[sage-devel] Re: European Horizon 2020 project OpenDreamKit accepted

[P Purkayastha]

Congratulations to everyone involved!

Cheers,
  basu.

On Wednesday, May 20, 2015 at 5:47:27 AM UTC+8, Nicolas M. Thiéry wrote:
>
>Dear Sage developers, 
>
> We are delighted to announce that the Horizon 2020 research proposal 
> OpenDreamKit was accepted by the European commission: 
>
> opendreamkit.org 
>
> Starting next Fall and for four years, this project will provide 
> substantial funding to the open source computational mathematics 
> ecosystem, and in particular popular tools such as LinBox, MPIR, 
> SageMath, GAP, Pari/GP, LMFDB, Singular, and the IPython/Jupyter 
> interactive computing environment. 
>
> The total budget is about 7.6 million euros. The largest portion of 
> that will be devoted to employing an average of 11 researchers and 
> developers working full time on the project in Europe. We will 
> announce job openings in the coming weeks; stay tuned! 
>
> Additionally, the participants will contribute the equivalent of six 
> other people working full time. Altogether the project involves about 
> 50 people spread over 15 sites in Europe. 
>
> This is a formidable recognition of the strength and maturity of this 
> ecosystem, of the power of open source development models, and of the 
> amazing hard work of many communities over the last decades. 
>
> The writing of the proposal itself was open and collaborative. It grew 
> out of a reflection on the long term needs of the community. It 
> benefited considerably from the feedback of many; we would like to 
> thank all those who helped shape this proposal and make it happen. 
>
> It is our hope that this financial support will help push forward 
> critical technical tasks. We tried hard in the proposal to make a 
> worthwhile selection of such tasks, within some constraints imposed by 
> the specific call. We are now legally committed to treat those tasks 
> in priority. This kind of long term prediction work is tough: one of 
> them has actually already been completed by the community in the mean 
> time! This is great; whenever this will happen we will be able 
> reprioritize the resources to whatever emerging needs that will arise. 
>
> Ultimately, this project belongs to the community. Get involved! 
>
> Cheers, 
> Nicolas 
> -- 
> Nicolas M. Thiéry "Isil" > 
> http://Nicolas.Thiery.name/ 
>

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Re: [sage-devel] Re: "Wrong results" or "Bad input" ?

[P Purkayastha]

On 03/07/2015 10:16 AM, William Stein wrote:

On Fri, Mar 6, 2015 at 6:10 PM, Michael Orlitzky  wrote:
> On 03/06/2015 08:10 PM, P Purkayastha wrote:
>>>
>>>
>> This is a serious bug. Is there a ticket for this?
>>
>
> It sort of falls under this one:
>
>http://trac.sagemath.org/ticket/7392
>
> even though a fix for that ticket might not affect some similar examples.

If you change the definition of rank, make sure to not do the
following, like I just thought I should do for a few minutes:

sage: n = matrix([ [-0.3, 0.2, 0.1], [0.2, -0.4, 0.4], [0.1, 0.2, -0.5] ])
sage: a = n.numpy()
sage: import numpy
sage: numpy.rank(a)
2

It looks right... but it's 2 because it's a 2-dimensional array :-)

sage: numpy.rank(numpy.zeros((1,2,4)))
3

Anyway, now you see how numerical people use the word "rank"...

William




Well, something is clearly very wrong with either rank() or with ==. Since the 
matrices can be changed from one ring to another and they give True on equality 
it makes no sense for them to give different ranks.



I don't think a typical user wants to go deep into mathematics and try to 
figure out what should be the correct way to determine the rank of a matrix. It 
should give the correct answer. Otherwise the method should be removed from 
fields that can give incorrect results.

sage: m.change_ring(RDF)
[-0.3  0.2  0.1]
[ 0.2 -0.4  0.4]
[ 0.1  0.2 -0.5]
sage: n.change_ring(QQ)
[-3/10   1/5  1/10]
[  1/5  -2/5   2/5]
[ 1/10   1/5  -1/2]
sage: m.change_ring(RDF).rank()
3
sage: n.change_ring(QQ).rank()
2

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Re: [sage-devel] Re: "Wrong results" or "Bad input" ?

[P Purkayastha]

On Saturday, March 7, 2015 at 6:48:46 AM UTC+8, Michael Orlitzky wrote:
>
> On 03/06/2015 04:51 PM, Travis Scrimshaw wrote: 
> >Yet this stopgap is not in a class in the global namespace, but a 
> > low-level class that almost always gets passed valid input. I am for 
> having 
> > checks for valid input (and most of the time it does error out), but 
> there 
> > is only one place I know of in the global namespace that can get invalid 
> > input ( Partitions(k, max_slope=m) with m >= 0 ). We have *years* of 
> > testing code which does pass valid input into IntegerListsLex that gives 
> > correct results (and it sometimes works on invalid input as well). 
> > 
> > Here are some tickets where Sage silently returns invalid results (from 
> 2 
> > minutes of looking through the bugs): 
> > 
>
> This might be the first bug I ever reported: 
>
>   sage: m = matrix([ [(-3/10), (1/5), (1/10)], 
>   : [(1/5), (-2/5), (2/5)], 
>   : [(1/10), (1/5), (-1/2)] ]) 
>   sage: 
>   sage: n = matrix([ [-0.3, 0.2, 0.1], 
>   : [0.2, -0.4, 0.4], 
>   : [0.1, 0.2, -0.5] ]) 
>   sage: 
>   sage: m.rank() 
>   2 
>   sage: n.rank() 
>   3 
>   sage: m == n 
>   True 
>
>
This is a serious bug. Is there a ticket for this? 

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[sage-devel] Let's encrypt

[P Purkayastha]

Hello devs,

  I hope someone here knows how the certificate system works for https
connections.

  I am raising this question because of the "Let's Encrypt" announcement
[1] made by EFF last month. It would make it easier to recommend the secure
mode for the sage notebook. Currently, all browsers give a big fat warning
if the notebook is started in secure mode.

[1]
https://www.eff.org/deeplinks/2014/11/certificate-authority-encrypt-entire-web

  Cheers,
 basu.

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[sage-devel] Re: Do we have a make target to clean upstream directory?

[P Purkayastha]

It is hard enough to clean it properly. If you have ideas, please 
see http://trac.sagemath.org/ticket/16327

On Monday, November 24, 2014 10:41:17 PM UTC+8, kcrisman wrote:
>
>
> As time goes it gets bigger and bigger...
>>
>
> +1 (only if it is documented properly!)
>  
>

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Re: [sage-devel] Code of Conduct

[P Purkayastha]

On Sun Nov 16 2014 at 12:44:39 AM Anne Schilling 
wrote:

> On 11/15/14 7:32 AM, P Purkayastha wrote:
> >
> >
> > On Friday, November 14, 2014 8:50:14 PM UTC+8, Dr. David Kirkby (Kirkby
> Microwave Ltd) wrote:
> >
> > On 13 November 2014 18:48, Volker Braun  > wrote:
> > > and welcome everyone to
> > > vote on it.
> > >
> > >
> > > Code of Conduct
> > > ---
> >
> > > If you believe someone is violating the code of conduct, we ask
> that you
> > > report it by emailing sage-...@googlegroups.com .
> The group administrators
> > > will consider the issue and explore resolutions.
> >
> > What will be the background of the "group administrators", and the
> > people who receive posts from sage-...@googlegroups.com
> ?
> >
> > Are these people going to have a background in human resources and/or
> > be trained in this area?
> >
> > Dave
> >
> >
> > You can just follow some guidelines. I am a member of the Gentoo Linux
> forums and they have very clear statements saying what is considered
> inappropriate in the forums. In gist,
> >
> > 1. No personal attacks,
> > 2. No offensive language
> >
> > The guidelines are quite comprehensive and I think it helps keep the
> forum in general very civil and helpful.
> >
> > Reference:
> > I) Guidelines for the forums: http://forums.gentoo.org/
> viewtopic-t-525.html
> > II) Guidelines for a less moderated subforum: http://forums.gentoo.org/
> viewtopic-t-120351.html
>
> Thanks for the links to the guidelines. It is interesting to see how other
> communities handle this.
> Dave's question was how situations will be handled when a violation occurs
> or that are reported.
> Does your community have experience with this?
>
> Best,
>
> Anne
>

Yes. Typically, they ban the user for a period of time. The violations are
dealt with on a case-by-case basis. It seems quite a few requests (code of
conduct violations, and otherwise) have piled up in
http://forums.gentoo.org/viewtopic-t-28820.html !

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Re: [sage-devel] Code of Conduct

[P Purkayastha]

On Friday, November 14, 2014 8:50:14 PM UTC+8, Dr. David Kirkby (Kirkby 
Microwave Ltd) wrote:
>
> On 13 November 2014 18:48, Volker Braun > 
> wrote: 
> > and welcome everyone to 
> > vote on it. 
> > 
> > 
> > Code of Conduct 
> > --- 
>
> > If you believe someone is violating the code of conduct, we ask that you 
> > report it by emailing sage-...@googlegroups.com . The 
> group administrators 
> > will consider the issue and explore resolutions. 
>
> What will be the background of the "group administrators", and the 
> people who receive posts from sage-...@googlegroups.com ? 
>
> Are these people going to have a background in human resources and/or 
> be trained in this area? 
>
> Dave 
>

You can just follow some guidelines. I am a member of the Gentoo Linux 
forums and they have very clear statements saying what is considered 
inappropriate in the forums. In gist,

1. No personal attacks,
2. No offensive language

The guidelines are quite comprehensive and I think it helps keep the forum 
in general very civil and helpful. 

Reference:
I) Guidelines for the forums: http://forums.gentoo.org/viewtopic-t-525.html
II) Guidelines for a less moderated subforum: 
http://forums.gentoo.org/viewtopic-t-120351.html


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[sage-devel] Typesetting maths - KaTeX

[P Purkayastha]

Might be interesting to keep an eye on this: http://khan.github.io/KaTeX
They claim to be faster than MathJax and also avoid page reflows.

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Re: [sage-devel] Re: Lists of sets S such that f(S)=1 somewhat efficiently (where should I write this function ?)

[P Purkayastha]

Put the function in combinat or sets? Apparently it is not just restricted
to coding theory or some other specific structure.
On 14 Sep, 2014 7:41 pm, "Nathann Cohen"  wrote:

> By the way, no idea about where I should write that in Sage ? :-/
>
> Nathann
>
> On 14 September 2014 13:19, Nathann Cohen  wrote:
> > Yo !
> >
> >> this is only one of the current trends - other ones argue that
> algorithms
> >> should be accompanied by implementations, and then there is a lot of
> things done
> >> on polynomial-time algorithms.
> >
> > Well, it should at the very least be implemented (with commented code)
> > indeed. It would also be cool if people cared about the actual
> > comutation times: using bitsets does not change anything
> > asymptotically but it does make a difference in the running times.
> >
> >> Anyhow, one speedup can come from your function being invariant under
> some
> >> permutations of variables; perhaps you can check this quickly.
> >
> > Does not apply to my case but there is a great thing about that in
> > Sage if it interests you: With just one line you can enumerate, from a
> > group acting G on a set of points, a representative of each orbit of
> > the action of G on the groups of size k.
> >
> > Example:
> >
> > sage:
> IntegerVectorsModPermutationGroup(groups.permutation.Cyclic(5),sum=3,max_part=1)
> > Vectors of length 5 and of sum 3 whose entries is in {0, ..., 1}
> > enumerated up to the action of Cyclic group of order 5 as a
> > permutation group
> >
> > Nathann
>
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Re: [sage-devel] Re: Can not add comments in trac

[P Purkayastha]

Thanks all. It was probably my (cable) internet provider. I could submit
comments using my mobile connection.
On 8 Sep, 2014 7:05 am, "Volker Braun"  wrote:

> PS: https://trac.sagemath.org/ should also work (self-signed certificate
> though)
>
> On Monday, September 8, 2014 12:04:02 AM UTC+1, Volker Braun wrote:
>>
>> Works for me. My guess would be that you have a not-so-transparent proxy
>> forced in front of you. Have you tried tunneling your browser connection
>> out? E.g. ssh -D 1234 boxen and then use localhost:1234 as socks proxy in
>> the browser.
>>
>> On Sunday, September 7, 2014 11:56:49 PM UTC+1, P Purkayastha wrote:
>>>
>>> I am unable to add comments in trac. If I login, then often the page
>>> refreshes to a state that indicates I am not logged in. Refreshing the page
>>> sometimes shows "logged in as..", but adding a comment results in "no
>>> permission" errors (and then I am showed as logged out). Is anyone else
>>> seeing this kind of errors?
>>>
>>  --
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[sage-devel] Can not add comments in trac

[P Purkayastha]

I am unable to add comments in trac. If I login, then often the page 
refreshes to a state that indicates I am not logged in. Refreshing the page 
sometimes shows "logged in as..", but adding a comment results in "no 
permission" errors (and then I am showed as logged out). Is anyone else 
seeing this kind of errors?

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[sage-devel] Re: reddit'ers at it again discussing sage...

[P Purkayastha]

Never used slrn, so I am just guessing that your terminal might be lacking 
in some aspect. Did you try urxvt?

On Thursday, August 28, 2014 7:39:58 AM UTC+8, Simon King wrote:
>
> Hi all! 
>
> On 2014-08-27, Francesco Biscani > 
> wrote: 
> >> On Wednesday, August 27, 2014 8:43:30 PM UTC+1, maldun wrote: 
> >>> 
> >>> With Ibus you can simply type every UTF-8 Character with ease like: 
> =E2= 
> >=88=9E, =CE=A3, 
> >>> =E2=88=AB=EF=BD=86(=CE=B1)=EF=BD=84=CE=B1 using the well known latex 
> com= 
> > mands =3DD 
> >>> =E4=BB=8A=E6=99=A9=E3=81=AF=E7=9A=86=E3=81=95 
> >>> 
> >> 
> > My browser was actually capable of rendering all that... What a time to 
> be 
> > alive! 
>
> I use slrn to read the sage lists. In my ~/.slrnc, I have set utf8 
> encoding: 
> charset display utf8 
> charset outgoing utf8 
>
> However, this is *not* enough to view anything meaningful in the text 
> above. 
>
> Can someone please give me a pointer how to make slrn capabable of 
> reading the stuff above? 
>
> Best regards, 
> Simon 
>
>

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Re: [sage-devel] Re: SageMathCloud / closed source / GPL / Spirit of Sage??

[P Purkayastha]

None of these arguments make any sense. If you want to run a local server 
with sage, you are very welcome to use the sage notebook that is 
distributed with sage itself. Also, this thread should definitely not be in 
sage-devel.

On Monday, August 18, 2014 7:45:36 AM UTC+8, Dr. David Kirkby (Kirkby 
Microwave Ltd) wrote:
>
>
> I think the whole closed source nature is likely to restrict the takeup of 
> Sage for several broad groups of people when they realise that to get high 
> performance they are going to need to store sensitive material on a Linux 
> server they don't control.
>
> As a 50 year old engineer I have worked at three institutions who I know 
> would not want to put workbooks on a server outside their institution.
>
> a) Ministry of Defence - no way.
> b) Airbus - no way. They are very strict on security.
> c) Marconi - most unlikely.
>
> 1) Many commercial companies are not going to be so keen to put 
> commercially sensitive material on a server they don't control. 
> Interlecural  property is valuable company asset. 
>
> Suddenly buying distributed licenses for Mathematica is more attractive 
> from a security point of view. At least Wolfram Research can't look at what 
> you are doing.
>
> 2) Military users are very unlikely to start working on something on a 
> distributed system they can't totally control.
>
> 3) Some academics,  especially those working on mathematics in areas they 
> know UW specialise in, would perhaps no want to put worksheets on a server 
> they know prying eyes will see. Why let someone else look at what you are 
> working on and possibly beat you to publish a paper?
>
> 4) Some individuals are just paranoid and will not use a distributed 
> system they don't control.
>
> No doubt HTTPS will be used to encrypt data in transit.  Maybe worksheets 
> are stored in an encrypted format on disk. But at some stage the data going 
> to be in plain text.
>
> Has anyone working on SageMathCloud ever considered that certain users 
> would not want data stored in a manner they have no control over? 
>
> Dave.
>  

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[sage-devel] Re: Reocvering from system crash during compile?

[P Purkayastha]

Try to rebuild the whole thing again, just so as to ensure that everything 
is properly built.

make distclean
make

On Wednesday, August 6, 2014 12:46:47 PM UTC+8, Alasdair wrote:
>
> I'm running Ubuntu 14.04 as a guest VM inside VirtualBox 4.3.12, with 
> Windows 7.1 Enterprise as the host OS.  (This gives me access to my 
> university's network, networked printers and drives etc, which are 
> unreachable from linux).  And in the middle of compling Sage 6.2 from 
> source, while I was fiddling about with a webcam, the system crashed with 
> the delightful, friendly BSOD.  Back in linux, the error messages I 
> received were
>
> checking for the distutils Python package... no
>> configure: error: cannot import Python module "distutils".
>> Please check your Python installation. The error was:
>> sys:1: RuntimeWarning: not adding directory '' to sys.path since it's 
>> writable by an untrusted group.
>> Untrusted users could put files in this directory which might then be 
>> imported by your Python code. As a general precaution from similar 
>> exploits, you should not execute Python code from this directory
>> make[3]: Entering directory 
>> `/opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2/src'
>> make[3]: *** No targets specified and no makefile found.  Stop.
>> make[3]: Leaving directory 
>> `/opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2/src'
>> Error building pynac.
>>
>> real0m1.585s
>> user0m0.254s
>> sys 0m0.159s
>> 
>> Error installing package pynac-0.3.2
>> 
>> Please email sage-devel (http://groups.google.com/group/sage-devel)
>> explaining the problem and including the relevant part of the log file
>>   /opt/sage-6.2/logs/pkgs/pynac-0.3.2.log
>> Describe your computer, operating system, etc.
>> If you want to try to fix the problem yourself, *don't* just cd to
>> /opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2 and type 'make' or 
>> whatever is appropriate.
>> Instead, the following commands setup all environment variables
>> correctly and load a subshell for you to debug the error:
>>   (cd '/opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2' && 
>> '/opt/sage-6.2/sage' --sh)
>> When you are done debugging, you can type "exit" to leave the subshell.
>> 
>> make[2]: *** [/opt/sage-6.2/local/var/lib/sage/installed/pynac-0.3.2] 
>> Error 1
>> make[2]: Leaving directory `/opt/sage-6.2/build'
>> make[1]: *** [all] Error 2
>> make[1]: Leaving directory `/opt/sage-6.2/build'
>>
>> real0m2.256s
>>
> user0m0.457s
>> sys 0m0.224s
>> ***
>> Error building Sage.
>>
>> The following package(s) may have failed to build:
>>
>> package: pynac-0.3.2
>> log file: /opt/sage-6.2/logs/pkgs/pynac-0.3.2.log
>> build directory: /opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2
>>
>
>
> I'm not sure if the errors were caused by the system crash, or are the 
> fault of the system itself.  But now that I've rebooted - how do I 
> recover?  Should I just throw everything away, and start from scratch?
>
> Thanks,
> Alasdair 
>
>

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Re: [sage-devel] Re: Remove webassets from sagenb?

