from:"Jason"

I looked more into it. I was wrong (or more correctly, I was outdated).
Indeed, recent versions of the notebook over the last while (years?) *have*
deprecated the header cells, and they have been removed from the notebook
format, I think since at least notebook format 4.0 in 2015 or so:

https://nbformat.readthedocs.io/en/latest/format_description.html#markdown-cells

"Heading cells have been removed, in favor of simple headings in markdown."

The shortcut commands that also used to exist now just insert markdown
cells with the appropriate header text (i.e., pressing '1', '2', etc.).

Jason


On Sat, Jan 6, 2018 at 3:14 PM Emmanuel Charpentier <
emanuel.charpent...@gmail.com> wrote:

>
> Le samedi 6 janvier 2018 22:10:46 UTC+1, Samuel Lelievre a écrit :
>>
>> Yet the attached screenshot seems to indicate that
>> the Jupyter notebook server launched by SageMath
>> does not include selecting the "Header" cell type.
>>
>
> Indeed. It's this difference between our notebook and the documentation
> <https://jupyter.brynmawr.edu/services/public/dblank/Jupyter%20Notebook%20Users%20Manual.ipynb#2.4-Header-Cells>
> found at Brywn Mawr College that led me to conclude that header cells were
> something different from Markdows cells containing headers.
>
> I haven't been able to find other references to those headers cells...  A
> slightly wider search tells me that "Heading cells have been removed in
> IPython 3 <https://github.com/jupyter/notebook/issues/255>". A similar
> feature has been developed
> <https://github.com/ipython-contrib/jupyter_contrib_nbextensions> for
> Jupyter 2.x to 4.x (documented here
> <http://jupyter-contrib-nbextensions.readthedocs.io/en/latest/index.html#>
> ).
>
> So the question may boil down to : does the feature alluded to by the
> original ask.sagemath.com question is
>
>- a standard feature we miss somehow,
>- a former, deprecated  feature , or
>- an unofficial extension, which turns out to be documented as
>standard at Brywn Mawr College ?
>
> and begets another question : should we add it to "our" notebook ?
>
>
> --
> Emmanuel Charpentier
>
>
>> Is there some configuration mechanism for deciding
>>
> which cell types are offered, which maybe would need
>> to be set up differently?
>>
>> Samuel
>>
>> 2018-01-06 14:47 GMT-06:00 Jason Grout :
>> >
>> > Cool, thanks, good to see things are getting up to date.
>>
> > Both of those definitely have the concept of header cells.
>> >
>> > Jason
>> >
>> >
>> > On Sat, Jan 6, 2018 at 11:29 AM Samuel Lelièvre 
>> wrote:
>> >>
>> >> Sage 8.1 has notebook 4.4.1, while Sage 8.2.beta0 up to Sage 8.2.beta1
>> have notebook 5.2.1.
>> >>
>> >> $ ls /path/to/sage-8.1/upstream | grep notebook
>> >> notebook-4.4.1.tar.gz
>> >>
>> >> $ ls /path/to/sage-8.beta0/upstream | grep notebook
>> >> notebook-5.2.1.tar.gz
>> >>
>> >> $ ls /path/to/sage-8.beta2/upstream | grep notebook
>> >> notebook-5.2.1.tar.gz
>> >>
>> >> --
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>> Groups "sage-devel" group.
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>
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>> >
>> > --
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>
> Le samedi 6 janvier 2018 22:10:46 UTC+1, Samuel Lelievre a écrit :
>
>> Yet the attached screenshot seems to indicate that
>> the Jupyter notebook server launched by SageMath
>> does not include selecting the "Header" cell type.
>>
>> Is there some configur

Re: [sage-devel] Jupyter header cells ?

Cool, thanks, good to see things are getting up to date. Both of those
definitely have the concept of header cells.

Jason


On Sat, Jan 6, 2018 at 11:29 AM Samuel Lelièvre 
wrote:

> Sage 8.1 has notebook 4.4.1, while Sage 8.2.beta0 up to Sage 8.2.beta1
> have notebook 5.2.1.
>
> $ ls /path/to/sage-8.1/upstream | grep notebook
> notebook-4.4.1.tar.gz
>
> $ ls /path/to/sage-8.beta0/upstream | grep notebook
> notebook-5.2.1.tar.gz
>
> $ ls /path/to/sage-8.beta2/upstream | grep notebook
> notebook-5.2.1.tar.gz
>
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Re: [sage-devel] Jupyter header cells ?

Thanks. The Jupyter notebook is in the "notebook" pip package.

Jason


On Sat, Jan 6, 2018 at 10:38 AM Samuel Lelievre 
wrote:

> Sat 2018-01-06 15:57:42 UTC, Jason Grout:
>
> >
> > What version of the Jupyter notebook is in Sage?
> > I'd be surprised if it didn't have header cells.
> >
> > Jason
>
> In Sage 8.1:
>
> $ cd /path/to/sage-8.1/upstream
> $ ls | grep jup
> jupyter_client-5.1.0.tar.gz
> jupyter_core-4.3.0.tar.gz
>
> In Sage 8.2.beta0:
>
> $ cd /path/to/sage-8.2.beta0/upstream
> $ ls | grep jup
> jupyter_client-5.1.0.tar.gz
> jupyter_core-4.4.0.tar.gz
>
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Re: [sage-devel] Jupyter header cells ?

Header cells in Jupyter notebooks have been around a very long time (since
essentially the beginning?). Years ago there was talk of deprecating them
in lieu of just using Markdown header syntax in markdown cells. There
aren't officially supported TOC or section-structuring features in the
notebook. We may see more section-structuring features in the notebook
going forward, though I don't know of anyone that has definite plans to
work on it right now.

You can convert a notebook to tex using nbconvert, and you can even write
latex in the notebook "raw" cells and have it output as part of the latex
in a conversion. And there's no technical problem that I know if in doing
something like sagetex using Jupyter kernels to give you the computation
engine of Jupyter inside of TeX.

What version of the Jupyter notebook is in Sage? I'd be surprised if it
didn't have header cells.

Jason


On Fri, Jan 5, 2018 at 2:55 PM Dima Pasechnik  wrote:

>
>
> On Friday, January 5, 2018 at 12:46:16 PM UTC, Erik Bray wrote:
>
>> On Wed, Jan 3, 2018 at 2:47 PM, Emmanuel Charpentier
>>
>  wrote:
>> > The documentation I referenced shows the presence of specific tools in
>> their
>> > implementation (specialized buttons, menus items, etc...) that seem to
>> be
>> > necessary for cross-referencing and auto-TOC. The "Header cells" seem
>> to be
>> > distinct from Markdown cells, code cells and raw cells.
>> >
>> > As far as I can tell, this is not available in "our" Jupyter.
>>
>> I'll have to take a closer look, but I'm still confused because
>> "header cells" have been in the notebook going way back (since early
>> versions of IPython Notebook).  The cross-referencing and TOC stuff
>> I'm less sure about.
>>
>> > I'm not sanguine about this enhancement :
>> >
>> > It certainly can be useful for heavy Jupyter users.
>> > OTOH, it is also a form of "LaTeX envy"...
>> >
>> > I see more and more proposals to add LaTeX-like features to Markdown
>> (such
>> > as citation management, cross-referencing, indexing,). But Markdown
>> was
>> > not created to be a LaTeX replacement, and these various proposals are
>> > problem-specific kludges, mutually inconsistent and, IMNSHO, not up to
>> the
>> > standard proposed by LaTeX.
>> >
>> > I see these "enhancements" as a way to avoid the Matterhorn-like
>> learnng
>> > curve of LaTeX ; but I think that, in the long term, the larger
>> investment
>> > on LaTeX yelds a better ROI. The key point is, of course "in the long
>> term"
>> > : someone not planning to  publish extensively might use Jupyter as a
>> way to
>> > meet a specific, one-time requirement (e. g. graduating) ; however,
>> someone
>> > planing to have to publish more than once or twice is probably better
>> off
>> > learning LaTeX which, as a scientific document preparation system, has
>> not
>> > yet been superseded (after about 30 years... !).
>>
>> I agree with all in theory. Though as I once learned, in an
>> embarrassing manner, one of the first times I taught Software
>> Carpentry to an audience that was not just astronomers/physicists,
>> outside those fields and mathematics LaTeX is *not* de facto.
>>
>
> Considering that Apple added a quite complete LaTeX support to Pages
> (their presentations editor)
> and iBooks Author (e-books writing tool) we'll hopefully see a wider use
> of LaTeX
> soon...
>
>
>
>>
>> Yes, maybe scientists in life science, social science, etc. should
>> also learn LaTeX but for many of those fields it's not nearly as
>> common and there's maybe far less ROI there.
>>
>> > In other words, "heavy Jupyter use" is a bit of an oxymoron in my eyes
>> (or,
>> > at least, a misguided choice).But I might be missing a point, hence my
>> > question.
>>
>> Maybe, but it's a whole new world...
>>
>> Best,
>> E
>>
>>
>> > Le mardi 2 janvier 2018 15:50:18 UTC+1, Erik Bray a écrit :
>> >>
>> >> On Tue, Dec 26, 2017 at 5:27 PM, Emmanuel Charpentier
>> >>  wrote:
>> >> > This question on ask.sagemath.org made me search Google about
>> something
>> >> > called "Header cells". I found such a thing in the Jupyter
>> documentation
>> >> > at
>> >> > Bryn Mawr College.
>> >> >
>> >> > It seems to

Re: [sage-devel] what happened to ipython?

2017-02-18 Thread Jason Grout

I'm able to reproduce it with multiline comments (but code seems to work
fine), in IPython in an SMC terminal. I'm also seeing it in JupyterLab and
Jupyter Notebook's terminal. I've filed an issue with JupyterLab too:
https://github.com/jupyterlab/jupyterlab/issues/1738

As a workaround, pasting multiline comments works in an SMC terminal if I
start ipython with --simple-prompt, which turns off a lot of the fancy
stuff.

Thanks,

Jason


On Sat, Feb 18, 2017 at 12:07 PM William Stein  wrote:

> Hi Jason,
>
> OK, Sage versus IPython is not relevant.  Try to paste in
>
> # a
> # b
> # c
>
> to Ipython in SMC via our terminal.  It just silently discards the
> last two lines.  In general it ignores everything after the first
> input block.
>
> If I ssh in via the apple terminal program, then lines are not discarded.
>
> William
>
>
>
> On Sat, Feb 18, 2017 at 9:00 AM, William Stein  wrote:
> >
> >
> > On Sat, Feb 18, 2017 at 8:53 AM, Jason Grout 
> wrote:
> >>
> >> Was it an upgrade to the 5.x IPython line? 5.0 introduced using prompt
> >> toolkit to do a lot of the fancy stuff (see
> >> http://ipython.readthedocs.io/en/stable/whatsnew/version5.html#id1).
> >> Minimally, you can start IPython with --simple-prompt to turn off a lot
> of
> >> the extra features. You can also turn off syntax highlighting, I think
> with
> >> --colors=nocolors
> >>
> >> I wasn't able to reproduce what I thought you were describing:
> >
> >
> > You didn't even try to reproduce it.  "Is there any way to disable this
> > fancy new
> > syntax-highlight-as-you-type-ninja command line interface to **Sage**".
> >
> > Can you try again?  Instead of typing "ipython", type "sage".   In case
> you
> > have a special version setup, type "sage-7.5".
> >
> > William
>
>
>
> --
> William (http://wstein.org)
>
> --
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Re: [sage-cell] Re: [sage-devel] Sage cells in interact wiki

2016-09-19 Thread Jason Grout

Some ideas:

Is the MoinMoin sage cell extension enabled?
https://github.com/sagemath/sagecell/blob/master/contrib/moinmoin/sagecell.py.
If
it is enabled, was MoinMoin updated and the extension no longer works?

Thanks,

Jason


On Mon, Sep 19, 2016 at 8:48 PM William Stein  wrote:

> On Mon, Sep 19, 2016 at 1:46 PM, Andrey Novoseltsev 
> wrote:
>
>> On Monday, 19 September 2016 10:53:27 UTC-6, William wrote:
>>>
>>> This seems to be an absolutely *massive* issue, which I'm sure was
>>> caused by some API change by Andrey.  These wiki pages have worked fine for
>>> about 7 years, so it's annoying that they are all suddenly broken.
>>>
>>> > I guess it was meant to use the Sage cell server to make the examples
>>> actually work but it doesn't do that anymore.
>>>
>>> They did actually work (and well) until very, very recently.
>>>
>>
>> Do you have a better idea of how recently? Week/month/several months?
>>
>
> Hmm.  This could also coincide with when Mike Hansen moved the wiki to GCE.
>
>
>>
>> Looking at the page source, I do not understand how embedded_sagecell.js
>> is supposed to load and there are no requests for it reported by browser.
>> Console complains about $, so something is off with jQuery, I guess. For
>> the record there is no need to load/use it with sagecell.makeSagecell at
>> all. And as "official API" that I am trying hard not to break (or at least
>> fix when I do) I consider
>> https://github.com/sagemath/sagecell/blob/master/doc/embedding.rst
>>
>> So - it does not work indeed, but I have no idea why and I hope that I am
>> not responsible ;-)
>>
>
> I now think that you are not responsible at all.  Thanks for the hints
> above!
>
>
>>
>> Thank you!
>> Andrey
>>
>>
>>>  -- William
>>>
>>> On Mon, Sep 19, 2016 at 6:04 AM, Jeroen Demeyer 
>>> wrote:
>>>
>>>> The "interact" wiki page
>>>> https://wiki.sagemath.org/interact
>>>> is seriously broken: I guess it was meant to use the Sage cell server
>>>> to make the examples actually work but it doesn't do that anymore. What is
>>>> worse: also the source code is not shown, making the examples almost
>>>> totally useless...
>>>>
>>>> Well, the Sage source code is still in the source of the wiki page, but
>>>> that's not very practical. However, there seem to be some
>>>> backslash-escaping going on, making the examples not 100% copy-pastable.
>>>>
>>>> Some context: I am working on an implementation of the SageNB interacts
>>>> in Jupyter at https://trac.sagemath.org/ticket/21267 and that page is
>>>> a valuable source of examples for me.
>>>>
>>>> --
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>>>>
>>>
>>>
>>>
>>> --
>>> William (http://wstein.org)
>>>
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>
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Re: [sage-devel] Jupyter notebook by default?

