# Jupyter notebook by default?

2000 views
Skip to first unread message

### Jeroen Demeyer

unread,
Dec 18, 2015, 5:35:53 AM12/18/15
to sage-devel
Should the Jupyter notebook be the default notebook for the next Sage
7.0 release? I don't really have an opinion on the matter.

Pros:

* Nice tracebacks!
* The Jupyter notebook is a mature well-maintained project, unlike
SageNB. It is widely used in the "scientific Python" community.
* Availability of other Jupyter kernels besides Sage.

Cons:

* Less compatible with Sage: Sage interacts don't work, some graphics
don't work.
* Certain features of SageNB are missing: live documentation,
sharing/publishing of worksheets.
* It clutters the file system with .ipynb files.

Don't cares:

* It's just a default choice, both options remain available.

### Emmanuel Charpentier

unread,
Dec 18, 2015, 9:47:24 AM12/18/15
to sage-devel
A few addenda :

Pros :
* The python debugger works in the IPython notebook. Damn useful !
* Some extensions developed for Python worksheets run in Sage worksheets.

Cons :
* (Currently) no standard way to create a cell in another language, as allowed by the Sage notebook's magics such as %maxima : in the current implementation, they create separate instances of interpreters, which do not return to the worksheet, even when explicitely terminated. Exceptions :
- Python (creates a separate subprocess)
- R, if rpy2 is young enough (but the interpreter used in %%R cells is different of the one used by r.... functions. This MUST be fixed).
* The lack of interacts is a sore point. But I hear there is work on this front...

I don't see what you mean when you say that live documentation is missing. You can access the online help by typing a function name and a question mark, and a pager will open on the right page. And the "help" menu contains a load of links to the manuals and tutorials (this should be extended, by the way...)

And I find that the "cluttering" of the filesystem (i.e. one worksheet, one file) is much saner that the Sage notebook "solution" (one worksheet, a $#!+load of anonymous files hidden in an invisble directory). Hoping that my two cents may help, -- Emmanuel Charpentier ### William Stein unread, Dec 18, 2015, 9:53:35 AM12/18/15 to sage-devel On Fri, Dec 18, 2015 at 6:47 AM, Emmanuel Charpentier <emanuel.c...@gmail.com> wrote: > A few addenda : > > Pros : > * The python debugger works in the IPython notebook. Damn useful ! > * Some extensions developed for Python worksheets run in Sage worksheets. > > Cons : > * (Currently) no standard way to create a cell in another language, as > allowed by the Sage notebook's magics such as %maxima : in the current > implementation, they create separate instances of interpreters, which do not > return to the worksheet, even when explicitely terminated. Exceptions : Wow, that's annoying; I didn't realize they had that limit. > - Python (creates a separate subprocess) > - R, if rpy2 is young enough (but the interpreter used in %%R cells is > different of the one used by r.... functions. This MUST be fixed). > * The lack of interacts is a sore point. But I hear there is work on this > front... > > I don't see what you mean when you say that live documentation is missing. > You can access the online help by typing a function name and a question > mark, and a pager will open on the right page. And the "help" menu contains > a load of links to the manuals and tutorials (this should be extended, by > the way...) > The Sage notebook lets you browse the entire 10K-page reference manual, tutorial, etc., of Sage as live, auto-converted worksheets. This is very useful for people learning Sage. You don't have to copy paste from the docs -- you directly play with them. This was a very cool feature Dorian Raymer added to the Sage notebook in maybe 2007 or 2008. There was some work on trying to create something similar at the Berkeley sage days. > And I find that the "cluttering" of the filesystem (i.e. one worksheet, one > file) is much saner that the Sage notebook "solution" (one worksheet, a >$#!+load of anonymous files hidden in an invisble directory).

Agreed... (in defense, the current design was something we came up
with in 2006, when we were planning to have *everything* stored in a
database, which was the sort of standard way to make websites back
then...)

>
> Hoping that my two cents may help,
>
> --
> Emmanuel Charpentier
>
>
>
> Le vendredi 18 décembre 2015 11:35:53 UTC+1, Jeroen Demeyer a écrit :
>>
>> Should the Jupyter notebook be the default notebook for the next Sage
>> 7.0 release? I don't really have an opinion on the matter.
>>
>>
>> Pros:
>>
>> * Nice tracebacks!
>> * The Jupyter notebook is a mature well-maintained project, unlike
>> SageNB. It is widely used in the "scientific Python" community.
>> * Availability of other Jupyter kernels besides Sage.
>>
>>
>> Cons:
>>
>> * Less compatible with Sage: Sage interacts don't work, some graphics
>> don't work.
>> * Certain features of SageNB are missing: live documentation,
>> sharing/publishing of worksheets.
>> * It clutters the file system with .ipynb files.
>>
>>
>> Don't cares:
>>
>> * It's just a default choice, both options remain available.
>
> --
> You received this message because you are subscribed to the Google Groups
> "sage-devel" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to sage-devel+...@googlegroups.com.
> To post to this group, send email to sage-...@googlegroups.com.
> Visit this group at https://groups.google.com/group/sage-devel.
> For more options, visit https://groups.google.com/d/optout.

--
William (http://wstein.org)

### Volker Braun

unread,
Dec 18, 2015, 10:27:29 AM12/18/15
to sage-devel
IMHO the Jupyter/IPython notebook is a clear winner, no real contest.

Nobody prevents you form using SageNB for existing worksheets or the live documentation; But if you start a new worksheet today then you really should be using Jupyter.

On Friday, December 18, 2015 at 11:35:53 AM UTC+1, Jeroen Demeyer wrote:
* Certain features of SageNB are missing: live documentation,
sharing/publishing of worksheets.

IMHO sharing is already better, you can just upload the ipynb file anywhere (including http://gist.github.com or any other pastebin) and then share it using the http://nbviewer.ipython.org service. For example:

* It clutters the file system with .ipynb files.

and .ipynb_checkpoints hidden directories. See also: http://trac.sagemath.org/19746

### Dima Pasechnik

unread,
Dec 20, 2015, 1:52:46 PM12/20/15
to sage-devel

On Friday, 18 December 2015 15:27:29 UTC, Volker Braun wrote:
IMHO the Jupyter/IPython notebook is a clear winner, no real contest.

Nobody prevents you form using SageNB for existing worksheets or the live documentation; But if you start a new worksheet today then you really should be using Jupyter.

On Friday, December 18, 2015 at 11:35:53 AM UTC+1, Jeroen Demeyer wrote:
* Certain features of SageNB are missing: live documentation,
sharing/publishing of worksheets.

IMHO sharing is already better, you can just upload the ipynb file anywhere (including http://gist.github.com or any other pastebin) and then share it using the http://nbviewer.ipython.org service. For example:

Some care will need to be taken, so that we don't have to deal with complaints of kind

" I run 'sage -n', and all my worksheets are gone!!! Help!!! "

### William Stein

unread,
Dec 20, 2015, 2:07:23 PM12/20/15
to sage-devel
On Sun, Dec 20, 2015 at 10:52 AM, Dima Pasechnik <dim...@gmail.com> wrote:
>
>
> On Friday, 18 December 2015 15:27:29 UTC, Volker Braun wrote:
>>
>> IMHO the Jupyter/IPython notebook is a clear winner, no real contest.
>>
>> Nobody prevents you form using SageNB for existing worksheets or the live
>> documentation; But if you start a new worksheet today then you really should
>> be using Jupyter.
>>
>>
>> On Friday, December 18, 2015 at 11:35:53 AM UTC+1, Jeroen Demeyer wrote:
>>>
>>> * Certain features of SageNB are missing: live documentation,
>>> sharing/publishing of worksheets.
>>
>>
>> IMHO sharing is already better, you can just upload the ipynb file
>> anywhere (including http://gist.github.com or any other pastebin) and then
>> share it using the http://nbviewer.ipython.org service. For example:
>>
>> http://nbviewer.ipython.org/url/sagepad.org/pub/sage-test.ipynb
>
>
> Some care will need to be taken, so that we don't have to deal with
> complaints of kind
>
> " I run 'sage -n', and all my worksheets are gone!!! Help!!! "

With every single upgrade of sagenb in the past, there was always an
automatic and safe migration step that would take care of this
problem, even if the notebook format changed completely (which
happened). I always wrote that code to do the migration, even though
it was a lot of work. Somebody should write something like that for
sagenb to jupyter.

