Re: [sage-devel] Re: Literal matrix syntax
On Thu, 2012-01-26 at 02:06 -0800, David Roe wrote: As for global defaults, it's nice for both examples and debugging for there to be as little global state as possible, and someone who wants RDF for reals probably wants CDF for complexes. The consistency argument is a good one, but changing matrix(...) would be much more invasive, and both defaults have their pros and cons, so the simpler syntax could be used for the simpler (i.e. more basic user that doesn't want to care about baserings but just wants to slice and dice some matrices) default. I agree that having very little global state is good, but right now I don't think that Sage is succeeding very well in our mission to provide a viable alternative to Matlab. I would like to see more users to Sage who care about floating point linear algebra, and I think it's worth having some global state if we can attract such people by making it easier to create matrices with floats. David Axiom associates the target type of the input so you type a:Matrix(Integer) := [[1]] or b:Matrix(Float) := [[1.1]] or for larger values c:Matrix(Integer) := [[1,2,3],[4,5,6]] d:Matrix(Float) := [[1.1,2.1,3.1],[4.1,5.1,6.1]] Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Literal matrix syntax
On Thu, 2012-01-26 at 02:24 -0800, Robert Bradshaw wrote: On Thu, Jan 26, 2012 at 2:16 AM, daly d...@axiom-developer.org wrote: On Thu, 2012-01-26 at 02:06 -0800, David Roe wrote: As for global defaults, it's nice for both examples and debugging for there to be as little global state as possible, and someone who wants RDF for reals probably wants CDF for complexes. The consistency argument is a good one, but changing matrix(...) would be much more invasive, and both defaults have their pros and cons, so the simpler syntax could be used for the simpler (i.e. more basic user that doesn't want to care about baserings but just wants to slice and dice some matrices) default. I agree that having very little global state is good, but right now I don't think that Sage is succeeding very well in our mission to provide a viable alternative to Matlab. I would like to see more users to Sage who care about floating point linear algebra, and I think it's worth having some global state if we can attract such people by making it easier to create matrices with floats. David Axiom associates the target type of the input so you type a:Matrix(Integer) := [[1]] or b:Matrix(Float) := [[1.1]] or for larger values c:Matrix(Integer) := [[1,2,3],[4,5,6]] d:Matrix(Float) := [[1.1,2.1,3.1],[4.1,5.1,6.1]] One can always make it explicit, e.g. matrix(QQ, [[1,2],[3,4]]) or (hypothetically) [1, 2; 3, 4; base_ring=QQ]; the question is about what to do in the implicit case. IMHO, the current default doesn't suit many users well, in particular it does disservice to those users who wouldn't even think to specify the basering. Sorry, I was unclear. Axiom associates the type with the target, so a:= [[1,2,3],[4,5,6]] == List List Integer b:Matrix(Float)== Type: Void c:Matrix(Integer) == Type: Void d:Matrix(RomanNumeral) == Type: Void e:Matrix(Fraction(Integer) == Type: Void b:=a + 1.0 2.0 3.0 + | | + 4.0 5.0 6.0 + == Type: Matrix Float so the line b:Matrix(Float) means that the symbol 'b' expects to hold something of the type Matrix(Float). The assignment b:=a assigned a List(List(Integer)) to the type of 'b' which causes an implicit coerce to the target type. c:=a + 1 2 3 + | | + 4 5 6 + == Type: Matrix Integer Working from the same List(List(Integer)) we get a different base ring of the matrix. d:=a + I II III+ | | + IV V VI + == Type: Matrix RomanNumeral I don't know how Sage handles the 'd:=a' case above. e:=a + 1 2 3 + | | + 4 5 6 + == Type: Matrix Fraction Integer Notice the output of the assignment 'c:=a' and 'e:=a' APPEAR to be the same but this is only because the denominator is 1. e:=[[1/2, 1/3, 1/4],[1/5,1/6,1/7]] + 1 1 1+ | - - -| | 2 3 4| | | | 1 1 1| | - - -| + 5 6 7+ It seems that if you have many possible base rings (which Axiom has) you need either an explicit coerce when the object is created or you need to know how to coerce a general input type (in this case, list) into the target type. So I am suggesting that a clean syntax is possible if the base ring is associated with the target symbol, not with the input tokens. Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Literal matrix syntax
On Thu, 2012-01-26 at 03:05 -0800, David Roe wrote: So I am suggesting that a clean syntax is possible if the base ring is associated with the target symbol, not with the input tokens. Apprently in Axiom you can statically type variable names, whereas in Python a variable is dynamically typed: you can't specify that a should hold an Integer for example. sage: a = 4; type(a) type 'sage.rings.integer.Integer' sage: a = 4/3; type(a) type 'sage.rings.rational.Rational' David The fact that the type is different seems to imply that Sage must manipulate the input somehow. Python does not know about rings. How is this done? Could the processing allow you to specify the type of the target with a particular syntax? All you need to do is keep a hash table of the specified target type. If the symbol is not found then do the usual process else use the specified target type. Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Two articles of interest to Sage in latest Notices
On Wed, 2012-01-18 at 23:45 +0100, Burcin Erocal wrote: On Wed, 18 Jan 2012 12:26:33 -0800 (PST) kcrisman kcris...@gmail.com wrote: Publishing Computational Mathematics, by Tim Daly (of Axiom, a frequent contributor on sage-devel) http://www.ams.org/notices/201202/rtx120200320p.pdf Literate programming is not just adding comments to code, but here are a few numbers nevertheless... FriCAS (I couldn't find Axiom on ohloh.net): https://www.ohloh.net/p/fricas # of lines of code: 1218007 # of comment lines: 205615 http://en.wikipedia.org/wiki/Axiom_computer_algebra_system http://axiom-developer.org Axiom has a project focus to become a literate program. FriCAS has a project focus to compete with Mathematica. Due to this philosophical difference the Axiom project forked. New computational mathematics is always interesting but it is more important to make sure that the code can be modified and maintained without devoting your life to the task. Projects die when the original authors leave. Sourceforge has 100,000 piles of dead code. In order to keep Axiom alive it must be possible to understand, modify, and maintain it. I firmly believe that literate programming is the only technology that can achieve this. Axiom is being rewritten to be fully literate. The code is being moved from a tree of little files to volumes with a particular focus. There are currently 21 volumes. These volumes contain actual executable source code which is extracted at build time. So the code you see in the books is the actual source code. There are still many small files to rewrite and distribute into their proper locations and there is still a great deal of explanation to be added to the volumes. However, this project has a 30 year horizon so this huge task is right on schedule. Singular: https://www.ohloh.net/p/Singular # of lines of code: 456764 # of comment lines: 73429 Sage: https://www.ohloh.net/p/sage # of lines of code: 474866 # of comment lines: 551813 Literate programming has nothing to do with comments. They are completely orthogonal. Think of literate programs as works of literature. You are telling a story (of why the code exists and what you are trying to solve). You need to motivate the characters (so procedures need to be introduced at the proper time in the explanation, not when the compiler needs it). You are trying to write a story for another human being, not code comments for the programmer. Write down the theory behind the code. The Hawaii test is a good benchmark. Can you bring a new person on the project, give them the literate books, send them away to an all-expense paid, 2 week vacation to Hawaii, and when they return they can maintain and modify the program as well as the original authors? I have found 2 literate programs that I consider examples: Lisp in Small Pieces by Queinnec (ISBN 0-521-56247-3) Implementing Elliptic Curve Cryptography by Rosing (ISBN 1-884777-69-4) I claim that literate programming improves code in 3 ways: A) the original programmer discovers errors while writing up the full explanation for peer review B) peer reviewers gain a deep understanding of the problem and can critique the original motivation for the code including how well the implementation covers it. C) future programmers can correctly modify and maintain the code in the spirit it was written. All of these are just opinions at this point but they can be tested. I am trying to find a university willing to run a test of hypothesis B. Students would be given either a literate program (e.g. Rosing's book) or the original source code (e.g. Rosing's downloadable source) and asked questions to test their comprehension, such as given #DEFINE NUMBITS 158 what is the significance of 158? Do you know? Elliptic curve code uses modular polynomial arithmetic which Rosing explains but would be really hard to reverse engineer from the source code. Gap wasn't available for comment at the time of publication: https://www.ohloh.net/p/gap-system This is also a good occasion to paste sage -coverageall output from 5.0.prealpha0: Overall weighted coverage score: 86.3% Total number of functions: 28917 We need 1056 more function to get to 90% coverage. We need 2502 more function to get to 95% coverage. We need 3658 more function to get to 99% coverage. Test coverage is an excellent idea. Commenting code is an excellent idea. Choosing descriptive variable names is an excellent idea. Code standards are an excellent idea. All of these have nothing to do with a literate program. Literate programming can be done in any language. I wrote an example using HTML: http://axiom-developer.org/axiom-website/litprog.html Are you creating computational mathematics useful for future generations or will they start yet-another- from-scratch-computer-algebra-system to replace Sage? Raise your game. Make your code live. Make
Re: [sage-devel] Re: Mathematica/Magma/Sage dictionaries ?
On Tue, 2011-12-13 at 18:15 -0600, Jason Grout wrote: On 12/13/11 5:51 PM, Nathann Cohen wrote: Hello everybody !!! I have been contacted by an enlightened colleague who planned to teach a bit of Sage at the local university, instead of Magma and Mathematica as it was formerly done. Now, enthusiasm is a wonderful thing that can achieve many things by itself, and for instance to the scary task of translating a semester's worth of Magma/Mathematica exercises and lecture notes into Sage ones. But really.. Wouldn't it be much much easier if someone around here already knew of an index of equivalents between Mathematica/Sage or Magma/Sage ? :-) Great idea. Tim Daly has long been asking people around here to contribute to the Rosetta Stone [1]. Jason [1] http://axiom-developer.org/axiom-website/rosetta.html or http://www.univ-orleans.fr/EXT/ASTEX/astex/doc/en/rosetta/htmla/roseta.htm -- I'm not sure where the original source is or how to add things to it. wget http://axiom-developer.org/axiom-website/rosetta.tex wget http://axiom-developer.org/axiom-website/rosettta.pdf -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Code style guidelines
diff has options to deal with whitespace. -b --ignore-space-change -w --ignore-all-space Tim Daly On Tue, 2011-10-25 at 07:35 +0200, Florent Hivert wrote: On Mon, Oct 24, 2011 at 11:20:47AM -0700, Keshav Kini wrote: Hmm. I have to say I'm surprised that people are advocating for using trailing whitespace at all, as it seemed to me to be quite universally reviled in the programming world. But on some reflection, the only real problem with trailing whitespace - other than that it bloats files and that it, er, grates on certain types of minds :) - is that people remove it from, or, though I imagine this is rare, add it to otherwise untouched lines. I guess if hypothetically we had stuck to a no trailing whitespace policy from day 1 of Sage development, such a policy would have minimized diff cruft. But Sage's codebase is already so big that perhaps the best policy is just don't purposelessly add or remove whitespace to lines that you aren't otherwise editing. As far as that goes, Jason's .emacs snippet seems useful for the developer's guide, indeed. +1 to this policy ! WE are trying to do that in the sage-combinat project. Systematically remove all trailing whitespaces creates a lot of conflicts in the patch queue so I'm strongly against it. Cheers, Florent -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Multiple databases and sage
On Wed, 2011-10-19 at 10:44 +0200, Paul-Olivier Dehaye wrote: Dear all, I am currently participating in a sage-based project that aims to integrate a lot of number theory databases (some of you know it, or are even participating!). Some of the goals of the project are to display, search across or perform further computations on archived objects that come from very different sources. The variety of sources can be due to human factors (more than one person has data, or people have overlapping but not identical interest), historical reasons (a legacy table has since been expanded but should be kept for compatibility reasons), and most importantly mathematical reasons (the archived objects can be computed using very different constructions that current mathematical results do not know how to unify, but all these objects should really be looked at through the same lens sometimes). I expect these to be very common problems when trying to integrate mathematical data from various sources into sage, regardless of the area of mathematics. Does this sound familiar to anyone? Some participants of the sage-combinat project are pushing for the concept of Categories ( mathematical categories) as a way to exploit object-oriented programming to its fullest and organize code in a flexible and efficient way. Categories are then used to incorporate purely mathematical information (of the type a Field is a Ring), that Python can also understand and use to build a whole class hierarchy. Axiom is based on a Category concept. Categories give a mathematical structure to the results that make it possible to use the algebra as a scaffold to organize the software. It has proven to be very effective. Can you point me at the sage-combinat project? Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Science Code Manifesto
Hmmm. I did work at CMU last year on a Journal article. It was based on about 3 years of research work. The article was completed, submitted for review, and accepted. CMU required that I sign over the copyright to them. Springer required that I sign over the copyright to them, despite an agreement between CMU and Springer. It turned out that the agreement was between CMU and Springer USA but the Journal is published by Springer Europe. Ultimately the two lawyers could not agree and my Journal article was withdrawn during production. CMU now holds the copyright. Three years of work and I have nothing, no rights and no publication. As a major advocate of Literate Programming I was hoping to publish a follow-on paper that included the actual source code. Why bother? Tim Daly On Sun, 2011-10-16 at 12:20 -0700, William Stein wrote: On Sunday, October 16, 2011, Dima Pasechnik dimp...@gmail.com wrote: Bill, are you sure that you have signed away to your employer rights to your ideas ? Technically Bill only said that Uni's consider employee work intellectual property, but he did not say they consider it *their* intellectual property... While some not so great universities are just degree-selling businesses, last time I had to obtain a permission from my employer for publishing something, was still in Soviet Union! So I really don't see how results of work done by a faculty member are university property. -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel +unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org -- William Stein Professor of Mathematics University of Washington http://wstein.org -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel +unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Science Code Manifesto
Oh, and as another aside, I left CMU in February (I'm now unemployed) but the last effort we had was to release our 6 year research project as open source. That effort is tied up in legal somewhere and has been since January. Since I'm no longer there I expect the code will never see the light of day. Which implies that I cannot use my last 6 years of work. Technically I cannot complain as I knew the rules while I worked there but it really does seem like a waste of good research. Nobody will be able to build on the results, which is a fundamental principle of scientific progress. Tim Daly On Sun, 2011-10-16 at 15:42 -0400, daly wrote: Hmmm. I did work at CMU last year on a Journal article. It was based on about 3 years of research work. The article was completed, submitted for review, and accepted. CMU required that I sign over the copyright to them. Springer required that I sign over the copyright to them, despite an agreement between CMU and Springer. It turned out that the agreement was between CMU and Springer USA but the Journal is published by Springer Europe. Ultimately the two lawyers could not agree and my Journal article was withdrawn during production. CMU now holds the copyright. Three years of work and I have nothing, no rights and no publication. As a major advocate of Literate Programming I was hoping to publish a follow-on paper that included the actual source code. Why bother? Tim Daly On Sun, 2011-10-16 at 12:20 -0700, William Stein wrote: On Sunday, October 16, 2011, Dima Pasechnik dimp...@gmail.com wrote: Bill, are you sure that you have signed away to your employer rights to your ideas ? Technically Bill only said that Uni's consider employee work intellectual property, but he did not say they consider it *their* intellectual property... While some not so great universities are just degree-selling businesses, last time I had to obtain a permission from my employer for publishing something, was still in Soviet Union! So I really don't see how results of work done by a faculty member are university property. -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel +unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org -- William Stein Professor of Mathematics University of Washington http://wstein.org -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel +unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Upstream projects
On Mon, 2011-09-05 at 07:32 +0200, Julien Puydt wrote: Le 05/09/2011 02:41, leif a écrit : One shouldn't upgrade packages just for the sake of higher version numbers in Sage though, and there are packages where upgrading is indeed non-trivial, because of functional changes in upstream, or a lot of changes made by Sage to its current version. I can't help but notice that last part of the sentence is part of Dave Neary's point. Snark on #sagemath Tracking upstream changes and feeding back bug reports and fixes takes time. Axiom has only one upstream package (GCL) and it is a major step to upgrade but it is done on a reasonably regular basis. We are fortunate that Camm tests GCL's changes by, among other things, compiling Axiom, Maxima, and other large packages. The other advantage is that Common Lisp is a standard so it is reasonably clear whether the failure is GCL or Axiom. Historically Axiom was written in MacLisp, then LispVM, and then Common Lisp. Since I had expertise in all three of these languages I did a fair amount of the porting and rewriting to Common Lisp. I have to say that it was not easy. The key advantage of Common Lisp is that we could change LispVM functions into either Common Lisp functions or macros without changing the code everywhere. If the new function implemented the LispVM or MacLisp semantics properly everything else just worked. I see Sage efforts to keep up with OS changes (e.g. Lion) and package changes (e.g. Maxima) but I am unaware of any work to keep up with Python. Python is up to version 3.2.2 which is incompatible with 2.7. Plus, there is no standard for the language. It is clear that Sage is losing ground on the upstream development path. What happens when the python-based spkgs, such as SciPy, convert to 3.x? The time will come when all published materials about Python use 3.x syntax and semantics, at which point Sage will no longer be programmed in Python. It happened to many languages (e.g. Fortran, C, Lisp, etc.). I don't believe that Python allows you to redefine standard Python functions and it doesn't have a macro facility so neither path used by Axiom is available for Sage. As pointed out in the article, the longer this continues, the harder, more expensive, and more disruptive the changes will be. Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Upstream projects
The Cost of Going it Alone by Dave Neary http://blogs.gnome.org/bolsh/2011/09/01/the-cost-of-going-it-alone/ -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: MATLAB: viable alternative...?
On Fri, 2011-08-19 at 05:27 -0700, leif wrote: ___ * I vaguely remember to have once seen some [quite old?] list / table mapping Mma function names to Sage's, but I'm not aware it is part of the Sage distribution or prominently advertised. I may be wrong of course. ;-) There is http://axiom-developer.org/axiom-website/rosetta.pdf which does not include Sage, although I'd be happy to replace it with a newer version that does. I'm not enough of a Sage person to do it properly. Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: MATLAB: viable alternative...?