[P Purkayastha]

Is any Sage developer working on Cantor? I used it a couple of years ago, 
and found it lacking (will have to look at it again to recall the issues I 
had with it). It seemed like it had a lot of potential though.

On Wednesday, August 6, 2014 11:46:07 AM UTC+8, François wrote:
>
> On Tue, 05 Aug 2014 07:06:36 kcrisman wrote: 
> > That took more time to track down than I would have liked.   So I guess 
> we 
> > can indeed scrap it, though if we can keep samuela's branch 
> compatibility 
> > (this is called the "newui" branch on github) that would be good for 
> > honoring that contribution, as someone may have time to do this in the 
> long 
> > run (sagenb may not be cutting-edge but it is still the best choice for 
> a 
> > lot of local work; I assume it is lighter-weight than whatever local SMC 
> > comes up but assumptions are dangerous).  Anyway, hope this detective 
> work 
> > was useful. 
> Actually if you are using KDE there is an interesting alternative to 
> sagenb: 
> "cantor" http://www.kde.org/applications/education/cantor 
> Pity it doesn't work on OS X. 
>
> Francois 
>

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Re: [sage-devel] Warn about long doctests (#16609 needs review)

[P Purkayastha]

Hmm.. sage.plot.{graphics,plot} can not be avoided. We need to show a lot 
of examples to the users, since the number of possible customizations is 
huge.

On Tuesday, July 29, 2014 8:32:43 PM UTC+8, Volker Braun wrote:
>
> sage: stats = json.load(open('/home/vbraun/.sage/timings2.json'))
> sage: sorted([(v['walltime'], k) for k,v in stats.items() if 'failed' not 
> in v])[-20:]
> [(103.71118903160095,
>   u'sage.combinat.rigged_configurations.tensor_product_kr_tableaux'),
>  (105.40626382827759, u'sage.combinat.root_system.plot'),
>  (105.58554887771606, u'sage.functions.bessel'),
>  (106.15052008628845, u'sage.plot.graphics'),
>  (108.91321992874146, 
> u'sage.schemes.elliptic_curves.isogeny_small_degree'),
>  (113.79727506637573, u'sage.matroids.catalog'),
>  (117.22659015655518, u'sage.symbolic.random_tests'),
>  (118.7537989616394, u'sage.combinat.ncsf_qsym.ncsf'),
>  (125.5258629322052, u'sage.combinat.backtrack'),
>  (126.43836998939514,
>   u'sage.schemes.hyperelliptic_curves.hyperelliptic_finite_field'),
>  (127.17231702804565, u'sage.plot.plot'),
>  (128.25516295433044, u'sage.calculus.riemann'),
>  (135.7807331085205,
>   u'sage.combinat.rigged_configurations.rigged_configurations'),
>  (149.45724391937256, u'sage.tests.book_schilling_zabrocki_kschur_primer'),
>  (158.25851893424988, u'sage.combinat.sf.macdonald'),
>  (171.6492350101471, u'sage.combinat.crystals.alcove_path'),
>  (203.31193494796753, u'sage.schemes.elliptic_curves.ell_rational_field'),
>  (214.14894604682922, 
> u'sage.combinat.cluster_algebra_quiver.mutation_type'),
>  (271.6959960460663, u'sage.combinat.similarity_class_type'),
>  (375.5583908557892,
>   u'sage.combinat.root_system.non_symmetric_macdonald_polynomials')]
>
> We don't need to change anything in these right away, hopefully the 
> warning will nag the authors into shortening their test ;-)  Maybe with the 
> exception of sage.plot.graphics, none of these are core functionality 
> making it very likely that they just demonstrate what can be done instead 
> of being necessary for coverage.
>  
>
> On Tuesday, July 29, 2014 4:20:09 AM UTC-4, John Cremona wrote:
>>
>> I would not be surprised if some of the offending long tests are by me (" 
>> just because the author wants to show off the capabilities of their code")  
>> so can you post a list of the longest ones?
>>
>> The other factor is that some modules are themselves very long (thousands 
>> of lines) withough -- necessarily -- having long individual tests.  Though 
>> probably they do.
>>
>> John
>>
>>
>> On 29 July 2014 03:58, Volker Braun  wrote:
>>
>>> A small handful of modules takes the majority of the doctest walltime, 
>>> see e.g. this lopsided distribution:
>>>
>>> 
>>> I'm proposing to 
>>>
>>> * turn the existing sage -t --warn-long parameter into a warning 
>>> (instead of an error)
>>>
>>> * enable it by default with a limit of 60s on a modern computer, 
>>> adjusted for slowness of the computer running the tests.
>>>
>>> This is implemented in http://trac.sagemath.org/ticket/16609. Please 
>>> review.
>>>
>>> -- 
>>> You received this message because you are subscribed to the Google 
>>> Groups "sage-devel" group.
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>>> an email to sage-devel+...@googlegroups.com.
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>>>
>>
>>

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Re: [sage-devel] Re: Notebook login - upper case letters

[P Purkayastha]

Seems like a problem with the notebook; not with the browser. It has
probably never worked as intended!
 On Jul 25, 2014 3:18 PM,  wrote:

>   Hello!
>
> On Thu, 24 Jul 2014 15:39:53 -0700 (PDT)
> P Purkayastha  wrote:
>
> > You can add a warning to the file (based on your error, I am giving
> > the file path):
> >
> > /usr/lib64/python2.7/site-packages/sagenb/data/sage/html/login.html
> >
> > Find the lines
> >
> > 
> > Sign into the Sage Notebook v{{ sage_version }}
> >
> > and append the following warning below it
> > Note that the user name is case
> > sensitive.
> >
>   Thank you for this hint. Now it draws the user's attention to the
> username letters. However:
>
> > You can also modify the lines:
> > {% if username_error %}
> > {{ gettext('Error') }}: {{
> > gettext('Username is not in the system') }}
> >
> > and modify the error to be like
> >
> > gettext('Username is not in the system. Note that the username is
> > case sensitive')
> >
>   I also added this text, but it does not show up on the web page if I
> enter a wrong username. My browser just shows me "Error code 500" and
> no text about incorrect username. Is it the problem with the Notebook
> or a browser?
>
>   Thanks!
> Vladimir
>
> -
>  
>

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Re: [sage-devel] Re: Notebook login - upper case letters

[P Purkayastha]

You can add a warning to the file (based on your error, I am giving the 
file path):

/usr/lib64/python2.7/site-packages/sagenb/data/sage/html/login.html

Find the lines


Sign into the Sage Notebook v{{ sage_version }}

and append the following warning below it
Note that the user name is case sensitive.

You can also modify the lines:
{% if username_error %}
{{ gettext('Error') }}: {{ 
gettext('Username is not in the system') }}

and modify the error to be like

gettext('Username is not in the system. Note that the username is case 
sensitive')



On Thursday, July 24, 2014 8:12:04 PM UTC+8, v_...@ukr.net wrote:
>
>  Is it possible to patch Notebook somehow to make it show the 
> clear error message (like "User does not exist.") and a hint (somethink 
> like "Please check the upper case letters in login name" or "Please 
> note that Sage Notebook distinguishes between lower case and upper case 
> letters in login name")? 
>
>   Regards, 
> Vladimir 
>   
>
> On Tue, 22 Jul 2014 13:59:35 -0700 (PDT) 
> Emmanuel Charpentier > wrote: 
>
> > See below. 
> > 
> > Le mardi 22 juillet 2014 19:31:49 UTC+2, v_...@ukr.net a écrit : 
> > > 
> > >  Hello! 
> > >   Today one of my students told me about the problems he 
> > > experiences trying to login into Sage Notebook server. In short, 
> > > the problem was that he entered his login name with the first 
> > > letter in upper case. I was surprised that Notebook distinguishes 
> > > between the names with upper case and lower case letters, since it 
> > > is usually ignored for logins everywhere. 
> > > 
> > 
> > Huh ? That happens on systems trying to emulate Windows' behaviour. 
> > Grownups' system are usually Unix-based and therefore case-sensitive. 
> > And Sage is *very* Unix-based (running a Unix VM or a Unix-like layer 
> > (Cygwin) are currently the *only* way torun it under windows (and 
> > only the first has reasonable behavior, notwithstanding the heroic 
> > eforts of the development team...)).   
> >   
> > 
> > >   However, what is worse, Sage Notebook does not give any message 
> > > about incorrect (non-existent in this case) login name - just and 
> > > "Error 500" screen. 
> > > 
> > 
> > There, you have a point ... :-) The error message below, however, 
> > *hints at the problem in the lines that read : 
> > "line 522, in _user raise LookupError("no user '{}'".format 
> > (username)) exceptions.LookupError: no user 'V_2e' " 
> > 
> > HTH, 
> > 
> > -- 
> > Emmanuel Charpentier 
> > 
> > 
> >   Meanwhile in the console log I can see the following message: 
> > > 
> > >  
> > > 
> > > 2014-07-22 20:01:15+0300 [-] WSGI application error 
> > > Traceback (most recent call last): 
> > >   File 
> > > "/usr/lib64/python2.7/site-packages/twisted/python/threadpool.py", 
> > > line 196, in _worker result = context.call(ctx, function, *args, 
> > > **kwargs) File 
> > > "/usr/lib64/python2.7/site-packages/twisted/python/context.py", 
> > > line 118, in callWithContext return self.currentContext 
> > > ().callWithContext(ctx, func, *args, **kw) File 
> > > "/usr/lib64/python2.7/site-packages/twisted/python/context.py", 
> > > line 81, in callWithContext return func(*args,**kw) File 
> > > "/usr/lib64/python2.7/site-packages/twisted/web/wsgi.py", line 332, 
> > > in run self.reactor.callFromThread(wsgiError, self.started, 
> > > *exc_info()) 
> > > ---  --- 
> > >   File 
> > > "/usr/lib64/python2.7/site-packages/twisted/web/wsgi.py", line 315, 
> > > in run appIterator = self.application(self.environ, 
> > > self.startResponse) File 
> > > "/usr/lib64/python2.7/site-packages/flask/app.py", line 1836, in 
> > > __call__ return self.wsgi_app(environ, start_response) File 
> > > "/usr/lib64/python2.7/site-packages/flask/app.py", line 1820, in 
> > > wsgi_app response = self.make_response(self.handle_exception(e)) 
> > > File "/usr/lib64/python2.7/site-packages/flask/app.py", line 1403, 
> > > in handle_exception reraise(exc_type, exc_value, tb) File 
> > > "/usr/lib64/python2.7/site-packages/flask/app.py", line 1817, in 
> > > wsgi_app response = self.full_dispatch_request() File 
> > > "/usr/lib64/python2.7/site-packages/flask/app.py", line 1477, in 
> > > full_dispatch_request rv = self.handle_user_exception(e) File 
> > > "/usr/lib64/python2.7/site-packages/flask/app.py", line 1381, in 
> > > handle_user_exception reraise(exc_type, exc_value, tb) File 
> > > "/usr/lib64/python2.7/site-packages/flask/app.py", line 1475, in 
> > > full_dispatch_request rv = self.dispatch_request() File 
> > > "/usr/lib64/python2.7/site-packages/flask/app.py", line 1461, in 
> > > dispatch_request return self.view_functions[rule.endpoint] 
> > > (**req.view_args) File 
> > > 
> "/usr/lib64/python2.7/site-packages/sagenb/flask_version/authentication.py", 
>
> > > 
> > > line 42, in login U = g.notebook.user_manager().user(username) File 
> > > "/usr/lib64/python2.7/site

Re: [sage-devel] Re: sage -t --optional=... skips the normal tests?

[P Purkayastha]

Thanks. This worked.

On Sun 13 Jul 2014 08:13:37 PM SGT, Volker Braun wrote:

sage -t --optional=sage,gap_packages src/sage/coding



On Sunday, July 13, 2014 7:52:32 AM UTC-4, P Purkayastha wrote:

I am trying to doctest the coding folder with the optional
gap_packages. But it seems to skip the statements without the "#
optional" statement. The result of it is that the optional tests
are all failing. Here is an output:

|
...allations/sage-git [128]»sage -t --optional=gap_packages
src/sage/coding
Runningdoctests withID 2014-07-13-19-47-19-ba9f5690.
Doctesting17files.
sage -t src/sage/coding/binary_code.pyx
[0tests,0.01s]
sage -t src/sage/coding/decoder.py
[0tests,0.00s]
sage -t src/sage/coding/codes_catalog.py
[0tests,0.00s]
sage -t src/sage/coding/code_constructions.py
[0tests,0.00s]
sage -t src/sage/coding/sd_codes.py
[0tests,0.00s]
sage -t src/sage/coding/all.py
[0tests,0.00s]
sage -t src/sage/coding/delsarte_bounds.py
[0tests,0.00s]
sage -t src/sage/coding/linear_code.py
**
File"src/sage/coding/linear_code.py",line
371,insage.coding.linear_code.min_wt_vec_gap
Failedexample:

sage.coding.linear_code.min_wt_vec_gap(Gstr,7,4,GF(2),algorithm="guava")#
optional - gap_packages (Guava package)
Exceptionraised:
Traceback(most recent call last):

File"/home/punarbasu/Installations/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py",line
480,in_run
self.execute(example,compiled,test.globs)

File"/home/punarbasu/Installations/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py",line
839,inexecute
execcompiled inglobs
File"",line
1,in


sage.coding.linear_code.min_wt_vec_gap(Gstr,Integer(7),Integer(4),GF(Integer(2)),algorithm="guava")#
optional - gap_packages (Guava package)
NameError:name 'Gstr'isnotdefined
**
|

This shouldn't fail because 'Gstr' is defined all right in the
actual file:

|
EXAMPLES::


sage:Gstr="Z(2)*[[1,1,1,0,0,0,0], [1,0,0,1,1,0,0],
[0,1,0,1,0,1,0], [1,1,0,1,0,0,1]]"
sage:sage.coding.linear_code.min_wt_vec_gap(Gstr,7,4,GF(2))
(0,1,0,1,0,1,0)


Thisoutput isdifferent but still a minimum weight vector::




sage:sage.coding.linear_code.min_wt_vec_gap(Gstr,7,4,GF(2),algorithm="guava")#
optional - gap_packages (Guava package)
(0,0,1,0,1,1,0)
|

Also, note that the files preceding "linear_code.py" all report "0
tests", which doesn't make any sense.

Is there some other argument I must provide with --optional?

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[sage-devel] sage -t --optional=... skips the normal tests?

[P Purkayastha]

I am trying to doctest the coding folder with the optional gap_packages. 
But it seems to skip the statements without the "# optional" statement. The 
result of it is that the optional tests are all failing. Here is an output:

...allations/sage-git [128] » sage -t --optional=gap_packages src/sage/
coding
Running doctests with ID 2014-07-13-19-47-19-ba9f5690.
Doctesting 17 files.
sage -t src/sage/coding/binary_code.pyx
[0 tests, 0.01 s]
sage -t src/sage/coding/decoder.py
[0 tests, 0.00 s]
sage -t src/sage/coding/codes_catalog.py
[0 tests, 0.00 s]
sage -t src/sage/coding/code_constructions.py
[0 tests, 0.00 s]
sage -t src/sage/coding/sd_codes.py
[0 tests, 0.00 s]
sage -t src/sage/coding/all.py
[0 tests, 0.00 s]
sage -t src/sage/coding/delsarte_bounds.py
[0 tests, 0.00 s]
sage -t src/sage/coding/linear_code.py
**
File "src/sage/coding/linear_code.py", line 371, in sage.coding.linear_code.
min_wt_vec_gap
Failed example:
sage.coding.linear_code.min_wt_vec_gap(Gstr,7,4,GF(2),algorithm="guava") 
   # optional - gap_packages (Guava package)
Exception raised:
Traceback (most recent call last):
  File 
"/home/punarbasu/Installations/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py"
, line 480, in _run
self.execute(example, compiled, test.globs)
  File 
"/home/punarbasu/Installations/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py"
, line 839, in execute
exec compiled in globs
  File "", line 1, in 

sage.coding.linear_code.min_wt_vec_gap(Gstr,Integer(7),Integer(4),GF
(Integer(2)),algorithm="guava")# optional - gap_packages (Guava package)
NameError: name 'Gstr' is not defined
**

This shouldn't fail because 'Gstr' is defined all right in the actual file:

EXAMPLES::


sage: Gstr = "Z(2)*[[1,1,1,0,0,0,0], [1,0,0,1,1,0,0], 
[0,1,0,1,0,1,0], [1,1,0,1,0,0,1]]"
sage: sage.coding.linear_code.min_wt_vec_gap(Gstr,7,4,GF(2))
(0, 1, 0, 1, 0, 1, 0)


This output is different but still a minimum weight vector::


sage: sage.coding.linear_code.min_wt_vec_gap(Gstr,7,4,GF(2),
algorithm="guava")# optional - gap_packages (Guava package)
(0, 0, 1, 0, 1, 1, 0)

Also, note that the files preceding "linear_code.py" all report "0 tests", 
which doesn't make any sense.

Is there some other argument I must provide with --optional?

