Migrate input types to BEAST 3 spec interfaces#25
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Brings the input-rule violations flagged by the beast3-migration
linter to zero. Three patterns across 17 classes:
CalcNodes / Parameters read from scalar inputs (3 classes):
Switch Input<RealScalarParam<Real>> to Input<RealScalar<Real>>;
replace per-input somethingIsDirty() with a NeDynamics.isDirtyInput()
helper that falls back to the underlying StateNode / CalculationNode
dirty signal (spec type interfaces deliberately don't expose
somethingIsDirty()).
ConstantNe, ExponentialNe, LogisticNe
CalcNodes / Distributions that reshape parameter dimensions at init
(5 classes): keep concrete RealVectorParam / RealScalarParam Inputs
(setDimension and per-index isDirty(int) aren't on the spec
interfaces) and implements StateNodeInitialiser. The marker exempts
them from the concrete-spec-param rule, same justification as the
Operator exemption (these classes write to the state nodes they're
handed).
NeSplineInterpolation, Skygrowth, StructuredSkygrid,
LogLinearGLM, GlmModel
Distributions where the input is read-only (3 classes): the holders
just iterate and call get(i) / size(), so the input swaps cleanly to
RealVector interface. Inline ParametricDistribution → spec
ScalarDistribution<?, Double> for the distr inputs; the body already
uses logDensity().
GrowthRateSmoothingPrior, LogSmoothingPrior, GLMPrior
(GLMPrior also keeps RealVectorParam / BoolVectorParam Inputs
plus StateNodeInitialiser, since it calls setDimension at init.)
Function-using utilities (2 classes): swap legacy Input<Function> for
the appropriate spec interface and translate the body calls
(getDimension() → size(), getArrayValue(i) → get(i), calcLogP(Function)
→ manual iid sum of logDensity).
LargerThan (Function → RealVector<? extends Real>)
ErrorSmoothing (Function → RealVector<? extends Real>,
ParametricDistribution → ScalarDistribution<?, Double>)
MaxRate: ParametricDistribution → ScalarDistribution<?, Double> with
an iid loop in place of the legacy calcLogP-over-a-Param-vector.
Legacy CalcNode parent (1 class): AncestralStateTreeLikelihood
swaps its parent import from beast.base.evolution.likelihood.TreeLikelihood
(@deprecated) to beast.base.spec.evolution.likelihood.TreeLikelihood.
Protected field surface (m_siteModel.Base, branchRateModel,
substitutionModel) matches between legacy and spec parents.
Bool inputs that aren't used in the body (2 classes): switch
Input<BoolVectorParam> to the BoolVector interface — these were
dead-but-declared anyway, no behaviour change.
mappedProbLogger, StructuredTreeLogger
Editor cast (1 class): NeDynamicsListInputEditor disconnects state
nodes by ID. The migrated Inputs return spec interfaces (RealScalar /
RealVector); cast to StateNode at the call site so getID() resolves
— runtime values will always be the concrete param.
Not addressed in this PR:
* Input<List<Function>> remains on mappedProbLogger,
StructuredTreeLogger, MappedMascot, and MappedMascotWithTipSampling.
Those four are CalcNode / StateNode / Distribution subclasses (not
pure Loggers) that implement Loggable as a mixin to log their own
tree state. The List<Function> metadata is threaded through their
toNewick() but never consumed, so the linter Input<@deprecated>
warning is pointing at a vestige; left untouched here pending a
refactor of the metadata-logging surface.
Mascot Code traffic light goes 🔴 → 🟡 (cleared input rule and the one
legacy CalcNode parent; the Function-typed Inputs on the four
above-mentioned classes are the remaining yellow). 8/8 tests pass.
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Summary
Clears the input-rule violations flagged by the beast3-migration linter (17 classes touched, plus one BEAUti editor call-site cast). Mascot Code traffic light goes 🔴 → 🟡.
CalcNodes / Parameters reading scalar inputs
Switch
Input<RealScalarParam<Real>>to the read-onlyInput<RealScalar<Real>>interface and replace per-inputsomethingIsDirty()with aNeDynamics.isDirtyInput()helper that falls back to the underlyingStateNode/CalculationNodedirty signal:ConstantNe,ExponentialNe,LogisticNeClasses that reshape parameter dimensions at init
Keep the concrete spec param Inputs (
setDimension, per-indexisDirty(int)aren't on the spec interfaces) andimplements StateNodeInitialiser. The marker exempts them from the concrete-spec-param rule, same justification as the Operator exemption — they write into the state nodes they're handed:NeSplineInterpolation,Skygrowth,StructuredSkygridLogLinearGLM,GlmModelGLMPrior(also swapsInput<ParametricDistribution>→Input<ScalarDistribution<?, Double>>)Distributions that just read
Swap
Input<RealVectorParam<? extends Real>>to theRealVectorinterface andInput<ParametricDistribution>toInput<ScalarDistribution<?, Double>>. Body already usessize()/get(int)/logDensity(double):GrowthRateSmoothingPrior,LogSmoothingPriorFunction-using utilities
Translate
Input<Function>to the appropriate spec interface (getDimension()→size(),getArrayValue(i)→get(i),calcLogP(Function)→ manual iid sum oflogDensity):LargerThan—Function→RealVector<? extends Real>ErrorSmoothing—Function→RealVector<? extends Real>,ParametricDistribution→ScalarDistribution<?, Double>MaxRate—ParametricDistribution→ScalarDistribution<?, Double>with an iid loopLegacy CalcNode parent
AncestralStateTreeLikelihoodswaps its parent import frombeast.base.evolution.likelihood.TreeLikelihood(@Deprecated) tobeast.base.spec.evolution.likelihood.TreeLikelihood. Protected field surface (m_siteModel.Base,branchRateModel,substitutionModel) matches between legacy and spec parents, so the body needs no further changes.BoolVector inputs
These two inputs are declared but never read in the body:
mappedProbLogger,StructuredTreeLogger—Input<BoolVectorParam>→Input<BoolVector>Editor call-site cast
NeDynamicsListInputEditordisconnects state nodes bygetID(); cast toStateNodeat the call site so the spec-interface Inputs resolve — runtime values will always be the concreteRealScalarParam.Not addressed in this PR
Input<List<Function>>remains onmappedProbLogger,StructuredTreeLogger,MappedMascot, andMappedMascotWithTipSampling. Those four are CalcNode / StateNode / Distribution subclasses (not pure Loggers) that implementLoggableas a mixin. TheList<Function>metadata is threaded through theirtoNewick()but never consumed inside the recursion — so the linterInput<@Deprecated>warning is pointing at a vestige. Left untouched pending a refactor of the metadata-logging surface.Test plan
mvn -DskipTests compileclean.mvn test— 8/8 pass.exec:execprofile on this repo; consider adding one if you want this baked into CI).