[sage-devel] Re: Ideals in LaurentPolynomialRing

[Kiran Kedlaya]

I wrote that code into the Sage library and it is supposed to be doing 
exactly what you proposed (clear denominators and do the computation in the 
polynomial ring). It is possible the regression was triggered by an update 
to Singular; it would indeed be helpful to identify a minimal example of 
the problem and then post it to a ticket.

I believe there are also some upstream bugs with minimal associated primes, 
e.g., https://github.com/sagemath/sage/issues/29671.

Kiran

On Monday, May 29, 2023 at 8:53:59 PM UTC-7 Travis Scrimshaw wrote:

> Dear Enrique,
>I am having a bit of trouble understanding exactly what computations 
> are slow and fast from your description. As Nils said, can you give us some 
> explicit code (with some comments about which parts are slow)?
>
> Best,
> Travis
>
> On Tuesday, May 30, 2023 at 3:28:39 AM UTC+9 Nils Bruin wrote:
>
>> Dear Enrique,
>>
>> From what you write I get the impression you may be talking about a 
>> regression in performance relative to earlier versions of sage. If you want 
>> to make an actionable item out of this, you'll probably have to file a 
>> ticket with explicit code on it that can be profiled; preferably with an 
>> indication why you think the performance could be significantly improved. 
>> That doesn't guarantee someone will work on it but it at least gives them a 
>> place to start if they want to, including you yourself! You could file it 
>> as an "enhancement" or even as a "bug" if you can convincingly show it's a 
>> regression. In the latter case you would probably end up identifying a 
>> version in which performance was significantly better. A git diff on some 
>> of the relevant files could then perhaps very quickly show what's happening.
>>
>>
>>
>> On Monday, 29 May 2023 at 09:07:07 UTC-7 enriqu...@gmail.com wrote:
>>
>>> Some time ago I had some computations on ideals in Laurent polynomial 
>>> rings, namely looking for minimal associated primes. Basically, I converted 
>>> any generator into a polynomial, study the ideal in the polynomial ring, 
>>> and forget the prime ideals containing monomials. From some time ago, it is 
>>> much easier since it can be done directly in the ring of Laurent 
>>> polynomials. 
>>> Yesterday these computations on an ideal with 80 generators were really 
>>> slow, but for some reason I checked that if the generators were converted 
>>> to elements in the associated polynomial ring, and then the ideal in the 
>>> Laurent polynomial ring is constructed, then those computations were solved 
>>> really fast. 
>>> I checked the code but I was not able to isolate the reason. Best, 
>>> Enrique.
>>>
>>

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[sage-devel] Re: Building Sage 9.4 (source) on Ubuntu 21.10 failed

[Kiran Kedlaya]

I have the same difficulty with 9.5beta8. I believe the issue with 
cysignals is the same one reported with other distributions, like Fedora:  
https://groups.google.com/g/sage-devel/c/jTlgRgLaZuM.

On Thursday, December 16, 2021 at 12:43:44 PM UTC-8 Marcus A. wrote:

> Hi,
> I tried to build sage 9.4 from source on Ubuntu 21.10.
> The package cysignals failed to build (see also the attached log files):
>
> ...
> Error building Sage.
>
> The following package(s) may have failed to build (not necessarily
> during this run of 'make all-start'):
>
> * package: cysignals-1.10.3
>   last build time: Dez 16 21:07
>   log file:/home/marcus/sage-9.4/logs/pkgs/cysignals-1.10.3.log
>   build directory: 
> /home/marcus/sage-9.4/local/var/tmp/sage/build/cysignals-1.10.3
>
> It is safe to delete any log files and build directories, but they
> contain information that is helpful for debugging build problems.
> WARNING: If you now run 'make' again, the build directory of the
> same version of the package will, by default, be deleted. Set the
> environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.
>
> make[1]: *** [Makefile:39: all-start] Error 1
> make[1]: Leaving directory '/home/marcus/sage-9.4'
> make: *** [Makefile:13: all] Error 2
>
>
>

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[sage-devel] Re: Notebook OpenSSL dependency

[Kiran Kedlaya]

My guess is the Sage build was somehow incomplete, I did a fresh rebuild 
and the issue went away.

If I'm able to reproduce this I'll post again...

On Saturday, July 17, 2021 at 4:13:35 PM UTC-7 Matthias Koeppe wrote:

> This has most likely nothing to do with openssl, despite the "helpful" 
> message issued by the script src/bin/sage-notebook
>
> On Saturday, July 17, 2021 at 3:07:21 PM UTC-7 Kiran Kedlaya wrote:
>
>> I'm building Sage 9.4beta4 on an Ubuntu 21.04 system, and the build 
>> superficially looks fine until I try to start Sage in notebook mode:
>>
>> Traceback (most recent call last):
>>   File 
>> "/home/kedlaya/sage/local/lib/python3.9/site-packages/sage/repl/ipython_kernel/install.py",
>>  
>> line 269, in have_prerequisites
>> from notebook.notebookapp import NotebookApp
>> ModuleNotFoundError: No module named 'notebook'
>>
>> The Jupyter notebook requires ssl, even if you do not use
>> https. Install the openssl development packages in your system and
>> then rebuild Python (sage -f python3).
>>
>> I presume this is an issue because Sage is using my systemwide Python 
>> (3.9.5) rather than building its own. Anyone know what Ubuntu package 
>> provides the appropriate dependency? Better yet, why isn't the configure 
>> script checking for this?
>>
>> Kiran
>>
>>

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[sage-devel] Notebook OpenSSL dependency

[Kiran Kedlaya]

I'm building Sage 9.4beta4 on an Ubuntu 21.04 system, and the build 
superficially looks fine until I try to start Sage in notebook mode:

Traceback (most recent call last):
  File 
"/home/kedlaya/sage/local/lib/python3.9/site-packages/sage/repl/ipython_kernel/install.py",
 
line 269, in have_prerequisites
from notebook.notebookapp import NotebookApp
ModuleNotFoundError: No module named 'notebook'

The Jupyter notebook requires ssl, even if you do not use
https. Install the openssl development packages in your system and
then rebuild Python (sage -f python3).

I presume this is an issue because Sage is using my systemwide Python 
(3.9.5) rather than building its own. Anyone know what Ubuntu package 
provides the appropriate dependency? Better yet, why isn't the configure 
script checking for this?

Kiran

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Re: [sage-devel] Ubuntu 20.10 build of 9.3beta1 failing on fplll

[Kiran Kedlaya]

Removing /usr/local/lib/libqd.a indeed took care of the issue. Thanks!

Kiran

On Thursday, November 12, 2020 at 4:13:39 PM UTC-8 François Bissey wrote:

> libqd.a in your /usr/local/lib folder has been compiled without -fPIC and 
> cannot
> be used to build a shared library.
> As stated by Dima, you shouldn’t need to install your own. If you insist 
> on using
> a libqd from /usr/local/lib, install one compiled with -fPIC.
>
> François
>
> > On 13/11/2020, at 10:40 AM, Kiran Kedlaya  wrote:
> > 
> > I'm trying to build Sage 9.3beta1 on my Ubuntu 20.10 laptop, and the 
> build is failing in fplll-5.3.3. The relevant lines seem to be
> > 
> > [fplll-5.3.3] /usr/bin/ld: /usr/local/lib/libqd.a(dd_const.o): warning: 
> relocation against `_ZN7dd_real4_pi4E' in read-only section `.text.startup'
> > [fplll-5.3.3] /usr/bin/ld: /usr/local/lib/libqd.a(dd_real.o): relocation 
> R_X86_64_PC32 against symbol `_ZSt4cerr@@GLIBCXX_3.4' can not be used when 
> making a shared object; recompile with -fPIC
> > 
> > I can include a more detailed log if needed, but let's see if this is 
> already enough to generate some suggestions...
> > 
> > Kiran
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
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> .
>
>

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[sage-devel] Ubuntu 20.10 build of 9.3beta1 failing on fplll

[Kiran Kedlaya]

I'm trying to build Sage 9.3beta1 on my Ubuntu 20.10 laptop, and the build 
is failing in fplll-5.3.3. The relevant lines seem to be

[fplll-5.3.3] /usr/bin/ld: /usr/local/lib/libqd.a(dd_const.o): warning: 
relocation against `_ZN7dd_real4_pi4E' in read-only section `.text.startup'
[fplll-5.3.3] /usr/bin/ld: /usr/local/lib/libqd.a(dd_real.o): relocation 
R_X86_64_PC32 against symbol `_ZSt4cerr@@GLIBCXX_3.4' can not be used when 
making a shared object; recompile with -fPIC

I can include a more detailed log if needed, but let's see if this is 
already enough to generate some suggestions...

Kiran

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Re: [sage-devel] Build of 9.2beta14 failing on Ubuntu - Python 3.8.5

[Kiran Kedlaya]

Thanks. I was trying to avoid the long compilation time, but I went ahead 
and redid the build after doing a 'make distclean' and that fixed the issue.

On Thursday, October 1, 2020 at 11:34:05 PM UTC-7 tdumont wrote:

> Yes, readline has changed since a recent upgrade of Ubuntu (20-04.
> make distclean
> and rebuild will solve the problem (after a long compilation time).
> t.d.
>
> Le 02/10/2020 à 02:27, Kiran Kedlaya a écrit :
> > I just tried to build 9.2beta14 on my Ubuntu laptop and am getting an
> > error in python3-3.8.5 (the systemwide Py3 is 3.8.2, although maybe I
> > should just wait a few days for Ubuntu to drop 20.10). 
> > 
> > The key line in the log seems to be
> > 
> > [python3-3.8.5] ModuleNotFoundError: No module named 'readline'
> > 
> > even though readline-8.0 itself built successfully.
> > 
> > Kiran
> > 
> > -- 
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> > 
> https://groups.google.com/d/msgid/sage-devel/870f0629-316c-47e8-ba48-1c51974d4d4fn%40googlegroups.com
> > <
> https://groups.google.com/d/msgid/sage-devel/870f0629-316c-47e8-ba48-1c51974d4d4fn%40googlegroups.com?utm_medium=email_source=footer
> >.
>

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[sage-devel] Build of 9.2beta14 failing on Ubuntu - Python 3.8.5

[Kiran Kedlaya]

I just tried to build 9.2beta14 on my Ubuntu laptop and am getting an error 
in python3-3.8.5 (the systemwide Py3 is 3.8.2, although maybe I should just 
wait a few days for Ubuntu to drop 20.10). 

The key line in the log seems to be

[python3-3.8.5] ModuleNotFoundError: No module named 'readline'

even though readline-8.0 itself built successfully.

Kiran

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Re: [sage-devel] Re: Python 3: gap interface issue

[Kiran Kedlaya]

I would definitely appreciate getting deprecation messages in calls to 
gap(...) as soon as possible!

Kiran

On Monday, February 4, 2019 at 7:18:31 AM UTC-8, E. Madison Bray wrote:
>
> On Mon, Feb 4, 2019 at 2:23 AM Simon King  > wrote: 
> > > Is the plan to make 
> > > "gap" and alias of (or a wrapper for) "libgap" in future releases? 
> > 
> > I think this would be a good idea in the long run, however would require 
> > a deprecation period. After all, libgap is not a drop-in replacement of 
> > gap, and I talk from experience (authoring the p_group_cohomology spkg) 
> > when I say that the transition from gap to libgap isn't trivial (but is 
> > a good idea). 
>
> That is my plan but it will be tricky.  Currently users expect 
> gap(...) to run in the pexpect interface (although that's also an 
> implementation detail that might be opaque to many users). 
>
> So I think the best plan is this: 
>
> 1) All code in Sage that uses GAP must first be ported over to the 
> libgap interface.  This is mostly straightforward but may be 
> non-trivial in some areas. 
>
> Now the next part is tricky to handle well.  Here's one idea, though 
> it's debatable: 
>
> 2) Add a deprecation message in calls to gap(...) that it will soon 
> use libgap, and users should switch to that. 
>
> 3) Eventually make gap() an alias for libgap(); at this point the old 
> pexpect interface will be available and deprecated, but not removed. 
>
> 4) Eventually remove old pexpect interface as well, after a deprecation 
> period. 
>
> 5) Maybe actually do away with libgap() and keep just gap().  Why have 
> both, at that point?  I think this last part is maybe the most 
> contentious, but would also be a long way off if at all. 
>

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Re: [sage-devel] Re: problem with 8.7.beta1

[Kiran Kedlaya]

For the record I just encountered this also; but since it appears to be 
fixed and just waiting for the branch to be merged, I omit further details.

On Sunday, January 27, 2019 at 10:28:22 PM UTC-8, Jeroen Demeyer wrote:
>
> On 2019-01-28 06:18, Travis Scrimshaw wrote: 
> > See possibly https://trac.sagemath.org/ticket/27114. 
>
> No, it's https://trac.sagemath.org/ticket/27109 
>

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Re: [sage-devel] divisions

[Kiran Kedlaya]

On Friday, June 8, 2018 at 10:25:10 AM UTC-7, Jeroen Demeyer wrote:
>
> I vote for 
>
> > 2) Laurent polynomials should conform to the rule (R0) and a / b 
> > should always be a rational fraction 
>
> by analogy with other parents, in particular polynomials. 
>

Not to mention integers! While I have seen plenty of first-timers being 
tripped up by:

{{{
sage: parent(4/2)
Rational Field
}}}

I think consensus has settled on this being the preferred behavior, in 
light of the availability of

{{{
sage: parent(4//2)
Integer Ring
}}}

Kiran

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[sage-devel] Re: Inverse of a p-adic matrix fails. Is this a bug?

[Kiran Kedlaya]

Would it make sense to implement a "generic pivot" method, which takes as 
an argument a function that does the pivot selection (that would then be 
handled separately over RR/CC vs p-adics)?

Kiran

On Wednesday, January 31, 2018 at 2:16:42 AM UTC-8, Nils Bruin wrote:
>
> I found this over CC and RR as well: the generic matrix inversion in sage 
> (which is probably what is getting invoked) looks like it's based on 
> straight-up row reduction: No pivoting (which it wouldn't know how to do in 
> the generic case). For CC and RR there's PLU decomposition in mpmath which 
> does use partial pivoting. It would be nice to have "natively" in sage and 
> would be easy to program and would be nice to have for non-square matrices. 
> The code is easily adapted (see 
> https://git.sagemath.org/sage.git/commit?id=f2ccf44acc673458aba3cf92d7692c7a92a505b6
>  
> for a POC).
>
> Partial pivoting for p-adic PLU decomposition would be straightforward to 
> implement as well, and very worthwhile to have. It's well-known that matrix 
> inversion is tricky business numerically, even for well-conditioned 
> matrices, but with pivoting one should get reasonable results in a lot more 
> cases. p-adics might be a little better behaved, but fundamentally the same 
> numerical considerations play a role.
>
> On Tuesday, January 30, 2018 at 3:50:45 PM UTC, Simon Brandhorst wrote:
>>
>> The following may be a bug or me not understanding p-adic floating point 
>> computations:
>>
>>
>> sage: R = Qp(2,type='floating-point',print_mode='terse')
>> sage: M = Matrix(R,4,[0, 0, 1, 1, 2^20, 1, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1])
>> sage: M.det()
>> 1048575
>> sage: M.inverse()
>>
>> ---
>> ZeroDivisionError Traceback (most recent call 
>> last)
>> 
>>
>> ZeroDivisionError: input matrix must be nonsingular
>>
>> sage: M = Matrix(R,4,[0, 0, 1, 1, 2^19, 1, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1])
>> sage: M.inverse()
>> [ 1048575201]
>> [274878955520   5242881  1048575]
>> [  524289   5242871   524287]
>> [274877382656   524289  1048575   524289]
>>
>> Works. 
>>
>

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[sage-devel] Including 64-bit-only code in Sage

[Kiran Kedlaya]

Currently, some code is unable to be included in Sage (except as an 
optional package) because it is not 32-bit safe. One example close to my 
heart is Drew Sutherland's smalljac package for computing L-series of 
hyperelliptic curves; Drew's position is that "life is too short to worry 
about overflowing a 32-bit integer."

I was reminded of this by Apple's announcement that iOS 11 will drop 
support for 32-bit apps. I agree with the position that now is not the time 
for Sage to follow suit; however, it would be helpful if some 64-bit-only 
code could be included in Sage's doctesting framework. Is it feasible now, 
or could it be in the near future, for some code to be configured so that 
it raises a NotImplementedError in a 32-bit environment, and is only 
doctested in a 64-bit environment?

I guess this is related to the ongoing discussions about package 
management. Right now, it is not so great to have something be relegated to 
a manual install just because it is 64-bit-only. But if the package 
management system could identify certain packages as being "64-bit-only but 
otherwise mandatory", then the installer could take care of including them 
whenever it detects a 64-bit platform. (And of course binaries could be 
distributed accordingly.)

Kiran



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Re: [sage-devel] Users can permanently modify GF(5).list()

[Kiran Kedlaya]

Eh? Shouldn't foo.list() return the same as list(foo) (a list) and 
foo.tuple() the same as tuple(foo) (a tuple)?

On Tuesday, May 31, 2016 at 6:08:51 AM UTC-7, Volker Braun wrote:
>
> I've said it before: list() should always return a tuple. Yes I know its 
> called list, but its just an English thing that verb and noun can't be 
> distinguished. Certainly no excuse to cache mutable data structures.
>
> On Tuesday, May 31, 2016 at 2:35:46 PM UTC+2, Jeroen Demeyer wrote:
>>
>> On 2016-05-31 14:06, Johan S. R. Nielsen wrote: 
>> > And that the small 
>> > penalty in returning a *copy* of the list in each call to list() is a 
>> > small price to pay for mitigating user errors? 
>> No. Better use a immutable data structure instead of a list. 
>>
>>

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Re: [sage-devel] Re: Rank of random dense matrices over GF(2)

[Kiran Kedlaya]

On Sunday, April 24, 2016 at 4:13:44 AM UTC-7, Jori Mäntysalo wrote:
>
> On Sun, 24 Apr 2016, Volker Braun wrote: 
>
> >Warning: Matrices generated are not uniformly distributed. For 
> >  unimodular matrices over finite field this function does not even 
> > 
> > At least its not THAT predictable ;-) 
> > 
> > ... after some attempts ... 
> > sage: MatrixSpace(GF(3), 2, 2).random_element() 
> > [2 0] 
> > [0 2] 
>
> Unimodular! This happens with algorithm='unimodular'. 
>
> Yes, but the docstring itself still needs to be corrected: it says 'for 
example "Matrix.random(GF(3), 2)" never generates "[[2,0],[0,2]]".' without 
the flag.

Kiran

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[sage-devel] Re: Rank of random dense matrices over GF(2)

[Kiran Kedlaya]

On Saturday, April 23, 2016 at 3:36:28 PM UTC-7, Dima Pasechnik wrote:
>
>
>
> On Saturday, April 23, 2016 at 10:16:33 PM UTC+1, Kiran Kedlaya wrote:
>>
>> I just tried the following experiment on several different machines; 
>> several different recent versions of Sage; algorithm = ple, m4ri; and n = 
>> 2, 25000, 3. In all cases, the result is identical:
>>
>> sage: M = MatrixSpace(GF(2), n)
>> sage: for i in range(10):
>> ...: print M.random_element().rank()
>> 19937
>> 19937
>> 19937
>> 19937
>> 19937
>> 19937
>> 19937
>> 19937
>> 19937
>> 19937
>>
>> Using the Internet, I also retroactively tested this in Sage 4.0.1. 
>> (Search in the page for "19937".)
>>
>> https://wiki.sagemath.org/sagebeatsmagma
>>
>> By contrast, I just tried a whole bunch of sparse examples coming from 
>> Cremona modular symbols that gave more plausible answers, e.g.:
>> sage: S = CremonaModularSymbols(31, sign=-1)
>> sage: T = 
>> hecke_matrix(2).sage_matrix_over_ZZ().change_ring(GF(2)).dense_matrix()
>> sage: T.dimensions()
>> (27549, 27549)
>> sage: T.rank()
>> 27461
>>
>> I'm not sure if this rank is correct, but at least it's not 19937.
>>
>
> well, this is hardly a surprise:
>
> sage: random_matrix?
> ...
>Warning: Matrices generated are not uniformly distributed. For
>  unimodular matrices over finite field this function does not even
>  generate all of them: for example "Matrix.random(GF(3), 2)" never
>  generates "[[2,0],[0,2]]". This function is made for teaching
>  purposes.
>
> Really?

sage: l = [Matrix.random(GF(3),2) for i in range(1)]
sage: len([i for i in l if i == 2])
114

The issue I raised appears to be distinct (see my response to Volker), but 
maybe there should also be a ticket to correct this docstring.
 

> -
> Improvements to this code are most welcome. 
> I looked at it many years ago, and it was a horrible broken mess.
> http://trac.sagemath.org/ticket/11772
> After that ticket it still was quite a mess, at least it did not hang our 
> teaching notebook server any more :-)
>
>  I haven't looked at that ticket, so I can't comment.

Kiran

 

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[sage-devel] Re: Rank of random dense matrices over GF(2)

[Kiran Kedlaya]

On Saturday, April 23, 2016 at 3:20:32 PM UTC-7, Volker Braun wrote:
>
> I'm guessing that its not a coincidence that Mersenne twister has a period 
> of 2^19937 ;-)
>
> Probably not!
 