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Re: [sage-devel] Re: cube roots in Sage

[P Purkayastha]

Hi Greg,

 Hope the following code helps you in implementing your function:

from sage.symbolic.function import SymbolicFunction
class real_nth_root_class(SymbolicFunction):
   def __init__(self):
   SymbolicFunction.__init__(self, 'real_nth_root', nargs=2)
   def _evalf_(self, x, n, parent=None):
   # Handle python floats which do not have the 'nth_root' method
   if isinstance(x, float):
   return float(RDF(x).nth_root(n))
   return parent(x).nth_root(n)

real_nth_root = real_nth_root_class()


In actual usage:

sage: real_nth_root( x, 3)
real_nth_root(x, 3)
sage: f(x) = real_nth_root( x, 3)
sage: f
x |--> real_nth_root(x, 3)
sage: plot( real_nth_root( x, 3), -5, 5 )
# plots the graph.


 Regards,
   basu.


On Fri 11 Jul 2014 06:23:21 AM SGT, Gregory Bard wrote:

I think we have a consensus that we should do *something* but unless I
am very much mistaken, the suggestion from Vincent Delecroix and Nils
Bruin that we make a symbolic function has advantages.

I was looking at Nils's code, but I have to confess that I don't
understand that code. Actually, I wasn't able to get the following to
work, but I have a feeling that I am making a minor and stupid mistake
with the syntax.


from sage.symbolic.function import SymbolicFunction
class nth_root(SymbolicFunction):
def __init__(self):
SymbolicFunction.__init__(self, 'nth_root', nargs=2)
def _evalf_(self, n, x, parent=None):
return parent(x).nth_root(n)

plot( nth_root( x, 3), -5, 5 )


Maybe someone here could explain exactly what the distinction is or
what the pros/cons are for my approach versus Nils's? I have no idea.

I have also posted this on Sage-Edu, but perhaps all future replies
should be restricted to Sage-Devel and not Sage-Edu?
---Greg

On Wednesday, June 25, 2014 1:10:06 AM UTC-4, Gregory Bard wrote:

As Vincent and Niles have brought up, there might be advantages to it
being a symbolic function. How does one actually go about making that
happen? Is this an intrusive change, or an easy one? I really have no
idea...
---Greg


On Sun, Jun 22, 2014 at 5:00 PM, Vincent Delecroix
<20100.delecr...@gmail.com > wrote:
> As Niles already said it would be better to have it as a
symbolic function
>
> sage: f(x) = real_nth_root(x, 5)
> sage: f
> x |--> real_nth_root(x,5)
>
> 2014-06-22 22:36 UTC+02:00, Gregory Bard
mailto:gregory.bard1...@gmail.com>>:
>> Yes, that is reasonable. Let us call it "real_nth_root"
instead, as
>> suggested by Nicolas Thiery. Any other requests/comments?
>>
>> It would be superb if this could be resolved by June 30th, when my
>> book goes to the American Mathematical Society for publication...
>> ---Greg
>>
>> On Sun, Jun 22, 2014 at 9:02 AM, William Stein
mailto:wst...@gmail.com>> wrote:
>>> On Sun, Jun 22, 2014 at 8:27 AM, Nicolas M. Thiery
>>> mailto:nicolas.thi...@u-psud.fr>>
wrote:
 On Fri, Jun 20, 2014 at 06:33:52PM -0700, Gregory Bard wrote:
> It seems that the consensus on both Sage-devel and Sage-edu
is to go
> with some sort of nth_real_root function. I propose the
following,
> which I have tested for evaluation, plotting,
differentiation, and
> integration. Sadly, the derivative has a Dirac delta in it,
which is
> ... perhaps unavoidable because of the vertical tangency of the
> cuberoot function at x=0. (Naturally, we can remove the
asserts once
> testing is completed.
> ---Greg
>
> def nth_real_root( x, n ):

 Just 2 cents of outsider feedback since I have not followed the
 discussion, and am not knowledgeable on the topic. This names
suggests
 to me that we look at all the real roots of n (for whatever this
 means), and then take the n-th one.  So maybe real_nth_root
instead?
>>>
>>> +1
>>>

 Cheers,
 Nicolas
 --
 Nicolas M. Thiéry "Isil" mailto:nthi...@users.sf.net>>
 http://Nicolas.Thiery.name/

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>>>
>>>
>>>
>>> --
>>> William Stein
>>> Professor of M

[sage-devel] Re: git trac

[P Purkayastha]

I suppose the steps are these

1 Send email to get account
2 Login to trac, change password (?), and set up ssh keys
3 git clone ...git-trac-command
4 ln -s git-trac-command/bin/git-trac ~/bin (assuming bin is in PATH)
5 add trac as a remote repository
6 git trac config --user=... --pass=...
7 review patches, etc.

Steps 2-6 can be automated. In particular, 2-6 should be possible to do in 
an automated way after asking the user for the password received during 
account setup. Something like "sage --setup-dev-environment"


On Sunday, June 15, 2014 8:20:16 AM UTC+8, William wrote:
>
> On Sat, Jun 14, 2014 at 5:12 PM, William Stein  > wrote: 
> > Hi Sage Devel, 
> > 
> > Sage comes with git, but Sage doesn't come with "git trac".  Why not? 
> > Is it just that nobody got around to including it, or is this on 
> > purpose. 
> > 
> > 
> http://www.sagemath.org/doc/developer/git_trac.html#installing-the-git-trac-command
>  
> > 
> > I'm just getting annoyed, due to copying the command from there (using 
> > Sage's git), and getting 
> > 
> > wstein$ git clone https://github.com/sagemath/git-trac-command.git 
> > Cloning into 'git-trac-command'... 
> > fatal: Unable to find remote helper for 'https' 
> > wstein$ git clone http://github.com/sagemath/git-trac-command.git 
> > Cloning into 'git-trac-command'... 
> > fatal: Unable to find remote helper for 'http' 
> > 
> > So we ship a git that can't even install git trac according to our 
> instructions? 
> > 
> > Is there any reason git-trac is distributed as a git repo?  Shouldn't 
> > it just be part of sage's git repo? 
> > 
> > 
> > I installed it using the system-wide git.  But then: 
> > 
> > sage-6.3.beta3$ git trac review 16479 
> > Fetching remote branch... 
> > Traceback (most recent call last): 
> >   File "/scratch/wstein/sage-6.3.beta3/git-trac-command/bin/git-trac", 
> > line 18, in  
> > cmdline.launch() 
> >   File 
> "/scratch/wstein/sage-6.3.beta3/git-trac-command/git_trac/cmdline.py", 
> > line 211, in launch 
> > app.review_diff(ticket_number) 
> >   File 
> "/scratch/wstein/sage-6.3.beta3/git-trac-command/git_trac/app.py", 
> > line 421, in review_diff 
> > diff = self.repo.review_diff(remote) 
> >   File 
> "/scratch/wstein/sage-6.3.beta3/git-trac-command/git_trac/git_repository.py", 
>
> > line 271, in review_diff 
> > self.git.fetch('trac', remote) 
> >   File 
> "/scratch/wstein/sage-6.3.beta3/git-trac-command/git_trac/git_interface.py", 
>
> > line 339, in meth 
> > return self.execute(git_cmd, *args, **kwds) 
> >   File 
> "/scratch/wstein/sage-6.3.beta3/git-trac-command/git_trac/git_interface.py", 
>
> > line 326, in execute 
> > popen_stderr=subprocess.PIPE) 
> >   File 
> "/scratch/wstein/sage-6.3.beta3/git-trac-command/git_trac/git_interface.py", 
>
> > line 261, in _run 
> > raise GitError(result) 
> > git_trac.git_error.GitError: git returned with non-zero exit code 
> > (128) when executing "git fetch trac u/vdelecroix/16479" 
> > STDERR: fatal: 'trac' does not appear to be a git repository 
> > STDERR: fatal: Could not read from remote repository. 
> > STDERR: Please make sure you have the correct access rights 
> > STDERR: and the repository exists. 
> > (sage-sh) 4cff879841d04d9bb516ba106ba89c57@compute8dc2:sage-6.3.beta3$ 
> > 
> > 
> > Is this because I have to setup ssh keys just to *read* a branch? 
> > Why?  I'm not pushing anything? 
> > 
> > Refereeing involves too much overhead. 
>
> I'm curious what the step-by-step list is to go from start to finish 
> to review a ticket.   E.g., starting with 
>
>  1. Send an email to "sage-trac-account AT googlegroups DOT com". 
>  2. ... 
>
> and ends with the ticket getting into Sage.I'm concerned that we 
> may be loosing development effort due to the process being needlessly 
> complicated.  We've been loosing my devel effort for that reason 
> for a long time already.  And my instincts with software are often 
> that if it is so complicated it scares me off, then it probably has a 
> similar effect on a lot of other people... 
>
>  -- William 
>
> -- 
> William Stein 
> Professor of Mathematics 
> University of Washington 
> http://wstein.org 
>

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Re: [sage-devel] Re: reduce compilation times during development

[P Purkayastha]

I put up a post in Google+ with my current observations regarding this:
https://plus.google.com/115114386497793444118/posts/2sUudfMLjmP


On Sat, Jun 7, 2014 at 3:08 PM, Ralf Stephan  wrote:

> On Monday, May 12, 2014 11:36:20 AM UTC+2, P Purkayastha wrote:
>
>> ... It shouldn't have upgraded anything, but it still decided to compile
>> a bunch of packages anyway.
>>
>
> I have witnessed the same thing recently. Someone with knowledge of the
> code please correct me. I think what is probably happening is that
> $HOME/.cycache over time fills with old entries. Some get cleaned but the
> ones not getting cleaned fill up, until the cleanup process is cleaning a
> part of the previously cached files every time a major build happens.
>
> The obvious workaround is to rm -rf $HOME/.cycache when this occurs.
>
> Regards,
>
> --
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[sage-devel] Re: Create a branch without a ticket

[P Purkayastha]

Looks like a bug to me.

On Wednesday, May 21, 2014 2:56:54 AM UTC+8, Štěpán Starosta wrote:
>
> Hi,
>
> I follow the guide (
> http://www.sagemath.org/doc/developer/walk_through.html#starting-without-a-ticket)
>  
> to create a new branch without a ticket. The command
>
> sage -dev checkout --branch my_branch
>
> outputs
> *Branch "my_branch" does not exist locally.*
>
> Any ideas what I might be doing wrong? I am running this on Sage 6.2.
>
> Thanks,
> Stepan
>
>
>

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[sage-devel] Re: Debugging the notebook

[P Purkayastha]

Currently, it is quite hard to develop with the notebook. If 
https://github.com/sagemath/sagenb/pull/204 gets merged then it will be 
much easier. It will then be possible to create a symbolic link to the git 
repository and develop in the git repository; something like this:

$ cd SAGE_ROOT/local/lib/python/site-packages/sagenb-*
$ mv sagenb sagenb.original
$ ln -s /path/to/sagenb-github/sagenb sagenb

If I get some time, I will upgrade the documentation too.

 - basu.

On Monday, May 19, 2014 9:38:45 AM UTC+8, RJB wrote:
>
> I’ve been hoping that someone with greater skill would come along and save 
> the day by fixing defect 15308, but no luck. Attach files have not worked 
> in the notebook since version 5.10. I’ve tried my hand at figuring out what 
> is going on, but it is a problem specific to the notebook and debugging is 
> a challenge.  
>
> The only thing I can find about debugging in the notebook is 
> http://www.sagemath.org/doc/reference/cmd/sage/misc/trace.html, which 
> basically does a very good job describing how to debug sage in command 
> mode… and ends by pointing out that the method does not work with the 
> notebook. And I have confirmed this.
>
> Can anybody point me to a method of debugging the notebook? Even if it’s 
> just to tell me how to put print statements in and look at the results 
> somewhere, I’d be grateful.
>
>

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Re: [sage-devel] Re: active testing

[P Purkayastha]

On Wednesday, May 14, 2014 6:51:23 PM UTC+8, Nathann Cohen wrote:
>
> > Ewww. 
> > 
> > By the way, sqrt("this was a string") (lower case) is slightly better, 
> > as the answer sounds like Yoda speech. 
>
> Indeed. We must patch it to cast everything into lower case first. 
>
>  
o.O 

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[sage-devel] Re: The latest development version is 6.1.beta1 released on 2013-12-21.

[P Purkayastha]

That will provide only the sage library, not the whole distribution. I 
think if people are going to download from the sagemath site, they are 
probably looking for the whole distribution, with all the packages needed 
to compile offline.

On Monday, May 12, 2014 1:03:05 AM UTC+8, leif wrote:
>
> leif wrote: 
> > http://sagemath.org/download-latest.html 
> > 
> > Ooops? 
>
> Should we perhaps also (add a) link to 
>
> https://github.com/sagemath/sage/releases ? 
>
> (There you can get e.g. 
> https://github.com/sagemath/sage/archive/6.3.beta0.tar.gz (and .zip) as 
> well.) 
>
>
> -leif 
>
> -- 
> () The ASCII Ribbon Campaign 
> /\   Help Cure HTML E-Mail 
>
>

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Re: [sage-devel] Re: reduce compilation times during development

[P Purkayastha]

Most of this time is spent in gcc. This can be seen if you grep the log 
file for "Finished Cythonizing". The commands following it are all gcc/g++ 
commands.

On Monday, May 12, 2014 7:30:20 PM UTC+8, Volker Braun wrote:
>
> Is the time spent in gcc or in Cython or both?
>
>
> On Monday, May 12, 2014 12:54:23 PM UTC+2, P Purkayastha wrote:
>>
>> Here is some more information. I checked out ticket/16325 and it differs 
>> from develop by only two commits to a single file.
>>
>> ~/Installations/sage-git» git l -n 3
>> * 2ecec6b - (HEAD, refs/heads/ticket/16325) bordercolor must not be a 
>> list. Fix this error. 24 hours ago 
>> * 2b1a65b - Enable fillcolor and bordercolor for implicit_plot 24 hours 
>> ago 
>> * fa885d9 - (refs/remotes/origin/develop, refs/heads/develop) Updated 
>> Sage version to 6.3.beta0 2 days ago %
>>
>> CCACHE is in the environment
>>
>> ~/Installations/sage-git» set|grep CCA
>> Binary file (standard input) matches
>> ~/Installations/sage-git» env|grep CCA
>> SAGE_INSTALL_CCACHE=yes
>>
>> I had just finished running sage -upgrade (and there was nothing to 
>> upgrade in reality - see my previous emails), so the commands below are run 
>> immediately after this upgrade command.
>>
>> ~/Installations/sage-git» local/bin/ccache -s
>> cache directory /home/punarbasu/.ccache
>> cache hit (direct)   4002297
>> cache hit (preprocessed)  166297
>> cache miss206048
>> called for link  2019701
>> called for preprocessing   21331
>> multiple source files226
>> compiler produced stdout  40
>> compile failed  6261
>> preprocessor error  3187
>> bad compiler arguments  3602
>> unsupported source language12963
>> autoconf compile/link  46173
>> unsupported compiler option12682
>> no input file  19175
>> files in cache 24529
>> cache size   3.5 Gbytes
>> max cache size   4.0 Gbytes
>>
>> ~/Installations/sage-git» git co ticket/16325
>> Switched to branch 'ticket/16325'
>> ~/Installations/sage-git» time sage -ba >& ~/sage.log
>> y
>> sage -ba >&~/sage.log  101.00s user 25.62s system 50% cpu 4:13.18 total
>>
>>
>> ~/Installations/sage-git» local/bin/ccache -s
>> cache directory /home/punarbasu/.ccache
>> cache hit (direct)   4002676
>> cache hit (preprocessed)  166331
>> cache miss206066
>> called for link  2020083
>> called for preprocessing   21331
>> multiple source files226
>> compiler produced stdout  40
>> compile failed  6261
>> preprocessor error  3187
>> bad compiler arguments  3602
>> unsupported source language12963
>> autoconf compile/link  46173
>> unsupported compiler option12682
>> no input file  19180
>> files in cache 24565
>> cache size   3.5 Gbytes
>> max cache size   4.0 Gbytes
>>
>>
>> The time required (4 min) is much better than yesterday, but still too 
>> long. Is this to be expected? The log file sage.log is attached.
>>
>> A copy of all the files is kept in src/build/lib.* - can it not just 
>> check the diff between those and the files in src/sage and decide which 
>> ones need recompiling?
>>
>>
>> On Monday, May 12, 2014 6:32:07 PM UTC+8, Volker Braun wrote:
>>>
>>> Try "sage -ba". If it is not very fast, tell us why cycache is not 
>>> working on your machine.
>>>
>>>
>>>
>>> On Monday, May 12, 2014 12:13:31 PM UTC+2, P Purkayastha wrote:
>>>>
>>>> All of this was on 6.3.beta0
>>>> On May 12, 2014 5:46 PM, "Volker Braun"  wrote:
>>>>
>>>>> With ccache and cycache the recompliation time of extension modules is 
>>>>> negligible. Should work automatically for Sage >= 6.2.rc0
>>>>>
>>>>

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Re: [sage-devel] Re: reduce compilation times during development

[P Purkayastha]

On Monday, May 12, 2014 6:54:23 PM UTC+8, P Purkayastha wrote:
>
> The time required (4 min) is much better than yesterday, but still too 
> long. Is this to be expected? The log file sage.log is attached.
>
> A copy of all the files is kept in src/build/lib.* - can it not just check 
> the diff between those and the files in src/sage and decide which ones need 
> recompiling?
>
>
I need to clarify something here. I forgot to set MAKE='make -j2', so it is 
using single thread. So, perhaps the build time is only 2 min and not 4min. 
Also, it seems only pyx or compiled files are kept in src/build.

