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As I understand from this open GitHub issue, multi-variable prompt templates are still not yet supported today.
In this Streamlit demo app for prompt engineering/optimization (which accepts arbitrary input QA datasets, so long as they have one reference answers column) - we worked around this by doing the prompt templating ourselves as a pre-processing step before FMEval. You can find screenshots and a walkthrough of the demo app's user experience here.
I believe the fmeval team are aware that both multi-variable prompt templating in general and in-context/RAG-based question answering in particular are important to customers, so these features might get expanded in future - but adding your voice on GitHub/etc may help drive their prioritization.
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