[sage-devel] gdb, doctests, strange behavior...

[Robert Miller]

I'm working on a new .pyx file, and everything has been working okay,
but something strange is now happening, and I can't quite get to the
bottom of it.

Some side notes- I am running on OS X 10.5, a fresh install of
sage-2.8.12. It failed building, I think it was scipy, but other than
that it has been working ok.

So I have some new cython classes, and I've written some doctests.
When I run through the doctests by hand, I can't reproduce what
happens when I doctest: I run
./sage -t -verbose .../relevant_file.pyx
and I watch as every test passes, then it pauses for a while as it
handles a bus error. Curious to see what is going on, I do the
following:

./sage -t -gdb .../relevant_file.pyx

gdb says lots of things like

warning: Could not find object file "/Volumes/HOME/sage/spkg/build/
python-2.5.1.p8/src/Modules/python.o" - no debug information available
for "./Modules/python.c".

before it loads, but it loads, and I type "r" to run the tests. It
complains more about symbols, such as

Reading symbols for shared libraries warning: Could not find object
file "/Volumes/HOME/sage/spkg/build/python-2.5.1.p8/src/build/
temp.macosx-10.3-i386-2.5/Volumes/HOME/sage/spkg/build/python-2.5.1.p8/
src/Modules/mathmodule.o" - no debug information available for "/
Volumes/HOME/sage/spkg/build/python-2.5.1.p8/src/Modules/
mathmodule.c".

Then it runs the tests. The problem is

Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: KERN_PROTECTION_FAILURE at address: 0x0015
0x000d1c50 in collect ()

So I backtrace:

(gdb) bt
#0  0x000d1c50 in collect ()
#1  0x000d276a in PyGC_Collect ()
#2  0x000c18d0 in Py_Finalize ()
#3  0x000c1376 in handle_system_exit ()
#4  0x000c15e5 in PyErr_PrintEx ()
#5  0x000c24ac in PyRun_SimpleFileExFlags ()
#6  0x000d0d97 in Py_Main ()
#7  0x1fdc in _start ()
#8  0x1f09 in start ()

I have reproduced what __dealloc__ does in another function, and have
tried over and over to reproduce this error outside of doctest mode,
to no avail. The fact that the garbage collector is accessing bad
memory seems to indicate that it has already been freed or something,
but this only only happens during doctests, or at least so it seems. I
have run the doctests again and again under gdb by hand, and they
never produce a problem, so I have it narrowed down to only every
doctest in the file. The crappy thing is that I don't know how to have
gdb tell me what the gc was trying to collect, and I can't reproduce
the problem in an environment where I can narrow anything down.

Given all these problems, I'm moving my project back to linux, for the
stability of a happy install, and the extra memory tools. However,
this situation is so confusing and bizarre I'd still like to figure
out what is happening... Any help is appreciated.

RLM


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: gdb, doctests, strange behavior...

[Robert Miller]

> Questions:
>
> (1) Do you or do you not actually have the same problem when
> you build the same code under Linux?   You don't say above.

I hadn't had the chance to try yet, but I have now. I can't get it to
give any error in linux at all. All the tests pass, in and out of gdb
mode. I tried several times.

> (2) What happens when you do
> grep "sage:" filename.pyx | sage

This produces the bus error also, but it's definitely after the
doctests have been run. My __dealloc__ functions are super-simple
though, just a list of sage_free's on variables that shouldn't already
be freed

- Robert M


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: gdb, doctests, strange behavior...

[Robert Miller]

> > (1) Do you or do you not actually have the same problem when
> > you build the same code under Linux?   You don't say above.
>
> I hadn't had the chance to try yet, but I have now. I can't get it to
> give any error in linux at all. All the tests pass, in and out of gdb
> mode. I tried several times.

Turns out I was testing the wrong branch. I can reproduce the problem
in linux, and here I actually get a useful-ish backtrace, since gdb
has enough information. The relevant line in my .pyx file is a simple
sage_free call. It looks like an array overflow problem or something.
I guess this is all good news, since it seems as if gdb in os x 10.5
could get me this information too if the build had finished.

(gdb) r
Starting program: /home/hd/sage/local/bin/
python .doctest_binary_code.py
[Thread debugging using libthread_db enabled]
[New Thread -1209636192 (LWP 5346)]
*** glibc detected *** free(): invalid next size (fast): 0x087836d0
***

Program received signal SIGABRT, Aborted.
[Switching to Thread -1209636192 (LWP 5346)]
0xe410 in __kernel_vsyscall ()
(gdb) bt
#0  0xe410 in __kernel_vsyscall ()
#1  0xb7e8f9a1 in raise () from /lib/tls/i686/cmov/libc.so.6
#2  0xb7e912b9 in abort () from /lib/tls/i686/cmov/libc.so.6
#3  0xb7ec387a in __fsetlocking () from /lib/tls/i686/cmov/libc.so.6
#4  0xb7ec9fd4 in malloc_usable_size () from /lib/tls/i686/cmov/
libc.so.6
#5  0xb7eca34a in free () from /lib/tls/i686/cmov/libc.so.6
#6  0xb427429d in
__pyx_tp_dealloc_4sage_6coding_11binary_code_PartitionStack
(o=0xb4c4c5cc) at sage/coding/binary_code.c:3413
#7  0x0808106b in insertdict (mp=0x6, key=0xb7e498c0, hash=-724865314,
value=0x8137720) at Objects/dictobject.c:412
#8  0x08081486 in PyDict_SetItem (op=0xb7e28824, key=0xb7e498c0,
value=0x8137720) at Objects/dictobject.c:637
#9  0x0808573a in PyObject_GenericSetAttr (obj=0xb7e2605c,
name=0xb7e498c0, value=0x8137720) at Objects/object.c:1427
#10 0x08084e0c in PyObject_SetAttr (v=0xb7e2605c, name=0xb7e498c0,
value=0x8137720) at Objects/object.c:1183
#11 0x08084f7b in PyObject_SetAttrString (v=0xb7e2605c, name=0x811bb0b
"_", w=0x8137720) at Objects/object.c:1097
#12 0x080e8144 in sys_displayhook (self=0x0, o=0xb7de6440) at Python/
sysmodule.c:105
#13 0x0805aa1c in PyObject_Call (func=0x14e2, arg=0x0, kw=0x0) at
Objects/abstract.c:1860
#14 0x080bc8f3 in PyEval_CallObjectWithKeywords (func=0x0,
arg=0xb42a9b6c, kw=0x0) at Python/ceval.c:3433
#15 0x080c23ca in PyEval_EvalFrameEx (f=0x8d43b5c, throwflag=0) at
Python/ceval.c:1530
#16 0x080c420e in PyEval_EvalCodeEx (co=0xb4c3ef50,
globals=0xb429e9bc, locals=0xb429e9bc, args=0x0, argcount=0, kws=0x0,
kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:
2831
#17 0x080c2b66 in PyEval_EvalFrameEx (f=0x877e1fc, throwflag=0) at
Python/ceval.c:494
#18 0x080c420e in PyEval_EvalCodeEx (co=0xb42ed9b0,
globals=0xb42e8b54, locals=0x0, args=0x8d421d0, argcount=4,
kws=0x8d421e0,
kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:
2831
#19 0x080c2367 in PyEval_EvalFrameEx (f=0x8d4207c, throwflag=0) at
Python/ceval.c:3660
#20 0x080c420e in PyEval_EvalCodeEx (co=0xb42edbf0,
globals=0xb42e8b54, locals=0x0, args=0x8c1b3b0, argcount=2,
kws=0x8c1b3b8,
kwcount=0, defs=0xb42ff1c8, defcount=3, closure=0x0) at Python/
ceval.c:2831
#21 0x080c2367 in PyEval_EvalFrameEx (f=0x8c1b244, throwflag=0) at
Python/ceval.c:3660
#22 0x080c420e in PyEval_EvalCodeEx (co=0xb42f1800,
globals=0xb42e8b54, locals=0x0, args=0x816b260, argcount=1,
kws=0x816b264,
kwcount=3, defs=0xb42f4278, defcount=9, closure=0x0) at Python/
ceval.c:2831
#23 0x080c2367 in PyEval_EvalFrameEx (f=0x816b124, throwflag=0) at
Python/ceval.c:3660
#24 0x080c420e in PyEval_EvalCodeEx (co=0xb7e01188,
globals=0xb7e3eacc, locals=0xb7e3eacc, args=0x0, argcount=0, kws=0x0,
kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:
2831
#25 0x080c4396 in PyEval_EvalCode (co=0x0, globals=0x0, locals=0x0) at
Python/ceval.c:494
#26 0x080e2c6e in PyRun_FileExFlags (fp=0x8161008, filename=0xbf8f739a
".doctest_binary_code.py", start=0, globals=0x0, locals=0x0,
closeit=1, flags=0xbf8f6b88) at Python/pythonrun.c:1271
#27 0x080e2fa9 in PyRun_SimpleFileExFlags (fp=,
filename=0xbf8f739a ".doctest_binary_code.py", closeit=1,
flags=0xbf8f6b88) at Python/pythonrun.c:877
#28 0x08056d0f in Py_Main (argc=1, argv=0xbf8f6c24) at Modules/main.c:
523
#29 0xb7e7bea2 in __libc_start_main () from /lib/tls/i686/cmov/libc.so.
6
#30 0x080561b1 in _start () at ../sysdeps/i386/elf/start.S:119


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: gdb, doctests, strange behavior...

[Robert Miller]

> If you want to send me a patch/bundle against 2.8.12 or so and
> instructions on how to reproduce this and I will take a look.

Thanks for the offer but I figured out what the problem with my code
was last night, as soon as I started using valgrind.

> ...
> I have seen the issue with gdb printing loads of output at startup of
> sage, but I didn't know that it also happened on 10.4 also. I might
> have a look on either how to get around this or actually solve the
> problem.

Just to be accurate, I wasn't using 10.4 at all, so I have no idea
what would happen there. This was only on 10.5.

William, Michael, thanks for the help! It turns out I was using the
wrong variable as an endpoint for a loop index, and it was just some
bad read/writes during those loops.


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: is anybody interesting lie groups, etc.

[Robert Miller]

I am interested in this, but it might be a while before I get some
spare time to look at it.

On Nov 21, 11:56 am, mabshoff <[EMAIL PROTECTED]
dortmund.de> wrote:
> On Nov 21, 8:50 pm, "David Joyner" <[EMAIL PROTECTED]> wrote:
>
> Hello David,
>
> > I think this is interesting but I wonder how easy it is to compile.
>
> It compiles on OSX, Linux, Solaris and Windows (probably Cygwin), the
> sources are at their website.
>
> > Also, is there also a plan to include lie?
>
> Mike Hansen did do an optional spkg and it should work. I am not sure
> how far integration has actually gone, but if ATLAS is integrated it
> might speed up the integration of lie, too.
>
>
>
> Cheers,
>
> Michael
>
> 
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: graph theory/combinatorics wishlist from Chris Godsil

[Robert Miller]

> > We need to be able to convert to and from the graph6 and sparse6 formats
> > to an adjacency matrix and to a graph.
Done.

> > We need some hooks to nauty.
Not done: we have reimplemented instead. If I don't do it before Sage
Days 7, I will do it there: create a (necessarily optional) spkg to
include nauty, and give all the relevant functions the option to call
nauty instead. I believe geng is part of nauty, so this would come
along for the ride. This should definitely be a wishlist trac ticket.

> > (a) Given a graph and a partition of its vertex set:
> > get generators, orbits and the order of the group of
> > automorphisms of the graph that preserve the partition.
Done. (Orbits are not part of the output, but can be easily read off
from the generators, and is a function of a permutation group (I
certainly hope))

> > (b) Determine if two graphs are isomorphic; if they are then provide the
> > isomorphism, if they are not, return canonical labels.
Done.

> > A python generator
> > based on geng. (This could be more useful in some respects than a
> > database.)
Done. For example:
sage: for g in graphs(3):
if g.order() != 0: print g.spectrum()
:
[0.0]
[0.0, 0.0]
[0.0, 0.0, 0.0]
[-1.0, 0.0, 1.0]
[-1.41421356237, 1.16280682999e-16, 1.41421356237]
[-1.0, 1.0]
[-1.0, -1.0, 2.0]

> > (a) Graphs on surfaces: [This item is a place-holder; I am not sure what
> > data structures people will want.]
> I'll pass on this for now until we know more about what we should do.
Comments: Emily Kirkman has done some extensive work on embedding
graphs in surfaces, and I'd love to see some conversation about this
at Sage Days 7.

> > (b) Cayley graphs: These can be dealt with in GAP, but I think it would be
> > useful to have a class, with the group and generating set explicit. Cayley
> > graphs could be directed or undirected. Circulants and Cayley graphs
> > for Zd (where p is prime) could be useful special cases.
Cayley graphs are implemented, but most likely not to the extent
anyone wants. For example, you can call cayley_graph on some groups,
and get the graph back, but the functionality is very limited. There
is certainly no CayleyGraph class, which would be a thousand times
better than the current situation. Definitely create a ticket for
this.

> > (c) Edge-colored graphs: A graph and functions from its edges to an index
> > set, and vice versa. These could also be represented as a set of
> > matchings,
> > and this data structure can be used to represent maps on surfaces.
> I think we should make a nice system for attaching arbitrary metadata to
> vertices and edges of a graph. Something like an attribute dictionary
> for each vertex and edge.
There is an existing trac ticket for improving the vertex association
setup- most likely these comments should just go on that ticket. Any
object at all can be the label for an edge, so I don't think there is
too much to do here.

Another ticket you might want to create, but that I would be most
likely to implement, is edge-labeled graph isomorphism.

> > (d) Bipartite graphs: We will need to deal with some incidence structures,
> > and these can be encoded as bipartite graphs. We want to get the point
> > graphs and line graphs of incidence structures. If we have a procedure to
> > convert a graph G to an incidence structure of vertices and edges, then
> > the line graph of the incidence structure is the line graph of G.
> Do we have a way to represent and work with incidence structures in Sage
> natively?
Graphs and codes are implemented, but I don't think designs are.
Ultimately, there should be an incidence structure class which they
inherit from etc etc etc. Definitely a wishlist ticket, and likely a
good coding sprint idea for Sage Days 7.


> > (e) Bundles: Start with a base graph G with vertices {1, . . . , n}.
> > For each
> > vertex i we are given a graph Ci . For each edge ij we are given a
> > bipartite
> > graph joining V (Ci ) to V (Cj ). (There is an implicit orientation here.)
> > Some examples:
> > (i) The Petersen graph: n = 2, C1 is the 5-cycle, C2 is its complement
> > and the bipartite graph is a 5-matching.
> > (ii) The Hoffman-Singleton graph can be constructed with n = 2, where
> > C1 is an independent set on 15 vertices, C2 is a nice distance regular
> > graph on 35 vertices,. . .
> > (iii) Covering graphs. Here the graphs Ci are empty on r vertices, and
> > each bipartite graphs is either an r-matching or is empty.
> Huh, I used this idea extensively in my dissertation and a research
> paper. I used the "blowup graph" terminology, though, from extremal
> graph theory. Is anyone working on this? If not, I'll make a trac ticket.
Nobody I know of. If you did this type of stuff in your dissertation,
then I nominate you! Create a ticket.

> > A database of small graphs. Put Ted Spence's strongly regular graphs
> > into a
> > database. (In this case the important thing is to have the graphs
> > themselves,
> > we would not necessarily need much dat

[sage-devel] is_integral_domain crappy output

[Robert Miller]

In sage/rings/quotient_ring.py, we have the following (line 220 in
2.8.14):
try:
return self.defining_ideal().is_prime()
except NotImplementedError:
return False

Why the heck don't we just propagate the NotImplementedError!?!
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: SAGE-2.8.15!

[Robert Miller]

I don't know if this is specific to my current install, but I thought
it could be useful to someone. Also, I'm not noticing any problems
resulting from this. During upgrade from 2.8.14 on Intel OS X 10.5.1:

g++ -fPIC -shared -o libntl.so FFT.o FacVec.o GF2.o GF2E.o GF2EX.o
GF2EXFactoring.o GF2X.o GF2X1.o GF2XFactoring.o GF2XVec.o GetTime.o
HNF.o ctools.o LLL.o LLL_FP.o LLL_QP.o LLL_RR.o LLL_XD.o RR.o
WordVector.o ZZ.o ZZVec.o ZZX.o ZZX1.o ZZXCharPoly.o ZZXFactoring.o
ZZ_p.o ZZ_pE.o ZZ_pEX.o ZZ_pEXFactoring.o ZZ_pX.o ZZ_pX1.o
ZZ_pXCharPoly.o ZZ_pXFactoring.o fileio.o lip.o lzz_p.o lzz_pE.o
lzz_pEX.o lzz_pEXFactoring.o lzz_pX.o lzz_pX1.o lzz_pXCharPoly.o
lzz_pXFactoring.o mat_GF2.o mat_GF2E.o mat_RR.o mat_ZZ.o mat_ZZ_p.o
mat_ZZ_pE.o mat_lzz_p.o mat_lzz_pE.o mat_poly_ZZ.o mat_poly_ZZ_p.o
mat_poly_lzz_p.o pair_GF2EX_long.o pair_GF2X_long.o pair_ZZX_long.o
pair_ZZ_pEX_long.o pair_ZZ_pX_long.o pair_lzz_pEX_long.o
pair_lzz_pX_long.o quad_float.o tools.o vec_GF2.o vec_GF2E.o
vec_GF2XVec.o vec_RR.o vec_ZZ.o vec_ZZVec.o vec_ZZ_p.o vec_ZZ_pE.o
vec_double.o vec_long.o vec_lzz_p.o vec_lzz_pE.o vec_quad_float.o
vec_vec_GF2.o vec_vec_GF2E.o vec_vec_RR.o vec_vec_ZZ.o vec_vec_ZZ_p.o
vec_vec_ZZ_pE.o vec_vec_long.o vec_vec_lzz_p.o vec_vec_lzz_pE.o
vec_xdouble.o xdouble.o G_LLL_FP.o G_LLL_QP.o G_LLL_XD.o G_LLL_RR.o
vec_ulong.o vec_vec_ulong.o
Undefined symbols:
  "___gmpn_sub_n", referenced from:
  _redc in lip.o
  "___gmpn_add", referenced from:
  __ntl_gadd in lip.o
  __ntl_gsub in lip.o
  "___gmpn_cmp", referenced from:
  __ntl_gcompare in lip.o
  __ntl_gcompare in lip.o
  __ntl_gadd in lip.o
  __ntl_gsub in lip.o
  __ntl_gexteucl in lip.o
  "___gmpn_gcd", referenced from:
  __ntl_ggcd in lip.o
  "___gmpn_mul", referenced from:
  __ntl_gmul in lip.o
  __ntl_gmul in lip.o
  "___gmpn_sub", referenced from:
  __ntl_gadd in lip.o
  __ntl_gadd in lip.o
  __ntl_gsub in lip.o
  __ntl_gsub in lip.o
  __ntl_gsubpos in lip.o
  "_main", referenced from:
  start in crt1.10.5.o
  "___gmpn_rshift", referenced from:
  __ntl_grshift in lip.o
  __ntl_gsdiv in lip.o
  "___gmpn_sqrtrem", referenced from:
  __ntl_gsqrt in lip.o
  __ntl_gsqrts in lip.o
  "___gmpn_addmul_1", referenced from:
  _redc in lip.o
  __ntl_gcrt_struct_eval in lip.o
  __ntl_gcrt_struct_eval in lip.o
  "___gmpn_divrem_1", referenced from:
  __ntl_gsdiv in lip.o
  "___gmpn_gcdext", referenced from:
  __ntl_gexteucl in lip.o
  __ntl_ginv in lip.o
  "___gmpn_mod_1", referenced from:
  __ntl_gsmod in lip.o
  __ntl_gcrt_struct_init in lip.o
  __ntl_grem_struct_eval in lip.o
  __ntl_grem_struct_eval in lip.o
  __ntl_grem_struct_eval in lip.o
  "___gmpn_mul_1", referenced from:
  __ntl_gsmul in lip.o
  "___gmpn_lshift", referenced from:
  __ntl_glshift in lip.o
  __ntl_gsmul in lip.o
  "___gmpn_tdiv_qr", referenced from:
  __ntl_gdiv in lip.o
  _gmod_simple in lip.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[2]: *** [libntl.so] Error 1
make[1]: *** [lib] Error 2

Error building libntl.so




--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: SAGE-2.8.15!

[Robert Miller]

Probably too late, but maybe this will help.

On thing I did that may have caused this is change branches on one
terminal while doing a maketest in another window.

I haven't moved sage root since install, so I don't know how relevant
#1358 is.

1. Tried to install cremona, ran into the same problem:

g++  -o ./tcurve tcurve_n.o curve_n.o curvedata_n.o curvered_n.o
curvemod_n.o pointsmod_n.o ffmod_n.o  -lpari -L/Volumes/HOME/sage/
local/lib -ljcntl -L../lib -L/Volumes/HOME/sage/local/lib -lntl -L../
lib -lgmp  -lpari -ljcntl  -lm
Undefined symbols:
  "initprimes(char*, int)", referenced from:
  _main in tcurve_n.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[1]: *** [tcurve] Error 1
make: *** [all] Error 2
Error building cremona

real1m55.506s
user1m36.765s
sys 0m9.635s
sage: An error occurred while installing cremona-20071116

2. Forced rebuild of gmp:

real4m3.257s
user1m14.718s
sys 2m53.891s
Successfully installed gmp-4.2.1.p12

3. Forced rebuild of ntl:

real5m39.132s
user5m6.040s
sys 0m17.611s
Successfully installed ntl-5.4.1.p7

4. Forced rebuild of cremona, ran into the same problem:

g++  -o ./tcurve tcurve_n.o curve_n.o curvedata_n.o curvered_n.o
curvemod_n.o pointsmod_n.o ffmod_n.o  -lpari -L/Volumes/HOME/sage/
local/lib -ljcntl -L../lib -L/Volumes/HOME/sage/local/lib -lntl -L../
lib -lgmp  -lpari -ljcntl  -lm
Undefined symbols:
  "initprimes(char*, int)", referenced from:
  _main in tcurve_n.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[1]: *** [tcurve] Error 1
make: *** [all] Error 2
Error building cremona

real2m4.148s
user1m36.826s
sys 0m9.547s
sage: An error occurred while installing cremona-20071116


On Dec 4, 11:43 am, mabshoff <[EMAIL PROTECTED]
dortmund.de> wrote:
> On Dec 4, 8:30 pm, Robert Miller <[EMAIL PROTECTED]> wrote:> I don't know if 
> this is specific to my current install, but I thought
> > it could be useful to someone. Also, I'm not noticing any problems
> > resulting from this. During upgrade from 2.8.14 on Intel OS X 10.5.1:
>
> > g++ -fPIC -shared -o libntl.so FFT.o FacVec.o GF2.o GF2E.o GF2EX.o
>
>^^^
>
> Arrg, these flags are wrong. I hate it when you figure out the problem
> right after one hits send. Let me check the spkg-install, maybe I can
> come up with something.
>
> Cheers,
>
> Michael
>
> > GF2EXFactoring.o GF2X.o GF2X1.o GF2XFactoring.o GF2XVec.o GetTime.o
> > HNF.o ctools.o LLL.o LLL_FP.o LLL_QP.o LLL_RR.o LLL_XD.o RR.o
> > WordVector.o ZZ.o ZZVec.o ZZX.o ZZX1.o ZZXCharPoly.o ZZXFactoring.o
> > ZZ_p.o ZZ_pE.o ZZ_pEX.o ZZ_pEXFactoring.o ZZ_pX.o ZZ_pX1.o
> > ZZ_pXCharPoly.o ZZ_pXFactoring.o fileio.o lip.o lzz_p.o lzz_pE.o
> > lzz_pEX.o lzz_pEXFactoring.o lzz_pX.o lzz_pX1.o lzz_pXCharPoly.o
> > lzz_pXFactoring.o mat_GF2.o mat_GF2E.o mat_RR.o mat_ZZ.o mat_ZZ_p.o
> > mat_ZZ_pE.o mat_lzz_p.o mat_lzz_pE.o mat_poly_ZZ.o mat_poly_ZZ_p.o
> > mat_poly_lzz_p.o pair_GF2EX_long.o pair_GF2X_long.o pair_ZZX_long.o
> > pair_ZZ_pEX_long.o pair_ZZ_pX_long.o pair_lzz_pEX_long.o
> > pair_lzz_pX_long.o quad_float.o tools.o vec_GF2.o vec_GF2E.o
> > vec_GF2XVec.o vec_RR.o vec_ZZ.o vec_ZZVec.o vec_ZZ_p.o vec_ZZ_pE.o
> > vec_double.o vec_long.o vec_lzz_p.o vec_lzz_pE.o vec_quad_float.o
> > vec_vec_GF2.o vec_vec_GF2E.o vec_vec_RR.o vec_vec_ZZ.o vec_vec_ZZ_p.o
> > vec_vec_ZZ_pE.o vec_vec_long.o vec_vec_lzz_p.o vec_vec_lzz_pE.o
> > vec_xdouble.o xdouble.o G_LLL_FP.o G_LLL_QP.o G_LLL_XD.o G_LLL_RR.o
> > vec_ulong.o vec_vec_ulong.o
> > Undefined symbols:
> >   "___gmpn_sub_n", referenced from:
> >   _redc in lip.o
> >   "___gmpn_add", referenced from:
> >   __ntl_gadd in lip.o
> >   __ntl_gsub in lip.o
> >   "___gmpn_cmp", referenced from:
> >   __ntl_gcompare in lip.o
> >   __ntl_gcompare in lip.o
> >   __ntl_gadd in lip.o
> >   __ntl_gsub in lip.o
> >   __ntl_gexteucl in lip.o
> >   "___gmpn_gcd", referenced from:
> >   __ntl_ggcd in lip.o
> >   "___gmpn_mul", referenced from:
> >   __ntl_gmul in lip.o
> >   __ntl_gmul in lip.o
> >   "___gmpn_sub", referenced from:
> >   __ntl_gadd in lip.o
> >   __ntl_gadd in lip.o
> >   __ntl_gsub in lip.o
> >   __ntl_gsub in lip.o
> >   __ntl_gsubpos in lip.o
> >   "_main", referenced from:
> >   start in crt1.10.5.o
> >   "___gmpn_rshift", referenced from:
> >   __ntl_grshift in lip.o
> >   __ntl_gsdiv in lip.o
> >   "___gmpn_sqrtrem", referenced from:
> >   __ntl_gsq

[sage-devel] Open for discussion

[Robert Miller]

Does anyone have any thoughts on the following? Luke Wolcott showed me
this example- the traceback looks suspect, but I don't know about the
internals here. Is this just something that is too big?