-- William

>
>
>>
>>
>>
>>> * It clutters the file system with .ipynb files.
>>
>>
>> and .ipynb_checkpoints hidden directories. See also:
>> http://trac.sagemath.org/19746
>>
>>

### Volker Braun

unread,
Dec 20, 2015, 3:47:08 PM12/20/15
to sage-devel
The ticket already has a notice printed that tells you how to run the old SageNB

Realistically, since we are switching to a model where notebooks are individual files there is always going to be somebody who won't read the hints. We'll have to do *that* switch anyways and it isn't going to be any easier if we wait.

### William Stein

unread,
Dec 20, 2015, 4:27:39 PM12/20/15
to sage-devel
On Sun, Dec 20, 2015 at 12:47 PM, Volker Braun <vbrau...@gmail.com> wrote:
> The ticket already has a notice printed that tells you how to run the old
> SageNB
>
> Realistically, since we are switching to a model where notebooks are
> individual files there is always going to be somebody who won't read the
> hints. We'll have to do *that* switch anyways and it isn't going to be any
> easier if we wait.

Notebooks in sagenb are basically individual files; it's just that
they are stored as a directory tree in the filesystem. The .sws file
that you get when you click "File --> Download" in sagenb is a file.
It represents almost exactly the same information as an ipynb file.
It is feasible to run a script that you automatically convert the
~/.sage/sagenb* (or whatever) directory into a collection of Jupyter
notebooks, say ~/.sage/jupyter. This would make life much easier for
users who have collections of notebooks. The hard part is
functionality that doesn't map from sagenb to jupyter, e.g.,
interacts, % modes, etc., etc.,

I wrote an sws parser, which is here in case anybody takes up
automating the above conversion (I won't):

https://github.com/sagemathinc/smc/blob/master/src/smc_pyutil/smc_pyutil/sws2sagews.py

The

>
>
> On Sunday, December 20, 2015 at 7:52:46 PM UTC+1, Dima Pasechnik wrote:
>>
>>
>>
>> On Friday, 18 December 2015 15:27:29 UTC, Volker Braun wrote:
>>>
>>> IMHO the Jupyter/IPython notebook is a clear winner, no real contest.
>>>
>>> Nobody prevents you form using SageNB for existing worksheets or the live
>>> documentation; But if you start a new worksheet today then you really should
>>> be using Jupyter.
>>>
>>>
>>> On Friday, December 18, 2015 at 11:35:53 AM UTC+1, Jeroen Demeyer wrote:
>>>>
>>>> * Certain features of SageNB are missing: live documentation,
>>>> sharing/publishing of worksheets.
>>>
>>>
>>> IMHO sharing is already better, you can just upload the ipynb file
>>> anywhere (including http://gist.github.com or any other pastebin) and then
>>> share it using the http://nbviewer.ipython.org service. For example:
>>>
>>> http://nbviewer.ipython.org/url/sagepad.org/pub/sage-test.ipynb
>>
>>
>> Some care will need to be taken, so that we don't have to deal with
>> complaints of kind
>>
>> " I run 'sage -n', and all my worksheets are gone!!! Help!!! "
>>
>>
>>>
>>>
>>>
>>>> * It clutters the file system with .ipynb files.
>>>
>>>
>>> and .ipynb_checkpoints hidden directories. See also:
>>> http://trac.sagemath.org/19746
>>>
>>>

### Volker Braun

unread,
Dec 20, 2015, 7:06:36 PM12/20/15
to sage-devel
On Sunday, December 20, 2015 at 10:27:39 PM UTC+1, William wrote:
Notebooks in sagenb are basically individual files; it's just that
they are stored as a directory tree in the filesystem.

Yes, what I meant was: SageNB doesn't show a filesystem view so nobody is going to know *where* they are stored in the file system.

Whereas Jupyter notebooks are always displayed as files. And the average user isn't going to find ~/.sage/jupyter with the jupyter file browser. In fact, if that is not a subdirectory of the directory where Jupyter is launched then you cannot open it. And you don't want a ton of converted notebooks dumped in the current directory either. Realistically, any notebook converter will have to be manually invoked. And thats not going to get easier by delaying when we change the defaults.

https://github.com/sagemathinc/smc/blob/master/src/smc_pyutil/smc_pyutil/sws2sagews.py

And its easy to programmatically generate new IPython notebooks:  http://nbviewer.ipython.org/gist/fperez/9716279

### William Stein

unread,
Dec 20, 2015, 7:12:57 PM12/20/15
to sage-devel
On Sun, Dec 20, 2015 at 4:06 PM, Volker Braun <vbrau...@gmail.com> wrote:
> On Sunday, December 20, 2015 at 10:27:39 PM UTC+1, William wrote:
>>
>> Notebooks in sagenb are basically individual files; it's just that
>> they are stored as a directory tree in the filesystem.
>
>
> Yes, what I meant was: SageNB doesn't show a filesystem view so nobody is
> going to know *where* they are stored in the file system.
>
> Whereas Jupyter notebooks are always displayed as files. And the average
> user isn't going to find ~/.sage/jupyter with the jupyter file browser. In
> fact, if that is not a subdirectory of the directory where Jupyter is
> launched then you cannot open it. And you don't want a ton of converted
> notebooks dumped in the current directory either. Realistically, any
> notebook converter will have to be manually invoked.

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.

> And thats not going to
> get easier by delaying when we change the defaults.

It will be much easier for our users to actually *use* a converter if
we delay changing the defaults until after such a converter is
written.

### Volker Braun

unread,
Dec 20, 2015, 7:25:52 PM12/20/15
to sage-devel
If you start Jupyter in ~/foo then you cannot open notebooks in ~/.sage/jupyter. Thats just how it is.

### Nils Bruin

unread,
Dec 20, 2015, 11:16:44 PM12/20/15
to sage-devel
On Sunday, December 20, 2015 at 2:12:57 PM UTC-10, William wrote:
It will be much easier for our users to actually *use* a converter if
we delay changing the defaults until after such a converter is
written.

++1 (OK, I guess that's an error in most language).

It's going to be a relatively unpleasant surprise for people if they start up the "sage notebook" and find a different notebook. We could possibly alleviate the problem of lack of information by somehow guessing if this is the first time this user starts up sage ipython notebook (and perhaps only if we detect there is evince of a sagenb) and startup with a document that explains how to do migration.

If the default changes, then most users will assume they are supposed to change with it (and we should only do this once we think users should change, e.g., when interacts work)

At the very least there should be a method to:
- start the classic notebook
- save a collection of worksheets (sagenb)
- convert them to ipynb, at least in a way that works for "simple" worksheets. Attached files etc. are obviously going to be an issue.

If we don't have a tool that makes it straightforward to do this migration then we're not ready to change defaults, in my opinion.

### Volker Braun

unread,
Dec 21, 2015, 3:40:23 AM12/21/15
to sage-devel
On Monday, December 21, 2015 at 5:16:44 AM UTC+1, Nils Bruin wrote:
different notebook. We could possibly alleviate the problem of lack of information by somehow guessing if this is the first time this user starts up sage ipython notebook

Thats inconsistent UX, now you open different notebooks on different computers / accounts. Unless you mean: print help to the terminal. The ticket does that already.

If the default changes, then most users will assume they are supposed to change with it (and we should only do this once we think users should change, e.g., when interacts work)

Interacts DO work. Its just Jupyter interacts and not SageNB interacts. There are many more published Jupyter interacts, and lots more documentation about them.

Not changing the default also sends a message to our users, namely that its a good idea to use SageNB for new projects and that it is the UI that we are actively maintaining.

