[sage-support] autoeval in sagecell

[davidp]

I am wondering why only the first cell in the following is automatically 
evaluated:

http://people.reed.edu/~davidp/211/sage/sagecell/tangent_plane.html

I have autoeval set to 'True' and notice that if I add


1+1


at the end, it is automatically evaluated.

Thanks in advance for any suggestions.

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[sage-support] Re: 3d graphics display problem

[davidp]

Fixed: I removed the .jmol directory from my home directory (allowing a new 
one to be formed the next time I ran jmol).  I thought I had tried that 
already.

On Thursday, July 25, 2013 4:15:37 PM UTC-7, davidp wrote:
>
> In the following, I expect p+s to be a picture of a plane with the word 
> 'hello' embedded at its center.  Instead, I get the word 'hello' in the 
> corner of the frame (where the number -1) might be expected.  Further, it 
> prints a number 2 way outside of the frame, and the axes labels are all in 
> the wrong order.  It is as if there is an off-by-one error in some labeling 
> code somewhere.  When I print p+s+t, I get 'hello' embedded in the center 
> as expected, and 'goodbye' is shifted to the corner of the frame now.
>
> ---
> sage: var('x y')
> (x, y)
> sage: p = plot3d(1,(x,-1,1),(y,-1,1))
> sage: s = text3d('hello',(0,0,1))  # hello appears in the wrong place
> sage: p + s
>
> sage: t = text3d('goodbye',(0,0,1))  # same coordinates as s
> sage: p + s + t   # hello now appears in the right place, but goodbye does 
> not
> 
>
> I am running sage-5.10 under Ubuntu 13.04 on a laptop.  The *same* setup 
> on my desktop does not produce this error.  I tried re-installing sage, 
> removing my old .sage, .jmol, and .java directories.  Same problem. 
>  Further, when I try the same code after logging in as guest on my laptop, 
> the code runs with no problem.  Any suggestions would be appreciated.
>
> Thanks.
>
>
>
>

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[sage-support] width of lines in plot legend

[davidp]

Is there a way to increase the linewidth of lines appearing in the legend 
of a plot without changing the linewidth in the plot, itself?

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[sage-support] 3d graphics display problem

[davidp]

In the following, I expect p+s to be a picture of a plane with the word 
'hello' embedded at its center.  Instead, I get the word 'hello' in the 
corner of the frame (where the number -1) might be expected.  Further, it 
prints a number 2 way outside of the frame, and the axes labels are all in 
the wrong order.  It is as if there is an off-by-one error in some labeling 
code somewhere.  When I print p+s+t, I get 'hello' embedded in the center 
as expected, and 'goodbye' is shifted to the corner of the frame now.

---
sage: var('x y')
(x, y)
sage: p = plot3d(1,(x,-1,1),(y,-1,1))
sage: s = text3d('hello',(0,0,1))  # hello appears in the wrong place
sage: p + s

sage: t = text3d('goodbye',(0,0,1))  # same coordinates as s
sage: p + s + t   # hello now appears in the right place, but goodbye does 
not


I am running sage-5.10 under Ubuntu 13.04 on a laptop.  The *same* setup on 
my desktop does not produce this error.  I tried re-installing sage, 
removing my old .sage, .jmol, and .java directories.  Same problem. 
 Further, when I try the same code after logging in as guest on my laptop, 
the code runs with no problem.  Any suggestions would be appreciated.

Thanks.



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Re: [sage-support] legends for 3d graphics

[davidp]

Cool!

On Thursday, July 25, 2013 10:58:56 AM UTC-7, William wrote:
>
> On Thu, Jul 25, 2013 at 9:16 AM, davidp > 
> wrote: 
> > I am using Sage to plot an arrangement of planes in 3-space.  Each plane 
> has 
> > its own color, and I would like a legend in the plot that associates the 
> > equation of each plane with its color.  This experiment seems to 
> indicate 
> > that legends are not available for 3d graphics: 
> > 
> > 
> --- 
> > sage: p = plot3d(x^2,(x,-1,1),(y,-1,1),legend_label='0') 
> > sage: q = plot3d(x^2+y^2,(x,-1,1),(y,-1,1),legend_label='1') 
> > sage: c = p+q 
> > sage: c.legend(true) 
> > 
> --- 
> > AttributeErrorTraceback (most recent call 
> last) 
> >  in () 
> > > 1 c.legend(true) 
> > 
> > AttributeError: 'Graphics3dGroup' object has no attribute 'legend' 
> > 
> --- 
> > 
> > As I rotate the 3d-object, I would like for the legend would stay in one 
> > place. 
> > 
> > Any suggestions? 
>
> This won't help you today, but an REU student -- Renford Alexander -- 
> is working fulltime right now on Three.js-based 3d graphics rendering 
> for https://cloud.sagemath.com.  He showed me some demos yesterday of 
> drawing text in 3d, the looked pretty useful.  In particular, he draws 
> arbitrary text on a 2d html5 canvas, then puts the canvas element in 
> the 3d scenes as a "sprite".This functionality should come to 
> https://cloud.sagemath.com within a month, hopefully. 
>
>  -- William 
>
> > 
> > Thanks. 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups 
> > "sage-support" group. 
> > To unsubscribe from this group and stop receiving emails from it, send 
> an 
> > email to sage-support...@googlegroups.com . 
> > To post to this group, send email to 
> > sage-s...@googlegroups.com. 
>
> > Visit this group at http://groups.google.com/group/sage-support. 
> > For more options, visit https://groups.google.com/groups/opt_out. 
> > 
> > 
>
>
>
> -- 
> William Stein 
> Professor of Mathematics 
> University of Washington 
> http://wstein.org 
>

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[sage-support] legends for 3d graphics

[davidp]

I am using Sage to plot an arrangement of planes in 3-space.  Each plane 
has its own color, and I would like a legend in the plot that associates 
the equation of each plane with its color.  This experiment seems to 
indicate that legends are not available for 3d graphics:

---
sage: p = plot3d(x^2,(x,-1,1),(y,-1,1),legend_label='0')
sage: q = plot3d(x^2+y^2,(x,-1,1),(y,-1,1),legend_label='1')
sage: c = p+q
sage: c.legend(true)
---
AttributeErrorTraceback (most recent call last)
 in ()
> 1 c.legend(true)

AttributeError: 'Graphics3dGroup' object has no attribute 'legend'
---

As I rotate the 3d-object, I would like for the legend would stay in one 
place.

Any suggestions?

Thanks.

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[sage-support] graphs: unexpected behavior from depth_first_search after relabeling

[davidp]

sage: g = graphs.CycleGraph(4)
sage: list(g.depth_first_search(0))
[0, 3, 2, 1]
sage: g.relabel([0,3,2,1])
sage: list(g.depth_first_search(0))
[0, 1, 2, 3]

I was expecting to get [0,3,2,1]  again after relabeling.

Dave

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[sage-support] Re: sage is filling up my directory with files

[davidp]

Yes!  This looks right.

Thanks,
Dave

On Wednesday, April 24, 2013 2:30:09 PM UTC-7, John H Palmieri wrote:
>
>
>
> On Wednesday, April 24, 2013 8:53:56 AM UTC-7, davidp wrote:
>>
>> I just installed Sage 5.8 and am running it from the command line.  For 
>> some reason, it is filling up my directory with what looks like temporary 
>> files, e.g., threshold.sageJmarTS.py,  threshold.sageR9Gfg9, and on and 
>> on.  (I  attached code contained in a file called 'threshold.sage'.  I get 
>> the same behavior from other attached files.)  These files remain in the 
>> directory after i quit Sage.  Could someone tell me what's wrong?
>>
>> Thanks,
>> Dave  
>>
>
> I think this is the problem reported here: <
> http://trac.sagemath.org/sage_trac/ticket/14149>. There does not seem to 
> be a fix right now.
>
> -- 
> John
>  
>

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Re: [sage-support] Re: sage is filling up my directory with files

[davidp]

I have been using attach and load for years, too, with no problem.  I just 
checked by attaching a file containing only a simple function called 
'hello' that prints 'hello world' when called.  I have the same problem.

Thanks,
Dave

On Wednesday, April 24, 2013 2:18:24 PM UTC-7, Dan Drake wrote:
>
> I've used attach and load for years without ever encountering this 
> problem. So there must be something about the code in your 
> threshold.sage file. Without seeing it, it's not likely we can help you. 
>
> On Wed, 24 Apr 2013 at 10:57AM -0700, davidp wrote: 
> > I think this problem has to do with attaching a file.  I noticed that 
> > "attach" has been deprecated.  Using either 'attach' or '%attach' seems 
> to 
> > cause the proliferation of extra files.  The 'load' command or 
> '%runfile' 
> > does not seem to have this behavior.  The problem with the 'attach' 
> command 
> > seems like a bug to me.  Shouldn't these extra files be stored in some 
> tmp 
> > file in the sage directory that get erased at the end of the session, or 
> > something like that? 
> > 
> > Thanks, 
> > Dave 
> > 
> > On Wednesday, April 24, 2013 8:53:56 AM UTC-7, davidp wrote: 
> > > 
> > > I just installed Sage 5.8 and am running it from the command line. 
>  For 
> > > some reason, it is filling up my directory with what looks like 
> temporary 
> > > files, e.g., threshold.sageJmarTS.py,  threshold.sageR9Gfg9, and on 
> and 
> > > on.  (I  attached code contained in a file called 'threshold.sage'.  I 
> get 
> > > the same behavior from other attached files.)  These files remain in 
> the 
> > > directory after i quit Sage.  Could someone tell me what's wrong? 
> > > 
> > > Thanks, 
> > > Dave   
> > > 
> > 
>
>
> Dan 
>
> -- 
> ---  Dan Drake 
> -  http://math.pugetsound.edu/~ddrake 
> --- 
>

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[sage-support] Re: sage is filling up my directory with files

[davidp]

I think this problem has to do with attaching a file.  I noticed that 
"attach" has been deprecated.  Using either 'attach' or '%attach' seems to 
cause the proliferation of extra files.  The 'load' command or '%runfile' 
does not seem to have this behavior.  The problem with the 'attach' command 
seems like a bug to me.  Shouldn't these extra files be stored in some tmp 
file in the sage directory that get erased at the end of the session, or 
something like that?

Thanks,
Dave

On Wednesday, April 24, 2013 8:53:56 AM UTC-7, davidp wrote:
>
> I just installed Sage 5.8 and am running it from the command line.  For 
> some reason, it is filling up my directory with what looks like temporary 
> files, e.g., threshold.sageJmarTS.py,  threshold.sageR9Gfg9, and on and 
> on.  (I  attached code contained in a file called 'threshold.sage'.  I get 
> the same behavior from other attached files.)  These files remain in the 
> directory after i quit Sage.  Could someone tell me what's wrong?
>
> Thanks,
> Dave  
>

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[sage-support] sage is filling up my directory with files

[davidp]

I just installed Sage 5.8 and am running it from the command line.  For 
some reason, it is filling up my directory with what looks like temporary 
files, e.g., threshold.sageJmarTS.py,  threshold.sageR9Gfg9, and on and 
on.  (I  attached code contained in a file called 'threshold.sage'.  I get 
the same behavior from other attached files.)  These files remain in the 
directory after i quit Sage.  Could someone tell me what's wrong?

Thanks,
Dave  

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[sage-support] Re: labels on the frame of a 3d plot

[davidp]

I am still interested in this question, in case anyone happens to know the 
answer.

