Notebook bug fix branch #1361

ellisonbg · 2012-02-01T17:45:01Z

I am using this branch to fix a number of bugs in the notebook. This branch is not done yet, but the changes are significant so testing should begin now.

Addresses: #1344, #1337, #1339, #1348, #1359

* Refactored the save widget so that the notebook doesn't depend on it. Now the notebook emits events and the save widget observes those events. * Created a new event system for all IPython events (events.js). We should start to use this to allow our classes to be loosely coupled. * Created a new notification widget that should be used for all notifications. Uses new event system. * Removed the kernel status widget. * All kernel status message use new event/notification system. * The print notebook view works again.

* Test suite passes. * nbformat put into a single location for easy update.

Hitting Shift-Enter on an already rendered text cell should simply move past it. It was causing the cell to enter edit mode. This is not fixed.

Previuosly we were using itex=True in the sympy latex printer. I don't know why where were doing this but we should use regular printing mode and put the $$ around the equations ourselves.

Pressing TAB to get the tooltip "range(TAB" was inserting a TAB. To get rid of this we are now telling CodeMirror to ignore it and also stopping the event from bubbling up the DOM.

ellisonbg · 2012-02-01T18:29:43Z

IPython/frontend/html/notebook/static/js/codecell.js

@@ -123,6 +123,10 @@ var IPython = (function (IPython) {
                return false;
            } else if ((pre_cursor.substr(-1) === "("|| pre_cursor.substr(-1) === " ") && tooltip_on_tab ) {
                that.request_tooltip_after_time(pre_cursor,0);
+                // Prevent the event from bubbling up.


@Carreau and @fperez: can you both test the tooltip behavior to make sure that TAB is not being inserted when the tooltip is brought up.

1. Users are warned when an older nbformat notebook is converted. 2. The notebook notifies the user when a notebook that is too new is attempted to load. To test these things, create a simple notebook. Then change its nbformat field by hand to 2 (to test 1) and then 4 (to test 2).

ellisonbg · 2012-02-02T00:50:44Z

OK, this is ready for review. @fperez, @Carreau, @takluyver, @minrk can you test this, the changes are significant and many bugs are fixed (list above).

fperez · 2012-02-02T04:31:54Z

Looking great so far, all but the mathjax bug seem completely gone; for that one I still see a slight glitch, best explained with an image:

The dollar signs shouldn't be there, though I don't know if that is somehow a sympy issue instead. I just want to point it out for now.

I haven't reviewed the code yet, but behavior-wise this is major progress, thanks a lot!

Carreau · 2012-02-02T07:19:41Z

Won't have time in the next 24h ... see maybe tomorow. i'ts on my to-do list.

miham · 2012-02-02T12:51:19Z

I'm not seeing the issue @fperez is having with dollar signs. I'm using Firefox 9.0.1, Sympy 0.7.1 and I started the notebook with $ python2 ipython.py notebook.

miham · 2012-02-02T13:05:59Z

When I run notebook in Epiphany 3.2.1 browser, $ BROWSER=epiphany python2 ipython.py notebook, and open a new notebook, I get the following error:

Websocket connection to
ws://127.0.0.1:8888/kernels/9645b519-b50f-4adf-aeca-5f08b012003d could not
be established. You will NOT be able to run code. Your browser may not be
compatible with the websocket version in the server, or if the url does not
look right, there could be an error in the server's configuration.

And I am indeed not able to run code - I entered 3+3 in the input cell and
nothing happened. The URL of the new notebook is http://127.0.0.1:8888/new.

Epiphany is great for IPython notebooks because it has a web application mode which makes IPython notebook behave like any other (native desktop) application you have installed - it appears in dash, application lists, etc.

