Raise an error for empty HybridTopology atom mappings

[jthorton]

The protocol currently allows atom mappings to be empty, resulting in an uninformative indexing error in validation, this PR adds validation specifically for this case.

LLM / AI generated code disclosure

LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes / no
If yes, please provide details here: No

Checklist

• All new code is appropriately documented (user-facing code must have complete docstrings).
• Added a news entry, or the changes are not user-facing.
• Ran pre-commit: you can run pre-commit locally or comment on this PR with pre-commit.ci autofix.
• Filled in the AI generated code disclosure.

Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion).

• GPU integration tests
• example notebook testing
• packaging tests: run this for any large feature PRs or PRs that add test data.

Developers certificate of origin

• I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[jthorton]

pre-commit.ci autofix

[github-actions]

No API break detected ✅

View workflow run

Griffe output

$ griffe check "openfe" -s src --no-inspection --no-color --verbose -a origin/main

$ griffe check "openfecli" -s src --no-inspection --no-color --verbose -a origin/main

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 90.46%. Comparing base (1692562) to head (577f9fc).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2120      +/-   ##
==========================================
- Coverage   95.13%   90.46%   -4.67%     
==========================================
  Files         213      213              
  Lines       20871    20878       +7     
==========================================
- Hits        19855    18887     -968     
- Misses       1016     1991     +975     

Flag	Coverage Δ
fast-tests	90.46% <100.00%> (?)
slow-tests	?

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