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Epic: execution improvements - #2113

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@atravitz atravitz commented Jul 30, 2026 •
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This PR covers the first section (non-breaking changes) of the Exorcist & Warehouse Integration Plan

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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).

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Codecov Report

❌ Patch coverage is 97.11090% with 31 lines in your changes missing coverage. Please review.
✅ Project coverage is 90.68%. Comparing base (1820817) to head (352ad4f).

Files with missing lines Patch % Lines
src/openfe/orchestration/worker.py 88.18% 15 Missing ⚠️
src/openfe/storage/warehouse.py 94.07% 9 Missing ⚠️
src/openfe/tests/orchestration/test_worker.py 98.42% 3 Missing ⚠️
src/openfe/orchestration/exorcist_utils.py 94.87% 2 Missing ⚠️
src/openfe/storage/utils.py 94.44% 1 Missing ⚠️
.../openfe/tests/orchestration/test_exorcist_utils.py 99.35% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main    #2113      +/-   ##
==========================================
- Coverage   95.07%   90.68%   -4.39%     
==========================================
  Files         206      222      +16     
  Lines       20697    21738    +1041     
==========================================
+ Hits        19677    19713      +36     
- Misses       1020     2025    +1005
Flag Coverage Δ
fast-tests 90.68% <97.11%> (?)
slow-tests ?

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@atravitz atravitz mentioned this pull request Aug 3, 2026
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atravitz force-pushed the epic/execution_improvements branch 2 times, most recently from 6fc30c6 to a07f1c8 Compare August 7, 2026 19:51
@atravitz atravitz mentioned this pull request Aug 11, 2026
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atravitz force-pushed the epic/execution_improvements branch 2 times, most recently from a6fd672 to cc8edd5 Compare August 14, 2026 16:01
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🚨 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

@atravitz
atravitz force-pushed the epic/execution_improvements branch from cc8edd5 to f93afcc Compare August 18, 2026 17:53
@atravitz atravitz mentioned this pull request Aug 21, 2026
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atravitz force-pushed the epic/execution_improvements branch 2 times, most recently from 4bf5974 to 15029e7 Compare August 24, 2026 15:25
atravitz
atravitz commented Aug 24, 2026
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Comment thread news/cli_headers.rst

**Changed:**

* Changed CLI sections from "Network Planning", "Quickrun Exectutor" and "Miscellaneous" to "Planning & Setup", "Execution", "Results Gathering", and "Miscellaneous".

@atravitz atravitz Aug 24, 2026

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TBD if this should stay. see #2171 (comment)

@atravitz
atravitz force-pushed the epic/execution_improvements branch from c4137e6 to 91f0310 Compare September 3, 2026 18:59
@atravitz atravitz added this to the 1.13.0 milestone Sep 8, 2026
@atravitz
atravitz force-pushed the epic/execution_improvements branch 2 times, most recently from 8e795d1 to ae8674b Compare September 15, 2026 20:30
@atravitz
atravitz force-pushed the epic/execution_improvements branch 2 times, most recently from e6e6f8d to ef24680 Compare September 19, 2026 00:07
@atravitz
atravitz force-pushed the epic/execution_improvements branch 2 times, most recently from e8b3f29 to 47d6440 Compare September 24, 2026 19:55
atravitz and others added 6 commits September 25, 2026 13:50
@atravitz @ethanholz
epic: add warehouse (#1864)
4ab9e20 
* refactor: remove result_server references in favor of gufe ExternalStorage (#1632)

* feat: remove result_server references in favor of gufe external_storage

Signed-off-by: Ethan Holz <ethan.holz@omsf.io>

* fix: remove extra external_store

* test: change from result_server to external_storage

* test: remove external_store reference

* test: change extension to item per class changes

* refactor: remove result server import

* chore: remove metadata store from resultclient

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* refactor: remove result server

* refactor: remove metadata store

---------

Signed-off-by: Ethan Holz <ethan.holz@omsf.io>
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* refactor: rename to WarehouseBaseClass (#1660)

* refactor(warehouse): rename to warehouse

* refactor: rename _ResultContainerTest to _ContainerTest

* refactor: rename _Container instances to _DataContainer

* feat/refactor: add setup store (#1671)

* refactor: remove extra implementations

We may end up adding these back later but for the time being, we are
going to remove them to keep life easy.