On Thursday, August 18, 2011 4:19:54 PM UTC-7, davidp wrote:
>
> Is there a way to turn off the labels on the frame in a 3d plot?  I 
> was hoping something like this might work: 
>
> var('x y') 
> plot3d(sin(x*y),(x,-2,2),(y,-2,2)).show(labels=false) 
>
> I know that I can set frame=false to get rid of the frame entirely, 
> but that is not what I am looking for.  Is there something like 
> plot.options for 3d graphic object? 
>
> Dave

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[sage-support] Re: ubuntu 12.04 + sage 5.1 + libgfortran

[davidp]

I had tried that, then got a further error, so I backtracked.  After 
reading your advice, I tried again, and everything worked.  

Thanks.   


On Saturday, July 28, 2012 1:00:57 PM UTC-7, P Purkayastha wrote:
>
> On 07/29/2012 03:29 AM, davidp wrote: 
> > I just made a clean install of ubuntu 12.04 on my thinkpad and installed 
> > sage from *sage-5.1-linux-64bit-ubuntu_12.04_lts-x86_64-Linux.tar.lzma* 
> > <
> http://boxen.math.washington.edu/home/sagemath/sage-mirror/linux/64bit/sage-5.1-linux-64bit-ubuntu_12.04_lts-x86_64-Linux.tar.lzma>,
>  
>
> > and have a problem, apparently with libgfortran (see below). Any help 
> > would be appreciated. 
> > 
> > Thanks! 
> > 
> > 
> > ImportError: libgfortran.so.3: cannot open shared object file: No such 
> > file or directory 
>
> You need to install libgfortran. 
>
>

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[sage-support] ubuntu 12.04 + sage 5.1 + libgfortran

[davidp]

I just made a clean install of ubuntu 12.04 on my thinkpad and installed 
sage from 
*sage-5.1-linux-64bit-ubuntu_12.04_lts-x86_64-Linux.tar.lzma*<http://boxen.math.washington.edu/home/sagemath/sage-mirror/linux/64bit/sage-5.1-linux-64bit-ubuntu_12.04_lts-x86_64-Linux.tar.lzma>,
 
and have a problem, apparently with libgfortran (see below).  Any help 
would be appreciated.

Thanks!

xyzzy> sage
--
| Sage Version 5.1, Release Date: 2012-07-09 |
| Type "notebook()" for the browser-based notebook interface.|
| Type "help()" for help.|
--
sage: plot(x^2,(x,0,1))
---
ImportError   Traceback (most recent call last)

/home/davidp/ in ()

/usr/local/sage/local/lib/python2.7/site-packages/IPython/Prompts.pyc in 
__call__(self, arg)
550 
551 # and now call a possibly user-defined print mechanism
--> 552 manipulated_val = self.display(arg)
553 
554 # user display hooks can change the variable to be 
stored in

/usr/local/sage/local/lib/python2.7/site-packages/IPython/Prompts.pyc in 
_display(self, arg)
576 return IPython.generics.result_display(arg)
577 except TryNext:
--> 578 return self.shell.hooks.result_display(arg)
579 
580 # Assign the default display method:

/usr/local/sage/local/lib/python2.7/site-packages/IPython/hooks.pyc in 
__call__(self, *args, **kw)
139 #print "prio",prio,"cmd",cmd #dbg
140 try:
--> 141 ret = cmd(*args, **kw)
142 return ret
143 except ipapi.TryNext, exc:

/usr/local/sage/local/lib/python2.7/site-packages/sage/misc/displayhook.pyc 
in result_display(ip_self, obj)
150 # IPython's default result_display() uses the 
IPython.genutils.Term.cout stream.
151 # See also local/lib/python2.6/site-packages/IPython/hooks.py.
--> 152 print_obj(IPython.genutils.Term.cout, obj)
153 
154 def displayhook(obj):

/usr/local/sage/local/lib/python2.7/site-packages/sage/misc/displayhook.pyc 
in print_obj(out_stream, obj)
142 if _check_tall_list_and_print(out_stream, obj):
143 return
--> 144 print >>out_stream, `obj`
145 
146 def result_display(ip_self, obj):

/usr/local/sage/local/lib/python2.7/site-packages/sage/structure/sage_object.so 
in sage.structure.sage_object.SageObject.__repr__ 
(sage/structure/sage_object.c:1496)()

/usr/local/sage/local/lib/python2.7/site-packages/sage/plot/graphics.pyc in 
_repr_(self)
801 """
802 if SHOW_DEFAULT:
--> 803 self.show()
804 return ''
805 else:

/usr/local/sage/local/lib/python2.7/site-packages/sage/misc/decorators.pyc 
in wrapper(*args, **kwds)
454 kwds[self.name + "options"] = suboptions
455 
--> 456 return func(*args, **kwds)
457 
458 #Add the options specified by @options to the signature of 
the wrapped

/usr/local/sage/local/lib/python2.7/site-packages/sage/plot/graphics.pyc in 
show(self, **kwds)
   1513 else:
   1514 kwds.setdefault('filename', 
sage.misc.misc.tmp_filename() + '.png')
-> 1515 self.save(**kwds)
   1516 os.system('%s %s 2>/dev/null 1>/dev/null &'
   1517   % (sage.misc.viewer.browser(), 
kwds['filename']))

/usr/local/sage/local/lib/python2.7/site-packages/sage/misc/decorators.pyc 
in wrapper(*args, **kwds)
454 kwds[self.name + "options"] = suboptions
455 
--> 456 return func(*args, **kwds)
457 
458 #Add the options specified by @options to the signature of 
the wrapped

/usr/local/sage/local/lib/python2.7/site-packages/sage/plot/graphics.pyc in 
save(self, filename, **kwds)
   2245 SageObject.save(self, filename)
   2246 else:
-> 2247 figure = self.matplotlib(**options)
   2248 # You can output in PNG, PS, EPS, PDF, or SVG format, 
depending on the file extension.
   2249 # matplotlib looks at the file extension to see what 
the renderer should be.

/usr/local/sage/local/lib/python2.7/site-packages/sage/plot/graphics.pyc in 
matplotlib(self, filename, xmin, xmax, ymin, ymax, figsize, figure, sub, 
axes, axes_labels, fontsize, frame, verify, aspect_ratio, gridlines, 
gridlinesstyle, vgridlinesstyle, hgridlinesstyle, show_legend, 
legend_options, axes_pad, ticks_integer, tick_formatter, ticks

[sage-support] labels on the frame of a 3d plot

[davidp]

Is there a way to turn off the labels on the frame in a 3d plot?  I
was hoping something like this might work:

var('x y')
plot3d(sin(x*y),(x,-2,2),(y,-2,2)).show(labels=false)

I know that I can set frame=false to get rid of the frame entirely,
but that is not what I am looking for.  Is there something like
plot.options for 3d graphic object?

Dave

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[sage-support] Re: drawing a graph that has only some of its edges oriented

[davidp]

My solution at the moment is to plot the graph setting save_pos=true.
Using the vertex positions determined by the plot, I create arrows for
the oriented edges.  I then plot the original plot of the graph plus
the arrows.

Dave

On Jun 29, 7:18 pm, davidp  wrote:
> Hi,
>
> I have found the need to think about "partially oriented" graphs: some
> edges have an orientation and others do not.  It would be natural to
> draw these with arrows for directed edges and lines for undirected
> edges.   What is the easiest way to do this with Sage?
>
> Thanks,
> Dave

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[sage-support] drawing a graph that has only some of its edges oriented

[davidp]

Hi,

I have found the need to think about "partially oriented" graphs: some
edges have an orientation and others do not.  It would be natural to
draw these with arrows for directed edges and lines for undirected
edges.   What is the easiest way to do this with Sage?

Thanks,
Dave

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[sage-support] mesh in parametric_plot3d

[davidp]

I would like to show my class a parametrized surface with mesh lines
(on Monday!).

1. The following code produces no mesh lines:

sage: var('x y')
sage: parametric_plot3d((x,x^2+y,x*y),(x,0,1),(y,
0,1),plot_points=10,mesh=true)

That seems odd to me.

2. The following code produces mesh lines, but they are very light in
color.  Is it possible to make the mesh lines thicker or to change
their color to black?

sage parametric_plot3d((x,x^2+y,x*y),(x,0,1),(y,
0,1),plot_points=10).show(mesh=true)

3. In general, I find it difficult to trace down which options are
applicable to the various plotting functions.  The documentation for
plot, plot3d, etc, list some options but not all, it seems.

I am using Sage 4.5.2 on Ubuntu 10.04.

Thanks,
Dave

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[sage-support] Re: matrix_plot

[davidp]

Thanks.

No problem.  I wrote a function to create what I wanted using
'polygon'.  It is useful to know that colormaps were not the answer.

Dave

On Aug 12, 3:47 pm, William Stein  wrote:
> On Thu, Aug 12, 2010 at 3:38 PM, davidp  wrote:
> > I am using Sage Version 4.3, Release Date: 2009-12-24.  The two plots:
>
> > matrix_plot(matrix(2,[2,2,3,3]),axes=false,frame=false)
> > matrix_plot(matrix(2,[1,1,3,3]),axes=false,frame=false)
>
> > look the same to me.  I tried various cmaps with the same result.  Is
> > there a way to set a cmap so that the plots of these matrices will be
> > distinct?
>
> No.  I think by default the input data is scaled to be between I think
> 0 and 1.  You'll have to try something besides color maps.
>
> William

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[sage-support] matrix_plot

[davidp]

I am using Sage Version 4.3, Release Date: 2009-12-24.  The two plots:

matrix_plot(matrix(2,[2,2,3,3]),axes=false,frame=false)
matrix_plot(matrix(2,[1,1,3,3]),axes=false,frame=false)

look the same to me.  I tried various cmaps with the same result.  Is
there a way to set a cmap so that the plots of these matrices will be
distinct?

Thanks,
Dave

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[sage-support] Re: missing eigenvectors

[davidp]

Thanks a lot!

