[sage-devel] [JOB] Software Engineering Positions at Galois Inc.

[Benjamin Jones]

Hi all,

It's been quite a while since I posted anything here, but it's great to see 
the Sagemath community is still humming!

I'm working for a company called Galois Inc. now and we have some positions 
open I thought I'd spam you with in case you or someone you know is on the 
job market.

https://galois.com/careers/software-engineer/

We're looking for strong candidates with BS/MS/PhD in CS, Math, or closely 
related field with good programming experience (e.g. contributing to a free 
open source alternative to Magma, Maple, Mathematica and Matlab). But who 
isn't, right?

There is more than one opening right now in the "software engineer" 
category, but don't let that spook you if you're not a computer scientist 
by birth. We have a bunch of folks who are mathematicians (myself 
included), essentially mathematicians, cryptographers, etc. We do a lot of 
work in Haskell, Python, C, Coq, Isabell, Proverif, and many domain 
specific languages.

There are positions both in Portland, OR (the main location) but also 
Arlington, VA. You can read all about the sorts of work we do 
at https://galois.com (and you can marvel at the abstract nonsense in the 
image on our homepage).


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Re: [sage-devel] Re: We need a new color?

[Benjamin Jones]

I will give that a positive review :)

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On Sun, Sep 29, 2013 at 11:26 PM, Maarten Derickx <
m.derickx.stud...@gmail.com> wrote:

> Speaking of xkcd and easter eggs, I have always thought that since sage
> already has an xgcd function, we should also have an xkcd function. I
> already wrote a first version at:
> https://sage.math.leidenuniv.nl/home/pub/22/
>
> Le vendredi 27 septembre 2013 18:03:00 UTC+2, kcrisman a écrit :
>
>>
>>>
>>> On Friday, September 27, 2013 4:57:51 AM UTC+2, kcrisman wrote:
>>>>
>>>> From a user.  I'm not sure how the matplotlib devels would feel about
>>>> adding this.
>>>>
>>>>
>>> I would assume they welcome a patch, especially when you quote xkcd.
>>> The definitions are here, i think:
>>> https://github.com/matplotlib/**matplotlib/blob/master/lib/**
>>> matplotlib/colors.py#L65<https://github.com/matplotlib/matplotlib/blob/master/lib/matplotlib/colors.py#L65>
>>>
>>>
>> I've submitted a pull request. https://github.com/**
>> matplotlib/matplotlib/pull/**2468<https://github.com/matplotlib/matplotlib/pull/2468>
>>
>> See also 
>> http://www.colourlovers.**com/palette/492360/Sage<http://www.colourlovers.com/palette/492360/Sage>
>>
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Re: [sage-devel] GSoC project: Mathematical functions library

[Benjamin Jones]

It would be fantastic for someone to take up the quest on #12289.

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On Tue, May 28, 2013 at 3:23 PM, Eviatar  wrote:

>
> On Tuesday, 28 May 2013 14:04:24 UTC-7, kcrisman wrote:
>>
>>
>>
>> On Tuesday, May 28, 2013 3:17:25 PM UTC-4, Benjamin Jones wrote:
>>>
>>> Awesome! Ping me if you need someone to help with code review.
>>>
>>>
>> +1, especially at SD 48 - looking forward to meeting you.
>>
>
> Thanks, looking forward to meeting you too!
>
>
>>
>>
>>> 1. Symbolic wrappers
>>>>> A pending patch, ticket 
>>>>> #4102<http://trac.sagemath.org/sage_trac/ticket/4102>,
>>>>> will make the Bessel functions symbolic. I will similarly update the rest
>>>>> of the special functions. This will involve defining methods for 
>>>>> evaluation
>>>>> and wrapping third-party libraries for handling simplification,
>>>>> integration, etc.
>>>>>
>>>>
>>>
>> This will be great, especially bringing back an "algorithm" keyword...
>>
>
> Right. There's also #12289<http://trac.sagemath.org/sage_trac/ticket/12289> 
> which
> will do this for _evalf_.
>
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Re: [sage-devel] GSoC project: Mathematical functions library

[Benjamin Jones]

Awesome! Ping me if you need someone to help with code review.

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On Tue, May 28, 2013 at 11:48 AM, Eviatar  wrote:

> Hello,
>
> I am grateful to have been selected as one of the Google Summer of Code
> students for this summer. I will be working on a benchmark framework for
> testing functions over different domains, making symbolic the special
> functions that are not yet, and implementing generalized hypergeometric
> functions. Here are some more details from my application:
>
> 1. Symbolic wrappers
>> A pending patch, ticket 
>> #4102<http://trac.sagemath.org/sage_trac/ticket/4102>,
>> will make the Bessel functions symbolic. I will similarly update the rest
>> of the special functions. This will involve defining methods for evaluation
>> and wrapping third-party libraries for handling simplification,
>> integration, etc.
>>
>
>
> From the open-source software listed at the 
> DLMF<http://dlmf.nist.gov/software/>,
>> Sage ships with Cephes (although it is not used for anything at the
>> moment), GSL, MPFR, Maxima, PARI/GP, SLATEC (through Maxima), and mpmath.
>> All these except Cephes and SLATEC have existing interfaces, facilitating
>> the wrapping of functionality.
>> The Bessel functions will be made symbolic by #4102, and the Airy
>> functions by the pending 
>> #12455<http://trac.sagemath.org/sage_trac/ticket/12455>.
>> hypergeometric_U, spherical_bessel_J, spherical_bessel_Y,
>> spherical_hankel1, spherical_hankel2, spherical_harmonic, elliptic_J,
>> jacobi, inverse_jacobi, elliptic_e, elliptic_ec, elliptic_eu, elliptic_f,
>> elliptic_kc, and elliptic_pi remain to be done.
>>
>
>
> 2. Benchmark framework
>> The benchmark framework is important for determining which backend is
>> appropriate for numeric evaluation of functions on different domains. Due
>> to implementation details, different algorithms will be suited to different
>> regions of the function's domain; for example, hypergeometric_U(-4, 10,
>> 100) is faster with PARI, but hypergeometric_U(-40, -40, 10) is faster
>> with SciPy. Picking the domains will require looking at the algorithm
>> implementation. A benchmark framework will allow Sage to more intelligently
>> decide between the backends depending on input, and also to detect and
>> track regressions. A sufficiently versatile implementation could also be
>> extended to other types of functions in the future.
>>
>
>
> I would begin by building on the benchmark system in tests/benchmark.py.
>> I would create a subclass of Benchmark designed for numerical functions;
>> it would accept arguments of domains on which to test functions, and
>> generate random test values using the underlying rings' 
>> random_elementmethod. For example, benchmark_function(gamma,
>> domains=[[1, 10], [50, 60]], ring=ZZ, systems=['maxima', 'sympy']) would
>> benchmark the gamma function on the integer domains [1, 10] and [50,60]
>> using Maxima and SymPy (this is only an example to illustrate the proposed
>> functionality; gamma does not currently have the option to be evaluated
>> with different backends). benchmark_function(gamma, domains=[[-10 -
>> 10*I, 10 - 5*I]], ring=CC) would benchmark gamma on the region of the
>> complex plane bounded by the two points -10 - 10i and 10 - 5i. The current
>> output format of the Benchmark class in benchmark.py should be changed
>> to be machine-readable.
>>
>
>
> After the benchmark framework is completed, I would determine appropriate
>> domains on which to test each of the special functions, and create a
>> benchmark suite. Using the results of these benchmarks, I will modify the
>> functions that have multiple backends to use the optimal one for a given
>> domain
>
>
>
> 3. Hypergeometric functions
>> #2516 <http://trac.sagemath.org/sage_trac/ticket/2516> is going to
>> implement generalized hypergeometric functions. These are a class of
>> holonomic functions, solutions to linear differential equations with
>> polynomial coefficients. Holonomic power series are closed under sum,
>> Cauchy product, and Hadamard product, so these operations could be
>> implemented. Useful references include 
>> 1<http://www.risc.jku.at/research/combinat/software/GeneratingFunctions/pub/mallinger96.pdf>
>>  and
>> 2<http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.187.6502&rep=rep1&type=pdf>
>> .
>
>
> My mentors for this project are Flavia Stan and Burcin Erocal.
>
> Now is the Community Bonding period; since

Re: [sage-devel] Matplotlib and sage's python

[Benjamin Jones]

Without building GUI support, it should work to replace show() with
savefig('plot.png'), for example. You won't get a window spawned with the
plot, but an image on disk.

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On Tue, May 21, 2013 at 11:30 PM, Julien Puydt wrote:

> Le 21/05/2013 21:57, William Stein a écrit :
>
>  Sage is by default built with any GUI support.
>>
>
> Is there a non-default and easy way to get a working
> matplotlib-on-bare-python?
>
> Snark on #sagemath
>
>
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Re: [sage-devel] Re: Public worksheet disabled on sagenb.org

[Benjamin Jones]

Seems like a reasonable first approximation would be to strip ALL
javascript from the worksheet archive.

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On Wed, May 15, 2013 at 7:05 AM, Volker Braun  wrote:

> Somebody needs to volunteer to strip out the malicious javascript from the
> archive of old worksheets, then we can host it...
>
>
> On Wednesday, May 15, 2013 2:31:28 PM UTC+1, leif wrote:
>>
>> It would probably at least be possible to freeze (by making them
>> read-only) some selected, (already published and) "approved" public
>> worksheets and make them available again to avoid dead links, perhaps by
>> (HTTP) redirection.
>>
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Re: [sage-devel] Re: Reasons for upgrading

[Benjamin Jones]

A, and B. D is nice but not essential.

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On Tue, Apr 30, 2013 at 11:24 AM, john_perry_usm  wrote:

> I know you said to move along if I don't upgrade, but I would like to
> upgrade if it weren't discommended or unreliable, for reasons (A) and (C).
> I actually thought it was discommended. I really need to pay more
> attention...
>
> john perry
>
>
> On Tuesday, April 30, 2013 5:14:58 AM UTC-5, Jeroen Demeyer wrote:
>>
>> Dear Sage upgraders,
>>
>> I would like to do a small survey considering upgrading (the "sage
>> --upgrade" command) to understand better what the important features
>> are. If you don't ever upgrade nor plan to upgrade, please move along.
>>
>> What are your major reasons for upgrading as opposed to building from
>> scratch? (multiple anwers possible, but only answer with things that are
>> important to you):
>>
>> A) Upgrades build faster.
>> B) Upgrading is easier.
>> C) I have a bunch of optional packages installed that I want to preserve.
>> D) I have various patches to the repos (e.g. devel/sage) that I want to
>> preserve.
>> E) Upgrading is cool!
>> F) None of the above, I do upgrade but I don't really care.
>>
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Re: [sage-devel] Race condition in singular doctest (#14371) needs review

[Benjamin Jones]

FWIW, I'm also experiencing some strange issues with doctesting that don't
occur in 5.8, but do in all the 5.9.betaX's. I posted about this on the
sage-release thread and at #4102.

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On Fri, Apr 5, 2013 at 4:33 AM, John Cremona  wrote:

> Is it not a blocker that (for some of us) "make ptestlong" cannot be
> run for fear of the rogue ecl processes?
>
> I successfully built 5.9.beta3 and ran "make testlong" without the p,
> watched it,  after a while saw two ecl processes using >8GB each and
> killed them both.  The rest of the test finished with no problems.
> But it is a real nuisance that I cannot just start the test and forget
> about it.
>
> Plain ubuntu 12.04.
>
> John
>
> On 5 April 2013 12:29, Jeroen Demeyer  wrote:
> > There is one more sage-5.9 blocker ticket which needs review:
> > http://trac.sagemath.org/sage_trac/ticket/14371
> >
> > It's a race condition in a doctest for the Singular pexpect interface,
> the
> > only solution I found was to insert a "sleep(0.5)" in the test.
> >
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Re: [sage-devel] Re: a problem in the new permutation groups code (and a solution ?)

[Benjamin Jones]

On Tue, Mar 26, 2013 at 3:34 AM, Volker Braun  wrote:
>
>
> In any case, http://trac.sagemath.org/14291 is about hooking up GAP and
> not creating a framework for group actions. So in the interest of a finite
> amout of work per ticket, we should probably fall back to only allow
> explicitly specified group actions (OnPoints/OnTuples etc) there. Once your
> group action framework is in place it'll be easy enough to hook that up
> into the orbit method as well.
>

+1

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Re: [sage-devel] Re: a problem in the new permutation groups code (and a solution ?)

[Benjamin Jones]

Big +1 to framework for explicitly instantiating group actions.

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On Mon, Mar 25, 2013 at 11:01 PM, tom d  wrote:

> Specify the action!  By making a group action framework, we would also be
> providing the possibility of changing the action to something contrary to
> the assumptions of the original developers Yes, in fact I think this is
> one of the natural reasons for doing an explicit group action framework.
>  Even for the action of S_n on the set {1,2,3,...,n} one can twist the
> 'usual' action with an automorphism \phi of S_n, so that \sigma acts on i
> by \phi(\sigma)(i).
>
> The 'usual' actions then become special predefined objects, like the
> special graphs, maybe summoned up automatically using the
> permutation/whatever's __call__ function if it's an idiomatic action like
> \sigma(3).
>
> As a category, I would imagine we would have a GroupAction category and/or
> a GroupWithAction category, which would put some requirements on the group
> and its elements.
>
> I've attached a bit of sample code, which could be used as a base to start
> a group action category.  (Currently just a class, as I need to go and read
> the category tutorials, though...)  The examples are at the bottom;
> includes products of actions, twisting by a group endomorphism, computing
> characters, orbits, checking the action definition, checking transitivity,
> and generating the Cayley graph of the action for a given generating
> set.
>
> On Monday, March 25, 2013 2:30:57 PM UTC+3, Volker Braun wrote:
>>
>> The group action category stuff would be nice, but you would run into
>> exactly the same question that Dima asked: What are you going to do if
>> there is more than one possible action. You'll have to either use some
>> heuristics (take the simpler / less nested action) or raise some exception
>> telling the user to explicitly disambiguate between them.
>>
>>
>>
>> On Monday, March 25, 2013 8:33:57 AM UTC+1, tom d wrote:
>>>
>>> Hm, wouldn't this just be a direct product of the individual group
>>> actions?  It seems to me that we're expecting the permutations to act
>>> according to an 'obvious' group action.  Should we also expect 'obvious'
>>> actions of things like a dihedral group when given a 2-dimensional vector?
>>> Probably the answer is to generalize and build up a proper group actions
>>> category (with obvious methods passing to representations!).
>>
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Re: [sage-devel] a problem in the new permutation groups code (and a solution ?)