2016-09-09 Thread Jason Grout

Nice! That's even better that it works out-of-the-box!

Jason


On Fri, Sep 9, 2016 at 6:06 PM Volker Braun  wrote:

>
> <https://lh3.googleusercontent.com/-mROFT73lCRs/V9MyE0CAH6I/b8A/w5ZN6NyVDg0LLGuBV6O3p-MR5uQWCq7AACLcB/s1600/table.png>
>
>
> On Friday, September 9, 2016 at 2:53:29 PM UTC+2, kcrisman wrote:
>>
>> Sorry for the necropost, but I couldn't find any other canonical place to
>> mention this:
>>
>> https://ask.sagemath.org/question/34782/how-to-render-html-or-latex-tables-in-jupyter-notebook/
>> Likely this is a fairly easy hook thing or the pretty_print issue but
>> thought it should be here for completeness.
>>
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Re: [sage-devel] Jupyter notebook by default?

2016-09-09 Thread Jason Grout

A bit more robust in escaping:

try:
from html import escape  # python 3.x
except ImportError:
from cgi import escape  # python 2.x
from IPython.display import HTML

def table(data):
rows = [["%s"%escape(str(i)) for i in data[0]]]
rows.extend([["%s"%escape(str(i)) for i in row] for row in
data[1:]])
s = '\n'.join(['%s'%(''.join(row)) for row in rows])
return HTML('%s'%s)

table([('Header 1', 'Header 2'), (1,'<'), (3,4)])

On Fri, Sep 9, 2016 at 9:28 AM Jason Grout  wrote:

> I don't think we have a good table-printing function built into IPython. A
> simple one is probably pretty straightforward:
>
> try:
> from html import escape  # python 3.x
> except ImportError:
> from cgi import escape  # python 2.x
> from IPython.display import HTML
>
> def table(data):
> rows = [["%s"%escape(i) for i in data[0]]]
> rows.extend([["%s"%i for i in row] for row in data[1:]])
> s = '\n'.join(['%s'%(''.join(row)) for row in rows])
> return HTML('%s'%s)
>
> table([('Header 1', 'Header 2'), (1,2), (3,4)])
>
>
> On Fri, Sep 9, 2016 at 8:53 AM kcrisman  wrote:
>
>> Sorry for the necropost, but I couldn't find any other canonical place to
>> mention this:
>>
>> https://ask.sagemath.org/question/34782/how-to-render-html-or-latex-tables-in-jupyter-notebook/
>> Likely this is a fairly easy hook thing or the pretty_print issue but
>> thought it should be here for completeness.
>>
>> --
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>

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Re: [sage-devel] Jupyter notebook by default?

2016-09-09 Thread Jason Grout

I don't think we have a good table-printing function built into IPython. A
simple one is probably pretty straightforward:

try:
from html import escape  # python 3.x
except ImportError:
from cgi import escape  # python 2.x
from IPython.display import HTML

def table(data):
rows = [["%s"%escape(i) for i in data[0]]]
rows.extend([["%s"%i for i in row] for row in data[1:]])
s = '\n'.join(['%s'%(''.join(row)) for row in rows])
return HTML('%s'%s)

table([('Header 1', 'Header 2'), (1,2), (3,4)])


On Fri, Sep 9, 2016 at 8:53 AM kcrisman  wrote:

> Sorry for the necropost, but I couldn't find any other canonical place to
> mention this:
>
> https://ask.sagemath.org/question/34782/how-to-render-html-or-latex-tables-in-jupyter-notebook/
> Likely this is a fairly easy hook thing or the pretty_print issue but
> thought it should be here for completeness.
>
> --
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Re: [sage-devel] Re: sage vs jupyter notebooks

2016-05-05 Thread Jason Grout

Thanks Volker. In general, Jupyter uses github-flavored markdown, which
supports tables and many other things:
https://help.github.com/articles/organizing-information-with-tables/, for
example.

Jason


On Thu, May 5, 2016 at 2:56 PM Volker Braun  wrote:

> A %%cython cell magic for commandline and Jupyter notebook is now at
> http://trac.sagemath.org/ticket/20562
> <http://trac.sagemath.org/ticket/20562#comment:1> (needs review)
>
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Re: [sage-devel] Deprecate the use of properties in all public API

2016-05-05 Thread Jason Grout

FYI, a relevant post just appeared on the ipython dev list:
https://mail.scipy.org/pipermail/ipython-dev/2016-May/017099.html



A few minutes ago we merged a PR[1] adding jedi[2] integration to
IPython, this make the IPython completer a bit smarter,
as it now knows about situation like:

In[1]: ('je'+'di').upper().

Where it will infer that you are actually calling a method on a
string, which before was requiring setting `IPCompleter.greedy` to
`true`
which has the drawback of evaluating your code with its side effects.




Thanks,

Jason



On Wed, May 4, 2016 at 11:50 AM Volker Braun  wrote:

> On Wednesday, May 4, 2016 at 5:26:03 PM UTC+2, mmarco wrote:
>>
>> Overall, I think that the problem with documentation is worse than the
>> gain with tab-completion, but it would be so nice if we could do something
>> like:
>> sage: n.transpose().[tab]
>>
>
> You can do that already:
>
> sage: n = matrix(QQ, 2)
> sage: %config IPCompleter.greedy=True
> sage: n.transpose().[TAB]
> Display all 230 possibilities? (y or n)
> n.transpose().C
>  n.transpose().hessenbergize
>  n.transpose().permute_rows_and_columns
> n.transpose().H  n.transpose().image
>n.transpose().pfaffian
> n.transpose().I
>  n.transpose().indefinite_factorization   n.transpose().pivot_rows
>
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Re: [sage-devel] Re: Proposal: move SageNB back to Sage

2016-04-16 Thread Jason Grout

On Fri, Apr 15, 2016 at 6:26 PM William Stein  wrote:

> On Fri, Apr 15, 2016 at 2:59 PM, Volker Braun 
> wrote:
> > Is there really going to be much activity on SageNB in the future? I
> > appreciate that you fixed the packaging and dependency nightmare, but it
> > seems that we are now (i.e. after #14840) at the point where we are
> likely
> > to just wait and eventually remove SageNB. I always found it frustrating
> to
> > do any kind of change on SageNB; there isn't really a good testsuite so
> you
> > basically have to check by hand that you don't break stuff. And none of
> the
> > core developers use SageNB so we don't really spot breakage that well
> > either. More than anything else, we can maintain Sage easily because we
> have
> > a pretty awesome testsuite.
> >
> > Having to do two separate commits, one to Sage and one to SageNB, isn't
> > really that much of a deal in comparison. Of course then waiting
> > indefinitely for a new SageNB release *IS* a big problem. So as a minimal
> > proposal, how about we just take over the SageNB github repo and make
> > releases whenever we need them. Which really isn't all that often.
>
> +1  -- I agree 100% with everything above.  If anybody wants added to
> the repo, let me know.
>
>
For what it's worth, +1 from me as well to Volker's proposal. That makes a
lot of sense.

Jason

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Re: [sage-devel] Re: Bye

2016-02-23 Thread Jason Grout

Definitely +1. Thanks for all your work, Nathann.

Jason

On Tue, Feb 23, 2016, 17:12 Nicolas M. Thiery 
wrote:

>
>
> On Mon, Feb 22, 2016 at 06:28:46PM -0800, kcrisman wrote:
> >...Though in open source development (at least in open development
> >projects like this one) meaning that sometimes people will hit the
> road
> >over disagreements, everyone should definitely thank Nathann for loads
> >and loads of work, especially in graphs and combinatorial objects:
> >...
> >So don't forget about breaks!
>
> Nicely phrased Karl. +1 all along.
>
> Cheers,
> Nicolas
> --
> Nicolas M. Thiéry "Isil" 
> http://Nicolas.Thiery.name/
>
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Re: [sage-devel] Re: Conversion Jupyter Notebook -> Doctests

2016-01-27 Thread Jason Grout

Min (in the Jupyter project) wrote a program to doctest .ipynb files a
while ago: https://gist.github.com/minrk/2620735.  I think it expects an
old version of the .ipynb format, but it is a good starting point to update
to the newest .ipynb format.

Thanks,

Jason

On Wed, Jan 27, 2016 at 3:39 PM kcrisman  wrote:

>
>
> On Wednesday, January 27, 2016 at 1:22:15 AM UTC-5, Clemens Heuberger
> wrote:
>>
>> Is there a way to convert a jupyter notebook .ipynb to a "doctestable
>> file"?
>> Such a thing existed for the sage notebook.
>>
>>
> Is it possible that there is an ipynb -> rst out there, or in
> development?  That might help fill the need.
>
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Re: [sage-devel] Re: Jupyter notebook by default?

2016-01-26 Thread Jason Grout

I should add that one of the major design goals for the next iteration of
the notebook is to be fully modular, so it would be easy to plug in your
own component to edit markdown, for example.

Thanks,

Jason

On Tue, Jan 26, 2016 at 10:59 PM Jason Grout  wrote:

> What if we used something like ProseMirror for the markdown editor?
> http://prosemirror.net/.  Would that help? Right now we use Codemirror.
>
> I'm writing a prototype for the next Jupyter notebook renderer as we speak
> (markdown cells are here, for example:
> https://github.com/jupyter/jupyter-js-cells/blob/master/src/widget.ts#L110).
> Pull requests welcome, as always :).
>
> Jason
>
>
> On Tue, Jan 26, 2016 at 10:55 PM kcrisman  wrote:
>
>> Another con I just discovered:
>> * You have to learn markdown to do anything useful in plain old text.
>>
>> Don't tell me this isn't a con.  (If it's not accurate, please tell me!
>> I just couldn't figure out how to get
>>
>> Now, I know enough md to get by.  Lots of people use it.  Lots of *other*
>> people (see, I used it!) would rather have at least SOME whizzy-wig
>> capability.  'Cuz why else does the interface I'm using right now in Google
>> Groups have things *like this or **this* or even bullet lists to click
>> (perhaps they use TinyMCE themselves)?  It should be just as much about
>> reducing learning curves as the "right" solution.  I hate having to
>> remember if links are [like this](url) or (this)[url] or even [url like
>> this] (oh wait, that's the Trac style).  Google lets me do this
>> <http://www.sagemath.org> with a simple click.
>>
>> To be productive on this front and not just complain, I did a fair amount
>> of searching for wysiwyg or tinymce and jupyter and found almost nothing.
>> Could this be a replacement?  https://github.com/bollwyvl/nb-wysiwyg  I
>> also found this nice article
>> <http://jupyter.cs.brynmawr.edu/hub/dblank/public/Jupyter%20Notebook%20Users%20Manual.ipynb#4.-Using-Markdown-Cells-for-Writing>
>> which (correctly) claims "Why is Markdown better? Well, it’s worth saying
>> that maybe it isn't. Mainly, it’s not actually a question of better or
>> worse, but of what’s in front of you and of who you are. A definitive
>> answer depends on the user and on that user’s goals and experience. These
>> Notebooks don't use Markdown because it's definitely better, but rather
>> because it's different and thus encourages users to think about their work
>> differently."  But not everyone, especially those instructors in a hurry,
>> have time to think about that on a first try.  If they end up writing a
>> book I hope they do!  But if they just want to make an example for class
>> it's a bit much.
>>
>> Hopefully Jupyter will be able to have an option to have wysiwyg
>> eventually, though I understand that might conflict with their design
>> goals. In which case their design goals are not really for
>> non-programmers.
>>
>> Practical example, lest someone think I'm beating up on a straw notebook
>> interface:
>> Someone makes an awesome 3d plot in Jupyter with vectors and parametric
>> things in red, blue, and green, labeling different things.  Now in the main
>> body of their text they want the same output, so they can talk about green
>> tangent vectors, blue normal vectors, and red curves, or something, in
>> those colors.  Lovely stuff.  They Google how to do this in md and get:
>>
>> http://stackoverflow.com/questions/19746350/how-does-one-change-color-in-markdown-cells-ipython-notebook
>> Result: the text stays all black for the presentation they have to do in
>> ten minutes.
>>
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Re: [sage-devel] Re: Jupyter notebook by default?

