltypes):
 new_list[index : index + 1] = list(new_list[index])
 index += 1
 return new_list


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[sage-devel] Re: flatten list command

[Hamptonio]

Whoops! - sorry about the misreporting on the GF(5) behavior.  I was
playing around with lots of similar versions and I must have gotten
confused.

That extra loop you deleted was put in to avoid errors on weird cases
like: flatten([[]]), which gives an IndexError: list index out of
range if the extra loop is removed.   But it was badly done.  Here is
another attempt which I think behaves OK on nested empty lists and
things that evaluate to False:

def flatten(in_list, ltypes=(list, tuple)):

Flattens a nested list.

INPUT:
in_list -- a list or tuple
ltypes -- optional list of particular types to flatten

OUTPUT:
a flat list of the entries of in_list

EXAMPLES:
sage: flatten([[1,1],[1],2])
[1, 1, 1, 2]
sage: flatten([[1,2,3], (4,5), [[[1],[2)
[1, 2, 3, 4, 5, 1, 2]

In the following example, the vector isn't flattened because
it is not given in the ltypes input.
sage: flatten((['Hi',2,vector(QQ,[1,2,3])],(4,5,6)))
['Hi', 2, (1, 2, 3), 4, 5, 6]

We give the vector type and then even the vector gets flattened:
sage: flatten((['Hi',2,vector(QQ,[1,2,3])], (4,5,6)),
ltypes=(list,
tuple,sage.modules.vector_rational_dense.Vector_rational_dense))
['Hi', 2, 1, 2, 3, 4, 5, 6]

We flatten a finite field.
sage: flatten(GF(5))
[0, 1, 2, 3, 4]
sage: flatten([GF(5)])
[Finite Field of size 5]
sage: flatten([GF(5)], ltypes = (list, tuple,
sage.rings.finite_field.FiniteField_prime_modn))
[0, 1, 2, 3, 4]


index = 0
new_list = [x for x in in_list]
while index  len(new_list):
while isinstance(new_list[index], ltypes):
if len(new_list[index]) != 0:
new_list[index : index + 1] = list(new_list[index])
else:
new_list.pop(index)
break
index += 1
return new_list


On Jun 28, 7:40 pm, William Stein [EMAIL PROTECTED] wrote:
 On 6/28/07, Hamptonio [EMAIL PROTECTED] wrote:

  Interesting.  I think I originally ripped mine off from one of [...]

 Hi,

 I've incorporated this into SAGE as a patch.  The main things I did
 were add more examples and delete part of the function which I
 consider stupid.  E.g., you wrote flatten(GF(5)) does return [0,1,2,3,4]
 but in fact it doesn't -- it returns [1,2,3,4] -- since it removes all things
 that evaluate to False because of this code:

if not new_list[index]:
new_list.pop(index)
continue

 So I deleted that code, since I see no reason for it, and all the examples
 work fine without it.

 Comments?

 William

 [EMAIL PROTECTED]:~/d/sage/sage/misc$ hg export 5194
 # HG changeset patch
 # User William Stein [EMAIL PROTECTED]
 # Date 1183076918 25200
 # Node ID 25f23d18288895f46a6aaa2bd8ef147cde5e31f3
 # Parent  65b460226d8173061face0c810fa6cffaf20dc08
 Marshall Hampton's flatten command (suitably modified)

 diff -r 65b460226d81 -r 25f23d182888 sage/misc/all.py
 --- a/sage/misc/all.py  Thu Jun 28 16:17:05 2007 -0700
 +++ b/sage/misc/all.py  Thu Jun 28 17:28:38 2007 -0700
 @@ -6,6 +6,8 @@ from misc import (alarm, srange, xsrange
repr_lincomb, tmp_dir, tmp_filename,
DOT_SAGE, SAGE_ROOT, SAGE_URL, SAGE_DB, SAGE_TMP,
is_32_bit, is_64_bit, newton_method_sizes)
 +
 +from flatten import flatten

  from remote_file import get_remote_file

 diff -r 65b460226d81 -r 25f23d182888 sage/misc/flatten.py
 --- /dev/null   Thu Jan 01 00:00:00 1970 +
 +++ b/sage/misc/flatten.py  Thu Jun 28 17:28:38 2007 -0700
 @@ -0,0 +1,42 @@
 +def flatten(in_list, ltypes=(list, tuple)):
 +   
 +   Flattens a nested list.
 +
 +   INPUT:
 +   in_list -- a list or tuple
 +   ltypes -- optional list of particular types to flatten
 +
 +   OUTPUT:
 +   a flat list of the entries of in_list
 +
 +   EXAMPLES:
 +   sage: flatten([[1,1],[1],2])
 +   [1, 1, 1, 2]
 +   sage: flatten([[1,2,3], (4,5), [[[1],[2)
 +   [1, 2, 3, 4, 5, 1, 2]
 +
 +   In the following example, the vector isn't flattened because
 +   it is not given in the ltypes input.
 +   sage: flatten((['Hi',2,vector(QQ,[1,2,3])],(4,5,6)))
 +   ['Hi', 2, (1, 2, 3), 4, 5, 6]
 +
 +   We give the vector type and then even the vector gets flattened:
 +   sage: flatten((['Hi',2,vector(QQ,[1,2,3])], (4,5,6)),
 ltypes=(list, tuple,sage.modules.vector_rational_dense.Vector_rational_dense))
 +   ['Hi', 2, 1, 2, 3, 4, 5, 6]
 +
 +   We flatten a finite field.
 +   sage: flatten(GF(5))
 +   [0, 1, 2, 3, 4]
 +   sage: flatten([GF(5)])
 +   [Finite Field of size 5]
 +   sage: flatten([GF(5)], ltypes = (list, tuple,
 sage.rings.finite_field.FiniteField_prime_modn))
 +   [0, 1, 2, 3, 4]
 +
 +   
 +   index = 0
 +   new_list = [x for x in in_list]
 +   while index  len(new_list):
 +   while isinstance(new_list[index], ltypes

[sage-devel] Re: SAGE notebook 2

[Hamptonio]

Hi,

I am getting some funny errors now on the new notebook.  In fact, the
first thing I tried failed, defining the following ring:

R7grev.w,r12,r13,r23,m1,m2,m3 = MPolynomialRing(QQ,7,order =
degrevlex)

gives the errors:

./t: line 2: syntax error near unexpected token `('
./t: line 2: `R7grev.w,r12,r13,r23,m1,m2,m3 =
MPolynomialRing(QQ,7,order = degrevlex)'

I get similar errors on simpler definitions too.

Cheers,
Marshall


On Jun 26, 1:35 am, William Stein [EMAIL PROTECTED] wrote:
 Hi,

 I fixed a number of issues with the notebook (see changelog below) and
 just made the changed version live.  If you're closing following this thread,
 please let me know if anything seems seriously broken as a result (I'm 
 suffering
 from the lack of a unit testing framework for the notebook -- help, Yi!).

