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workflow patches #451
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)
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Looks good to me.
Regarding the naming, maybe better prio_tasks
? intermediate_tasks
is a bit long
Or maybe full circle back to |
I like |
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How many tests are failing for this branch?
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 |
The charged peptide simulation doesn't fail? Did you pull grappa recently? |
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
A collection of fixes as we explore various ways of interacting with kimmdy both for users and plugin developers.
Task
s are now consistently called tasks to not confuse them withstep
s (as inRecipeStep
s)nrexcl
of the reactive moleculetype is more exposedconfig.cwd
Up for discussion:
RunManager.crr_tasks
have been renamed toslotted_tasks
to 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.