From fc79e268422b16edbaddbd94cc62b31c123c0bd3 Mon Sep 17 00:00:00 2001 From: Curtis Rueden Date: Wed, 28 Aug 2024 10:11:38 -0500 Subject: [PATCH 01/10] mega-melt: split the process into more sections Specifically: the "Adjusting the melting pot" section was rather long, performing a series of different sorts of adjustments. This patch splits that step into multiple more fine-grained sections, in an attempt to ease navigation of the shell script code. --- tests/run.sh | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/tests/run.sh b/tests/run.sh index 0b64a7d..d50cf81 100755 --- a/tests/run.sh +++ b/tests/run.sh @@ -114,7 +114,7 @@ chmod +x "$meltingPotScript" && test "$(grep -F "[ERROR]" "$meltingPotLog" | grep -v "using default branch")" && die 'Melting pot generation failed!' -sectionStart 'Adjusting the melting pot' +sectionStart 'Adjusting the melting pot: build.sh script' buildScript="$meltingPotDir/build.sh" buildScriptTemp="$buildScript.tmp" @@ -177,6 +177,10 @@ chmod +x "$buildScript" && rm "$buildScriptTemp" || die 'Error adjusting melting pot build script!' +sectionEnd # Adjusting the melting pot: build.sh script + +sectionStart 'Adjusting the melting pot: component POMs' + # HACK: Adjust component POMs to satisfy Maven HTTPS strictness. find "$meltingPotDir" -name pom.xml | while read pom @@ -195,6 +199,10 @@ do perl -0777 -i -pe 's/(\s*org.scijava<\/groupId>\s*pom-scijava<\/artifactId>\s*)[^\n]*/${1}999-mega-melt<\/version>/igs' "$pom" done +sectionEnd # Adjusting the melting pot: component POMs + +sectionStart 'Adjusting the melting pot: melt.sh script' + # HACK: Skip tests for projects with known problems. mv "$meltScript" "$meltScript.original" && @@ -207,6 +215,10 @@ grep -qxF "$f" $dir/skipTests.txt \&\& buildFlags=-DskipTests\ chmod +x "$meltScript" || die "Failed to adjust $meltScript" +sectionEnd # Adjusting the melting pot: melt.sh script + +sectionStart 'Adjusting the melting pot: unit test hacks' + # HACK: Remove flaky tests from imagej-ops builds. # CachedOpEnvironmentTest fails intermittently. Of course, it should be # somehow fixed in imagej-ops. But for now, let's not let it ruin the melt. @@ -219,7 +231,7 @@ echo "org.janelia.saalfeldlab/n5-aws-s3" >> "$skipTestsFile" && echo "sc.fiji/labkit-pixel-classification" >> "$skipTestsFile" || die "Failed to generate $skipTestsFile" -sectionEnd # Adjusting the melting pot +sectionEnd # Adjusting the melting pot: unit test hacks # Run the melting pot now, unless -s flag was given. doMelt=t From d240bfd48e2a87e7088fe0df044206318b3ed2e6 Mon Sep 17 00:00:00 2001 From: Curtis Rueden Date: Wed, 28 Aug 2024 12:49:40 -0500 Subject: [PATCH 02/10] mega-melt: eliminate buildScriptTemp variable It doesn't actually save any characters. --- tests/run.sh | 27 +++++++++++++-------------- 1 file changed, 13 insertions(+), 14 deletions(-) diff --git a/tests/run.sh b/tests/run.sh index d50cf81..260fe74 100755 --- a/tests/run.sh +++ b/tests/run.sh @@ -117,31 +117,30 @@ test "$(grep -F "[ERROR]" "$meltingPotLog" | grep -v "using default branch")" && sectionStart 'Adjusting the melting pot: build.sh script' buildScript="$meltingPotDir/build.sh" -buildScriptTemp="$buildScript.tmp" cp "$buildScript" "$buildScript.original" && # HACK: Remove known-duplicate short version properties, keeping # the short version declaration only for the more common groupId. # E.g.: org.antlr:antlr is preferred over antlr:antlr, so we set # antlr.version to match org.antlr:antlr, not antlr:antlr. -mv -f "$buildScript" "$buildScriptTemp" && -sed -E 