BUG Fix install with src layout

[drewejohnson]

Realized after trying to install from the build wheel for 0.10.0 (that I also pushed to pypi 🤦) that things weren't quite right. It didn't really seem to be installing serpentTools package, but each individual sub-package (e.g., data., io) so you couldn't really do import serpentTools.

After an hour of fighting w/ the flat-style layout and setuptools, I decided the easier fix was just to git mv serpentTools src/serpentTools. So while there are lots of changed files, the real changes are specific to

• MANIFEST.in
• pyproject.toml
• docs/examples/nodal_writer.py :: previously broken symlink

I've done more testing on the wheel built from this version, and it looks much better. Gives us the versions we want, in the layout we expect, with the modules we want.

After this goes through, we should do the following

1. Make a new tag + release for 0.10.1
2. Push 0.10.1 wheel to pypi (later we can automate this CI Auto-deploy wheel and source distribution to pypi on release #505)
3. "yank" release 0.10.0 from pypi so that no one gets version 0.10.0 with pip install serpentTools
   • They will still get 0.10.1 and other 0.10.* later, just not literally 0.10.0

I should have caught this sooner. The jupyter issue in testing (#493) should have tipped me off to this install problem

[drewejohnson]

@DanKotlyar can you "yank" release 0.10.0 from pypi?

• https://peps.python.org/pep-0592/
  -https://pypi.org/help/#yanked

I do not have this ability

[DanKotlyar]

@drewejohnson Can you provide more details on how to "yank"?
I understand why "yanking" is needed but couldn't understand what exactly should I do.

[drewejohnson]

Yeah there don't appear to be any documentation for it. Looks like the steps are

1. Log in to pypi.org
2. Go to "Your projects" from top right profile or https://pypi.org/manage/projects/
3. Select "Manage" option for serpent tools
4. There you should see all the releases that have been made
5. Select "Options" for release 0.10.0
6. Select "Yank"

We can also merge this and I'll work on 0.11.0 release notes that include this MR