 

>
> On Monday, May 12, 2014 6:32:07 PM UTC+8, Volker Braun wrote:
>>
>> Try "sage -ba". If it is not very fast, tell us why cycache is not 
>> working on your machine.
>>
>>
>>
>> On Monday, May 12, 2014 12:13:31 PM UTC+2, P Purkayastha wrote:
>>>
>>> All of this was on 6.3.beta0
>>> On May 12, 2014 5:46 PM, "Volker Braun"  wrote:
>>>
>>>> With ccache and cycache the recompliation time of extension modules is 
>>>> negligible. Should work automatically for Sage >= 6.2.rc0
>>>>
>>>

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Re: [sage-devel] Re: reduce compilation times during development

[P Purkayastha]

All of this was on 6.3.beta0
On May 12, 2014 5:46 PM, "Volker Braun"  wrote:

> With ccache and cycache the recompliation time of extension modules is
> negligible. Should work automatically for Sage >= 6.2.rc0
>
>
> On Monday, May 12, 2014 11:36:20 AM UTC+2, P Purkayastha wrote:
>>
>> Yes, this is set. I tried it again just now. I changed to develop using
>>
>> git checkout develop
>>
>> and re-ran the upgrade process. It shouldn't have upgraded anything, but
>> it still decided to compile a bunch of packages anyway. Thankfully, it
>> found most in ccache, except for R. But for sage, the following message was
>> spit out during compilation:
>>
>> ...
>> Found compiled sage/rings/polynomial/polynomial_ring_homomorphism.pyx incache
>> Found compiled sage/rings/polynomial/polynomial_zmod_flint.pyx in cache
>> Found compiled sage/rings/polynomial/polynomial_zz_pex.pyx in cache
>> Finished Cythonizing, time: 24.08 seconds.
>> running install
>> running build
>> running build_py
>> copying sage/plot/contour_plot.py -> build/lib.linux-x86_64-2.7/sage/plot
>> running build_ext
>> building 'sage.algebras.quatalg.quaternion_algebra_element' extension
>> building 'sage.algebras.letterplace.free_algebra_letterplace' extension
>> ...
>> building 'sage.ext.interpreters.wrapper_py' extension
>> building 'sage.ext.interpreters.wrapper_el' extension
>> Executing 321 commands (using 2 threads)
>>
>> So, it decided to still recompile 321 files. This is far from optimal.
>>
>> On Sunday, May 11, 2014 9:14:02 PM UTC+8, Ralf Stephan wrote:
>>>
>>>
>>>
>>> On Sunday, May 11, 2014 12:41:24 PM UTC+2, P Purkayastha wrote:
>>>>
>>>> I have both ccache and cycache enabled.
>>>>
>>> Is this set?
>>> $ set|grep CCA
>>> SAGE_INSTALL_CCACHE=yes
>>>
>>> I occasionally look at what changes in the output of "local/bin/ccache
>>> -s"
>>> before and after compilation.
>>>
>>> Regards,
>>>
>>  --
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[sage-devel] Re: reduce compilation times during development

[P Purkayastha]

Yes, this is set. I tried it again just now. I changed to develop using

git checkout develop

and re-ran the upgrade process. It shouldn't have upgraded anything, but it 
still decided to compile a bunch of packages anyway. Thankfully, it found 
most in ccache, except for R. But for sage, the following message was spit 
out during compilation:

...
Found compiled sage/rings/polynomial/polynomial_ring_homomorphism.pyx incache
Found compiled sage/rings/polynomial/polynomial_zmod_flint.pyx in cache
Found compiled sage/rings/polynomial/polynomial_zz_pex.pyx in cache
Finished Cythonizing, time: 24.08 seconds.
running install
running build
running build_py
copying sage/plot/contour_plot.py -> build/lib.linux-x86_64-2.7/sage/plot
running build_ext
building 'sage.algebras.quatalg.quaternion_algebra_element' extension
building 'sage.algebras.letterplace.free_algebra_letterplace' extension
...
building 'sage.ext.interpreters.wrapper_py' extension
building 'sage.ext.interpreters.wrapper_el' extension
Executing 321 commands (using 2 threads)

So, it decided to still recompile 321 files. This is far from optimal.

On Sunday, May 11, 2014 9:14:02 PM UTC+8, Ralf Stephan wrote:
>
>
>
> On Sunday, May 11, 2014 12:41:24 PM UTC+2, P Purkayastha wrote:
>>
>> I have both ccache and cycache enabled.
>>
> Is this set?
> $ set|grep CCA
> SAGE_INSTALL_CCACHE=yes
>
> I occasionally look at what changes in the output of "local/bin/ccache -s"
> before and after compilation.
>
> Regards,
>

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[sage-devel] reduce compilation times during development

[P Purkayastha]

Currently, what methods are there to reduce the compilation times during 
development?

I have a desktop which is not that fast and it takes ages to get sage ready 
if I change branches. As an example, I ran the following commands
$ sage -upgrade develop   # this upgraded to sage-6.3.beta0
$ sage --dev checkout --ticket 16325  # somehow this was not based off 
develop
$ git rebase develop  # this rebased the branch ticket/16325 on develop
$ # made changes to only one file: sage/plot/contour_plot.py
$ sage -btp --long src/sage/plot

The build took 15 min to complete - it is running the tests now.

I have both ccache and cycache enabled. The last command above identified a 
lot of files which do not need compilation, but then it also identified 
over 300 files which needed to be compiled. This is a recurring problem 
that I face when changing branches and is really time consuming.

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[sage-devel] Re: Spurious(?) ValueErrors when plotting on a loglog scale

[P Purkayastha]

http://trac.sagemath.org/ticket/13422

On Saturday, April 26, 2014 3:17:00 PM UTC-7, Michael Orlitzky wrote:
>
> If we try to plot some values in sage on a loglog scale where there will 
> be fewer than 2 ticks on the (say) x-axis, it throws a ValueError: 
>
>   ValueError: Either expand the range of the independent variable to 
>   allow two different integer powers of your `base`, or change your 
>   `base` to a smaller number. 
>
> I see no reason to disallow this; I often want to plot values between 
> zero and ten on a log_10 scale. In fact if I comment out the "raise" in 
> sage, I get the plot I want with no other (apparent) negative effects. 
>
> Does anyone remember why this is in place? Can we get rid of it? Here is 
> some code that will throw the ValueError: 
>
>   from sage.all import * 
>
>   u1_points = [(1,17.10095360023844), 
>(3,11.390822965745611), 
>(7,7.572843732189597), 
>(15,5.020820222090607), 
>(31,3.322248387376159)] 
>
>   u2_points = [(3.0,7.062958467518104), 
>(7.0,4.653624065352839), 
>(15.0,3.0687723922185906), 
>(31.0,2.0241074994435957), 
>(63.0,1.3351289174481258)] 
>
>   u1_label=r'$uniform_{1}$' 
>   u2_label=r'$uniform_{2}$' 
>   p1 = list_plot_loglog(u1_points, 
> plotjoined=True, 
> legend_label=u1_label, 
> base=10) 
>   p2 = list_plot_loglog(u2_points, 
> plotjoined=True, 
> color='red', 
> legend_label=u2_label, 
> base=10) 
>   p = p1 + p2 
>   p.show() 
>

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[sage-devel] Re: Spurious(?) ValueErrors when plotting on a loglog scale

[P Purkayastha]

http://trac.sagemath.org/ticket/13422

On Saturday, April 26, 2014 3:17:00 PM UTC-7, Michael Orlitzky wrote:
>
> If we try to plot some values in sage on a loglog scale where there will 
> be fewer than 2 ticks on the (say) x-axis, it throws a ValueError: 
>
>   ValueError: Either expand the range of the independent variable to 
>   allow two different integer powers of your `base`, or change your 
>   `base` to a smaller number. 
>
> I see no reason to disallow this; I often want to plot values between 
> zero and ten on a log_10 scale. In fact if I comment out the "raise" in 
> sage, I get the plot I want with no other (apparent) negative effects. 
>
> Does anyone remember why this is in place? Can we get rid of it? Here is 
> some code that will throw the ValueError: 
>
>   from sage.all import * 
>
>   u1_points = [(1,17.10095360023844), 
>(3,11.390822965745611), 
>(7,7.572843732189597), 
>(15,5.020820222090607), 
>(31,3.322248387376159)] 
>
>   u2_points = [(3.0,7.062958467518104), 
>(7.0,4.653624065352839), 
>(15.0,3.0687723922185906), 
>(31.0,2.0241074994435957), 
>(63.0,1.3351289174481258)] 
>
>   u1_label=r'$uniform_{1}$' 
>   u2_label=r'$uniform_{2}$' 
>   p1 = list_plot_loglog(u1_points, 
> plotjoined=True, 
> legend_label=u1_label, 
> base=10) 
>   p2 = list_plot_loglog(u2_points, 
> plotjoined=True, 
> color='red', 
> legend_label=u2_label, 
> base=10) 
>   p = p1 + p2 
>   p.show() 
>

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Re: [sage-devel] Re: Spurious(?) ValueErrors when plotting on a loglog scale

[P Purkayastha]

On Sun, Apr 27, 2014 at 2:46 PM, Michael Orlitzky wrote:

> On 04/27/2014 04:57 PM, P Purkayastha wrote:
> > This is strange. Two of my earlier messages got deleted. Does anyone
> > know why? Perhaps because I only wrote the URL to the ticket?
> >
> > Getting back to the question, this was fixed two years ago and is
> > awaiting a review. See #13422
> >
>
> Ah, thanks for the link. Do I understand correctly that this would still
> throw a ValueError, but allow the user to avoid it by supplying his own
> (at least two) ticks?
>
> If so, I would rather see it done automatically. Why throw a ValueError
> and make me supply a second tick when sage can do it automatically? If I
> don't like the ticks that sage comes up with, *then* I can supply my
> own. I think that will be less cumbersome in the common case of
> just-plot-the-thing-already. (And if I supply only one tick, just let me
> do it.)
>

The patch is to do it automatically. It will raise an error *only* if you
give ticks manually, and what you give is insufficient (see the examples in
the doctests).

Another ticket #13528 is positively reviewed but depends on this patch. So,
please review this one #13422 if you are interested.

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[sage-devel] Re: Spurious(?) ValueErrors when plotting on a loglog scale

[P Purkayastha]

This is strange. Two of my earlier messages got deleted. Does anyone know 
why? Perhaps because I only wrote the URL to the ticket?

Getting back to the question, this was fixed two years ago and is awaiting 
a review. See #13422

On Sunday, April 27, 2014 6:17:00 AM UTC+8, Michael Orlitzky wrote:
>
> If we try to plot some values in sage on a loglog scale where there will 
> be fewer than 2 ticks on the (say) x-axis, it throws a ValueError: 
>
>   ValueError: Either expand the range of the independent variable to 
>   allow two different integer powers of your `base`, or change your 
>   `base` to a smaller number. 
>
> I see no reason to disallow this; I often want to plot values between 
> zero and ten on a log_10 scale. In fact if I comment out the "raise" in 
> sage, I get the plot I want with no other (apparent) negative effects. 
>
> Does anyone remember why this is in place? Can we get rid of it? Here is 
> some code that will throw the ValueError: 
>
>   from sage.all import * 
>
>   u1_points = [(1,17.10095360023844), 
>(3,11.390822965745611), 
>(7,7.572843732189597), 
>(15,5.020820222090607), 
>(31,3.322248387376159)] 
>
>   u2_points = [(3.0,7.062958467518104), 
>(7.0,4.653624065352839), 
>(15.0,3.0687723922185906), 
>(31.0,2.0241074994435957), 
>(63.0,1.3351289174481258)] 
>
>   u1_label=r'$uniform_{1}$' 
>   u2_label=r'$uniform_{2}$' 
>   p1 = list_plot_loglog(u1_points, 
> plotjoined=True, 
> legend_label=u1_label, 
> base=10) 
>   p2 = list_plot_loglog(u2_points, 
> plotjoined=True, 
> color='red', 
> legend_label=u2_label, 
> base=10) 
>   p = p1 + p2 
>   p.show() 
>

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Re: [sage-devel] Notebooks: Show running vs. calculating sheets

[P Purkayastha]

Yes. There was some discussion about this in either sage-devel  or
sage-notebook.
On Apr 16, 2014 5:49 PM, "mmarco"  wrote:

> So, what is the plan for the future? Switch from the current notebook to
> something like the cloud interface? Will William release that part under
> the GPL?
>
> El miércoles, 16 de abril de 2014 10:24:29 UTC+2, P Purkayastha escribió:
>>
>> Some of these concerns are already addressed in cloud.sagemath. The
>> current notebook is very much in maintenance stage at present.
>>
>>
>> On Tuesday, April 15, 2014 8:50:04 PM UTC+8, Jori Mantysalo wrote:
>>>
>>> On Tue, 15 Apr 2014, John Cremona wrote:
>>>
>>> > One thing you can do is run top on your server: assuming that all
>>> > notebooks are running under the account with username sage, you can
>>> > look to see if any processes owned by sage are using a non-trivial
>>> > amount of CPU.  If not, you can go ahead and restart the server with a
>>> > small chance of annoying some of your users...
>>>
>>> Yes, I have done this too.
>>>
>>> Actually Sage needs few more tweaks from admin viewpoint. There should
>>> be
>>> easy way to notify users about coming reboot, something that
>>> shutdown-command on Linux can do for command line users.
>>>
>>> Also just logging in as admin is quite slow when there is, say, few
>>> hundred worksheets.
>>>
>>> And then removing users should be possible.
>>>
>>> --
>>> Jori Mäntysalo
>>>
>>  --
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Re: [sage-devel] Notebooks: Show running vs. calculating sheets

[P Purkayastha]

Some of these concerns are already addressed in cloud.sagemath. The current 
notebook is very much in maintenance stage at present.


On Tuesday, April 15, 2014 8:50:04 PM UTC+8, Jori Mantysalo wrote:
>
> On Tue, 15 Apr 2014, John Cremona wrote: 
>
> > One thing you can do is run top on your server: assuming that all 
> > notebooks are running under the account with username sage, you can 
> > look to see if any processes owned by sage are using a non-trivial 
> > amount of CPU.  If not, you can go ahead and restart the server with a 
> > small chance of annoying some of your users... 
>
> Yes, I have done this too. 
>
> Actually Sage needs few more tweaks from admin viewpoint. There should be 
> easy way to notify users about coming reboot, something that 
> shutdown-command on Linux can do for command line users. 
>
> Also just logging in as admin is quite slow when there is, say, few 
> hundred worksheets. 
>
> And then removing users should be possible. 
>
> -- 
> Jori Mäntysalo 
>

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Re: [sage-devel] Re: new layout breaks sagenb development?

[P Purkayastha]

I have set up a pull request to move the flask_version directory to inside
sagenb.

The documentation can be fixed later, but this should enable anyone to
start working on sagenb dev immediately. I also checked that the newly
generated sagenb tarball installs and works correctly.

- basu.



On Tue, Apr 8, 2014 at 11:35 PM, R. Andrew Ohana wrote:

> The symbolic link exists for the sole reason that previously you could not
> install sagenb as a standard python package (it cared deeply about its
> location in the SAGE_ROOT); this was necessary for getting sagenb to
> initially work on the git version of Sage. The symbolic link was made (as a
> hack) because I didn't know what (and didn't want to deal with) other
> things might be affected if I actually moved that directory. However, it
> should probably be physically moved, and not just linked.
>
>
> On Tue, Apr 8, 2014 at 8:30 AM, P Purkayastha  wrote:
>
>> Hello Jonathan,
>>
>>  In my experience, making a symbolic link to the root of the sagenb
>> directory does not work. Making a symbolic link to the sagenb directory
>> *inside the sagenb root* also does not work.
>>
>>  My suggestion would be to change the layout of the sagenb root directory
>> and move flask_version to inside the sagenb/sagenb, instead of having it as
>> a symbolic link.
>>
>> - basu.
>>
>>
>>
>> On Tue, Apr 8, 2014 at 11:21 PM, Jonathan  wrote:
>>
>>> Another solution that works is to work with a separate sagenb git
>>> repository and then rename the directory sagenb inside the egg to something
>>> like sagenb_old.  Then create a symlink to your development git repository
>>> named sagenb.  This is almost the same solution as Basu's.
>>>
>>> On Tuesday, April 8, 2014 10:07:30 AM UTC-5, kcrisman wrote:
>>>>
>>>> Hey Basu,  thanks!  That sounds great.
>>>>
>>>> Can you open a ticket to fix the developer guide with this information
>>>> (the last section on sagenb development)?  (Suitably generic, of course.)
>>>>
>>>> - kcrisman
>>>>
>>>> On Tuesday, April 8, 2014 10:45:24 AM UTC-4, P Purkayastha wrote:
>>>>>
>>>>> There is an easy fix. The main reason why it has broken sagenb
>>>>> development is because "sagenb/sagenb/flask_version" is a symbolic link to
>>>>> "sagenb/flask_version" - I do not know why it is set up like this. So,
>>>>> doing the following will allow you to work on sagenb dev - I will assume
>>>>> that your sage is in ~/sage and sagenb is in ~/sagenb:
>>>>>
>>>>> $ cd ~/sagenb/sagenb
>>>>> $ rm flask_version
>>>>> $ mv ../flask_version .
>>>>> $ cd ~/sage/local/lib/python/site-packages/sagenb-0.10.8.2-py2.7.egg
>>>>> $ mv sagenb{,-0.10.8.2}
>>>>> $ ln -s ~/sagenb/sagenb .
>>>>>
>>>>>
>>>>> And now, you can continue to work on sagenb dev in ~/sagenb.
>>>>>
>>>>> - basu.
>>>>>
>>>>> On Tuesday, April 8, 2014 10:33:03 AM UTC+8, kcrisman wrote:
>>>>>>
>>>>>> With the new directory layout, http://www.sagemath.org/doc/
>>>>>> developer/sagenb/index.html no longer makes any sense, and I don't
>>>>>> see any easy way to do any sagenb development without making new (s)pkgs.
>>>>>>  Is that correct?  Any ideas for making this simpler?
>>>>>>
>>>>>> Thanks,
>>>>>> - kcrisman
>>>>>>
>>>>>  --
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>>
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Re: [sage-devel] Re: new layout breaks sagenb development?

[P Purkayastha]

Hello Jonathan,

 In my experience, making a symbolic link to the root of the sagenb
directory does not work. Making a symbolic link to the sagenb directory
*inside the sagenb root* also does not work.

 My suggestion would be to change the layout of the sagenb root directory
and move flask_version to inside the sagenb/sagenb, instead of having it as
a symbolic link.

- basu.