   -- William

 ---

 changeset:   5127:5c77fa34a543
 tag: tip
 user:William Stein [EMAIL PROTECTED]
 date:Tue Jun 26 00:20:29 2007 -0700
 summary: make changing evaluation system much clearer

 changeset:   5126:659b25b295df
 user:William Stein [EMAIL PROTECTED]
 date:Tue Jun 26 00:06:37 2007 -0700
 summary: Unified the save button in text edit mode.

 changeset:   5125:5138ee7b363b
 user:William Stein [EMAIL PROTECTED]
 date:Mon Jun 25 23:54:02 2007 -0700
 summary: tiny fixes for some possible security problems

 changeset:   5124:550f2062e641
 user:William Stein [EMAIL PROTECTED]
 date:Mon Jun 25 23:47:43 2007 -0700
 summary: Add download link for published worksheets.

 changeset:   5123:2b6c13c613e6
 user:William Stein [EMAIL PROTECTED]
 date:Mon Jun 25 23:40:26 2007 -0700
 summary: Added 0 as a possible rating and user comments in ratings.

 changeset:   5122:0cb80f3e387f
 user:William Stein [EMAIL PROTECTED]
 date:Mon Jun 25 22:48:49 2007 -0700
 summary: fix output bug and error in revisions.

 changeset:   5121:ed788cc5989d
 user:William Stein [EMAIL PROTECTED]
 date:Mon Jun 25 22:46:17 2007 -0700
 summary: SAGE Notebook: Fix large output link.

 changeset:   5120:172b14df6514
 user:William Stein [EMAIL PROTECTED]
 date:Mon Jun 25 22:27:05 2007 -0700
 summary: Get rid of insane stupid global username variable in
 twist.py, which was just there
 to get the ball rolling.


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[sage-devel] Re: a SD4 video

[Hamptonio]

Small but the sound is good.  Thanks for putting it up, I was
disappointed I couldn't make it to SD4 and videos help a lot.

-MH

On Jun 22, 2:01 pm, William Stein [EMAIL PROTECTED] wrote:
 What do you guys think of this video:

 http://sage.math.washington.edu/home/was/tmp/sd4/

 Size?  Format? Etc.

 --
 William Stein
 Associate Professor of Mathematics
 University of Washingtonhttp://www.williamstein.org


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[sage-devel] Re: SAGE notebook 2

[Hamptonio]

Nils Bruin has addressed most of the points I was going to make, but I
did notice one minor thing in testing the new notebook - it actually
effects the old one too:

If you have a comment with a question mark, the question mark gets
parsed by the help system.  I consider this undesirable behavior.  For
example, the line

# Is this a bug?

has output:

No object 'sh.bug' currently defined.

...which certainly isn't what I would expect.

Cheers,
Marshall Hampton

On Jun 21, 12:52 pm, William Stein [EMAIL PROTECTED] wrote:
 Hi,

 I spent the last 3 days synthesizing the ideas from the workshop and writing
 a lot of code and have put together the first version of the SAGE Notebook 
 2.
 I've posted a server running it here:

https://sage.math.washington.edu:8102/

 Unless anybody *else* wants to put a lot of hard work into this now, it is in
 feature freeze.  I implemented the minimum of what I really wanted.

 I'm sure there are *lots* of bugs in the notebook.  I don't know of any
 in particular, but I wrote a lot of new code, so there are bound to be
 numerous issues.

 I want to use this new notebook server in a class for high school
 students that I'm teaching next week, so I would be very grateful if
 people could try it out and report bugs or points about the design
 that they find very confusing.  You can also report features you wish
 were there, but I'm not going to implement anything new on the notebook
 myself for a while.

 By the way, the general document model greatly resembles Google
 Documents, as I'm sure will be clear once you try the notebook out.

  --  William

 Important note -- I implemented a secure separate process model for
 the notebook.  Unfortunately, ssh doesn't work at all in the chroot jail
 that the server runs in (Bobby -- why!?  -- just create two new accounts
 with dumb passwords -- it isn't possible to ssh from one to the other),
 so I can't use it in the chroot jail yet.   So it is trivial to vandalize the
 server...

 --
 William Stein
 Associate Professor of Mathematics
 University of Washingtonhttp://www.williamstein.org


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[sage-devel] Re: printing MPolynomialRing

[Hamptonio]

I agree, the singular output is nice.I don't use such big rings,
but I very often use two blocks: variables and parameters.

On Jun 19, 7:26 am, Martin Albrecht [EMAIL PROTECTED]
wrote:
 On Tuesday 19 June 2007 14:55, Martin Albrecht wrote:

  Hi there,

  I would like to gather some options on the way multivariate polynomial
  rings are printed in SAGE.

 Sorry for replying to myself, I meant to gather opinions not options of
 course. In case you wondered ...

 Martin

 --
 name: Martin Albrecht
 _pgp:http://pgp.mit.edu:11371/pks/lookup?op=getsearch=0x8EF0DC99
 _www:http://www.informatik.uni-bremen.de/~malb
 _jab: [EMAIL PROTECTED]


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[sage-devel] Re: Dynamical systems support

[Hamptonio]

http://www.cam.cornell.edu/~rclewley/cgi-bin/moin.cgi/ProjectOverview#head-702b485f9c8e1152ee4a6cd65f2cc5974da6a8ea

There's a link to the project overview, I forgot to put it in the
original post.

On Jun 8, 1:14 pm, Hamptonio [EMAIL PROTECTED] wrote:
 Hi,

 I was just at the SIAM dynamical systems meeting in Snowbird, and it
 got me curious about how support for dynamical systems could be put
 into sage.  Unfortunately, the research I was presenting was done
 entirely in Mathematica, so I couldn't give sage a lot of press.  I
 did show sage to various people, and one of them pointed me to
 PyDSTool, a python-based project for dynamical systems.  It is
 currently in a beta state, but it looks like a healthy project that
 might already be useful.

 The other options are AUTO (written in fortran, and I'm not sure what
 the license is), or XPP (in C).  Apparently XPP has some AUTO-calling
 capability as well.

 I would be interested in comments familiar with these projects, and
 what their licenses really are.

 -Marshall


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[sage-devel] plot_vector_field

[Hamptonio]

At the moment, plot_vector_field is only capable of plotting product
vector fields, which is unacceptable for my use of it in an ODE
class.  Since it is a crucial issue for my use, I plan on trying to
extend it to handle arbitrary 2d fields, unless Alex Clemesha feels
like doing it for me.  Any tips are appreciated.

actually I think my first attempt works, I just modified
GraphicPrimitiveFactory_plot_field so that it evaluates functions of
two arguments.  A diff patch file is at

http://www.d.umn.edu/~mhampton/plotpatch

If this looks okay I will try to update the documentation as well.

-Marshall Hampton


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[sage-devel] Re: plot_vector_field

[Hamptonio]

One thing I can't figure out is how to make the arrows a constant
length.  Any suggestions?

Thanks,
Marshall

On Jun 5, 9:39 am, Hamptonio [EMAIL PROTECTED] wrote:
 At the moment, plot_vector_field is only capable of plotting product
 vector fields, which is unacceptable for my use of it in an ODE
 class.  Since it is a crucial issue for my use, I plan on trying to
 extend it to handle arbitrary 2d fields, unless Alex Clemesha feels
 like doing it for me.  Any tips are appreciated.

 actually I think my first attempt works, I just modified
 GraphicPrimitiveFactory_plot_field so that it evaluates functions of
 two arguments.  A diff patch file is at

 http://www.d.umn.edu/~mhampton/plotpatch

 If this looks okay I will try to update the documentation as well.

 -Marshall Hampton


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[sage-devel] Re: plot_vector_field

[Hamptonio]

OK, thanks. I will look into hacking the quiver function.

It is unclear to me, from your response, if you understand the problem
with plot_vector_field in its current form.  The example from the
wolfram site is somewhat misleading, since it uses a vector field of
the form (f(x),g(y)), but this is not necessary in mathematica - it
can handle fields of the form (f(x,y),g(x,y)), which is what my patch
fixes.

Cheers,
Marshall Hampton

On Jun 5, 1:09 pm, alex clemesha [EMAIL PROTECTED] wrote:
  At the moment, plot_vector_field is only capable of plotting product
  vector fields, which is unacceptable for my use of it in an ODE
  class.  Since it is a crucial issue for my use, I plan on trying to
  extend it to handle arbitrary 2d fields, unless Alex Clemesha feels
  like doing it for me.  Any tips are appreciated.

