From 03a12a6ff481947f26ff490fa70a27fbb923391a Mon Sep 17 00:00:00 2001
From: Jean-Yves TINEVEZ <tinevez@pasteur.fr>
Date: Thu, 16 Jul 2026 09:40:18 +0200
Subject: [PATCH 1/2] Add maven-assembly-plugin to produce
 jar-with-dependencies

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.
---
 pom.xml | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/pom.xml b/pom.xml
index 4926b2a..fcac363 100644
--- a/pom.xml
+++ b/pom.xml
@@ -191,6 +191,30 @@
                             <argLine>-Xmx4g -Djna.library.path=/opt/homebrew/opt/c-blosc/lib</argLine>
                         </configuration>
                     </plugin>
+
+					<plugin>
+						<artifactId>maven-assembly-plugin</artifactId>
+						<configuration>
+							<archive>
+								<manifest>
+									<mainClass>org.mastodon.geff.RoundTripGeff</mainClass>
+								</manifest>
+							</archive>
+							<descriptorRefs>
+								<descriptorRef>jar-with-dependencies</descriptorRef>
+							</descriptorRefs>
+						</configuration>
+						<executions>
+							<execution>
+								<id>make-assembly</id>
+								<phase>package</phase>
+								<goals>
+									<goal>single</goal>
+								</goals>
+							</execution>
+						</executions>
+					</plugin>
+                    
                 </plugins>
             </build>
         </profile>

From 0fb39489aeaf4a7d3533fc881c57609d7783a47a Mon Sep 17 00:00:00 2001
From: Jean-Yves TINEVEZ <tinevez@pasteur.fr>
Date: Thu, 16 Jul 2026 09:40:46 +0200
Subject: [PATCH 2/2] Use -Djna.library.path for blosc native library lookup

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
---
 cross-language-tests/run_tests.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cross-language-tests/run_tests.py b/cross-language-tests/run_tests.py
index c49a9ee..231976a 100644
--- a/cross-language-tests/run_tests.py
+++ b/cross-language-tests/run_tests.py
@@ -89,7 +89,7 @@ def run_java_roundtrip(
 
     # Add library path if blosc is found
     if blosc_path:
-        cmd.append(f"-Djava.library.path={blosc_path}")
+        cmd.append(f"-Djna.library.path={blosc_path}")
 
     cmd.extend(
         [