[sage-devel] High level architectural design document of Sage

2012-11-30 Thread Wai Man Chung
Hi, I am new to Sage and I am interested to participate in the development work of Sage. I would like to understand the codes of Sage. I would like to know if there is any high level architectural design document on Sage. I can find fragments of information related to this, e.g. - Sage use so

[sage-devel] Application specific module in Sage

2012-11-30 Thread Wai Man Chung
Hi, I would like to know if Sage will go to implement some specific module for application ? e.g. Signal processing, Bioinformatics, Queuing networks, computational linguistics, etc. I think implementation of modules in specific areas is worthy to consider. Currently I do find some in the ma

[sage-devel] Re: Testing new MPIR spkg on old Mac OSX

2012-11-30 Thread Dima Pasechnik
On 2012-12-01, Greg McWhirter wrote: > --=_Part_1437_25379457.1354339928090 > Content-Type: text/plain; charset=ISO-8859-1 > > It is a few years old. I don't know if that qualifies it as "old" or not. > It has dual quad-core Intel Xeons in it I believe. what does Apple's "about this mac" tel

[sage-devel] Re: Testing new MPIR spkg on old Mac OSX

2012-11-30 Thread Greg McWhirter
It is a few years old. I don't know if that qualifies it as "old" or not. It has dual quad-core Intel Xeons in it I believe. The i7 may be an artifact of what the 5.0 binary was built on. The 5.4.1 source attempt thinks the processor is core2 to the best of my ability reading the logs. - Greg

[sage-devel] Re: Testing new MPIR spkg on old Mac OSX

2012-11-30 Thread Dima Pasechnik
On 2012-12-01, Greg McWhirter wrote: > --=_Part_1340_24540346.1354327647430 > Content-Type: text/plain; charset=ISO-8859-1 > > It does error out similarly. I tried it both on a clean source download of > sage 5.4.1 (forced to use the OS X gcc 4.2 instead of the 4.0.1) and a > working binary

[sage-devel] Re: Normalization of a vector

2012-11-30 Thread Keshav Kini
Kannappan Sampath writes: > Perhaps, I should explain my rationale for the terms I chose, my > first preference is `echelonize(v)`  (although I wrote it second) > because, what the function returns amounts to its reduced row echelon > form, if you think of it as 1 x n matrix.  My rationale for "m

[sage-devel] Re: Testing new MPIR spkg on old Mac OSX

2012-11-30 Thread Greg McWhirter
It does error out similarly. I tried it both on a clean source download of sage 5.4.1 (forced to use the OS X gcc 4.2 instead of the 4.0.1) and a working binary download of sage 5.0 (using sage's gcc 4.6.3). Log snips are at the end. - Greg Snip from 5.0: /bin/sh ../libtool --tag=CC --mode=

[sage-devel] Re: Testing new MPIR spkg on old Mac OSX

2012-11-30 Thread Jean-Pierre Flori
On Saturday, December 1, 2012 1:57:38 AM UTC+1, Greg McWhirter wrote: > > Ah, yes. It was with the older 2.4 (2.4.0.p6). I should have confirmed > that it was the same one before replying. Sorry for the potential confusion > there. > > At any rate, the last bits of the log are appended below (a

[sage-devel] Re: Testing new MPIR spkg on old Mac OSX

2012-11-30 Thread Greg McWhirter
Ah, yes. It was with the older 2.4 (2.4.0.p6). I should have confirmed that it was the same one before replying. Sorry for the potential confusion there. At any rate, the last bits of the log are appended below (and if you need more, let me know). I'd be happy to help test future changes as wel

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

2012-11-30 Thread Benjamin Jones
On Fri, Nov 30, 2012 at 3:57 PM, Eviatar wrote: > I think echelonize is a bit misleading, because it's not really doing > Gaussian elimination. Besides, I think it would have to be rref to be > consistent with matrices (it's reduced row echelon form, not simply row > echelon form): > > sage: matr

[sage-devel] Re: Inverting elements of polynomial_modn_dense_ntl

2012-11-30 Thread Jean-Pierre Flori
On Friday, November 30, 2012 11:23:55 PM UTC+1, Michael Orlitzky wrote: > > I accidentally noticed that most of the doctests for this module were > testing the flint implementation instead: > > http://trac.sagemath.org/sage_trac/ticket/13781 > > The patch is straight-forward, but there's a hi

