Beast3

[walterxie]

Summary

Migrates model-selection from BEAST2 (2.7.x) / Ant to BEAST3 (2.8.0-beta7) / Maven across 17 commits. Tracked in #14 ("Migrate to beast3").

Build system: Ant → Maven

• Replaced build.xml with pom.xml (Java 25 release target, Maven Central publishing plugin).
• Reorganized source tree into standard Maven layout: src/main/java, src/main/resources, src/test/java, src/test/resources.
• Added module-info.java (JPMS), declaring requires/exports/provides, including the new org.apache.commons.statistics.distribution dependency and optional BEAST FX/JavaFX modules for the GUI.
  • Fixed two categories of service-provider registration errors here: MCMC2IS was dropped from the provides list because it's abstract and doesn't qualify (its shared logic was split into a new abstract MCMC2Abstract base class); ExponentialProductPosteriorMeansLikelihood, LogTransformedNormalKDEDistribution, and LogitTransformedNormalKDEDistribution each gained a public no-arg constructor so they do qualify.
• Added .github/workflows/ci-publish.yml for tag-triggered CI + zip release, and src/assembly/beast-package.xml for the BEAST package zip (including sources jar and BeAUti fxtemplates).
• Bumped version.xml to 1.7.0, depending on BEAST.base/BEAST.app >=2.8.0; registered the new MCMC2IS provider.

Parameter → Tensor

BEAST3 replaced beast.base.inference.parameter.Parameter/RealParameter with a generic Tensor type system (beast.base.spec.type.Tensor, RealScalarParam, RealVectorParam, etc.). Updated throughout:

• KernelDensityEstimatorDistribution and its subclasses (NormalKDEDistribution, LogTransformedNormalKDEDistribution, LogitTransformedNormalKDEDistribution, MultivariateKccept Tensor<?, ? extends Double> instead ofParameter/RealParameter, including bounds-checking logic previously done via Parameter.getLower()/getUpper().
• CPOAnalyser and the *SamplingStep classes updated d Prior wrapper distribution: LogNormal/Gamma/etc.now extend TensorDistribution directly, so the code pulls the target Tensor out via tensorDistribution.paramInput.get() instead of unwrapping a RealParameter from a Prior.
• Related type fix in MCMC2IS: BEAST3's StateNode no longer implements Function, so a raw StateNode can no longer be pasFunction is expected. Narrowed via pattern-matching <?> before use.
• PathSampler also gained fallback code paths so all example XMLs run correctly against the new type hierarchy.
  Commons Math → Commons Statistics
  BEAST3 dropped org.apache.commons.math (BetaDistribution/BetaDistributionImpl, GammaDistribution/GammaDistributionImpl, ExponentialDistribution/ExponentialDistributionImpl,athException). Replaced withorg.apache.commons.statistics.distribution in GSSTreeDistribution, PathSampler, PathSampleAnalyser, GeneralisedSteppingStone, and the KDE distribution classes. Mostly mechanical: newnstructors became static XDistribution.of(...)factory calls (e.g. BetaDistribution.of(alpha, 1.0)), and the checked MathException is gone, so the surrounding try/catch was
  removed. Declared the new module dependency in modul

Evaluator removed

BEAST3 deleted beast.base.inference.Evaluator and si() to a zero-arg method. In PathSamplingStep,PairedPathSamplingStep, and GeneralisedSteppingStoneStep, the old Evaluator-based block is commented out (not deleted) with a TODO explaining why: it was only ever exercised by BEAST2esn't exist in BEAST3 and wasn't used by this package anyway — replaced with a plain operator.proposal() call.

JUnit 4 → 5

• GSSTreeDistributionTest migrated from org.junit.Test/junit.framework.TestCase to org.junit.jupiter.api.Test with static org.junit.jupiter.api.Assertions.assertEquals.
• pom.xml adds junit-jupiter 5.8.2 and assertj-core as test dependencies, with Surefire configured for JPMS (--add-reads flags) and a BEAST_PACKAGE_PATH system property so tests can ret runtime.

Maven release beta1 is https://central.sonatype.com/artifact/io.github.beast2-dev/model-selection

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TODO:

• Could not find class beast.base.core.BEASTInterface as service when loading BEAUti template
  Could not find class beast.base.core.BEASTInterface as service when loading BEAUti template #15