> The relevant code is 
> in sage.matrix.matrix_mod2_dense.Matrix_mod2_dense.randomize
>
> Not sure exactly whats wrong but taking rstate.c_random() % (number of 
> columns) at the very least leads to modulo bias
>
>
I've created ticket #20493 for this issue. One observation I made there is 
that when density != 1 this problem seems to go away, probably because 
randomize is running different code in that case. The key snippet seems to 
be:
{{{
mask = __M4RI_LEFT_BITMASK(self._entries.ncols % m4ri_radix)
for i from 0 <= i < self._nrows:
for j from 0 <= j < self._entries.width:
# for portability we get 32-bit twice rather than 
64-bit once
low = gmp_urandomb_ui(rstate.gmp_state, 32)
high = gmp_urandomb_ui(rstate.gmp_state, 32)
self._entries.rows[i][j] = m4ri_swap_bits( 
((high)<<32) | (low) )
self._entries.rows[i][self._entries.width - 1] &= mask
}}}
This seems to be filling out each row using successive random 32-bit words 
from gmp, lopping off the extra bits at the end. Is that a bad idea for 
some reason?

Kiran
 

>
> On Saturday, April 23, 2016 at 11:16:33 PM UTC+2, Kiran Kedlaya wrote:
>>
>> I just tried the following experiment on several different machines; 
>> several different recent versions of Sage; algorithm = ple, m4ri; and n = 
>> 2, 25000, 3. In all cases, the result is identical:
>>
>> sage: M = MatrixSpace(GF(2), n)
>> sage: for i in range(10):
>> ...: print M.random_element().rank()
>> 19937
>> 19937
>> 19937
>> 19937
>> 19937
>> 19937
>> 19937
>> 19937
>> 19937
>> 19937
>>
>> Using the Internet, I also retroactively tested this in Sage 4.0.1. 
>> (Search in the page for "19937".)
>>
>> https://wiki.sagemath.org/sagebeatsmagma
>>
>> By contrast, I just tried a whole bunch of sparse examples coming from 
>> Cremona modular symbols that gave more plausible answers, e.g.:
>> sage: S = CremonaModularSymbols(31, sign=-1)
>> sage: T = 
>> hecke_matrix(2).sage_matrix_over_ZZ().change_ring(GF(2)).dense_matrix()
>> sage: T.dimensions()
>> (27549, 27549)
>> sage: T.rank()
>> 27461
>>
>> I'm not sure if this rank is correct, but at least it's not 19937.
>>
>> Kiran
>>
>>

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[sage-devel] Rank of random dense matrices over GF(2)

[Kiran Kedlaya]

I just tried the following experiment on several different machines; 
several different recent versions of Sage; algorithm = ple, m4ri; and n = 
2, 25000, 3. In all cases, the result is identical:

sage: M = MatrixSpace(GF(2), n)
sage: for i in range(10):
...: print M.random_element().rank()
19937
19937
19937
19937
19937
19937
19937
19937
19937
19937

Using the Internet, I also retroactively tested this in Sage 4.0.1. (Search 
in the page for "19937".)

https://wiki.sagemath.org/sagebeatsmagma

By contrast, I just tried a whole bunch of sparse examples coming from 
Cremona modular symbols that gave more plausible answers, e.g.:
sage: S = CremonaModularSymbols(31, sign=-1)
sage: T = 
hecke_matrix(2).sage_matrix_over_ZZ().change_ring(GF(2)).dense_matrix()
sage: T.dimensions()
(27549, 27549)
sage: T.rank()
27461

I'm not sure if this rank is correct, but at least it's not 19937.

Kiran

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[sage-devel] Re: Request to extend the binomial function by the reflection formula

[Kiran Kedlaya]

I haven't thought about this carefully enough to have an opinion yet. But 
definitely -1 to the status quo! If we don't implement binomial(n, k) in a 
mathematically meaningful way for k < 0, it would be better to raise a 
ValueError rather than silently returning 0.

Kiran

On Sunday, April 3, 2016 at 11:03:41 AM UTC-7, Peter Luschny wrote:
>
> Hi all,
>
> I have already reported the unsatisfactory state of the binomial
> function as implemented in Sage on 'Ask Sage' and had opened 
> a request for enhancement with ticket #17123. 
>
> Here I take up a suggestion of John Palmieri to discuss the
> issue on this list. The request is:
>
>Extend binomial(n,k) by the reflection formula, i. e. set
>for n>=1 and k>=1
>   
>binomial(-k, -n) = (-1)^(n+k) binomial(n-1, k-1).
>   
> The reasons are:
>
> (1) The current behavior introduces incompatibility with
> Maple and Mathematica. This does not only question Sage as an
> alternative for the other M-systems; because of the ubiquity
> and importance of the binomial function it becomes difficult 
> to recommended Sage for implementing sequences on the OEIS. 
>
> The behaviour of Maple and Mathematica (which support the
> reflection formula) seems to be the de facto standard. Many 
> mathematicians write their formulas in the OEIS without 
> explicitly mentioning when they assume the reflection formula.
> And this extension was used by mathematicians prior to Maple
> and Mathematica. (So it is certainly not a question of 'do we
> have to mimic all the crap of other M-systems' like some 
> commentators seem to suggest.) 
>
> (2) The extension appears natural as the extended binomial
> has the same behaviour as:
>
> def limit_binomial(n,r):
> return limit(gamma(n+x+1)/(gamma(r+x+1)*gamma(n+x-r+1)), x=0) 
>
> for n in (-5..5): print [limit_binomial(n,k) for k in (-5..5)]
>
> Indeed I find it confusing that the current implementation 
> does not exhibit this behavior.
>
> (3) Also the basic representation of Pascal's triangle in terms
> of the matrix exponential (see the Wikipedia reference below)
> makes the reflection extension appear natural as it is an extension
> from the matrix with 1, 2, 3, ... subdiagonal and zero everywhere
> else to the matrix with .., -3, -2, -1, 0, 1, 2, 3, .. as subdiagonal.
>
> (4) For a comparison of different extensions run this:
>
> def _binomial(n,k, pascal = true, reflection = true, uppernegation = true):
> def b(n,k): return factorial(n)/(factorial(k)*factorial(n-k))
> if pascal and n >= 0 and k >= 0 and k <= n: return b(n,k) 
> if reflection and n < 0 and k < 0 and k <= n: return 
> (-1)^(n-k)*b(-k-1,n-k) 
> if uppernegation and n < 0 and k >= 0: return (-1)^k*b(k-n-1,k) 
> return 0
>
> R = [n for n in (-5..5)]
> print "(1) Pascal's triangle, for the ultra-orthodox."
> print "(cf. [BP])" 
> for n in R: print [_binomial(n,k,true,false,false) for k in R]
> print "(2) Current behavior of Sage, also Magma, extends (1)."
> for n in R: print [_binomial(n,k,true,false,true) for k in R]
> print "(3) Suggested behavior."
> print "Also Maple and Mathematica, extends (1) and (2)."
> print "(cf. [RS], p.5071)" 
> for n in R: print [_binomial(n,k,true,true,true) for k in R]
> print "(4) Extends (1) by reflection only."
> print "(cf. [LMMS], p.637)" 
> for n in R: print [_binomial(n,k,true,true,false) for k in R]
>
> (5) References
>
> [BP] Blaise Pascal; Traité du triangle arithmétique; G. Desprez, 1665. 
> [LMMS] Ana Luzón, Donatella Merlini, Manuel A. Morón, Renzo Sprugnoli;
> Identities induced by Riordan arrays; Linear Algebra and its Applications, 
> 436 (2012) 631-647
> [WP] Pascal's triangle
> https://en.wikipedia.org/wiki/Pascal's_triangle#Extensions
> [MJK] M. J. Kronenburg; The Binomial Coefficient for Negative Arguments; 
> arXiv:1105.3689v2
> [RS] Renzo Sprugnoli; Negation of binomial coefficients; Discrete 
> Mathematics 308 (2008) 5070–5077
> [PL] Peter Luschny; Extensions of the binomial; Blog post;
> http://oeis.org/wiki/User:Peter_Luschny/ExtensionsOfTheBinomial
> [trac] http://trac.sagemath.org/ticket/17123
>
> I'd like to hear your opinions.
>
> Peter
>
>

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[sage-devel] Acknowledgments on sagemath.org

[Kiran Kedlaya]

The page

http://www.sagemath.org/development-ack.html

lists the funders of various Sage Days up to 23. We are a long way past 
that now!

I propose that we crowdsource the problem of getting this up to date. If 
you organized a Sage Days since 23, get on GitHub and edit the file:

https://github.com/sagemath/website/blob/master/src/development-ack.html

to include your conference and its funders. Remember that GitHub makes this 
easy: you can edit the file in place, and then GitHub will take care of the 
niceties of creating a fork, setting up your changes in a branch, and 
issuing a pull request.

Kiran

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Re: [sage-devel] Re: Sage 7.1 build fails on patch

[Kiran Kedlaya]

On Wednesday, March 23, 2016 at 4:05:51 AM UTC-7, Dima Pasechnik wrote:
>
>
>
> On Tuesday, March 22, 2016 at 10:49:44 PM UTC, John H Palmieri wrote:
>>
>>
>>
>> On Tuesday, March 22, 2016 at 3:24:13 PM UTC-7, David Roe wrote:
>>>
>>>
>>>
>>> On Tue, Mar 22, 2016 at 10:13 PM, Dima Pasechnik  
>>> wrote:
>>>
 we now decompress tarfiles with python

 https://docs.python.org/2/library/tarfile.html

 and all the features of it are only in Python 2.7. Hmm...

>>>
>>> This seems like a bad idea; there are lots of systems that won't have 
>>> Python 2.7.
>>> David 
>>>
>>
>> Python 2.7 was released 5 years ago. 
>>
>
> moreover, 2.6 is unsupported since Oct 2013. It's really bad idea to still 
> use it, 
> as there are security problems which are no longer fixed by the upstream.
>

Be that as it may, apparently my work server is running CentOS 6.7, and the 
supported version of Python in that distro is 2.6.6. (That being said, my 
sysadmin installed a newer Python locally, which solves my immediate 
problem.)

Kiran 

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[sage-devel] Sage 7.1 build fails on patch

[Kiran Kedlaya]

I just failed to build Sage 7.1 on my work server, on which I have built 
many previous versions. Any ideas?

patch-2.7.5

Setting up build directory for patch-2.7.5
Traceback (most recent call last):
  File "/home/kkedlaya/sage-7.1/build/bin/sage-uncompress-spkg", line 21, 
in 
with tarfile.open(filename, 'r:*') as archive:
AttributeError: 'TarFile' object has no attribute '__exit__'
Error: failed to extract /home/kkedlaya/sage-7.1/upstream/patch-2.7.5.tar.gz
/home/kkedlaya/sage-7.1/logs/pkgs/patch-2.7.5.log (END) 

Internals of this machine are reasonably standard:
uname -a: Linux variety 2.6.32-573.8.1.el6.x86_64 #1 SMP Tue Nov 10 
18:01:38 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
lscpu:
Architecture:  x86_64
CPU op-mode(s):32-bit, 64-bit
Byte Order:Little Endian
CPU(s):24
On-line CPU(s) list:   0-23
Thread(s) per core:2
Core(s) per socket:6
Socket(s): 2
NUMA node(s):  2
Vendor ID: GenuineIntel
CPU family:6
Model: 44
Stepping:  2
CPU MHz:   3457.923
BogoMIPS:  6915.71
Virtualization:VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache:  256K
L3 cache:  12288K
NUMA node0 CPU(s): 0,2,4,6,8,10,12,14,16,18,20,22
NUMA node1 CPU(s): 1,3,5,7,9,11,13,15,17,19,21,23

Kiran

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[sage-devel] Re: [sage-nt] Re: On Sage-days

[Kiran Kedlaya]

As it happens, I just got back from visiting BICMR about a week ago: one of 
my former PhD students (Ruochuan Liu) just started as a full-time 
researcher there. Note for future reference: middle of winter is not the 
ideal time to visit either Beijing in general or BICMR in particular! Their 
building is very nice but is highly optimized for warmer weather (most 
corridors are external).

That said, BICMR is starting to ramp up its mathematical activity and seems 
to have plenty of resources at hand, so I imagine they could afford to 
bring in enough of an international group to make a Sage Days of the form 
introduce Sage to the Chinese mathematical community viable. I for one 
hope this happens!

Kiran

On Friday, January 11, 2013 2:23:00 AM UTC-8, Volker Braun wrote:

 I guess the sports part is a mistranslation; Sometimes, a sprint is not 
 a sports activity... 

 Perhaps off-topic, but how nearby is the lab doing OpenBLAS  (
 http://www.rdcps.ac.cn)? It might be useful for Sage to talk to them...



 On Friday, January 11, 2013 5:31:31 AM UTC, Robert Bradshaw wrote:

 what topics you would expect the Sage Days to revolve around (do you 
 mean sports like football, hockey, ?



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[sage-devel] Re: Android app

[Kiran Kedlaya]

I get similar errors on my Droid 3 running Android 2.3.4 (and I can
also see aleph.sagemath.org in my browser).

Kiran

On Jan 24, 10:04 am, Volker Braun vbraun.n...@gmail.com wrote:
 On Tuesday, January 24, 2012 5:07:33 AM UTC-8, jason wrote:

  Can you reach aleph.sagemath.org with your web browser on that phone?

 The results are html created on the phone, so one should never get a Web
 page not available error. Looks like the android WebView widget works
 slightly different here.









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[sage-devel] Re: Bug Days in/near Boston after Joint Meetings?

[Kiran Kedlaya]

On Nov 4, 9:03 pm, kcrisman kcris...@gmail.com wrote:
 Well, we're currently just assessing interest; I'm sure it would be
 possible to do it closer in, but then we'd need someplace different to
 do it.  I have no idea whether the usual suspects in Cambridge or some
 of the other Boston institutions (or CMI where one Sage Days was held)
 would be available but I bet there are people on this list who might :)

In case that's referring to me, I won't be able to be in the Boston
area during the days after the meeting. But it's IAP at MIT, so
availability of space there is probably not a problem. (Ditto at
Harvard now that they have changed their academic calendar, but I
don't have any pull there.)

Kiran

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[sage-devel] Re: Indented code in terminal

[Kiran Kedlaya]

I just tried this in sage -ipython (to get directly to the ipython
interpreter) and got a similar error, so I'd call this an ipython
issue. And +1 for it being a bug.

Kiran

On Apr 19, 5:50 am, Jeroen Demeyer jdeme...@cage.ugent.be wrote:
 On 2011-04-19 14:40, Fredrik Johansson wrote:

  Hi all,

  Maybe it's just me, but I find it terribly annoying that one cannot
  paste code fragments containing indentation in a Sage terminal
  session, as one can with the ordinary Python interpreter. Simple
  example:

  def f(x):
      if x == 1:
          return 2
      return 1

 I agree it is annoying, but not sure whether it can be considered a bug.

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[sage-devel] Re: Multidimensional root finding with GSL

[Kiran Kedlaya]

I have some old Cython code (based on some code from Josh Kantor,
which I may also still have) that wrapped gsl_poly_complex_solve for
taking roots of complex univariate polynomials. That could at least
serve as a starting point...

Kiran

On Feb 7, 11:24 am, Joris Vankerschaver
joris.vankerscha...@gmail.com wrote:
 Dear all,

 Has there been any effort so far in wrapping the root-finding routines
 in GSL?  Or are there better alternatives for numerical root finding
 of vector-valued functions in Sage?  All I could find is this mission
 statement, but it doesn't look as if this was ever completed (I'd
 love to be wrong):

    http://wiki.sagemath.org/days4/projects/numerical

 I wouldn't mind wrapping these beasts myself (using, say, the code in
 sage/gsl/ode as a starting point), but I have no experience with
 Cython so it will take some time...

 All the best,
 Joris

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[sage-devel] Re: weird bug in mod()

[Kiran Kedlaya]

I'm sure I'm not the only one on this list to have made this mistake
before...

Running a .py file is not the same as typing commands into an
interactive session, because Sage doesn't do preprocessing on .py
files. There is a way to call the preprocessor directly, but that's
not necessary here; rename your file from foo.py and foo.sage, and
then it should run fine (I just tried it).

Omitting the preprocessing wreaks all kinds of havoc on Sage syntax;
for instance, ^ reverts to its Python meaning (bitwise XOR).

Kiran

On Apr 23, 12:08 pm, John Cremona john.crem...@gmail.com wrote:
 This works fine from the command line (4.4.alpha1):

 sage: K.a = NumberField(x^3 - 7)
 sage: R.y = K[]
 sage: f = y^2 + 3
 sage: g = y^3 - 5
 sage: h,alpha,beta = XGCD(f,g)
 sage: c = 1+((a-1))*alpha*f
 sage: l = lcm(f,g)
 sage: c.mod(l)
 (-3/52*a + 3/52)*y^4 + (5/52*a - 5/52)*y^3 + (15/52*a - 15/52)*y +
 27/52*a + 25/52
 sage: c % l
 (-3/52*a + 3/52)*y^4 + (5/52*a - 5/52)*y^3 + (15/52*a - 15/52)*y +
 27/52*a + 25/52

 but when I put this into a .py file, c%l returns 0 while c.mod(l)
 throws an error:

 /home/jec/sage-current/local/lib/python2.6/site-packages/sage/rings/ideal.p yc
 in reduce(self, f)
    1005         if self.gen() == 0:
    1006             return f
 - 1007         q, r = f.quo_rem(self.gen())
    1008         return r
    1009

 /home/jec/sage-current/local/lib/python2.6/site-packages/sage/structure/ele 
 ment.so
 in sage.structure.element.FieldElement.quo_rem
 (sage/structure/element.c:16544)()

 /home/jec/sage-current/local/lib/python2.6/site-packages/sage/structure/ele 
 ment.so
 in sage.structure.element.Element.__getattr__
 (sage/structure/element.c:2617)()

 /home/jec/sage-current/local/lib/python2.6/site-packages/sage/structure/par 
 ent.so
 in sage.structure.parent.getattr_from_other_class
 (sage/structure/parent.c:2817)()

 /home/jec/sage-current/local/lib/python2.6/site-packages/sage/structure/par 
 ent.so
 in sage.structure.parent.raise_attribute_error
 (sage/structure/parent.c:2584)()

 AttributeError:
 'sage.rings.fraction_field_element.FractionFieldElement' object has no
 attribute '_parent'

 I was trying to improve #8378...  am I doing something stupid?  Or what?

 John

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[sage-devel] Re: GeoGebra GSoC

[Kiran Kedlaya]

On Mar 31, 9:58 pm, Dan Drake dr...@kaist.edu wrote:
 We should also figure out exactly what we want to do. Using Javascript
 to communicate with the GeoGebra applet is nice, but what will be
 communicated? I'm guessing what would be useful is being able to use
 Sage to compute things that GeoGebra cannot, or is slow at. It might
 also be nice to control GeoGebra from an @interact. I don't know any
 details of accomplishing those things.


I can tell you one thing I'd like to do. Once upon a time, I wrote
(but never really finished) a book on Euclidean geometry, which I now
distribute as an open-source document:

http://math.mit.edu/~kedlaya/geometryunbound/

I would love to turn this (or vastly more likely, to hire a student to
turn this) into an interactive textbook, in the spirit of the CCLI
proposal that several of us (me, William, Rob Beezer, Jason Grout, Tom
Judson) have in to NSF right now. I'm thinking Sage notebooks with
full TeX (that much we have now) and every diagram an @interact
powered by GeoGebra.

Kiran

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[sage-devel] Build failure on 4.3.4.rc0: 32/64 bit issue?

[Kiran Kedlaya]

Alert readers of sage-devel and sage-release may know that since
4.3.4.alpha0, I haven't been able to compile sage on my somewhat
eccentric Fedora 10 system. It's a 64-bit system with 64-bit compilers
and such under /usr/lib, but it's on a network with mostly 32-bit
machines and their compilers are also visible under /usr/local/lib.

I keep hitting a build error in gd, with a linking error for iconv). I
put up the last install log:

http://math.mit.edu/~kedlaya/sage-434rc0.log

and the libtool script from the gd build directory:

http://math.mit.edu/~kedlaya/libtool

The latter has the following odd feature which may be causing the
problem. When the libtool script defines sys_lib_search_path_spec, it
includes

/scratch/sage-4.3.4.rc0/local/lib/../lib64/

which does not exist, but it doesn't include

/scratch/sage-4.3.4.rc0/local/lib/

which is where libiconv.so is actually located. Is this a symptom of
32/64 confusion?

Kiran

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[sage-devel] Re: Sage 4.3.4.rc0 released

[Kiran Kedlaya]

I only noticed after starting this separate thread:

http://groups.google.com/group/sage-devel/t/4f67007cbdd9e1e

that Jaap's problem looks the same as mine (since 4.3.4.alpha0),
although I can't guarantee that fixing one will fix the other.

Kiran

On Mar 17, 1:46 pm, Jaap Spies j.sp...@hccnet.nl wrote:
 Minh Nguyen wrote:
  Hi folks,

  This release candidate cleans up warnings resulting from building the
  Sage documentation. If there are no show stoppers, then this release
  is considered the final release candidate.

