Fix cross language tests at least on macOS - #8
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mvn package only produced target/classes/ with no dependency JARs. The cross-language test runner looks for a *-jar-with-dependencies.jar first; without it, it fell back to target/classes/ alone, leaving n5, n5-zarr, imglib2, etc. off the classpath at runtime. Done with the help of Claude Sonnet and Tobias Pietzsch.
JNA ignores -Djava.library.path and uses its own -Djna.library.path property to locate native libraries. The cross-language test runner was passing the wrong property, so libblosc.dylib was never found regardless of whether c-blosc was installed via homebrew. Again, Claude and Tobias
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Two issues prevented the Python/Java round-trip tests from running at all.
mvn packageproduced no runnable jarThe
pom.xmlhad nomaven-assembly-plugin, somvn packageonly wrote compiled classes totarget/classes/with no dependency JARs alongside them. The test runner looks for a*-jar-with-dependencies.jarfirst; without it, it fell back to
target/classes/alone, leaving n5, n5-zarr, imglib2 and friends off the classpath. Every test failed immediately withNoClassDefFoundError: org/janelia/saalfeldlab/n5/N5Reader.Fix: add
maven-assembly-pluginto thebuildprofile somvn packagealso producestarget/geff-*-jar-with-dependencies.jar.Blosc native library was never found
JNA (used by
n5-bloscto loadlibblosc) ignores-Djava.library.pathand uses its own-Djna.library.pathproperty instead. The test runner was passing the wrong property, so even with c-blosc correctly installedvia Homebrew, JNA could not locate
libblosc.dyliband every run crashed withUnsatisfiedLinkError.Fix: pass
-Djna.library.pathinrun_tests.py, consistent with how the Maven Surefire config already does it inpom.xml.Done with the help of Claude Sonnet to make sense of the error, and @tpietzsch