sagemath_doc_html: Use jupyter-sphinx for 3D graphics #33507

mkoeppe · 2022-03-15T20:50:22Z

We use jupyter-sphinx

https://jupyter-sphinx.readthedocs.io/en/latest/

to facilitate live sage documentation based on jupyter and Thebe.

For documentation authors, new directives are available:

.. ONLY:: pdf

.. JUPYTER-EXECUTE::

in addition to

.. ONLY:: html

See the branch for examples.

Related tickets: #31027

Depends on #33529

CC: @kwankyu @jhpalmieri @nthiery @egourgoulhon @dimpase

Component: documentation

Author: Kwankyu Lee, Matthias Koeppe

Branch: 72c8378

Reviewer: Matthias Koeppe, Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/33507

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

kwankyu · 2022-03-16T03:58:33Z

comment:2

It uses nbsphinx: https://nbsphinx.readthedocs.io/en/0.8.8/

nbsphinx allows including jupyter notebooks in toctrees. It seems that we cannot include a single cell of a jupyter notebook as a part of our documentation, which I guess is what we want.

kwankyu · 2022-03-16T05:05:54Z

Branch: public/33507

sagetrac-git · 2022-03-16T05:06:23Z

Commit: 1b7e46b

sagetrac-git · 2022-03-16T05:06:23Z

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

`1b7e46b`	`Experiments with jupyter-spinx`

sagetrac-git · 2022-03-16T05:08:40Z

Changed commit from 1b7e46b to 58f1338

sagetrac-git · 2022-03-16T05:08:40Z

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

`58f1338`	`Experiments with jupyter-sphinx`

kwankyu · 2022-03-16T05:10:33Z

comment:6

This tool

https://jupyter-sphinx.readthedocs.io/en/latest/

works well.

I uploaded a branch to experiment with the tool. First sage -pip install jupyter-sphinx.

mkoeppe · 2022-03-16T05:28:00Z

comment:7

This package would be easy to add, we already have all dependencies - https://github.com/jupyter/jupyter-sphinx/blob/master/setup.py#L30

sagetrac-git · 2022-03-16T05:33:20Z

Changed commit from 58f1338 to 8f8cd2b

sagetrac-git · 2022-03-16T05:33:20Z

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

`8f8cd2b`	`Activate Thebelab`

kwankyu · 2022-03-16T08:30:50Z

comment:10

We need a sagemath binder repo for Thebe to work.

sagetrac-git · 2022-03-17T04:53:13Z

Changed commit from 8f8cd2b to 84cec60

sagetrac-git · 2022-03-17T04:53:13Z

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

`84cec60`	`For pdf documentation`

kwankyu · 2022-03-17T05:07:38Z

comment:12

The last commit provides an example to provide live images to htmls and static images to pdfs.

kwankyu · 2022-03-17T05:18:05Z

comment:13

One annoying thing is that .. only:: latex works but .. only:: pdf doesn't.

sagetrac-git · 2022-03-17T05:22:00Z

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

`5f01f21`	`Forgotten images`

sagetrac-git · 2022-03-17T05:22:00Z

Changed commit from 84cec60 to 5f01f21

sagetrac-git · 2022-03-17T07:13:05Z

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

`73c8c37`	`build/pkgs/jupyter_sphinx: New`
`bbc276e`	`build/pkgs/sagemath_doc_html/dependencies: Add jupyter_sphinx`
`6133f9f`	`configure.ac (--disable-doc): Disable jupyter_sphinx too`

sagetrac-git · 2022-03-17T07:13:05Z

Changed commit from 5f01f21 to 6133f9f

mkoeppe · 2022-03-17T07:13:22Z

comment:16

Here's the package

nthiery · 2022-03-17T08:15:03Z

comment:17

Replying to @kwankyu:

We need a sagemath binder repo for Thebe to work.

I fixed 'Sage binder env' about a month ago:

https://github.com/sagemath/sage-binder-env

It now uses conda to install Sage which is more maintained than
Sage's docker image.

kwankyu · 2022-03-17T08:29:38Z

comment:18

Replying to @mkoeppe:

Here's the package

Thank you!

kwankyu · 2022-03-17T08:52:36Z

comment:19

Replying to @nthiery:

Replying to @kwankyu:

We need a sagemath binder repo for Thebe to work.

I fixed 'Sage binder env' about a month ago:

https://github.com/sagemath/sage-binder-env

It now uses conda to install Sage which is more maintained than
Sage's docker image.

I have no experience with Thebe. Jupyter-sphinx supports Thebe. But running an interact example cell through jupyter-sphinx only shows Waiting for kernel.... Is this supposed to take long? Would the interact work well once the kernel is up?

sagetrac-git · 2022-03-18T09:00:11Z

Changed commit from 6133f9f to 7641a72

mkoeppe · 2022-03-22T04:34:52Z

comment:74

Sorry, fixed now

dimpase · 2022-03-22T15:46:00Z

comment:75

I am still getting this docbuild error on macOS, even after git clean -fdx.