[Benjamin Jones]

It seems to me that the ambiguity arises from the original statement, "the
orbit (1,2) under G", not the fact that the domain is non-homogeneous. It's
less ambiguous to say directly G.{1, 2} (the orbit of the _element_ {1, 2})
versus G.1 \union G.2 (the orbit of the subset {1, 2}). Then, which group
action you are talking about is clear.

For the API, it seems best (to me) to have the standard orbit function
(which takes an element of the domain and returns its orbit) and add to
that an optional parameter which changes the semantics to orbits of sets.
The user would have to supply a subset of the domain then, instead of an
element or you'd raise a TypeError.

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Re: [sage-devel] Review needed : short patch exposes a Group method from GAP in Sage

[Benjamin Jones]

On Wed, Feb 27, 2013 at 3:53 PM, Nathann Cohen  wrote:
> Helloo everybody !!
>
> There's a small patch I wrote aaages ago and there has been no activity
> on the ticket for the last 7 months. Would anybody here feel like giving it
> a review ? It just exposes a method from GAP and I would like to have it in
> order to plot some graphs..
>
> http://trac.sagemath.org/sage_trac/ticket/13102
>
> I would be glad to review one of yours in exchange, for as long as I can
> understand what it does :-)
>
> THaaanksss !!
>
> Nathann


Hi Nathann,

I left a comment on the ticket and made myself a reviewer.

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Re: [sage-devel] Re: Fwd: [gdr-im] Inria : Manuel Bronstein's codes / Open source diffusion

[Benjamin Jones]

On Mon, Feb 25, 2013 at 3:52 AM, Jason Grout
 wrote:
> On 2/23/13 6:32 PM, Benjamin Jones wrote:
>
>> I've been working (somewhat slowly) on an implementation of
>> Bronstein's pmint (Poor Man's Integrator) in Sage. I'd heard a while
>> back that someone's student had done an implementation of it in Sage,
>> but I don't know if it was released. Does anyone have more info on
>> that?
>
>
> You might check out Sympy's work in that area:
>
> http://docs.sympy.org/dev/modules/integrals/integrals.html#sympy.integrals.heurisch
>
> Thanks,
>
> Jason
>

Thanks Jason! That's a great pointer. It looks like this "heurisch"
integrator was added in sympy 0.7.2 and Sage includes 0.7.1 at the
moment. Also, unfortunately, the conversion to and from sympy isn't
implemented for a lot of our special functions (something that is on
my todo list).

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Re: [sage-devel] Fwd: [gdr-im] Inria : Manuel Bronstein's codes / Open source diffusion

[Benjamin Jones]

On Sat, Feb 23, 2013 at 3:56 AM, John Cremona  wrote:
> I expect that James Davenport might have an opinion!
>
> John
>
> On 23 February 2013 11:51, Sébastien Labbé  wrote:
>> Hi sage-devel,
>>
>> I am forwarding this email to the sage-devel mailing list (see below).
>> The question is : May it be usefull for Sage? Here are some more links
>> :
>>
>> "In Memory of Manuel Bronstein"
>> http://www.ccas.ru/sabramov/ps/PCS56.pdf
>>
>> http://en.wikipedia.org/wiki/Risch_algorithm
>>
>> Cheers,
>>
>> Sébastien
>>

Since most (all?) of that code released is written in Aldor or Maple,
I'm not sure any of it naturally fits into Sage. Maybe as a series of
optional packages?

I've been working (somewhat slowly) on an implementation of
Bronstein's pmint (Poor Man's Integrator) in Sage. I'd heard a while
back that someone's student had done an implementation of it in Sage,
but I don't know if it was released. Does anyone have more info on
that?

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Re: [sage-devel] Please test this if you have OS X 10.8

[Benjamin Jones]

On Tue, Feb 12, 2013 at 12:53 PM, kcrisman  wrote:
> Hi!  Thanks to very hard work by Ivan Andrus, we have Sage double-clicking
> sws files on Mac.  We just need one more test to make it complete.
>
> If you DO have OS X 10.8 Mountain Lion but have NOT ever made something that
> makes sws files open with Sage.app on a double-click, please download
> http://sage.math.washington.edu/home/palmieri/misc/sage-Sage-testing-doubleclick-x86_64-Darwin.dmg
> and try it out.  We particularly would like people who don't even have
> Sage.app to try this, since with multiple versions of Sage.app there can be
> natural confusion as to which one is supposed to open the file, though in
> principle this should work there as well.  Thanks to John Palmieri for
> helping with this.
>
> - kcrisman

Works for me (OS X 10.8.2). I've never installed any .app Sage distro
on this particular machine before. I downloaded this one, dragged to
/Applications, waiting quite a while, and then tried double clicking a
sws I had laying around. Worked perfectly. Nice work!

The helpful messages that pop up along the way have really improved
too! I think this will go a long way to getting new folks started with
Sage on OS X.

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Re: [sage-devel] Re: How to make Sage worksheets publically available

[Benjamin Jones]

On Mon, Jan 21, 2013 at 12:17 PM, Jason Grout
 wrote:

>
> I couldn't figure out how to get the attached file from that pdf. Here's
> another way to embed files (see the first answer):
> http://tex.stackexchange.com/questions/17926/how-do-i-make-an-attached-file-display-like-a-link
>
>
> Thanks,
>
> Jason
>

If you download the source (from "other formats"), you get a .tar.gz
that has the .sage file in it.

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Re: [sage-devel] How to automatically download the newest sage?

[Benjamin Jones]

On Wed, Jan 16, 2013 at 2:12 PM, Maarten Derickx
 wrote:
> Dear all,
>
> I want to create a script that when I run it automatically downloads the
> latest sage developement version. I was wondering what would be the best way
> to do so?
>
> Thanks Maarten
>

A while back, I copied a script that Harald wrote, made some trivial
modifications, and use it regularly to download a command line
specified sage version (including beta versions)

https://github.com/benjaminfjones/sage-devel/blob/master/sage-from-source.sh
(pull requests welcome!)

usage example

$ ./sage-from-source.sh 5.6.beta3

You could easily modify it to scrape the latest published development
version from http://sagemath.org/download-latest.html

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Re: [sage-devel] Re: Why does - (x > 100) return -x > -100 ?

[Benjamin Jones]

On Mon, Jan 7, 2013 at 10:53 AM, Keshav Kini  wrote:
> Benjamin Jones  writes:
>
>> On Mon, Dec 17, 2012 at 9:32 PM, P Purkayastha 
>> wrote:
>>
>> On 12/18/2012 10:10 AM, Benjamin Jones wrote:
>>
>> if y > 0 is true,
>> is x*(y > 0) true or false?
>>
>>
>> Why is this kind of operation (+,-,*, etc) distributive over
>> comparison operators? Is this distributive operation well defined
>> in general, maybe according to some theory?
>>
>>
>>
>> If you think about the comparison operators as type constructors (for
>> the SR type), it's useful for them to be functors. In other words,
>> it's useful to be able to map over them, e.g. map the function that
>> is multiplication by a constant element of SR over a comparison:
>>
>> sage: y = var('y')
>> sage: x * (y > 0)
>> x*y > 0
>>
>> Just like applying the operator (x*_) over a list [ y, 0 ].
>
> Couldn't you apply the same logic to "*" as well? Now (a * b) * c
> becomes (a * c) * (b * c), which is obviously not what we want.
>
> Certainly it's nice to be able to map over things. I would think that
> there should be some actual syntax for this, though, rather than just
> implicitly distributing all operations over relational operators. As far
> as I can see, the only thing that's special here about relational
> operators as opposed to arithmetic operators is that we don't currently
> have a coherent way of resolving the application of other operators to
> relational expressions. I don't think that should mean that by default
> we just distribute.
>
> See also http://trac.sagemath.org/sage_trac/ticket/7660#comment:8 .
>
> -Keshav
>
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>
>

I agree that an explicit syntax for mapping over relations would be
better than having it done implicitly. But, then again, it would be
nice to  implicitly map over equality, there would be no confusion
there.

So, what should x*(y > 0) do, raise a NotImplementedError? And x*(y ==
0)? I guess we just special case inequalities.

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Re: [sage-devel] Inconsitent output of the domain for the automorphism group of graph?

[Benjamin Jones]

On Fri, Dec 28, 2012 at 12:27 PM, David Roe  wrote:
> In the long term, I think the right solution is to copy what is done for
> Galois groups of number fields: depending on a keyword option to
> automorphism_group(), we should return either the abstract permutation group
> (as is done now) or a group equipped with an action on the edges and
> vertices of the graph.
> David
>

This is a good idea. For the lurkers, azi created ticket #13874 for this.

--
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> On Fri, Dec 28, 2012 at 2:36 AM, Jernej Azarija 
> wrote:
>>
>>
>>
>> On Thursday, 27 December 2012 23:51:07 UTC+1, Benjamin Jones wrote:
>>>
>>> On Thu, Dec 27, 2012 at 1:07 PM, Jernej Azarija 
>>> wrote:
>>> >
>>> >
>>> > On Thursday, 27 December 2012 20:59:45 UTC+1, Benjamin Jones wrote:
>>> >>
>>> >> On Thu, Dec 27, 2012 at 11:39 AM, Jernej Azarija 
>>> >> wrote:
>>> >> > Hello!
>>> >> >
>>> >> > I apologize for posting this question here but somehow I am not
>>> >> > allowed
>>> >> > to
>>> >> > drop questions to sage-support. Moreover I do not feel confident
>>> >> > enough
>>> >> > to
>>> >> > post this thing as a bug on the trac wiki.
>>> >> >
>>> >> > Working with a large graph G on ~250 vertices I have noticed that
>>> >> > elements
>>> >> > of the automorphism group of G permute ~50 vertices and that most
>>> >> > vertices
>>> >> > are fixed by any automorphism. Hence most orbits of the automorphism
>>> >> > group
>>> >> > contain just singletons. However sage simply discards all vertices
>>> >> > that
>>> >> > are
>>> >> > fixed by the automorphism . In my case this resulted in an
>>> >> > "incomplete"
>>> >> > orbit containing just 50 elements. An extreme case happens when one
>>> >> > deals
>>> >> > with an asymmetric graph
>>> >> >
>>> >> > ===
>>> >> > sage: G = graphs.RandomRegular(7,50)
>>> >> > sage: G.vertices()
>>> >> > [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
>>> >> > 19,
>>> >> > 20,
>>> >> > 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,
>>> >> > 38,
>>> >> > 39,
>>> >> > 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]
>>> >> > sage: G.automorphism_group().domain()
>>> >> > {1}
>>> >> > sage: G.automorphism_group().orbits()
>>> >> > [[1]]
>>> >> > ===
>>> >> >
>>> >> > This of course is not the desired result since one assumes orbits
>>> >> > partition
>>> >> > the group.
>>> >> >
>>> >> > Is this a bug or am I simply missing some parameter to resolve this
>>> >> > issue?
>>> >> >
>>> >>
>>> >> I don't think this is a bug.
>>> >
>>> >
>>> > Hello! Thanks for your reply!
>>> >>
>>> >>
>>> >> It looks to me like G.automorphism_group() is returning an abstract
>>> >> permutation group. For a lot of random graphs this is going to be the
>>> >> trivial group "Permutation Group with generators [()]" (a random graph
>>> >> is likely to have no symmetry). The natural (non-empty) domain for the
>>> >> action of such a group is a singleton set and there is of course only
>>> >> one orbit there. Notice that G.automorphism_group().domain() returns
>>> >> {1}, it's the domain of a permutation group on {1, ... , n}.
>>> >
>>> > I am not sure this is consistent with the mathematical definition of
>>> > the
>>> > domain of a group acting on a set S.
>>>
>>> G.automorphism_group() is not returning "a group acting on a set S",
>>> merely a permutation group. Observe that the trivial group is
>>> isomorphic to the trivial permutation subgroup of {1} as well as {0,
>>> 1, ... , 50}.
>>>
>>> > Even *if* I take this convention for
>>> > granted, it becomes a mess if I try to obtain the orbits of a
>>> > ve

Re: [sage-devel] Inconsitent output of the domain for the automorphism group of graph?

[Benjamin Jones]

>>
>> The documentation (G.automorphism_group?) describes how to get the
>> subgroup of the automorphism group that preserves a given partition of
>> the vertex set.
>
> The documentation about the partition thing is quite shallow (just one
> sentence) and the expected usage does not seem to work:
> ===
> sage: G = graphs.PetersenGraph()
> sage: G.automorphism_group(partition=[[1]])
> ---
> KeyError  Traceback (most recent call last)
>
> /home/foo/ in ()
>
> /home/foo/sage-5.5.rc0/local/lib/python2.7/site-packages/sage/graphs/generic_graph.pyc
> in automorphism_group(self, partition, translation, verbosity, edge_labels,
> order, return_group, orbits)
>   16466 HB = H._backend
>   16467 for u,v in self.edge_iterator(labels=False):
>> 16468 u = G_to[u]; v = G_to[v]
>   16469 HB.add_edge(u,v,None,self._directed)
>   16470 GC = HB._cg
>
> KeyError: 0
>
> =
>
> does anyone happen to know how is this thing used? I need to compute the
> automorphism group that fixes the specified vertex (the stabilizer of a
> vertex v of the automorphism of G)

The partition you give should be a partition of the vertex set.
`partition=[[1]]` would only work if you had a vertex set {1}. Here
are some examples:

sage: G = graphs.PetersonGraph()
sage: G.vertices()
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
sage: G.automorphism_group(partition=[[0], [1..9]])
Permutation Group with generators [(3,7)(4,5)(8,9),
(2,6)(3,8)(4,5)(7,9), (1,4,5)(2,3,8,6,9,7)]
sage: G.automorphism_group(partition=[[0,1,2], [3..9]])
Permutation Group with generators [(3,7)(4,5)(8,9), (2,10)(3,5)(4,7)]

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Re: [sage-devel] Inconsitent output of the domain for the automorphism group of graph?