2016-01-26 Thread Jason Grout

What if we used something like ProseMirror for the markdown editor?
http://prosemirror.net/.  Would that help? Right now we use Codemirror.

I'm writing a prototype for the next Jupyter notebook renderer as we speak
(markdown cells are here, for example:
https://github.com/jupyter/jupyter-js-cells/blob/master/src/widget.ts#L110).
Pull requests welcome, as always :).

Jason


On Tue, Jan 26, 2016 at 10:55 PM kcrisman  wrote:

> Another con I just discovered:
> * You have to learn markdown to do anything useful in plain old text.
>
> Don't tell me this isn't a con.  (If it's not accurate, please tell me!  I
> just couldn't figure out how to get
>
> Now, I know enough md to get by.  Lots of people use it.  Lots of *other*
> people (see, I used it!) would rather have at least SOME whizzy-wig
> capability.  'Cuz why else does the interface I'm using right now in Google
> Groups have things *like this or **this* or even bullet lists to click
> (perhaps they use TinyMCE themselves)?  It should be just as much about
> reducing learning curves as the "right" solution.  I hate having to
> remember if links are [like this](url) or (this)[url] or even [url like
> this] (oh wait, that's the Trac style).  Google lets me do this
> <http://www.sagemath.org> with a simple click.
>
> To be productive on this front and not just complain, I did a fair amount
> of searching for wysiwyg or tinymce and jupyter and found almost nothing.
> Could this be a replacement?  https://github.com/bollwyvl/nb-wysiwyg  I
> also found this nice article
> <http://jupyter.cs.brynmawr.edu/hub/dblank/public/Jupyter%20Notebook%20Users%20Manual.ipynb#4.-Using-Markdown-Cells-for-Writing>
> which (correctly) claims "Why is Markdown better? Well, it’s worth saying
> that maybe it isn't. Mainly, it’s not actually a question of better or
> worse, but of what’s in front of you and of who you are. A definitive
> answer depends on the user and on that user’s goals and experience. These
> Notebooks don't use Markdown because it's definitely better, but rather
> because it's different and thus encourages users to think about their work
> differently."  But not everyone, especially those instructors in a hurry,
> have time to think about that on a first try.  If they end up writing a
> book I hope they do!  But if they just want to make an example for class
> it's a bit much.
>
> Hopefully Jupyter will be able to have an option to have wysiwyg
> eventually, though I understand that might conflict with their design
> goals. In which case their design goals are not really for
> non-programmers.
>
> Practical example, lest someone think I'm beating up on a straw notebook
> interface:
> Someone makes an awesome 3d plot in Jupyter with vectors and parametric
> things in red, blue, and green, labeling different things.  Now in the main
> body of their text they want the same output, so they can talk about green
> tangent vectors, blue normal vectors, and red curves, or something, in
> those colors.  Lovely stuff.  They Google how to do this in md and get:
>
> http://stackoverflow.com/questions/19746350/how-does-one-change-color-in-markdown-cells-ipython-notebook
> Result: the text stays all black for the presentation they have to do in
> ten minutes.
>
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Re: [sage-devel] Re: Jupyter notebook by default?

I'm not sure exactly what you mean here.  Can you give an example?

Thanks,

Jason

On Tue, Jan 5, 2016 at 3:16 PM, kcrisman  wrote:

> I know this is now hijacking the thread... but if we are on those lines,
> when it comes to "too much output", making sure that this is something that
> can allow people to easily see and compare an "old" "too much output" to a
> "new" "too much output" after evaluating a cell/command a second/several
> time/s would be very helpful - we've had numerous requests along those
> lines.  Doubtless this is already in the works though - nice to hear from
> you, Jason! :)
>
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Re: [sage-devel] Re: Jupyter notebook by default?

Brian, Sylvain, and Jon talked and came to an agreement.

Jason


On Tue, Jan 5, 2016 at 2:42 PM, Jeroen Demeyer 
wrote:

> On 2016-01-05 19:27, Jason Grout wrote:
>
>> FYI, Sylvain Corlay is making some changes to ipywidgets to bring them
>> more into line with the Sage syntax.  He said in the Jupyter dev meeting
>> just now that he'll be making a PR today.
>>
>
> Cool, however it seems from
> https://github.com/ipython/ipywidgets/issues/238 that @ellisonbg was the
> main person who needed to be convinced.
>
>
> Jeroen.
>
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Re: [sage-devel] Re: Jupyter notebook by default?



On Tuesday, January 5, 2016 at 8:17:45 AM UTC-7, William wrote:
>
>
> One example of a subtle feature in Sage (notebook and worksheets) not 
> in Jupyter, which I was just reminded of, is output limiting.  In Sage 
> there are numerous rules/options to deal with people doing stuff like: 
>
> while True: 
>print "hi!" 
>
> ... which is exactly what students will tend to do by accident... 
> Jupyter doesn't deal with this, but it might not be too hard to 
> implement in theory.  One of the main problems is figuring out what 
> the arbitrary rate limiting defaults "should" be; it's arbitrary, and 
> depends a lot on whether everything is local, over the web, etc. so 
> getting a bunch of people to agree is hard, which might mean they will 
> never implement anything. 
>


William,

Jon Frederic in the Jupyter dev meeting happening right now said that he 
will be working on output limiting as one of his next things.

Jason

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Re: [sage-devel] Re: Jupyter notebook by default?

FYI, Sylvain Corlay is making some changes to ipywidgets to bring them more 
into line with the Sage syntax.  He said in the Jupyter dev meeting just 
now that he'll be making a PR today.

Thanks,

Jason

On Sunday, January 3, 2016 at 7:45:19 AM UTC-7, Jeroen Demeyer wrote:
>
> On 2016-01-03 14:41, Emmanuel Charpentier wrote: 
> >   * Interacts : In a Python worksheet, ipywidgets offers a nice 
> > interactive framework, ... which turns out no be non obvious to use 
> > from a Sage worksheet. A replacement and/or a compatibility layer 
> > are needed. (Even if we offer a replacement, a compatibility layer 
> > might be useful to ease transition/conversion of old sagenb 
> worksheets). 
>
> During Sage Days 70, some work was done to make ipywidgets interacts 
> usable within Sage. This now works using the git master for ipywidgets 
> (which is not in Sage yet). 
>
> Unfortunately, the API of @interact has some significant differences 
> between SageNB and Jupyter. IMHO, that of SageNB makes more sense but I 
> have not been able to convince upstream Jupyter of this fact. Jupyter 
> might have more fancy stuff (like a game controller widget), but fewer 
> basic "just works" stuff. 
>
> I think that a compatibility layer might be possible, but I don't know 
> if it can cover all features of SageNB interacts. 
>
> Jeroen. 
>

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Re: [sage-devel] Re: Jupyter notebook by default?

(cross-posting to ipython-dev)

Jon,

At the recent San Francisco meetings, we talked about this.  What do you
think about:

1. keeping track of the size of the io messages sent from any specific
kernel execution
2. When the total size of io reaches some specific size
(user-configurable), transmitting a special "throwing away output, but
here's how to save the output to a file if you want in the future, or how
to increase the limit" message
3. keep a running buffer of the last bit of output attempted to be sent,
and send it when the execution finishes (so basically a ring buffer that
overwrites the oldest message)

This:

* allows small output through
* provides an explanatory message
* provides the last bit of output as well

One thing to figure out: a limit on size of output that is text may not be
appropriate for output that is images, etc.

Thanks,

Jason


On Tue, Jan 5, 2016 at 12:11 PM, Jason Grout  wrote:

>
> -- Forwarded message --
> From: Jonathan Frederic 
> Date: Tue, Jan 5, 2016 at 11:42 AM
> Subject: Re: [sage-devel] Re: Jupyter notebook by default?
> To: Jason Grout 
> Cc: sage-devel 
>
>
> Jason,
>
> Thanks for pulling me in on this.
>
> William,
>
> I agree, getting a bunch of people to agree on stuff can seem impossible.
> However, you mention Sage offers a couple options to mitigate output
> overflows, can you point me to those options?  The Jupyter Notebook should
> provide multiple options too - this will also make it easier for everyone
> to agree.
>
> Also, in you experience, which of these options work the best?
>
> I was thinking initially of doing something simple, like hard limiting
> data/time, then printing an error if that's exceeded.  In the Jupyter
> Notebook, we have to worry about
> - Too many messages sent on the websocket
> - The notebook json file growing too large and consequently becoming
> unopenable
> - Too much data being appended to the DOM, crashing the browser
>
>
> Thanks!
> -Jon
>
> On Tue, Jan 5, 2016 at 10:19 AM, Jason Grout 
> wrote:
>
>>
>>
>> On Tuesday, January 5, 2016 at 8:17:45 AM UTC-7, William wrote:
>>>
>>>
>>> One example of a subtle feature in Sage (notebook and worksheets) not
>>> in Jupyter, which I was just reminded of, is output limiting.  In Sage
>>> there are numerous rules/options to deal with people doing stuff like:
>>>
>>> while True:
>>>print "hi!"
>>>
>>> ... which is exactly what students will tend to do by accident...
>>> Jupyter doesn't deal with this, but it might not be too hard to
>>> implement in theory.  One of the main problems is figuring out what
>>> the arbitrary rate limiting defaults "should" be; it's arbitrary, and
>>> depends a lot on whether everything is local, over the web, etc. so
>>> getting a bunch of people to agree is hard, which might mean they will
>>> never implement anything.
>>>
>>
>>
>> William,
>>
>> Jon Frederic in the Jupyter dev meeting happening right now said that he
>> will be working on output limiting as one of his next things.
>>
>> Jason
>>
>
>
>

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Re: [sage-devel] Re: Jupyter notebook by default?

FYI, you can set the notebook directory with a command line switch:

jupyter notebook --NotebookApp.notebook_dir=~/.sage/jupyter

Thanks,

Jason

On Sunday, December 20, 2015 at 5:25:52 PM UTC-7, Volker Braun wrote:
>
> If you start Jupyter in ~/foo then you cannot open notebooks in 
> ~/.sage/jupyter. Thats just how it is.
>
> On Monday, December 21, 2015 at 1:12:57 AM UTC+1, William wrote:
>>
>> I clearly don't agree with that, since that's never been the case 
>> before, as I mentioned.  I'll not press this any further. 
>>
>

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[sage-devel] Re: Sources of funding - perhaps computer manufacturers?

2015-10-03 Thread Jason Grout


On 10/3/15 05:27, Jeroen Demeyer wrote:

On 2015-10-02 04:01, Jonathan wrote:

interactively zoomable by click and drag. To be useable for most people
they also need GUI adjustment of colors, symbols, etc.


I saw some demo of a IPython/Jupyter widget which does exactly this: the
plot is essentially a Javascript applet which allows zooming client-side
(even without having Jupyter running).


We have several implementations of such a thing in Jupyter community. 
Matplotlib has a basic implementation of this if you use "%matplotlib 
notebook" to change to the interactive backend.  Bokeh may be what you 
saw, as it works also without a kernel running.  We (at Bloomberg) also 
just open-sourced a plotting library we've been working on at Bloomberg 
for the last year or so which has interactivity, based on the Jupyter 
widgets: https://github.com/bloomberg/bqplot.


Thanks,

Jason



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[sage-devel] Re: History of notebooks.

2015-10-03 Thread Jason Grout


On 10/3/15 11:35, Thierry Dumont wrote:

Hello,

I am preparing a talk I will give to a group of engineers, about
"Notebooks". I mean web technology based notebooks (not java, qt or
something else, but notebooks which use your web browser); so I will
speak about Sage Notebook, Ipython and Jupyter notebooks.

My question is:

-> Was Sage notebook at the origin of all ?


The Sage notebook certainly preceded the IPython and Jupyter notebooks 
and served as one of the main inspirations for them.  I've CCd Fernando 
and Brian from the Jupyter project to get a more definitive statement.


Thanks,

Jason

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[sage-devel] python-ideas thread on python random functions

2015-09-12 Thread Jason Grout

Just FYI, there's a long discussion going on right now on python-ideas 
mailing list about the standard random number generator in python, and 
whether it would be a better idea to have cryptographically secure 
random number generation by default.  I'm mentioning it here since 
there's likely people in this community who have interesting things to 
say about cryptographically secure random numbers.  Apparently Theo de 
Raadt (OpenBSD founder) emailed Guido about it, which started the 
discussion.


You can see the discussion at 
https://mail.python.org/pipermail/python-ideas/2015-September/thread.html, 
for example, with subject lines like "Python's Source of Randomness 
and the random.py	module Redux" and "Should our default random number 
generator be secure?"


Thanks,

Jason


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[sage-devel] Re: Compiling error for Sage 6.7 on OS X 10.10.3, XCode 6.3.1

2015-05-28 Thread Jason Grout


On 5/27/15 22:09, Jason Grout wrote:

On 5/27/15 18:38, Justin C. Walker wrote:

Are you building multi-threaded?



Interestingly, this may be the problem.  When I do:

export MAKE="make -j1"

and then build, it seems like I pass the point where I had errors before
in building gcc.


