BEASTLabs

BEAST utility library containing generally useful classes used by other BEAST packages.

Building

Requires Java 25 and Maven.

mvn compile

BEAST3 dependencies are resolved from GitHub Packages. You may need a GitHub personal access token configured in your ~/.m2/settings.xml:

<servers>
  <server>
    <id>github</id>
    <username>YOUR_GITHUB_USERNAME</username>
    <password>YOUR_GITHUB_TOKEN</password>
  </server>
</servers>

Module

JPMS module name: beast.labs

Key exports:

• beastlabs.core.util — Slice, ParameterConstrainer
• beastlabs.util — BEASTVector, Transform
• beastlabs.math.distributions — BernoulliDistribution, WeightedDirichlet, WeibullDistribution
• beastlabs.evolution.tree — RNNIMetric, RobinsonsFouldMetric, MonophyleticConstraint
• beastlabs.evolution.likelihood — ExperimentalTreeLikelihood, MultiPartitionTreeLikelihood
• beastlabs.evolution.operators — tree operators, CombinedOperator
• beastlabs.parsimony — Fitch parsimony implementations

BEAST3 migration status

Branch: beast3

All 142 source files compile against beast3 (beast-base 2.8.0-SNAPSHOT).

Changes from BEAST2:

• Maven multi-module build (was Ant)
• JPMS module beast.labs with requires static for beast-fx/javafx
• commons-math 2.x replaced with commons-statistics (immutable distribution API)
• cern.colt.Arrays replaced with java.util.Arrays
• org.json replaced with beast.base.internal.json
• Nashorn scripting via standalone nashorn-core dependency (removed from JDK)

TODO:

• Migrate tests from JUnit 4 to JUnit 5
• Add CI workflow (GitHub Actions)
• Add version.xml for BEAST package manager
• Add release script

IntelliJ

It should look like this after following the developer guide https://github.com/CompEvol/beast3/blob/master/scripts/DevGuideIntelliJ.md