At the very least there should be a method to:
- start the classic notebook

This whole thread is ONLY about changing the default, nobody was talking about removing SageNB

### Jeroen Demeyer

unread,
Dec 21, 2015, 3:52:15 AM12/21/15
to sage-...@googlegroups.com
On 2015-12-21 09:40, Volker Braun wrote:
> Interacts DO work. Its just Jupyter interacts and not SageNB interacts.
I think that the SageNB @interact API is much better designed and more
consistent than the Jupyter @interact API. Unfortunately, I am not able
to convince upstream Jupyter (really: ipywidgets) that this is the case.
See https://github.com/ipython/ipywidgets/issues/238

It's true that ipywidgets might be able to do more fancy stuff (like
support for game controllers), but the basic stuff works better in SageNB.

Jeroen.

### John H Palmieri

unread,
Dec 21, 2015, 12:20:37 PM12/21/15
to sage-devel

I think we need a migration tool and a deprecation warning: "The old Sage notebook is deprecated in favor of Jupyter notebooks. For information about converting old-style notebooks to Jupyter notebooks, see ... To use Jupyter notebooks now, run 'sage -notebook=jupyter'." Then the next version of Sage can change the default behavior.

--
John

### Nils Bruin

unread,
Dec 22, 2015, 3:16:55 PM12/22/15
to sage-devel
On Sunday, December 20, 2015 at 10:40:23 PM UTC-10, Volker Braun wrote:
On Monday, December 21, 2015 at 5:16:44 AM UTC+1, Nils Bruin wrote:
different notebook. We could possibly alleviate the problem of lack of information by somehow guessing if this is the first time this user starts up sage ipython notebook

Thats inconsistent UX, now you open different notebooks on different computers / accounts. Unless you mean: print help to the terminal. The ticket does that already.

The reason why I expect that  printing on the terminal is insufficient, is because most notebook users will not look there at all: they're just looking at the browser that pops up. There are quite some precedents for informational pop-ups: firefox and chrome are usually quite insistent on start-up to ask you about migrating information to themselves and/or selecting them as default browser.

We could make the UX more consistent by "preinstalling" a migration ipy notebook. In fact, that notebook could include code to open and read the sagenb worksheets (jupyter kernels don't run chrooted by default, right? so their code can still access HOME/.sagenb) and help with translating the worksheets.

The main scenario is that of single-user notebooks. multi-user setups don't translate easily to jupyter anyway, so a more manual translation approach will be required anyway.

### Volker Braun

unread,
Dec 22, 2015, 4:08:37 PM12/22/15
to sage-devel
On Tuesday, December 22, 2015 at 9:16:55 PM UTC+1, Nils Bruin wrote:
We could make the UX more consistent by "preinstalling" a migration ipy notebook.

Into which directory are we going to put that MigrateFromSagenb.ipynb file?

In fact, that notebook could include code to open and read the sagenb worksheets (jupyter kernels don't run chrooted by default, right? so their code can still access HOME/.sagenb)

The kernel and the file browser ui are two separate components, potentially running on separate computers. The kernel can execute arbitrary code (and access ~/.sage if the OS allows), the file browser is restricted to the directory tree below the startup directory.

### kcrisman

unread,
Dec 30, 2015, 8:43:56 PM12/30/15
to sage-devel, Ivan Andrus
Regardless of how "useful" or awesome the Jupyter notebook is and how many people in scientific computing are using it, there is a substantial ecosystem now designed around the Sage notebook proper - including perhaps even the not-yet-one-year-old "Sage for Undergraduates" book? - and a lot of people "know" how to use it to do various things. Some of the below were mentioned above.
* Access to documentation
* Access to live documentation
* things like %auto, %hide - presumably some of these are in Jupyter
* difference in @interact API
* It can't handle attached files properly, really? I was surprised to read that
* Different way to create math markup/'text' cells
I'll also point out that William apparently felt it was useful to create a .sagews format rather than just have ipynb be the default in SMC, which presumably has different features?  Or was that only because Jupyter was not as good when he started SMC?

Another issue would be how to deal with the Mac app, what its default should be, etc.  Similarly for the virtual Windows solution - will people even be able to find their stuff?

> 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.

I'll press it further: not doing this is basically flipping the bird to a lot of long-time users.  I don't mean this sarcastically.

> >  And thats not going to get easier by delaying when we change the defaults.

> It will be much easier for our users to actually *use* a converter if we delay changing the defaults until after such a converter is written.

Uh, duh.

All these comments are predicated upon a "strong" change of default.  In a normal user interface (to me, as a user) there would be a really easy way to decide *not* to change the default when first downloading/upgrading.  I think someone mentioned this before as well.

### Volker Braun

unread,
Dec 31, 2015, 4:36:04 AM12/31/15
to sage-devel, darth...@gmail.com
On Thursday, December 31, 2015 at 2:43:56 AM UTC+1, kcrisman wrote:
Regardless of how "useful" or awesome the Jupyter notebook is and how many people in scientific computing are using it, there is a substantial ecosystem now designed around the Sage notebook proper

And we are not removing it for all the legacy reasons that you listed. This thread is about what format new notebooks are supposed to be. Anybody who prefers SageNB can still use SageNB

But the fact is: Its unmaintained/-able, and the longer we wait the more painful it'll be to switch. How is waiting another year going to help? Because by then there will be another book explaining how to use SageNB? Do you think the book author is going to be happy that we never made it clear that SageNB is on the way out? SageNB is an evolutionary dead end, and the only question is how deep into that hole do we want to go.

### kcrisman

unread,
Jan 1, 2016, 10:01:18 AM1/1/16
to sage-devel

And we are not removing it for all the legacy reasons that you listed. This thread is about what format new notebooks are supposed to be. Anybody who prefers SageNB can still use SageNB

But how easy will that be?  It already sounds like sagenb notebooks are not really portable to Jupyter.

But the fact is: Its unmaintained/-able, and the longer we wait the more painful it'll be to switch. How is waiting another year going to help? Because by then there will be another book explaining how to use SageNB? Do you think the book author is going to be happy that we never made it clear that SageNB is on the way out? SageNB is an evolutionary dead end, and the only question is how deep into that hole do we want to go.

As William said, the answer is to either find a way to make them port, or to find a way to gracefully detect that someone has existing sagenb worksheets (perhaps slightly more gracefully than just checking DOT_SAGENB since that doesn't mean they actually did anything) and either ask to upgrade to Jupyter worksheets, if that's possible, or make it very easy to change a default setting.

Could there be an environment variable DEFAULT_SAGE_NOTEBOOK that one could have incredibly explicit instructions for how to use?  (Would making an alias work in this context?  Not in the sage: notebook() situation, I guess.)

But it has to be idiot-proof.  Imagine the following conversation at the Sage table:

Customer (yes they are customers!): Will I ever have any problems with upgrading?
Sage rep: Yep, we will make it so all your old stuff is never upgradeable with essentially no warning other than some cryptic command line thing you don't even see because you only look at your browser!
Customer: I didn't hear you right, I think? You mean, "we'll support legacy stuff so long it will make Microsoft look good."  I mean, I don't want to still be using .doc in 2020.
Sage rep: Nope, we're sort of the opposite; we won't have any 'compatibility mode' nor any incentive to upgrade your old documents; you either go to the new one - oh, by the way, it doesn't do everything the old one does yet - or you just stick with the old kind forever.

Yup, I see that as a real winner.  And of course this conversation can happen again whenever the next new hit comes out in five years, which it no doubt will.

Writing up a very accessible (perhaps even linked to in the warning) translation guide to getting started in Jupyter would be good too.  As much as there might be a bigger ecosystem for them, that is not a very compelling argument to me; otherwise we should all be using RStudio and shiny, and well basically just using R for everything.  How many of those zillions of easy-to-search sample worksheets are about something like calculating elliptic curve invariants or a nice demo for a graph theory course?  Probably just a tiny proportion of the ones about data science or scientific computing.

On a separate note, I'm wondering how changing the default will impact those running servers.    Which is a higher knowledge crowd but also one who might not be reading sage-devel (in fact likely isn't).  Basically, I'm asking about any worst-case scenarios when someone upgrades from (say) 6.7 to 7.2 at the end of a school year and either doesn't read the 'release notes', doesn't even know there are release notes, or our release notes are so minimal as to be useless, or something.  (I assume that commercial software has that problem of non-reading too.)