MIT's online linear algebra course with Gilbert Strang mentions rref as one of the very first functions in Matlab. On Tue, 2011-08-16 at 00:44 -0700, Rob Beezer wrote: On Aug 15, 11:38 pm, William Stein wst...@gmail.com wrote: It sound like it wouldn't be difficult for you to name one single Matlab matrix function that engineers would actually use that Numpy/Scipy doesn't have? I wonder why it's not in numpy yet. Sorry, I couldn't parse that. Did you mean would instead of wouldn't? More directly - it appeared to me that the popular matrix decompositions in MATLAB were all (or almost all) available to be wrapped from SciPy/NumPy as Sage methods for RDF/CDF matrices. I know one example sort of like this, which is rref, for reduced row echelon form. However, in a numerical setting, my understanding is that engineers would never ever use rref directly anyways. Nonetheless, Matlab has it and Numpy/Scipy don't, because there is no point in having it. I have to be careful, because I would not claim to be a numerical linear algebraist, so I am willing to be corrected - but I think an LU decomposition would be the first choice for an alternative to rref. It is basically what we used to call Gaussian elimination, rather than Gauss-Jordan elimination, but with more care about pivoting in a numerical setting. Enabling LU decomposition for rectangular matrices (not just square), which is now possible in NumPy/SciPy, is a patch with a positive review (iirc) and I have posted a patch for an exact LU decomposition, which is able to run over generic rings twice as fast as echelon form (as theory would predict). Needs review. An LU decomposition is the lever for a similar speedup (2x) in solve_left() over generic rings. Incidentally, as I discovered by putting this on a homework assignment for my class, it genuinely is really easy to implement rref in Numpy, and the result from almost anybody is very impressively fast, even in pure Python (Cython barely helps in this case, since Numpy is already so optimized). I would vote for not allowing a naive/classical rref algorithm from Sage to be applied to a matrix over RDF/CDF. Also, with your 75% above, do you mean when working with Sage matrices or Numpy arrays? Consider the primary numerical matrix decompositions - LU, QR, SVD, Cholesky, Schur. Rough recollection - and it depends on patches in- progress - these are available in MATLAB, and almost all are also available for Sage RDF/CDF matrices (maybe just Cholesky needs attention). Some are available for exact Sage matrices (modulo finding exact eigenvalues in some cases). Along with straight-out numerical eigenvalues for Sage RDF/CDF matrices, and exact Jordan canonical form and exact rational canonical form (over *any* field), I'd posit roughly 75% coverage by Sage in this area, exact and RDF/CDF combined. Maybe higher. Rob -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Sage Pari
Again I have to credit Sebastian Pancratz and Fredrik Johansson here for raising the standard in flint. I thought I had been producing beautiful code until Sebastian started rewriting some of it for me. :-) I downloaded Flint and looked at the source code and documentation. First, I applaud you on the PDF. It looks very nice and it includes quite a bit of information. I especially liked the hyperlinks to Wolfram's site and the fact that you included a bibliography. The inline mathematics is very useful (a TeX advantage). As an experiment I tried to understand Bell Numbers, of which I know nothing. Since the algorithm for bell_number_vec_recursive is small I can see what is being computed. However, I also see that bell_number_vec contains a magic number 7000 as the defining value to split the computation. One advantage of a literate form of the documentation would be the obvious need to explain this number. The pdf simply says that it Automatically switches... but not when or why. The hard part of a fully literate document is the need to explain the special tricks that make an algorithm fast. Mathematically they might not matter but computational math hinges on the details. Many an algorithm in Sage has been carefully tuned to get speed and it is this careful tuning that makes the algorithm worthwhile. It also makes it obscure. But this tuning includes crucial knowledge that cannot be reverse-engineered and is only known to the author. Eventually the author dies, as has happened with several Axiom authors. If a future maintainer needed to port Flint to run on the ARM or the Apple5 or the GPU/CPU/APU setup what are the critical things to optimize? Is 7000 machine independent? Knowing these details is the difference between a classroom algorithm and a world class one. If I write Bell Numbers in Axiom, does 7000 matter? The reason to favor a fully-embedded literate program is that you can't ignore or hide any implementation detail. The magic number 7000 would cry out for an explanation. Keeping the code in one file and the documentation in another file makes it trivial to skip details. A peer review of a literate program would certainly notice that this was skipped. I am tempted to make a literate paper about bell numbers that is built on your code but I'd obviously make a fool of myself in front of a crowd of number theorists :-) Never the less, a small pamphlet on the implementation of Bell Numbers would make a good starting example to critique. I would be willing to provide the tools and techniques if you'd be willing to provide the explanations. Feel free to decline. Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Sage Pari
On Jul 27, 11:58 am, John Cremona john.crem...@gmail.com wrote: My innocent posting to sage-devel on this subject two days ago seems to have done something to increase the number of postings this month, even if a lot of the discussion has been much wider than the orginal title (Sage Pari) suggests! Well, credit is the coin of the realm in open source so it is important to make sure that those who work get recognized (paid). This is especially sensitive in an academic environment. If you spend a year writing software but don't publish then the tenure committee won't see any of that work. I managed to widen (hijack) this thread to the larger topic of computational math and literate programming. Apologies for that. Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Sage Pari
the standards for published mathematical software will help us all in the long run. We can look forward to a time when we can read, understand, and cite particular Pari and Sage algorithms which are their actual implementations in literate form. Tim Daly d...@literatesoftware.com d...@axiom-developer.org -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Sage Pari
don't know where to integrate literate tools into the process. Raising the standards for published mathematical software will help us all in the long run. We can look forward to a time when we can read, understand, and cite particular Pari and Sage algorithms which are their actual implementations in literate form. It's not the only important step that needs to be taken though. My epiphany regarding automated program checking came when I serendipitously encountered a fantastic book on Prolog on the exact same day that I sat down to implement Damas-Hindley-Milner type inference for an interpreter I have been writing. I marvel that a 20 line implementation of the unification algorithm saves me so much hassle. After this little epiphany I have not had any problems seeing the future. Type inference and unification have been around for ages, but I feel like someone who has been in a time machine and returned and who has to sit around and watch the inevitable development of the compiler technology that I have already seen. Progress feels like a slow motion replay. Ah, indeed. Another direction is the development of automated proofs. I don't know about Sage but Axiom has an algebraic scaffold that looks like it will allow us to attach definitions and theorems (e.g. around Groups, Rings, Fields, etc) and then prove the algorithms that, say Ring, implements. I have had many discussions, some with the people at UTexas, working on ACL2. There are other efforts (e.g. COQ) in this same direction. The root question is How do we connect mathematical theory to computational mathematics in a rigorous, automatable way that can be published and peer-reviewed?. The task is too big and the goal is too distant for a single leap. It would be better if we could begin to have something like a Sage track (like HICSS tracks), that calls for, reviews, and accepts literate software. Each example paper could slowly raise the standards of good practice. Flint might be a good place to start. Perhaps there is an ACM connection to this effort. (I am no longer an ACM member though). ACM might help sponsor some of the presentations. NIST is also a potential partner as these algorithm papers could become standards. Oak Ridge National Labs has a numeric library interest and might be convinced to help fund a literate form of the library. Sage has a reach and connection with a large number of academic researchers. It would certainly help a tenure review if the software algorithms were in literate, peer-reviewed paper form. This might help get tenure-track people more involved in the creation of software since it seems that only papers count in the tenure process. In any case, if the papers were literate then it would be clear who, what, and how to cite prior work. Literate Pari papers would be an obvious example. Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: LaTeX code to Sage expression?
Since TeX is turing complete and allows macros,
would it be possible to create a set of macros
that are not ambiguous? For instance, an integral
macro that specifies the limits and differential
variable?
\integrate{0}{\infty}{r}{sin(\theta)}
In this case it seems to me that the latex macros
would closely approximate the actual linear input
to the CAS.
Tim Daly
On Sat, 2011-05-14 at 08:25 -0700, rjf wrote:
Look at
http://moralfiber.org/eylon/berkeley/cs282/
to see a paper,
Parsing Mathematics Typeset in TeX
that successfully parsed many many formulas
from Gradshteyn and Rhyzik, a table of integrals.
The result was Lisp, which presumably could be Maxima.
If you have a result in Maxima, presumably Sage can make sense of it.
Or the same design can directly produce whatever Sage-speak you had in
mind.
--
To post to this group, send an email to sage-devel@googlegroups.com
To unsubscribe from this group, send an email to
sage-devel+unsubscr...@googlegroups.com
For more options, visit this group at http://groups.google.com/group/sage-devel
URL: http://www.sagemath.org
Re: [sage-devel] Re: profiling Sage startup
Sage could follow the same technique used by Gimp. Gimp loads a huge number of files at startup and can take over a minute to start on small systems. They have a startup splash screen that shows the files which are being loaded. That way the user sees progress during startup. -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Support contracts for commercial customers.
On Sat, 2011-02-26 at 20:09 -0800, Nils Bruin wrote: On Feb 25, 10:52 pm, William Stein wst...@gmail.com wrote: 2) Pay for advertising Sage in maths journals, New Scientist, or if deemed appropriate, anywhere where the 4 M's are advertised. b) Is 2) something that will annoy anybody reading this? I could see somebody being annoyed that valuable Sage money is being spent on advertising. (I personally think advertising is a good idea.) Do you have good reasons for thinking that? Not that you need them or need to share them. I am just wondering. I would personally like to see sage develop into a platform that I can use for my research needs. When I look at other programs that fit in that category (magma, kant/kash, pari, singular, gap, python, gcc), I notice that none of those feel the need to advertise. Is there something that sage might gain from advertising that those other programs wouldn't? Are those other projects missing opportunities? Well, missing opportunities has a lot to do with project goals. If you are advertising, what is it you are advertising? Are you trying to get more developers? Why not use sourceforge, etc to post help requests? Are you trying to get more users? Why not use a direct phone/mail campaign to your likely targets, which for Sage would be other schools and peers at other schools. A table at the math conferences is a great idea and you should continue that. If you are advertising to attract money then what would your ad copy be about? Money only goes where it can grow. Why would someone invest in Sage if it is not already a commercial entity? I am a little unclear about the financial growth potential of any open source computational mathematics package. What is the business plan? What is the elevator pitch? What are the 3 year payback goals? Is it 1) advertise 2)... 3) profit! If you are advertising to attract attention then Google might not be the best place. Most universities probably already have MMA and Maple so professors and students know about them. If they are using these tools in class they are probably already aware of what is available. I know that when I taught, say compilers, I reviewed pretty much every compiler textbook I could find. I doubt that a professor is going to be swayed by a Google ad. I could be wrong in an individual instance but less likely to be wrong in the general case. Are you advertising to a particular niche market? For instance, Mathcad is very engineering oriented and has a lot of special purpose packages such as a way to get GPIB data off your spiffy HP equipment. Lab guys love it and will pay for this ability. Sage has no GPIB support. Some projects, like Axiom, are not missing opportunities since there is nothing about the project goals that would make a Google ad relevant. What Sage project goals require ads? Is Sage really ready to compete head-to-head with MMA and Maple? Would Sage know what to do with ten thousand end-users (students) demanding support? Personally I would love to see Sage win big because I fear the dark ages that will occur when MMA and Maple disappear. You might not think this could happen but how many companies do you know that are 50 years old? And what ever happened to Macsyma (Symbolics died but you can still buy it for DOS). What about Derive? (TI bought it, rewrote it into C++ but refused to release the original Lisp code to me). Reduce? (Tony Hearn released the code as open source but I don't know who is maintaining it). Axiom was one of the commercial big three with MMA and Maple. When MMA and Maple (recently bought by a company in Japan) go under where will computational mathematics be? Will MMA and Maple become open source? Who will maintain them? Who but the original authors could understand their internals? What happens to all of those thousands of algorithms? So I hope that you advertise well. I hope you start a company. I hope you all get rich and famous. But I also think that there needs to be a bit more thought about exactly what it is you would advertise and what you are trying to achieve by it. Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Support contracts for commercial customers.
I'm also curious about honest *opinions* about how people in the Sage community would feel about a company making potentially gobs of money selling support contracts? What balance between profit and giving back to the community would be appropriate? What services might be offensive, and what would be OK? For example: * I could see how some people might be annoyed if there were a Sage version of EPD (http://www.enthought.com/products/epd.php) that fully supported Windows (say), even though Sage didn't, and cost $199/license. On the other hand, perhaps a $199 Sage-for-Windows might be better than no-sage-at-all for Windows for free. Funding always has the upside and the downside. One upside is that you could afford to pay someone to actually do porting and support work. As you know, there are a lot of tasks that rarely get done because they are just not interesting enough to do. I spend a week every two months on porting and platform issues. With funds coming in you could set up a limited liability corp to manage negotiation with schools, etc. The downside is that you begin to compete with MMA, Maple, etc. commercially. Can Sage compete on a level playing field? If I am going to give my research away should I write it in Sage or MMA? Which one will give me a larger audience? There is the question about where the profit would go. If I do the research and you make the money it seems a little out of balance. There might be limitations on free. For instance, a Windows port might use proprietary software to make Sage run well on Windows. There are a few people in Sage who are quite passionate about GPL-ish issues and this might lead to a fork. Redhat seems to have walked the thin line but they always styled themselves as a service company. They did a lot to support the community. Eventually they ended up with a deliberate split of redhat vs fedora. Would you end up with a Sage vs Wage split? * I'm curious if something like sagenb.org, but with Google ads, would be offensive. I could see somebody starting a small business that is just public notebook servers that also have ads. I haven't personally made up my mind about any of this. -- William -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Support contracts for commercial customers.
On Thu, 2011-02-24 at 11:18 -0800, Tom Boothby wrote: I'm also curious about honest *opinions* about how people in the Sage community would feel about a company making potentially gobs of money selling support contracts? What balance between profit and giving back to the community would be appropriate? What services might be offensive, and what would be OK? For me, it all depends on what the company does with said gobs of money, and who is at the helm. If some enterprising stranger starts a company providing support contracts, that's their own business -- we develop free software, and people are allowed to use it. But somehow, if you (William Stein) were to start the company and profit from it, the situation gets hairy. Keith Geddes (Maple's version of William) had to choose between being part of Maple management and being a professor. He decided to be a professor. I've talked to him about it and it was not a simple decision on his part. You can be rich or you can be famous. Which one would you choose? :-) For example, if you were to start a company which was primarily devoted to making you lots of money, that would kinda suck. If, on the other hand, you devoted the majority of the profit to a good cause, I'd be all for it. My definition of good cause here is pretty loose, too: if you used the profit to (say) buy and operate a server farm which replaced the public notebook, that'd be *awesome* in my book. If the money went to an institute which pays mathematicians to do research which is tangentially related to the interests of Sage users, great. If Sage could follow the Redhat model I think this would be a win for the whole community. It would be great to see ANY kind of a funding stream for computational mathematics. Funding grants for general research questions (e.g. what is a general way to handle simplification?) would be great. If the money went to some Sage developers and not others, then I foresee some big problems, though. I don't know how this would be handled, and I assume that some people would get pissed off and leave the project over it. On the other hand, it would be nice to be able to hire talented programmers to do dirty work that current Sage developers don't want to do. For example: * I could see how some people might be annoyed if there were a Sage version of EPD (http://www.enthought.com/products/epd.php) that fully supported Windows (say), even though Sage didn't, and cost $199/license. On the other hand, perhaps a $199 Sage-for-Windows might be better than no-sage-at-all for Windows for free. Is this option GPL-compatible? * I'm curious if something like sagenb.org, but with Google ads, would be offensive. I could see somebody starting a small business that is just public notebook servers that also have ads. Knock yourself out. If it was made obvious that sagenb.org requires huge amounts of computing power and the ads enabled us to pay for CPU time on a distributed solution, I'm all for it. On the other hand, if the ads only make a few bucks a month, it isn't worth it. Free services on the net have ads or are donation-driven -- people are used to that. I'm thoroughly opposed to obnoxious flash ads, pop-ups, etc., but text google ads are fine by me. It's going to be HILARIOUS when we start seeing Mathematica ads on sagenb.org, though. -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Rapid growth in Python popularity
The python community is huge, skills are available, and often the needs are not in the core science algorithm which is well looked after, but in the glue and interface, which requires a less in-depth understanding of the science than the core algorithm. It allows non-niche programmers to assist more easily than... FORTRAN. I do think Sage has proven the conjecture that Python is an excellent choice for a glue language (although a lot of the actual glue seems to be in Cython?). Since Sage is growing by accretion, William made an excellent choice. I don't think Sage has proven the conjecture that Python is good for computational mathematics. My experience with computational mathematicians is that they will program in obscure (APL) or dead (Fortran) languages. Every one I have met over the years is perfectly capable of writing their algorithms in anything. There are two ways to look at any computational mathematics problem. Either you want something very close to the math, (e.g. Spad) for conceptual efficiency or very close to the machine (e.g. C) for execution efficiency. Python sits somewhere between these two extremes, making it a non-optimal choice for either. If I were working with Sage I'd write my algorithm in some other language and glue it on with python. As for the conjecture that Python is wildly popular and therefore the perfect choice for computational mathematics I can only point to history. Pascal was everywhere, including in the universities. Smalltalk took the world by storm. PL/I was universal. Ada was the ultimate language. Most people probably don't even list these languages on their resume anymore. Wait 10 years. Nobody will admit to knowing Python. Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Rapid growth in Python popularity
As for the conjecture that Python is wildly popular and therefore the perfect choice for computational mathematics I can only point to history. Pascal was everywhere, including in the universities. Smalltalk took the world by storm. PL/I was universal. Ada was the ultimate language. Most people probably don't even list these languages on their resume anymore. Wait 10 years. Nobody will admit to knowing Python. Your summarization of history indicates that no language will survive 10 years, so we should pick a language not on its long-term merits but based on getting something out of it before it fades. Hasty generalization. Fortran, Lisp and C are still active and they are 50 years old so some languages are still resume material. Pascal, in its day, was HOT. Universities switched to Pascal for teaching, books were using it as pseudocode, and great debates raged about its bike-shed issues (e.g. a lack of strings). It was the easiest language to write. It was easy to compile. It was required as a line-item on your resume. It cured cancer and was the key to worldwide understanding. Famous people in history were renamed after the language! Surely everyone you know codes in Pascal, right? Is Python a Fortran or a Pascal? Well, lets look for some data about how others choose. I have touched nearly every computational math program on the planet over the years. On my Ubuntu linux system almost every python program I didn't write is some sort of a system script so it seems to have moved into Perl's primary domain. From that data point I'd say that Python is a great language to know if you plan to be a sysadmin. (I excluded Sage, of course). Sympy and numpy are exceptions. But even Java people use python for scripting and test (e.g. inside ant). On my Ubuntu linux system almost every computational math program I didn't write is either Fortran, Lisp, C, C++, assembler or some specialized math language like Spad, MMA, Maple, etc. From that data point I'd say that Python is not a computational mathematics language of note. From the data it seems that Python is the new Perl, a new, improved system scripting language; a glue language for the new millenium. That might explain why it appears to be so popular and why Perl is sinking in the TIOBE ratings. Would you do computational math in Perl? Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Rapid growth in Python popularity
An interesting article about computational science programming: http://www.nature.com/news/2010/101013/full/467775a.html?ref=nf Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: gcd lcm and numberfields
On Fri, 2011-02-11 at 09:20 +, David Kirkby wrote: On 10 February 2011 14:51, rjf fate...@gmail.com wrote: in maxima, gcd(1/4,1/6) is 1/12, lcm is 1/2 Since maxima immediately simplifies 2/1 to 2, there is no distinction between gcd(2/1, ) and gcd(2, ...) FWIW, I just noticed that Mathematica treats 2/1 as an integer and not as a rational. In[1]:= Head[2] Out[1]= Integer In[2]:= Head[1/3] Out[2]= Rational In[3]:= Head[2/1] Out[3]= Integer What does MMA do with gcd(2/1,4) -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: sage thoughts
On Fri, 2011-02-11 at 01:49 -0800, Simon King wrote: Hi, On 11 Feb., 09:56, Simon King simon.k...@uni-jena.de wrote: Well, I had the impression that a couple of people are in favour of the following: gcd(a/b,c/d) := gcd(a,c)/lcm(b,d) lcm(a/b,c/d) := lcm(a,c)/gcd(b,d) It just occurs to me that I am incredibly stupid. The definition above wouldn't work at all, it isn't even well-defined. Just replace gcd(1/4,1/6) by gcd(3/12,9/54). You obtain gcd(1,1)/ lcm(4,6) = 1/12, but gcd(3,9)/lcm(12,54) = 1/36. Does anyone have a better idea? Would it be a correct definition if one insisted on reduced fractions? Cheers, Simon That's why I was asking for an algorithm for gcd and lcm in the subdomain. I'm not sure what answer is expected. The unit (1) is correct but not by your definition, and apparently not helpful for the original poster. Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: sage thoughts
On Thu, 2011-02-10 at 22:57 -0800, Simon King wrote: Hi Bruno! On 11 Feb., 01:37, Bruno Le Floch blfla...@gmail.com wrote: You could have both consistencies. That depends on how you define gcd and lcm: - Quotient fields as described by Bruno. - Fields: zero if both elements are zero. A non-zero element otherwise (most fields would choose 1 here). - PID: a generator of the corresponding ideal. I don't see how this brings in both consistencies. Algebraic consistency requires gcd and lcm on QQ to have different outputs depending on whether QQ is seen a Field, a PID, a Quotient Field... Is there a clear way for the user to indicate which QQ he wants? I am sorry for the FUD that I spread in my earlier posts. Meanwhile people convinced me that it is indeed possible to have both consistencies. The point is: In a PID, the lcm of a and b is only defined up to a unit - it is only required that lcm(a,b) generates the intersection of the ideals generated by a and b. My mistake was: 1 is certainly the canonical choice of a generator of the ideal a\cap b (a,b non-zero); but that does not mean that it is the best return value of lcm(a,b)! So, if lcm(a,b) for a,b non-zero returns *any* non-zero element, then consistency from the category point of view is granted - lcm(1/2,1/4) = 42 is not wrong in QQ. But that freedom means: We can *in addition* achieve consistency with respect to sub-structures, namely by seeing QQ as a quotient field. Cheers, Simon Can you suggest an algorithm to implement this? Is there an agreed-upon answer (i.e., not 42?) Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: sage thoughts
On Wed, 2011-02-09 at 22:18 -0800, rjf wrote: You say, gcd(2/1,4) returns 1 for simplicity (!), because 2/1 is a rational. This is shockingly silly. I don't know exactly how this came up, but if 2/1 is in a different domain (rational) from 2, (integer), then gcd should probably be 1, since any non- zero rational number divides any other, and one commonly uses the positive unit 1 for such a case. You could argue that since you can coerce 2/1, you should. That's sometimes OK, but not always. Really, the issue is much broader. for example, do you also want to treat the complex number 1+0*i the same as 1? do you want to treat the floating point number 1.0 the same as 1? What about 1X1 matrices? Is 1^0 the same as 1^0.0 or 1.0^0 or 1.0^0.0? Do you perhaps wish to consider/dismiss the existence of number systems with signed zeros (IEEE floating-point standard) on the grounds that -0 = +0, [true, for numerical comparison] and therefore there should be only a single zero? While I don't know the exact formulation of this GCD problem, the issue of implicit coercion is one of the troubling sore spots in a system design, and should not be decided by counting up casual +1 votes. I think the Axiom people might have thought more about it than others. It is a question of domains. In Axiom you can specify the domains. 2/1 is a Fraction(Integer) aka rational 4 is an Integer (2/1)::Integer = 2 where 2 is an Integer. 4::Fraction(Integer) is a Fraction(Integer) So there are several cases: gcd((2/1),4::Fraction(Integer)) = 1 of type Fraction(Integer) gcd((2/1)::Integer,4)) = 2 of type PositiveInteger gcd(2/1,4) = 1 of type Fraction(Integer) gcd(2,4)= 2 of type PositiveInteger gcd(2,4::Fraction(Integer)) = 1 of type Fraction(Integer) Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: FAQ suggestion: I'm a programmer, how can I contribute to Sage?
