DOC: Add interactive notebooks to pages in the "Usage Examples" section

[agriyakhetarpal]

Description

Tip

Those interested can try it at https://pywavelets--741.org.readthedocs.build/en/741/regression/index.html

The Usage Examples section, following #728 and as requested in #737 (comment), is rendered interactive through the changes in this PR through the use of jupyterlite-sphinx and Markdown-based notebooks that are executed by MyST-NB. Please read below for a granular overview of all of these details:

Which issue does this PR solve/reference?

Addresses a part of #706

Key changes made

1. All .rst based files under doc/source/regression converted to Markdown and reformatted as notebooks
2. Jupytext frontmatter added to all of the notebooks so that they can be executed at the time of building the documentation
3. Code cells that raise an error marked with cell-based tags
4. MyST-NB is configured in conf.py
5. NotebookLite directive used from jupyterlite-sphinx to run the notebooks under WASM in the same tab (and something like Add the option to open JupyterLite window in new tab jupyterlite/jupyterlite-sphinx#165 can be added for this directive as well)
6. A custom, minimal Sphinx extension added to execute the Jupytext CLI before the sources and toctrees are read, and to selectively ignore the .ipynb-based notebooks that get generated during the process in order to keep the documentation build warning-free. Generating them at build time is for the NotebookLite directive to be able to access them and load them, since the NotebookLite directive currently does not load .md files or notebook files in other formats.
   i. I imagine this will be helpful for DOC: stats: Convert sampling tutorial to MyST-md scipy/scipy#20303 as well where it is required to load the notebooks in an interactive manner under a specific folder. The notebooks are not executed by Jupytext at the time of conversion, and therefore, based on past experiments, it takes ~10 seconds to convert 30 or so notebooks.

Additional context

This is just a pilot run of how notebook-based examples can be configured for Sphinx-based documentation websites, so there are a few corner cases that I have noticed so far:

1. The styling of the NotebookLite directive can be improved because it takes way too much of the screen's space, perhaps through a user-provided option in conf.py just like how the TryExamples directive can be configured.
2. References to the API for a package (in this case, public classes and methods for PyWavelets) are not linked to when running the notebook in its inline frame, because the notebook is not running under Sphinx and cannot access Sphinx's generated HTML pages. This can be worked around via better writing the notebooks by exploring other ways to reference pages and sections from the API (say, by adding Markdown-based headings or links, etc.).

A brief to-do list

Besides the points mentioned above, smaller tasks can be looked into:

• Hide reST-based syntax (at least the irrelevant top parts of each page) using MyST
• Improve the styling in other ways
• Provide a button to download notebooks (both .md and .ipynb)

[agriyakhetarpal]

Quite strange. The documentation is building without any problems locally...

Edit: I can reproduce locally if I delete a few of the previously generated files – this is coming from jupyterlite-sphinx. I think that Read the Docs is using a cached version of the documentation and is not purging the files properly, or it isn't allowing the subprocess to execute at the config-inited builder hook.

Edit, again: they were failing because the jupytext command was failing silently and was not converting any notebooks. Removing the hardcoded path fixed it.

[rgommers]

Is this how it's done in scikit-learn as well? I don't mind if it's needed, but it seems easy to forget this kind of snippet in larger projects.

[agriyakhetarpal]

It should be possible to write another minimal Sphinx extension that can automate adding these admonitions and connect to the HTML builder at an event, similar to convert_md_to_ipynb. We don't need it here, however.

As for scikit-learn, I think they switched to the PyData Sphinx Theme as well in their recent release, and I feel like I like their solution much more than using an admonition – the JupyterLite/Binder/download buttons are very conveniently placed in the secondary sidebar. I can try to explore that and see how they did it, and whether we can do it conditionally for just these six pages through the theme's API.

[agriyakhetarpal]

Here's an example: https://scikit-learn.org/stable/auto_examples/classification/plot_classifier_comparison.html#sphx-glr-auto-examples-classification-plot-classifier-comparison-py

[agriyakhetarpal]

sphinx-gallery/sphinx-gallery#1312 is a non-minimal implementation, so we can't copy it that easily unless it were a Sphinx extension of its own.

[rgommers]

That looks really nice! I suggest then that we merge this as is, and explore the option of how to have support either in pydata-sphinx-theme or in a separate Sphinx extension for having a right sidebar like done in sphinx-gallery.

