Jupyter documentation fails for notebooks in subdirectories #19885

vbraun · 2016-01-13T21:07:20Z

Exactly the same as #19469, but for help links.

Steps to reproduce:

Start sage --notebook=jupyter
In the Jupyter file browser, select New -> Folder
Click on the newly-created "Untitled Folder" (name does not matter)
Create a new Sage kernel notebook in this subfolder
Click on Help -> Sage Documentation

Opened URL is http://localhost:8888/notebooks/Untitled%20Folder/kernelspecs/sagemath/doc/index.html

Correct URL would be http://localhost:8888/kernelspecs/sagemath/doc/reference/index.html

Upstream: Fixed upstream, but not in a stable release.

CC: @EmmanuelCharpentier

Component: notebook

Author: Volker Braun

Branch/Commit: 65cd4d2

Reviewer: Emmanuel Charpentier

Issue created by migration from https://trac.sagemath.org/ticket/19885

The text was updated successfully, but these errors were encountered:

jdemeyer · 2016-01-13T21:45:29Z

comment:1

This should be trivial to fix for somebody who knows javascript (i.e. not me). That javascript should determine whether the help link is relative and prepend base_url if it is.

vbraun · 2016-01-13T23:00:54Z

comment:2

But the SageKernel.help_links doesn't have a place to add javascript. Sure we could shove it somewhere into the notebook but its somewhat ugly.

An alternative might be to add a Jupyter notebook extension for Sage static files, as it is also useful elsewhere (e.g. mathjax).

vbraun · 2016-01-14T00:11:39Z

comment:3

On second thought that still doesn't give the kernel knowledge about the url prefix...

vbraun · 2016-01-14T00:37:43Z

comment:4

And there is currently no good way of installing them without mucking with user configuration: jupyter/notebook#878

EmmanuelCharpentier · 2016-01-14T08:34:55Z

comment:5

Please note, that, with Sage 7.0rc0 :

I cannot create a subdirectory (I see a message such as [I 08:41:36.043 NotebookApp] Creating new directory in (yes, the subdirectory is created ... nowhere !)
Starting sage -n jupyter in my home directory, creating a new sheeet : I can access the Reference manual.
Navigating to a subdirectory, creating a new worksheet : 404...
Opening an existing worksheet : 404...
navigating back to my home directory and opening an existing worksheet : access to the Reference Manual works.

The obvious workaround is to start a notebook server in each work directory. Not inconsiderable loss of functionality, but tolerable.

vbraun · 2016-01-14T23:42:51Z

comment:6

You need to have write permissions in the original directory... which one is it?

vbraun · 2016-01-15T00:46:10Z

comment:7

Upstream PR at jupyter/notebook#958

EmmanuelCharpentier · 2016-01-15T06:34:27Z

comment:8

Replying to @vbraun:

You need to have write permissions in the original directory... which one is it?

I suppose that "the original directory" is the directory from where i launched "sage -n jupyter". It was my home directory.

vbraun · 2016-01-15T09:27:41Z

Branch: u/vbraun/jupyter_documentation_fails_for_notebooks_in_subdirectories

vbraun · 2016-01-15T09:29:03Z

New commits:

`92e10ba`	`Fix help_links to work with base_url and notebooks in subdirectories`

vbraun · 2016-01-15T09:29:03Z

Commit: 92e10ba

vbraun · 2016-01-15T09:29:03Z

Author: Volker Braun

EmmanuelCharpentier · 2016-01-15T10:56:26Z

comment:11

On a small (notebook) machine, running 7.0rc1+Trac#19885 :

Doesn't work for me : starting from my home directory and navigating to ~/Boulot/Bayes/Strat1/, opening an existing worksheet and trying to access the Sage Reference manual gives me a 404. The browser tries to access http://localhost:8888/notebooks/Boulot/Bayes/Strat1/kernelspecs/sagemath/doc/faq/index.html.

Note : I just typed "make" (i. e. didn't rebuild the docs, which need more than 30 minutes on this small machine). Does this influence the result ?

needs_work

sagetrac-git · 2016-01-15T10:58:32Z

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

`9c5cee2`	`Update patchlevel`

sagetrac-git · 2016-01-15T10:58:32Z

Changed commit from 92e10ba to 9c5cee2

vbraun · 2016-01-15T10:58:59Z

comment:13

Try again

EmmanuelCharpentier · 2016-01-15T11:16:33Z

comment:14

Works now.

I can't reasonably testlong on this notebook (takes 5-8 hours usually...). I'll do that tonight on a "reasonable" machine.

Thank you very much !