[sage-devel] Re: Testing new MPIR spkg on old Mac OSX

2012-11-30 Thread Jean-Pierre Flori
On Friday, November 30, 2012 10:55:12 PM UTC+1, Greg McWhirter wrote: > > Unfortunately (for me at least) it is still broken as of this morning. I > was unable to compile 4.5.1 or upgrade from 5.0 as a result on 10.5. hat > information would be useful for potentially pursuing a fix? > > - Greg

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

2012-11-30 Thread Eviatar
I think echelonize is a bit misleading, because it's not really doing Gaussian elimination. Besides, I think it would have to be rref to be consistent with matrices (it's reduced row echelon form, not simply row echelon form): sage: matrix([0,3,4]).echelon_form() [0 3 4] sage: matrix([0,3,4]).r

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

2012-11-30 Thread Benjamin Jones
On Fri, Nov 30, 2012 at 1:36 PM, Eviatar wrote: > Hello, > > I was planning to work on the patch for this; however, is "normal form" > known terminology for dividing a vector by the leading entry? A Google > search returns no such use. Wouldn't it be better for it to be named > something like div

[sage-devel] Inverting elements of polynomial_modn_dense_ntl

2012-11-30 Thread Michael Orlitzky
I accidentally noticed that most of the doctests for this module were testing the flint implementation instead: http://trac.sagemath.org/sage_trac/ticket/13781 The patch is straight-forward, but there's a hidden issue that the doctests should have caught: sage: R. = PolynomialRing(Integers(101

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

2012-11-30 Thread Kannappan Sampath
Perhaps, I should explain my rationale for the terms I chose, my first preference is `echelonize(v)` (although I wrote it second) because, what the function returns amounts to its reduced row echelon form, if you think of it as 1 x n matrix. ~KnS. On Sat, Dec 1, 2012 at 3:47 AM, Keshav Kini wr

[sage-devel] Re: Normalization of a vector

2012-11-30 Thread Jason Grout
On 11/30/12 3:36 PM, Eviatar wrote: I was planning to work on the patch for this; however, is "normal form" known terminology for dividing a vector by the leading entry? A Google search returns no such use. Wouldn't it be better for it to be named something like divided_by_leading, to remove ambi

[sage-devel] Re: Normalization of a vector

2012-11-30 Thread Keshav Kini
Kannappan Sampath writes: > Here's a "natural" place where I can see this is helpful:  > > To carry out, Gauss-Jordan like row reductions, where you'd like the > first non-zero entry in a row (the so-called pivot) to be 1, I think > this is very helpful. > > So, I'd be **for** keeping this, perhap

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

2012-11-30 Thread Kannappan Sampath
Here's a "natural" place where I can see this is helpful: To carry out, Gauss-Jordan like row reductions, where you'd like the first non-zero entry in a row (the so-called pivot) to be 1, I think this is very helpful. So, I'd be **for** keeping this, perhaps in a different name, that would reflec

[sage-devel] hg.sagemath.org server error

2012-11-30 Thread Keshav Kini
Hi, The sage-root repo seemingly isn't being served correctly, as the following URL returns an HTTP 500: http://hg.sagemath.org/sage-root/ -Keshav -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To post to this group, send email to sage-devel@g

[sage-devel] Re: Testing new MPIR spkg on old Mac OSX

2012-11-30 Thread Greg McWhirter
Unfortunately (for me at least) it is still broken as of this morning. I was unable to compile 4.5.1 or upgrade from 5.0 as a result on 10.5. hat information would be useful for potentially pursuing a fix? - Greg McWhirter -- You received this message because you are subscribed to the Google

[sage-devel] Re: Normalization of a vector

2012-11-30 Thread Eviatar
Hello, I was planning to work on the patch for this; however, is "normal form" known terminology for dividing a vector by the leading entry? A Google search returns no such use. Wouldn't it be better for it to be named something like divided_by_leading, to remove ambiguity and potential confus

Re: [sage-devel] Re: License issues if linking Mathematica and Sage

2012-11-30 Thread David Kirkby
On 30 November 2012 15:53, kcrisman wrote: > > > On Friday, November 30, 2012 6:36:32 AM UTC-5, Dr. David Kirkby wrote: >> >> It's clear there might be legal issues if Mathematica linked to Sage >> using Mathlink, so I was thinking of sending the email below to both >> the FSF and Wolfram Research

Re: [sage-devel] Re: License issues if linking Mathematica and Sage

2012-11-30 Thread David Kirkby
On 30 November 2012 17:35, Keshav Kini wrote: > David Kirkby writes: >> Sage >> >> http://www.sagemath.org/ >> >> is an open-source mathematical package released under the GPL version >> 2, or if the user wishes, any later version of the GPL. > > Well, according to William as of October 2011 in a

[sage-devel] Re: [sage-support] Typo in documentation of free modules

2012-11-30 Thread kcrisman
On Friday, November 30, 2012 1:21:13 PM UTC-5, KnS wrote: > > This is trac #13780 now. Thanks Philipp for reporting here. (I'll submit a > patch now; but, I am ccing to the sage-devel to ask if issues that are so > trivial to fix but still can be considered major, deserve a separate > ticket).

