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TreePriors.xml missing BICEPS operators (EpochTop, EpochAll, TreeFlex) #1

@alexeid

Description

@alexeid

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 (EpochFlexOperator with fromOldestTipOnly="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 — expects YuleModelBICEPSEpochTop.t:anolis
  • SimpleTreePriorTest — expects CoalescentConstantBICEPSEpochTop.t:anolis
  • CloneTest, 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.

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