[walterxie]

Migrate TreeStat2 to BEAST 3 (BEAST v2.8)

Moves TreeStat2 from the BEAST 2.7 Ant build to a BEAST 3 Maven package that runs as a Java module (Java 25), following the beast3-migration skills and using starbeast2 as the reference.

Build and packaging

• Maven layout: sources moved with git mv (history kept). Java is under src/main/java; the GUI images are under src/main/resources/treestat2/images.
• pom.xml (new): io.github.compevol:treestat2:0.3.0-SNAPSHOT, Java 25.
  • BEAST 3 beast-base/beast-pkgmgmt 2.8.0-rc1.
  • io.github.compevol:ccd 1.2.2 and io.github.beast2-dev:beast-labs 2.1.1 from Maven Central.
  • beast-fx and javafx as optional dependencies, because CCD's API refers to beast-fx's TreeAnnotator.
  • commons-math3 3.6.1.
• jam.jar: it isn't on Maven Central, so it moved to a Maven repository inside the project, lib/local/jam/1.0/, as local:jam:1.0.
• module-info.java (new): module treestat2, with 3 exported packages and 57 BEASTInterface providers.
• src/assembly/beast-package.xml (new): builds target/TreeStat2.v.zip. Its lib/ contains treestat2, jam and commons-math3, which the BEAST 3 runtime doesn't provide.
• Zip name: ${beast.pkg.name}.v${project.version}, the same as beast3 and CCD, so there's no separately derived version property.
• version.xml: version 0.2.0 → 0.3.0. Minimum dependency versions are now BEAST.base/BEAST.app 2.8.0, CCD 1.2.2 and BEASTLabs 2.1.1. Nothing else changed.
• Removed: build.xml (Ant), .classpath and .project (Eclipse).
• CI: added .github/workflows/ci-publish.yml, copied unchanged from beast3. It builds on master and publishes on v* tags.

Code changes

• No BEAST 3 class replacements were needed. TreeStat2 only uses Tree, Node, TreeParser, TreeUtils and TreeIntervals, which are unchanged in BEAST 3 and not deprecated.
• CCD API rename: CCD 1.2.2 renamed averageRFDistances(Tree) to expectedRFDistances(Tree), so CCD{0,1,2}ExpectedRFDistance were updated to match.

Documentation

• README.md:
  • Updated for BEAST v2.8, with new Installation and "Running from source with Maven" sections.
  • Every existing applauncher TreeStatApp … examplehing mvn -q compile exec:exec@treestat-Dbeast.args="…" command.
• tutorial/treestat2logger.md: builds with mvn packatalls into the BEAST 2.8 package directory.
• Tutorial XML:
  • tutorial/updated_aln268_b3_draft.xml is a draft sn't run yet: it depends on BDMM and MultiTypeTree,which have no BEAST 3 release.
  • tutorial/TODO.md explains what's blocking it, whwhat's left.
  • The original updated_aln268.xml is unchanged, for BEAST 2.7.

Testing

• mvn clean package passes. The project has no unit tests.
• Every README command was run exactly as written, w-help, single and multiple statistics,--out-file/--out-tag, control file, full class names, --ccd-burn-in, and the RNNI/RF jump distances. The output files and columns
  were checked.
  • Via Maven, against the build.
  • Via applauncher on an installed BEAST 2.8.0, witough BEAST_PACKAGE_PATH alongside the installed CCD1.2.2 and BEASTLabs 2.1.1.
• beast -validate on the draft tutorial XML fails astiTypeTree classes can't be found.

Known issues / follow-ups

• How to handle jam: if treestat2 is published to Maven Central, its pom will list local:jam, which isn't on Central, so other projects can't depend on treestat2 there. A proposed solution is at jam.jar is not on Maven Central: published treestat2 can't be used as a Maven dependency #12.
• Providers missing from version.xml: CCD2ExpectedRFDistance, CCD2Information, CCD2RFDistance, RFJumpDistance and RNNIJumpDistance are in module-info.java but not in version.xml. Check Confirm release status of 5 statistics registered in module-info.java but missing from version.xml #11.
• Untracked work in progress: src/treestat2/ccd/{binomialess,ess} is untracked and wasn't migrated.
• Tutorial XML: finish once BDMM and MultiTypeTree aTODO.md).