[wait to merge] move to src layout

[atravitz]

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 by making a comment with pre-commit.ci autofix before requesting review.

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:
  -https://github.com/OpenFreeEnergy/openfe/actions/runs/20286805952
• example notebook testing:
  • https://github.com/OpenFreeEnergy/openfe/actions/runs/20287275628/job/58263774921
• packaging tests: run this for any large feature PRs or PRs that add test data.
  • https://github.com/OpenFreeEnergy/openfe/actions/runs/20287676262

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/.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.04%. Comparing base (ea1ae64) to head (eefd61f).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1752      +/-   ##
==========================================
- Coverage   95.39%   93.04%   -2.36%     
==========================================
  Files         189      190       +1     
  Lines       16646    16897     +251     
==========================================
- Hits        15880    15721     -159     
- Misses        766     1176     +410     

Flag	Coverage Δ
fast-tests	93.04% <ø> (?)
slow-tests	?

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[github-actions]

No API break detected ✅