[sage-devel] Re: [sage-support] Typo in documentation of free modules

2012-11-30 Thread Kannappan Sampath
This is trac #13780 now. Thanks Philipp for reporting here. (I'll submit a patch now; but, I am ccing to the sage-devel to ask if issues that are so trivial to fix but still can be considered major, deserve a separate ticket). Thank you, ~KnS On Wed, Nov 28, 2012 at 11:54 PM, Philipp Kerling wr

Re: [sage-devel] License issues if linking Mathematica and Sage

2012-11-30 Thread Andrea Lazzarotto
2012/11/30 David Kirkby > Sage is an open-source mathematical package released under the GPL > I forgot one thing: FSF will kill all of your family if you use the term "open source". IMHO you should use "free software" so they're happy. Best regards, -- *Andrea Lazzarotto* - http://andrealazz

[sage-devel] Re: License issues if linking Mathematica and Sage

2012-11-30 Thread Keshav Kini
David Kirkby writes: > Sage > > http://www.sagemath.org/ > > is an open-source mathematical package released under the GPL version > 2, or if the user wishes, any later version of the GPL. Well, according to William as of October 2011 in an email to me: > The complete Sage distribution is GPLv3

Re: [sage-devel] Re: License issues if linking Mathematica and Sage

2012-11-30 Thread Andrea Lazzarotto
2012/11/30 kcrisman > I guess I don't see the point. Are we really thinking Wolfram would want > to do that? I agree. Also, probably the FSF doesn't care a lot about this because basically they exclude the possibility of existence of any nonfree software... -- *Andrea Lazzarotto* - http://an

[sage-devel] Re: Crash in graph_generators with MALLOC_CHECK_=3

2012-11-30 Thread Jean-Pierre Flori
On Friday, November 30, 2012 5:21:24 PM UTC+1, Simon King wrote: > > Hi! > > I don't know if the following is related with the recently discussed > problems in the graph backend or whether it is from one of my dreaded > "fix memleaks by weak caching" patches - can experts please have a > look

Re: [sage-devel] Documentation problems

2012-11-30 Thread John H Palmieri
On Friday, November 30, 2012 8:11:11 AM UTC-8, Nicolas M. Thiéry wrote: > > On Fri, Nov 16, 2012 at 08:29:16PM -0800, Andrew Mathas wrote: > >To build the documentation I typically use something like > >sage -b && sage --docbuild reference html > >Often this works without a hitch a

[sage-devel] Crash in graph_generators with MALLOC_CHECK_=3

2012-11-30 Thread Simon King
Hi! I don't know if the following is related with the recently discussed problems in the graph backend or whether it is from one of my dreaded "fix memleaks by weak caching" patches - can experts please have a look at #13779 ? The problem: If one does "export MALLOC_CHECK_=3", then the tests for

Re: [sage-devel] Documentation problems

2012-11-30 Thread Nicolas M. Thiery
On Fri, Nov 16, 2012 at 08:29:16PM -0800, Andrew Mathas wrote: >To build the documentation I typically use something like >sage -b && sage --docbuild reference html >Often this works without a hitch and just as often I get numerous warnings >like >categories.rst:44: WARNING: toc

Re: [sage-devel] Re: mathematica 9

2012-11-30 Thread Harald Schilly
On Fri, Nov 30, 2012 at 4:57 PM, kcrisman wrote: > I did NOT like rpy/rpy2 syntax, so something preferable to that would be > helpful. Yes, it's not so nice, but for me it seems to be quite stable and helpful. What - in my eyes - also need some mentioning is scikit.learn: http://scikit-learn.org

[sage-devel] Re: mathematica 9

2012-11-30 Thread kcrisman
On Friday, November 30, 2012 7:28:55 AM UTC-5, Volker Braun wrote: > > Also, if you look at the statsmodels dependency list (NumPy, SciPy, > Pandas, Cython, Matplotlib) it seems like it (together with Pandas) would > fit nicely into our infrastructure. In fact, I think statistics is an area >