{{{id=14|
P = QQ[2^(1/2), 2^(1/3), 2^(1/5)]
}}}

{{{id=11|
P.gens()
///
(sqrt2, a, b)
}}}

{{{id=10|
aaa,bbb,ccc = P.gens()
}}}

{{{id=17|
print aaa.absolute_minpoly();
print bbb.absolute_minpoly();
print ccc.absolute_minpoly();
///
x^2 - 2
x^3 - 2
x^5 - 2
}}}

{{{id=19|
P.order(aaa)
///
Traceback (most recent call last):
  File "", line 1, in 
  File "/Volumes/HOME/sage/sage_notebook/worksheets/admin/6/code/
56.py", line 4, in 
exec compile(ur'P.order(aaa)' + '\n', '', 'single')
  File "/Volumes/HOME/sage/data/extcode/sage/", line 1, in 

  File "/Volumes/HOME/sage/local/lib/python2.5/site-packages/sage/
rings/number_field/number_field.py", line 3890, in order
base = self.base_field().maximal_order()
  File "/Volumes/HOME/sage/local/lib/python2.5/site-packages/sage/
rings/number_field/number_field.py", line 3224, in maximal_order
OK = self.order(B, check_is_integral=False, check_rank=False)
  File "/Volumes/HOME/sage/local/lib/python2.5/site-packages/sage/
rings/number_field/number_field.py", line 3891, in order
return order.relative_order_from_ring_generators(gens, base,
**kwds)
  File "/Volumes/HOME/sage/local/lib/python2.5/site-packages/sage/
rings/number_field/order.py", line 1465, in
relative_order_from_ring_generators
absolute_order_module_gens = monomials(module_gens, n)
  File "/Volumes/HOME/sage/local/lib/python2.5/site-packages/sage/
rings/monomials.py", line 40, in monomials
return _monomials(v, R, n, 0)
  File "/Volumes/HOME/sage/local/lib/python2.5/site-packages/sage/
rings/monomials.py", line 15, in _monomials
v = monomials(w, n)
  File "/Volumes/HOME/sage/local/lib/python2.5/site-packages/sage/
rings/monomials.py", line 40, in monomials
return _monomials(v, R, n, 0)
  File "/Volumes/HOME/sage/local/lib/python2.5/site-packages/sage/
rings/monomials.py", line 15, in _monomials
v = monomials(w, n)
  File "/Volumes/HOME/sage/local/lib/python2.5/site-packages/sage/
rings/monomials.py", line 40, in monomials
return _monomials(v, R, n, 0)
  File "/Volumes/HOME/sage/local/lib/python2.5/site-packages/sage/
rings/monomials.py", line 15, in _monomials
v = monomials(w, n)
  File "/Volumes/HOME/sage/local/lib/python2.5/site-packages/sage/
rings/monomials.py", line 40, in monomials
return _monomials(v, R, n, 0)
  File "/Volumes/HOME/sage/local/lib/python2.5/site-packages/sage/
rings/monomials.py", line 15, in _monomials
v = monomials(w, n)
  File "/Volumes/HOME/sage/local/lib/python2.5/site-packages/sage/
rings/monomials.py", line 40, in monomials
return _monomials(v, R, n, 0)
  File "/Volumes/HOME/sage/local/lib/python2.5/site-packages/sage/
rings/monomials.py", line 15, in _monomials
v = monomials(w, n)
  File "/Volumes/HOME/sage/local/lib/python2.5/site-packages/sage/
rings/monomials.py", line 40, in monomials
return _monomials(v, R, n, 0)
  File "/Volumes/HOME/sage/local/lib/python2.5/site-packages/sage/
rings/monomials.py", line 15, in _monomials
v = monomials(w, n)
  File "/Volumes/HOME/sage/local/lib/python2.5/site-packages/sage/
rings/monomials.py", line 40, in monomials
return _monomials(v, R, n, 0)
  File "/Volumes/HOME/sage/local/lib/python2.5/site-packages/sage/
rings/monomials.py", line 19, in _monomials
v.append(v[j]*z)
  File "element.pyx", line 1372, in
sage.structure.element.RingElement.__mul__
  File "coerce.pxi", line 126, in sage.structure.element._mul_c
KeyboardInterrupt
>>>
>>>
}}}

--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: Animate

[Robert Miller]

> If you don't mind, I have two sage/graphics questions.  First, how do you 
> animate tachyon objects?  If I have a list L of t.cylinder()'s and I do
> sage: a = animate(L)

The problem here is that T.cylinder() returns a "Tachyon" object
instead of a "Graphics" object.

sage: type(L[0])


When animate runs, it checks whether each item is a Graphics object or
not. If it isn't, then it calls .plot() on it. So the animate function
isn't ready for Tachyon objects.

> Is there a special tachyon animate?

What you could do is follow the source code for animate, to see how to
use the convert command to create a gif from a list of images instead.
I'm looking at sage/plot/animate.py, line 249:

cmd = 'cd "%s"; convert -delay %s -loop %s *.png "%s"'%(d,
int(delay), int(iterations), outfile)

so if 'dir' is a directory of images, specifically .png files, then

cd "dir"
convert -delay 20 -loop 1 *.png "result.gif"

will create an animation that plays through them once, with a 20/100
second delay per frame. -loop 0 will loop forever.

> Second, how do you get cylinders to only show up from the origin out to a 
> specified point?

Those are fcylinders. If you want, the graphs in sage use Tachyon, so
you could look at the source code there. E.g.,
G = graphs.CubeGraph(4)
G.plot3d??
The edges are fcylinders.

-- 
Robert L. Miller
University of Washington
Department of Mathematics
http://www.rlmiller.org/

--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: having authors names in .py files

[Robert Miller]

> > > Again I strongly disagree with removing all the AUTHOR: blocks from
> > > the Sage docstrings.

The following is from the GPL v3:

"""
...
Notwithstanding any other provision of this License, for material you
add to a covered work, you may (if authorized by the copyright holders
of that material) supplement the terms of this License with terms:

* a) ...
* b) Requiring preservation of specified reasonable legal notices
or author attributions ...
"""

Disturbing discussions like this seriously make me consider adding
some provision like this to at least the code I have contributed. If
people were to start removing my name from software I have spent hard
time writing, Sage would be down one developer. The example with
graph.py is great, because in fact many code submissions Jason was
making were coming in without names corresponding to the patches,
simply because Jason was using a slightly different revision control
program. If it weren't for his name in the code itself, it might not
be there at all.

Recall: we are not the borg. We all have names. What is the real
objective here? I'd like to help develop the best math software in the
world, and get credit for it. In the kind of job market many of us
face, this is what differentiates different people vying for the same
job. Ownership and credit are very different things. Tell me this- why
are we so worried about owning something that is free, that anyone can
change and distribute, and whose goal is to be available to everyone?

-- Robert L. Miller


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: Fwd: banner

[Robert Miller]

> Obviously
> the 5-cube has to go somewhere ...

Just some input on the 5-cube. The one line that everyone is using to
make the 5-cube could be a little nicer:

sage: graphs.CubeGraph(5).show3d()
http://www.rlmiller.org/ok.png
versus
sage: graphs.CubeGraph(5).show3d(iterations=300)
http://www.rlmiller.org/better.png

--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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] Is -7 a prime number?

[Robert Miller]

The algebraic definition is that its only divisors are itself and 1,
up to units-- yes. The cultural definition is that it is in {2,
3, ...}-- no. It seems weird to use the cultural definition, since if
we pass to another ring that contains ZZ, chances are the definition
there will be the cultural definition. If -7 goes from not prime to
prime when we extend, say, to the ring of integers of a number field,
then that feels weird. Anyway, the ticket is question is:

http://trac.sagemath.org/sage_trac/ticket/1399
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: Is -7 a prime number?

[Robert Miller]

On Dec 14, 4:15 am, "John Cremona" <[EMAIL PROTECTED]> wrote:
> Where in ring theory (outside of number theory) is the notion of a
> prime element of a ring used?

In basic commutative algebra, e.g. a beginning graduate student is
playing around with rings to get a sense of things... It might be
misleading to just say, no -7 is not a prime in the ring ZZ. In most
other situations, I'll admit that prime ideal is a more natural way of
working with things. I'm just wary of returning False, and having a
beginner in algebra getting confused. The fact is, if -7 divides a
times b, then it divides a or it divides b.


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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] Call for reviews, beginning 2.9.1

[Robert Miller]

2.9.1 is due out on Saturday. I'd like to start with the following
tickets:

- Possibly fixed or invalid:
http://trac.sagemath.org/sage_trac/ticket/678
http://trac.sagemath.org/sage_trac/ticket/1144
http://trac.sagemath.org/sage_trac/ticket/1476

- Easy, should be done:
http://trac.sagemath.org/sage_trac/ticket/526 - this only requires an
update for the manual and changing make --> $MAKE
http://trac.sagemath.org/sage_trac/ticket/1064 - the involved files
have changed, but everything is stable now so someone should make a
patch

- Tickets related to packages:
http://trac.sagemath.org/sage_trac/ticket/705
http://trac.sagemath.org/sage_trac/ticket/780
http://trac.sagemath.org/sage_trac/ticket/950 & #1452
http://trac.sagemath.org/sage_trac/ticket/954
http://trac.sagemath.org/sage_trac/ticket/1002
http://trac.sagemath.org/sage_trac/ticket/1137
http://trac.sagemath.org/sage_trac/ticket/1259
http://trac.sagemath.org/sage_trac/ticket/1277
http://trac.sagemath.org/sage_trac/ticket/1415
http://trac.sagemath.org/sage_trac/ticket/1438
http://trac.sagemath.org/sage_trac/ticket/1470
http://trac.sagemath.org/sage_trac/ticket/1495
http://trac.sagemath.org/sage_trac/ticket/1505
http://trac.sagemath.org/sage_trac/ticket/1510
http://trac.sagemath.org/sage_trac/ticket/1522
http://trac.sagemath.org/sage_trac/ticket/1533
http://trac.sagemath.org/sage_trac/ticket/1540
http://trac.sagemath.org/sage_trac/ticket/1541
http://trac.sagemath.org/sage_trac/ticket/1545 (and #490 and #542)
http://trac.sagemath.org/sage_trac/ticket/1546
http://trac.sagemath.org/sage_trac/ticket/1553

- Someone should look into the following tickets, all of which are
Solaris-related:
http://trac.sagemath.org/sage_trac/ticket/678
http://trac.sagemath.org/sage_trac/ticket/1178
http://trac.sagemath.org/sage_trac/ticket/1325
http://trac.sagemath.org/sage_trac/ticket/1326
http://trac.sagemath.org/sage_trac/ticket/1328
http://trac.sagemath.org/sage_trac/ticket/1329



--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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] Notebook listing usernames

[Robert Miller]

As pointed out by Michael Abshoff, it seems like an information leak
to list all the usernames on a notebook when you fail to use a valid
one to log in. Thoughts?
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: #1426: new trac view: tickets ***reported by*** given user

[Robert Miller]

David,

Did you mean to attach something to that ticket?


-- Robert M

On Dec 20, 8:07 pm, David Harvey <[EMAIL PROTECTED]> wrote:
> Hi paul,
>
> is this what you wanted?
>
> http://sagetrac.org/sage_trac/report/9
>
> david
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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] Sage 2.9.1.alpha2

[Robert Miller]

Sage 2.9.1 alpha2 is out, available at:

http://sage.math.washington.edu/home/rlmill/sage-2.9.1.alpha2.tar

Closed tickets:
alpha2:
#1064 - Robert Miller - permutation __call__ type check
#1175 - Michael Abshoff - circular link in sage/local/lib/python2.5
#1233 - Michael Abshoff, John Cremona - mwrank wrapper causes crashes
and error on non-minimal curves
#1240 - Michael Abshoff - wrong unix rights of some files
#1424 - William Stein - threaded map function, as requested by Peter
Doyle
#1459 - Mike Hansen - make notebook ? behavior like command line
behavior
#1546 - Michael Abshoff - Update FLINT.spkg to 1.03 release
#1556 - Yi Qiang - make usernames legible on bad login name to
notebook
#1562 - Robert Bradshaw - inverse trig
#1563 - Robert Miller - ./sage -r main
#1569 - William Stein - solve() fails if one list element is True
#1572 - Michael Abshoff - memleak in graph_fast.pyx
#1573 - Michael Abshoff - Mismatched free() / delete / delete [] in
wrap.cc

alpha1:
#1139 - Mike Hansen - nintegral raises helpful error if precision is
too high
#1318 & #1319 - Robert Miller - eigenspaces/charpoly of a graph
#1363 - Carl Witty - sqrt for complex intervals
#1380 - Martin Albrecht - R.=QQ[]; x.subs(x=1/y); now works
#1421 - Paul Zimmerman, Craig Citro - finer control in ECM interface
#1432 - William Stein - plotting examples
#1540 - Michael Abshoff - remove linux elf binaries during lapack
build
#1542 & #1543 - Craig Citro - R/rpy build issues fixed
#1548 - Michael Abshoff - numerical noise in doctests in calculus.py
#1551 - Robert Miller - is_subgraph
#1555 - bill.p, William Stein - typos in documentation



--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: Sage 2.9.1.alpha2

[Robert Miller]

> What needs to happen to go from 2.9.1.alpha2 to a release
> candidate and a release?
>
>  -- William

1. I would like to get patches in for all the critical tickets. In
particular, I'd like to see #1366 fixed up.

2. The following tickets could use review:
#1130, #1155, #1371, #1413, #1418, #1448, #1485, #1505, (#1516 &
#1536), #1533, #1558, #1561, (#1567 & #1568)
Also, I think Robert Bradshaw is currently reviewing #980. It would be
good to get at least a majority of these reviewed before Saturday.

3. Tickets #1495 & #1547 should also get patches soon, to improve the
way ATLAS builds.

4. At least by 2.9.2, we should have a pretty robust system for jmol.
I know there are one or two issues left, including #1580...

The plan is to do an rc0 by about 2:00am EST 12/22, then a release by
2am the next day.

-- Robert M
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: Sage 2.9.1.alpha2

[Robert Miller]

> > What needs to happen to go from 2.9.1.alpha2 to a release
> > candidate and a release?

Also, we *really* need to update COPYING.txt to reflect the new
packages.
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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] Sage-2.9.1.alpha3

[Robert Miller]

is here:

http://sage.math.washington.edu/home/rlmill/sage-2.9.1.alpha3.tar

summary:
alpha3:
 #668 - Michael Abshoff - numerical noise doctest in calculus.py
 #670 - Michael Abshoff - numerical noise doctest in piecewise.py
 #924 -   William Stein - the matplotlib spkg patches break underlying
functionality
#1561 -  Nick Alexander - add ._matrix_() and .transpose() to vector/
FreeModuleElement.
#1579 - Michael Abshoff - memleak in GSL's ComplexDoubleVector
#1582 -   Robert Miller - 2.9.1.alph2: doctest failure in sage/graphs/
graph.py with x86 Linux
#1584 -   Robert Miller - calculus.py doctest failure on Fermat

alpha2:
#1064 - Robert Miller - permutation __call__ type
check
#1175 -   Michael Abshoff - circular link in sage/local/
lib/python2.5
#1233 - Michael Abshoff, John Cremona - mwrank wrapper causes crashes
and error on non-minimal curves
#1240 -   Michael Abshoff - wrong unix rights of some
files
#1424 - William Stein - threaded map function, as
requested by Peter Doyle

#1459 -   Mike Hansen - make notebook ? behavior like
command line behavior
#1546 -   Michael Abshoff - Update FLINT.spkg to 1.03
release
#1556 -  Yi Qiang - make usernames legible on bad
login name to notebook
#1562 - Dan Drake - inverse trig
#1563 - Robert Miller - ./sage -r main
#1569 - William Stein - solve() fails if one list
element is True
#1572 -   Michael Abshoff - memleak in graph_fast.pyx
#1573 -   Michael Abshoff - Mismatched free() / delete /
delete [] in wrap.cc

alpha1:
#1139 - Mike Hansen - nintegral raises helpful
error if precision is too high
#1318 & #1319 -       Robert Miller - eigenspaces/charpoly of
a graph
#1363 -  Carl Witty - sqrt for complex
intervals
#1380 - Martin Albrecht - R.=QQ[]; x.subs(x=1/
y); now works
#1421 - Paul Zimmerman, Craig Citro - finer control in ECM
interface
#1432 -   William Stein - plotting examples
#1540 - Michael Abshoff - remove linux elf
binaries during lapack build
#1542 & #1543 - Craig Citro - R/rpy build issues fixed
#1548 - Michael Abshoff - numerical noise in
doctests in calculus.py
#1551 -       Robert Miller - is_subgraph
#1555 -   bill.p, William Stein - typos in documentation

--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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] Sage 2.9.1.rc0

[Robert Miller]

is here:

http://sage.math.washington.edu/home/rlmill/sage-2.9.1.rc0.tar

summary:
rc0:
 #405 -Mike Hansen - set rows and cols of matrices
 #649  Mike Hansen - create a special symbolic
matrix data type
 #857 - Michael Abshoff, Robert Miller - updates to COPYING.txt
#1106 -Mike Hansen - speed up dense matrix
comparison
#1448 - Mike Hansen, ref. David Harvey - iterate over a matrix space
#1459 -Mike Hansen - make notebook ? behavior like
command line behavior
#1505 -Martin Albrecht - make M4RI a shared library
#1533 -Robert Bradshaw - finish converting java3d to
an spkg
#1566 -Mike Hansen - Symbolic substitution
infinite recursion
#1586 -  Robert Miller - preparser.py doctest failures

alpha3:
 #668 - Michael Abshoff - numerical noise doctest in calculus.py
 #670 - Michael Abshoff - numerical noise doctest in piecewise.py
 #924 -   William Stein - the matplotlib spkg patches break underlying
functionality
#1561 -  Nick Alexander - add ._matrix_() and .transpose() to vector/
FreeModuleElement.
#1579 - Michael Abshoff - memleak in GSL's ComplexDoubleVector
#1582 -   Robert Miller - 2.9.1.alph2: doctest failure in sage/graphs/
graph.py with x86 Linux
#1584 -   Robert Miller - calculus.py doctest failure on Fermat

alpha2:
#1064 - Robert Miller - permutation __call__ type
check
#1175 -   Michael Abshoff - circular link in sage/local/
lib/python2.5
#1233 - Michael Abshoff, John Cremona - mwrank wrapper causes crashes
and error on non-minimal curves
#1240 -   Michael Abshoff - wrong unix rights of some
files
#1424 - William Stein - threaded map function, as
requested by Peter Doyle
#1546 -   Michael Abshoff - Update FLINT.spkg to 1.03
release
#1556 -  Yi Qiang - make usernames legible on bad
login name to notebook
#1562 - Dan Drake - inverse trig
#1563 - Robert Miller - ./sage -r main
#1569 - William Stein - solve() fails if one list
element is True
#1572 -   Michael Abshoff - memleak in graph_fast.pyx
#1573 -   Michael Abshoff - Mismatched free() / delete /
delete [] in wrap.cc

alpha1:
#1139 - Mike Hansen - nintegral raises helpful
error if precision is too high
#1318 & #1319 -       Robert Miller - eigenspaces/charpoly of
a graph
#1363 -  Carl Witty - sqrt for complex
intervals
#1380 - Martin Albrecht - R.=QQ[]; x.subs(x=1/
y); now works
#1421 - Paul Zimmerman, Craig Citro - finer control in ECM
interface
#1432 -   William Stein - plotting examples
#1540 - Michael Abshoff - remove linux elf
binaries during lapack build
#1542 & #1543 - Craig Citro - R/rpy build issues fixed
#1548 - Michael Abshoff - numerical noise in
doctests in calculus.py
#1551 -       Robert Miller - is_subgraph
#1555 -   bill.p, William Stein - typos in documentation



--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: Sage 2.9.1.rc0

[Robert Miller]

There is a build failure due to m4ri importing from the wrong place,
but this is fixed, rc1 will be up shortly.