FYI, gcc built fine with "make -j1".  I stopped the build process 
halfway through building the singular package and unset the MAKE="make 
-j1" environment variable, so then make reverted to the default (which I 
guess is "make -j6 -l5" for my case), and the rest of the build 
proceeded smoothly.


Weird.  Given the issues others were having, would it make sense to 
build gcc on XCode 6.3.1 single-threaded by default?  I can also post my 
install.log with errors if someone wants to take a look.


Thanks,

Jason


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[sage-devel] Re: Compiling error for Sage 6.7 on OS X 10.10.3, XCode 6.3.1


On 5/27/15 18:38, Justin C. Walker wrote:


On May 27, 2015, at 13:15 , Jason Grout wrote:


I'm running into an error compiling gcc in Sage 6.7 on OS X 10.10.3 with XCode 
6.3.1.  Here's the end of the build log (I can post the entire install log, if 
needed).  Is Sage supposed to compile on OS X 10.10.3 with XCode 6.3.1?  I saw 
some messages and trac tickets about compiling gcc in Sage on this platform 
from before 6.7, but it seemed like they were fixed.


FWIW, I have no problems building on 10.10.3.  I have Xcode 6.1, but 6.3 
command-line tools (which App Store has installed three times for some reason).

Are you building multi-threaded?



Interestingly, this may be the problem.  When I do:

export MAKE="make -j1"

and then build, it seems like I pass the point where I had errors before 
in building gcc.


Thanks,

Jason



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[sage-devel] Re: Compiling error for Sage 6.7 on OS X 10.10.3, XCode 6.3.1


On 5/27/15 18:38, Justin C. Walker wrote:


On May 27, 2015, at 13:15 , Jason Grout wrote:


I'm running into an error compiling gcc in Sage 6.7 on OS X 10.10.3 with XCode 
6.3.1.  Here's the end of the build log (I can post the entire install log, if 
needed).  Is Sage supposed to compile on OS X 10.10.3 with XCode 6.3.1?  I saw 
some messages and trac tickets about compiling gcc in Sage on this platform 
from before 6.7, but it seemed like they were fixed.


FWIW, I have no problems building on 10.10.3.  I have Xcode 6.1, but 6.3 
command-line tools (which App Store has installed three times for some reason).

Are you building multi-threaded?



I'm just typing "make" in the sage directory (after doing make distclean 
and git clean -df).  So I'm doing whatever is the default.  The start of 
the install.log is (snipping lines with paths in my system):


Installing GCC because you have g++ version 4.2.1, which is quite old.
Installing GCC because a Fortran compiler is missing.
*** ALL ENVIRONMENT VARIABLES BEFORE BUILD: ***
[snip]
SAGE_KEEP_BUILT_SPKGS=yes
[snip]
SAGE_MP_LIBRARY=MPIR
SAGE_ORIG_PATH=/usr/bin:/bin:/usr/sbin:/sbin
SAGE_ORIG_PATH_SET=True
SAGE_PARALLEL_SPKG_BUILD=
[snip]
SAGE_VERSION=6.7
***
make -j6 -l5 base
make[2]: warning: -jN forced in submake: disabling jobserver mode.

Does that answer your question?

Thanks,

Jason


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[sage-devel] Re: Compiling error for Sage 6.7 on OS X 10.10.3, XCode 6.3.1


On 5/27/15 18:18, Volker Braun wrote:

Thats what the OSX buildbot is on, so it should work. Do you actually
have commandline tools 6.3.1? Whats the output of clang --version?




% xcodebuild -version
Xcode 6.3.1
Build version 6D1002
% clang --version
Apple LLVM version 6.1.0 (clang-602.0.49) (based on LLVM 3.6.0svn)
Target: x86_64-apple-darwin14.3.0
Thread model: posix

Does that look right?

I do see that the app store now has XCode 6.3.2 available.  I can 
install that if it helps.


Thanks for your help!

Jason


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[sage-devel] Compiling error for Sage 6.7 on OS X 10.10.3, XCode 6.3.1

I'm running into an error compiling gcc in Sage 6.7 on OS X 10.10.3 with 
XCode 6.3.1.  Here's the end of the build log (I can post the entire 
install log, if needed).  Is Sage supposed to compile on OS X 10.10.3 
with XCode 6.3.1?  I saw some messages and trac tickets about compiling 
gcc in Sage on this platform from before 6.7, but it seemed like they 
were fixed.


Thanks,

Jason




[snip]
/usr/bin/clang++  -I../../src/libcpp -I. -I../../src/libcpp/../include 
-I../../src/libcpp/include  -g  -W -Wall -Wno-narrowing -Wwrite-strings 
-Wmissing-format-attribute -pedantic -Wno-long-long  -fno-exceptions 
-fno-rtti -I../../src/libcpp -I. -I../../src/libcpp/../include 
-I../../src/libcpp/include   -c -o errors.o -MT errors.o -MMD -MP -MF 
.deps/errors.Tpo ../../src/libcpp/errors.c
clang: warning: treating 'c' input as 'c++' when in C++ mode, this 
behavior is deprecated
/usr/bin/clang++  -I../../src/libcpp -I. -I../../src/libcpp/../include 
-I../../src/libcpp/include  -g  -W -Wall -Wno-narrowing -Wwrite-strings 
-Wmissing-format-attribute -pedantic -Wno-long-long  -fno-exceptions 
-fno-rtti -I../../src/libcpp -I. -I../../src/libcpp/../include 
-I../../src/libcpp/include   -c -o directives-only.o -MT 
directives-only.o -MMD -MP -MF .deps/directives-only.Tpo 
../../src/libcpp/directives-only.c
clang: warning: treating 'c' input as 'c++' when in C++ mode, this 
behavior is deprecated
/usr/bin/clang++  -I../../src/libcpp -I. -I../../src/libcpp/../include 
-I../../src/libcpp/include  -g  -W -Wall -Wno-narrowing -Wwrite-strings 
-Wmissing-format-attribute -pedantic -Wno-long-long  -fno-exceptions 
-fno-rtti -I../../src/libcpp -I. -I../../src/libcpp/../include 
-I../../src/libcpp/include   -c -o directives.o -MT directives.o -MMD 
-MP -MF .deps/directives.Tpo ../../src/libcpp/directives.c
clang: warning: treating 'c' input as 'c++' when in C++ mode, this 
behavior is deprecated

rm -f libcpp.a
ar cru libcpp.a charset.o directives.o directives-only.o errors.o expr.o 
files.o identifiers.o init.o lex.o line-map.o macro.o mkdeps.o pch.o 
symtab.o traditional.o

ranlib libcpp.a
TARGET_CPU_DEFAULT="" \
HEADERS="auto-host.h ansidecl.h" DEFINES="" \
/bin/sh ../../src/gcc/mkconfig.sh bconfig.h
/usr/bin/clang++ -c   -g  -DIN_GCC-fno-exceptions -fno-rtti 
-fasynchronous-unwind-tables -W -Wall -Wno-narrowing -Wwrite-strings 
-Wcast-qual -Wno-format -Wmissing-format-attribute -pedantic 
-Wno-long-long -Wno-variadic-macros -Wno-overlength-strings -fno-common 
 -DHAVE_CONFIG_H -DGENERATOR_FILE -I. -Ibuild -I../../src/gcc 
-I../../src/gcc/build -I../../src/gcc/../include 
-I../../src/gcc/../libcpp/include  \

-DBASEVER="\"4.9.2\"" -DDATESTAMP="\"\"" \
-DREVISION="\"\"" \
-DDEVPHASE="\"\"" -DPKGVERSION="\"(GCC) \"" \
	-DBUGURL="\"<http://gcc.gnu.org/bugs.html>\"" -o build/version.o 
../../src/gcc/version.c
clang: warning: treating 'c' input as 'c++' when in C++ mode, this 
behavior is deprecated
awk -f ../../src/gcc/opt-gather.awk 
../../src/gcc/ada/gcc-interface/lang.opt ../../src/gcc/fortran/lang.opt 
../../src/gcc/go/lang.opt ../../src/gcc/java/lang.opt 
../../src/gcc/lto/lang.opt ../../src/gcc/c-family/c.opt 
../../src/gcc/common.opt ../../src/gcc/config/fused-madd.opt 
../../src/gcc/config/i386/i386.opt ../../src/gcc/config/darwin.opt > 
tmp-optionlist

/bin/sh ../../src/gcc/../move-if-change tmp-optionlist optionlist
echo timestamp > s-options
/bin/sh ../../src/gcc/../move-if-change tmp-gi.list gtyp-input.list
echo timestamp > s-gtyp-input
echo "#define BUILDING_GCC_MAJOR `echo 4.9.2 | sed -e 
's/^\([0-9]*\).*$/\1/'`" > bversion.h
echo "#define BUILDING_GCC_MINOR `echo 4.9.2 | sed -e 
's/^[0-9]*\.\([0-9]*\).*$/\1/'`" >> bversion.h
echo "#define BUILDING_GCC_PATCHLEVEL `echo 4.9.2 | sed -e 
's/^[0-9]*\.[0-9]*\.\([0-9]*\)$/\1/'`" >> bversion.h
echo "#define BUILDING_GCC_VERSION (BUILDING_GCC_MAJOR * 1000 + 
BUILDING_GCC_MINOR)" >> bversion.h

echo timestamp > s-bversion
if test no = yes \
   || test -n ""; then \
  /bin/sh ../../src/gcc/genmultilib \
"m32" \
"i386" \
"" \
"" \
"" \
"" \
"" \
"" \
"" \
"" \
"no" \
> tmp-mlib.h; \
else \
  /bin/sh ../../src/gcc/genmultilib '' '' '' '' '' '' '' '' \
"" '' no \
> tmp-mlib.

[sage-devel] Re: hosting the sage cell server


On 5/22/15 01:02, William Stein wrote:

I think the license of SageCell has always been BSD.


Like William and Rob said, the license has always been open source, and 
the sage cell server has always been developed in the open.  The license 
of the source files is BSD, with the caveat that (to my understanding) 
GPLv2+ is forced on us from importing Sage several places, as pointed 
out in the license file 
(https://github.com/sagemath/sagecell/blob/master/LICENSE.txt#L36):


"Some files (like interact_compatibility.py and interact_sagecell.py)
are licensed GPLv2+ for the sole reason that they import Sage GPLv2+
code (see the header for those files).  If those imports are removed,
the files may be licensed with the modified BSD license."

"Since this package includes GPLv2+ code (namely those files above),
the repository as a whole is licensed GPLv2+."

Thanks,

Jason


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[sage-devel] Re: sage and jupyterhub for classroom teaching

2015-04-02 Thread Jason Grout

If I recall correctly, Kyle Kelly (who works at Rackspace) has worked a 
lot with setting up JupyterHub with Docker containers.  That's how 
http://tmpnb.org works, for example.  He would be one of the best people 
to contact about how to set something like that up.


Thanks,

Jason


On 4/2/15 02:59, Volker Braun wrote:

Very rougly, JH is right now an authenticating reverse proxy. Every user
gets basically a single-user notebook running in a separate process
(possibly on a different machine). The upside is that it is simple and
if you can run a single-user notebook then you can also run JH, and it
scales much easier. The downside is that communication between different
users (like collaborative editing) is more difficult / currently missing.

The minimal sensible JH install for a classroom, say, would be

* Jupyter hub running as a service
* A bunch of unix accounts, one per stundent

Authentication for unix users is already baked into JH.

A docker image with that would probably not be difficult to make, though
I haven't had time to try it. And if you can't run a docker image
nowadays then you shouldn't expose stuff to the network.



On Thursday, April 2, 2015 at 6:21:52 AM UTC+2, Nils Bruin wrote:

It appears that sagenb is in maintenance-only, and that for
graphical interface, the IPython notebook is the way forward. The
IPython notebook looks wonderful and will probably be a very able
replacement for single-user scenarios, but it lacks the multiuser
capability that sagenb provides.
I noticed that IPython notebook is now Jupyter, and that there *IS*
a multiuser offshoot for that now: Jupyterhub. Does anyone here have
experience deploying Jupyterhub and/or using it to interface with
sage? It looks like a very attractive option for cases where
SageMathCloud isn't appropriate.

The blog post here:

https://developer.rackspace.com/blog/deploying-jupyterhub-for-education/
<https://developer.rackspace.com/blog/deploying-jupyterhub-for-education/>

looks promising as far as how mature Jupyterhub is, but I have no
idea how it would work with sage.

Comments and insights welcome!

Nils

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[sage-devel] Re: Sage Notebook shutdown

2015-03-30 Thread Jason Grout




I just cracked open the users.pickle for sagenb, and found that there
are 250443 total users.   Of these, only 18688 (or 7.4%) actually have
the email field set -- all others are blank.  I guess these might be
exactly the openid accounts. Of these, 15058 are gmail accounts, which
are probably the Google openid accounts.

Oh, for some reason many emails are duplicated, e.g.,
dimp...@gmail.com appears twice.  In any case, there are 17705
uniques.


Was that just the pickle file for sagenb.org, or was that looking at all 
of the users.pickle files and combining the results for all of the 
*.sagenb.org users?


Thanks,

Jason


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[sage-devel] Re: Sage Notebook shutdown

2015-03-26 Thread Jason Grout


On 3/26/15 22:42, William Stein wrote:

Another offer - I could delay a bit longer if somebody could move sagenb
to oauth2...