[sage-devel] Re: License issues if linking Mathematica and Sage

2012-11-30 Thread kcrisman
On Friday, November 30, 2012 6:36:32 AM UTC-5, Dr. David Kirkby wrote: > > It's clear there might be legal issues if Mathematica linked to Sage > using Mathlink, so I was thinking of sending the email below to both > the FSF and Wolfram Research. Any comments? > > I guess I don't see the point

[sage-devel] Re: Testing new MPIR spkg on old Mac OSX

2012-11-30 Thread Jean-Pierre Flori
On Friday, November 30, 2012 3:50:43 PM UTC+1, Dima Pasechnik wrote: > > On 2012-11-30, Jean-Pierre Flori > wrote: > > --=_Part_1212_10818395.1354274078891 > > Content-Type: text/plain; charset=ISO-8859-1 > > > > Dear all, > > > > While updating MPIR in #13137, we remarked the old fix f

[sage-devel] Re: Testing new MPIR spkg on old Mac OSX

2012-11-30 Thread Dima Pasechnik
On 2012-11-30, Jean-Pierre Flori wrote: > --=_Part_1212_10818395.1354274078891 > Content-Type: text/plain; charset=ISO-8859-1 > > Dear all, > > While updating MPIR in #13137, we remarked the old fix for compilation on > OSX 10.4 (and maybe 10.5) running in 32 bit mode on 64 bit Intel hardware

[sage-devel] Re: mathematica 9

2012-11-30 Thread Volker Braun
Also, if you look at the statsmodels dependency list (NumPy, SciPy, Pandas, Cython, Matplotlib) it seems like it (together with Pandas) would fit nicely into our infrastructure. In fact, I think statistics is an area where Sage is lagging. On Friday, November 30, 2012 12:04:20 PM UTC, jason wr

Re: [sage-devel] Re: mathematica 9

2012-11-30 Thread Harald Schilly
On Fri, Nov 30, 2012 at 1:04 PM, Jason Grout wrote: > http://pandas.pydata.org/ > > ... Also, the > statsmodel package deserves mention: http://statsmodels.sourceforge.net/. Yes, 100% ack. Google Summer of Code 2013 is coming soon, i.e. Dec. 1st is my (personal) reminder to start digging into tha

[sage-devel] Re: mathematica 9

2012-11-30 Thread Jason Grout
On 11/30/12 5:02 AM, Harald Schilly wrote: On Thursday, November 29, 2012 4:35:08 PM UTC+1, Dr. David Kirkby wrote: Unfortunately, I've never been that impressed with pexpect. Just for the record, over here in the "Python world", we already have rpy2. Here is a link to the introduction o

Re: [sage-devel] Re: mathematica 9

2012-11-30 Thread David Kirkby
On 29 November 2012 09:45, Andrea Lazzarotto wrote: > BTW the fact they also started to copy Sage features (such as R integration) > is a clear signal. > > Best regards, > > -- > Andrea Lazzarotto - http://andrealazzarotto.com You might just as well say the fact that * Sage has copied Mathemati

[sage-devel] License issues if linking Mathematica and Sage

2012-11-30 Thread David Kirkby
It's clear there might be legal issues if Mathematica linked to Sage using Mathlink, so I was thinking of sending the email below to both the FSF and Wolfram Research. Any comments? = Hi, I would like to seek some clarification on software license conditions. Since this affects Wolfra

[sage-devel] Testing new MPIR spkg on old Mac OSX

2012-11-30 Thread Jean-Pierre Flori
Dear all, While updating MPIR in #13137, we remarked the old fix for compilation on OSX 10.4 (and maybe 10.5) running in 32 bit mode on 64 bit Intel hardware was not maintained properly and does not do what it was supposed to do anymore. This is not so bad because it seems to indicate that the

Re: [sage-devel] mathematica 9

2012-11-30 Thread Harald Schilly
On Thursday, November 29, 2012 4:35:08 PM UTC+1, Dr. David Kirkby wrote: > > Unfortunately, I've never been that impressed with pexpect. > Just for the record, over here in the "Python world", we already have rpy2. Here is a link to the introduction of the latest stable version: http://rpy.sou

Re: [sage-devel] Re: which letter to use for the universal cyclotomics ?

2012-11-30 Thread Christian Stump
Hi, I implemented the desired changes and updated the ticket (and actually got a "green" for the very first time!). The patch is again for review, and I would appreciate if some of the people contributed to the discussion would check if the requested changes are implemented the way they wanted it