[Benjamin Jones]

On Thu, Dec 27, 2012 at 1:07 PM, Jernej Azarija  wrote:
>
>
> On Thursday, 27 December 2012 20:59:45 UTC+1, Benjamin Jones wrote:
>>
>> On Thu, Dec 27, 2012 at 11:39 AM, Jernej Azarija 
>> wrote:
>> > Hello!
>> >
>> > I apologize for posting this question here but somehow I am not allowed
>> > to
>> > drop questions to sage-support. Moreover I do not feel confident enough
>> > to
>> > post this thing as a bug on the trac wiki.
>> >
>> > Working with a large graph G on ~250 vertices I have noticed that
>> > elements
>> > of the automorphism group of G permute ~50 vertices and that most
>> > vertices
>> > are fixed by any automorphism. Hence most orbits of the automorphism
>> > group
>> > contain just singletons. However sage simply discards all vertices that
>> > are
>> > fixed by the automorphism . In my case this resulted in an "incomplete"
>> > orbit containing just 50 elements. An extreme case happens when one
>> > deals
>> > with an asymmetric graph
>> >
>> > ===
>> > sage: G = graphs.RandomRegular(7,50)
>> > sage: G.vertices()
>> > [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
>> > 20,
>> > 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,
>> > 39,
>> > 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]
>> > sage: G.automorphism_group().domain()
>> > {1}
>> > sage: G.automorphism_group().orbits()
>> > [[1]]
>> > ===
>> >
>> > This of course is not the desired result since one assumes orbits
>> > partition
>> > the group.
>> >
>> > Is this a bug or am I simply missing some parameter to resolve this
>> > issue?
>> >
>>
>> I don't think this is a bug.
>
>
> Hello! Thanks for your reply!
>>
>>
>> It looks to me like G.automorphism_group() is returning an abstract
>> permutation group. For a lot of random graphs this is going to be the
>> trivial group "Permutation Group with generators [()]" (a random graph
>> is likely to have no symmetry). The natural (non-empty) domain for the
>> action of such a group is a singleton set and there is of course only
>> one orbit there. Notice that G.automorphism_group().domain() returns
>> {1}, it's the domain of a permutation group on {1, ... , n}.
>
> I am not sure this is consistent with the mathematical definition of the
> domain of a group acting on a set S.

G.automorphism_group() is not returning "a group acting on a set S",
merely a permutation group. Observe that the trivial group is
isomorphic to the trivial permutation subgroup of {1} as well as {0,
1, ... , 50}.

> Even *if* I take this convention for
> granted, it becomes a mess if I try to obtain the orbits of a
> vertex-stabilizer. Being more concrete:
>
> sage: G = graphs.RandomRegular(7,50)
> sage: G.automorphism_group().stabilizer(1).orbits()
> [[1]]
>
> which is clearly not the desired output.

This in consistent with what I said above. In this case
G.automorphism_group() is the trivial group (permutation group with no
generators). So, G.automorphism_group().stabilizer(1) is again the
trivial group.

>>
>> One simple thing you can do is call:
>>
>> sage: A = G.automorphism_group(orbits=True)
>
> Yes. Is there a way to extend this answer to the case when I wish to obtain
> the orbit of a specific subgroup of the automorphism group?
>

The documentation (G.automorphism_group?) describes how to get the
subgroup of the automorphism group that preserves a given partition of
the vertex set. Other than that it would depend on what subgroup you
want. Check out the generic group methods that construct subgroups.

Also, see this discussion:
https://groups.google.com/forum/?fromgroups=#!topic/sage-support/HX0QfXgwO5s

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Re: [sage-devel] Inconsitent output of the domain for the automorphism group of graph?

[Benjamin Jones]

On Thu, Dec 27, 2012 at 11:39 AM, Jernej Azarija  wrote:
> Hello!
>
> I apologize for posting this question here but somehow I am not allowed to
> drop questions to sage-support. Moreover I do not feel confident enough to
> post this thing as a bug on the trac wiki.
>
> Working with a large graph G on ~250 vertices I have noticed that elements
> of the automorphism group of G permute ~50 vertices and that most vertices
> are fixed by any automorphism. Hence most orbits of the automorphism group
> contain just singletons. However sage simply discards all vertices that are
> fixed by the automorphism . In my case this resulted in an "incomplete"
> orbit containing just 50 elements. An extreme case happens when one deals
> with an asymmetric graph
>
> ===
> sage: G = graphs.RandomRegular(7,50)
> sage: G.vertices()
> [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
> 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39,
> 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]
> sage: G.automorphism_group().domain()
> {1}
> sage: G.automorphism_group().orbits()
> [[1]]
> ===
>
> This of course is not the desired result since one assumes orbits partition
> the group.
>
> Is this a bug or am I simply missing some parameter to resolve this issue?
>

I don't think this is a bug.

It looks to me like G.automorphism_group() is returning an abstract
permutation group. For a lot of random graphs this is going to be the
trivial group "Permutation Group with generators [()]" (a random graph
is likely to have no symmetry). The natural (non-empty) domain for the
action of such a group is a singleton set and there is of course only
one orbit there. Notice that G.automorphism_group().domain() returns
{1}, it's the domain of a permutation group on {1, ... , n}.

I guess what you want is the automorphism group along with it's action
on the set of vertices of the graph.

One simple thing you can do is call:

sage: A = G.automorphism_group(orbits=True)

to get the abstract group back along with the set of orbits. Also, by
setting `translation=True` you can also get a dictionary back that
provides translation from vertices {0, 1, ..., n} to the domain set of
the permutation group (a subset of {1, ... , n+1}).

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Re: [sage-devel] Re: Why does - (x > 100) return -x > -100 ?

[Benjamin Jones]

On Mon, Dec 17, 2012 at 9:32 PM, P Purkayastha  wrote:

> On 12/18/2012 10:10 AM, Benjamin Jones wrote:
>
>> if y > 0 is true,
>> is x*(y > 0) true or false?
>>
>
> Why is this kind of operation (+,-,*, etc) distributive over comparison
> operators? Is this distributive operation well defined in general, maybe
> according to some theory?
>
>
If you think about the comparison operators as type constructors (for the
SR type), it's useful for them to be functors. In other words, it's useful
to be able to map over them, e.g. map the function that is multiplication
by a constant element of SR over a comparison:

sage: y = var('y')
sage: x * (y > 0)
x*y > 0

Just like applying the operator (x*_) over a list [ y, 0 ].

Another example:

sage: f(x) = x + 1
sage: y = var('y')
sage: expr = y > 0
sage: f(expr)
(y > 0) + 1

If > was a functor, you would expect to get f(y) > f(0), which is y + 1 >
1. And indeed,

sage: (y > 0) + 1
y + 1 > 1

So things look consistent. This even works for non-linear functions:

sage: f(x) = x^2+1
sage: f(y > 0)
(y > 0)^2 + 1
sage: (y > 0)^2 + 1
y^2 + 1 > 1

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Re: [sage-devel] Re: Why does - (x > 100) return -x > -100 ?

[Benjamin Jones]

On Mon, Dec 17, 2012 at 6:10 PM, Benjamin Jones
 wrote:
>
>
> On Mon, Dec 17, 2012 at 5:32 PM, Travis Scrimshaw  wrote:
>>
>> Hey Sebastien,
>>
>>> But not for multiplication by a negative number :
>>>
>>> sage: - (x > 100)
>>> -x > -100
>>>
>>> Do you consider this to be a bug? I would prefer the answer "-x < -100" to 
>>> preserve the space of solutions. Do you?
>>>
>>
>> The result is not what I would expect. However, I will let someone more 
>> versed with the symbolic ring officially call it a bug.
>>
>> It's also not just negation, but honest multiplication:
>>
>>sage: (-1)*(x > 100)
>>-x > -100
>>sage: ZZ(-1)*(x > 100)
>>-x > -100
>>sage: SR(-1)*SR(x > 100)
>>-x > -100
>>
>> Best,
>> Travis
>>
>>
>> --
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>>
>>
>
>
> It's hard to tell from the implementation if this behavior is intentional, 
> unintentional, or a bug. The implementation is just that multiplication maps 
> over relational operators like ==, <, <=, etc. But I think it's not possible 
> in the current framework to make multiplication preserve the truth of a 
> statement, e.g.
>
> if y > 0 is true,
> is x*(y > 0) true or false?
>
> You can't decide unless you know more about x. If you want to make 
> multiplying by elements in SR preserve truth of a statement you have to 
> decide this.
>
> The same question has come up on ask.sagemath: 
> http://ask.sagemath.org/question/1656/multiplying-an-inequality-by-1
>
> --
> Benjamin Jones

Sorry for the noise..  I meant to say (at the top) that from the
implementation (of sage.symbolic.expression.Expression._mul_) it's
pretty clear that this behavior *is* intentional, not a bug, but
that's not to say it's desirable in all situations.

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Re: [sage-devel] Re: Why does - (x > 100) return -x > -100 ?

[Benjamin Jones]

On Mon, Dec 17, 2012 at 5:32 PM, Travis Scrimshaw wrote:

> Hey Sebastien,
>
> But not for multiplication by a negative number :
>>
>> sage: - (x > 100)
>> -x > -100
>>
>> Do you consider this to be a bug? I would prefer the answer "-x < -100"
>> to preserve the space of solutions. Do you?
>>
>>
> The result is not what I would expect. However, I will let someone more
> versed with the symbolic ring officially call it a bug.
>
> It's also not just negation, but honest multiplication:
>
>sage: (-1)*(x > 100)
>-x > -100
>sage: ZZ(-1)*(x > 100)
>-x > -100
>sage: SR(-1)*SR(x > 100)
>-x > -100
>
> Best,
> Travis
>
>
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>
>

It's hard to tell from the implementation if this behavior is intentional,
unintentional, or a bug. The implementation is just that multiplication
maps over relational operators like ==, <, <=, etc. But I think it's not
possible in the current framework to make multiplication preserve the truth
of a statement, e.g.

if y > 0 is true,
is x*(y > 0) true or false?

You can't decide unless you know more about x. If you want to make
multiplying by elements in SR preserve truth of a statement you have to
decide this.

The same question has come up on ask.sagemath:
http://ask.sagemath.org/question/1656/multiplying-an-inequality-by-1

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Re: [sage-devel] Re: Normalization of a vector

[Benjamin Jones]

On Fri, Nov 30, 2012 at 3:57 PM, Eviatar  wrote:

> I think echelonize is a bit misleading, because it's not really doing
> Gaussian elimination. Besides, I think it would have to be rref to be
> consistent with matrices (it's reduced row echelon form, not simply row
> echelon form):
>
> sage: matrix([0,3,4]).echelon_form()
> [0 3 4]
> sage: matrix([0,3,4]).rref()
> [  0   1 4/3]
>
> Even if "normal form" is used in some specific contexts, I don't think
> many people would associate it with that function, and it might create
> confusion with normalize().
>
> How about a vote?
>
>1. reduce() (kind of ambiguous and might be mistaken for the Python
>function reduce)
>2. echelonize() (probably echelon_form() is more appropriate, since
>it's not mutating the vector)
>3. rref()
>4. normal_form()
>5. monicize()
>6. divide_by_leading()
>
> I vote (6).
>
>
The name 'normal_form' refers to the property of the returned vector. From
that point of view, how about

7. monic()

I vote (7).

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Re: [sage-devel] Re: Normalization of a vector

[Benjamin Jones]

On Fri, Nov 30, 2012 at 1:36 PM, Eviatar  wrote:

> Hello,
>
> I was planning to work on the patch for this; however, is "normal form"
> known terminology for dividing a vector by the leading entry? A Google
> search returns no such use. Wouldn't it be better for it to be named
> something like divided_by_leading, to remove ambiguity and potential
> confusion?
>
>
The author of that method may have named it in the context of projective
geometry.

See http://en.wikipedia.org/wiki/Homogeneous_coordinates. For example, in
the projective space P_2, each non-zero vector (x, y, z) corresponds to a
point and two vectors correspond to the same point iff one is a scalar
multiple of the other. So for each point with representative vectors
satisfying x \ne 0 (i.e. the points in one of the standard coordinate
patches), there is a unique "normal form" coordinate (1, y/x, z/x).

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Re: [sage-devel] Bug in functions sin, cos, exp...

[Benjamin Jones]

On Tue, Oct 30, 2012 at 2:58 PM, David Roe  wrote:
> I think this is a bug: the type of the result should be consistent.
> David
>
>
> On Tue, Oct 30, 2012 at 3:54 PM, mmarco  wrote:
>>
>> There is an inconsistency in the behaviour of the cosine function
>> sage: type(cos(1))
>> 
>> sage: type(cos(pi))
>> 
>> sage: type(cos(0))
>> 
>>
>> It also happens with the sine:
>>
>> sage: type(sin(0))
>> 
>> sage: type(sin(pi))
>> 
>>
>> and the exponential:
>> sage: type(exp(0))
>> 
>> sage: type(exp(1))
>> 
>>
>>  the logarithm:
>>
>> sage: type(log(1))
>> 
>> sage: type(log(2))
>> 
>> sage: type(log(0))
>> 
>>
>>
>>
>> Is there some reason for this or is it a bug? Shouldn't the answer be,
>> at least, a sage Integer and not a python int?
>>

There is a ticket for this on trac somewhere.. can't locate its number ATM.

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Re: [sage-devel] Defining anti-commutator

[Benjamin Jones]

On Tue, Oct 9, 2012 at 7:46 AM, Dox  wrote:
> Dear all,
>
> I'm interested in defining the anti-commutator (function or method) for
> matrices. I look up the definition of the commutator, and it's very simple
>
> def acomm(self,other):
> return self*other + other*self
>
> providing (of course) the additional information about the usage.
>
> However I tried to add this function to my sage-test branch... and I
> couldn't find where the methods for matrices are.
>
> Where should I include this changes?
>
> Thx.
>

The commutator method is located in sage/matrix/matrix0.pyx which I
found by doing:

{{{
sage: search_src("commutator")
...
matrix/matrix0.pyx:2154:def commutator(self, other):
...
}}}

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Re: [sage-devel] Re: When will OS X 10.8 be supported, officially?