Edit: Notebook doesn't work in Epiphany in master too. I am pretty sure that it worked a couple of days ago though.

takluyver · 2012-02-02T13:30:03Z

Miha, the notebook will only work in modern browsers which support
websockets. We recommend using recent versions of Firefox or Chrome. This
requirement isn't going to change on our end, so it won't work with
Epiphany until Epiphany gets websocket support.

ellisonbg · 2012-02-02T16:45:09Z

@fperez: I don't see this issue with the dollar signs either. This was on both Chrome and FF on Mac OS X. I am wondering if it is a MathJax version issue. Of what vintage is your MathJax - mine is late summer.

fperez · 2012-02-02T17:02:55Z

Mmh, that's quite odd. Just to be safe, I've re-downloaded mathjax with a fresh copy from their site and re-installed locally, and I've tested both Ffox and Chrome. I see those $ signs in both browsers (after multiple javascript reloads).

It's really bizarre. On the one hand I am not using sympy so much that this is a huge deal for me (I hadn't seen the issue in the first place), but on the other, if I see the problem, chances are someone else out there will too. So it really would be better to get to the bottom of it.

It almost looks as if we were inserting extra $ signs... If I manually call Math(latex(a)), it works fine:

Uploaded with Shutter

ellisonbg · 2012-02-02T17:07:19Z

On Thu, Feb 2, 2012 at 9:02 AM, Fernando Perez
reply@reply.github.com
wrote:

Mmh, that's quite odd. Just to be safe, I've re-downloaded mathjax with a fresh copy from their site and re-installed locally, and I've tested both Ffox and Chrome. I see those $ signs in both browsers (after multiple javascript reloads).

Hmm, that is a puzzle.

It's really bizarre. On the one hand I am not using sympy so much that this is a huge deal for me (I hadn't seen the issue in the first place), but on the other, if I see the problem, chances are someone else out there will too. So it really would be better to get to the bottom of it.

Yes, what about other types of sympy expressions? Is this problem
localized to root?

It almost looks as if we were inserting extra $ signs... If I manually call Math(latex(a)), it works fine:

Yes, that is what I am thinking. I will give you some JS code to
enter into the console to look at that.

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Reply to this email directly or view it on GitHub:
#1361 (comment)

Brian E. Granger
Cal Poly State University, San Luis Obispo
bgranger@calpoly.edu and ellisonbg@gmail.com

ellisonbg · 2012-02-02T17:11:52Z

@fperez: here is the code to type into the console:

IPython.notebook.get_cell(1).outputs[0]

This assumes that the cell with the output is cell 1 (0-indexed) and that there is one output. It will give you a JS object you can introspect. There will be a latex attribute that has the raw text that was returned by the server.

fperez · 2012-02-02T17:18:41Z

Yes, what about other types of sympy expressions? Is this problem localized to root?

OK, the problem is actually in all sympy expressions:

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I double-checked, and with master it's OK, no spurious $ signs anywhere. They only show up with this branch.

fperez · 2012-02-02T17:22:30Z

Yup, I just typed sqrt(2) into a cell after loading sympy/sympyprinting, and got, using your JS snippet, this in the object's latex field:

latex: "$$$\sqrt{2}$$$"

so there seem to be indeed spurious $ in there.

ellisonbg · 2012-02-02T17:26:43Z

OK, now let's track down where the extra $ is coming from. In the
sympy printing extension, we call:

def print_latex(o):
"""A function to generate the latex representation of sympy expressions."""
s = latex(o, mode='plain')
s = s.replace('\dag','\dagger')
return '$$%s$$' % s

You can see where we are adding the double pair if $$. You can call
the latex function (it is sympy.latex) in the notebook to see if it is
adding $:

latex(3**(S(1)/4))

Try that on a few expressions - it comes back with no $ on my system.
What a funny problem...

On Thu, Feb 2, 2012 at 9:22 AM, Fernando Perez
reply@reply.github.com
wrote:

Yup, I just typed sqrt(2) into a cell after loading sympy/sympyprinting, and got, using your JS snippet, this in the object's latex field:
latex: "$$$\sqrt{2}$$$"
so there seem to be indeed spurious $ in there.

Reply to this email directly or view it on GitHub:
#1361 (comment)

Brian E. Granger
Cal Poly State University, San Luis Obispo
bgranger@calpoly.edu and ellisonbg@gmail.com

ellisonbg · 2012-02-02T17:26:58Z

@fperez: let's pull up IRC and figure this out.