### David Roe

unread,
Jan 1, 2016, 4:47:00 PM1/1/16
to sage-devel
On Fri, Jan 1, 2016 at 7:01 AM, kcrisman wrote:

And we are not removing it for all the legacy reasons that you listed. This thread is about what format new notebooks are supposed to be. Anybody who prefers SageNB can still use SageNB

But how easy will that be?  It already sounds like sagenb notebooks are not really portable to Jupyter.

But the fact is: Its unmaintained/-able, and the longer we wait the more painful it'll be to switch. How is waiting another year going to help? Because by then there will be another book explaining how to use SageNB? Do you think the book author is going to be happy that we never made it clear that SageNB is on the way out? SageNB is an evolutionary dead end, and the only question is how deep into that hole do we want to go.

As William said, the answer is to either find a way to make them port, or to find a way to gracefully detect that someone has existing sagenb worksheets (perhaps slightly more gracefully than just checking DOT_SAGENB since that doesn't mean they actually did anything) and either ask to upgrade to Jupyter worksheets, if that's possible, or make it very easy to change a default setting.

If we change the default to Jupyter, detecting existing Sage notebooks and presenting a choice to the user to upgrade their existing notebooks is a great idea.
David

Could there be an environment variable DEFAULT_SAGE_NOTEBOOK that one could have incredibly explicit instructions for how to use?  (Would making an alias work in this context?  Not in the sage: notebook() situation, I guess.)

But it has to be idiot-proof.  Imagine the following conversation at the Sage table:

Customer (yes they are customers!): Will I ever have any problems with upgrading?
Sage rep: Yep, we will make it so all your old stuff is never upgradeable with essentially no warning other than some cryptic command line thing you don't even see because you only look at your browser!
Customer: I didn't hear you right, I think? You mean, "we'll support legacy stuff so long it will make Microsoft look good."  I mean, I don't want to still be using .doc in 2020.
Sage rep: Nope, we're sort of the opposite; we won't have any 'compatibility mode' nor any incentive to upgrade your old documents; you either go to the new one - oh, by the way, it doesn't do everything the old one does yet - or you just stick with the old kind forever.

Yup, I see that as a real winner.  And of course this conversation can happen again whenever the next new hit comes out in five years, which it no doubt will.

Writing up a very accessible (perhaps even linked to in the warning) translation guide to getting started in Jupyter would be good too.  As much as there might be a bigger ecosystem for them, that is not a very compelling argument to me; otherwise we should all be using RStudio and shiny, and well basically just using R for everything.  How many of those zillions of easy-to-search sample worksheets are about something like calculating elliptic curve invariants or a nice demo for a graph theory course?  Probably just a tiny proportion of the ones about data science or scientific computing.

On a separate note, I'm wondering how changing the default will impact those running servers.    Which is a higher knowledge crowd but also one who might not be reading sage-devel (in fact likely isn't).  Basically, I'm asking about any worst-case scenarios when someone upgrades from (say) 6.7 to 7.2 at the end of a school year and either doesn't read the 'release notes', doesn't even know there are release notes, or our release notes are so minimal as to be useless, or something.  (I assume that commercial software has that problem of non-reading too.)

--

### Volker Braun

unread,
Jan 2, 2016, 8:08:15 AM1/2/16
to sage-devel
You still haven't understood that this is about how to create new notebooks. We have the legacy support covered by shipping the old notebook. Also, I don't recall Microsoft bundling a free copy of word 2007 with word 2010, you are comparing apples and oranges.

On Friday, January 1, 2016 at 4:01:18 PM UTC+1, kcrisman wrote:
How many of those zillions of easy-to-search sample worksheets are about something like calculating elliptic curve invariants or a nice demo for a graph theory course?

And maybe we have the market for EC invariants saturated, and the reason for not growing any more is that we don't fit into the larger scientific Python ecosystem?

### William Stein

unread,
Jan 2, 2016, 9:22:18 AM1/2/16
to sage-...@googlegroups.com
+1000!

--
You received this message because you are subscribed to the Google Groups "sage-devel" group.
To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+...@googlegroups.com.
To post to this group, send email to sage-...@googlegroups.com.
Visit this group at https://groups.google.com/group/sage-devel.
For more options, visit https://groups.google.com/d/optout.

--
Sent from my massive iPhone 6 plus.

### kcrisman

unread,
Jan 2, 2016, 1:41:15 PM1/2/16
to sage-devel

You still haven't understood that this is about how to create new notebooks. We have the legacy support covered by shipping the old notebook. Also, I don't recall Microsoft bundling a free copy of word 2007 with word 2010, you are comparing apples and oranges.

??

MS Word still supports pretty old .doc files - and cheerfully asks to upgrade them to .docx or whatever.  LibreOffice is even better - I can open ClarisWorks documents well over a decade old with it.  And I bet (though I haven't used Maple in many years) that when they switched to their Java-based "Clickable Calculus" thing (that was how it worked, right?) that they upgraded worksheets for use in the new system.  Ditto for Mma?

That's what I'm talking about.  "Legacy support" for us cannot be about treating people with a lot of sagenb worksheets like a company with COBOL programs that need continued support but will not have new stuff written from scratch in.  If Jupyter really is the future, and Sage really wants to be professional about a transition to it, it needs to provide an *easy* and *effective* upgrade path for worksheets created in sagenb (and, presumably, in sagews format, I don't know if they convert?) to that.  (See the rst2sws and sws2rst and tex2sws and sws2tex for some interesting conversions in addition to the several successive conversions William has written over the years.)

Think of all of the people we have not been able to gain to Sage over the years because we don't have a simple Maple -> Sage or Mma -> Sage converter.  (I'm not complaining about that! I don't think such people recognize the technical hurdle there.  But if there were such things, we would have a lot more users, I think it's fairly clear.)  Similarly, not having a sagenb -> ipynb (or whatever the future brings) converter that is reliable may cause people to just go back to whatever they were using beforehand, or to say the heck with it.

(By the way, as to location - one could let the user decide, with a default of ~/MyOldSageWorksheets or some such nonsense, if there was an interactive GUI or script or web thing on the sagenb or sage or jupyter side.  No need to have a specific default because not everyone will upgrade.)

Otherwise, I don't want to hear any complaints about people sticking with proprietary solutions that do cover such upgrades.  The reality is that most people stick with the devil they know.  This isn't about technical superiority; it's about treating our users as if they have exactly enough time to use Sage, and very little to do anything else regarding upgrades or whatever.   Because who will guarantee that in five years there won't be some brand-new toy instead of Jupyter?  We already see Julia and Nemo as the hot new thing (in a different direction than the notebooks, of course); what can we predict for the next five years in terms of anything?  (Perhaps OpenDreamKit will help in that regard.)

By the way, 'whatever' means not just 'upgrades to notebooks' but also 'hard documentation to search' and 'I still don't know if Sage works in El Capitan' and lots of other things I get personal message about fairly regularly that I don't necessarily pass on here.  This is just a symptom of the usual F/LOSS problem of being written largely for the developers - which is way, way less fair to say about Sage than many other projects, due largely to some of the very people I'm arguing with in this thread!  But we still have the same symptoms, even if it's a relatively mild infection.  (Sorry, I just got over a pretty bad case of the flu so I've been using that kind of analogy too much.)

### William Stein

unread,
Jan 2, 2016, 2:13:58 PM1/2/16
to sage-devel
Karl,

It's not "the usual F/LOSS problem", it's the usual problem of a
volunteer project with almost no funding. There is a ton of high
quality well funded FLOSS software out there that doesn't have this
problem (e.g., Firefox, Chromium, parts of OS X, the swift language,
...)

For better or worse, I think we just have to acknowledge the reality of the
situation, and move on and do a very bad job in the above
regards compared to the well funded alternatives until/if we do
eventually get funding. Right now, it is best of the Sage project
focuses squarely on its core competence, which is research level pure
mathematics, (and I hope also undergrad math teaching).

I think there is no question that if some group popped up and
implemented all the automated backwards compatibility, and other nice
things that you describe above, all very good quality, and with proper
review on trac, then Volker would smile and merge it in seconds.
Implementing this stuff we want is precisely what is nearly
impossibly hard for any sane research mathematician to justify
spending serious time on.

