Add support for tetrahedral connectivity and use scipy to generate it

[nilsdeppe]

Proposed changes

This provides an easy way to fill gaps in for domains with Gauss points. There are several optimizations possible to make it run faster if needed.

Upgrade instructions

Code review checklist

• The code is documented and the documentation renders correctly. Run
  make doc to generate the documentation locally into BUILD_DIR/docs/html.
  Then open index.html.
• The code follows the stylistic and code quality guidelines listed in the
  code review guide.
• The PR lists upgrade instructions and is labeled bugfix or
  new feature if appropriate.

Further comments

[nilsvu]

(optional) Maybe just name triangulate?

[nilsdeppe]

I don't feel too strongly, I used this so it matches up with GenerateXdmf use-tetrahedral-connectivity but I agree it's very long

[nilsvu]

Up to you

[nilsvu]

You can relatively easily show a progress bar here so the script doesn't appear "frozen" without any indication that it is doing anything. Here's how:

import rich.progress

progress = rich.progress.Progress(
        rich.progress.TextColumn("[progress.description]{task.description}"),
        rich.progress.BarColumn(),
        rich.progress.MofNCompleteColumn(),
        rich.progress.TimeRemainingColumn(),
        disable=(len(h5files) == 1),
    )
task_id = progress.add_task("Processing files", total=len(h5files))

with progress:
    for h5file, filename in progress.track(h5files, task_id=task_id):
        # ...
        progress.update(task_id, advance=1) # don't remember if this is needed

Docs are here: https://rich.readthedocs.io/en/stable/progress.html

[nilsvu]

(optional) showing a progress bar (over timesteps rather than files as suggested before) instead of the log messages would be nicer

[nilsvu]

Question: how does this handle shared grid points on LGL element boundaries? The tetrahedra connecting these points would be degenerate.

[nilsdeppe]

I haven't read the paper that describes qhull, but as far as I can tell it works fine and doesn't produce any double connectivity.

[nilsvu]

LGTM please squash.