[Benjamin Jones]

On Wed, Sep 26, 2012 at 9:20 PM, Benjamin Jones
 wrote:
> On Wed, Sep 26, 2012 at 7:14 PM, John H Palmieri  
> wrote:
>>
>>
>> On Wednesday, September 26, 2012 6:45:48 PM UTC-7, JBT wrote:
>>>
>>> Just out of curiosity, when will be OS X 10.8 (Mountain Lion) supported by
>>> SAGE, officially?
>>
>>
>> Well, we need to get enough people running OS X 10.8 to build and test Sage
>> successfully. Three of us (as far as I can tell) have done this, while you
>> haven't. We need to understand why you're having problems, and we need to
>> get more people involved. I personally think that the scipy spkg at
>> http://trac.sagemath.org/sage_trac/ticket/13309 is safe enough, and solves
>> the problem for enough people, that it should be merged. Given your
>> experience, that doesn't mean that Mountain Lion will be "officially
>> supported", though.
>>
>> --
>> John
>>
>
> I have a macbook-pro running 10.8.2 now, I'll give building 5.3 with
> the special instructions a shot tomorrow and report back.
>
> --
> Benjamin Jones

I built sage-5.3 with the scipy-0.9.p2 package successfully on Mac OS
X 10.8.2 today. Here is what I did:

1. update OS to 10.8.2 using Software Update
2. install latest XCode v4.5 (not just the command line tools)
3. download sage-5.3 source tarball, run make
--> make fails at scipy
4. run `./sage -i `
--> scipy builds successfully!
5. run make again
--> make finishes successfully!

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Re: [sage-devel] Re: When will OS X 10.8 be supported, officially?

[Benjamin Jones]

On Wed, Sep 26, 2012 at 7:14 PM, John H Palmieri  wrote:
>
>
> On Wednesday, September 26, 2012 6:45:48 PM UTC-7, JBT wrote:
>>
>> Just out of curiosity, when will be OS X 10.8 (Mountain Lion) supported by
>> SAGE, officially?
>
>
> Well, we need to get enough people running OS X 10.8 to build and test Sage
> successfully. Three of us (as far as I can tell) have done this, while you
> haven't. We need to understand why you're having problems, and we need to
> get more people involved. I personally think that the scipy spkg at
> http://trac.sagemath.org/sage_trac/ticket/13309 is safe enough, and solves
> the problem for enough people, that it should be merged. Given your
> experience, that doesn't mean that Mountain Lion will be "officially
> supported", though.
>
> --
> John
>

I have a macbook-pro running 10.8.2 now, I'll give building 5.3 with
the special instructions a shot tomorrow and report back.

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Re: [sage-devel] LibGAP spkg vote!

[Benjamin Jones]

On Sun, Sep 23, 2012 at 6:40 AM, Volker Braun  wrote:
> LibGAP (the C library interface to GAP) is finally usable and ready to be
> released into the wild! We will ship it as a separate spkg since
>   * Upstream doesn't build a shared library
>   * The build system is replaced by standard autotools
>   * To avoid symbol collisions every gap function and global variable is
> renamed with a libGAP_ prefix
>   * We add hooks to input/output, error handling, and the GAP memory
> manager.
>
> Actually, prefixing the symbols in a library might be a good idea in other
> libraries that were not originally written with sharing in mind. If two
> functions have the same name in two shared libraries, then (at least on
> Linux) the first one wins which is almost certainly not what the second
> library wants. LibGAP does the prefixing with a script using the python ply
> module to identify the globals.
>
> Per the usual rules, new spkgs need a vote so now is your chance to be heard
> ;-)
>

Thanks Volker, libGAP us a great contribution!

+1

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Re: [sage-devel] Re: inner product of complex vectors

[Benjamin Jones]

On Wed, Sep 12, 2012 at 2:04 PM, Jason Grout
 wrote:
>
> Fair enough.  That's convincing to me.  I wish there was a nice notation in
> Sage for v.inner_product(w) that wasn't so cumbersome and wordy, then!
>
>
> Thanks,
>
> Jason
>

I have wished for the same thing on occasion. One idea would be to
introduce some new abstract binary operators, say <*> and <+> and have
the preparser magic v <*> w into v.__abstract_mul__(w). In Haskell,
arbitrary infix operators can be defined using special characters
(e.g. <++>, +-+, and  are allowable) and many people find it quite
handy.

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Re: [sage-devel] sage startup time hasn't improved...

[Benjamin Jones]

On Fri, Aug 10, 2012 at 7:51 PM, William Stein  wrote:
> Hi,
>
> I'm sad that on a fast SSD repeatedly doing the following:
>
> wstein@geom:/usr/local/sage/sage-5.2$ time echo "" | ./sage
> --
> | Sage Version 5.2, Release Date: 2012-07-25 |
> | Type "notebook()" for the browser-based notebook interface.|
> | Type "help()" for help.|
> --
> sage: sage:
> Exiting Sage (CPU time 0m0.03s, Wall time 0m0.03s).
>
> real0m1.902s
> user0m1.428s
> sys 0m0.424s
>
> always outputs 1.9 seconds!   That test was < 1 second on sage.math
> when I put in a doctest to make sure it didn't exceed that 1 second,
> when we were trying to improve the sage startup time.  In the
> intervening year (?), the test is ignored or gone, and the startup
> time seems to have got a bit worse.  Dang.
>
> On another faster machine, I'm getting:
>
> wstein@combinat:/usr/local/sage/sage-5.2$ time echo "" | ./sage
> --
> | Sage Version 5.2, Release Date: 2012-07-25 |
> | Type "notebook()" for the browser-based notebook interface.|
> | Type "help()" for help.|
> --
> sage: sage:
> Exiting Sage (CPU time 0m0.04s, Wall time 0m0.05s).
>
> real0m1.580s
> user0m1.224s
> sys 0m0.356s
>
>
> Any ideas?
>
>
>
>
> William
>

Another data point: I also get (just barely) under 1s on a ~1 year old
server running debian 6.0.5.


jonesbe@sage:~/sage/sage-5.2$ time echo "" | ./sage
--
| Sage Version 5.2, Release Date: 2012-07-25 |
| Type "notebook()" for the browser-based notebook interface.|
| Type "help()" for help.|
--
Loading Sage library. Current Mercurial branch is: 11143
sage: sage:
Exiting Sage (CPU time 0m0.02s, Wall time 0m0.02s).

real0m0.977s
user    0m0.676s
sys 0m0.300s


This is a VM running on Intel(R) Xeon(R) CPU X5690  @ 3.47GHz and
RAID-5 server grade hard drives. Mount options:


/dev/xvda4 on /home type ext3
(rw,nosuid,nodev,relatime,errors=continue,data=ordered)



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Re: [sage-devel] erf - numerical calculation tracs

[Benjamin Jones]

On Fri, Aug 10, 2012 at 4:30 PM, MartinX  wrote:
> I am slightly puzzled.  Trac #1173, #13050 and #13003 all aim to improve
> numerical calculation of erf() and are still open.  In the meantime, at
> least as far as 5.2 is concerned, it appears that erf() has been updated too
> be consistent with the template developed in #11143 and now uses mpmath and
> deals with complex numbers for numerical calculation.  Should we now close
> the open tracs?  Or am I missing the point?
>
> Martin
>

I think #13003 can be closed; it is marked "Reported upstream.
Developers deny it's a bug." and the original reason for the ticket
has been solved in the meantime by #13193 (see
http://trac.sagemath.org/sage_trac/ticket/13193#comment:6).

On the other hand, #1173, and #13050 are still around to address a
different enhancement: allowing the user to pass an `algorithm`
parameter to change the backend used for numerical evaluation. This
latter enhancement depends on modifications to Pynac, see #12289.

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Re: [sage-devel] Hoodies and other clothing with logo

[Benjamin Jones]

On Thu, Jul 12, 2012 at 10:08 PM, kcrisman  wrote:
>
>
> On Thursday, July 12, 2012 11:05:06 PM UTC-4, kcrisman wrote:
>>>
>>>
>>>  - topaz: part of polymake. polymake is an experimental Sage package,
>>> which is currently broken. The new version of polymake insists that on Mac
>>> OS X, Fink is a prerequisite, so this does not seem like a good option.
>>> (Maybe Fink isn't really necessary, but I don't want to figure it out.)
>>>
>>
>> I had a query the other day about using polymake in Sage.  And
>> http://polymake.org/doku.php/howto/mac does eventually get to non-Fink
>> instructions.  Not that this necessarily relates directly to the vote, but I
>> figured some enterprising person might make a working spkg for polymake.
>> Note that it apparently only works on 10.6+ with the most recent versions?
>> They even give some pretty specific patches (further down than I copied) to
>> put in the configuration files... it looks at least as detailed as most
>> spkg-installs!
>
>
> Sorry for hijacking this, John ...  does chomp have hoodies?
>
> http://polymake.spreadshirt.de/
>
> I would buy a Sage hoodie.  Just sayin'.  There HAS to be a larger market
> for those than polymake hoodies, wouldn't you think?
>

I would also buy a Sage hoodie, even though I wouldn't be allowed to
wear it on the floor of the house of reps. I think a line of
skateboard decks with Sage logos might be a hit also (not entirely
joking).

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Re: [sage-devel] Re: Please test sage-5.1.rc1

[Benjamin Jones]

On Sat, Jul 7, 2012 at 10:36 AM, mmarco  wrote:
> Builds and passes the doctest in my gentoo box (intel core i7).
>
> --
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sage-5.1.rc1 also builds and passes all (long) tests on

 * Debian (testing) x86_64 VM using 10 cores
 * Fedora 17 x86_64 using 8 cores

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Re: [sage-devel] Please test sage-5.1.rc1

[Benjamin Jones]

On Fri, Jul 6, 2012 at 2:05 AM, Jeroen Demeyer  wrote:
> Because many of the Sage testing machines (redhawk and all of Skynet)
> are down, version sage-5.1.rc1 has been tested much less than usual.
>
> So, please build sage-5.1.rc1 and report unexpected problems, especially
> if you have an unusual system.  Downloads at:
> http://www.sagemath.org/download-latest.html
>
> If there are no problems, then sage-5.1 will be released identical to
> sgae-5.1.rc1.
>
>
> Jeroen.
>
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Builds and passes long tests on my Mac OS X 10.7.4 (Intel Core 2 Duo).

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Re: [sage-devel] Re: Skynet

[Benjamin Jones]

On Mon, Jul 2, 2012 at 1:39 AM, Jeroen Demeyer  wrote:
> On 2012-06-30 16:57, Volker Braun wrote:
>> There are still power outages all over the east coast after some
>> thunderstorms. I wouldn't be surprised if it comes back after the power
>> is switched back on ;-)
> And what if... there is nobody to switch on the power?
>
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Where is skynet? In a hardened bunker that only Mariah had the keys to?

But seriously, has anyone thought about applying for access to the GCC
compile farm [1] ? It looks like they will give shell access accounts
to developers working on free software projects (GPL, BSD, MIT, .. )

[1] http://gcc.gnu.org/wiki/CompileFarm

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Re: [sage-devel] sage release plan

[Benjamin Jones]

On Thu, Jun 28, 2012 at 4:20 PM, kcrisman  wrote:
>
>
> On Thursday, June 28, 2012 4:45:00 PM UTC-4, Jeroen Demeyer wrote:
>>
>> On 2012-06-28 17:17, William Stein wrote:
>> > We took *forever* to release sage-5.0 -- certainly it was the longest
>> > time between releases ever.
>> Sure, the longest time ever.  On the other hand, it was *only* 4 months,
>> which I wouldn't call "forever".  But it did take so long for a good
>> reason: we wanted to support OS X 10.7.  If you set explicit goals like
>> that, it takes as long as it needs to take.
>
>
> Okay, but to play devil's advocate - if the explicit goal is merging #11080
> and releasing something without problems otherwise, could that take shorter?
>  For instance, all that currently seems needed there is for someone other
> than the author of the Lion patch for
> http://trac.sagemath.org/sage_trac/ticket/13126 to test the new openssl
> package.
>
> Of all the 74 current positive review tickets, 17 are invalid or dupes, many
> are pending (such as regarding #13121, which could be in a Sage 5.3), and
> most of the rest have nothing to do with the notebook (many are graph theory
> or upgrading various other spkgs).
>

I just finished the last part of the review on #13126, it's ready to go.

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Re: [sage-devel] Bad interaction between differents types of integers in sage?

[Benjamin Jones]

On Sat, Jun 23, 2012 at 3:34 PM, Julien Puydt  wrote:
> Hi,
>
> wouldn't the following be a bug?
>
> sage: E=ModularForms(1,12).cuspidal_subspace()
> sage: f=E.0
> sage: dim=len([1,2,4,8,16])
> sage: dim
> 5
> sage: f.coefficients(5)
> [1, -24, 252, -1472, 4830]
> sage: f.coefficients(dim)
> ---
> TypeError                                 Traceback (most recent call
> last)
>
> /home/jpuydt/sage-5.0/ in ()
>
> /home/jpuydt/sage-5.0/local/lib/python2.7/site-packages/sage/modular/modform/element.pyc
> in coefficients(self, X) 316         if isinstance(X, rings.Integer):
>    317             X = range(1,X+1)
> --> 318         Y = [n for n in X   if  not (n in
> self.__coefficients.keys())] 319         v = self._compute(Y)
>    320         for i in range(len(v)):
>
> TypeError: 'int' object is not iterable
>
>
> Snark on #sagemath
>
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It may not be desirable, but `f.coefficients?` does specify that it's
input should be an Integer, not and `int`.

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Re: [sage-devel] Proposal: by default, at least in Makefile, build docs using jsMath

[Benjamin Jones]

On Tue, Jun 19, 2012 at 11:29 PM, John H Palmieri
 wrote:
>
> [X]  Yes, make jsMath the default when running 'make'.

The difference is huge. I get

(without -j) real   0m13.313s (average over 3 runs)
(with -j) real  1m18.227s (average over 3 runs)

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Re: [sage-devel] And the 2012 Spies Sage Development Prize Winner is...

