Update components for new major ImgLib2 versions

In testing this upgrade, I needed to write a custom script facilitating
execution of the mega-melt test with some SNAPSHOT components built from
branches. The script I used is preserved in SNAPSHOTS.md here, so that
we can more easily reuse it in the future. This commit also makes a
minor adjustment to the tests/run.sh script allowing the mega-melt to
continue even if the version to be cloned is a SNAPSHOT.

Base components with breaking changes:

* imglib2: 5.12.0 -> 6.1.0
* imglib2-realtransform: 3.1.2 -> 4.0.1

Downstream affected components:

* imagej-deprecated: 0.1.5 -> 0.2.0
* imagej-ops: 1.0.0 -> 2.0.0
* imglib2-algorithm: 0.13.0 -> 0.13.2
* imglib2-algorithm-gpl: 0.3.0 -> 0.3.1
* imglib2-cache: 1.0.0-beta-16 -> 1.0.0-beta-17
* imglib2-imglyb: 1.1.0 -> 2.0.0
* imglib2-roi: 0.13.0 -> 0.14.1
* scifio: 0.44.1 -> 0.45.0
* Colocalisation_Analysis: 3.0.5 -> 3.0.6
* SPIM_Registration: 5.0.24 -> 5.0.25
* z_spacing: 1.1.1 -> 1.1.2
* bigdataviewer-core: 10.4.5 -> 10.4.6
* bigdataviewer-server: 3.1.1 -> 3.1.2
* bigdataviewer-vistools: 1.0.0-beta-31 -> 1.0.0-beta-32
* bigdataviewer_fiji: 6.2.3 -> 6.2.4
* TrackMate: 7.11.0 -> 7.11.1
* n5-imglib2: 4.4.0 -> 5.0.0
* BigStitcher: 1.1.5 -> 1.1.6
* multiview-reconstruction: 1.2.8 -> 2.0.0
* labkit-pixel-classification: 0.1.16 -> 0.1.17
* labkit-ui: 0.3.10 -> 0.3.11

Co-authored-by: Mark Hiner <hiner@wisc.edu>

Author: ctrueden

SNAPSHOTS.md

@@ -0,0 +1,52 @@
+So, you want to run the mega-melt, but with some SNAPSHOTs built from branches?
+
+Here is an example script that does so for the labkit-pixel-classification and
+labkit-ui components. Copy this script into a file called `go`, change the
+`adjust`... lines below to match the branches of your SNAPSHOT component(s),
+  and then give it a try with `sh go`!
+
+```shell
++#!/bin/sh
++
++# Fail on error.
++set -e
++
++# Generate the mega melt structure.
++tests/run.sh -s
++
++# Pull appropriate branches, build artifacts, and install them locally.
++adjust() {
++  dir=$1
++  remote=$2
++  branch=$3
++  cd "target/mega-melt/melting-pot/$dir"
++
++  # fetch the needed branch
++  git remote add upstream "$remote"
++  git fetch upstream
++
++  # discard pom.xml hacks
++  git checkout pom.xml
++
++  # switch to the needed branch
++  git checkout "upstream/$branch"
++
++  # reapply pom.xml hacks
++  mv pom.xml pom.xml.original &&
++  sed -E -e 's_(https?://maven.imagej.net|http://maven.scijava.org)_https://maven.scijava.org_g' \
++    -e 's_http://maven.apache.org/xsd_https://maven.apache.org/xsd_g' pom.xml.original > pom.xml ||
++    die "Failed to adjust pom.xml"
++  perl -0777 -i -pe 's/(<parent>\s*<groupId>org.scijava<\/groupId>\s*<artifactId>pom-scijava<\/artifactId>\s*<version>)[^\n]*/${1}999-mega-melt<\/version>/igs' pom.xml
++
++  # build and install the component
++  mvn -Denforcer.skip -DskipTests -Dmaven.test.skip -Dinvoker.skip clean install
++
++  cd - >/dev/null
++}
++adjust sc.fiji/labkit-pixel-classification https://github.com/ctrueden/labkit-pixel-classification bump-to-imglib2-6.1.0
++adjust sc.fiji/labkit-ui https://github.com/ctrueden/labkit-ui bump-to-imglib2-6.1.0
++
++# Run the mega melt!
++cd target/mega-melt/melting-pot
++./melt.sh 2>&1 | tee melt.log
+```

pom.xml

@@ -487,7 +487,7 @@
 		<net.imagej.imagej-common.version>${imagej-common.version}</net.imagej.imagej-common.version>
 