For now, let's just move on, make Jupyter (which just got $6,000,000 in funding recently) the default, and deal with the pain and continued failure to grow. Maybe someday things will be different. -- William -- William (http://wstein.org) ### Jonathan unread, Jan 2, 2016, 3:12:45 PM1/2/16 to sage-devel William, Volker, et al... I think you misunderstand Karl. He has stated what is ideal, but I think from his messages that he understands we do not have the manpower within the group of people who can commit time to Sage to make his ideal happen. What he is asking is that you avoid doing this transition in a manner that blindsides many people who are using Sage (especially for teaching using servers they maintain). If ipynb is going to be the default it needs to launch the first time with messages on the command line and in the browser that explain how to use the Old notebook if necessary and with some advice on conversion, if any exists. It would also be nice to have a brief list of key notebook features that do not yet work in ipynb. I suggest language like: WARNING!! If you have been using Sagemath using the Sagenotebook (default prior to ____) for interactive Sagemath sessions in a browser, you should be aware that Sagenotebook is no longer the default. The default is ipynb (web link..). You can launch the older Sagenotebook as described below. However, unless you need the following features which do not yet exist in ipynb we recommend you use the new ipynb, as it has better support: ___list of missing features___. To use the the old default ... Regards, Jonathan ### Volker Braun unread, Jan 2, 2016, 7:15:01 PM1/2/16 to sage-devel I'm adding a Jupyter notebook extension to the sagenb exporter (https://github.com/vbraun/ExportSageNB) to hook into the GUI. So my proposal would be that the initial window will be something like this: On Friday, December 18, 2015 at 11:35:53 AM UTC+1, Jeroen Demeyer wrote: Should the Jupyter notebook be the default notebook for the next Sage 7.0 release? I don't really have an opinion on the matter. Pros: * Nice tracebacks! * The Jupyter notebook is a mature well-maintained project, unlike SageNB. It is widely used in the "scientific Python" community. * Availability of other Jupyter kernels besides Sage. Cons: * Less compatible with Sage: Sage interacts don't work, some graphics don't work. * Certain features of SageNB are missing: live documentation, sharing/publishing of worksheets. * It clutters the file system with .ipynb files. ### Jonathan unread, Jan 2, 2016, 9:52:35 PM1/2/16 to sage-devel This looks like you are on the correct track. I would just urge you to indicate what features of Sagenb are not available yet. I think things are close to the point that the only significant thing will be interacts. If plotly is installed, I think good interactive 2D and 3D graphs will be available. Jonathan ### Emmanuel Charpentier unread, Jan 3, 2016, 8:41:51 AM1/3/16 to sage-devel Le dimanche 3 janvier 2016 03:52:35 UTC+1, Jonathan a écrit : This looks like you are on the correct track. I would just urge you to indicate what features of Sagenb are not available yet. A few things pop to my mind. I already signaled some f them (some might say I ranted about them), but I think that they are stumbling blocks. • "other language" cells : %maxima and %r (possibly other interpreters such as %octave) do not work as expected. Both %maxima and %r open new instances of their respective interpreters and enter an REPL that cannot be exited (even with an explicit "quit();" or "q('no')". In other words, they never return. • r("<some call to R graphics>") doesn't display anything in the Jupyter notebook, even when bracketed by r.png() and r.dev_off(). You have to save (r.dev_copy()) the graph and display it in the notebook explicitely. Annoying... Rpy2 (part of Sage) offers the rpy2.ipython extension, which offer %R loine magic an %%R celle magic that work well (including graphics) ... in an R instance different of the one used by sage "r.xxx" functions. The data interchange format is different of the one used by the current r interface. • The latex (mathjax) interface seems to have a few Jupyter-specific quirks. For example, I have been unable to use a "$\frac{a}{b}\$" tick marker in a Sage jupyter worksheet. I suspect that the Jupyter notebook doesn't use the (user-configurable) Latex configuration of Sage n the same way as the Sage notebook does.
• I noted that plot3d seems to call a Web-based  utility for some plots (one sees messages related to loading data flashing in the region where the jsmol (?) result will be displayed). This might implu that these finctions might be unusable on an unconnected system (I didn't check that yet...).
• In the current implementation, one cannot use some of the features the default 3D renderer (jsmol ?). For example, when one attempts animation, a right-click displays the relevant options, but one cannot activate them.

I think things are close to the point that the only significant thing will be interacts.  If plotly is installed, I think good interactive 2D and 3D graphs will be available.

• 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).

Yet another interact interface ? That might be interesting if and only if the "new" interface has significantl enhancements over the "old" one...

HTH,

--
Emmanuel Charpentier

### Jeroen Demeyer

unread,
Jan 3, 2016, 9:45:19 AM1/3/16
to sage-...@googlegroups.com
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.

### Emmanuel Charpentier

unread,
Jan 3, 2016, 9:50:10 AM1/3/16
to sage-devel
Omitted from the previous ran^Kpost (and thus is probably still quite incomplete...) :

• (Very ?) serious : no %cython cells, and no "obvious" shortcut to get them. The "semi-obvious" replacement (%%writefile + load()) is not *that* obvious to realize "cleanly" (no left-over files, etc...). a cell magic would be (more than) nice
• Annoying more than serious : no obvious way to get rid of the "sage:" and "...  " prompts when cutting-and-pasting from examples. Not a problem for Sage function, but this pasted medley of code and prompts won't load() cleanly from a file ('indentation error').

HTH,

--
Emmanuel Charpentier

### Volker Braun

unread,
Jan 3, 2016, 10:33:36 AM1/3/16
to sage-devel
On Sunday, January 3, 2016 at 2:41:51 PM UTC+1, Emmanuel Charpentier wrote:
• "other language" cells : %maxima and %r (possibly other interpreters such as %octave) do not work as expected. Both %maxima and %r open new instances of their respective interpreters and enter an REPL that cannot be exited (even with an explicit "quit();" or "q('no')". In other words, they never return
Interactive line magics obviously can't work in the browser like on the command line

The lack of appropriate cell magics (%%maxima)  is just an existing bug on the commandline.

Of course if you care about it then send in a patch.

On the plus side, the jupyter notebook comes with an official R kernel available as Sage optional package: sage -r r_jupyter.

### Emmanuel Charpentier

unread,
Jan 3, 2016, 11:36:30 AM1/3/16
to sage-devel
Dear Volker,

Le dimanche 3 janvier 2016 16:33:36 UTC+1, Volker Braun a écrit :
On Sunday, January 3, 2016 at 2:41:51 PM UTC+1, Emmanuel Charpentier wrote:
• "other language" cells : %maxima and %r (possibly other interpreters such as %octave) do not work as expected. Both %maxima and %r open new instances of their respective interpreters and enter an REPL that cannot be exited (even with an explicit "quit();" or "q('no')". In other words, they never return
Interactive line magics obviously can't work in the browser like on the command line

The lack of appropriate cell magics (%%maxima)  is just an existing bug on the commandline.

Indeed. We should have %%maxima, %%r , %%pari, etc...

[ BTW : that's not really a bug, but rather a design conflict : the original %mode functions were designed to switch (for an indefinite scope) the behaviour of the REPL.This was transposed in the Sage notebook as what amounts to the equivalent of Jupyter's cell magics (scope defined as the current cell). Whereas line magics are, as far as I understand, Jupyter-specific... We can't be consistent across notebooks without redefining our "mode switch" magics as "cell magics", and rename them with "%%"...  ]

Of course if you care about it then send in a patch.

I do and I plan to. Therefore, I'm trying to understand how to add such magics to Jupyter. I'm currently swimming (drowning...) on my source tree in order to understand how this should be done. The difficulty is not the code itself, but how to package it as a magic.

Same question about %cython (which should become %%cython ?), with another difficulty : how to define the function in the global namespace as in the command line or Sage notebook... The relevant compile_and_load() function returns a module (from which one can of course import *, which would mimic the current Sage notebook behavior) ; the point is to do this automatically from the magic function).

