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…d spec classes Two modules: beast-morph-models (core, depends on beast-base) and beast-morph-models-fx (BEAUti integration, depends on beast-fx). - LewisMK extends spec Base, adds getRateMatrix(), renames internal freqValues field to avoid shadowing parent Frequencies - NStatesNoRatesSubstitutionModel extends spec BasicGeneralSubstitutionModel, now abstract (setupRelativeRates inherited as abstract) - Ordinal/NestedOrdinal: clean unused imports - BEAUti template: update namespace, replace ScaleOperator/Uniform/SubtreeSlide with UpDownOperator/BactrianNodeOperator/BactrianSubtreeSlide - Add JPMS module-info.java for both modules - Add LewisMKTest with 8 unit tests
- Move legacy 2.7 example XMLs to examples/legacy-2.7/ - Add M3982.xml using BEAST 3 spec classes (spec SiteModel, TreeLikelihood, StrictClockModel, YuleModel, ScaleTreeOperator, BactrianNodeOperator, RealScalarParam, TreeWithMetaDataLogger) - Fix exec-maven-plugin to use commandlineArgs with %classpath so multi-word beast.args are tokenized correctly - Remove test resource copies of examples needing external packages - Update README with module structure, build/run instructions
- Delete build.xml (legacy Ant build) - Update version.xml to BEAST 3 format (remove BEAST 2 depends) - Migrate fxtemplate: RealScalarParam for estimated params, spec distributions-as-priors, spec SiteModel/TreeLikelihood/ YuleModel/ScaleOperator/UpDownOperator/TreeWithMetaDataLogger - Remove unused ExtensionFileFilter import
Builds JARs, assembles flat ZIP matching the BEAST package convention (version.xml, lib/, fxtemplates/, examples/ at root), and optionally creates a GitHub release with --release flag. Version and package name are extracted from version.xml.
Replaces the morph-models-specific script with the generic version that auto-discovers JARs, fxtemplates, and examples. Works for both single-module and multi-module layouts. Also adds *.v*.zip to gitignore.
Move BEAST package ZIP assembly from shell script into Maven so `mvn package` reproducibly produces the correct ZIP on any platform. BEAST core and JavaFX deps marked as provided scope to exclude them and their transitives from the package. Assembly descriptor placed in beast-morph-models-fx (last reactor module). release.sh becomes a thin wrapper for GitHub release creation only.
Updates all POMs and README to use the CompEvol organisation namespace.
Notes Maven Central as alternative source if published there.
Allows third-party developers to run BEAST via exec:exec to test their package. The assembly descriptor now uses an includes whitelist to keep only morph-models JARs in the distribution ZIP.
Move fxtemplates to beast.morph.models.fx/fxtemplates/ to avoid JPMS split-package conflict with beast-fx. Add exec-maven-plugin to beast-morph-models-fx for running BEAUti with morph-models on the module path. Add beast.main and beast.args default properties.
Add <depends on='BEAST.base' atleast='2.8.0'/> to version.xml for consistency with other BEAST3 packages. Add GitHub Actions workflow for running tests on push/PR.
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Summary
io.github.compevolContext
Prepares morph-models for beta1 release to Maven Central alongside beast3 2.8.0-beta1, so
packagemanager -mavencan be tested end-to-end.🤖 Generated with Claude Code