On Dec 22, 2:07 pm, Robert Miller <[EMAIL PROTECTED]> wrote:
> is here:
>
> http://sage.math.washington.edu/home/rlmill/sage-2.9.1.rc0.tar
>
> summary:
> rc0:
>  #405 -Mike Hansen - set rows and cols of matrices
>  #649  Mike Hansen - create a special symbolic
> matrix data type
>  #857 - Michael Abshoff, Robert Miller - updates to COPYING.txt
> #1106 -Mike Hansen - speed up dense matrix
> comparison
> #1448 - Mike Hansen, ref. David Harvey - iterate over a matrix space
> #1459 -Mike Hansen - make notebook ? behavior like
> command line behavior
> #1505 -Martin Albrecht - make M4RI a shared library
> #1533 -Robert Bradshaw - finish converting java3d to
> an spkg
> #1566 -Mike Hansen - Symbolic substitution
> infinite recursion
> #1586 -  Robert Miller - preparser.py doctest failures
>
> alpha3:
>  #668 - Michael Abshoff - numerical noise doctest in calculus.py
>  #670 - Michael Abshoff - numerical noise doctest in piecewise.py
>  #924 -   William Stein - the matplotlib spkg patches break underlying
> functionality
> #1561 -  Nick Alexander - add ._matrix_() and .transpose() to vector/
> FreeModuleElement.
> #1579 - Michael Abshoff - memleak in GSL's ComplexDoubleVector
> #1582 -   Robert Miller - 2.9.1.alph2: doctest failure in sage/graphs/
> graph.py with x86 Linux
> #1584 -   Robert Miller - calculus.py doctest failure on Fermat
>
> alpha2:
> #1064 - Robert Miller - permutation __call__ type
> check
> #1175 -   Michael Abshoff - circular link in sage/local/
> lib/python2.5
> #1233 - Michael Abshoff, John Cremona - mwrank wrapper causes crashes
> and error on non-minimal curves
> #1240 -   Michael Abshoff - wrong unix rights of some
> files
> #1424 - William Stein - threaded map function, as
> requested by Peter Doyle
> #1546 -   Michael Abshoff - Update FLINT.spkg to 1.03
> release
> #1556 -      Yi Qiang - make usernames legible on bad
> login name to notebook
> #1562 - Dan Drake - inverse trig
> #1563 - Robert Miller - ./sage -r main
> #1569 - William Stein - solve() fails if one list
> element is True
> #1572 -   Michael Abshoff - memleak in graph_fast.pyx
> #1573 -   Michael Abshoff - Mismatched free() / delete /
> delete [] in wrap.cc
>
> alpha1:
> #1139 - Mike Hansen - nintegral raises helpful
> error if precision is too high
> #1318 & #1319 -   Robert Miller - eigenspaces/charpoly of
> a graph
> #1363 -  Carl Witty - sqrt for complex
> intervals
> #1380 - Martin Albrecht - R.=QQ[]; x.subs(x=1/
> y); now works
> #1421 - Paul Zimmerman, Craig Citro - finer control in ECM
> interface
> #1432 -   William Stein - plotting examples
> #1540 - Michael Abshoff - remove linux elf
> binaries during lapack build
> #1542 & #1543 - Craig Citro - R/rpy build issues fixed
> #1548 - Michael Abshoff - numerical noise in
> doctests in calculus.py
> #1551 -   Robert Miller - is_subgraph
> #1555 -   bill.p, William Stein - typos in documentation
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: Sage 2.9.1.rc0

[Robert Miller]

Build testers: please instead try

http://sage.math.washington.edu/home/rlmill/sage-2.9.1.rc1.tar


On Dec 22, 4:46 pm, Robert Miller <[EMAIL PROTECTED]> wrote:
> There is a build failure due to m4ri importing from the wrong place,
> but this is fixed, rc1 will be up shortly.
>
> On Dec 22, 2:07 pm, Robert Miller <[EMAIL PROTECTED]> wrote:
>
> > is here:
>
> >http://sage.math.washington.edu/home/rlmill/sage-2.9.1.rc0.tar
>
> > summary:
> > rc0:
> >  #405 -Mike Hansen - set rows and cols of matrices
> >  #649  Mike Hansen - create a special symbolic
> > matrix data type
> >  #857 - Michael Abshoff, Robert Miller - updates to COPYING.txt
> > #1106 -Mike Hansen - speed up dense matrix
> > comparison
> > #1448 - Mike Hansen, ref. David Harvey - iterate over a matrix space
> > #1459 -Mike Hansen - make notebook ? behavior like
> > command line behavior
> > #1505 -Martin Albrecht - make M4RI a shared library
> > #1533 -Robert Bradshaw - finish converting java3d to
> > an spkg
> > #1566 -Mike Hansen - Symbolic substitution
> > infinite recursion
> > #1586 -  Robert Miller - preparser.py doctest failures
>
> > alpha3:
> >  #668 - Michael Abshoff - numerical noise doctest in calculus.py
> >  #670 - Michael Abshoff - numerical noise doctest in piecewise.py
> >  #924 -   William Stein - the matplotlib spkg patches break underlying
> > functionality
> > #1561 -  Nick Alexander - add ._matrix_() and .transpose() to vector/
> > FreeModuleElement.
> > #1579 - Michael Abshoff - memleak in GSL's ComplexDoubleVector
> > #1582 -   Robert Miller - 2.9.1.alph2: doctest failure in sage/graphs/
> > graph.py with x86 Linux
> > #1584 -   Robert Miller - calculus.py doctest failure on Fermat
>
> > alpha2:
> > #1064 - Robert Miller - permutation __call__ type
> > check
> > #1175 -   Michael Abshoff - circular link in sage/local/
> > lib/python2.5
> > #1233 - Michael Abshoff, John Cremona - mwrank wrapper causes crashes
> > and error on non-minimal curves
> > #1240 -   Michael Abshoff - wrong unix rights of some
> > files
> > #1424 - William Stein - threaded map function, as
> > requested by Peter Doyle
> > #1546 -   Michael Abshoff - Update FLINT.spkg to 1.03
> > release
> > #1556 -  Yi Qiang - make usernames legible on bad
> > login name to notebook
> > #1562 - Dan Drake - inverse trig
> > #1563 - Robert Miller - ./sage -r main
> > #1569 - William Stein - solve() fails if one list
> > element is True
> > #1572 -   Michael Abshoff - memleak in graph_fast.pyx
> > #1573 -   Michael Abshoff - Mismatched free() / delete /
> > delete [] in wrap.cc
>
> > alpha1:
> > #1139 - Mike Hansen - nintegral raises helpful
> > error if precision is too high
> > #1318 & #1319 -   Robert Miller - eigenspaces/charpoly of
> > a graph
> > #1363 -  Carl Witty - sqrt for complex
> > intervals
> > #1380 - Martin Albrecht - R.=QQ[]; x.subs(x=1/
> > y); now works
> > #1421 - Paul Zimmerman, Craig Citro - finer control in ECM
> > interface
> > #1432 -   William Stein - plotting examples
> > #1540 - Michael Abshoff - remove linux elf
> > binaries during lapack build
> > #1542 & #1543 - Craig Citro - R/rpy build issues fixed
> > #1548 - Michael Abshoff - numerical noise in
> > doctests in calculus.py
> > #1551 -   Robert Miller - is_subgraph
> > #1555 -   bill.p, William Stein - typos in documentation
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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] Sage 2.9.1.rc2

[Robert Miller]

The URL:
http://sage.math.washington.edu/home/rlmill/sage-2.9.1.rc2.tar

summary:
rc2: four spaces -> tab in spkg/standard/deps, and
#1558 - Joel Mohler
  - more NTL wrapping, coefficient access and factoring
#1564 - Robert Bradshaw, William Stein
  - 3d graphics via jmol!
#1580 - Robert Miller
  - notebook shows graphics out of order

rc1: just fixed spkg/install and spkg/standard/deps from #1505

The jmol spkg isn't for certain, but it won't hurt to see what various
build environments expose. Tomorrow we will wrap up the remaining
issues and release 2.9.1.
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: Bug Day 8 proposal: Dec. 27th or 28th

[Robert Miller]

2nd sounds good to me!

On Dec 22, 11:51 pm, Robert Bradshaw <[EMAIL PROTECTED]>
wrote:
> On Dec 22, 2007, at 6:38 PM, mabshoff wrote:
>
>
>
> > On Dec 23, 3:30 am, William Stein <[EMAIL PROTECTED]> wrote:
> >> On Dec 22, 2007, at 7:09 PM, Martin Albrecht <[EMAIL PROTECTED]
> >> bremen.de
>
> >>> wrote:
>
> >>> I'll be away from keyboard then till January.
>
> >> dec 27 is my 5th anniversary so that won't work for me.
>
> > Hah, we finally found an occasion when William won't work on Sage. But
> > I have to admit that you have your priorities straight. If other
> > people are interested we should still try to do something coordinated
> > on that day.
>
> >> i propose jan 4 at 1am as the release date for 2.9.2, and that we
> >> have
> >> bug days on irc starting jan 2.
>
> > Sounds good to me, too. I plan to pretty much work on 2.9.2 from now
> > until the release date.
>
> The 2nd would work well for me too, I'm flying home that morning and
> should be free the rest of that day. I hope to work on the 3D stuff
> before then, but it'll be pretty sporadic when I'll be free so I
> can't promise I'll be able to be around on the 27th.
>
> - Robert
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: Sage 2.9.1.rc2

[Robert Miller]

Testall on sage.math:

Following tests failed:
sage -t  const.tex

sage -t  devel/sage-main/sage/libs/mwrank/mwrank.pyx
sage -t  devel/sage-main/sage/libs/mwrank/interface.py
sage -t  devel/sage-main/sage/schemes/elliptic_curves/
ell_rational_field.py
sage -t  devel/sage-main/sage/schemes/elliptic_curves/sha.py
sage -t  devel/sage-main/sage/schemes/elliptic_curves/padic_lseries.py
sage -t  devel/sage-main/sage/schemes/elliptic_curves/padics.py
sage -t  devel/sage-main/sage/schemes/elliptic_curves/lseries_ell.py

'str' object not callable is a common theme to these...
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: Sage 2.9.1.rc2

[Robert Miller]

OK, I've fixed the mwrank issues, so const.tex is the only thing left.
The error:
sage: show(line([zeta(1/2 + k*I/6) for k in range(180)]),
rgbcolor=(3/4,1/2,5/8))
---
 Traceback (most recent call
last)

/home/rlmill/release/sage-2.9.1.rc3/ in ()

/home/rlmill/release/sage-2.9.1.rc3/local/lib/python2.5/site-packages/
sage/plot/plot.py in __call__(self, points, coerce, **kwds)
   1705 if coerce:
   1706 for z in points:
-> 1707 if len(z) == 3:
   1708 return self._graphic3d()(points,
coerce=coerce, **kwds)
   1709 xdata.append(float(z[0]))

: object of type
'sage.rings.complex_number.ComplexNumber' has no len()


On Dec 23, 10:34 am, Robert Miller <[EMAIL PROTECTED]> wrote:
> Testall on sage.math:
>
> Following tests failed:
> sage -t  const.tex
>
> sage -t  devel/sage-main/sage/libs/mwrank/mwrank.pyx
> sage -t  devel/sage-main/sage/libs/mwrank/interface.py
> sage -t  devel/sage-main/sage/schemes/elliptic_curves/
> ell_rational_field.py
> sage -t  devel/sage-main/sage/schemes/elliptic_curves/sha.py
> sage -t  devel/sage-main/sage/schemes/elliptic_curves/padic_lseries.py
> sage -t  devel/sage-main/sage/schemes/elliptic_curves/padics.py
> sage -t  devel/sage-main/sage/schemes/elliptic_curves/lseries_ell.py
>
> 'str' object not callable is a common theme to these...
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: Sage 2.9.1.rc2

[Robert Miller]

There is an rc3, but there are still issues with the new matplotlib
spkg on Darwin. We may just roll back to what we were using before...
http://sage.math.washington.edu/home/rlmill/release/sage-2.9.1.rc3/dist/sage-2.9.1.rc3.tar

On Dec 23, 11:08 am, "William Stein" <[EMAIL PROTECTED]> wrote:
> See attached patch to fix problem below...
>
> On Dec 23, 2007 8:52 AM, Robert Miller <[EMAIL PROTECTED]> wrote:
>
>
>
>
>
> > OK, I've fixed the mwrank issues, so const.tex is the only thing left.
> > The error:
> > sage: show(line([zeta(1/2 + k*I/6) for k in range(180)]),
> > rgbcolor=(3/4,1/2,5/8))
> > ---
> >  Traceback (most recent call
> > last)
>
> > /home/rlmill/release/sage-2.9.1.rc3/ in ()
>
> > /home/rlmill/release/sage-2.9.1.rc3/local/lib/python2.5/site-packages/
> > sage/plot/plot.py in __call__(self, points, coerce, **kwds)
> >1705 if coerce:
> >1706 for z in points:
> > -> 1707 if len(z) == 3:
> >1708 return self._graphic3d()(points,
> > coerce=coerce, **kwds)
> >1709     xdata.append(float(z[0]))
>
> > : object of type
> > 'sage.rings.complex_number.ComplexNumber' has no len()
>
> > On Dec 23, 10:34 am, Robert Miller <[EMAIL PROTECTED]> wrote:
> > > Testall on sage.math:
>
> > > Following tests failed:
> > > sage -t  const.tex
>
> > > sage -t  devel/sage-main/sage/libs/mwrank/mwrank.pyx
> > > sage -t  devel/sage-main/sage/libs/mwrank/interface.py
> > > sage -t  devel/sage-main/sage/schemes/elliptic_curves/
> > > ell_rational_field.py
> > > sage -t  devel/sage-main/sage/schemes/elliptic_curves/sha.py
> > > sage -t  devel/sage-main/sage/schemes/elliptic_curves/padic_lseries.py
> > > sage -t  devel/sage-main/sage/schemes/elliptic_curves/padics.py
> > > sage -t  devel/sage-main/sage/schemes/elliptic_curves/lseries_ell.py
>
> > > 'str' object not callable is a common theme to these...
>
> --
> William Stein
> Associate Professor of Mathematics
> University of Washingtonhttp://wstein.org
>
>  7837.patch
> 2KDownload
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: Sage 2.9.1.rc2

[Robert Miller]

On Dec 23, 12:30 pm, "William Stein" <[EMAIL PROTECTED]> wrote:
> We *have* to get the new matplotlib package to fully work.  The one we
> currently ship is very very out of date.   I will hopefully be able to
> work on this tonight if nobody else resolves the problems; what are
> they?

It seems to be one commonly occuring error (it is all over the Darwin
tests)
"No module named _locale"
e.g.

**
File "plot.py", line 10:
sage: from pylab import *
Exception raised:
Traceback (most recent call last):
  File "/Users/was/build/sage-2.9.1.rc2/local/lib/python2.5/
doctest.py", line 1212, in __run
compileflags, 1) in test.globs
  File "", line 1, in 
from pylab import *###line 10:
sage: from pylab import *
  File "/Users/was/build/sage-2.9.1.rc2/local/lib/python2.5/site-
packages/pylab.py", line 1, in 
from matplotlib.pylab import *
  File "/Users/was/build/sage-2.9.1.rc2/local/lib/python2.5/site-
packages/matplotlib/pylab.py", line 197, in 
from cbook import flatten, is_string_like, exception_to_str,
popd, \
  File "/Users/was/build/sage-2.9.1.rc2/local/lib/python2.5/site-
packages/matplotlib/cbook.py", line 18, in 
preferredencoding = locale.getpreferredencoding()
  File "/Users/was/build/sage-2.9.1.rc2/local/lib/python2.5/
locale.py", line 494, in getpreferredencoding
import _locale
ImportError: No module named _locale
**

>
> On 12/23/07, Robert Miller <[EMAIL PROTECTED]> wrote:
>
>
>
>
>
> > There is an rc3, but there are still issues with the new matplotlib
> > spkg on Darwin. We may just roll back to what we were using before...
> >http://sage.math.washington.edu/home/rlmill/release/sage-2.9.1.rc3/di...
>
> > On Dec 23, 11:08 am, "William Stein" <[EMAIL PROTECTED]> wrote:
> > > See attached patch to fix problem below...
>
> > > On Dec 23, 2007 8:52 AM, Robert Miller <[EMAIL PROTECTED]> wrote:
>
> > > > OK, I've fixed the mwrank issues, so const.tex is the only thing left.
> > > > The error:
> > > > sage: show(line([zeta(1/2 + k*I/6) for k in range(180)]),
> > > > rgbcolor=(3/4,1/2,5/8))
>
> > ---
> > > >  Traceback (most recent call
> > > > last)
>
> > > > /home/rlmill/release/sage-2.9.1.rc3/ in ()
>
> > > > /home/rlmill/release/sage-2.9.1.rc3/local/lib/python2.5/site-packages/
> > > > sage/plot/plot.py in __call__(self, points, coerce, **kwds)
> > > >1705 if coerce:
> > > >1706         for z in points:
> > > > -> 1707 if len(z) == 3:
> > > >1708 return self._graphic3d()(points,
> > > > coerce=coerce, **kwds)
> > > >1709 xdata.append(float(z[0]))
>
> > > > : object of type
> > > > 'sage.rings.complex_number.ComplexNumber' has no len()
>
> > > > On Dec 23, 10:34 am, Robert Miller <[EMAIL PROTECTED]> wrote:
> > > > > Testall on sage.math:
>
> > > > > Following tests failed:
> > > > > sage -t  const.tex
>
> > > > > sage -t  devel/sage-main/sage/libs/mwrank/mwrank.pyx
> > > > > sage -t  devel/sage-main/sage/libs/mwrank/interface.py
> > > > > sage -t  devel/sage-main/sage/schemes/elliptic_curves/
> > > > > ell_rational_field.py
> > > > > sage -t  devel/sage-main/sage/schemes/elliptic_curves/sha.py
> > > > > sage -t  devel/sage-main/sage/schemes/elliptic_curves/padic_lseries.py
> > > > > sage -t  devel/sage-main/sage/schemes/elliptic_curves/padics.py
> > > > > sage -t  devel/sage-main/sage/schemes/elliptic_curves/lseries_ell.py
>
> > > > > 'str' object not callable is a common theme to these...
>
> > > --
> > > William Stein
> > > Associate Professor of Mathematics
> > > University of Washingtonhttp://wstein.org
>
> > >  7837.patch
> > > 2KDownload
>
> --
> William Stein
> Associate Professor of Mathematics
> University of Washingtonhttp://wstein.org
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: Sage 2.9.1.rc2

[Robert Miller]

Actually, I don't know if matplotlib has anything to do with this
issue, as:

File "matrix2.pyx", line 2280, in
sage.matrix.matrix2.Matrix.echelon_form
RuntimeError

ImportError: No module named _locale


On Dec 23, 12:35 pm, Robert Miller <[EMAIL PROTECTED]> wrote:
> On Dec 23, 12:30 pm, "William Stein" <[EMAIL PROTECTED]> wrote:
>
> > We *have* to get the new matplotlib package to fully work.  The one we
> > currently ship is very very out of date.   I will hopefully be able to
> > work on this tonight if nobody else resolves the problems; what are
> > they?
>
> It seems to be one commonly occuring error (it is all over the Darwin
> tests)
> "No module named _locale"
> e.g.
>
> **
> File "plot.py", line 10:
> sage: from pylab import *
> Exception raised:
> Traceback (most recent call last):
>   File "/Users/was/build/sage-2.9.1.rc2/local/lib/python2.5/
> doctest.py", line 1212, in __run
> compileflags, 1) in test.globs
>   File "", line 1, in 
> from pylab import *###line 10:
> sage: from pylab import *
>   File "/Users/was/build/sage-2.9.1.rc2/local/lib/python2.5/site-
> packages/pylab.py", line 1, in 
> from matplotlib.pylab import *
>   File "/Users/was/build/sage-2.9.1.rc2/local/lib/python2.5/site-
> packages/matplotlib/pylab.py", line 197, in 
> from cbook import flatten, is_string_like, exception_to_str,
> popd, \
>   File "/Users/was/build/sage-2.9.1.rc2/local/lib/python2.5/site-
> packages/matplotlib/cbook.py", line 18, in 
> preferredencoding = locale.getpreferredencoding()
>   File "/Users/was/build/sage-2.9.1.rc2/local/lib/python2.5/
> locale.py", line 494, in getpreferredencoding
> import _locale
> ImportError: No module named _locale
> **
>
>
>
> > On 12/23/07, Robert Miller <[EMAIL PROTECTED]> wrote:
>
> > > There is an rc3, but there are still issues with the new matplotlib
> > > spkg on Darwin. We may just roll back to what we were using before...
> > >http://sage.math.washington.edu/home/rlmill/release/sage-2.9.1.rc3/di...
>
> > > On Dec 23, 11:08 am, "William Stein" <[EMAIL PROTECTED]> wrote:
> > > > See attached patch to fix problem below...
>
> > > > On Dec 23, 2007 8:52 AM, Robert Miller <[EMAIL PROTECTED]> wrote:
>
> > > > > OK, I've fixed the mwrank issues, so const.tex is the only thing left.
> > > > > The error:
> > > > > sage: show(line([zeta(1/2 + k*I/6) for k in range(180)]),
> > > > > rgbcolor=(3/4,1/2,5/8))
>
> > > ---
> > > > >  Traceback (most recent call
> > > > > last)
>
> > > > > /home/rlmill/release/sage-2.9.1.rc3/ in ()
>
> > > > > /home/rlmill/release/sage-2.9.1.rc3/local/lib/python2.5/site-packages/
> > > > > sage/plot/plot.py in __call__(self, points, coerce, **kwds)
> > > > >1705 if coerce:
> > > > >1706 for z in points:
> > > > > -> 1707 if len(z) == 3:
> > > > >1708 return self._graphic3d()(points,
> > > > > coerce=coerce, **kwds)
> > > > >1709 xdata.append(float(z[0]))
>
> > > > > : object of type
> > > > > 'sage.rings.complex_number.ComplexNumber' has no len()
>
> > > > > On Dec 23, 10:34 am, Robert Miller <[EMAIL PROTECTED]> wrote:
> > > > > > Testall on sage.math:
>
> > > > > > Following tests failed:
> > > > > > sage -t  const.tex
>
> > > > > > sage -t  devel/sage-main/sage/libs/mwrank/mwrank.pyx
> > > > > > sage -t  devel/sage-main/sage/libs/mwrank/interface.py
> > > > > > sage -t  devel/sage-main/sage/schemes/elliptic_curves/
> > > > > > ell_rational_field.py
> > > > > > sage -t  devel/sage-main/sage/schemes/elliptic_curves/sha.py
> > > > > > sage -t  
> > > > > > devel/sage-main/sage/schemes/elliptic_curves/padic_lseries.py
> > > > > > sage -t  devel/sage-main/sage/schemes/elliptic_curves/padics.py
> > > > > > sage -t  devel/sage-main/sage/schemes/elliptic_curves/lseries_ell.py
>
> > > > > > 'str' object not callable is a common theme to these...
>
> > > > --
> > > > William Stein
> > > > Associate Professor of Mathematics
> > > > University of Washingtonhttp://wstein.org
>
> > > >  7837.patch
> > > > 2KDownload
>
> > --
> > William Stein
> > Associate Professor of Mathematics
> > University of Washingtonhttp://wstein.org
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: Sage 2.9.1.rc2

[Robert Miller]

http://mail.python.org/pipermail/python-list/2000-June/041688.html

On Dec 23, 1:13 pm, Robert Miller <[EMAIL PROTECTED]> wrote:
> Actually, I don't know if matplotlib has anything to do with this
> issue, as:
>
> File "matrix2.pyx", line 2280, in
> sage.matrix.matrix2.Matrix.echelon_form
> RuntimeError
>
> ImportError: No module named _locale
>
> On Dec 23, 12:35 pm, Robert Miller <[EMAIL PROTECTED]> wrote:
>
> > On Dec 23, 12:30 pm, "William Stein" <[EMAIL PROTECTED]> wrote:
>
> > > We *have* to get the new matplotlib package to fully work.  The one we
> > > currently ship is very very out of date.   I will hopefully be able to
> > > work on this tonight if nobody else resolves the problems; what are
> > > they?
>
> > It seems to be one commonly occuring error (it is all over the Darwin
> > tests)
> > "No module named _locale"
> > e.g.
>
> > **
> > File "plot.py", line 10:
> > sage: from pylab import *
> > Exception raised:
> > Traceback (most recent call last):
> >   File "/Users/was/build/sage-2.9.1.rc2/local/lib/python2.5/
> > doctest.py", line 1212, in __run
> > compileflags, 1) in test.globs
> >   File "", line 1, in 
> > from pylab import *###line 10:
> > sage: from pylab import *
> >   File "/Users/was/build/sage-2.9.1.rc2/local/lib/python2.5/site-
> > packages/pylab.py", line 1, in 
> > from matplotlib.pylab import *
> >   File "/Users/was/build/sage-2.9.1.rc2/local/lib/python2.5/site-
> > packages/matplotlib/pylab.py", line 197, in 
> > from cbook import flatten, is_string_like, exception_to_str,
> > popd, \
> >   File "/Users/was/build/sage-2.9.1.rc2/local/lib/python2.5/site-
> > packages/matplotlib/cbook.py", line 18, in 
> >     preferredencoding = locale.getpreferredencoding()
> >   File "/Users/was/build/sage-2.9.1.rc2/local/lib/python2.5/
> > locale.py", line 494, in getpreferredencoding
> > import _locale
> > ImportError: No module named _locale
> > **
>
> > > On 12/23/07, Robert Miller <[EMAIL PROTECTED]> wrote:
>
> > > > There is an rc3, but there are still issues with the new matplotlib
> > > > spkg on Darwin. We may just roll back to what we were using before...
> > > >http://sage.math.washington.edu/home/rlmill/release/sage-2.9.1.rc3/di...
>
> > > > On Dec 23, 11:08 am, "William Stein" <[EMAIL PROTECTED]> wrote:
> > > > > See attached patch to fix problem below...
>
> > > > > On Dec 23, 2007 8:52 AM, Robert Miller <[EMAIL PROTECTED]> wrote:
>
> > > > > > OK, I've fixed the mwrank issues, so const.tex is the only thing 
> > > > > > left.
> > > > > > The error:
> > > > > > sage: show(line([zeta(1/2 + k*I/6) for k in range(180)]),
> > > > > > rgbcolor=(3/4,1/2,5/8))
>
> > > > ---
> > > > > >  Traceback (most recent 
> > > > > > call
> > > > > > last)
>
> > > > > > /home/rlmill/release/sage-2.9.1.rc3/ in ()
>
> > > > > > /home/rlmill/release/sage-2.9.1.rc3/local/lib/python2.5/site-packages/
> > > > > > sage/plot/plot.py in __call__(self, points, coerce, **kwds)
> > > > > >1705 if coerce:
> > > > > >1706 for z in points:
> > > > > > -> 1707 if len(z) == 3:
> > > > > >1708 return self._graphic3d()(points,
> > > > > > coerce=coerce, **kwds)
> > > > > >1709 xdata.append(float(z[0]))
>
> > > > > > : object of type
> > > > > > 'sage.rings.complex_number.ComplexNumber' has no len()
>
> > > > > > On Dec 23, 10:34 am, Robert Miller <[EMAIL PROTECTED]> wrote:
> > > > > > > Testall on sage.math:
>
> > > > > > > Following tests failed:
> > > > > > > sage -t  const.tex
>
> > > > > > > sage -t  devel/sage-main/sage/libs/mwrank/mwrank.pyx
> > > > > > > sage -t  devel/sage-main/sage/libs/m

[sage-devel] jmol in Sage 2.9.1

[Robert Miller]

Running in a notebook, in a fresh version of 2.9.1, I can't display the sphere.