On Thu, Feb 2, 2012 at 9:26 AM, Brian Granger ellisonbg@gmail.com wrote:

OK, now let's track down where the extra $ is coming from. In the
sympy printing extension, we call:

def print_latex(o):
"""A function to generate the latex representation of sympy expressions."""
s = latex(o, mode='plain')
s = s.replace('\dag','\dagger')
return '$$%s$$' % s

You can see where we are adding the double pair if $$. You can call
the latex function (it is sympy.latex) in the notebook to see if it is
adding $:

latex(3**(S(1)/4))

Try that on a few expressions - it comes back with no $ on my system.
What a funny problem...

On Thu, Feb 2, 2012 at 9:22 AM, Fernando Perez
reply@reply.github.com
wrote:
Yup, I just typed sqrt(2) into a cell after loading sympy/sympyprinting, and got, using your JS snippet, this in the object's latex field:
latex: "$$$\sqrt{2}$$$"
so there seem to be indeed spurious $ in there.

Reply to this email directly or view it on GitHub:
#1361 (comment)
Brian E. Granger
Cal Poly State University, San Luis Obispo
bgranger@calpoly.edu and ellisonbg@gmail.com

Brian E. Granger
Cal Poly State University, San Luis Obispo
bgranger@calpoly.edu and ellisonbg@gmail.com

fperez · 2012-02-02T17:30:09Z

Will hop on irc now... The problem may be a sympy version issue...

Older versions of sympy put in an extra $ when using latex(e, mode='plain'). We are removing those before we add our own to make sure it works.

* Math now adds $$ if the user doesn't provide them. * Latex is like Math, but doesn't add delimiters.

fperez · 2012-02-02T19:41:30Z

Just to confirm for the PR record, that with the updates discussed on IRC to Math and the new Latex display object, this puppy is good to go.

miham · 2012-02-02T19:54:38Z

Miha, the notebook will only work in modern browsers which support websockets. We recommend using recent
versions of Firefox or Chrome. This requirement isn't going to change on our end, so it won't work with
Epiphany until Epiphany gets websocket support.

Just for the record: It turns out that the Tornado upgrade (2.1.1 -> 2.2) broke notebooks in Epiphany. With tornado 2.1.1 both master and nbissues branches work fine in Epiphany. I sent mail to Epiphany mailing list and i hope that they figure out why Tornado 2.2 (which was released on jan 30) is causing problems.

fperez · 2012-02-02T21:09:12Z

IPython/frontend/html/notebook/static/js/notebook.js

    // Persistance and loading

+    Notebook.prototype.get_notebook_id = function () {


Is it really necessary to have explicit getters and setters? I'm just curious: in Java/C++ they are ubiquitous, in Python rarely used. I just don't know if JS really requires them, and what the issues may be with explicitly setting the attribute from the outside. Basically, does the extra indirection layer really buy us anything?

I am not sure what the usual patterns are in Javascript. It is surely more like Python than Java/C++. In this case, it was a gut feel that I wanted a layer of abstraction, in case I needed to ever change how the attribute was handled. I haven't done many of these though and I guess you could argue that it is not needed yet.

I think the principal reason is that there is no equivalent of @property. If it seems like changing the notebook name might have side effects (even if it doesn't start out with any), it should be a setter because you can't turn an attribute into a property without changing the API, unlike in Python.

I think it's a minor style issue really, but that's the usual motivation.

OK, it's no big deal and I don't have any major objection, really. Since we're all finding our way through JS, I'm sure we'll learn more and will find our own style over time. I think it's fine to leave these as-is for now, following your instinct.

I'll merge now then, since we're good on review and you updated the example nb, which was the last point in my mind. Thanks for the great job, this fixes a number of key issues!