On Wed, 2011-02-02 at 10:43 -0600, Jason Grout wrote: On 2/2/11 10:33 AM, rjf wrote: 1. What happens if you don't have a plan? 2. Who makes a plan? You have long experience with other open-source projects. Have they had plans? (I'm really genuinely curious). Who made it? How comprehensive/detailed was it? Was the plan a success (i.e., was it worth making?) Was the plan followed? How did you give incentive to follow the plan? Axiom has a set of goals, made by me, such as http://axiom-developer.org/axiom-website/currentstate.html This gives a place to capture ideas and long term plans. A plan might imply a schedule and, as far as I'm aware, nobody knows how to schedule software development. This is especially true of free software. Is it a success? Well, a lot of the tasks have been accomplished, some have been abandoned, and some will take years to finish (e.g. making Axiom fully literate). How did I give incentive to follow the plan? Ideas that were discussed and agreed upon were added to the list of goals. Some of them have been completed (e.g. the boot language is gone), some of them have died (e.g. the CCL port is dead), and some of them caused much controversy (e.g. competing with MMA, autoconf, boot language) and were decided by me. Those who disagreed forked. A project cannot be all things to all people and someone has to decide what the long term goals are. But I don't think that a plan is useful except maybe in the short term among a group of developers. Open source does not really attract groups in my experience. It is usually a set of single-person efforts. Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: FAQ suggestion: I'm a programmer, how can I contribute to Sage?
On Tue, 2011-02-01 at 08:40 -0800, William Stein wrote: On Tue, Feb 1, 2011 at 8:32 AM, William Stein wst...@gmail.com wrote: On Tue, Feb 1, 2011 at 6:21 AM, Dr. David Kirkby * No documented plan * No real documented estimates of time scales * No status reports for the project as a whole. If you think a plan as you describe it for overall Sage development is so important, why don't you make one? -- William How about this plan? 1. Make a plan. 2. ??? 3. Profit! -- William There is a patent on that business plan. The Supreme Court just ruled that it is valid. I'm sure you'll be hearing from MicroGooglzon shortly. Oh, and step 2 is considered a trade secret, which you just revealed, so you've REALLY stepped in it now :-) Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: FAQ suggestion: I'm a programmer, how can I contribute to Sage?
3) I think the issue of crackpots and bad code dragging things down is not much of a problem. The reason is that it takes quite a bit of perseverance to get code into Sage. My experience with my Jmol contributions is an example. I would not claim to be the best coder, but think my Jmol contributions addressed some issues people had. And certainly the code is not yet ideal, but it does do most of what I understood people to want. Because of the load on people doing testing, it has taken months to get much feedback on it. This means anybody submitting code has to be willing to stick with it and prod it along over the long term. People who are not serious won't do this. My example may be a little slower than many people's because I also have very little time to contribute to this, but I still think you are unlikely to get really bad code included using the present model. To quote the above This means anybody submitting code has to be willing to stick with it and prod it over the long term. The real problem with Sage's development model will not show up for a few years. At the moment most of the code being contributed is supported by the original authors. The algorithms are complex and some implementations are only competitive when optimized into Cython, despite the Sage is Python mantra. The real problem will arise when these authors leave the project. Code rots. People make simple changes. Linux changes libraries. Who will be able to debug research-level elliptic curve code when some minor, unrelated change breaks it? Who will even know that it is broken? Is it broken now? And since the Sage code base is owned by other people with other goals, that is, all of the spkg files from upstream projects, the potential for code rot is much larger and the debugging problem is much harder. Is the elliptic curve code failure due to Sage-owned python changes or spkg changes? What happens when python itself changes and upstream packages make the move to python 3.0? The problem isn't really bad code. The problem is code rot. What does a programmer need to know to maintain the system? How can a new programmer join the project and contribute? If it is not easy now it won't be possible later. How do we architect systems to survive the loss of the authors? How do we architect systems to survive the changing platforms? Will Sage live? Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: FAQ suggestion: I'm a programmer, how can I contribute to Sage?
On Sun, 2011-01-30 at 13:52 -0800, William Stein wrote: On Sun, Jan 30, 2011 at 9:23 AM, daly d...@axiom-developer.org wrote: 3) I think the issue of crackpots and bad code dragging things down is not much of a problem. The reason is that it takes quite a bit of perseverance to get code into Sage. My experience with my Jmol contributions is an example. I would not claim to be the best coder, but think my Jmol contributions addressed some issues people had. And certainly the code is not yet ideal, but it does do most of what I understood people to want. Because of the load on people doing testing, it has taken months to get much feedback on it. This means anybody submitting code has to be willing to stick with it and prod it along over the long term. People who are not serious won't do this. My example may be a little slower than many people's because I also have very little time to contribute to this, but I still think you are unlikely to get really bad code included using the present model. To quote the above This means anybody submitting code has to be willing to stick with it and prod it over the long term. The real problem with Sage's development model will not show up for a few years. How long do you mean by a few years? The major packages, Maxima, Reduce, Axiom, Mathematica, Maple, and others of that ilk are 30+ years old. So I would define a few years as the time it took the project to move from the primary authors to a second generation support role. How long will this take for Sage? Well, as I recall you have said that you plan to move on to doing number theory work rather than system development. Indeed, I suspect that the pSage effort is a first move in that direction. However, a good computational mathematics platform is a forever thing in the sense that the results it gets ought to be forever valid. So given the difference between the startup timeframe and the lifetime timeframe of Sage there is a question of how to survive that transition. At the moment most of the code being contributed is supported by the original authors. I don't know what you're basing this vague claim on... The algorithms are complex and some implementations are only competitive when optimized into Cython, despite the Sage is Python mantra. There is no Sage is Python mantra. Sage is a mathematical software system, some parts of which are written using Python, and the interpreted user language of Sage is indeed Python. Umm...ok. It has been my impression that Sage is Python has been one of the major bullet points of the project. I remember a discussion about rewriting things like integration into python. But my memory is not what it used to be so perhaps I'm mistaken. The real problem will arise when these authors leave the project. Code rots. People make simple changes. Linux changes libraries. Who will be able to debug research-level elliptic curve code when some minor, unrelated change breaks it? I can easily think of at least a dozen people immediately. But given that you're worried about a few years, and you didn't define what this phrase means, it's perhaps not possible to answer your question. There is a distinction between those who can (e.g. Victor Miller) and those who will, especially if the bug is upstream. Tracing a bug through the inheritance hierarchy, into Cython, and then into an upstream linked library is not a trivial exercise. Who will even know that it is broken? Is it broken now? Yes, it is broken. It's computer software, after all. And since the Sage code base is owned by other people with other goals, that is, all of the spkg files from upstream projects, the potential for code rot is much larger and the debugging problem is much harder. And for exactly these reasons there are far more people involved in fixing bugs in various parts of Sage. If you total all the people who have worked on code that is part of Sage during the last year, you would likely easily get over 1000 programmers. I bet you can't say that about Axiom (and perhaps not about Mathematica, Matlab or Maple, either.) Also, the modularity of Sage makes the problem easier in some ways. Is the elliptic curve code failure due to Sage-owned python changes or spkg changes? Sometimes one, sometimes the other, sometimes both. What happens when python itself changes and upstream packages make the move to python 3.0? There are no Python packages at all in Sage that involve elliptic curves. I agree that you win the pedantic point about elliptic curves in python. Pick a python-implemented algorithm of high complexity and we can reconsider the point, possibly algorithms with subfield structures and uniqueness of finite fields? Surely there must be some high complexity algorithm in python that depends on upstream libraries. Choose one. But incidentally, when the Python dependencies
Re: [sage-devel] Re: Free advertising on Stack Overflow
Advertising images target the emotions, not the intellect. What images bring strong emotional responses to mathematicians? Are Mandelbrot sets the leading edge of cool? For the Sage crowd wouldn't an elliptic curve be better? Tim Daly On 1/23/2011 7:56 AM, Martin Albrecht wrote: On Sunday 23 January 2011, you wrote: Here is a basic design: http://tinyurl.com/48xqfm5 Thoughts? Hi, I like the general idea but would suggest a few optimisations design wise. - I think the font isn't optimal. A sans serif font is a good choice I think but I would play around with some other fonts (from that family) to get an idea how they look. - I'd drop the gradients around the edges or the darker stuff in the edges. The gradients remind me of website 4-5 years ago whereas the modern style seems to be flat, like on sagemath. Almost any website logo these days is flat with clear contrasts. - I think some spaces between text and images is too small, giving it a slight uneasy feel. Feel free to ignore these comments, just my five cents. Martin -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Why Sage? Website Section
I don't really have anything more worth saying on this subject. Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Why Sage? Website Section
On 11/15/2010 8:54 PM, Robert Bradshaw wrote: On Sun, Nov 14, 2010 at 11:45 AM, Dr. David Kirkby david.kir...@onetel.net wrote: On 11/14/10 07:00 PM, Tim Daly wrote: I find it amusing that mathematicians are being told that a math-specific language is a liability. Mathematics is, after all, a specialized language that took me years to learn. Creating, learning, and maintaining a math-specific language is not free, and perhaps one of the few strands of consensus in this thread is that it's very difficult to do right. The marginal advantages over using a (suitable) general purpose language is, IMHO, not worth the cost. Using a general purpose language has several advantages, most of which have been discussed to death already. Actually, I do not believe that the current way we do mathematics by computers is correct but that discussion takes us WAY off thread and this isn't the forum for that anyway. Was the adoption of the special(er) purpose Spad language helpful in attracting users and/or developers for Axiom? No, I'm sure that it did not attract more users. What it did do was make the language much closer to the mathematics. Spad is a general purpose programming language, uses indentation like Python, and is quite similar to python syntax and semantics. In fact, it allows things quite beyond python, like nested list comprehensions, full multiline closures, general argument destructuring, etc. If you are a python programmer you would find Spad to be python 4.0. It also compiles to exceptionally efficient code without needing Cython. I do think that python is not actually the language of Sage. I think the Sage language is unnamed at the moment. I've been a paid professional python programmer and I still struggle with Sage (which I build occasionlly to cross-check Axiom). The Sage language has a lot of things like QQ which is nowhere in the python language. Saying that Sage is written in python seems like saying that mathematics is written in english (there I go with those analogies again...). Most english speakers cannot read or write mathematics and most python programmers cannot read or write sage programs. Maple is a very C-like language, which has a much larger audience than python. I am not sure that this attracted more users to Maple. I am not sure that attracting users to CAS systems has anything to do with the language. Generally you don't reach the language issue until you've used a CAS as a fancy calculator for a while. In any case, my original point was that in becoming a computational mathematician the CAS language is the least of your problems. Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Why Sage? Website Section
I find it amusing that mathematicians are being told that a math-specific language is a liability. Mathematics is, after all, a specialized language that took me years to learn. In any problem you wish to solve with a program there is always an impedance mismatch (like hooking a soda straw to a firehose). You can choose a language close to the machine (e.g assembler) and port your problem across the chasm. Or you can choose a language close to the problem (e.g. APL) and let the machine do the port across the chasm. Python is somewhere in the middle where mathematics is concerned. Python is a poor match for the machine (interpreted) and it is a poor match for the mathematics (needing lots of supporting superstructure the user needs to learn). As a pragmatic choice for design-by-accretion it is excellent. But as a selling point for developing mathematics I'm somewhat more skeptical. What is the ultimate purpose of Sage (beyond competition)? Is it a platform for doing computational mathematics? If so, why wouldn't I want a language close to my problem, that is, a language that directly supports well-founded mathematics? And what can that possibly have to do with Python? Python is the glue. Who chooses a workbench based on the glue? Tim Daly On 11/13/2010 10:13 AM, rjf wrote: On Nov 13, 6:32 am, Johan S. R. Nielsenj.s.r.niel...@mat.dtu.dk wrote: two info boxes on this suggested Why Sage-page. I don't think that Python is the perfect language to write mathematics software with; I would definitely vote on a much more functional language here, e.g. OCaml or maybe even Haskell. However, this would cut out so many potential developers, ... yada yada... excessive boosterism. Consider that symbolic software systems like Maxima/Macsyma, Reduce, Axiom, Jacal ... were written in Lisp, and that Mathematica and Maple were written in C dialects... and even YOU would prefer a different, more functional language. And then you say Python is still better. Certainly not for writing math software.Maybe for writing web applications? Because it has a coherent syntax Compared to Lisp or Haskell or OCaml? Because people who know little mathematics and little about programming can write/alter/debug applications for SAGE??? About which they presumably know nothing? And this is because Python is such a winner? And of course so much of SAGE is not even in Python, but C, Fortran, C+ +, Lisp, whatever, that even that is nonsense. excessive boosterism. At best, you might say, some features of Sage can be augmented by writing in Python, and the user interface looks like Python (actually it is not, but has to be pre-processed). RJF -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Why Sage? Website Section
I am not the best person to ask as I have a vested interest. I find that mathematical notation is strongly context sensitive which gets translated into types when done as computational mathematics. Thus, I believe that a mathematical language needs to be strongly typed. Python is not strongly typed. Axiom has two levels of type-strength. The interpreter does its best to guess types so the user can give short and reasonable inputs. The compiler requires extremely strong typing to ensure that the algorithms match the intentions. The fact that the compiler does not make guesses makes it more challenging to develop library code but increases the chance that the algorithm is correct. Python does not compile. In addition, I believe that a computational mathematics language has to have a strong connection to the underlying mathematics. In Axiom's case, abstract algebra provides the mathematical framework for providing categories around which the algorithms are structured. Sage does not seem to have a strong scaffold for adding new packages. It appears to be growing by accretion. There are two extensions I would like to have which is the use of unicode and the use of two dimensional input. Sage/Python has a chance for a big win here. I think that unicode input which allows greek and other symbols would make the input closer to the original mathematics notation. Unfortunately, my thesis work showed me that mathematical notation is highly ambiguous. In fact, I have come to the conclusion that the equations in a book are pretty much content free. The real mathematics is actually contained in the surrounding text. To see this effect take your favorite textbook, remove everything but the equations and you'll find that you have lost the meaning of the symbols. Without context, E=MC^2 is a meaningless jumble of symbols. I think that two dimensional input is also a huge win. However, I worked on two dimensional input at IBM Research. I know of several attempts to do the same thing. The most recent attempt that I saw was at the University of Waterloo. I do not know what became of this effort but I know that two dimensional input is hard and very ambiguous. In any case, computational mathematics is more about the algorithms than about the notation. A strong mathematical framework and strong typing are more important than I/O. By the way, the Axiom Spad language is very much like Python. It uses indentation to group code. It has list comprehensions. It has many more data structures than Python. It dispatches not only on the types of the arguments but also on the type of the result (something few languages allow even today). Spad can be either interpreted or compiled. It can communicate with lisp (the implementation language), C (the whole graphics subsystem is written in C), javascript (the browser frontend is AJAX/Javascript/HTML), Fortran (the commercial version called the NAG fortran library routines), etc. The claim that Python is an exceptional language for computation mathematics or is exceptional as a glue language completely ignores history which tends to make us old people cranky. I think the Sage language designers could steal a few useful ideas from the Spad language. I also find the Python/Lisp debate useless. In Axiom, Lisp is the implementation language but you can use Axiom for years and not know that because Spad is the computational algorithm language. In Sage there is confusion about the implementation language of Python and the computational mathematics language built in Python which appears not to have a name. Tim Daly On 11/14/2010 2:45 PM, Dr. David Kirkby wrote: On 11/14/10 07:00 PM, Tim Daly wrote: I find it amusing that mathematicians are being told that a math-specific language is a liability. Mathematics is, after all, a specialized language that took me years to learn. I asked RJF what languge he thought the interface should be. As 10 options I consider might be viable choises where 1) Create an entirely new language. 2) Python 3) Maxima 4) A Mathematica like interface 5) A MATLAB like interface 6) A Maple-like interface 7) A Magma-like interface 8) Lisp 9) Q - see http://en.wikipedia.org/wiki/Q_%28equational_programming_language%29 10) Pure http://code.google.com/p/pure-lang/ is another possibility, but that did not exist until 2008, but is based on Q, which existed prior to Sage He failed to response. (He would rather tell me on the Maxima list that I can create an infinite set of integers to do some testing.) But that is to be expected from Richard - a signal to noise ratio of about -30 dB. But what do you think is the ideal language for a user interface? There have been endless attempts at cleating new languages (#1 above). I've even done it myself, to the extent of writing a couple of hundred lines of code for lex and yacc. But it's a very difficult problem to get right, and quite honestly requires a set of sills I don't think a single Sage
Re: [sage-devel] Re: Why Sage? Website Section
On 11/14/2010 10:37 PM, William Stein wrote:
On Sun, Nov 14, 2010 at 6:48 PM, Eviatareviatarb...@gmail.com wrote:
I thought Python was strongly typed. Definition from Wikipedia:
Most generally, strong typing implies that the programming language
places severe restrictions on the intermixing that is permitted to
occur, preventing the compiling or running of source code which uses
data in what is considered to be an invalid way. For instance, an
integer division operation may not be used upon strings; a procedure
which operates upon linked lists may not be used upon numbers.
However, the nature and strength of these restrictions is highly
variable.
What do you mean by saying it isn't?
FYI, I've learned from experience that even using the phrases
strongly typed and weakly typed is a bad idea.
The problem is that there aren't any good accepted definitions of
them, and it is easy to find reputable sources that flatly disagree
with the definition at Wikipedia, unfortunately.
The original poster probably meant that Python is not statically
typed. (Another can of worms, but less of a problem.)
- William
I agree with William that the strongly typed question is a
(well, I can't bring myself to use the can of worms analogy
given my prior analogy chastizing :-) )
To illustrate an example, it is possible to define:
integer foo(integer x, integer y) {}
matrix foo(integer x, integer y) {}
and then write:
integer a := foo(3,4)
matrix b := foo(3,4)
The question of which foo to call requires function dispatching
on the return type of the function. Few existing languages do this.
One place where this is useful is the construction of canonical forms.
The question of which result is simplest depends on the result you
expect. Consider that
1 11
- x + --
7 13
is a polynomial with fractional coefficients and cannot be reduced. But
13x + 77
91
is a fraction of two polynomials with integer coefficients. They also
happen to represent the same value. Simplification of the value depends
on whether the desired result is a
Polynomial(Fraction(Integer))
or a
Fraction(Polynomial(Integer))
By specifying the target type you can define the simple form.
Tim Daly
--
To post to this group, send an email to sage-devel@googlegroups.com
To unsubscribe from this group, send an email to
sage-devel+unsubscr...@googlegroups.com
For more options, visit this group at http://groups.google.com/group/sage-devel
URL: http://www.sagemath.org
Re: [sage-devel] Re: ECL / Maxima / Fedora 14 issues.
