#20690 closed enhancement (fixed)
Live documentation in Jupyter using Thebe
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: | 8c8e731 (Commits, GitHub, GitLab) | Commit: | |
Dependencies: | #21309 | Stopgaps: |
Description (last modified by )
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:
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?
TODO:
- [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 from a dedicated spkg (#21309).
This ticket solves #17269. Follow-up ticket for possible improvements: #20893.
Change History (55)
comment:1 Changed 5 years ago by
- Branch set to u/nthiery/live_documentation_in_jupyter_using_thebe
comment:2 Changed 5 years ago by
- Branch changed from u/nthiery/live_documentation_in_jupyter_using_thebe to public/live_documentation_in_jupyter_using_thebe-20690
comment:3 Changed 5 years ago by
- Commit set to 19f31f8567ac77094d2ee483e7adf9d6963a8dd7
- Description modified (diff)
- Summary changed from Live documentation in Jupyter using thebe to Live documentation in Jupyter using Thebe
comment:4 Changed 5 years ago by
- Branch changed from public/live_documentation_in_jupyter_using_thebe-20690 to public/live_documentation_in_jupyter_using_thebe-20690-experimental
comment:5 Changed 5 years ago by
- 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 5 years ago by
- Branch changed from public/live_documentation_in_jupyter_using_thebe-20690 to public/live_documentation_in_jupyter_using_thebe-20690-experimental
comment:7 Changed 5 years ago by
- Description modified (diff)
comment:8 Changed 5 years ago by
- Description modified (diff)
comment:9 Changed 5 years ago by
- Commit changed from 19f31f8567ac77094d2ee483e7adf9d6963a8dd7 to 5016cd83634381cd6be0f42154ea759744a7b272
Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:
5016cd8 | 20690: First implementation of a live documentation in Jupyter using Thebe
|
comment:10 Changed 5 years ago by
- Description modified (diff)
comment:11 Changed 5 years ago by
- Cc vdelecroix vbraun added
comment:12 Changed 5 years ago by
- Cc rbeezer added
- Description modified (diff)
- Keywords days77 jupyter thebe notebook added
comment:13 Changed 5 years ago by
- Description modified (diff)
comment:14 Changed 5 years ago by
- Commit changed from 5016cd83634381cd6be0f42154ea759744a7b272 to 07035fd4b6db42b55131c19026f274e4e624f33b
Branch pushed to git repo; I updated commit sha1. New commits:
32c9e64 | 20690: Only show the activate button when there are cells to be activated
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d6aaed2 | 20690: Disable the activate button once clicked
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b5e95e4 | 20690: Factor out a thebe-sage setup function before complexifying it for upcoming functionalities
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07035fd | 20690: On live doc activation, hide expected results and add a Run button before them
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comment:15 Changed 5 years ago by
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 5 years ago by
- Description modified (diff)
comment:17 Changed 5 years ago by
- Description modified (diff)
- Reviewers set to Vincent Delecroix
comment:18 Changed 5 years ago by
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 5 years ago by
- 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 5 years ago by
- 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: ↓ 22 Changed 5 years ago by
- Cc slelievre tmonteil added
- Description modified (diff)
This ticket solves #17269.
comment:22 in reply to: ↑ 21 Changed 5 years ago by
comment:23 follow-up: ↓ 29 Changed 5 years ago by
- 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 5 years ago by
- 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: ↓ 26 Changed 5 years ago by
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.
comment:26 in reply to: ↑ 25 Changed 5 years ago by
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.
comment:27 Changed 5 years ago by
- Branch changed from u/fcayre/thebe-20690 to u/tmonteil/thebe-20690
comment:28 follow-up: ↓ 30 Changed 5 years ago by
- 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.
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f508730 | Merge branch 'u/fcayre/thebe-20690' of trac.sagemath.org:sage into t/21309/package_thebe_js
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ef6657d | #20690 : use thebe.js from the thebejs package instead of the hardcoded one.
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comment:29 in reply to: ↑ 23 Changed 5 years ago by
- Status changed from needs_work to needs_review
Replying to vdelecroix:
With the current version, the button
activate
does not appear in all situation. It does for the reference manual but not forHelp -> Thematic Tutorials -> Tutorial: Sage Introductory Programming (PREP)
.