[sagemath_doc_html-none] [repl     ] executing interact
[sagemath_doc_html-none] [repl     ] /Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/jsonschema/validators.py:188: DeprecationWarning: Passing a schema to Validator.iter_errors is deprecated and will be removed in a future release. Call validator.evolve(schema=new_schema).iter_errors(...) instead.
[sagemath_doc_html-none] [repl     ]   warnings.warn(
[sagemath_doc_html-none] [repl     ] Extension error:
[sagemath_doc_html-none] [repl     ] Notebook execution failed (exception: [Errno 2] No such file or directory: '/Users/dima/sage/local/bin/sage')
...
[sagemath_doc_html-none] [plot3d   ] executing plot3d
[sagemath_doc_html-none] [plot3d   ] /Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/jsonschema/validators.py:188: DeprecationWarning: Passing a schema to Validator.iter_errors is deprecated and will be removed in a future release. Call validator.evolve(schema=new_schema).iter_errors(...) instead.
[sagemath_doc_html-none] [plot3d   ]   warnings.warn(
[sagemath_doc_html-none] [plot3d   ] Extension error:
[sagemath_doc_html-none] [plot3d   ] Notebook execution failed (exception: [Errno 2] No such file or directory: '/Users/dima/sage/local/bin/sage')
...
sagemath_doc_html-none] [reference] ... done (500 todos, 2546 index, 1665 citations, 2139 modules)
[sagemath_doc_html-none] [reference] WARNING: Unable to fetch /Users/dima/sage/local/share/doc/sage/doctrees/en/reference/plot3d/environment.pickle
[sagemath_doc_html-none] [reference] WARNING: Unable to fetch /Users/dima/sage/local/share/doc/sage/doctrees/en/reference/repl/environment.pickle
[sagemath_doc_html-none] [reference] preparing documents... skipping loading of indexes... done
[sagemath_doc_html-none] [reference] /Users/dima/sage/src/doc/en/reference/index.rst:17: WARNING: unknown document: repl/index
[sagemath_doc_html-none] [reference] /Users/dima/sage/src/doc/en/reference/index.rst:24: WARNING: unknown document: plot3d/index
[sagemath_doc_html-none] [reference] The inventory files are in local/share/doc/sage/inventory/en/reference.
[sagemath_doc_html-none] Error building the documentation.
[sagemath_doc_html-none] Traceback (most recent call last):
[sagemath_doc_html-none]   File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197, in _run_module_as_main
[sagemath_doc_html-none]     return _run_code(code, main_globals, None,
[sagemath_doc_html-none]   File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87, in _run_code
[sagemath_doc_html-none]     exec(code, run_globals)
[sagemath_doc_html-none]   File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/__main__.py", line 2, in <module>
[sagemath_doc_html-none]     main()
[sagemath_doc_html-none]   File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/__init__.py", line 1751, in main
[sagemath_doc_html-none]     builder()
[sagemath_doc_html-none]   File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/__init__.py", line 141, in f
[sagemath_doc_html-none]     runsphinx()
[sagemath_doc_html-none]   File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/sphinxbuild.py", line 326, in runsphinx
[sagemath_doc_html-none]     sys.stderr.raise_errors()
[sagemath_doc_html-none]   File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/sphinxbuild.py", line 262, in raise_errors
[sagemath_doc_html-none]     raise OSError(self._error)
[sagemath_doc_html-none] OSError: WARNING: Unable to fetch /Users/dima/sage/local/share/doc/sage/doctrees/en/reference/plot3d/environment.pickle 
[sagemath_doc_html-none] 
[sagemath_doc_html-none]     Note: incremental documentation builds sometimes cause spurious
[sagemath_doc_html-none]     error messages. To be certain that these are real errors, run
[sagemath_doc_html-none]     "make doc-clean doc-uninstall" first and try again.
[sagemath_doc_html-none] make[6]: *** [doc-inventory--reference_top] Error 1
[sagemath_doc_html-none] make[5]: *** [doc-inventory-reference] Error 2
make[4]: *** [sagemath_doc_html-SAGE_DOCS-no-deps] Error 2

something in these two modules wants to call '/Users/dima/sage/local/bin/sage' -
which is absent, naturally, and probably this leads to absent environment.pickle in plot3d.