 Hi Marshall,

 The motivation behind the function 'plot_vector_field' is it is one of
 several from Mathematica's 'PlotField' plotting functions, 
 see:http://reference.wolfram.com/mathematica/Compatibility/tutorial/Graph...

 If you go to the above link, I think you will find that the other couple
 'missing' functions (not in SAGE yet), are the others listed on the page.

 Actually, in SAGE, is the class 'GraphicPrimitive_PlotField', which is a
 more general
 class that was designed to enable the implementation all the functions of
 Mathematica's 'PlotField' package ... and actually implementing the rest of
 those functions might be 'easy'.  (but if you want to do that and you want
 them to look really nice, get ready to chase around pixels ;)

 What is really going on with the class 'GraphicPrimitive_PlotField' is it is
 a wrapper
 on top of matplotlib's (see google if you are not familiar) 'quiver'
 function.
 The quiver function is a pretty general function, and it holds all the
 underlying parameters (arrows of constant length) that can be manipulated.

 Alex

 p.s. I'm glad you are interested in some of the more 'advanced'-ish plotting
 functions
 in SAGE, you can make some beautiful and illuminating images with them,
 and they definitely couldn't hurt being improved.


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[sage-devel] Re: more licensing discussion

[Hamptonio]

What email have you been using for John Stone?


On May 28, 4:33 pm, William Stein [EMAIL PROTECTED] wrote:
 On 5/28/07, Robert Bradshaw [EMAIL PROTECTED] wrote:



  I'm just glad those are the only two sticky issues. I think we're
  fine with jsmath, as you said it's not linked--just distributed and
  run (separately) on the user's browser. We don't have to place
  license restrictions on the browser...

 Yep, that should be fine.

  Hopefully the author of Tachyon gets back to us--I would be surprised
  if he didn't free it up.

 The problem is that he's never responded to any
 email I've ever sent him.  I suggest we wait a few days,
 and if he doesn't response then:
   (1) people on sage-devel who really like Tachyon could
 write their own emails to him asking in their own words
 that he consider removing the obnoxious licensing clause,
 and ,
   (2) we try even hard to figure out if distributing Tachyon with
 SAGE is actually a copyright violation.  It's not completely
 100% crystal clear to me, since SAGE does no C library linking
 with Tachyon. And fortunately the Tachyon license is the BSD
 license (not something like the lame gnuplot license), so
 it's not restrictive. That said, we very well might want to do some
 C library linking with Tachyon in the future, and it would be very
 bad to not have this option.

 --
 William Stein
 Associate Professor of Mathematics
 University of Washingtonhttp://www.williamstein.org


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[sage-devel] Re: automatic sage upgrade notification?

[Hamptonio]

Pop-up windows about upgrades are really annoying.  But a simple text
output of the sort described, that doesn't ask for any input, would be
a good idea I think.

-M.Hampton

On May 18, 11:18 am, William Stein [EMAIL PROTECTED] wrote:
 Hi,

 This is a discussion of update/upgrade notification for SAGE for normal users.
 Feel free to read it and share your thoughts.

 -- Forwarded message --
  Another suggestion I have, automatic notification of major new
  version releases:

  Say once a week, when  you start SAGE, it checks with the canonical
  SAGE server on the Net and if a significant version (like  2.5) has
  been released, it just says something like A newer version of SAGE
  with software enhancements, version 2.5, is now available.  If you
  have administrative privileges for SAGE you may wish to install it
  with the command sage -upgrade from the command line.  Note that
  this may take some time, depending on the speed of your computer and
  network connection.

 Maybe.  I'll running it by sage-devel.  One of the things I hate most
 about software is stupid frickin' automatic notifications about upgrades...
 They drive me crazy. Especially Adobe Acrobat's.



  Otherwise, people may get way behind without ever knowing it, and run
  into problems/difficulties/errors/frustrations you've already long
  since solved.

  I don't know how often, for example, I see people still running
  Firefox 1.0 or 1.5, both insecure and  long since superceded, with no
  idea that there's a newer, better version available.

  And, on the SysAdmin side, the mathematicians bugging the SysAdmins
  due to the upgrade message will get the SysAdmins to install the
  newer version, which they otherwise may have no clue was even released.

  Of course,  you've got to be real sure that the -upgrade works real
  well!

  Arthur
   Maybe.  I'll running it by sage-devel.  One of the things I hate most
   about software is stupid frickin' automatic notifications about
   upgrades...
   They drive me crazy. Especially Adobe Acrobat's.

  You don't want to make it too obtrusive, but if someone's not on Sage-
  announce (or one of the other mailing lists) which I assume most
  normal users aren't,

 True.

  or you don't go to sagmath.org (which I assume
  most wouldn't  much if they're just a normal user) how would someone
  ever know if a new and improved version came out?

 They wouldn't, unless they type upgrade().

  I mean, I'm in the new and improved software business, mathematicians
  just want to do math... they mostly don't want to screw around with
  computers so mostly don't pay much attention to software at all,
  unless something breaks, and often not so much even then.

  Adobe Acrobat's upgrade notifications suck.  But so do Adobe's
  installs, especially their network installs.

  *Don't* ever make it an automatic upgrade, though.  I hate those.
  Those massively suck.

 --
 William Stein
 Associate Professor of Mathematics
 University of Washingtonhttp://www.williamstein.org


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[sage-devel] Re: Fwd: [sage-devel] Re: automatic sage upgrade notification?

[Hamptonio]

I would like to register to use sage.

Marshall Hampton,
SAGE user #1

:)

On May 18, 3:47 pm, mabshoff [EMAIL PROTECTED]
dortmund.de wrote:
 On May 18, 10:07 pm, [EMAIL PROTECTED] wrote:

  I HATE it when software phones home.  There should be, at least, a config 
  entry available to disable this behavior.  And IMO, it should be disabled 
  by default.

 Yes, Opt in is the way to go. Anything else is just plain EVIL(tm).

 The other suggestion about counting uniq IPs won't tell you much about
 the number of installations of SAGE either, because with my DSL
 connection at home I get a shiny new one every 24 hours. The same more
 or less applies to my IP at the office I get via dhcp. You could log
 the MACs, but let's just say that this isn't exactly nice either.

 Another possibility would be that people who use SAGE and like it
 should send an email to some specified address. Then somebody could
 send them back an email stating you are registered SAGE user #,
 similar to the Linux user counter one sees in signatures every once in
 a while. Should I venture a guess who will be SAGE user #1?

 Cheers,

 Michel


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[sage-devel] Re: a press release

[Hamptonio]

I could volunteer some time at the joint meetings at a table.  I hope
by then to be at least a small scale developer.

I am very interested in using sage in the courses I teach, but I
initially became interested for research reasons.  It would be great
to have a special session at the 2009 joint meetings for research
using sage.  I would be happy to help organize that if any help is
needed.

On wikipedia there are alreay quite a few examples of code snippets
written in Python or Perl.  Depending on the context, I think pure
python makes more sense than sage for what I've seen since it is more
portable/accessible to most people.  If you are illustrating one
specific idea, you can usually do it in python.  Of course, for very
mathematical subject matter (like modular forms) it may make more
sense to use sage.