FYI, this looks like the migration guide: 
https://developers.google.com/accounts/docs/OpenID


Thanks,

Jason


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[sage-devel] Re: Sage Notebook shutdown

2015-03-26 Thread Jason Grout

On 3/26/15 15:59, kcrisman wrote:

 > We've posted the following message on the http://sagenb.org site:
 >
 >   "This Sage notebook server will be shut down April 17, 2015.

I am very worried about the extremely short notice. Many users will be
disappointed to lose their work. Why not just keep it running without
supporting it?

One could change the notice fairly trivially for that.  And it's true
that, although we've often said "sagenb is disappearing eventually",
exactly when "eventually" happens was not specified.

That said, William is right that the proximate cause is that Google is
no longer supporting OpenID in the same way (at all?) and that is
probably how many current users are using it, and undoubtedly no one
will have time or knowledge to give those people passwords (is this even
possible?).

I'm also worried by the short notice.  As Karl-Dieter says, the impetus 
behind this is that many, many users will lose access due to Google 
retiring OpenID.  We could, of course, keep it up for those not using 
Google OpenID, for a bit longer - I'll leave that up to William.  That 
could get really confusing to a lot of people.  I personally won't have 
time to respond to a huge number of inquiries about why logins aren't 
working.

Thanks,

Jason

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[sage-devel] Re: Sage is grown up; needs a last name

2015-02-19 Thread Jason Grout


+1 to SageMath

Jason


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[sage-devel] Re: Maple versus Mathematica

2014-12-01 Thread Jason Grout


On 12/1/14, 6:00, mmarco wrote:


P.S. 2: Is there some easy way to embed sagecell code in a wiki?



Yes, we have plugins for MoinMoin, Dokuwiki, and Drupal.  See the 
interact pages at http://wiki.sagemath.org/interact/ for examples of how 
to do this on the Sage wiki.


Jason



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[sage-devel] Re: The "code of conduct" is getting out of hand - please stop for 2 weeks.

2014-11-29 Thread Jason Grout


On 11/29/14, 6:58, Dr. David Kirkby (Kirkby Microwave Ltd) wrote:

Discussions on this are not going in a positive direction. The tone of
the discussions is far worst than anything I have seen on here in a
long time.

I think it would be best if everyone stopped discussing it for a
couple of weeks, and revisited it later (I propose Monday the 15th
December).

Maybe if people stop for a while, it will cool the discussions, and
perhaps they can more forward in a positive direction. Since at the
minute, the whole thing is getting quite nasty.


+1.  While I've been reading the whole discussion, I've stayed out of it 
because of the direction, emotion, and tone of it.  I think this is the 
first suggestion I wholeheartedly vote +1 on.


Thanks,

Jason


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[sage-devel] Re: Maple versus Mathematica

2014-11-21 Thread Jason Grout

The ith element of a list is M[[i]].  An expression ending in & is a 
lambda function, with # being the first parameter.  f /@ B is equivalent 
to map(f, B) (f is applied to each element of B).  If[# == 0, 0, 1] is 
equivalent to lambda x: x==0 ? 0 : 1


So to me, it looks like:

m2 = [m[2][i] for i in [x[2] for x in m[3]]
m3 = [m2[i] for i in [x[2] for x in m[4]]
lM = [[0 if i==0 else 1 for i in x] for x in m3]

There's a decent chance that I missed something, though.  It's been a 
long while since I did anything in mathematica, and I've realized that 
mathematica quickly starts looking like line noise after I've stopped 
using it.


Thanks,

Jason

P.S. I was curious about the online mathematica the other night.  If I 
understood the marketing material correctly, it seems you get 
interactive computation included in the base price, and you are charged 
for offline computation.  I checked the prices, and saw that the credit 
system they offer sells computational time for about $10.80/hour (in $15 
increments), down to $6.47/hour (if you buy $180 at a time), billed in 
100ms chunks [1].  In comparison, the highest price an Amazon Linux EC2 
On Demand instance is a 32 processor, 244GB Ram, 8 800GB SSD instance 
for $6.82/hour.  I realize I didn't count Amazon's bandwidth charges 
($0.12/GB after 1GB out from EC2 to internet each month), but 
regardless, that seems like relatively expensive computational time.


[1] http://www.wolfram.com/cloud-credits/ (down at the bottom)
[2] http://aws.amazon.com/ec2/pricing/



On 11/21/14, 20:45, William Stein wrote:


On Nov 21, 2014 11:46 AM, "Dr. David Kirkby (Kirkby Microwave Ltd)"
mailto:drkir...@kirkbymicrowave.co.uk>>
wrote:
 >
 >
 > On 18 Nov 2014 22:37, "Stefan" mailto:stefanvanz...@gmail.com>> wrote:
 > >
 > > I don't know if I simply lack the appropriate Mathematica
knowledge, but years ago, when I implemented matroids
 > > lM = Map[If[# == 0, 0, 1] &, M[[2]][[#[[2]] & /@ M[[3]], #[[2]] &
/@ M[[4, {2}];
 >
 > I am no expert on Mathematica, but Mathematica code does not need to
be so cryptic.
 >

Can anybody rewrite the above line of mathematica code so that it does
something equivalent, but is less cryptic?

 > Anyway,  is it any less readable than this code to plot the
Mandelbrot set?
 >
 >
http://preshing.com/20110926/high-resolution-mandelbrot-in-obfuscated-python/
 >
 > Or this C code
 >
 > http://www.ioccc.org/2013/birken/birken.c
 >
 > Dave.
 >
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[sage-devel] Nature article mentions Sage

2014-11-05 Thread Jason Grout

FYI, this nature article from today, mainly about the IPython notebook, 
also mentions Sage: 
http://www.nature.com/news/interactive-notebooks-sharing-the-code-1.16261


"A number of notebooks and notebook-like programs exist in the 
open-source world; knitr works with the R coding language, which is 
especially powerful for statistical analysis. And the Sage mathematical 
software system, which is also based on the Python language, supports 
its own notebook."


Kyle Kelly from Rackspace, who works a lot with the IPython lead devs 
with the nbviewer, also set up a tmpnb to allow for small interactive 
notebooks for random internet users: 
http://www.nature.com/news/ipython-interactive-demo-7.21492


Thanks,

Jason

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[sage-devel] Re: The Misfortunes of a Trio of Mathematicians Using Computer Algebra Systems

2014-11-04 Thread Jason Grout


On 11/4/14, 7:04, Volker Braun wrote:

I can see that there could be a number of follow up comments about
the article. But too much emphasis on Sage's ability to perform the
computation correctly would make it like a childish pi**ing contest.

Agree. A reasonable article should

a) give some overview over the algorithms involved

b) talk about bug tracking and prioritization, stopgaps

c) automated testing to prevent the same issue in the future

There have been subtle bugs in determinants of integer matrices in Sage
before, e.g. http://trac.sagemath.org/ticket/14032 "determinant() of
integer matrices of size in [51,63] broken". Open source doesn't make
Sage magically bug-free. But Linus' law applies: "given enough eyeballs,
all bugs are shallow".


I agree with both of you.  Given that a significant part of this article 
dwelt on the closed-source bug-reporting frustration, it might be even 
more interesting if the user was taken through an actual bug found in 
Sage, and the bug-reporting and bug-fixing process was described, 
emphasizing the open approach and the role the authors could play.  I 
was disappointed with the original article's conclusions---it gave the 
impression that the best we could hope for in finding, reporting, and 
fixing bugs in mathematical software was that we might be able to find 
them in comparing the output of two different black boxes.


Thanks,

Jason


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[sage-devel] [ANN - JOB] Assistant Researcher - Berkeley Institute for Data Science

2014-10-30 Thread Jason Grout

See below for a posting about a job opportunity involving open source 
tools for scientific computing.


Thanks,

Jason


 Original Message 
Subject:[Numpy-discussion] [ANN - JOB] Assistant Researcher - Berkeley
Institute for Data Science
Date:   Wed, 29 Oct 2014 19:15:51 -0700
From:   Fernando Perez 


Hi all,

the newly founded Berkeley Institute for Data Science is hiring
researchers with a focus on open source tools for scientific computing,
please see here for details:

https://aprecruit.berkeley.edu/apply/JPF00590

Cheers,

f
--
Fernando Perez (@fperez_org; http://fperez.org)
fperez.net-at-gmail: mailing lists only (I ignore this when swamped!)
fernando.perez-at-berkeley: contact me here for any direct mail

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[sage-devel] Re: determinant calculation, was: The Misfortunes of a Trio of Mathematicians [...]

2014-10-29 Thread Jason Grout

On 10/28/14, 15:53, Robert Dodier wrote:

On 2014-10-25, Jason Grout wrote:

http://www.ams.org/notices/201410/rnoti-p1249.pdf

P.S. It would be interesting to see if Sage can do the calculation they
identified as buggy in mathematica. That would make for a cool
follow-up editorial.

I've reimplemnted the buggy determinant calculation in Maxima.
Presumably from this it would be easy to redo it in any other system;
I don't know how Sage manages such calculations.

I am happy to report that Maxima, despite its many and varied bugs,
doesn't have this particular one:

bfloat (determinant (big_matrix));
=> 1.951242191319868b9762

Reported value in paper is 1.95124219131987 * 10^9762.

Script is attached as a PS. The function foo(n) can be used to generate
random examples, as the authors did to find one which tickles the bug.

Thanks so much for typing up those long matrices. It looks like Sage
also gets the right answer for that particular example:

https://cloud.sagemath.com/#projects/49a2531d-9d02-42c9-9db6-f9551fbfa59e/files/2014-10-24-212837.sagews

Thanks,

Jason

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[sage-devel] Re: The Misfortunes of a Trio of Mathematicians Using Computer Algebra Systems

2014-10-27 Thread Jason Grout

On 10/25/14, 21:38, William Stein wrote:

On Sat, Oct 25, 2014 at 6:34 PM, William Stein wrote:

On Oct 25, 2014 5:53 PM, "Jason Grout" wrote:

On 10/25/14, 15:04, William Stein wrote:

On Sat, Oct 25, 2014 at 6:37 AM, Jason Grout
wrote:

On 10/25/14, 0:07, William Stein wrote:

They are fun aren't they -- no login required.

It seems that often, though, the login page or the project settings page
flashes up for a second or less, which is confusing. Do you know why
the
signup page or settings page might come up first, then be replaced with
the
worksheet?

It's fixed now.

Not for me. There's a blank white page, then a page that says Sage and
something like "loading", then the settings page for a project, then the
published worksheet. Each page flashes up for maybe 1/2 second or so. I've
made sure my cache is disabled when I reloaded.

This is with this page:
https://cloud.sagemath.com/projects/4a5f0542-5873-4eed-a85c-a18c706e8bcd/files/support/ams-article-mathematica-bugs.sagews

Try it when you are not logged in, eg in a new private browsing session.

Disregard my message -- I would guess you already are using private
browsing mode for testing.

I was going back and forth. Let me be more precise. Using incognito,
it does indeed appear that (now) the flashes of setting screen, etc.,
are gone---all I see is a blank screen, then a header, then the page.
When I am logged in, I still see the flashes of the settings page, etc.

Thanks,

Jason

[sage-devel] Re: The Misfortunes of a Trio of Mathematicians Using Computer Algebra Systems

2014-10-25 Thread Jason Grout


On 10/25/14, 15:04, William Stein wrote:

On Sat, Oct 25, 2014 at 6:37 AM, Jason Grout
 wrote:

On 10/25/14, 0:07, William Stein wrote:


They are fun aren't they -- no login required.



It seems that often, though, the login page or the project settings page
flashes up for a second or less, which is confusing.  Do you know why the
signup page or settings page might come up first, then be replaced with the
worksheet?


It's fixed now.



Not for me.  There's a blank white page, then a page that says Sage and 
something like "loading", then the settings page for a project, then the 
published worksheet.  Each page flashes up for maybe 1/2 second or so. 
I've made sure my cache is disabled when I reloaded.


This is with this page: 
https://cloud.sagemath.com/projects/4a5f0542-5873-4eed-a85c-a18c706e8bcd/files/support/ams-article-mathematica-bugs.sagews


Thanks,

Jason



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[sage-devel] Re: The Misfortunes of a Trio of Mathematicians Using Computer Algebra Systems

2014-10-25 Thread Jason Grout


On 10/25/14, 0:07, William Stein wrote:

They are fun aren't they -- no login required.


It seems that often, though, the login page or the project settings page 
flashes up for a second or less, which is confusing.  Do you know why 
the signup page or settings page might come up first, then be replaced 
with the worksheet?


Thanks,

Jason


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[sage-devel] Re: The Misfortunes of a Trio of Mathematicians Using Computer Algebra Systems

2014-10-24 Thread Jason Grout


On 10/24/14, 20:55, Jason Grout wrote:

P.S. It would be interesting to see if Sage can do the calculation they
identified as buggy in mathematica.  That would make for a cool
follow-up editorial.



And here's a public worksheet: 
https://cloud.sagemath.com/projects/49a2531d-9d02-42c9-9db6-f9551fbfa59e/files/2014-10-24-212837.sagews


(Thanks, William, for making public worksheets!)

Next challenge: implement their mathematica notebooks in Sage.

