pom-scijava

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The **Java-8** update site currently ships `json-20090211.jar` as a runtime dependency of `SPIM_Registration` (via `formats-gpl`), but the version isn't managed here in `pom-scijava` and the currently shipped version is outdated...

imagejan

[Trainable Segmentation](https://github.com/fiji/Trainable_Segmentation/tree/update-tests) needs ImageJ 1.53u to complete its updated unit tests. It can then be re-enabled in melting pot.

hinerm

Decide whether to stop excluding xalan and serializer

2

The `ome:formats-api` and `ome:formats-bsd` and `ome:bio-formats-tools` components have runtime dependencies on `xalan:xalan` and `xalan:serializer`. Right now pom-scijava excludes these dependencies—and also from `org.apache.xmlgraphics:batik-bridge` and `org.apache.xmlgraphics:batik-dom` and `ch.qos.logback:logback-classic`—for reasons that have...

ctrueden

After adding the TrackMate extensions to pom-scijava (9ec5bc2380334e1d9ce9bb479b0141e2fecd8363), there are duplicate classes in the mega-melt: ``` No Duplicate Classes Allowed! - For duplicate transitive dependencies, add dependency exclusions. - For...

ctrueden

cisd.base needs an update for its native binaries

1

While we added macosx-arm binaries to `cisd.jhdf5`, `cisd.base` also contains binaries and needs an update: https://sissource.ethz.ch/sispub/base/-/tree/master/libs/native I'll figure out how to compile this and get in touch with Bernd Rinn.

mkitti

Convert remaining repositories to GitHub Actions

1

Here's a list of artifacts still using Travis, according to status.scijava.org: #### Infrastructure * [x] sc.fiji : fiji-builds [ @ctrueden ] #### First party * [ ] [net.imagej : imagej-launcher](https://github.com/imagej/imagej-launcher/)...

ctrueden

Improve our approach to javadoc linking

3

The [pom-scijava-base](https://github.com/scijava/pom-scijava-base) ancestor POM includes [configuration hardcoding several links](https://github.com/scijava/pom-scijava-base/blob/master/pom.xml#L412-L455) for the javadoc tool. This configuration makes classes for SciJava-based projects clickable, pointing uniformly to [javadoc.scijava.org](https://javadoc.scijava.org/) endpoints aggregating multiple components. For...

ctrueden

Ensure imagej-server works with latest BOM

1

The ImageJ Server codebase needs some updates to work with pom-scijava 29. Updating the imagej-server POM (see `pom-sj-29` branch) yields the following compile errors: ``` [ERROR] .../imagej-server/src/main/java/net/imagej/server/resources/ObjectsResource.java:[29,18] cannot find symbol...

ctrueden

building ComDet plugin as maven artifact

2

Hello @ctrueden, following on this topic https://github.com/imagej/pyimagej/issues/173#issuecomment-1038473992 If you can point me towards some docs on how I can build and publish the plugin in maven. Thanks in advance for...

ekatrukha

Melting-pot failures with Java 11

3

I ran into the following failures when building the melting pot with a J11 JDK: ``` [FAILURE] io.scif/scifio [FAILURE] io.scif/scifio-hdf5 [FAILURE] io.scif/scifio-jai-imageio [FAILURE] net.imagej/ij1-patcher [FAILURE] net.imagej/imagej-tensorflow [FAILURE] net.imglib2/imglib2-label-multisets [FAILURE] net.imglib2/imglib2-unsafe...

hinerm