-Marshall Hampton

On May 16, 2:13 pm, William Stein [EMAIL PROTECTED] wrote:
 On 5/16/07, Nathan Ryan [EMAIL PROTECTED] wrote:

   Is anyone actively using this, daily, as part of their course work,
   as would be done with Matlab, Mathematica, and the like?  Perhaps at
   Sage Days 4, there could be some discussion of how well it works in
   practice, both for full-time classroom use (i.e., not as an off to
   the side curiosity), and for math research.  One aspect to consider
   is how often, in these uses, do you run into dead-ends, parts of the
   package that aren't yet implemented.

 I use SAGE for an undergrad number theory course I'm teaching right
 now, where SAGE already blows away the competition.

  I'm teaching multivariable calc in the fall and plan on using it then.
  In order to prepare for that, I'm having a student at UCLA go through
  Mathematica packets used here to look for exactly these kinds of
  dead-ends.  He and I will report on what we find.

 If we still don't have 3-d graphing by then, will it be a major obstruction?
 Obviously I hope we do have good 3-d graphics in the notebook by
 the end of the summer...

  On a similar note, I have a couple of ideas to increase SAGE's
  visibility (okay, maybe 3):

  1.  Once we have a feature-frozen version of the calculus package up and

   
 ^^

 That will never happen :-).  But SAGE-2.5 now does have a pretty usable
 calculus package up and running.

  running, it might be nice to get a table at the joint meetings.  I think
  it's pretty expensive, but there might be some other way to have a
  significant commercial-like presence at the meetings.  This seems to be
  a sure-fire way to get thousands of new people exposed to SAGE in a weekend.

 David Joyner checked on this yesterday.  The next joint meeting is in San 
 Diego
 in January, and it costs $400 for us to get a table, since we are First 
 timers
 and they have a discount for first timers.  Would you be willing to
 help out with
 such a booth?

  2.  I think it would also be interesting to organize special sessions on
  SAGE (either in sectional or national meetings) couched as either
  teaching or research sessions.

 The deadline already passed for the national meeting in January in 2008.
 We could aim for a special session in 2009.  Let's not forget and miss
 the deadline again!
 Regarding sectional meetings, that's a great idea.  I'm actually giving a
 plenary talk on SAGE at the AMS Sectional Meeting, Salt Lake City, UT
 July 30-Aug 3, 2007.

  3.  Just like Mathworld has a bunch of Mathematica code interspersed, I
  think it would be interesting to have a bunch of sage code interspersed
  throughout Wikipedia or PlanetMath.

 There might be massive amounts of politics involved in doing that, which we'll
 have to figure out how to negotiate.
 I don't contribute much to Wikipedia or PlanetMath, so maybe somebody who is
 involved could make some comments.   Remember that MathWorld is owned
 by Mathematica, so they don't have to worry about such politics since they're
 in their own little world.

  I understand there are a bunch  of possible issues with these ideas, but
  I just wanted to throw them out there.

 They are all good ideas.  The issues are all just challenges that we should
 find ways to deal with.

 --
 William Stein
 Associate Professor of Mathematics
 University of Washingtonhttp://www.williamstein.org


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[sage-devel] Re: Fwd: Kudos on a fabulous system!

[Hamptonio]

Absolutely.  I've been thinking about this a fair amount lately as I
would like to use sage in teaching undergrads (mostly multivariable
calc, ODEs, and linear algebra).  At first I was thinking of them
installing it on their laptops, but most of them use Windows.  Having
a notebook server for a class is actually much better, since they can
pick up where they left off in lab seamlessly.  It would be nice if
there was a way to hide worksheets - i.e. I can foresee not wanting to
have people be able to easily copy code from anyone else in the
class.  A crude solution is to have a seperate notebook for each
student, but there must be a better way.

Marshall

On May 16, 11:50 am, Nick Alexander [EMAIL PROTECTED] wrote:
 Martin Albrecht [EMAIL PROTECTED] writes:
  On Wednesday 16 May 2007 16:07, William Stein wrote:
  Hi,

  Here is some fan mail from a new user of SAGE on Windows (via VMware)
  -- see below.
  I think we're going to have to make a hard choice about whether to continue
  to support Cygwin or just distribute SAGE on Windows via VMware, since it
  is so frickin' hard to get everything to work on Cygwin, and there are many
  efficiency issues.  It's a hard choice since many people have put in so
  much time to get SAGE to work on Cygwin (I've put in weeks myself).
  Comments welcome.

 +1 for removing it.

 This is where the notebook *really* shines: it lets us offer SAGE to
 unsupported hardware platforms.  If Google can do it...

 Nick


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[sage-devel] Re: SAGE-2.5 (!)

[Hamptonio]

Yes, I was upgrading.

-MH

On May 9, 12:14 pm, David Harvey [EMAIL PROTECTED] wrote:
 On May 9, 2007, at 1:06 PM, Hamptonio wrote:



  Hi,

  I have the following 'make test' failure for sage 2.5 on a PPC OS X
  powerbook:

  The following tests failed:
  sage -t  devel/sage-main/sage/libs/cf/cf.pyx
  Total time for all tests: 4614.8 seconds

 Ummm I just did a clean install of sage 2.5 on a powerpc OS X, and
 the cf directory doesn't even exist.

 david


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[sage-devel] Re: sage-2.5.alpha3

[Hamptonio]

For my OS X intel mac pro:

All tests passed!
Total time for all tests: 1516.7 seconds

I also fired up the notebook and ran a few pieces of my own code, no
problems.

Marshall Hampton

On May 6, 11:24 am, William Stein [EMAIL PROTECTED] wrote:
 Hello,

 I've posted sage-2.5.alpha3 here:

http://sage.math.washington.edu/home/was/sage2.5/

 Feedback is welcome.   This still won't build on OS X PowerPC or
 Cygwin, but should build on Linux and Intel OS X and pass make test
 there.  Also, it should have most code that people have sent me for
 inclusion in SAGE.   The official sage-2.5 is getting close, so any
 testing feedback is greatly appreciated.  In particular, if people
 could try out some of the new features in sage-2.5, especially symbolic
 computation, this would be quite valuable.

 Here's a list of the main things that are new in sage-2.5.alpha3:

 2.5: * new packages:
  - flintqs
  - ipython-0.8.0 (w stein)
  - maxima-5.12.0 (w stein)
  - python-2.5.1 (y qiang) -- important bug fixes
  - tachyon3d-0.98beta (w stein)
  * m abshoff:  cputime bugfix for cygwin
  * m albrecht: major new singular library mode interface for SAGE 
 which
provides the world's fastest polynomial
 arithmetic to SAGE (not
yet enabled by default!)
  * r bradshaw: tons of polynomial and power series optimizations;
Coleman p-adic integration; Kedlaya for genus  1
  * t clemens:  source browser bugfix
  * p de napoli:fix some bugs in rationals and integers
  * d deshomme: (refereed by r bradshaw and w stein) very good support
for Hida's quad-double field RQDF.
  * w hart: quadratic sieve update (SAGE's qsieve command):
 It is MUCH faster,
especially for large factorizations, on account
 of having implemented the
large prime variant. it will factor an 81 digit
 number in  20 minutes.
On the Athlon it is the fastest generally
 available implementation of the
quadratic sieve in the world for certain sized
 factorizations, and
only slightly behind at other sizes.
Another example: n =
 next_prime(2^110)*next_prime(2^120) has these
times on 32-bit 2Ghz linux: qsieve (107s), PARI
 (223s), Magma 2.13 (336s).
  * d harvey:   improvements, bug fixes.
  * d kohel:quaternion algebra improvements
  * k minola:   tmp file clean bugfix; misc build fixes.
  * k minola, d joyner:  updated the conway polynomial table
  * w stein and b moretti: major new symbolic calculus functionality
  * w stein:rewrite of SAGE/maxima interface.
  * c witty:(refereed by n alexandar) a new algebraic reals field
(Qbar meet RR!).  mpfr improvements


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[sage-devel] Re: [EMAIL PROTECTED]

[Hamptonio]

I would love to attend, but during the week I am teaching a summer
course.