I experimented with using Amazon's cloud for (Axiom) builds. It is trivially easy to set up custom images that can be used for builds. It is also very cheap for an hour of CPU. So consider setting up a cloud buildbot. Tim Daly On 10/30/2010 1:30 PM, David Kirkby wrote: On 30 October 2010 07:17, Mike Wittmsg...@gmail.com wrote: On Oct 29, 6:48 pm, Mike Wittmsg...@gmail.com wrote: I don't suppose there's a way I can initiate the buildbot from my end and have the results go to the right place? Once I get time to install Fedora 14, I imagine I could at least make that system available. I suppose that I should try to understand how the buildbot scheme works. Is there one place you can point me to that describes it pretty well? If so, I could probably find an hour or two Saturday or Sunday to see if I can understand its workings and then give you a more coherent answer. OK, well I did find the documentation on buildbot.net, and if I'm understanding correctly from my brief scan of some of the manual it appears that the communication is initiated from the build slaves. So, I think that means that my machines could be used. So I have two questions: (1) Do the machines have to be available all the time, or can they just be available some of the time. (2) Would someone be willing set this up for me (or at least provide an example configuration that works for sage builds on some linux type box) or will I have to *actually* study the buildbot manual until I can figure out how to do that myself. -Mike It's not practical unless the machine runs 24 hours per day, 7 days per week. The release manager can currently click a button on a GUI and start the build on all the slaves when he wants to. That's just not going to be practical with your setup. There is a plan to use Virtual machines on Boxen as build slaves soon. Perhaps you could manage one of those running Fedora 14. That machine would then stay on 24/7. Dave -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Python 2.7 vs 3.2
There was an interesting comment here about the question of Python 2.8 and the smooth upgrade path. Apparently the only Pythonic path is a 3.2 version. http://sayspy.blogspot.com/2010/10/viewing-python-32-as-successor-to.html -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Supported platforms - once again
I would expect significant pushback from the Gentoo people on the issue of including other projects inside Sage. GCL packaged gmp4 (now fixed) and their response was that this should not be part of GCL. I'm not sure if independently available projects (e.g. ECL, Maxima, etc) would fit the compile-from-source Gentoo model. Certainly the packaging of OSX binaries for Fortran will raise a few eyebrows. Tim Daly On 10/27/2010 3:38 PM, François Bissey wrote: On 10/27/10 04:26 PM, mmarco wrote: A few words about the gentoo platform. Since gentoo does not follow the usual system of versions, but is based on continuous incremental upgrades, there is no way to ensure that sage binaries would work on a given gentoo box. As far as i know, the usual binaries available for other platform don't run over gentoo. Although in all the cases i have tried, i was able to build sage from source. I think it would be a good idea to change the sentence Gentoo binaries are regularly available at ??? by a note with a link to the sage-on-gentoo project. What's the best URL to use? I found http://github.com/cschwan/sage-on-gentoo but is that the most suitable? I guess since Gentoo uses a different system, it's not exactly comparable to any Sage build. There's a few bits I'm lacking on that page, but I think it's a big improvement over the previous system, where there were several different references to supported platforms, no two of which agreed with each other. I should pipe in since we are talking about that. Generally speaking sage should work on a reasonably up to date stable Gentoo system. However it would be a good thing to point user to sage-on-gentoo as it is aimed at properly integrating to their system. Eventually we plan to make sage available directly from the main Gentoo tree like any other package. we may keep the overlay around for alpha/experimental stuff. The caveats are as follow. The sage-on-gentoo project is focused on the end user. That is someone gets sage from it and starts working. It is not meant as a development platform - unless you know how to write ebuilds for Gentoo. If you want to get new code in sage it may be best to get the tarball. Francois -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Function assume() has no effect on Maxima via desolve()
The problem is called the proviso problem, as in things like 1/x provided x != 0 I did thesis work in this area. One of the attacks is to use cylindrical algebraic decomposition (CAD). A second approach is to create a tree of expressions based on intervals such as [1/x where x 0] [1/x where x = 0] [1/x where x 0] The computation proceeds in 3 parts, each one under an interval assumption. If a new proviso is added the program tree-forks again: [1/x where x 0 1/y where y 0] [1/x where x 0 1/y where y = 0] [1/x where x 0 1/y where y 0] [1/x where x = 0 1/y where y 0] [1/x where x = 0 1/y where y = 0] [1/x where x = 0 1/y where y 0] [1/x where x 0 1/y where y 0] [1/x where x 0 1/y where y = 0] [1/x where x 0 1/y where y 0] Note that these can all be run in parallel and the results combined after the computation. This approach lends itself to massively parallel computations. I did a literature analysis of a couple hundred textbooks and found that approximately 80 percent of all equation provisos could be rewritten into interval constraints. A simple assume facility does not begin to address the problem for many reasons, such as the fact that provisos can arise during intermediate computations. Tim Daly On 9/23/2010 8:36 AM, Burcin Erocal wrote: On Wed, 22 Sep 2010 11:40:44 -0700 (PDT) rjffate...@gmail.com wrote: Many features in Maxima do not use the assume features at all. If Macsyma were to be redesigned from the ground up, the issues related to assume etc would probably be addressed at a foundational level. To the extent that other computer algebra systems claim to be a fresh look at issues, it appears that they have all failed to address this one. Instead they ignore assumptions and later patch them on in peculiar ways and provide access to this information only from some specific programs, e.g Mathematica's Integrate, Reduce, Simplify. But probably not much else. So this known problem (at least since 1974) was off the radar of the brainiacs who designed all those subsequent systems, including I suppose, Sage. I think it would be a huge overstatement to say that the symbolics subsystem in Sage was designed in any way. IMHO, it was mostly patched together to support educational use, then acquired more cruft through several rewrite attempts and cramped schedules. I am definitely not an expert in this field and have no idea how the assumptions should work. If you can provide some references, perhaps these could be used as starting points when/if somebody decides to work on this. Here is the only reference I found on this topic: http://portal.acm.org/citation.cfm?id=680466 The article is available for download here (for those with access): http://www.springerlink.com/content/p77364025wh6j7h5/ Burcin -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Function assume() has no effect on Maxima via desolve()
To implement the proviso system I mentioned would require that it be deeply embedded in the algorithms. Whenever an algorithm (say, division) did an operation that involved a proviso it would need to (a) decorate the result with the proviso and (b) potentially split the answer into separate sub-answers for further computation. Note that I did not make any restrictions on the provisos so they could be anything (not even necessarily computable), such as polynomials or roots (e.g. [x suchthat x in roots of ] and they don't need to be intervals (e.g. f(x) is holonomic, the so-called is provisos). There are deep research questions here involving reformulating normal algorithmic computations to collect the provisos, splitting the collection into (not necessarily decidable) disjoint sets, doing parallel computation under a proviso set (generating further subsets as the computation proceeds), combining partial results to poison other branches of the parallel computation tree (which implies computing partial CAD results and a blackboard architecture) and the question of combining results under proviso constraints (e.g. combining intervals if the representations are intervals, in order to recover the real line or the complex plane). There is a whole research program here but the NSF doesn't seem to know or care so its unlikely to be explored except by open source. Axiom has a long term goal of refactoring the algebra to include this in the design at the fundamental level (which was the point of the thesis work). It is only in recent years that hundred-core machines are becoming available to support the huge parallel trees this generates. A proviso-based system will enable parallel computation in a natural manner as opposed to the current ideas that depend on simple cases (like matrix multiply). An assume facility that is bolted-on after the fact cannot possibly handle issues that arise as part of the computation since intermediate expressions can contain computations that are not apparent in the final result. An assume facility could create some initial conditions but would naturally be expressed using something like Axiom's suchthat. Tim Daly On 9/23/2010 11:19 AM, rjf wrote: On Sep 23, 5:36 am, Burcin Erocalbur...@erocal.org wrote: I think it would be a huge overstatement to say that the symbolics subsystem in Sage was designed in any way. IMHO, it was mostly patched together to support educational use, then acquired more cruft through several rewrite attempts and cramped schedules. I think that is true of ALL the subsystems in Sage. In terms of my own interests, that is why the idea of rewriting Maxima in Python is pointless. Wouldn't you prefer to write a system that addressed the shortcomings of Macsyma (etc.) And by shortcomings I don't mean written in Lisp instead of Python. There are perhaps papers hinting at the Macsyma assume system capabilities by Michael Genesereth, but a quick search did not reveal them. The Maple system has a more ambitious capability, but it is still patched on. I do not know where the Mathematica version contains, at the moment. It seems to grow, every so often. But it is still patched on. The note from Tim suggests that (I think) linear inequalities and rectangular regions can encode most conditions of interest. Or maybe polynomial conditions? Certainly not all. And cylindrical algebraic decomposition may be useful, though potentially quite expensive, there is all that other stuff that is not algebraic. Like log, exp, cos, ... I am definitely not an expert in this field and have no idea how the assumptions should work. If you can provide some references, perhaps these could be used as starting points when/if somebody decides to work on this. Well, you can probably start with that Maple reference, the next time you design a system. Unfortunately, Sage is already built, and it is probably too late. But Stein is doing something else, so you don't have to worry about him getting in the way. Maybe UberSage; you can call Sage if you need to. Here is the only reference I found on this topic: http://portal.acm.org/citation.cfm?id=680466 The article is available for download here (for those with access): http://www.springerlink.com/content/p77364025wh6j7h5/ Burcin -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Suggestion to provide external links in documentation.
You might find this document useful: http://axiom-developer.org/axiom-website/rosetta.pdf On 9/21/2010 5:11 AM, Dr. David Kirkby wrote: I was just looking at a post of Minh's, in which he suggested others had suggested adding to docstrings the names of related commands. That seems very sensbile - just like the man pages of a Unix system. How would people feel about providing links to MathWorld and Wikipedia on the docstrings too? i.e. for norm http://trac.sagemath.org/sage_trac/ticket/8825 add links to http://en.wikipedia.org/wiki/Matrix_norm http://mathworld.wolfram.com/Norm.html http://mathworld.wolfram.com/MatrixNorm.html http://mathworld.wolfram.com/VectorNorm.html IMHO, it would also be worth adding the nearest equivalent commands in Macsyma, Mathematica, Maple and MATLAB, though I doubt that will be possible for many commands. sin() would have Sin[] - nearest equivalent command for Mathematica sin() - nearest equivalent command for MATLAB I don't know about the command for 'sine' in other packages, but no doubt someone is familiar with them. One could also add for packages where there is no similar command for the commercial packages. foobar() - As of version 7.0, Mathematica has no similar functionality. I think at one point, providing a list of equivalent commands in these packages should be done, to aid people porting code from these packages to Sage. A start would be to document the nearest equivalent commands in the actual docstrings. At least if a conversion list was ever made, the docstrings would provide some help to those compiling such a list. Dave -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Cliquer - upstream modifications and dubious code
This might be of interest on security grounds: http://www.amazon.com/Secure-Coding-Robert-C-Seacord/dp/0321335724 On 9/15/2010 6:46 AM, Dr. David Kirkby wrote: On 09/15/10 06:17 AM, Minh Nguyen wrote: I'm disheartened that this happened. One should not modify upstream source, but place patches against upstream source under the directory patch/. I think you mean patches. I did notice a patch directory in Cliquer, but http://www.sagemath.org/doc/developer/patching_spkgs.html#overview-of-patching-spkg-s says patches. That's a minor point though. I worked on getting Cliquer to build as a shared library on Cygwin, Linux, Mac OS X and Solaris (t2.math). I take your comments as an encouragement for me (or anyone) to further investigate how to polish up the Cliquer spkg. In my programming work, I have been following advice from E. S. Raymond's book The Art of Unix Programming [1] and D. A. Wheeler's book Secure Programming for Linux and Unix HOWTO -- Creating Secure Software [2]. I hope you would continue to share your thoughts, as you have generous done, on good programming practices so that contributors to the Sage community can benefit from your experience. Clearly Minh you take the time to read up on what are considered good practices, but your attention to such issues is not universal among Sage developers. #1 seems pretty useful for all Sage developers to read. #2 is a bit less so, though clearly anyone dealing with the notebook should look at #2. IMHO, the notebook is very bad from a security point of view, but I have some sympathy for William over that. He probably never expected to get a large number of people using one sage server, so security was not high on his priority list. It's s shame there are not any decent books online about best practices in software engineering. Whatever I've found tends to be in expensive books. [1] http://catb.org/~esr/writings/taoup/html/ [2] http://www.dwheeler.com/secure-programs/ [3] http://en.wikipedia.org/wiki/Clique_(graph_theory) -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: A Mathematica parser for Sage.
Some of the questions you have about why lisp are answered in: http://channel9.msdn.com/shows/Going+Deep/Expert-to-Expert-Rich-Hickey-and-Brian-Beckman-Inside-Clojure/ which is about Clojure, a more recent lisp although the ideas are essentially the same in Common Lisp. Tim Daly David Kirkby wrote: On 5 September 2010 10:14, Mitesh Patel qed...@gmail.com wrote: Hi David, On 09/05/2010 03:52 AM, David Kirkby wrote: I'm quite happy to be that someone who learns Lisp - I'm serious thinking of buying a book on it. Unfortunately, they tend to be quite expensive, as do books on writing compilers. Some time ago, I found Practical Common Lisp by P. Seibel, which is available for free online: http://www.gigamonkeys.com/book/ But I have not read it and am not familar with Lisp. Sincerely, Mitesh Thank you for that - it is one of the books on Amazon I was considering. http://www.amazon.com/Practical-Common-Lisp-Peter-Seibel/dp/1590592395 It's $52.29 on Amazon - to find it free is quite nice. I also found Common Lisp: A Gentle Introduction to Symbolic Computation - all http://www.cs.cmu.edu/~dst/LispBook/index.html I want to finish the Solaris port first, getting it building properly on 64-bit systems. But then I might take a look trying to parse Mathematica and do something useful with it. Dave -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] A Mathematica parser for Sage.
Without knowing Lisp it is hard for me to really tell how valid your arguments are, but I must admit a couple of people who know both Lisp and Python have said Lisp would be easier. You are RJF are not the only ones to express that opinion. Dave Consider the MMA code as a source language and write a simple compiler stage that translates that MMA code to a tree structure. You have to do this in any modern compiler architecture. For this purpose you can think of lisp as a printable form of AST structures. So the lisp data structures are just these parse trees. MMA parse trees are easy to make. Lisp gives execution semantics to these AST data structures since, in lisp, data is code and code is data. So once you finish the first stage of your compiler using lisp as your AST target language you're done. Just execute it. In fact, lisp implements the rest of the compiler for you. Axiom's Spad language does the same thing. The Spad language gets parsed into an AST which just happens to be list data structures. These data structures also happen to be executable lisp. Gnu Common Lisp compiles the lisp code to C and GCC compiles the C code to machine code. So Spad algebra is implemented in machine code, or implemented in C, or implemented in lisp depending on where you want to focus. But all we had to write was the source-language (spad) to-source-language (lisp) parser. Writing in lisp gives you all the power of the python-cython but the whole process is automated and you don't have to change language level. The generated machine code is extremely efficient (matching Fortran machine instruction sequences for numeric code). So when a lisper sees the whole rewrite it in cython to make it faster debate and hears that python is an interpretation-only language you can begin to see why python seems so primitive. The whole interpreter/compiler issue was solved and automated 30 years ago, only to be recreated by python/cython in a more primitive, hand-processed form. Writing an MMA compiler on top of the python/cython stack is a LOT more work and re-invents technology that is 30 years old. Just parse Foo[x] into (Foo x) and execute it. Problem solved. Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] A Mathematica parser for Sage.
David Kirkby wrote: On 5 September 2010 22:13, William Stein wst...@gmail.com wrote: On Sunday, September 5, 2010, David Kirkby david.kir...@onetel.net wrote: RJF thinks Lisp is the best language William thinks Python is God No I don't. I chose Python for Sage because in 2004 it was the closest popular open source language to Magma. God was the wrong word. But you have said Python is a beautiful language. Your view of the language contrasts greatly with that of RJF. It's not clear to me the best way to tackle something able to parse Mathematica. It is however very clear there are far more people know Python than Lisp, so use of Python is more attractive to more developers. Dave What does the number of python developers have to do with the question? If we look at the problem domain it appears that the task is a source-to-source transformation followed by an execution of the result. Which language makes this task easier? MMA-to-lisp followed by execution involves changing MMA data structures into lisp data structures which, because of the data-code equivalence of lisp, just involves evaluating the resulting expression in Maxima. It would be possible to write a Sage pexpect front end that takes MMA syntax as input, calls a (translate-and-execute) function in Maxima, and returns the result. Thus you get both Maxima and MMA in the same code pile at little cost. MMA-to-python is a compiler task (lex/yacc/AST/codegen). The generated code would have to know which subsystems would be involved because the syntax of the calls vary. An alternative is an MMA interpreter, which is a lot of work. Adding MMA syntax to the python top-level would involve much more pre-parser effort in Sage, moving the Sage language farther from python than it already is. While they are conceptually equivalent tasks, the lisp version seems to me to be mechanically easier to implement. It is considerably more flexible and more easily extended. Lisp could easily add new syntax, something a MMA-to-python based compiler would find a struggle. Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Random banter about Sage standards
William Stein wrote: On Wed, Sep 1, 2010 at 6:08 PM, Jason Grout jason-s...@creativetrax.com wrote: On 9/1/10 10:32 AM, Bill Hart wrote: Tim, all screwing around aside for a moment. I broadly agree with your sentiments. However, there are also some issues with what you are suggesting. And I mean to make these observations in all seriousness. I'm reading this thread with great interest. Though I don't have strong feelings one way or the other at this time, your post made a lot of sense to me. Thanks for the post. Jason I've written a blog post that is relevant to this thread: http://389a.blogspot.com/2010/09/purple-sage.html As I understand your post, you are creating software for your own personal use. Clearly the only standards that matter are your own. Do you agree that creating software that the world should use might require different standards? What would you expect those standards to be? Should the code be required to do more than just compile and run a simple test? -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Random banter about Sage standards
I think the claim was that it is becoming the M$ of mathematical software. I suspect that means default standard or something. Actually, I didn't ask. Tim, what does it mean? I was making the assumption that Sage managed achieve success by being widely adopted and replacing the 4Ms. The bulk of the discussion rests on that assumption. If that assumption is not true and Sage disappears, nobody cares. Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Random banter about Sage standards
If I understand you correctly, you want to set the goal for Sage much higher than just a free, open alternative to the Ma*s. - Robert Yes, but why am I trying to do that? Computation mathematics is a new field of study, at least in the symbolic area. It is the child of the union of mathematics and computers. Unlike other forms of software, computational mathematics software (CMS) has the property that it will always be able to give timeless answers, making it useful forever. Being useful forever does not imply that the software survives forever. You can argue that this is good darwinian attrition. But CMS software is very hard to build and requires a great deal of very scarce expertise that can disappear at any time (e.g. changing jobs, being hired into a company like MapleSoft/Wolfram/Magma/etc., companies being bought or closed) When that happens, and it will, then that portion of the software becomes unmaintainable or unavailable. The natural response to dead software is to write new software. You can see this in CMS-land as there are over one hundred attempts at building CAS programs (I collected them at one point, similar to the Sage goal). But due to the expertise issue these programs don't get very far. Sage wants to rewrite the Trager/Bronstein integration but that seems unlikely as the required expertise (Bronstein) is dead and the code isn't documented (yet). Sage is trying to avoid the darwin problem by gluing together existing systems. This is a very clever idea, a second generation response. What I am trying to do is ask the question... What does a computational mathematics system need to do to live forever? in particular, in this forum, What does Sage need to do to live forever? Sage is exciting, fast moving, has no time to do it right, would die of documentation ossification, couldn't possibly prove anything (as if proofs are foreign to mathematics), needs to be released twice a day, is in a foot-race with the 4Ms for mind-share, needs quantity not quality, will let the next-generation-slubs document their work, is 3ns faster than M*, etc. I am one of the first generation dinosaurs trying to impart some of the lessons learned to the next generation. I am taking the long view, trying to figure out how to impart computational mathematics to my grandchildren. Will they still be writing new polynomial packages and arguing over ZZ? Will they have to watch yet another hundred threads discussion the same issues? Will they suggest that William Stein should move his comments to the flame thread? Or will they have a broad legacy of excellent CMS work upon which to build? My experience tells me that William will move on, python will move on, the funding will dry up, the students will be hired into real jobs and Sage will die of code rot as GCC/python/architecture/build-complexity/etc all work away at its foundations. The system will devolve into tracking down hard bugs in other peoples code, people will find that hard without documentation and not worth doing because it isn't flashy. Suppose William had instead proposed that Sage was a project to find and fix all the bugs in Maxima. How many people would join? Now imagine Barry Brightspot proposing a project to find and fix all the bugs in Sage To those who work on Sage... Why? Do you just want to build yet-another-CAS? Do you just want a platform for your thesis work? Do you just want to write code that gets thrown away? Or would you rather have your name appear in the credits list of Sage-2090 as one of the Newtons of computational mathematics? I am advocating that Sage set its goals much higher than replacing the Ms. If you don't, then my experience tells me that the project will die. If you do then the project may die anyway but other people can build on the remains rather than from scratch. Or you just might have a formula for the long-term. What do *you* think needs to be done to make Sage live forever? I have thought about this question for a long time and I'm trying to pass it on. Your experience may tell you that my suggestions are wrong but you'll only be able to know after the fact and by then it will be too late. Anyway, I've said about all I want to say so I'm abandoning this topic. Good luck and thanks for all the fish. Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: test suites for Sage
Nicolas,
This is similar to the CATS pamphlet files.
They use noweb format but they could use the \begin...\end
latex environment. I plan to make that change anyway.
If we look at one of the files, e.g.
http://axiom-developer.org/axiom-website/CATS/schaum1.input.pamphlet
it is a sequence of blocks. The Axiom comment character is -- so
any line beginning with -- is ignored by Axiom.
Each block is of the form
--S (number)
An Axiom Command Line
--R
--R The expected output from Axiom
--R
--E (number)
So when this file is run Axiom sees a command line followed by
a set of comments. The comments contain the expected output.
