Initial documentation setup with mkdocs

[melissawm]

Here is an attempt at fixing #70. This is not a jupyterbook setup, but a plain mkdocs setup that also uses mkdocs-gallery.

I am still trying to figure out the correct way to execute gallery examples. As of now, they will run but the napari viewer window will not close by itself, which prevents correct execution of the gallery. qtgallery still doesn't work correctly but I'm working on it.

[alisterburt]

great stuff @melissawm - please ping when you think this is ready! Alternatively I'm happy to give you write access to the repo for docs work, let me know what you prefer

[psobolewskiPhD]

@melissawm Do you think we can use the same fix as in the napari/docs repo? https://github.com/napari/docs/pull/207

def napari_scraper(block, block_vars, gallery_conf):
    """Basic napari window scraper.

    Looks for any QtMainWindow instances and takes a screenshot of them.

    `app.processEvents()` allows Qt events to propagateo and prevents hanging.
    """
    imgpath_iter = block_vars['image_path_iterator']

    if app := napari.qt.get_app():
        app.processEvents()
    else:
        return ""

    img_paths = []
    for win, img_path in zip(
        reversed(napari._qt.qt_main_window._QtMainWindow._instances),
        imgpath_iter,
    ):
        img_paths.append(img_path)
        win._window.screenshot(img_path, canvas_only=False)

    napari.Viewer.close_all()
    app.processEvents()

    return scrapers.figure_rst(img_paths, gallery_conf['src_dir'])

[melissawm]

I'll try!

[melissawm]

I think I've made progress with the scraper but now I'm hitting #181, so I'll wait for that to go in and will update accordingly. Cheers!

[psobolewskiPhD]

@melissawm #181 is merged! Let me know if I can help get this one over the line! ❤️

[Czaki]

Why mkadocs? I know that it is simpler, but as it is napari project then may be nice to use the same theme.

[psobolewskiPhD]

Why mkadocs? I know that it is simpler, but as it is napari project then may be nice to use the same theme.

Good point. I do think that mkdocs was @alisterburt preference, see: https://github.com/napari/napari-animation/issues/70#issuecomment-1520385125

[melissawm]

I'm going to get this in shape, but if the preference is to use the new napari theme I am happy to come up with an alternative version :relaxed:

[psobolewskiPhD]

@melissawm I certainly don't want to throw away your efforts with this PR! But beyond the theme, I think using the same docs tooling (sphinx & myst) as for napari docs would make maintenance easier? What do you think?

As an aside, I think this plugin has such unique napari value that it should become part of "napari[all]" so consistent theme does make sense in that context.

[GenevieveBuckley]

@psobolewskiPhD

I certainly don't want to throw away your efforts with this PR! But beyond the theme, I think using the same docs tooling (sphinx & myst) as for napari docs would make maintenance easier? What do you think?

As an aside, I think this plugin has such unique napari value that it should become part of "napari[all]" so consistent theme does make sense in that context.

I'm +1 on the idea that napari-animation should be included with "napari[all]".

I think it might be nice to have the same website theme as core napari, but I do not think it is worth spending developer time on if this is going to be annoying. That could be a future PR, but I don't think it's important.

Previously, @alisterburt expressed a strong preference for using the mkdocs-material theme, and staying away from sphinx (here and here). I agree with Alister, I think a sphinx/myst setup would be much more complicated to maintain than mkdcos-gallery.

It is much more important to me personally that we get the functional benefits of good documentation (i.e. the info and gallery examples are readable on the website). I do not care about branding & whether the website uses the same shade of blue, font, or theme, etc. At this stage of the project, it's better to spend that developer time on functionality (eg: fixing bugs, or generating more/better content for documentation, etc.)

[GenevieveBuckley]

This looks close, so I'd like for us to try and get this across the finish line @melissawm. Are there any blockers remaining from your point of view?

The only big thing I think is to make sure github actions updates the docs and gallery examples when needed.

I've previously done something similar here for the napari-threedee project. We update the github actions yaml, and make sure we have secrets.DOCS_DEPLOY_TOKEN set up for the repository, eg:

    # Build the book
    - name: Build the book
      run: |
        mkdocs build
    # Push the book's HTML to github-pages whenever the main repo branch changes
    - name: GitHub Pages action
      if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
      uses: peaceiris/actions-gh-pages@v3.8.0
      with:
        deploy_key: ${{ secrets.DOCS_DEPLOY_TOKEN }}
        external_repository: napari-animation/napari-animation.github.io
        publish_dir: ./site

[GenevieveBuckley]

I will say that when I run mkdocs serve, the gallery examples output static images, rather than the movies shown here https://napari-animation-docs.readthedocs.io/en/latest/ (like this).

Having actual animations would be ideal for the napari-animation docs eventually, but I think the static 2D images are a big step forward regardless (essentially they are an infinite improvement all on their own, because otherwise new users would never even know from the docs that examples exist at all).

[psobolewskiPhD]

Ironically that site ( https://github.com/kolibril13/napari-animation-docs/blob/main/docs/source/conf.py ) uses sphinx. Anyhow I think the key to the animations showing is the helper function, see: https://github.com/kolibril13/napari-animation-docs/blob/main/docs/source/notebook.ipynb We could try something similar as a hidden cell showing just output? Edit: actually I think it would require changing the scraper...

BTW it doesn't look like on that site that the examples are run on CI, but rather locally and the videos are embedded in the notebooks. So a bit different case I think, but maybe would work

[melissawm]

Yup, I was waiting on a decision regarding the sphinx vs. mkdocs discussion to then figure out the actual animations. I guess I didn't want to spend time on one stack if we're going with the other in the end 😅

[jni]

fwiw my leaning is the opposite to Alister's. You make good points @GenevieveBuckley about "whatever gets us going", and I definitely agree, but that may or may not be what helps us maintain the documentation in the long term — having two stacks is not going to be helpful re long term maintenance here. (I do agree very much about theming being a low priority.)

imho mkdocs filled a niche three years ago when Alister made those comments of allowing easy authoring with markdown, which was not easy at all in sphinx. Today myst and myst-nb have got that use case well covered, so I don't think the pain points with sphinx are what they used to be, and there is lots of value in using the same toolchain for all our projects.

Additionally, if we get automatic movies going with napari-animation in mkdocs it may be additional work to display automatic movies in napari docs proper, whereas the work can get used by multiple napari projects if it happens in sphinx-land.

[melissawm]

Ok - I am happy to set up an alternate version with sphinx, it should be simple enough to get up and running quickly. If that makes the animations easier, at least we'll have that data point for the decision. Does that sound reasonable?

[jni]

imho yes! Thank you @melissawm!

[GenevieveBuckley]

I've built working video scrapers for both mkdocs and sphinx setups now. They work fine on my local projects, so I guess the question is do we have a sphinx setup here (assuming the mkdocs plan is overruled) that I can slot them into.

[melissawm]

Let me do that today - I'll push a different pr and then we can check. I'll ping you when ready

[GenevieveBuckley]

Let me do that today - I'll push a different pr and then we can check. I'll ping you when ready

Ok, sure. Tomorrow is a public holiday, so I can either work on it today or get to it next week.

[GenevieveBuckley]

Superseded by https://github.com/napari/napari-animation/pull/200