's;(-D('"$shortVersionClashes"').version=[^ ]*) -D[^ ]*;\1;' "$buildScriptTemp" > "$buildScript" && +mv -f "$buildScript" "$buildScript.tmp" && +sed -E 's;(-D('"$shortVersionClashes"').version=[^ ]*) -D[^ ]*;\1;' "$buildScript.tmp" > "$buildScript" && # HACK: Add leading underscore to version properties that start with a digit. -mv -f "$buildScript" "$buildScriptTemp" && -sed -E 's; -D([0-9][^ ]*);& -D_\1;' "$buildScriptTemp" > "$buildScript" && +mv -f "$buildScript" "$buildScript.tmp" && +sed -E 's; -D([0-9][^ ]*);& -D_\1;' "$buildScript.tmp" > "$buildScript" && # HACK: Add non-standard version properties used prior to # pom-scijava 32.0.0-beta-1; see d0bf752070d96a2613c42e4e1ab86ebdd07c29ee. -mv -f "$buildScript" "$buildScriptTemp" && -sed -E 's; -Dsc.fiji.3D_Blob_Segmentation\.version=([^ ]*);& -DFiji_3D_Blob_Segmentation.version=\1;' "$buildScriptTemp" > "$buildScript" && -mv -f "$buildScript" "$buildScriptTemp" && -sed -E 's; -Dsc.fiji.(3D_Objects_Counter|3D_Viewer)\.version=([^ ]*);& -DImageJ_\1.version=\2;' "$buildScriptTemp" > "$buildScript" && +mv -f "$buildScript" "$buildScript.tmp" && +sed -E 's; -Dsc.fiji.3D_Blob_Segmentation\.version=([^ ]*);& -DFiji_3D_Blob_Segmentation.version=\1;' "$buildScript.tmp" > "$buildScript" && +mv -f "$buildScript" "$buildScript.tmp" && +sed -E 's; -Dsc.fiji.(3D_Objects_Counter|3D_Viewer)\.version=([^ ]*);& -DImageJ_\1.version=\2;' "$buildScript.tmp" > "$buildScript" && # HACK: Add non-standard net.imagej:ij version property used prior to # pom-scijava 28.0.0; see 7d2cc442b107b3ac2dcb799d282f2c0b5822649d. -mv -f "$buildScript" "$buildScriptTemp" && -sed -E 's; -Dij\.version=([^ ]*);& -Dimagej1.version=\1;' "$buildScriptTemp" > "$buildScript" && +mv -f "$buildScript" "$buildScript.tmp" && +sed -E 's; -Dij\.version=([^ ]*);& -Dimagej1.version=\1;' "$buildScript.tmp" > "$buildScript" && # HACK: Add explicit kotlin.version to match our pom-scijava-base. # Otherwise, components built on older pom-scijava-base will have @@ -170,11 +169,11 @@ enforcerVersion=$( mvn -B -U -q -Denforcer.skip=true -Dexec.executable=echo \ -Dexec.args='${maven-enforcer-plugin.version}' --non-recursive validate exec:exec 2>&1 | head -n1 | sed 's;\(.\[[0-9]m\)*;;') && -mv -f "$buildScript" "$buildScriptTemp" && -sed -E "s;mvn -Denforcer.skip;& -Dmaven-enforcer-plugin.version=$enforcerVersion -Dkotlin.version=$kotlinVersion;" "$buildScriptTemp" > "$buildScript" && +mv -f "$buildScript" "$buildScript.tmp" && +sed -E "s;mvn -Denforcer.skip;& -Dmaven-enforcer-plugin.version=$enforcerVersion -Dkotlin.version=$kotlinVersion;" "$buildScript.tmp" > "$buildScript" && chmod +x "$buildScript" && -rm "$buildScriptTemp" || +rm "$buildScript.tmp" || die 'Error adjusting melting pot build script!' sectionEnd # Adjusting the melting pot: build.sh script From 4a38357ca084a56f071ad3db5540c4bb545c0de2 Mon Sep 17 00:00:00 2001 From: Curtis Rueden Date: Wed, 28 Aug 2024 15:06:31 -0500 Subject: [PATCH 03/10] mega-melt: use absolute path for base directories So that while in a different directory, the various path strings are all still correct and functional. --- tests/run.