On Apr 27, 5:56 pm, David Joyner [EMAIL PROTECTED] wrote:
 Hello SAGE people:

 This is proposal for 4th SAGE days 2007, to be held the week of
 June 11-16, 2007 (a Monday thru Saturday) in the Mathematics Department of
 the University of Washington in scenic Seattle.

 The focus will be on coding sprints, rather than talks on various
 SAGE-related topics. Namely, it is planned to be a developers workshop,
 with fewer general audience talks.

 If you think you can make it and are interested in attending, please email
 me ([EMAIL PROTECTED]) or this list. If there is sufficient interest,
 then we will try to get funding and take it from there.

 - David Joyner and William Stein


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[sage-devel] Re: Slightly OT: A SAGE Review

[Hamptonio]

My current bioinformatics textbook uses R for all its coding examples,
and since I wanted to use python/biopython for my course, I tried to
install the R-python interface.  As is often the case with such
things, it turned out to be far from self-contained, and I needed a
whole bunch of libraries I didn't have (this was on OS X 10.4).  Since
I am impatient and low on time, I gave up after about 1/2 hour, since
there is a very nice R.app for OS X available already and I didn't
have any specific connection in mind.  However, it looks like I will
often have statistics grad students in that course and they might use
such an interface.  So I will give another vote in favor of getting R
into sage.  Currently I think sage should appeal to everyone in math
except perhaps math ed and stats folks, and having R included would
win over the stats people.

-Marshall Hampton

On Apr 5, 11:39 pm, William Stein [EMAIL PROTECTED] wrote:
 Hi,

 Regarding the review, which mentions the stats package R, a lot of people have
 written me off list about creating an interface to R.  Note that there
 has been a Python -- R
 interface since before SAGE was ever written:

  http://rpy.sourceforge.net/

 I haven't used it, but imagine it would be easy to install into SAGE.
 (??)  If somebody
 investigates, please post their experiences.

 William


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[sage-devel] phc interface; numerical roots

[Hamptonio]

Hi,

I am interested in using phc through sage, and it looks like phc.py is
pretty broken.  I've hacked it up to work in blackbox mode (i.e. you
type 'phc -b inputfile outputfile' and it doesn't ask any questions),
and if there is any interest I can try to clean up my efforts.

Does anyone know if there are tools in SAGE for parsing the output of
phc?  That is what I am really interested in; I will start writing one
if it doesn't exist.

A related question is: what is the easiest/best way to get the
numerical roots of a polynomial in SAGE?  For simplicity, assume that
the polynomial has coefficients in QQ.

-Marshall Hampton


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[sage-devel] Re: sage-2.4-rc3

[Hamptonio]

I installed 2.4-rc3 on a powerpc g4 powerbook.  I had 4 tests fail,
but it looked like that was because I didn't install the gap
packages.  The four failures were:

sage -t  devel/sage-main/sage/graphs/graph.py
sage -t  devel/sage-main/sage/graphs/graph_isom.py
sage -t  devel/sage-main/sage/groups/perm_gps/permgroup.py
sage -t  devel/sage-main/sage/gsl/dft.py

I'll try to install gap and check again.

-Marshall Hampton

On Mar 25, 11:53 am, William Stein [EMAIL PROTECTED] wrote:
 Thanks for all your feedback.  It looks like a release of sage-2.4 is 
 imminent!

 On 3/25/07, David Joyner [EMAIL PROTECTED] wrote:





  All tests passed on suse 10.2 amd 64 bit.

  Jaap Spies wrote:
   Jaap Spies wrote:

   There were no problems what so ever with sage-2.4.rc3 on FC5:
   --
   All tests passed!
   Total time for all tests: 1093.9 seconds
   [EMAIL PROTECTED] sage-2.4.rc3]$

   The same for Fedora Core 6.

   Jaap

 --
 William Stein
 Associate Professor of Mathematics
 University of Washingtonhttp://www.williamstein.org


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[sage-devel] Re: sage-2.4-rc3

[Hamptonio]

As I mentioned, they were all due to the lack of the gap packages.
After installing those 2 optional packages, everything is fine:

All tests passed!
Total time for all tests: 3473.6 seconds

-twice the time of the MacBook Pro, I'm jealous...

Do you still want to see the logs?

-Marshall

On Mar 25, 4:52 pm, William Stein [EMAIL PROTECTED] wrote:
 Can you send the part of SAGE_ROOT/test.log that describes
 the failures for

  sage -t  devel/sage-main/sage/graphs/graph.py
  sage -t  devel/sage-main/sage/graphs/graph_isom.py
  sage -t  devel/sage-main/sage/groups/perm_gps/permgroup.py

 The dft.py is just a rounding randomness.  But I don't know what
 would have caused the above three failures.

 On 3/25/07, Hamptonio [EMAIL PROTECTED] wrote:





  I installed 2.4-rc3 on a powerpc g4 powerbook.  I had 4 tests fail,
  but it looked like that was because I didn't install the gap
  packages.  The four failures were:

  sage -t  devel/sage-main/sage/graphs/graph.py
  sage -t  devel/sage-main/sage/graphs/graph_isom.py
  sage -t  devel/sage-main/sage/groups/perm_gps/permgroup.py
  sage -t  devel/sage-main/sage/gsl/dft.py

  I'll try to install gap and check again.

  -Marshall Hampton

  On Mar 25, 11:53 am, William Stein [EMAIL PROTECTED] wrote:
   Thanks for all your feedback.  It looks like a release of sage-2.4 is 
   imminent!

   On 3/25/07, David Joyner [EMAIL PROTECTED] wrote:

All tests passed on suse 10.2 amd 64 bit.

Jaap Spies wrote:
 Jaap Spies wrote:

 There were no problems what so ever with sage-2.4.rc3 on FC5:
 --
 All tests passed!
 Total time for all tests: 1093.9 seconds
 [EMAIL PROTECTED] sage-2.4.rc3]$

 The same for Fedora Core 6.

 Jaap

   --
   William Stein
   Associate Professor of Mathematics
   University of Washingtonhttp://www.williamstein.org

 --
 William Stein
 Associate Professor of Mathematics
 University of Washingtonhttp://www.williamstein.org


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[sage-devel] Re: sage-2.4-rc3

[Hamptonio]

OK, I will directly email you the whole test.log since I don't know
how to attach it in the group interface.  I first loaded the
gap_packages-4.4.9 and ran 'make test' again, and then I installed the
database_gap-4.4.9 package and tried again.

-Marshall

On Mar 25, 6:40 pm, William Stein [EMAIL PROTECTED] wrote:
 On 3/25/07, Hamptonio [EMAIL PROTECTED] wrote:



  As I mentioned, they were all due to the lack of the gap packages.
  After installing those 2 optional packages, everything is fine:

  All tests passed!
  Total time for all tests: 3473.6 seconds

  -twice the time of the MacBook Pro, I'm jealous...

  Do you still want to see the logs?

 Yes, since make test should pass with no need to install
 any optional packages.   This is very odd.





  -Marshall

  On Mar 25, 4:52 pm, William Stein [EMAIL PROTECTED] wrote:
   Can you send the part of SAGE_ROOT/test.log that describes
   the failures for

sage -t  devel/sage-main/sage/graphs/graph.py
sage -t  devel/sage-main/sage/graphs/graph_isom.py
sage -t  devel/sage-main/sage/groups/perm_gps/permgroup.py

   The dft.py is just a rounding randomness.  But I don't know what
   would have caused the above three failures.