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[sage-devel] The Misfortunes of a Trio of Mathematicians Using Computer Algebra Systems

2014-10-24 Thread Jason Grout

The AMS Notices has a column about using computers to do math, dwelling 
on some problems they had with Mathematica:


 http://www.ams.org/notices/201410/rnoti-p1249.pdf

The HackerNews discussion immediately brings up Sage, of course: 
https://news.ycombinator.com/item?id=8505665


Funny quote (that I don't necessarily agree with): "This resembles the 
well- known Pentium division bug discovered by Thomas Nicely in 1994, 
which only affected certain kinds of numbers. But it seems Mathematica 
is a black box even darker that the internals of a microprocessor, so it 
is difficult to try to understand what kinds of numbers are affected by 
the Mathematica bug that we are describing."


Interestingly, throughout the article, they emphasize what a hard time 
they had when the found MMA and Maple conflicting, and the problems with 
having MMA be closed-source.  You'd think they'd end with a resounding 
recommendation to use open-source software whereever possible, and fund 
and motivate it's development.  However, their final recommendation 
backpedals quite a bit and is just "However, for the time being, when 
dealing with a problem whose answer cannot be easily verified without a 
computer, it is highly advisable to perform the computations with at 
least two computer algebra systems."


Thanks,

Jason

P.S. It would be interesting to see if Sage can do the calculation they 
identified as buggy in mathematica.  That would make for a cool 
follow-up editorial.


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[sage-devel] Re: Official interact API needed

2014-10-23 Thread Jason Grout

On 10/23/14, 17:27, William Stein wrote:

On Thu, Oct 23, 2014 at 2:03 PM, kcrisman wrote:

Hi all! Based on on-and-off discussion with some other developers and the
disconnect between interacts on SMC and sagecell and sagenb, it seems time
to at least find out what an API for interacts currently is.

The one for sagenb is pretty well documented, I think, in interact.py. I
have no idea where the other two are.

Type

interact?

for the documentation in SMC (it's very similar to Sage). Then for
each control, type "interact.controls.[tab]" and look at their
docstrings.

In sagecell, doing

interact?

and hitting enters silently fails. Doing interact?[tab] shows some
very minimal/useless documentation. So I also don't know where the
interact docs are for SMC.

There is some very rough documentation at:

https://github.com/sagemath/sagecell/blob/master/doc/interact_protocol.rst

There is some more comprehensive documentation for our rewrite in the
source file:

https://github.com/sagemath/sagecell/blob/master/interact_sagecell.py

and for the sage compatibility layer at:

https://github.com/sagemath/sagecell/blob/master/interact_compatibility.py

Andrey has volunteered ;-) to combine all current documentation into
something. So let us know!!

Naturally there could still be further extensions in SMC if needed but we
really need a place for a consistent API or it will just be too confusing.
(That includes nested interacts, presumably, though I don't know whether
sagenb could do them without some upgrades in its dependencies - jQuery is
being updated, which is a start, but it might need other widgets?)

Nested interacts isn't really something that need documentation or an
API. They are something that should "just work", but which don't in
sagenb, and probably won't ever.

To add to the confusion, there is something like interacts for
ipython, which is maybe somewhat different API-wise from what is in
sage...

http://nbviewer.ipython.org/github/ipython/ipython/blob/master/examples/Interactive%20Widgets/Index.ipynb

Right. The IPython interact system is what I've been working a lot on
for the last year. There is little to no documentation on it at this
point, and we're having a Google hangout about the scope of the IPython
interactive widget system next week.

Thanks,

Jason

[sage-devel] Re: On scientific computing, Python and Julia

2014-08-22 Thread Jason Grout


On 8/21/14, 11:36, Bill Hart wrote:

You can define the A.b syntax in Julia if you should so desire. It's
essentially just another kind of method overload in Julia.

And then, it supports A. giving a list of all the things that could
follow the dot, just as Python would.


Are you saying you can overload the dot operator?  I thought that was 
still an open issue (https://github.com/JuliaLang/julia/issues/1974).


Harold: Julia does have a module system, which Bill illustrated, that 
uses the dot to access members of the module.  And a dot also accesses 
fields of a type instance.


Thanks,

Jason


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[sage-devel] Re: Crazy/dumb idea about Sage on Windows...

2014-08-22 Thread Jason Grout


On 8/22/14, 0:45, Fernando Perez wrote:

Because our execution model decouples the kernel from the filesystem,
the user gets their 'normal' environment, files, etc, and they don't
really need to know anything about the VM to get to their work, their
directories, etc.


Their .sage and .ipynb files would live on the windows side, but if they 
have some data they want to analyze (like a file to read in, or a file 
to save to), they'd still have to somehow get that data into/out of the 
VM.  You're right that it's easier than what we have, though!


Thanks,

Jason


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[sage-devel] Re: On scientific computing, Python and Julia

2014-08-22 Thread Jason Grout


On 8/21/14, 18:08, Bill Hart wrote:

In theory, I can do generic programming in Julia that is faster (at
runtime) than you can do in *any* C compiler. And I don't just mean a
little bit. I mean a lot. I don't even think the Julia people fully
realise this yet (I might be wrong about that, I don't know). And it's
not been realised in practice for many cases. But it is true.


Are you talking about the sort of things illustrated in this julia issue 
with the various macros they talk about?


https://github.com/JuliaLang/julia/issues/7033

Thanks,

Jason

P.S. I've been following Julia for a while and I'm very intrigued by it. 
 I've also started keeping an eye on Nemo recently---very interesting!



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

2014-08-21 Thread Jason Grout


On 8/18/14, 17:33, kcrisman wrote:



On Monday, August 18, 2014 3:22:00 PM UTC-4, wstein wrote:

Hi,

Andrey Novoseltsev kindly pointed out that interact.sagemath.org
<http://interact.sagemath.org> is
deluged with spam, e.g.,

http://interact.sagemath.org/node/1194
<http://interact.sagemath.org/node/1194>

Can somebody volunteer to deal with this ASAP?   Either clean up the
spam, or move hosting somewhere else (i'll point DNS their way).   I'm
afraid UW is  likely to disconnect sagemath.org
<http://sagemath.org> from the internet if
we don't.


  I don't know who is currently administering this or has such
privileges... One easy fix is to disable comments, perhaps.  Wow, I had
no idea.



Just following up---that's exactly what I did, and made the site 
essentially read-only except for "trusted author" accounts.  If you'd 
like one of those, email me.  If someone wants to take over the site, 
let me know.


Thanks,

Jason



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[sage-devel] Re: what is the plot3D viewer used in sagemath cloud

2014-08-21 Thread Jason Grout


On 8/21/14, 15:27, Frédéric Chapoton wrote:

Thanks ! Do you know which file format is used by sagemath cloud to
communicate with threejs ? Is it .obj or .x3d or json ? Where can I find
the code ? and some documentation ?


The relevant files for smc are the 3d.* files here:

https://github.com/sagemath/cloud

(at least, those were the files a while ago, and I doubt much has 
changed with the 3d rendering since then.)


My students and I rewrote that 3d renderer for the sage cell server, and 
then we again rewrote a system to use the IPython widget infrastructure 
(so it works in the sage cell server and the IPython notebook).  If 
you're interested in either of those, let me know.


Thanks,

Jason


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[sage-devel] R build script is unable to find file that exists at path

2014-06-25 Thread Jason Wu

Hello again,

I'm (still) trying to build sage on cygwin64 using the /u/jpflori/cygwin64 
branch from trac. I've run into quite a few errors but I've been able to 
fix them usually by following the wiki. However, I've run into a strange 
problem

Screenshot:


(link: http://i.imgur.com/I6245eD.png)

The problem is that R fails while building one of its packages (grDevices) 
with the message:

byte-compiling package 'grDevices'
Warning in solve.default(rgb) :
  unable to load shared object 
'/home/jwpilly/sage/local/var/tmp/sage/build/r-3.0.2.p1/src/modules//lapack.dll':
  *No such file or directory*
Error in solve.default(rgb) : LAPACK routines cannot be loaded
Error: unable to load R code in package 'grDevices'
Execution halted
../../../share/make/lazycomp.mk:7: recipe for target 
'../../../library/grDevices/R/grDevices.rdb' failed
make[7]: *** [../../../library/grDevices/R/grDevices.rdb] Error 1

As you can see, the build script complains that there is no such file 
" 
'/home/jwpilly/sage/local/var/tmp/sage/build/r-3.0.2.p1/src/modules//lapack.dll'"
 
even though in the screenshot, you can see that there clearly is a file 
named "lapack.dll" at that path in windows explorer. I noticed that the 
file path contains a double forward slash, but I thought in linux this 
resolves to a single slash? Anyway, this strange bug is preventing sage 
from successfully building.

Any help is appreciated and thanks in advance

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[sage-devel] Re: curl 404 on cygwin64 branch

2014-06-22 Thread Jason Wu

It worked! I initially tried this, but it didn't work because the tarball 
from mpir.org was named "mpir-2.7.0[DASH]alpha4.tar.bz2" where the one it 
was trying to download was "mpir-2.7.0[DOT]alpha4.tar.bz2".

Thanks again!

On Sunday, June 22, 2014 7:20:25 PM UTC-4, Dima Pasechnik wrote:
>
> On 2014-06-22, Jason Wu > wrote: 
> > Hello, 
> > I'm fairly new to sage and I was trying to build sage on cygwin64. I 
> cloned 
> > the git repo and checked out u/jpflori/cygwin64 but it gets stuck when 
> it 
> > tries to download mpir 2.7.0.alpha4. mpir2.6.0 (used in master branch) 
> > won't build on cygwin64. anyways, sage-spkg uses curl to try and 
> download 
> > the 2.7.0 alpha package from the sagemath.org server but it doesn't 
> exist: 
> > 
> > /home/jwpilly/sage/build/pipestatus "sage-spkg ${SAGE_SPKG_OPTS} 
> > mpir-2.7.0.alpha4 2>&1" "tee -a 
> > /home/jwpilly/sage/logs/pkgs/mpir-2.7.0.alpha4.log" 
> > Found local metadata for mpir-2.7.0.alpha4 
> > Attempting to download package mpir-2.7.0.alpha4 
> >>>> Trying to download 
> > http://www.sagemath.org/packages/upstream/mpir/mpir-2.7.0.alpha4.tar.bz2 
> >   % Total% Received % Xferd  Average Speed   TimeTime Time 
> >  Current 
> >  Dload  Upload   Total   SpentLeft 
> >  Speed 
> >   0 00 00 0  0  0 --:--:-- --:--:-- --:--:-- 
>   
> >   0 
> > curl: (22) The requested URL returned error: 404 Not Found 
> > Error: failed to download package mpir-2.7.0.alpha4 
> > Makefile:582: recipe for target 
> > '/home/jwpilly/sage/local/var/lib/sage/installed/mpir-2.7.0.alpha4' 
> failed 
> > 
> > 
> > I know the real location of mpir2.7.0.alpha4 is here: 
> > http://mpir.org/mpir-2.7.0-alpha4.tar.bz2 
> > 
> > is there any config files i can edit so that sage downloads from there? 
> i 
> > can download the tarball manually but i don't know how to make the make 
> > script use the local tarball instead of trying to download it 
>
> just download the file and place it in $SAGEROOT/upstream/ 
> The installed should be able to pick it up from there. 
> HTH, 
> Dmitrii 
>
> > 
> > Thanks in advance! 
> > 
>
>

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[sage-devel] curl 404 on cygwin64 branch

2014-06-22 Thread Jason Wu

Hello,
I'm fairly new to sage and I was trying to build sage on cygwin64. I cloned 
the git repo and checked out u/jpflori/cygwin64 but it gets stuck when it 
tries to download mpir 2.7.0.alpha4. mpir2.6.0 (used in master branch) 
won't build on cygwin64. anyways, sage-spkg uses curl to try and download 
the 2.7.0 alpha package from the sagemath.org server but it doesn't exist:

/home/jwpilly/sage/build/pipestatus "sage-spkg ${SAGE_SPKG_OPTS} 
mpir-2.7.0.alpha4 2>&1" "tee -a 
/home/jwpilly/sage/logs/pkgs/mpir-2.7.0.alpha4.log"
Found local metadata for mpir-2.7.0.alpha4
Attempting to download package mpir-2.7.0.alpha4
>>> Trying to download 
http://www.sagemath.org/packages/upstream/mpir/mpir-2.7.0.alpha4.tar.bz2
  % Total% Received % Xferd  Average Speed   TimeTime Time 
 Current
 Dload  Upload   Total   SpentLeft 
 Speed
  0 00 00 0  0  0 --:--:-- --:--:-- --:--:--   
  0
curl: (22) The requested URL returned error: 404 Not Found
Error: failed to download package mpir-2.7.0.alpha4
Makefile:582: recipe for target 
'/home/jwpilly/sage/local/var/lib/sage/installed/mpir-2.7.0.alpha4' failed


I know the real location of mpir2.7.0.alpha4 is here: 
http://mpir.org/mpir-2.7.0-alpha4.tar.bz2

is there any config files i can edit so that sage downloads from there? i 
can download the tarball manually but i don't know how to make the make 
script use the local tarball instead of trying to download it

Thanks in advance!