 Sorry, but once again the build failed:

 gcc -fPIC -g -I/home/jaap/downloads/sage-4.3.4.rc0/local/include 
 -I/home/jaap/downloads/sage-4.3.4.rc0/local/include/freetype2/ -Wl,--rpath
 -Wl,/home/jaap/downloads/sage-4.3.4.rc0/local/lib -o .libs/gd2copypal 
 gd2copypal.o  -L/home/jaap/downloads/sage-4.3.4.rc0/local/lib ./.libs/libgd.so
 -lfontconfig /home/jaap/downloads/sage-4.3.4.rc0/local/lib/libfreetype.so 
 /home/jaap/downloads/sage-4.3.4.rc0/local/lib/libpng12.so -lz -lm -Wl,--rpath
 -Wl,/home/jaap/downloads/sage-4.3.4.rc0/local/lib
 ./..libs/libgd.so/:. undefined referencelibs /to libgd.so`: libiconv'undefined
   .reference/ .tolibs /`libgd.solibiconv:' undefined
   .reference/ .tolibs /`libgd.so:libiconv_close '
 undefined. /reference. libsto/ `libgd.so:libiconv_close 'undefined
   .reference/ .tolibs /`libgd.solibiconv_open:'
 undefined reference to `libiconv_open'
 collect2: collect2: ld returned 1 exit status
 ld returned 1 exit status
 make[4]: *** [gdtopng] Error 1
 make[4]: *** Waiting for unfinished jobs
 make[4]: *** [annotate] Error 1
 ./.libs/libgd.so: undefined reference to `libiconv'
 ./.libs/libgd.so: undefined reference to `libiconv_close'
 ./.libs/libgd.so: undefined reference to `libiconv_open'
 collect2: ld returned 1 exit status
 make[4]: *** [gdparttopng] Error 1
 ./.libs/libgd.so: undefined reference to `libiconv'
 ./.libs/libgd.so: undefined reference to `libiconv_close'
 ./.libs/libgd.so: undefined reference to `libiconv_open'
 collect2: ld returned 1 exit status
 make[4]: *** [gd2copypal] Error 1
 make[4]: Leaving directory 
 `/home/jaap/downloads/sage-4.3.4.rc0/spkg/build/gd-2.0.35.p4/src'
 make[3]: *** [all-recursive] Error 1
 make[3]: Leaving directory 
 `/home/jaap/downloads/sage-4.3.4.rc0/spkg/build/gd-2.0.35.p4/src'
 make[2]: *** [all] Error 2
 make[2]: Leaving directory 
 `/home/jaap/downloads/sage-4.3.4.rc0/spkg/build/gd-2.0.35.p4/src'
 Error building gd.

 real    0m8.984s
 user    0m7.703s
 sys     0m5.884s
 sage: An error occurred while installing gd-2.0.35.p4
 Please email sage-develhttp://groups.google.com/group/sage-devel
 explaining the problem and send the relevant part of
 of /home/jaap/downloads/sage-4.3.4.rc0/install.log.  Describe your computer, 
 operating system, etc.
 If you want to try to fix the problem yourself, *don't* just cd to
 /home/jaap/downloads/sage-4.3.4.rc0/spkg/build/gd-2.0.35.p4 and type 'make 
 check' or whatever is appropriate.
 Instead, the following commands setup all environment variables
 correctly and load a subshell for you to debug the error:
 (cd '/home/jaap/downloads/sage-4.3.4.rc0/spkg/build/gd-2.0.35.p4'  
 '/home/jaap/downloads/sage-4.3.4.rc0/sage' -sh)
 When you are done debugging, you can type exit to leave the
 subshell.
 make[1]: *** [installed/gd-2.0.35.p4] Error 1
 make[1]: Leaving directory `/home/jaap/downloads/sage-4.3.4.rc0/spkg'

 real    11m4.109s
 user    14m5.462s
 sys     2m28.947s
 Error building Sage.

 This is on Fedora 12 64 bit.

 Jaap

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[sage-devel] Re: Sage 4.3.4.rc0 builds ok on Solaris 10 (SPARC)

[Kiran Kedlaya]

On Mar 18, 3:56 am, Robert Bradshaw rober...@math.washington.edu
wrote:
 Actually, I think all such posts belong on sage-release; all 1000+  
 subscribers to sage-devel don't need to know every time Sage alpha X  
 builds or brakes on system Y. (Of course, these replies are invaluable  
 for the release manager, so I don't want to discourage people from  
 sending them in.) Fortunately all such posts usually occur in one  
 thread, so I can delete them in bulk when they show up on sage-devel.


All well and good, but I sometimes get the sense that no one is
actually checking sage-release. For instance, as of now, the thread
Sage 4.3.4.rc0 released on sage-devel has 11 replies, while the same
thread on sage-release has none. So why should David (and why should
I) bother posting to sage-release?

The concept of separate mailing lists seems to be working in some
cases (sage-combinat-devel is quite active, sage-nt somewhat less so)
and not others (the last post to sage-finance was a spam from 6 months
ago). I think the Windows port is a special case, since it involves
issues quite apart from the rest of Sage development. But Solaris !=
Windows, and if it is going to become an officially supported system,
then now is precisely *not* the time for a separate forum.

What might be appropriate is a division between general Sage
development and build system issues. The latter would include all the
Solaris traffic, and probably everything currently posted on sage-
release (including all the Sage-x.y.z.alpha/rc released threads). In
fact, it might suffice to change the same of sage-release to something
like sage-build!

Kiran

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[sage-devel] Re: Sage 4.3.4.rc0 builds ok on Solaris 10 (SPARC)

[Kiran Kedlaya]

On Mar 18, 5:01 am, William Stein wst...@gmail.com wrote:
 I have been receiving regular off list complaints from people that
 there are too many Solaris posts (as explained above).  It is only
 natural to create:

    * sage-solaris:     the primary list for Solaris porting discussion.

 ...

 Of course only David can speak for his own motives, but do you really
 think David is quitting because of me creating a sage-solaris mailing
 list?

I think David may be quitting because he feels marginalized by a
substantial segment of the Sage development community, which has been
expressing its antipathy towards discussion of the Solaris port by
complaining previously off-list, now on-list. I personally give David
credit for holding out as long as he did!

Kiran

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[sage-devel] Re: Build failure on 4.3.4.rc0: 32/64 bit issue?

[Kiran Kedlaya]

A good suggestion, but it doesn't help in this case. This may be a
Fedora issue rather than a 32/64 bit issue, since Jaap Spies had
similar trouble.

There seems to be a configuration issue. The spkg runs the config
script with the options
---
./configure --prefix=/scratch/sage-4.3.4.rc0/local --without-jpeg --
without-x --with-zlib=/scratch/sage-4.3.4.rc0/local --with-freetype=/
scratch/sage-4.3.4.rc0/local --without-xpm
---
If I remove the --with-freetype option, the build succeeds. Why that
is the case is completely beyond me!

Kiran

On Mar 18, 11:38 am, Dima Pasechnik dimp...@gmail.com wrote:
 Kiran,
 it should be possible by simply setting PATH appropriately to make all
 the
 unwanted /usr/local stuff invisible.
 Did you try doing this?
 (assuming you use bash as the shell, you can do PATH=whatever_stuff_you_need
  export PATH )

 A similar problem arises on MacOSX, when one has some extra things,
 like fink, installed.
 E.g. I have
 $ echo $PATH
 /usr/local/texlive/2007/bin/powerpc-darwin:/sw/bin:/sw/sbin:/usr/bin:/
 bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/X11R6/bin

 In order to build, successfully, Sage, I need to do something like

 $ PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin
 $ export PATH

 and then proceed to build Sage (without quitting this shell, cause
 then you'd get the unneeded parts of the PATH back)

 HTH,
 Dmitrii

 On Mar 18, 7:40 pm, Kiran Kedlaya ksk...@gmail.com wrote:



  Alert readers of sage-devel and sage-release may know that since
  4.3.4.alpha0, I haven't been able to compile sage on my somewhat
  eccentric Fedora 10 system. It's a 64-bit system with 64-bit compilers
  and such under /usr/lib, but it's on a network with mostly 32-bit
  machines and their compilers are also visible under /usr/local/lib.

  I keep hitting a build error in gd, with a linking error for iconv). I
  put up the last install log:

 http://math.mit.edu/~kedlaya/sage-434rc0.log

  and the libtool script from the gd build directory:

 http://math.mit.edu/~kedlaya/libtool

  The latter has the following odd feature which may be causing the
  problem. When the libtool script defines sys_lib_search_path_spec, it
  includes

  /scratch/sage-4.3.4.rc0/local/lib/../lib64/

  which does not exist, but it doesn't include

  /scratch/sage-4.3.4.rc0/local/lib/

  which is where libiconv.so is actually located. Is this a symptom of
  32/64 confusion?

  Kiran

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[sage-devel] Re: Exhibit booth for 2011 joint meetings

[Kiran Kedlaya]

On a related note: between now and the 2011 JMM is this summer's
International Congress. The information about exhibits is in a PDF
downloadable from here:

http://www.icm2010.com/exh_manual.asp

The smallest booth (6 m^2) runs about $3000, plus $25/day for internet
access.

My guess is that there aren't going to be nearly enough Sagers who
have other reason to make the trip to Hyderabad for a Sage booth to be
viable. So far I can think of myself and William. If I'm missing
anyone, feel free to counterargue...

Kiran

On Mar 2, 10:10 am, mhampton hampto...@gmail.com wrote:
 I've made a wiki page for this, at:

 http://wiki.sagemath.org/jmms2011

 I took the liberty of adding Karl and Rob to the list, since they
 seemed pretty definitive about going.  Anyone else who is interested
 in helping with the booth please sign up!

 The call for exhibitors and sponsors will be in early May according
 to the AMS website.

 -Marshall

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[sage-devel] Re: Sage 4.3.3.alpha0 released

[Kiran Kedlaya]

All doctests pass under 64-bit Fedora 10.

Kiran

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[sage-devel] Segfault: Polynomials over RealField

[Kiran Kedlaya]

The following input segfaults sage 4.3.2 on sage.math, as well as sage
4.3 on various other machines.

P.x = PolynomialRing(RealField())
print sum(P(0)*P(0) for k in range(1))

This example seems quite fragile; for instance, the segfault goes away
if you change RealField to RationalField, RealDoubleField, or Complex
Field.

Kiran

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[sage-devel] Re: Exhibit booth for 2011 joint meetings

[Kiran Kedlaya]

This would definitely be called for if the AMS approves William's
Short Course application. I can help with funding if needed.

Kiran

On Jan 26, 11:30 pm, mhampton hampto...@gmail.com wrote:
 Since this sort of decision should be made pretty early in the year I
 wanted to open a discussion on it.

 Sage has had two exhibition booths at the national (US) joint math
 meetings, in 2008 and 2009.  This year we did not have a booth.

 I think those booths were extremely helpful in making people more
 aware of Sage.  My impression is that now somewhere around 1/3 to 1/2
 of academic mathematicians have heard of Sage, but most do not have a
 clear idea of exactly what it is and what it can do.  If we had a
 booth at the 2011 meetings, I think it would be important to have a
 good graphical display - i.e. at least one good-sized monitor, ideally
 2.  William Stein obtained a great monitor for 2008, but its unclear
 how to repeat that in New Orleans.

 Overall I think it would be worthwhile to have another booth if enough
 people can pitch in.  It does take a lot of effort.  While it costs
 money, at least 2 people get exhibitor registrations (maybe 3?).  For
 the money (less than $1000 total I think) its probably the most
 effective way to get the attention of many mathematicians.

 I would be willing to help organize and run a booth in 2011 if some
 other people could commit to that as well.  I do not have a source of
 funding for it at the moment but if we start now it shouldn't be too
 hard to find.

 Any thoughts?

 -Marshall Hampton

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[sage-devel] Re: ISSAC 2011

[Kiran Kedlaya]

Am I reading correctly that the per diem fee is 80 USD per person per
day? Those must be some serious refreshments...

Kiran

On Dec 4, 12:06 pm, kcrisman kcris...@gmail.com wrote:
 Just FYI:

 From an email forwarded to the Maxima list:

 *---*

  Call for Proposals for Workshops

   ISSAC 2011

 June 8-11, 2011

 *---*

 We solicit proposals for satellite workshops to be held in conjunction
 with ISSAC 2011.

 For the first time, ISSAC will participate in the Federated Computing
 Research Conference (FCRC). FCRC occurs once every four years, and is
 the world's largest computing research conference.  FCRC consists of a
 collection of conferences that agree to share the same conference
 facility. To learn more, seehttp://acm.org/fcrc/ .

 The FCRC week in 2011 will run June 4-11  The ACM is able to offer
 space for workshops or small conferences at no additional charge.
 Participants are responsible for paying a modest FCRC registration fee
 (approx. 50 USD for the entire FCRC week) and a ``per diem'' fee to
 cover refreshments (approx. 80 USD per day).  These fees are the same
 regardless of how many events one attends, i.e., there is no penalty
 to register for one conference and attend a different workshop.  ISSAC
 will take place at the end of the FCRC week, and space for workshops
 is available for us starting the day before, June 7.

 Opportunities abound for making connections with other fields of
 computer science. Conferences that have confirmed their participation
 include the

 * ACM Symposium on Theory of Computing (STOC),

 * ACM Symposium on Parallelism in Algorithms and Architectures (SPAA),

 * ACM Conference on Programming Language Design and Implementation
 (PLDI),

 * CRA-W Career Mentoring Workshop.

 Potential ideas for workshops that take advantage of the presence of
 these related conferences might then be Complexity in Computer
 Algebra, Parallel Symbolic Computation, Programming Languages for
 Computer Algebra, or Mentoring Women in Computer Algebra.

 We also welcome proposals for other topics.  Holding your workshop at
 an event with international presence might heighten participation.

 Please email your proposal to General Chair Eric Schost at
 esch...@uwo.ca.  There is no hard deadline, but because space is
 limited, we encourage you to submit by December 14, 2009. We will make
 decisions on a ``first come, first served'' basis and may close
 submissions before December 1st.

 For questions concerning the Federated Computing Research Conference,
 any organizational details, current list of participating conferences,
 or current availability of space, please contact Local Arrangements
 Chair Emil Volcheck at volch...@acm.org.

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[sage-devel] Magma false is true

[Kiran Kedlaya]

This is now ticket #7504.

sage: bool(pari(False))
False
sage: bool(gap(False))
False
sage: bool(maxima(False))
False
sage: bool(maple(False))
False
sage: bool(mathematica(False))
False
sage: bool(magma(False))
True

Kiran

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[sage-devel] Re: Implementation of Q(t) and monomials

[Kiran Kedlaya]

On Nov 14, 9:05 pm, William Stein wst...@gmail.com wrote:

 Could you add something to this email about performance comparisons with 
 Magma?
 It's one thing to say Sage is slow compared to my custom optimized C
 code (no surprise), and another to say Sage is 1000 times slower
 than some easy-to-write interpreter code in Magma (ouch, and is the
 case here, right?).

I'm guessing the latter. I actually have done exactly this type of
calculation (computing a Gauss-Manin connection) in a couple of
examples using Magma and it seemed to work pretty well. I didn't try
Sage's rational function field per se, since at the time we didn't
wrap Singular to do Groebner bases over such a field (do we even do it
now?), but Singular was hopelessly bad at doing Groebner bases over Q
(t) (as in, what Magma did in a fraction of a second wouldn't
terminate in two hours under Singular). I'm guessing that among other
improvements, Magma's method (based on F4) has less intermediate
coefficient explosion.

Kiran

P.S. Sebastian: I'll be interested in this code eventually, for
possible applications to computing zeta functions of varieties over
finite fields (Lauder's deformation method in p-adic cohomology).
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[sage-devel] Re: Sage 4.2.1.alpha0 released!

[Kiran Kedlaya]

All long tests pass under 64 bit Fedora 10.

Kiran

On Nov 9, 1:04 pm, Mike Hansen mhan...@gmail.com wrote:
 Hello all,

 Sage 4.2.1.alpha0 is out.  Source and binary areavailable at

 http://sage.math.washington.edu/home/mhansen/release/4.2.1/alpha0/sag...http://sage.math.washington.edu/home/mhansen/release/4.2.1/alpha0/sag...

 The upgrade path is

 http://sage.math.washington.edu/home/mhansen/release/4.2.1/alpha0/sag...

 Tickets merged in 4.2.1.alpha0:

 #7111: Robert Miller: timeout when doctesting partition refinement
 code [Reviewed by Mike Hansen]
 #7204: Mitesh Patel: issue building sage docs since notebook moved
 [Reviewed by ]
 #7200: Valentin Féray: Fixing longest increasing subsequence
 (permutation method) [Reviewed by Florent Hivert]
 #7285: William Stein: remove hgmerge from list of installed scripts
 [Reviewed by Mike Hansen]
 #385: Karl-Dieter Crisman: implement at for symbolics [Reviewed by David 
 Joyner]
 #2646: Jason Grout: create plot_vector_field3d function [Reviewed by
 Marshall Hampton]
 #3666: Alex Ghitza: pari(infinity) looks like it works, but it doesn't
 [Reviewed by Karl-Dieter Crisman]
 #5680: Burcin Erocal: Use new bits from FLINT 1.2.4 (followup to
 #5240) [Reviewed by Mike Hansen]
 #5800: Jason Grout: Nice wrapper for bitset [Reviewed by Robert Bradshaw]
 #5911: Nathann Cohen: greatly improve the documentation one gets from
 Graph? [Reviewed by Robert Miller, Minh Van Nguyen, Mike Hansen]
 #6541: Luis Felipe Tabera: functions numerator and denominator for
 univariate polynomials [Reviewed by Karl-Dieter Crisman]
 #6543: Marshall Hampton: improve doctests for tachyon [Reviewed by
 Minh Van Nguyen, Tim Dumol]
 #6673: Mitesh Patel: Set up jsMath extensions, macros, etc., for the
 documentation [Reviewed by John Palmieri]
 #6676: William Stein: DeprecationWarning on twisted after starting
 notebook(). [Reviewed by Mike Hansen]
 #6759: David Kirkby: Update sqlite to latest release - needed for
 Sun's compiler [Reviewed by Minh Van Nguyen]
 #6761: Kwankyu Lee: solve_left on a vector returns a matrix [Reviewed
 by Robert Bradshaw]
 #6831: Andrey Novoseltsev: No more maximal dimension requirement for
 lattice polytopes [Reviewed by Marshall Hampton]
 #7052: Anders Jonsson, Robert Miller: Chromatic polynomial calculated
 incorrectly [Reviewed by Mike Hansen]
 #7096: Christian Wuthrich: bug in dual isogeny computation [Reviewed
 by John Cremona]
 #7124: Minh Van Nguyen: affine cipher and its cryptanalysis [Reviewed
 by Rob Beezer]
 #7159: Nathann Cohen: Graph.merge_vertices, and a bug in edge_boundary
 [Reviewed by Anders Jonsson]
 #7227: Sebastien Labbe: Improving factor complexity of words functions
 [Reviewed by Vincent Delecroix]
 #7241: Mike Hansen: sage -upgrade will try to redownload spkg's that
 are already present [Reviewed by Florent Hivert]
 #7266: William Stein: implement computation of Silverman height bounds
 [Reviewed by Robert Bradshaw]
 #7306: Rob Beezer: Documentation fix for Generalized Petersen graph
 [Reviewed by AJonsson]
 #7315: Karl-Dieter Crisman: Can only forget one GenericDeclaration at
 a time for some reason [Reviewed by Jason Grout]
 #7324: Yann Laigle-Chapuy: improve order_from_multiple [Reviewed by
 Francis Clarke]
 #7326: Jason Grout: html.table should automatically typeset math
 inside of strings [Reviewed by Wilfried Huss]
 #7327: Jason Grout, Karl-Dieter Crisman: Make integrate accept a
 variable range as a tuple [Reviewed by Karl-Dieter Crisman, Jason
 Grout, Mike Hansen]
 #7329: Jason Grout: Make integration of vectors work (component-wise)
 [Reviewed by Rob Beezer]
 #7366: Martin Albrecht: fix GF(4,'a').list() [Reviewed by Rob Beezer]
 #7370: Martin Albrecht: fix FiniteFieldIterator [Reviewed by Yann 
 Laigle-Chapuy]
 #7373: David Kirkby: Disable assembly code in libgcrypt on risky
 platforms. [Reviewed by Mike Hansen]
 #7393: Mike Hansen: Update ECL to the latest version [Reviewed by William 
 Stein]
 #7399: Robert Bradshaw: fix ugliness for default graph plot3d
 [Reviewed by William Stein]
 #3128: Simon King: PolynomialRing's behaviour does not match docstring
 [Reviewed by Martin Albrecht, Mike Hansen]
 #4264: Christian Wuthrich: change E.a_invariants() for an elliptic
 curve to return a tuple [Reviewed by Mike Hansen]
 #6309: D. Benjamin Antieau: miscellaneous additions to simplicial
 complex class; clique complex method for graphs [Reviewed by John
 Palmieri]
 #6747: Tom Boothby: Improve plotting of trees [Reviewed by Nathann
 Cohen, Michael Yurko]
 #7244: Rob Beezer: Implement dicyclic groups as permutation groups
 [Reviewed by David Joyner]
 #7295: François Bissey: typo in ecm spkg-install [Reviewed by Minh Van Nguyen]
 #7320: John Palmieri: search_src and friends are case-sensitive
 [Reviewed by Karl-Dieter Crisman]
 #7323: John Palmieri: tinkering with documentation for simplicial
 complexes [Reviewed by Phillipe Saade]
 #7328: Jason Grout: latex doesn't handle python floats correctly
 [Reviewed by Karl-Dieter Crisman]
 #7331: 

[sage-devel] Re: Sage 4.2.alpha0 released

[Kiran Kedlaya]

All long doctests pass under 64-bit Fedora 10.

