Opened 11 years ago

# Upgrade the notebook to use MathJax instead of jsMath — at Version 76

Reported by: Owned by: mpatel jason, was major sage-5.4 notebook sd41 rbeezer, robert.marik, jhpalmieri, rkirov, kcrisman, kini Rob Beezer, Davide Cervone, John Palmieri, Jason Grout, Nathan Carter Jason Grout, John Palmieri, Punarbasu Purkayastha, Keshav Kini Fixed upstream, but not in a stable release. fix sagenb #11080

MathJax is the successor to jsMath.

This will also fix #1608

apply:

Also install the new notebook from the sagenb git fork https://github.com/jasongrout/sagenb/tree/mathjax.

### comment:1 Changed 11 years ago by rbeezer

• Cc rbeezer added

### comment:2 follow-up: ↓ 4 Changed 11 years ago by rbeezer

• Cc robert.marik added

I've been experimenting a bit with MathJax, outside of the notebook. Mostly thinking about how it will handle tex4ht output in jsMath mode, but here are some some observations that might be useful:

1. Easier in most ways to structure a page to use MathJax. Just insert something like
<script type="text/javascript" src="path-to-MathJax/MathJax.js"></script>


No need for a "process()" call at the end, etc.

1. Default is to not recognize single dollar-signs as delimiters. Alternative is $$..$$. This would be a good thing, since if a user adds text (via TinyMCE) right now jsMath tries to parse the following as math. $$..$$ and $..$ both work for display math. We would break lots of old worksheets if we stopped recognizing $..$.
1. There is a jsMath compatibility mode. I believe I've found one bug in this already (reported upstream). I'd imagine this is not a development priority, but who knows?
1. Modes and configuration is controlled globally by config/MathJax.js which is just one huge well-commented Javascript object. It can be overridden in a web page by adding a new version into the script block mentioned above. Maybe we want to make this easy for users to access, or maybe it is easy already, or maybe we don't want to bother.
1. This looks to me like the best introduction to the types of decisions we will want to make about what to cut over to:
1. MathJax is HUGE. Fonts for lots of Unicode points, I guess. SVN checkout is 53 MB, after unzipping fonts.zip it all occupies 171 MB.
1. I just noticed this morning that html.table() uses class="math" which is a jsMath way to tag span's or div's for processing. I haven't found how to do something similiar in MathJax, though this will work in jsMath compatibility mode. A very small test would indicate that the two modes can be used at the same time.
1. Consonant with (2) and (7), I'd love to see the notebook formatting move to something closer to rigorous XML (ie XHTML, I guess). Certain types of processing would be easier if we did, but that is not really what this ticket is all about.

### comment:3 Changed 11 years ago by robert.marik

Thanks for comment, I feel that MathJax? is much slower on cheap/older computer. This could be an important issue for using Sage in highschools and universities. Is it possible to keep both MathJax? and jsMath and let the notebook admin to choose, which one will be used?

### comment:4 in reply to: ↑ 2 ; follow-up: ↓ 10 Changed 11 years ago by jason

1. MathJax is HUGE. Fonts for lots of Unicode points, I guess. SVN checkout is 53 MB, after unzipping fonts.zip it all occupies 171 MB.

I think MathJax? includes the equivalent of our jsmath-image-fonts spkg. If we added MathJax? to Sage, it might be good to strip out the image fonts and distribute them separately as a mathjax-image-fonts spkg (mathjax faq tells how to do this, I believe). Somewhere I have a half-finished prototype of this solution.

### comment:5 Changed 11 years ago by jhpalmieri

• Cc jhpalmieri added

### comment:6 Changed 11 years ago by jason

• Description modified (diff)

### comment:7 Changed 11 years ago by jason

• Description modified (diff)

### comment:8 Changed 11 years ago by jason

• Status changed from new to needs_work

### comment:9 Changed 11 years ago by jason

• Description modified (diff)

### comment:10 in reply to: ↑ 4 ; follow-up: ↓ 11 Changed 11 years ago by rminer

1. MathJax is HUGE. Fonts for lots of Unicode points, I guess. SVN checkout is 53 MB, after unzipping fonts.zip it all occupies 171 MB.

I think MathJax? includes the equivalent of our jsmath-image-fonts spkg. If we added MathJax? to Sage, it might be good to strip out the image fonts and distribute them separately as a mathjax-image-fonts spkg (mathjax faq tells how to do this, I believe). Somewhere I have a half-finished prototype of this solution.