[agriyakhetarpal]

Thanks! I'm still figuring out a solution for preprocessing the notebooks to add the directives on-demand (it's not that easy to do without a Markdown parser that allows me to change things programmatically through a document's AST).

Another option I have explored is an extension that runs at the time of the source-read event, and I have it working partially. If this doesn't work, I can ping you to merge this – because the content looks complete and I guess we will have better things to spend more time on.

[rgommers]

Unresolving this to keep the discussion visible - this is an important topic I think. The sphinx-gallery example renders a lot nicer visually; the sidebar links are much cleaner and it shouldn't require as much boilerplate in the .md files to get those links. It looks like it'd be good for pydata-sphinx-theme or a separate extension to have something similar.

Not a show-stopper for PyWavelets, because there's only a handful of .md files. But I doubt that what we have here will work for a much larger project.

[agriyakhetarpal]

I added a basic extension to clean up the generated IPython notebooks in 6bc9c60 using nbformat, works quite well. I am now exploring a method to add the directives based on #741 (comment) automatically – it requires some configuration but I feel that it can be achieved at the source-read event before the Markdown files are processed.

[agriyakhetarpal]

Processing Markdown programmatically doesn't bear good fruit – it would have been easier if we used IPyNB, and we don't plan to. I would suggest that we should merge this for now, @rgommers.

The issue with Markdown was that there isn't a clean way to add both the Jupytext frontmatter and the notebook directives and that requires some obtrusive, prone-to-failure file manipulation by processing the contents as a string (we can keep the notebook directives at the bottom and the frontmatter intact, but it's easier to provide the download buttons at the top of the page rather than at the bottom).

[agriyakhetarpal]

Weird, the local docs build and RTD both produce cleaner downloadable notebooks, but the NotebookLite directive on RTD doesn't have the cleaner notebooks (they still have the Sphinx directives). This does not happen locally. I think RTD has some caching troubles, because I removed the redundant module headings from the notebooks (such as (reg-dwt-idwt)= and so on), but they are still there on RTD.

Local build

Read the Docs

Edit: some notebooks are as expected, and some don't.

Edit 2: this is most likely the case of a cached build or some updates that don't trickle down the RTD, the logs say that all the notebooks are converted. I can't reproduce locally, and I feel that the issue will go away automatically on a fresh build.

[agriyakhetarpal]

I had a revelation just now and I think 07a0926 should fix the synchronisation issue for good – the RTD build is just buggy for some reason or the other and the local documentation builds where the issue doesn't arise can be trusted upon. Ready for review and further proceedings.

[agriyakhetarpal]

Tagging @melissawm and @steppi for a review as discussed during the 14/06/2024 interactive docs meeting – thanks, both!

[melissawm]

This seems to work really well- I love the buttons and dropdowns.

How flexible can we make this to share with other projects? Ideally, we could have an extension (or as a part of jupyterlite-sphinx) that adds the preprocess notebooks event, common settings and looks without having to turn them on manually for each project?

[steppi]

This seems to work really well- I love the buttons and dropdowns.

How flexible can we make this to share with other projects? Ideally, we could have an extension (or as a part of jupyterlite-sphinx) that adds the preprocess notebooks event, common settings and looks without having to turn them on manually for each project?

I had a discussion with @agriyakhetarpal offline where we discussed how this preprocessing could be added to jupyterlite-sphinx. I think he's working on it.

[steppi]

Thanks @agriyakhetarpal. Don't forget to set jupyterlite_silence = True again now that we're done debugging. After that I think this is good to merge.

cc @rgommers

[rgommers]

Don't forget to set jupyterlite_silence = True again now that we're done debugging. After that I think this is good to merge.

Looks like that last action was done, and everything is green. Are you happy with this PR as is @agriyakhetarpal?

[agriyakhetarpal]

In the last few comments, I bumped to the latest https://github.com/jupyterlite/pyodide-kernel/releases/tag/v0.5.1, which brings https://github.com/pyodide/pyodide/releases/tag/0.27.1.

[agriyakhetarpal]

Now that all tests are passing, this PR should be ready – thanks to @gabalafou's help with the styling 🙈

cc: @melissawm and @Carreau; tagging you here as I can't request a review from GitHub directly.