[WIP] SepTop Protocol

[hannahbaumann]

Checklist

• [ ] Added a news entry

Developers certificate of origin

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

[codecov[bot]]

Codecov Report

:x: Patch coverage is 93.03323% with 130 lines in your changes missing coverage. Please review. :white_check_mark: Project coverage is 92.35%. Comparing base (1cb3ac7) to head (dffae05).

Files with missing lines	Patch %	Lines
.../tests/protocols/openmm_septop/test_septop_slow.py	67.41%	58 Missing :warning:
openfe/protocols/openmm_septop/base.py	85.09%	38 Missing :warning:
...nfe/protocols/openmm_septop/equil_septop_method.py	94.77%	26 Missing :warning:
openfe/protocols/openmm_septop/utils.py	95.31%	3 Missing :warning:
openfe/tests/protocols/conftest.py	90.32%	3 Missing :warning:
...e/protocols/openmm_septop/equil_septop_settings.py	98.03%	2 Missing :warning:

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1057      +/-   ##
==========================================
- Coverage   95.54%   92.35%   -3.20%     
==========================================
  Files         163      172       +9     
  Lines       12593    14454    +1861     
==========================================
+ Hits        12032    13349    +1317     
- Misses        561     1105     +544     

Flag	Coverage Δ
fast-tests	92.35% <93.03%> (?)
slow-tests	?

Flags with carried forward coverage won't be shown. Click here to find out more.

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

:rocket: New features to boost your workflow:

• :snowflake: Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[jthorton]

Docs look awesome, great job @hannahbaumann!

[hannahbaumann]

Thanks @IAlibay !

• I removed the femto_constants code, that one was leftover from when I still was using the other alchemical factory, thank you for pointing that out!
• I switched from is_close to assert_allclose
• I moved the compute_energy function into the protocol conftest and made the suggested changes
• I then also removed the femto_utils file as it was no longer needed.

[hannahbaumann]

Thanks @jthorton , I think I addressed all your comments, except the ones we will address in follow up PRs. Whenever you have some time this would be ready for re-review!

[mikemhenry]

fix for the docs is here: https://github.com/hannahbaumann/openfe_septop/pull/4

[hannahbaumann]

@atravitz : Could you maybe have a look at the mypy errors in the plan_network_options.py script raised here? I'm not sure why I'm getting these in this PR, and it would be helpful to know if you think we need to fix them or if it should be ok as is!

[IAlibay]

Ran long tests today, got this:

FAILED openfe/tests/protocols/openmm_septop/test_septop_slow.py::test_openmm_run_engine[CUDA] - KeyError: 'last_checkpoint'

[hannahbaumann]

@IAlibay I fixed the long test, it should be working now!

[github-actions[bot]]

No API break detected ✅