User-installable BEAST.base / BEAST.app packages (off the boot module path)#95
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Split the entangled root version.xml into a clean BEAST.base descriptor and a new BEAST.app descriptor (beast-fx/version.xml), moving the FX service blocks and packageapp entries out of BEAST.base. Embed the BEAST.app descriptor in beast-fx.jar (mirroring beast-base), and add maven-assembly descriptors producing BEAST.base.package.v*.zip and BEAST.app.package.v*.zip with a correct lib/ split: BEAST.base carries its third-party deps but not beast-pkgmgmt; BEAST.app carries beast-fx plus JavaFX only, relying on BEAST.base for the rest. The package id is kept as BEAST.app (not BEAST.fx) for backward compatibility with existing <depends on="BEAST.app"> declarations.
createAndRegisterModuleLayer built each package's layer with the boot layer as its only parent, so a package's module dependency could be resolved only when that dependency was on the boot module path. Build each layer with boot plus all previously-registered plugin layers as parents, so a package can read modules provided by other packages (e.g. beast.fx requires beast.base once the core modules are no longer on the boot path). Backward-compatible: boot remains a parent. Covered by ModuleLayerCrossDependencyTest.
Add BeastLauncher.seedBundledPackage(), which extracts a bundled <app>/packages/<pkg>.package*.zip into the user package dir, version-aware (a same-or-newer user copy is preserved). getPath() seeds both core packages, falling back to the legacy single-jar copy in dev/IDE runs. build-sign-dmg.sh removes beast-base/beast-fx from the boot module path and bundles both package zips in the app image; on first launch they are seeded into the user dir and load as plugin module layers, so the package manager can upgrade them in place. beast.fx requires beast.base, so both move together; beast-pkgmgmt and third-party deps stay on boot, JavaFX is provided by the bundled JRE+FX. package.path is already invalidated on install/uninstall. Runtime-unverified: needs a DMG build + BEAUti launch to confirm beast.fx works from a plugin layer reading boot JavaFX. Covered by SeedBundledPackageTest and CorePackagesInstalledTest.
The synthetic BEAST.app registration in addInstalledPackages() always marks it installed, so the follow-up network auto-install and the RuntimeException hard-fail in loadExternalJars were unreachable in every normal path while wiring a network call and a hard crash into the universal startup sequence (and conceptually requiring the GUI layer for headless runs). Remove both; keep the genuinely useful part -- deferring checkInstalledDependencies until after all packages are loaded so deps resolved via plugin layers are not flagged as missing. A real BEAST.app load failure now surfaces naturally (e.g. main class not found) rather than being masked by a synthetic-installed flag.
alexeid
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The developer version works, but the Mac release is broken. I think you need to keep core jars, and when I commented out To replicate: cd $beast3/release/Mac/
# rm dmg-staging
rm -rf dmg-staging
./build-sign-dmg.sh
# clean the lib path
rm -rf ~/Library/Application\ Support/BEAST/2.8
# go to release version
cd dmg-staging/BEAST 2.8.0
# use released script to test
./bin/beast -validate ~/WorkSpace/beast3/beast-base/src/test/resources/beast.base/examples/testHKY.xml |
…t-fx.jar
Removing beast-fx from the boot module path also removed JavaFX from the
boot layer -- JavaFX was only resolved there because beast.fx (on boot)
required it and pulled it out of the bundled JRE+FX. With beast.fx gone the
BEAST.app plugin layer could not find JavaFX, so beast.fx failed to load
(ClassNotFoundException: beastfx.app.beast.BeastMain).
- Add javafx.controls/fxml/swing/web + jdk.jsobject to the runtime
--add-modules so the JRE+FX modules resolve into the boot layer, where the
beast.fx plugin layer reads them (transitive graphics/base/media follow).
- Drop JavaFX from the BEAST.app package zip: it carried both the empty
automatic-module jars and the platform jars, and the empty ones fail
resolution ('javafx.graphics not found'); JavaFX comes from the JRE+FX
anyway. The zip is now beast-fx.jar + version.xml.