Kiran

On Oct 19, 3:10 am, Mike Hansen mhan...@gmail.com wrote:
 Hello all,

 Sage 4.2.alpha0 is out.  Source and binary areavailable at

 http://sage.math.washington.edu/home/mhansen/release/4.2/alpha0/sage-...http://sage.math.washington.edu/home/mhansen/release/4.2/alpha0sage-4...

 The upgrade path is

 http://sage.math.washington.edu/home/mhansen/release/4.2/alpha0/sage-...

 The tickets merged in 4.2.alpha0 are:

 #5556: Karl-Dieter Crisman: symbolic gamma function is incoherent
 [Reviewed by Mike Hansen]
 #5985: Craig Citro, Nicolas M. Thiéry: cPickle: adds support for class
 pickling customization [Reviewed by Craig Citro, Nicolas M. Thiéry]
 #6482: Martin Albrecht: multivariate polynomial substitution has a
 design flaw [Reviewed by Mike Hansen]
 #1509: Matthew Trumbell: Allow text rotation in plotting [Reviewed by
 Karl-Dieter Crisman]
 #2341: Karl-Dieter Crisman, Ricardo Massaro: vector subs over symbolic
 does not work [Reviewed by Jason Grout]
 #2900: Karl-Dieter Crisman: matplotlib bug in imshow (probably fixed
 in new version) [Reviewed by Jason Grout]
 #3718: Karl-Dieter Crisman: calculus -- sage treats limits involving
 floor and ceil completely wrong [Reviewed by Tim Dumol]
 #4807: Michael Yurko: bug in exponential integral [Reviewed by Mike Hansen]
 #4941: Yann Laigle-Chapuy: pari list slicing is extremely slow -- make
 it much faster [Reviewed by Mike Hansen]
 #5755: Karl-Dieter Crisman: error converting symbolic expression to
 polynomial [Reviewed by Mike Hansen]
 #5899: Tim Abbott: Update Debian build support for Sage spkg [Reviewed
 by Mike Hansen]
 #5986: Craig Citro, Nicolas M. Thiéry: Workaround mishandled nested
 classes in Python and cPickle [Reviewed by Robert Bradshaw]
 #5991: Nicolas M. Thiéry: Add a standard constructor for dynamic
 classes [Reviewed by David Roe]
 #6118: Robert Bradshaw, Craig Citro: integer shifting slow [Reviewed
 by Mike Hansen, Craig Citro]
 #6187: John Palmieri, Mitesh Patel: Fix post-cloning docbuild problems
 and add new command-line options [Reviewed by John Cremona, Mike
 Hansen]
 #6189: Karl-Dieter Crisman: 'integrate' produces incorrect answer
 [Reviewed by Mike Hansen]
 #6228: Karl-Dieter Crisman: Wrong multiplicities when solving a
 univariate polynomial equation [Reviewed by Mike Hansen]
 #6304: David Harvey: intermittent crash in bernmm (4.0.2.rc0)
 [Reviewed by Mike Hansen]
 #6420: Karl-Dieter Crisman: Maxima integration error with 1/x^3
 [Reviewed by Mike Hansen]
 #6572: John Palmieri: tutorial: put double colon on its own line
 [Reviewed by Mike Hansen]
 #6586: John Palmieri: update Sphinx to version 0.6.2 or 0.6.3
 [Reviewed by John Cremona, Tim Dumol, Mitesh Patel]
 #6605: John Palmieri: sage -docbuild DOC FORMAT should do better error
 checking on DOC [Reviewed by Mitesh Patel]
 #6642: Karl-Dieter Crisman: problem with solve (from the tutorial)
 [Reviewed by John Palmieri]
 #6823: Nathann Cohen: Kneser Graph in graph_generators [Reviewed by Rob 
 Beezer]
 #6892: John Palmieri: change dollar signs to backticks [Reviewed by Mike 
 Hansen]
 #6899: Mike Hansen, Burcin Erocal: weird bug taking float of real part
 of a symbolic [Reviewed by Burcin Erocal, Karl-Dieter Crisman]
 #6906: John Palmieri: update Mercurial to version 1.3.1 [Reviewed by
 Mike Hansen]
 #6909: Martin Albrecht: move some commutative algebra to libSingular
 functions interface [Reviewed by Michael Brickenstein, Burcin Erocal]
 #6958: Robert Miller: prove_BSD function for elliptic curves over QQ
 [Reviewed by William Stein]
 #6977: Nicolas M. Thiéry: Implement __len__ to add support for MuPAD
 objects as Python containers [Reviewed by Mike Hansen]
 #6986: Jason Grout: Make PIL standard [Reviewed by Mike Hansen]
 #7007: Mike Hansen: variables() method for polynomial rings returns
 the constant as well as the variable. [Reviewed by Jason Grout]
 #7010: Minh Van Nguyen: sanity check key value of the shift
 cryptosystem [Reviewed by Rob Beezer]
 #7015: William Stein, Minh Van Nguyen: cygwin port -- ratpoints --
 don't build executable since we don't need it (and fails on cygwin)
 [Reviewed by Mike Hansen]
 #7045: David Kirkby: update libgcrypt to the latest version 1.4.4
 [Reviewed by Adam Webb]
 #7081: Tim Dumol: sage -c ... runs from the local/bin/ directory.
 ugh [Reviewed by William Stein]
 #7084: Karl-Dieter Crisman: Make assumption comparison work for
 GenericDeclarations [Reviewed by Tim Dumol]
 #7117: John Palmieri: latex fix for RIF [Reviewed by Mike Hansen]
 #3970: Mike Hansen: MaximaElements should not coerce into SR.
 [Reviewed by Adam Webb]
 #5243: Florent Hivert: non decreasing parking functions (depend now on
 5255) [Reviewed by Dan Drake, Mike Hansen]
 #5812: Wilfried Huss: option zorder has no effect for point() and
 polygon() [Reviewed by Karl-Dieter Crisman, Volker Braun]
 #6828: Nathann Cohen: Random Bipartite Graph [Reviewed by Rob Beezer]
 #6891: Karl-Dieter Crisman: Bring functions.spike_functions.py to 

[sage-devel] Re: Sage Days: MSRI

[Kiran Kedlaya]

Bart confirms the dates, although they are not yet completely official
(the Lorentz Center administration still has to formally approve the
proposal, but he seems confident that will happen).

Kiran

On Oct 7, 4:50 pm, Kiran Kedlaya ksk...@gmail.com wrote:
 On Oct 7, 11:56 am, Burcin Erocal bur...@erocal.org wrote:



  On Wed, 7 Oct 2009 06:17:32 -0700

  William Stein wst...@gmail.com wrote:
   On Wed, Oct 7, 2009 at 1:27 AM, John Cremona john.crem...@gmail.com
   wrote:

Isn't the second of those weeks the week of the planned Sage Days in
Leiden?  Which will specialise in Number Theory?

   Good point -- there were so many possible dates for Leiden that what
   is posted in various places (e.g.,http://wiki.sagemath.org/) is
   wrong at this point.

   I checked withMSRIand one week earlier: June 21-July 2, 2010, also
   works for them.

  What are the final dates for Leiden?

  I thought the dates on the wiki were final, since we used them to set
  the dates for the Sage Days at RISC (July 18-22). Another item to keep
  in mind when deciding the schedule is ISSAC 2010 in Munich (July 25-28).

  Cheers,
  Burcin

 I guess that means the Sage Days at RISC conflicts with ANTS (July
 19-23). Ah well, it's a busy summer, especially with August largely
 off limits due to the ICM.

 In other news, I'm in Leiden this week, so I can check with Bart about
 the dates in case he doesn't answer.

 Kiran
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[sage-devel] Re: Sage Days: MSRI

[Kiran Kedlaya]

On Oct 7, 11:56 am, Burcin Erocal bur...@erocal.org wrote:
 On Wed, 7 Oct 2009 06:17:32 -0700

 William Stein wst...@gmail.com wrote:
  On Wed, Oct 7, 2009 at 1:27 AM, John Cremona john.crem...@gmail.com
  wrote:

   Isn't the second of those weeks the week of the planned Sage Days in
   Leiden?  Which will specialise in Number Theory?

  Good point -- there were so many possible dates for Leiden that what
  is posted in various places (e.g.,http://wiki.sagemath.org/) is
  wrong at this point.

  I checked with MSRI and one week earlier: June 21-July 2, 2010, also
  works for them.

 What are the final dates for Leiden?

 I thought the dates on the wiki were final, since we used them to set
 the dates for the Sage Days at RISC (July 18-22). Another item to keep
 in mind when deciding the schedule is ISSAC 2010 in Munich (July 25-28).

 Cheers,
 Burcin

I guess that means the Sage Days at RISC conflicts with ANTS (July
19-23). Ah well, it's a busy summer, especially with August largely
off limits due to the ICM.

In other news, I'm in Leiden this week, so I can check with Bart about
the dates in case he doesn't answer.

Kiran

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[sage-devel] Re: Sage Days: India?

[Kiran Kedlaya]

On Sep 30, 11:18 pm, William Stein wst...@gmail.com wrote:
 On Wed, Sep 30, 2009 at 5:44 PM, Kiran Kedlaya ksk...@gmail.com wrote:

  On Sep 30, 5:15 pm, William Stein wst...@gmail.com wrote:
  Hi Sage-Devel,

  Jarrod Millman, Prabhu Ramachandran, and I have been kicking around
  the idea of having a Sage Days in India as a satellite conference near
  when the next ICM (International Congress of Mathematicians) will
  happen in India next year (Aug 19-27, 2010 -- 
  seehttp://www.icm2010.org.in/).

  Who here is highly interested in the possibility of attending such a Sage 
  Days?

   -- William

  I'll be in India for the ICM, but I've already booked the week before
  for a pair of satellite conferences in Goa, and I don't think I can
  stay any later. So I'm interested but very likely not actually
  available.

 I'm also likely going to a number theory satellite conference in Goa
 the week before (maybe the same as you).   So this Sage Days would be
 either two weeks before or the week after ICM.

 William

For the recond, ECC 2010 is scheduled to be in Princeton sometime in
August, either before or just after the ICM (e.g., during the week
August 30-September 3). I'm not sure when they (meaning Victor Miller)
will know the exact dates.

Any thoughts about the location? If Prabhu is at IITB, I suppose
that's an option.

Kiran
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[sage-devel] Re: Sage 4.1.2.rc0 released

[Kiran Kedlaya]

On Oct 1, 3:39 am, Minh Nguyen nguyenmi...@gmail.com wrote:
 Hi folks,

 This is the first release candidate for Sage 4.1.2, which mostly fixed
 bugs. With the Sage 4.1.2.rc0 release, I'm stepping down as release
 manager for the 4.1.2 release cycle and hand over the release chair to
 William Stein.

Using the updated cliquer package from #6681, on my 64-bit Fedora 10
machine, 4.1.2rc0 builds and passes all long doctests except for
these:

sage -t -long devel/sage/sage/server/notebook/notebook.py
sage -t -long devel/sage/sage/interfaces/sage0.py

However, I wasn't able to reproduce these failures. The second one
looks like an out-of-memory or something. The first is at line 1475;
it looks like the xxx seconds ago at the end of the docstring became
1 second ago in my first test.

Kiran
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[sage-devel] Re: Sage Days: India?

[Kiran Kedlaya]

On Sep 30, 5:15 pm, William Stein wst...@gmail.com wrote:
 Hi Sage-Devel,

 Jarrod Millman, Prabhu Ramachandran, and I have been kicking around
 the idea of having a Sage Days in India as a satellite conference near
 when the next ICM (International Congress of Mathematicians) will
 happen in India next year (Aug 19-27, 2010 -- seehttp://www.icm2010.org.in/).

 Who here is highly interested in the possibility of attending such a Sage 
 Days?

  -- William

I'll be in India for the ICM, but I've already booked the week before
for a pair of satellite conferences in Goa, and I don't think I can
stay any later. So I'm interested but very likely not actually
available.

Kiran
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[sage-devel] Re: Sage 4.1.1 source released

[Kiran Kedlaya]

On 64-bit Fedora 10, I get a build failure in cliquer. The relevant
snippet from the install log is below.

This looks like a case of 32/64 confusion, which I am no stranger to.
This machine runs on a primarily 32-bit network, and in the past we've
discovered various build problems due to this. For instance, the local
gcc in /usr/bin is 64-bit, but the NFS one in /usr/local/bin is 32-
bit, so I have to configure my path appropriately. In this case, it's
somehow trying to find stubs-32.h instead of stubs-64.h, but I don't
know why.

Kiran
---

Host system
uname -a:
Linux dwork.mit.edu 2.6.27.25-170.2.72.fc10.x86_64 #1 SMP Sun Jun 21
18:39:34 EDT 2
009 x86_64 x86_64 x86_64 GNU/Linux


CC Version
gcc -v
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --
infodir=/usr/
share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-
bootstrap --e
nable-shared --enable-threads=posix --enable-checking=release --with-
system-zlib --
enable-__cxa_atexit --disable-libunwind-exceptions --enable-
languages=c,c++,objc,ob
j-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-
plugin --with-
java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-
multifile --enabl
e-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar
--disable-lib
java-multilib --with-cpu=generic --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.3.2 20081105 (Red Hat 4.3.2-7) (GCC)

scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
gcc -o src/cl.os -c -fPIC src/cl.c
In file included from /usr/include/features.h:359,
 from /usr/include/stdio.h:28,
 from src/cl.c:2:
/usr/include/gnu/stubs.h:7:27: error: gnu/stubs-32.h: No such file or
directory
scons: *** [src/cl.os] Error 1
scons: building terminated because of errors.
(et cetera)
---

On Aug 14, 12:30 pm, Minh Nguyen nguyenmi...@gmail.com wrote:
 Hi folks,

 This is a source release of Sage 4.1.1.

 Sage 4.1.1 was released on August 14, 2009. It is available at

http://www.sagemath.org/download.html

 * About Sage (http://www.sagemath.org)

 Sage is developed by volunteers and combines over 90 open source packages.
 It is available for download fromwww.sagemath.organd its mirrors in
 source or binary form. If you have any questions and/or problems,
 please report them to the Google groups sage-devel or sage-support.
 You can also drop by in #sage-devel or #sage-support in freenode.


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[sage-devel] Indents in notebook cells

[Kiran Kedlaya]

What would you expect from the following input into the notebook?

CELL 1:
u = 2+2
u = 2+3

CELL 2:
print u

If you try something like this at a command line, the first line gives
an error due to the spaces in front. But on my notebook server
(running 4.1), the first cell evaluates without an error, and the
second one returns 4, not 5. ?!

Kiran

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[sage-devel] Re: Sage 4.1.1.alpha1 released

[Kiran Kedlaya]

Build from upgrade works flawlessly, and all doctests pass, on 64-bit
(Opteron) Fedora 10.

Kiran

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[sage-devel] Re: Sage and Singular Talk

[Kiran Kedlaya]

One pet complaint that you might bring up with the Singular team: I
have had trouble using Singular for Groebner basis computations over
the rational function field Q(t). Certain computations that Magma
handles easily cause Singular to choke up. I posted an example
upstream:

http://www.singular.uni-kl.de/forum/viewtopic.php?f=10t=1683sid=a8f16c64febeaa83ca01675a38070c36

but got no reply. (By contrast, I haven't had any problems working in
F_p(t).)

Kiran

On Jul 15, 7:25 am, Martin Albrecht m...@informatik.uni-bremen.de
wrote:
 Hi there,

 next week I'll visit the Singular group in Kaiserslautern. As a part of my
 visit I will give a talk on Sage. The talk will be focused on topics I assume
 to be relevant to the Singular team.

 I have uploaded a draft of my slides to:

  http://sage.math.washington.edu/home/malb/talks/sage-singular.pdf

 Btw. they are in English because this way the Sage community can help me to
 improve the slides ;) and it increases accountability: I am invited to
 represent the Sage project there, so the project should know what I am up to.

 The slides contain a wish list at the end, so if you care about commutative
 and non-commutative algebra (implemented in Singular and/or PolyBoRi) let me
 hear, what you'd like to see.

 Cheers,
 Martin

 --
 name: Martin Albrecht
 _pgp:http://pgp.mit.edu:11371/pks/lookup?op=getsearch=0x8EF0DC99
 _otr: 47F43D1A 5D68C36F 468BAEBA 640E8856 D7951CCF
 _www:http://www.informatik.uni-bremen.de/~malb
 _jab: martinralbre...@jabber.ccc.de
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[sage-devel] Re: Sage-4.1.alpha1

[Kiran Kedlaya]

On 64-bit Fedora 10, I see these doctest failures:

sage -t  devel/sage/doc/fr/tutorial/programming.rst
sage -t  devel/sage/sage/misc/darwin_utilities.pyx

Kiran

On Jun 25, 2:18 pm, Robert Miller rlmills...@gmail.com wrote:
 This release is primarily the Python upgrade. The source tarball and
 sage.math binary are here:

 http://sage.math.washington.edu/home/rlmill/release/sage-4.1.alpha1.tarhttp://sage.math.washington.edu/home/rlmill/release/sage-4.1.alpha1-s...

 If you care to try upgrading (do so at your own risk -- upgrading has
 been seen to not work, but not seen to work), the bits are here:

 http://sage.math.washington.edu/home/rlmill/release/sage-4.1.alpha1/

 I owe much gratitude to Mike Hansen, Martin Albrecht and particularly
 William Stein for help with getting the Python upgrade to work.

 These are the known doctest failures:

sage -t -long devel/sage/sage/modules/
 vector_real_double_dense.pyx # 1 doctests failed
sage -t -long devel/sage/doc/fr/tutorial/programming.rst # 1
 doctests failed

 I haven't looked into these, since I have spent about eleven hours out
 of the last thirty on the Python upgrade.

 Tom Boothby will take over for alpha2, and I will merge more spkg's
 for alpha3, which will also be rc0.

 Cheers,

 Robert Miller
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[sage-devel] Re: Sage 4.0.2.rc0 released

[Kiran Kedlaya]

All tests pass under 64-bit Fedora 10.

Kiran

On Jun 15, 3:13 am, Nick Alexander ncalexan...@gmail.com wrote:
 Hi all,

 Here's Sage 4.0.2.rc0. Come and get it while it's hot:

  http://sage.math.washington.edu/home/ncalexan/releases

 We merged all of the tickets with positive review on trac (save one
 that depended on a still-unreviewed ticket), and updated to the
 current upstream for seven spkgs. You're probably wondering why this
 is rc0 instead of alpha0 -- we'd like to get 4.0.2 pushed out the door
 pretty soon, and we've already merged all the code we could from trac,
 so we're cutting it off here. In addition, William is giving a talk at
 MEGA on Thursday, and it would be nice to have a fresh new release for
 that. So please build and test soon, and we'll get this tested and
 released.

 == Notable new features ==

 * Updated to current upstream of Singular, MPIR, FLINT, numpy, scipy,
 m4ri, and pynac
 * sage -br calls gcc in parallel when MAKE is set
 * New script for automatically downloading and testing patches from a
 trac ticket -- this was used to create this release, but will be
 packaged with rc1

 == Known issues ==

 * There's a doctest failure with Singular on 32-bit machines, where
 Singular seems to be choosing different representatives for the
 integers mod 2^32 on 32 and 64 bit architectures. Martin Albrecht will
 hopefully chime in on the right fix for this.
 * The new scipy will have doctest failures with gfortran, but works
 fine with g95. In particular, we patch scipy.optimize.optimize for
 g95, but not gfortran -- and the unpatched version has unusual
 behavior for find_maximum_on_interval (which calls
 scipy.optimize.optimize.fminbound).

 == List of closed tickets ==

 This will come with the release email for the next rc; if you want to
 see it right away, it's here:

  http://trac.sagemath.org/sage_trac/query?status=closedgroup=resoluti...

 Thanks,
 -Craig and Nick
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[sage-devel] Re: Sage 4.0.1.rc0

[Kiran Kedlaya]

On 64-bit Fedora 10, I see the same html failure as previous reported,
and no other failures.

Kiran

On Jun 5, 1:24 am, Justin C. Walker jus...@mac.com wrote:
 On Jun 4, 2009, at 13:18 , William Stein wrote:





  On Thu, Jun 4, 2009 at 1:04 PM, Kiran Kedlaya ksk...@gmail.com  
  wrote:
 [snip]
  There's now an rc1 with that #6209 thing fixed:

 http://sage.math.washington.edu/home/mhansen/release/4.0.1/rc1/sage-4...

  and

 http://sage.math.washington.edu/home/mhansen/release/4.0.1/rc1/sage-4...

 Built as an upgrade to sage-4.0.rc0.  Build completed w/o problems  
 (Mac OS X, 10.5.7, Dual Quad Xeon).

 Testing yielded two failures:

          sage -t  devel/sage/doc/en/bordeaux_2008/birds_other.rst
          sage -t  devel/sage/sage/misc/html.py

 The test log is at sage.math.washington.edu:~justin/logs/log-4.0.1.rc1.

 The failure in the html test is as reported by others.

 The failure in the test for the birds is similar to the error I  
 previously reported: a mysterious error occurred this time (no  
 timeout).  The crash log (available on request) shows an illegal  
 instruction.  Oddly, the crashed thread seems to be in a semaphore  
 wait system call.  I don't see that the kernel throws an illegal  
 instruction signal during this call, but the kernel code is a bit  
 twisty...

 Repeated tests of this file will succeed and fail, more or less  
 randomly.