A post-process reads the output from Axiom and compares it
to the comments. The --S/--E numbering scheme allow the compare
function to check that all tests run and list the number of the
failing function.
This allows us to automate the testing.
Tim Daly
Nicolas M. Thiery wrote:
On Mon, Aug 30, 2010 at 03:33:23PM +1000, Minh Nguyen wrote:
A few months ago I experimented with writing test cases in LaTeX as
part of a detailed discussion of underlying relevant theory. So for
example you want to write some test cases for graph theory. You start
by writing a short document explaining any relevant theory and runtime
complexity of algorithms you want to cover, with references to any
literature where appropriate. Next write down properties you're
interested in together with any expected results, followed by a
transcript of a Sage session that verify the stated properties. All of
these are written up as a LaTeX document just like your normal LaTeX
document. To run the test cases through Sage, I used a little tool [1]
to extract the test cases and run them through the Sage doctesting
framework. As an example of what I mean, refer to this document [2]
which is a work in progress.
For the record: the (relatively new) sageexample environment of
sagetex allows for including doctest like examples in the latex file:
\begin{sageexample}
sage: 1 + 1
2
\end{sageexample}
Upon compilation, those examples are all extracted to a separate file
which you can test using sage -t. That's what we use to check the
examples in our French introductory Sage book. This still has a couple
glitches, but the more people use it, the better it will become :-)
Best,
Nicolas
--
Nicolas M. Thiéry Isil nthi...@users.sf.net
http://Nicolas.Thiery.name/
--
To post to this group, send an email to sage-devel@googlegroups.com
To unsubscribe from this group, send an email to
sage-devel+unsubscr...@googlegroups.com
For more options, visit this group at http://groups.google.com/group/sage-devel
URL: http://www.sagemath.org
Re: [sage-devel] Re: Random banter about Sage standards
How do you expect Wolfram Research, Maplesoft and similar deal with such issues? They must hit them too. I suspect they have a few nightmares with this, but the best way is probably to have decent documentation. If code is well commented, and has references to papers where the algorithms are published, then it sill probably be maintainable. Actually I've had the same literate programming, deep documentation discussion with developers from Wolfram and Maple. According to them, neither program has good internal documentation. They can rely on the fact that they can pay people to maintain the source and the knowledge continuity. I have begged them to improve it. Why would *I* care? Because of the future. Think about things in the long term. There are very few companies that last 50 years. Indeed, Maplesoft was bought recently. What would happen if Wolfram and MapleSoft died? Well, in the worst case, the failing company just disappears. Nobody can run MMA or Maple code anymore. This creates a *huge* black hole in computational mathematics. (Think Derive and Texas Instruments). There is the possibility that the code might be released but it is a very slim chance. Companies that go bankrupt get their assets sold. The source code would be the major asset and there would be a lot of people wanting to get paid so they won't likely make the code open source. (Think Macsyma and Symbolics) But lets assume the best case, that MMA and/or Maple became open source. Here I have a great deal of experience because *I* got the open source version of Axiom which was a very large, very complex program. Axiom was sold commercially as one of the big 3. Internally it was mostly code with about 3 lines of useful documentation. The released version of the code lacked the front end (saturn), the back end (nag libraries), the new compiler (aldor), and required a running Axiom in order to build Axiom so it had to be restructured to self-bootstrap. The only reason that Axiom came back to life is that I was one of the original developers and had a deep understanding of the system internals. I'm not bragging, I'm simply pointing out that it is difficult to organize and repair a million things of code. Even with my deep understanding of internals (some of which I wrote) it still took a year to make it available. I found that I couldn't understand my own code and I always try to write dirt-simple code, unfortunately without comments. Now imagine that someone handed you the (partial but mostly complete) source code for MMA or Maple. And imagine that it contained 3 useful comments. Is there any chance of rebuilding these programs into runnable systems? I think not. Now imagine that MMA and Maple were fully literate and could be read like a novel. Which would you prefer? Which scenerio benefits computational mathematics in the long term? Now apply the same lesson to Sage. Assume that 30 years from now, none of the original developers are connected with the code and there is no one to ask. It will happen. Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Random banter about Sage standards
of the arguments but also on the type of the return (something that is still not common). But Axiom was developed as research software, not with the intention of being brought to market as a product (free or commercial). Sage is being developed with this intention. Our choice of standards was to build on abstract algebra. There were a great many debates about the right way to do things and we always went back to the touchstone of what abstract algebra implied. At the time (40 years ago) there were no existing examples of computational mathematics for many of the ideas so we had to invent them. Axiom set the standards (e.g. integration) and they were quite high (Axiom still has the most complete implementation). Sage has existing examples to guide it. So at the time Sage was being developed there *were* standards in place. You seem to feel that Sage was started pre-standard (2005?) and pre-referee (ISSAC?). I think this was necessary for the time--Sage would have gotten off the ground if it couldn't have been useful so quickly. This includes in particular many of the spkgs that have been grandfathered in and wouldn't make the cut now, but it takes time to remove/replace/clean them up. Of course there's room for improvement, but do you think the current review process is insufficient and lots of new bad code is being written and included? If so, what should we do better? I *do* feel that the current review process in Sage is insufficient (see my earlier diatriabe). I see reviews of bug fixes but I don't see reviews of spkgs. We are now over 50 years into the development of computational mathematics and Sage has the goal of competing with systems developed in the 1970/1980s, over 30 years ago. This would be a great thing if Sage were to deeply document the algorithms, develop the standards, and/or prove the code correct but I don't see anyone advocating any of these. I don't see anyone advocating alternative ideas that would raise the bar in computational mathematics. Even in the area of education I don't see anyone hammering on the NSF to fund more efforts in computational mathematics. I don't see pushback to NIST to standardize the algorithms. Obama wants to bring science back to life and encourage research. As the largest group of academics I would wish that you would petition the funding sources. Even if all of the funds went to Sage I'd still feel that this was worthwhile. In short, I don't see *change*. Tim Daly (curmudgeon and rjf wannabe) -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Random banter about Sage standards
Bill Hart wrote: Why is this entire thread not on sage-flame? What does software engineering, documentation, test code, etc. have to do with Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab.? Despite what appears to be competitive badgering I really do want Sage to succeed. But I don't want Sage to spread the impression that mathematical software can't be trusted. I badger because computational mathematics is my chosen field of study and I feel it is *vital* to raise the standards to professional, high quality, trustworthy levels. If Sage is going to be the M$ of mathematical software, will it also convince everyone that math software just gives highly questionable answers? Every program makes mistakes but hand-waving about it's not my problem, it's the upstream code gives the whole field a bad reputation. And I very much care about that. This *isn't* software, this is *computational mathematics*. If advocating such project goals is considered sage-flame material then we all lose. ...[snip]... Why attack Sage. It is what it is. Why defend it. It certainly didn't/ doesn't get everything right. One thing is for sure. Whatever is wrong with Sage, it is almost certainly too late to fix it. Whatever is right with Sage certainly made it popular. *sigh* If you want to make Sage seriously innovate to solve one or more of the above, you need a *large* group of like-minded volunteers who can help you. You won't do it on your own, no matter how many years you work, nor how hard. Many of the things Tim and David say resonate with me. I'd really, really love a tremendously efficient, well-documented, reliable, Open Source mathematical project. Having seen how insanely difficult even just goal number 1 is for just the domain of arithmetic, I honestly think we haven't got a chance. Not ever. The expertise don't exist in sufficient quantity. And even those with the expertise, don't have the time. So, looks like we are stuck with what we got. Re: don't have the time... Unlike any other software effort, programs like Sage are timeless. The integral of the sin(x) will always give the same answer, now or 30 years from now. Any one individual does not have the time but the project does, assuming it lasts. Would you read a mathematics journal with the editorial policy we'll print anything because we don't have the time?. By the way, does anyone know what the current state of program proving is? How does this work? Does one write the proof by hand then formalise it in code in a formal system until it parses? Can someone give me some references on this. I am genuinely interested. I've read some comments about SML being good for program proving (why?), and that the Haskell type system amounts to giving a proof under some circumstances. But it is baking my noodle how any of this has anything to do with proving programs, especially in mathematics. The monad idea in Haskell gave me some hope, because it sounds mathematical, but I simply didn't understand it, at the end of the day. See http://en.wikipedia.org/wiki/Curry%E2%80%93Howard_correspondence and http://userweb.cs.utexas.edu/users/kaufmann/tutorial/rev3.html#top and http://coq.inria.fr/a-short-introduction-to-coq The first one shows that writing programs and proving programs have a correspondence. The second one shows ACL2 which is basically a way of writing program proofs in lisp. The third one shows COQ which has a very strong connection between mathematics and types. In systems like Maxima and Axiom it would be possible to embed ACL2 directly into the system (lisp is lisp after all) and perform the proofs inline. Given the mathematical definition of a Ring and a function on the Ring elements you could prove the function correct. For Axiom this is part of the stated long term goals of the project. On the other side (at the machine level) there is a program called FX, that is, Function Extraction. FX grew out of the work by Richard Linger, Harlan Mills, and Bernard Witt. It is being constructed at the Software Engineering Institute. FX reads machine language, extracts the semantics, and composes the instructions into blocks of behavior. You can't fully test a program but FX covers *all* of the program behavior so you can identify failing cases. See http://daly.axiom-developer.org/TimothyDaly_files/publications/sei/Man75586.pdf (disclaimer: I am one of the authors of the FX technology) Testing programs is as ineffective as testing theorems. No matter how many examples you create, you don't have a proof. Tim Daly -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Re: test suites for Sage
I am working on 2 new test suites. One involves the Rubi test suite using patterns for integration. This is a very large test suite, well over 9000 integrals. I have created test cases for Axiom but not yet written the rule-based integration patterns. I'll move them into the CATS area in the near future. This establishes a baseline against which the new rule-based integration patterns can test. I have to add special functions like polylogs which Axiom does not yet recognize before I can go further and then write the pattern rules. Piezas's work is also pattern matching. The difficulty for computational mathematics is that some of the patterns might not hold true across all domains. They are identities so this should not be a problem but I'd have to look at them in more detail to be convinced. I've done no more than glance at the pages. The second test suite involves graphing. I am using the CRC Standard Curves and Surfaces (David von Seggern) book which covers a huge range of graphs, from random (fractal, gaussian, non-guassian) to determinate (algebraic, integral, transcendental, piecewise continuous). This is moving, but slowly, and will probably not see the light of day until 2011. I tried to write a test suite based on Yudell Luke's The Special Functions and Their Approximations that involved expansions of MeijerG function but I don't know that I've got the chops to do it. Maybe in my next life :-) Tim (somebody, I can't find his name) was going to try the CATS integration test suite in Sage. It should be rather easy as Sage uses Maxima and the syntax is very close. I don't know what became of that effort. If you do a test suite on graphs I'd be happy to try to make it work in Axiom. This would likely involve writing new algebra code so it would be helpful if you included citations of algorithms (if you know them) as you develop it. It looks like Gross and Yellin includes high level algorithms so that would be exceptionally helpful. I strongly favor basing test suites on books containing algorithms. A test suite for sequences and series is on my wish list but I have not found a good reference for it. I think it would be useful to collect good reference books for any of the mathematics we want to test. This would give other people a good starting point for developing test suites. For the CATS test suite each file contains the problem, the expected answer, and Axiom's answer. The format of the files makes it possible to run them automatically which I do with every system build. Does Sage have such a file format? Tim Daly Minh Nguyen wrote: This is a split off from the thread Random banter about Sage standards at http://groups.google.com/group/sage-devel/browse_thread/thread/c80b87648c213c5 Hi Tim, On Fri, Aug 27, 2010 at 9:59 PM, Tim Daly d...@axiom-developer.org wrote: For *standard test suites*, I believe we should have these in many different areas. We should collect a set of reference books that are fairly comprehensive and jointly develop tests that run on all systems. Rubi is doing this with rule based integration. http://www.apmaths.uwo.ca/~arich/ Axiom is doing this with the Computer Algebra Test Suite http://axiom-developer.org/axiom-website/CATS/index.html This is a point I at least agree on. I think it would be a moderately difficult project to write a Sage counterpart to the Axiom CATS. It would be an interesting project to see how one could develop a similar test suite based on T. Piezas III's book A Collection of Algebraic Identities available at https://sites.google.com/site/tpiezas/Home I've have been thinking about writing a test suite for Sage's graph theory functionalities. The following comprehensive book provides a good starting point on what to include: * Jonathan L. Gross and Jay Yellen (eds). Handbook of Graph Theory. CRC Press, 2004. All of these items are on my todo list [1], but I haven't made any headway on any of them in the last few months. [1] http://sage.math.washington.edu/home/mvngu/todo.html -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Textbook converted to Sage worksheets
Rob Beezer wrote: I've converted Tom Judson's open-source Abstract Algebra textbook (http://abstract.pugetsound.edu) from Latex to a series of Sage worksheets (one per chapter) with almost no compromises (ie the same source also builds a faithful PDF). Cross-worksheet links are not supported yet in the notebook, and I've not yet started adding Sage code to the book, but adding compute cells is possible and feasible right now. Available as the first example on the wiki page: http://wiki.sagemath.org/devel/LatexToWorksheet Rob, This is excellent. It would be useful if these kinds of textbooks were available in versions for every CAS. I'll look at what it might take to generate an Axiom version. Like the CATS test suites, this could give everyone a common touchstone for discussion and debate as well as a common reference for teaching. The worksheets are packaged into a single zip file, which the notebook will upload and unpack (mostly even in the right order). There is a live compute cell at the bottom of each chapter for experiments or annotation via Tiny MCE. The graphics all begin life as tikz diagrams, so even these have editable source code. Tom has done a lot of work to modernize the source, since this book was originally written in the late 1980's. He had to also update the Historical Note about Fermat's Last Theorem. ;-) I'll be working over the next several months to add in material about using Sage to study groups, rings, fields, etc. Any extra non-obvious ideas about how to leverage Sage in the study of these topics would be appreciated. Reports of any typos or technical problems with the current state-of-the-art would also be appreciated. I have a few other books in various states of conversion, some have Sage code already. I'm also going to use Tom's book to further stress-test MathJax, which has already resulted in two bug-fixes for the MathJax jsMath-compatibility extension. I've had help from several people on this, notably Tom Judson, Robert Marik, Dan Drake, Minh van Nyugen and Davide Cervone. I'll contribute any examples from Axiom that have direct conversions to Sage. (I've cross-posted to sage-devel and sage-edu - sorry for the noise if you read both.) Rob -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Random banter about Sage standards
this with rule based integration. http://www.apmaths.uwo.ca/~arich/ Axiom is doing this with the Computer Algebra Test Suite http://axiom-developer.org/axiom-website/CATS/index.html If we publish and maintain the test suite results for all systems there will be great pressure to conform to these results, great pressure to develop standard algorithms that everyone uses, and great pressure to improve areas of weakness. For *program proofs* I can see where ACL2 and COQ can be integrated into systems so that a published paper can include an automated proof. This will raise the standard expected for professional publications in computational mathematics. It will also move us away from depending on domain experts who have the unfortunate tendency to die off, both personally and professionally. The 30 year horizon ... We are nearly 50 years into computational mathematics. It is time to develop departments and textbooks, raise the level of expectation for peer-reviewed publications, develop not only software engineering practices but also computational engineering practices. Computational mathematics is the one area of software where you can independently check your answers and you can expect to write timeless software that gets the same answers 30 years later. It really is worth the time to get it right. To bring this diatribe back to earth and the original subject, you have identified a symptom of a much larger problem with the current systems. Unfortunately there is no peer-pressure to have higher standards. I was hoping that the NIST Digital Library of Mathematical Functions would be the touchstone of algorithms but that is clearly not the case. Perhaps someday there will be sub-department of the NSF that tried to organize, guide, and fund it but nobody there has the vision and the will to get it done. Maybe we should nominate William as an NSF director :-) Tim Daly Dr. David Kirkby wrote: On 08/24/10 02:06 PM, kcrisman wrote: Anyway, I think (as you have correctly noted before) we have a bit of a culture clash between software engineering and mathematics. SNIP Just have patience with those of us who aren't from a software background - and trust that we are trying hard to internalize your lessons, but that we have more immediate needs to fill as well for our next course or paper. I think that just as Minh's messages about documentation are slowly taking hold in the whole ecosystem, so are yours about software engineering. - kcrisman Just to make a point, my own background is not software engineering. My first degree is in electrical and electronic engineering, my masters in microwaves and optoelectronics and my PhD in medical physics. Apart from a very brief spell (about 6 months), I have never worked in the IT industry. I first became aware of the subject of software engineering when an Australian guy joined the department I worked at University College London. Russel's task was to develop some hardware and software for a research project. He quite rightly realised that developing software by the seat of your pants as he called it was not the way to go about it. So before starting to write the software, he purchased a book on the subject of software engineering. I never gave this topic much more thought until I started working on Sage. I then because to realise that Sage needs to take a more professional approach to the development, as it seems a bit add-hock to me. My own view is I'd rather have something with less features, which I could rely on, than lots of features I don't trust. When there is little in the way of project management, and a culture of not doing anything properly, then attitude tends to spread like a virus. I'm currently running the doctests 100 times on a machine, with the same build of Sage that passed all doc tests. This is an interesting failure I observed: sage -t -long devel/sage/doc/en/constructions/linear_algebra.rst ** File /export/home/drkirkby/sage-4.5.3.alpha2/devel/sage-main/doc/en/constructions/linear_algebra.rst, line 202: sage: A.eigenvalues() Expected: [3, 2, 1] Got: [3, 1] ** The tests have been run 41 times now, and only once has that test failed. The answer looks quite reasonable, but I assume is wrong, as the other 40 times the code gave the expected value. It's these sorts of things that concern me. Why should the same build of Sage, running exactly the same doctests each time, not produce repeatable results? There's been a few failures, though that is the only one I've noticed where the answer looks very reasonable, but is in fact incorrect. Dave -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http
Re: [sage-devel] Re: How does real_lazy work?