On the plus side, the jupyter notebook comes with an official R kernel available as Sage optional package: sage -r r_jupyter.

Indeed ! And that's appreciable (and apprecied). The same could be done for various  Sage-inclu(ded-dable) languages (pari, octave) for which a Jupyter kernel exists (see this list). Maxima is a special case : the existing Maxima-Jupyter kernel wont't adapt to our ECL-compiled implementation (I asked)...

BTW, your r_jupyter package doesn't appear in the output of sage -installed, nor in the output of sage -optional...

--
Emmanuel Charpentier

### William Stein

unread,
Jan 3, 2016, 12:19:53 PM1/3/16
to sage-devel
On Sun, Jan 3, 2016 at 8:36 AM, Emmanuel Charpentier
<emanuel.c...@gmail.com> wrote:
> Dear Volker,
>
> Le dimanche 3 janvier 2016 16:33:36 UTC+1, Volker Braun a écrit :
>>
>> On Sunday, January 3, 2016 at 2:41:51 PM UTC+1, Emmanuel Charpentier
>> wrote:
>>>
>>> "other language" cells : %maxima and %r (possibly other interpreters such
>>> as %octave) do not work as expected. Both %maxima and %r open new instances
>>> of their respective interpreters and enter an REPL that cannot be exited
>>> (even with an explicit "quit();" or "q('no')". In other words, they never
>>> return
>>
>> Interactive line magics obviously can't work in the browser like on the
>> command line
>>
>>
>> The lack of appropriate cell magics (%%maxima) is just an existing bug on
>> the commandline.
>
>
> Indeed. We should have %%maxima, %%r , %%pari, etc...
>
> [ BTW : that's not really a bug, but rather a design conflict : the original
> %mode functions were designed to switch (for an indefinite scope) the
> behaviour of the REPL.This was transposed in the Sage notebook as what
> amounts to the equivalent of Jupyter's cell magics (scope defined as the
> current cell). Whereas line magics are, as far as I understand,
> Jupyter-specific... We can't be consistent across notebooks without
> redefining our "mode switch" magics as "cell magics", and rename them with
> "%%"... ]

In case you are curious, in SageMathCloud worksheets a line mode is

%foo <stuff on the line>

and a cell mode is

%foo(optional, arguments)
<rest of the cell>

In SMC %foo is just foo('... rest of line or cell...'), with some
optional hooks (e.g., support foo.eval for backwards compat with
sage). So a "magic" is much less magic -- just define any function
that takes a string as input, and you've written one.

I don't use %% anywhere.

I don't care what you do with Jupyter, but I'm sticking with this
design for cell modes, and definitely won't change.

-- William

### Volker Braun

unread,
Jan 3, 2016, 1:00:40 PM1/3/16
to sage-devel
On Sunday, January 3, 2016 at 6:19:53 PM UTC+1, William wrote:
In case you are curious, in SageMathCloud worksheets a line mode is

%foo <stuff on the line>

and a cell mode is

%foo(optional, arguments)
<rest of the cell>

Thats almost the same except for the second percent sign in the cell magic

%%foo
<rest of the foo cell>

FWIW the line magic in the command line (and by extension jupyter) is such that

%foo
1+1

runs %foo (whatever that does) and then "1+1" as the subsequent Sage command. E.g.

sage: %cpaste
Pasting code; enter '--' alone on the line to stop or use Ctrl-D.
:%ls
:1+1
:--
aclocal.m4       bootstrap*  config/      config.status*  configure.ac  dist/  local/  m4/       README.txt  src/  upstream/
autom4te.cache/  build/      config.log@  configure*      COPYING.txt   home/  logs/   Makefile  sage*       tmp/  VERSION.txt
2

### Jeroen Demeyer

unread,
Jan 3, 2016, 1:48:01 PM1/3/16
to sage-...@googlegroups.com
On 2016-01-03 17:36, Emmanuel Charpentier wrote:
> how to define the function in the global namespace
> as in the command line or Sage notebook... The relevant
> compile_and_load() function returns a module (from which one can of
> course import *, which would mimic the current Sage notebook behavior) ;
> the point is to do this automatically from the magic function).

No, the point is to fix cython() such that this works *without* special
support in the magic function.

This is part of http://trac.sagemath.org/ticket/18083

### Volker Braun

unread,
Jan 3, 2016, 3:23:56 PM1/3/16
to sage-devel
On Sunday, January 3, 2016 at 5:36:30 PM UTC+1, Emmanuel Charpentier wrote:
[ BTW : that's not really a bug, but rather a design conflict : the original %mode functions were designed to switch (for an indefinite scope) the behaviour of the REPL.This was transposed in the Sage notebook as what amounts to the equivalent of Jupyter's cell magics (scope defined as the current cell). Whereas line magics are, as far as I understand, Jupyter-specific... We can't be consistent across notebooks without redefining our "mode switch" magics as "cell magics", and rename them with "%%"...  ]

IMHO we should just switch the interface line magics to work like other line magics in Jupyter/IPython, and also SMC: Take the rest of the line as string and evaluate

Example for IPython default magic:

sage: %system ls Makefile
['Makefile']

Example for how we currently handle line magics on the commandline (BAD: we just forget about the argument)

sage: %gap 1+1;

--> Switching to Gap <--

gap: ^C

--> Exiting back to Sage <--

Expected behavoir of %gap 1+1; is to be like

sage: gap('1+1;')
2

On the commandline ONLY line magics without arguments could still switch the interface

### Emmanuel Charpentier

unread,
Jan 3, 2016, 4:49:17 PM1/3/16
to sage-devel

Le dimanche 3 janvier 2016 21:23:56 UTC+1, Volker Braun a écrit :
On Sunday, January 3, 2016 at 5:36:30 PM UTC+1, Emmanuel Charpentier wrote:
[ BTW : that's not really a bug, but rather a design conflict : the original %mode functions were designed to switch (for an indefinite scope) the behaviour of the REPL.This was transposed in the Sage notebook as what amounts to the equivalent of Jupyter's cell magics (scope defined as the current cell). Whereas line magics are, as far as I understand, Jupyter-specific... We can't be consistent across notebooks without redefining our "mode switch" magics as "cell magics", and rename them with "%%"...  ]

IMHO we should just switch the interface line magics to work like other line magics in Jupyter/IPython, and also SMC: Take the rest of the line as string and evaluate

As stated, that would break the compatibility with SMC magics that William just declared intangible (and always "cell magic"). This could be (more or less) restored  if the magic function had access to the current interface. Pseudo-Python ahead :

args, input=(RestOfTheFirstLline(), RestOfTheCell())
if(SMC):
ReturnAndPrint(magicfun(input))
if(commandline): ## In that case, by definition, input==None
if(restofthefirstline=""):
switchREPLuntilEOFOrOtherMagic(magicfun())
else:
ReturnAndPrint(magicfun(args))
else: ## Jupyter
ProcessOptions(args)
ReturnAndPrint(magicfun(input, ProcessedOptions))

The difficulty is, of course, that the same part of the command structure (the rest of the first line) would mean two different things :
- source code to execute in a command line
- possible options to be  passed to a cell magic in Jupyter (some interface, already supported (rpy2, the IRkernel for R) already use this convention !).

Furthermore, I supposed that SMC ignored the rest of the first line. This is what the %r magic does
%r print(2+2)
print(3+2)

## prints [1] 5, even if the pasted result is a bit more complicated :
︡3c5a5418-14e0-46fe-a34d-3fa7a0eb1b7d︡︡{"stdout":"[1] 4","done":false}︡{"stdout":" 5\n","done":false}︡{"done":true}
︠68da460a-f070-4758-9fbb-667f85c4819es︠

but not the %maxima magic :

%maxima diff(log(x),x)
integrate(arctan(x),x)

## prints 1/x on one line, then x*arctan(x) - 1/2*log(x^2 + 1) on the next line, but again the reality is a bit more complicated :

︡410cbb81-a181-4e01-92a0-0c3e28da800a︡︡{"stdout":"1/x","done":false}︡{"stdout":"\n","done":false}︡{"stdout":"x*arctan(x) - 1/2*log(x^2 + 1)\n","done":false}︡{"done":true}
︠e820fb8a-cd58-4173-9d99-95dd022e4a6f︠

Therefore, we have a specification/consistency problem, to be solved BEFORE the coding problem(s).

