OpenFreeEnergy / OpenFreeEnergy/openfe
cli gather: add alchemical_network.json awareness
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@atravitz is already working on this.
Since Mar 28, 2025.
cli
usability
- Dominant language
- Python
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- 331
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- Avg merge
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Description
As discussed in openfe dev meeting, we should add the alchemical network as a cli gather argument, so that we can use it as the source of truth when checking for failed or missing runs.
The industry benchmarking scripts already do this, and we can achieve this without an api break by:
- make alchemical_network cli arg optional
- if alchemical_network arg is not passed, raise a warning that strongly encourages the user to pass in alchemical_network
in 2.0, we can discuss removing the legacy behavior.
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