OpenFreeEnergy / OpenFreeEnergy/openfe

Gather error when less than two repeats are present

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Dominant language
Python
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Description

I was wondering whether we could change the behavior with this Error:

https://github.com/OpenFreeEnergy/openfe/blob/35a999907e6c3567e8173e8ef3ad11cf0b5785f4/openfecli/commands/gather.py#L494
I've been running into this error during benchmarking. I would like to get a preliminary result while other calculations are still running. I think what's confusing to me was that I would have expected the --allow-partial flag to handle this differently; to skip edges when only one leg is present instead of giving an error.

I wonder how many people will run multiple repeats of openfe in production, so I think long term supporting single repeats will be important. I'm not sure which would be the best way to do that, I know it's tricky because of using the standard deviation as error vs picking an analytical for a single repeat. I thought I'd just raise it here to maybe collect some ideas on that?

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Research direction

Start in openfecli/commands/gather.py around line 494 and inspect how the error and --allow-partial are handled. Clarify the intended behavior for a single repeat or an edge with one leg, then define completion as an agreed behavior that produces preliminary results without invalid error estimates.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
cli
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
30/100

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