 		<!-- ImageJ Deprecated - https://github.com/imagej/imagej-deprecated -->
-		<imagej-deprecated.version>0.1.5</imagej-deprecated.version>
+		<imagej-deprecated.version>0.2.0</imagej-deprecated.version>
 		<net.imagej.imagej-deprecated.version>${imagej-deprecated.version}</net.imagej.imagej-deprecated.version>
 
 		<!-- ImageJ Launcher - https://github.com/imagej/imagej-launcher -->
@@ -527,7 +527,7 @@
 		<net.imagej.imagej-opencv.version>${imagej-opencv.version}</net.imagej.imagej-opencv.version>
 
 		<!-- ImageJ Ops - https://github.com/imagej/imagej-ops -->
-		<imagej-ops.version>1.0.0</imagej-ops.version>
+		<imagej-ops.version>2.0.0</imagej-ops.version>
 		<net.imagej.imagej-ops.version>${imagej-ops.version}</net.imagej.imagej-ops.version>
 
 		<!-- ImageJ Plugins: Batch - https://github.com/imagej/imagej-plugins-batch -->
@@ -581,39 +581,39 @@
 		<!-- ImgLib2 - https://github.com/imglib -->
 
 		<!-- ImgLib2 - https://github.com/imglib/imglib2 -->
-		<imglib2.version>5.12.0</imglib2.version>
+		<imglib2.version>6.1.0</imglib2.version>
 		<net.imglib2.imglib2.version>${imglib2.version}</net.imglib2.imglib2.version>
 
 		<!-- ImgLib2 Algorithms - https://github.com/imglib/imglib2-algorithm -->
-		<imglib2-algorithm.version>0.13.0</imglib2-algorithm.version>
+		<imglib2-algorithm.version>0.13.2</imglib2-algorithm.version>
 		<net.imglib2.imglib2-algorithm.version>${imglib2-algorithm.version}</net.imglib2.imglib2-algorithm.version>
 
 		<!-- ImgLib2 Algorithms FFT - https://github.com/imglib/imglib2-algorithm-fft -->
 		<imglib2-algorithm-fft.version>0.2.1</imglib2-algorithm-fft.version>
 		<net.imglib2.imglib2-algorithm-fft.version>${imglib2-algorithm-fft.version}</net.imglib2.imglib2-algorithm-fft.version>
 
 		<!-- ImgLib2 Algorithms GPL - https://github.com/imglib/imglib2-algorithm-gpl -->
-		<imglib2-algorithm-gpl.version>0.3.0</imglib2-algorithm-gpl.version>
+		<imglib2-algorithm-gpl.version>0.3.1</imglib2-algorithm-gpl.version>
 		<net.imglib2.imglib2-algorithm-gpl.version>${imglib2-algorithm-gpl.version}</net.imglib2.imglib2-algorithm-gpl.version>
 
 		<!-- ImgLib2 Cache - https://github.com/imglib/imglib2-cache -->
-		<imglib2-cache.version>1.0.0-beta-16</imglib2-cache.version>
+		<imglib2-cache.version>1.0.0-beta-17</imglib2-cache.version>
 		<net.imglib2.imglib2-cache.version>${imglib2-cache.version}</net.imglib2.imglib2-cache.version>
 
 		<!-- ImgLib2 IJ - https://github.com/imglib/imglib2-ij -->
 		<imglib2-ij.version>2.0.0</imglib2-ij.version>
 		<net.imglib2.imglib2-ij.version>${imglib2-ij.version}</net.imglib2.imglib2-ij.version>
 
 		<!-- ImgLib2 ImgLyb - https://github.com/imglib/imglib2-imglyb -->
-		<imglib2-imglyb.version>1.1.0</imglib2-imglyb.version>
+		<imglib2-imglyb.version>2.0.0</imglib2-imglyb.version>
 		<net.imglib2.imglib2-imglyb.version>${imglib2-imglyb.version}</net.imglib2.imglib2-imglyb.version>
 
 		<!-- ImgLib2 RealTransform - https://github.com/imglib/imglib2-realtransform -->
-		<imglib2-realtransform.version>3.1.2</imglib2-realtransform.version>
+		<imglib2-realtransform.version>4.0.1</imglib2-realtransform.version>
 		<net.imglib2.imglib2-realtransform.version>${imglib2-realtransform.version}</net.imglib2.imglib2-realtransform.version>
 