[Benjamin Jones]

On Tue, Jun 19, 2012 at 12:27 PM, Robert Bradshaw
 wrote:
> Congratulations, Jason. Well deserved!
>
> On Mon, Jun 18, 2012 at 9:32 PM, William Stein  wrote:
>> ... Jason Grout!
>>
>> CITATION:
>>
>> Jason Grout is a constant presence across the Sage landscape.  He is
>> extremely active in the discussion groups, comments on many tickets,
>> contributes code to the core Sage library, improves the documentation,
>> and works tirelessly to improve the notebook interface.  He
>> contributes in many ways to make Sage a better tool for mathematics
>> research, but he is perhaps most recognized for his efforts to make
>> Sage an effective tool for teaching mathematics.
>>
>> Jason's mathematical tastes have resulted in major code contributions
>> for linear algebra, graph theory, plotting and symbolics.  These are
>> all important areas for the undergraduate mathematics curriculum.  But
>> he is equally interested in Sage infrastructure, such as LaTeX
>> representation, usability improvements to Trac server, format and
>> delivery of documentation, and NumPy/SciPy integration.  With a strong
>> background in web applications, his work on the notebook interface is
>> both visionary and technically strong.  A recent project he runs is
>> the Sage Cell Server, which allows a remote server to accept Sage code
>> and return results without any account or login.  This can power
>> interactive demonstrations on web pages or computations via mobile
>> devices, and the principles and implementations will be used in
>> increasing the scalability of Sage servers.  As an example of his
>> interest in education, this project has involved several undergraduate
>> students in significant ways.  Jason also gives freely of his time to
>> help other users and developers.  He is the second most numerous
>> poster of all time in the sage-support forum, in the top five for the
>> sage-devel, sage-edu and sage-notebook forums, and he has the
>> fifth-highest karma at the Ask Sage site.
>>
>> For his significant and inspiring technical contributions, his massive
>> contributions to the vitality of the Sage community, his work on
>> making Sage available via the notebook and cell servers, and his
>> interest in education, Jason Grout is awarded the 2012 Spies Sage
>> Development Prize. This award carries a prize of $500 from the Sage
>> Foundation (thanks to Jaap Spies).
>>
>> Join us in congratulating him!
>>
>>  - The Prize Committee
>>

Congratulations, Jason. As has already been said, well deserved!

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Re: [sage-devel] Trac is slow and now it's affecting patchbot

[Benjamin Jones]

On Wed, Jun 13, 2012 at 2:08 PM, Starx  wrote:
>> To fix the patchbot problem, you can always run a patchbot
>> instance yourself on this particular ticket and the new results will
>> show up.
>
> Can I?  I assumed I would need some kind of admin access to fiddle
> with patchbot.  How does one do this?
>
> -Jim
>

Clone the Robert Bradshaw's patchbot repo here:
https://github.com/robertwb/sage-patchbot

and run something like:

$ python patchbot.py --sage-root=$HOME/sage/sage-5.1.beta3 --ticket=14341

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Re: [sage-devel] Trac is slow and now it's affecting patchbot

[Benjamin Jones]

On Wed, Jun 13, 2012 at 11:53 AM, Starx  wrote:
> Trac has been very slow for me these last few days and now it's cause
> patchbot to fail on one of my patches:
> http://trac.sagemath.org/sage_trac/ticket/12630
>
> So two questions:
>
> 1) Is trac slow for anyone else?  Can something be done?
> 2) Will patchbot sort itself out or do I need to do something to make
> it try again?
>
> -Jim
>
> --
> Die Dunkelheit... leitet die Musik.
> Die Musik... leitet die Seele.
>
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Trac has been super slow for me this morning and the URL timeout error
from the patchbot indeed seems to have caused the "Apply failure".
Since William has restarted apache and postgres, Trac seems pretty
responsive. To fix the patchbot problem, you can always run a patchbot
instance yourself on this particular ticket and the new results will
show up.

In fact, I can do so now and see what happens..

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[sage-devel] trac connection error

[Benjamin Jones]

I haven't seen this before, after logging in to trac.sagemath.org:

Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/trac/web/api.py", line 436, in send_error
data, 'text/html')
  File "build/bdist.linux-x86_64/egg/trac/web/chrome.py", line 803, in
render_template
message = req.session.pop('chrome.%s.%d' % (type_, i))
  File "build/bdist.linux-x86_64/egg/trac/web/api.py", line 212, in __getattr__
value = self.callbacks[name](self)
  File "build/bdist.linux-x86_64/egg/trac/web/main.py", line 298, in
_get_session
return Session(self.env, req)
  File "build/bdist.linux-x86_64/egg/trac/web/session.py", line 156, in __init__
if req.authname == 'anonymous':
  File "build/bdist.linux-x86_64/egg/trac/web/api.py", line 212, in __getattr__
value = self.callbacks[name](self)
  File "build/bdist.linux-x86_64/egg/trac/web/main.py", line 157, in
authenticate
authname = authenticator.authenticate(req)
  File "build/bdist.linux-x86_64/egg/trac/web/auth.py", line 83, in authenticate
authname = self._get_name_for_cookie(req, req.incookie['trac_auth'])
  File "build/bdist.linux-x86_64/egg/trac/web/auth.py", line 205, in
_get_name_for_cookie
db = self.env.get_db_cnx()
  File "build/bdist.linux-x86_64/egg/trac/env.py", line 335, in get_db_cnx
return get_read_db(self)
  File "build/bdist.linux-x86_64/egg/trac/db/api.py", line 90, in get_read_db
return _transaction_local.db or DatabaseManager(env).get_connection()
  File "build/bdist.linux-x86_64/egg/trac/db/api.py", line 152, in
get_connection
return self._cnx_pool.get_cnx(self.timeout or None)
  File "build/bdist.linux-x86_64/egg/trac/db/pool.py", line 172, in get_cnx
return _backend.get_cnx(self._connector, self._kwargs, timeout)
  File "build/bdist.linux-x86_64/egg/trac/db/pool.py", line 105, in get_cnx
cnx = connector.get_connection(**kwargs)
  File "build/bdist.linux-x86_64/egg/trac/db/postgres_backend.py",
line 87, in get_connection
    params)
  File "build/bdist.linux-x86_64/egg/trac/db/postgres_backend.py",
line 203, in __init__
port))
OperationalError: FATAL:  connection limit exceeded for non-superusers

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Re: [sage-devel] Re: new computer - any special Lion instructions?

[Benjamin Jones]

On Tue, Jun 5, 2012 at 9:37 PM, kcrisman  wrote:
>
>> I'm using Lion as well. I installed the command line tools package
>> from Apple and have had no problems building sage-5+. No idea about
>
> Is that different from the $5 Xcode or whatever?  I could ask my IT
> people to preinstall certain optional things from the installation
> materials.
>

Yes -- I didn't pay anything to install the command line tools. See
[2] for more info. The full xcode includes all the Apple specific
libraries that one needs to build Mac and iOS apps.


>> Mountain Lion, compatibility probably depends more on what Apple does
>> with their dev tools from here. But the gcc package seems to solve
>> these problems for now.
>>
>> Just think how fast you'll be able to build sage!
>
> Well, especially once we get the documentation building serially!
>
> - kcrisman
>

[2] http://kennethreitz.com/xcode-gcc-and-homebrew.html

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Re: [sage-devel] Article of interest: A Multi-Language Computing Environment for Literate Programming and Reproducible Research

[Benjamin Jones]

On Tue, Jun 5, 2012 at 5:42 PM, Fernando Perez  wrote:
> Hi John,
>
> thanks for the pointer, useful reference to have.
>
> It bugs me that Sage not listed on page 6 in the table of existing
> tools.  It covers much of the same ground... (so does the ipython
> notebook, but that didn't exist when this was written; but Sage most
> certainly did).
>
> Cheers,
>
> f
>

As another pointer, one of the authors on that paper, Eric Schulte,
maintains a very nice "Emacs starter kit" [1] for people that use
emacs but who are not (yet) at the guru level. The starter pack is
very useful for putting the ideas in the paper into practice.

I've been using this setup for a sort of "sagetex" in org-mode. I like it.

[1] http://eschulte.me/emacs-starter-kit/

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Re: [sage-devel] new computer - any special Lion instructions?

[Benjamin Jones]

On Tue, Jun 5, 2012 at 9:11 PM, kcrisman  wrote:
> So although my 3-year-old MacBook Pro with Snow Leopard on it works
> fine, due to warranty issues my employer is basically forcing me to
> get a new machine.  (I won't be paying for it, or I'd say no - I love
> this little guy.)
>
> I'm still a little hesitant because of the past issues with building
> on Lion, and the constant Xcode upgrades.   I won't have a choice
> about Lion, though I will be able to not cash in the free upgrade to
> Mountain Lion.  Does anyone who has a Lion machine know of any
> problems I would have with the very latest Xcode and building Sage?
>
> And does anyone know what the Mountain Lion situation will be?
> Presumably the new GCC package will make it "just work", but I'm still
> nervous.
>
> On the plus side, it would be a Quad Core i7 and maybe the new
> graphics card would render WebGL graphics better if we get them?  I
> could also choose a MacBook Air, but needing a special adaptor to
> connect to wired internet isn't a good option with our flaky wifi :(
>
> Thanks for any input,
> - kcrisman
>

I'm using Lion as well. I installed the command line tools package
from Apple and have had no problems building sage-5+. No idea about
Mountain Lion, compatibility probably depends more on what Apple does
with their dev tools from here. But the gcc package seems to solve
these problems for now.

Just think how fast you'll be able to build sage!

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Re: [sage-devel] Re: trac.sagemath.org

[Benjamin Jones]

On Mon, May 28, 2012 at 3:06 PM, Keshav Kini  wrote:
> Jason Grout  writes:
>> On 5/28/12 12:13 AM, William Stein wrote:
>>> Hi,
>>>
>>> Warning: we at sd40.5 [1] are coloring the bikeshed [2].
>>>
>>> [1] http://trac.sagemath.org/sage_trac/wiki/sd40.5
>>> [2] http://trac.sagemath.org/sage_trac/
>>
>> Wow, this is the shortest bikeshedding thread I've ever seen.
>>
>> Are you looking for comments?  Personally, I prefer the previous
>> theme. It was warmer (felt more inviting, with a yellowish background
>> instead of a blue background)
>
> I think the blue background matches our various logos and sagemath.org a
> lot better than the old background color did, at least. Personally I
> like the new color theme, but I don't really have any justification for
> my purely personal preference.
>
> -Keshav
>

"Seeing the color blue actually causes the body to produce chemicals
that are calming;" [1]

[1] http://www.precisionintermedia.com/color.html

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Re: [sage-devel] Re: Poll: Making sage-mode a standard package

[Benjamin Jones]

On Sat, May 26, 2012 at 10:23 AM, Ivan Andrus  wrote:
> On May 26, 2012, at 7:09 PM, Benjamin Jones wrote:
>> On Sat, May 26, 2012 at 6:55 AM, Ivan Andrus  wrote:
>>
>>>
>>> No offense taken.  Who knows what's going to happen after I graduate for
>>> example—maybe I'll get a full time job fixing bugs in Sage, or maybe I'll be
>>> flipping burgers. :-)
>>>
>>> It's important to remember that if it's standard someone _has_ to maintain
>>> it.  Of course, it's also more likely that someone _will_ maintain it.
>>>
>>> -Ivan
>>>
>>
>> From the point of view that making sage-mode a standard package would
>> increase the likelihood that it is maintained, I would support it
>> being included as a standard package.
>
> Do you say that because you feel it hasn't been maintained well, or that it 
> might not be in the future since the original author has moved on?
>
> -Ivan
>

I said that in the spirit that I think sage-mode is a useful package
and any steps we can take to ensure that useful packages continue to
be well maintained is a good thing. I haven't been using it for all
that long, so I can't comment on if it has or hasn't been maintained
well in the past. As for the future, who knows, but making it a
standard package will increase its chances to thrive compared to
making it an optional package.

What is your opinion as the current maintainer?

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Re: [sage-devel] Re: Poll: Making sage-mode a standard package

[Benjamin Jones]

On Sat, May 26, 2012 at 6:55 AM, Ivan Andrus  wrote:

>
> No offense taken.  Who knows what's going to happen after I graduate for
> example—maybe I'll get a full time job fixing bugs in Sage, or maybe I'll be
> flipping burgers. :-)
>
> It's important to remember that if it's standard someone _has_ to maintain
> it.  Of course, it's also more likely that someone _will_ maintain it.
>
> -Ivan
>

>From the point of view that making sage-mode a standard package would
increase the likelihood that it is maintained, I would support it
being included as a standard package.

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Re: [sage-devel] Poll: Making sage-mode a standard package

[Benjamin Jones]

On Fri, May 25, 2012 at 4:57 PM, Justin C. Walker  wrote:
>
> On May 25, 2012, at 16:07 , William Stein wrote:
>
>> On Fri, May 25, 2012 at 3:41 PM, Justin C. Walker  wrote:
>>> On Fri, May 25, 2012 at 2:24 PM, Ivan Andrus  wrote:
>>>
>>>> [X] Don't make it standard and close the ticket.  Include as optional 
>>>> package.
>>
>> I'm curious -- why are people against sage-mode being a standard package?
>
> For me, it's not about "sage-mode": it's got more to do with the number of 
> moving parts.  Fewer is better, all things equal, and we ought to put things 
> into Sage if there are really good reasons.
>
> If it's standard, tests are needed.
>
> Also, emacs, as delivered on a given platform may not change much, but a 
> number of people use GUI versions of the app, which are separate from the 
> regular distributions (Mac OS X, for example). Version change for those apps 
> is unpredictable, and based on the user.
>
> Is emacs even a standard part of Linux distributions?
>
> Finally, I think most emacs users would have little problem installing an 
> optional package, while most non emacs users aren't interested :-}  That's a 
> rash generalization, but it resonates...
>
> One guy's opinion...
>
> Justin
>

I agree with Justin; well put.

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Re: [sage-devel] Poll: Making sage-mode a standard package

[Benjamin Jones]

On Fri, May 25, 2012 at 2:24 PM, Ivan Andrus  wrote:
> Dear all sage and emacs (or not) users,
>
> Since I've been working on sage-mode a bit recently I thought I would look at 
> trac and try to fix any sage-mode related bugs there.  I found #2666 which 
> wants to make sage-mode a standard package.
>
> If people want this then I'd like to get it done.  But if not then I'd like 
> to close the ticket.  Personally, I'm not sure it should be standard since 
> people who wish to use it still have to add something to their .emacs, and 
> hence they still need to know about it and take some action.  However, I'm 
> open to being persuaded.  The spkg is 272K.
>
> [ ] Make it standard at some point in the "near" future.
> [ ] Don't make it standard and close the ticket.
> [ ] Don't make it standard now, but don't close the ticket.
>
> -Ivan
>

I've been using the sage-mode spkg you made and I like it, but I'd say
this should be an optional package. So I vote:

[X ] Don't make it standard and close the ticket. ** Include it as an
optional package.**

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Re: [sage-devel] maxima error on calls like solve((A+p^B,p), is that the intended behavior?