Just in case you haven't thought of this, what Gollum (the GitHub forum) folks did was host the MathJax? fonts on Amazon S3, and then not include them in their distribution. I don't know if that would work for you, but I wanted to point it out.

### comment:11 in reply to: ↑ 10 Changed 11 years ago by jason

1. MathJax is HUGE. Fonts for lots of Unicode points, I guess. SVN checkout is 53 MB, after unzipping fonts.zip it all occupies 171 MB.

I think MathJax? includes the equivalent of our jsmath-image-fonts spkg. If we added MathJax? to Sage, it might be good to strip out the image fonts and distribute them separately as a mathjax-image-fonts spkg (mathjax faq tells how to do this, I believe). Somewhere I have a half-finished prototype of this solution.

Just in case you haven't thought of this, what Gollum (the GitHub forum) folks did was host the MathJax? fonts on Amazon S3, and then not include them in their distribution. I don't know if that would work for you, but I wanted to point it out.

That's a very interesting solution. I suppose we could host them on the main sage webserver, for example. Or maybe Google Code or something like that so we had redundant sources.

### comment:12 Changed 11 years ago by jhpalmieri

I just found the web page http://bitbucket.org/kevindunn/sphinx-extension-mathjax/wiki/Home, which allows the use of Sphinx with MathJax. Assuming it works, we could upgrade all of Sage (not just the notebook but also the docs), to use MathJax instead of jsMath.

### comment:13 Changed 11 years ago by drkirkby

MathJax is very impressive looking. I like the idea the user does not have to have any fonts installed on his computer, which is a major advantage over jsMath

Dave

### Changed 11 years ago by rbeezer

Screenshot of double integral

### Changed 11 years ago by rbeezer

Screenshot of matrix

### comment:14 Changed 11 years ago by rbeezer

• Cc rkirov added

Steps that will install MathJax with the new Flask notebook.

1. Install the Flask version of the notebook.
http://code.google.com/r/rkirov-flask/

1. Download v1.1 of MathJax as zip file (from bottom of page).
http://www.mathjax.org/download/

1. Unzip the MathJax? distribution into
$SAGE_ROOT/devel/sagenb/sagenb/data and rename the new directory: mathjax-MathJax-5a7e4d7 (or whatever) to be just the directory: MathJax 1. jsmath compatibility. Edit $SAGE_ROOT/devel/sagenb/sagenb/data/MathJax/config/default.js

by adding "jsMath2jax.js" as the first entry of the "extensions" list, so it becomes
extensions: ["jsMath2jax.js", "tex2jax.js"]