We should also specify what happens with the computed results : are they just displayed in the output cell and kept in the target interpreterv instance ? (In that case, we should be damn sure that we vcan get the results back by other means, such as r() after an %r cell, or maxima() after a %maxima computation). Or should we try to return something ? If so, how ?

We should also specify how to pass data to the called interpreter, and back to Sage. At least in the case of r(), it is hard to get anything else than string representations. One point of using %R is that this dat interchange problem is at least treated consistently.

Note that the "coding problems" are not that small : ensuring that r(...), %r, %R and %%R "speak" to the same instance of R does not seem trivial (at least for my midget capacities)...

Example for IPython default magic:

sage: %system ls Makefile
['Makefile']

Example for how we currently handle line magics on the commandline (BAD: we just forget about the argument)

sage: %gap 1+1;

--> Switching to Gap <--

gap: ^C

--> Exiting back to Sage <--

Expected behavoir of %gap 1+1; is to be like

sage: gap('1+1;')
2

On the commandline ONLY line magics without arguments could still switch the interface

Should we open a ticket for this, or should we continue to discuss the specificatin here, opening tickets for the actual coding ?

HTH (but doubting it...),

--
Emmanuel Charpentier

### Volker Braun

unread,
Jan 3, 2016, 5:06:38 PM1/3/16
to sage-devel
We can't (and shouldn't) change how Jupyter extracts arguments. Its either line magic

%magic one line of argument

or cell magic

%%magic
argument
more argument

Note that the "coding problems" are not that small : ensuring that r(...), %r, %R and %%R "speak" to the same instance of R does not seem trivial

Thats the easy part, just call r(...) with the magic argument (as a string).

### William Stein

unread,
Jan 3, 2016, 7:38:02 PM1/3/16
to sage-devel
On Sun, Jan 3, 2016 at 1:49 PM, Emmanuel Charpentier
<emanuel.c...@gmail.com> wrote:
>
>
> Le dimanche 3 janvier 2016 21:23:56 UTC+1, Volker Braun a écrit :
>>
>> On Sunday, January 3, 2016 at 5:36:30 PM UTC+1, Emmanuel Charpentier
>> wrote:
>>>
>>> [ BTW : that's not really a bug, but rather a design conflict : the
>>> original %mode functions were designed to switch (for an indefinite scope)
>>> the behaviour of the REPL.This was transposed in the Sage notebook as what
>>> amounts to the equivalent of Jupyter's cell magics (scope defined as the
>>> current cell). Whereas line magics are, as far as I understand,
>>> Jupyter-specific... We can't be consistent across notebooks without
>>> redefining our "mode switch" magics as "cell magics", and rename them with
>>> "%%"... ]
>>
>>
>> IMHO we should just switch the interface line magics to work like other
>> line magics in Jupyter/IPython, and also SMC: Take the rest of the line as
>> string and evaluate
>
>
> As stated, that would break the compatibility with SMC magics that William
> just declared intangible (and always "cell magic").

Just to be clear: I don't care whether or not whatever design you
guys are coming up with in this thread is compatible with SMC Sage
worksheets. SMC provides both Sage worksheets and Jupyter notebooks
on an equal footing; each has its pros and cons, and will continue to
be fully supported (likely with a converter between them, that at
least converts what can be converted).
> --
> You received this message because you are subscribed to the Google Groups
> "sage-devel" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to sage-devel+...@googlegroups.com.
> To post to this group, send email to sage-...@googlegroups.com.
> Visit this group at https://groups.google.com/group/sage-devel.
> For more options, visit https://groups.google.com/d/optout.

--
William (http://wstein.org)

### kcrisman

unread,
Jan 4, 2016, 1:21:04 PM1/4/16
to sage-devel
Thank you Jonathan for clarifying what I thought was obvious in what I was saying.

> As stated, that would break the compatibility with SMC magics that William
> just declared intangible (and always "cell magic").

Just to be clear:  I  don't care whether or not whatever design you
guys are coming up with in this thread is compatible with SMC Sage
worksheets.  SMC provides both Sage worksheets and Jupyter notebooks
on an equal footing; each has its pros and cons, and will continue to
be fully supported (likely with a converter between them, that at
least converts what can be converted).

I would be interested in why SMC provides Sage worksheets if Jupyter is so *clearly* the most superior option.  [Rhetorical question]

And what of the long-term in Sage itself - would an eventual "SMC personal edition" become the default?  [Not rhetorical but probably too far in the future to speculate]

### William Stein

unread,
Jan 4, 2016, 1:24:39 PM1/4/16
to sage-devel
On Mon, Jan 4, 2016 at 10:21 AM, kcrisman wrote:
Thank you Jonathan for clarifying what I thought was obvious in what I was saying.

> As stated, that would break the compatibility with SMC magics that William
> just declared intangible (and always "cell magic").

Just to be clear:  I  don't care whether or not whatever design you
guys are coming up with in this thread is compatible with SMC Sage
worksheets.  SMC provides both Sage worksheets and Jupyter notebooks
on an equal footing; each has its pros and cons, and will continue to
be fully supported (likely with a converter between them, that at
least converts what can be converted).

I would be interested in why SMC provides Sage worksheets if Jupyter is so *clearly* the most superior option.  [Rhetorical question]

Weird question, given that I literally just wrote "Sage worksheets and Jupyter notebooks on an equal footing; each has its pros and cons, and will continue to be fully supported". There are many ways in which Sage worksheets are superior to Jupyter notebooks, and some very nontrivial subtle new things I've been working on the last month that will lead to more...

And what of the long-term in Sage itself - would an eventual "SMC personal edition" become the default?  [Not rhetorical but probably too far in the future to speculate]

No clue.  There's no legal or technical reason it couldn't happen... This year it likely won't as SMC is still changing way too much.

-- William

--
You received this message because you are subscribed to the Google Groups "sage-devel" group.
To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+...@googlegroups.com.
To post to this group, send email to sage-...@googlegroups.com.
Visit this group at https://groups.google.com/group/sage-devel.
For more options, visit https://groups.google.com/d/optout.

--

### kcrisman

unread,
Jan 5, 2016, 8:57:58 AM1/5/16
to sage-devel

> As stated, that would break the compatibility with SMC magics that William
> just declared intangible (and always "cell magic").

Just to be clear:  I  don't care whether or not whatever design you
guys are coming up with in this thread is compatible with SMC Sage
worksheets.  SMC provides both Sage worksheets and Jupyter notebooks
on an equal footing; each has its pros and cons, and will continue to
be fully supported (likely with a converter between them, that at
least converts what can be converted).

I would be interested in why SMC provides Sage worksheets if Jupyter is so *clearly* the most superior option.  [Rhetorical question]

Weird question, given that I literally just wrote "Sage worksheets and Jupyter notebooks on an equal footing; each has its pros and cons, and will continue to be fully supported". There are many ways in which Sage worksheets are superior to Jupyter notebooks, and some very nontrivial subtle new things I've been working on the last month that will lead to more...

The question wasn't for you, but for all those who early in this thread said how awesome Jupyter was.  But thank you for confirming.

And what of the long-term in Sage itself - would an eventual "SMC personal edition" become the default?  [Not rhetorical but probably too far in the future to speculate]

No clue.  There's no legal or technical reason it couldn't happen... This year it likely won't as SMC is still changing way too much.

So technical reason in the sense that even if someone did it, it would require a lot of maintenance to keep up with official SMC.

+++

On a less sarcastic note (and my apologies for that) I'm wondering what the status of Jupyterhub (the multi-user Jupyter, right?) is right now.  Active development, but so is HURD... not that I am expecting it to take 30 years to produce!  Just curious if there are any inside scoops.  Proper migration of entire servers being possible would be a much bigger reason to change the default.

