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* feat(warehouse): initial re-implementation of StorageManager * feat(warehouse): initial implementation with test * feat(warehouse): add support for new context object * feat(warehouse): experimental implementation of executing a DAG * feat!: Replace Context with new implementation BREAKING CHANGE: This completely breaks existing `Context` to leverage our new context management. * test(warehouse): add a context test * test: cleanup test_protocolunit.py * refactor(StorageManager)!: make _convert_to_namespace a static method * test(ProtocolDAG): fix ProtocolDAG tests * test(Protocol): cleanup testing for transformation and protocol * test(Protocol): remove reliance on mixin in two cases since StorageManger isn't tokenizable * chore: remove commented out code * Revert "chore: remove commented out code" This reverts commit 7e6bb03. * chore: fix comments and cleanup code * fix: satisfy typing * refactor(StorageManager)!: make _convert_to_namespace, convert_to_namespace * docs: storagemanager * docs: add docstrings to Context object * Update gufe/protocols/protocolunit.py Co-authored-by: Alyssa Travitz <[email protected]> * Apply suggestions from code review Co-authored-by: Alyssa Travitz <[email protected]> * fix: indents from code review web ui * fix: remove TODO * chore: rename scratch_path to scratch_dir * chore: remove dead comment * chore: remove redudndant fixtures * refactor: rename convert_to_namespace to append_to_namespace * docs: added news * Apply suggestions from code review on news item Co-authored-by: Alyssa Travitz <[email protected]> * fix docs env build by mocking zstandard * test: add a context test for validating cleanup --------- Co-authored-by: Alyssa Travitz <[email protected]> Co-authored-by: Alyssa Travitz <[email protected]>
* feat: return namespaced handles so other untis can ingest these handles * test: add a test to validate * Update gufe/storage/storagemanager.py Co-authored-by: Alyssa Travitz <[email protected]> --------- Co-authored-by: Alyssa Travitz <[email protected]>
… backend (#745) * refactor: split out transfer functionality * test: split out transfer functionality tests Signed-off-by: Ethan Holz <[email protected]> --------- Signed-off-by: Ethan Holz <[email protected]> Co-authored-by: Alyssa Travitz <[email protected]>
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
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- Coverage 98.89% 98.75% -0.14%
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* docs: add information on storage Signed-off-by: Ethan Holz <[email protected]> * docs: initial draft on context * docs: improve context docs * docs: migrate how to write a custom implementation * doc: update with comments from review Co-authored-by: Alyssa Travitz <[email protected]> * fix docs build * docs: Add information on changes in feat/return-storage-handles This adds new information on how storage is handled, and how storage gets passed around by units. * docs: add information on pre-namespaced objects from other branch * docs: add suggestion to back link to Context docs * docs: add becomes in migration guide per suggestion * docs: add link to protocol how to * docs: add more informaton on StorageManagers * docs: clean up storage code example * Apply suggestions from code review Co-authored-by: Alyssa Travitz <[email protected]> * fix typo * Apply suggestions from code review Co-authored-by: Alyssa Travitz <[email protected]> * docs: add more context on context * fix note formatting * move serialization constraints to the end * Apply suggestions from code review Co-authored-by: Alyssa Travitz <[email protected]> * Apply suggestions from code review Co-authored-by: Alyssa Travitz <[email protected]> * Apply suggestion from @atravitz Co-authored-by: Alyssa Travitz <[email protected]> * fix formatting for docs build * Apply suggestions from code review Co-authored-by: Alyssa Travitz <[email protected]> * clean up --------- Signed-off-by: Ethan Holz <[email protected]> Co-authored-by: Alyssa Travitz <[email protected]> Co-authored-by: Alyssa Travitz <[email protected]>
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No API break detected ✅ |
dotsdl
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Apr 10, 2026
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This is looking excellent! Did a quick review of the new concept docs; just a couple notes I think should be addressed.
Will give the rest of the PR a thorough review at a later time! Can't wait to use this in alchemiscale to finally support result file retention!
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| .. code-block:: python | ||
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| path = ctx.shared.scratch_dir / "myfile.dat" |
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| path = ctx.shared.scratch_dir / "myfile.dat" | |
| path = ctx.shared / "myfile.dat" |
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| 3. **Handle ctx.permanent.** There was no equivalent in the legacy API. | ||
| Decide which results must persist between DAG executions and write them via | ||
| ``ctx.permanent``. For migration you can start by mirroring whatever used | ||
| to live in ``ctx.shared`` and refine later. |
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I don't think we should recommend that protocol authors switch from shared to permanent by default, as this could result in large in-DAG intermediate files getting held by execution engines for no good reason.
The recommendation here should be to switch to permanent any files that must survive DAG execution for the purposes of continuation or understanding results later; the default should not be keep everything.
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To elaborate: in alchemiscale, we plan to retain permanent files by default (unless opted out of by the Task creator) for DAGs, and only retain shared during the duration of DAG execution (for continuation if interrupted) or retain shared indenfinitely if opted into by the Task creator (for debugging problematic cases).
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Changes to how we handle contexts and storage.
Implemented by @ethanholz - this epic is to track the work as a long-lived branch.
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