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[sage-devel] Re: Logs for aleph.sagemath.org

2014-06-06 Thread Jason Grout


On 6/5/14, 2:33, Ivan Andrus wrote:

Are there logs (and if so where are they?) for aleph.sagemath.org?  I'm trying 
to figure out what sorts of things the iOS app is used for.


Yes, there are logs.   Right now, we log remote ip, referer, execution 
type, kernel id, and the code text: 
https://github.com/sagemath/sagecell/blob/master/log.py


That's a good idea to log the user agent too, but we don't have 
historical data on that (at least from the ios app)


Thanks,

Jason



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[sage-devel] Re: Sage Stack Exchange Site

2014-06-02 Thread Jason Grout


On 6/2/14, 11:12, William Stein wrote:

In fact, as you suggest above, go one further:   Python -->
"mathematical software"

Having such a site, which is like mathoverflow, but for open source
math software, sounds attractive (if such a thing does not already
exist).


Related: http://scicomp.stackexchange.com/ "Computational Science Stack 
Exchange is a question and answer site for scientists using computers to 
solve scientific problems."


It's seems more about scientific computing rather than more pure 
mathematical software, though.


Jason


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[sage-devel] Re: optional graph database?

2014-05-23 Thread Jason Grout


On 5/21/14, 13:21, William Stein wrote:

On Wed, May 21, 2014 at 11:18 AM, kcrisman  wrote:

I'm about to give a very intro talk about graph theory in Sage, and
the graph database section [1] of the reference manual begins: "...
This class will also interface with the optional database package
containing all unlabeled graphs with 8 or fewer nodes."

I can't find any optional package to install to get these extra graphs
up to 8 vertices.   Anybody have any idea what happened to this?   I
realize that this stuff was originally done by Robert Miller and Emily
Kirkman, who have moved on to other things (Home Depot and Actuarial
work, I think...), but maybe somebody has kept track...  If not, we
should delete that line from the reference manual.

There is a database included in Sage with graphs up to 7 nodes:

for k in [1..9]:
 print k, GraphQuery(display_cols=['num_vertices'],
num_vertices=k).number_of()

1 1
2 2
3 4
4 11
5 34
6 15
7 1044
8 0
9 0

So the builtin database is pretty tiny -- only just over a thousand
graphs total?



Well, the problem is that there is a LOT of information in the database,
some of which is quite expensive to compute for all isomorphism classes.


I appreciate that.



Also, the database must still exist in some sense, or
http://artsci.drake.edu/grout/graphs/ wouldn't work... I just found all
three graphs with degree sequence  - which leads me to wonder how
that syntax would have to change if two-digit (in decimal) values for degree
were possible if the database were bigger ;-)


That database http://artsci.drake.edu/grout/graphs/  was maybe a key
part of Jason Grout's Ph.D. work -- and making a Sage version of it
(which is what is in Sage up to 7 vertices) was one of the things that
got him involved with Sage development.


It was actually for my masters thesis that I originally did the 
database.  And it was the very first thing that got me involved in Sage 
development.


You can see at the http://artsci.drake.edu/grout/graphs/ page that I 
still have the 8-vertex database up.  It's a mysql database, and I just 
dumped it to a sql file and posted it here:


http://boxen.math.washington.edu/home/jason/graph-database.sql.gz

To answer Karl-Dieter's question, obviously the degree sequence string 
format would change, or we could count in hex or something.


Thanks,

Jason


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[sage-devel] Re: free private github repos

2014-05-16 Thread Jason Grout


On 5/15/14, 7:36, Dima Pasechnik wrote:

And, by the way, should Sage get a DOI?
This looks doable, only one probably needs to be an "Owner" of
https://github.com/sagemath/sage
and not just "team member".



Interesting.  So would this mean that we can tell people at 
http://wiki.sagemath.org/Publications_using_SAGE to cite the specific 
version of Sage that they used and include the DOI?


Thanks,

Jason


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[sage-devel] Re: sage--gram-schmidt

2014-05-09 Thread Jason Grout


(CCd to sage-devel)

On 5/9/14, 13:32, David Guichard wrote:

Is there some deep reason I'm not seeing that G-S doesn't work for SR?
It seems like everything should be fine. Is the problem in detecting
dependent sets over SR? This keeps me from being able to do simple
examples for a linear algebra class. I can do it over QQbar, but
that's pretty ugly.



I ran into similar problems at one point with the LU decomposition, 
where it complained that the base ring was not exact.  I think the 
problem ultimately is that if you are working in an 'inexact' ring, 
round-off error can be a bear (so you're right that detecting linear 
dependence is hard).  The RDF and CDF matrices try to use numpy and 
stable algorithms for computing these sorts of things for real/complex 
floating point matrices.


Mike Hansen and I had a conversation about this at one point, and I 
think we concluded that instead of looking at the base ring in the case 
of SR, we should instead look at the specific matrix and decide if it 
was "exact" or an approximation.  For example, an SR matrix with just 
integers and/or variables could be considered exact, while an SR matrix 
with floating point numbers wouldn't.


Thanks,

Jason

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

2014-05-09 Thread Jason Grout


On 5/7/14, 0:41, Ivan Andrus wrote:

On May 6, 2014, at 11:47 AM, Jason Grout  wrote:


On 5/5/14, 14:20, Daniel Bell wrote:

Hi

I am one of the students who was selected for working with Sage for
Google Summer of Code.  I will be working on the iOS app.  One of the
features I want to implement is the ability to interact with
interact.sagemath.org <http://interact.sagemath.org/top-rated-posts>

Is there an API I can use, or a database I can interact with?


interact.sagemath.org is using Drupal, so I imagine it would be a pretty 
standard thing to enable a REST API or something of that sort.  Would you like 
to take over the website and do that?


I take it from this that you were the maintainer, and it will therefore be 
abandoned soon?


One of my students built the site and was the maintainer until our 
project was over.  I would probably be considered the maintainer now.  I 
haven't done much with the site recently.  I realized that having a 
separate, sort of 'heavyweight' site was not as conducive to sharing the 
examples as much as I originally thought (not nearly as conducive as, 
for example, the published worksheets on sagenb.org).  I think somehow 
tying the original creation and sharing a lot more closely would be much 
better.  That's what we had with sagenb.org published worksheets---one 
button from creation would share, and one more click would update to the 
most recent version.  In some sense, we have that with the cell server 
too---two clicks from creation give a link you can share.  We don't have 
the concept of updating a link in the cell server, though.  The IPython 
notebook viewer has a different take on how to tie together sharing and 
creation---content is hosted where ever is convenient, and the viewer 
simply makes it easy to interact with that content.


So in general, I think it was a valuable experiment and direction to 
explore, but I also think the concept should be rethought and 
incorporated more fully in the tools creating the content.  If we had 
people that could devote part or full-time work to creation and curation 
of examples, that might change things, but even in that case you have to 
deal with scaling the work.


So I'm not planning on doing much more work upgrading and expanding the 
site.  That said, if someone else wants to take over it, they are more 
than welcome to do so.


Thanks,

Jason


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[sage-devel] Re: test message

2014-05-06 Thread Jason Grout


On 5/6/14, 9:05, Simon King wrote:

I wouldn't mind to stay with google-groups, *IF* one could use it via
gmane (which is currently not the case).


I'm replying to this on gmane (via thunderbird).  If you see this 
message, I guess it shows it is possible.


Jason


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

2014-05-06 Thread Jason Grout


On 5/5/14, 14:20, Daniel Bell wrote:

Hi

I am one of the students who was selected for working with Sage for
Google Summer of Code.  I will be working on the iOS app.  One of the
features I want to implement is the ability to interact with
interact.sagemath.org <http://interact.sagemath.org/top-rated-posts>

Is there an API I can use, or a database I can interact with?



interact.sagemath.org is using Drupal, so I imagine it would be a pretty 
standard thing to enable a REST API or something of that sort.  Would 
you like to take over the website and do that?


Thanks,

Jason


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[sage-devel] Google Summer of Code

2014-04-22 Thread Jason Grout

Does anyone have an update about what projects are Google Summer of Code 
projects are running under the Sage umbrella?


Thanks,

Jason

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[sage-devel] Re: Heartbleed

2014-04-10 Thread Jason Grout


On 4/8/14, 22:06, kcrisman wrote:

What version does sagenb, cloud, sage cell use?


For the cell server, I have automatic security updates enabled.  I 
checked yesterday and the openssl package had been automatically 
upgraded already.


Jason


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[sage-devel] handing off *.sagenb.org and sage cell server

2014-04-10 Thread Jason Grout


Hi everyone,

Very recently, I had an unexpected opportunity come up, and after a lot 
of thinking and praying with my family, decided to accept a job in 
industry starting in June (in the quantitative finance research group at 
Bloomberg in New York).  I don't plan to completely disappear from the 
Sage community, but I think it would be best to hand off the 
administration for two pieces of major infrastructure that I help 
maintain, as I won't have the time that I have now to work on these.


* the sage notebook servers at *.sagenb.org.  These are effectively in 
maintenance mode right now, with very few updates.  We are actively 
encouraging people to switch to cloud.sagemath.com.


* the sage cell server at http://sagecell.sagemath.org.  This service 
now serves about 2000 computations a day, and consists of 6 virtual 
machines spread across 2 computers, with another virtual machine doing 
remote logging and permalink URL storage. The build and deployment 
process for the cell server consists of about 5 commands to create and 
deploy a virtual machine from scratch.


If you are interested in taking over the administration of either of 
these, please let me and/or William know.


Thanks,

Jason

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[sage-devel] Re: Need contact who can provide direction on default jquery-ui theme for sage-notebook...

2014-03-25 Thread Jason Grout


On 3/25/14, 9:02, kcrisman wrote:



As I have posted to the sage-notebook list, I have pure javascript
Jmol working in the notebook (see track ticket #16004:
http://trac.sagemath.org/ticket/16004
<http://trac.sagemath.org/ticket/16004>).  However, this requires an
up-to-date version of jquery.  It appears that the jquery-ui-1.8.11
(about 3 years old) which we are using is not compatible.  Can
somebody tell me what the theme choices were to roll an updated
jquery-ui-1.10.4?


I don't think it should be horrible to update, for a JS expert - for me,
probably very horrible :)

Jason, what version of Jquery-ui do you use in the cell server?  Maybe
that is a starting point for thinking about this.


1.10.2: https://github.com/sagemath/sagecell/blob/master/Makefile#L16

See 
https://raw.githubusercontent.com/sagemath/sagecell/master/static/jquery-ui/js/jquery-ui-1.10.2.custom.min.js


See also 
https://github.com/sagemath/sagecell/blob/master/static/jquery-ui/css/sagecell/jquery-ui-1.10.2.custom.min.css, 
which points to this theme: 
http://jqueryui.com/themeroller/?ffDefault=Verdana%2CArial%2Csans-serif&fwDefault=normal&fsDefault=1.1em&cornerRadius=4px&bgColorHeader=cc&bgTextureHeader=highlight_soft&bgImgOpacityHeader=75&borderColorHeader=aa&fcHeader=22&iconColorHeader=22&bgColorContent=f3f3f3&bgTextureContent=flat&bgImgOpacityContent=0&borderColorContent=dd&fcContent=362b36&iconColorContent=22&bgColorDefault=99bbff&bgTextureDefault=highlight_hard&bgImgOpacityDefault=60&borderColorDefault=cc&fcDefault=11&iconColorDefault=77&bgColorHover=99bbff&bgTextureHover=highlight_hard&bgImgOpacityHover=90&borderColorHover=88&fcHover=11&iconColorHover=22&bgColorActive=ffc53d&bgTextureActive=highlight_hard&bgImgOpacityActive=60&borderColorActive=a85700&fcActive=00&iconColorActive=00&bgColorHighlight=fbf9ee&bgTextureHighlight=glass&bgImgOpacityHighlight=55&borderColorHighlight=fcefa1&fcHighlight=363636&iconColorHighlight=2e83ff&bgColorError=fef1ec&bgTextureError=highlight

_
hard&bgImgOpacityError=95&borderColorError=cd0a0a&fcError=cd0a0a&iconColorError=cd0a0a&bgColorOverlay=aa&bgTextureOverlay=flat&bgImgOpacityOverlay=0&opacityOverlay=30&bgColorShadow=aa&bgTextureShadow=flat&bgImgOpacityShadow=0&opacityShadow=30&thicknessShadow=8px&offsetTopShadow=-8px&offsetLeftShadow=-8px&cornerRadiusShadow=8px&ctl=themeroller

Thanks,

Jason

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[sage-devel] Re: %load

2014-03-25 Thread Jason Grout


On 3/24/14, 3:25, Volker Braun wrote:

I find the various commands to evaluate code from a file confusing (and
not really documented). When was the English language changed so that
"load" implies evaluation?


Probably when it was programmed into magma: 
http://linux.math.tifr.res.in/manuals/html/magma/text93.html (which I 
think the Sage %load originally derived from, right William?)




Also, changing the way IPython works is only
going to confuse me more, not less.

IMHO we should have

%load # as provided by ipython
%run   # evaluate file content, preparsed depending on the file
extension
%attach  # like run, but watch for changes







Also:

* No new statements, i.e. no "load" without percent sign is not allowed.


in other words:

load 'filename'

is not allowed? (unless, I suppose, you turn on %automagics)


* But do support them as global functions load('filename.py').
* No %runfile. Whats the difference with %run?