Dave

On Aug 6, 7:29 pm, Jason Grout  wrote:
> On 8/6/10 11:56 AM, davidp wrote:
>
>
>
> > Sage has no trouble finding the eigenvectors of the 3x3 matrix below
> > but something is wrong in the 4x4 example.  Am I doing something
> > silly?
>
> > sage: version()
> > 'Sage Version 4.3, Release Date: 2009-12-24'
> > sage: m=matrix(CC,[[1,0,I],[1,1,0],[I,0,1]])
> > sage: m.eigenvectors_right()
> > [(1.00 + 1.00*I, [
> > (1.00, -1.00*I, 1.00)
> > ], 1), (1.00, [
> > (0, 1.00, 0)
> > ], 1), (1.00 - 1.00*I, [
> > (1.00, 1.00*I, -1.00)
> > ], 1)]
> > sage: n=matrix(CC,[[1,0,I,0],[1,1,0,I],[I,0,1,1],[0,I,0,2]])
> > sage: n.eigenvectors_right()
> > [(1.77621849241320 + 1.01489897201814*I, [
>
> > ], 1), (1.77621849241320 - 1.01489897201814*I, [
>
> > ], 1), (0.723781507586799 + 1.07181709265703*I, [
>
> > ], 1), (0.723781507586799 - 1.07181709265703*I, [
>
> > ], 1)]
>
> Short answer: use CDF, not CC.
>
> sage: n=matrix(CDF,[[1,0,I,0],[1,1,0,I],[I,0,1,1],[0,I,0,2]])
> sage: n.eigenvectors_right()
> [(0.723781507587 - 1.07181709266*I, [(-0.512558924324 -
> 0.132091804021*I, 0.462262927873 - 0.251444224409*I, 0.585855615051,
> -0.293915958782 - 0.115371137717*I)], 1), (1.77621849241 -
> 1.01489897202*I, [(0.340477754428 - 0.0450332871844*I, 0.598345310973,
> -0.38050619325 - 0.218580892372*I, -0.562226753834 - 0.123968940799*I)],
> 1), (0.723781507587 + 1.07181709266*I, [(0.512558924324 -
> 0.132091804021*I, -0.462262927873 - 0.251444224409*I, 0.585855615051,
> -0.293915958782 + 0.115371137717*I)], 1), (1.77621849241 +
> 1.01489897202*I, [(0.340477754428 + 0.0450332871844*I, 0.598345310973,
> 0.38050619325 - 0.218580892372*I, 0.562226753834 - 0.123968940799*I)], 1)]
>
> That will use LAPACK under the hood (via scipy).
>
> Medium answer: We will (very?!) soon have linear algebra over CC be very
> good, pending completion of ongoing work in wrapping ALGLIB in Sage.
>
> Long answer: Our generic algorithms are woefully inadequate for
> multiprecision linear algebra (we just do the textbook algorithms, which
> can have really bad roundoff error).  That is what CC employs.  In fact
> there is an error displayed to this effect the first time you try it:
>
> sage: n=matrix(CC,[[1,0,I,0],[1,1,0,I],[I,0,1,1],[0,I,0,2]])
> sage: n.eigenvectors_right()
> /Users/grout/sage/local/bin/sage-ipython:1: UserWarning: Using generic
> algorithm for an inexact ring, which may result in garbage from
> numerical precision issues.
>    #!/usr/bin/env python
> /Users/grout/sage/local/bin/sage-ipython:1: UserWarning: Using generic
> algorithm for an inexact ring, which will probably give incorrect
> results due to numerical precision issues.
>    #!/usr/bin/env python
> [(1.77621849241320 + 1.01489897201814*I, [
>
> ], 1), (1.77621849241320 - 1.01489897201814*I, [
>
> ], 1), (0.723781507586799 + 1.07181709265703*I, [
>
> ], 1), (0.723781507586799 - 1.07181709265703*I, [
>
> ], 1)]
>
> Thanks,
>
> Jason

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[sage-support] missing eigenvectors

[davidp]

Sage has no trouble finding the eigenvectors of the 3x3 matrix below
but something is wrong in the 4x4 example.  Am I doing something
silly?

sage: version()
'Sage Version 4.3, Release Date: 2009-12-24'
sage: m=matrix(CC,[[1,0,I],[1,1,0],[I,0,1]])
sage: m.eigenvectors_right()
[(1.00 + 1.00*I, [
(1.00, -1.00*I, 1.00)
], 1), (1.00, [
(0, 1.00, 0)
], 1), (1.00 - 1.00*I, [
(1.00, 1.00*I, -1.00)
], 1)]
sage: n=matrix(CC,[[1,0,I,0],[1,1,0,I],[I,0,1,1],[0,I,0,2]])
sage: n.eigenvectors_right()
[(1.77621849241320 + 1.01489897201814*I, [

], 1), (1.77621849241320 - 1.01489897201814*I, [

], 1), (0.723781507586799 + 1.07181709265703*I, [

], 1), (0.723781507586799 - 1.07181709265703*I, [

], 1)]

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[sage-support] image of a complex function

[davidp]

For a class I am teaching, I would like to display an image in the
plane---say a png-file--- and show how it is transformed under a
complex function f: C --> C.  What is the best way to do this?

Thanks,
Dave

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[sage-support] sage -t problems with semicolons and line breaks

[davidp]

On the file test.py, consisting of

"""
EXAMPLES::

sage: gcd(4,6);
sage: a = {1:'a',
   2:'b'}
"""

running sage -t produces two error messages (see below).  Is it true
that sage -t does not recognize semicolons and does not parse line
breaks correctly?  (Cutting and pasting the code in the examples into
sage produces no errors.)

Thanks,
Dave





| Sage Version 4.0.alpha0, Release Date: 2009-05-15

sage -t  "test.py"
******
File "/home/davidp/math/sandpile/sage/sage-sandpile1.4/test.py", line
4:
sage: gcd(4,6);
Expected nothing
Got:
2
******
File "/home/davidp/math/sandpile/sage/sage-sandpile1.4/test.py", line
5:
e: a = {1:'a',
Exception raised:
Traceback (most recent call last):
  File "/home/davidp/download/sage-devel/local/bin/ncadoctest.py",
line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
  File "/home/davidp/download/sage-devel/local/bin/
sagedoctest.py", line 38, in run_one_example
    OrigDocTestRunner.run_one_example(self, test, example,
filename, compileflags)
  File "/home/davidp/download/sage-devel/local/bin/ncadoctest.py",
line 1172, in run_one_example
compileflags, 1) in test.globs
  File "", line 1
 a = {Integer(1):'a',###line 5:
e: a = {1:'a',

^
 SyntaxError: unexpected EOF while parsing
**
1 items had failures:
   2 of   4 in __main__.example_0
***Test Failed*** 2 failures.

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[sage-support] Re: problem running sage -t

[davidp]

Same problem:

sage -t  "sandpile.py"
Traceback (most recent call last):
  File "./sandpile.py", line 18, in 
from sandpile import *
  File "/home/davidp/math/sandpile/sage/sage-sandpile1.4/sandpile.py",
line 167, in 
class Sandpile(DiGraph):
NameError: name 'DiGraph' is not defined

 [1.4 s]
exit code: 1024

--
The following tests failed:


sage -t  "sandpile.py"
Total time for all tests: 1.4 seconds


On Jun 4, 2:46 pm, Marshall Hampton  wrote:
> What happens if you rename it "sandpile.py"?  I'm not sure that will
> help but there are some funny differences between running .py
> and .sage files.
>
> -Marshall
>
> On Jun 2, 8:35 pm, davidp  wrote:
>
> > I would like to run the doctests in my file, "sandpile.sage", but get
> > the following error message:
>
> > ++===
> > xyzzy> sage -t sandpile.sage
> > sage -t  "sandpile.sage"
> > /usr/local/sage-devel/local/bin/sage-preparse: File file_name is
> > missing
> > Traceback (most recent call last):
> >   File "./sandpile.py", line 18, in 
> >     from sandpile import *
> >   File "/home/davidp/math/sandpile/sage/sage-sandpile1.4/sandpile.py",
> > line 167, in 
> >     class Sandpile(DiGraph):
> > NameError: name 'DiGraph' is not defined
>
> >          [1.6 s]
> > exit code: 1024
>
> > --
> > The following tests failed:
>
> >         sage -t  "sandpile.sage"
> > Total time for all tests: 1.6 seconds
> > ++
>
> > I tried adding
>
> >     from sage.graphs.graph import DiGraph
>
> > to the file but got the same error message.
>
> > Any suggestions?
>
> > Thanks,
> > Dave
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[sage-support] Re: fast slicing of matrix

[davidp]

Success!

sage: G = graphs.GridGraph([100,100])
sage: L = G.laplacian_matrix()
sage: L
1 x 1 sparse matrix over Integer Ring
sage: sage: time M = L[1:]
CPU times: user 21.98 s, sys: 0.01 s, total: 21.99 s
Wall time: 22.93 s
sage: sage: time N = L._delete_row_(0)
CPU times: user 0.01 s, sys: 0.00 s, total: 0.01 s
Wall time: 0.01 s
sage: sage: timeit('N = L._delete_row_(0)')
25 loops, best of 3: 10.9 ms per loop

I am travelling for the next several days but will follow up on this
soon.

Thanks a lot!


On Jun 2, 10:12 pm, William Stein  wrote:
> On Tue, Jun 2, 2009 at 10:10 PM, davidp  wrote:
>
> > I might be going down the wrong path, but is seems like I would want
> > to add a
>
> >         copy_mpz_vector_init
>
> > function to  vector_integer_sparse_c.pxi that would make a copy of an
> > mpz_vector.  Is that overkill?
>
> That sounds like a good idea to me.
>
> William
>
>
>
>
>
> > My first idea was to use add_mpz_vector_init(sum, v, w, mul), which
> > sets sum equal to v + mul*w, but let mul = 0.  However
> > add_mpz_vector_init returns the zero vector when mul = 0 !
>
> > Dave
>
> > On Jun 2, 9:06 pm, William Stein  wrote:
> >> On Tue, Jun 2, 2009 at 8:45 PM, davidp  wrote:
>
> >> > I can't figure out how to create a new sparse matrix (see below).
>
> >> > Sorry,
> >> > Dave
>
> >> You can make a new matrix with the analogous parent but a different
> >> shape using the new_matrix method.
>
> >> sage: a = random_matrix(ZZ,3,4,sparse=True)
> >> sage: a.new_matrix(2,4)
> >> [0 0 0 0]
> >> [0 0 0 0]
>
> >> In your cython code you would write something like
>
> >> cdef Matrix_integer_sparse M = a.new_matrix(2,4)
>
> >> William
>
> >> > M = Matrix_integer_sparse.__new__(Matrix_integer_sparse,
> >> > sage.matrix.matrix_space.MatrixSpace(ZZ, self._nrows-1, self._ncols,
> >> > sparse=True), None, None, None)
>
> >> > ---
> >> > ...
> >> >    def _delete_row_(self, Py_ssize_t row_number):
> >> >        cdef Py_ssize_t i
> >> >        cdef mpz_vector* self_row, *M_row
> >> >        cdef Matrix_integer_sparse M
>
> >> >        M = Matrix_integer_sparse.__new__(Matrix_integer_sparse,
> >> > sage.matrix.matrix_space.MatrixSpace(ZZ, self._nrows-1, self._ncols,
> >> > sparse=True), None, None, None)
>
> >> > ^
> >> > 
>
> >> > /usr/local/sage-devel/devel/sage-devel/sage/matrix/
> >> > matrix_integer_sparse.pyx:221:101: Compiler crash in
> >> > AnalyseExpressionsTransform
>
> >> > ModuleNode.body = StatListNode(matrix_integer_sparse.pyx:23:0)
> >> > StatListNode.stats[13] = StatListNode(matrix_integer_sparse.pyx:43:5)
> >> > StatListNode.stats[0] = CClassDefNode(matrix_integer_sparse.pyx:43:5,
> >> >    as_name = u'Matrix_integer_sparse',
> >> >    base_class_module = u'matrix_sparse',
> >> >    base_class_name = u'Matrix_sparse',
> >> >    class_name = u'Matrix_integer_sparse',
> >> >    module_name = '',
> >> >    visibility = 'private')
> >> > CClassDefNode.body = StatListNode(matrix_integer_sparse.pyx:55:4)
> >> > StatListNode.stats[9] = DefNode(matrix_integer_sparse.pyx:216:4,
> >> >    name = u'_delete_row_',
> >> >    num_required_args = 2,
> >> >    reqd_kw_flags_cname = '0')
> >> > File 'Nodes.py', line 360, in analyse_expressions: StatListNode
> >> > (matrix_integer_sparse.pyx:217:8)
> >> > File 'Nodes.py', line 2835, in analyse_expressions:
> >> > SingleAssignmentNode(matrix_integer_sparse.pyx:221:41)
> >> > File 'Nodes.py', line 2928, in analyse_types: SingleAssignmentNode
> >> > (matrix_integer_sparse.pyx:221:41)
> >> > File 'ExprNodes.py', line 2281, in analyse_types: SimpleCallNode
> >> > (matrix_integer_sparse.pyx:221:41)
> >> > File 'ExprNodes.py', line 3105, in analyse_types: TupleNode
> >> > (matrix_integer_sparse.pyx:221:41,
> >> >    is_sequence_constructor = 1)
> >> > File 'ExprNodes.py', line 2972, in analyse_types: TupleNode
> >> > (matrix_integer_sparse.pyx:221:41,
> >> >    is_sequence_constructor = 1)
> >> > File 'ExprNodes.py'

[sage-support] Re: fast slicing of matrix

[davidp]

I might be going down the wrong path, but is seems like I would want
to add a

 copy_mpz_vector_init

function to  vector_integer_sparse_c.pxi that would make a copy of an
mpz_vector.  Is that overkill?