1. Edit
$SAGE_ROOT/devel/sagenb/sagenb/data/sage/html/notebook/base.html  and change <script type="text/javascript" src="/javascript/sage/jsmath.js"></script>  to <script type="text/javascript" src="/static/MathJax/MathJax.js?config=default"></script>  This will install MathJax and the notebook will use it. But the setup is buggy, so needs work. I'm sure there is some configuration on the Sage side and/or the MathJax side that will need changes. • A mix of black and green symbols. • Only renders on a reload - adding new TeX via TinyMCE returns with an error about not finding fonts. • Some stray tags are being rendered, or something. Screenshots attached: $$(2\pi h)^{-d}\iint_{\{H(x,\xi) <\tau\}} dx d\xi$$  Matrix: $\begin{bmatrix}
x^2 & y^2\\
x^3 & \cos(z)
\end{bmatrix}$ ### comment:15 Changed 11 years ago by kcrisman • Cc kcrisman added ### comment:16 Changed 10 years ago by jhpalmieri I'm attaching a draft of a patch for the Sage library. The integration with Sphinx is completely untested, and is probably broken. See the top of the patch file for a list of things to do. ### Changed 10 years ago by rbeezer ### comment:17 Changed 10 years ago by rbeezer Added patch to Flask notebook code to support MathJax, built with Davide Cervone's help. 1. This is a hand-edited patch to recover from an hg mess-up. I think it is OK, but be wary. 2. Fonts are coming from MathJax CDN. Comment in code indicates change for local MathJax installation. 3. <script> tags added by Palmieri's Sage library patch need to be handled with care on notebook side, so notebook does not evaluate them. Right now when "Typeset" box is checked, evaluated cells raise a Javascript error in evaluate_script_tags (or a function with a similar name). ### comment:18 follow-up: ↓ 19 Changed 10 years ago by jason John's patch doesn't apply cleanly to stock 4.7; does it apply to the most recent alpha of 4.7.1? applying mathjax.patch patching file sage/misc/latex.py Hunk #15 succeeded at 1750 with fuzz 2 (offset 2 lines). Hunk #23 FAILED at 2382 1 out of 25 hunks FAILED -- saving rejects to file sage/misc/latex.py.rej patch failed, unable to continue (try -v) patch failed, rejects left in working dir errors during apply, please fix and refresh mathjax.patch  ### comment:19 in reply to: ↑ 18 Changed 10 years ago by rbeezer Replying to jason: John's patch doesn't apply cleanly to stock 4.7; does it apply to the most recent alpha of 4.7.1? Yes. rob@tiger:/sage/dev/devel/sage$ ../../sage -version
| Sage Version 4.7.1.alpha2, Release Date: 2011-06-07                |
* Warning: this is a prerelease version, and it may be unstable.     *
rob@tiger:/sage/dev/devel/sage$hg qimport -P http://trac.sagemath.org/sage_trac/raw-attachment/ticket/9774/mathjax.patch adding mathjax.patch to series file applying mathjax.patch now at: mathjax.patch  ### comment:20 follow-up: ↓ 22 Changed 10 years ago by jason Don't we need the actual MathJax? spkg or files somewhere? Rob: do you have instructions for putting these in the directory, or do we use my half-finished patch mentioned in the description, or something else? ### Changed 10 years ago by rbeezer ### comment:21 Changed 10 years ago by rbeezer Attached a patch to add sagenb/notebook/mathjax.py New file is similar to, but not identical to, sagenb/notebook/jsmath.py We did not delete the latter, but I think it can safely go away. ### comment:22 in reply to: ↑ 20 Changed 10 years ago by rbeezer Replying to jason: Don't we need the actual MathJax? spkg or files somewhere? Rob: do you have instructions for putting these in the directory, or do we use my half-finished patch mentioned in the description, or something else? We need an spkg to be Internet-independent. We did not experiment with your old one. I think it would be best to make a new one. This requires a small edit (once you are sure all works with CDN version). Font suggestions coming up. ### comment:23 Changed 10 years ago by rbeezer Davide Cervone says for an spkg we need only keep font subdirectories called otf, eot, svg  In particular png subdirectories are huge-est and can go away. Rob ### comment:24 Changed 10 years ago by jason ah; I bet it's because the svg fonts replace the png fonts for all browsers we care about, or something. Okay, Davide is the final authority on what browsers support what... ### comment:25 follow-up: ↓ 26 Changed 10 years ago by jason I get an error from the line: response = make_response(render_template('js/mathjax.js', theme_mathjax_macros=mathjax_macros)) in flask_version/base.py. I see a jsmath.js template in sagenb/data/sage/js/jsmath.js template. Is this another file that didn't get added to the patch? ### Changed 10 years ago by rbeezer ### comment:26 in reply to: ↑ 25 Changed 10 years ago by rbeezer Replying to jason: Is this another file that didn't get added to the patch? Yes, same situation - "old" file could be removed. "file-add-two" should create the missing file. Sorry about all the problems - my hg status is useless with the hg mess-up. This file will require an edit when we move from CDN to spkg. Thank-you!!!!!!!!!!!!!! ### comment:27 Changed 10 years ago by jason I have a working version, but there still seems to be something slightly different about Typeset mode compared to before. I'm posting my patch, but there is still *lots* of debugging stuff in the patch that should be taken out before a final version is posted. ### Changed 10 years ago by jason apply to sagenb repository; apply on top of previous patches ### comment:28 Changed 10 years ago by rbeezer The problem with the Sage notebook code intercepting (and evaluating) the contents of <script>,</script> tags can probably be rectified in one, or both, of the functions of the Flask notebook: In sagenb/data/sage/js/notebook_lib.js: eval_script_tags separate_script_tags  ### comment:29 Changed 10 years ago by jason rbeezer: yes, that's what my patch does. The current remaining problem is something different. ### comment:30 Changed 10 years ago by jhpalmieri In the current version of mathjax.patch, look at the top of the file for some unfinished business. For example, the pathname at the end of doc/common/themes/sage/static/mathjax_sage.js_t might be wrong, which might break MathJax? in the Sphinx documentation. ### comment:31 Changed 10 years ago by rbeezer In the current state, the --mathjax switch seems to work with a build of the html version of the reference manual. Mathematics in the documentation is being wrapped with $$,$$ pairs, which are the default MathJax? delimiters for inline mathematics. However these snippets are not being rendered when viewed in a browser. In the page source of a page of the html documentation, I see a script in a file named mathjax_sage.js which we are not generating. We do have jsmath_sage.js lying about in the doc directories, which have the full jsmath configuration information. So this likely needs repair before an HTML documentation page with MathJax? support is built properly. ### comment:32 Changed 10 years ago by rbeezer OK, I can force mathjax_sage.js to be created by totally trashing some of the documentation output with devel/sage/doc/output/html$ rm -rf en