{{{
from sage.plot.plot3d.all import Sphere
Sphere(1).show()
}}}

"""
The page at https://localhost:8000 says:

Reference Error: jmol SetDocument is not defined
"""

Looking in plot/plot3d/all.py, the third line was commented out before
release, but uncommenting it does not change anything. Any ideas about
this?

-- 
Robert L. Miller
University of Washington
Department of Mathematics
http://www.rlmiller.org/

--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: San Diego!

[Robert Miller]

> It's beautiful, though there are terrifying rumors that it might rain. :-)
>
>  --William

Well I assure you it is raining here in Seattle (it was -10 F at my
parents' house Thursday!). My plane is due in at 3:12 tomorrow
afternoon, so I will see you all at the booth!
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: sage.graphs, lad

[Robert Miller]

On Jan 3, 2008 8:48 PM, Brent Woodruff <[EMAIL PROTECTED]> wrote:
> Robert Miller wrote:
> > Right now, it's there but somewhat hidden. I'm not sure why it's
> > hidden. You can do something like
> >
> > sage: G = graphs.PetersenGraph()
> > sage: G.__get_pos__()
>
> When I first looked at the Sage source I missed this storage of
> position. Is there a standard set of properties you have decided to
> keep? As you can see in LAD's GUI, I have decided to store labels
> (string), weights (float), and colors (int), as well as a positions (num
> array of floats).

I'd say anything but standard. Sage's graphs have evolved as people's
needs have influenced them. The positions are there just to give the
graphs a default layout. You can also associate arbitrary python
objects with vertices and edges in Sage, although again these need a
bit of cleanup (http://trac.sagemath.org/sage_trac/ticket/743). Over
the summer, Emily and I were part of an REU on electrical networks.
Not much code came of this, other than a Kirchoff matrix constructor,
mainly because the NetworkX XGraphs and XDiGraphs together with the
linear algebra in Sage were enough for everyone's purposes. Here is a
quick example of what you can do in Sage:

sage: G = Graph()
sage: G.add_vertices(['strings', 77, ('tuples',9,3), 7.6])
sage: G.add_edges([(77,('tuples',9,3),'edgelabel'),
(77,7.6,EllipticCurve('37a'))])
sage: G.show(layout='circular', edge_labels=True,
partition=[['strings'],[77,('tuples',9,3),7.6]])

As you'll see, the partitions argument doesn't specify which color,
but it does display colorings. You can use the vertex_colors option to
specify which vertices get which colors, however we don't store
colorings at this point.

> I am wondering if we could, for the benefit of both projects, settle on
> a common base class or conventions for interoperability. For that
> matter, it wouldn't be difficult to agree to use XGraph/XDiGraph and
> decorate with a common class. I assume any of you would know better than
> me at this point.

That's what Sage uses, XGraph/XDiGraph. Aric, Emily and I will be at
IPAM in the beginning of February (http://wiki.sagemath.org/days7),
and one of our goals is to try to factor as much as we can upstream to
NetworkX. If you aren't able to make it, you should still involve
yourself via wiki and IRC. Several people in the past have "virtually"
participated in Sage days conferences.

Also, I am CCing sage-devel on this letter, mainly for the following
discussion. For those of you who haven't heard of LAD, here is a link
(http://www.fprimex.com/lad).

> > I don't have any experience with wx widgets yet. One of the big
> > challenges Sage developers have been working on lately is interactive
> > widget like features. The main challenge is the existing notebook
> > structure, which uses web browsers to serve an application. Java seems
> > to be the only option, and until recently we hadn't found much
> > (although jmol has potential). How is your experience with wxPython?
>
> First let me say that I'd be happy to lend my assistance to Sage if you
> all decided to use wxPython for something. Here's my take on it:
>
> LAD is my first full blown wxPython application, however I have
> previously worked on C++ wxWidgets projects. I find that the Python API
> almost exactly matches the C++ API so I am able to be very productive.
> Others might see this similarity as a drawback; perhaps that it is not
> pythonic. The documentation is excellent. Traditionally, wxWidget's weak
> spot has been its Mac support (QT is further along), although with
> wxPython 2.8 the quality and portability of the library has greatly
> improved. It is even included in Mac OS X 10.5. I think only QT/PyQT can
> compete in the long run, but I have a personal distaste for QT's layout
> schemes (spacers instead of sizers) and widgets. For the other side of
> the story, you could check with the VLC folks - they are switching from
> wx to QT.
>
> I have spent a significant amount of time building up a set of best
> practices for myself, so I can't say that the Sage developers would
> initially like wxPython. Additionally, I don't know that Sage users
> wouldn't prefer the web based approach already implemented (ala MapleNet).
>
> Brent W.

-- 
Robert L. Miller
University of Washington
Department of Mathematics
http://www.rlmiller.org/

--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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] (graphviz) Help! Autoconf hurts my head...

[Robert Miller]

The ticket

http://trac.sagemath.org/sage_trac/ticket/1762

aims to provide an optional graphviz spkg, but I can't get the
autoconf crap to work... All the relevant details are on the ticket,
so if you know anything about this, please help out!
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Re: sage features/bugs

[Robert Miller]

> >> Let A be a matrix not over ZZ or QQ:
>
> >>   A.adjoint()
> >>   A.inverse()
>
> >> are not implemented.
>
> > I don't think they should be.   There are already (at least) 3 ways
> > to do this:
>
> Wait a sec I agree with David K on the adjoint issue. The adjoint
> doesn't require the fraction field to even be constructed, and it
> makes perfect sense over non-domains.
>
> > sage: A = random_matrix(ZZ,2)
> > sage: ~A
>
> > [ 1/34  1/17]
> > [-6/17  5/17]
> > sage: A.__invert__()
>
> > [ 1/34  1/17]
> > [-6/17  5/17]
> > sage: A^(-1)
>
> > [ 1/34  1/17]
> > [-6/17  5/17]
>
> I vaguely recall being stung several times by the lack of an inverse
> () method. For someone who doesn't know python that well, neither ~
> nor __invert__ are obvious alternatives. I don't think it would hurt
> at all to have an inverse() method.

I actually think both should be methods, just because ~ and ^(-1)
don't show up on tab completion...


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Re: Missed patent opportunity

[Robert Miller]

PS - Software patents are EVIL!

On Feb 20, 1:30 pm, "alex clemesha" <[EMAIL PROTECTED]> wrote:
> On Feb 20, 2008 1:22 PM, <[EMAIL PROTECTED]> wrote:
>
>
>
> > This just got posted to slashdot.
>
> >http://oreillyschool.com/why/interview.php
>
> Oh Geez!
>
> > 
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Re: exact cover problem

[Robert Miller]

Just a technical note: Mod 2 matrices are not the natural way to think
about adjacency matrices (I learned this the hard way) - the entry is
actually better thought of as the number of paths of length one from
one vertex to another. That way taking nth powers of the matrices
counts the number of n-paths from one vertex to another.

Let's not try to reduce NP-complete to polynomial in this thread... ;)

Sorry, my point is an emphatic ++1 for including DLX in Sage.

-- Robert M
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Re: Sage 2.10.2.rc2 release!

[Robert Miller]

Mabshoff,

In rc2, I get that glibc problem sometimes when simply exiting the
program:

"""
[EMAIL PROTECTED]:~/sage-2.10.3.rc2-sage.math-only-x86_64-Linux$ ./sage
--
| SAGE Version 2.10.3.rc2, Release Date: 2008-03-05  |
| Type notebook() for the GUI, and license() for information.|
--
The SAGE install tree may have moved.
Regenerating Python.pyo and .pyc files that hardcode the install PATH
(please wait at most a few minutes)...
Please do not interrupt this.

sage: exit
Exiting SAGE (CPU time 0m0.02s, Wall time 0m15.75s).
Exiting spawned Gap process.
*** glibc detected *** double free or corruption (out):
0x00ea1e50 ***
/home/rlmill/sage-2.10.3.rc2-sage.math-only-x86_64-Linux/local/bin/
sage-sage: line 214: 15440 Aborted sage-ipython "$@" -
c "$SAGE_STARTUP_COMMAND;"
"""

This is the problem causing "sage -t  devel/sage/sage/graphs/graph.py"
to fail. In verbose mode, I get:

"""
1210 passed and 0 failed.
Test passed.
*** glibc detected *** double free or corruption (out):
0x00ecf3d0 ***

 [44.0 s]
exit code: 256

--
The following tests failed:


sage -t -verbose devel/sage-main/sage/graphs/graph.py
Total time for all tests: 44.0 seconds
"""

I have to make a remark (that probably won't help you...): When you
recompile Python --without-pymalloc to valgrind something, this looks
like the message you start getting upon exit...

- RLM

--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Re: interact versus manipulate

[Robert Miller]

+1 interact

On Mar 8, 1:57 pm, mhampton <[EMAIL PROTECTED]> wrote:
> The advantage of vivify is all the derivative terms that flow from it
> - you could cache images with revivify, explore 4D graphs with
> vivisection...hmm...
>
> +1 to interact.
>
> -M. Hampton
>
> On Mar 8, 3:11 pm, Chris Swierczewski <[EMAIL PROTECTED]> wrote:
>
> > +1 vivify (actually, make it +1 interact)
>
> > --
> > Chris Swierczewski
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Re: Glib algorithms #2436 vote

[Robert Miller]

On Mar 25, 5:12 pm, Gary Furnish <[EMAIL PROTECTED]> wrote:
> Trac #2436 adds the following algorithms from glib to libcsage:
> Multiplatform threads
> Thread pools
> Asynchronous Queues
> Memory Slices
> Doubly and Singly linked lists
> Queues
> Sequences
> Hash Tables
> Arrays
> Balanced Binary Trees
> N-ary Trees
> Quarks

+1, I've been waiting for this!
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Re: Sage Journal

[Robert Miller]

On Mar 26, 10:33 am, "William Stein" <[EMAIL PROTECTED]> wrote:
> >  On Wed, 26 Mar 2008 09:32:36 -0700 (PDT)
> >  Harald Schilly <[EMAIL PROTECTED]> wrote:
> >  > I had the idea of publishing an online Journal with articles about
> >  > Sage - a mixture between blogs and a real journal. This could be an
> >  > excellent vehicle to promote Sage and the ideas behind to a bigger
> >  > audience.
> Yes, the name should either change as you suggest, or
> this should somehow merge with JSage, and JSage itself
> would become less academic.  (Note that JSage hasn't really
> started yet, in any real sense.)Maybe something like Harald
> is proposing is a better direction to go in that the current
> JSage direction (which is to be purely very academic and
> research-oriented).
>
> William

Perhaps this would also be a good way of getting the original JSage
intentions rolling. Quite a few people have recently been doing the
kind of work that would make ideal articles for that. If JSage were a
real thing you might start seeing submissions in the research-oriented
sector, anyway. I also like the idea of the journal as a recruiting
possibility. Having articles about Sage internals is probably the
right way to attract the kind of developers we are looking for. As for
politics/philosophy/community/..., this might be best left in "letters
to the editor," for the journal's sake.
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Vertex colors

[Robert Miller]

I thought it appropriate to put this one to vote. As someone has
pointed out( http://trac.sagemath.org/sage_trac/ticket/2684 ), red is
not an ideal color for vertices, since it is too dark. I propose we
change them to white.

Thoughts?
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Re: Vertex colors

[Robert Miller]

http://sage.math.washington.edu/home/rlmill/vert_red.png

http://sage.math.washington.edu/home/rlmill/vert_white.png

On Mar 28, 6:36 pm, "William Stein" <[EMAIL PROTECTED]> wrote:
> On Fri, Mar 28, 2008 at 6:17 PM, Robert Miller <[EMAIL PROTECTED]> wrote:
>
> >  I thought it appropriate to put this one to vote. As someone has
> >  pointed out(http://trac.sagemath.org/sage_trac/ticket/2684), red is
> >  not an ideal color for vertices, since it is too dark. I propose we
> >  change them to white.
>
> >  Thoughts?
>
> Post some screen shots.   Press shift-applekey-4 and select a region.
>
> Wouldn't white be invisible since the background is white?
>
> William
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Re: Vertex colors

[Robert Miller]

Also try:

http://sage.math.washington.edu/home/rlmill/vert_ff.png

http://sage.math.washington.edu/home/rlmill/vert_99.png

On Mar 29, 10:31 am, Robert Miller <[EMAIL PROTECTED]> wrote:
> http://sage.math.washington.edu/home/rlmill/vert_red.png
>
> http://sage.math.washington.edu/home/rlmill/vert_white.png
>
> On Mar 28, 6:36 pm, "William Stein" <[EMAIL PROTECTED]> wrote:
>
> > On Fri, Mar 28, 2008 at 6:17 PM, Robert Miller <[EMAIL PROTECTED]> wrote:
>
> > >  I thought it appropriate to put this one to vote. As someone has
> > >  pointed out(http://trac.sagemath.org/sage_trac/ticket/2684), red is
> > >  not an ideal color for vertices, since it is too dark. I propose we
> > >  change them to white.
>
> > >  Thoughts?
>
> > Post some screen shots.   Press shift-applekey-4 and select a region.
>
> > Wouldn't white be invisible since the background is white?
>
> > William
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Re: Vertex colors

[Robert Miller]

For completeness:

http://sage.math.washington.edu/home/rlmill/vert_99ff99.png

http://sage.math.washington.edu/home/rlmill/vert_99.png

--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Re: Sage 3.0.alpha3 released

[Robert Miller]

On OSX 10.5/Firefox 2, I cannot delete cells in a notebook worksheet
as of sage-3.0.alpha2.

On Apr 9, 9:48 pm, "Justin C. Walker" <[EMAIL PROTECTED]> wrote:
> On Apr 9, 2008, at 12:56 , mabshoff wrote:
>
> > On Apr 9, 8:40 pm, mabshoff <[EMAIL PROTECTED]
> > dortmund.de> wrote:
> > Can somebody on OSX 10.4 try the spkg at
> >http://sage.math.washington.edu/home/mabshoff/SPKG/polybori-0.3.1.p0
> > You need to first install the updated linbox.spkg at
> >http://sage.math.washington.edu/home/mabshoff/release-cycles-3.0/alph...
> > to get past the LinBox build problem.
>
> > Josh Kantor will check if it builds in a couple hours, but I wouldn't
> > be hurt about some feedback sooner.
>
> Mac OS X, 10.4.11 (Core 2 Duo, "-j2"):
>
>  real   123m10.195s
>  user   88m28.361s
>  sys26m32.847s
>  ...
>  SAGE build/upgrade complete!
>
>  All tests passed!
>  Total time for all tests: 4608.7 seconds
>
> Cheers,
>
> Justin
>
> --
> Justin C. Walker, Curmudgeon-At-Large, Director
> Institute for the Enhancement of the Director's Income
> 
> The path of least resistance:
> it's not just for electricity any more.
> 
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Re: Sage 3.0.alpha3 released

[Robert Miller]

Tom,

Confirmed working in 3.0.alpha3.

On Apr 9, 10:39 pm, [EMAIL PROTECTED] wrote:
> Try alpha3, and ignore my last email.  William and I have been re-working 
> js.py quite a bit.  As of alpha2, I think you needed to use ctrl-backspace to 
> delete a cell.  That didn't last long, and backspace is back in alpha3.  
> Please tell me if you find otherwise.
>
> On Wed, 9 Apr 2008, Robert Miller wrote:
>
> > On OSX 10.5/Firefox 2, I cannot delete cells in a notebook worksheet
> > as of sage-3.0.alpha2.
>
> > On Apr 9, 9:48 pm, "Justin C. Walker" <[EMAIL PROTECTED]> wrote:
> >> On Apr 9, 2008, at 12:56 , mabshoff wrote:
>
> >>> On Apr 9, 8:40 pm, mabshoff <[EMAIL PROTECTED]
> >>> dortmund.de> wrote:
> >>> Can somebody on OSX 10.4 try the spkg at
> >>>http://sage.math.washington.edu/home/mabshoff/SPKG/polybori-0.3.1.p0
> >>> You need to first install the updated linbox.spkg at
> >>>http://sage.math.washington.edu/home/mabshoff/release-cycles-3.0/alph...
> >>> to get past the LinBox build problem.
>
> >>> Josh Kantor will check if it builds in a couple hours, but I wouldn't
> >>> be hurt about some feedback sooner.
>
> >> Mac OS X, 10.4.11 (Core 2 Duo, "-j2"):
>
> >>  real   123m10.195s
> >>  user   88m28.361s
> >>  sys26m32.847s
> >>  ...
> >>  SAGE build/upgrade complete!
>
> >>  All tests passed!
> >>  Total time for all tests: 4608.7 seconds
>
> >> Cheers,
>
> >> Justin
>
> >> --
> >> Justin C. Walker, Curmudgeon-At-Large, Director
> >> Institute for the Enhancement of the Director's Income
> >> 
> >> The path of least resistance:
> >> it's not just for electricity any more.
> >> 
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Re: Bad example with NICE graph isomorphism

[Robert Miller]

Just to verify, the ticket

> #2765: Robert Miller: bug in graph_isom, Hoffman-Singleton
>constructor

was a fix to a bug which Chris Godsil reported to me a week ago (which
I was able to fix in one day!). In particular, two permutations of the
Hoffman-Singleton graph were giving different canonical labels.
Stephen, I meant to warn you about this bug since I know you are
working closely with this graph. Although I haven't traced your
example down since it now works, I would bet it was a manifestation of
the same bug. The exact location of the bug is recorded on the
ticket-- essentially my invariant wasn't quite invariant. As a follow
up, do you have enough theoretical knowledge of these graphs? In
particular, do you know what the size of the automorphism group should
be, and is NICE (as of the latest alpha release of Sage 3.0) reporting
it correctly?

It is amusing to me that both you and Chris used the word "bad" in the
example files you sent. Would "naughty" not be more appropriate?

Cheers,
Robert

On Apr 14, 11:19 am, mabshoff <[EMAIL PROTECTED]
dortmund.de> wrote:
> On Apr 14, 8:08 pm, "David Joyner" <[EMAIL PROTECTED]> wrote:
>
>
>
> > Perhaps this has been fixed already?
>
> > sage: version()
> > 'SAGE Version 3.0.alpha2, Release Date: 2008-04-06'
> > sage: import sage.graphs
> > sage: import sage.graphs.graph_isom
> > sage:
> > sage: G=Graph("[EMAIL PROTECTED]@[EMAIL PROTECTED]@[EMAIL PROTECTED]@[EMAIL 
> > PROTECTED]@[EMAIL PROTECTED]@KN~_^}?~{")
> > <, 17, 18, 0, 5, 4, 2, 6, 1, 3, 9, 7, 8, 20, 25, 24, 22, 26, 21, 23,
> > 29, 27, 28, 31, 30, 32]
> > sage: H=G.relabel(perm,inplace=False)
> > sage:
> > sage: _,Gcan=sage.graphs.graph_isom.search_tree(G,[range(G.order())])
> > sage: _,Hcan=sage.graphs.graph_isom.search_tree(H,[range(H.order())])
> > sage: if Gcan==Hcan:
> > : print "NICE says the graphs are isomorphic"
> > : else:
> > : print "NICE says the graphs are NOT isomorphic"
> > :
> > NICE says the graphs are isomorphic
>
> Hi Stephan,
>
> Thanks for the bug report.
>
> > Since bugs are usually reported to sage-support (not sage-devel), I am
> > cross-posting.
>
> Nah, if is is something focused like this posting here is alright in
> my book. Especially since not every dev reads sage-support
>
> > On Mon, Apr 14, 2008 at 2:03 PM, Stephen Hartke <[EMAIL PROTECTED]> wrote:
> > > Attached is an example where NICE does not correctly determine the
> > > isomorphism between two graphs.  I tested this with Sage 2.11.  I have not
> > > had an opportunity to examine the NICE code, so I'm not sure where the
> > > problem is.
>
> > > I do not currently have a Trac account, so I am sending the example here.
>
> > > Best wishes,
> > > Stephen
>
> I get:
>
> sage: version()
> 'SAGE Version 3.0.alpha4, Release Date: 2008-04-12'
> sage: import sage.graphs
> sage: import sage.graphs.graph_isom
> sage: G=Graph("[EMAIL PROTECTED]@[EMAIL PROTECTED]@[EMAIL PROTECTED]@[EMAIL 
> PROTECTED]@?
> [EMAIL PROTECTED]@KN~_^}?~{")
> sage: perm=[10, 15, 14, 12, 16, 11, 13, 19, 17, 18, 0, 5, 4, 2, 6, 1,
> 3, 9, 7, 8, 20, 25, 24, 22, 26, 21, 23, 29, 27, 28, 31, 30, 32]
> sage: H=G.relabel(perm,inplace=False)
> sage: _,Gcan=sage.graphs.graph_isom.search_tree(G,[range(G.order())])
> sage: _,Hcan=sage.graphs.graph_isom.search_tree(H,[range(H.order())])
> sage:
> sage: Gcan==Hcan
> True
>
> 3.0.alpha1 contained the following fix:
>
>
> which sounds like it fixed your problem.
>
> Cheers,
>
> Michael
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Re: Initial support for posets

[Robert Miller]

We might want to think about the naming conventions for Lattice. As
with all words in mathematics, this one has multiple meanings. A
lattice can be a poset with a meet and a join, or it can be a free
abelian group with an inner product. Normally I wouldn't bring such a
thing up, but I'm working with a group thinking about implementing the
latter, and you have already (it seems) implemented the former.