Axiom solves this problem by separating the category information from the specific domain information. Thus you can have a categorical implementation that works for every domain in the category but you can supply a specific implementation for a given domain. So a dense matrix and a sparse matrix are both matrices but each can override the default multiply routine for efficiency reasons. Domains can take parameters that specify information. Polynomials are represented by a domain that supplies the coefficient ring R so that you can create a polynomial over integers, a polynomial over fractions, a polynomial over the roman numerals, etc. Thus you say you want a Polynomial(Fraction(Integer)), a polynomial with fraction coefficients. Fraction(Polynomial(Integer)), a fraction with polynomials in the numerator and denomiator where the coefficients of the polynomials are integers. So if p is a polynomial with fractional coefficients (that is, Polynomial(Fraction(Integer)) 1 3 1 2 - x + - x 7 3 we can ask for the same thiing as a fraction of polynomials (that is, Fraction(Polynomial(Integer)) 3 2 3x + 7x - 21 which is known as rearranging the type tower Sage can use a similar scheme to separate the category information from the domain information and from the domain representation. From a mathematical point of view this has been a very successful way to separate concerns. Tim Daly Johan S. R. Nielsen wrote: On Aug 11, 1:28 pm, koffie m.derickx.stud...@gmail.com wrote: Hej Johan, It indeed seems to be at the core of a wider problem. The core of the problem seems that sometimes you can represent various objects in different ways. - So in the coding theory example you can represent a general linear code by a generator matrix. While you can represent a cyclic linear code by a generator polynomial. - In real_lazy you represent sqrt(2) as an algebraic element. But you want to execute functions on it's binary representation (1.011010100 etc.). - In linear algebra you can represent a matrix as a sparse or a dense matrix. - In commutative algebra you can represent a polynomial in a sparse or a dense way. - More suggestions are welcome :) In all these cases you might sometimes want to execute functions as implemented for the other representation. The big question of this topic was how to nicely make these functions available as attributes without breaking class inheritance and docstrings. I guess the best solution suggested is Robert Bradshaw's solution. It would be nice to have a working example of it's suggestion to be able to test it. And maybe also add a section to the structuring code in Sage part in the sage developers guide. This is exactly it, and it crops up more or less everywhere in mathematics. What I want to do for the error-correcting codes case (exemplified via the one question posed above), is to begin with the representation which is mostly used (or the representation most tightly encompassing the object in question), so for a cyclical code, I would use the generator polynomial. Whenever one wants to access it as a linear code, this should be seamlessly (or close to) allowed, and should generate the generator matrix in the background and cache it for later use. Unfortunately, inheritance seems to me to be at the same time too rigid and too weak, so I would sidestep that entirely and rely on ducktyping (and manual implementing of inherited attributes -- perhaps using solutions inspired by Robert's here). Problems like this and the one of this thread arise all the time, but I have yet to see an agreed or standardised solution ideology in Sage. Has it ever been decided? Or is it empirically defined through the current Sage code? I would very much like to see it in a section called Structuring code in Sage -- just as much as I would like to see such a section. The existing documentation in Writing code for Sage is only concerned with micro-level problems such as doc-strings and naming conventions; there is no discussion on macro-level stuff like structuring. I guess this is also to encourage taking these discussions on this board but sometimes general stuff is agreed on such discussion which could be written down. I guess; I am new here, so I might easily have missed something fundamental. @Johan, is the problem I describe here the only one that was mentioned in the other google thread or are there more? There are several more, and some of them less specific. More or less my entire first post is a discussion of how to solve the general case of your example problem for the codes as well as related problems regarding how to encode and decode. I invite everyone (also those not familiar with error-correcting codes) with an opinion on these structuring issues to join the discussion. Cheers, Johan -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel
Re: [sage-devel] Re: complementary problem
mda_ wrote: Hopefully this all agrees with you, and if not, I guess I can start learning Lisp... My apologies for the cross-posting (I am not yet approved for sage- flame) http://www.buayacorp.com/wp-content/uploads/2007/10/john-mccarthy-poster1.jpg The fact that you're doing it at all implies the imperative which, as we all know, is not the way to program (this week). (Above: A portrait, and tribute! ;-), to the inventor of lisp!) http://en.wikipedia.org/wiki/John_McCarthy_(computer_scientist) -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Python, Sage, categories
You might find this interesting... http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.110.7221rep=rep1type=pdf Taivalsaari, Antero On the Notion of Inheritance ACM Computing Surveys, Vol 28 No 3 Sept 1996 Robert Bradshaw wrote: On Sat, Jul 24, 2010 at 10:46 AM, Harald Schilly harald.schi...@gmail.com wrote: On Jul 24, 8:10 am, Robert Bradshaw rober...@math.washington.edu wrote: We should do this as part of the tests, collect timing data on each test block (and perhaps even each line?). I don't think this would work for all lines because completing all the tests would take too long (if we want to use timeit, each line is repeated several times) I rather suggest to add something to the doctest infrastructure, that executes those lines in timeit(..) that are tagged via # timeit appended to the line. e.g. sage: x = 1 sage: _ = x*x # timeit Data for these timings are collected in a key-value dictionary that is pickled into a file named after the current date+time (maybe also revision number?) ... The key should also be something useful, e.g. a 3-tuple consisting of the relative path and name to the file, the line number and the string literal of the exectued line. Based on that it should be straightforward to write some code that analyzes execution time regressions. +1 to the idea of a timeit decorator, which would be useful for microbenchmarking. I think timing whole blocks would be useful as well to make sure there's no macro regressions. Though any one datapoint isn't as useful, if everyone was consistently getting a slowdown for a given doctest, that would be an indicator that something is going on. - Robert -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] About mpmath and sympy
Paulo César Pereira de Andrade wrote: 2010/7/17 François Bissey f.r.bis...@massey.ac.nz: As an aside, if two upstream packages include another upstream package (e.g. both include GMP) what does Sage do? Are there two copies of GMP? They could have different versions of the same package since project 1 could have stopped at one version and project 2 could have stopped at another. Sage could be using a third. Funny you mentioned GMP. At one point givaro was shipping its own GMP. It was actually an accident on the givaro devs part - and I had notified them. But I didn't notify this list. So in at least one release givaro was actually overwriting part of GMP. I think there may be still duplicates somewhere, not just GMP, but probably don't affect sage because either sage doesn't build it by default, e.g. gap optional modules, or sage talks to it using the pexpect interface. For your question I guess it depends if it is kept internally without clash with anything else or it actively tries to overwrite things that have been installed already. The second one is a no-no, and the first one should be fixed to use upstream but not as a matter of emergency I would guess. If it is linked statically, and provides only an opaque interface, usually it should just work, but that may depend on how the duplicates access external resources, like files, kernel interface, etc. Problems can get serious on shared objects when there are name clashes (I remember when I tried LD_PRELOAD=libpolybori.so and discovered that it builds stubs to several libc calls if UNIX is not defined, and it is not in Linux). About Tim Daly comment that I think may be related to axiom :-) The axiom package was broken for quite some time in Mandriva. My first work on it I got it to work with system gmp, but need several gcl patches. When someone else in Mandriva updated to gmp 5, I rebuilt axiom using its internal copy of gmp3 (I am using git axiom). In case you want to check it: http://svn.mandriva.com/cgi-bin/viewvc.cgi/packages/cooker/axiom/ Axiom for mandriva is at the usual download site. I was curious how Sage was planning to handle the multiple-version problem. If you look at the way software can be layered you find that each layer tries to reduce errors by including the upstream software. So MPIR is included in the distro for some packages but each package usually has its own version. Axiom only depends on two packages (GCL and noweb (noweb is going away)) but including Axiom under Sage will end up including gmp since that is included in GCL. Including Axiom under Sage also includes a lisp but Maxima in Sage uses ECL these days so there would be two complete lisps. Maxima can build on GCL. Would it be reasonable for Sage to establish fundamental spkgs (like gmp) which were used by all of the spkgs? I think Sage could play the role of a normalizing force, suggesting that upstream packages use the same distros. This would be similar to the (decades-old) push to use standard system libraries. There was a day when everyone included their own copy of printf in every program. Maybe it is time for a new spkg substrate push, at least in the computer algebra community. Francois Paulo -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] About mpmath and sympy
As an aside, if two upstream packages include another upstream package (e.g. both include GMP) what does Sage do? Are there two copies of GMP? They could have different versions of the same package since project 1 could have stopped at one version and project 2 could have stopped at another. Sage could be using a third. François Bissey wrote: Hi, Newer sympy has a bundled copy of mpmath, what causes several problems in my sagemath package. I was in vacation during most of Mandriva 2010.1 freeze, and did not fully test the package for some time, but I am working on an update for it; basically an 's/import mpmath/import sympy.mpmath as mpmath/', but would like to know what would be the better approach. (just letting the code use both leads to SEGvs). The new sagemath package will conflict with python-mpmath-0.14-1mdv2010.1 (forcing it to be uninstalled), because the sympy is python-sympy-0.6.7-1mdv2010.1. Hi Paulo, that will probably be a pain for us in gentoo as well. At the moment we are sticking with sympy-0.6.6 as sympy-0.6.7 gives us trouble. The gentoo philosophy at this point will be to remove mpmath from sympy and make it a requirement. But I haven't been actively working on that. Francois -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Vote on making GNU patch a standard package
It is officially none of my business what you decide. However, given that developers are the only people likely to know how to create and post a diff-Naur patch file and developers are likely able to install tools and 'patch' is a well-known, widely used, and standard tool ... does it make sense to have your own copy? Adam Webb wrote: [Yes] Include GNU patch as a standard package in Sage Sounds good to me. Adam -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Patches overwriting patches in singular
I'm surprised you don't use patch. Mercurial can generate patches. François Bissey wrote: On Jun 29, 4:13 pm, François Bissey f.r.bis...@massey.ac.nz wrote: sage doesn't assume that the patch command is installed but rely on cp being there. That's why patch aren't used. I agree not ideal but that's a lowest common denominator issue. Perhaps compare the md5sum of the original and bail if it's not the expected number? Any time a file changes, the file we replace it with in the spkg-install should probably change as well. Do our prerequisites include some checksumming or hashing utility? that's an interesting idea. On the linux side usually distro do checksums on packages so it has to be a part of the base system if you want to update. It's probably the case on most other platform in one way or another. That wouldn't have taken care of Dave's original problem in any case, which was double copying the same file. Which I stupidly parroted in Gentoo. Francois -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Patches overwriting patches in singular
Perhaps I'm being thick about this. In Axiom's build we have a zip file for GCL source code. At build time we unzip the GCL source, THEN apply our patches, THEN we do a build. Why wouldn't this process work in Sage? Sage requires all of GCC to be installed. Surely requiring patch is not a lot more overhead. In the worst case, add the source for patch and build your own copy early in the build process. Sending/posting/trading diff -Naur patches is a long standing tradition in open source. Sage is the only project I've ever heard of that doesn't use them. Mike Hansen wrote: On Tue, Jun 29, 2010 at 4:54 PM, Tim Daly d...@axiom-developer.org wrote: I'm surprised you don't use patch. Mercurial can generate patches. The issue is not generating the patches -- it's applying them. All of the spkgs (should) have the diff as well as the file with the patch applied. --Mike -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Patches overwriting patches in singular
We use a naming convention for patches. Thus the 3rd new patch created today by me would have the name: 20100629.03.tpd.patch which orders the patches by date, sub-sequence, and author. You might want to use your spkg name instead as in: 20100629.03.singular.patch This would ensure that patches are unique. Mike Hansen wrote: On Tue, Jun 29, 2010 at 5:57 PM, Dr. David Kirkby david.kir...@onetel.net wrote: But if there are two three files src/foo.c patches/foo.c patches/foo.c.diff what does patches/foo.c.diff possibly give me that could could get by running diff src/foo.c patches/foo.c ? This requires that patches/foo.c was made from src/foo.c. This is the case for the current version, but if you look at a previous version of patches/foo.c in the repository, you have to go out and get the corresponding src/foo.c from the internet in order to see what the change actually was. --Mike -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Is 'flex' needed to build Sage?
I'm sure Singular has a process to fix the problems you mention. All you have to do is send a 'diff -Naur' patch that improves the build. You got hundreds of megabytes of code for free and you're complaining because the install script isn't written the way you advocate? Advocacy is volunteering. Send them a thank-you note for all the free code and include a patch file. Tim Open source... now it's YOUR problem to solve -- daly Dr. David Kirkby wrote: On 06/ 6/10 11:48 PM, François Bissey wrote: yes singular is a downright mess, upstream and in sage. I'm glad I'm not alone in my view. Apart from moving to the latest upstream I think the singular spkg is due for a spring clean. It build an enormous amount of targets in a way that looks like a very careful choreography and apart from libsingular and the singular binary there is no indication sage uses any of the other stuff built. It does take a long time to build compared to most other packages, which is probably due to the fact the package is large and so has a lot of source code. If a lot of the targets are unnecessary, then I suspect the build time could be reduced. It took 40 minutes on my old 900 MHz SPARC, though I could probably reduce that if targets can be built in parallel. But even then, it is still going to be quite lengthy. I have just read William's opinion and it may be true that is generally easy to build. But reproducing the set up used in the sage spkg from a packaging point of view is quite difficult. Francois Dave -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] new paper on sage by myself and Burcin Erocal
I was commenting on the version of Axiom shown in your note. :-)
Axiom prints a banner on startup containing 2 pieces of information.
The second line is the release version of the system (September 2005)
The third line is the date this version was built (December 2006)
That's quite amusing given the Sage discussion about release schedules
and user-update frequency. The latest version of Axiom is May 2010.
AXIOM Computer Algebra System
Version: Axiom 3.9 (September 2005)
Timestamp: Saturday December 2, 2006 at 09:30:31
William Stein wrote:
On Wed, Jun 2, 2010 at 6:10 AM, Tim Daly d...@axiom-developer.org wrote:
You have Axiom from 2005?
You do realize it is updated every 2 months :-)
Tim
Huh? I can't figure out what you're referring to above.
William
William Stein wrote:
On Tue, Jun 1, 2010 at 11:31 PM, Martin Rubey
martin.ru...@math.uni-hannover.de wrote:
William Stein wst...@gmail.com writes:
Hi,
Burcin Erocal and I wrote a paper
The Sage Project: Unifying Free Mathematical Software to Create a
Viable Alternative to Magma, Maple, Mathematica and Matlab
for http://www.math.kobe-u.ac.jp/icms2010/index.html
Here it is:
http://wstein.org/papers/icms/icms_2010.pdf
A tiny correction to the list on 6, Table 2: as far as I know, sage does
not communicate with axiom, but rather with fricas. But I admit, I am
not 100% certain, what the default installation does. Please correct
me, if I'm mistaken.
Martin
Thanks for raising this point. I remember Tim Daly complaining at
some point that I should rename the axiom command in sage to
fricas. So this is worth looking into, which I just did. The result
is that the Sage interface called axiom really is an interface to
Axiom, as claimed.
I think the Sage interface that is called axiom does in fact work
fine with Axiom. On my computer, I don't have fricas installed, but
I do have axiom:
wst...@sage:~$ which fricas
wst...@sage:~$ which axiom
/usr/bin/axiom
This is the read-deal axiom, from Debian I think:
wst...@sage:~$ axiom
GCL (GNU Common Lisp) 2.6.7 CLtL1Nov 10 2006 14:25:02
Source License: LGPL(gcl,gmp), GPL(unexec,bfd,xgcl)
Binary License: GPL due to GPL'ed components: (XGCL READLINE BFD UNEXEC)
Modifications of this banner must retain notice of a compatible license
Dedicated to the memory of W. Schelter
Use (help) to get some basic information on how to use GCL.
Temporary directory for compiler files set to /tmp/
AXIOM Computer Algebra System
Version: Axiom 3.9 (September 2005)
Timestamp: Saturday December 2, 2006 at 09:30:31
-
Issue )copyright to view copyright notices.
Issue )summary for a summary of useful system commands.
Issue )quit to leave AXIOM and return to shell.
-
Re-reading compress.daase Re-reading interp.daase
Re-reading operation.daase
Re-reading category.daase
Re-reading browse.daase
(1) - )quit
Now I run Sage, and verify that it doesn't know about any fricas
command, only Axiom, which is the systemwide genuine axiom:
wst...@sage:~$ sage
--
| Sage Version 4.4.1, Release Date: 2010-05-02 |
| Type notebook() for the GUI, and license() for information.|
--
sage: !which axiom
/usr/bin/axiom
sage: !which fricas
And now I run a command, which calls Axiom:
sage: axiom('2 + 3')
5
Consulting the source shows that the command that Sage runs when the
axiom interface is invoked is axiom -nox -noclef:
sage: axiom.__init__??
...
Source:
def __init__(self, name='axiom', command='axiom -nox -noclef',
script_subdirectory=None, logfile=None,
server=None, server_tmpdir=None,
init_code=[')lisp (si::readline-off)']):
See http://trac.sagemath.org/sage_trac/ticket/5111
There is a *separate* fricas interface:
sage: fricas.__init__??
Definition: fricas.__init__(self, name='fricas', command='fricas
-nox -noclef', script_subdirectory=None, logfile=None, server=None,
server_tmpdir=None, init_code=[')lisp (si::readline-off)'])
Source:
def __init__(self, name='fricas', command='fricas -nox -noclef',
The upshot is that maybe I should list both fricas and axiom in the
interfaces table?
William
--
To post to this group, send an email to sage-devel@googlegroups.com
To unsubscribe from this group, send an email to
sage-devel+unsubscr...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/sage-devel
URL: http://www.sagemath.org
--
To post to this group, send an email to sage-devel@googlegroups.com
Re: [sage-devel] new paper on sage by myself and Burcin Erocal
You have Axiom from 2005?
You do realize it is updated every 2 months :-)
Tim
William Stein wrote:
On Tue, Jun 1, 2010 at 11:31 PM, Martin Rubey
martin.ru...@math.uni-hannover.de wrote:
William Stein wst...@gmail.com writes:
Hi,
Burcin Erocal and I wrote a paper
The Sage Project: Unifying Free Mathematical Software to Create a
Viable Alternative to Magma, Maple, Mathematica and Matlab
for http://www.math.kobe-u.ac.jp/icms2010/index.html
Here it is:
http://wstein.org/papers/icms/icms_2010.pdf
A tiny correction to the list on 6, Table 2: as far as I know, sage does
not communicate with axiom, but rather with fricas. But I admit, I am
not 100% certain, what the default installation does. Please correct
me, if I'm mistaken.
Martin
Thanks for raising this point. I remember Tim Daly complaining at
some point that I should rename the axiom command in sage to
fricas. So this is worth looking into, which I just did. The result
is that the Sage interface called axiom really is an interface to
Axiom, as claimed.
I think the Sage interface that is called axiom does in fact work
fine with Axiom. On my computer, I don't have fricas installed, but
I do have axiom:
wst...@sage:~$ which fricas
wst...@sage:~$ which axiom
/usr/bin/axiom
This is the read-deal axiom, from Debian I think:
wst...@sage:~$ axiom
GCL (GNU Common Lisp) 2.6.7 CLtL1Nov 10 2006 14:25:02
Source License: LGPL(gcl,gmp), GPL(unexec,bfd,xgcl)
Binary License: GPL due to GPL'ed components: (XGCL READLINE BFD UNEXEC)
Modifications of this banner must retain notice of a compatible license
Dedicated to the memory of W. Schelter
Use (help) to get some basic information on how to use GCL.
Temporary directory for compiler files set to /tmp/
AXIOM Computer Algebra System
Version: Axiom 3.9 (September 2005)
Timestamp: Saturday December 2, 2006 at 09:30:31
-
Issue )copyright to view copyright notices.
Issue )summary for a summary of useful system commands.
Issue )quit to leave AXIOM and return to shell.
-
Re-reading compress.daase Re-reading interp.daase
Re-reading operation.daase
Re-reading category.daase
Re-reading browse.daase
(1) - )quit
Now I run Sage, and verify that it doesn't know about any fricas
command, only Axiom, which is the systemwide genuine axiom:
wst...@sage:~$ sage
--
| Sage Version 4.4.1, Release Date: 2010-05-02 |
| Type notebook() for the GUI, and license() for information.|
--
sage: !which axiom
/usr/bin/axiom
sage: !which fricas
And now I run a command, which calls Axiom:
sage: axiom('2 + 3')
5
Consulting the source shows that the command that Sage runs when the
axiom interface is invoked is axiom -nox -noclef:
sage: axiom.__init__??
...
Source:
def __init__(self, name='axiom', command='axiom -nox -noclef',
script_subdirectory=None, logfile=None,
server=None, server_tmpdir=None,
init_code=[')lisp (si::readline-off)']):
See http://trac.sagemath.org/sage_trac/ticket/5111
There is a *separate* fricas interface:
sage: fricas.__init__??
Definition: fricas.__init__(self, name='fricas', command='fricas
-nox -noclef', script_subdirectory=None, logfile=None, server=None,
server_tmpdir=None, init_code=[')lisp (si::readline-off)'])
Source:
def __init__(self, name='fricas', command='fricas -nox -noclef',
The upshot is that maybe I should list both fricas and axiom in the
interfaces table?
William
--
To post to this group, send an email to sage-devel@googlegroups.com
To unsubscribe from this group, send an email to
sage-devel+unsubscr...@googlegroups.com
For more options, visit this group at http://groups.google.com/group/sage-devel
URL: http://www.sagemath.org
Re: [sage-devel] Re: What's the point of two stable releases in two days?
The Axiom project had a long debate about releases and version numbers which I see is about to happen here. Axiom decided that a reasonable balance was to make 2 decisions, one about releases and one about versions. RELEASES There is a choice between releasing often and releasing, say, yearly. Sage releases about every week or two at the moment. The upside of this strategy is that people get the latest version immediately. The downside of this strategy is that people are ALWAYS in update mode and big changes are very hard to manage in a small window (2 days?) First, there would be a silver and a gold releases. The silver version is updated continuously and available from most of the sites with a git pull or git clone. The gold release would be a time-boxed release every 2 months. This gives people who care about a particular change a way to get the latest release immediately. It allows others who just want the system, a way to update at a more reasonable pace, maximally, every 2 months. The gold release is maintained on github, the silver is on all other sites. VERSIONS Version numbers get religious really fast and the debate is not very productive. Essentially, a single number is not sufficient to carry all of the information about what might have changed, especially if you have a component system. Since git maintains a 40-digit SHA1 hash for every commit it is sufficient for a version number. Any reference to a single hash number gives all of the required information. This is sufficient for silver releases. Since the time-boxed gold releases are 2 months apart it is sufficient to use the form May 2010 as the unique release number. This is easy to distinguish from March 2010. I'm sure that the Sage list will find this method not right for a variety of reasons but I can tell you that there is no perfect solution. The Axiom debate raged on for about a year. Time-boxing isn't perfect but it allows big changes to occur without breaking everyone and little changes to occur without annoying everyone. Every project seems to have this debate. Good luck with it. Tim Daly kcrisman wrote: On May 26, 3:56 pm, William Stein wst...@gmail.com wrote: On Wed, May 26, 2010 at 12:50 PM, Dr. David Kirkby david.kir...@onetel.net wrote: On 05/26/10 05:34 PM, leif wrote: On 26 Mai, 18:09, Robert Bradshawrober...@math.washington.edu I like the risk assessment field idea. Me too, perhaps give it a different name. What would you call it? There are at least three things to consider I can think of. 1) What are the risks associated with a change? 2) The probability of the change causing a problem. 3) The impact such a problem would cause. There might be others. Even things that have a fairly high probability of causing a problem are probably not worth worrying about too much if the impact would be minimal. Conversely, even something which has a low probability of causing a problem, but would have major consequences, needs to be taken seriously. However, unless there was a *major* change in Sage release practices, it would be a bit pointless doing any sort of risk analysis. I don't detect much of an appetite for a major change in Sage release practices. In fact, I detect quite the converse. At a bare minimum, any major change should be designed by people who have actually done some Sage releases. Wouldn't it be easiest for someone to change the 5.0 release date thingie on Trac to sometime in June, but may be pushed to July or later in order to fulfill goals (Cygwin, etc.)? This seems like even more of a tempest in a teapot than the SPKG.txt thread ;) - kcrisman -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: What's the point of two stable releases in two days?