The wrapper .app/.bat/shell launchers and the Windows .cfg patch launched with `--add-modules ALL-MODULE-PATH` only. Since the bundled JRE+FX provides JavaFX as platform modules and the javafx jars were dropped from the module path, ALL-MODULE-PATH no longer pulls JavaFX into the module graph, so the beast.fx plugin layer (which requires javafx.*) fails to resolve and the GUI tools die silently on launch — BEAUti/TreeAnnotator/LogCombiner/AppLauncher on all platforms, plus BEAST itself on Windows. Name javafx.controls/fxml/swing/web + jdk.jsobject explicitly in --add-modules, matching what BEAST.cfg already does for the jpackage launcher.
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Makes
BEAST.baseandBEAST.appuser-installable packages and loads them from the user package directory, so the package manager can upgrade them in place. Builds on master's #94 fix (BEAST.appis registered as a core package there).Changes
Packaging
version.xmlinto a cleanBEAST.basedescriptor and a newbeast-fx/version.xml(BEAST.app), moving the FX service blocks +packageappentries out ofBEAST.base.beast-fx.jarembeds itsversion.xml.maven-assemblydescriptors produceBEAST.base.package.v*.zip(beast-base.jar+ its third-party deps, nobeast-pkgmgmt) andBEAST.app.package.v*.zip(beast-fx.jar+version.xmlonly;beast-base,beast-pkgmgmtand JavaFX are provided at runtime).Module-layer resolution
createAndRegisterModuleLayer()parents each package layer on boot + all previously-registered plugin layers (was boot only), so a package can read modules from another package's layer (e.g.beast.fx→beast.base). Backward-compatible — boot remains a parent. Covered byModuleLayerCrossDependencyTest.Core loaded from the user dir (Mac)
BeastLauncher.seedBundledPackage()extracts a bundled<app>/packages/<pkg>.package*.zipinto the user package dir, version-aware (a same-or-newer user copy is preserved).getPath()seeds both core packages, with the legacy single-jar copy as the dev/IDE fallback.build-sign-dmg.shkeepsbeast-base/beast-fxoff the boot module path and bundles both package zips in the app image; on first launch they seed into the user dir and load as plugin module layers, so the package manager can upgrade them in place.beast-pkgmgmtand third-party deps stay on boot. JavaFX +jdk.jsobjectare named in the runtime--add-modulesso the bundled JRE+FX modules resolve into the boot layer, where thebeast.fxplugin layer reads them (needed becausebeast.fx, which used to pull them in, is no longer on boot).Startup loading
loadExternalJarsno longer network-auto-installsBEAST.appor hard-fails when it is missing (both unreachable given the synthetic registration, and they put a network call and a hard crash on the universal startup path).checkInstalledDependenciesruns after all packages load, so dependencies resolved via plugin layers are not flagged as missing.Tests:
CorePackagesInstalledTest,SeedBundledPackageTest,ModuleLayerCrossDependencyTest(fullbeast-pkgmgmtsuite green, 43 tests).Testing plan for @walterxie
#94 regression —
./bin/packagemanager -listshowsBEAST.appinstalled;-add SSM/BDMM-Primeresolve and install.Package zips —
mvn -DskipTests package→BEAST.appzip isbeast-fx.jar+version.xml;BEAST.basezip isbeast-base.jar+ third-party deps with nobeast-pkgmgmt/JavaFX.Runtime gate (needs a DMG build + launch) —
release/Mac/build-sign-dmg.sh, then./bin/beast -validate <xml>and launch BEAUti. Confirmbeast.fxloads from a plugin layer (reading JavaFX from the boot layer), and~/Library/Application Support/BEAST/2.8/{BEAST.base,BEAST.app}are seeded. Upgrade check: bump a user-dirversion.xml/jar and confirm it is picked up after restart.Remaining (not in this PR)
BEAST.base/BEAST.appentries topackages2.8.xmland host the zips. TheBEAST.appzip carries no JavaFX (the app image provides it via the JRE+FX), so a standalone/CBAN install on a plain JRE needs JavaFX provided separately, per platform.--add-moduleschange to those release scripts.