SepTop: slightly refactor _execute calls

[IAlibay]

Fixes #1919

Main tasks:

• Moved _execute back into the base units.
• Move deserialization back into _execute rather than run

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/.

[IAlibay]

pre-commit.ci autofix

[codecov]

Codecov Report

❌ Patch coverage is 80.76923% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 91.34%. Comparing base (fab07ca) to head (29f2b7a).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/openfe/protocols/openmm_septop/base.py	58.33%	5 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1930      +/-   ##
==========================================
- Coverage   94.60%   91.34%   -3.27%     
==========================================
  Files         206      206              
  Lines       18296    18285      -11     
==========================================
- Hits        17309    16702     -607     
- Misses        987     1583     +596     

Flag	Coverage Δ
fast-tests	91.34% <80.76%> (?)
slow-tests	?

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[hannahbaumann]

Thanks @IAlibay , lgtm! The missing lines in codecov are probably covered by a slow test?

[IAlibay]

Thanks @IAlibay , lgtm! The missing lines in codecov are probably covered by a slow test?

Just looked and that's indeed the case. It's the five lines in the execute call 😅. They will only get called when you do the integration tests.

[github-actions]

No API break detected ✅