[Benjamin Jones]

On Tue, May 22, 2012 at 8:27 AM, Jonathan  wrote:
> Yes, I made a typo..Thanks for realizing what I meant.
>
> However, I still think that a solution that has complex answers is OK.  If
>  you are finding the symbolic solution isn't it better to find the general
> solution and then deal with specific cases?  I don't see what is wrong with:
> p = (-A)^(1/B), even when B = 2 and A > 0.  This just means p =
> (+/-)sqrt(-A). I just don't see any problem with having two possible
> answers, even if they are complex.  Is the problem that Maxima is trying to
> solve the problem restricting it to RR?
>
> I believe this is a case where Sage should try to catch this kind of Maxima
> error and allow the user to get the general answer without having to drop
> into Maxima.
>
> So, I am arguing that Sage really should return: p = (-A)^(1/B) in cases
> like this and that when Maxima asks a question, we need a better explanation
> for the user of how to respond.
>
> Jonathan
>

Well, I agree. I guess I was trying to say that a solution, if one
exists, depends on the context (the underlying ring and also the
values of A and B) so I don't think it's unreasonable for Maxima to
ask for more information before giving an apparent solution which may
or may not really exist.

Mathematica seems to agree with you to:

http://www.wolframalpha.com/input/?i=solve+A+%2B+p%5EB+%3D+0+for+p

I definitely agree that Sage could be more helpful here as the middle
man. I wonder if Maxima has any flags related to this, e.g.
`return_purely_symbolic_solutions = true` would return `[ p =
(-A)^(1/B) ]` and we could wrap this flag as an option to solve?

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Re: [sage-devel] maxima error on calls like solve((A+p^B,p), is that the intended behavior?

[Benjamin Jones]

On Mon, May 21, 2012 at 3:10 PM, Jonathan  wrote:
> sage: var('x y z p q A B C')
> sage: solve((A + p^B),p)
>
> results in:
>
> ...
> TypeError: ECL says: Maxima asks: Is B an integer?
>
>
> Shouldn't it result in:
>
> [p = (-A)^(1/p)]
>
>
> Jonathan

I guess you mean: [p = (-A)^(1/B)]

Think about what happens when A = 2 and B = 2, or when A = 2 and B = 1/2.

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Re: [sage-devel] Introduction, Symbolic Expressions, Pynac, GSOC 2012

[Benjamin Jones]

On Fri, May 18, 2012 at 6:06 AM, Titus Nicolae  wrote:
> Hello,
> My name is Titus Nicolae, I am a 3rd year student at Politehnica University
> Timisoara.
> I am working on Pynac during Google Summer of Code 2012.
> With the help of Burcin Erocal I'll be implementing support for MPFR, GMP,
> MPFC
> in Pynac and solve some old issues. I'll post updates related to Pynac on
> this blog.
>
> Cheers,
> Titus Nicolae
>

Great! I'm glad you can work on this. I'm looking forward to seeing
your progress.

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Re: [sage-devel] sage-5.0.rc0 released

[Benjamin Jones]

On Wed, May 2, 2012 at 2:02 AM, Jeroen Demeyer  wrote:
> Dear Sage lovers,
>
> We're releasing Sage 5.0.rc0.
>
> Source archive:
>
> http://boxen.math.washington.edu/home/release/sage-5.0.rc0/sage-5.0.rc0.tar
>
> Upgrade path:
>
> http://boxen.math.washington.edu/home/release/sage-5.0.rc0/sage-5.0.rc0/
>
> The source and upgrade path can also be found on the mirror network
> (you might need to wait a while before the mirrors are synchronized):
>
> http://www.sagemath.org/download-latest.html
>
>
> Please build, test, and report!  We'd love to hear about your
> experiences with this release.
>

Sage-5.0.rc0 builds and passes all tests (make ptestlong) on my fedora
16 x86_64 machine:

> uname -a
Linux kimchi.homenetwork 3.3.2-6.fc16.x86_64 #1 SMP Sat Apr 21
12:43:20 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

Also, regarding #12857, I looked through the live documentation on 2D
/ 3D plotting and everything looks good, as expected.

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Re: [sage-devel] Re: Can we develop a plan to get 100% doctest coverage?

[Benjamin Jones]

>>
>> Is there an easy way to find a list of undocumented functions?
>
> sage -coverage
>
> For example,
>
> cd SAGE_ROOT/devel/sage/sage/coding
> sage -coverage .
>
> Outputs:
>
> ag_code.py: 100% (1 of 1)
> binary_code.pyx: 91% (41 of 45)
> code_bounds.py: 100% (17 of 17)
> code_constructions.py: 96% (25 of 26)
> decoder.py: 100% (3 of 3)
> guava.py: 100% (3 of 3)
> linear_code.py: 82% (52 of 63)
> sd_codes.py: 20% (1 of 5)
> source_coding/huffman.py: 100% (9 of 9)
>
> Overall weighted coverage score:  88.1%
> Total number of functions:  172
> We need    3 more function to get to 90% coverage.
> We need   11 more function to get to 95% coverage.
> We need   18 more function to get to 99% coverage.
>
> ---
>
> You can then do the following to see what is wrong with a given file:
>
>   sage -coverage sd_codes.py
>
> --
> sd_codes.py
> SCORE sd_codes.py: 20% (1 of 5)
>
> Missing documentation:
>         * MS(n):
>         * matA(n):
>         * matId(n):
>         * MS2(n):
>



> --
> William Stein
> Professor of Mathematics
> University of Washington
> http://wstein.org
>

Here [1] is a patch I just wrote to increase the doctest coverage of
one file mentioned here (linear_code.py) to 100%. Please review! I'm
going to work on the other files in that directory as I have time.

[1] http://trac.sagemath.org/sage_trac/ticket/12893

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Re: [sage-devel] Can we develop a plan to get 100% doctest coverage?

[Benjamin Jones]

On Sun, Apr 29, 2012 at 9:35 AM, David Kirkby  wrote:
> The fact there are functions in Sage untested is worrying, and I think
> its fair to say most people would like to see 100% doctest coverage,
> but IMHO, we need a plan for this to happen, and the plan inforced,
> otherwise this will not happen soon. So I'm suggesting we collect
> ideas for a plan.
>
> Two things that do NOT appear to work, at least in isolation are:
>
> A) Saying coverage should be x % in release Y, then hoping it is.
> B) Saying coverage should be x % by the date DD/MM/YY, then hoping it is.
>
> Both of these have been tried, and niether are working. The graph here
>
> http://thales.math.uqam.ca/~labbes/blogue/2011/03/evolution-of-the-overall-doctest-coverage-of-sage/
>
> seems to indicate that progress on this has slowed over the last year
> or so, where progress was about 4.7% per year. (I'm not actually sure
> I agree with his line of best fit, which would suggest to me the
> situation has slowed even more.)
>
>
> A few ideas that might work, are below. I would add, I'm not
> suggesting they are all very good (in particular 1 and 4 are a bit
> excessive), but I mention them anyway.
>
> 1) Having a release, where the only aim is to increase doctest
> coverage. No patches are accepted, unless they increase coverage.
> 2) Finding sections of code which are not tested, and depreciating
> them, unless someone writes the doctests, in which case the
> depreciation can be removed.
> 3) Having a release, where anyone can submit a patch which gets
> reviewed, but the release manager does not merge it unless the author
> of the patch can provide another patch which increase doctest
> coverage.
> 4) Finding individuals that have written code that is not tested, and
> not merging any more patches from them unless they first add tests to
> the ALL code they have already written.
> 5) Finding individuals that have written code that is not tested, and
> not merging any more patches from them unless they first add tests to
> a number (say 5) tests for all the code they have written which is
> untested.
> 6) Not accepting any patches, unless a equal number of lines of code
> are submitted which add doctests.
> 7) Paying individuals to just write tests.
>
> I believe if we want to achieve 100% coverage, we need to do more than
> A and B above, as they are proved not to work.
>
> Can anyone suggest anything else, or have any comments.
>
> Dave
>
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Option 1) seems like a good idea to me. The others might also work,
but would surely require a lot of extra work on the part the release
manager or whoever ends up having to enforce / implement the
restrictions. That extra work would be better funneled into increasing
doctest coverage in my opinion.

We might consider combining option 1 and plan A, as you put it, but
set a realistic target %.

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Re: [sage-devel] Re: reply to Trac via e-mail?

[Benjamin Jones]

On Mon, Apr 16, 2012 at 8:50 PM, kcrisman  wrote:
>
>
> On Apr 16, 7:55 pm, Robert Bradshaw 
> wrote:
>> On Mon, Apr 16, 2012 at 6:51 AM, Niles Johnson  wrote:
>> > Another -- perhaps more trivial -- way to make posting replies on trac
>> > easier would be to have each email from trac include a link to the ticket.
>>
>> +1. I find it quite surprising and annoying that they don't do this
>> already! (I'd love email reply as well, but that's likely quite a bit
>
> Here is an example from an email I just got.  At the bottom:
>
> Ticket URL:  8>
> Sage 
> Sage: Creating a Viable Open Source Alternative to Magma, Maple,
> Mathematica, and MATLAB
>
> How is this not what we are asking for (I mean the first part, not the
> "reply" part)?  Do some mail programs filter this out, maybe?
>

In gmail, I usually have to click on the ... image to get the trac URL
to reveal. I guess gmail thinks it's a signature.

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Re: [sage-devel] Re: inferior sage in emacs, bug?

[Benjamin Jones]

On Wed, Apr 11, 2012 at 4:16 AM, Ivan Andrus  wrote:
> On Apr 11, 2012, at 10:34 AM, Ivan Andrus wrote:
>
>> FWIW, I've been meaning to make an spkg with my changes (adding AUCTeX 
>> support for SageTeX). It would also include customization of the preamble 
>> and possibly a fix for this problem.
>
> I made spkg that you can try [1].
>
> I can confirm the Unknown button type `help-xref' error if I revert Nick's 
> fix [2], but not otherwise.  The new spkg contains the latest from my 
> repository [3] including this fix. If desired I can open a trac ticket and 
> get this to be the new official spkg, though I would like to add a make-spkg 
> script first so that it's easier (create sage-load.el and rename directory) 
> in the future.
>
> -Ivan
>
> [1] http://boxen.math.washington.edu/home/iandrus/sage_mode-0.8.spkg
> [2] https://bitbucket.org/ncalexan/sage-mode/changeset/4e9e72fc639f
> [3] https://bitbucket.org/gvol/sage-mode/overview
>

Thanks Ivan, your sage_mode-0.8.0.spkg works for me! By the way,
should it be "sage_mode" or "sage-mode"? It looks like the 0.7 spkg
was called "sage-mode".
If you make a ticket, please CC me on it and I'll help review.

Thanks again,

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Re: [sage-devel] inferior sage in emacs, bug?

[Benjamin Jones]

On Tue, Apr 10, 2012 at 5:56 PM, Florent Hivert  wrote:
>      Hi
>
>> I've got the correct spkg file now, and emacs doesn't complain on
>> loading a .py file, but now I get another error after `M-x sage`:
>> "Unknown button type `help-xref'"
>
> Hum ! As I said, I'm not the maintainer of the package and this is going
> quickly out of my expertise range...
>
> I would guess that the problem is now with your emacs install. As far as I
> understand, on my computer this is defined in standard with emacs in the file
>    /usr/share/emacs/23.1/lisp/help-mode.elc
> which is distributed in the base emacs package (emacs-23.1-18.1.x86_64.rpm
> on an outdated OpenSuSE 11.3).
>
> Cheers,
>
> Florent
>

Yes, that could be it. I'm using emacs 23.3.1 on Mac OS X which I
installed using the Homebrew project ("brew install emacs").
It seems that help-xref is referred to in my distribution at:

/usr/local/Cellar/emacs/23.3b/share/emacs/23.3/lisp/loaddefs.el

but I can't find where it's defined. For example, this appears in loaddefs.el:

{{{
(autoload 'help-xref-button "help-mode" "\
Make a hyperlink for cross-reference text previously matched.
MATCH-NUMBER is the subexpression of interest in the last matched
regexp.  TYPE is the type of button to use.  Any remaining arguments are
passed to the button's help-function when it is invoked.
See `help-make-xrefs'.

\(fn MATCH-NUMBER TYPE &rest ARGS)" nil nil)
}}}

So it turns out if I load a .py file, then enable help-mode `M-x
help-mode`, and then load sage mode `M-x sage-mode` I get no
complaints out of emacs.

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Re: [sage-devel] inferior sage in emacs, bug?

[Benjamin Jones]

On Tue, Apr 10, 2012 at 5:23 PM, Florent Hivert  wrote:
>    Hi,
>
>> I was playing around with sage-mode recently too, but I couldn't even
>> get it to load. I did `sage -f sage-mode-0.7.spkg` and added the lines
>> {{{
>> (add-to-list 'load-path (expand-file-name
>> "/Users/jonesbe/sage/sage-4.8/data/emacs"))
>> (require 'sage "sage")
>> (setq sage-command "/Users/jonesbe/sage/sage-4.8/sage")
>> }}}
>>
>> to my .emacs file, but when I load a python or sage script now, I get
>> an error: "File error: Cannot open load file, sage-load". I don't see
>> a sage-load.el file anywhere in the spkg.
>
> Where did you get the spkg ? I just downloaded the spkg from
> <http://wiki.sagemath.org/sage-mode?action=AttachFile&do=view&target=sage-mode-0.7.spkg>
> and the file is there:
>
> $ wget -q 
> 'http://wiki.sagemath.org/sage-mode?action=AttachFile&do=get&target=sage-mode-0.7.spkg'
>  -O sage-mode-0.7.spkg
> $ tar tf sage-mode-0.7.spkg | grep sage-load
> sage-mode-0.7/emacs/sage-load.el
>
> Cheers,
>
> Florent

I cloned the hg repo and produced an spkg from that directory. I see
the problem now.

I've got the correct spkg file now, and emacs doesn't complain on
loading a .py file, but now I get another error after `M-x sage`:
"Unknown button type `help-xref'"

Thanks for the help, Florent.

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Re: [sage-devel] inferior sage in emacs, bug?

[Benjamin Jones]

On Tue, Apr 10, 2012 at 4:38 PM, Ezequiel Birman
 wrote:
> Are sage-mode inferior-sage-mode and sage-view still supported?
>
> I (kind of) managed to get an Inferior Sage. Is there a way to eval last
> expresion in sage-mode instead of the whole buffer (C-c C-r)?
>
> I am using latest sage (4.8) and sage-mode cloned from mercurial
> repo.  (by the way, I've built and installed sage-mode python packages in
> the default location: /usr/lib/python2.7/site-packages/ Should I move
> them under the sage dir hierarchy? ie. overwrite the old python packages
> installed by sage 4.8?)
>


I was playing around with sage-mode recently too, but I couldn't even
get it to load. I did `sage -f sage-mode-0.7.spkg` and added the lines
{{{
(add-to-list 'load-path (expand-file-name
"/Users/jonesbe/sage/sage-4.8/data/emacs"))
(require 'sage "sage")
(setq sage-command "/Users/jonesbe/sage/sage-4.8/sage")
}}}

to my .emacs file, but when I load a python or sage script now, I get
an error: "File error: Cannot open load file, sage-load". I don't see
a sage-load.el file anywhere in the spkg.