On Apr 23, 12:48 pm, mhampton <[EMAIL PROTECTED]> wrote:
> I'm not really qualified to comment in detail, but I thought I would
> mention that I am interested in computing face lattices of polytopes
> as part of my polytope module.  Perhaps you could comment on whether
> there is (or could be) anything in your code that might help me out
> with that.
>
> I think its exciting that we are getting more sage-native
> functionality like this.
>
> Cheers,
> M. Hampton
>
> On Apr 23, 7:53 pm, "Franco Saliola" <[EMAIL PROTECTED]> wrote:
>
> > Dear all,
>
> > I've posted on trac the current version of my posets code.
> > There is still much to be done, some algorithms need
> > to be improved and others need to be implemented. (There
> > are no NotImplementedErrors.)
>
> >  http://trac.sagemath.org/sage_trac/ticket/2519
>
> > But before I continue working, I'd like some feedback. I've
> > made some decisions, and I don't know if they are the
> > best decisions. So please offer suggestions.
>
> > I've defined a HasseDiagram class that inherits from
> > DiGraph. A Hasse diagram are transitively-reduced, directed,
> > acyclic graph without loops or multiple edges. NOTE: We
> > assume that range(n) is a linear extension of the Hasse
> > diagram. This decision was taken in the hopes that it
> > increases the efficiency of algorithms.
>
> > There is a FinitePoset class that stores the list of
> > elements of the poset (_elements), the HasseDiagram
> > (_hasse_diagram, or hasse_diagram()), and maps
> > _element_to_vertex and _vertex_to_element. So FinitePoset is
> > just a vertex labelling of the HasseDiagram.
>
> > There is a constructor called Poset that takes various forms
> > of data describing a finite poset and returns a FinitePoset
> > object.
>
> > There are also Lattice, MeetSemilattice, JoinSemilattice...,
> > and PosetElement, LatticeElement,  So one create poset
> > elements and compare them with <, >, etc. And lattice
> > elements can by multiplied and added (for meet and join).
>
> > There are a few toy posets included (eventually there
> > should be a poset database): BooleanLattice, Chain,
> > Antichain, Pentagon, Diamond, PosetOfIntegerCompositions,
> > RandomPoset, SymmetricGroupBruhatOrder,
> > SymmetricGroupWeakOrder.
>
> > So what do you think?
>
> > Franco
>
> > --
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] A Sage Enhancement Proposal: Lattice Modules

[Robert Miller]

SEP

Implement Lattices over ZZ, with pairings into QQ or ZZ

0. (Maybe) Implement a FreeModule_ZZ_quotient class. This would also
allow for constructing abelian groups in the sort of canonical way
(something people have been asking for...)

1. Implement a LatticeModule class, which will inherit from
FreeModule_generic_pid: instances of LatticeModule will inherit an
underlying free ZZ module and make use of the optional
inner_product_matrix property.

This shouldn't just be a free ZZ module with inner product matrix,
since we want specific functions for computing the dual lattice, etc.
which are more appropriate in a Lattice class.
  a. Attributes will include
- is_euclidean (whether the inner product matrix is symmetric,
rather than skew-symmetric)
- is_integral (whether the image of the pairing is in ZZ or QQ)
- discriminant (the determinant of the matrix [], where
{a_i} is a basis for the module).  A lattice is nondegenerate if its
discriminant is nonvanishing.
  b.  Euclidean lattices also have the attributes:
- signature
- even/odd (whether  \in 2 ZZ for all a)
  c. Use L. for the pairing induced on module elements by the
inner product matrix.

2. Implement a SubLatticeModule class, which will inherit from
FreeModule_submodule_with_basis_pid and from Lattice, but override
L. for the inner product.
   a.  Function is_primitive (a sublattice M of a lattice L is
primitive if L/M is a free ZZ-module)
   b.  Functions to get parent lattice and sublattice as LatticeModule
objects.

3. Implement a LatticeQuotient class (for now, just full sublattices,
i.e., finite quotients).
  -- Inherit from FreeModule_ZZ_quotient?
  -- Inherit from AbelianGroup?
  -- Inherit from nothing?
( The question here is what the underlying structure for a
LatticeQuotient should actually be. The important thing is how will
someone want to access elements of a LatticeQuotient? )
   a.  Attributes will include a quadratic_form_matrix with entries
defined over QQ/ZZ or QQ/2ZZ

4. Create a dual_lattice function for integral euclidean lattices,
with optional "embedding" argument

5. Implement a dual_quotient function for integral euclidean lattices
which returns a LatticeQuotient.

6. Implement isomorphism tests for indefinite integral euclidean
lattices.

-- Robert Miller, Andrey Novoseltsev, Ursula Whitcher

--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Re: A Sage Enhancement Proposal: Lattice Modules

[Robert Miller]

I believe all that David was saying was that our LatticeQuotients
should probably inherit from a new FreeModule_ZZ_quotient class
instead of from AbelianGroups, since the latter are not fully
developed sage objects yet...

On Apr 28, 11:29 am, "John Cremona" <[EMAIL PROTECTED]> wrote:
> David, I don't think you understood my suggestion.   We are talking
> about groups A which are finitely-generated and torsion-free, so
> abstractly isomorphic to Z^n, together with a suitable blinear
> function on AxA taking values in Z or Q, and I wish to include R
> -valued forms.
>
> John
>
> 2008/4/28 David Joyner <[EMAIL PROTECTED]>:
>
>
>
> >  On Mon, Apr 28, 2008 at 2:02 PM, Robert Miller <[EMAIL PROTECTED]> wrote:
>
> >  >  SEP
>
> >  >  Implement Lattices over ZZ, with pairings into QQ or ZZ
>
> >  >  0. (Maybe) Implement a FreeModule_ZZ_quotient class. This would also
> >  >  allow for constructing abelian groups in the sort of canonical way
> >  >  (something people have been asking for...)
>
> >  >  1. Implement a LatticeModule class, which will inherit from
> >  >  FreeModule_generic_pid: instances of LatticeModule will inherit an
> >  >  underlying free ZZ module and make use of the optional
> >  >  inner_product_matrix property.
>
> >  >  This shouldn't just be a free ZZ module with inner product matrix,
> >  >  since we want specific functions for computing the dual lattice, etc.
> >  >  which are more appropriate in a Lattice class.
> >  >   a. Attributes will include
> >  > - is_euclidean (whether the inner product matrix is symmetric,
> >  >  rather than skew-symmetric)
> >  > - is_integral (whether the image of the pairing is in ZZ or QQ)
> >  > - discriminant (the determinant of the matrix [], where
> >  >  {a_i} is a basis for the module).  A lattice is nondegenerate if its
> >  >  discriminant is nonvanishing.
> >  >   b.  Euclidean lattices also have the attributes:
> >  > - signature
> >  > - even/odd (whether  \in 2 ZZ for all a)
> >  >   c. Use L. for the pairing induced on module elements by the
> >  >  inner product matrix.
>
> >  >  2. Implement a SubLatticeModule class, which will inherit from
> >  >  FreeModule_submodule_with_basis_pid and from Lattice, but override
> >  >  L. for the inner product.
> >  >a.  Function is_primitive (a sublattice M of a lattice L is
> >  >  primitive if L/M is a free ZZ-module)
> >  >b.  Functions to get parent lattice and sublattice as LatticeModule
> >  >  objects.
>
> >  >  3. Implement a LatticeQuotient class (for now, just full sublattices,
> >  >  i.e., finite quotients).
> >  >   -- Inherit from FreeModule_ZZ_quotient?
> >  >   -- Inherit from AbelianGroup?
>
> >  -1 is my vote on this. Infinite AbelianGroup instances are not
> >  completely implemented.
>
> >  >   -- Inherit from nothing?
> >  >  ( The question here is what the underlying structure for a
> >  >  LatticeQuotient should actually be. The important thing is how will
> >  >  someone want to access elements of a LatticeQuotient? )
> >  >a.  Attributes will include a quadratic_form_matrix with entries
> >  >  defined over QQ/ZZ or QQ/2ZZ
>
> >  >  4. Create a dual_lattice function for integral euclidean lattices,
> >  >  with optional "embedding" argument
>
> >  >  5. Implement a dual_quotient function for integral euclidean lattices
> >  >  which returns a LatticeQuotient.
>
> >  >  6. Implement isomorphism tests for indefinite integral euclidean
> >  >  lattices.
>
> >  >  -- Robert Miller, Andrey Novoseltsev, Ursula Whitcher
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Re: SSE2 not so useless after all

[Robert Miller]

> I can't tell exactly what GAP does. It is beautifully documented, but
> it talks about "grease units", which is terminology I don't
> understand. It does look like M4RM though.

Grease is a concept for speeding up certain things using caching. For
example, suppose I have the permutation group S_{32} acting on ints. I
can represent a particular permutation as a permutation matrix, which
means that applying that permutation is just vector-matrix
multiplication. However, instead of computing the full matrix
multiplication, we can cut the matrix into pieces (probably of length
"grease units" or something). Essentially, we compute every possible
sum of the first four rows, then the next four rows, etc. Then, to see
how to multiply the vector by the matrix, we cut the vector into
chunks of four, and simply look up the corresponding entry in the
"grease table", finally adding them together in the end.

-- RLM
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Trac #1284

[Robert Miller]

Hello,

During the last bug day, I found several tickets related to
inconsistencies in abelian groups. I think I've fixed the circular
logic, etc. causing the problems in the patch included in #1284.
However, there is a difference of opinion on notation that I need to
ask about here.

Q: Should the output of
sage: G <= H
for G and H abelian groups be whether G is a subgroup of H?

I know the answer seems simple, but here's why you might want to
answer no (William suggested this to me). If you have a list of
abelian groups L = [G1,...,Gn], and you want to quickly sort it, if
you do sorted(L), you may not get back what you are expecting, since
the subgroup ordering on abelian groups isn't linear.

gfurnish proposes the alternative sorted(L,
cmp=canonical_ab_group_cmp), with G <= H returning whether G is a
subgroup of H. I think I favor this approach.

The other option is G.is_subgroup(H).
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Re: Notebook feature request

[Robert Miller]

> > Python
> > has amnesia, in a sense -- it never knows where code really came
> > from, but there are ways around this.

It is also the case that when you load a file, tracebacks simply say
that the error is in "module"... I wish those tracebacks were more
helpful too...

--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Re: Letting users shoot themselves in the foot?

[Robert Miller]

> > sage: V = QQ**2
> > sage: W = V.subspace([[1,2]])
> > sage: W([2,1], check=False) in W
> > True

If a user must do "check=False" in order to shoot themselves in the
foot, then we're doing pretty well.


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Re: Proposal for Inclusion into Sage: Sphinx, Docutils, Pygments, and Jinja

[Robert Miller]

[X] Yes, include these in Sage

--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Re: Sage public notebook servers

[Robert Miller]

> A security researcher decided to purposely take down sage.math to
> demonstrate that it is possible to fork bomb the machine through the
> public sage notebook servers.   I had always plan to run these comletley
> public servers until something like this happened.  Therefore,
> sagenb.org (and the other public sage notebook servers I host) will be
> completely disable until further notice.

Tell him where to put his next fork bomb for me.


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Source on webpage

[Robert Miller]

I propose that there should be links from the front page of
sagemath.org to:

1. The source download

2. The source browser

Since, after all the emphasis is on open source. It's a pretty trivial
point, but it would be nice to be one click away...
--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Re: updating the _pos dictionary for graphs

[Robert Miller]

Jason,

> Does anyone know if it is assumed that if the _pos dictionary in a graph
> is not None, then it contains each vertex as a key?  It seems like it is
> assumed several places in the code (e.g., in the subgraph() function).
> However, _pos isn't updated properly (e.g., in the delete_vertex
> function, the add_vertex function, etc.).  This is leading to bugs in
> several other functions.
>
> If there isn't a policy, then I think we ought to allow _pos to carry
> partial information about the graph, i.e., not all vertices have to have
> positions specified, if possible.

This was my original assumption, but I and/or others working on the
code have probably made the assumption that each vertex was a key from
time to time -- this should be fixed.

> Also, the _boundary list isn't being updated when vertices are deleted
> or a subgraph is made.  I can patch this easily, though.

+1

Robert L. Miller
http://www.rlmiller.org/

--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---

[sage-devel] Graph Labels

[Robert Miller]

William,

Sorry about the failed tests. I'm not sure why XGraphs take up 50%
more space than Graphs: for an unlabelled graph, the adjacency dicts
are the same:

sage: import networkx
sage: N = graphs.PetersenGraph().networkx_graph()
sage: N

sage: N2 = networkx.Graph(N)
sage: N2

sage: N.adj

{0: {1: None, 4: None, 5: None},
 1: {0: None, 2: None, 6: None},
 2: {1: None, 3: None, 7: None},
 3: {2: None, 4: None, 8: None},
 4: {0: None, 3: None, 9: None},
 5: {0: None, 7: None, 8: None},
 6: {1: None, 8: None, 9: None},
 7: {2: None, 5: None, 9: None},
 8: {3: None, 5: None, 6: None},
 9: {4: None, 6: None, 7: None}}
sage: N2.adj

{0: {1: None, 4: None, 5: None},
 1: {0: None, 2: None, 6: None},
 2: {1: None, 3: None, 7: None},
 3: {2: None, 4: None, 8: None},
 4: {0: None, 3: None, 9: None},
 5: {0: None, 7: None, 8: None},
 6: {1: None, 8: None, 9: None},
 7: {2: None, 5: None, 9: None},
 8: {3: None, 5: None, 6: None},
 9: {4: None, 6: None, 7: None}}

The labels for edges just take the place of the None entries. I'm
actually not sure why NetworkX has two classes at all.

-Robert M

On 1/23/07, William Stein <[EMAIL PROTECTED]> wrote:
> Robert,
>
> Make sure to do hg_sage.pull() before working further on the graph code,
> since I fixed a bunch of problems that were introduced.
>
>(1) Tons of doctests were broken by your changes.
> I fixed them all.  In the future, though, you should
> *always* do "sage -t " in the graphs directory before
> sending me anything, and make sure all tests pass.
>
>(2) I made sure the examples in the tutorial you wrote get
> doctested.
>
>(3) I fixed some bug related to printing...
>
>(4) I programmed around a weird bug in printing where self._nxg.name
> sometimes didn't get set.  (?)
>
> Also, I have a question or worry.   Robert, you seem to have changed
> *all* graphs in SAGE to have to be labeled.  This means that unlabeled
> graphs now take 50% more space to store than they used to.  Are you sure
> it is a good idea that all graphs *have* to be labeled by default,
> especially given that NetworkX is not designed that way.  Just curious.
>
> William
>


-- 
Robert L. Miller
http://www.robertlmiller.com/

--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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] Build error in matrix_integer_dense.pyx

[Robert Miller]

Getting the following error when building the latest version of SAGE:

robert-millers-powerbook-g4-12:/Volumes/DATA/sage-1.7 robert$ sage -br

--
sage: Building and installing modified SAGE library files.

pyrexc --embed-positions -I/Volumes/DATA/sage-1.7/devel/sage-main
sage/matrix/matrix_integer_dense.pyx

Error converting Pyrex file to C:

...
#moduli = [ start_prime ]
residues = [ left._mod_int(start_prime) *
right._mod_int(start_prime) ]
cur_prime = start_prime
while product < height:
cur_prime = next_prime(cur_prime)
product *= cur_prime
^


/Volumes/DATA/sage-1.7/devel/sage-main/sage/matrix/matrix_integer_dense.pyx:614:21:
Expected an identifier or literal
sage: Error running pyrexc.
sage: There was an error installing modified sage library code.


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: Build error in matrix_integer_dense.pyx

[Robert Miller]

This only emphasizes my frustration with mercurial:

robert-millers-powerbook-g4-12:/Volumes/DATA/sage-1.7 robert$ sage
-update
Using SAGE Server http://sage.math.washington.edu/sage//packages
http://sage.math.washington.edu/sage//packages/install --> install
[.]
http://sage.math.washington.edu/sage//packages/standard/list --> list
[.]
http://sage.math.washington.edu/sage//packages/standard/deps --> deps
[.]
http://sage.math.washington.edu/sage//packages/standard/newest_version
--> newest_version
[.]
http://sage.math.washington.edu/sage//packages/standard/README -->
README
[.]
http://sage.math.washington.edu/sage//packages/standard/doc-1.8.2.1.spkg
--> doc-1.8.2.1.spkg
[..]
http://sage.math.washington.edu/sage//packages/standard/examples-1.8.2.1.spkg
--> examples-1.8.2.1.spkg
[..]
http://sage.math.washington.edu/sage//packages/standard/extcode-1.8.2.1.spkg
--> extcode-1.8.2.1.spkg
[..]
http://sage.math.washington.edu/sage//packages/standard/mpfi-1.3.4-rc3.p2.spkg
--> mpfi-1.3.4-rc3.p2.spkg
[...]
http://sage.math.washington.edu/sage//packages/standard/sage-1.8.2.1.spkg
--> sage-1.8.2.1.spkg
[..]
http://sage.math.washington.edu/sage//packages/standard/sage_c_lib-1.8.2.1.spkg
--> sage_c_lib-1.8.2.1.spkg
[]
http://sage.math.washington.edu/sage//packages/standard/sage_scripts-1.8.2.1.spkg
--> sage_scripts-1.8.2.1.spkg
[..]
robert-millers-powerbook-g4-12:/Volumes/DATA/sage-1.7 robert$ sage -br

--
sage: Building and installing modified SAGE library files.

pyrexc --embed-positions -I/Volumes/DATA/sage-1.7/devel/sage-main
sage/matrix/matrix_integer_dense.pyx

Error converting Pyrex file to C:

...
#moduli = [ start_prime ]
residues = [ left._mod_int(start_prime) *
right._mod_int(start_prime) ]
cur_prime = start_prime
while product < height:
cur_prime = next_prime(cur_prime)
product *= cur_prime
^


/Volumes/DATA/sage-1.7/devel/sage-main/sage/matrix/matrix_integer_dense.pyx:614:21:
Expected an identifier or literal
sage: Error running pyrexc.
sage: There was an error installing modified sage library code.


On Jan 24, 8:02 pm, "William Stein" <[EMAIL PROTECTED]> wrote:
> You have an old old version of sagex, which is before Robert Bradshaw
> added support for "+=" (etc.).  You must do
>
> sage -upgrade
>
> not just hg_sage.pull(), which only gets the Python/SageX library code.
>
> In particular, Nick's guess is exactly right:
>
> On Wed, 24 Jan 2007 19:23:58 -0800, Nick Alexander <[EMAIL PROTECTED]> wrote:
> > Just a guess, but I believe that in place update (+=, *=) were just
> > added to sagex.  You might try updating that package.
> > Nick  -- William
>
> On Wed, 24 Jan 2007 17:47:40 -0800, Robert Miller <[EMAIL PROTECTED]> wrote:
>
> > Getting the following error when building the latest version of SAGE:
>
> > robert-millers-powerbook-g4-12:/Volumes/DATA/sage-1.7 robert$ sage -br
>
> > --
> > sage: Building and installing modified SAGE library files.
>
> > pyrexc --embed-positions -I/Volumes/DATA/sage-1.7/devel/sage-main
> > sage/matrix/matrix_integer_dense.pyx
>
> > Error converting Pyrex file to C:
> > 
> > ...
> > #moduli = [ start_prime ]
> > residues = [ left._mod_int(start_prime) *
> > right._mod_int(start_prime) ]
> > cur_prime = start_prime
> > while product < height:
> > cur_prime = next_prime(cur_prime)
> > product *= cur_prime
> > ^
> > 
>
> > /Volumes/DATA/sage-1.7/devel/sage-main/sage/matrix/matrix_integer_dense.pyx:614:21:
> > Expected an identifier or literal
> > sage: Error running pyrexc.
> > sage: There was an error installing modified sage library code.


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: Build error in matrix_integer_dense.pyx

[Robert Miller]

Look carefully at my previous post: all I did was sage -upgrade
followed by sage -br.

On Jan 24, 11:23 pm, Robert Bradshaw <[EMAIL PROTECTED]>
wrote:
> Doesn't look like it got the new sagex package, have you tried sage -
> upgrade?
>
> On Jan 24, 2007, at 11:14 PM, Robert Miller wrote:
>
> > This only emphasizes my frustration with mercurial:
>
> > robert-millers-powerbook-g4-12:/Volumes/DATA/sage-1.7 robert$ sage
> > -update
> > Using SAGE Serverhttp://sage.math.washington.edu/sage//packages
> >http://sage.math.washington.edu/sage//packages/install--> install
> > [.]
> >http://sage.math.washington.edu/sage//packages/standard/list--> list
> > [.]
> >http://sage.math.washington.edu/sage//packages/standard/deps--> deps
> > [.]
> >http://sage.math.washington.edu/sage//packages/standard/newest_version
> > --> newest_version
> > [.]
> >http://sage.math.washington.edu/sage//packages/standard/README-->
> > README
> > [.]
> >http://sage.math.washington.edu/sage//packages/standard/
> > doc-1.8.2.1.spkg
> > --> doc-1.8.2.1.spkg
> > [..]
> >http://sage.math.washington.edu/sage//packages/standard/
> > examples-1.8.2.1.spkg
> > --> examples-1.8.2.1.spkg
> > [..]
> >http://sage.math.washington.edu/sage//packages/standard/
> > extcode-1.8.2.1.spkg
> > --> extcode-1.8.2.1.spkg
> > [..]
> >http://sage.math.washington.edu/sage//packages/standard/mpfi-1.3.4-
> > rc3.p2.spkg
> > --> mpfi-1.3.4-rc3.p2.spkg
> > [...]
> >http://sage.math.washington.edu/sage//packages/standard/
> > sage-1.8.2.1.spkg
> > --> sage-1.8.2.1.spkg
> > [..]
> >http://sage.math.washington.edu/sage//packages/standard/
> > sage_c_lib-1.8.2.1.spkg
> > --> sage_c_lib-1.8.2.1.spkg
> > []
> >http://sage.math.washington.edu/sage//packages/standard/
> > sage_scripts-1.8.2.1.spkg
> > --> sage_scripts-1.8.2.1.spkg
> > [..]
> > robert-millers-powerbook-g4-12:/Volumes/DATA/sage-1.7 robert$ sage -br
>
> > --
> > sage: Building and installing modified SAGE library files.
>
> > pyrexc --embed-positions -I/Volumes/DATA/sage-1.7/devel/sage-main
> > sage/matrix/matrix_integer_dense.pyx
>
> > Error converting Pyrex file to C:
> > 
> > ...
> > #moduli = [ start_prime ]
> > residues = [ left._mod_int(start_prime) *
> > right._mod_int(start_prime) ]
> > cur_prime = start_prime
> > while product < height:
> > cur_prime = next_prime(cur_prime)
> > product *= cur_prime
> > ^
> > 
>
> > /Volumes/DATA/sage-1.7/devel/sage-main/sage/matrix/
> > matrix_integer_dense.pyx:614:21:
> > Expected an identifier or literal
> > sage: Error running pyrexc.
> > sage: There was an error installing modified sage library code.
>
> > On Jan 24, 8:02 pm, "William Stein" <[EMAIL PROTECTED]> wrote:
> >> You have an old old version of sagex, which is before Robert Bradshaw
> >> added support for "+=" (etc.).  You must do
>
> >> sage -upgrade
>
> >> not just hg_sage.pull(), which only gets the Python/SageX library
> >> code.
>
> >> In particular, Nick's guess is exactly right:
>
> >> On Wed, 24 Jan 2007 19:23:58 -0800, Nick Alexander
> >> <[EMAIL PROTECTED]> wrote:
> >>> Just a guess, but I believe that in place update (+=, *=) were just
> >>> added to sagex.  You might try updating that package.
> >>> Nick  -- William
>
> >> On Wed, 24 Jan 2007 17:47:40 -0800, Robert Miller
> >> <[EMAIL PROTECTED]> wrote:
>
> >>> Getting the following error when building the latest version of
> >>> SAGE:
>
> >>> robert-millers-powerbook-g4-12:/Volumes/DATA/sage-1.7 robert$
> >>> sage -br
>
> >>> --
> >>> sage: Building and installing modified SAGE library files.
>
> >>> pyrexc --embed-positions -I/Volumes/DATA/sage-1.7/devel/sage-main
> >>> sage/matrix/ma

[sage-devel] Re: Build error in matrix_integer_dense.pyx

[Robert Miller]

Ok, I got it mixed up, what I did was -update followed by -br. Point
is, after update, my sage fails to build.