On Tue, Apr 8, 2014 at 11:21 PM, Jonathan  wrote:

> Another solution that works is to work with a separate sagenb git
> repository and then rename the directory sagenb inside the egg to something
> like sagenb_old.  Then create a symlink to your development git repository
> named sagenb.  This is almost the same solution as Basu's.
>
> On Tuesday, April 8, 2014 10:07:30 AM UTC-5, kcrisman wrote:
>>
>> Hey Basu,  thanks!  That sounds great.
>>
>> Can you open a ticket to fix the developer guide with this information
>> (the last section on sagenb development)?  (Suitably generic, of course.)
>>
>> - kcrisman
>>
>> On Tuesday, April 8, 2014 10:45:24 AM UTC-4, P Purkayastha wrote:
>>>
>>> There is an easy fix. The main reason why it has broken sagenb
>>> development is because "sagenb/sagenb/flask_version" is a symbolic link to
>>> "sagenb/flask_version" - I do not know why it is set up like this. So,
>>> doing the following will allow you to work on sagenb dev - I will assume
>>> that your sage is in ~/sage and sagenb is in ~/sagenb:
>>>
>>> $ cd ~/sagenb/sagenb
>>> $ rm flask_version
>>> $ mv ../flask_version .
>>> $ cd ~/sage/local/lib/python/site-packages/sagenb-0.10.8.2-py2.7.egg
>>> $ mv sagenb{,-0.10.8.2}
>>> $ ln -s ~/sagenb/sagenb .
>>>
>>>
>>> And now, you can continue to work on sagenb dev in ~/sagenb.
>>>
>>> - basu.
>>>
>>> On Tuesday, April 8, 2014 10:33:03 AM UTC+8, kcrisman wrote:
>>>>
>>>> With the new directory layout, http://www.sagemath.org/doc/
>>>> developer/sagenb/index.html no longer makes any sense, and I don't see
>>>> any easy way to do any sagenb development without making new (s)pkgs.  Is
>>>> that correct?  Any ideas for making this simpler?
>>>>
>>>> Thanks,
>>>> - kcrisman
>>>>
>>>  --
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[sage-devel] Re: new layout breaks sagenb development?

[P Purkayastha]

There is an easy fix. The main reason why it has broken sagenb development 
is because "sagenb/sagenb/flask_version" is a symbolic link to 
"sagenb/flask_version" - I do not know why it is set up like this. So, 
doing the following will allow you to work on sagenb dev - I will assume 
that your sage is in ~/sage and sagenb is in ~/sagenb:

$ cd ~/sagenb/sagenb
$ rm flask_version
$ mv ../flask_version .
$ cd ~/sage/local/lib/python/site-packages/sagenb-0.10.8.2-py2.7.egg
$ mv sagenb{,-0.10.8.2}
$ ln -s ~/sagenb/sagenb .


And now, you can continue to work on sagenb dev in ~/sagenb.

- basu.

On Tuesday, April 8, 2014 10:33:03 AM UTC+8, kcrisman wrote:
>
> With the new directory layout, 
> http://www.sagemath.org/doc/developer/sagenb/index.html no longer makes 
> any sense, and I don't see any easy way to do any sagenb development 
> without making new (s)pkgs.  Is that correct?  Any ideas for making this 
> simpler?
>
> Thanks,
> - kcrisman
>

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[sage-devel] Re: help with sage -b under Git

[P Purkayastha]

I suggest that you upgrade to the develop branch using the following, when 
a new develop version is released:

# Assuming you are in SAGE_ROOT
$ git checkout develop
$ ./sage -upgrade develop 

These two lines are at the core of a zsh function in my ~/.zshrc. The full 
function can be found here: http://dpaste.com/hold/1750080/
I use it to fake the ATLAS installation (**), and build sage with a custom 
MAKE and "-march=native" CFLAGS.

- basu.

(**) I have to fake the ATLAS installation because sage never detects my 
system ATLAS correctly (installed from science overlay in Gentoo), and I 
really do not want to compile ATLAS every time on my laptop.


On Thursday, March 20, 2014 11:20:42 AM UTC+8, kcrisman wrote:
>
> I'm getting more used to sage -dev and/or git.  But weird things can 
> happen.  Tonight, on Mac OS X 10.7:
>
> 0) I was already at the 6.2.beta4 develop branch.
> 1) Checked out a ticket and sage -b and sage -docbuild reference html 
> (presumably branch changed to ticket/9321 since that is there)
> 2) Used sage -dev -create-ticket to create a new ticket
> 3) Checked out a new branch for that ticket ticket/15977
> 4) Did some documentation-only changes.
> 5) Did sage -b with disastrous results (below).  Help!  I really hope it 
> isn't this fragile, and if it is, we need massive warnings.
> 6) Committed my changes anyway, switched to develop branch, did ./sage -b 
> and zillions of Cythonizing and warnings... apparently the new branch was 
> based off 6.1.1, not 6.2.beta4?  But how do I control that?  Presumably not 
> good because of the possible spkg differences, oh no.
>
> $ ./sage -b
> g++ -o src/ZZ_pylong.os -c -fPIC -I/Users/.../sage/local/include 
> -I/Users/.../sage/local/include/python2.7 
> -I/Users/.../sage/local/include/NTL -Iinclude src/ZZ_pylong.cpp
> In file included from src/ZZ_pylong.cpp:13:0:
> include/ntl_wrap.h:255:35: error: using typedef-name 'NTL::mat_ZZ' after 
> 'struct'
> In file included from include/ntl_wrap.h:13:0,
>  from src/ZZ_pylong.cpp:13:
> /Users/.../sage/local/include/NTL/mat_ZZ.h:12:17: note: 'NTL::mat_ZZ' has 
> a previous declaration here
> In file included from src/ZZ_pylong.cpp:13:0:
> include/ntl_wrap.h:256:15: error: using typedef-name 'NTL::mat_ZZ' after 
> 'struct'
> In file included from include/ntl_wrap.h:13:0,
>  from src/ZZ_pylong.cpp:13:
> /Users/.../sage/local/include/NTL/mat_ZZ.h:12:17: note: 'NTL::mat_ZZ' has 
> a previous declaration here
> In file included from src/ZZ_pylong.cpp:13:0:
> include/ntl_wrap.h:256:47: error: using typedef-name 'NTL::mat_ZZ' after 
> 'struct'
> In file included from include/ntl_wrap.h:13:0,
>  from src/ZZ_pylong.cpp:13:
> /Users/.../sage/local/include/NTL/mat_ZZ.h:12:17: note: 'NTL::mat_ZZ' has 
> a previous declaration here
> In file included from src/ZZ_pylong.cpp:13:0:
> include/ntl_wrap.h:256:65: error: invalid type in declaration before ';' 
> token
> include/ntl_wrap.h:257:39: error: using typedef-name 'NTL::mat_ZZ' after 
> 'struct'
> In file included from include/ntl_wrap.h:13:0,
>  from src/ZZ_pylong.cpp:13:
> /Users/.../sage/local/include/NTL/mat_ZZ.h:12:17: note: 'NTL::mat_ZZ' has 
> a previous declaration here
> In file included from src/ZZ_pylong.cpp:13:0:
> include/ntl_wrap.h:258:39: error: using typedef-name 'NTL::mat_ZZ' after 
> 'struct'
> In file included from include/ntl_wrap.h:13:0,
>  from src/ZZ_pylong.cpp:13:
> /Users/.../sage/local/include/NTL/mat_ZZ.h:12:17: note: 'NTL::mat_ZZ' has 
> a previous declaration here
> In file included from src/ZZ_pylong.cpp:13:0:
> include/ntl_wrap.h:259:35: error: using typedef-name 'NTL::mat_ZZ' after 
> 'struct'
> In file included from include/ntl_wrap.h:13:0,
>  from src/ZZ_pylong.cpp:13:
> /Users/.../sage/local/include/NTL/mat_ZZ.h:12:17: note: 'NTL::mat_ZZ' has 
> a previous declaration here
> In file included from src/ZZ_pylong.cpp:13:0:
> include/ntl_wrap.h:260:47: error: using typedef-name 'NTL::mat_ZZ' after 
> 'struct'
> In file included from include/ntl_wrap.h:13:0,
>  from src/ZZ_pylong.cpp:13:
> /Users/.../sage/local/include/NTL/mat_ZZ.h:12:17: note: 'NTL::mat_ZZ' has 
> a previous declaration here
> In file included from src/ZZ_pylong.cpp:13:0:
> include/ntl_wrap.h:261:51: error: using typedef-name 'NTL::mat_ZZ' after 
> 'struct'
> In file included from include/ntl_wrap.h:13:0,
>  from src/ZZ_pylong.cpp:13:
> /Users/.../sage/local/include/NTL/mat_ZZ.h:12:17: note: 'NTL::mat_ZZ' has 
> a previous declaration here
> In file included from src/ZZ_pylong.cpp:13:0:
> include/ntl_wrap.h:262:15: error: using typedef-name 'NTL::mat_ZZ' after 
> 'struct'
> In file included from include/ntl_wrap.h:13:0,
>  from src/ZZ_pylong.cpp:13:
> /Users/.../sage/local/include/NTL/mat_ZZ.h:12:17: note: 'NTL::mat_ZZ' has 
> a previous declaration here
> In file included from src/ZZ_pylong.cpp:13:0:
> include/ntl_wrap.h:262:

[sage-devel] Is sagenb.org ok?

[P Purkayastha]

There are a couple of recent reports with non-functioning or incorrect 
openid authentications at the end of the google bug reports:

https://spreadsheets.google.com/pub?key=pCwvGVwSMxTzT6E2xNdo5fA

The versions are all 5.11 which is what sagenb.org is running.

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[sage-devel] Re: Adding plot to polyhedron plot has side effects

[P Purkayastha]

On 02/24/2014 01:55 AM, Robert Lipshitz wrote:

Hi,

When I add a 3d plot to a polyhedron plot, it doesn't just return a new plot 
object but also changes the polyhedron plot. On the other hand, adding two 3d 
plots does not change either of them. For example:

sage: x = var('x')
sage: y = var('y')
sage: plot1 = plot3d(x^2+y^2,(x,-2,2),(y,-2,2))
sage: plot2 = plot3d(x^2-y^2, (x,-2,2), (y,-2,2))
sage: plot3 = plot3 = Polyhedron(vertices = list(Permutations(3))).plot() #A 
hexagon in 3-space (the 2d permutohedron)
sage: plot4 = plot3+plot1
sage: plot5 = plot2+plot1

After this, plot2 has not changed, but plot3 is now the union of a hexagon and 
a paraboloid. Check it:

sage: plot2
sage: plot4

I assume this is a bug, but thought I would check before reporting it to trac. 
Is this desired behavior?

(I'm using Sage 6.1.1.)

Thanks,
Robert



This is known: http://trac.sagemath.org/ticket/13288

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[sage-devel] Re: Saving .show() Output as a Vector Graphic

[P Purkayastha]

On 02/24/2014 12:22 PM, Evan Oman wrote:

I am using Sage to make visual representations of Graphs(ie of the vertex and 
edge variety) via the show command.

However as far as I can tell I can only save these as a raster in the form of a 
PNG or JPEG? I have been a vector graphic snob as of late and would like to 
save graphs as PDF like I can regular plots. Is this possible?

Thanks!


instead of show() simply use save(). You can give the same arguments to 
save() as you give to show(), except for the first one - that should be 
the filename, like


plot(x).save('/tmp/a.pdf', )
plot(x).save('./a.eps', )
plot(x).save('./a.svg', )

If the latter two are done in a notebook cell, it will show a link to 
the file.




PS: I am not sure if this is an appropriate venue to post such a question, if 
this is the case let me know where I should direct my related inquirers.



You should direct such requests to sage-support.

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[sage-devel] Re: drop future first-class SPARC support?

[P Purkayastha]

On 02/23/2014 03:32 PM, Jeroen Demeyer wrote:

On 2014-02-22 16:58, P Purkayastha wrote:

Add another ticket to that list. SPARC also blocks an improvement in
#12798.

I totally disagree with that. That ticket has *nothing* at all to do
with SPARC. There's an obvious right fix (not rendering plots with
NaNs). If you write code which depends on the fact that a 3D renderer
will work correctly if you feed it NaNs, that's dangerous in any case.



Well, the discussion in the ticket goes into more details. But here is 
the summary


1. *we* are not generating NaNs in Sage code. Those are happening from 
matplotlib:

https://github.com/matplotlib/matplotlib/blob/master/lib/matplotlib/delaunay/interpolate.py#L81

2. I am definitely not interested in rewriting / reimplementing working 
matplotlib code.


3. The bad behavior happens *only* on SPARC and *only* during doctest.

4. The current output is *wrong*. And it has been so ever since the 
function was introduced six years ago.


Personally, incorrect output is something that I am definitely not 
supportive of. It is worse than not having a functionality to begin with.


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[sage-devel] Re: drop future first-class SPARC support?

[P Purkayastha]

On 02/22/2014 06:07 PM, Volker Braun wrote:

SPARC also blocks the gap-4.7 upgrade, and gap upstream appears not interested 
in fixing that anytime soon.

On the other hand, ARM and POWER7 are actually relevant platforms that we could 
support.



Add another ticket to that list. SPARC also blocks an improvement in #12798.

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[sage-devel] Re: admin for ask.sagemath

[P Purkayastha]

On 02/21/2014 04:45 PM, Ralf Stephan wrote:

On Thursday, February 20, 2014 7:18:55 PM UTC+1, kcrisman wrote:

And this is a good time to remind people not to *close* posts, but
flag them, so they can be deleted, if they are truly spam.  I
haven't tried to actually delete a closed post with my new
superpowers yet, but with karma it was not possible.


um, how would I do that?  short of downvoting I cannot seem to find a
flag button.
at stackoverflow there is "share/edit/flag"...


I hope those with admin permissions ban that ip. The amount of spam is 
simply ridiculous at present.


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[sage-devel] Re: arcsec(float(.1)) throws error

[P Purkayastha]

On 02/13/2014 06:50 AM, Jason Grout wrote:

David Smith just pointed this out: arcsec(float(.1)) throws an error
that doesn't make much sense.  Yes, it's outside of the domain, but it
should probably deal with this by returning NaN or something rather than
a type error.  This came up when David was trying to plot arcsec.

On a related note, maybe we should have some sort of error that can be
thrown for values outside of domains?  Plot could catch an out-of-domain
error and break the drawing there, so you wouldn't end up with something
like http://sagecell.sagemath.org/?q=llweji

Thanks,

Jason



The patch to plot() needs review since nearly two years. You may want to 
review, or check that ticket:


http://trac.sagemath.org/ticket/13246

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[sage-devel] Re: Embedded LaTeX do not show up in Sage 6.1 notebook

[P Purkayastha]

Thanks goes to Jeroen :)

On 02/02/2014 04:45 PM, Eric Gourgoulhon wrote:

Thank you for this rapid fix !

Eric.

Le samedi 1 février 2014 23:45:29 UTC+1, P Purkayastha a écrit :


You can fix it temporarily by doing the modification in
https://github.com/sagemath/sagenb/issues/195#issuecomment-33885044
<https://github.com/sagemath/sagenb/issues/195#issuecomment-33885044>

The modification has to be made to the file
SAGE_ROOT/local/lib/python/site-packages/sagenb-0.10.7*/sagenb/misc/misc.py


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[sage-devel] Re: Embedded LaTeX do not show up in Sage 6.1 notebook

[P Purkayastha]

On 02/01/2014 10:14 PM, Eric Gourgoulhon wrote:

Hi,

I've just made a fresh install of Sage 6.1 from the sources (via git
clone) and noticed that LaTeX formulas in the notebook are not rendered
by Mathjax: they remain between $ symbols, as they have been typed. This
regards LaTeX formulas typed as comments in the text between the cells,
not the output cells (in the latter, the LaTeX display is OK, except for
a color problem: there is some mix of blue and dark green). There are
some error messages displayed in the console, which I copy below.

I tried with two different browsers (Firefox and Chromium). With Sage
6.0 everything was OK.
Do others have the same problem ?

Eric.


You can fix it temporarily by doing the modification in
https://github.com/sagemath/sagenb/issues/195#issuecomment-33885044

The modification has to be made to the file
SAGE_ROOT/local/lib/python/site-packages/sagenb-0.10.7*/sagenb/misc/misc.py

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[sage-devel] Re: Embedded LaTeX do not show up in Sage 6.1 notebook

[P Purkayastha]

On 02/01/2014 11:56 PM, P Purkayastha wrote:

Thanks for the report. I have opened an issue in sagenb [1]. It's
puzzling since I didn't see this during the 6.1.beta* versions.

[1] https://github.com/sagemath/sagenb/issues/195


sagenb-0.10.8 (the latest sagenb) + sage-6.1.beta4 works fine. So, the 
bug is probably introduced in sage after the release of 6.1.beta4.


- basu.

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[sage-devel] Re: Embedded LaTeX do not show up in Sage 6.1 notebook

[P Purkayastha]

Thanks for the report. I have opened an issue in sagenb [1]. It's 
puzzling since I didn't see this during the 6.1.beta* versions.


[1] https://github.com/sagemath/sagenb/issues/195

On 02/01/2014 10:14 PM, Eric Gourgoulhon wrote:

Hi,

I've just made a fresh install of Sage 6.1 from the sources (via git
clone) and noticed that LaTeX formulas in the notebook are not rendered
by Mathjax: they remain between $ symbols, as they have been typed. This
regards LaTeX formulas typed as comments in the text between the cells,
not the output cells (in the latter, the LaTeX display is OK, except for
a color problem: there is some mix of blue and dark green). There are
some error messages displayed in the console, which I copy below.

I tried with two different browsers (Firefox and Chromium). With Sage
6.0 everything was OK.
Do others have the same problem ?

Eric.

