8000 Update components for new major ImgLib2 versions · scijava/pom-scijava@7464ac6 · GitHub
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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>
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‎SNAPSHOTS.md

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

‎pom.xml

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

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

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