For reference, here's the discussion from last time, which talks about 
the differences: 
https://groups.google.com/forum/#!topic/sage-devel/6UXXRtMvxBk.  tl;dr: 
+1 to unifying %run and %runfile, and pushing these changes upstream. 
Not surprisingly, that's essentially what you voted for too in that 
thread, Volker.


Thanks,

Jason


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[sage-devel] A PEP for adding infix matrix multiply to Python

2014-03-15 Thread Jason Grout

There has been lots of conversation recently on adding an infix matrix 
multiplication operator to Python, pushed by some folks from the 
numpy/scipy community, and backed by pandas and some other projects. 
Guido has practically accepted the proposal to make @ an infix matrix 
multiplication operator (like A @ B).  There are ongoing conversations 
about operator precedence, binding, etc., as well as the possibility of 
a matrix power operator @@ (like A @@ 2).


Anyways, see the message below from Nathaniel, who has been the one 
spearheading this.


Thanks,

Jason

 Original Message 
Subject: [pydata] Re: A PEP for adding infix matrix multiply to Python
Date: Sun, 16 Mar 2014 02:40:11 +
From: Nathaniel Smith 
Reply-To: pyd...@googlegroups.com
To: pyd...@googlegroups.com

Hi again,

As an update on this for anyone not following python-ideas or
numpy-discussion: Guido has accepted the addition of @ as a matrix
multiplication operator in principle, once some details are worked
out:
https://mail.python.org/pipermail/python-ideas/2014-March/027109.html

So if you have any feedback you've been sitting on, now is a good time
to speak up :-). The current PEP draft can be seen here:
http://legacy.python.org/dev/peps/pep-0465/

I've also started threads on numpy-discussion specifically about the
details to be worked out, in case anyone wants to comment -- input on
these points would be especially helpful:

Precedence/associativity of @:
http://mail.scipy.org/pipermail/numpy-discussion/2014-March/069444.html

Do we care about @@:
http://mail.scipy.org/pipermail/numpy-discussion/2014-March/069448.html

I believe that if you aren't subscribed to numpy-discussion, then you
can still post through gmane (though unfortunately their anti-spam
munging of the @ character makes these threads kind of hard to read!):
http://news.gmane.org/gmane.comp.python.numeric.general

Or, worst case, just email me directly, and I'll collate.

Cheers,
-n

On Sat, Feb 22, 2014 at 10:00 PM, Nathaniel Smith  wrote:

[Apologies for wide distribution -- please direct followups to either
the github PR linked below, or else numpy-discuss...@scipy.org]

After the numpy-discussion thread about np.matrix a week or so back, I
got curious and read the old PEPs that attempted to add better
matrix/elementwise operators to Python.
  http://legacy.python.org/dev/peps/pep-0211/
  http://legacy.python.org/dev/peps/pep-0225/
And I was a bit surprised -- if I were BDFL I probably would have
rejected these PEPs too. One is actually a proposal to make
itertools.product into an infix operator, which no-one would consider
seriously on its own merits. And the other adds a whole pile of
weirdly spelled new operators with no clear idea about what they
should do.

But it seems to me that at this point, with the benefit of multiple
years more experience, we know much better what we want -- basically,
just a nice clean infix op for matrix multiplication. And that just
asking for this directly, and explaining clearly why we want it, is
something that hasn't been tried. So maybe we should try and see what
happens.

As a starting point for discussion, I wrote a draft. It can be read
and commented on here:
   https://github.com/numpy/numpy/pull/4351

It's important that if we're going to do this at all, we do it right,
and that means being able to honestly say that this document
represents our consensus when going to python-dev. So if you think you
might object please do so now :-)

-n

--
Nathaniel J. Smith
Postdoctoral researcher - Informatics - University of Edinburgh
http://vorpus.org




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http://vorpus.org

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[sage-devel] Re: 2d interactive graphs

2014-03-11 Thread Jason Grout


On 3/10/14 7:18 PM, Gehad Elrobey wrote:

hi , I am a software engineering student interested in gsoc 2d
interactive graphs project.

I Think that interactive 2d graphs is one interesting feature that must
be added to both sage-nb and sage cloud.
In the Projects ideas its mentioned that this features must be added to
sage-nb at least, but from the discussions here it seems that the
notebook view will not be continued and will be replaced by the sage
cloud. can you clarify if the 2d notebook is really on its way out ?


As far as I know, the sage-nb codebase is in maintenance mode, with no 
huge changes or features planned (if someone is working actively on the 
codebase, please post here!)


William is planning to make a personal version of the sage cloud 
available as a next generation sage notebook (and he's proposed such a 
thing as a GSOC project).


Thanks,

Jason



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Re: [sage-devel] wolfram language

2014-03-07 Thread Jason Aubrey

A perspective on the wolfram language in Slate:

http://www.slate.com/articles/technology/bitwise/2014/03/stephen_wolfram_s_new_programming_language_can_he_make_the_world_computable.html

(Sage gets a mention.)


On Mon, Feb 24, 2014 at 8:13 PM, Jason Grout wrote:

> I just saw this on HackerNews:
>
> http://blog.stephenwolfram.com/2014/02/starting-to-demo-
> the-wolfram-language/
>
> I understand that they are trying to release the mathematica cloud thing
> sometime this quarter.  This video (above) is kind of interesting.  The
> cloud interface to mathematica is talked about at 9:18, and I thought the
> comments in the code shown at 10:28 were kind of funny.
>
> Thanks,
>
> Jason
>
>
>
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[sage-devel] Re: wolfram language

2014-03-03 Thread Jason Grout


On 3/2/14, 4:45, Harald Schilly wrote:

Second, functionalities are not discoverable. In Sage there is more
and more a trend to group top-level functions by a topic, e.g. someone
types "graphs.[TAB]" and the tab key expands a list of functions only
for graphs. Additionally, once you have constructed a data structure
holding the information for a concrete incarnation of a concept - AKA
variable name - you can do variable.[TAB] to see operations you can do
on that given instance.
This struck me briefly in the MMA demo video, where the UI gave a list
of common functions you can apply on the given object. (It was only
limited to those functions with only one argument, though.)


Yes, it is nice that we have namespaces and objects/methods.  I should 
note that maple has long had some capabilities for intelligently acting 
on a selected object (via a menu), and that Nathan Carter has a vision 
of doing stuff like that with the sage cloud.  He was writing a short 
prototype up during the Joint Math Meetings in January, and I think 
he'll be coming to the dev days in June.


Thanks,

Jason


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[sage-devel] sage version announcement

2014-03-01 Thread Jason Grout

I just noticed that the version announcement on sage-announce for 
6.1/6.1.1 has a dead link to the ticket list.


https://groups.google.com/d/msg/sage-announce/J3-zKIh3Wc4/u4GNq_zCzVcJ

has two links:

* We closed 193 tickets in this release. For details, see

  http://boxen.math.washington.edu/home/release/sage-6.1/tickets.html

* We closed 4 tickets in this release. For details, see

  http://boxen.math.washington.edu/home/release/sage-6.1.1/tickets.html

but both links give 404 errors.

Thanks,

Jason

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[sage-devel] Re: Problem installing sagecell

2014-03-01 Thread Jason Grout


On 2/28/14, 8:13, Jason Grout wrote:

On 2/28/14, 4:07, Jesus Escribano wrote:

Hello
thank you for your answer. Sorry for asking again, I'm not an expert in
this subject.

I understand I should change the Makefile, introducing the line

/canvas3d   = /
/$(sage-root)/local/lib/python/site-packages/sagenb-0.10.*.egg/sagenb/data/sage/js/canvas3d_lib.js

/

But .. how can I do this? The Makefile is in the sagecell-2013-08-12
package, isn't it? I think that I could do the following:

1. Open the sagecell-2013-08-12 package (I'm not sure how)
2. Modify the Makefile
3. Create a new sagecell package (again, I'm not sure how).


Is this correct?


No need to change the spkg.  That make command is run as the last step
in the installation; you can do it manually after the installation. Just
go into the sagecell directory, modify the makefile, and then run:

sage -sh -c "make -B"

to remake everything. (you may need to put in the path to sage in order
to do that).

Does that help?


I just updated the sagecell spkg: 
http://boxen.math.washington.edu/home/jason/sagecell-spkg/sagecell-2014-03-01.spkg


I also updated my sage sagecell branch to 6.1.1.

Jason


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[sage-devel] Re: Problem installing sagecell

2014-02-28 Thread Jason Grout


On 2/28/14, 4:07, Jesus Escribano wrote:

Hello
thank you for your answer. Sorry for asking again, I'm not an expert in
this subject.

I understand I should change the Makefile, introducing the line

/canvas3d   = /
/$(sage-root)/local/lib/python/site-packages/sagenb-0.10.*.egg/sagenb/data/sage/js/canvas3d_lib.js
/

But .. how can I do this? The Makefile is in the sagecell-2013-08-12
package, isn't it? I think that I could do the following:

1. Open the sagecell-2013-08-12 package (I'm not sure how)
2. Modify the Makefile
3. Create a new sagecell package (again, I'm not sure how).


Is this correct?


No need to change the spkg.  That make command is run as the last step 
in the installation; you can do it manually after the installation. 
Just go into the sagecell directory, modify the makefile, and then run:


sage -sh -c "make -B"

to remake everything. (you may need to put in the path to sage in order 
to do that).


Does that help?

Thanks,

Jason


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[sage-devel] Re: wolfram language

2014-02-27 Thread Jason Grout


On 2/27/14 4:26 PM, rjf wrote:

So how does it stack up as
(a) user experience?
(b) programming environment?


For what it's worth, it took me a couple of hours to implement a live 
camera widget:


http://sagecell.sagemath.org/?q=bttssr

I believe the cloud has something like this too.

(and yes, I know I'm not comprehensively answering your question.  Just 
thought I'd throw this out there, though...)


Thanks,

Jason


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[sage-devel] Re: Problem installing sagecell

2014-02-26 Thread Jason Grout


On 2/26/14 4:18 PM, Jesus Escribano wrote:

Hello
yes, you are right. The path is slightly different:

/home/sagecell/sage/local/lib/python2.7/site-packages/sagenb-0.10.7.2-py2.7.egg/sagenb/data/sage/js/canvas3d_lib.js

(that is, python2.7 instead of python)

Should I change it in the makefile?



Sure.  This is what is currently in the Makefile:

canvas3d   = 
$(sage-root)/local/lib/python/site-packages/sagenb-0.10.*.egg/sagenb/data/sage/js/canvas3d_lib.js



That should be path-agnostic.  It's possible that the sagecell spkg from 
August had a more specific path.  Perhaps I should just create a new spkg.


Thanks,

Jason


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[sage-devel] Re: Problem installing sagecell

2014-02-25 Thread Jason Grout


On 2/25/14 5:46 AM, Jesus Escribano wrote:

make: *** No hay ninguna regla para construir el objetivo 
`/home/sagecell/sage/local/lib/python/site-packages/sagenb-0.10.4-py2.7.egg/sagenb/data/sage/js/canvas3d_lib.js',
 necesario para `static/all.js'.  Alto.


It's looking for the file it mentions.  Is that file where it is looking?

I think those instructions are slightly out of date now, but they're 
probably basically correct still.


Thanks,

Jason


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

On 2/24/14 3:21 PM, Evan Oman wrote:

On Monday, February 24, 2014 1:18:00 AM UTC-6, P Purkayastha wrote:

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.

Thanks for the redirect to sage-support! I will be using that for all
future questions.

As for this problem I am using the Graph module which doesn't seem to
work with the save command. I tried the following:

|
graphObject =Graph({1:[2,3,4],2:[1,3,4],3:[1,2,4],4:[1,2,3]})
figure =graphObject.plot(layout="circular")
figure.save('./test.pdf')
|

and I got an *AssertionError *referring to a bunch of the matplotlib
packages.

The only way I have been able to save so far has been through saving the
the outputted image via a right click in the browser.

  Is the Graph module incompatible with saving in this manner?

It seems to work for me: http://sagecell.sagemath.org/?q=gpscvj

Thanks,

Jason

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


On 2/24/14 1:22 AM, P Purkayastha wrote:

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


And a preliminary patch is up at http://trac.sagemath.org/ticket/9089

Volunteers are more than welcome to update the patches at #9089 or write 
new patches, of course!


Jason



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[sage-devel] wolfram language


I just saw this on HackerNews:

http://blog.stephenwolfram.com/2014/02/starting-to-demo-the-wolfram-language/

I understand that they are trying to release the mathematica cloud thing 
sometime this quarter.  This video (above) is kind of interesting.  The 
cloud interface to mathematica is talked about at 9:18, and I thought 
the comments in the code shown at 10:28 were kind of funny.


Thanks,

Jason



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[sage-devel] Re: Sage library license


On 2/24/14 9:01 AM, Jeroen Demeyer wrote:

Sage-the-distribution is GPL v3 only. This is the only license which is
compatible with all components of Sage.


IIRC, that is because some components are licensed as GPL 2 or 3, while 
others are GPLv3+, right?


Thanks,

Jason


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[sage-devel] Re: Sage library license