William Stein wrote: On Wed, May 26, 2010 at 3:08 PM, Tim Daly d...@axiom-developer.org wrote: The Axiom project had a long debate about releases and version numbers which I see is about to happen here. Axiom decided that a reasonable balance was to make 2 decisions, one about releases and one about versions. RELEASES There is a choice between releasing often and releasing, say, yearly. Sage releases about every week or two at the moment. The upside of this strategy is that people get the latest version immediately. The downside of this strategy is that people are ALWAYS in update mode and big changes are very hard to manage in a small window (2 days?) First, there would be a silver and a gold releases. The silver version is updated continuously and available from most of the sites with a git pull or git clone. The gold release would be a time-boxed release every 2 months. This gives people who care about a particular change a way to get the latest release immediately. It allows others who just want the system, a way to update at a more reasonable pace, maximally, every 2 months. The gold release is maintained on github, the silver is on all other sites. VERSIONS Version numbers get religious really fast and the debate is not very productive. Essentially, a single number is not sufficient to carry all of the information about what might have changed, especially if you have a component system. Since git maintains a 40-digit SHA1 hash for every commit it is sufficient for a version number. Any reference to a single hash number gives all of the required information. This is sufficient for silver releases. Since the time-boxed gold releases are 2 months apart it is sufficient to use the form May 2010 as the unique release number. This is easy to distinguish from March 2010. I'm sure that the Sage list will find this method not right for a variety of reasons but I can tell you that there is no perfect solution. The Axiom debate raged on for about a year. Time-boxing isn't perfect but it allows big changes to occur without breaking everyone and little changes to occur without annoying everyone. Every project seems to have this debate. Good luck with it. Thanks for sharing the above. 1. How do you think your choice of releases and version numbers impacted the number of Axiom users? Developers? I have no way to track the number of users so I can't say. Axiom forked (twice) and the forks have their own version numbering schemes, each one different and neither one is clear, at least to me. Developers will track whatever scheme you use and they won't like it :-) It is very difficult to introduce large changes to the system if the updates are too frequent. I'm introducing a new package that includes over 50 new pieces of algebra in this next release. The developer silver version has seen each new piece of algebra as it was introduced, with updates happening several times a day all month long but each new piece is useless standalone. The gold version will have a fully implemented and tested piece so users won't see the intermediate states. At the rate you are currently releasing I don't know how you can introduce fundamental changes like a reorganization of the categories. If there is a mistake the whole user community gets hit. And if it takes a couple weeks to debug then you'll have the world at your throat. The silver releases give your developers a chance to play before it goes out to the general public. I make NO guarantees about silver releases. They might not even build (although breaking the build is on my list of major sins). If you succeed wildly then you'll have thousands of universities downloading versions, students will each have a different version depending on the day of the week they decided to download. A gold version would give professors something concrete to point at e.g. the September 2010 version. 2. Now that you've had the above version/release schedule for a few years, is there anything you would change? Well you'd be amazed at how quickly 8 weeks goes by The pace of 8 weeks between releases leaves 7 weeks of work and a week of deep test, binary builds, etc. Fedora always seems to break things on every release so it just takes a lot of time. I see you have the same breakage happening on certain platforms. It is very frustrating. Having done the silver/gold release mechanism for about 4 years now I think it is just about right. It gives lots of pressure to hit the timebox but enough time to plan for a major change. Timeboxing also allows estimates of when to stop adding new features (a freeze) and start cleaning up the little details. This subtle side-effect forces fixing the little annoying things that nobody notices but make it cleaner and more professional. 3. How did your debate about the above end? Was their some definitive argument, or? Originally the development was released every 2 months
Re: [sage-devel] A function to compute Bezout coefficients ?
Is anyone else getting duplicate copies of Sage messages? -- Tim Mike Hansen wrote: Hello, I've been looking for a function that allows one to compute Bezout coefficients of two numbers (say natural numbers). There is the GCD function, but I haven't found anything about Bezout coefficients. This is not complicated to write one, but it would be better if it was included somehwere in Sage. Is there already something like that ? You should use xgcd: sage: xgcd(5, 7) (1, 3, -2) sage: g,a,b = xgcd(5, 7) sage: a*5 + b*7 1 --Mike -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: icc
how about using:
find . -name *.pyx -exec touch {} \;
William A. Stein wrote:
On May 23, 2010, at 1:12 PM, leif wrote:
On 23 Mai, 21:40, Dr. David Kirkby david.kir...@onetel.net wrote:
'lcalc' had a particularly annoying attempt to cover up warnings from the
assembler, as it actually caused the build to break on Solaris, as the option to
cover up the warnings was passed directly to the Sun assembler, but it did not
accept the option.
They seem to think gcc (the compiler driver) will be smart enough to
know all options passed to any component of the tool chain, even if
passed verbatim ;-)
IMHO, the quality of the coding in Sage leaves a lot to be desired in places.
One of my current favorites is a snippet from sage-build:
cd $SAGE_ROOT/devel/sage/sage
echo *** TOUCHING ALL CYTHON (.pyx) FILES ***
touch */*.pyx */*/*.pyx */*/*/*.pyx */*/*/*/*.pyx */*/*/*/*/*.pyx */
*/*/*/*/*.pyx */*/*/*/*/*/*.pyx 2 /dev/null
Reminds me of M$-DOS, where the shell did not expand wildcards. (If
you have fun, count the asterisks...)
-Leif
Instead of keeping this as a favorite, implement a better version, and post a
patch.
-- William
--
To post to this group, send an email to sage-devel@googlegroups.com
To unsubscribe from this group, send an email to
sage-devel+unsubscr...@googlegroups.com
For more options, visit this group at http://groups.google.com/group/sage-devel
URL: http://www.sagemath.org
--
To post to this group, send an email to sage-devel@googlegroups.com
To unsubscribe from this group, send an email to
sage-devel+unsubscr...@googlegroups.com
For more options, visit this group at http://groups.google.com/group/sage-devel
URL: http://www.sagemath.org
Re: [sage-devel] Re: numerically stable fast univariate polynomial multiplication over RR[x]
Bill Hart wrote: That's actually a very interesting paper. I've recently been playing with Forth, which is a kind of Lisp type language (yeah I know you won't agree with that), based on a data stack. I also worked through a book on Lisp up to the point where macros were defined, as I wanted to understand how that was handled in Lisp. I actually get Lisp now, but it was a round about way that I got there. It's clearly not for everyone. I've also been experimenting with how short programs can be that still give reasonable performance. The answer is, amazingly short, if one spends a lot of time thinking about it before coding. Another thing I've been enjoying lately is literate programming. Amazingly it turns out to be faster to write a literate program than an ordinary program because debugging takes almost no time. Can I quote you on that in the Axiom system (which is moving toward being fully literate)? Anyhow, I'm going to read this paper of yours now. Bill. On May 3, 3:37 pm, rjf fate...@gmail.com wrote: If you are not doing floating point arithmetic with machine arithmetic, but using MPFR, then you are sacrificing a huge amount of time. You might as well be using rational arithmetic, or the kind of arithmetic that Collins once proposed, where the denominator is a power of 2. Makes reducing to lowest terms relatively fast because the GCD is trivial. Compare that to boosting the overall precision in MPFR to big enough. If you want to read more about multiplying polynomials, you can read the (unpublished, unfinished, too-long) paper here: www.cs.berkeley.edu/~fateman/papers/shortprog.tex RJF -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group athttp://groups.google.com/group/sage-devel URL:http://www.sagemath.org -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: numerically stable fast univariate polynomial multiplication over RR[x]
I have also found that it has the side-effect you mention. It makes debugging easier, if it is needed at all. Hopefully this will also be true of the person who ends up maintaining our code after we're gone. Thanks for the permission. Your quote appears on the documentation page of the axiom website (which I won't link here) Tim Bill Hart wrote: Ah you arrived right on cue. LOL! Ha ha, you can quote me if you want, but I have written a couple of literate programs in my life, so I'm hardly an expert. But I was surprised at how much difference it made to the debugging time. Bill. On May 3, 10:04 pm, Tim Daly d...@axiom-developer.org wrote: Bill Hart wrote: That's actually a very interesting paper. I've recently been playing with Forth, which is a kind of Lisp type language (yeah I know you won't agree with that), based on a data stack. I also worked through a book on Lisp up to the point where macros were defined, as I wanted to understand how that was handled in Lisp. I actually get Lisp now, but it was a round about way that I got there. It's clearly not for everyone. I've also been experimenting with how short programs can be that still give reasonable performance. The answer is, amazingly short, if one spends a lot of time thinking about it before coding. Another thing I've been enjoying lately is literate programming. Amazingly it turns out to be faster to write a literate program than an ordinary program because debugging takes almost no time. Can I quote you on that in the Axiom system (which is moving toward being fully literate)? Anyhow, I'm going to read this paper of yours now. Bill. On May 3, 3:37 pm, rjf fate...@gmail.com wrote: If you are not doing floating point arithmetic with machine arithmetic, but using MPFR, then you are sacrificing a huge amount of time. You might as well be using rational arithmetic, or the kind of arithmetic that Collins once proposed, where the denominator is a power of 2. Makes reducing to lowest terms relatively fast because the GCD is trivial. Compare that to boosting the overall precision in MPFR to big enough. If you want to read more about multiplying polynomials, you can read the (unpublished, unfinished, too-long) paper here: www.cs.berkeley.edu/~fateman/papers/shortprog.tex RJF -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group athttp://groups.google.com/group/sage-devel URL:http://www.sagemath.org -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group athttp://groups.google.com/group/sage-devel URL:http://www.sagemath.org -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Fwd: numerically stable fast univariate polynomial multiplication over RR[x]
Bill Hart wrote: On Apr 27, 8:55 pm, rjf fate...@gmail.com wrote: Oh, just another note. There are people who have made their whole careers on devising asymptotically fast algorithms which have never been implemented, or (if they have been implemented) are not fast because their overly-simplified analysis does not fit the currently available computer efficiency profile. Indeed, their analysis may not fit any past profile of computers, and their algorithms were never practical. Interesting observation. Furer's algorithm is not practical, as are some matrix multiplication algorithms. Do you have any other examples in mind? Note, for example, that memory access is far more expensive than arithmetic, and that many computers now can multiply or add in comparable time; and they have several multipliers. Etc. I would say that memory access if far more expensive than addition, but not arithmetic in general. FFT multiplication is n log n (sometimes with a log log n, depending on what you are multiplying) and I would say the memory access perhaps adds a hidden log n factor. Can you perhaps be more specific as to what you are hinting at? On current microprocessors a multiply can be done in a few clock ticks (probably one apparent clock tick if the in-processor pipelines are fully overlapped). An L1 cache access is about 3 clock ticks, an L2 can be dozens, and a memory access can be several hundred or more (depending on DDR/2/3/..., inter-processor MESI cache, prefetch instructions, etc.) By analogy, it is more expensive to peel an egg than to slice a carrot but the time is buried under the time it takes to get one out of the fridge (L1), the supermarket (L2), the farm (main memory) or grow a new one (disk). So if an FFT that is optimized for, say 128 byte cache lines with minimal cache collisions, then the multiply times will matter. But changing the FFT to ignore cache line sizes so the fetch breaks a cache line on each read and the multiply times are completely irrelevant. RJF -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group athttp://groups.google.com/group/sage-devel URL:http://www.sagemath.org -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Sage and Amazon EC2?
I haven't used Sage on EC2 but I have done Axiom builds there (about a 1.5 hour compile/test). Its simple to configure a machine. They have hundreds of prebuilt instances. I used an ubuntu instance, ssh'ed to it, added a few packages, did a build and test. Worked as expected with no problems. If you're used to working on linux nothing should come as a surprise. Tim Daly Dan Drake wrote: The current thread about using the notebook server with classes of students made me think about the possibility of using Amazon EC2 instances to do the computing for a notebook server. I haven't used EC2 and don't know too much about it, but the idea seem to be that you can spin up a web-accessible virtual machine very easily -- it seems to be about as hard as creating a Google group. You pay for the VM by the hour. The notebook server does its computing by ssh'ing to an account and running Sage there. Imagine you provision a bunch of EC2 machines with a copy of Sage, and point the notebook server to those machines. If your notebook server needs more power, you just make some more EC2 machines. You only pay for what you use, so this seems like it could be a very effective and efficient way to run a heavily-used notebook server. I looked up prices, and it looks like about 17 cents an hour for a CPU intensive instance. If 20 students each used a notebook server and each accessed their own instance, that's $3.40 for each class hour. For a 45-hour semester-long class, that's roughly $150, which seems pretty cheap. (Consider that for some classes, a single *textbook* is $150.) Has anyone experimented with using EC2 and Sage? It seems like an interesting possibility. Dan -- --- Dan Drake - http://mathsci.kaist.ac.kr/~drake --- -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: code review tools
Speaking of that, why not institute a program committee where people volunteer to do reviews before your Sage days? I do a lot of program committee work, which is painful but is a professional giving back to the community task. It is always done against a deadline which is a great motivation. Tim Daly Jason Grout wrote: On 04/14/2010 03:04 PM, William Stein wrote: On Wed, Apr 14, 2010 at 12:43 PM, John Cremonajohn.crem...@gmail.com wrote: I have been strongly encouraging new students starting out with Sage to make small (initially) patches on their very own ticket, so that they can feel good when these get reviewed positively and then merged. But those same people might take quite a while longer before they feel confident about reviewing others people's tickets. It's usually a long time after one has started submitting papers for publication that one starts to get requests for refereeing other papers -- not that long, but a while. Isn't that similar? Yes. The main intent of what I'm suggesting is that people who are contributing a *lot* of code, but not doing any reviewing, will be very, very strongly encouraged to do more reviewing. Maybe a more balanced system would address the concerns. You get a little karma for posting a patch, a little more karma for posting a patch on a ticket with someone else's patch (because you're probably sort of reviewing their code as you make your patch), and a lot more karma for reviewing a ticket. You'd get a first-time bonus karma for posting your first patch. Of course, this also might make it more complicated than it is worth. Jason -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org To unsubscribe, reply using remove me as the subject.
Re: [sage-devel] Randomised testing against Mathematica
There are two test suites with validated results at http://axiom-developer.org/axiom-website/CATS/ The CATS (Computer Algebra Test Suite) effort targets the development of known-good answers that get run against several systems. These end result suites test large portions of the system. As they are tested against published results they can be used by all systems. The integration suite found several bugs in the published results which are noted in the suite. It also found a bug introduced by an improper patch to Axiom. It would be generally useful if Sage developed known-good test suites in other areas, say infinite sequences and series. Perhaps such a suite would make a good GSOC effort with several moderators from different systems. I have done some more work toward a trigonometric test suite. So far I have found that Mathematica and Maxima tend to agree on branch cuts and Axiom and Maple tend to agree on branch cuts. The choice is arbitrary but it affects answers. I am having an internal debate about whether to choose MMA/Maxima compatible answers just to regularize the expected results users will see. Standardized test suites give our users confidence that we are generating known-good results for some (small) range of expected inputs. An academic-based effort (which Axiom is not) could approach NIST for funding an effort to develop such suites. NIST has a website (http://dlmf.nist.gov/) Digital Library of Mathematical Functions. I proposed developing Computer Algebra test suites for their website but NIST does not fund independent open source projects. Sage, however, could probably get continuous funding to develop such suites which would benefit all of the existing CAS efforts. NSF might also be convinced since such test suites raise the level of expected quality of answers without directly competing against commercial efforts. I'd like to see a CAS testing research lab that published standardized answers to a lot of things we all end up debating, such as branch cuts, sqrt-of-squares, foo^0, etc. Tim Daly Dr. David Kirkby wrote: Joshua Herman wrote: Is there a mathematica test suite we could adapt or a standardized set of tests we could use? Maybe we could take the 100 most often used functions and make a test suite? I'm not aware of one. A Google found very little of any real use. I'm sure Wolfram Research have such test suites internally, but they are not public. There is discussion of how they have an internal version of Mathematica which runs very slowly, but tests things in greater detail. http://reference.wolfram.com/mathematica/tutorial/TestingAndVerification.html Of course, comparing 100 things is useful, but comparing millions of them in the way I propose would more likely show up problems. I think we are all aware that it is best to test on the hardware you are using to be as confident as possible that the results are right. Of course, Wolfram Research could supply a test suite to check Mathematica on an end user's computer, but they do not do that. They could even encrypt it, so users did not know what was wrong, but could at least alert Wolfram Research. I'm aware of one bug in Mathematica that only affected old/slower SPARC machines if Solaris was updated to Solaris 10. I suspect it would have affected newer machines too, had they been heavily loaded. (If I was sufficiently motivated, I would probably prove that, but I'm not, so my hypothesis is unproven). It did not produce incorrect results, but pegged the CPU at 100% forever if you computed something as simple as 1+1.) It was amazing how that was solved between myself, Casper Dik a kernel engineer at Sun and various other people on the Internet. It was Casper who finally nailed the problem, after I posted the output of lsof, he could see what Mathematica was doing. I've got a collection of a few Mathematica bugs, mainly affecting only Solaris, although one affected at least one Linux distribution too. http://www.g8wrb.org/mathematica/ One thing I know Mathematica does do, which Sage could do, is to automatically generate bug report if it finds a problem. At the most primitive level, that code might be if (x 0) function_less() else if (x == 0) function_equal() else if (x 0) function_greater() else function_error() If the error is generated, a URL is given, which you click and can send a bug report to them. It lists the name of the file and line number which generated the error. That's something that could be done in Sage and might catch some bugs. Dave LOOK ITS A SIGNATURE CLICK IF YOU DARE--- http://www.google.com/profiles/zitterbewegung On Wed, Mar 3, 2010 at 12:04 AM, David Kirkby david.kir...@onetel.net wrote: Has anyone ever considered randomised testing of Sage against Mathematica? As long as the result is either a) True or False b) An integer then comparison should be very easy. As a dead simple example, 1) Generate a large random number n
Re: [sage-devel] GPL issues again - trivial ones this time !!!
Try sending a question to FSF. I'm sure they'd give you an authoritative answer. Stallman has answered every question I ever sent him. Tim Daly Tom Boothby wrote: Context is important. The GPL doesn't say that every GPL'd interactive program must print a banner. It says that if such a banner is printed by a current GPL'd programs, then *if you distribute a modified copy*, that copy must also print the banner. The most ordinary manner of running Sage isn't running a modified interactive GPL'd program. Looks to me like the closest we've got is iPython, which is BSD'd, so we don't need to print its banner. And the notebook is its own project, so it doesn't have to inherit anybody's banner either. -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] A Challenge - what is wrong with this *simple* patch?
Dr. David Kirkby wrote:
I submitted a patch which I believe is very simple and should not
break anything, but it could not be merged into sage-4.3.1.rc0 because
it breaks the Singular installation on Sage. (It was marked as fixed,
then changed to 'needs work' as it fails.)
Can anyone spot what is wrong with it?
Here's the patch.
http://trac.sagemath.org/sage_trac/attachment/ticket/7898/singular-variables-to-names.patch
heres the ticket.
http://trac.sagemath.org/sage_trac/ticket/7898
Note sage-env has for a long time defined there, and that is
unchanged. So why should that break.
if [ $RM = ]; then
RM=rm export RM
fi
if [ $LN = ]; then
LN=ln export LN
fi
if [ $CHMOD = ]; then
CHMOD=chmod export CHMOD
fi
Is this change in a Makefile?
Then the syntax is wrong. Try
${CHMOD}
because
$CHMOD is interpreted as $C
Tim
--
To post to this group, send an email to sage-devel@googlegroups.com
To unsubscribe from this group, send an email to
sage-devel+unsubscr...@googlegroups.com
For more options, visit this group at http://groups.google.com/group/sage-devel
URL: http://www.sagemath.org
Re: [sage-devel] Re: doctest failures due to rounding errors on Solaris.
