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[WIP] CLI results gathering from warehouse - #2157

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[WIP] CLI results gathering from warehouse#2157
atravitz wants to merge 19 commits into
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feat/cli_raw_results

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@atravitz atravitz commented Aug 18, 2026

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  • 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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atravitz and others added 19 commits August 14, 2026 09:01
@atravitz @ethanholz
epic: add warehouse (#1864)
f278d4f 
* 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)
1f6ae4d 
* 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)
cc8edd5 
* 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
first thoughts on implementation
2379fa5
@atravitz
add get_task_df
832a726
@atravitz
add get_unit_results to warehouse
c408766
@atravitz
first pass at fuller gather_result approach
a8de805 
fix protocol dag store deduplication order
@atravitz
update docstrings
e5beea9
@atravitz
guardrails and docstrings
0de5cd8
@atravitz
add helper functions
65674f3
@atravitz
add example warehouse for testing
1becba1
@atravitz
warehouse loading
350421f
@atravitz
separate creating new filesystem warehouse from loading an existing one
e90ee88
@atravitz
update tests
a8cff0c
@atravitz
make alchemical_network_to_task_graph private
1dcc3c2
@atravitz
warehouse root_dir instead of obj
e096c32
@atravitz
require warehouse and db paths
0b8c49d
@atravitz
update test to use from_dir
2107dc3
@atravitz
add cli to gather raw results
3fa24d6
@atravitz atravitz mentioned this pull request Aug 18, 2026
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@codecov

codecov Bot commented Aug 18, 2026

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Codecov Report

❌ Patch coverage is 94.31193% with 62 lines in your changes missing coverage. Please review.
✅ Project coverage is 90.13%. Comparing base (ca92919) to head (3fa24d6).

Files with missing lines Patch % Lines
src/openfecli/commands/gather_warehouse.py 0.00% 17 Missing ⚠️
src/openfe/orchestration/__init__.py 88.09% 15 Missing ⚠️
src/openfe/storage/warehouse.py 93.54% 10 Missing ⚠️
src/openfe/orchestration/exorcist_utils.py 83.33% 7 Missing ⚠️
src/openfecli/commands/worker.py 93.75% 4 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 99.25% 1 Missing ⚠️
src/openfecli/commands/plan_rbfe_network.py 80.00% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main    #2157      +/-   ##
==========================================
- Coverage   95.20%   90.13%   -5.08%     
==========================================
  Files         213      218       +5     
  Lines       21134    21526     +392     
==========================================
- Hits        20121    19402     -719     
- Misses       1013     2124    +1111
Flag Coverage Δ
fast-tests 90.13% <94.31%> (?)
slow-tests ?

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2 participants

@atravitz @ethanholz