My first idea was to use add_mpz_vector_init(sum, v, w, mul), which
sets sum equal to v + mul*w, but let mul = 0.  However
add_mpz_vector_init returns the zero vector when mul = 0 !

Dave

On Jun 2, 9:06 pm, William Stein  wrote:
> On Tue, Jun 2, 2009 at 8:45 PM, davidp  wrote:
>
> > I can't figure out how to create a new sparse matrix (see below).
>
> > Sorry,
> > Dave
>
> You can make a new matrix with the analogous parent but a different
> shape using the new_matrix method.
>
> sage: a = random_matrix(ZZ,3,4,sparse=True)
> sage: a.new_matrix(2,4)
> [0 0 0 0]
> [0 0 0 0]
>
> In your cython code you would write something like
>
> cdef Matrix_integer_sparse M = a.new_matrix(2,4)
>
> William
>
>
>
>
>
> > M = Matrix_integer_sparse.__new__(Matrix_integer_sparse,
> > sage.matrix.matrix_space.MatrixSpace(ZZ, self._nrows-1, self._ncols,
> > sparse=True), None, None, None)
>
> > ---
> > ...
> >    def _delete_row_(self, Py_ssize_t row_number):
> >        cdef Py_ssize_t i
> >        cdef mpz_vector* self_row, *M_row
> >        cdef Matrix_integer_sparse M
>
> >        M = Matrix_integer_sparse.__new__(Matrix_integer_sparse,
> > sage.matrix.matrix_space.MatrixSpace(ZZ, self._nrows-1, self._ncols,
> > sparse=True), None, None, None)
>
> > ^
> > 
>
> > /usr/local/sage-devel/devel/sage-devel/sage/matrix/
> > matrix_integer_sparse.pyx:221:101: Compiler crash in
> > AnalyseExpressionsTransform
>
> > ModuleNode.body = StatListNode(matrix_integer_sparse.pyx:23:0)
> > StatListNode.stats[13] = StatListNode(matrix_integer_sparse.pyx:43:5)
> > StatListNode.stats[0] = CClassDefNode(matrix_integer_sparse.pyx:43:5,
> >    as_name = u'Matrix_integer_sparse',
> >    base_class_module = u'matrix_sparse',
> >    base_class_name = u'Matrix_sparse',
> >    class_name = u'Matrix_integer_sparse',
> >    module_name = '',
> >    visibility = 'private')
> > CClassDefNode.body = StatListNode(matrix_integer_sparse.pyx:55:4)
> > StatListNode.stats[9] = DefNode(matrix_integer_sparse.pyx:216:4,
> >    name = u'_delete_row_',
> >    num_required_args = 2,
> >    reqd_kw_flags_cname = '0')
> > File 'Nodes.py', line 360, in analyse_expressions: StatListNode
> > (matrix_integer_sparse.pyx:217:8)
> > File 'Nodes.py', line 2835, in analyse_expressions:
> > SingleAssignmentNode(matrix_integer_sparse.pyx:221:41)
> > File 'Nodes.py', line 2928, in analyse_types: SingleAssignmentNode
> > (matrix_integer_sparse.pyx:221:41)
> > File 'ExprNodes.py', line 2281, in analyse_types: SimpleCallNode
> > (matrix_integer_sparse.pyx:221:41)
> > File 'ExprNodes.py', line 3105, in analyse_types: TupleNode
> > (matrix_integer_sparse.pyx:221:41,
> >    is_sequence_constructor = 1)
> > File 'ExprNodes.py', line 2972, in analyse_types: TupleNode
> > (matrix_integer_sparse.pyx:221:41,
> >    is_sequence_constructor = 1)
> > File 'ExprNodes.py', line 2522, in analyse_types: GeneralCallNode
> > (matrix_integer_sparse.pyx:221:101)
>
> > Compiler crash traceback from this point on:
> >  File "/usr/local/sage-devel/local/lib/python2.5/site-packages/Cython/
> > Compiler/ExprNodes.py", line 2532, in analyse_types
> >    if hasattr(self.function, 'entry') and not
> > self.function.entry.as_variable:
> > AttributeError: 'NoneType' object has no attribute 'as_variable'
> > Error running command, failed with status 256.
> > sage: There was an error installing modified sage library code.
>
> > On Jun 2, 7:28 pm, William Stein  wrote:
> >> On Tue, Jun 2, 2009 at 7:22 PM, davidp  wrote:
>
> >> > I tried adding a delete_row method to matrix_integer_sparse.pyx but
> >> > stopped after getting the error message:
>
> >> Just def your method -- do not cpdef it.  You can still use Cython
> >> code in a cpdef's method and it will be just as fast.
>
> >> Make sure that your "delete row" method returns a *new* matrix by the 
> >> way...
>
> >> William
>
> >> > +
> >> > Error convert

[sage-support] Re: fast slicing of matrix

[davidp]

I can't figure out how to create a new sparse matrix (see below).

Sorry,
Dave

M = Matrix_integer_sparse.__new__(Matrix_integer_sparse,
sage.matrix.matrix_space.MatrixSpace(ZZ, self._nrows-1, self._ncols,
sparse=True), None, None, None)


---
...
def _delete_row_(self, Py_ssize_t row_number):
cdef Py_ssize_t i
cdef mpz_vector* self_row, *M_row
cdef Matrix_integer_sparse M

M = Matrix_integer_sparse.__new__(Matrix_integer_sparse,
sage.matrix.matrix_space.MatrixSpace(ZZ, self._nrows-1, self._ncols,
sparse=True), None, None, None)
 
^


/usr/local/sage-devel/devel/sage-devel/sage/matrix/
matrix_integer_sparse.pyx:221:101: Compiler crash in
AnalyseExpressionsTransform

ModuleNode.body = StatListNode(matrix_integer_sparse.pyx:23:0)
StatListNode.stats[13] = StatListNode(matrix_integer_sparse.pyx:43:5)
StatListNode.stats[0] = CClassDefNode(matrix_integer_sparse.pyx:43:5,
as_name = u'Matrix_integer_sparse',
base_class_module = u'matrix_sparse',
base_class_name = u'Matrix_sparse',
class_name = u'Matrix_integer_sparse',
module_name = '',
visibility = 'private')
CClassDefNode.body = StatListNode(matrix_integer_sparse.pyx:55:4)
StatListNode.stats[9] = DefNode(matrix_integer_sparse.pyx:216:4,
name = u'_delete_row_',
num_required_args = 2,
reqd_kw_flags_cname = '0')
File 'Nodes.py', line 360, in analyse_expressions: StatListNode
(matrix_integer_sparse.pyx:217:8)
File 'Nodes.py', line 2835, in analyse_expressions:
SingleAssignmentNode(matrix_integer_sparse.pyx:221:41)
File 'Nodes.py', line 2928, in analyse_types: SingleAssignmentNode
(matrix_integer_sparse.pyx:221:41)
File 'ExprNodes.py', line 2281, in analyse_types: SimpleCallNode
(matrix_integer_sparse.pyx:221:41)
File 'ExprNodes.py', line 3105, in analyse_types: TupleNode
(matrix_integer_sparse.pyx:221:41,
is_sequence_constructor = 1)
File 'ExprNodes.py', line 2972, in analyse_types: TupleNode
(matrix_integer_sparse.pyx:221:41,
is_sequence_constructor = 1)
File 'ExprNodes.py', line 2522, in analyse_types: GeneralCallNode
(matrix_integer_sparse.pyx:221:101)

Compiler crash traceback from this point on:
  File "/usr/local/sage-devel/local/lib/python2.5/site-packages/Cython/
Compiler/ExprNodes.py", line 2532, in analyse_types
if hasattr(self.function, 'entry') and not
self.function.entry.as_variable:
AttributeError: 'NoneType' object has no attribute 'as_variable'
Error running command, failed with status 256.
sage: There was an error installing modified sage library code.


On Jun 2, 7:28 pm, William Stein  wrote:
> On Tue, Jun 2, 2009 at 7:22 PM, davidp  wrote:
>
> > I tried adding a delete_row method to matrix_integer_sparse.pyx but
> > stopped after getting the error message:
>
> Just def your method -- do not cpdef it.  You can still use Cython
> code in a cpdef's method and it will be just as fast.
>
> Make sure that your "delete row" method returns a *new* matrix by the way...
>
> William
>
>
>
>
>
> > +
> > Error converting Pyrex file to C:
> > 
> > ...
> >            add_mpz_vector_init(&M._matrix[i], &self._matrix[i], &
> > (right)._matrix[i], mul)
> >        mpz_clear(mul)
> >        return M
>
> > # added by David Perkinson
> >    cpdef ModuleElement _delete_row_(self, Py_ssize_t row_number):
> >         ^
> > 
>
> > /usr/local/sage-devel/devel/sage-devel/sage/matrix/
> > matrix_integer_sparse.pyx:216:10: C method '_delete_row_' not
> > previously declared in definition part of extension type
> > Error running command, failed with status 256.
> > sage: There was an error installing modified sage library code.
>
> > ++
>
> > I might have to actually read the Cython documentation!
>
> > Dave
>
> > On Jun 2, 5:43 pm, Jason Grout  wrote:
> >> William Stein wrote:
> >> > On Mon, Jun 1, 2009 at 5:16 PM, davidp  wrote:
> >> >> Is there a fast way to create a submatrix?
>
> >> >> -
>
> >> >> sage: version()
> >> >> 'Sage Version 4.0.alpha0, Release Date: 2009-05-15'
> >> >> sage: G = graphs.GridGraph([100,100])
> >> >> sage: L = G.laplacian_matrix()
> >> >> 

[sage-support] problem running sage -t

[davidp]

I would like to run the doctests in my file, "sandpile.sage", but get
the following error message:

++===
xyzzy> sage -t sandpile.sage
sage -t  "sandpile.sage"
/usr/local/sage-devel/local/bin/sage-preparse: File file_name is
missing
Traceback (most recent call last):
  File "./sandpile.py", line 18, in 
from sandpile import *
  File "/home/davidp/math/sandpile/sage/sage-sandpile1.4/sandpile.py",
line 167, in 
class Sandpile(DiGraph):
NameError: name 'DiGraph' is not defined

 [1.6 s]
exit code: 1024

--
The following tests failed:


sage -t  "sandpile.sage"
Total time for all tests: 1.6 seconds
++

I tried adding

from sage.graphs.graph import DiGraph

to the file but got the same error message.

