Fix 1-4 interpolation for core-dummy interactions

[jthorton]

This fixes the treatment of 1-4 interactions between core and dummy atoms and extensive tests to the hybrid topology factory to ensure they are handled correctly.

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.

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

[jthorton]

The 4 tests introduced to show that 1-4 interactions between the core-dummy atoms has failed as expected https://github.com/OpenFreeEnergy/openfe/actions/runs/22312817357/job/64549319567?pr=1856#step:11:6546. Now turning on the setting by default which should fix the tests.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 90.55%. Comparing base (82558ea) to head (0d3ad8d).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1856      +/-   ##
==========================================
- Coverage   94.72%   90.55%   -4.18%     
==========================================
  Files         216      216              
  Lines       19546    20480     +934     
==========================================
+ Hits        18515    18545      +30     
- Misses       1031     1935     +904     

Flag	Coverage Δ
fast-tests	90.55% <100.00%> (?)
slow-tests	?

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[hannahbaumann]

Thanks @jthorton , lgtm! Thank you for adding all those thorough tests, I tried to go through all of them, but since it's so many I may have missed something, so it will be great to have another set of eyes on this!

[IAlibay]

Just realising it's on the 1.11 milestone - going to put a block until the results come through. It's possible we won't be able to include it in this release (purely a "too many things to do before the free energy workshop")

[IAlibay]

GPU tests here: https://github.com/OpenFreeEnergy/openfe/actions/runs/25015486410

[IAlibay]

CPU tests here: https://github.com/OpenFreeEnergy/openfe/actions/runs/25015503017

[IAlibay]

This looks good to me, thanks! Could you just address @hannahbaumann's comments please?

Sorry it took so long for me to wrap my head around the exceptions stuff - it makes sense now.

[jthorton]

pre-commit.ci autofix

[IAlibay]

Two very small things, otherwise lgtm! (edit: merged as discussed on slack)

[github-actions]

No API break detected ✅