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Description
Problem
BEAUti tests (e.g. BeautiSimpleTest, SimpleTreePriorTest, CloneTest) fail because they expect BICEPS operators like YuleModelBICEPSEpochTop.t:anolis, CoalescentConstantBICEPSEpochTop.t:anolis, etc., but these operators are not generated.
The TreeOperators fragment in TreePriors.xml does not include the three BICEPS operators:
BICEPSEpochTop(EpochFlexOperator)BICEPSEpochAll(EpochFlexOperatorwithfromOldestTipOnly="false")BICEPSTreeFlex(TreeStretchOperator)
These operators are present in LegacyStandard.xml (lines 301-303), where they are hardcoded per tree prior, but were not carried over to the new TreeOperators fragment in TreePriors.xml.
Question
Should these BICEPS operators be added to the TreeOperators fragment in TreePriors.xml? Are they still appropriate for the new spec-based template system, or should they be handled differently?
Affected tests (~20 failures)
BeautiSimpleTest— expectsYuleModelBICEPSEpochTop.t:anolisSimpleTreePriorTest— expectsCoalescentConstantBICEPSEpochTop.t:anolisCloneTest,DivergenceDatingTest,LinkUnlinkTest, and others
Context
These failures surfaced after fixing BEAUti template discovery so that tests no longer crash with Standard.xml not found. The underlying operator omission has been present since TreePriors.xml was created.