 Justin

 --
 Justin C. Walker, Curmudgeon-at-Large
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[sage-devel] Re: What can Magma do that Sage can't do?

[Kiran Kedlaya]

William mentioned an area dear to my heart:

On Jun 5, 10:47 pm, William Stein wst...@gmail.com wrote:
   * Magma's linear algebra over p-adics is better than in Sage.

 PROJECT: Design and implement good algorithms for linear algebra over
 p-adics (subtle and interesting research area).

There is actually some room for improvement in Magma's handling of p-
adics. Consider the following example:

 F := Qp(3, 10);
 M := Matrix([[F!1, F!2, F!1], [F!1, F!5, F!4], [F!4, F!8, F!1]]);
 CharacteristicPolynomial(M);
$.1^3 - (7 + O(3^10))*$.1^2 - (3^3 + O(3^10))*$.1 + 3^2 + O(3^10)

This is valid but not best possible. If you do a bit of row reduction
on the matrix you get

[1 + O(3^10) 2 + O(3^10) 1 + O(3^10)]
[0 + O(3^10) 3 + O(3^10) 3 + O(3^10)]
[3 + O(3^10) 6 + O(3^10) 0 + O(3^10)]

from which it is not hard to see that the determinant of M is actually
3^2 + O(3^11). (Divide the second and third rows by 3, and then you
can do all the arithmetic in Z/3^9 Z.)

The best way to handle this seems to be using Newton polygons, which
will have to wait for roed's p-adic polynomials code to come online.
After that, there is a nice project waiting here, which has important
applications to computing zeta functions of varieties using p-adic
cohomology (in which it is crucial to use as little working precision
as you can get away with, for efficiency).

Kiran
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[sage-devel] Re: Sage 4.0.1.rc0

[Kiran Kedlaya]

I have the same problem. Has the fix to #6209 been put in yet? I ran
into this problem when I was reviewing the FLINT spkg, but it seemed
to have been fixed the last time I downloaded the spkg (otherwise I
wouldn't have given a positive review!).

Kiran

On Jun 4, 11:51 am, William Stein wst...@gmail.com wrote:
 2009/6/4 Mike Hansen mhan...@gmail.com:

  Hello,

  Now that sage.math is back up, I've cut rc0 and put it in
  /home/mhansen/sage-4.0.1.rc0.tar.  All tests passed on sage.math.

 Thanks.  On OSX 32-bit it fails quickly when trying to buid FLINT:

 gcc -std=c99 -I/Users/was/build/sage-4.0.1.rc0/local/include/
 -I/Users/was/build/sage-4.0.1.rc0/local/include  -fPIC -funroll-loops
  -O3 -c ZmodF_mul-tuning.c -o ZmodF_mul-tuning.o
 gcc -std=c99 -I/Users/was/build/sage-4.0.1.rc0/local/include/
 -I/Users/was/build/sage-4.0.1.rc0/local/include  -fPIC -funroll-loops
  -O3 -c fmpz.c -o fmpz.o
 fmpz.c:40:29: error: zn_poly/zn_poly.h: No such file or directory
 make[2]: *** [fmpz.o] Error 1
 Failed to build FLINT dylib.

 real0m6.449s
 user0m5.773s
 sys 0m0.633s
 sage: An error occurred while installing flint-1.2.5
 Please email sage-develhttp://groups.google.com/group/sage-devel
 explaining the problem and send the relevant part of
 of /Users/was/build/sage-4.0.1.rc0/install.log.  Describe your
 computer, operating system, etc.
 If you want to try to fix the problem, yourself *don't* just cd to
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[sage-devel] Re: sage-4.0

[Kiran Kedlaya]

There's an spkg on track but it hasn't been reviewed yet. I was hoping
to look at it this weekend, but feel free to beat me to it. :)

Kiran

On May 30, 2:27 pm, simon.k...@uni-jena.de wrote:
 Hi William,

 On 30 Mai, 16:34, William Stein wst...@gmail.com wrote:

  I have release sage-4.0.  It's now available athttp://sagemath.org/src/.   
  Binaries will follow in a day.

 Wasn't it claimed (AFAIK off list by you or Michael Abshoff) that sage
 4.0 would contain Singular 3-1-0? It isn't there, the spkg is
 singular-3-0-4-4-20090511.spkg.
 Sniff :(

 Best regards
 Simon
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[sage-devel] Re: Sage 4.0.rc1 released!

[Kiran Kedlaya]

Besides numerical noise, I get a bunch of doctest failures triggered
by errors of the form

OSError: [Errno 12] Cannot allocate memory: '/scratch/sage-4.0.rc1/
tmp'

I think this is believed to be a known issue with Python 2.5 on Fedora
x86-64; see tickets #5218 and #6151, which I believe are due to be
addressed in 4.0.rc2.

Kiran

On May 28, 4:46 am, Mike Hansen mhan...@gmail.com wrote:
 Hello,

 Sage 4.0.rc1 has been released.  This should hopefully take care of
 the rest of the fallout from the switch to Pynac.  The tarball can be
 found at

 http://sage.math.washington.edu/home/mhansen/sage-4.0.rc1.tar

 and a copy of it to be used for upgrading can be found at

 http://sage.math.washington.edu/home/mhansen/release/4.0/rc1/sage-4.0...

 I will post the list of patches, authors, and reviewers later on.

 --Mike
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[sage-devel] Re: Taking a break from release management

[Kiran Kedlaya]

I think it's safe to say that without your work, we would be nowhere
near 4.0; having patches getting into releases so quickly was
reassuring to a lot of us that our work on those patches would not be
lost to bitrot. Enjoy a well-deserved vacation; I hope to see you back
in the forums soon thereafter!

Kiran

On May 25, 10:45 am, mabshoff mabsh...@googlemail.com wrote:
 Hello folks,

 for various reasons I am taking a break from release management. Post
 4.0.rc0 I have merged only a few patches that can be found in

  http://sage.math.washington.edu/home/mabshoff/release-cycles-4.0/rc1/

 and should simply be reimported. It would also be good if someone
 could deal with trac accounts since I am not likely to be around much
 in the next four weeks.

 Cheers,

 Michael
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[sage-devel] Re: Sage 4.0.rc0 released!

[Kiran Kedlaya]

On a fresh build on 64-bit Fedora 10 (Opteron), only one doctest
fails:

sage -t  devel/sage/sage/matrix/matrix2.pyx

due to numerical noise as follows:
**
File /scratch/sage-4.0.rc0/devel/sage/sage/matrix/matrix2.pyx, line
4964:
sage: m.change_ring(CDF).eigenvalues() # again for display
purposes
Expected:
[10.463115298 - 4.98835989975e-16*I, 7.42365754809 -
5.05298436852e-16*I, 3.36964641458 + 5.59670199836e-17*I,
1.25904669699 + 4.34508443713e-17*I, 0.00689184179485 -
5.75358699674e-17*I, 0.330700789655 + 5.1816322259e-16*I]
Got:
[10.463115298 - 3.57021884933e-16*I, 7.42365754809 +
2.91121322571e-17*I, 3.36964641458 - 1.54788874696e-16*I,
1.25904669699 - 5.01646753379e-17*I, 0.00689184179485 -
3.97030024181e-16*I, 0.330700789655 + 1.32245788594e-16*I]
**

Kiran

On May 21, 10:14 am, mabshoff mabsh...@googlemail.com wrote:
 Hi,

 I gotta run to the airport, but sources and upgrade bits of 4.0.rc0
 are in

http://sage.math.washington.edu/home/mabshoff/release-cycles-4.0/rc0/

 Once I get online I will post more info, but I am sure this will take
 a couple hours. Sorry.

 Cheers,

 Michael

 Merged in Sage 4.0.rc0:

 #6104: Michael Abshoff: Fix Solaris specific build issue for
 libfplll.spkg [Needs review]

 #3932: Ryan Dingman: generate size n trees in linear time [Reviewed by
 Robert Miller]
 #4875: Marshall Hampton: Polyhedron.show(fill=True) fails [Reviewed by
 David Perkison]
 #5076: David Roe: bug with (coercion in?) p-adic extension fields
 [Reviewed by Robert Bradshaw]
 #5120: Nicolas Thiery: An alternative implementation of the Unique
 Representation design pattern [Reviewed by David Roe]
 #5236: David Roe: x^(-pm) in ramified extensions of Qp [Reviewed by
 Kiran Kedlaya]
 #5554: Nick Alexander: implement cholesky_decomposition for matrices
 other than RDF [Reviewed by Rob Beezer, Michael Abshoff]
 #5581: Marshall Hampton: Face lattices and f-vectors for polytopes;
 bug fixes for polyhedra.py [Reviewed by David Perkison]
 #5619: Minh Van Nguyen: doctests for error messages in groebner_fan.py
 [Reviewed by Marshall Hampton]
 #5621: Minh Van Nguyen, Mike Hansen: doctests for calculus.py
 [Reviewed by John Palmieri]
 #5753: Burcin Erocal: update to pynac 0.1.4 [Reviewed by Mike Hansen]
 #5777: Burcin Erocal: update to pynac 0.1.6 [Reviewed by Mike Hansen]
 #5783: Nicolas Thiery: Lazy attribute fixes and improvements [Reviewed
 by David Roe]
 #5582: Robert Bradshaw: Coercion from float to QQ is missing [Reviewed
 by Jason Bandlow, Mike Hansen]
 #5837: Luiz Berlioz: bug in rational_diagonal_form() from
 QuadraticForm class [Reviewed by John Cremona, Gonzalo Tornaria]
 #5879: Dan Bump: Added crystal of letters for type E [Reviewed by Anne
 Schilling, Michael Abshoff]
 #5907: Gonzalo Tornaria, Carl Witty: incorrect fast_float evaluation
 of constant polynomials [Reviewed by Mike Hansen]
 #5930: Mike Hansen, William Stein, Carl Witty, Robert Bradshaw: switch
 from maxima to pynac for core symbolic manipulation system [Reviewed
 by Carl Witty, Robert Bradshaw, William Stein, Mike Hansen, Tom
 Boothby, Michael Abshoff]
 #5940: Emily Kirkman: graph theory -- bug in is_circular_planar
 [Reviewed by Robert Miller]
 #5944: Burcin Erocal: fix a nasty pynac bug in exp [Reviewed by Mike
 Hansen]
 #5954: Jon Hanke: Added documentation/doctests for all quadratic form
 genus symbol routines [Reviewed by Gonzalo Tornaria]
 #6088: Nicolas Thiery: LatticePolytope: Removed a try/catch which
 could involuntarily hide exceptions from lower code [Reviewed by
 Andrey Novoseltsev]
 #6029: Robert Bradshaw: bug in floor() for python types [Reviewed by
 Mike Hansen]
 #6035: Wilfried Huss: Don't draw vertical asympotes [Reviewed by
 Marshall Hampton]
 #6036: Kwankyu Lee: a bug in polynomial() for PolynomialRing(GF(5),2)
 [Reviewed by Mike Hansen]
 #6037: Jon Hanke: Major Upgrade to QuadraticForm Local Density
 Routines [Reviewed by Gonzalo Tornaria]
 #6040: Jon Hanke: Added Doctests for QuadraticForms methods [Reviewed
 by Gonzalo Tornaria]
 #6042: John Cremona: Bring doctests of modular/modsym/ambient.py up to
 100% [Reviewed by David Loeffler, Alex Ghitza]
 #6048: John Palmieri: fix non-ASCII character in mpolynomialsystem
 [Reviewed by Martin Albrecht]
 #6049: Jason Grout: bitset complement zeroes out last word if the
 bitset is a multiple of the word size [Reviewed by Carl Witty]
 #6052: Gonzalo Tornaria: partial_fraction_decomposition is broken for
 irreducible denominators [Reviewed by Mike Hansen]
 #6054: Mike Hansen: fix display2d with ecl on OSX [Reviewed by Michael
 Abshoff]
 #6059: Gonzalo Tornaria: speed regresion in hilbert_symbol after #5834
 [Reviewed by John Cremona]
 #6060: Fredrik Johansson: divmod fails when one argument is Integer
 and the other is a Python int [Reviewed by Mike Hansen]
 #6061: William Stein: refresh the pickle jar [Reviewed by Michael

[sage-devel] Re: Sage 4.0.alpha0 released!

[Kiran Kedlaya]

On May 16, 10:55 am, mabshoff mabsh...@googlemail.com wrote:
 As usual please build, doctest and report any issues.


All tests pass on my 64-bit Opteron box under Fedora 10.

Kiran

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[sage-devel] Re: Sage 3.4.2.rc0 release!

[Kiran Kedlaya]

Clean build on 64-bit Fedora 10 (Opteron) fails one doctest:

sage -t  devel/sage/sage/sets/primes.py
**
File /opt/sage/sage-3.4.2.rc0/devel/sage/sage/sets/primes.py, line
80:
sage: Px^2+x
Expected:
True
Got:
False
**
1 items had failures:
   1 of  12 in __main__.example_4
***Test Failed*** 1 failures.
For whitespace errors, see the file /opt/sage/sage-3.4.2.rc0/
tmp/.doctest_primes.py
 [1.7 s]
exit code: 1024

--
Kiran

On Apr 30, 8:23 am, mabshoff mabsh...@googlemail.com wrote:
 Hello folks,

 here goes 3.4.2.rc0 - a little later than planned, but it seems like
 we fixed all the issues (and more) that needed to be fixed. We finally
 merged the symbolic logic code written well over *18* months ago, but
 no doctests, no merge is something we take seriously. On top of that
 we are at

 Overall weighted coverage score:  71.1%
 Total number of functions:  22348
 We need  881 more function to get to 75% coverage.
 We need 1999 more function to get to 80% coverage.
 We need 3116 more function to get to 85% coverage.

 Note that this is also due to splitting DSage into its own spkg. We
 will discuss what to do with the DSage codebase at SD15 I assume.

 The source tarball, upgrade bits as well as a sage.math binary are in
 the usual place at

http://sage.math.washington.edu/home/mabshoff/release-cycles-3.4.2/

 I have done some preliminary build testing and it seems to at least
 build. From here on we will only merge truly critical bugs that fix
 doctests and grave issues, otherwise better luck in Sage 4.0 :).

 Please build, doctest and report any issues.

 Cheers,

 Michael

 Merged, but needs review:

 #5849: Michael Abshoff: Update MPIR to 1.1.1

 Merged in Sage 3.4.2.rc0:

 #545: Chris Gorecki: polish the new symbolic logic code [Reviewed by
 Minh Van Nguyen, Georg Weber, Wilfried Huss, Michael Abshoff]
 #2740: Robert Bradshaw: Downloading and uploading folders of
 worksheets [Reviewed by William Stein]
 #4435: John Palmieri: %latex -- don't use \usepackage{fullpage}
 [Reviewed by William Stein]
 #5479: Alex Ghitza: schemes/generic/spec.py: Spec.__call__ is
 basically not implemented [Reviewed by David Roe]
 #5588: John Palmieri: developer's guide: more information about
 docstrings [Reviewed by John Cremona]
 #5765: Alex Ghitza: improve doctest coverage for schemes/generic/
 algebraic_scheme.py [Reviewed by John Cremona]
 #5791: John Palmieri: Allow custom packages to be injected or %latex
 and the Sage latex mode [Reviewed by Rob Beezer]
 #5804: William Stein, Bill Hart, Michael Abshoff: Solaris 10/Sparc:
 number_of_partitions(10) is broken [Reviewed by Mike Hansen]
 #5820: Alex Ghitza: implement comparison of ring coercion morphisms
 [Reviewed by David Roe]
 #5824: William Stein: Move DSage to its own spkg [Reviewed by Michael
 Abshoff]
 #5846: Chris Wuthrich: small bug in caching the precision for p-adic L-
 series [Reviewed by Georg Weber]
 #5853: Chris Wuthrich: Restify and include more documentation on
 elliptic curves [Reviewed by John Cremona]
 #5855: Robert Miller: implement squarefree_divisors function [Reviewed
 by William Stein]
 #5856: Alex Ghitza: elliptic curves over Z/pZ are treated totally
 differently than elliptic curves over GF(p) [Reviewed by John Cremona]
 #5860: William Stein: delete sage/catalogue [Reviewed by David Harvey]
 #5877: Franco Saliola: calling a group character is broken [Reviewed
 by David Harvey]
 #5880: William Stein, Rob Beezer: notebook -- greatly reduce the
 number of actions that trigger taking a snapshot [Reviewed by Rob
 Beezer, William Stein]
 #5881: Mike Hansen: __cmp__ is random-ish in root_system/type_dual.py
 also (analog to #5811) [Reviewed by Michael Abshoff]
 #5890: Alex Ghitza: clean up schemes/elliptic_curves/ell_generic.py
 [Reviewed by John Cremona]
 #5896: Craig Ctiro: Documentation fix for lcalc interface [Reviewed by
 John Cremona]
 #5898: Karl-Dieter Crisman: Plot Field doc [Reviewed by Minh Van
 Nguyen]
 #5904: Alex Ghitza: improve doctest coverage for schemes/jacobians/
 abstract_jacobian.py [Reviewed by John Cremona]
 #5905: John Cremona: minor fix to ReST markup in ell_rational_field.py
 [Reviewed by John Palmieri]
 #5912: William Stein: %fortran mode is broken in the notebook
 [Reviewed by Chris Swierczewski]
 #5914: Robert Miller: default edge color is *invisible* [Reviewed by
 William Stein]
 #5918: Franco Saliola: bring doctest coverage for posets to 100%
 [Reviewed by Dan Drake]
 #5919: John Cremona: bug in conversion of polys over GF(2,e) from NTL
 to singular [Reviewed by Martin Albrecht]
 #5921: Alex Ghitza: factoring integer polynomials does not factor the
 content [Reviewed by John Cremona]
 #5926: William Stein: solaris top sometimes fails due to race
 condition [Reviewed by Michael Abshoff]
 #5928: 

[sage-devel] Re: Sage 3.4.1.rc2 released

[Kiran Kedlaya]

Built from scratch on Fedora 10 (64-bit Opteron 250), failed two
doctests on the first try:

sage -t  devel/sage/sage/calculus/calculus.py
sage -t  devel/sage/sage/calculus/equations.py

both on timeouts. I tried them both individually: equations.py ran in
30 seconds, calculus.py took long enough that I didn't have the
patience to let it finish (I killed it after 288 seconds).

Kiran

On Apr 11, 4:22 am, mabshoff mabsh...@googlemail.com wrote:
 Hello,

 this is 3.4.1.rc2. Loads of Solaris fixes for doctests, additional
 doctests, several spkg updates and misc fixes. All the details can be
 seen in the list below, but note that the number of patches merged is
 much larger than originally intended and announced. This build will be
 the basis of Doc Day 4 this Saturday, so if you plan to participate
 please build this as soon as possible. As usual a sage.math binary,
 the sources and the update tree are all available at or in

http://sage.math.washington.edu/home/mabshoff/release-cycles-3.4.1/

 Compared to 3.4.1.rc1 two doctests failures were fixed, but it seems
 that a new OSX and Solaris specific one popped up:

 bsd:sage-3.4.1.rc2 mabshoff$ ./sage -t  devel/sage/sage/rings/
 infinity.py
 sage -t  devel/sage/sage/rings/infinity.py
 **
 File /Users/mabshoff/sage-3.4.1.rc2/devel/sage/sage/rings/
 infinity.py, line 408:
 sage: CDF(-infinity)
 Expected:
 -infinity
 Got:
 +infinity
 **

 This is now #5748. Tomorrow should bring plenty of doctest patches and
 merges, so a 3.4.1.rc3 is in the card. My main goal is to fix some
 ATLAS issues, downgrade GAP and update clisp and enable the no
 readline option for Maxima.

 Please build, test and report any failures you do find. It is now
 planned to get this release out as soon as possible with the bounty
 from DocDay 4 since tomorrow a months will have passed since the
 release of Sage 3.4.