Dr. David Kirkby wrote: rjf wrote: On Dec 31, 11:15 am, Dr. David Kirkby david.kir...@onetel.net wrote: RJF The point you are missing is that we want to compare the output what Sage prints to a human. The point you are missing is that the following item, which presumably could be printed by Sage, is perfectly readable to a human: 6121026514868073 * 2^(-51). It exactly dictates the bits in an IEEE double-float, and does not require any conversion from binary to decimal. It does not need rounding. This kind of representation does not have any hidden unprinted digits. It does not ever need to be longer because of delicate edge conditions of certain numbers. It happens to evaluate to APPROXIMATELY 2.718281828459045 Sure, Sage could print that. It would also be worth printing the sign bit, so we could verify the values of 1) Sign bit 2) Significand 3) Exponent. All of those could be correct. But there is still the software which does the non-trivial task of converting that into the base 10 representation used by humans. Then in additon to that, there is the software which takes a base 10 number, shows it with the Sage prompt, adding carriage returns etc where necessary. All of these can go wrong. I would think in an almost ideal world, the test would be done at a higher level, using hardware/software which checked what the monitor actually displayed. That's not quite as easy to do though. Even better would be some way to scan the brain of the user to see what he/she believes Sage is showing. Perhaps we use a font that is not very good, so despite being displayed properly, it misunderstood. Given most of time people want to see a base 10 representation of a number, and not a base 2, base 16 or IEE 754 representation, I believe most testing should be done at the base 10 level. If there is a reason for testing the IEEE 754 representation as first choice, then you have yet to convince me of it. Dave Dave, Axiom has the same issues. My take on this is that what you check depends on the reason you are checking. If you are generating the output for human use (e.g. a table) then you want decimal. If you are generating the output for regression testing (e.g. checking the answers on multiple hardware) then you probably want Fateman's solution. Tim -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: doctest failures due to rounding errors on Solaris.
William Stein wrote: On Thu, Dec 31, 2009 at 9:13 PM, Tim Daly d...@axiom-developer.org wrote: Dr. David Kirkby wrote: rjf wrote: On Dec 31, 11:15 am, Dr. David Kirkby david.kir...@onetel.net wrote: RJF The point you are missing is that we want to compare the output what Sage prints to a human. The point you are missing is that the following item, which presumably could be printed by Sage, is perfectly readable to a human: 6121026514868073 * 2^(-51). It exactly dictates the bits in an IEEE double-float, and does not require any conversion from binary to decimal. It does not need rounding. This kind of representation does not have any hidden unprinted digits. It does not ever need to be longer because of delicate edge conditions of certain numbers. It happens to evaluate to APPROXIMATELY 2.718281828459045 Sure, Sage could print that. It would also be worth printing the sign bit, so we could verify the values of 1) Sign bit 2) Significand 3) Exponent. All of those could be correct. But there is still the software which does the non-trivial task of converting that into the base 10 representation used by humans. Then in additon to that, there is the software which takes a base 10 number, shows it with the Sage prompt, adding carriage returns etc where necessary. All of these can go wrong. I would think in an almost ideal world, the test would be done at a higher level, using hardware/software which checked what the monitor actually displayed. That's not quite as easy to do though. Even better would be some way to scan the brain of the user to see what he/she believes Sage is showing. Perhaps we use a font that is not very good, so despite being displayed properly, it misunderstood. Given most of time people want to see a base 10 representation of a number, and not a base 2, base 16 or IEE 754 representation, I believe most testing should be done at the base 10 level. If there is a reason for testing the IEEE 754 representation as first choice, then you have yet to convince me of it. Dave Dave, Axiom has the same issues. My take on this is that what you check depends on the reason you are checking. If you are generating the output for human use (e.g. a table) then you want decimal. If you are generating the output for regression testing (e.g. checking the answers on multiple hardware) then you probably want Fateman's solution. Tim The output is used both for human use and for regression testing. Its primary use is human -- it's an example in the Sage reference manual: sage: float(e) 2.7182818284590451 This is something a user will look at when reading the documentation for some function. It illustrates what happens when they convert the symbolic constant e to float. William And therein lies the problem. We use a regression that does a comparison of the printed representation of the output of the run with a stored copy of the output. All of our regression tests were passing until I installed another, unrelated program. Suddenly about 30 regression tests started failing. It turns out that the unrelated program upgraded one of the system libraries. The net effect of that change was to cause the last digit in the output to wobble so that some of the table values differ in the nth place (20th, 30th, or thereabouts digit). This caused the regression comparisons to fail. Common lisp will give you the exact bit pattern of the float and this value does not wobble so the text comparison succeeds with both the old and the new libraries against the bit pattern. So I can tell you from experience that what you would like to do is not going to succeed. Our solution to the human vs regression problem is to include the stable bit values in the actual compare and keep the human values in a latex table. This is easy to do with literate input. Tim -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] new version of compmath proposal
William Stein wrote: Hi, I've posted a new version of the compmath proposal here: http://wstein.org/grants/compmath09/project_summary.pdf http://wstein.org/grants/compmath09/project_description.pdf http://wstein.org/grants/compmath09/references_cited.pdf This is basically the final version, though I could probably fix some typos. So if you read it and see typos, let me know. If you see anything technically seriously wrong/stupid, also let me know. Thanks, -- William I'm not on the NSF committee to review this but it appears that you are asking for funding for Sage days. One of the innovative Sage days listed for funding is a Bug Smash day. So one of the four days of funding is for debugging work. Am I misreading the proposal? Is a Bug Smash day innovative? If nothing else, you might retitle the day to something else. Believe me, I understand the critical importance of bug smashing to the progress and success of the project. I'm just not sure that the committee might not consider it worth funding. I see a lot of words, like the S-Dyer proposal but I couldn't get funding at CCNY to work on the Andrews-Curtis conjecture from Infinite Group Theory (see http://daly.axiom-developer.org in the bottom right corner) Magnus is the largest Infinite Group Theory project and was originally created through NSF funding. At one point, the funding dried up, about the time I became lead developer, although I'm not sure that correlation implies causation in this case. Tim -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: A Sage NSF proposal to the Computational Mathematics Program
Jaap Spies wrote: mark mcclure wrote: On Nov 23, 3:30 pm, William Stein wst...@gmail.com wrote: That is true. In fact, I hope in the proposal to not insult or snub non-free commercial software either. But William, just two days ago on sage-support you wrote: Let's put Mathworks out of business. http://groups.google.com/group/sage-support/browse_thread/thread/b56450bab6d43bf7/a82a770db1abd6dc#msg_d72f94b7ff856c29 Ever heard of the word humor? Even without a smiley this is possible in a message. Jaap I believe Sage is a very useful piece of software for many people. But I have had numerous discussions (the last one was at the NSF workshop in Rhode Island prior to ECCAD) about funding open source computational mathematics. The definitive statement seems to be: NSF will not fund software development that competes with existing commercial software. I pointed out that nowhere in Axiom's goals was there any sense of competing with commercial software but that response was unheard. But given the definitive reply from NSF I am somewhat surprised that NSF funds Sage at all. -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: A Sage NSF proposal to the Computational Mathematics Program
Is there a plan for what happens if funding is not approved? Do the servers continue? Are the students reassigned? Do the Sage days continue? Does the code move to sourceforge or github? Does this become a free-time only, non-academic activity? Once Sage becomes a non-academic free and open source project there is no hope of getting NSF to pay attention again. (Axiom used to be funded at IBM). Computational mathematics suffers from one critical flaw (which I pointed out to the NSF). Someone in an academic position only gets tenure track credit for published PAPERS. Source code does not count and it is a net loss to write working code if you are on a tenure track. This makes it hard for someone to aspire to a tenure position and also participate effectively in open-source computational math. So if (when) Sage is no longer a hot topic, funded, and a top-of-the-interest-pile for new papers then the momentum slows a bit. NSF funding is critical for keeping the conference papers flowing. Without it there will be no papers and Sage will become venerable software. It is very difficult to run a large open source project with no funding at all. Axiom costs me between $4000 and $5000 per year for hosting costs, equipment, personal travel, free books (I buy old copies of the Axiom book and give them away), etc. So while Axiom is technically free-as-in-beer the reality is that it comes out of my personal budget. I assume that Sage has similar direct and indirect costs. If these are no longer receiving NSF and/or academic funding (e.g. free server hosting) what becomes of the Sage project? Tim -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Axiom trademark and ethics
Hi, I looked at http://www.uspto.gov/teas/e-TEAS/index.html where one can search for trademarks, file a trademark application, etc. It looks like it costs $325. I think filing an application for SageMath would be an appropriate use of Sage foundation funds. There is a search form here: http://tess2.uspto.gov/bin/gate.exe?f=tessstate=4001:pj0t1h.1.1 I've only ever heard of trademarking math software in the context of Tim Daly remarking that Axiom is his registered trademark, so I searched Axiom first and found 103 hits -- the first I clicked on was for Axiom: Providing Christian evangelistic and ministerial services directed towards athletes, athletic coaches and those whom they influence, in the sport of skateboarding. I tried searching Axiom and software (and similar searches) but couldn't find anything about the Axiom math software (I just thought it would be a good example). There are at least 359 registered trademarks that contain the word Sage in them. Searching for just Sage and software yields just 5 or so, including http://tess2.uspto.gov/bin/showfield?f=docstate=4001:pj0t1h.13.29 which is the one for the accounting software. Their description is: Computer software for use in managing accounting and business information, retrieving accounting and business information, viewing accounting and business information, managing contacts and performing accounting functions in the fields of business management, information services, and research systems; computer software for use in electronic commerce to allow users to perform electronic business transactions via a global computer network, electronic mail, Internet website hosting, Internet website development, and Internet access; and accompanying user manual documentation for use with all of the above. If there were a problem trademarking the name Sage, it would I guess be most likely to be because of the accounting software. The word SageMath does not have any entries at all in the trademark database. The point of this email is to discuss: (1) Should we trademark SageMath (pretty obvious yes)? (2) Should we also trademark Sage in the context of math software, if possible? (3) Is there somebody who like legal stuff who is willing to help out with the application? Because I'm not such a person. I'm not in a hurry, but think it's about time to start moving this process forward. I am not a lawyer but I DID speak to a lawyer about the Axiom trademark. The issue of a trademark is to make sure that the mark implies the particular product named. So the trademark is used to identify a particular product and to protect the reputation of that product. You do not want someone posting bugs about Sage that do not apply to your software, thereby possibly damaging the Sage reputation. Since the GPL2 allows all of your code to be cloned, the name IS the project. Trademarks in the United States (I have no idea how this works in the rest of the world...) can be obtained in two ways (according to a trademark lawyer). You can register a trademark or you can use the mark in an exclusive manner for 7 years and obtain a common law trademark. Axiom has been unregistered since NAG dropped the registration in 2000. It has been used in a computer algebra sense to apply to this project since that time. Legally, then, I am the common law holder of the Axiom trademark as it applies to Computer Algebra software (there are, as you have noticed, hundreds of 'Axiom' trademarks in different areas). In either case, in order to keep a trademark, you need to defend against any and all infringing uses of the mark or you might lose it. You also need to keep the mark current with active use, which Axiom does. Keeping or losing a trademark does not depend on registration. Registration makes it easier to show that you are the holder but you can still lose the mark if it is not actively defended. My campaign with Sage to stop using the name Axiom as a command to invoke Fricas was part of the necessary defense of the mark. The Axiom BSD license is copyright-based and allows forking the code but not use of the name. Trademark is a different area of intellectual property law and nothing in the GPL2 or BSD license allows infringing of a trademark. You'll have the same problems when defending Sage. I have sent you notes about the use of Sage in the area of mathematics when I have found other math software using the same name. If another math software project uses the same name you would have to show that you were using it first. Even then you might not be able to be able to defend the name. If you want a trademark you will need a unique name in the field of use and you will need to defend it. Registration is little more than publicly stating ownership but it is not required. I hated consulting a real, live lawyer. It costs me time and money I'd rather not have spent. But at this point I am reasonably certain that I
[sage-devel] Re: Categories restart: call for reviewers
Nicolas Do you have the inheritance graph of the categories? Tim Daly Nicolas M. Thiery wrote: Hi John! On Sun, Aug 23, 2009 at 12:37:11PM +0100, John Cremona wrote: 2009/8/23 Nicolas M. Thiery nicolas.thi...@u-psud.fr: So you can focus on looking at the code, doc, and tests in the files mentioned in: http://trac.sagemath.org/sage_trac/wiki/CategoriesCategoriesReview possibly simply by browsing: http://combinat.sagemath.org/hgwebdir.cgi/code/file/tip/sage/categories) and make sure they makes sense. I don't really know how this type of reviewing differs from normal Sage reviewing of patches attached to trac tickets. Just that you don't need to worry about the technical side (checking that the patch applies, pass test, ...). Also setting a positive review will be on the wiki page, file by file, rather than on the trac ticket. Finally, there is essentially no datastructure/algorithm issue in the current code (that will change!) But anyway, I looked at one file, finite_fields.py, and the method _call_() in there looks wrong -- it raises an error whatever the input, while the dicstring suggests that it is supposed to try using __call__() and only change the error message if that does not work. It's the converse: __call__ tries to do generic stuff (like C(P) returns P if P is readilly a parent in the category C), and if that does not work calls _call_ (similar to what happens for __mul__ / _mul). I actually haven't changed that part; that's how it is in the original category framework. See the doc of _call_ / __call__ in Category (sage.category.category.py). Suggestions to improve the doctests to clarify this are welcome! If I have completely misunderstood what is going on, then I will carry on ignoring the category activity until it is finished, Please don't! at which point I'm sure I will use it all the time! Which is why I want as much early feedback from you as possible :-) Cheers, Nicolas -- Nicolas M. Thiéry Isil nthi...@users.sf.net http://Nicolas.Thiery.name/ --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Sage build failure
The install.log file is at http://daly.axiom-developer.org/install.log This fails on fedora 5 [EMAIL PROTECTED] sage-3.0]# uname -a Linux localhost.localdomain 2.6.18-1.2239.fc5 #1 Fri Nov 10 13:04:06 EST 2006 i686 i686 i386 GNU/Linux You have new mail in /var/spool/mail/root [EMAIL PROTECTED] sage-3.0]# cat /proc/cpuinfo processor : 0 vendor_id : GenuineIntel cpu family : 6 model : 14 model name : Genuine Intel(R) CPU T2050 @ 1.60GHz stepping: 8 cpu MHz : 1595.293 cache size : 2048 KB fdiv_bug: no hlt_bug : no f00f_bug: no coma_bug: no fpu : yes fpu_exception : yes cpuid level : 10 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat clflush dts acpi mmx fxsr sse sse2 ss nx constant_tsc pni bogomips: 3233.79 building 'sage.modules.real_double_vector' extension gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DGSL_DISABLE_DEPRECATED=1 -I/research/sage-3.0/local/lib/python2.5/site-packages/numpy/core/include/numpy -I/research/sage-3.0/local//include -I/research/sage-3.0/local//include/csage -I/research/sage-3.0/devel//sage/sage/ext -I/research/sage-3.0/local/include/python2.5 -c sage/modules/real_double_vector.c -o build/temp.linux-i686-2.5/sage/modules/real_double_vector.o -w -w sage/modules/real_double_vector.c: In function '__pyx_pf_4sage_7modules_18real_double_vector_28RealDoubleVectorSpaceElement___init__': sage/modules/real_double_vector.c:2014: internal compiler error: in merge_alias_info, at tree-ssa-copy.c:235 Please submit a full bug report, with preprocessed source if appropriate. See URL:http://bugzilla.redhat.com/bugzilla for instructions. Preprocessed source stored into /tmp/ccwUCwx8.out file, please attach this to your bugreport. error: command 'gcc' failed with exit status 1 sage: There was an error installing modified sage library code. ERROR installing SAGE real13m47.698s user11m26.741s sys 2m9.727s sage: An error occurred while installing sage-3.0 Please email sage-devel http://groups.google.com/group/sage-devel explaining the problem and send the relevant part of of /research/sage-3.0/install.log. Describe your computer, operating system, etc. If you want to try to fix the problem, yourself *don't* just cd to /research/sage-3.0/spkg/build/sage-3.0 and type 'make'. Instead type /research/sage-3.0/sage -sh in order to set all environment variables correctly, then cd to /research/sage-3.0/spkg/build/sage-3.0 (When you are done debugging, you can type exit to leave the subshell.) make[1]: *** [installed/sage-3.0] Error 1 make[1]: Leaving directory `/research/sage-3.0/spkg' real150m43.177s user74m23.338s sys 69m26.373s --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Sage 3.0 notebook fails to display
On a clean build (see specs below) (log is at http://daly.axiom-developer.org/install.log) ./sage sage: notebook() on Fedora 8 86_64 on processor : 0 vendor_id : AuthenticAMD cpu family : 15 model : 104 model name : AMD Athlon(tm) 64 X2 Dual-Core Processor TK-57 stepping: 2 cpu MHz : 1900.113 cache size : 256 KB fpu : yes fpu_exception : yes cpuid level : 1 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 syscall nx mmxext fxsr_opt rdtscp lm 3dnowext 3dnow up rep_good pni cx16 lahf_lm extapic misalignsse bogomips: 3803.70 TLB size: 1024 4K pages clflush size: 64 cache_alignment : 64 address sizes : 36 bits physical, 48 bits virtual power management: ts fid vid ttp tm stc 100mhzsteps this opens Firefox (version 2.0.0.8) to: https://:8000/?startup_token=(long hex string) and says Server not found tar -xf sage-3.0.tar [EMAIL PROTECTED] sage]# cd sage-3.0 [EMAIL PROTECTED] sage-3.0]# make cd spkg ./install all 21 | tee -a ../install.log make[1]: Entering directory `/space/sage/sage-3.0/spkg' . Host system uname -a: Linux localhost.localdomain 2.6.23.1-42.fc8 #1 SMP Tue Oct 30 13:18:33 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux GCC Version gcc -v Using built-in specs. Target: x86_64-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --with-cpu=generic --host=x86_64-redhat-linux Thread model: posix gcc version 4.1.2 20070925 (Red Hat 4.1.2-33) I tried sage: hg_sage.pull() sage: hg_sage.update() sage: hg_sage.merge() but it says there is nothing to merge. Tim --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Approximating Ei using polynomials
The AS handbook lists polynomial coefficients for approximation of E1, the exponential integral. Does anyone know how these coefficients were derived? Is it a chebyshev polynomial? I want to dynamically compute these coefficients to the required precision. Tim --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://sage.scipy.org/sage/ and http://modular.math.washington.edu/sage/ -~--~~~~--~~--~--~---
[sage-devel] Axiom and the Numerical Mathematics Consortium
I have been concentrating on Axiom's numerical capabilities. I am making a set of regression tests against the published values in Abramowitz and Stegun (1965). You might find it interesting to run these same tests in Sage. I can send them to anyone who would like to volunteer. They are basically the published table values versus the computed values. For instance, one row reads: [0.01, 0.00841468254, sin(0.01), sin(0.01)-0.00841468254] where the first entry is the point, the second entry is the AS table value, the third entry is a function call, and the fourth entry is the computed difference. I'm a member of the Numerical Mathematics Consortium (http://www.nmconsortium.org).A recently published draft standard, which I'm reviewing, is available at: http://www.nmconsortium.org/docs/NMC_Technical_Specification%20(9-24-2007).pdf You might find it useful to track these standards. Tim --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://sage.scipy.org/sage/ and http://modular.math.washington.edu/sage/ -~--~~~~--~~--~--~---
[sage-devel] Two Computational Mathematics Job Openings
City College of New York (my prior place of employment) and the Center for Algorithms and Interactive Scientific Software (CAISS) has two tenure track job openings. Headed by Gilbert Baumslag, the designer of Magnus http://sourceforge.net/projects/magnus, this is a group dedicated to computational mathematics. There is a strong emphasis on group-theoretic work, as Dr. Baumslag is the leading expert in infinite group theory. Dr. Baumslag has invented and reduced to practice a new interface idea called the zero learning curve front end. It changes the way users think about solving problems, allows parallel computations naturally, and, as you'd expect from the title, is trivial to learn. As a former employee I can highly recommend the people and the working environment. There are many visitors to the group who are known worldwide so there are many interesting connections. Visit http://grouptheory.org Tim Daly --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Axiom and Sage
Well,per your request, I logged in to the Sage VM and did sage -f fricas-0.3.1 simply hangs. However, sage -f axiom4sage-0.3.1 succeeds and shows a total time of real 18m42 or, if I include network time real 19.6 which is about the wall-clock time. So there appears to be a suggestion that it might be a good idea to do package installs directly rather than thru the notebook interface. Potentially this could be due to the large amount of screen output. Apparently the package rename didn't work. Tim --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://sage.scipy.org/sage/ and http://modular.math.washington.edu/sage/ -~--~~~~--~~--~--~---
