Address melting-pot incompatibilities to facilitate 32.0.0 final release

[ctrueden]

This is a catch-all issue to keep track of problems across the SciJava component collection which must be resolved in order to regain harmony across the bill of materials. Please edit this summary with issues as they are discovered.

• ImageJ 1.53h breaks line bounds imagej/imagej-legacy#279 (behavior breakage in 1.53h)
• Make SNT available in scijava-pom morphonets/SNT#108
• Update to pom-scijava 29 API imagej/imagej-omero#107
• Error with latest Fiji + imagej-server update site imagej/imagej-server#41
• Error when starting the server in Fiji imagej/imagej-server#44
• bigdataviewer-core.version needs to be >=10.3.1 in order to be compatible with jhdf5.version=19.04.0 (e6e17ce)
• `bigdataviewer-core 10.4.0 breaks compilation trackmate-sc/MaMuT#30
• Fix CI build for fiji/H5J_Loader_Plugin, so that it can be released

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/timeline-for-the-next-fiji-update/69640/3

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/timeline-for-the-next-fiji-update/69640/4

[ctrueden]

2022-08-16 status update

Fixed but release needed

• org.janelia.saalfeldlab/n5-hdf5 -- jhdf5 version skew (fixed by Use datasetExists for dataset specific attributes saalfeldlab/n5-hdf5#17)
• sc.fiji:bigwarp_fiji -- bdv version skew (fixed by Fix compile errors with bigdataviewer-core-10.4.1 saalfeldlab/bigwarp#145)

Compile errors (API breakage)

• io.scif/scifio-ome-xml -- scifio version skew (0.39.1 -> 0.43.1) -- no such method io.scif.formats.ICSFormat.Metadata.getPixelSizes() -- Project does not build against scifio 0.43.x scifio/scifio-ome-xml#30
• sc.fiji/bigdataviewer-server -- missing dependencies: net.imglib2:imglib2-ui, commons-lang:commons-lang
• sc.fiji:MaMuT -- bdv version skew -- display has private access in bdv.viewer.ViewerPanel -- bigdataviewer-core 10.4.0 breaks compilation trackmate-sc/MaMuT#30

Test errors (behavior breakage)

• net.imagej/imagej-legacy -- ij version skew -- ImageJ 1.53h breaks line bounds imagej/imagej-legacy#279
• org.janelia.saalfeldlab/n5-aws-s3 -- The specified bucket does not exist
• org.scijava/scripting-kotlin -- kotlin version skew
• sc.fiji/KymographBuilder -- ij or imagej-legacy version skew -- javassist.NotFoundException: ij.plugin.MacAdapter
• sc.fiji/labkit-pixel-classification -- CLIJ2 problem: Error while checking the CLIJ2 installation: null
• org.janelia.saalfeldlab/n5-viewer_fiji -- java.lang.NoClassDefFoundError: org/w3c/dom/ElementTraversal
  • HACK: add xml-apis dependency (just depending on new pom-scijava 32 doesn't fix it, maybe because some dependency upstream already has xml-apis excluded by its use of an older pom-scijava)

EJML 0.24 -> 0.25

• net.imglib2/imglib2-realtransform -- java.lang.NoSuchMethodError: org.ejml.factory.LinearSolverFactory.linear(I)Lorg/ejml/factory/LinearSolver
• jitk/jitk-tps -- no such class org.ejml.factory.LinearSolver

502 Bad Gateway from dl.bintray.com

• sc.fiji/FS_Align_TrakEM2
• sc.fiji/Reconstruct_Reader
• sc.fiji/T2-NIT
• sc.fiji/T2-TreelineGraph
• sc.fiji/TrakEM2_
• sc.fiji/TrakEM2_Archipelago
• sc.fiji/blockmatching_
• sc.fiji/register_virtual_stack_slices
• sc.fiji/z_spacing

[tpietzsch]

@ctrueden trackmate-sc/MaMuT#31 fixes trackmate-sc/MaMuT#30

I released MaMuT-7.0.6 with the fix.