before rebuilding the HTML reference documentation. It comes from a template file mathjax_sage.js_t that one of the patches creates properly.

Mathematics still does not render, but I think the MathJax? configuration is looking locally. Time for a local MathJax? install, I think.

### comment:33 follow-up: ↓ 34 Changed 10 years ago by rbeezer

In a page of the documentation, I inserted manually

<script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS_HTML-full">


and the mathematics rendered properly with MathJax.

Then I installed the mathjax 1.1a distribution alongside jsmath in the Flask notebook tree and used

<script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS_HTML-full">


which also caused the math to render properly. (/sage/notebook is my SAGE_ROOT)

In both cases the fonts did not look too great to my eye.

Questions:

(a) How do we get these scripts commands to be placed properly in each page of the docs, with a proper relative path?

(b) Is there really a clean separation between Sage and the notebook if --mathjax mode for documentation requires the MathJax code from the notebook?

### comment:34 in reply to: ↑ 33 Changed 10 years ago by rbeezer

Then I installed the mathjax 1.1a distribution alongside jsmath in the Flask notebook tree and

which also caused the math to render properly. (/sage/notebook is my SAGE_ROOT)

Oops, the incantation for a local install of MathJax should have been

<script type="text/javascript" src="/sage/notebook/devel/rkirov-flask/sagenb/data/mathjax/MathJax.js?config=TeX-AMS_HTML-full"></script>


### comment:35 Changed 10 years ago by jhpalmieri

Here's a new version of my patch. With a locally installed version of MathJax, the documentation seems to render properly. I don't know if this is the best solution, but at least it seems to work.

(I installed MathJax by downloading a zip file: https://github.com/mathjax/MathJax/zipball/v1.1a. I unzipped it and renamed the resulting directory to mathjax, and moved it to SAGE_ROOT/local/lib/python/site-packages/sagenb-0.9.0-py2.6.egg/sagenb/data/, alongside of the old jsmath directory. I also put a copy of the mathjax directory in SAGE_ROOT/devel/sagenb/sagenb/data/. I haven't tried to install local fonts.)

### Changed 10 years ago by jhpalmieri

(experimental) patch for Sage library

### comment:36 Changed 10 years ago by jhpalmieri

By the way, one comment about the latest version of my patch: it fixes the problem Rob mentioned about getting the appropriate invocation to MathJax in each piece of documentation. It does this by setting the variable mathjax_path to

file://[path to MathJax.js]?config=TeX-AMS_HTML-full,file://[path to mathjax_sage.js]


The paths here are absolute ones, in SAGE_ROOT/devel/sage/doc/output/html/en/_static/. This directory is created by sage -docbuild website html, so now if you build the docs with the -j flag (to enable MathJax), it first builds the website target, then builds whatever you requested. There might be a better way to do this, using relative paths, but I couldn't get it to work. For example, using

    <script type="text/javascript" src="_static/MathJax.js?config=TeX-AMS_HTML-full"></script>


successfully turns on MathJax, but without the local configuration turning on the custom macros. Using

    <script type="text/javascript" src="_static/MathJax.js?config=TeX-AMS_HTML-full,mathjax_sage.js"></script>


doesn't work, nor does any variation of it that I tried. (Note that when you change the path specifying the local configuration file, you also need to change the last line of that configuration file to match it, according to http://www.mathjax.org/docs/1.1/configuration.html.) If we could copy the file mathjax_sage.js to _static/config/local/, then we could use

    <script type="text/javascript" src="_static/MathJax.js?config=TeX-AMS_HTML-full,local/mathjax_sage.js"></script>


for the invocation, and

MathJax.Ajax.loadComplete("[MathJax]/config/local/mathjax_sage.js")


for the last line in mathjax_sage.js. But I don't know how to put this file in the right place: it's autogenerated, so we can't put it in the MathJax local directory ahead of time, and I can't figure out how to get Sphinx to do it when it's building the documentation.