 		<!-- ImgLib2 ROI - https://github.com/imglib/imglib2-roi -->
-		<imglib2-roi.version>0.13.0</imglib2-roi.version>
+		<imglib2-roi.version>0.14.1</imglib2-roi.version>
 		<net.imglib2.imglib2-roi.version>${imglib2-roi.version}</net.imglib2.imglib2-roi.version>
 
 		<!-- ImgLib2 Unsafe - https://github.com/imglib/imglib2-unsafe -->
@@ -623,7 +623,7 @@
 		<!-- SCIFIO - https://github.com/scifio -->
 
 		<!-- SCIFIO - https://github.com/scifio/scifio -->
-		<scifio.version>0.44.1</scifio.version>
+		<scifio.version>0.45.0</scifio.version>
 		<io.scif.scifio.version>${scifio.version}</io.scif.scifio.version>
 
 		<!-- SCIFIO-BF-compat - https://github.com/scifio/scifio-bf-compat -->
@@ -709,7 +709,7 @@
 		<Cell_Counter.version>3.0.0</Cell_Counter.version>
 		<sc.fiji.Cell_Counter.version>${Cell_Counter.version}</sc.fiji.Cell_Counter.version>
 
-		<Colocalisation_Analysis.version>3.0.5</Colocalisation_Analysis.version>
+		<Colocalisation_Analysis.version>3.0.6</Colocalisation_Analysis.version>
 		<sc.fiji.Colocalisation_Analysis.version>${Colocalisation_Analysis.version}</sc.fiji.Colocalisation_Analysis.version>
 
 		<Color_Histogram.version>2.0.7</Color_Histogram.version>
@@ -858,7 +858,7 @@
 		<SPIM_Opener.version>2.0.2</SPIM_Opener.version>
 		<sc.fiji.SPIM_Opener.version>${SPIM_Opener.version}</sc.fiji.SPIM_Opener.version>
 
-		<SPIM_Registration.version>5.0.24</SPIM_Registration.version>
+		<SPIM_Registration.version>5.0.25</SPIM_Registration.version>
 		<sc.fiji.SPIM_Registration.version>${SPIM_Registration.version}</sc.fiji.SPIM_Registration.version>
 
 		<Samples.version>2.0.3</Samples.version>
@@ -1002,25 +1002,25 @@
 		<sc.fiji.trakem2_tps.version>${trakem2_tps.version}</sc.fiji.trakem2_tps.version>
 
 		<!-- Z-Spacing correction - https://github.com/saalfeldlab/z-spacing -->
-		<z_spacing.version>1.1.1</z_spacing.version>
+		<z_spacing.version>1.1.2</z_spacing.version>
 		<sc.fiji.z_spacing.version>${z_spacing.version}</sc.fiji.z_spacing.version>
 
 		<!-- BigDataViewer - https://github.com/bigdataviewer -->
 
 		<!-- BigDataViewer Core - https://github.com/bigdataviewer/bigdataviewer-core -->
-		<bigdataviewer-core.version>10.4.5</bigdataviewer-core.version>
+		<bigdataviewer-core.version>10.4.6</bigdataviewer-core.version>
 		<sc.fiji.bigdataviewer-core.version>${bigdataviewer-core.version}</sc.fiji.bigdataviewer-core.version>
 
 		<!-- BigDataServer - https://github.com/bigdataviewer/bigdataviewer-server -->
-		<bigdataviewer-server.version>3.1.1</bigdataviewer-server.version>
+		<bigdataviewer-server.version>3.1.2</bigdataviewer-server.version>
 		<sc.fiji.bigdataviewer-server.version>${bigdataviewer-server.version}</sc.fiji.bigdataviewer-server.version>
 
 		<!-- BigDataViewer Visualization Tools - https://github.com/bigdataviewer/bigdataviewer-vistools -->
-		<bigdataviewer-vistools.version>1.0.0-beta-31</bigdataviewer-vistools.version>
+		<bigdataviewer-vistools.version>1.0.0-beta-32</bigdataviewer-vistools.version>
 		<sc.fiji.bigdataviewer-vistools.version>${bigdataviewer-vistools.version}</sc.fiji.bigdataviewer-vistools.version>
 
 		<!-- BigDataViewer Fiji - https://github.com/bigdataviewer/bigdataviewer_fiji -->
-		<bigdataviewer_fiji.version>6.2.3</bigdataviewer_fiji.version>
+		<bigdataviewer_fiji.version>6.2.4</bigdataviewer_fiji.version>
 		<sc.fiji.bigdataviewer_fiji.version>${bigdataviewer_fiji.version}</sc.fiji.bigdataviewer_fiji.version>
 