   On 3/25/07, Hamptonio [EMAIL PROTECTED] wrote:

I installed 2.4-rc3 on a powerpc g4 powerbook.  I had 4 tests fail,
but it looked like that was because I didn't install the gap
packages.  The four failures were:

sage -t  devel/sage-main/sage/graphs/graph.py
sage -t  devel/sage-main/sage/graphs/graph_isom.py
sage -t  devel/sage-main/sage/groups/perm_gps/permgroup.py
sage -t  devel/sage-main/sage/gsl/dft.py

I'll try to install gap and check again.

-Marshall Hampton

On Mar 25, 11:53 am, William Stein [EMAIL PROTECTED] wrote:
 Thanks for all your feedback.  It looks like a release of sage-2.4 is 
 imminent!

 On 3/25/07, David Joyner [EMAIL PROTECTED] wrote:

  All tests passed on suse 10.2 amd 64 bit.

  Jaap Spies wrote:
   Jaap Spies wrote:

   There were no problems what so ever with sage-2.4.rc3 on FC5:
   --
   All tests passed!
   Total time for all tests: 1093.9 seconds
   [EMAIL PROTECTED] sage-2.4.rc3]$

   The same for Fedora Core 6.

   Jaap

 --
 William Stein
 Associate Professor of Mathematics
 University of Washingtonhttp://www.williamstein.org

   --
   William Stein
   Associate Professor of Mathematics
   University of Washingtonhttp://www.williamstein.org

 --
 William Stein
 Associate Professor of Mathematics
 University of Washingtonhttp://www.williamstein.org


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To post to this group, send email to sage-devel@googlegroups.com
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For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://sage.scipy.org/sage/ and http://modular.math.washington.edu/sage/
-~--~~~~--~~--~--~---

[sage-devel] Re: Biopython package

[Hamptonio]

Stupid of me not to try that - i.e. the 'http://'.  Ah well.  I have
written to the biopython dev list to let them know of the SAGE-
biopython connection.

I tried to take a look at what was causing those installation
hangups.  It looks like its not the mxTextTools, but rather the
components that immediately follow - namely the lack of Reportlab
(optional, I've never used its functionality) and the compilation of
part of Bio.PDB (basically a parser for molecular structure files).  I
cut out the relevant section and pasted it below.  If I have time, I
will try to figure out a workaround for this in the installation
script.

I am now spending a great deal of time working in the SAGE notebook
environment, which should inspire me eventually to do more development
work on SAGE.

Here's the installation snippet of interest:

*** Reportlab *** is either not installed or out of date.

This package is optional, which means it is only used in a few
specialized modules in Biopython.  You probably don't need this if you
are unsure.  You can ignore this requirement, and install it later if
you see ImportErrors.
You can find Reportlab at http://www.reportlab.org/downloads.html.

Do you want to continue this installation? (Y/n)
*** Bio.KDTree *** NOT built by default

The Bio.PDB.NeighborSearch module depends on the Bio.KDTree module,
which in turn, depends on C++ code that does not compile cleanly on
all platforms. Hence, Bio.KDTree is not built by default.

Would you like to build Bio.KDTree ? (y/N)  running build

On Mar 20, 12:39 pm, William Stein [EMAIL PROTECTED] wrote:
 On Tuesday 20 March 2007 9:30 am, Hamptonio wrote:

  Just to clarify: the downloading problem isn't biopython-specific - I
  can't get anything fromwww.sagemath.orgthrough sage, only from a
  browser.  For example, 'sage -optional' fails as well.

 Sorry, you have to do this (note the http://) -- I forgot to mention
 this before -- my mistake.

 export SAGE_SERVER=http://www.sagemath.org;
 sage -optional
 ...





  -MH

  On Mar 20, 10:31 am, Hamptonio [EMAIL PROTECTED] wrote:
   Woo-hoo! Thank you!!!

   I had the same error as before on my Mac Pro - the
   '...
   in open_local_file
   raise IOError(e.errno, e.strerror, e.filename)
   IOError: [Errno 2] No such file or directory: 'www.sagemath.org/
   packages/optional/biopython-1.43.spkg'
   sage: Failed to download package biopython-1.43 fromwww.sagemath.org'

   error, so I manually downloaded the spkg fromwww.sagemath.org, and it
   installed fine apart from the weird need for 'enter'  commands that
   you warned me about.  I have tested a few of my more commonly used
   tasks and it seems to work.

   I can tell the biopython developers about this once the package
   download problems get a little sorted out.

   Thanks again,
   Marshall

   On Mar 20, 7:53 am, Hamptonio [EMAIL PROTECTED] wrote:
Great!  I am once again amazed by your speed.

I set SAGE_SERVER as you said, but my attempt at installing fails to
get the package.  The output is appended below.  I doing this on a PPC
(G4) Apple powerbook, with sage 2.0 upgraded to 2.3.

I had tried to read the documentation you suggested - I was only
volunteering to try this because it seemed relatively simple!   I've
installed biopython 1.42 on linux, apple, and windows machines, but I
haven't tried a normal install of 1.43 yet (its quite recent).  I am
not sure what mxTextTools is doing; in a python install I just do
'sudo python setup.py install' although I am not sure that the sudo is
necessary.

I'll also give this a try on the Mac Pro (Intel) in my office when I
get in.

Thanks,
Marshall

~/sage-2.0:07:43:42:./sage -i biopython-1.43
Installing biopython-1.43
Calling sage-spkg on biopython-1.43
WARNING: Using SAGE_ROOT variable that was already set to '/Users/mh/
sage-2.0'.
biopython-1.43
Machine:
Darwin medmgmt-3.tajen.edu.tw 8.8.0 Darwin Kernel Version 8.8.0: Fri
Sep  8 17:18:57 PDT 2006; root:xnu-792.12.6.obj~1/RELEASE_PPC Power
Macintosh powerpc
Deleting directories from past builds of previous/current versions of
biopython-1.43
/Users/mh/sage-2.0/local/bin/sage-spkg: file /Users/mh/sage-2.0/
biopython-1.43 does not exist
Attempting to download
it.www.sagemath.org/packages/optional/biopython-1.43.spkg--
biopython-1.43.spkg
[
Traceback (most recent call last):
  File /Users/mh/sage-2.0/local/bin/sage-download_package, line 53,
in module
if not download_file(optional/%s%F):
  File /Users/mh/sage-2.0/local/bin/sage-download_package, line 45,
in download_file
urllib.urlretrieve(url, file, reporthook)
  File /Users/mh/sage-2.0/local/lib/python2.5/urllib.py, line 89, in
urlretrieve
return _urlopener.retrieve(url, filename, reporthook, data)
  File /Users/mh/sage-2.0/local/lib/python2.5/urllib.py, line 222,
in retrieve
fp = self.open(url

[sage-devel] Re: Biopython package

[Hamptonio]

Great!  I am once again amazed by your speed.

I set SAGE_SERVER as you said, but my attempt at installing fails to
get the package.  The output is appended below.  I doing this on a PPC
(G4) Apple powerbook, with sage 2.0 upgraded to 2.3.

I had tried to read the documentation you suggested - I was only
volunteering to try this because it seemed relatively simple!   I've
installed biopython 1.42 on linux, apple, and windows machines, but I
haven't tried a normal install of 1.43 yet (its quite recent).  I am
not sure what mxTextTools is doing; in a python install I just do
'sudo python setup.py install' although I am not sure that the sudo is
necessary.

I'll also give this a try on the Mac Pro (Intel) in my office when I
get in.