Another option would be to try to get Sphinx to write this into each html file:

<script type="text/x-mathjax-config">
[contents of mathjax_sage.js]
</script>
<script type="text/javascript" src="_static/MathJax.js?config=TeX-AMS_HTML-full"></script>


We can get the last line by specifing mathjax_path in conf.py, but I don't know how to get the first part.

I'll keep working on it...

### comment:37 Changed 10 years ago by rbeezer

Hi John,

Are you testing with the Flask notebook? If not, it might be easier to build what look like absolute paths to the MathJax files in the data directory of the notebook, because of the way Flask sets up paths with the "route()" command? I can't tell if this will solve the problem you are wrestling with or not.

The <script> tags were being messed with by the notebook on the server side just before being dispatched. But then the client sees two versions - wrapped and unwrapped, and totally trashes one of them to prevent running a script twice. I thought Jason had a patch for this too, but I haven't seen it. The symptom would be when you cycle through wrap, no-wrap, and hide for some output, then one of them is missing. I guess we can press on and fix this eventually.

About to go off-line shortly for the long weekend, but will come back to this when I can stick with it.

Rob

### comment:38 Changed 10 years ago by jhpalmieri

For building the documentation, the notebook isn't relevant: they get built from the command line. I think that when trying to make MathJax work with the notebook, we'll want to construct the URLs differently than I'm doing for the docs, but I don't know enough about the paths, etc., in the notebook to say exactly how to do it. For what it's worth, though, I have been using the flask notebook.

### comment:39 Changed 10 years ago by jason

I've uploaded my current flask patch queue here: http://sage.math.washington.edu/home/jason/mathjax-flask-patches.tar.gz My current (probably non-working) patch queue for my sage library, including two mathjax patches, is here: http://sage.math.washington.edu/home/jason/mathjax-sage-patches.tar.gz

These are both works-in-progress, but currently stalled for at least a week or two.

### comment:40 Changed 10 years ago by jason

I stalled working on it because of other time pressures with the single-cell, but also because I realized that the *next* version of Sphinx supports Mathjax out of the box, while I thought the current version would require patches.

### comment:41 Changed 10 years ago by jhpalmieri

I think that the implementation of MathJax in Sphinx comes from the file mathjax.py, which is available for download separately. So my patch just adds it.

I'm attaching another version ("v2") of my patch; this one writes the MathJax local configuration file to a file in SAGE_ROOT/local/lib/python/site-libraries/sagenb.../, which may not be a good idea. But it allows for a simpler invocation of MathJax. I'm really not sure which approach is better.

### Changed 10 years ago by jhpalmieri

(experimental) patch for Sage library, alternate version

### comment:42 Changed 10 years ago by jason

What is the current status on this now? Where should we start working on it again?

### comment:43 Changed 10 years ago by rkirov

The last patch involving MathJax?, that I rebased from the ones here is on google code:

Unless Jonathan Gutow did something else on top of it, this is latest work.

### Changed 10 years ago by jason

Rebased version of comprehensive mathjax patch to 4.8.alpha4

### Changed 10 years ago by jason

Apply only this patch

### comment:44 Changed 10 years ago by jason

• Description modified (diff)
• Milestone set to sage-5.0

### comment:45 Changed 10 years ago by jason

• Description modified (diff)

### comment:46 Changed 10 years ago by jason

• Authors set to Rob Beezer, Davide Cervone, John Palmieri, Jason Grout
• Description modified (diff)
• Reviewers set to Jason Grout
• Status changed from needs_work to needs_review

### comment:47 Changed 10 years ago by jason

• Description modified (diff)

### comment:48 Changed 10 years ago by jason

• Description modified (diff)

### comment:49 Changed 10 years ago by jason

• Authors changed from Rob Beezer, Davide Cervone, John Palmieri, Jason Grout to Rob Beezer, Davide Cervone, John Palmieri, Jason Grout, Nathan Carter

### Changed 10 years ago by jason

apply to scripts repository

### Changed 10 years ago by jason

apply to sage repository

### comment:50 Changed 10 years ago by jason

• Description modified (diff)

### comment:51 Changed 10 years ago by kini

• Cc kini added

### comment:52 Changed 10 years ago by kini

• Description modified (diff)
• Status changed from needs_review to needs_work

I assume the description was incorrect, but even with the correction I made, trac_9774-mathjax-try3.patch does not apply cleanly on top of 4.8.alpha6. On 4.8.alpha4 (at least by hg up 4.8.alpha4 && sage -b) it fails a couple of doctests. Rebasing and fixing doctests now.

