Update apps#104
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## compute-layer #104 +/- ##
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- Coverage 70.64% 69.26% -1.38%
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Files 17 19 +2
Lines 1475 1604 +129
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mattwthompson
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| """ | ||
| @python_app | ||
| def prepare_openmm_system( | ||
| packing_future: dict[str, BulkLiquid | Topology], | ||
| job_dir: str, | ||
| ) -> dict[str, BulkLiquid | openmm.System]: | ||
| """ |
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Pull request overview
This PR updates the simulation “apps” pipeline and workflow interface to support a multi-step run (packing → OpenMM setup → minimization → equilibration → production → density analysis), and adds a helper to fetch job output trajectories from target metadata (supporting the “decouple compute and targets” direction referenced in the linked issues).
Changes:
- Extend the Parsl workflow to run equilibration/production steps and then perform density analysis.
- Add typed config structures (ensemble/equilibration/minimization) and broaden compute config typing through the workflow/prep/jobs layers.
- Add a
fetch_trajectory_paths_from_targethelper and update the density example to usesubmit_target.
Reviewed changes
Copilot reviewed 10 out of 11 changed files in this pull request and generated 11 comments.
Show a summary per file
| File | Description |
|---|---|
| examples/run_density.py | Updates example to submit targets via SimulationWorkflow and fetch resulting trajectories. |
| dimsim/configs/minimization.py | Adds a typed minimization config and defaults. |
| dimsim/configs/equilibration.py | Adds a typed equilibration config structure. |
| dimsim/configs/ensemble.py | Introduces an Ensemble enum for config typing. |
| dimsim/compute/workflow.py | Refactors submission to support target-based submission and new pipeline stages. |
| dimsim/compute/prep.py | Tightens typing for target→compute-config conversion and updates supported tags. |
| dimsim/compute/jobs.py | Generalizes job-id creation to BaseComputeConfig and adjusts hashed parameters. |
| dimsim/compute/fetch.py | Adds helper to locate production trajectory paths based on target + compute parameters. |
| dimsim/compute/apps.py | Adds equilibration/production/analysis apps and expands minimization outputs for downstream steps. |
| dimsim/_tests/compute/test_apps.py | Extends test coverage to system creation and energy minimization behaviors. |
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Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> Fix Update Fix
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This was referenced Jul 21, 2026
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Closes #37
Closes #70
Closes #102