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Re: [sage-devel] zeromq and @parallel for clusters

[Benjamin Jones]

On Mon, Apr 9, 2012 at 6:07 AM, Volker Braun  wrote:
> Are we going to make zeromq+pyzmq a standard spkg anytime soon, or is
> anybody opposed to doing so? I think a communication framework would be
> potentially of more use than just for the notebook server, but I haven't
> seen any efforts towards including zeromq. Also, the new IPython can make
> use of zeromq so why not enable that functionality? Do we have a roadmap?
>
> I did write an extension to @parallel to work with a cluster/grid/cloud of
> independent machines. It logs in via ssh, sets up tunnels, and then uses
> zeromq to communicate with the worker processes. And reliably sends
> stdout/err back to the server, so you actually get to see e.g. segfaults in
> worker processes. And kills off workers if something goes wrong. And
> (optionally) copies a working directory to the nodes. I think it would be of
> general interest, but of course depends on zeromq.
>

I think making zmq a standard package is a great idea, as well as
enabling ipython's zmq functions. Maybe this would be a good project
for bug days 19 in May?

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Re: [sage-devel] plot() is plotting undefined/imaginary points

[Benjamin Jones]

On Tue, Mar 20, 2012 at 10:13 PM, Dan Drake  wrote:

> plot(sqrt(2*x^2-3)/(5*x-2), (x,-10,10),ymin=-5,ymax=5)
>
> merrily plots points when the numerator is imaginary:
>
>
> http://aleph.sagemath.org/?z=eJwryMkv0SguLCrRMNKqiDPSNdbU1zDVqtA10tRR0KjQ0TU00DE00NSpzM3Ms9U1BdKJFbammgCoDQ7n
>
> I don't mind that it complains about failing to evaluate the function,
> but the plot is totally wrong. I want something more like:
>
> http://www.google.com/#q=sqrt(2*x%5E2-3)/(5*x-2)<http://www.google.com/#q=sqrt%282*x%5E2-3%29/%285*x-2%29>
>
>
> Dan
>
>
Hi Dan,

It looks to me like a line is being drawn across the gap in the domain. You
can verify that this is what's going on if you do something like:

plot(sqrt(2*x^2-3)/(5*x-2), (x,-10,10),ymin=-5,ymax=5,linestyle="none",
marker=".")

This is the same artifact that you run into when plotting over a vertical
asymptote on most graphing calculators, you get a (nearly) vertical line
drawn because the plotter is joining computed points with lines. It would
be nice to add a feature like the `detect_poles` option where the domain
could be detected better.

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Re: [sage-devel] Re: Irreps of Lie groups

[Benjamin Jones]

Hi Dox,

I would love for more representation theory to be available in Sage. I
think what you are doing is already implemented (in a different form).
See the Thematic Tutorial called "Lie Methods and Related
Combinatorics in Sage" [1]. In particular, enumerating the irreducible
representations (by highest weight) and computing their degrees
(dimensions) is possible in the Weyl Character Ring.

I might suggest contacting the sage-combinat mailing list and asking
if your code would fit in somewhere.


.. [1] http://sagemath.org/doc/thematic_tutorials/lie.html

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On Mon, Mar 5, 2012 at 8:34 AM, daveloeffler  wrote:
> When you say "computing the irreps", it is not clear what it is about the
> irreps you are computing. I guess it is the dimension?
>
>
> On Monday, 5 March 2012 10:50:20 UTC, Dox wrote:
>>
>> Dear all,
>> a couple of weeks ago I wrote a small program for computing the irreps
>> of a Lie group,
>> http://sagenb.org/home/pub/4395/
>> I'd like to help implementing it for future versions of SAGE...
>> However, I guess it needs a lot of work for the sake of optimization.
>>
>> * Could you help me optimize it?
>>
>> * Where should it be included as a class? (in case it is possible)
>>
>> Thank you!
>>
>> DOX
>
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Re: [sage-devel] Re: tachyon -- are we building it incorrectly or?

[Benjamin Jones]

I can verify that tachyon renders using multiple threads on linux. In
fact it looks like it uses all available threads by default (!).
Rendering the 1000 random platonic solids from William's 3d plot
worksheet took 1.07 seconds using 10 Xeon cores.

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On Fri, Mar 2, 2012 at 3:20 PM, Volker Braun  wrote:
> From the spkg-install:
>
> # The threaded version of the 0.98 beta doesn't work on OS X.
>
> I haven't tried it myself.
>
>
>
> On Friday, March 2, 2012 11:17:55 AM UTC-8, William wrote:
>>
>> I thought that if I rendered a 3d scene using viewer='tachyon', then
>> it would use the multiple cores of my computer to render the scene
>> more quickly.  However, I was just rendering a complicated 3d scene
>> for my class (that takes about 30 seconds), and in top I see the
>> attached screenshot -- in particular, there is only 1 thread.
>> I'm using a Core i7 OS X 10.7 laptop that has at least 2 processors
>> (and "4 hardware threads", I think), and Sage Version 5.0.beta2.
>
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Re: [sage-devel] sage, gentoo-prefix & lmonade was: log messages

[Benjamin Jones]

On Mon, Feb 20, 2012 at 5:13 PM, John H Palmieri  wrote:
>
>
> On Monday, February 20, 2012 2:43:29 PM UTC-8, Benjamin Jones wrote:
>>
>> On Mon, Feb 20, 2012 at 2:39 PM, François Bissey wrote:
>> 
>> > There are efforts to parallelize the building of the doc and I would say
>> > that
>> > if it gets merged we may very well put the doc back into sage and just
>> > build
>> > it. We could keep fetching pre-built doc for thos who want on slow
>> > systems.
>> >
>> > Francois
>> >
>>
>> Is there currently any way to prevent Sage from building the docs when
>> one downloads a new tarball, i.e. something like setting
>> SAGE_ATLAS_LIB="..." to avoid building atlas every time a new beta is
>> released?
>
> As François points out, running "make build" will build Sage and its
> component parts without building the documentation.  Since the documentation
> is viewed as an integral part of Sage, if you run doctests on Sage in this
> state, there will be failures (in devel/sage/sage/misc/sagedoc.py, if I
> remember right).
>
> I don't think we need another environment variable for this.
>

I didn't realize there is a 'build' target. That makes sense, thanks!
This will save my poor old laptop many cpu cycles. I agree there's no
need to another environment variable.

> --
> John
>

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Re: [sage-devel] sage, gentoo-prefix & lmonade was: log messages

[Benjamin Jones]

On Mon, Feb 20, 2012 at 2:39 PM, François Bissey
 wrote:

> There are efforts to parallelize the building of the doc and I would say that
> if it gets merged we may very well put the doc back into sage and just build
> it. We could keep fetching pre-built doc for thos who want on slow systems.
>
> Francois
>

Is there currently any way to prevent Sage from building the docs when
one downloads a new tarball, i.e. something like setting
SAGE_ATLAS_LIB="..." to avoid building atlas every time a new beta is
released?

If not, would people support adding an environment variable to this
effect? Maybe that variable could be set to the location of online
docs for the last major release, or that variable would cause a script
to run that downloads pre-built docs (as happens with the
gentoo-prefix?)

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Re: [sage-devel] Re: VirtualBox

[Benjamin Jones]

On Tue, Jan 10, 2012 at 7:48 PM, Volker Braun  wrote:
> Instead of shutting down the virtual machine you can just save the machine
> state. Loading the vm then circumvents the whole boot process.
>

It looks like it works great on Mac OS X. The VM boots, and right away
the browser loads full screen logged into the notebook.

There are some testing worksheets there (says Volker) and the Java
runtime is missing (Volker is aware of this also). I was wondering a
couple of things about the usability of Sage in the VM browser (and
bear in mind that I haven't used the VM appliance at all before).

After a minute or two I couldn't figure out how to save a worksheet or
plots or other data files and access them in the host OS.

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Re: [sage-devel] Re: ask.sagemath spam

[Benjamin Jones]

On Wed, Nov 9, 2011 at 7:25 AM, kcrisman  wrote:
>
>
> On Nov 9, 8:11 am, kcrisman  wrote:
>> I had to close five questions just now that were spam.
>>
>> But I can't actually *delete* them, as far as I can tell.
>
> Of course, now that I closed them, it seems like one can't further
> flag them... sigh.  Is there no admin on the site that can do such
> things?
>

The "flag offensive" button is still there and seems to work (I can
click it and get a popup asking me to confirm). It's not clear if it
does anything though.

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

[Benjamin Jones]

I'm interested in attending after the Joint meetings. Currently, I
have a hotel arranged until the 6th on Jan. If some funding is
available for hotel stay I would definitely participate.

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On Fri, Nov 4, 2011 at 4:31 PM, kcrisman  wrote:
> There is the potential to have Sage Days 36+k, another Bug Days format
> like http://wiki.sagemath.org/days27, immediately after the Joint
> Mathematics Meetings in Boston.
>
> The idea would be to have it near there (for instance, on my campus,
> which is otherwise pretty quiet that time of year) so that people only
> had to do one flight.  Funding would be available, on the usual terms
> (William, what are those?).
>
> William says that there doesn't have to be any particular focus,
> though if specific people were coming in a focus area (linear algebra,
> porting, etc.) then we could try to make a list of top priority bugs
> in that area.  Also, I am reasonably sure that we could convince a
> couple knowledgeable R folks to stop in for a time.
>
> Anyway, reply to this thread or off-list if you would be interested in
> this; we need to know fairly soon to start definitive planning.   At
> least for those of us at semester schools, this is a fairly convenient
> time and location.   Dates would probably depend on folks'
> availability, but keep in mind the Joint Meetings end on a Saturday.
> Days 27 went Friday through Tuesday or Thursday, I believe.
>
> - kcrisman
>
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Re: [sage-devel] Proposal for "3-D" logo for Sage...

[Benjamin Jones]

On Sun, Oct 16, 2011 at 3:16 PM, Jonathan  wrote:
> I was preparing a poster for a Univ. Wisc. System Chemistry meeting
> and was playing with Jmol.  I mocked up a 3-D version of the Sage logo
> which can be rotated in Jmol [also found a bug in Jmol by doing
> this ;)].  Anyway, I thought a static version might be useful as an
> update to the Sage logo.  I've posted it to the logo section of the
> Sage Wiki.  What do people think?  You can see it at this link:
>
> http://wiki.sagemath.org/logos?action=AttachFile&do=view&target=Sage+logo+3D.png
>
> Jonathan
>


Very cool. Are you willing to post the code that produces it? (just
out of curiosity about how you made it..)

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[sage-devel] Choosing names for exponential integral type special functions

[Benjamin Jones]

In Trac ticket #11143, there is some discussion [1] about the naming
of exponential integral type special functions which are added to the
global namespace there. Here are the names of the functions which are
wrapped in #11143, according to Maxima:

expintegral_e (v,z)Exponential integral E
expintegral_e1 (z) Exponential integral E1
expintegral_ei (z) Exponential integral Ei
expintegral_li (z) Logarithmic integral Li
expintegral_si (z) Exponential integral Si
expintegral_ci (z) Exponential integral Ci
expintegral_shi (z)Exponential integral Shi
expintegral_chi (z)Exponential integral Chi

In the patch provided (by me) for #11143, all the functions are called
``exp_integral_*`` where * is e, e1, ei, li, etc..

It was suggested to change the names to something more intuitive, for
example ``log_integral`` intstead of ``exp_integral_li``. This would
match the names of these functions in Mathematica and Maple, for
example. On the other hand, having the whole group of function named
starting with ``exp_integral_*`` allows the user to type
``exp_integral`` and see the list of all the functions in this
group easily.

We (the participants on #11143) would like to know the community's
thoughts on the naming convention.

Thanks,

--
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[1] http://trac.sagemath.org/sage_trac/ticket/11143#comment:36

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Re: [sage-devel] Writing a piece about import in the developers guide.

[Benjamin Jones]

On Wed, Aug 31, 2011 at 1:09 AM, Volker Braun  wrote:

> +1 for any tool to reduce/simplify the number of imports. Everybody adds
> imports if something is missing, but nobody takes out imports after
> rewriting a module. Its not hard to find unused imports, as a random example
> sage/rings/polynomial/polynomial_rational_flint.pyx imports is_Polynomial
> but doesn't use it. But without manually searching around in the source code
> its hard to find which imports are seldomly-used and hence good candidates
> to move function/methods.
>
>
Are there any tools for automating the process of finding out which imports
aren't used in a large module?

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Re: [sage-devel] Re: interacts within interacts

[Benjamin Jones]

On Fri, Aug 19, 2011 at 11:00 PM, Rob Beezer  wrote:
> On Aug 19, 7:56 pm, Jason Grout  wrote:
>> To whet your appetite, though, I took the example Rob Beezer
>> now has on his front page:
>>
>> http://buzzard.ups.edu/
>
> Thanks, Jason, for slash-dotting my site when my students are all
> looking for their reading assignments on a Friday night, a week before
> classes start.  ;-)
>
>> What should happen is that it will get all the special graphs that Sage
>> knows about.  It then figures out what parameters Sage needs and creates
>> a nested interact with those parameters.  Fill in the parameters, and a
>> picture and the eigenvalues appear.
>
> I had to hit the evaluate button twice, the first time it failed to do
> anything (perhaps what Benjamin Jones saw).  Then every time I select
> a new graph type, I get a bunch of error output.  Ignore it.  Enter
> new parameters for the graph (if needed) and hit Return.  Then you get
> some nice looking output.  Very nice, even if a bit rough.
>
> Rob
>
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>

Woops. That might have been me pasting:

while True:
os.fork()

into the textbox on your homepage, Rob. Sorry..

