Opened 3 years ago

Last modified 3 years ago

#20690 closed enhancement

Live documentation in Jupyter using Thebe — at Version 28

Reported by: nthiery Owned by:
Priority: major Milestone: sage-7.4
Component: documentation Keywords: days77, jupyter, thebe, notebook, sd75
Cc: vdelecroix, vbraun, rbeezer, slelievre, tmonteil Merged in:
Authors: Florent Cayré, Nicolas M. Thiéry Reviewers: Vincent Delecroix, Thierry Monteil
Report Upstream: N/A Work issues:
Branch: u/tmonteil/thebe-20690 (Commits) Commit: ef6657d0dbd9c0008c5dae50bf18e47bee6f2e6c
Dependencies: #21309 Stopgaps:

Description (last modified by tmonteil)

Thebe is a Jupyter javascript plugin for static sites that allows for rendering selected divs of the HTML as live cells connected to a Jupyter server:

https://oreillymedia.github.io/thebe/

The goal of this ticket is to use this technology to implement live documentation in the Jupyter notebook as we had in the legacy Sage notebook.

Kudos to Rob Beezer for pointing us to Thebe in his presentation of MathBookXML at Sage Days 77.

Steps:

  • [X] Configure Sphinx to add the Thebe javascript library in the static page
  • [X] Configure Sphinx to add a small header to our html page with:
    • [X] Inclusion of the Thebe javascript
    • [X] Thebe configuration: which divs to make live

Currently, we include all <pre> tags that contain the "sage:" prompt TODO: shall we change to <pre> tags that start with the "sage:" prompt ?

to do?

  • [X] Only activate Thebe if the page is served by a Jupyter instance

Currently we check that the protocol is http

  • [X] A button to activate live cells
  • [X] Configure the Jupyter notebook in Sage to somehow provide the

server configuration to Thebe (not needed in fact)

  • [X] Preparse or customize/configure Thebe to support Sage's doctest syntax:
    • [X] Strip out the "sage: " prompts and "....:" and "... " continuation prompts
    • [X] Strip out the outputs

Bonus: show the included outputs below the cell until the new output is computed

What's been done here is: output is show until the "activate" button is clicked.

  • [X] Support doctests with several commands by spliting into several cells
  • [X] Ship thebe.js from a dedicated spkg (#21309).

Follow-up ticket for possible improvement: #20893. This ticket solves #17269.

Change History (28)

comment:1 Changed 3 years ago by nthiery

  • Branch set to u/nthiery/live_documentation_in_jupyter_using_thebe

comment:2 Changed 3 years ago by nthiery

  • Branch changed from u/nthiery/live_documentation_in_jupyter_using_thebe to public/live_documentation_in_jupyter_using_thebe-20690

comment:3 Changed 3 years ago by nthiery

  • Commit set to 19f31f8567ac77094d2ee483e7adf9d6963a8dd7
  • Description modified (diff)
  • Summary changed from Live documentation in Jupyter using thebe to Live documentation in Jupyter using Thebe

New commits:

19f31f820690: added some examples of sage code in a fast-to-compile document. DONT MERGE IN SAGE

comment:4 Changed 3 years ago by nthiery

  • Branch changed from public/live_documentation_in_jupyter_using_thebe-20690 to public/live_documentation_in_jupyter_using_thebe-20690-experimental

comment:5 Changed 3 years ago by nthiery

  • Branch changed from public/live_documentation_in_jupyter_using_thebe-20690-experimental to public/live_documentation_in_jupyter_using_thebe-20690

The current branch is not to be merged in Sage, as it contains some edits in the Sage's faq that are just here for quick testing (compiling the faq is fast!).

comment:6 Changed 3 years ago by nthiery

  • Branch changed from public/live_documentation_in_jupyter_using_thebe-20690 to public/live_documentation_in_jupyter_using_thebe-20690-experimental

comment:7 Changed 3 years ago by nthiery

  • Description modified (diff)

comment:8 Changed 3 years ago by nthiery

  • Description modified (diff)

comment:9 Changed 3 years ago by git

  • Commit changed from 19f31f8567ac77094d2ee483e7adf9d6963a8dd7 to 5016cd83634381cd6be0f42154ea759744a7b272

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

5016cd820690: First implementation of a live documentation in Jupyter using Thebe

comment:10 Changed 3 years ago by nthiery

  • Description modified (diff)

comment:11 Changed 3 years ago by nthiery

  • Cc vdelecroix vbraun added

comment:12 Changed 3 years ago by nthiery

  • Cc rbeezer added
  • Description modified (diff)
  • Keywords days77 jupyter thebe notebook added

comment:13 Changed 3 years ago by nthiery

  • Description modified (diff)

comment:14 Changed 3 years ago by git

  • Commit changed from 5016cd83634381cd6be0f42154ea759744a7b272 to 07035fd4b6db42b55131c19026f274e4e624f33b

Branch pushed to git repo; I updated commit sha1. New commits:

32c9e6420690: Only show the activate button when there are cells to be activated
d6aaed220690: Disable the activate button once clicked
b5e95e420690: Factor out a thebe-sage setup function before complexifying it for upcoming functionalities
07035fd20690: On live doc activation, hide expected results and add a Run button before them

comment:15 Changed 3 years ago by vdelecroix

Everything seems to work (nice!). Some naive questions from a user point of view:

  • would it be possible to remove the "sage: " string in the cells? It would be convenient since it perturb the editor. It would even be worse with the continuation "....:" since these are not ignored by the sage preparser...