 Cheers,

 Michael

 3.4.1 Blockers:

  * #5219: Build ATLAS in dist mode with SSE2 only
  * #5559: roots issue on fedora core 32-bit and gcc 4.3.3
  * #5662: Gonzalo Tonoria: [with patch, needs review] Timing issue in
 clisp-readline (Nasty hang (deadlock?) in maxima pexpect interface on
 core 2 quad
  * #5697: downgrade GAP due to Itanium issues
  * #5702: make make check  friends doctest the documentation too
  * #5741: Detect Atom CPUs as Core2 in the ATLAS detection script
  * #5742: ATLAS.spkg: parallel make breaks on system with real sh
  * #5743: Solaris 10/Sparc: Fix numerical noise issues in doctests
  * #5748: Sage 3.4.1.rc2: isinf() related doctest failure in sage/
 rings/infinity.py

 Merged in Sage 3.4.1.rc2:

 #673: William Stein: Solaris 10: rings/complex_double.pyx doctests
 failure: inf vs. Infinity [Reviewed by Michael Abshoff]
 #1595: William Stein: do something about the pari overflow test
 [Reviewed by Michael Abshoff]
 #3812: Nick Alexander: add apply_morphism to ideal [Reviewed by John
 Cremona]
 #5002: Anne Schilling: CrystalOfTableaux call method breaks on
 legitimate data [Reviewed by Dan Bump]
 #5140: Lars Fischer, John Cremona: is_irreducible() reports units as
 irreducible [Reviewed by Alex Ghitza]
 #5156: William Stein: implement computation of the conjectural
 (analytic) order of Sha for elliptic curves over Heegner quadratic
 imaginary fields [Reviewed by Robert Miller, John Cremona]
 #5230: Bill Cauchois: implement boundary_style parameter for
 parametric 3d plots [Reviewed by William Stein]
 #5306: Maite Aranes: More number field ideal utilities [Reviewed by
 John Cremona, David Loeffler]
 #: John Palmieri: make some TeX macros available to docstrings
 [Reviewed by Dan Drake]
 #5606: Robert Bradshaw: color complex plotting [Reviewed by William
 Stein]
 #5628: Gonzalo Tornaria, William Stein: work arroud annoying false
 positive SSE4a sage-flags.txt issue [Reviewed by Michael Abshoff]
 #5678: Golam Mortuza Hossain: LaTeX typesetting for two letters phi
 and Phi [Reviewed by John Palmieri]
 #5689: William Stein: hitting control c while computing pi results in
 wrong answers later [Reviewed by Michael Abshoff]
 #5693: William Stein: sloane_sequence -- very confusing error message
 [Reviewed by Jaap Spies]
 #5694: William Stein: _ for previous output is completely broken in
 the notebook due to the preparser [Reviewed by Robert Bradshaw]
 #5695: Michael Abshoff: Sage 3.4.1.rc1: doctest failure in combinat/
 words/words.py on 32 bit boxen [Reviewed by Jaap Spies]
 #5696: Michael Abshoff: update libpng to latest release (security)
 [Reviewed by Mike Hansen]
 #5698: William Stein, Bill Hart: Sage 3.4.1.rc1: doctest failure in
 schemes/elliptic_curves/monsky_washnitzer.py [Reviewed by Michael
 Abshoff]
 #5699: William Stein: notebook -- %r mode is completely broken
 (trivial to fix) [Reviewed by Mike Hansen]
 #5703: William Stein: notebook -- fix major bug introduced by #5687
 

[sage-devel] Re: Fedora 10 binary of Sage 3.4 doesn't work

[Kiran Kedlaya]

I had a similar problem building from source, but running make just
now seems to have fixed it. (FYI, my 64-bit office machine, formerly
of RHEL5 fame, now runs Fedora 10.)

Kiran

On Mar 14, 12:45 pm, William Stein wst...@gmail.com wrote:
 On Sat, Mar 14, 2009 at 9:43 AM, mabshoff mabsh...@googlemail.com wrote:

  On Mar 14, 8:20 am, Carl Witty carl.wi...@gmail.com wrote:

  Hi Carl,

  The tar 
  filehttp://www.sagemath.org/bin/linux/64bit/sage-3.4-linux-Fedora_release...
  is missing big chunks of Sage (for instance, there's nothing in
  local/lib/python2.5/site-packages/Jinja*).  (The tar file is about
  40MB smaller than other 64-bit Linux builds, so presumably there's a
  lot of stuff missing.)

  This should be fixed now. Thanks for reporting it.

 But Carl -- please test again :-)

 William
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[sage-devel] Re: Cardinality of a set...

[Kiran Kedlaya]

Just to make life complicated, have a look at

http://en.wikipedia.org/wiki/Positive_number

and then

http://fr.wikipedia.org/wiki/Nombre_positif

Yes, it seems that positive means 0 in English and =0 in French.
(I suppose nonnegative means =0 in English and 0 in French. The
French for 0 is strictement positive).

Kiran

mabshoff wrote:
 On Feb 26, 5:26 am, Ralf Hemmecke r...@hemmecke.de wrote:
   Please vote for your favorite names:
    - NaturalNumbers
    - Naturals
    - NaturalIntegers
    - NonNegativeIntegers
   /
    - PositiveNaturals
    - PositiveIntegers
 
  If I'd have a say... then I would choose NonNegativeInteger and
  PositiveIntegers, because nobody agrees on whether or not 0 is a natural
  number. So with NNI and PI one would avoid that confusion.

 +1

 In Dortmund there is a regularly given class about non-negative
 matrices and way back as a beginning student in math this seemed like
 an odd title to me until I thought about it for a second. There is no
 ambiguity there, so that is a good thing.

  Ralf

 Cheers,

 Michael
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[sage-devel] Re: Sage 3.3.alpha1 released

[Kiran Kedlaya]

All tests pass on my Opteron 64-bit RHEL5 box.

Kiran

On Jan 23, 1:55 pm, mabshoff mabsh...@googlemail.com wrote:
 On Jan 23, 10:11 am, Nick Alexander ncalexan...@gmail.com wrote:

 Hi,

  This credit is incorrect.  The patch was reviewed by Martin Albrecht.

  #2789: Nick Alexander: multivariate polynomials over residue fields of
  number fields are broken [Reviewed by Nick Alexander]

 Oops, which idiot wrote that in the release notes? :), Since Nick
 wrote and reviewed his own patch I have to removed that code at once
 from 3.3.alpha2 :p

 Anyway, thanks for pointing that out and I has been corrected in my
 notes for 3.3.alpha2. I am somewhat certain that my error rate on
 credit will be above average in this release since I have not slept a
 whole lot and it has been a while since I merged 50+ in a single six
 hour or so session. I plan to sit down after SD12 and make sure that
 all credit has been properly assigned since I want to compile detailed
 statistics about what happened at SD12 since it seems to be working
 out really well.

  Nick

 Cheers,

 Michael
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[sage-devel] Re: Sage 3.2.2.rc1 released

[Kiran Kedlaya]

I get the same failure in multi_polynomial_ideal.py in 64-bit RHEL5
(and nothing else).

Kiran

On Dec 17, 4:43 pm, Jaap Spies j.sp...@hccnet.nl wrote:
 mabshoff wrote:
  On Dec 17, 1:27 pm, Jaap Spies j.sp...@hccnet.nl wrote:
  Jaap Spies wrote:

  Hi Jaap,

  --
  The following tests failed:
     sage -t  
  pha2/devel/sage/sage/rings/polynomial/multi_polynomial_ideal.py # 1 
  doctests failed
  --
  Total time for all tests: 4613.0 seconds
  I don't like the prefix pha2 :(!  I prefer the possibility to copy and 
  paste in a new test.

  Hmm, looks like a line wrap, but I guess this might be a side effect
  of #4811. Can you post the actual full failure of that test, i.e
  showing how you invoke the test and so on?

 Hi Michael,

 [j...@paix sage-3.2.2.alpha2]$ ./sage -t  
 devel/sage/sage/rings/polynomial/multi_polynomial_ideal.py # 1 doctests failed
 sage -t  devel/sage/sage/rings/polynomial/multi_polynomial_ideal.py
 **
 File 
 /home/jaap/work/downloads/sage-3.2.2.alpha2/devel/sage/sage/rings/polynomi 
 al/multi_polynomial_ideal.py, line 58:
      sage: S.a,b = R.quotient((x^2 + y^2, 17))
 Expected:
      verbose 0 ... Warning: falling back to very slow toy implementation.
 Got nothing
 **
 1 items had failures:
     1 of  47 in __main__.example_0
 ***Test Failed*** 1 failures.
 For whitespace errors, see the file 
 /home/jaap/downloads/sage-3.2.2.alpha2/tmp/.doctest_multi_polynomial_ideal. py
          [16.5 s]
 exit code: 1024

 --
 The following tests failed:

         sage -t  devel/sage/sage/rings/polynomial/multi_polynomial_ideal.py
 Total time for all tests: 16.5 seconds

 At the end of ./sage -tp 2 devel/sage/sage

 I got

   --
  
   The following tests failed:
  
     sage -t  pha2/devel/sage/sage/rings/polynomial/multi_polynomial_ideal.py 
 # 1 doctests failed
   --

 Jaap
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[sage-devel] Re: Sage 3.2.1.rc1 released

[Kiran Kedlaya]

This is also the unique doctest failure under RHEL5 on my 64-bit
Opteron box (upgraded from rc0).

Kiran

On Dec 1, 10:35 am, Jaap Spies [EMAIL PROTECTED] wrote:
 mabshoff wrote:

  On Dec 1, 7:27 am, Jaap Spies [EMAIL PROTECTED] wrote:
  mabshoff wrote:

  SNIP

  Upgrade from rc0 on Fedora 9 has the known issues in
  sage/rings/polynomial/multi_polynomial_ideal.py

  Jaap

  Hi Jaap,

  can you repost the output? I made another one of those GBasis over ZZ
  computations optional for now since I observed different results on
  various boxen.

 sage -t  devel/sage/sage/rings/polynomial/multi_polynomial_ideal.py
 **
 File 
 /home/jaap/work/downloads/sage-3.2.1.alpha2/devel/sage/sage/rings/polynomi 
 al/multi_polynomial_ideal.py, line 58:
      sage: S.a,b = R.quotient((x^2 + y^2, 17))
 Expected:
      verbose 0 ... Warning: falling back to very slow toy implementation.
 Got nothing
 **
 1 items had failures:
     1 of  47 in __main__.example_0
 ***Test Failed*** 1 failures.
 For whitespace errors, see the file 
 /home/jaap/downloads/sage-3.2.1.alpha2/tmp/.doctest_multi_polynomial_ideal. py
          [13.6 s]
 exit code: 1024

 The other M2 issue seems to be gone!

 Jaap

  Cheers,

  Michael
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[sage-devel] Re: Hilbert Class Polynomial function in SAGE...

[Kiran Kedlaya]

For the record, Drew Sutherland (cc'd on this) has some screamingly
fast code for the CRT method, which he spoke about at ECC this year.

Kiran

eduardo wrote:
 Hi there!

 I attended the SAGE DAYS 10 in Nancy (Thanks the people there for
 everything!). As other colleague and me are interested in crypto
 interesting Elliptic Curves, we noticed that the SAGE function that
 calculates the Hilbert class polynomial needs magma, so we proposed at
 the
 Coding Sprint the implementation of this function, for instance with
 CM
 Methods or/and the CRT Methods. After some time spending on it we got
 some issues that surely can be corrected with some help/discussion:

 We implemented the CM-version of it in purely sage-python code.
 Comparing timings with Magma our implementation was almost (here)-
 times
 slower. So we can emphasize 3 bottlenecks apart from computation of a
 j-Invariant: the computation of the appropriate precision, generating
 of all
 different reduced primitive quadratic forms and the using of Python.

 1. An idea of the computation of the appropriate precision we
 gathered
 from Andreas Enge's article  [http://hal.inria.fr/inria-1040]. He
 gives
 an upper bound for the size of the largest coefficient of the
 polynomial.

 2. To generate all reduced primitive quadratic forms we used first the
 function
 called BinaryQF_reduced_representatives() from quadratic forms
 library. After
 that we implemented our version of this function and got about 50%
 speed up,
 and the present code doesn't generate primitive forms if the
 discriminant is
 non-fundamental.

 3. But anyway our implementation was a snail comparing to magma's one.
 And then
 we tried to use Cython to implement the same function. As a result
 our
 implementation was a bit faster than magma's at least in experiments
 we ran.
 The only thing worried us was the using of type long long for
 discriminant of
 quadratic field. It means the input parameter is bounded by 2^63. It
 is
 O.K. for D around -2^63; even magma will break down since the
 complexity
 of the algorithm is O(|D|).

 Now I would like to ask some questions:
 * Shall we consider the bigger value of D then values fit in long
 long?
 * Is it safe to use long long? Is it 64-bit on all platforms?
 Does Cython care about that?
 * We can perhaps use mpz_t (from GMP) instead of long long. Then we
 need
 to know how can we input/ouput a variable of this type in Cython. Is
 there
 some documentation about that?

 thanks in Advance!

 cheers
 Ed
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[sage-devel] Re: MSRI SAGE Days on Algebraic Geometry this March

[Kiran Kedlaya]

The announced dates overlap the proposed dates for the Sage Days at
Georgia (right before the Arizona Winter School). Does this mean that
there will be more than one Sage Days conference going on at once? (If
so, surely world domination is not long behind.)

Kiran

William Stein wrote:
 Hi!

 There's going to be a surprise Sage Days at MSRI this March 2009 on
 Algebraic Geometry.  See

 http://www.msri.org/calendar/workshops/WorkshopInfo/502/show_workshop

 for the preliminary web page.   Funding is available.

 William

 --
 William Stein
 Associate Professor of Mathematics
 University of Washington
 http://wstein.org
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[sage-devel] Factoring multivariate polynomials over Z

[Kiran Kedlaya]

The following is apparently not implemented (see 3.1.2 traceback at
bottom):
---
sage: R.x1, x2 = PolynomialRing(Integers(), 2)
sage: (x1*x2).factor()
---
However, I think it would be trivial to implement: change the base
ring of the polynomial to Rationals() and then factor. I believe the
result returned by Singular is then guaranteed to have integer
coefficients, so it can be coerced back.

Can someone more familiar with Singular confirm that? And if I am
correct, would it be worth hacking factor() to enable this?

Kiran
---
TypeError Traceback (most recent call
last)

/home/sdb1/r1/kedlaya/ipython console in module()

/scratch/sage-x64/local/lib/python2.5/site-packages/sage/rings/
polynomial/multi_polynomial_element.py in factor(self)
   1349 pass
   1350
- 1351 R._singular_().set_ring()
   1352 S = self._singular_().factorize()
   1353 factors = S[1]

/scratch/sage-x64/local/lib/python2.5/site-packages/sage/rings/
polynomial/polynomial_singular_interface.py in _singular_(self,
singular, force)
172 return R
173 except (AttributeError, ValueError):
-- 174 return self._singular_init_(singular, force)
175
176 def _singular_init_(self, singular=singular_default,
force=False):

/scratch/sage-x64/local/lib/python2.5/site-packages/sage/rings/
polynomial/polynomial_singular_interface.py in _singular_init_(self,
singular, force)
243
244 else:
-- 245 raise TypeError, no conversion to a Singular ring
defined
246
247 return self.__singular

TypeError: no conversion to a Singular ring defined

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[sage-devel] Re: Zeta functions for schemes over F_p

[Kiran Kedlaya]

For the record, a version of my generic code (with a bit of help from
craigcitro) has been merged into 3.0.1alpha1, as ticket #3031. Anyone
now interested in tackling #793 should let me know.

Kiran

On Apr 15, 1:56 pm, Kiran Kedlaya [EMAIL PROTECTED] wrote:
 There is an old ticket #793 about implementing a zeta_function method
 for hyperelliptic curves. Such a method would have to have a default
 behavior in case none of the special-purpose methods we have already
 implemented are appropriate.

 So I thought I'd try writing a generic method for schemes over finite
 fields. Unfortunately, it's limited right now to schemes over prime
 fields because it requires at least a random coercion from F_q to
 F_{q^n}, which we don't yet support for q composite. (Maybe soon...)

 It's also a bit stupid because it counts rational points over F_q by
 actually constructing the list of them. Better would be to construct a
 scheme consisting of these points and then compute the length of this
 over the field. For example, if your scheme were the affine scheme
 V(I) for I an ideal in F_q[x_1, ..., x_n], you could form the ideal J
 = I + (x_1^q - x_1, ..., x_n^q-x_n) and then call
 J.vector_space_dimension().

 But in any case, see
    http://math.mit.edu/~kedlaya/Zeta_functions.sws
 for a notebook containing what I have so far. Comments and
 improvements welcome...

 Kiran
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[sage-devel] Re: fast linear algebra over cyclotomic fields

[Kiran Kedlaya]

Is the strategy to work multimodularly using completely split primes?
Or does someone have a better idea?

Kiran

On Apr 25, 5:46 pm, Craig Citro [EMAIL PROTECTED] wrote:
 I'm in.

 -cc

 -- Forwarded message --
 From: William Stein [EMAIL PROTECTED]
 Date: Fri, Apr 25, 2008 at 10:48 AM
 Subject: [sage-devel] fast linear algebra over cyclotomic fields
 To: sage-devel@googlegroups.com sage-devel@googlegroups.com

  Hi,

  Is anybody interested in helping me to implement very fast linear algebra 
 over
  cyclotomic number fields?

  We're going to need this big time for

      http://wiki.l-functions.org/School2008

  and

      http://wiki.l-functions.org/LfunctionsAndModularFormsII

   -- William

  --
  William Stein
  Associate Professor of Mathematics
  University of Washington
  http://wstein.org
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[sage-devel] Re: Sage 3.0.alpha5 released

[Kiran Kedlaya]

All tests pass on 64-bit RHEL (Opteron), and no more segfaults at exit
either.

Kiran

mabshoff wrote:
 Hello folks

 here we go with 3.0.alpha5. So, that happened to 3.0.alpha4? It was
 never announced in public since it was a snapshot I initially
 considered
 potentially unstable, but that didn't happen. We have closed a total
 of *221* tickets so far. This alpha should build and doctest without
 any significant problems [famous last words]. All the mysterious
 segfaults at exit should be fixed. Besides numerous fixes to padics
 and
 the notebook there were also a boat load of other fixes. The  most
 visible change to users should be the gcc 4.3 support out of the box.
 This release has been build tested on x86-64 Arch Linux. The only
 thing
 needed is to use the system's Fortran compiler by setting
 SAGE_FORTRAN
 and SAGE_FORTRAN_LIB - see the README.txt. The list of blockers has
 gotten much shorter and we should start winding things down for the
 final 3.0 release. On the list of goals we still need 64 bit OSX
 support
 which is doable and the merge of the benchmarking code. Stay tuned
 for the next alpha coming soon ;)

 Sources and binaries are in the usual place:

 http://sage.math.washington.edu/home/mabshoff/release-cycles-3.0/sage-3.0.alpha5.tar

 http://sage.math.washington.edu/home/mabshoff/release-cycles-3.0/sage-3.0.alpha5-sage.math-only-x86_64-Linux.tar.gz

 Cheers,

 Michael


 List of blockers:
  * #2303: bessel_I(1,1,scipy) segfaults with gcc 4.2.3 on Linux x86
   [nobody has been able to reproduce this so far. gcc 4.2.3
on x86-64 does not have this problem]
  * #2344: python -- upgrade to version 2.5.2 [the spkg works fine,
   but causes a segfault in integer.pyx on OSX. Getting this
   spkg is essential for the 64 bit OSX port]
  * #2592: NTL abort in Integers(125)[]
  * #2877: security risk -- several constructors use eval to parse
 input

 Memory leaks:
  * _fast_eval
  * PolyBoRi
  * latin squares

 Merged in alpha5:

 #449: Michael Abshoff: lcalc Solaris build fixes
 #848: Alex Ghitza: Using strings for infinity in GSL
 #1626: Michael Abshoff: update lcalc to 20080205, add gcc 4.3 support
 #1763: Alex Ghitza, Didier Deshommes: implement norms for matrices
 #1766: Dan Drake, Harald Schilly, Mike Hansen: enhancing latex
embedding with plots
 #2195: Willem Jan Palenstijn: odd Givaro-related crash in finite
 fields
 #2219: Alex Ghitza: docs for root_field should say the polynomial
 needs
to be irreducible
 #2347: Robert Bradshaw: better parsing for symbolics
 #2616: Didier Deshommes: Replace all matrix.submatrix() instances
 #2704: Martin Albrecht: bug in lcm(a,b) for a,b polynomials in QQ[]
if a is constant
 #2850: Chris Swierczewski: Docstrings and doctests for permgroup.py
 #2851: William Stein: clean binary install of sage followed by
sage -br is broken
 #2857: Didier Deshommes: numerical_approx for matrices
 #2875: William Stein: notebook -- save_session is completely broken
in the notebook
 #2879: John Voight: Bug fix in totallyreal_rel
 #2880: John Cremona: Special code for elliptic curve cardinality for
j=0 and j=1728
 #2901: William Stein: rewrite load_session and save_session to use
much better modern techniques (in particular merge the
 notebook
and non-notebook implementations)
 #2904: Didier Deshommes: sage/matrix/matrix_misc.py has no copyright
info
 #2905: Gary Furnish: Various speedups
 #2911: Michael Abshoff: Use $@ instead of $* in sage-* local/bin
 #2912: Martin Albrecht: M4RI should be built with -O3
 #2913: William Stein: notebook -- deleting a running cell results in
a bug
 #2914: William Stein: integers are immutable but set_str breaks that;
having this function is a *major* bug.
 #2915: Mike Hansen, William Stein: bug in symbolic integration or
stupid bug in the sage/maxima interface?
 #2916: Willem Jan Palenstijn: invalid coercion between non-prime
 finite
fields
 #2917: William Stein: internal server error in notebook
 sage-3.0.alpha4
 #2919: Michael Abshoff: gcc 4.3: compilation issues in partitions_c.cc
 #2920: Michael Abshoff: gcc 4.3: fix rubiks.spkg build
 #2921: Michael Abshoff: gcc 4.3: Fix flintqs.spkg build
 #2923: Michael Abshoff: gcc 4.3: matplotlib build fix
 #2924: William Stein: programming guide section on style is terrible!
 #2925: Michael Abshoff: gcc 4.3: givaro-3.2.10.rc3 is broken
 #2927: Michael Abshoff: gcc 4.3: make Singular.spkg compile
 #2929: Michael Abshoff: gcc 4.3: fix gmp.spkg
 #2931: Michael Abshoff: gcc 4.3: fix linbox.spkg compilation

 Merged in alpha4:

 #1689: William Stein, Michael Abshoff: document SAGE_FORTRAN_LIB
 #1948: John Cremona, Alex Ghitza: K.factor_integer needs a name
 change,
since now it does much more
 #2199: Tim Abbott, Michael Abshoff: Copyright files for Debian
 packages
 #2394: Tom Boothby: Wrap Cremona's newforms class
 #2590: Jason Grout: plotting a line 

[sage-devel] sage -n?