I tried hitting evaluate multiple times with no difference on
sagemath.org:5467. Maybe something is timing out?
Update-   I just tried again and I get something like what Rob is
describing. I see interact controls, but lots of errors as well. Some
of the graph types seem to work, some return things like:
NetworkXError: Invalid graph description, r should be >=2

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Re: [sage-devel] interacts within interacts

[Benjamin Jones]

On Fri, Aug 19, 2011 at 9:56 PM, Jason Grout
 wrote:
> As soon as things slow down a bit, Alex Kramer or I will document some of
> the new things that Ira, Alex, and I did with interacts over the summer.  To
> whet your appetite, though, I took the example Rob Beezer now has on his
> front page:
>
> http://buzzard.ups.edu/
>
> and made it work with any of the special graphs in Sage.  Try pasting the
> following into the singlecell on his page, or at sagemath.org:5467
>
>
> import inspect
> @interact
> def _(g=dir(graphs)):
>    f = getattr(graphs, g)
>    extra_args=inspect.getargs(f.im_func.func_code)[0][1:]
>    @interact(controls=extra_args)
>    def my(**kwargs):
>        P = getattr(graphs, g)(**kwargs)
>        print 'n:', P.num_verts(), ' e:', P.num_edges()
>        print 'Eigenvalues:', P.spectrum()
>        P.plot().show()
>
> What should happen is that it will get all the special graphs that Sage
> knows about.  It then figures out what parameters Sage needs and creates a
> nested interact with those parameters.  Fill in the parameters, and a
> picture and the eigenvalues appear.
>
> Anyways, stay tuned.  There will be more later.  This isn't integrated into
> Sage yet, but exists in the singlecell server.
>
> Thanks,
>
> Jason
>
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>

Jason-

When I paste this code into the single cell textbox and click
"evaluate", all I get is:

Session 357a084a-857d-4c2b-9284-a893bb9244ea done

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Re: [sage-devel] public single cell server

[Benjamin Jones]

On Fri, Jul 29, 2011 at 7:11 PM, Jason Grout
 wrote:
> Hi everyone,
>
> I'd like to announce a trial beta run of a public single cell server:
>
> http://sagemath.org:5467/
>
> The idea is that this is a single cell that can very easily be embedded in
> any webpage.  This is the start of a comprehensive Sage web service as well,
> and lays a piece of the ground work for a much more scalable model for doing
> computations in the normal notebook.
>
> It's ready to be hammered by the larger community at this point.  I will be
> mentioning this next week at Mathfest, so please try to break it :).  I
> think just about any normal Sage computation should work.  Please report any
> errors to me.
>
> We've also rewritten interacts, so please especially test interacts. There
> are some exciting new features for interacts in this rewrite that I can
> detail later.  The main focus for this testing is that current existing
> interacts should work unchanged, hopefully.
>

This is fantastic. I've been thinking about potential uses for this
since I watched the recording of your talk about it at the recent Sage
notebook days.

One suggestion, is it possible to make the input text box resizeable
so that the user can see more than 15 lines at a time? I didn't look
into the docs closely so maybe this is already an option.

Thanks!

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Re: [sage-devel] Re: Citing used Sage components automatically

[Benjamin Jones]

On Fri, Jul 29, 2011 at 7:50 AM, Niles  wrote:
>
> Indeed, one of the things that first piqued my curiosity was the
> message when quitting a Sage session: "Exiting spawned Maxima
> process." or "Exiting spawned Gap process."  Another approach to
> raising user awareness might be to have each component of Sage
> "register" its use in a session, even if it doesn't require spawning a
> new process.  Then the list of used components could be printed when
> quitting a session.  But can this be done without adding tons of
> overhead?
>
> -Niles
>

+1

Something like "Today's Sage session brought to you by ... "

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Re: [sage-devel] Plotting a dirac_delta

[Benjamin Jones]

Dox-

The Dirac delta "function" is not strictly speaking a function. It is
a distribution (see
http://en.wikipedia.org/wiki/Dirac_delta_function). Maybe you want to
plot a diagram like the one in the upper left hand corner of the
wikipedia article?

That would be a nice feature to add to Sage.

--
Benjamin Jones
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On Tue, Jul 5, 2011 at 8:56 AM, Dox  wrote:
> Hi group!
> I'm trying to plot a dirac_delta function, with the command
> sage: var('x')
> sage: plot(dirac_delta(x), (x,-1,1), detect_poles=False)
> and I get just a line through the x axis. Can this function be plotted with
> the singularity? because I'd like to plot a more complex function and detect
> the singular behaviour by looking at it!
> Thx.!!!
> Dox
>
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Re: [sage-devel] Call for vote: lrcalc as standard or optional spkg?

[Benjamin Jones]

On Tue, Jun 28, 2011 at 9:29 AM, Nicolas M. Thiery
 wrote:
>        Dear Sage and Sage-Combinat developers,
>
> With Mike and Anne we are about to finalize an interface with lrcalc:
>

I've used lrcalc extensively in the past and I am very impressed with
it. I vote:

[ X ] A standard spkg
[ ] An optional spkg

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Re: [sage-devel] Newly upgraded and consolidate notebook servers: millions of bugs?

[Benjamin Jones]

Problem solved, thanks!

--
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On Tue, Jun 14, 2011 at 11:45 PM, William Stein  wrote:
> On Tue, Jun 14, 2011 at 9:17 PM, Benjamin Jones
>  wrote:
>> On sagenb.org, I created a new account using openID. When I try to
>> edit a copy of a published worksheet, I get:
>>
>> Internal Server Error
>>
>> An error occurred rendering the requested page. More information is
>> available in the server log.
>
> Can you try again now?
>
> William
>
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Re: [sage-devel] Newly upgraded and consolidate notebook servers: millions of bugs?

[Benjamin Jones]

Sorry for double posting, my problem seems to be related to the openID
account I created. I logged in using my pre-existing account and
everything seems to work great (so far), including editing copies of
published worksheets.

--
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On Tue, Jun 14, 2011 at 11:17 PM, Benjamin Jones
 wrote:
> On sagenb.org, I created a new account using openID. When I try to
> edit a copy of a published worksheet, I get:
>
> Internal Server Error
>
> An error occurred rendering the requested page. More information is
> available in the server log.
>
> --
> Benjamin Jones
> benjaminfjo...@gmail.com
>
>
>
> On Tue, Jun 14, 2011 at 10:40 PM, William Stein  wrote:
>> Hi,
>>
>> Mike Hansen and I made some dangerous optimizations to the Sage
>> notebook codebase, then moved all notebook servers to run on the same
>> machine, and upgraded all sage notebook servers to use the new
>> notebook and Sage-4.7.  The notebook servers I'm referring to are the
>> following:
>>
>>       http://sagenb.org
>>       http://prep.sagenb.org
>>       http://tutorial.sagenb.org
>>       http://480.sagenb.org
>>       http://alpha.sagenb.org
>>       http://demo.sagenb.org
>>       http://demo2.sagenb.org
>>       http://nt.sagenb.org
>>       http://standalone.sagenb.org
>>       http://test.sagenb.org
>>       http://uw.sagenb.org
>>
>> Not upgraded:  http://flask.sagenb.org, because we don't want to
>> delete 150 openid accounts there...
>>
>> We made some nontrivial changes that could have introduced "millions
>> of new bugs".   If (when) anybody runs into *new* bugs on any of the
>> above servers, or find that any of them just don't work at all, please
>> respond to this message and/or report the issues here [1], so we have
>> something to do at Sage Days 31 [2] tomorrow.
>>
>> [1]  http://code.google.com/p/sagenb/issues/list
>> [2]  http://wiki.sagemath.org/days31
>>
>> On the plus side, http://sagenb.org might not totally suck now.
>>
>>  -- William
>>
>>
>> --
>> William Stein
>> Professor of Mathematics
>> University of Washington
>> http://wstein.org
>>
>> --
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>> http://groups.google.com/group/sage-devel
>> URL: http://www.sagemath.org
>>
>

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Re: [sage-devel] Newly upgraded and consolidate notebook servers: millions of bugs?

[Benjamin Jones]

On sagenb.org, I created a new account using openID. When I try to
edit a copy of a published worksheet, I get:

Internal Server Error

An error occurred rendering the requested page. More information is
available in the server log.

--
Benjamin Jones
benjaminfjo...@gmail.com



On Tue, Jun 14, 2011 at 10:40 PM, William Stein  wrote:
> Hi,
>
> Mike Hansen and I made some dangerous optimizations to the Sage
> notebook codebase, then moved all notebook servers to run on the same
> machine, and upgraded all sage notebook servers to use the new
> notebook and Sage-4.7.  The notebook servers I'm referring to are the
> following:
>
>       http://sagenb.org
>       http://prep.sagenb.org
>       http://tutorial.sagenb.org
>       http://480.sagenb.org
>       http://alpha.sagenb.org
>       http://demo.sagenb.org
>       http://demo2.sagenb.org
>       http://nt.sagenb.org
>       http://standalone.sagenb.org
>       http://test.sagenb.org
>       http://uw.sagenb.org
>
> Not upgraded:  http://flask.sagenb.org, because we don't want to
> delete 150 openid accounts there...
>
> We made some nontrivial changes that could have introduced "millions
> of new bugs".   If (when) anybody runs into *new* bugs on any of the
> above servers, or find that any of them just don't work at all, please
> respond to this message and/or report the issues here [1], so we have
> something to do at Sage Days 31 [2] tomorrow.
>
> [1]  http://code.google.com/p/sagenb/issues/list
> [2]  http://wiki.sagemath.org/days31
>
> On the plus side, http://sagenb.org might not totally suck now.
>
>  -- William
>
>
> --
> William Stein
> Professor of Mathematics
> University of Washington
> http://wstein.org
>
> --
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Re: [sage-devel] chrome and trac

[Benjamin Jones]

On Wed, Jun 8, 2011 at 1:51 PM, Jason Grout  wrote:
> For a long time now (maybe several months?), when I access trac using Chrome
> on OSX, it seems like a stylesheet isn't loaded, so the page is missing a
> lot of the nice formatting.  I posted a screenshot here:
>
> http://sage.math.washington.edu/home/jason/chrome-no-style.png
>
> Does anyone else see this problem?  Info:
>
> Chrome 12.0.742.91
> OSX 10.6.7
>
> When I look in Developer Tools, I don't see any errors about files not
> loading, even when I option-refresh to clear the cache.
>
> Thanks,
>
> Jason

That's weird. I'm using the exact same Chrome and OSX versions and I
don't see any problems with the Trac pages. Did you try a complete
"clear browsing data"?

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[sage-devel] Re: implementing mma's InverseFunction

[Benjamin Jones]

The `symbolic_inverse` function you posted on ask.sagemath looks good.
I might suggest catching the RuntimeError when no roots are found and
raising a more informative error, e.g. "Sage could not find a symbolic
inverse" ...

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On Apr 23, 3:38 am, Kelvin Li  wrote:
> On Apr 23, 1:22 am, Kelvin Li  wrote:
>
>
>
>
>
>
>
>
>
> > On Apr 14, 1:09 pm, Kelvin Li  wrote:
>
> > > On Apr 14, 1:03 am, Burcin Erocal  wrote:
>
> > > > Hi Kelvin,
>
> > > > On Tue, 12 Apr 2011 10:43:25 -0700 (PDT)
>
> > > > Kelvin Li  wrote:
> > > > > Is anybody working on implementing something similar to mathematica's
> > > > > InverseFunction? Or is there already a trac ticket out there? If there
> > > > > is interest and it is not on trac, I can open a ticket.
>
> > > > > Here is the link to mma's docs on InverseFunction:
>
> > > > >http://reference.wolfram.com/mathematica/ref/InverseFunction.html
>
> > > > > The question of finding the inverse to a given callable symbolic
> > > > > function has popped up a few times. In the cases that I have seen, it
> > > > > seems that Sage does not have this sort of feature. Here is one
> > > > > instance from AskSage:
>
> > > > >http://ask.sagemath.org/question/502/can-sage-compute-the-inverse-of-...
>
> > > > > Anybody know what is being done (or has been done)?
>
> > > > I don't think anybody is working on this. Feel free to open a ticket
> > > > and give the link to the MMA documentation in the description. A full
> > > > solution to this would probably require adding an attribute to all
> > > > symbolic functions to point to their inverses.
>
> > > This is now #11202 (http://trac.sagemath.org/sage_trac/ticket/11202).
>
> > > > Are you interested in working on this? I could try to explain how to go
> > > > about this in more detail if there is interest.
>
> > > Thanks Burcin, I will give it a shot. I have never hacked Sage before
> > > (or any large software project, for that matter), so expect lots of
> > > mistakes from me. :-)
>
> > > Is there something I should be aware of before I dive into the
> > > symbolics code? I am imagining adding an `inverse` method to the
> > > symbolic functions classes, wherever that may be. In the end, I also
> > > imagine being able to find the inverses of vector functions (but both
> > > input and output must have the same number of dimensions).
>
> > > Would it be okay to call Sage's `solve` function to find the inverse,
> > > or would there be problems with that?
>
> > > > Cheers,
> > > > Burcin
>
> > This thread has been dormant for a while, but I thought it would be
> > worth mentioning that I found a way to find the inverse of symbolic
> > expressions in one variable, using the "roots" method. See my latest
> > answer at:
>
> >http://ask.sagemath.org/question/502/can-sage-compute-the-inverse-of-...
>
> > Even with this, I would like to find inverses of vector functions
> > (i.e. more than one variable). Not sure if this is possible yet with
> > the same approach of using "roots". The relevant Trac ticket is #11202
> > (http://trac.sagemath.org/sage_trac/ticket/11202).
>
> > Ideas? Comments?
>
> > -- Kelvin
>
> A quick look at the code for the "roots" method shows that it simply
> calls Maxima's "solve". Therefore, finding the inverse of vector
> functions should be relatively easy to implement, using the same
> approach.
>
> Updating Trac ticket #11202 again...
>
> -- Kelvin

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[sage-devel] Re: http://flask.sagenb.org -- test it!!!

[Benjamin Jones]

On Mar 28, 10:45 pm, mhampton  wrote:
> Hey Harald (et al)-
>
> I am wondering if this is a general bug in the sage notebook - I seem
> to be having this problem with sage-4.7.alpha2 (not running the flask
> notebook, just the usual one).  Can someone else try this to confirm?
>
> -Marshall
>
> On Mar 27, 4:56 am, Harald Schilly  wrote:
>

Could it be that this is a problem with Chrome and the non-bleeding
edge jmol package as in this thread:

http://groups.google.com/group/sage-support/browse_thread/thread/47046e1c81d75d24/48e4b7d7beb19035?lnk=gst&q=jmol#48e4b7d7beb19035

??

--
Benjamin Jones

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