Updating cookbook recipes and notebooks to reflect yt4 changes

[chummels]

This is a pass at updating the docs to reflect the current state of code in yt4. Namely, this updates the cookbook, fixing some breakages in the notebooks, and ensuring full tuples are used to specify each field reference, among some other changes.

Note, I'm removing the description surrounding n_ref in the Gadget loading data page, since it is no longer relevant in yt4: http://yt-project.org/docs/dev/examining/loading_data.html#indexing-criteria

[chummels]

In response to the concerns about adding parentheses on the various tuples: I know it's not necessary and that the code will function correctly either way. I just thought it was cleaner to consistently specify tuples with parens surrounding them. But I can remove these if people have strong feelings about it.

[chummels]

I'm reviewing this -- thank you for the big effort to update this. One thing I do want to flag for further thought is whether we're doing a service or a disservice when we always use explicit tuples, even when there is no ambiguity.

It was my understanding that we were meant to be using the full tuple specification as much as possible to avoid possible field clashes.

[matthewturk]

@chummels I'm not saying that it's wrong; I was flagging that I am not sure that I fully support having it everywhere, especially where there aren't conflicts or ambiguity. I apologize for the unclear message that I sent -- I was not asking for any work to be done.

[chummels]

No, I get it. It's a valid concern. I just thought we were moving to full-tuple specification everywhere. We can talk about it today in the meeting.

[neutrinoceros]

I just thought it was cleaner to consistently specify tuples with parens surrounding them. But I can remove these if people have strong feelings about it.

Consistency > all

That said, here's a surprise argument in favour of leaving parens out, and encouraging the paren-free syntax:
ipython/ipython#12395

Last year, @cphyc contributed this patch to IPython (and thus, to JupyterLab and Notebook), which allows auto-completion to work on the second member of a two-tuple key in an accessor, while it previously used to work only on the first one (which wasn't really useful to us since it would then only auto-complete field types and never field names). The feature isn't released yet, and it's targeted for IPython 8.0, which is a big deal, hence the delay.

[jzuhone]

@neutrinoceros let me know if you are going to review again or not--if not, I will merge.

[neutrinoceros]

Oh sorry I forgot about this, I'll give it a go now

[neutrinoceros]

here are more suggestions in line with my first batch. I think I got all of them now.