* refactor: remove load_* and store_* functions

Signed-off-by: Ethan Holz <ethan.holz@omsf.io>

* refactor: keys are being stored really strangely

* refactor(warehouse): huge refactor to simplify working with Warehouse

* refactor(warehouse): remove dead code

* fix: delete failed due to incorrect object

* test: add a test for the FileSystemWarehouse

* refactor: remove dead code

* Update openfe/storage/warehouse.py

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* docs: update warehouse docstrings

* feat(warehouse): leverage keyed_chain for object dedup

* Update openfe/storage/warehouse.py

* import Literal

* Update openfe/storage/warehouse.py

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* Update openfe/storage/warehouse.py

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* Update openfe/storage/warehouse.py

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* Update openfe/storage/warehouse.py

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* Update openfe/storage/warehouse.py

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* Update openfe/storage/warehouse.py

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* Update openfe/storage/warehouse.py

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* docs(warehouse): change from return, to raises

* refactor(warehouse): move _key_exists to exists

* chore(warehouse): remove extra todo

* chore(warehouse): remove _load_stream

* fix(warehouse): deduplicate objects on the filesystem

* chore(warehouse): add typehint to exists

---------

Signed-off-by: Ethan Holz <ethan.holz@omsf.io>
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
Co-authored-by: Alyssa Travitz <alyssa.travitz@omsf.io>

* Temporarily build pooch from main w/ hotfix (#1806)

* build with pooch@main to see if hotfix works

* add link

* Add support for result tokenizables to warehouse (#1763)

* feat(warehouse): add result tokenizable store

* docs(warehouse): add docs on the result store

* chore: add property for result store

* fix: use the correct function signature for handling setup

---------

Co-authored-by: Alyssa Travitz <alyssa.travitz@omsf.io>

* test: cleanup warehouse test to be more modular (#1809)

* fix dict type

* add news item

* run mypy CI on PRs into all branches (not just main) (#2112)

* ignore a couple type check violations for now

---------

Signed-off-by: Ethan Holz <ethan.holz@omsf.io>
Co-authored-by: Ethan Holz <ethan.holz@omsf.io>
@ethanholz @atravitz
feat: filesystem exorcist worker (#1833)
3897efc 
* refactor: remove result_server references in favor of gufe ExternalStorage (#1632)

* feat: remove result_server references in favor of gufe external_storage

Signed-off-by: Ethan Holz <ethan.holz@omsf.io>

* fix: remove extra external_store

* test: change from result_server to external_storage

* test: remove external_store reference

* test: change extension to item per class changes

* refactor: remove result server import

* chore: remove metadata store from resultclient

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* refactor: remove result server

* refactor: remove metadata store

---------

Signed-off-by: Ethan Holz <ethan.holz@omsf.io>
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* refactor: rename to WarehouseBaseClass (#1660)

* refactor(warehouse): rename to warehouse

* refactor: rename _ResultContainerTest to _ContainerTest

* refactor: rename _Container instances to _DataContainer

* feat/refactor: add setup store (#1671)

* refactor: remove extra implementations

We may end up adding these back later but for the time being, we are
going to remove them to keep life easy.

* refactor: remove load_* and store_* functions

Signed-off-by: Ethan Holz <ethan.holz@omsf.io>

* refactor: keys are being stored really strangely

* refactor(warehouse): huge refactor to simplify working with Warehouse

* refactor(warehouse): remove dead code

* fix: delete failed due to incorrect object

* test: add a test for the FileSystemWarehouse

* refactor: remove dead code

* Update openfe/storage/warehouse.py

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* docs: update warehouse docstrings

* feat(warehouse): leverage keyed_chain for object dedup

* Update openfe/storage/warehouse.py

* import Literal

* Update openfe/storage/warehouse.py

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* Update openfe/storage/warehouse.py

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* Update openfe/storage/warehouse.py

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* Update openfe/storage/warehouse.py

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* Update openfe/storage/warehouse.py

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* Update openfe/storage/warehouse.py

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* Update openfe/storage/warehouse.py

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* docs(warehouse): change from return, to raises

* refactor(warehouse): move _key_exists to exists

* chore(warehouse): remove extra todo

* chore(warehouse): remove _load_stream

* fix(warehouse): deduplicate objects on the filesystem

* chore(warehouse): add typehint to exists

---------

Signed-off-by: Ethan Holz <ethan.holz@omsf.io>
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
Co-authored-by: Alyssa Travitz <alyssa.travitz@omsf.io>

* Temporarily build pooch from main w/ hotfix (#1806)

* build with pooch@main to see if hotfix works

* add link

* Add support for result tokenizables to warehouse (#1763)

* feat(warehouse): add result tokenizable store

* docs(warehouse): add docs on the result store

* chore: add property for result store

* fix: use the correct function signature for handling setup

---------

Co-authored-by: Alyssa Travitz <alyssa.travitz@omsf.io>

* test: cleanup warehouse test to be more modular (#1809)

* feat: add warehouse primitives for handling protocol units

* feat: inital worker for exorcist

* test: add tests for warehouse

* fix: can now return protocol unit

* refactor: make things more consistent

* test: initial test setup for orchestration subpackage

* test: initial exorcist utility testing

* refactor: provide a root path to the exorcist DB

* test: inital worker testing

* feat: add shared_store

* feat: add better handling for CLI application

Signed-off-by: Ethan Holz <ethan.holz@omsf.io>

* test: add new worker tests

* feat: add exorcist worker to CLI

* test: add for worker CLI command

* docs: add numpy docstrings

* feat: add support for planning an RBFE to a Warehouse

* fix: correct edge direction for task graph

* refactor: remove extra debugging from warehouse

* refactor: cleanup handling of tasks for worker

* refactor: fix issues in the CLI for running the worker

* Update src/openfe/orchestration/__init__.py

* fix dict type

* add news item

* ignore a couple type check violations for now

* fix type checking

* add exorcist to docs build

---------

Signed-off-by: Ethan Holz <ethan.holz@omsf.io>
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
Co-authored-by: Alyssa Travitz <alyssa.travitz@omsf.io>
@atravitz
updates to filesystem warehouse worker-based execution (#2153)
d073f35 
* only use protocolunit as key

