Update our Jupyter Notebooks

[alongd]

As spotted by @LeenFahoum, some imports were outs=dated in our Jupyter notebooks.
This PR updates them

[Copilot]

Pull request overview

This PR updates several ARC utility Jupyter notebooks to reflect recent internal API/module changes (notably parser and xyz-perception utilities) and strips execution metadata/outputs to keep notebooks clean in version control.

Changes:

• Update notebook imports to current module paths (e.g., arc.parser.parser.parse_1d_scan_energies).
• Replace removed/obsolete xyz parsing helpers with arc.species.perceive.perceive_molecule_from_xyz.
• Clear cell outputs and reset execution_count to null across updated notebooks.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
ipython/Tools/Visualize 1D Torsion scan.ipynb	Updates parser import path and strips cell outputs/execution counts.
ipython/Tools/TS Guesses.ipynb	Removes legacy RMG DB setup, adjusts reaction-family call site, strips outputs/execution counts (but currently has API mismatches).
ipython/Tools/Plot xyz.ipynb	Switches from removed xyz-to-molecule utilities to perceive_molecule_from_xyz, strips outputs/execution counts.
ipython/Tools/Perceive_xyz_(xyz_to_smiles).ipynb	Updates xyz perception flow to use perceive_molecule_from_xyz, strips outputs/execution counts.
ipython/Tools/External symmetry and optical isomers.ipynb	Updates xyz perception import/usage and strips outputs/execution counts.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 63.05%. Comparing base (ce7de27) to head (96893fc).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #884   +/-   ##
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  Coverage   63.05%   63.05%           
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  Files         114      114           
  Lines       38069    38069           
  Branches     9967     9967           
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  Hits        24005    24005           
  Misses      11175    11175           
  Partials     2889     2889           

Flag	Coverage Δ
functionaltests	63.05% <ø> (ø)
unittests	63.05% <ø> (ø)

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[LeenFahoum]

This path seems user-specific, so the notebook may fail for other users. Could we make it more general/relative?

[alongd]

Do you mean this: path = '/path/to/ESS/output/file/output.out'?
It's already "generic" (path to your ESS output...). Anything we put won't work for the user, they have to point to their output file anyway.
I added a comment to make it clearer

[LeenFahoum]

Looks good