A number of bug fixes for notebook issues that had crept up recently with all the major improvements done on multiple fronts. In closing #1359, we've changed slightly how Math() works: it now unconditionally surrounds its input with $$...$$, so that it always appears in displayed math mode. We have also introduced a new display object, Latex(), which does *not* add any latex markup, for other constructs beyond simple math expressions. This change makes Math() friendlier to use in simple cases and means that Math(sympy.latex(foo)) will produce the expected displayed math results without the user having to add any $ markup. Summary of fixes: Fixes #1344: Ctrl + M + L does not toggle line numbering in htmlnotebook. Fixes #1337: Tab in the notebook after `(` should not indent, only give a tooltip. Fixes #1339: Notebook printing broken. Fixes #1348: `Ctrl-m-Ctrl-m` does not switch to markdown cell Fixes #1359: [sympyprinting] MathJax can't render \root{m}{n}

fperez · 2012-02-02T21:41:16Z

Merged, thanks @ellisonbg!!

A number of bug fixes for notebook issues that had crept up recently with all the major improvements done on multiple fronts. In closing ipython#1359, we've changed slightly how Math() works: it now unconditionally surrounds its input with $$...$$, so that it always appears in displayed math mode. We have also introduced a new display object, Latex(), which does *not* add any latex markup, for other constructs beyond simple math expressions. This change makes Math() friendlier to use in simple cases and means that Math(sympy.latex(foo)) will produce the expected displayed math results without the user having to add any $ markup. Summary of fixes: Fixes ipython#1344: Ctrl + M + L does not toggle line numbering in htmlnotebook. Fixes ipython#1337: Tab in the notebook after `(` should not indent, only give a tooltip. Fixes ipython#1339: Notebook printing broken. Fixes ipython#1348: `Ctrl-m-Ctrl-m` does not switch to markdown cell Fixes ipython#1359: [sympyprinting] MathJax can't render \root{m}{n}

ellisonbg added 3 commits January 31, 2012 21:42

Fixing minor issues with nbformat.

981f2ab

* Test suite passes. * nbformat put into a single location for easy update.

Fixing ipython#1348 to allow Ctrl-M M to work w/o releasing Ctrl.

648d2de

This was referenced Feb 1, 2012

Notebook printing broken #1339

Closed

Ctrl + M + M does not switch to markdown cell #1348

Closed

ellisonbg added 3 commits February 1, 2012 09:57

Fixing Shift-Enter bug in text cells.

1be7dfb

Hitting Shift-Enter on an already rendered text cell should simply move past it. It was causing the cell to enter edit mode. This is not fixed.

Fixing ipython#1359. We are not using itex mode in sympyprinting.

5cf294c

Previuosly we were using itex=True in the sympy latex printer. I don't know why where were doing this but we should use regular printing mode and put the $$ around the equations ourselves.

Fixing ipython#1337. Tooltip stops TAB from being handled by others.

07435e3

Pressing TAB to get the tooltip "range(TAB" was inserting a TAB. To get rid of this we are now telling CodeMirror to ignore it and also stopping the event from bubbling up the DOM.

ellisonbg reviewed Feb 1, 2012
View reviewed changes

ellisonbg added 3 commits February 1, 2012 14:36

Updating CodeMirror to c813c94 to fix ipython#1344.

ecc950e

Making keyboard shortcut for showing line numbers consistent.

de28679

This was referenced Feb 2, 2012

Ctrl + M + L does not toggle line numbering in htmlnotebook #1344

Closed

Tab in the notebook after ( should not indent, only give a tooltip #1337

Closed

[sympyprinting] MathJax can't render \root{m}{n} #1359

Closed

ellisonbg added 2 commits February 2, 2012 09:33

Related to ipython#1359. Removing extra $ that older versions sympy add.

8247cb1

Older versions of sympy put in an extra $ when using latex(e, mode='plain'). We are removing those before we add our own to make sure it works.

Changes to Math class and added Latex class.

4aa7390

* Math now adds $$ if the user doesn't provide them. * Latex is like Math, but doesn't add delimiters.

fperez reviewed Feb 2, 2012
View reviewed changes

fperez merged commit 54c3e06 into ipython:master Feb 2, 2012

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Notebook bug fix branch #1361

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ellisonbg commented Feb 1, 2012

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fperez commented Feb 2, 2012

		// Persistance and loading

		Notebook.prototype.get_notebook_id = function () {

Notebook bug fix branch #1361

Notebook bug fix branch #1361

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