feat: exorcist worker

[ethanholz]

Adds support for a Filesystem-backed exorcist worker that can run ProtocolUnits from an AlchemicalNetwork. Adding @atravitz and @IAlibay for reference. Still in progress but sharing for the initial workflow.

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/.

[codecov]

Codecov Report

❌ Patch coverage is 96.08586% with 31 lines in your changes missing coverage. Please review.
⚠️ Please upload report for BASE (feat/warehouse@fd24777). Learn more about missing BASE report.

Files with missing lines	Patch %	Lines
src/openfe/orchestration/__init__.py	88.09%	15 Missing ⚠️
src/openfecli/commands/worker.py	93.75%	4 Missing ⚠️
src/openfe/storage/warehouse.py	86.36%	3 Missing ⚠️
src/openfe/tests/orchestration/test_worker.py	98.43%	3 Missing ⚠️
src/openfecli/plan_alchemical_networks_utils.py	87.50%	3 Missing ⚠️
src/openfe/tests/orchestration/conftest.py	97.22%	1 Missing ⚠️
.../openfe/tests/orchestration/test_exorcist_utils.py	99.29%	1 Missing ⚠️
src/openfecli/commands/plan_rbfe_network.py	80.00%	1 Missing ⚠️

Additional details and impacted files

@@                Coverage Diff                @@
##             feat/warehouse    #1833   +/-   ##
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  Coverage                  ?   92.27%           
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  Files                     ?      208           
  Lines                     ?    18008           
  Branches                  ?        0           
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  Hits                      ?    16616           
  Misses                    ?     1392           
  Partials                  ?        0           

Flag	Coverage Δ
fast-tests	92.27% <96.08%> (?)

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[ethanholz]

Seems I still have some unit testing to finish up, but this should be enough to highlight the use case for interested partners.

[ethanholz]

A few notes on how to run this code:

We need to first generate a warehouse that contains everything to run. Currently, only RBFE planning works. When using openfe plan-rbfe-network, you just need to add the --warehouse flag. This will generate a FilesystemWarehouse.

To run a single task you use something like this:

openfe worker warehouse

This will only run a task to completion and then stop. To run this in a loop, you can do something like this: https://gist.github.com/ethanholz/775027b469d6038f3dc958110c635c4c

[IAlibay]

@atravitz I think we need to discuss this at some point soon. My understanding was that warehouse & exorcist was going to be decoupled from planning?

[ethanholz]

@atravitz I think we need to discuss this at some point soon. My understanding was that warehouse & exorcist was going to be decoupled from planning?

The exorcist implementation is built to accept units as discussed. To demonstrate capabilities, I have added a flag to warehouse so that you can test and validate some of the functionality today.