On Jan 24, 11:27 pm, Robert Bradshaw <[EMAIL PROTECTED]>
wrote:
> Yeah, upgrade != update (though to be honest I don't know the
> intricacies of the differences).
>
> On Jan 24, 2007, at 11:26 PM, Robert Miller wrote:
>
> > Look carefully at my previous post: all I did was sage -upgrade
> > followed by sage -br.
>
> > On Jan 24, 11:23 pm, Robert Bradshaw <[EMAIL PROTECTED]>
> > wrote:
> >> Doesn't look like it got the new sagex package, have you tried sage -
> >> upgrade?
>
> >> On Jan 24, 2007, at 11:14 PM, Robert Miller wrote:
>
> >>> This only emphasizes my frustration with mercurial:
>
> >>> robert-millers-powerbook-g4-12:/Volumes/DATA/sage-1.7 robert$ sage
> >>> -update
> >>> Using SAGE Serverhttp://sage.math.washington.edu/sage//packages
> >>>http://sage.math.washington.edu/sage//packages/install--> install
> >>> [.]
> >>>http://sage.math.washington.edu/sage//packages/standard/list--> list
> >>> [.]
> >>>http://sage.math.washington.edu/sage//packages/standard/deps--> deps
> >>> [.]
> >>>http://sage.math.washington.edu/sage//packages/standard/
> >>> newest_version
> >>> --> newest_version
> >>> [.]
> >>>http://sage.math.washington.edu/sage//packages/standard/README-->
> >>> README
> >>> [.]
> >>>http://sage.math.washington.edu/sage//packages/standard/
> >>> doc-1.8.2.1.spkg
> >>> --> doc-1.8.2.1.spkg
> >>> [..]
> >>>http://sage.math.washington.edu/sage//packages/standard/
> >>> examples-1.8.2.1.spkg
> >>> --> examples-1.8.2.1.spkg
> >>> [..]
> >>>http://sage.math.washington.edu/sage//packages/standard/
> >>> extcode-1.8.2.1.spkg
> >>> --> extcode-1.8.2.1.spkg
> >>> [..]
> >>>http://sage.math.washington.edu/sage//packages/standard/mpfi-1.3.4-
> >>> rc3.p2.spkg
> >>> --> mpfi-1.3.4-rc3.p2.spkg
> >>> [...]
> >>>http://sage.math.washington.edu/sage//packages/standard/
> >>> sage-1.8.2.1.spkg
> >>> --> sage-1.8.2.1.spkg
> >>> [..]
> >>>http://sage.math.washington.edu/sage//packages/standard/
> >>> sage_c_lib-1.8.2.1.spkg
> >>> --> sage_c_lib-1.8.2.1.spkg
> >>> []
> >>>http://sage.math.washington.edu/sage//packages/standard/
> >>> sage_scripts-1.8.2.1.spkg
> >>> --> sage_scripts-1.8.2.1.spkg
> >>> [..]
> >>> robert-millers-powerbook-g4-12:/Volumes/DATA/sage-1.7 robert$
> >>> sage -br
>
> >>> --
> >>> sage: Building and installing modified SAGE library files.
>
> >>> pyrexc --embed-positions -I/Volumes/DATA/sage-1.7/devel/sage-main
> >>> sage/matrix/matrix_integer_dense.pyx
>
> >>> Error converting Pyrex file to C:
> >>> 
> >>> ...
> >>> #moduli = [ start_prime ]
> >>> residues = [ left._mod_int(start_prime) *
> >>> right._mod_int(start_prime) ]
> >>> cur_prime = start_prime
> >>> while product < height:
> >>> cur_prime = next_prime(cur_prime)
> >>> product *= cur_prime
> >>> ^
> >>> 
>
> >>> /Volumes/DATA/sage-1.7/devel/sage-main/sage/matrix/
> >>> matrix_integer_dense.pyx:614:21:
> >>> Expected an identifier or literal
> >>> sage: Error running pyrexc.
> >>> sage: There was an error installing modified sage library code.
>
> >>> On Jan 24, 8:02 pm, "William Stein" <[EMAIL PROTECTED]> wrote:
> >>>> You have an old old version of sagex, which is before Robert
> >>>> Bradshaw
> >>>> added support for "+=" (etc.).  You must do
>
> >>>> sage -upgrade
>
> >>>> not just hg_sage.pull(), which only gets the Python/SageX 

[sage-devel] Re: Build error in matrix_integer_dense.pyx

[Robert Miller]

Ok, I think I know a little more about what went wrong:

After doing sage -update-build, sage compiles just fine. My assumption
was that

sage -update
sage -br

would do the trick, but it seems as if sage -br doesn't build the
downloaded updates... I'm wondering, what does sage -br actually do?
Where is the dividing line?

On Jan 24, 11:31 pm, "Robert Miller" <[EMAIL PROTECTED]> wrote:
> Ok, I got it mixed up, what I did was -update followed by -br. Point
> is, after update, my sage fails to build.
>
> On Jan 24, 11:27 pm, Robert Bradshaw <[EMAIL PROTECTED]>
> wrote:
>
> > Yeah, upgrade != update (though to be honest I don't know the
> > intricacies of the differences).
>
> > On Jan 24, 2007, at 11:26 PM, Robert Miller wrote:
>
> > > Look carefully at my previous post: all I did was sage -upgrade
> > > followed by sage -br.
>
> > > On Jan 24, 11:23 pm, Robert Bradshaw <[EMAIL PROTECTED]>
> > > wrote:
> > >> Doesn't look like it got the new sagex package, have you tried sage -
> > >> upgrade?
>
> > >> On Jan 24, 2007, at 11:14 PM, Robert Miller wrote:
>
> > >>> This only emphasizes my frustration with mercurial:
>
> > >>> robert-millers-powerbook-g4-12:/Volumes/DATA/sage-1.7 robert$ sage
> > >>> -update
> > >>> Using SAGE Serverhttp://sage.math.washington.edu/sage//packages
> > >>>http://sage.math.washington.edu/sage//packages/install--> install
> > >>> [.]
> > >>>http://sage.math.washington.edu/sage//packages/standard/list--> list
> > >>> [.]
> > >>>http://sage.math.washington.edu/sage//packages/standard/deps--> deps
> > >>> [.]
> > >>>http://sage.math.washington.edu/sage//packages/standard/
> > >>> newest_version
> > >>> --> newest_version
> > >>> [.]
> > >>>http://sage.math.washington.edu/sage//packages/standard/README-->
> > >>> README
> > >>> [.]
> > >>>http://sage.math.washington.edu/sage//packages/standard/
> > >>> doc-1.8.2.1.spkg
> > >>> --> doc-1.8.2.1.spkg
> > >>> [..]
> > >>>http://sage.math.washington.edu/sage//packages/standard/
> > >>> examples-1.8.2.1.spkg
> > >>> --> examples-1.8.2.1.spkg
> > >>> [..]
> > >>>http://sage.math.washington.edu/sage//packages/standard/
> > >>> extcode-1.8.2.1.spkg
> > >>> --> extcode-1.8.2.1.spkg
> > >>> [..]
> > >>>http://sage.math.washington.edu/sage//packages/standard/mpfi-1.3.4-
> > >>> rc3.p2.spkg
> > >>> --> mpfi-1.3.4-rc3.p2.spkg
> > >>> [...]
> > >>>http://sage.math.washington.edu/sage//packages/standard/
> > >>> sage-1.8.2.1.spkg
> > >>> --> sage-1.8.2.1.spkg
> > >>> [..]
> > >>>http://sage.math.washington.edu/sage//packages/standard/
> > >>> sage_c_lib-1.8.2.1.spkg
> > >>> --> sage_c_lib-1.8.2.1.spkg
> > >>> []
> > >>>http://sage.math.washington.edu/sage//packages/standard/
> > >>> sage_scripts-1.8.2.1.spkg
> > >>> --> sage_scripts-1.8.2.1.spkg
> > >>> [..]
> > >>> robert-millers-powerbook-g4-12:/Volumes/DATA/sage-1.7 robert$
> > >>> sage -br
>
> > >>> --
> > >>> sage: Building and installing modified SAGE library files.
>
> > >>> pyrexc --embed-positions -I/Volumes/DATA/sage-1.7/devel/sage-main
> > >>> sage/matrix/matrix_integer_dense.pyx
>
> > >>> Error converting Pyrex file to C:
> > >>> 
> > >>> ...
> > >>> #moduli = [ start_prime ]
> > >>> residues = [ left._mod_int(start_prime) *
> > >>> right._mod_int(start_prime) ]
> > >>> cur_prime = start_prime
> > >>> while product < height:
> > >>> cur_prime = next_prime(cur_prime)
> > >>> product *= cur_prime
> > >>> ^

[sage-devel] Re: Build error in matrix_integer_dense.pyx

[Robert Miller]

A relevant conversation with William, earlier:

William wrote:
>> By the way, what are the differences between the following?
>>
>> sage -update
>
>This is the first step of doing "sage -upgrade".  It downloads new
>packages but doesn't apply them.  It confuses WAY more people (at least 3)
>than it helps (David Kohel), so I'm removing it.
>
>> hg_sage.pull()
>> hg_sage.update()

>This refers only the SAGE library hg repository.

What is the difference between "new packages" and the "SAGE library hg
repository"?

On Jan 24, 11:39 pm, "Robert Miller" <[EMAIL PROTECTED]> wrote:
> Ok, I think I know a little more about what went wrong:
>
> After doing sage -update-build, sage compiles just fine. My assumption
> was that
>
> sage -update
> sage -br
>
> would do the trick, but it seems as if sage -br doesn't build the
> downloaded updates... I'm wondering, what does sage -br actually do?
> Where is the dividing line?
>
> On Jan 24, 11:31 pm, "Robert Miller" <[EMAIL PROTECTED]> wrote:
>
> > Ok, I got it mixed up, what I did was -update followed by -br. Point
> > is, after update, my sage fails to build.
>
> > On Jan 24, 11:27 pm, Robert Bradshaw <[EMAIL PROTECTED]>
> > wrote:
>
> > > Yeah, upgrade != update (though to be honest I don't know the
> > > intricacies of the differences).
>
> > > On Jan 24, 2007, at 11:26 PM, Robert Miller wrote:
>
> > > > Look carefully at my previous post: all I did was sage -upgrade
> > > > followed by sage -br.
>
> > > > On Jan 24, 11:23 pm, Robert Bradshaw <[EMAIL PROTECTED]>
> > > > wrote:
> > > >> Doesn't look like it got the new sagex package, have you tried sage -
> > > >> upgrade?
>
> > > >> On Jan 24, 2007, at 11:14 PM, Robert Miller wrote:
>
> > > >>> This only emphasizes my frustration with mercurial:
>
> > > >>> robert-millers-powerbook-g4-12:/Volumes/DATA/sage-1.7 robert$ sage
> > > >>> -update
> > > >>> Using SAGE Serverhttp://sage.math.washington.edu/sage//packages
> > > >>>http://sage.math.washington.edu/sage//packages/install--> install
> > > >>> [.]
> > > >>>http://sage.math.washington.edu/sage//packages/standard/list--> list
> > > >>> [.]
> > > >>>http://sage.math.washington.edu/sage//packages/standard/deps--> deps
> > > >>> [.]
> > > >>>http://sage.math.washington.edu/sage//packages/standard/
> > > >>> newest_version
> > > >>> --> newest_version
> > > >>> [.]
> > > >>>http://sage.math.washington.edu/sage//packages/standard/README-->
> > > >>> README
> > > >>> [.]
> > > >>>http://sage.math.washington.edu/sage//packages/standard/
> > > >>> doc-1.8.2.1.spkg
> > > >>> --> doc-1.8.2.1.spkg
> > > >>> [..]
> > > >>>http://sage.math.washington.edu/sage//packages/standard/
> > > >>> examples-1.8.2.1.spkg
> > > >>> --> examples-1.8.2.1.spkg
> > > >>> [..]
> > > >>>http://sage.math.washington.edu/sage//packages/standard/
> > > >>> extcode-1.8.2.1.spkg
> > > >>> --> extcode-1.8.2.1.spkg
> > > >>> [..]
> > > >>>http://sage.math.washington.edu/sage//packages/standard/mpfi-1.3.4-
> > > >>> rc3.p2.spkg
> > > >>> --> mpfi-1.3.4-rc3.p2.spkg
> > > >>> [...]
> > > >>>http://sage.math.washington.edu/sage//packages/standard/
> > > >>> sage-1.8.2.1.spkg
> > > >>> --> sage-1.8.2.1.spkg
> > > >>> [..]
> > > >>>http://sage.math.washington.edu/sage//packages/standard/
> > > >>> sage_c_lib-1.8.2.1.spkg
> > > >>> --> sage_c_lib-1.8.2.1.spkg
> > > >>> []
> > > >>>http://sage.math.washington.edu/sage//packages/standard/
> > > >>> sage_scripts-1.8.2.1.spkg
> > > >>> --> sage_scripts-1.8.2.1.spkg
> > > >>> [..]
> > > >>>

[sage-devel] Re: Build error in matrix_integer_dense.pyx

[Robert Miller]

Awesome. Not only is my confusion cleared, but the option that was
causing it no longer exists...

On Jan 24, 11:45 pm, Robert Bradshaw <[EMAIL PROTECTED]>
wrote:
> I think it's a distinction between packages (optional or otherwise)
> and the core sage library (found in devel/sage/...). The latter is
> under the repository and you can have many branches ("clones")
> whereas the former is not.
>
> - Robert
>
> On Jan 24, 2007, at 11:39 PM, Robert Miller wrote:
>
> > Ok, I think I know a little more about what went wrong:
>
> > After doing sage -update-build, sage compiles just fine. My assumption
> > was that
>
> > sage -update
> > sage -br
>
> > would do the trick, but it seems as if sage -br doesn't build the
> > downloaded updates... I'm wondering, what does sage -br actually do?
> > Where is the dividing line?
>
> > On Jan 24, 11:31 pm, "Robert Miller" <[EMAIL PROTECTED]> wrote:
> >> Ok, I got it mixed up, what I did was -update followed by -br. Point
> >> is, after update, my sage fails to build.
>
> >> On Jan 24, 11:27 pm, Robert Bradshaw <[EMAIL PROTECTED]>
> >> wrote:
>
> >>> Yeah, upgrade != update (though to be honest I don't know the
> >>> intricacies of the differences).
>
> >>> On Jan 24, 2007, at 11:26 PM, Robert Miller wrote:
>
> >>>> Look carefully at my previous post: all I did was sage -upgrade
> >>>> followed by sage -br.
>
> >>>> On Jan 24, 11:23 pm, Robert Bradshaw <[EMAIL PROTECTED]>
> >>>> wrote:
> >>>>> Doesn't look like it got the new sagex package, have you tried
> >>>>> sage -
> >>>>> upgrade?
>
> >>>>> On Jan 24, 2007, at 11:14 PM, Robert Miller wrote:
>
> >>>>>> This only emphasizes my frustration with mercurial:
>
> >>>>>> robert-millers-powerbook-g4-12:/Volumes/DATA/sage-1.7 robert$
> >>>>>> sage
> >>>>>> -update
> >>>>>> Using SAGE Serverhttp://sage.math.washington.edu/sage//packages
> >>>>>>http://sage.math.washington.edu/sage//packages/install--> install
> >>>>>> [.]
> >>>>>>http://sage.math.washington.edu/sage//packages/standard/list--
> >>>>>> > list
> >>>>>> [.]
> >>>>>>http://sage.math.washington.edu/sage//packages/standard/deps--
> >>>>>> > deps
> >>>>>> [.]
> >>>>>>http://sage.math.washington.edu/sage//packages/standard/
> >>>>>> newest_version
> >>>>>> --> newest_version
> >>>>>> [.]
> >>>>>>http://sage.math.washington.edu/sage//packages/standard/README-->
> >>>>>> README
> >>>>>> [.]
> >>>>>>http://sage.math.washington.edu/sage//packages/standard/
> >>>>>> doc-1.8.2.1.spkg
> >>>>>> --> doc-1.8.2.1.spkg
> >>>>>> [..]
> >>>>>>http://sage.math.washington.edu/sage//packages/standard/
> >>>>>> examples-1.8.2.1.spkg
> >>>>>> --> examples-1.8.2.1.spkg
> >>>>>> [..]
> >>>>>>http://sage.math.washington.edu/sage//packages/standard/
> >>>>>> extcode-1.8.2.1.spkg
> >>>>>> --> extcode-1.8.2.1.spkg
> >>>>>> [..]
> >>>>>>http://sage.math.washington.edu/sage//packages/standard/
> >>>>>> mpfi-1.3.4-
> >>>>>> rc3.p2.spkg
> >>>>>> --> mpfi-1.3.4-rc3.p2.spkg
> >>>>>> [...]
> >>>>>>http://sage.math.washington.edu/sage//packages/standard/
> >>>>>> sage-1.8.2.1.spkg
> >>>>>> --> sage-1.8.2.1.spkg
> >>>>>> [..]
> >>>>>>http://sage.math.washington.edu/sage//packages/standard/
> >>>>>> sage_c_lib-1.8.2.1.spkg
> >>>>>> --> sage_c_lib-1.8.2.1.spkg
> >>>>>> []
> >>>>>>http://sage.math.washington.edu/sage//packages/standard/
> >>>>>> sage_scripts-1.8.2.1.spkg
> >>&g

[sage-devel] Re: mercurial

[Robert Miller]

I have to go with David on this one. I've been confused many times by
Mercurial, and I would look forward to any SD3 workshops etc.


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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] NetworkX Development

[Robert Miller]

-- Forwarded message --
From: Dan Schult <[EMAIL PROTECTED]>
Date: Feb 20, 2007 7:22 AM
Subject: Re: NetworkX Development
To: Robert Miller <[EMAIL PROTECTED]>
Cc: Aric Hagberg <[EMAIL PROTECTED]>


Hi Robert,
I have also looked at SAGE, though I haven't seen a talk about it.
I am impressed and interested.  Aric and I would appreciate any
help/ideas you have about NetworkX and we'll try to help make
NetworkX part of sage.

I agree with Aric's list of areas where we could use some help.
The big picture issue is perhaps the most difficult:
How do we provide graph classes which encompass all major areas
of graph theory without code explosion?  And how do we make it
clear which algorithms work with which graph classes?

At this point we have split digraph from graph, and kept simple
graphs separate from multiedge/selfloop/edge_data graphs.  That
means we have 4 graph classes.  But we are starting to see a need
for a numerically weighted graph class--and I could envision hanging
spectral data and numpy matrix data on a graph class in a way that
you have done with position data.

You are clearly interested in the graphics side of the package and so
maybe you and Aric could talk about how to get interactive graphs via
matplotlib.

I also notice the graph database project that Emily is working on.
It would be nice if that included spectral information too (for
adjacency spectra and laplacian spectra).

What do you think?
Dan

On Feb 20, 2007, at 8:28 AM, Aric Hagberg wrote:

> Hi Robert,
> [also cc: to Dan]
>
> Thanks for your note.  I do know about SAGE (I saw William talk about
> it at Scipy06) and I like the approach you are taking.  We're happy to
> work with you in whatever way to help make NewtworkX work with SAGE
> and would be grateful to have you or any of the team help with
> development.
>
> Briefly, here is the current status of NetworkX as I see it:
>
> Dan Schult and I are the primary developers.
> Development is a slower than I like since neither of us
> are paid to work on software (but we do as part of our research).
>
> There are plenty of parts that could use improvement, modification,
> or addition.  For example
>
> - The documentation is incomplete.  I've been watching what your
>   project and numpy is doing regarding standard formats.
>
> - Many standard graph theory parts are missing since we primarily
>   added code that solved our research problems without any
>   systematic attempt to cover all of graph theory.
>
> - There are some warts that we'd like to fix.  One example is the
>   inability for us to enforce which functions work with which
>   algorithms.  E.g. XGraph with multiple edges probably breaks
>   many algorithms.  We have had some internal discussions on this
>   and could use a fresh perspective.
>
> - The drawing is a hack that I made because everyone wants to "see"
>   the graph.  So I hacked up something with matplotlib and there is an
>   interface to graphviz. Plenty of room for improvement there
>   including adding interactive control of the drawing in matplotlib.
>   John Hunter showed me how to do it but I haven't had the time
>   to follow up on that.  Also there are many layout algorithms
>   that could be added.
>
> I'll take a look at what you have done in SAGE and let me know
> what you think is the best way to proceed.  The sourceforge site,
> which hosts the mailing lists, is currently offline but hopefully
> will be back real soon.
>
> Aric
>
> On Tue, Feb 20, 2007 at 12:15:51AM -0800, Robert Miller wrote:
>> Hello Aric,
>>
>> My name is Robert Miller, and I am a mathematics graduate student at
>> the University of Washington, Seattle. I am also a developer for the
>> open source mathematics program SAGE
>> (http://sage.math.washington.edu/sage/). We have recently included
>> NetworkX, after determining that it is the best open source graph
>> theory software out there. I have noticed some places where the code
>> could be improved, and I would very much like to be a part of the
>> development team of NetworkX. I have already submitted a couple
>> things
>> to the trac, as rlmill. You can see what we've done so far in SAGE at
>>
>> http://sage.math.washington.edu:9001/graph
>>
>> In particular, you can check out the survey we did of every piece of
>> software we could find, which led us to believe that yours was the
>> best. Also, if you'd like to try out the software itself, you can go
>> to
>>
>> http://sage.math.washington.edu:8100/graphs
>>
>> I've left a few examples up there for you. Most of what I've done so
>> far has been pretty basic. I've be

[sage-devel] Python/C API

[Robert Miller]

David,

I was wondering if you could help get me started here. I've been
reading the Python/C API, and I've been browsing both sides of a lot
of Pyrex: for argument's sake, let's say the Complex double matrices.
First, I'm wondering how they're cdef-ing classes that they're then
calling from Python. Also, what do .so files in site-packages have to
do with specific classes in the repository?

(
sage: sage.matrix.matrix_complex_double_dense.Matrix_complex_double_dense??
Type:   type
Base Class: 
String Form:
Namespace:  Interactive
File:
/Volumes/DATA/sage/local/lib/python2.5/site-packages/sage/matrix/matrix_complex_double_dense.so
)

I have some questions also about reference counting, but let's start here.

-- 
Robert L. Miller
http://www.robertlmiller.com/

--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: Python/C API

[Robert Miller]

FYI this is a completely hypothetical situation here. I am not doing
any developing in the Python/C API, and may never do so. But I'm
experimenting with different levels of architecture, mainly just to
see how things work. Right now the situation is, suppose I have some
function I want to call from Python, but in the end I want to
implement it in basically raw C. One approach I thought of was, okay,
I'll Pyrex a really simple function, compile it and go into the c
file, then write most of what I need from there. My main thought about
reference counting:

Python objects seem to need heavy babysitting in terms of reference
counting, especially if you look at some Pyrex autogen code. But it
seems like the C compiler will keep track of reference counts for C
types. Just supposing (again, completely hypothetical) I decide to
write something in the P/C API completely without Pyrex or SageX, but
I want a Python function or two to get called at the top, and I want C
to do the rest. My impression is that I need to keep track of
reference counts for PyObjs but not C variables. Is this true? I have
never had to worry about reference counting when writing pure C, so
why do PyObjects need that extra help?