### comment:53 Changed 10 years ago by kini

Whoops, looks like "a couple of doctests" was an understatement. I guess it should be done in a separate patch. Here's the new patch, rebased only.

### Changed 10 years ago by kini

apply to \$SAGE_ROOT/devel/sage

### comment:54 Changed 10 years ago by jason

The try3 patches were against alpha4. Late last night I patched 5.0.beta1, and realized there were some patch failures, which I fixed. I'll compare your rebase with mine.

I also realized last night during dinner that I hadn't run doctests, so those should be run on sage and sagenb. Thanks for checking this.

### comment:55 follow-up: ↓ 58 Changed 10 years ago by jason

You don't happen to have your changes as a separate patch on top of mine, do you? I'd love to review your changes, but it's a bit hard to see where your additions are.

If you don't have it, I'll just diff the two patches, but that's a little harder to read than a separate patch.

### comment:56 Changed 10 years ago by jhpalmieri

I wonder if the reported problems with "<" and ">" are due to line 1685 in latex.py:

x = x.replace('<', '&lt;').replace('>', '&gt;')


This was put in for use with jsMath, but maybe MathJax doesn't have the same issues.

### comment:57 Changed 10 years ago by jason

It was more complicated than that, but I've fixed it by getting rid of the math_parse function and conditional typesetting we were doing. We've configured MathJax? to make the math_parse function obsolete, and it's inconsistent to typeset only conditionally. See https://github.com/jasongrout/sagenb/commit/6a4eed4d6baf78cd19fe634144c727843d1af08d and https://github.com/jasongrout/sagenb/commit/8d6b0a071c13850cea983faaa6b910be498cd0ae

I've updated test.sagenb.org with the newest mathjax changes.

### comment:58 in reply to: ↑ 55 Changed 10 years ago by kini

You don't happen to have your changes as a separate patch on top of mine, do you? I'd love to review your changes, but it's a bit hard to see where your additions are.

If you don't have it, I'll just diff the two patches, but that's a little harder to read than a separate patch.

Er, no, I don't, unfortunately. You can get such a diff by doing hg qfinish on my patch on top of 4.8.alpha6, then hg up 4.8.alpha4, then hg qimport -P [your patch], then hg diff -r tip -r [revid of my patch] (you would probably want to hg strip [revid of my patch] later).

But I don't see how that's very useful to you since it will be some gigantic patch subsuming everything that was merged in alpha5 and alpha6. In your position I would just diff the two patches, but maybe I don't understand what you're asking for. If you just want diffs for the files touched by the patch, that would also be possible, but maybe a bit messier. Do as above, except also qfinish your patch, and then merge the two qfinished patches' commits into a new commit, with your patch as the primary parent. Then do hg log -r [the merge commit] -p [the file names]. (I think that should work.) Or I guess you could just make the gigantic patch and ignore the parts that are on irrelevant files.

### comment:59 Changed 10 years ago by jason

• Description modified (diff)
• Status changed from needs_work to needs_review

kini: your try4 patch looks fine to me. It applies cleanly on 5.0.some_version_of_prealpha1_or_beta1

### comment:60 Changed 10 years ago by ppurka

I seem to have a broken install here (2nd try). I followed this sequence of steps to install mathjax + jmol (output of history in zsh).

  663  local/bin
664  ../../sage -hg qimport http://trac.sagemath.org/sage_trac/raw-attachment/ticket/9774/trac_9774-scripts-mathjax.patch
***  ../../sage -hg qpush  # This line is missing because of my zsh setup
666  ../../
667  l
668  cd devel/sage
669  ../../sage -hg qimport http://trac.sagemath.org/sage_trac/raw-attachment/ticket/9774/trac_9774-mathjax-try4.patch
670  ../../sage -hg qpush
671  ../../sage -b
672  ../..
674  ./sage -f http://sage.math.washington.edu/home/jason/mathjax/sagenb-0.9.0.spkg
675  ./sage -f http://sage.math.washington.edu/home/jason/jmol/jmol-12.0.45.p4.spkg
676  ./sage -b
678  ./sage -n
679  BROWSER="firefox" ./sage -n


Mathjax is broken and so is jmol. Do I need to install something extra for mathjax + jmol to work? These steps were followed on a freshly compiled sage-4.8. Screenshot: http://i.imgur.com/A6wrQ.png

### comment:61 Changed 10 years ago by jason

• Dependencies set to #11080

I only tested it on a 5.0 beta. I see that #11080 isn't explicitly listed as a dependency (though it is mentioned in the description).