Error messages:

2014-02-01 14:50:14+0100 [-] WSGI application error
 Traceback (most recent call last):
   File
"/home/eric/sage-git/sage-6.1/sage/local/lib/python2.7/site-packages/Twisted-13.1.0-py2.7-linux-x86_64.egg/twisted/python/threadpool.py",
line 212, in _worker
 o = self.q.get()
   File
"/home/eric/sage-git/sage-6.1/sage/local/lib/python2.7/site-packages/Twisted-13.1.0-py2.7-linux-x86_64.egg/twisted/python/context.py",
line 118, in callWithContext
 return self.currentContext().callWithContext(ctx, func, *args,
**kw)
   File
"/home/eric/sage-git/sage-6.1/sage/local/lib/python2.7/site-packages/Twisted-13.1.0-py2.7-linux-x86_64.egg/twisted/python/context.py",
line 83, in callWithContext
 self.contexts.pop()
   File
"/home/eric/sage-git/sage-6.1/sage/local/lib/python2.7/site-packages/Twisted-13.1.0-py2.7-linux-x86_64.egg/twisted/web/wsgi.py",
line 340, in run
 self.started = True
 ---  ---
   File
"/home/eric/sage-git/sage-6.1/sage/local/lib/python2.7/site-packages/Twisted-13.1.0-py2.7-linux-x86_64.egg/twisted/web/wsgi.py",
line 315, in run
 appIterator = self.application(self.environ, self.startResponse)
   File
"/home/eric/sage-git/sage-6.1/sage/local/lib/python2.7/site-packages/Flask-0.10.1-py2.7.egg/flask/app.py",
line 1836, in __call__
 return self.wsgi_app(environ, start_response)
   File
"/home/eric/sage-git/sage-6.1/sage/local/lib/python2.7/site-packages/Flask-0.10.1-py2.7.egg/flask/app.py",
line 1820, in wsgi_app
 response = self.make_response(self.handle_exception(e))
   File
"/home/eric/sage-git/sage-6.1/sage/local/lib/python2.7/site-packages/Flask-0.10.1-py2.7.egg/flask/app.py",
line 1403, in handle_exception
 reraise(exc_type, exc_value, tb)
   File
"/home/eric/sage-git/sage-6.1/sage/local/lib/python2.7/site-packages/Flask-0.10.1-py2.7.egg/flask/app.py",
line 1817, in wsgi_app
 response = self.full_dispatch_request()
   File
"/home/eric/sage-git/sage-6.1/sage/local/lib/python2.7/site-packages/Flask-0.10.1-py2.7.egg/flask/app.py",
line 1477, in full_dispatch_request
 rv = self.handle_user_exception(e)
   File
"/home/eric/sage-git/sage-6.1/sage/local/lib/python2.7/site-packages/Flask-0.10.1-py2.7.egg/flask/app.py",
line 1381, in handle_user_exception
 reraise(exc_type, exc_value, tb)
   File
"/home/eric/sage-git/sage-6.1/sage/local/lib/python2.7/site-packages/Flask-0.10.1-py2.7.egg/flask/app.py",
line 1475, in full_dispatch_request
 rv = self.dispatch_request()
   File
"/home/eric/sage-git/sage-6.1/sage/local/lib/python2.7/site-packages/Flask-0.10.1-py2.7.egg/flask/app.py",
line 1461, in dispatch_request
 return self.view_functions[rule.endpoint](**req.view_args)
   File
"/home/eric/sage-git/sage-6.1/sage/local/lib/python2.7/site-packages/sagenb-0.10.7.2-py2.7.egg/sagenb/flask_version/base.py",
line 144, in mathjax_js
 data = render_template('js/mathjax_sage.js',
theme_mathjax_macros=mathjax_macros)
   File
"/home/eric/sage-git/sage-6.1/sage/local/lib/python2.7/site-packages/Flask-0.10.1-py2.7.egg/flask/templating.py",
line 128, in render_template
 context, ctx.app)
   File
"/home/eric/sage-git/sage-6.1/sage/local/lib/python2.7/site-packages/Flask-0.10.1-py2.7.egg/flask/templating.py",
line 110, in _render
 rv = template.render(context)
   File
"/home/eric/sage-git/sage-6.1/sage/local/lib/python2.7/site-packages/Jinja2-2.5.5-py2.7.egg/jinja2/environment.py",
line 891, in render
 return self.environment.handle_exception(exc_info, True)
   File
"/home/eric/sage-git/sage-6.1/sage/local/lib/python2.7/site-packages/sagenb-0.10.7.2-py2.7.egg/sagenb/data/sage/js/mathjax_sage.js",
line 30, in top-level template code
 {{ theme_mathjax_macros|join(',\n') }}
   File
"/home/eric/sage-git/sage-6.1/sage/local/lib/python2.7/site-packages/Jinja2-2.5.5-py2.7.egg/jinja2/filters.py",
line 241, in do_join
 return unicode(d).join(imap(unicode, value))
 exceptions.TypeError: 'function' object is not iterable



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[sage-devel] Re: Giant email subjects from Trac

[P Purkayastha]

On 02/01/2014 11:27 AM, Michael Orlitzky wrote:

On 01/31/2014 11:33 AM, Keshav Kini wrote:

Hi,

Check this out: http://i.imgur.com/sbNIk6J.png

I *literally* cannot read this mail, because my monitor is not large
enough for the message body to even appear in my mail client!  :)  Even
"View Source" doesn't work, since the thing is UUencoded!

I guess someone will say I should use a better mail client...



https://addons.mozilla.org/en-us/thunderbird/addon/compactheader/



+1
Recommend this addon. I have been using it for years. Very nice addon.

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[sage-devel] Re: Giant email subjects from Trac

[P Purkayastha]

On 02/01/2014 12:33 AM, Keshav Kini wrote:

Hi,

Check this out: http://i.imgur.com/sbNIk6J.png

I *literally* cannot read this mail, because my monitor is not large
enough for the message body to even appear in my mail client!  :)  Even
"View Source" doesn't work, since the thing is UUencoded!

I guess someone will say I should use a better mail client...


Yeah, a better mail client and a bigger monitor. That one is not even 
full HD. You need 4K resolution at least.


On topic -- can the milestone bumps be done without the mass emails? It 
used to work earlier, somehow.


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[sage-devel] Re: Git reviewing help needed

[P Purkayastha]

On 01/30/2014 09:42 AM, kcrisman wrote:

Volker's last thing makes a lot more sense.  What I want to do is to get
back to the "master" or "develop" from there with "sage -dev checkout"
but I guess I need to already have known about the "--branch" parameter

$ ./sage -dev checkout --branch master
On local branch "master" without associated ticket.

#  Use "sage --dev merge" to include another ticket/branch.
#  Use "sage --dev commit" to save changes into a new commit.


2. What is the output of "git branch"?



$ git branch
   master
* ticket/13576
   ticket/15693
(well, now it's probably on master since I switched)

I think it would be very useful to have very explicit instructions for
how to create and stay on "develop" from upstream *using the sage -dev
scripts*.  I'll eventually figure it out but it's nice to have it within
Sage, again.  Unified context.


1. Staying on develop was my personal suggestion. To stay on that, you 
will need to run git directly:


$ git checkout -b develop --track origin/develop

(now you are on a local branch called "develop")

2. do your reviewing, etc, and after you are done

$ git checkout develop
- OR -
$ sage --dev checkout --branch develop

$ sage -b

(recompile to get back to the files from develop, assuming you had run 
sage -b earlier while reviewing the ticket)



3. If a new development version of sage gets released then run

$ sage -upgrade develop
$ git checkout develop # check out your local branch
$ git status   # check if develop is up to date. If not..
$ git rebase origin/develop # ... if not.. do this.

  - basu.

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[sage-devel] Re: Git reviewing help needed

[P Purkayastha]

On 01/29/2014 11:36 PM, kcrisman wrote:



 > Oh, and it's not clear to me
 > from
http://sagemath.org/doc/developer/walk_through.html#reviewing
 what
 > to do when I'm *done* reviewing!  I guess one "checks out master"
but
 > that is just something I sort of got through osmosis and I don't
know if
 > it's right, nor the sage -dev syntax for this.

As I mentioned above, I check out develop. This is most important when
packages are updated.



Unfortunately, the simple syntax didn't work.  Maybe I have to do
something else so it knows what "develop" is?  But that isn't in the doc.


1. What command are you running?

2. What is the output of "git branch"?


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[sage-devel] Re: Error: environment variable $HOME is not set.

[P Purkayastha]

On 01/28/2014 09:41 PM, Jeremy McFarland wrote:

Hello,

I am very impressed with sage, and would love to use it on my Ubuntu server. I 
attempted to install sagecell, but that was a huge mess and I gave up. I do not 
want to make calls to another system outside my network, so I need sage (or 
sagecell) to run locally.

I am running Ubuntu 12.04 Server with the latest version of Sage binary 
installed. When I attempt to execute a sage -python call I receive the 
following error in my Apache2 error.log:

Error: environment variable $HOME is not set.
Error setting environment variables by sourcing 
'/usr/lib/sagemath/spkg/bin/sage-env'

Setting $HOME in the python script does not fix this. /var/www/.sage exists in 
the www-data home directory of /var/www. www-data owns and has r/w on 
/var/www/.sage.

Is there a fix for this? If not, is there a successful install instruction set 
for installing sagecell on Ubuntu with the latest release of Sage? Any other 
alternatives for execution of python code using the Sage libraries so I can 
execute things in sage and return them to my PHP script being run on the 
webserver?


You can try to set $HOME in SAGE_ROOT/local/bin/sage-env, like

export HOME="some directory"

This file is not a python script, but is a bash script.
The problem you are facing is that Sage expects $HOME to be defined and 
the directory actually present. It uses $HOME/.sage by default where it 
stores all configuration.





Thanks in advance,

-Jeremy



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[sage-devel] Re: Git reviewing help needed

[P Purkayastha]

On 01/25/2014 10:14 AM, P Purkayastha wrote:

As mentioned earlier in this ML, using ccache will help. I haven't tried
using cycache.


I was trying to figure out how to enable cython caching. I can not find 
any documentation on it. Only #15430.


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[sage-devel] Re: Git reviewing help needed

[P Purkayastha]

On 01/24/2014 09:22 AM, kcrisman wrote:

$ ./sage -dev checkout --ticket 15693


At this point I usually do a "manual" diff against develop.

$ git diff origin/develop

I usually keep my "current version" at develop. I also keep my develop 
up to date by creating a local branch called develop that tracks 
origin/develop. This helps avoid big changes between tickets, especially 
when the changes involve package updates. Switching between a ticket and 
master is suboptimal in those cases, since there is no way to revert 
package updates.


$ git checkout -b develop origin/develop

If I find that a ticket is based off master or some old develop branch, 
I try to create another local branch based off my (very up to date) 
develop. Let's say the current branch is develop, then I will do


$ sage --dev checkout --ticket 1234567
$ git checkout -b my_1234567 origin/develop
$ git merge ticket/1234567  # if merge is unsuccessful, then tell author
$ sage -b
$ git diff origin/develop   # Now we can review the changes.

After I am done reviewing and if I have given positive review, then I 
can delete this branch.


$ git checkout develop
$ git branch -D my_1234567


Resuming my attempt:

$ ./sage -b


  Didn't I JUST BUILD SAGE?  Note that the ticket in question
touches one .pyx file and doesn't even change any code - it's a nearly
trivial documentation fix.


This is a problem with the git build. I think all the files that have 
been "touched" are recompiled, even though there are zero changes. This 
happens even if I change branch from develop to ticket/123456 that may 
be based off the most up to date develop branch.


As mentioned earlier in this ML, using ccache will help. I haven't tried 
using cycache.




Oh, and it's not clear to me
from http://sagemath.org/doc/developer/walk_through.html#reviewing what
to do when I'm *done* reviewing!  I guess one "checks out master" but
that is just something I sort of got through osmosis and I don't know if
it's right, nor the sage -dev syntax for this.


As I mentioned above, I check out develop. This is most important when 
packages are updated.



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[sage-devel] Re: Precision problems in taking determinant?

[P Purkayastha]

Well, my patch in that ticket is similar - give both a warning and 
autoconvert. This way one gets an answer immediately, and knows what to 
do later on.



On 01/21/2014 01:47 AM, Volker Braun wrote:

An argument against would be that you then can't contrast the two
implementations. One would at least need a way of disabling the
automatic change.

One could just raise a warning: "Use matrix(RDF, ...) instead".


On Monday, January 20, 2014 5:33:10 PM UTC, P Purkayastha wrote:

Would it be proper to autoconvert matrices over RR to RDF in case of
the
default precision


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Re: [sage-devel] Re: Precision problems in taking determinant?

[P Purkayastha]

On 01/21/2014 01:22 AM, Volker Braun wrote:

Your matrix easily exceeds the precision limit if the determinant is
computed naively.

sage: A.change_ring(RealIntervalField(53)).det()
0.?e10
sage: A.change_ring(RealIntervalField(60)).det()
0.?e8
sage: A.change_ring(RealIntervalField(80)).det()
1.68?e4
sage: A.change_ring(RealIntervalField(100)).det()
16801.79800?

B turns out to be correct since it uses a numerically more stable
algorithm. As a rule of thumb, computations with hardware floating point
numbers tend to be implemented best (at the cost of supporting only a
singe choice for precision)


On Monday, January 20, 2014 4:28:45 PM UTC, P Purkayastha wrote:

Which of these outputs should we trust?


In the face of numerical instability you should trust neither ;-)


Thanks, Volker and Vincent. RDF seems to be the recommended field. :)

Would it be proper to autoconvert matrices over RR to RDF in case of the 
default precision, so that the more stable numerical algorithms from RDF 
can be used? I had proposed one such change in #13660 ( 
http://trac.sagemath.org/13660 ) in case of eigenvalue/eigenvector 
computations.


- basu.

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[sage-devel] Precision problems in taking determinant?

[P Purkayastha]

The following matrix gives wildly different results

A = matrix([[  1.0,-1.50614628068, 2.26847661882,-
3.41665762226, 5.14598617013, -7.7506079306, 11.6735493077,-
17.5820728722],
[  1.0,   -0.936702701875,0.877411951699,   -0.821874145813,   
0.769851732984,   -0.721122198329,0.675477111557,   -0.632721235449],
[  1.0,   -0.443181140009, 0.19640952286,  -0.0870449962496,
0.03857670067,  -0.0170964661807,  0.00757683137208, -0.00335790876514],
[  1.0,0.352786603689,0.124458387743,   0.0439072519123,  
0.0154898902795,  0.00546462578321,  0.00192784677049, 0.000680118514595],
[  1.0,0.647213396311,0.418885180364,0.271108100248,   
0.175464794329, 0.11356316547, 0.07349960202,   0.0475699270508],
[  1.0, 1.44318114001, 2.08277180288, 3.00581698486,
4.33793838286, 6.26043086067, 9.03493574645, 13.0390488705],
[  1.0, 1.93670270187, 3.75081735545, 7.26421810653,
14.0686308339, 27.2467553477, 52.7688646993, 102.197602838],
[  1.0, 2.50614628068, 6.28076918019, 15.7405263208,
39.4480614948, 98.8626125954, 247.764168855, 620.933250262]])


B = A.change_ring(RDF)


print "det(A) = {}, det(B) = {}".format(A.determinant(), B.determinant())
print "parent(A) = {}\nparent(B) = {}".format(A.parent(), B.parent())

The output is the totally unexpected:

det(A) = -4.194304e6, det(B) = 16801.7979988
parent(A) = Full MatrixSpace of 8 by 8 dense matrices over Real Field with 53 
bits of precision
parent(B) = Full MatrixSpace of 8 by 8 dense matrices over Real Double Field

Which of these outputs should we trust? And what is the preferred field over 
which something as simple as a determinant should be computed?


- basu.

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[sage-devel] bug in doctesting framework

[P Purkayastha]

>From what I remember, doctesting a file using 
sage -btnew

used to work from all directories. It doesn't right now because it doesn't 
take the relative path or absolute path into account. The paths are all 
relative to SAGE_ROOT.

...ations/sage/src/sage/plot» sage -btnew
scons: `install' is up to date.
Updating Cython code
Finished compiling Cython code (time = 2.20727992058 seconds)
running install
running build
running build_py
copying sage/plot/matrix_plot.py -> build/lib.linux-x86_64-2.7/sage/plot
running build_ext
Executing 0 commands (using 1 thread)
Time to execute 0 commands: 0.0022029876709 seconds
Total time spent compiling C/C++ extensions:  0.0984809398651 seconds.
running install_lib
copying build/lib.linux-x86_64-2.7/sage/plot/matrix_plot.py -> 
/home/punarbasu/tmp/sage/local/lib/python2.7/site-packages/sage/plot
byte-compiling 
/home/punarbasu/tmp/sage/local/lib/python2.7/site-packages/sage/plot/matrix_plot.py
 
to matrix_plot.pyc
running install_egg_info
Removing 
/home/punarbasu/tmp/sage/local/lib/python2.7/site-packages/sage-6.1.beta5-py2.7.egg-info
Writing 
/home/punarbasu/tmp/sage/local/lib/python2.7/site-packages/sage-6.1.beta5-py2.7.egg-info
Running doctests with ID 2014-01-19-21-31-24-f65200e9.
Doctesting files changed since last git commit
Doctesting 1 file.
sage -t src/sage/plot/matrix_plot.py
IOError in doctesting framework
**
Traceback (most recent call last):
  File 
"/home/punarbasu/tmp/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py",
 
line 2086, in __call__
doctests, extras = self.source.create_doctests(sage_namespace)
  File 
"/home/punarbasu/tmp/sage/local/lib/python2.7/site-packages/sage/doctest/sources.py",
 
line 627, in create_doctests
raise IOError(errno.ENOENT, "File does not exist", self.path)
IOError: [Errno 2] File does not exist: 'src/sage/plot/matrix_plot.py'

--
sage -t src/sage/plot/matrix_plot.py  # IOError in doctesting framework
--
Total time for all tests: 0.0 seconds
cpu time: 0.0 seconds
cumulative wall time: 0.0 seconds



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[sage-devel] Re: untracked git files

[P Purkayastha]

Sorry, I had just created the ticket but not rebased on to develop. That 
got rid of all the untracked files (they are in gitignore) except for the 
last two. I don't know why they are present.

On Sunday, January 19, 2014 12:14:10 AM UTC+8, P Purkayastha wrote:
>
> In trying to import a patch, I ran across this problem:
>
> ~/Installations/sage» ./sage --dev import-patch --url "
> http://trac.sagemath.org/raw-attachment/ticket/13576/trac_13576-add_options_to_points.patch
> "
> There are untracked files in your working directory:
> aclocal.m4
> autom4te.cache/output.0
> autom4te.cache/output.1
> autom4te.cache/requests
> autom4te.cache/traces.0
> autom4te.cache/traces.1
> build/Makefile-auto
> build/Makefile-auto.in
> config.log
> config.status
> config/config.guess
> config/install-sh
> config/missing
> configure
> src/doc/en/reference/diophantine_approximation/conf.py
> src/doc/en/reference/diophantine_approximation/index.rst
> The patch cannot be imported unless these files are removed.
>
> What would be a good way to fix this? Should I add them or delete them 
> from git? Maybe add them to gitignore?
>

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[sage-devel] untracked git files

[P Purkayastha]

In trying to import a patch, I ran across this problem:

~/Installations/sage» ./sage --dev import-patch --url 
"http://trac.sagemath.org/raw-attachment/ticket/13576/trac_13576-add_options_to_points.patch";
There are untracked files in your working directory:
aclocal.m4
autom4te.cache/output.0
autom4te.cache/output.1
autom4te.cache/requests
autom4te.cache/traces.0
autom4te.cache/traces.1
build/Makefile-auto
build/Makefile-auto.in
config.log
config.status
config/config.guess
config/install-sh
config/missing
configure
src/doc/en/reference/diophantine_approximation/conf.py
src/doc/en/reference/diophantine_approximation/index.rst
The patch cannot be imported unless these files are removed.

