From f6903f3fd8be89a3e22611a496b11016d3c8d477 Mon Sep 17 00:00:00 2001
From: Mark Kittisopikul <markkitt@gmail.com>
Date: Fri, 16 Oct 2026 06:40:58 -0400
Subject: [PATCH] Switch from cisd:jhdf5 to janelia-jhdf5

Replace ch.systems.cisd:jhdf5:14.12.0 in Viewer3D with
org.scijava:janelia-jhdf5 (22.03.01-SNAPSHOT for now). H5JLoader.java
compiles unchanged. Temporary plumbing (snapshot version property,
bytedeco snapshot repository, CI step that installs the janelia-jhdf5
snapshot) is to be removed once janelia-jhdf5 is released.

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
---
 .github/workflows/maven.yml | 11 +++++++++++
 modules/Viewer3D/pom.xml    |  7 ++++---
 pom.xml                     | 11 +++++++++++
 3 files changed, 26 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml
index 9bf9270dd..ba4fd7e8d 100644
--- a/.github/workflows/maven.yml
+++ b/.github/workflows/maven.yml
@@ -28,6 +28,17 @@ jobs:
         java-version: '8'
         distribution: 'zulu'
         cache: maven
+    # Temporary: janelia-jhdf5 22.03.01-SNAPSHOT is not published anywhere, so build and
+    # install it into ~/.m2 first. Remove once janelia-jhdf5 is released.
+    - name: Check out janelia-jhdf5
+      uses: actions/checkout@v4
+      with:
+        repository: JaneliaSciComp/janelia-jhdf5
+        ref: main
+        path: janelia-jhdf5
+    - name: Install janelia-jhdf5 snapshot
+      working-directory: janelia-jhdf5
+      run: mvn -B -U install -DskipTests -Djacoco.skip=true -Djavacpp.platform=linux-x86_64
     - name: Build with Maven
       run: mvn -P janeliaws clean install
 
diff --git a/modules/Viewer3D/pom.xml b/modules/Viewer3D/pom.xml
index 5b5db29c9..c6a5144b1 100644
--- a/modules/Viewer3D/pom.xml
+++ b/modules/Viewer3D/pom.xml
@@ -51,9 +51,10 @@
 
         <!-- HDF5 -->
         <dependency>
-            <groupId>ch.systems.cisd</groupId>
-            <artifactId>jhdf5</artifactId>
-            <version>14.12.0</version>
+            <groupId>org.scijava</groupId>
+            <artifactId>janelia-jhdf5</artifactId>
+            <!-- Temporary: remove the explicit version once janelia-jhdf5 is released (use a release version then). -->
+            <version>${janelia-jhdf5.version}</version>
         </dependency>
 
     </dependencies>
diff --git a/pom.xml b/pom.xml
index c0670724f..cad2af3ab 100644
--- a/pom.xml
+++ b/pom.xml
@@ -165,6 +165,9 @@
 
         <janeliaws.maven-enforcer-plugin.version>3.0.0-M2</janeliaws.maven-enforcer-plugin.version>
 
+        <!-- Temporary: remove once janelia-jhdf5 is released (then use the release version). -->
+        <janelia-jhdf5.version>22.03.01-SNAPSHOT</janelia-jhdf5.version>
+
     </properties>
 
     <repositories>
@@ -183,6 +186,14 @@
                 <enabled>false</enabled>
             </snapshots>
         </repository>
+        <!-- Temporary: remove once janelia-jhdf5 is released.
+             org.bytedeco snapshots (javacpp, hdf5) needed by janelia-jhdf5 until they are released. -->
+        <repository>
+            <id>central-portal-snapshots</id>
+            <url>https://central.sonatype.com/repository/maven-snapshots/</url>
+            <releases><enabled>false</enabled></releases>
+            <snapshots><enabled>true</enabled></snapshots>
+        </repository>
     </repositories>
 
     <distributionManagement>