Thanks,
Marshall

~/sage-2.0:07:43:42:./sage -i biopython-1.43
Installing biopython-1.43
Calling sage-spkg on biopython-1.43
WARNING: Using SAGE_ROOT variable that was already set to '/Users/mh/
sage-2.0'.
biopython-1.43
Machine:
Darwin medmgmt-3.tajen.edu.tw 8.8.0 Darwin Kernel Version 8.8.0: Fri
Sep  8 17:18:57 PDT 2006; root:xnu-792.12.6.obj~1/RELEASE_PPC Power
Macintosh powerpc
Deleting directories from past builds of previous/current versions of
biopython-1.43
/Users/mh/sage-2.0/local/bin/sage-spkg: file /Users/mh/sage-2.0/
biopython-1.43 does not exist
Attempting to download it.
www.sagemath.org/packages/optional/biopython-1.43.spkg --
biopython-1.43.spkg
[
Traceback (most recent call last):
  File /Users/mh/sage-2.0/local/bin/sage-download_package, line 53,
in module
if not download_file(optional/%s%F):
  File /Users/mh/sage-2.0/local/bin/sage-download_package, line 45,
in download_file
urllib.urlretrieve(url, file, reporthook)
  File /Users/mh/sage-2.0/local/lib/python2.5/urllib.py, line 89, in
urlretrieve
return _urlopener.retrieve(url, filename, reporthook, data)
  File /Users/mh/sage-2.0/local/lib/python2.5/urllib.py, line 222,
in retrieve
fp = self.open(url, data)
  File /Users/mh/sage-2.0/local/lib/python2.5/urllib.py, line 190,
in open
return getattr(self, name)(url)
  File /Users/mh/sage-2.0/local/lib/python2.5/urllib.py, line 451,
in open_file
return self.open_local_file(url)
  File /Users/mh/sage-2.0/local/lib/python2.5/urllib.py, line 465,
in open_local_file
raise IOError(e.errno, e.strerror, e.filename)
IOError: [Errno 2] No such file or directory: 'www.sagemath.org/
packages/optional/biopython-1.43.spkg'
sage: Failed to download package biopython-1.43 from www.sagemath.org


On Mar 19, 10:52 pm, William Stein [EMAIL PROTECTED] wrote:
 On Monday 19 March 2007 8:28 pm, Hamptonio wrote:



  Hi,

  I became interested in SAGE after I found it to be the easiest way to
  install cddlib and gmp, and now I am getting hooked.  My research is
  very schizophrenic: besides some computational algebra/geometry coming
  from dynamical systems, I am also interested in mathematical biology
  and bioinformatics.  There is an open-source project called biopython
  (http://biopython.org/wiki/Biopython) that I am using in a
  bioinformatics course right now. It would be very nice if there was a
  biopython optional package for SAGE.  I am willing to try and create
  one, but I thought I would post here first to see if anyone had any
  preliminary advice before I waste my time.

  Biopython currently requires Numeric, but all the parts I need seem to
  work OK using numpy.  The developers are currently working on
  switching over entirely to numpy.  It also requires something called
  mxTextTools, but I think that should be OK since its open source and
  has a very permissive license.

 Adding biopython is a good idea.  Prompted by your email, I created
 a package for it, which I've posted here:

  http://www.sagemath.org/packages/optional/

 If you do
$ export SAGE_SERVER=www.sagemath.org
 from bash, you can get it with
sage -i biopython-1.43

 My biophython-1.43 package includes mxTextTools, so it's very easy to install.
 Also, it seems that biophython-1.43 works fine with numpy.  If it doesn't,
 Numeric is a well-supported optional sage package: sage -i numeric-24.2.

 One very annoying thing that somebody needs to get to the bottom of, is that
 it seems necessary to hit enter several times half-way through the install,
 or it just pauses forever.   This probably has something to do with maybe
 mxTextTools's installing doing something obnoxious.  Feedback is appreciated.

 By the way, this document gives a basic idea of how spkg's are created:
  http://www.sagemath.com/doc/html/prog/node23.html

 In short, an spkg is just a bzip2'd tarball, with a file spkg-install that
 gets run in the environment of SAGE, e.g., python is SAGE's Python, etc.,
 and it is supposed to install code to $SAGE_LOCAL.

 William

 William


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For more options, visit this group at http

[sage-devel] Re: Biopython package

[Hamptonio]

Woo-hoo! Thank you!!!

I had the same error as before on my Mac Pro - the
'...
in open_local_file
raise IOError(e.errno, e.strerror, e.filename)
IOError: [Errno 2] No such file or directory: 'www.sagemath.org/
packages/optional/biopython-1.43.spkg'
sage: Failed to download package biopython-1.43 from www.sagemath.org'

error, so I manually downloaded the spkg from www.sagemath.org, and it
installed fine apart from the weird need for 'enter'  commands that
you warned me about.  I have tested a few of my more commonly used
tasks and it seems to work.

I can tell the biopython developers about this once the package
download problems get a little sorted out.

Thanks again,
Marshall

On Mar 20, 7:53 am, Hamptonio [EMAIL PROTECTED] wrote:
 Great!  I am once again amazed by your speed.

 I set SAGE_SERVER as you said, but my attempt at installing fails to
 get the package.  The output is appended below.  I doing this on a PPC
 (G4) Apple powerbook, with sage 2.0 upgraded to 2.3.

 I had tried to read the documentation you suggested - I was only
 volunteering to try this because it seemed relatively simple!   I've
 installed biopython 1.42 on linux, apple, and windows machines, but I
 haven't tried a normal install of 1.43 yet (its quite recent).  I am
 not sure what mxTextTools is doing; in a python install I just do
 'sudo python setup.py install' although I am not sure that the sudo is
 necessary.

 I'll also give this a try on the Mac Pro (Intel) in my office when I
 get in.

 Thanks,
 Marshall

 ~/sage-2.0:07:43:42:./sage -i biopython-1.43
 Installing biopython-1.43
 Calling sage-spkg on biopython-1.43
 WARNING: Using SAGE_ROOT variable that was already set to '/Users/mh/
 sage-2.0'.
 biopython-1.43
 Machine:
 Darwin medmgmt-3.tajen.edu.tw 8.8.0 Darwin Kernel Version 8.8.0: Fri
 Sep  8 17:18:57 PDT 2006; root:xnu-792.12.6.obj~1/RELEASE_PPC Power
 Macintosh powerpc
 Deleting directories from past builds of previous/current versions of
 biopython-1.43
 /Users/mh/sage-2.0/local/bin/sage-spkg: file /Users/mh/sage-2.0/
 biopython-1.43 does not exist
 Attempting to download 
 it.www.sagemath.org/packages/optional/biopython-1.43.spkg--
 biopython-1.43.spkg
 [
 Traceback (most recent call last):
   File /Users/mh/sage-2.0/local/bin/sage-download_package, line 53,
 in module
 if not download_file(optional/%s%F):
   File /Users/mh/sage-2.0/local/bin/sage-download_package, line 45,
 in download_file
 urllib.urlretrieve(url, file, reporthook)
   File /Users/mh/sage-2.0/local/lib/python2.5/urllib.py, line 89, in
 urlretrieve
 return _urlopener.retrieve(url, filename, reporthook, data)
   File /Users/mh/sage-2.0/local/lib/python2.5/urllib.py, line 222,
 in retrieve
 fp = self.open(url, data)
   File /Users/mh/sage-2.0/local/lib/python2.5/urllib.py, line 190,
 in open
 return getattr(self, name)(url)
   File /Users/mh/sage-2.0/local/lib/python2.5/urllib.py, line 451,
 in open_file
 return self.open_local_file(url)
   File /Users/mh/sage-2.0/local/lib/python2.5/urllib.py, line 465,
 in open_local_file
 raise IOError(e.errno, e.strerror, e.filename)
 IOError: [Errno 2] No such file or directory: 'www.sagemath.org/
 packages/optional/biopython-1.43.spkg'
 sage: Failed to download package biopython-1.43 fromwww.sagemath.org

 On Mar 19, 10:52 pm, William Stein [EMAIL PROTECTED] wrote:

  On Monday 19 March 2007 8:28 pm, Hamptonio wrote:

   Hi,

   I became interested in SAGE after I found it to be the easiest way to
   install cddlib and gmp, and now I am getting hooked.  My research is
   very schizophrenic: besides some computational algebra/geometry coming
   from dynamical systems, I am also interested in mathematical biology
   and bioinformatics.  There is an open-source project called biopython
   (http://biopython.org/wiki/Biopython) that I am using in a
   bioinformatics course right now. It would be very nice if there was a
   biopython optional package for SAGE.  I am willing to try and create
   one, but I thought I would post here first to see if anyone had any
   preliminary advice before I waste my time.