What would be a good way to fix this? Should I add them or delete them from 
git? Maybe add them to gitignore?

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[sage-devel] bug in sage command line

[P Purkayastha]

Here is a weird bug in the sage command line. As you may have noticed, 
the sage: prompt does not return, and the command is actually still 
inside the for loop.


┌┐
│ Sage Version 6.1.beta5, Release Date: 2014-01-15   │
│ Type "notebook()" for the browser-based notebook interface.│
│ Type "help()" for help.│
└┘
┏┓
┃ Warning: this is a prerelease version, and it may be unstable. ┃
┗┛
sage: V = Integers(2)**2
sage: for v in V:
: print v # pressing ^C now
KeyboardInterrupt
: # This line is not indented. Let's press Enter
: # This line is indented.
: 2+2 # Still indented (and in reality we are inside the for loop)
KeyboardInterrupt
: 2+2
:
KeyboardInterrupt
:
  File "", line 4
Integer(2)+Integer(2)
  ^
IndentationError: expected an indented block

If you want to paste code into IPython, try the %paste and %cpaste magic 
functions.


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[sage-devel] Error in doctest

[P Purkayastha]

I see the following error in doctesting lately,

[padics   ] Exception occurred:
[padics   ] File "pow_computer.pxd", line 6, in init 
sage.rings.padics.padic_base_generic_element 
(sage/rings/padics/padic_base_generic_element.c:5658)
[padics   ] ValueError: sage.rings.padics.pow_computer.PowComputer_class 
has the wrong size, try recompiling
[padics   ] The full traceback has been saved in 
/tmp/sphinx-err-TyJgUm.log, if you want to report the issue to the 
developers.
[padics   ] Please also report this if it was a user error, so that a 
better error message can be provided next time.
[padics   ] Either send bugs to the mailing list at 
,
[padics   ] or report them in the tracker at 
. Thanks!

[combinat ] no targets are out of date.

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[sage-devel] Re: Python as build-time dependency

[P Purkayastha]

On 01/08/2014 03:39 PM, Jean-Pierre Flori wrote:

What scripting language use Gentoo in ebuilds?


Essentially, ebuilds are in bash, although portage is in python.

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[sage-devel] Re: sage crashes when current working directory is $SAGE_ROOT/src/sage !?

[P Purkayastha]

Same crash on Linux x86_64.


On 01/07/2014 11:19 PM, Vincent Delecroix wrote:

I do have the problem.

2014/1/7, Niles Johnson :

Am I confused?  My sage root directory is /Applications/sage.  I cd to

/Applications/sage/src/sage

and then attempt to start sage with either

/Applications/sage/sage

or

../../sage

Either of these results in a crash which looks related to ipython


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[sage-devel] Re: [sage-trac] #15107: Projective Plane designs

[P Purkayastha]

On 01/04/2014 10:46 PM, Nathann Cohen wrote:


I feel better now.

Nathann


^_^ \o/

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[sage-devel] Re: [sage-trac] #15107: Projective Plane designs

[P Purkayastha]

On 01/04/2014 10:20 PM, Nathann Cohen wrote:


The docstring will read :

- ``type`` -- When set to "Pappian", the method only returns Pappian
projective planes. No other value is available.


From what I understand, Dima is more concerned about future 
extendability of the function. If someone comes along with a different 
construction two years from now then that person can simply set a 
different type and the same function will work. Right *now*, there is no 
advantage other than the prospect of being maintainable and extendable 
in the far future.


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[sage-devel] Re: sage -upgrade idiosyncracies

[P Purkayastha]

Yes.

The output of make (run again; nothing to update) is attached. There are 
no differences between github, trac and my local develop branch.


~/Installations/sage» git rev-parse --abbrev-ref HEAD
develop
~/Installations/sage» git diff develop origin/develop
~/Installations/sage» diff -q local/bin/sage-upgrade src/bin/sage-upgrade
Files local/bin/sage-upgrade and src/bin/sage-upgrade differ
~/Installations/sage [1] »  git diff develop trac/develop
~/Installations/sage»

On 12/26/2013 12:32 AM, Volker Braun wrote:

You need to run "make" to install the updated scripts in local/, did you
do that?

On Wednesday, December 25, 2013 4:21:51 PM UTC, P Purkayastha wrote:

Well, that's the problem. local/bin is not tracked by git. And I am not
sure how else I can force the upgrade of the scripts. In terms of the
sage library, I am already on sage-6.1.beta2.

On 12/26/2013 12:12 AM, Volker Braun wrote:
 > It seems your first installation is pre-6.0. Before that was
released
 > there were bugs in the upgrade script. Use git to manually
upgrade to
 > 6.0 first, then "sage -upgrade" will (should) work.
 >
 >
 > On Wednesday, December 25, 2013 2:22:43 PM UTC, P Purkayastha wrote:
 >
 > With the second method it is all very smooth. I did a
 > .../src/sage/sage-6.0.server> git fetch origin
 >
 >
 > The fetch is also performed by the upgrade script, no need to do it
 > manually.
 >
 > followed by
 > .../src/sage/sage-6.0.server> ./sage -upgrade develop
 >
 >
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~/Installations/sage» make
cd build && \
"../build/pipestatus" \
"env SAGE_PARALLEL_SPKG_BUILD='' ./install all 2>&1" \
"tee -a ../logs/install.log"
Nothing to (re)build / all up-to-date.
./sage -b
scons: `install' is up to date.
Updating Cython code
Finished compiling Cython code (time = 2.21100997925 seconds)
running install
running build
running build_py
running build_ext
warning: Replacing library search directory in linker command:
  "/tmp/sage/local/lib" -> "/mnt/usb/Installations/sage/local/lib"

Executing 0 commands (using 1 thread)
Time to execute 0 commands: 0.00230002403259 seconds
Total time spent compiling C/C++ extensions:  0.0993618965149 seconds.
running install_lib
running install_egg_info
Removing 
/mnt/usb/Installations/sage/local/lib/python2.7/site-packages/sage-6.1.beta2-py2.7.egg-info
Writing 
/mnt/usb/Installations/sage/local/lib/python2.7/site-packages/sage-6.1.beta2-py2.7.egg-info

real0m3.227s
user0m2.853s
sys 0m0.267s
[ -f local/etc/sage-started.txt ] || local/bin/sage-starts
build/pipestatus "./sage --docbuild --no-pdf-links all html  2>&1" "tee -a 
logs/dochtml.log"

Building reference manual, first pass.

[combinat ] no targets are out of date.
[polynomia] no targets are out of date.
[cmd  ] no targets are out of date.
[dynamics ] no targets are out of date.
[arithgrou] no targets are out of date.
[graphs   ] no targets are out of date.
[homology ] no targets are out of date.
[misc ] no targets are out of date.
[notebook ] no targets are out of date.
[algebras ] no targets are out of date.
[calculus ] no targets are out of date.
[categorie] no targets are out of date.
[coding   ] no targets are out of date.
[coercion ] no targets are out of date.
[constants] no targets are out of date.
[cryptogra] no targets are out of date.
[databases] no targets are out of date.
[dev  ] no targets are out of date.
[diophanti] Configuration error:
[diophanti] There is a syntax error in your configuration file: invalid syntax 
(conf.py, line 1)
[doctest  ] no targets are out of date.
[finance  ] n

[sage-devel] Re: sage -upgrade idiosyncracies

[P Purkayastha]

Well, that's the problem. local/bin is not tracked by git. And I am not 
sure how else I can force the upgrade of the scripts. In terms of the 
sage library, I am already on sage-6.1.beta2.


On 12/26/2013 12:12 AM, Volker Braun wrote:

It seems your first installation is pre-6.0. Before that was released
there were bugs in the upgrade script. Use git to manually upgrade to
6.0 first, then "sage -upgrade" will (should) work.


On Wednesday, December 25, 2013 2:22:43 PM UTC, P Purkayastha wrote:

With the second method it is all very smooth. I did a
.../src/sage/sage-6.0.server> git fetch origin


The fetch is also performed by the upgrade script, no need to do it
manually.

followed by
.../src/sage/sage-6.0.server> ./sage -upgrade develop


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[sage-devel] sage -upgrade idiosyncracies

[P Purkayastha]

I had set up sage-git in two ways. The first one was by following the 
quickstartguide [1]. The second way was by using the sage-6.0 tarball.


First method (Quickstartguide):
---

Now, with the first method, it seems impossible to run sage -upgrade and 
have it behave properly. Here is an example output:


~/Installations/sage» ./sage -upgrade develop
fatal: 'develop' does not appear to be a git repository
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
There was a failure downloading Sage's sources. Please make sure you are 
connected to the internet. Aborting...

~/Installations/sage [1] »


This error is present even though the develop branch is present in the 
remote repository:


~/Installations/sage [1] » git branch -r | grep origin
  origin/HEAD -> origin/master
  origin/develop
  origin/master
  origin/upstream

The following command partially works:

~/Installations/sage» ./sage -upgrade g...@trac.sagemath.org:sage.git develop
From trac.sagemath.org:sage
 * [new branch]  develop-> zKYBy6_CBUB4D3fkr1eEgEY5-lmwod6sahiGr0V8
Already up-to-date.
Deleted branch zKYBy6_CBUB4D3fkr1eEgEY5-lmwod6sahiGr0V8 (was 036984d).
/mnt/usb/Installations/sage/local/bin/sage-upgrade: line 59: 
sage-real-upgrade: command not found


Followed this by a "make" and it recompiled maxima, and other than that 
I do not see any other changes.


Second method (sage-6.0 tarball):
-

With the second method it is all very smooth. I did a

.../src/sage/sage-6.0.server> git fetch origin

followed by

.../src/sage/sage-6.0.server> ./sage -upgrade develop



The main problem:
-

After a bit more investigating, it turns out that most of the scripts in 
SAGE_ROOT/local/bin are all at some old version from Dec 14. A bunch of 
questions:


1. So, even though I started out with sage-git from pre-6.0 version, at 
some point sage itself got upgraded but not installed (at least the 
scripts)?


2. How can I (manually) install the new scripts? Should I just copy the 
files from src/bin?


3. How can I prevent this problem from recurring in the future?


[1] http://trac.sagemath.org/wiki/QuickStartSageGit

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[sage-devel] Re: A bash script to find old deprecated code

[P Purkayastha]

This is very good. I think this should become a part of some dev script. So 
that it creates warnings every time there is an old deprecation (>1y old) 
while sage is being packaged!!

On Tuesday, December 24, 2013 5:13:32 AM UTC+8, Nathann Cohen wrote:
>
> Hellooo !!
>
> I just wrote this script, which lets you find old deprecations in Sage's 
> code. Just some bash and calls to git. If you run "./fdep . | sort -u" (and 
> wait a bit) you will get the list of occurrences of "deprecation(" in 
> Sage, sorted by age.
>
> Which makes it a nice tool to spot stuff which should have been 
> deprecated long ago.
>
> Now, is there a way to use it collectively ? Like in "sage -coverage" or 
> stuff like that ? I tried to remove all these codes by myself a couple of 
> days ago, to just notice it was beyond me :-P
>
> 2011-04-29 #3416 ./schemes/elliptic_curves/constructor.py
> 2011-05-20 #9265 ./combinat/skew_tableau.py
> 2011-05-20 #9265 ./combinat/tableau.py
> 2011-08-03 #11360 ./groups/perm_gps/cubegroup.py
> 2011-08-22 #7748 ./functions/exp_integral.py
> 2011-09-08 #11634 ./geometry/polyhedron/base.py
> 2011-09-08 #11763 ./geometry/polyhedron/base.py
> 2012-01-01 #10358 ./databases/sloane.py
> 2012-06-15 #12930 ./combinat/alternating_sign_matrix.py
> 2012-06-30 #12484 ./misc/misc.py
>
> Nathann
>
> P.S. : Some calls to deprecations are actually older than that, but this 
> script works by asking git when each line was last modified. Thus 
> some deprecation can appear to be younger than they are ;-)
>  

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[sage-devel] D3 viewer for matplotlib

[P Purkayastha]

This blog article might be of interest:
http://jakevdp.github.io/blog/2013/12/19/a-d3-viewer-for-matplotlib/

 - basu.

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[sage-devel] Re: Several years of bug reports

[P Purkayastha]

On 12/20/2013 06:40 PM, Harald Schilly wrote:

On Fri, Dec 20, 2013 at 6:24 AM, P Purkayastha  wrote:

So, is it confirmed that the redirect will be to ask.sagemath?



Well, I'm not aware of a "formal" decision, but I think it's the best
place for a first stop to help users. In any circumstance, the
redirect can be changed very quickly.

Harald



Ok. So, I will merge the changes and later we can decide where the 
redirect will go to. :)


basu.

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[sage-devel] Re: Several years of bug reports

[P Purkayastha]

So, is it confirmed that the redirect will be to ask.sagemath? If so, I 
will merge the changes in #186 and #187 which links the notebook to the URL 
provided by Harald.

- basu.

On Wednesday, December 11, 2013 1:22:05 PM UTC+8, P Purkayastha wrote:
>
> On 12/10/2013 11:08 PM, Harald Schilly wrote: 
> > On Tue, Dec 10, 2013 at 3:55 PM, kcrisman wrote: 
> >>> This is a very good idea. Then the notebook doesn't need to be 
> changed. 
> >> 
> >> 
> >> +1 
> > 
> > The 301 redirect works now: 
> > http://sagemath.org/report-issue 
> > 
> > Harald 
> > 
>
> Thanks. I have put up a pull request: 
> https://github.com/sagemath/sagenb/pull/186 
>

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[sage-devel] Re: Errors with long integers in Mathematica

[P Purkayastha]

On 12/16/2013 10:50 PM, Eric Gourgoulhon wrote:

You are not totally wrong, although I do not feel very qualified with
the charpoly stuff. So I tried to review the patch: it works well under
Sage 5.10 but fails to install under 5.11 and 5.12, with the following
error message:

sage:
hg_sage.apply("/home/eric/sage-5.12/trac_local/trac_14403_symbolic_charpoly_v3.patch")

cd "/home/eric/sage-5.11/devel/sage" && sage --hg import
"/home/eric/sage-5.12/trac_local/trac_14403_symbolic_charpoly_v3.patch"
application de
/home/eric/sage-5.12/trac_local/trac_14403_symbolic_charpoly_v3.patch
patching file sage/matrix/matrix_symbolic_dense.pyx
Hunk #1 FAILED at 103
1 out of 2 hunks FAILED -- saving rejects to file
sage/matrix/matrix_symbolic_dense.pyx.rej
abandon : patch failed to apply

What does this mean ?


It means that the underlying code on which the patch was based has 
changed. So, the patch does not apply properly any more.


The exact change that failed to apply is in the file
sage/matrix/matrix_symbolic_dense.pyx.rej

Ideally, one would have to make the changes manually after looking at 
that .rej file. If you are unfamiliar with this, then leave it up to the 
author to reimplement (rebase) the patch on sage-5.12, or preferably 
sage-5.13, which is ready to be released.


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[sage-devel] Re: Several years of bug reports

[P Purkayastha]

On 12/10/2013 11:08 PM, Harald Schilly wrote:

On Tue, Dec 10, 2013 at 3:55 PM, kcrisman  wrote:

This is a very good idea. Then the notebook doesn't need to be changed.



+1


The 301 redirect works now:
http://sagemath.org/report-issue

Harald



Thanks. I have put up a pull request:
https://github.com/sagemath/sagenb/pull/186

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[sage-devel] Re: Several years of bug reports

[P Purkayastha]

On 12/10/2013 02:15 AM, Harald Schilly wrote:

additional idea: we should change the URL to an indirect one. Then we
can change this more easily! e.g. "http://sagemath.org/report-issue";
which is a 301 redirect to ask or whatever we want.


This is a very good idea. Then the notebook doesn't need to be changed.

basu.

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[sage-devel] Re: About groups., designs., and the brand-new codes.

[P Purkayastha]

On 11/22/2013 09:34 PM, John Cremona wrote:

On 22 November 2013 13:31, Nathann Cohen  wrote:

Hellooo !!


Backwards compatibility issues?


Well, we can deprecate stuff for a start. And the message could say "What
you are looking for moved to a different place ! It's larger, there is a lot
of light and a comfy couch. Come join us !"


I have a lot of code where I would
not want to change every NumberField(...) to fields.NumberField(...)
and similarly with QuadraticField() and CyclotomicField().  Is this
just a question of scale, i.e. those are almost all the special field
constructors while there are lots and lots of codes?


Hmmm... There is no "fields." object in the version of Sage I run, so I
don't get your question O_o


You are right -- but I thought that your proposal was that there
should be, instead of what there is now.



My reason for suggesting this change (at least for the sage/coding) is 
so that the codes are more easily discoverable.


 Right now, if I want a specific code, say Hamming code, I have to 
remember "oh.. the name of the code is Hamming, so it probably starts 
with Hamming in Sage too. Oh great! That works! Hamming gives 
HammingCode. Let's try LDPC.. nothing, ok.. maybe.. ldp, nope. 
Low, nope." And then I will have to go around searching through the 
documentation and realize that ldpc codes are not there in Sage.


With the codes. introduced by Nathann, it can easily be checked 
what codes are there - by simply doing a codes.. Once this ticket 
is in place, it would be in fact nice to not have all these codes also 
in the global namespace. Having them in both places is a duplication, 
and might even be confusing to a new user. It is not for now, but rather 
for later - as the components inside Sage themselves grow in size with 
new constructions they will be better organized if they are under the 
general names and discoverable via tab completion beyond that. 
Temporarily, one's programs may not run or may give deprecation errors. 
Over the long term everyone should benefit from a neatly organized 
namespace.


Just my opinion. :)

- basu.

