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Temporary: depends on janelia-jhdf5 22.03.01-SNAPSHOT, adds the bytedeco snapshot repository and a CI step that builds janelia-jhdf5 first. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
This was referenced Oct 16, 2026
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What changed
components/formats-bsd/pom.xml: replacecisd:jhdf5:19.04.1withorg.scijava:janelia-jhdf5:22.03.01-SNAPSHOT. Thetest-no-hdfsurefire execution now excludesorg.scijava:janelia-jhdf5from the classpath.JHDFServiceImpl: the "JHDF is required" message no longer points to the obsoletecisd-jhdf5-batteries_included_lin_win_mac.jar.ch.systemsx.cisd.hdf5.*/ch.systemsx.cisd.base.*packages.pom.xml, and two steps in.github/workflows/maven.ymlthat build and install the janelia-jhdf5 snapshot before the Bio-Formats build.Why
cisd:jhdf5 19.04.1 is unmaintained, bundles old HDF5 1.10 natives and only supports a few platforms. janelia-jhdf5 is a drop-in replacement with the same API that runs on HDF5 2.x through bytedeco and supports more platforms (including macOS arm64, Linux arm64, Windows). Many downstream projects get JHDF5 transitively through Bio-Formats.
Draft: waiting on a janelia-jhdf5 release
janelia-jhdf5 is not released yet (22.03.01-SNAPSHOT, which also needs javacpp/hdf5 1.5.15-SNAPSHOT / 2.2.0 from the bytedeco snapshot repo). When released: set the real version in formats-bsd/pom.xml, remove the snapshot repository from the root pom.xml, and remove the two janelia-jhdf5 steps from maven.yml.
Testing
Locally on JDK 21, with janelia-jhdf5 installed in ~/.m2:
mvn -pl components/formats-bsd -am installpassed: formats-bsd 1525 tests (includes JHDFServiceTest) plus thetest-no-hdfrun (MissingJHDFServiceTest) with 0 failures; formats-api 224 tests passed.dependency:treeshows nocisd:*artifacts. Only formats-bsd referenced jhdf5, so other modules were not rebuilt. Not run: the CI matrix (Java 11/17/21/25 on 3 OSes) and the Java 8 baseline.Licensing
janelia-jhdf5: BSD-3-Clause for new code, Apache-2.0 for inherited JHDF5/cisd:base code. Dependencies: bytedeco hdf5/javacpp (HDF5 license, Apache-2.0 or GPLv2+Classpath), jnr-posix (EPL-2.0 / GPL-2 / LGPL-2.1 multi-license).
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