Enable extending NonEquilibriumCyclingProtocols #44
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* Added new (de)compression + (de)serialize functions in feflow.utils.data * Include compressed System, State, and Integrator as a result for the main simulation unit. * SetupUnits now take `extends_data`, which when populated, spoof the running of the `SetupUnit._execute` method. It instead immediately returns results with values consistent to the end state of the extended SimulationUnit. * Added new test `test_pdr_extend` to test the extension functionality.
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One limitation of Is this the case for the outputs added in this PR? |
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These are not json serializable. I can add another step in (de)serialization for converting to and from base64. |
GufeTokenizables must be JSON serializable, so including bytes is not an option. Instead, we take the compressed bytes and encode them into a Base64 string.
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* When `mapping` is `None`, use the mapping provided by the ProtocolDAGResult
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@ijpulidos any idea why my tests fail on license keys? |
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@ianmkenney My guess is that the secrets fail since it's coming from a fork? Let me dig around and see if there's a way to make this work. One way would be making a separate PR in the repo, but I'll see if there's another way. |
That is exactly what is going on, the quick fix is for someone who has write access, to push this branch to the |
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to kick off ci (you need write access to the repo for this to work) |
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This is currently blocked by #38. |
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@ianmkenney @dotsdl Is this ready to be reviewed? If so, can you mark it as such? Thanks! |
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@ijpulidos I think an initial review works, not sure if you want to wait for gufe/openfe v1.0.0 before merging though. |
This PR introduces the ability to extend a NonEquilibriumCycling protocol by including serialized and compressed OpenMM State, System, and Integrator in the main simulation units. When instantiating new NonEquilbriumProtocols which extend a previous result, these objects are used to bypass the normal function of the SetupUnit. Closes #2.