So please follow the directions on #11080 first (which involves a lot more patches). My guess is that things won't apply cleanly to 4.8, and you'll need a 5.0 beta.

### comment:62 Changed 10 years ago by jason

And thanks for looking at this! This ticket is also live at test.sagenb.org.

### comment:63 Changed 10 years ago by ppurka

There seems to be some problem with mathjax rendering with LatexExpr. Compare the jsmath rendering here: http://sagenb.org/home/pub/4337/ to the mathjax here: http://test.sagenb.org/home/pub/19/

### comment:64 Changed 10 years ago by ppurka

Some doctest failures with this patch:

...sage-5.0.beta2/devel/sage> ../../sage -t sage/misc/latex.py
sage -t  "devel/sage-main-backup/sage/misc/latex.py"
**********************************************************************
File "/home/punarbasu/Installations/sage-5.0.beta2/devel/sage-main-backup/sage/misc/latex.py", line 1765:
sage: MathJax().eval(type(3), mode='inline')
Expected:
<html><script type="math/tex">\newcommand{\Bold}[1]{\mathbf{#1}}\hbox{ < type 'sage.rings.integer.Integer' > }</script></html>
Got:
<html><script type="math/tex">\newcommand{\Bold}[1]{\mathbf{#1}}\verb|&lt;type|\phantom{\verb!x!}\verb|'sage.rings.integer.Integer'&gt;|</script></html>
**********************************************************************
File "/home/punarbasu/Installations/sage-5.0.beta2/devel/sage-main-backup/sage/misc/latex.py", line 2199:
sage: sys.displayhook
Expected:
<html>...\verb|&lt;function|\phantom{x}\verb|pretty_print|...</html>
Got:
<html><script type="math/tex">\newcommand{\Bold}[1]{\mathbf{#1}}\verb|&lt;function|\phantom{\verb!x!}\verb|pretty_print|\phantom{\verb!x!}\verb|at|\phantom{\verb!x!}\verb|0x150b050&gt;|</script></html>
**********************************************************************
2 items had failures:
1 of   7 in __main__.example_52
1 of   7 in __main__.example_59
***Test Failed*** 2 failures.
For whitespace errors, see the file /home/punarbasu/.sage//tmp/latex_7938.py
[3.1 s]

----------------------------------------------------------------------
The following tests failed:

sage -t  "devel/sage-main-backup/sage/misc/latex.py"
Total time for all tests: 3.1 seconds


### Changed 9 years ago by ppurka

Apply to devel/sage

### comment:65 Changed 9 years ago by ppurka

• Status changed from needs_review to needs_work
• Work issues set to does not work in DOT_SAGE

rebased patch to sage-5.1beta2.

There is however a very weird problem with mathjax, both 1.0 and 2.0 branches. The math is not rendered as long as the sagenb directory is under DOT_SAGE. To reproduce, try the steps below. Use any branch (mathjax-1 or mathjax-2) for instance jasongrout/mathjax (mathjax-1) in github.

1. mkdir /tmp/a
2. DOT_SAGE=/tmp/a sage -n.
3. First, note that the above command launches the nb in port 8000 instead of 8080. But if we use some other command such as the one below, then it does open in port 8080.
sage -n directory=/tmp/a.sagenb

4. Open a new worksheet, and try to print latex, for instance run the command view('?'). You will get a js error popup saying (in Opera 12.00RC, and Opera-11.64)
SyntaxError: at index 0 in "\newcommand{\Bold}[1]{\mathbf{#1}}?": invalid character escape sequence


In firefox-10.0.4 I simply get the error: SyntaxError: illegal character. This error is not present if I run sage instead as sage -n directory=/tmp/a.sagenb, and the mathjax output is all good.

### comment:66 Changed 9 years ago by ppurka

• Description modified (diff)

### comment:67 follow-up: ↓ 68 Changed 9 years ago by kini

It looks like Samuel Ainsworth has independently got MathJax working in his "newui" branch (I haven't tested it). At a glance it seems he's using the MathJax CDN.