I presume the message "Notebook execution failed" comes from jupyter-sphinx:
https://github.com/jupyter/jupyter-sphinx/blob/master/jupyter_sphinx/execute.py

dimpase · 2022-03-22T20:30:43Z

Changed reviewer from Matthias Koeppe, ... to Matthias Koeppe, Dima Pasechnik

dimpase · 2022-03-22T20:30:43Z

comment:76

after

ln -s /Users/dima/sage/sage /Users/dima/sage/local/bin/sage

the docbuild completes, but it's certainly a problem to be fixed that needs this workaround.

kwankyu · 2022-03-23T01:12:09Z

comment:77

Replying to @dimpase:

I am still getting this docbuild error on macOS, even after git clean -fdx.

[sagemath_doc_html-none] [repl     ] executing interact
[sagemath_doc_html-none] [repl     ] /Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/jsonschema/validators.py:188: DeprecationWarning: Passing a schema to Validator.iter_errors is deprecated and will be removed in a future release. Call validator.evolve(schema=new_schema).iter_errors(...) instead.
[sagemath_doc_html-none] [repl     ]   warnings.warn(
[sagemath_doc_html-none] [repl     ] Extension error:
[sagemath_doc_html-none] [repl     ] Notebook execution failed (exception: [Errno 2] No such file or directory: '/Users/dima/sage/local/bin/sage')

...

I presume the message "Notebook execution failed" comes from jupyter-sphinx:
https://github.com/jupyter/jupyter-sphinx/blob/master/jupyter_sphinx/execute.py

I am on macOS too. Do you have no problem in running sagemath kernel in jupyter from your sage installation?

dimpase · 2022-03-23T09:56:15Z

comment:78

If I remove the symlink as in comment:76 I get a jupyter kernel error

Traceback (most recent call last):
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/tornado/web.py", line 1704, in _execute
    result = await result
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/tasks.py", line 328, in __wakeup
    future.result()
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/tornado/gen.py", line 769, in run
    yielded = self.gen.throw(*exc_info)  # type: ignore
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/notebook/services/sessions/handlers.py", line 74, in post
    model = yield maybe_future(
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/tornado/gen.py", line 762, in run
    value = future.result()
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/tornado/gen.py", line 769, in run
    yielded = self.gen.throw(*exc_info)  # type: ignore
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/notebook/services/sessions/sessionmanager.py", line 98, in create_session
    kernel_id = yield self.start_kernel_for_session(session_id, path, name, type, kernel_name)
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/tornado/gen.py", line 762, in run
    value = future.result()
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/tornado/gen.py", line 769, in run
    yielded = self.gen.throw(*exc_info)  # type: ignore
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/notebook/services/sessions/sessionmanager.py", line 110, in start_kernel_for_session
    kernel_id = yield maybe_future(
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/tornado/gen.py", line 762, in run
    value = future.result()
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/futures.py", line 201, in result
    raise self._exception
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/tasks.py", line 256, in __step
    result = coro.send(None)
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/notebook/services/kernels/kernelmanager.py", line 176, in start_kernel
    kernel_id = await maybe_future(self.pinned_superclass.start_kernel(self, **kwargs))
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/jupyter_client/utils.py", line 26, in wrapped
    raise e
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/jupyter_client/utils.py", line 23, in wrapped
    return loop.run_until_complete(future)
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/nest_asyncio.py", line 81, in run_until_complete
    return f.result()
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/futures.py", line 201, in result
    raise self._exception
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/tasks.py", line 256, in __step
    result = coro.send(None)
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/jupyter_client/multikernelmanager.py", line 187, in _async_start_kernel
    starter = ensure_async(km.start_kernel(**kwargs))
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/jupyter_client/utils.py", line 26, in wrapped
    raise e
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/jupyter_client/utils.py", line 23, in wrapped
    return loop.run_until_complete(future)
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/nest_asyncio.py", line 81, in run_until_complete
    return f.result()
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/futures.py", line 201, in result
    raise self._exception
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/tasks.py", line 256, in __step
    result = coro.send(None)
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/jupyter_client/manager.py", line 362, in _async_start_kernel
    raise e
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/jupyter_client/manager.py", line 351, in _async_start_kernel
    await ensure_async(self._launch_kernel(kernel_cmd, **kw))
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/jupyter_client/utils.py", line 26, in wrapped
    raise e
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/jupyter_client/utils.py", line 23, in wrapped
    return loop.run_until_complete(future)
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/nest_asyncio.py", line 81, in run_until_complete
    return f.result()
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/futures.py", line 201, in result
    raise self._exception
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/tasks.py", line 256, in __step
    result = coro.send(None)
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/jupyter_client/manager.py", line 269, in _async_launch_kernel
    connection_info = await self.provisioner.launch_kernel(kernel_cmd, **kw)
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/jupyter_client/provisioning/local_provisioner.py", line 179, in launch_kernel
    self.process = launch_kernel(cmd, **scrubbed_kwargs)
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/jupyter_client/launcher.py", line 169, in launch_kernel
    raise ex
  File "/Users/dima/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/jupyter_client/launcher.py", line 157, in launch_kernel
    proc = Popen(cmd, **kwargs)
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 951, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 1821, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: '/Users/dima/sage/local/bin/sage'

With the link it works. It turns out I have outdated things in ~/Library/Jupyter, in particular sagemath/kernel.json with the obsolete path to sage (version 9.4.beta3).