EmmanuelCharpentier · 2016-01-15T20:33:32Z

comment:15

ptestlong has one failure :

sage -t --long --warn-long 74.3 src/sage/repl/ipython_kernel/kernel.py  # 1 doctest failed

However, it's probably a booboo :

charpent@asus16-ec:/usr/local/sage-7.0$ sage -t --long --warn-long 74.3 src/sage/repl/ipython_kernel/kernel.py
Running doctests with ID 2016-01-15-21-29-51-29b6b7be.
Git branch: t/19885/jupyter_documentation_fails_for_notebooks_in_subdirectories
Using --optional=database_gap,dot2tex,mpir,python2,sage,sage_mode,threejs
Doctesting 1 file.
sage -t --long --warn-long 74.3 src/sage/repl/ipython_kernel/kernel.py
**********************************************************************
File "src/sage/repl/ipython_kernel/kernel.py", line 88, in sage.repl.ipython_kernel.kernel.SageKernel.help_links
Failed example:
    sk.help_links
Expected:
    [{'text': 'Sage Documentation',
      'url': '../kernelspecs/sagemath/doc/index.html'},
     ...]
Got:
    [{'text': 'Sage Documentation', 'url': 'kernelspecs/sagemath/doc/index.html'},
     {'text': 'Sage Tutorial',
      'url': 'kernelspecs/sagemath/doc/tutorial/index.html'},
     {'text': 'Thematic Tutorials',
      'url': 'kernelspecs/sagemath/doc/thematic_tutorials/index.html'},
     {'text': 'FAQs', 'url': 'kernelspecs/sagemath/doc/faq/index.html'},
     {'text': 'PREP Tutorials', 'url': 'kernelspecs/sagemath/doc/prep/index.html'},
     {'text': 'Sage Reference',
      'url': 'kernelspecs/sagemath/doc/reference/index.html'},
     {'text': "Developer's Guide",
      'url': 'kernelspecs/sagemath/doc/developer/index.html'},
     {'text': 'Python', 'url': 'http://docs.python.org/2.7'},
     {'text': 'IPython', 'url': 'http://ipython.org/documentation.html'},
     {'text': 'Singular',
      'url': 'http://www.singular.uni-kl.de/Manual/latest/index.htm'},
     {'text': 'GAP', 'url': 'http://gap-system.org/Manuals/doc/ref/chap0.html'},
     {'text': 'NumPy', 'url': 'http://docs.scipy.org/doc/numpy/reference/'},
     {'text': 'SciPy', 'url': 'http://docs.scipy.org/doc/scipy/reference/'},
     {'text': 'SymPy', 'url': 'http://docs.sympy.org/latest/index.html'},
     {'text': 'Matplotlib', 'url': 'http://matplotlib.org/contents.html'},
     {'text': 'Markdown',
      'url': 'http://help.github.com/articles/github-flavored-markdown'}]
**********************************************************************
1 item had failures:
   1 of   4 in sage.repl.ipython_kernel.kernel.SageKernel.help_links
    [8 tests, 1 failure, 0.06 s]
----------------------------------------------------------------------
sage -t --long --warn-long 74.3 src/sage/repl/ipython_kernel/kernel.py  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 0.1 seconds
    cpu time: 0.1 seconds
    cumulative wall time: 0.1 seconds

==> needs_work

sagetrac-git · 2016-01-15T22:16:54Z

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

`65cd4d2`	`Fix documentation`

sagetrac-git · 2016-01-15T22:16:54Z

Changed commit from 9c5cee2 to 65cd4d2

vbraun · 2016-01-15T22:46:08Z

comment:17

fixed

vbraun · 2016-01-15T23:50:54Z

Upstream: Fixed upstream, but not in a stable release.

EmmanuelCharpentier · 2016-01-15T23:52:32Z

Reviewer: Emmanuel Charpentier

EmmanuelCharpentier · 2016-01-15T23:52:32Z

Changed upstream from Fixed upstream, but not in a stable release. to none

EmmanuelCharpentier · 2016-01-15T23:52:32Z

comment:19

Passes ptestlong with no errors
Works as advertised

==>positive_review

vbraun · 2016-01-15T23:54:40Z

Upstream: Fixed upstream, but not in a stable release.

vbraun · 2016-01-20T10:19:44Z

Changed branch from u/vbraun/jupyter_documentation_fails_for_notebooks_in_subdirectories to 65cd4d2

vbraun added this to the sage-7.0 milestone Jan 13, 2016

vbraun added c: user interface labels Jan 13, 2016

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EmmanuelCharpentier mannequin added s: needs work and removed s: needs review labels Jan 15, 2016

vbraun added s: needs review and removed s: needs work labels Jan 15, 2016

EmmanuelCharpentier mannequin added s: needs work and removed s: needs review labels Jan 15, 2016

vbraun added s: needs review and removed s: needs work labels Jan 15, 2016

EmmanuelCharpentier mannequin added s: positive review and removed s: needs review labels Jan 15, 2016

vbraun removed the s: positive review label Jan 20, 2016

vbraun closed this as completed in 7841f42 Jan 20, 2016

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Jupyter documentation fails for notebooks in subdirectories #19885

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Jupyter documentation fails for notebooks in subdirectories #19885

Jupyter documentation fails for notebooks in subdirectories #19885

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