On Feb 21, 10:57 am, Robert Bradshaw <[EMAIL PROTECTED]>
wrote:
> I'll jump in and answer you questions.
>
> On Feb 21, 2007, at 10:18 AM, Robert Miller wrote:
>
> > David,
>
> > I was wondering if you could help get me started here. I've been
> > reading the Python/C API, and I've been browsing both sides of a lot
> > of Pyrex: for argument's sake, let's say the Complex double matrices.
> > First, I'm wondering how they're cdef-ing classes that they're then
> > calling from Python.
>
> cdef has two uses. The first is to declare a class as an extension
> type (so it can contain cdef'd property and functions), and the
> second is to declare a property/function as a c type. Cdef'd
> extension types are accessible from python, just not their cdef'd
> properties/functions.
>
> > Also, what do .so files in site-packages have to
> > do with specific classes in the repository?
>
> > (
> > sage:
> > sage.matrix.matrix_complex_double_dense.Matrix_complex_double_dense??
> > Type:   type
> > Base Class: 
> > String Form: > 'sage.matrix.matrix_complex_double_dense.Matrix_complex_double_dense'>
> > Namespace:  Interactive
> > File:
> > /Volumes/DATA/sage/local/lib/python2.5/site-packages/sage/matrix/
> > matrix_complex_double_dense.so
> > )
>
> Each .pyx file has an associated shared object library containing all
> the classes/methods/etc. needed.
>
>
>
> > I have some questions also about reference counting, but let's
> > start here.
>
> You shouldn't have to worry about it too much. Basically, if you
> malloc something manually, you have to worry about freeing it. If you
> call the C/Python API directly (which you probably won't need to do),
> you have to worry if the returned PyObject* is a borrowed or new
> copy. But otherwise pyrex will take care of it all for you.
>
>
>
> > --
> > Robert L. Miller
> >http://www.robertlmiller.com/


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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] Feature request

[Robert Miller]

In the command line, I can do

$ sage -b branch

to build the branch, and

$ sage -br branch

to build and then run the branch, so why shouldn't I be able to do

$ sage -r branch

if I'm on a different repository and I want to just run the branch?


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: Combinatorics in SAGE

[Robert Miller]

Maybe something for partitions too... I'm working on stuff that's all
partitions and permutations, and SAGE doesn't seem to speak fluently
in this area yet.

On Feb 23, 3:02 pm, "Nick Alexander" <[EMAIL PROTECTED]> wrote:
> On Feb 23, 1:01 pm, "William Stein" <[EMAIL PROTECTED]> wrote:
>
>
>
> > On 2/23/07, Mike Hansen <[EMAIL PROTECTED]> wrote:
>
> > > The last couple days I've been working on adding a fair amount of
> > > functionality to the combinat module of SAGE.  Mostly, I'd like to get
> > > it roughly as feature-complete as mupad-combinat or combinatorica.
>
> > Excellent!  Also look at the combinatorics functionality in MAGMA and
> > Maple...
>
> > > I was wondering the best way to go about integrating these changes
> > > into SAGE, specifically naming conventions.  For example, there are
> > > about 75 functions that apply to permuations of the form [1,2,3].
> > > Right now, I just have them in permutation.py in combinat/ and am
> > > importing them all through all.py.  Would it be better / more
> > > consistent to just have all.py import permuation and then call the
> > > routines through something like permutation.descents(p) ?
>
> > Yes, that would help a lot to not pollute the global namespace
> > too much.  Alternatively, all functions on permutations could
> > be methods on PermutationGroupElements, which are defined
> > in sage/groups/perm_gps/.  This would be a nice way of unifying
> > things a bit more, and would make a lot of sense.
>
> This makes a lot of sense for things like permutation.order(),
> permutation.descents(), etc, but not a lot of sense for "number of
> permutations with no three ascents" or similar.  Those should be
> methods in PermutationGroup.
>
> But in general, I second the "methods in class hierarchy" layout.
> It's working well for EllipticCurves.
>
> Thanks, Mike, for implementing much needed functionality!
>
> Nick


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: NetworkX Development

[Robert Miller]

Aric,

I've been working in a few different directions lately:
1- I'm working on a C implementation of the base class structure,
which will vastly speed up many algorithms. I'm not sure whether you
want to keep everything in Python or not, but Python is great at
interfacing C.
2- I'm reading Brendan McKay's paper on graph isomorphisms, and
reproducing it piece by piece in python. Eventually, I hope to provide
an open source alternative to his eminent yet restrictively licensed
program nauty (http://cs.anu.edu.au/~bdm/nauty/   ---   note the
non-military restriction).
3- I have some immediate ideas for speeding up the spring layout algorithm.

If I implement my changes to, say, the spring layout function, how do
I go about submitting those changes to you? Are you using a revision
control system? Would this involve the mailing lists on sourceforge?

Eagerly awaiting response,

Robert L Miller

On 2/20/07, Aric Hagberg <[EMAIL PROTECTED]> wrote:
> Hi Robert,
> [also cc: to Dan]
>
> Thanks for your note.  I do know about SAGE (I saw William talk about
> it at Scipy06) and I like the approach you are taking.  We're happy to
> work with you in whatever way to help make NewtworkX work with SAGE
> and would be grateful to have you or any of the team help with
> development.
>
> Briefly, here is the current status of NetworkX as I see it:
>
> Dan Schult and I are the primary developers.
> Development is a slower than I like since neither of us
> are paid to work on software (but we do as part of our research).
>
> There are plenty of parts that could use improvement, modification,
> or addition.  For example
>
> - The documentation is incomplete.  I've been watching what your
>   project and numpy is doing regarding standard formats.
>
> - Many standard graph theory parts are missing since we primarily
>   added code that solved our research problems without any
>   systematic attempt to cover all of graph theory.
>
> - There are some warts that we'd like to fix.  One example is the
>   inability for us to enforce which functions work with which
>   algorithms.  E.g. XGraph with multiple edges probably breaks
>   many algorithms.  We have had some internal discussions on this
>   and could use a fresh perspective.
>
> - The drawing is a hack that I made because everyone wants to "see"
>   the graph.  So I hacked up something with matplotlib and there is an
>   interface to graphviz. Plenty of room for improvement there
>   including adding interactive control of the drawing in matplotlib.
>   John Hunter showed me how to do it but I haven't had the time
>   to follow up on that.  Also there are many layout algorithms
>   that could be added.
>
> I'll take a look at what you have done in SAGE and let me know
> what you think is the best way to proceed.  The sourceforge site,
> which hosts the mailing lists, is currently offline but hopefully
> will be back real soon.
>
> Aric
>
> On Tue, Feb 20, 2007 at 12:15:51AM -0800, Robert Miller wrote:
> > Hello Aric,
> >
> > My name is Robert Miller, and I am a mathematics graduate student at
> > the University of Washington, Seattle. I am also a developer for the
> > open source mathematics program SAGE
> > (http://sage.math.washington.edu/sage/). We have recently included
> > NetworkX, after determining that it is the best open source graph
> > theory software out there. I have noticed some places where the code
> > could be improved, and I would very much like to be a part of the
> > development team of NetworkX. I have already submitted a couple things
> > to the trac, as rlmill. You can see what we've done so far in SAGE at
> >
> > http://sage.math.washington.edu:9001/graph
> >
> > In particular, you can check out the survey we did of every piece of
> > software we could find, which led us to believe that yours was the
> > best. Also, if you'd like to try out the software itself, you can go
> > to
> >
> > http://sage.math.washington.edu:8100/graphs
> >
> > I've left a few examples up there for you. Most of what I've done so
> > far has been pretty basic. I've been trying to implement everyone's
> > requests, which for the most part have been for "pretty graphics" type
> > features. You should in particular check out
> >
> > http://sage.math.washington.edu:9001/graph_plotting
> >
> > which shows my latest accomplishment, "pretty" 3d pictures of graphs.
> > I look forward to hearing back from you soon.
> >
> > --
> > Robert L. Miller
> > http://www.robertlmiller.com/
>


-- 
Robert L. Miller
http://www.robertlmiller.com/

--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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] magma interface

[Robert Miller]

In magma, I do this:

> F := FiniteField(2);
> F;
Finite field of size 2
> FiniteField(2);
Finite field of size 2
>

I can't reproduce this with the interface in sage:

sage: F = magma('FiniteField(2);')
sage: magma(F.name())
 _sage_[17] := _sage_[12];
sage: magma('%s;'%F.name())
sage: magma.eval('FiniteField(2);')
' _sage_[18] := Type(_sage_[17]);
\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08'
sage: magma.eval('F := FiniteField(2);')
''
sage: magma.eval('F')
' _sage_[18];\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08\x08'

This isn't necessarily on the latest version, but maybe someone can
tell me why I'm being stupid


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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] Rational construction

[Robert Miller]

Say I want a function to return a rational, and I have the integers
for numerator and denominator. Right now, I have to call the Rational
constructor twice:

return Rational(self.size())/Rational(n)

It seems natural to have something like
elif isinstance(x, tuple):
..

around line 165 or so in rational.pyx, to allow something like

return Rational(  (self.size()  ,  n)  )

Does anyone mind if I implement this?


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: open source "nauty"

[Robert Miller]

Special thanks to David Harvey for instigating.

On Mar 23, 10:19 pm, "William Stein" <[EMAIL PROTECTED]> wrote:
> On 3/23/07, David Joyner <[EMAIL PROTECTED]> wrote:
>
>
>
> > Let me be the first on this list to congratulate you! IMHO, this is a
> > big contribution..
>
> > I'm not sure how to browse a patch and even if I did, I'm not sure I'd
> > understand your code. How much is Sagex and how much is Python?
>
> Just apply the patch using hg_sage.apply(patchname), and then
> browse the code.  Probably the patch will be in sage-2.4, anyways, so
> when I release that you'll get it.
>
> > Can you give some timings, comparing your package vs nauty?
>
> It's probably way slower for now, since we haven't made any attempt
> whatever to optimize it for speed, and it's in pure Python.  The point was
> simply to implement exactly the same algorithm, and get it right.  I
> think that's done now.
>
> William


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: open source "nauty"

[Robert Miller]

Talk notes and a more mathematical explanation of
the isomorphism algorithm are available at:

Talk notes:
http://sage.math.washington.edu/home/rlmill/graph_isom/2007-03-29.pdf
Paper:
http://sage.math.washington.edu/home/rlmill/graph_isom/Isomorphism.pdf

On Mar 24, 11:47 am, "Robert Miller" <[EMAIL PROTECTED]> wrote:
> Special thanks to David Harvey for instigating.
>
> On Mar 23, 10:19 pm, "William Stein" <[EMAIL PROTECTED]> wrote:
>
> > On 3/23/07, David Joyner <[EMAIL PROTECTED]> wrote:
>
> > > Let me be the first on this list to congratulate you! IMHO, this is a
> > > big contribution..
>
> > > I'm not sure how to browse a patch and even if I did, I'm not sure I'd
> > > understand your code. How much is Sagex and how much is Python?
>
> > Just apply the patch using hg_sage.apply(patchname), and then
> > browse the code.  Probably the patch will be in sage-2.4, anyways, so
> > when I release that you'll get it.
>
> > > Can you give some timings, comparing your package vs nauty?
>
> > It's probably way slower for now, since we haven't made any attempt
> > whatever to optimize it for speed, and it's in pure Python.  The point was
> > simply to implement exactly the same algorithm, and get it right.  I
> > think that's done now.
>
> > William


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: sage-2.4.1

[Robert Miller]

Upgrading from 2.3 to 2.4.1.2, and getting very strange behavior:

[EMAIL PROTECTED]:~/sage$ ./sage
--
| SAGE Version 2.4.1.2, Release Date: 2007-03-28 |
| Type notebook() for the GUI, and license() for information.|
--

---
  Traceback (most recent call
last)

/home/rlmill/sage/local/bin/ in ()

/home/rlmill/sage/local/lib/python2.5/site-packages/sage/
all_cmdline.py in ()
  1 """nodoctest"""
> 2 from sage.all import *
  3

/home/rlmill/sage/local/lib/python2.5/site-packages/sage/all.py in
()
 43 del _l
 44 except KeyError:
---> 45  raise RuntimeError, "To use the SAGE libraries, set the
environment variable SAGE_ROOT to the SAGE build directory and
LD_LIBRARY_PATH to $SAGE_ROOT/local/lib"
 46
 47

: To use the SAGE libraries, set the
environment variable SAGE_ROOT to the SAGE build directory and
LD_LIBRARY_PATH to $SAGE_ROOT/local/lib
sage: exit
---
Traceback (most recent call
last)

/home/rlmill/sage/local/lib/python2.5/site-packages/sage/misc/
interpreter.py in sage_prefilter(self, block, continuation)
388 for i in range(len(B)):
389 L = B[i]
--> 390 M = do_prefilter_paste(L, continuation or (not
first))
391 first = False
392 # The L[:len(L)-len(L.lstrip())]  business here
preserves

/home/rlmill/sage/local/lib/python2.5/site-packages/sage/misc/
interpreter.py in do_prefilter_paste(line, continuation)
342 raise ImportError, "Attaching of '%s' not
implemented (load .py, .spyx, and .sage files)"%name
343 if len(line) > 0:
--> 344 line = preparser_ipython.preparse_ipython(line, not
continuation)
345 return line
346

/home/rlmill/sage/local/lib/python2.5/site-packages/sage/misc/
preparser_ipython.py in preparse_ipython(line, reset)
 65 # but I don't know how yet...
 66 L = L[1:].strip()
---> 67 import sage.interfaces.all
 68 if L.lower() in sage.interfaces.all.interfaces:
 69 switch_interface(L.lower())

/home/rlmill/sage/local/lib/python2.5/site-packages/sage/interfaces/
all.py in ()
  8 from genus2reduction import genus2reduction, Genus2reduction
  9 from gfan import gfan,  Gfan
---> 10 from gp import gp, gp_console, gp_version, is_GpElement, Gp
 11 #from gnuplot import gnuplot, gnuplot_console
 12 from kash import  kash, kash_console, kash_version,
is_KashElement, Kash

/home/rlmill/sage/local/lib/python2.5/site-packages/sage/interfaces/
gp.py in ()
 91 from sage.misc.misc import verbose
 92 from sage.libs.pari.all import pari
---> 93 import sage.rings.all
 94
 95 class Gp(Expect):

/home/rlmill/sage/local/lib/python2.5/site-packages/sage/rings/all.py
in ()
 40
 41 # Ideals
---> 42 from ideal import Ideal, is_Ideal
 43
 44 # Quotient

/home/rlmill/sage/local/lib/python2.5/site-packages/sage/rings/
ideal.py in ()
 29 from sage.structure.element import MonoidElement
 30 from sage.interfaces.singular import singular as
singular_default, is_SingularElement
---> 31 import sage.rings.infinity
 32 from sage.structure.sequence import Sequence
 33

/home/rlmill/sage/local/lib/python2.5/site-packages/sage/rings/
infinity.py in ()
124 #import sage.rings.real_double
125 #import sage.rings.real_mpfr
--> 126 import sage.rings.integer
127 import sage.rings.rational
128

/home/rlmill/sage/local/bin/integer.pyx in integer()
132
133
--> 134
135
136

/home/rlmill/sage/local/bin/rational.pxd in integer_ring()
  5
  6
> 7
  8
  9

/home/rlmill/sage/local/bin/rational.pyx in rational()
 39
 40
---> 41
 42
 43

/home/rlmill/sage/local/bin/real_double.pxd in real_mpfr()
  6
  7
> 8
  9
 10

/home/rlmill/sage/local/bin/real_double.pyx in real_double()
 36
 37
---> 38
 39
 40

/home/rlmill/sage/local/bin/complex_double.pyx in complex_double()
 77
 78
---> 79
 80
 81

/home/rlmill/sage/local/bin/real_mpfr.pxd in complex_number()
 13
 14
---> 15
 16
 17

: 'module' object has no attribute
'RealNumber'
sage: exit
---
   Traceback (most recent call
last)

/home/rlmill/sage/local/lib/python2.5/site-packages/sage/misc/
interpreter.py in sage_prefilter(self, block, continuation)
388 for i in range(len(B)):
389 L = B[i]
--> 390 M = do_prefilter_paste(L, continuation or (not
first))
391 first = False
392 # The L[:len(L)-len(L.lstrip())]  business here
preserves

/ho

[sage-devel] Re: sage-2.4.1

[Robert Miller]

PS- I also tried renaming sage-main to sage-old and doing sage-upgrade
again,
but I'm not getting a new sage-main that way...

On Mar 30, 11:28 am, "Robert Miller" <[EMAIL PROTECTED]> wrote:
> Upgrading from 2.3 to 2.4.1.2, and getting very strange behavior:
>
> [EMAIL PROTECTED]:~/sage$ ./sage
> --
> | SAGE Version 2.4.1.2, Release Date: 2007-03-28 |
> | Type notebook() for the GUI, and license() for information.|
> --
>
> ---
>   Traceback (most recent call
> last)
>
> /home/rlmill/sage/local/bin/ in ()
>
> /home/rlmill/sage/local/lib/python2.5/site-packages/sage/
> all_cmdline.py in ()
>   1 """nodoctest"""
> > 2 from sage.all import *
>   3
>
> /home/rlmill/sage/local/lib/python2.5/site-packages/sage/all.py in
> ()
>  43 del _l
>  44 except KeyError:
> ---> 45  raise RuntimeError, "To use the SAGE libraries, set the
> environment variable SAGE_ROOT to the SAGE build directory and
> LD_LIBRARY_PATH to $SAGE_ROOT/local/lib"
>  46
>  47
>
> : To use the SAGE libraries, set the
> environment variable SAGE_ROOT to the SAGE build directory and
> LD_LIBRARY_PATH to $SAGE_ROOT/local/lib
> sage: exit
> ---
> Traceback (most recent call
> last)
>
> /home/rlmill/sage/local/lib/python2.5/site-packages/sage/misc/
> interpreter.py in sage_prefilter(self, block, continuation)
> 388 for i in range(len(B)):
> 389 L = B[i]
> --> 390 M = do_prefilter_paste(L, continuation or (not
> first))
> 391 first = False
> 392 # The L[:len(L)-len(L.lstrip())]  business here
> preserves
>
> /home/rlmill/sage/local/lib/python2.5/site-packages/sage/misc/
> interpreter.py in do_prefilter_paste(line, continuation)
> 342 raise ImportError, "Attaching of '%s' not
> implemented (load .py, .spyx, and .sage files)"%name
> 343 if len(line) > 0:
> --> 344 line = preparser_ipython.preparse_ipython(line, not
> continuation)
> 345 return line
> 346
>
> /home/rlmill/sage/local/lib/python2.5/site-packages/sage/misc/
> preparser_ipython.py in preparse_ipython(line, reset)
>  65 # but I don't know how yet...
>  66 L = L[1:].strip()
> ---> 67 import sage.interfaces.all
>  68 if L.lower() in sage.interfaces.all.interfaces:
>  69 switch_interface(L.lower())
>
> /home/rlmill/sage/local/lib/python2.5/site-packages/sage/interfaces/
> all.py in ()
>   8 from genus2reduction import genus2reduction, Genus2reduction
>   9 from gfan import gfan,  Gfan
> ---> 10 from gp import gp, gp_console, gp_version, is_GpElement, Gp
>  11 #from gnuplot import gnuplot, gnuplot_console
>  12 from kash import  kash, kash_console, kash_version,
> is_KashElement, Kash
>
> /home/rlmill/sage/local/lib/python2.5/site-packages/sage/interfaces/
> gp.py in ()
>  91 from sage.misc.misc import verbose
>  92 from sage.libs.pari.all import pari
> ---> 93 import sage.rings.all
>  94
>  95 class Gp(Expect):
>
> /home/rlmill/sage/local/lib/python2.5/site-packages/sage/rings/all.py
> in ()
>  40
>  41 # Ideals
> ---> 42 from ideal import Ideal, is_Ideal
>  43
>  44 # Quotient
>
> /home/rlmill/sage/local/lib/python2.5/site-packages/sage/rings/
> ideal.py in ()
>  29 from sage.structure.element import MonoidElement
>  30 from sage.interfaces.singular import singular as
> singular_default, is_SingularElement
> ---> 31 import sage.rings.infinity
>  32 from sage.structure.sequence import Sequence
>  33
>
> /home/rlmill/sage/local/lib/python2.5/site-packages/sage/rings/
> infinity.py in ()
> 124 #import sage.rings.real_double
> 125 #import sage.rings.real_mpfr
> --> 126 import sage.rings.integer
> 127 import sage.rings.rational
> 128
>
> /home/rlmill/sage/local/bin/integer.pyx in integer()
> 132
> 133
> --> 134
> 135
> 136
>
> /home/rlmill/sage/local/bin/rational.pxd in integer_ring()
>   5
>   6
> > 7
>   8
>   9
>
> /home/rlmill/sage/local/bin/rational.pyx in rational()
>  39
>  40
> ---> 41
>  42
>  43
>
> /home/rlm

[sage-devel] Re: sage-2.4.1

[Robert Miller]

(1) I did ./sage -upgrade.
(2) Yes
(3) The last 4 lines of install.log are
"""
Successfully installed gap_packages-4.4.9
Now cleaning up tmp files.
Making SAGE/Python scripts relocatable...
Making script relocatable
"""
(?)
(4) Nothing
(5) Waiting to see... (to be continued)

On Mar 30, 11:32 am, "William Stein" <[EMAIL PROTECTED]> wrote:
> 1) how did you upgrade?  Did you do "sage -upgrade"?
> 2) Is this on a (=my) Macbook Pro?
> 3) Were there any errors in the install.log during the upgrade, or did
> it complete fine?
> 4) If you do "./sage -upgrade" again what happens?
> 5) If you move devel/sage-main elsewhere and delete the devel/sage symlink,
>   and the file spkg/installed/sage-2.4.1.2, then do "./sage -upgrade",
> what happens?
>
>  -- William
>
> On 3/30/07, Robert Miller <[EMAIL PROTECTED]> wrote:
>
>
>
> > Upgrading from 2.3 to 2.4.1.2, and getting very strange behavior:
>
> > [EMAIL PROTECTED]:~/sage$ ./sage
> > --
> > | SAGE Version 2.4.1.2, Release Date: 2007-03-28 |
> > | Type notebook() for the GUI, and license() for information.|
> > --
>
> > ---
> >   Traceback (most recent call
> > last)
>
> > /home/rlmill/sage/local/bin/ in ()
>
> > /home/rlmill/sage/local/lib/python2.5/site-packages/sage/
> > all_cmdline.py in ()
> >   1 """nodoctest"""
> > > 2 from sage.all import *
> >   3
>
> > /home/rlmill/sage/local/lib/python2.5/site-packages/sage/all.py in
> > ()
> >  43 del _l
> >  44 except KeyError:
> > ---> 45  raise RuntimeError, "To use the SAGE libraries, set the
> > environment variable SAGE_ROOT to the SAGE build directory and
> > LD_LIBRARY_PATH to $SAGE_ROOT/local/lib"
> >  46
> >  47
>
> > : To use the SAGE libraries, set the
> > environment variable SAGE_ROOT to the SAGE build directory and
> > LD_LIBRARY_PATH to $SAGE_ROOT/local/lib
> > sage: exit
> > ---
> > Traceback (most recent call
> > last)
>
> > /home/rlmill/sage/local/lib/python2.5/site-packages/sage/misc/
> > interpreter.py in sage_prefilter(self, block, continuation)
> > 388 for i in range(len(B)):
> > 389 L = B[i]
> > --> 390 M = do_prefilter_paste(L, continuation or (not
> > first))
> > 391 first = False
> > 392 # The L[:len(L)-len(L.lstrip())]  business here
> > preserves
>
> > /home/rlmill/sage/local/lib/python2.5/site-packages/sage/misc/
> > interpreter.py in do_prefilter_paste(line, continuation)
> > 342 raise ImportError, "Attaching of '%s' not
> > implemented (load .py, .spyx, and .sage files)"%name
> > 343 if len(line) > 0:
> > --> 344 line = preparser_ipython.preparse_ipython(line, not
> > continuation)
> > 345 return line
> > 346
>
> > /home/rlmill/sage/local/lib/python2.5/site-packages/sage/misc/
> > preparser_ipython.py in preparse_ipython(line, reset)
> >  65 # but I don't know how yet...
> >  66 L = L[1:].strip()
> > ---> 67 import sage.interfaces.all
> >  68 if L.lower() in sage.interfaces.all.interfaces:
> >  69 switch_interface(L.lower())
>
> > /home/rlmill/sage/local/lib/python2.5/site-packages/sage/interfaces/
> > all.py in ()
> >   8 from genus2reduction import genus2reduction, Genus2reduction
> >   9 from gfan import gfan,  Gfan
> > ---> 10 from gp import gp, gp_console, gp_version, is_GpElement, Gp
> >  11 #from gnuplot import gnuplot, gnuplot_console
> >  12 from kash import  kash, kash_console, kash_version,
> > is_KashElement, Kash
>
> > /home/rlmill/sage/local/lib/python2.5/site-packages/sage/interfaces/
> > gp.py in ()
> >  91 from sage.misc.misc import verbose
> >  92 from sage.libs.pari.all import pari
> > ---> 93 import sage.rings.all
> >  94
> >  95 class Gp(Expect):
>
> > /home/rlmill/sage/local/lib/python2.5/site-packages/sage/rings/all.py
> > in ()
> >  40
> >  41 # Ideals
> > ---> 42 from ideal import Ideal, is_Ideal
> 