[Kiran Kedlaya]

Currently the command-line option to start sage directly in (secure)
notebook mode is -notebook. What do people think of adding a shorter
alternative, such as sage -n? If people are wary about assigning
single-letter options, then sage -nb is another possibility.

Kiran

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[sage-devel] Zeta functions for schemes over F_p

[Kiran Kedlaya]

There is an old ticket #793 about implementing a zeta_function method
for hyperelliptic curves. Such a method would have to have a default
behavior in case none of the special-purpose methods we have already
implemented are appropriate.

So I thought I'd try writing a generic method for schemes over finite
fields. Unfortunately, it's limited right now to schemes over prime
fields because it requires at least a random coercion from F_q to
F_{q^n}, which we don't yet support for q composite. (Maybe soon...)

It's also a bit stupid because it counts rational points over F_q by
actually constructing the list of them. Better would be to construct a
scheme consisting of these points and then compute the length of this
over the field. For example, if your scheme were the affine scheme
V(I) for I an ideal in F_q[x_1, ..., x_n], you could form the ideal J
= I + (x_1^q - x_1, ..., x_n^q-x_n) and then call
J.vector_space_dimension().

But in any case, see
   http://math.mit.edu/~kedlaya/Zeta_functions.sws
for a notebook containing what I have so far. Comments and
improvements welcome...

Kiran

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[sage-devel] Re: Preliminary Sage Days Announcements

[Kiran Kedlaya]

The Joint Meetings are themselves fairly early (Jan 5-8). Does fairly
early in January mean before or after that? Before might be awkward
because of the New Year's holiday.

Kiran

On Apr 13, 6:51 am, David Joyner [EMAIL PROTECTED] wrote:
 On Sun, Apr 13, 2008 at 2:13 AM, William Stein [EMAIL PROTECTED] wrote:

   Hello Sage Devel,

   1. There will be a Sage Days in January 2009 in San Diego, CA.  The
   exact dates haven't
   been determined yet, though it will probably be fairly early in January.

 AFAIK, there is no word yet on the SAGE presence at the Jan 2009 AMS
 national meeting in
 Washington DC. If anyone on this list knows anything more, please post.



   2. There will be a Sage Days in Athen, Georgia at University of Georgia 
  (UGA)
   March 7 - 13, 2009 mainly on quadratic forms and lattices.   Mark your
   calendars.
   Jon Hanke will be our host, there will be funding, etc.  More details
   to come later.
   (Note for number theorists, this is right before the Arizona Winter 
  School.)

    -- William

   --
   William Stein
   Associate Professor of Mathematics
   University of Washington
   http://wstein.org
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[sage-devel] Noncanonical coercion (finite fields)

[Kiran Kedlaya]

Any opinions about what

sage: F9.a = GF(9); F81.b = GF(81); F81(a)

should return? There is no canonical answer, so it may be better to
throw an exception rather than pick one of the two correct answers.
But any of these would be better than the current behavior, which is
to return 0.

Kiran


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[sage-devel] Re: p-adic crash error

[Kiran Kedlaya]

It was pointed out (by mabshoff, I think) that ticket #2592 may be a
similar issue, so we might be able to knock that one off now. In other
news, #2325 was fixed by this page, so it as well as #2843 have now
been closed.

Kiran

David Roe wrote:
 No, I forgot to change it back.  Use the patch I posted instead, which
 changes all the eis_shift_a's back to eis_shift.  The p-adics folder
 passes sage -t now.
 David

 On Thu, Apr 10, 2008 at 8:53 PM, mabshoff
 [EMAIL PROTECTED] wrote:
 
 
 
   On Apr 11, 12:35 am, David Roe [EMAIL PROTECTED] wrote:
I think Willem fixed this bug.  I've made the same change a few other
places and added a doctest.
David
 
   Hi David,
 
   I posted a one line patch to make you patch compile. It is attached to
   #2843. Can you have a look? craigcitro just said in IRC that you
   intend to remove the extra _a
 
   Cheers,
 
   Michael
 
 
  
 
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[sage-devel] Re: hyperlinks for Colloquy users

[Kiran Kedlaya]

+1 (on the error message)

Kiran

On Apr 9, 9:12 am, David Harvey [EMAIL PROTECTED] wrote:
 Yi,

 This sounds like a much better approach than what I did, but when I  
 run that I get an error message about not being able to find the objc  
 module?

 david

 On Apr 9, 2008, at 2:54 AM, Yi Qiang wrote:



  Hey,
  I thought this was a great idea but I found the patching Colloquy
  approach to be a bit hardcore, especially since it does the wrong
  things for channel urls in other channels.

  I whipped up a quick python plugin using Colloquy's plugin framework.
  To install it, just drop it into ~/Library/Application
  Support/Colloquy/PlugIns/ and type /reload plugins or restart
  Colloquy.

  You can get the plugin here:

 http://yiqiang.org/sage-devel-trac.py

  Cheers,
  Yi

 http://yiqiang.org 

  On Fri, Apr 4, 2008 at 10:22 AM, David Harvey  
  [EMAIL PROTECTED] wrote:

   Hi all,

   This message is for Sage developers who use the Colloquy IRC chat
   client.

   I have patched Colloquy so that text like #1234 gets  
  hyperlinked to
   the sage trac server.

   Here is the patch file, which should get applied to the file Panels/
   JVDirectChatPanel.m in the root of the colloquy tree (you can get  
  the
   original source via svn from the main colloquy web site):

     http://math.harvard.edu/~dmharvey/sage-colloquy.patch

   Also I made a binary. I think I made it Universal. But really I have
   no idea what I'm doing, since I don't really know how to use XCode,
   but it seems to work for me (OSX 10.4.11, intel):

     http://math.harvard.edu/~dmharvey/Colloquy.app.zip

   david
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[sage-devel] p-adic crash error

[Kiran Kedlaya]

Jen Balakrishnan spent time with some of the usual suspects during the
Arizona Winter School tracking down bugs in the p-adics, but more
remain. We've isolated a code snippet that makes sage 2.11 go boom on
multiple platforms:
{{{
sage: R.x = QQ[]
sage: K = Qp(11,10)
sage: J.a = K.extension(x^30-11)
sage: M.t = PowerSeriesRing(J)
sage: S.x,y = QQ[]
sage: xr = O(a^152)*t + (8*a^2 + 10*a^32 + 7*a^62 + 10*a^92 + 7*a^122
+ O(a^152))*t^2 + O(a^154)*t^3 + (2*a^4 + 10*a^64 + 2*a^124 +
O(a^154))*t^4 + O(a^156)*t^5 + (5*a^6 + 2*a^96 + a^126 + O(a^156))*t^6
+ O(a^158)*t^7 + (7*a^8 + 6*a^38 + 8*a^68 + 2*a^98 + 5*a^128 +
O(a^158))*t^8 + O(a^160)*t^9 + (8*a^10 + 10*a^40 + a^70 + 5*a^130 +
O(a^160))*t^10 + O(a^162)*t^11 + (9*a^12 + 7*a^42 + 8*a^72 + 6*a^102 +
9*a^132 + O(a^162))*t^12 + O(a^164)*t^13 + (2*a^14 + 5*a^44 + 3*a^74 +
a^104 + 4*a^134 + O(a^164))*t^14 + O(a^166)*t^15 + (2*a^16 + 5*a^46 +
8*a^76 + 5*a^106 + 7*a^136 + O(a^166))*t^16 + O(a^168)*t^17 + (7*a^18
+ 3*a^48 + 6*a^78 + 9*a^138 + O(a^168))*t^18 + O(a^172)*t^19 + (7*a^50
+ 3*a^80 + 5*a^110 + 5*a^140 + 7*a^170 + O(a^172))*t^20 +
O(a^172)*t^21 + (a^22 + a^52 + 3*a^82 + 3*a^112 + 2*a^142 +
O(a^172))*t^22 + O(a^174)*t^23 + (4*a^24 + 7*a^54 + 9*a^84 + 4*a^114 +
7*a^144 + O(a^174))*t^24 + O(a^176)*t^25 + (3*a^26 + 8*a^56 + 8*a^116
+ 5*a^146 + O(a^176))*t^26 + O(a^178)*t^27 + (2*a^28 + 2*a^58 + 6*a^88
+ a^118 + 10*a^148 + O(a^178))*t^28 + O(a^180)*t^29 + (8*a^30 + 5*a^60
+ 8*a^90 + 5*a^120 + 6*a^150 + O(a^180))*t^30 + O(a^184)*t^31 +
(7*a^62 + 9*a^92 + 2*a^182 + O(a^184))*t^32
sage: yr = xr^2
sage: dtr = xr.derivative()
sage: f_dtr = yr*dtr # boom
FFTRep: inconsistent use
(and then sage exits uncleanly)
}}}
I wasn't able to find a shorter value of xr that reproduces this
(removing the t^32 term alleviates the error).

We've opened ticket #2843 for this.

Kiran


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[sage-devel] Re: plot taking a very, very long time

[Kiran Kedlaya]

For the record, I ran into more or less the same phenomenon a couple
of days ago, and again floor() was the culprit.

Kiran

On Apr 6, 1:16 pm, mabshoff [EMAIL PROTECTED]
dortmund.de wrote:
 On Apr 6, 7:05 pm, Jaap Spies [EMAIL PROTECTED] wrote:



  mabshoff wrote:

   On Apr 6, 6:36 pm, Jaap Spies [EMAIL PROTECTED] wrote:
   In the notebook of sage-2.11:

   time plot(1.0 - x * floor(1/x), (x,0.1,1.0)

   CPU time: 143.77 s,  Wall time: 1660.39 s

   with a correct image.

   Maple is almost immediate.

   Even worse:
   time plot(1.0 - x * floor(1/x), (x, 0.0, 1.0), plot_points=1000)

   CPU time: 244.71 s,  Wall time: 5155.23 s

   Thoughts? See trac ticket #2831

   Hi Jaap,

   The problem is that floor(1/x) calls maxima. If you drop it the
   whole thing takes about a second.

  Yes, I know. But why should I drop it, if this is what I want to plot!

 This indicates that _fast_eval is not used. I assume it doesn't have a
 floor() method or if it has one it isn't used. That is the bug.

  Jaap

 Cheers.

 Michael
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[sage-devel] Re: Sage 2.11.alpha2 released!

[Kiran Kedlaya]

Am I first to respond? w00t! But I have an unfair advantage this week,
being in an unusual time zone (India).

Anyway, on 64-bit RH (Opteron), I get one doctest failure (not in
parallel):

sage -t  devel/sage-main/sage/dsage/tests/testdoc.py

which fails as follows:
-
sage -t  devel/sage-main/sage/dsage/tests/testdoc.pyException
exceptions.TypeError: TypeError('NoneType' object is not callable,)
in bound method Popen.__del__ of subprocess.Popen object at
0x1bb1a850 ignored
Exception in thread Thread-1 (most likely raised during interpreter
shutdown):
Traceback (most recent call last):
  File /scratch/sage-2.11.alpha2/local/lib/python2.5/threading.py,
line 460, in __bootstrap
  File /scratch/sage-2.11.alpha2/local/lib/python2.5/site-packages/
sage/dsage/interface/dsage_interface.py, line 46, in run
  File /scratch/sage-2.11.alpha2/local/lib/python2.5/site-packages/
twisted/internet/posixbase.py, line 220, in run
  File /scratch/sage-2.11.alpha2/local/lib/python2.5/site-packages/
twisted/internet/posixbase.py, line 233, in mainLoop
type 'exceptions.AttributeError': 'NoneType' object has no attribute
'msg'
Unhandled exception in thread started by
Error in sys.excepthook:

Original exception was:

 [17.3 s]
exit code: 1024
-
Kiran

mabshoff wrote:

 Hello folks,

 this is 2.11.alpha2. It is a little later than I had hoped and
 planned mostly due to the fact that Easter and Spring break
 put somewhat of a damper on development. So far we merged 111
 patches into this release.

 There were fixes all over the map. This build should now also
 build fine on OSX 10.5.2 and higher. If you had some major
 feature merged in this release please add some info about it
 at the Sage 2.11 Release Tour wiki page located at

http://wiki.sagemath.org/sage-2.11

 This is likely the last release before 2.11.final unless we
 hit some major show stopper. Please build, doctest and report
 any issue you hit in this thread. But I am sure by now you
 know the drill :=)

 Please also correct and spelling issues as well as wrongly
 assigned credit in the list below.

 Cheers,

 Michael


 Merged in alpha2:

 #1010: Marshall Hampton: upgrade gfan to version 0.3
 #1618: Michael Abshoff: Make SCons ignore Intel ifort's
linker options
 #1707: Carlo Hamalainen: add Carlo Hamalainen's latin square
stuff to Sage
 #2276: Martin Albrecht: M.divides(N) gives an error if M and
N are monomials in R.x,y = PolynomialRing(QQ)
 #2355: Didier Deshommes, Gary Furnish: Write a clearer
submatrix implementation
 #2415: Michael Abshoff: update NTL to 5.4.2 (bugfix release)
 #2417: Alex Ghitza: discriminant method sometimes returns
values in the fraction field
 #2470: Yi Qiang: dsage docs in tutorial -- can't tex them
 #2498: Alex Ghitza: PARI's is_irreducible being used
inappropriately
 #2565: Dan Drake: logging is extremely broken
 #2596: William Stein: Sage 2.11.alpha0: sage/plot/plot.py
doctest failure
 #2597: Ryan HintonAdd reduced adjacency matrix and a list
file format support to BipartiteGraph
 #2600: Carl Witty: vector plot throws error when function
contains a float
 #2609: Robert Miller: generators for congruence subgroups
 #2611: Martin Albrecht: add monomial_coefficent to boolean
polynomials
 #2612: Robert Bradshaw: String to Integer Conversion
 #2614: Joel Mohler: MPolynomial coefficient/
polynomial_coefficient merging
 #2627: Robert Bradshaw: Integer(abs(gamma(n+1))) is not always
equal to factorial(n) for n a positive integer
 #2634: Martin Albrecht: Unable to create certain multivariate
polynomial rings since libsingular is invoked instead
of generic code
 #2642: Martin Albrecht, Carl Witty: doctest failure in
polynomial_modn_dense_ntl.pyx: .small_roots()
 #2645: Jason Grout: arrow3d is sometimes too long
 #2653: Robert Bradshaw: norm and trace of elements of orders
are Rational not Integer
 #2657: Tim Abbott: Debian fplll cleanup
 #2660: Michael Abshoff: copy work around stdint.h on Solaris 9
 #2661: Mike Hansen: sage cannot compute floor / ceil of
log(8)/log(2)
 #2664: Nick Alexander: implement a symplectic form for
finding symplectic bases
 #2668: Nick Alexander, Carl Witty: loads/dumps do not work
with QQbar and AA
 #2672: Michael Abshoff: Fix OSX 10.5 detection code - it
fails for the currect OSX 10.5.2
 #2674: Craig Citro, Justin Walker: Bug in modforms
 #2676: Robert Miller: equitable partitions: two bugs
 #2677: Didier Deshommes: sage 2.11.alpha1: doctest failures
in real_double_dense.pyx
 #2681: Alex Ghitza:improve doctest coverage in libs/pari/gen.pyx
 #2683: Mike Hansen: Add initial support of k-Schur functions
 #2685: Robert Miller: compute the girth of a graph
 #2689: Robert Miller: compute blocks and cut-vertices of a
graph
 #2690: Emily Kirkman: add circular argument to genus command
 #2691: Robert Miller: generate 

[sage-devel] Re: Sage 2.11.alpha2 released!

[Kiran Kedlaya]

OK, this is weird. With -verbose on, the test claims to pass, even
though the outcome seems to be the same! It looks like the test proper
is passing but something weird is happening upon exit. See below.

Kiran
-
sage -t -verbose devel/sage-main/sage/dsage/tests/testdoc.pyTrying:
from sage.dsage.misc.misc import find_open_port###line 4:_sage_
 from sage.dsage.misc.misc import find_open_port
Expecting nothing
ok
Trying:
port = find_open_port().next()###line 5:_sage_ port =
find_open_port().next()
Expecting nothing
ok
Trying:
dsage.server(blocking=False, port=port, verbose=False, ssl=False,
log_level=Integer(3))###line 6:_sage_
dsage.server(blocking=False, port=port, verbose=False, ssl=False,
log_level=3)
Expecting:
Going into testing mode...
ok
Trying:
dsage.worker(blocking=False, port=port, verbose=False, ssl=False,
log_level=Integer(3), poll=RealNumber('0.1'),
authenticate=False)###line 8:_sage_
dsage.worker(blocking=False, port=port, verbose=False, ssl=False,
log_level=3, poll=0.1, authenticate=False)
Expecting nothing
ok
Trying:
sleep(RealNumber('2.0'))###line 9:_sage_ sleep(2.0)
Expecting nothing
ok
Trying:
d = dsage.connect(port=port, ssl=False)###line 10:_sage_ d
= dsage.connect(port=port, ssl=False)
Expecting nothing
ok
Trying:
sleep(RealNumber('2.0'))###line 11:_sage_ sleep(2.0)
Expecting nothing
ok
Trying:
a = d('2 + 3')###line 12:_sage_ a = d('2 + 3')
Expecting nothing
ok
Trying:
a.wait(timeout=Integer(30))###line 13:_sage_
a.wait(timeout=30)
Expecting nothing
ok
Trying:
a###line 14:_sage_ a
Expecting:
5
ok
Trying:
job_id = a.kill()###line 19:_sage_ job_id = a.kill()
Expecting nothing
ok
Trying:
v = [d('%s^2'%i) for i in range(Integer(100),Integer(103))]###line
20:_sage_ v = [d('%s^2'%i) for i in range(100,103)]
Expecting nothing
ok
Trying:
_ = [x.kill() for x in v]###line 28:_sage_ _ = [x.kill()
for x in v]
Expecting nothing
ok
Trying:
a = Integer(5)###line 29:_sage_ a = 5
Expecting nothing
ok
Trying:
b = Integer(5)###line 30:_sage_ b = 5
Expecting nothing
ok
Trying:
j = d('a+b', user_vars={'a': a, 'b': b})###line 31:_sage_ j
= d('a+b', user_vars={'a': a, 'b': b})
Expecting nothing
ok
Trying:
j.wait()###line 32:_sage_ j.wait()
Expecting nothing
ok
Trying:
j###line 33:_sage_ j
Expecting:
10
ok
1 items had no tests:
__main__
1 items passed all tests:
  18 tests in __main__.example_0
18 tests in 2 items.
18 passed and 0 failed.
Test passed.
Exception exceptions.TypeError: TypeError('NoneType' object is not
callable,) in bound method Popen.__del__ of subprocess.Popen object
at 0x18563850 ignored
Exception in thread Thread-1 (most likely raised during interpreter
shutdown):
Traceback (most recent call last):
  File /scratch/sage-2.11.alpha2/local/lib/python2.5/threading.py,
line 460, in __bootstrap
  File /scratch/sage-2.11.alpha2/local/lib/python2.5/site-packages/
sage/dsage/interface/dsage_interface.py, line 46, in run
  File /scratch/sage-2.11.alpha2/local/lib/python2.5/site-packages/
twisted/internet/posixbase.py, line 220, in run
  File /scratch/sage-2.11.alpha2/local/lib/python2.5/site-packages/
twisted/internet/posixbase.py, line 233, in mainLoop
type 'exceptions.AttributeError': 'NoneType' object has no attribute
'msg'
Unhandled exception in thread started by
Error in sys.excepthook:

Original exception was:

 [16.0 s]

--
All tests passed!
Total time for all tests: 16.0 seconds

-

Yi Qiang wrote:

 Hey Kiran,
 Can you run
 sage -t -verbose devel/sage-main/sage/dsage/tests/

 and attach the output of that?

 Thanks,
 Yi

 On Fri, Mar 28, 2008 at 11:01 PM, Kiran Kedlaya [EMAIL PROTECTED] wrote:
 
   Am I first to respond? w00t! But I have an unfair advantage this week,
   being in an unusual time zone (India).
 
   Anyway, on 64-bit RH (Opteron), I get one doctest failure (not in
   parallel):
 
  sage -t  devel/sage-main/sage/dsage/tests/testdoc.py
 
   which fails as follows:
   -
   sage -t  devel/sage-main/sage/dsage/tests/testdoc.pyException
   exceptions.TypeError: TypeError('NoneType' object is not callable,)
   in bound method Popen.__del__ of subprocess.Popen object at
   0x1bb1a850 ignored
   Exception in thread Thread-1 (most likely raised during interpreter
   shutdown):
   Traceback (most recent call last):
File /scratch/sage-2.11.alpha2/local/lib/python2.5/threading.py,
   line 460, in __bootstrap
File /scratch/sage-2.11.alpha2/local/lib/python2.5/site-packages/
   sage/dsage/interface/dsage_interface.py, line 46, in run
File /scratch/sage-2.11.alpha2/local/lib/python2.5/site-packages/
   twisted/internet/posixbase.py, line 220, in run
File /scratch/sage-2.11.alpha2/local/lib/python2.5/site-packages/
   twisted/internet/posixbase.py, line 233, in mainLoop
   type 'exceptions.AttributeError': 'NoneType

[sage-devel] spyx files and compiler flags

[Kiran Kedlaya]

I was trying to compile an spyx file using FLINT, and I got some error
messages of the form:

error: 'for' loop initial declaration used outside C99 mode

That suggests that along the lines of cinclude, clib, etc. which are
discussed in ticket 1994 (http://trac.sagemath.org/sage_trac/ticket/
1994), there should also be a compiler directive called ccflags, as in

#ccflags -std=c99

Is this extant under another name, or does it also need to be added?

