Epic: execution improvements

[atravitz]

This PR covers the first section (non-breaking changes) of the Exorcist & Warehouse Integration Plan

LLM / AI generated code disclosure

LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: no
If yes, please provide details here:

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.
• Filled in the AI generated code disclosure.

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 95.66532% with 43 lines in your changes missing coverage. Please review.
✅ Project coverage is 90.57%. Comparing base (ca92919) to head (cc8edd5).

Files with missing lines	Patch %	Lines
src/openfe/orchestration/__init__.py	88.18%	15 Missing ⚠️
src/openfe/storage/warehouse.py	86.91%	14 Missing ⚠️
src/openfecli/commands/worker.py	93.75%	4 Missing ⚠️
src/openfe/tests/orchestration/test_worker.py	98.42%	3 Missing ⚠️
src/openfecli/plan_alchemical_networks_utils.py	87.50%	3 Missing ⚠️
.../openfe/tests/orchestration/test_exorcist_utils.py	98.61%	2 Missing ⚠️
src/openfe/tests/orchestration/conftest.py	97.22%	1 Missing ⚠️
src/openfecli/commands/plan_rbfe_network.py	80.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2113      +/-   ##
==========================================
- Coverage   95.20%   90.57%   -4.63%     
==========================================
  Files         213      217       +4     
  Lines       21134    21522     +388     
==========================================
- Hits        20121    19494     -627     
- Misses       1013     2028    +1015     

Flag	Coverage Δ
fast-tests	90.57% <95.66%> (?)
slow-tests	?

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[github-actions]

🚨 API breaking changes detected! 🚨

View workflow run

Griffe output

$ griffe check "openfe" -s src --no-inspection --no-color --verbose -a origin/main
src/openfe/tests/storage/test_resultclient.py:0: <module>:
Public object was removed

src/openfe/tests/storage/test_metadatastore.py:0: <module>:
Public object was removed

src/openfe/tests/storage/test_resultserver.py:0: <module>:
Public object was removed

src/openfe/storage/resultclient.py:0: <module>:
Public object was removed

src/openfe/storage/resultserver.py:0: <module>:
Public object was removed

src/openfe/storage/metadatastore.py:0: <module>:
Public object was removed


$ griffe check "openfecli" -s src --no-inspection --no-color --verbose -a origin/main
src/openfecli/commands/plan_rbfe_network.py:121: plan_rbfe_network(warehouse):
Parameter was added as required