workflow patches #451
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workflow patches #451
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to reflect its function for a user, not the mode of operation
and format json
(since this the only time we do it is after initializing the config, using the config)
KRiedmiller
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Jul 9, 2024
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Or maybe full circle back to |
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I like |
ehhartmann
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Jul 9, 2024
tests/test_files/test_integration/hexalanine_single_reaction/kimmdy2.yml
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None of the ones that we run in CI, see https://github.com/graeter-group/kimmdy/actions/runs/9809976871/job/27089067802 but the restarting is still broken. and |
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The charged peptide simulation doesn't fail? Did you pull grappa recently? |
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It probably would, I'm not running the tests that require PLUMED, but that's entirely out of scope for this PR. |
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changes from #451 fix: properly compare to empty dicts refactor(config): rename recursive_dict argument to opts to reflect its function for a user, not the mode of operation feat: add xtc option to config refactor: format json feat: always setup tasks on init of RunManager feat: configure logger from init of Config (since this the only time we do it is after initializing the config, using the config) refactor(runmanager): rename step to task_name for consistency docs: update quarto version fix: resolve all non-relative paths in config relative to config.cwd refactor(runmanager): rename crr_tasks to priority_tasks
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A collection of fixes as we explore various ways of interacting with kimmdy both for users and plugin developers.
Tasks are now consistently called tasks to not confuse them withsteps (as inRecipeSteps)nrexclof the reactive moleculetype is more exposedconfig.cwdUp for discussion:
RunManager.crr_taskshave been renamed toslotted_tasksto highlight the role of slotting in tasks between the predetermined queue. Since it is now easier to run kimmdy interactively this property is more exposed and I wanted a proper word and less angry animal sounds. Still not entirely happy with the name, naming things is hard.