[sage-devel] Re: sage-2.4.1

[Robert Miller]

Sorry, amend (2)- I'm on sage.math

On Mar 30, 11:38 am, "Robert Miller" <[EMAIL PROTECTED]> wrote:
> (1) I did ./sage -upgrade.
> (2) Yes
> (3) The last 4 lines of install.log are
> """
> Successfully installed gap_packages-4.4.9
> Now cleaning up tmp files.
> Making SAGE/Python scripts relocatable...
> Making script relocatable
> """
> (?)
> (4) Nothing
> (5) Waiting to see... (to be continued)
>
> On Mar 30, 11:32 am, "William Stein" <[EMAIL PROTECTED]> wrote:
>
> > 1) how did you upgrade?  Did you do "sage -upgrade"?
> > 2) Is this on a (=my) Macbook Pro?
> > 3) Were there any errors in the install.log during the upgrade, or did
> > it complete fine?
> > 4) If you do "./sage -upgrade" again what happens?
> > 5) If you move devel/sage-main elsewhere and delete the devel/sage symlink,
> >   and the file spkg/installed/sage-2.4.1.2, then do "./sage -upgrade",
> > what happens?
>
> >  -- William
>
> > On 3/30/07, Robert Miller <[EMAIL PROTECTED]> wrote:
>
> > > Upgrading from 2.3 to 2.4.1.2, and getting very strange behavior:
>
> > > [EMAIL PROTECTED]:~/sage$ ./sage
> > > --
> > > | SAGE Version 2.4.1.2, Release Date: 2007-03-28 |
> > > | Type notebook() for the GUI, and license() for information.|
> > > --
>
> > > ---
> > >   Traceback (most recent call
> > > last)
>
> > > /home/rlmill/sage/local/bin/ in ()
>
> > > /home/rlmill/sage/local/lib/python2.5/site-packages/sage/
> > > all_cmdline.py in ()
> > >   1 """nodoctest"""
> > > > 2 from sage.all import *
> > >   3
>
> > > /home/rlmill/sage/local/lib/python2.5/site-packages/sage/all.py in
> > > ()
> > >  43 del _l
> > >  44 except KeyError:
> > > ---> 45  raise RuntimeError, "To use the SAGE libraries, set the
> > > environment variable SAGE_ROOT to the SAGE build directory and
> > > LD_LIBRARY_PATH to $SAGE_ROOT/local/lib"
> > >  46
> > >  47
>
> > > : To use the SAGE libraries, set the
> > > environment variable SAGE_ROOT to the SAGE build directory and
> > > LD_LIBRARY_PATH to $SAGE_ROOT/local/lib
> > > sage: exit
> > > ---
> > > Traceback (most recent call
> > > last)
>
> > > /home/rlmill/sage/local/lib/python2.5/site-packages/sage/misc/
> > > interpreter.py in sage_prefilter(self, block, continuation)
> > > 388 for i in range(len(B)):
> > > 389 L = B[i]
> > > --> 390 M = do_prefilter_paste(L, continuation or (not
> > > first))
> > > 391 first = False
> > > 392 # The L[:len(L)-len(L.lstrip())]  business here
> > > preserves
>
> > > /home/rlmill/sage/local/lib/python2.5/site-packages/sage/misc/
> > > interpreter.py in do_prefilter_paste(line, continuation)
> > > 342 raise ImportError, "Attaching of '%s' not
> > > implemented (load .py, .spyx, and .sage files)"%name
> > > 343 if len(line) > 0:
> > > --> 344 line = preparser_ipython.preparse_ipython(line, not
> > > continuation)
> > > 345 return line
> > > 346
>
> > > /home/rlmill/sage/local/lib/python2.5/site-packages/sage/misc/
> > > preparser_ipython.py in preparse_ipython(line, reset)
> > >  65 # but I don't know how yet...
> > >  66 L = L[1:].strip()
> > > ---> 67 import sage.interfaces.all
> > >  68 if L.lower() in sage.interfaces.all.interfaces:
> > >  69 switch_interface(L.lower())
>
> > > /home/rlmill/sage/local/lib/python2.5/site-packages/sage/interfaces/
> > > all.py in ()
> > >   8 from genus2reduction import genus2reduction, Genus2reduction
> > >   9 from gfan import gfan,  Gfan
> > > ---> 10 from gp import gp, gp_console, gp_version, is_GpElement, Gp
> > >  11 #from gnuplot import gnuplot, gnuplot_console
> > >  12 from kash import  kash, kash_console, kash_v

[sage-devel] Re: sage-2.4.1

[Robert Miller]

To finish answering (5),

[EMAIL PROTECTED]:~/sage$ ./sage
--
| SAGE Version 2.4.1.2, Release Date: 2007-03-28 |
| Type notebook() for the GUI, and license() for information.|
--

sage:

yay!

On Mar 30, 11:44 am, "Robert Miller" <[EMAIL PROTECTED]> wrote:
> Sorry, amend (2)- I'm on sage.math
>
> On Mar 30, 11:38 am, "Robert Miller" <[EMAIL PROTECTED]> wrote:
>
> > (1) I did ./sage -upgrade.
> > (2) Yes
> > (3) The last 4 lines of install.log are
> > """
> > Successfully installed gap_packages-4.4.9
> > Now cleaning up tmp files.
> > Making SAGE/Python scripts relocatable...
> > Making script relocatable
> > """
> > (?)
> > (4) Nothing
> > (5) Waiting to see... (to be continued)
>
> > On Mar 30, 11:32 am, "William Stein" <[EMAIL PROTECTED]> wrote:
>
> > > 1) how did you upgrade?  Did you do "sage -upgrade"?
> > > 2) Is this on a (=my) Macbook Pro?
> > > 3) Were there any errors in the install.log during the upgrade, or did
> > > it complete fine?
> > > 4) If you do "./sage -upgrade" again what happens?
> > > 5) If you move devel/sage-main elsewhere and delete the devel/sage 
> > > symlink,
> > >   and the file spkg/installed/sage-2.4.1.2, then do "./sage -upgrade",
> > > what happens?
>
> > >  -- William
>
> > > On 3/30/07, Robert Miller <[EMAIL PROTECTED]> wrote:
>
> > > > Upgrading from 2.3 to 2.4.1.2, and getting very strange behavior:
>
> > > > [EMAIL PROTECTED]:~/sage$ ./sage
> > > > --
> > > > | SAGE Version 2.4.1.2, Release Date: 2007-03-28 |
> > > > | Type notebook() for the GUI, and license() for information.|
> > > > --
>
> > > > ---
> > > >   Traceback (most recent call
> > > > last)
>
> > > > /home/rlmill/sage/local/bin/ in ()
>
> > > > /home/rlmill/sage/local/lib/python2.5/site-packages/sage/
> > > > all_cmdline.py in ()
> > > >   1 """nodoctest"""
> > > > > 2 from sage.all import *
> > > >   3
>
> > > > /home/rlmill/sage/local/lib/python2.5/site-packages/sage/all.py in
> > > > ()
> > > >  43 del _l
> > > >  44 except KeyError:
> > > > ---> 45  raise RuntimeError, "To use the SAGE libraries, set the
> > > > environment variable SAGE_ROOT to the SAGE build directory and
> > > > LD_LIBRARY_PATH to $SAGE_ROOT/local/lib"
> > > >  46
> > > >  47
>
> > > > : To use the SAGE libraries, set the
> > > > environment variable SAGE_ROOT to the SAGE build directory and
> > > > LD_LIBRARY_PATH to $SAGE_ROOT/local/lib
> > > > sage: exit
> > > > ---
> > > > Traceback (most recent call
> > > > last)
>
> > > > /home/rlmill/sage/local/lib/python2.5/site-packages/sage/misc/
> > > > interpreter.py in sage_prefilter(self, block, continuation)
> > > > 388 for i in range(len(B)):
> > > > 389 L = B[i]
> > > > --> 390 M = do_prefilter_paste(L, continuation or (not
> > > > first))
> > > > 391 first = False
> > > > 392 # The L[:len(L)-len(L.lstrip())]  business here
> > > > preserves
>
> > > > /home/rlmill/sage/local/lib/python2.5/site-packages/sage/misc/
> > > > interpreter.py in do_prefilter_paste(line, continuation)
> > > > 342 raise ImportError, "Attaching of '%s' not
> > > > implemented (load .py, .spyx, and .sage files)"%name
> > > > 343 if len(line) > 0:
> > > > --> 344 line = preparser_ipython.preparse_ipython(line, not
> > > > continuation)
> > > > 345 return line
> > > > 346
>
> > > > /home/rlmill/sage/local/lib/python2.5/site-packages/sage/misc/
> > > > prep

[sage-devel] Mod 2 Matrix Row Space Hangs

[Robert Miller]

On both sage.math and my macbook, the following hangs:

--
| SAGE Version 2.4, Release Date: 2007-03-25 |
| Type notebook() for the GUI, and license() for information.|
--

sage: M = Matrix(FiniteField(2), [[1, 1, 1, 1, 0, 0, 0, 0, 0, 0]])
sage: M.row_space()


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: Slightly OT: A SAGE Review

[Robert Miller]

> > 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

>From the installation instructions for rpy:

...(b) Then, configure the path to the R library.  You have several
ways to do
this (substitute RHOME with the path where R is installed, usually
/usr/local/lib/R):

o make a link to RHOME/bin/libR.so in /usr/local/lib or /usr/
lib, then
  run 'ldconfig',

o or, put the following line in your .bashrc (or equivalent):

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:RHOME/bin

o or, edit the file /etc/ld.so.conf and add the following
line:

RHOME/bin

  and then, run 'ldconfig'.

To accomplish this in the spkg-install script, should I do the first
option
in SAGE_ROOT/local/lib?


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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] Mysterious doctest failures

[Robert Miller]

When doctesting after the newest pull, I get:

sage -t -long devel/sage-nice/sage/graphs/graph.py  Exception
exceptions.AttributeError: "'NumberField_cyclotomic' object has no
attribute 'polynomial_ntl'" in
'number_field_element.NumberFieldElement._parent_poly_c_' ignored
Exception exceptions.AttributeError: "'NumberField_cyclotomic' object
has no attribute 'polynomial_ntl'" in
'number_field_element.NumberFieldElement._parent_poly_c_' ignored
MulMod: bad args

This is really confusing, since I have no idea which of the over 500
doctests could be throwing this error. Also, it doesn't make sense to
me, since none of the graph doctests have anything to do with number
fields, at least as far as I can see. I mean, cyclotomics??

1) How can I find out which doctest is generating this error?
2) Anyone have any idea what is causing this?

Thanks,
Robert M


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: Mysterious doctest failures

[Robert Miller]

After some investigating, I have found that the problem was coming
from the character_table command for groups: this was a bug in 2.4,
and is fixed in 2.4.1.2. Sorry for the inconvenience, but it would
still
be nice to be able to know where an exception came from in a doctest.

On Apr 8, 1:04 pm, "Robert Miller" <[EMAIL PROTECTED]> wrote:
> When doctesting after the newest pull, I get:
>
> sage -t -long devel/sage-nice/sage/graphs/graph.py  Exception
> exceptions.AttributeError: "'NumberField_cyclotomic' object has no
> attribute 'polynomial_ntl'" in
> 'number_field_element.NumberFieldElement._parent_poly_c_' ignored
> Exception exceptions.AttributeError: "'NumberField_cyclotomic' object
> has no attribute 'polynomial_ntl'" in
> 'number_field_element.NumberFieldElement._parent_poly_c_' ignored
> MulMod: bad args
>
> This is really confusing, since I have no idea which of the over 500
> doctests could be throwing this error. Also, it doesn't make sense to
> me, since none of the graph doctests have anything to do with number
> fields, at least as far as I can see. I mean, cyclotomics??
>
> 1) How can I find out which doctest is generating this error?
> 2) Anyone have any idea what is causing this?
>
> Thanks,
> Robert M


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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] block sums

[Robert Miller]

sage: A = Matrix( GF(2), [[]] )
sage: B = Matrix( GF(2), [[0]] )
sage: A
[]
sage: B
[0]
sage: A.block_sum(B)

[0]
[0]
sage: A = Matrix( GF(2), [] )
sage: A
[]
sage: A.block_sum(B)
[0]


--~--~-~--~~~---~--~~
To post to this group, send email to [EMAIL PROTECTED]
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: block sums

[Robert Miller]

There should be no difference between the matrices [[]] and [],
especially if they're printing as the same matrix. There is no
mathematical reason for having a matrix consisting of one row and zero
columns. Even if there were, there doesn't seem to be a way to create
a matrix with zero rows and one column. I'm of the opinion that [[]]
should be treated as having zero rows *and* zero columns.

On Apr 13, 11:18 am, David Harvey <[EMAIL PROTECTED]> wrote:
> On Apr 13, 2007, at 2:08 PM, Robert Miller wrote:
>
> > sage: A = Matrix( GF(2), [[]] )
> > sage: B = Matrix( GF(2), [[0]] )
> > sage: A
> > []
> > sage: B
> > [0]
> > sage: A.block_sum(B)
>
> > [0]
> > [0]
> > sage: A = Matrix( GF(2), [] )
> > sage: A
> > []
> > sage: A.block_sum(B)
> > [0]
>
> I don't understand the problem. In all cases, the number of rows of A
> plus the number of rows of B equals the number of rows of
> A.block_sum(B), and similarly for columns. What am I missing?
>
> david


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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] more mod2 row space trouble

[Robert Miller]

sage: M = Matrix(GF(2), [[1,1,0],[0,1,0]])
sage: M.row_space()

Vector space of degree 3 and dimension 2 over Finite Field of size 2
Basis matrix:
[1 0 0]
[0 1 0]
sage: M = Matrix(GF(2), [[1,1,0],[0,0,1]])
sage: M.row_space()

Vector space of degree 3 and dimension 1 over Finite Field of size 2
Basis matrix:
[1 1 0]


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: bugs in graphs?

[Robert Miller]

The attached bundle fixes these bugs and also includes some of the
latest optimizations to NICE. Thanks for the bug report!

On 4/27/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
> Tried to show3d a digraph, got the following:
>

>
>
> Tried to compute the automorphism group for a graph with (apparently) no 
> symmetry:
>

>
>


-- 
Robert L. Miller
http://www.robertlmiller.com/

--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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/
-~--~~~~--~~--~--~---



graph.hg
Description: Binary data

[sage-devel] Re: web page redesign

[Robert Miller]

Perhaps you could have the menus that appear at the top and bottom of
the main page appear on each sub-page, as well as the grey borders. It
would give the overall site more consistency, and give the user a
feeling of still being at the same site. You could add the download,
documentation, etc. links to the menus on the sub-pages too. It's good
for a user to be able to navigate from any page towards where they're
trying to get.

The front page is quite nice. As I continue to navigate downward (as a
n00b user), I keep seeing comforting familiar things, like Gnu,
Python, and Firefox, and I start to think, what is this new,
intriguing math software wait it's *free*!?

I completely disagree that two columns are confusing. The fundamental
flaw of so many annoying websites is an abundance of gimmicks and no
real content. Personally, I hate mouseOver effects.

One reaction I had was to "instead of an obscure language designed for
mathematics." ...designed for, maybe a particular mathematics program,
or... there's something kind of pejorative about the way the word
mathematics fits in there... And there are still critics out there who
might say Python was such (although, to hell with 'em).

And of course I liked the first graphic...


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: sage-2.5.alpha3

[Robert Miller]

William,

First of all, alpha3 builds on the macbook perfectly.

Please include the patch below in sage-2.5. It fixes a subtle bug in
NICE where I was using a global variable locally.

# HG changeset patch
# User Robert L Miller <[EMAIL PROTECTED]>
# Date 1178570314 25200
# Node ID 0e3e8e80f792ca31157a9156ceae5e3fd30168fe
# Parent  cc90d781b4537dd2ab8def52ec1164be2c8a4bd0
Fixed subtle typo in NICE

diff -r cc90d781b453 -r 0e3e8e80f792 sage/graphs/graph_isom.py
--- a/sage/graphs/graph_isom.py Sun May 06 07:31:35 2007 -0700
+++ b/sage/graphs/graph_isom.py Mon May 07 13:38:34 2007 -0700
@@ -1290,7 +1290,7 @@ def search_tree(G, Pi, lab=True, dig=Fal
 elif state == 17:
 if verbosity > 0: print 'state: 17'
 if e[k] == 0:
-l = W[k]
+li = W[k]
 for i in range(1,l+1):
 boo = True
 for j in range(1,k):
@@ -1298,7 +1298,7 @@ def search_tree(G, Pi, lab=True, dig=Fal
 boo = False
 break
 if boo:
-l = [v for v in l if v in Omega[i]]
+li = [v for v in li if v in Omega[i]]
 W[k] = l
 e[k] = 1
 VVV = [v for v in W[k] if v > v[k]]


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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] Python 2.5.1 bug?

[Robert Miller]

I know this isn't a bug in sage, but it is good to be aware of... If
the contents of the file crash.py is:


def crash():
n = 5
k = 2
return [( 2**(n-2*i-2) - 2**(floor(n/2)-i-1) - 1 ) for i in
range(k)]


Then you get bizarre behavior:

sage: load crash.py
sage: crash()


Unhandled SIGSEGV: A segmentation fault occured in SAGE.



So far my ignorance has prevented me from reproducing this in Python
alone (I'm too dependent on the sage environment).


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: sage-2.5.0.2

[Robert Miller]

Hrmm... Sorry to observe and not fix, but:

sage: V = VectorSpace(GF(Integer(2)), n)
---
 Traceback (most recent call
last)

/home/rlmill/sage-2.5/ in ()

/home/rlmill/sage-2.5/local/lib/python2.5/site-packages/sage/modules/
free_module.py in VectorSpace(K, dimension, sparse,
inner_product_matrix)
295 if not K.is_field():
296 raise TypeError, "K must be a field"
--> 297 return FreeModule(K, dimension, sparse,
inner_product_matrix)
298
299 def span(R, gens, check=True, already_echelonized=False):

/home/rlmill/sage-2.5/local/lib/python2.5/site-packages/sage/modules/
free_module.py in FreeModule(base_ring, rank, sparse,
inner_product_matrix)
231 """
232 global _cache
--> 233 rank = int(rank)
234 if not (inner_product_matrix is None):
235 inner_product_matrix =
sage.matrix.matrix_space.MatrixSpace(base_ring, rank)
(inner_product_matrix)

/home/rlmill/sage-2.5/local/lib/python2.5/site-packages/sage/calculus/
calculus.py in __int__(self)
638 return int(repr(self))
639 except (ValueError, TypeError):
--> 640 return int(float(self))
641
642 def __long__(self):

: float() argument must be a string or a
number

On May 11, 10:36 am, "William Stein" <[EMAIL PROTECTED]> wrote:
> Hi,
>
> I've released sage-2.5.0.2, which is a minor bugfix release.  Numerous
> heroic people
> observed (and fixed!) several minor issues with sage-2.5, and many of these
> fixes are in sage-2.5.0.2.  You should definitely consider upgrade using
>
> sage -upgrade
>
> --
> William Stein
> Associate Professor of Mathematics
> University of Washingtonhttp://www.williamstein.org


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: sage-2.5.0.2

[Robert Miller]

Oops. It wasn't declared, and the traceback was confusing... I'll give
it more time before I post again, sorry.

On May 12, 11:11 am, Robert Bradshaw <[EMAIL PROTECTED]>
wrote:
> What is n?
>
> On May 12, 2007, at 11:10 AM, Robert Miller wrote:
>
>
>
> > Hrmm... Sorry to observe and not fix, but:
>
> > sage: V = VectorSpace(GF(Integer(2)), n)
> > --
> > -
> >  Traceback (most recent call
> > last)
>
> > /home/rlmill/sage-2.5/ in ()
>
> > /home/rlmill/sage-2.5/local/lib/python2.5/site-packages/sage/modules/
> > free_module.py in VectorSpace(K, dimension, sparse,
> > inner_product_matrix)
> > 295 if not K.is_field():
> > 296 raise TypeError, "K must be a field"
> > --> 297 return FreeModule(K, dimension, sparse,
> > inner_product_matrix)
> > 298
> > 299 def span(R, gens, check=True, already_echelonized=False):
>
> > /home/rlmill/sage-2.5/local/lib/python2.5/site-packages/sage/modules/
> > free_module.py in FreeModule(base_ring, rank, sparse,
> > inner_product_matrix)
> > 231 """
> > 232 global _cache
> > --> 233 rank = int(rank)
> > 234 if not (inner_product_matrix is None):
> > 235 inner_product_matrix =
> > sage.matrix.matrix_space.MatrixSpace(base_ring, rank)
> > (inner_product_matrix)
>
> > /home/rlmill/sage-2.5/local/lib/python2.5/site-packages/sage/calculus/
> > calculus.py in __int__(self)
> > 638 return int(repr(self))
> > 639 except (ValueError, TypeError):
> > --> 640 return int(float(self))
> > 641
> > 642 def __long__(self):
>
> > : float() argument must be a string or a
> > number
>
> > On May 11, 10:36 am, "William Stein" <[EMAIL PROTECTED]> wrote:
> >> Hi,
>
> >> I've released sage-2.5.0.2, which is a minor bugfix release.
> >> Numerous
> >> heroic people
> >> observed (and fixed!) several minor issues with sage-2.5, and many
> >> of these
> >> fixes are in sage-2.5.0.2.  You should definitely consider upgrade
> >> using
>
> >> sage -upgrade
>
> >> --
> >> William Stein
> >> Associate Professor of Mathematics
> >> University of Washingtonhttp://www.williamstein.org


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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: sage-2.5.0.2

[Robert Miller]

> It's an interesting illustration of the adverse affects of us
> predefining symbolic
> variables at startup.  Thoughts?  Comments?   It's nice to be able to do this:
>
>sage: x^n + y^n == z^n
>(y^n + x^n) == z^n
>
> But the error message you got was confusing.  Note that we could improve
> the error message for the vector space constructor, e.g., specifically check
> for a symbolic variable and make a remark about it if it appears.

I like the idea here, but this confusing behavior isn't specific to
any particular constructor...

>
> Alternatively, maybe we should allow symbolic vector
> spaces with an undefined dimension :-)   (that was a joke).
>

Not a bad idea... You could override every method with a
return NotWellDefinedError...


--~--~-~--~~~---~--~~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
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/
-~--~~~~--~~--~--~---