Any suggestions?

Thanks,
Dave
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[sage-support] Re: fast slicing of matrix

[davidp]

I tried adding a delete_row method to matrix_integer_sparse.pyx but
stopped after getting the error message:

+
Error converting Pyrex file to C:

...
add_mpz_vector_init(&M._matrix[i], &self._matrix[i], &
(right)._matrix[i], mul)
mpz_clear(mul)
return M

# added by David Perkinson
cpdef ModuleElement _delete_row_(self, Py_ssize_t row_number):
 ^


/usr/local/sage-devel/devel/sage-devel/sage/matrix/
matrix_integer_sparse.pyx:216:10: C method '_delete_row_' not
previously declared in definition part of extension type
Error running command, failed with status 256.
sage: There was an error installing modified sage library code.

++

I might have to actually read the Cython documentation!

Dave



On Jun 2, 5:43 pm, Jason Grout  wrote:
> William Stein wrote:
> > On Mon, Jun 1, 2009 at 5:16 PM, davidp  wrote:
> >> Is there a fast way to create a submatrix?
>
> >> -
>
> >> sage: version()
> >> 'Sage Version 4.0.alpha0, Release Date: 2009-05-15'
> >> sage: G = graphs.GridGraph([100,100])
> >> sage: L = G.laplacian_matrix()
> >> sage: L
> >> 1 x 1 sparse matrix over Integer Ring
> >> sage: time M = L[1:,1:]
> >> CPU times: user 24.93 s, sys: 0.04 s, total: 24.97 s
> >> Wall time: 25.27 s
>
> >> 
>
> >> I am just interested in deleting a single row and column of the matrix
> >> (not necessarily the first).
>
> >> Thanks,
>
> > There is no fast way to do that right now.  One could easily add code
> > to SAGE_ROOT/devel/sage/sage/matrix/matrix_integer_sparse.pyx that
> > would provide blazingly fast deletion of a row, and reasonably fast
> > deletion of a column.   Of course it would be better to implement
> > arbitrary slicing in some optimized way in matrix_integer_sparse.pyx.
> > I hope somebody does so.
>
> Just looking at the generic code, it seems that it goes through each and
> every index position in the slice, setting the new matrix entry to the
> old one.  This is obviously the wrong thing to do for sparse matrices,
> and can likely trivially be made faster.  I think all you may have to do
> is override the matrix_from_rows_and_columns for sparse matrices.
>
> Jason
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[sage-support] fast slicing of matrix

[davidp]

Is there a fast way to create a submatrix?

-


sage: version()
'Sage Version 4.0.alpha0, Release Date: 2009-05-15'
sage: G = graphs.GridGraph([100,100])
sage: L = G.laplacian_matrix()
sage: L
1 x 1 sparse matrix over Integer Ring
sage: time M = L[1:,1:]
CPU times: user 24.93 s, sys: 0.04 s, total: 24.97 s
Wall time: 25.27 s




I am just interested in deleting a single row and column of the matrix
(not necessarily the first).

Thanks,
Dave
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[sage-support] Re: using sphinx to create a manual

[davidp]

I guess I figured it out.  In the conf.py file:

# The reST default role (used for this markup: `text`) to use for all
documents.
default_role = 'math'

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[sage-support] using sphinx to create a manual

[davidp]

I am writing a manual for a Sage package I am developing.  It seems
natural to use Sphinx/reST.  I made an independent installation of
Sphinx and eventually realized that to typeset mathematics, I need to
write, for example, :math:`\Gamma` instead of Sage's cleaner version: `
\Gamma`.  The latter is obviously preferable (and $'s would be even
better, of course).

Any suggestions?

Thanks,
Dave
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[sage-support] odd behavior from integral

[davidp]

The following seems like odd behavior to me.

Dave

I. No problem:
sage: integral(log(x)/x^(1.002),x)
500*(-log(x)/x^(1/500) - 500/x^(1/500))
sage: s(10)-s(1)
500*(-log(10)/10^(1/500) - 500/10^(1/500)) + 25
sage: n(_)
2.64282437870861

II. Problem:
sage: integral(log(x)/x^(1.002),x,1,10)
---
TypeError Traceback (most recent call
last)

/home/davidp/ in ()

/usr/local/sage-3.4-Fedora_release_9-i686-Linux/local/lib/python2.5/
site-packages/sage/misc/functional.pyc in integral(x, *args, **kwds)
435 """
436 if hasattr(x, 'integral'):
--> 437 return x.integral(*args, **kwds)
438 else:
439 from sage.calculus.calculus import SR

/usr/local/sage-3.4-Fedora_release_9-i686-Linux/local/lib/python2.5/
site-packages/sage/calculus/calculus.pyc in integral(self, v, a, b)
   3068 else:
   3069 try:
-> 3070 return self.parent()(self._maxima_().integrate
(v, a, b))
   3071 except TypeError, error:
   3072 s = str(error)

/usr/local/sage-3.4-Fedora_release_9-i686-Linux/local/lib/python2.5/
site-packages/sage/interfaces/maxima.pyc in integral(self, var, min,
max)
   1994 if max is None:
   1995 raise ValueError, "neither or both of min/max
must be specified."
-> 1996 return I(var, min, max)
   1997
   1998 integrate = integral

/usr/local/sage-3.4-Fedora_release_9-i686-Linux/local/lib/python2.5/
site-packages/sage/interfaces/expect.pyc in __call__(self, *args,
**kwds)
   1332
   1333 def __call__(self, *args, **kwds):
-> 1334 return self._obj.parent().function_call(self._name,
[self._obj] + list(args), kwds)
   1335
   1336 def help(self):

/usr/local/sage-3.4-Fedora_release_9-i686-Linux/local/lib/python2.5/
site-packages/sage/interfaces/expect.pyc in function_call(self,
function, args, kwds)
   1252 self._check_valid_function_name(function)
   1253 return self.new("%s(%s)"%(function, ",".join([s.name()
for s in args]+
-> 1254  ['%s=%s'%
(key,value.name()) for key, value in kwds.items()])))
   1255
   1256 def call(self, function_name, *args, **kwds):

/usr/local/sage-3.4-Fedora_release_9-i686-Linux/local/lib/python2.5/
site-packages/sage/interfaces/expect.pyc in new(self, code)
   1065
   1066 def new(self, code):
-> 1067 return self(code)
   1068
   1069
###

/usr/local/sage-3.4-Fedora_release_9-i686-Linux/local/lib/python2.5/
site-packages/sage/interfaces/expect.pyc in __call__(self, x, name)
   1000 return x
   1001 if isinstance(x, basestring):
-> 1002 return cls(self, x, name=name)
   1003 try:
   1004 return self._coerce_from_special_method(x)

/usr/local/sage-3.4-Fedora_release_9-i686-Linux/local/lib/python2.5/
site-packages/sage/interfaces/expect.pyc in __init__(self, parent,
value, is_name, name)
   1375 except (TypeError, KeyboardInterrupt,
RuntimeError, ValueError), x:
   1376 self._session_number = -1
-> 1377 raise TypeError, x
   1378 self._session_number = parent._session_number
   1379

TypeError: Computation failed since Maxima requested additional
constraints (try the command 'assume(>0)' before integral or limit
evaluation, for example):
 an integer?

III.  Problem:
sage: numerical_integral(log(x)/x^(1.002),x,1,10)
---
TypeError Traceback (most recent call
last)

/home/davidp/ in ()

/usr/local/sage-3.4-Fedora_release_9-i686-Linux/local/lib/python2.5/
site-packages/sage/gsl/integration.so in
sage.gsl.integration.numerical_integral (sage/gsl/integration.c:2008)
()

TypeError: invalid integration algorithm


Dave



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[sage-support] Re: new cell in worksheet

[davidp]

I am running Sage 3.4 under Fedora 10.  I am having trouble inserting
a cell (of any type) right before a text cell in a worksheet.

I have tried the following:

1. Hovering the mouse just above the text cell.
2. Going to a calculation cell just above the text cell and trying
shift-click, alt-click, control-click.

My solution has been to leave an empty calculation cell between the
text cell and the cells preceding the text cell.

Thanks for any suggestions.

Dave

On Mar 24, 2:41 am, Stan Schymanski  wrote:
> Hi Jason,
>
> Thanks a lot for that! Your proposal sounds good. Pity it hasn't been
> implemented yet, but perhaps the tickets you submitted will help. I'll
> contribute my thoughts when I have an account.
>
> Stan
>
> On Mar 23, 4:01 pm, Jason Grout  wrote:
>
> > Stan Schymanski wrote:
> > > Thanks for your feedback, Jason! Could you submit a ticket for this to
> > > be fixed/enhanced? Unfortunately, I can't do it myself.
>
> > We should get you a trac account, then.  You can follow the instructions
> > onhttp://trac.sagemath.org/sage_trac/
>
> > The bugs are nowhttp://trac.sagemath.org/sage_trac/ticket/5591
>
> > and
>
> > The bug is nowhttp://trac.sagemath.org/sage_trac/ticket/5592
>
> > As for the alt-enter and ctrl-enter thing, can you look at my proposal
> > in the last few messages in this 
> > thread:http://groups.google.com/group/sage-devel/browse_thread/thread/5892dd...
>
> > (specifically,http://groups.google.com/group/sage-devel/msg/e351edd7b62437b9)
>
> > That proposal deals with splitting cells.
>
> > Note that two adjacent text cells are merged whenever the sheet is saved
> > and reopened.  I don't know that alt-enter and ctrl-enter makes sense
> > right now (however, maybe the text cells shouldn't be merged, and maybe
> > alt-enter and ctrl-enter should make sense...)
>
> > Jasno
>
> > > Cheers,
> > > Stan
>
> > > Jason Grout wrote:
> > >> Stan Schymanski wrote:
>
> > >>> In this context, I'm having trouble inserting a calculationcellbefore
> > >>> a htmlcellor between two html cells in Sage 3.4. The Alt-Enter or
> > >>> Ctrl-Enter methods don't not work in html cells.
>
> > >> Both of these are because they have not been implemented.  Contributions
> > >> are definitely welcome!
>
> > >>> If I want toinserta
> > >>> calculationcellbefore an htmlcell, I can't just press Alt-Enter in
> > >>> the foregoing calculationcell, because this creates anewcalculation
> > >>>cellAFTER the htmlcell. Is there another way?
>
> > >> Hmmm...I'd consider this a bug.  The Alt-enter should make anew
> > >> calculationcellright after the old calculationcell(before the
> > >> following htmlcell).
>
> > >> Jason
>
> > >>> Cheers,
> > >>> Stan
>
> > >>> kcrisman wrote:
>
> >  Dear Kwankyu,
>
> > > If I write and evaluate in acellin aworksheetand if there are
> > > already cells below the one which I am evaluating, then the cursor
> > > moves into thecelljust below instead of creating anewcellfor next
> > > input. Is this behavior preferable? This is annoying at least to me.
>
> >  One of the designers can answer for the technical reasons for this
> >  design decision, but let me tell you it is very useful when you are
> >  running through aworksheetyou have already created, but changing a
> >  few things (e.g. some initial constant defined at the top)!
>
> >  But actually, if you click on "Help" you will see that Alt-Enter
> >  actually does what you require, while Ctrl-Enter splits thecelland
> >  evaluates both things.  I didn't know either of these until I looked
> >  just now, and will definitely use them now too.
>
> >  Enjoy!
>
> >  - kcrisman
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[sage-support] opening a saved jmol file

[davidp]

In the sage notebook, how can I open (display) a file I saved in jmol
format?