I double checked this. Actually, the button does not appear when the pages do not have cells (the first pages of the PREP are just pictures, no computations), but it does otherwise (see e.g. the "Calculus 1" page), so it is somehow a good feature.
comment:30 in reply to: ↑ 28 Changed 5 years ago by
Replying to tmonteil:
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.
Ça c'est gentil!
For the record, I had Florent Cayré on the phone this morning. He started looking at this, but somehow he has a technical issue posting messages on trac which we did not manage to debug. Anyway, we should be able to review this shortly (e.g. tomorrow during the Sage Days).
comment:31 Changed 5 years ago by
- Keywords sd75 added
Great ! (i just arrived at Cernay, barbecue tonight!)
comment:32 Changed 5 years ago by
- Branch changed from u/tmonteil/thebe-20690 to u/nthiery/thebe-20690
comment:33 Changed 5 years ago by
- Commit changed from ef6657d0dbd9c0008c5dae50bf18e47bee6f2e6c to 427875361ce7799bcce2b06641ba8624184b42c9
Branch pushed to git repo; I updated commit sha1. New commits:
4278753 | 20690: Added comment about Thebe and Sage's thebejs package
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comment:34 Changed 5 years ago by
- Description modified (diff)
(Just editing ticket description, fixing formatting.)
comment:35 follow-up: ↓ 38 Changed 5 years ago by
Hi Vincent, Thierry, Besides merging the latest #21309 when it's polished, do you consider this as ready to go? It would be nice to be done with this! Thanks,
comment:36 Changed 5 years ago by
- Branch changed from u/nthiery/thebe-20690 to u/tmonteil/thebe-20690
comment:37 Changed 5 years ago by
- Commit changed from 427875361ce7799bcce2b06641ba8624184b42c9 to 11720b4c7f8bfdfb06f678c02a677754e7870553
I changed the symlink from local/share/thebejs/thebe.js
to local/share/thebe/thebe.js
according to the renaming done in #21309. Since the two branches were completely entangled (lot of merges), i went back to the last Florent's commit, fixed the symlink and added (and updated) Nicola's comment in thebe-sage.js
header. Now the two branches are completely independant, apart from the very last merge.
If you plan to modify something in the current ticket or in #21309, please undo the last merge before, or it will start to knit again.
New commits:
e4768df | #20690 : use thebe.js from the thebe package instead of the hardcoded one.
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7199979 | #20690 : report updated version of Nicola's change in the disentangled branch.
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520cdd0 | #21309 : thebejs -> thebe ; use hash in pkg name ; link to trac URL.
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11720b4 | Merge branch 't/21309/package_thebe_js' into t/20690/thebe-20690
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comment:38 in reply to: ↑ 35 Changed 5 years ago by
Replying to nthiery:
Hi Vincent, Thierry, Besides merging the latest #21309 when it's polished, do you consider this as ready to go? It would be nice to be done with this! Thanks,
I did not inspect thebe-sage.js
as i would have done for Python files. But its behaviour corresponds to the claimed feature and the code seem not malicious. So i guess it will be OK for me once the dependencies will be satisfied.
comment:39 Changed 5 years ago by
Thanks Thierry for the final version of #21309 (Jeroen is double checking it right now) and for cleaning the history.
I agree that we are on a thin line here since we don't have strong review standards set for js files like this one. For example we are missing tests! However writing such tests would take some infrastructure; we should discuss how to setup such infrastructure with the Jupyter people at some point, but for now I guess that's ok.
Vincent, any further comment?
Cheers,
Nicolas
comment:40 follow-up: ↓ 43 Changed 5 years ago by
- Status changed from needs_review to needs_work
I have a doubt: to avoid race condition, i guess we should add thebe to the doc build dependencies.
comment:41 Changed 5 years ago by
- Commit changed from 11720b4c7f8bfdfb06f678c02a677754e7870553 to 22ae6378d820d7ad644c452c15ba335c27b1a6ab
comment:42 Changed 5 years ago by
- Commit changed from 22ae6378d820d7ad644c452c15ba335c27b1a6ab to 8c8e731a11790c135c906dbdf00dffd9fe616a9a
Branch pushed to git repo; I updated commit sha1. New commits:
7d4fe86 | #21309 : package thebejs.
|
28346f6 | 21309: added a brief line stating why Sage uses thebe
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520cdd0 | #21309 : thebejs -> thebe ; use hash in pkg name ; link to trac URL.