* add specific protocol dag store

* add get_protocol_dags

* fix protocol dag store deduplication order

* type checking and require a name

* default task db to use warehouse name

* update docstrings

* update type hint for python 3.12
@atravitz @ethanholz
filesystem warehouse usability improvements (#2155)
39301f0 
* warehouse loading

* separate creating new filesystem warehouse from loading an existing one

* update tests

* make alchemical_network_to_task_graph private

* warehouse root_dir instead of obj

* require warehouse and db paths

* placeholder note for cli planning

* planning function returns db and warehouse

* add get_task_df

* add dependency df getter

* allow 'scratch' arg to be string

* add simple df getter tests

* fix get dep test

* move import to speed up CLI

* Update src/openfe/tests/orchestration/test_exorcist_utils.py

Co-authored-by: Ethan Holz <ethan.holz@thoriumworks.com>

* update env to point back to gufe main (gufe PR #827 merged)

---------

Co-authored-by: Ethan Holz <ethan.holz@thoriumworks.com>
@atravitz @IAlibay
add exorcist status check cli command (#2156)
cda4e0a 
* move pd df printing to utils

* add status check cli command

* remove task_type column for now

* truncate cli output to seconds

* add news item

* add news item

* Update src/openfe/orchestration/exorcist_utils.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

* fix example table

* Apply suggestions from code review

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

* rename fixture for clarity

---------

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
@atravitz
update cli sections (#2171)
5e80eb5 
* update CLI header sections

* add news item

* bump recent additions to min openfe v1.13

* update test
atravitz and others added 5 commits September 25, 2026 13:50
@atravitz
move Worker to its own module (#2172)
2b4be37
@atravitz @IAlibay
add results handling for new worker-based execution (#2114)
9d41033 
* first thoughts on implementation

* add get_unit_results to warehouse

* first pass at fuller gather_result approach

fix protocol dag store deduplication order

* update docstrings

* guardrails and docstrings

* add helper functions

* add example warehouse for testing

* update tests

* update test to use from_dir

* add type hints

* add output_in_quickrun_format

* remove placeholder function

* update test be order agnostic

* refactor for clarity

* move protocol dag instance check

* clearer error messages

* rename purs -> unit_results

* result -> results for consistency

* update test to be order agnostic

* add tests for read/write type checking

* fix file exists check

* move convert_to_quickrun_output to utils and add a test

* Apply suggestions from code review

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

* add docstring

* add docstring

---------

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
@atravitz @IAlibay
CLI: support worker-based execution (#2174)
bfe0308 
* CLI: updates to `openfe worker` (#2173)

* add notes

* cli worker require taskdb

* add example slurm submission script

* add CLI for creating a warehouse (#2170)

* add warehouse option to plan_rhfe for consistent behavior

* add alchemical network parameter

* add build_warehouse command

* add CLI plugin

* add alchemical network getter

* fix file exists check

* clean up default naming

* add write statements

* add TODO

* add smoke test

* add cli to gather raw results (#2166)

* don't resolve root_dir

* require tasks.db as cli input

* rename worker -> run_worker

* add outline for docs

* rename to warehouse_to_legacy_json

* adding to_legacy_json and test

* add news item placeholder so we don't forget

* tutorial draft

* move docs to be in User Guide with 'Execution with Quickrun'

* add docs text

* rename

* cleaning up names

* use exist_ok=True

* clean up print statements

* add note to add n_repeats

* handle task df columns better

* fix test fixtures

* run_worker -> run_task

* warehouse flag -> networks_only flag

* update CLI instructions

* add status check to docs

* remove straggling file

* update docs for accuracy

* update plan_rhfe_network

* update docs

* --warehouse and --task-db

* rename build_task_db_from_alchemical_network to setup_task_campaign

* require task_db_path

* modify test to execute entire codepath without mocking

* add null legacy_json test

* fixing and adding tests for --networks-only

* update test_plan_rhfe_network to use --networks-only option

* remove redundant check/test

* move example slurm script inline

* add link to Create an AlchemicalNetwork

* Apply suggestion from @IAlibay

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

* add clarifying sentence on naming

* first pass at fuller gather_result approach

* update docs based on reviews

---------

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
@atravitz
openfe status: add summary table (#2201)
477c65f 
* add status check counts to CLI

* docstring

* add news

* rename count -> summary

* add docs

* add write statement

* fix function call
@atravitz
use conda-forge exorcist (#2209)
352ad4f
@atravitz
atravitz force-pushed the epic/execution_improvements branch from 47d6440 to 352ad4f Compare September 25, 2026 20:50
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@atravitz @ethanholz