Thanks,
Dave
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[sage-support] Re: showing graphs with multiple edges

[davidp]

Sorry.  I was not being clear.  I was surprised by the fact that
*only* the latter shows multiple edges.

I am also surprised that arrowheads don't appear with multiple edges.
This is especially a problem with weighted digraphs.

(By the way, it probably would have been better for me to have written

sage: G = DiGraph({1:{2: 2}, 2:{1:1}}, weighted=True)

so that the Laplacian comes out correctly.  However, this doesn't help
with my problem.)

Dave

On Mar 19, 6:01 pm, Jason Grout  wrote:
> davidp wrote:
> > Hi,
>
> > I was a bit surprised by the difference exhibited below:
>
> > sage: G = DiGraph({1:{2: 2}, 2:{1:1}})
> > sage: G.show()
>
> I'm surprised by the output of this.  There are clearly two edges in the
> graph: 1->2 and 2->1, but only one edge is shown.
>
> > sage: DiGraph(G.laplacian_matrix()).show()
>
> The Laplacian matrix has nonzero entries indicating edges from each
> vertex to each other vertex, so why do you find it surprising that there
> are two edges?
>
> sage: H=DiGraph(G.laplacian_matrix())
> sage: H.edges()
> [(0, 0, 1), (0, 1, -1), (1, 0, -1), (1, 1, 1)]
>
> I find it surprising that arrowheads don't appear in the following, though:
>
> sage: DiGraph(G.laplacian_matrix()).show()
>
> Thanks,
>
> Jason
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[sage-support] showing graphs with multiple edges

[davidp]

Hi,

I was a bit surprised by the difference exhibited below:

sage: G = DiGraph({1:{2: 2}, 2:{1:1}})
sage: G.show()
sage: DiGraph(G.laplacian_matrix()).show()

The latter draws multiple edges.

Dave
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[sage-support] resetting vertex labels

[davidp]

Suppose G is a DiGraph.  Is there a way to change the vertex labels of
G so that they are shown when G.show() is called?  The method,
G.set_vertex() does not seem to do that.

Sample code

sage: G = DiGraph({1:{2: 2}, 2:{1:1}})
sage: G.show()
sage: G.set_vertex(1,4)
sage: G.show() # <-- there is no change

What I am really after is this: I have a collection of integers, one
for each vertex.  Over time the integers change.  I would like to show
the graph with vertices labeled by these integers.  Best of all would
be to do this via @interact.

Thanks,
Dave
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[sage-support] Re: Small groups library is missing

[davidp]

That works.  Thanks a lot.

Dave


On Mar 16, 3:54 pm, David Joyner  wrote:
> Please try
>
> http://sage.math.washington.edu/home/wdj/patches/gap_packages-4.4.12_...http://sage.math.washington.edu/home/wdj/patches/database_gap-4.4.12
>
> instead. If you have problem, please email me.
>
> Thanks.
>
> On Mon, Mar 16, 2009 at 6:50 PM, davidp  wrote:
>
> > I have just installed Sage 3.4, database_gap-4.4.10, and
> > gap_packages-4.4.10_6.  It seems that I can't access 'SmallGroups':
>
> > sage: gap.eval('SmallGroups(8,1)')
> > ---
> > RuntimeError                              Traceback (most recent call
> > last)
>
> > /home/davidp/download/ in ()
>
> > /usr/local/sage-3.4-Fedora_release_9-i686-Linux/local/lib/python2.5/
> > site-packages/sage/interfaces/gap.pyc in eval(self, x, newlines,
> > strip, **kwds)
> >    477             input_line += ';'
> >    478
> > --> 479         result = Expect.eval(self, input_line, **kwds)
> >    480
> >    481         if not newlines:
>
> > /usr/local/sage-3.4-Fedora_release_9-i686-Linux/local/lib/python2.5/
> > site-packages/sage/interfaces/expect.pyc in eval(self, code, strip,
> > synchronize, locals, **kwds)
> >    972         try:
> >    973             with gc_disabled():
> > --> 974                 return '\n'.join([self._eval_line(L, **kwds)
> > for L in code.split('\n') if L != ''])
> >    975         except KeyboardInterrupt:
> >    976             # DO NOT CATCH KeyboardInterrupt, as it is being
> > caught
>
> > /usr/local/sage-3.4-Fedora_release_9-i686-Linux/local/lib/python2.5/
> > site-packages/sage/interfaces/gap.pyc in _eval_line(self, line,
> > allow_use_file, wait_for_prompt)
> >    721                         return ''
> >    722                 else:
> > --> 723                     raise RuntimeError, message
> >    724
> >    725         except KeyboardInterrupt:
>
> > RuntimeError: Gap produced error output
> > Variable: 'SmallGroups' must have a value
>
> >   executingSmallGroups(8,1);
> > sage: gap('SmallGroup(8,1)')
> > ---
> > TypeError                                 Traceback (most recent call
> > last)
>
> > /home/davidp/download/ in ()
>
> > /usr/local/sage-3.4-Fedora_release_9-i686-Linux/local/lib/python2.5/
> > site-packages/sage/interfaces/expect.pyc in __call__(self, x, name)
> >   1000             return x
> >   1001         if isinstance(x, basestring):
> > -> 1002             return cls(self, x, name=name)
> >   1003         try:
> >   1004             return self._coerce_from_special_method(x)
>
> > /usr/local/sage-3.4-Fedora_release_9-i686-Linux/local/lib/python2.5/
> > site-packages/sage/interfaces/expect.pyc in __init__(self, parent,
> > value, is_name, name)
> >   1375             except (TypeError, KeyboardInterrupt,
> > RuntimeError, ValueError), x:
> >   1376                 self._session_number = -1
> > -> 1377                 raise TypeError, x
> >   1378         self._session_number = parent._session_number
> >   1379
>
> > TypeError: Gap produced error output
> > Error, the Small Groups library is required but not installed
>
> >   executing $sage1:=SmallGroup(8,1);;
>
> > I am running Sage under Fedora 10, 32bit.  The command "sage -i"
> > seemed to install the two packages without complaint.
>
> > So is this still a known problem?
>
> > Thanks,
> > Dave
>
> > On Mar 2, 6:33 pm, David Joyner  wrote:
> >> On Mon, Mar 2, 2009 at 3:51 PM, David Joyner  wrote:
> >> > I am trying and failing to get the sage-install script to work.
>
> >> ...
>
> >> > 
> >> > /bin/ls: cannot access gap-*.spkg: No such file or directory
>
> >> > /bin/ls: cannot access gap-*.spkg: No such file or directory
> >> > ./spkg-install: line 13: patches: command not found
>
> >> > ./spkg-install: line 14: Installing: command not found
>
> >> > ./spkg-install: line 15: Installing: command not found
>
> >> > ./spkg-install: line 16: patches: command not found
>
> >> > 
> >> > 
>
> >> > Does anyone have an idea what the problem could be?
>
> >> I finally figured out that (a) I was in the wrong directory
> >> and (b) spaces matter for shell scripts. It now works in Linux.
> >> I'm going to test in on a mac OS 10.4 and then post a link to the trac 
> >> ticket
> >> if that works.
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[sage-support] Re: Small groups library is missing

[davidp]

I have just installed Sage 3.4, database_gap-4.4.10, and
gap_packages-4.4.10_6.  It seems that I can't access 'SmallGroups':

sage: gap.eval('SmallGroups(8,1)')
---
RuntimeError  Traceback (most recent call
last)

/home/davidp/download/ in ()

/usr/local/sage-3.4-Fedora_release_9-i686-Linux/local/lib/python2.5/
site-packages/sage/interfaces/gap.pyc in eval(self, x, newlines,
strip, **kwds)
477 input_line += ';'
478
--> 479 result = Expect.eval(self, input_line, **kwds)
480
481 if not newlines:

/usr/local/sage-3.4-Fedora_release_9-i686-Linux/local/lib/python2.5/
site-packages/sage/interfaces/expect.pyc in eval(self, code, strip,
synchronize, locals, **kwds)
972 try:
973 with gc_disabled():
--> 974 return '\n'.join([self._eval_line(L, **kwds)
for L in code.split('\n') if L != ''])
975 except KeyboardInterrupt:
976 # DO NOT CATCH KeyboardInterrupt, as it is being
caught

/usr/local/sage-3.4-Fedora_release_9-i686-Linux/local/lib/python2.5/
site-packages/sage/interfaces/gap.pyc in _eval_line(self, line,
allow_use_file, wait_for_prompt)
721 return ''
722 else:
--> 723 raise RuntimeError, message
724
725 except KeyboardInterrupt:

RuntimeError: Gap produced error output
Variable: 'SmallGroups' must have a value


   executing SmallGroups(8,1);
sage: gap('SmallGroup(8,1)')
-------
TypeError Traceback (most recent call
last)

/home/davidp/download/ in ()

/usr/local/sage-3.4-Fedora_release_9-i686-Linux/local/lib/python2.5/
site-packages/sage/interfaces/expect.pyc in __call__(self, x, name)
   1000 return x
   1001 if isinstance(x, basestring):
-> 1002 return cls(self, x, name=name)
   1003 try:
   1004 return self._coerce_from_special_method(x)

/usr/local/sage-3.4-Fedora_release_9-i686-Linux/local/lib/python2.5/
site-packages/sage/interfaces/expect.pyc in __init__(self, parent,
value, is_name, name)
   1375 except (TypeError, KeyboardInterrupt,
RuntimeError, ValueError), x:
   1376 self._session_number = -1
-> 1377 raise TypeError, x
   1378 self._session_number = parent._session_number
   1379

TypeError: Gap produced error output
Error, the Small Groups library is required but not installed

   executing $sage1:=SmallGroup(8,1);;


I am running Sage under Fedora 10, 32bit.  The command "sage -i"
seemed to install the two packages without complaint.

So is this still a known problem?

Thanks,
Dave

On Mar 2, 6:33 pm, David Joyner  wrote:
> On Mon, Mar 2, 2009 at 3:51 PM, David Joyner  wrote:
> > I am trying and failing to get the sage-install script to work.
>
> ...
>
>
>
> > 
> > /bin/ls: cannot access gap-*.spkg: No such file or directory
>
> > /bin/ls: cannot access gap-*.spkg: No such file or directory
> > ./spkg-install: line 13: patches: command not found
>
> > ./spkg-install: line 14: Installing: command not found
>
> > ./spkg-install: line 15: Installing: command not found
>
> > ./spkg-install: line 16: patches: command not found
>
> > 
> > 
>
> > Does anyone have an idea what the problem could be?
>
> I finally figured out that (a) I was in the wrong directory
> and (b) spaces matter for shell scripts. It now works in Linux.
> I'm going to test in on a mac OS 10.4 and then post a link to the trac ticket
> if that works.
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[sage-support] Re: Sage 3.4 on Fedora: cannot execute binary file

[davidp]

Thanks!

On Mar 14, 11:19 am, mabshoff  wrote:
> Ok, there is now a 32 bit FC9 binary - I had it on sage.math all along
> and it did get lost in the shuffle when putting things in the various
> directories.
>
> Cheers,
>
> Michael
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[sage-support] Re: Sage 3.4 on Fedora: cannot execute binary file

[davidp]

Is it strange, then, to list this binary under 32bit:

http://sagemath.org/bin/linux/32bit/index.html

Also, I don't see a release for i686.  Perhaps that will come later.

