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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>
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What changed
modules/Viewer3D/pom.xml: replacech.systems.cisd:jhdf5:14.12.0withorg.scijava:janelia-jhdf5. janelia-jhdf5 is a drop-in replacement for cisd:jhdf5 19.04.x (samech.systemsx.cisd.hdf5.*packages) running on HDF5 2.x via javacpp-presets, and it vendors cisd:base.IHDF5LegacyReaderandncsa.hdf.hdf5lib).H5JLoader.javaonly usesIHDF5Reader,object().hasAttributeandint64().getAttr, so no source changes were needed.Draft status
Draft until janelia-jhdf5 is released, which needs a stable javacpp-presets 1.5.15 with HDF5 2.2.0. Until then it depends on
22.03.01-SNAPSHOTplus temporary plumbing, each part commented "remove once janelia-jhdf5 is released":pom.xml:janelia-jhdf5.versionproperty and the bytedeco snapshot repository (https://central.sonatype.com/repository/maven-snapshots/).github/workflows/maven.yml: steps that check out andmvn installjanelia-jhdf5 into~/.m2before the buildBuild/test results
mvn -pl modules/Viewer3D -am compile(JDK 21, linux-x86_64, janelia-jhdf5 snapshot installed locally): BUILD SUCCESS. The CI workflow uses JDK 8, which was not available here, so the CI change is untested. No tests were run (the module has no H5J tests), and H5J loading was not exercised at runtime.Open issues (need attention before merging)
modules/Viewer3D/pom.xmlpinsorg.bytedeco:javacpp:0.10andjavacpp-presets:ffmpeg:2.5.1-0.10. Because that is a direct dependency it wins over the javacpp 1.5.15-SNAPSHOT that janelia-jhdf5/hdf5 need, so HDF5 would almost certainly fail to load at runtime until the ffmpeg/javacpp stack is upgraded (or isolated) as well. I did not change this.librariesmodule pulls incisd:jhdf5:19.04.1(andcisd:base) transitively viaorg.janelia.saalfeldlab:n5-hdf5:2.2.0(through jacsstorage-clients / n5-universe). That duplicates thech.systemsx.cisd.hdf5classes if they share a class path with janelia-jhdf5. As these are separate NetBeans modules it may be fine, but it should be checked.🤖 Generated with Claude Code