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[sage-devel] Re: Changing branch on a trac ticket

[P Purkayastha]

On 11/04/2013 06:25 AM, Volker Braun wrote:

On Sunday, November 3, 2013 9:29:09 PM UTC, Nils Bruin wrote:

For purpose (b), however, it would be nicer if 


The git log is easily accessible from code. Its easy to write all kinds
of analysis scripts if you care to.


If you check out the branch locally, you can run a

git diff  

to see the cumulative changes.



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

[P Purkayastha]

On 09/27/2013 10:57 AM, kcrisman wrote:

 From a user.  I'm not sure how the matplotlib devels would feel about
adding this.  And which RGB value would it be, anyway? ;-)
+++
One of my students pointed out a weird flaw in Sage today.  Namely, in
the plotting color options, 'sage' is not a known color name.  So, e.g.,
plot((e^(sin(x))),(x,-5,5),color='sage')
generates an error.

My entire class felt that this was a problematic oversight on the part
of the Sage developers.  In fact, they proposed that sage be the default
plotting color in Sage.

Any insights here?  Are the developers humorless?  Have they just not
noticed this gaping color hole?


We need easter eggs inside Sage! I will get to inserting some eggs right 
away!



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[sage-devel] Re: Matplotlib: Error when building sage and possible fix

[P Purkayastha]

Did you try the compilation with the environment variable 

SAGE_INSTALL_GCC="no"

This should avoid installing gcc. Also, gcc 4.6 does support "-march" 
option. Is that what you meant to write when you wrote "-arch"?

On Saturday, August 24, 2013 5:46:41 PM UTC+8, ASageWoodpecker wrote:
>
> When trying to build sage, I came across a weird situation with matplotlib 
> on OS X.
>
> The setup deemed my default version of gcc (LLVM) to be too old 
> (equivalent to 4.2) and downloaded GNU GCC 4.6. However, the build script 
> for matplotlib insisted on having the '-arch' option for compilation via 
> the local version of gcc. Presumably, this helps the executable work with 
> the x86_64 architecture on OS X or as a fat binary. But GNU GCC 4.6 does 
> not support the '-arch' flag, only LLVM gcc does. As a result, the whole 
> build script fails.
>
> I eventually got around this problem by going to the matplotlib build 
> directory within the sage-root directory, invoking the sage-shell for the 
> environment and temporarily renaming the sage-installed version of GNU GCC 
> before invoking the build script. This let the build script use the default 
> compiler on my system and the matplotlib build finished without a hitch 
> thereafter.
>
> I'm not sure of the best way to fix this bug. But I think one of the 
> following would work:
> 1. Use a local version of gcc that supports the '-arch' flag that 
> matplotlib wants to use
> 2. Change the matplotlib build script to provide the '-arch' information 
> through a valid flag.
>
> Hope this is helpful to others in working around the problem or maybe 
> committing a fix to the source.
>

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[sage-devel] Re: Getting sage-git or sage- to compile

[P Purkayastha]

Well, the 3.10 series is a disaster here. It doesn't even boot properly. My 
kernel config is essentially unchanged from 3.9.11. Trying out 3.8 series 
now :-(

On Friday, August 23, 2013 1:44:39 PM UTC+8, P Purkayastha wrote:
>
> On 08/23/2013 10:48 AM, Dima Pasechnik wrote: 
> > On 2013-08-22, P Purkayastha  wrote: 
> >> Yes. The kernel was one of the things that I upgraded. I am currently 
> on 
> >> 3.9.11, which I upgraded from 3.7.10.  I will try using some other 
> kernel. 
> >> 
> >> If it is the kernel, it is very unfortunate and troubling. I had 
> >> upgraded to 3.10.2 from 3.7.10, and had to immediately downgrade to 
> >> 3.9.11 because of issues with mounting one particular usb stick. 
> > 
> > isn't 3.10.9 the latest stable? 
>
> Yes. As I mentioned earlier, 3.10.2 had a bad bug with handling usb 
> disks. I will try upgrading and check whether 3.10.9 has the usb bug and 
> whether it exhibits the bug in sage or not. 
>
>
>

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[sage-devel] Re: Getting sage-git or sage- to compile

[P Purkayastha]

On 08/23/2013 10:48 AM, Dima Pasechnik wrote:

On 2013-08-22, P Purkayastha  wrote:

Yes. The kernel was one of the things that I upgraded. I am currently on
3.9.11, which I upgraded from 3.7.10.  I will try using some other kernel.

If it is the kernel, it is very unfortunate and troubling. I had
upgraded to 3.10.2 from 3.7.10, and had to immediately downgrade to
3.9.11 because of issues with mounting one particular usb stick.


isn't 3.10.9 the latest stable?


Yes. As I mentioned earlier, 3.10.2 had a bad bug with handling usb 
disks. I will try upgrading and check whether 3.10.9 has the usb bug and 
whether it exhibits the bug in sage or not.



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[sage-devel] Re: Getting sage-git or sage- to compile

[P Purkayastha]

Yes. The kernel was one of the things that I upgraded. I am currently on 
3.9.11, which I upgraded from 3.7.10.  I will try using some other kernel.


If it is the kernel, it is very unfortunate and troubling. I had 
upgraded to 3.10.2 from 3.7.10, and had to immediately downgrade to 
3.9.11 because of issues with mounting one particular usb stick.


On 08/22/2013 08:02 PM, Volker Braun wrote:

This sounds to me like a kernel issue, did you recently switch it?
Various programs that benchmark implementations hang forever. I'm pretty
sure something is wrong with timers and/or signals.


On Thursday, August 22, 2013 9:30:54 AM UTC+1, P Purkayastha wrote:

Hi all,

   Due to some change in my system sage no longer finishes compiling.
This is irrespective of whether it is sage-git or some released
version.
Usually it is some tuning process that remains stuck for ever.

* At one point, it was atlas that was tuning for two whole days and
never finished (irrespective of whether I gave the ARCH as "base" or
"Core2" or let it decide by itself). A system installation of atlas
finished compiling and installing in 20 min. Thanks to Burcin, I have
been able to use the system atlas and tricked sage into continuing with
the rest of the installation.

* Now, it is g2fx that is stuck for ever. It remains stuck at again a
tuning program that doesn't use any cpu and it will remain stuck like
this for days on end without any resolution. The log file of g2fx is
attached and a screenshot is attached which shows at which command
it is
stuck.

I am at a loss and I can't understand what exactly is impeding these
tuning processes. It is also a hindrance since I am unable to install
any newer version of sage on this particular machine, beyond what I had
last compiled (sage-5.11.beta3):
model name: Intel(R) Core(TM)2 CPU  6400  @ 2.13GHz

If anyone can let me know how I can use a system installation of
g2fx or
just let it use some generic tuning parameters, it will be great, and I
can continue with actually working with sage instead of fighting it!

Thanks,
basu.

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[sage-devel] Re: Getting sage-git or sage- to compile

[P Purkayastha]

It is just sitting there doing nothing.

...tallations/sage/logs/pkgs» strace -p 3679
Process 3679 attached
^CProcess 3679 detached
...tallations/sage/logs/pkgs»


~» cat gdb.3679.log
(gdb) #0  0x004011d8 in tuning_gf2x_mul1 (c=c@entry=0x658010, 
a=1084672390, b=1756245403) at gen_mul1_w64k2.c:63

hi = 
lo = 
tmp = 
A = {0, 1084672390, 2169344780, 3253426826}
#1  0x00400ba1 in main (argc=, argv=out>) at tuneup_1.c:127

i = 
c0 = 0x658030
c = 0x658010
a = 0x7fa29ea52010
b = 0x7fa29e9d1010
st = 0
benchtime = 
btime = 100
progname = 0x7fff89641610 
"/home/punarbasu/Installations/sage/local/var/tmp/sage/build/gf2x-1.1/src/src/.libs/tune_gen_mul1_w64k2"

m = 313810596090
(gdb) A debugging session is active.

Inferior 1 [process 3679] will be detached.

Quit anyway? (y or n) [answered Y; input not from terminal]
Detaching from program: 
/home/punarbasu/Installations/sage/local/var/tmp/sage/build/gf2x-1.1/src/src/.libs/tune_gen_mul1_w64k2, 
process 3679




On 08/22/2013 04:55 PM, Francois Bissey wrote:

Can you attach with strace or gdb to see what the process is doing? If it does 
anything at all that is.

Francois

On 22/08/2013, at 20:30, "P Purkayastha"  wrote:


Hi all,

Due to some change in my system sage no longer finishes compiling. This is 
irrespective of whether it is sage-git or some released version. Usually it is 
some tuning process that remains stuck for ever.

* At one point, it was atlas that was tuning for two whole days and never finished (irrespective of 
whether I gave the ARCH as "base" or "Core2" or let it decide by itself). A 
system installation of atlas finished compiling and installing in 20 min. Thanks to Burcin, I have 
been able to use the system atlas and tricked sage into continuing with the rest of the 
installation.

* Now, it is g2fx that is stuck for ever. It remains stuck at again a tuning 
program that doesn't use any cpu and it will remain stuck like this for days on 
end without any resolution. The log file of g2fx is attached and a screenshot 
is attached which shows at which command it is stuck.

I am at a loss and I can't understand what exactly is impeding these tuning 
processes. It is also a hindrance since I am unable to install any newer 
version of sage on this particular machine, beyond what I had last compiled 
(sage-5.11.beta3):
model name: Intel(R) Core(TM)2 CPU  6400  @ 2.13GHz

If anyone can let me know how I can use a system installation of g2fx or just 
let it use some generic tuning parameters, it will be great, and I can continue 
with actually working with sage instead of fighting it!

Thanks,
  basu.

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[sage-devel] Re: Getting sage-git or sage- to compile

[P Purkayastha]

On 08/22/2013 05:22 PM, Jeroen Demeyer wrote:

On 2013-08-22 10:30, P Purkayastha wrote:

Hi all,

  Due to some change in my system sage no longer finishes compiling.
This is irrespective of whether it is sage-git or some released version.
Usually it is some tuning process that remains stuck for ever.


Have you tried a different C compiler (or installing Sage from scratch
with SAGE_INSTALL_GCC=yes)?



Yes. I have tried gcc-4.6.3 which is the stable version in gentoo and 
also gcc-4.7.3 which is the highest unstable version in gentoo.



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[sage-devel] Re: Weird banner

[P Purkayastha]

On 08/20/2013 09:53 PM, John Cremona wrote:

On 20 August 2013 14:50, William Stein  wrote:


On Aug 20, 2013 6:45 AM, "David Loeffler" 
wrote:


Hi John,

Are you maybe using Sage inside a screen session? Apparently screen
doesn't play nicely with UTF-8 characters, unless you invoke it with
"screen -U".


If so, time to switch to tmux!!!


Never heard of it -- some kind of screen only better?

John


Some people would say that you should ditch X and switch to console+tmux 
if you are currently using a tiling window manager with only xterm windows.


Another example of such a tiling console is dvtm.



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[sage-devel] Re: atlas tuning

[P Purkayastha]

On 08/19/2013 09:26 PM, Volker Braun wrote:

Different ATLAS versions have different routines so the architectural
defaults for one version don't necessarily match another version.

If you don't want top performance then you can always set
SAGE_ATLAS_ARCH=fast or SAGE_ATLAS_ARCH=base when compiling Sage, this
will use some generic settings but will build much faster.


I have tried all of these tricks and still couldn't get atlas, g2fx to 
build. Both of them remain stuck at some tuning stage.


On the git version, with make -j2, givaro fails to build because it 
seems to get built before gmp. This is completely reproducible every 
time I run a "make distclean; make -j2" cycle.


I looked at my base system packages (gentoo linux) and the only major 
thing that has changed since the last time I could build sage 
(sage-5.11-beta3) is the kernel which I upgraded from 3.7.10 to 3.9.11. 
For some reason, I can't get any version of sage to build now.


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[sage-devel] Re: atlas tuning

[P Purkayastha]

On 08/19/2013 07:36 PM, John Cremona wrote:

What would make atlas suddenly decide to start running its tuning code
(building 5.12.beta1) on a machine which a few days ago built 5.11
without that happening?  It's frustrating since even though I am using
make -j32 the tuning code is taking forever...

Would killing the make and rerunning it save time or just risk
restarting the tuning process from scratch?

John



Well, you have run into the problems I have been facing (see my posts on 
sage-git). It never finishes tuning. Last time I checked it was going on 
for two days, and I just decided to kill it and instead compiled sage on 
a different machine. I now feel that I should just compile sage on 
cloud.sagemath and do my development from there because it is so fast. 
My only other nice option is an ultrabook, which may or may not be able 
to sustain long compile times and the heat it generates.



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[sage-devel] Re: bug in plot_field.py if unknown options are set

[P Purkayastha]

On 08/07/2013 11:38 PM, Tobias Weich wrote:

Hi,
durings some work on the unification of linestyle options I found the
following little bug:

|
var('y')
plot_vector_field((sin(x),cos(y)),(x,-3,3),(y,-3,3),linestyle='dotted')
|

crashes with a "maximum recursion depth" error|.

One would however expect that it prints out a warning, that the
linestyle option is ignored, togehter with a lis of the allowed options.

The reason| for this problem is simple: .options() checks whether there
are unknown options and if this is the case prints a warning. While
printing this it calls ._repr_. Unfortunately in .plot_field.py the
function ._repr_() calls options again which reates the infinite loop:

|
def_repr_(self):
"""
 String representation of PlotField graphics primitive.

 EXAMPLES::

 sage: x,y = var('x,y')
 sage: P=plot_vector_field((sin(x), cos(y)), (x,-3,3), (y,-3,3))
 sage: P[0]
 PlotField defined by a 20 x 20 vector grid
 """
return"PlotField defined by a %s x %s vector
grid"%(self.options()['plot_points'],self.options()['plot_points'])

|

I would propose openig a ticket and uploading a patch which replaces
|
self.options()
|
by
|
self._options
|

However being completely unexperienced with fixing bugs in sage I wanted
to mail it to the list first and ask whether some more experienced
developpers see some problems, better solutions or other functions that
could be affacted.

Thanks for your feed-back

Tobi


Did you open a ticket about this bug? If so, can you mention the ticket 
here? Thanks!





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[sage-devel] Re: GSoC "New decoding error-correcting codes algorithm for Sage"

[P Purkayastha]

On 08/06/2013 07:47 PM, Johan S. R. Nielsen wrote:

Hi Veronica,

This seems really interesting. How is progress on your project?

I work in algebraic coding theory myself, and I have been writing lots
of Sage code for this. Most of it is generally useful, but I have not
had time to add it to Sage proper, since that would require
restructuring a lot of Sage's current error correcting code
functionality (where a code is just a generator matrix and all known
structure is thrown away).


Hi Johan,

  If you have suggestions how to improve the coding theory functions in 
Sage, please open some tickets! Some of us have been adding some 
functionality and fixing bugs (over the past year) in sage.coding. More 
improvements are definitely welcome!




My library is released as GPL and is available at
www.jsrn.dk/codinglib

Most functionality is related to algebraic codes such as Reed--Solomon
codes and Goppa codes, as well as algebraic decoders for these. If any
of it is useful for your project, then don't hesitate to use it. I have
also been thinking how error correcting codes could be better
represented in Sage, and if you have such concerns with your project, I
would gladly join discussions.

Best,
Johan S. R. Nielsen


On Thursday, May 30, 2013 5:48:38 PM UTC+2, Verónica Suaste wrote:

Hi all,

I'm Verónica, an undergraduate math student. I'm glad to share with
you the fact that my project for GSoC 2013 has been selected. The
main idea of these work is to implement new decoding algorithm of
linear codes and make this contribution to Sage.
You can check the full proposal in this link Project proposal
. This blog will
be updated with any progress about the project.
I'll be glad to hear any comment or suggestion from you. So please,
just let me know.

Also, it is very likely I'll be attending the next Sage Day in
Seattle. Which I consider a good start for this project.
Hope to meet some of you there!

Cheers,
Verónica.

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[sage-devel] Re: New Trac Server

[P Purkayastha]

On 07/18/2013 02:49 PM, R. Andrew Ohana wrote:

On Wed, Jul 17, 2013 at 11:44 PM, P Purkayastha mailto:ppu...@gmail.com>> wrote:

The new trac looks good! Almost every link has a square box next to
it. Is that intentional?


Looking at the front page of trac it appears to indicate links that
leave trac, so I imagine yes, it was an intentional change made
upstream. No clue on if it is configurable or not.


It's next to (and related to) the download link on every patch too.


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[sage-devel] Re: New Trac Server

[P Purkayastha]

On 07/18/2013 12:59 PM, R. Andrew Ohana wrote:




On Wed, Jul 17, 2013 at 9:38 PM, Keshav Kini mailto:keshav.k...@gmail.com>> wrote:

"R. Andrew Ohana" mailto:andrew.oh...@gmail.com>> writes:

 > Ok, everything should be back up and running now.

Cool!

Bug report: http://trac.tangentspace.org/ doesn't work anymore. If that
is intended behavior, then I guess the fact that trac email
notifications link to trac.tangentspace.org
 is correspondingly
unintended behavior.


Ok, hopefully this is fixed now. I fixed a bunch of references to
tangentspace that were still laying around.


The new trac looks good! Almost every link has a square box next to it. 
Is that intentional?



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[sage-devel] Re: Sage graphics in javascript ?

[P Purkayastha]

On 07/14/2013 12:17 AM, Nathann Cohen wrote:

Hello everybody !!!

Have you ever seen this thing ?
https://github.com/mbostock/d3/wiki/Gallery

It's a javascript library which seems to handle quite a range of things,
and I am thinking of writing a patch that would let us draw Sage graphs
using it instead of Matplotlib.

Perhaps we could also use it to obtain a small interface to visually
edit graphs too. Perhaps we could also use it to draw more complicated
graphs, like the ones that the combinat guys like to print, with a lot
of information on edges and vertices.



What happened to the graph editor that was written by Rado? I forget how 
it was supposed to be called.




Is there anybody else around here who would like to replace matplotlib
with something easier to work with ? Or at least to provide another
output to our objects for a while, and see how it goes ?

The library seems to be GPL-compatible.

See youuu !

Nathann

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[sage-devel] Re: The 2013 Spies Prize winner is...

[P Purkayastha]

Congrats Jeroen - a thorough and excellent release manager. :-)

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