### comment:68 in reply to: ↑ 67 Changed 9 years ago by ppurka

It looks like Samuel Ainsworth has independently got MathJax working in his "newui" branch (I haven't tested it). At a glance it seems he's using the MathJax CDN.

Has he applied the mathjax patches to the sage repo? Without those patches it won't work. And these patches were not applying for quite sometime. I just updated one today.

There are more changes to make actually. SAGE_ROOT/devel/sage/doc has lots of jsmath references, which all need to be converted to mathjax.

If you can independently confirm the behavior in comment:65 then it will be good.

### comment:69 Changed 9 years ago by jhpalmieri

• Description modified (diff)
• Reviewers changed from Jason Grout to Jason Grout, John Palmieri
• Status changed from needs_work to positive_review

Regarding your comment: the spkg in the ticket description is quite old, and that was probably the problem. The notebook has now been upgraded to use MathJax, and it does not have the problem you described.

### comment:70 Changed 9 years ago by jhpalmieri

• Work issues does not work in DOT_SAGE deleted

### comment:71 Changed 9 years ago by kcrisman

• Milestone changed from sage-5.1 to sage-5.2

Fantastic news!

This was merged in the notebook at this github pull request, just for completeness.

Since #11080 is for Sage 5.2, this should be too.

### comment:72 Changed 9 years ago by kcrisman

• Reviewers changed from Jason Grout, John Palmieri to Jason Grout, John Palmieri, Punarbasu Purkayastha, Keshav Kini

### comment:73 Changed 9 years ago by kcrisman

Just checking on this - Jason, will this indeed fix #1608? That is, will we be shipping (the relevant) MathJax fonts? From what I'm reading above, that seems to be the case. Anyone who confirms this, please give positive review to #1608 and add your name as a reviewer.

### comment:74 follow-up: ↓ 75 Changed 9 years ago by jhpalmieri

• Status changed from positive_review to needs_work

We have doctest failures:

        sage -t  --long -force_lib devel/sagenb-main/sagenb/notebook/jsmath.py # 5 doctests failed
sage -t  --long -force_lib devel/sagenb-main/sagenb/misc/sphinxify.py # 1 doctests failed
sage -t  --long -force_lib devel/sage/doc/de/tutorial/latex.rst # 27 doctests failed
sage -t  --long -force_lib devel/sage/doc/en/tutorial/latex.rst # 27 doctests failed
sage -t  --long -force_lib devel/sage/sage/matrix/matrix0.pyx # 1 doctests failed


The problem with sphinxify is easy to fix. Should we delete jsmath.py, or is it still needed for something?

The problems with the tutorial are a bit more involved, since (a) it explicitly discusses using JSMath and (b) I don't speak German.

I don't understand the matrix0.pyx problem at all, at least not yet.

### comment:75 in reply to: ↑ 74 Changed 9 years ago by kcrisman

The problems with the tutorial are a bit more involved, since (a) it explicitly discusses using JSMath and (b) I don't speak German.

There are a number of Sage folks who do, though, so hopefully the second one won't be a problem. Once you fix the English one let us know.

I wonder why the other tutorial versions don't cause problems? In particular, there is a tutorial in Russian and one in French in 5.1.beta3 that you don't mention as having caused problems - maybe they're based on different versions of the English tutorial.

### comment:76 Changed 9 years ago by jhpalmieri

• Description modified (diff)
• Work issues set to fix sagenb

Here is a patch fixing the doctests in the Sage library. For the English tutorial, I did a little bit more than a search-and-replace, changing "JSMath" to "MathJax". For the German tutorial, that's essentially all I did.

sagenb also needs fixing, and I don't have the energy to do this right now. If someone else wants to, that would be great. Here's what I think should be done: delete notebook/jsmath.py, and patch misc/sphinxify.py:

• ## sagenb/misc/sphinxify.py

diff --git a/sagenb/misc/sphinxify.py b/sagenb/misc/sphinxify.py
index 837b40a..85c9f4d 100644
 a def sphinxify(docstring, format='html'): sage: sphinxify('**Testing**\nmonospace') '\n
Testing\n\n\n\n
\n    \n

x=y

\n\n\n' '\n
\n    \n

\$$x=y\$$

\n\n\n
sage: sphinxify('x=y', format='text') 'x=y\n' sage: sphinxify(':math:x=y', format='text')
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