Kiran

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[sage-devel] Re: upgrade to 2.10.1 - zlib headers taken from the host?

[Kiran Kedlaya]

Apparently I need to read my install.log more closely. Correction to
my previous message:

I *did* receive this error when I again built 2.10 from scratch and
then upgraded to 2.10.1. (This means mabshoff and I might be able to
investigate at SAGE Days 7 this week.)

I *did not* receive an error on a scratch 2.10.1 install. (So my
recommendation still holds.)

Kiran

On Feb 4, 1:50 pm, Kiran Kedlaya [EMAIL PROTECTED] wrote:
 I was the one who reported something like this to mabshoff. However,
 it was not so easily reproducible. I built 2.10.1 from scratch without
 an error. I then built 2.10 from scratch and then upgraded it to
 2.10.1, and again no error.

 The install which originally gave the error had been progressively
 upgraded from (I think) 2.9. So it's possible that a fresh install
 will work in your case too.

 Kiran

 On Feb 4, 9:56 am, philt [EMAIL PROTECTED] wrote:

  http://sage.math.washington.edu/home/mabshoff/SPKG/libpng-1.2.22.p5.spkg
   that should fix the issue. Since you already installed the system zlib
   headers testing it won't verify that the problem was fixed for you
   unless you deinstall zlib1g-dev first. The ticket number is #2043.

  Hello,
  I tried the following:
  apt-get remove zlib1g-dev
  cd spkg/standard
  wgethttp://sage.math.washington.edu/home/mabshoff/SPKG/libpng-1.2.22.p5.spkg
  sage -i libpng-1.2.22.p5.spkg

  then the logs =
  Installing libpng-1.2.22.p5.spkg
  Calling sage-spkg on libpng-1.2.22.p5.spkg
  libpng-1.2.22.p5
  Machine:
  Linux sage 2.6.21.6-grsec2.1.10-200706182032-vs2.2.0.3 #1 SMP Fri Aug
  17 20:53:31 CES
  T 2007 x86_64 GNU/Linux
  Deleting directories from past builds of previous/current versions of
  libpng-1.2.22.p
  5
  Extracting package /opt/sage-2.10/spkg/standard/
  libpng-1.2.22.p5.spkg ...
  [...]
  Finished extraction
  
  Host system
  uname -a:
  Linux sage 2.6.21.6-grsec2.1.10-200706182032-vs2.2.0.3 #1 SMP Fri Aug
  17 20:53:31 CEST 2007 x86_64 GNU/Linux
  
  
  GCC Version
  gcc -v
  Using built-in specs.
  Target: x86_64-linux-gnu
  Configured with: ../src/configure -v --enable-languages=c,c+
  +,fortran,objc,obj-c++,treelang --prefix=/usr --enable-shared --with-
  system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-
  threads=posix --enable-nls --program-suffix=-4.1 --enable-__cxa_atexit
  --enable-clocale=gnu --enable-libstdcxx-debug --enable-mpfr --enable-
  checking=release x86_64-linux-gnu
  Thread model: posix
  gcc version 4.1.2 20061115 (prerelease) (Debian 4.1.1-21)
  
  checking for a BSD-compatible install... /usr/bin/install -c
  [...]
  checking for zlibVersion in -lz... no
  configure: error: zlib not installed
  Error configuring libpng

  So it seems I've still exactly the same problem.
  While I've local/include/zlib.h and local/lib/libz.so/.so.1/.so.1.2.3

  Phil
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[sage-devel] Re: upgrade to 2.10.1 - zlib headers taken from the host?

[Kiran Kedlaya]

I was the one who reported something like this to mabshoff. However,
it was not so easily reproducible. I built 2.10.1 from scratch without
an error. I then built 2.10 from scratch and then upgraded it to
2.10.1, and again no error.

The install which originally gave the error had been progressively
upgraded from (I think) 2.9. So it's possible that a fresh install
will work in your case too.

Kiran

On Feb 4, 9:56 am, philt [EMAIL PROTECTED] wrote:
 http://sage.math.washington.edu/home/mabshoff/SPKG/libpng-1.2.22.p5.spkg
  that should fix the issue. Since you already installed the system zlib
  headers testing it won't verify that the problem was fixed for you
  unless you deinstall zlib1g-dev first. The ticket number is #2043.

 Hello,
 I tried the following:
 apt-get remove zlib1g-dev
 cd spkg/standard
 wgethttp://sage.math.washington.edu/home/mabshoff/SPKG/libpng-1.2.22.p5.spkg
 sage -i libpng-1.2.22.p5.spkg

 then the logs =
 Installing libpng-1.2.22.p5.spkg
 Calling sage-spkg on libpng-1.2.22.p5.spkg
 libpng-1.2.22.p5
 Machine:
 Linux sage 2.6.21.6-grsec2.1.10-200706182032-vs2.2.0.3 #1 SMP Fri Aug
 17 20:53:31 CES
 T 2007 x86_64 GNU/Linux
 Deleting directories from past builds of previous/current versions of
 libpng-1.2.22.p
 5
 Extracting package /opt/sage-2.10/spkg/standard/
 libpng-1.2.22.p5.spkg ...
 [...]
 Finished extraction
 
 Host system
 uname -a:
 Linux sage 2.6.21.6-grsec2.1.10-200706182032-vs2.2.0.3 #1 SMP Fri Aug
 17 20:53:31 CEST 2007 x86_64 GNU/Linux
 
 
 GCC Version
 gcc -v
 Using built-in specs.
 Target: x86_64-linux-gnu
 Configured with: ../src/configure -v --enable-languages=c,c+
 +,fortran,objc,obj-c++,treelang --prefix=/usr --enable-shared --with-
 system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-
 threads=posix --enable-nls --program-suffix=-4.1 --enable-__cxa_atexit
 --enable-clocale=gnu --enable-libstdcxx-debug --enable-mpfr --enable-
 checking=release x86_64-linux-gnu
 Thread model: posix
 gcc version 4.1.2 20061115 (prerelease) (Debian 4.1.1-21)
 
 checking for a BSD-compatible install... /usr/bin/install -c
 [...]
 checking for zlibVersion in -lz... no
 configure: error: zlib not installed
 Error configuring libpng

 So it seems I've still exactly the same problem.
 While I've local/include/zlib.h and local/lib/libz.so/.so.1/.so.1.2.3

 Phil
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[sage-devel] Re: Sage 2.10.1.rc2 released!

[Kiran Kedlaya]

Doctest failure on my machine (64 bit Opteron, RHEL 5); see below.

Kiran

--
The following tests failed:

sage -t  devel/sage-main/sage/interfaces/sage0.py
**
File sage0.py, line 143:
sage: _= sage0.cputime() # random output
Exception raised:
Traceback (most recent call last):
  File /scratch/sage-x64/local/lib/python2.5/doctest.py, line
1212, in __run
compileflags, 1) in test.globs
  File doctest __main__.example_2[0], line 1, in module
_= sage0.cputime() # random output###line 143:
sage: _= sage0.cputime() # random output
  File /scratch/sage-x64/local/lib/python2.5/site-packages/sage/
interfaces/expect.py, line 502, in cputime
raise NotImplementedError
NotImplementedError
**
File sage0.py, line 147:
sage: _= sage0.cputime() # random output
Exception raised:
Traceback (most recent call last):
  File /scratch/sage-x64/local/lib/python2.5/doctest.py, line
1212, in __run
compileflags, 1) in test.globs
  File doctest __main__.example_2[2], line 1, in module
_= sage0.cputime() # random output###line 147:
sage: _= sage0.cputime() # random output
  File /scratch/sage-x64/local/lib/python2.5/site-packages/sage/
interfaces/expect.py, line 502, in cputime
raise NotImplementedError
NotImplementedError
**
File sage0.py, line 286:
sage: F == sage0(F)._sage_()
Exception raised:
Traceback (most recent call last):
  File /scratch/sage-x64/local/lib/python2.5/doctest.py, line
1212, in __run
compileflags, 1) in test.globs
  File doctest __main__.example_7[2], line 1, in module
F == sage0(F)._sage_()###line 286:
sage: F == sage0(F)._sage_()
  File /scratch/sage-x64/local/lib/python2.5/site-packages/sage/
interfaces/sage0.py, line 273, in _sage_
return loads(open(P._local_tmpfile()).read())
  File sage_object.pyx, line 532, in
sage.structure.sage_object.loads
  File sage_object.pyx, line 530, in
sage.structure.sage_object.loads
error: Error -3 while decompressing data: incorrect header check
**
2 items had failures:
   2 of   3 in __main__.example_2
   1 of   3 in __main__.example_7
***Test Failed*** 3 failures.
For whitespace errors, see the file .doctest_sage0.py
 [14.1 s]
exit code: 256

--
The following tests failed:


sage -t  devel/sage-main/sage/interfaces/sage0.py



On Jan 28, 6:48 am, mabshoff [EMAIL PROTECTED]
dortmund.de wrote:
 Hello folks,

 here we go with Sage 2.10.1.rc2. We finally have the eclib.spkg
 updated as well as various fixes like the empty ideal comparison
 segfault and the abs norm vector issue. Those attempting to
 build on Solaris will also be glad to hear that I made progress
 merging build fixes and we are getting close to a build out of
 the box for the vast majority of spkgs.

 The meh*.txt are still there, I only found them hiding in some
 spkg after I rolled rc2. Expect rc3 with progress on ATLAS,
 the notebook interface and various build improvements in the
 next 24 hours. I assume that we will release in the next 72
 hours.

 If you have been suffering from the sage0 doctest failure please
 try out the patch attached to #1958. It hasn't made it in to rc2,
 but the way it currently looks it will be in there.

 The tarball [201MB] is available at the ususal place:

 http://sage.math.washington.edu/home/mabshoff/release-cycles-2.10.1/s...

 I am currently having problems connecting to the webserver - if
 it persists I will move the tarball somewhere else.

 Cheers,

 Michael

 ###

 To Do:

 * reviews, i.e. #1922, #1923 (Jason) - for details see below
 * resolve notebook issue (GNUTLS related)
 * update mfpr to 2.3.1.rc2
 * ATLAS: add profiles for Pentium M, Athlon
 * disable mandatory FLINT check
 * update documentation for new ATLAS options
 * #1689: update documentation for new SAGE_FORTRAN_LIB
 * #1884: leak in coercion
 * #1874: PolyBoRi leak: fix it or get somebody else to do it
 * pygnutls: bump for update - look for update?
 * remove opencdk since it is included in gnutls 2.2.1
 * add two open valgrind issues to track: Valgrind issues in 2.9.2

 sage-memcheck.3056: Conditional jump or move depends on uninitialised
 value(s), Invalid read of size 1
 doctest calculus.py
 sage-memcheck.19097:
 doctest: real_rqdf.py

 sage-memcheck.24275: longest_match - libz: Conditional jump or move
 depends on uninitialised value(s)

 ###

 spkg audit:

 * ensure that 

[sage-devel] Re: Sage 2.10.1.rc2 released!

[Kiran Kedlaya]

This is also fixed by that patch, yes.

Kiran

On Jan 29, 11:55 am, mabshoff [EMAIL PROTECTED]
dortmund.de wrote:
 On Jan 29, 5:52 pm, Kiran Kedlaya [EMAIL PROTECTED] wrote:

  Doctest failure on my machine (64 bit Opteron, RHEL 5); see below.

 Hi Kiran,

  Kiran

  --
  The following tests failed:

 can you confirm that the patch attached to

 #1958: Craig Citro: fix problems with ANSI codes in sage0.py

 fixes the issue for you, too? The patch did work for Jaap and Craig,
 so it has already been merged in rc3.

 SNIP

 Cheers,

 Michael
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[sage-devel] Re: Multiple return values

[Kiran Kedlaya]

Before proceeding, let me thank William for answering my original
question. In the case I was interested in, the number of return values
does not vary in any funny way, so I can use nvals to get what I want
back out.

But in the example of IsIsomorphic, there seems to be a problem. If I
start Magma and type

 E := EllipticCurve([2,1]);
 F := EllipticCurve([5,1]);
 bool, phi := IsIsomorphic(E,F);

then the identifier phi remains undefined! And in Sage, if I type

sage: E = magma.EllipticCurve([2,1]);
sage: F = magma.EllipticCurve([5,1])
sage: bool, phi = magma.IsIsomorphic(E, F, nvals=2)

this generates an error:

type 'exceptions.RuntimeError': Error evaluation Magma code.
IN:_sage_[9], _sage_[10] := IsIsomorphic(_sage_[4],_sage_[8]);
OUT:
 _sage_[9], _sage_[10] := IsIsomorphic(_sage_[4],_sage_[8]);
^
Runtime error in :=: Illegal undefined assignment for LHS index
assignment

In a perfect world, the above would run and produce bool == False, phi
== None. Sigh.

Kiran

On Jan 16, 12:26 pm, Robert Bradshaw [EMAIL PROTECTED]
wrote:
 There is no way in python to detect how many arguments a function
 result will be assigned to, and I'm not a fan of magma's way of doing
 it. WIth variable length tuples one has to check the length of a
 tuple before unpacking it.

 There is a function E1.isomorphism_to(E2) that actually computes the
 isomorphism. I think is_isomorphism should just return True or False
 (is_* has that convention). Then one can do such things as

 if E.is_isomporhic(F):
  ...

 Perhaps an optional argument compute which computes and then caches
 or returns the actual isomorphism.

 - Robert

 On Jan 16, 2008, at 6:03 AM, John Cremona wrote:

  What a coincidence -- the patch I am working on *will* (have the
  capability to) return both a boolean and an isomorphism for
  is_isomorphic() on elliptic curves.  I was wondering how to do that
  and assumed that it would be a tuple.  Rather than make the tuple's
  length (1 or 2) depend on the input I would always return a tuple of
  length 2 but the second item would be None iff the first has false.
  Isn't that a reasonable way of doing it?

  I don't like requiring the trapping of errors, though I realise that
  it is very Pythonesque to do so.  But if we allow the input line
  sage: phi = E1.isomorphism(E2)

  then we *must* raise an error when the things are not isomorphic,
  just as
  sage: QQ(2).nth_root(2)
  raises as ValueError (though sqrt(2) does not as it creates a
  symbolic sqrt(2)).

  This is going beyond the original thread, I know.

  On 16/01/2008, David Kohel [EMAIL PROTECTED] wrote:

  There was a thread on multiple return values coming from Magma,
  since renamed to Integer points on conics

  William pointed out that one can access the multiple return values
  using nvals:

   x = magma.XGCD(15, 10)
   x,y,z = magma.XGCD(15, 10, nvals = 3)

  The first returns an integer, while the second returns a tuple.

  Q1: Is this an acceptable general construction for Python and/or
  SAGE,
  namely to return a different type depending on the values passed into
  it?  Is it acceptable when it is controlled by nvals in exactly this
  way?

  As William pointed out, very different algorithms can be called
  depending on the
  number of arguments requested in Magma.  The following is an example:

  sage: E = magma.EllipticCurve([1,3])
  sage: magma.IsIsomorphic(E,E)
  true
  sage: bool, phi = magma.IsIsomorphic(E,E,nvals=2)
  sage: phi
  Elliptic curve isomorphism from: Elliptic Curve defined by y^2 =
  x^3 +
  x + 3 over Rational Field to Elliptic Curve defined by y^2 = x^3 +
  x +
  3 over Rational Field
  Taking (x : y : 1) to (x : y : 1)

  Currently in SAGE we have:

  sage: E = EllipticCurve([1,3])
  sage: E.is_isomorphic(E)
  True

  Q2: Would the following be acceptable way of implementing equivalent
  functionality in SAGE?:

  sage: bool, phi = E.is_isomorphic(E, nvals=2)

  Note that often (in many concexts) it more expensive to return an
  isomorphism, but only slightly more so compared with recomputing the
  isomorphism test.  If the answer to my question is no, it not
  acceptable SAGE/Python syntax, then how should we implement this
  functionality?  One possibility is:

  sage: phi = E1.isomorphism(E2)

  and to trap an error if is_isomorphic returns false.  Is this a
  better?

  --
  John Cremona
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[sage-devel] Magma multiple return values

[Kiran Kedlaya]

In Magma, many commands return multiple values, for instance:

sage: %magma
magma: XGCD(15, 10)
5 1 -1

However, the following happens in SAGE:

sage: magma.XGCD(15, 10)
5

Is there a good way for the Magma interface to detect multiple return
values and bundle them into a Python tuple? Then I'd be able to say

sage: x, y, z = magma.XGCD(15, 10)

and have now x == 5, y == 1, z == -1.

Kiran


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[sage-devel] Re: hodge number calculator

[Kiran Kedlaya]

Thank you for contributing this! Even without being integrated into
SAGE, this is very useful for me; I need these numbers reasonably
often, and I hate having to reconstruct the calculation from scratch
every time I need to do it.

Kiran

On Jan 14, 8:38 am, D. Benjamin Antieau [EMAIL PROTECTED]
wrote:
 To all,

 I've created a sage file to calculate, among other things, the Hodge numbers
 of an arbitrary complete intersection. Attached is the .sage file. I also
 attempted to create a .spkg file, but it does not seem to work. Mine
 contains simply a .py file that the install script puts it
 $SAGE_ROOT/local/bin. But, I cannot seem to use it from within sage. Any
 help on that front would be appreciated. On the other hand, loading the
 .sage file works fine.

 The file itself is well-documented. I would love suggestions for further
 methods to add. For instance, at some point I will add the ability to
 compute the degrees of the top Chern classes of a threefold.

 I don't see putting this in sage at the moment, but it does lead to the
 question: should there be a CompleteIntersection class, which would inherit
 from AlgebraicScheme_subscheme_projective. If so, then I could put this code
 in that class in the characteristic zero case.

 Ben Antieau

 Example:

 The Hodge numbers of a crazy fourfold. The list of integers is the list of
 degrees of the complete intersection.
sage: hodge_numbers_ci([2,4,6,3,6,4,3,2,9,5],4)
[  1   0   0   0  2658146543]
[  0   1   0 22238665343   0]
[  0   0 42452753184   0   0]
[  0 22238665343   0   1   0]
[ 2658146543   0   0   0   1]

 The file provides the following functions:
 chiy_characteristic_ci(degrees,index,yprecision,zprecision)
 hodge_numbers_ci(degrees,dimension)
 betti_numbers_ci(degrees,dimension)
 euler_characteristic_ci(degrees,dimension)
 topological_euler_characteristic_ci(degrees,dimension)
 arithmetic_genus_ci(degrees,dimension)
 geometric_genus_ci(degrees,dimension) [==arithmetic_genus_ci]
 K_squared_surface_ci(degrees,dimension) [computes the degree of K^2 of a
 complete intersection surface]
 c2_surface_ci(degrees,dimension) [computes the degree of the second Chern
 class of a complete intersection surface]

  hodge_numbers_ci.sage
 22KDownload

  hodge_numbers_ci-0.1.spkg
 5KDownload
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[sage-devel] Re: SAGE 2.10.alpha0 released

[Kiran Kedlaya]

Works for me. That means #1553 is solved, though the larger SCons
issue remains in case we bring in any more software that uses it.

On my box (again, that's 64-bit RHEL5), sage -testall passes all
tests.

Kiran

On Jan 7, 9:30 pm, mabshoff [EMAIL PROTECTED]
dortmund.de wrote:
 Hello folks,

 and a new merge cycle has been opened. Every time I finish one they
 pull me back in again ;)

 Anyways, tarball is in

 http://sage.math.washington.edu/home/mabshoff/release-cycles-2.10/

 Inside that directory you see another directory alpha0 which contains
 all updated spkgs as well as all patches. So that way you can keep an
 eye on development and just grab patches and spkgs as they get merged.
 Once I start alpha1 expect that directory to appear there, too.

 As usual I will ask people to do reviews and fix open bugs. Come on
 over to the tracker and do your best. alpha0 was mostly about mem leak
 fixes, I did discover a whole bunch of new ones when I did an audit
 with the help of valgrind of 2.9.3 and with the help of various people
 (see below) we fixed a whole bunch of them. We are getting to the
 point where the number of known leaks is going toward zero, the main
 culprit at the moment is Givaro.

 As usual let us know about any issue you encounter. I am catching some
 sleep now - see you in the morning.

 Cheers,

 Michael

 Merged in alpha0:

 #1092: Willem Jan Palenstijn, Michael Abshoff: small memleaks exposed
        by ntl_ZZ_pE
 #1093: Michael Abshoff, Willem Jan Palenstijn: small memleaks exposed
        by ntl_ZZ_pX.py
 #1541: Burcin Erocal: improve PolyBoRi integration
 #1544: David Joyner, Rich Morin: SAGE Tutorial nits #2
 #1553: Kiran Kedlaya, Michael Abshoff: SCons related build failure
        of PolyBoRi on 64-bit RHEL5
 #1598: Martin Albrecht: fix SIGSEGV in libSINGULAR interface on
        Solaris
 #1694: Michael Abshoff, Bill Hart: Update FLINT to 1.05 release
 #1701: Martin Albrecht: attempt to clean up currRing if deallocated
 #1702: Martin Albrecht: fix memleak in fplll.pyx
 #1703: Michael Abshoff: memleak in Singular: one mpz is leaked in
        longrat.cc

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