Less importantly:

  • why did you decide to have this "Run" and "Run Again" buttons? These do not exist in the standard Jupyter notebook. Would it be possible to simply remove them?
  • the cells are properly executed when pressing "Shift + Enter" but, contrarily to the case of the notebook, after pressing "Shift + Enter" the focus is kept in the same cell. Not sure that it is desirable to move the focus (since the next cell might be very far).

comment:16 Changed 3 years ago by vdelecroix

  • Description modified (diff)

comment:17 Changed 3 years ago by vdelecroix

  • Description modified (diff)
  • Reviewers set to Vincent Delecroix

comment:18 Changed 3 years ago by vdelecroix

I moved the part related to improvements to #20893. I definitely think that we should try to have something ready for the next beta release. And it is in good shape!

comment:19 Changed 3 years ago by fcayre

  • Branch changed from public/live_documentation_in_jupyter_using_thebe-20690-experimental to u/fcayre/thebe-20690
  • Commit changed from 07035fd4b6db42b55131c19026f274e4e624f33b to 5f9fc0e62bfe1c37f6a3419e9170ef0159f615f8
  • Description modified (diff)

comment:20 Changed 3 years ago by vdelecroix

  • Status changed from new to needs_review

As discussed with Florent (by mail) the first step should be ready (see #20893 for next steps). I am going through the changes and testing this version.

comment:21 follow-up: Changed 3 years ago by slelievre

  • Cc slelievre tmonteil added
  • Description modified (diff)

This ticket solves #17269.

comment:22 in reply to: ↑ 21 Changed 3 years ago by tmonteil

Replying to slelievre:

This ticket solves #17269.

Thanks for letting me know about the current ticket. This is indeed a blocker to leave sage notebook for good (this, and the fact that jupyter doen not handle .rst files as worksheets, let me continue to use the former during tutorials).

comment:23 Changed 3 years ago by vdelecroix

  • Milestone changed from sage-7.3 to sage-7.4
  • Status changed from needs_review to needs_work

With the current version, the button activate does not appear in all situation. It does for the reference manual but not for Help -> Thematic Tutorials -> Tutorial: Sage Introductory Programming (PREP).

comment:24 Changed 3 years ago by tmonteil

  • Reviewers changed from Vincent Delecroix to Vincent Delecroix, Thierry Monteil

thebe.js should not be raw copied to Sage source code. Instead, it should be installed as a Sage package, so that it is easier to keep it up-to-date. Typically, the script you copied is adapted to Jupyter 4.0.5.

comment:25 follow-up: Changed 3 years ago by nthiery

Hi Thierry,

Thanks for looking at this!

It was Volker's suggestion to just raw copy thebe.js in the sources.

One part of the rationale is simplicity. The other is that, once jupyterlab will have matured out, thebe.js is likely to become a thin layer on top of it, if not just a part of it. So it's not that crucial to take the efforts of a super clean long term solution.

But I don't have a strong opinion either.

Last edited 3 years ago by nthiery (previous) (diff)

comment:26 in reply to: ↑ 25 Changed 3 years ago by tmonteil

Having a dedicated spkg is not such a huge effort, and there are tons of temporary things in Sage that wait to be cleaned for years, let us not make things worse when we can avoid it. Let me just give a try.

Last edited 3 years ago by tmonteil (previous) (diff)

comment:27 Changed 3 years ago by tmonteil

  • Branch changed from u/fcayre/thebe-20690 to u/tmonteil/thebe-20690

comment:28 Changed 3 years ago by tmonteil

  • Commit changed from 5f9fc0e62bfe1c37f6a3419e9170ef0159f615f8 to ef6657d0dbd9c0008c5dae50bf18e47bee6f2e6c
  • Dependencies set to #21309
  • Description modified (diff)

I wrote #21309 to package thebe.js (needs review) and let the current branch depend on that one (i.e. i replaced the hardcoded code to a symlink to the file provided by the spkg). It works well on my machine.


New commits:

7d4fe86#21309 : package thebejs.
f508730Merge branch 'u/fcayre/thebe-20690' of trac.sagemath.org:sage into t/21309/package_thebe_js
ef6657d#20690 : use thebe.js from the thebejs package instead of the hardcoded one.
Note: See TracTickets for help on using tickets.