### William Stein

unread,
Jan 5, 2016, 10:17:45 AM1/5/16
to sage-devel, Jason Grout
On Tue, Jan 5, 2016 at 5:57 AM, kcrisman <kcri...@gmail.com> wrote:
> The question wasn't for you, but for all those who early in this thread said
> how awesome Jupyter was. But thank you for confirming.

Some people tend to use/develop either Jupyter or SageMath notebooks
exclusively, and remain a little ignorant of the other one. There are
notable exceptions though, like Jason Grout who works a huge amount on
Jupyter development now (for pay!), but is also very knowledgable
about Sage. Personally, I'm looking at Jupyter-related stuff today,
since I'm rewriting (again) how synchronized editing works, and trying
to address various issue...

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.

Another basic -- and much harder to implement(!) -- subtle feature of
the sage notebook (and SMC) that Jupyter doesn't have is the
following. Try typing

import time
for i in range(10):
time.sleep(1)
print i

and closing your browser half way through. In Sagenb (and sagews)
it'll compute all the output and put it in the browser, where you'll
find it later when you visit the page. In Jupyter, all the output
that appears when you aren't observing the computation is lost. I
remember in maybe 2006 or 2007 implementing this and that it was very
important to researchers -- you can just start:

for n in range(100):
print n, important_function_of(n)

and come back tomorrow and see the result -- researchers *love* to be
able to do that without having to worry. With Jupyter, you have no
choice but to create a file, and output each result to that file, then
look in the file later; this is a bigger cognitive load.

Implementing the above (recording all output without the browser
client open) requires adding a slightly nontrivial idea to how
Jupyter is implemented, so I don't think it's likely to be really
easy.

Don't worry -- I've repeatedly mentioned the above differences to many
Jupyter developers, and I'm sure they will get addressed, since there
are a ton of people working on Jupyter.

Anyway, there are many subtle differences... Everything can be worked
around, of course.

>
>>>
>>> And what of the long-term in Sage itself - would an eventual "SMC
>>> personal edition" become the default? [Not rhetorical but probably too far
>>> in the future to speculate]
>>
>>
>> No clue. There's no legal or technical reason it couldn't happen... This
>> year it likely won't as SMC is still changing way too much.
>
>
> So technical reason in the sense that even if someone did it, it would
> require a lot of maintenance to keep up with official SMC.
>
> +++
>
> On a less sarcastic note (and my apologies for that) I'm wondering what the
> status of Jupyterhub (the multi-user Jupyter, right?) is right now. Active
> development, but so is HURD... not that I am expecting it to take 30 years
> to produce! Just curious if there are any inside scoops. Proper migration
> of entire servers being possible would be a much bigger reason to change the
> default.
>

### Volker Braun

unread,
Jan 5, 2016, 11:14:30 AM1/5/16
to sage-devel, grout...@gmail.com
I'd also be more than happy to ship the personal SMC edition with sage when its ready; But sticking with the essentially unsupported SageNB for 1+years just to wait&see is not a sane plan. Even then, jupyter notebooks are a forward-safe choice so we have nothing to gain from waiting while people write new SageNB notebooks.

As for the Jupyter wishlist, proper output capture would also be nice. Right now only the Python-internal stdout is captured, but for example

sage: cython(r'printf("test\n")')
test

yields no output in Jupyter.

There are at least two different multi-user Jupyter versions that are of interest; the authenticated (via unix account, much better than SageNB) jupyterhub and the anonymous https://tmpnb.org (try it now if you haven't seen it)

### William Stein

unread,
Jan 5, 2016, 11:26:24 AM1/5/16
to sage-devel, Jason Grout
On Tue, Jan 5, 2016 at 8:14 AM, Volker Braun <vbrau...@gmail.com> wrote:
> I'd also be more than happy to ship the personal SMC edition with sage when
> its ready; But sticking with the essentially unsupported SageNB for 1+years
> just to wait&see is not a sane plan. Even then, jupyter notebooks are a
> forward-safe choice so we have nothing to gain from waiting while people
> write new SageNB notebooks.

+1 and "personal SMC" is going to fully support using Jupyter no
matter what, which makes Jupyter notebooks even safer.

> As for the Jupyter wishlist, proper output capture would also be nice. Right
> now only the Python-internal stdout is captured, but for example
>
> sage: cython(r'printf("test\n")')
> test
>
> yields no output in Jupyter.
>
> There are at least two different multi-user Jupyter versions that are of
> interest; the authenticated (via unix account, much better than SageNB)
> jupyterhub and the anonymous https://tmpnb.org (try it now if you haven't
> seen it)

And SageMathCloud, which also provides multi-user Jupyter. At the
moment I write this, there are 59 jupyter notebooks running on SMC --
see "Running Instances" here:

https://cloud.sagemath.com/b97f6266-fe6f-4b40-bd88-9798994a04d1/raw/metrics/metrics.html

### Volker Braun

unread,
Jan 5, 2016, 11:35:09 AM1/5/16
to sage-devel
Indeed, there are at least three different multi-user Jupyter servers.

### kcrisman

unread,
Jan 5, 2016, 12:55:06 PM1/5/16
to sage-devel, grout...@gmail.com

I'd also be more than happy to ship the personal SMC edition with sage when its ready; But sticking with the essentially unsupported SageNB for 1+years just to wait&see is not a sane plan. Even then, jupyter notebooks are a forward-safe choice so we have nothing to gain from waiting while people write new SageNB notebooks.

As for the Jupyter wishlist, proper output capture would also be nice. Right now only the Python-internal stdout is captured, but for example

sage: cython(r'printf("test\n")')
test

yields no output in Jupyter.

There are at least two different multi-user Jupyter versions that are of interest; the authenticated (via unix account, much better than SageNB) jupyterhub and the anonymous https://tmpnb.org (try it now if you haven't seen it)

It's nice, though it didn't compute anything for me (likely I have a bad connection).

> Don't worry -- I've repeatedly mentioned the above differences to many Jupyter developers, and I'm sure they will get addressed, since there are a ton of people working on Jupyter.

Right.

### Jason Grout

unread,
Jan 5, 2016, 2:21:52 PM1/5/16
to sage-devel
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.

### Jason Grout

unread,
Jan 5, 2016, 2:21:52 PM1/5/16
to sage-devel, grout...@gmail.com, Jonathan Frederic

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

### Jason Grout

unread,
Jan 5, 2016, 2:21:52 PM1/5/16
to sage-devel
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

### Jonathan Frederic

unread,
Jan 5, 2016, 2:21:53 PM1/5/16
to sage-devel
Jason,

Thanks for pulling me in on this.

William,

I agree, getting a bunch of people to agree about stuff can be impossible.  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 for this too.  Also, in your experience, which of the Sage 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

### Jason Grout

unread,
Jan 5, 2016, 2:21:53 PM1/5/16
to William Stein, Jonathan Frederic, sage-...@googlegroups.com, IPython developers list
(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 <grout...@gmail.com>
Cc: sage-devel <sage-...@googlegroups.com>

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:

### William Stein

unread,
Jan 5, 2016, 2:32:46 PM1/5/16
to Jason Grout, Jonathan Frederic, sage-devel, IPython developers list
On Tue, Jan 5, 2016 at 11:19 AM, Jason Grout wrote:
(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.

The above strategy is a good start, but I've found it to be too naive in practice.  For example, in SMC there is a different limit on the amount of output that will be rendered with mathjax, versus the amount of stdout output.  This is because mathjax rendering is vastly more resource intensive than text rendering.  Also, if your graphics images are just contents of messages in base64 (say), they can be relatively large, but easy to render quickly.

You might also want to distinguish between local users and people using Jupyter via a remote server.  If everything is running on your laptop, the network situation is completely different than a remote server talking to a cell phone.

I know you wrote "user-configurable" above, but it's a possibly bad sign when user configuration is required.

Have fun at the Jupyter dev meeting!

William

--

### Jeroen Demeyer

unread,
Jan 5, 2016, 4:42:32 PM1/5/16
to sage-...@googlegroups.com
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.

### kcrisman

unread,
Jan 5, 2016, 5:16:18 PM1/5/16
to sage-devel
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! :)

### Jason Grout

unread,
Jan 5, 2016, 5:16:38 PM1/5/16