Thanks,
Dave

On Mar 14, 8:37 am, Jaap Spies  wrote:
> davidp wrote:
> > I am having trouble starting Sage 3.4 on two machines running Fedora:
>
> > 1.
> > poly> cd sage-3.4-Fedora_release_9-x86_64-Linux/
> > poly> ./sage
> > --
> > | Sage Version 3.4, Release Date: 2009-03-11                         |
> > | Type notebook() for the GUI, and license() for information.        |
> > --
> > /home/davidp/download/sage-3.4-Fedora_release_9-x86_64-Linux/local/bin/
> > sage.bin: /home/davidp/download/sage-3.4-Fedora_release_9-x86_64-Linux/
> > local/bin/sage.bin: cannot execute binary file
> > poly> uname -a
> > Linux poly 2.6.27.19-78.2.30.fc9.i686 #1 SMP Tue Feb 24 20:09:23 EST
> > 2009 i686 i686 i386 GNU/Linux
>
> > 2.
> > xyzzy> cd sage-3.4-Fedora_release_9-x86_64-Linux/
> > xyzzy> ./sage
> > --
> > | Sage Version 3.4, Release Date: 2009-03-11                         |
> > | Type notebook() for the GUI, and license() for information.        |
> > --
> > /usr/local/sage-3.4-Fedora_release_9-x86_64-Linux/local/bin/sage.bin: /
> > usr/local/sage-3.4-Fedora_release_9-x86_64-Linux/local/bin/sage.bin:
> > cannot execute binary file
> > xyzzy> uname -a
> > Linux xyzzy 2.6.27.19-170.2.35.fc10.i686.PAE #1 SMP Mon Feb 23
> > 13:09:26 EST 2009 i686 i686 i386 GNU/Linux
>
> > Thanks for any help,
>
> Seems you downloaded the 64 bit version and try to run it on 33 bit.
>
> Jaap
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[sage-support] Sage 3.4 on Fedora: cannot execute binary file

[davidp]

I am having trouble starting Sage 3.4 on two machines running Fedora:

1.
poly> cd sage-3.4-Fedora_release_9-x86_64-Linux/
poly> ./sage
--
| Sage Version 3.4, Release Date: 2009-03-11 |
| Type notebook() for the GUI, and license() for information.|
--
/home/davidp/download/sage-3.4-Fedora_release_9-x86_64-Linux/local/bin/
sage.bin: /home/davidp/download/sage-3.4-Fedora_release_9-x86_64-Linux/
local/bin/sage.bin: cannot execute binary file
poly> uname -a
Linux poly 2.6.27.19-78.2.30.fc9.i686 #1 SMP Tue Feb 24 20:09:23 EST
2009 i686 i686 i386 GNU/Linux

2.
xyzzy> cd sage-3.4-Fedora_release_9-x86_64-Linux/
xyzzy> ./sage
--
| Sage Version 3.4, Release Date: 2009-03-11 |
| Type notebook() for the GUI, and license() for information.|
--
/usr/local/sage-3.4-Fedora_release_9-x86_64-Linux/local/bin/sage.bin: /
usr/local/sage-3.4-Fedora_release_9-x86_64-Linux/local/bin/sage.bin:
cannot execute binary file
xyzzy> uname -a
Linux xyzzy 2.6.27.19-170.2.35.fc10.i686.PAE #1 SMP Mon Feb 23
13:09:26 EST 2009 i686 i686 i386 GNU/Linux

Thanks for any help,
Dave
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[sage-support] Re: ideals of points

[davidp]

That works.

Thanks!

Dave

On Feb 26, 5:31 pm, Alex Raichev  wrote:
> Hi Dave:
>
> I'm also just learning the basics of interacting with Singular through
> Sage.  So probably someone else on the list can answer your question
> better than me.  Still, i'll take a stab at it.
>
> Carrying on with your/Singular's notation, try
>
> sage: singular.setring(AC)
> sage: sol= singular('SOL').sage_structured_str_list()
>
> to save the output of SOL as a structured list of Sage strings.  (I
> found this command by typing help(sage.interfaces.singular) and
> browsing the documentation page that popped up.)  Now all you have to
> do is convert those Sage strings to Sage numbers with the eval()
> command.  For instance,
>
> sage: a= eval(sol[1][1][1][1])
>
> Does that work?
>
> Alex
>
> P.S. I'll be jumping for joy if/when the Singular people fix the bug
> that's breaking the potentially super-useful variety() command.
>
> On Feb 27, 5:54 am,davidp wrote:
>
> > Thanks for your response.  I tried what you suggested and got the
> > error you anticipated.  So it looks like I need to work within
> > Singular.  The relevant page at the Singular site:
>
> >http://www.singular.uni-kl.de/Manual/latest/sing_1168.htm#SEC1227
>
> > Using the notation from the site just referenced, I end up with a
> > ring, AC, in which the solutions are supposed to be stored in 'SOL'.
> > I can execute singular.setring(AC), but cannot subsequently access the
> > solutions.
>
> > Thanks,
> > Dave
>
> > On Feb 25, 1:49 pm, Alex Raichev  wrote:
>
> > > Hi Dave:
>
> > > Once you have your zero-dimensional ideal K within a Sage ring, you
> > > could try the variety() command
>
> > > K.variety(ring=QQbar) or
> > > K.variety(ring=CC)
>
> > > to get its solutions as algebraic numbers or complex floating point
> > > numbers, respectively.  See 'variety()' under
>
> > >http://www.sagemath.org/doc/ref/module-sage.rings.polynomial.multi-po...
>
> > > for more details. Problem is, variety() sometimes 
> > > fails:http://sagetrac.org/sage_trac/ticket/4622.
>
> > > Alex
>
> > > On Feb 25, 7:27 am,davidp wrote:
>
> > > > Hi,
>
> > > > I have the following homogeneous Singular ideal defining a finite set
> > > > of points in projective space.  I would like to get numerical
> > > > approximations for these points.
>
> > > > sage: S.ring()
>
> > > > //   characteristic : 0
> > > > //   number of vars : 4
> > > > //        block   1 : ordering dp
> > > > //                  : names    x_3 x_2 x_1 x_0
> > > > //        block   2 : ordering C
> > > > sage: S.ideal()
>
> > > > x_1^3-x_3*x_2*x_0,
> > > > x_3*x_2*x_1-x_0^3,
> > > > x_2^3-x_3*x_1*x_0,
> > > > x_3^3-x_2*x_1*x_0,
> > > > x_2^2*x_1^2-x_3^2*x_0^2,
> > > > x_3^2*x_1^2-x_2^2*x_0^2,
> > > > x_3^2*x_2^2-x_1^2*x_0^2
> > > > sage: type(S.ideal())
> > > > 
>
> > > > One way to go might be to map to a new ring, setting x_0 = 1, then use
> > > > the nice Singular algorithm for finding the solutions:
>
> > > >http://www.singular.uni-kl.de/Manual/3-0-4/sing_582.htm
>
> > > > I couldn't figure out how to get the Singular "map" function to work
> > > > with Sage, so I just converted equations using string commands (saved
> > > > in "y" in the following code) then tried:
>
> > > > sage: R = singular.ring(0,'(x_3,x_2,x_1)','lp')
> > > > sage: J = singular.ideal(y)
> > > > sage: J
>
> > > > -x_3*x_2+x_1^3,
> > > > x_3*x_2*x_1-1,
> > > > -x_3*x_1+x_2^3,
> > > > x_3^3-x_2*x_1,
> > > > -x_3^2+x_2^2*x_1^2,
> > > > x_3^2*x_1^2-x_2^2,
> > > > x_3^2*x_2^2-x_1^2
> > > > sage: K = J.groebner()
> > > > sage: M = K.solve(10,1)
>
> > > > I'm not sure where to go from there.  Of course, I might be taking the
> > > > wrong approach altogether.
>
> > > > Any advice would be appreciated.
>
> > > > Thanks,
> > > > Dave
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[sage-support] Re: ideals of points

[davidp]

Thanks for your response.  I tried what you suggested and got the
error you anticipated.  So it looks like I need to work within
Singular.  The relevant page at the Singular site:

http://www.singular.uni-kl.de/Manual/latest/sing_1168.htm#SEC1227

Using the notation from the site just referenced, I end up with a
ring, AC, in which the solutions are supposed to be stored in 'SOL'.
I can execute singular.setring(AC), but cannot subsequently access the
solutions.

Thanks,
Dave

On Feb 25, 1:49 pm, Alex Raichev  wrote:
> Hi Dave:
>
> Once you have your zero-dimensional ideal K within a Sage ring, you
> could try the variety() command
>
> K.variety(ring=QQbar) or
> K.variety(ring=CC)
>
> to get its solutions as algebraic numbers or complex floating point
> numbers, respectively.  See 'variety()' under
>
> http://www.sagemath.org/doc/ref/module-sage.rings.polynomial.multi-po...
>
> for more details. Problem is, variety() sometimes 
> fails:http://sagetrac.org/sage_trac/ticket/4622.
>
> Alex
>
> On Feb 25, 7:27 am,davidp wrote:
>
> > Hi,
>
> > I have the following homogeneous Singular ideal defining a finite set
> > of points in projective space.  I would like to get numerical
> > approximations for these points.
>
> > sage: S.ring()
>
> > //   characteristic : 0
> > //   number of vars : 4
> > //        block   1 : ordering dp
> > //                  : names    x_3 x_2 x_1 x_0
> > //        block   2 : ordering C
> > sage: S.ideal()
>
> > x_1^3-x_3*x_2*x_0,
> > x_3*x_2*x_1-x_0^3,
> > x_2^3-x_3*x_1*x_0,
> > x_3^3-x_2*x_1*x_0,
> > x_2^2*x_1^2-x_3^2*x_0^2,
> > x_3^2*x_1^2-x_2^2*x_0^2,
> > x_3^2*x_2^2-x_1^2*x_0^2
> > sage: type(S.ideal())
> > 
>
> > One way to go might be to map to a new ring, setting x_0 = 1, then use
> > the nice Singular algorithm for finding the solutions:
>
> >http://www.singular.uni-kl.de/Manual/3-0-4/sing_582.htm
>
> > I couldn't figure out how to get the Singular "map" function to work
> > with Sage, so I just converted equations using string commands (saved
> > in "y" in the following code) then tried:
>
> > sage: R = singular.ring(0,'(x_3,x_2,x_1)','lp')
> > sage: J = singular.ideal(y)
> > sage: J
>
> > -x_3*x_2+x_1^3,
> > x_3*x_2*x_1-1,
> > -x_3*x_1+x_2^3,
> > x_3^3-x_2*x_1,
> > -x_3^2+x_2^2*x_1^2,
> > x_3^2*x_1^2-x_2^2,
> > x_3^2*x_2^2-x_1^2
> > sage: K = J.groebner()
> > sage: M = K.solve(10,1)
>
> > I'm not sure where to go from there.  Of course, I might be taking the
> > wrong approach altogether.
>
> > Any advice would be appreciated.
>
> > Thanks,
> > Dave
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[sage-support] ideals of points

[davidp]

Hi,

I have the following homogeneous Singular ideal defining a finite set
of points in projective space.  I would like to get numerical
approximations for these points.

sage: S.ring()

//   characteristic : 0
//   number of vars : 4
//block   1 : ordering dp
//  : namesx_3 x_2 x_1 x_0
//block   2 : ordering C
sage: S.ideal()

x_1^3-x_3*x_2*x_0,
x_3*x_2*x_1-x_0^3,
x_2^3-x_3*x_1*x_0,
x_3^3-x_2*x_1*x_0,
x_2^2*x_1^2-x_3^2*x_0^2,
x_3^2*x_1^2-x_2^2*x_0^2,
x_3^2*x_2^2-x_1^2*x_0^2
sage: type(S.ideal())


One way to go might be to map to a new ring, setting x_0 = 1, then use
the nice Singular algorithm for finding the solutions:

http://www.singular.uni-kl.de/Manual/3-0-4/sing_582.htm

I couldn't figure out how to get the Singular "map" function to work
with Sage, so I just converted equations using string commands (saved
in "y" in the following code) then tried:

sage: R = singular.ring(0,'(x_3,x_2,x_1)','lp')
sage: J = singular.ideal(y)
sage: J

-x_3*x_2+x_1^3,
x_3*x_2*x_1-1,
-x_3*x_1+x_2^3,
x_3^3-x_2*x_1,
-x_3^2+x_2^2*x_1^2,
x_3^2*x_1^2-x_2^2,
x_3^2*x_2^2-x_1^2
sage: K = J.groebner()
sage: M = K.solve(10,1)

I'm not sure where to go from there.  Of course, I might be taking the
wrong approach altogether.