[ctrueden]

@tpietzsch Do you have time to fix bigdataviewer-server today or tomorrow?

[tpietzsch]

@tpietzsch Do you have time to fix bigdataviewer-server today or tomorrow?

Sure!

[ctrueden]

@tpietzsch Thanks! This diff should be enough to find the problems:

diff --git a/pom.xml b/pom.xml
index 5643f41..09d9b1c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,7 +5,7 @@
        <parent>
                <groupId>org.scijava</groupId>
                <artifactId>pom-scijava</artifactId>
-               <version>28.0.0</version>
+               <version>32.0.0-beta-5</version>
                <relativePath />
        </parent>

@@ -86,12 +86,6 @@

                <commons-cli.version>1.2</commons-cli.version>
                <stringtemplate.version>3.2.1</stringtemplate.version>
-
-               <!-- TODO: Remove these version pins and update the code. -->
-               <bigdataviewer-core.version>9.0.3</bigdataviewer-core.version>
-               <imglib2.version>5.9.0</imglib2.version>
-               <imglib2-cache.version>1.0.0-beta-13</imglib2-cache.version>
-               <spim_data.version>2.2.4</spim_data.version>
        </properties>

        <repositories>

[ctrueden]

2022-08-18 status update

SOLVED

• scifio-ome-xml -- released 0.17.1
• imagej-omero -- released 1.0.0-5.5
• imagej-omero-legacy -- released 1.0.0-5.5
• sc.fiji:MaMuT -- released 7.0.6
• org.janelia.saalfeldlab/n5-aws-s3 -- SKIP TESTS (The specified bucket does not exist)
• sc.fiji/labkit-pixel-classification -- SKIP TESTS (Error while checking the CLIJ2 installation: null)
• org.janelia.saalfeldlab/n5-blosc -- SKIP TESTS (java.lang.UnsatisfiedLinkError: Unable to load library 'blosc')
• org.janelia.saalfeldlab/n5-zarr -- SKIP TESTS (java.lang.UnsatisfiedLinkError: Unable to load library 'blosc')

Fixed but release needed

• org.janelia.saalfeldlab/n5-hdf5 -- jhdf5 version skew (fixed by Use datasetExists for dataset specific attributes saalfeldlab/n5-hdf5#17)
• sc.fiji:bigwarp_fiji -- bdv version skew (fixed by Fix compile errors with bigdataviewer-core-10.4.1 saalfeldlab/bigwarp#145)

Compile errors (API breakage)

• sc.fiji/bigdataviewer-server -- missing dependencies: net.imglib2:imglib2-ui, commons-lang:commons-lang

Test errors (behavior breakage)

• net.imagej/imagej-legacy -- ij version skew -- ImageJ 1.53h breaks line bounds imagej/imagej-legacy#279
• org.scijava/scripting-kotlin -- kotlin version skew
• sc.fiji/KymographBuilder -- ij or imagej-legacy version skew -- javassist.NotFoundException: ij.plugin.MacAdapter (affects macOS ONLY)
• org.janelia.saalfeldlab/n5-viewer_fiji -- java.lang.NoClassDefFoundError: org/w3c/dom/ElementTraversal -- needs to inherit xml-apis as a dependency

EJML 0.24 -> 0.25

• net.imglib2/imglib2-realtransform -- java.lang.NoSuchMethodError: org.ejml.factory.LinearSolverFactory.linear(I)Lorg/ejml/factory/LinearSolver
• jitk/jitk-tps -- no such class org.ejml.factory.LinearSolver

502 Bad Gateway from dl.bintray.com (see morphonets/SNT#108)

• sc.fiji/FS_Align_TrakEM2
• sc.fiji/Reconstruct_Reader
• sc.fiji/T2-NIT
• sc.fiji/T2-TreelineGraph
• sc.fiji/TrakEM2_
• sc.fiji/TrakEM2_Archipelago
• sc.fiji/blockmatching_
• sc.fiji/register_virtual_stack_slices
• sc.fiji/z_spacing

[tpietzsch]

@ctrueden I fixed bigdataviewer-server and released bigdataviewer-server-3.1.0