Add visualize doc and ignore ipynb for pre-commit

[lsetiawan]

This PR adds a small documentation about visualize subpackage.

[lsetiawan]

Can someone help me in adding the create_echogram function into the api reference dropdown list in the sidebar?? I'm not sure how to do that 😞

[emiliom]

Can someone help me in adding the create_echogram function into the api reference dropdown list in the sidebar?? I'm not sure how to do that

I'll do this. But not right now 😢

[emiliom]

Can someone help me in adding the create_echogram function into the api reference dropdown list in the sidebar?? I'm not sure how to do that

Hmm, I'm realizing now that I don't know how this is behaving since the conversion to Jupyter Book. See the dynamic table of content on the upper right; that's what I would expect, except it should be exposing 3rd-level section headers but it's only exposing 2nd-level ones (I imagine this is a configuration we can change; this may be a good starting point). The dropdown on the left sidebar seems to be a selective set corresponding exclusively to automodapi-generated entities that are specified like this:

.. automodapi:: echopype.echodata
   :no-inheritance-diagram:
   :no-heading:

I don't know how Jupyter Book is deciding to grab those and create sub-headings in the left sidebar. No other page entry on the left sidebar has sub-headings.

This is a Jupyter Book problem. In the original RTD Sphinx theme, the section navigation on the left was doing exactly what I expect. See this example from v0.5.4. This will require research.

[emiliom]

The new "Data visualization" page has instructions for including plotting dependencies during installation with pip install: pip install echopype[plot]. How about with conda? In the Installation and Examples page, we have instructions for installation with both pip and conda, so we should have conda instructions here, too.

[lsetiawan]

For conda, everything is included, so it already comes with the dependencies for plotting also.

[lsetiawan]

This is a Jupyter Book problem. In the original RTD Sphinx theme, the section navigation on the left was doing exactly what I expect. See this example from v0.5.4. This will require research.

Thank you so much @emiliom for looking into this in depth! Hmm... I was hoping it would be a simple change! I'll look into further. Appreciate your help 😄

[emiliom]

This is a Jupyter Book problem. In the original RTD Sphinx theme, the section navigation on the left was doing exactly what I expect. See this example from v0.5.4. This will require research.

Thank you so much @emiliom for looking into this in depth! Hmm... I was hoping it would be a simple change! I'll look into further. Appreciate your help smile

As the next step, ideally I would suggest trying to "turn off" the drop down menu on the left sidebar and enabling 3rd-level section headers on the table of content on the right. In practice, it'll depend on how hard each of those tasks is!

[emiliom]

See #686. I give up trying to tweak the behavior of the table of contents. I'll merge this (the new visualization page), and we can revisit the table of content issue in the future.