Any advice would be appreciated.

Thanks,
Dave

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[sage-support] Singular Hilbert series

[davidp]

Hi,

Singular's hilb command does not work as expected:

sage: R = singular.ring(0,'(x,y,z)','dp')
sage: I = singular.ideal(['x^3-y^2*z','z^2-x*y'])
sage: I.hilb()
`sage90`

Could someone please explain this?

Thanks,
Dave
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[sage-support] problem with GraphDatabase

[davidp]

Hi,

Cutting and pasting commands from the Reference:

http://sagemath.org/doc/ref/node47.html

gives me:

===
>> sage
--
| Sage Version 3.2.2, Release Date: 2008-12-18   |
| Type notebook() for the GUI, and license() for information.|
--
sage: graphs_query = GraphDatabase()
sage: L = graphs_query.get_list(num_vertices=7, diameter=5)
---
AttributeErrorTraceback (most recent call
last)

/home/davidp/math/sandpile/sage/sage-sandpile1.2/ in
()

AttributeError: 'GraphDatabase' object has no attribute 'get_list'
sage:
===
I have also tried cutting and pasting code from the online
documentation for GenericGraphQuery and similar functions, also
getting errors.

I am running sage under Fedora.

Any suggestions would be much appreciated.  (I have a thesis student
who would like to use these functions.)

Thanks,
Dave

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[sage-support] gap documentation

[davidp]

I will be teaching abstract algebra this semester and want to
introduce my students to Sage and GAP.  I have installed
gap_packages-4.4.10_6, but I am still having trouble with
documentation:

--
| Sage Version 3.2.3, Release Date: 2009-01-05   |
| Type notebook() for the GUI, and license() for information.|
--
sage: gap_console()
GAP4, Version: 4.4.10 of 02-Oct-2007, i686-pc-linux-gnu-gcc
gap> ?SymmetricGroup
Help: Showing `Reference: SymmetricGroup'
Record: '.tempfile' must have an assigned value at
str := OutputTextFile( $SAGE.tempfile, false );
 called from
HELP_VIEWER_INFO.(viewer).show( data ); called from
HELP_PRINT_MATCH( i ); called from
HELP_SHOW_MATCHES( books, str, true ) called from
(  ) called from read-eval-loop
Entering break read-eval-print loop ...
you can 'quit;' to quit to outer loop, or
you can 'return;' after assigning a value to continue
brk>


I am running Sage on a thinkpad with Fedora 10.

Any suggestions would be appreciated.

Thanks,
Dave
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[sage-support] Re: problem running combinatorial functions

[davidp]

My set-up:

Linux Fedora 9, 2.6.27.7-53.fc9.i686
Thinkpad X40
shell = bash  (with pretty minimal .bashrc and .bash_profile)
Sage Version 3.2.2, Release Date: 2008-12-18 from a binary, not an
upgrade

I do have a .gaprc and had installed gap before installing sage.  I
tried removing .gaprc, but that didn't fix the problem.

By the end of January, I will have a different laptop, running Fedora
10.  So almost certainly the problem will disappear for me then.  So
this is not to pressing.

About the laplacian bug (really the weighted_adjacency_matrix bug),
could someone else please make a patch?  I am travelling non-stop
between semesters now and have not had time to learn how to do this.

Thanks,
Dave


On Jan 7, 6:06 pm, mabshoff  wrote:
> On Jan 7, 3:38 pm, davidp  wrote:
>
> Hi Dave,
>
> > Oops.  I take back my last post.  Running Sage 3.2.2, I got the
> > following:
>
> > sage: combinations([1,2,3,4],2)
> > 
> >    File "", line 1
> >      [ [ 1, 2 ], [ 1, 3 ], [ 1, 4 ], [ 2, 3 ], [ 2, 4 ], [ 3, 4 ] ]
> > gap>
>
> I tried in Sage 3.2, 3.2.1, 3.2.2 and 3.2.3 and it always worked for
> me.
>                                                                     ^
>
>
>
> > SyntaxError: invalid syntax
>
> > The problem seems to occur on line 1580 of combinat.py:
>
> > 1579    ans=gap.eval("Combinations(%s,%s)"%(mset,ZZ(k))).replace
> > ("\n","")
> > 1580   return eval(ans)
>
> > For the example above:
>
> > sage: gap.eval("Combinations([1,2,3,4],2)")
> > '[ [ 1, 2 ], [ 1, 3 ], [ 1, 4 ], [ 2, 3 ], [ 2, 4 ], [ 3, 4 ] ]\n\x1b
> > [1m\x1b[34mgap> \x1b[0m'
> > sage: eval(gap.eval("Combinations([1,2,3,4],2)").replace("\n",""))
> > 
> >    File "", line 1
> >      [ [ 1, 2 ], [ 1, 3 ], [ 1, 4 ], [ 2, 3 ], [ 2, 4 ], [ 3, 4 ] ]
> > gap>
> >                                                                    ^
> > SyntaxError: invalid syntax
>
> > sage: eval(gap.eval("Combinations([1,2,3,4],2)").replace("\n",""))
> > 
> >    File "", line 1
> >      [ [ 1, 2 ], [ 1, 3 ], [ 1, 4 ], [ 2, 3 ], [ 2, 4 ], [ 3, 4 ] ]
> > gap>
> >                                                                    ^
> > SyntaxError: invalid syntax
>
> > Thanks for any suggestions.
>
> Hmm, this looks like some escape characters from the shell. What shell
> are you using? . What platform is this on? Did you build this Sage
> yourself or is it a binary? Did you upgrade it from a previous release
> of Sage?
>
>  Do you have any gap config file around? This problem sounds familiar,
> but I cannot put my finger on it.
>
> > Dave
>
> One last think: Do you have a patch for the laplacian_matrix()
> problem, i.e.http://trac.sagemath.org/sage_trac/ticket/4888or do you
> want someone from our end to make a patch? Robert Miller looked at the
> suggested fix and he agrees that it is the right way to go.
>
> Cheers,
>
> Michael
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[sage-support] Re: problem running combinatorial functions

[davidp]

Oops.  I take back my last post.  Running Sage 3.2.2, I got the
following:

sage: combinations([1,2,3,4],2)

   File "", line 1
 [ [ 1, 2 ], [ 1, 3 ], [ 1, 4 ], [ 2, 3 ], [ 2, 4 ], [ 3, 4 ] ]
gap>
   ^
SyntaxError: invalid syntax

The problem seems to occur on line 1580 of combinat.py:

1579ans=gap.eval("Combinations(%s,%s)"%(mset,ZZ(k))).replace
("\n","")
1580   return eval(ans)

For the example above:

sage: gap.eval("Combinations([1,2,3,4],2)")
'[ [ 1, 2 ], [ 1, 3 ], [ 1, 4 ], [ 2, 3 ], [ 2, 4 ], [ 3, 4 ] ]\n\x1b
[1m\x1b[34mgap> \x1b[0m'
sage: eval(gap.eval("Combinations([1,2,3,4],2)").replace("\n",""))

   File "", line 1
 [ [ 1, 2 ], [ 1, 3 ], [ 1, 4 ], [ 2, 3 ], [ 2, 4 ], [ 3, 4 ] ]
gap>
   ^
SyntaxError: invalid syntax

sage: eval(gap.eval("Combinations([1,2,3,4],2)").replace("\n",""))

   File "", line 1
 [ [ 1, 2 ], [ 1, 3 ], [ 1, 4 ], [ 2, 3 ], [ 2, 4 ], [ 3, 4 ] ]
gap>
       ^
SyntaxError: invalid syntax

Thanks for any suggestions.

Dave



On Jan 4, 10:44 am, davidp  wrote:
> Thanks.  By problem went away with Sage 3.2.2.
>
> Dave
>
> On Dec 27 2008, 10:55 am, mabshoff 
> dortmund.de> wrote:
> > On Dec 27, 9:11 am,DavidPerkinson wrote:
>
> > Hi Dave,
>
> > > Here is a typical error when I try to run a combinatorial function:
>
> > > sage: combinations([1,2],3)
> > > 
> > >    File "", line 1
> > >      [  ]gap>
> > >          ^
> > > SyntaxError: invalid syntax
>
> > > Linux Fedora 9, 2.6.27.7-53.fc9.i686 on a Thinkpad
> > > SAGE Version 3.1.4, Release Date: 2008-10-16
> > > installed from a binary
>
> > > Thanks for any suggestions.
>
> > > Dave
>
> > This works for me in Sage 3.2.2:
>
> > sage: combinations([1,2],1)
> > [[1], [2]]
> > sage: combinations([1,2],2)
> > [[1, 2]]
> > sage: combinations([1,2],3)
> > []
>
> > Note that this code was recently (In Sage 3.2.0 or so IIRC) fixed.
>
> > Cheers,
>
> > Michael
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[sage-support] Re: problem running combinatorial functions

[davidp]

Thanks.  By problem went away with Sage 3.2.2.

Dave

On Dec 27 2008, 10:55 am, mabshoff  wrote:
> On Dec 27, 9:11 am,DavidPerkinson wrote:
>
> Hi Dave,
>
>
>
> > Here is a typical error when I try to run a combinatorial function:
>
> > sage: combinations([1,2],3)
> > 
> >    File "", line 1
> >      [  ]gap>
> >          ^
> > SyntaxError: invalid syntax
>
> > Linux Fedora 9, 2.6.27.7-53.fc9.i686 on a Thinkpad
> > SAGE Version 3.1.4, Release Date: 2008-10-16
> > installed from a binary
>
> > Thanks for any suggestions.
>
> > Dave
>
> This works for me in Sage 3.2.2:
>
> sage: combinations([1,2],1)
> [[1], [2]]
> sage: combinations([1,2],2)
> [[1, 2]]
> sage: combinations([1,2],3)
> []
>
> Note that this code was recently (In Sage 3.2.0 or so IIRC) fixed.
>
> Cheers,
>
> Michael
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