 		<!-- SPIM Data - https://github.com/bigdataviewer/spimdata -->
@@ -1030,7 +1030,7 @@
 		<!-- TrackMate - https://github.com/trackmate-sc -->
 
 		<!-- TrackMate - https://github.com/trackmate-sc/TrackMate -->
-		<TrackMate.version>7.11.0</TrackMate.version>
+		<TrackMate.version>7.11.1</TrackMate.version>
 		<sc.fiji.TrackMate.version>${TrackMate.version}</sc.fiji.TrackMate.version>
 
 		<!-- TrackMate-Cellpose - https://github.com/trackmate-sc/TrackMate-Cellpose -->
@@ -1129,7 +1129,7 @@
 		<org.janelia.saalfeldlab.n5-ij.version>${n5-ij.version}</org.janelia.saalfeldlab.n5-ij.version>
 
 		<!-- N5 ImgLib2 Bindings - https://github.com/saalfeldlab/n5-imglib2 -->
-		<n5-imglib2.version>4.4.0</n5-imglib2.version>
+		<n5-imglib2.version>5.0.0</n5-imglib2.version>
 		<org.janelia.saalfeldlab.n5-imglib2.version>${n5-imglib2.version}</org.janelia.saalfeldlab.n5-imglib2.version>
 
 		<!-- N5 Viewer for Fiji - https://github.com/saalfeldlab/n5-viewer_fiji -->
@@ -1166,8 +1166,8 @@
 		<net.haesleinhuepf.clijx-weka_.version>${clijx-weka_.version}</net.haesleinhuepf.clijx-weka_.version>
 
 		<!-- BigStitcher - https://imagej.net/plugins/bigstitcher -->
-		<BigStitcher.version>1.1.5</BigStitcher.version>
-		<multiview-reconstruction.version>1.2.8</multiview-reconstruction.version>
+		<BigStitcher.version>1.1.6</BigStitcher.version>
+		<multiview-reconstruction.version>2.0.0</multiview-reconstruction.version>
 		<multiview-simulation.version>0.2.0</multiview-simulation.version>
 		<net.preibisch.BigStitcher.version>${BigStitcher.version}</net.preibisch.BigStitcher.version>
 		<net.preibisch.multiview-reconstruction.version>${multiview-reconstruction.version}</net.preibisch.multiview-reconstruction.version>
@@ -1195,8 +1195,8 @@
 		<sc.fiji.MaMuT.version>${MaMuT.version}</sc.fiji.MaMuT.version>
 
 		<!-- Labkit - https://imagej.net/plugins/labkit -->
-		<labkit-pixel-classification.version>0.1.16</labkit-pixel-classification.version>
-		<labkit-ui.version>0.3.10</labkit-ui.version>
+		<labkit-pixel-classification.version>0.1.17</labkit-pixel-classification.version>
+		<labkit-ui.version>0.3.11</labkit-ui.version>
 		<sc.fiji.labkit-pixel-classification.version>${labkit-pixel-classification.version}</sc.fiji.labkit-pixel-classification.version>
 		<sc.fiji.labkit-ui.version>${labkit-ui.version}</sc.fiji.labkit-ui.version>
 

tests/run.sh

@@ -111,7 +111,7 @@ chmod +x "$meltingPotScript" &&
 # NB: The pipe to tee eats the melting-pot error code.
 # Even with the POSIX-unfriendly pipefail flag set.
 # So we resort to this hacky error check of the log.
-grep -qF "[ERROR]" "$meltingPotLog" &&
+test "$(grep -F "[ERROR]" "$meltingPotLog" | grep -v "using default branch")" &&
   die 'Melting pot generation failed!'
 
 sectionStart 'Adjusting the melting pot'
@@ -190,7 +190,7 @@ chmod +x "$meltScript" ||
 # fixed in imagej-ops. But for now, let's not let it ruin the melt.
 rm -f "$meltingPotDir/net.imagej/imagej-ops/src/test/java/net/imagej/ops/cached/CachedOpEnvironmentTest.java"
 
-# TEMP: Until saalfeldlab/n5-aws-s3#13 is fixed.
+# TEMP: Until saalfeldlab/n5-aws-s3#13 is released.
 echo "org.janelia.saalfeldlab/n5-aws-s3" >> "$skipTestsFile" &&
 
 # Error while checking the CLIJ2 installation: null