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8c8e731 | Merge branch 't/21309/package_thebe_js' into t/20690/thebe-20690
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comment:43 in reply to: ↑ 40 ; follow-up: ↓ 44 Changed 5 years ago by
Replying to tmonteil:
I have a doubt: to avoid race condition, i guess we should add thebe to the doc build dependencies.
For this, i had to merge with sage.7.3 because the exact same line in build/make/deps
changed there. Let us test the build like this (it might take some time). Again, if you plan to do some modifications, do not forget to undo the very last merge (with #21309) before.
comment:44 in reply to: ↑ 43 Changed 5 years ago by
Replying to tmonteil:
Replying to tmonteil:
I have a doubt: to avoid race condition, i guess we should add thebe to the doc build dependencies.
For this, i had to merge with sage.7.3 because the exact same line in
build/make/deps
changed there. Let us test the build like this (it might take some time).
Ok, thanks!
Again, if you plan to do some modifications, do not forget to undo the very last merge (with #21309) before.
We discussed this with Jeroen this morning. Unless Vincent has a specific requestion, we don't plan for further modifications.
comment:45 Changed 5 years ago by
(good for me)
comment:46 Changed 5 years ago by
- Status changed from needs_work to positive_review
comment:47 Changed 5 years ago by
I don't want to remove the positive review but I would like some info about diff --git a/src/doc/common/themes/sage/static/thebe.js
which reads
../../../../../../local/share/thebe/thebe.js
Would there be a better way to refer to the thebe.js
file installed by the thebe
package? The above assume a particular sage install. I don't usually let people get away with putting /local/
in anything these days as it is bad for stuff like sage-on-gentoo and more broadly sage-on-distro.
comment:48 Changed 5 years ago by
I have no idea on how to do that. This kind of symlink already appears for mathjax
, but the symlink is done when sagenb is installed. Unfortunately, there is no sage_documentation
package where we could add a spkg-install
script to install the symlink at build time. I you have an idea to improve this situation, it would be nice to implement it here and for mathjax as well.
comment:49 Changed 5 years ago by
I have no solution right now. I will have to find a way to live with it. I'll come up with something, I usually do in the end. It doesn't always make sense in vanilla sage unfortunately.
comment:50 Changed 5 years ago by
- Branch changed from u/tmonteil/thebe-20690 to 8c8e731a11790c135c906dbdf00dffd9fe616a9a
- Resolution set to fixed
- Status changed from positive_review to closed
comment:51 Changed 5 years ago by
- Commit 8c8e731a11790c135c906dbdf00dffd9fe616a9a deleted
Adding a symbolic link from the sources to some installation directory really makes no sense, especially because it is hardcoded. Having it installed by the thebe
package would at least make slightly more sense. Of course, ideally we would just use thebe.js
from the installation directory.
comment:52 Changed 5 years ago by
See #21527 for a follow-up on the symbolic link issue.
comment:53 Changed 5 years ago by
Here is some feedback after real-life testing. I am currently teaching for a 3-week Sage tutorial, and there is a workflow issue, somehow thebe.js
miss the main point of the sagenb live documentation.
On sagenb notebook, say the students work on some thematic tutorial, they do some tests, copy some lecturer's examples and want to keep their changes. What they can do is to click on File
(top left) and then Copy worksheet
so that the live documentation becomes a true sagenb worksheet they can save to come back on it later.
In the current case, we can do some tests and modifications (which is great), but all the work is lost when we close the webpage. We should have a button to export the current state into a (possibly degradated, we do not really care about the subtle html structure) .ipynb
file that can then be saved.
comment:54 Changed 5 years ago by
Thanks Thierry for the feedback!
Yes, this is a very desirable feature, which we had already listed on #20893:
- [ ] Add support in Thebe for basic export to Jupyter notebooks. A quality loss (in particular in terms of the hierarchical structure) is acceptable.
Do you mind merging this item with the new one you added there?
comment:55 Changed 4 years ago by
While preparing the report for OpenDreamKit?, I just noticed that this is completely broken: #22458
New commits:
20690: added some examples of sage code in a fast-to-compile document. DONT MERGE IN SAGE