Sorry for noise, it's OK.

mkoeppe · 2022-03-23T18:36:45Z

comment:79

Probably the docbuild should try to isolate from such user settings.

kwankyu · 2022-03-23T23:49:40Z

comment:80

Replying to @mkoeppe:

Probably the docbuild should try to isolate from such user settings.

I don't understand the precise mechanism. But it seems that jupyter-sphinx just runs a new jupyter notebook with sagemath kernel. Then there is nothing to do with the docbuild.

kwankyu · 2022-03-23T23:52:54Z

comment:81

Replying to @dimpase:

Thank you for review.

mkoeppe · 2022-03-24T00:16:54Z

comment:82

Replying to @kwankyu:

Replying to @mkoeppe:

Probably the docbuild should try to isolate from such user settings.

I don't understand the precise mechanism. But it seems that jupyter-sphinx just runs a new jupyter notebook with sagemath kernel. Then there is nothing to do with the docbuild.

But its happening during the docbuild according to the output that Dima shared

kwankyu · 2022-03-24T00:27:17Z

comment:83

Replying to @mkoeppe:

But its happening during the docbuild according to the output that Dima shared

The source of the problem may be in our jupyter kernel configuration in repl.ipython_kernel.kernel.

dimpase · 2022-03-24T08:55:55Z

comment:84

Replying to @mkoeppe:

Replying to @kwankyu:

Replying to @mkoeppe:

Probably the docbuild should try to isolate from such user settings.

I don't understand the precise mechanism. But it seems that jupyter-sphinx just runs a new jupyter notebook with sagemath kernel. Then there is nothing to do with the docbuild.

But its happening during the docbuild according to the output that Dima shared

I could reproduce this issue just by running ./sage -n. So this is indeed a "pure" notebook problem.

vbraun · 2022-04-02T10:52:54Z

Changed branch from public/33507 to 72c8378

mkoeppe · 2022-04-05T19:18:00Z

Changed commit from 72c8378 to none

mkoeppe · 2022-04-05T19:18:00Z

comment:86

The first bug report on this may have arrived: https://groups.google.com/g/sage-release/c/-0luW4DPEPs/m/1bST2lbcCAAJ

dimpase · 2022-04-05T20:59:07Z

comment:87

Replying to @mkoeppe:

The first bug report on this may have arrived: https://groups.google.com/g/sage-release/c/-0luW4DPEPs/m/1bST2lbcCAAJ

You mean

[sagemath_doc_html-none] [plot3d   ] Notebook execution failed (exception: [Errno 2] No such file or directory: '/home/furutaka/work/sage/sage-9.0-git-bld/local/bin/sage')

I suppose.

This looks identical to comment:75 - a stale Jupyter kernel somewhere.

mkoeppe · 2022-04-06T04:38:14Z

comment:88

Yes. I have opened #33650 for this.

mkoeppe added this to the sage-9.7 milestone Mar 15, 2022

mkoeppe added c: documentation labels Mar 15, 2022

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mkoeppe changed the title ~~sagemath_doc_html: Use pythreejs for 3D graphics~~ sagemath_doc_html: Use jupyter-sphinx for 3D graphics Mar 16, 2022

dimpase added s: needs work and removed s: needs review labels Mar 22, 2022

dimpase added s: positive review and removed s: needs work labels Mar 23, 2022

vbraun removed the s: positive review label Apr 2, 2022

vbraun closed this as completed in 08a9423 Apr 2, 2022

videlec mentioned this issue Jan 29, 2023

Meta-ticket: Improve live documentation in the Jupyter notebook #20893

Open

13 tasks

kwankyu mentioned this issue Mar 22, 2022

Provide live documentation support in Jupyter using Thebe #24593

Closed

mkoeppe mentioned this issue Mar 20, 2022

Make jmol optional #31027

Closed

kwankyu mentioned this issue Jan 29, 2023

Rework on live sage documentation #33320

Closed

vbraun mentioned this issue Mar 31, 2022

Modernize coercion for SpecialHyperellipticQuotientRing #33576

Closed

mkoeppe mentioned this issue May 4, 2022

Set JUPYTER_DATA_DIR etc. during docbuild #33650

Closed

kwankyu mentioned this issue Aug 25, 2023

Improve the part on LaTeX of the Sage Tutorial #36130

Closed

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sagemath_doc_html: Use jupyter-sphinx for 3D graphics #33507

sagemath_doc_html: Use jupyter-sphinx for 3D graphics #33507

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