   Biopython currently requires Numeric, but all the parts I need seem to
   work OK using numpy.  The developers are currently working on
   switching over entirely to numpy.  It also requires something called
   mxTextTools, but I think that should be OK since its open source and
   has a very permissive license.

  Adding biopython is a good idea.  Prompted by your email, I created
  a package for it, which I've posted here:

   http://www.sagemath.org/packages/optional/

  If you do
 $ export SAGE_SERVER=www.sagemath.org
  from bash, you can get it with
 sage -i biopython-1.43

  My biophython-1.43 package includes mxTextTools, so it's very easy to 
  install.
  Also, it seems that biophython-1.43 works fine with numpy.  If it doesn't,
  Numeric is a well-supported optional sage package: sage -i numeric-24.2.

  One very annoying thing that somebody needs to get

[sage-devel] Biopython package

[Hamptonio]

Hi,

I became interested in SAGE after I found it to be the easiest way to
install cddlib and gmp, and now I am getting hooked.  My research is
very schizophrenic: besides some computational algebra/geometry coming
from dynamical systems, I am also interested in mathematical biology
and bioinformatics.  There is an open-source project called biopython
(http://biopython.org/wiki/Biopython) that I am using in a
bioinformatics course right now. It would be very nice if there was a
biopython optional package for SAGE.  I am willing to try and create
one, but I thought I would post here first to see if anyone had any
preliminary advice before I waste my time.

Biopython currently requires Numeric, but all the parts I need seem to
work OK using numpy.  The developers are currently working on
switching over entirely to numpy.  It also requires something called
mxTextTools, but I think that should be OK since its open source and
has a very permissive license.

Cheers,
Marshall Hampton


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URLs: http://sage.scipy.org/sage/ and http://modular.math.washington.edu/sage/
-~--~~~~--~~--~--~---

[sage-devel] Re: ode_solver

[Hamptonio]

Very nice!  Things seem fine so far after a few crude tests (on a Mac
Pro, sage 1.6, no packages installed).  I will try to push it harder
soon.  I think there is one small typo in the documentation: for the
initial condition example shouldn't it be

   y_0=1,y_1=1, would do

   sage: T.y_0=[1,1]

instead of

   y_0=1,y_1=1, would do

   sage: T.y_0=[1,0]

Cheers,
Marshall Hampton


Joshua Kantor wrote:
 In response to Williams sage-2.0 plan I wanted to describe what I had done
 with using gsl to implement a numerical ode solver. I believe that the
 patch containing this  will be applied after
 doing a recent pull or upgrade but I'm not sure(is this true?). If not I
 can send patches for people to play with. I have included the
 documentation at the end so people can look at the syntax.

 To see the documentation and examples

 sage: ode_solver?

 To be done

 1. Testing/feedback: Is it easy to use compared to matlab,mathematica.
 Any bugs or ways to crash it (unexpected input or user specified
 functions that do weird things)?

 2. More examples, doctests, improved documentation (I noticed a bunch of
 typos just copying the documentation below)

 3. Obvious additions people think would be useful. Currently it has a
 plotting routine and a routine to produce an interpolated function from
 the data points.


 Ideas for extension:

 1. It would be nice if there was some facility for automatically
 converting a nth order ODE
 to a system of first order ones.

 2. It would be nice if there was some facility for automatically computing
 the jacobian when the functions involved are rational functions and
 elementary functions.


 3. Numerically computing the jacobian: For the algorithms that require the
 jacobian It would be possible to numerically compute the jacobian,
 however I was wary of doing this by default. Does anyone have any knowledge
 about
 the benefits of this, can it cause instability (using the numerical
 jacobian
 instead of the exact one).


 Accuracy testing:

 1. I believe there are standard batches of tests for ode solvers.
 it would be interesting if some of these could be applied to compare the
 accuracy with matlab for example. This ode solver will be slower than
 matlab's on systems that require many function evaluations because we are
 forced to use python functions and there is significant overhead in
 calling these. Still comparisons would be interesting. There is a way to
 use compiled functions describe in the documentation but requires
 writing the functions in C and so isn't really suitable for
 general users.



   


 ode_solver is a class that wraps the GSL libraries ode solver routines
   To use it instantiate a class,
   sage: T=ode_solver()

   To solve a system of the form dy_i/dt=f_i(t,y), you must supply a
   vector or tuple/list valued function f representing f_i.
   The functions f and the jacobian should have the form foo(t,y) or
 foo(t,y,params).
   params which is optional allows for your function to depend on
 one or a tuple of parameters.
   Note if you use it, params must be a tuple even if it only has
 one component.
   For example if you wanted to solve y''+y=0. You need to write it
 as a first order system
   y_0' = y_1
   y1_1 = -y_0

   In code,

   sage: f = lambda t,y:[y[1],-y[0]]
   sage: T.function=f

   For some algorithms the jacobian must be supplied as well,
   the form of this should be a function return a list of lists of
 the form
   [ [df_1/dy_1,...,df_1/dy_n], ..., [df_n/dy_1,...,df_n,dy_n],
   [df_1/dt,...,df_n/dt] ]. There are examples below, if your
 jacobian was the function my_jacobian
   you would do.

   sage: T.jacobian=my_jacobian


   There are a variety of algorithms available for different types
 of systems. Possible algorithms are
   rkf45 - runga-kutta-felhberg (4,5)
   rk2 - embedded runga-kutta (2,3)
   rk4 - 4th order classical runga-kutta
   rk8pd - runga-kutta prince-dormand (8,9)
   rk2imp - implicit 2nd order runga-kutta at gaussian points
   rk4imp - implicit 4th order runga-kutta at gaussian points
   bsimp - implicit burlisch-stoer (requires jacobian)
   gear1 - M=1 implicit gear
   gear2 - M=2 implicit gear

   The default algorithm if rkf45. If you instead wanted to use
 bsimp you would do

   sage: T.algorithm=bsimp

   The user should supply initial conditions in y_0. For example if
 your initial conditions are
   y_0=1,y_1=1, would do

   sage: T.y_0=[1,0]

   The actual solver is invoked by the method ode_solve.
   It has arguments t_span, y_0,num_points, params.
   y_0 must be supplied either as an argument or above by
 

[sage-devel] Re: sage-2.0 !

[Hamptonio]

Hi,

I would be interested in helping with Kantor's ODE solver , although
I don't know what that is.  I have a long-term goal of replacing
Mathematica with SAGE for our department's ODE and Calc III labs, but I
don't think the time is right yet.

-Marshall Hampton
University of Minnesota, Duluth


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