toward HDF5 2.2.0

[bogovicj]

waiting on bytedeco/javacpp-presets#1808 and a new release of https://github.com/JaneliaSciComp/janelia-jhdf5/

[mkitti]

Downstream check of this PR against the HDF5 2.2.0 work in janelia-jhdf5, on macOS arm64.

It works once janelia-jhdf5 loads its own native library. Built against janelia-jhdf5 with JaneliaSciComp/janelia-jhdf5#13 and #14 (installed locally as 22.03.01-SNAPSHOT) and org.bytedeco:hdf5:2.2.0-1.5.15-SNAPSHOT, mvn test passes 47 tests with 5 skipped. That's identical to master (cbabb1a) with cisd:jhdf5.

Depends on janelia-jhdf5 #13. Against the janelia-jhdf5 stack without #13, 40 of 47 tests error with UnsatisfiedLinkError: 'int hdf.hdf5lib.H5.H5dont_atexit()', because nothing in janelia-jhdf5's main code loaded hdf5_java. #13 fixes that, and #14 fixes the case where an enum such as CharacterEncoding or HDF5DataClass is touched before a factory.

Before this can merge:

• Snapshot dependencies. pom-scijava's RequireReproducibleBuilds enforcer rule fails on org.scijava:janelia-jhdf5:22.03.01-SNAPSHOT. The local check used -Denforcer.skip=true. This needs releases of janelia-jhdf5 and of the bytedeco presets.
• CI can't resolve the snapshots. The janelia-jhdf5 snapshot isn't published anywhere, and the org.bytedeco snapshots live at https://central.sonatype.com/repository/maven-snapshots/, which isn't among this project's repositories. Fine for a draft.
• Natives on other platforms. janelia-jhdf5's published pom currently brings only macosx-arm64 natives. JaneliaSciComp/janelia-jhdf5#11 switches it to hdf5-platform; until then, this would fail on Linux, Windows and Intel Macs.
• Windows additionally needs bytedeco/javacpp-presets#1814: without it, the two HDF5 Java bindings load separate HDF5 libraries on Windows.

Small suggestions:

• slf4j: slf4j-api is only needed because org.bytedeco:hdf5 leaves it optional while hdf.hdf5lib.H5 requires it. That's better declared once in janelia-jhdf5 as a regular dependency, so each consumer doesn't have to. Keeping it here meanwhile is fine.
• Version overrides: the javacpp.version/hdf5.version overrides must stay in step with whatever janelia-jhdf5 is built against. They can be dropped once pom-scijava manages those versions.

🤖 Generated with Claude Code

[mkitti]

Suggestions to make this draft build in CI while it waits on the releases. These mirror what we did for the other repos in the migration to janelia-jhdf5 (e.g. fiji/HDF5_Vibez#22, bigdataviewer/bigdataviewer-core#228), so the temporary plumbing looks the same everywhere and is easy to find and remove later.

1. pom.xml: add the snapshot repository that org.bytedeco:hdf5:2.2.0-1.5.15-SNAPSHOT and javacpp come from, and mark the temporary parts:

<repositories>
	<!-- Temporary: 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>

(If the project already declares scijava.public, keep it alongside.) A "remove once janelia-jhdf5 is released" comment on janelia-jhdf5.version makes the cleanup list obvious.

2. .github/workflows/build-pr.yml and build-main.yml: build and install the janelia-jhdf5 snapshot first, and skip the SNAPSHOT-rejecting enforcer rule:

      # 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
        shell: bash

and on the build step:

        env:
          # pom-scijava's enforcer rejects SNAPSHOT dependencies.
          MAVEN_ARGS: -Denforcer.skip=true

platform-test.yml (plain mvn -B clean test) would need the same two additions, plus -Denforcer.skip=true; its other platforms also need the hdf5-platform natives from JaneliaSciComp/janelia-jhdf5#11 as noted above, so it can stay red until then.

3. Downstream note: since n5-hdf5 currently brings cisd:jhdf5:19.04.1 into consumers transitively, projects that depend on n5-hdf5 and already moved to janelia-jhdf5 (e.g. saalfeldlab/transform-helpers#8) have to exclude it, otherwise both jars (with duplicate ch.systemsx.cisd.* classes) are on the classpath. Once this PR merges and is released, those exclusions can be dropped.

If it helps, I can push these changes to a branch on mkitti/n5-hdf5 for you to cherry-pick, or open a PR against saalfeldlab:janelia-jhdf5.

🤖 Generated with Claude Code