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/run.sh b/tests/run.sh index 260fe74..2a5c0b1 100755 --- a/tests/run.sh +++ b/tests/run.sh @@ -19,14 +19,14 @@ sectionEnd() { sectionStart 'Generating mega-melt project' -dir=$(dirname "$0") +dir=$(cd "$(dirname "$0")" && pwd) pom="$dir/../pom.xml" test -f "$pom" || die 'Where is pom.xml?!' generateMegaMeltScript="$dir/generate-mega-melt.py" filterBuildLogScript="$dir/filter-build-log.py" -megaMeltDir="$dir/../target/mega-melt" +megaMeltDir=$(cd "$dir/../target/mega-melt" && pwd) pomParent="$megaMeltDir/../pom.xml" versionSwapLog="$megaMeltDir/version-swap.log" dependencyTreeLog="$megaMeltDir/dependency-tree.log" From a9c0e8685e595cbe5701014ba1932247b50029d6 Mon Sep 17 00:00:00 2001 From: Curtis Rueden Date: Wed, 28 Aug 2024 12:50:12 -0500 Subject: [PATCH 04/10] mega-melt: add in a section for changed components Empty by default, but configurable to mix in PRs and such. --- tests/run.sh | 124 ++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 123 insertions(+), 1 deletion(-) diff --git a/tests/run.sh b/tests/run.sh index 2a5c0b1..01304ad 100755 --- a/tests/run.sh +++ b/tests/run.sh @@ -114,9 +114,131 @@ chmod +x "$meltingPotScript" && test "$(grep -F "[ERROR]" "$meltingPotLog" | grep -v "using default branch")" && die 'Melting pot generation failed!' +buildScript="$meltingPotDir/build.sh" + +echo +echo 'Hacking in any changed components...' + +# Mix in changed components. Syntax is: +# +# groupId|artifactId|path-to-remote|remote-ref +# +# Example: +# +# components=' +# org.janelia.saalfeldlab|n5-imglib2|git@github.com:saalfeldlab/n5-imglib2|pull/54/head +# sc.fiji|SPIM_Registration|git@github.com:fiji/SPIM_Registration|pull/142/head +# sc.fiji|labkit-ui|git@github.com:juglab/labkit-ui|pull/115/head +# sc.fiji|labkit-pixel-classification|git@github.com:juglab/labkit-pixel-classification|pull/12/head +# sc.fiji|z_spacing|git@github.com:saalfeldlab/z-spacing|pull/28/head +# net.imagej|imagej-common|git@github.com:imagej/imagej-common|pull/112/head +# sc.fiji|TrackMate|git@github.com:trackmate-sc/TrackMate|pull/289/head +# sc.fiji|TrackMate-Skeleton|git@github.com:trackmate-sc/TrackMate-Skeleton|pull/2/head +# sc.fiji|bigwarp_fiji|git@github.com:saalfeldlab/bigwarp|pull/170/head +# net.imagej|imagej-ops|git@github.com:imagej/imagej-ops|pull/654/head +# ' +# +# One entry per line inside the components variable declaration. +# No leading or trailing whitespace anywhere. +# +# Each component will: +# 1. Be updated to that ref (cloning as needed); +# 2. Have its version adjusted to 999 in its pom.xml and gav marker; +# 3. Be `mvn install`ed to the local repo cache at that version; +# 4. Have its version adjusted to 999 in melting pot's build.sh; +# 5. Be added to the list of components to build in melt.sh (if not already present). +components=' +' +failFile="$meltingPotDir/fail" +rm -f "$failFile" +echo "$components" | while read component +do + test "$component" || continue + + g=${component%%|*}; r=${component#*|} + a=${r%%|*}; r=${r#*|} + remote=${r%%|*}; ref=${r#*|} + test "$g" -a "$a" -a "$remote" -a "$ref" || { + touch "$failFile" + die "Invalid component line: $component" + } + d="$meltingPotDir/$g/$a" + printf "[$g:$a] " + + # Update component working copy to desired ref (cloning as needed). + mkdir -p "$d" && + echo "Log of actions for custom version of $g:$a" > "$d/surgery.log" && + echo >> "$d/surgery.log" && + test -f "$d/.git" || git init "$d" >> "$d/surgery.log" || { + touch "$failFile" + die "Failed to access or initialize repository in directory $d" + } + printf . + cd "$d" && + git remote add mega-melt "$remote" >> surgery.log && + printf . && + git fetch mega-melt --depth 1 "$ref":mega-melt >> surgery.log 2>&1 && + printf . && + git switch mega-melt >> surgery.log 2>&1 || { + touch "$failFile" + die "$g:$a: failed to fetch ref '$ref' from remote $remote" + } + printf . + + # Adjust component version to 999. + mvn versions:set -DnewVersion=999 >> surgery.log || { + touch "$failFile" + die "$g:$a: failed to adjust pom.xml version" + } + printf . + if [ -f gav ] + then + mv gav gav.prehacks + sed -E "s;:[^:]*$;:999;" gav.prehacks > gav || { + touch "$failFile" + die "$g:$a: failed to adjust gav version" + } + fi + printf . + + # Install changed component into the local repo cache. + mvn -Denforcer.skip -Dmaven.test.skip install >> surgery.log || { + touch "$failFile" + die "$g:$a: failed to build and install component" + } + printf . + + # Adjust component version to 999 in melting pot's build.sh. + cd "$meltingPotDir" + test -f "$buildScript.prehacks" || cp "$buildScript" "$buildScript.prehacks" || { + touch "$failFile" + die "$g:$a: failed to back up $buildScript" + } + printf . + mv -f "$buildScript" "$buildScript.tmp" && + sed -E "s;(-D($g\\.)?$a\\.version)=[^ ]*;\1=999;g" "$buildScript.tmp" > "$buildScript" || { + touch "$failFile" + die "$g:$a: failed to adjust component version in $buildScript" + } + printf . + + # Add component to the build list in melt.sh (if not already present). + grep -q "\b$g/$a\b" "$meltScript" || { + test -f "$meltScript.prehacks" || cp "$meltScript" "$meltScript.prehacks" + mv -f "$meltScript" "$meltScript.tmp" && + perl -0777 -pe 's;\n+do\n;\n '"$g/$a"' \\$&;igs' "$meltScript.tmp" > "$meltScript" + } || { + touch "$failFile" + die "$g:$a: failed to add component to the build list in $meltScript" + } + printf ".\n" +done +rm -f "$buildScript.tmp" "$meltScript.tmp" +test ! -f "$failFile" || + die "Failed to hack in changed components!" + sectionStart 'Adjusting the melting pot: build.sh script' -buildScript="$meltingPotDir/build.sh" cp "$buildScript" "$buildScript.original" && # HACK: Remove known-duplicate short version properties, keeping From f3f2db3382bfbfd071f794dd38ac69fa00160233 Mon Sep 17 00:00:00 2001 From: Curtis Rueden Date: Wed, 28 Aug 2024 09:54:43 -0500 Subject: [PATCH 05/10] WIP: Test components built on ImgLib2 v7 --- pom.xml | 28 ++++++++++++++-------------- tests/run.sh | 9 +++++++++ 2 files changed, 23 insertions(+), 14 deletions(-) diff --git a/pom.xml b/pom.xml index 12a3838..4ce2471 100644 --- a/pom.xml +++ b/pom.xml @@ -482,7 +482,7 @@ ${ij1-patcher.version} - 2.1.0 + 2.1.1 ${imagej-common.version} @@ -580,11 +580,11 @@ - 6.3.0 + 7.1.0 ${imglib2.version} - 0.14.0 + 0.15.3 ${imglib2-algorithm.version} @@ -596,15 +596,15 @@ ${imglib2-algorithm-gpl.version} - 1.0.0-beta-17 + 1.0.0-beta-18 ${imglib2-cache.version} - 2.0.1 + 2.0.2 ${imglib2-ij.version} - 2.0.0 + 2.0.1 ${imglib2-imglyb.version} @@ -612,15 +612,15 @@ ${imglib2-mesh.version} - 4.0.2 + 4.0.3 ${imglib2-realtransform.version} - 0.14.1 + 0.15.0 ${imglib2-roi.version} - 1.0.0 + 1.1.0 ${imglib2-unsafe.version} @@ -1012,7 +1012,7 @@ - 10.4.14 + 10.6.0 ${bigdataviewer-core.version} @@ -1020,11 +1020,11 @@ ${bigdataviewer-server.version} - 1.0.0-beta-34 + 1.0.0-beta-36 ${bigdataviewer-vistools.version} - 6.3.0 + 6.4.0 ${bigdataviewer_fiji.version} @@ -1178,8 +1178,8 @@ ${clijx-weka_.version} - 1.2.10 - 3.2.7 + 1.3.0 + 3.4.0 0.2.0 ${BigStitcher.version} ${multiview-reconstruction.version} diff --git a/tests/run.sh b/tests/run.sh index 01304ad..7a4a7d3 100755 --- a/tests/run.sh +++ b/tests/run.sh @@ -148,6 +148,15 @@ echo 'Hacking in any changed components...' # 4. Have its version adjusted to 999 in melting pot's build.sh; # 5. Be added to the list of components to build in melt.sh (if not already present). components=' +org.janelia.saalfeldlab|n5-imglib2|git@github.com:saalfeldlab/n5-imglib2|pull/54/head +sc.fiji|SPIM_Registration|git@github.com:fiji/SPIM_Registration|pull/142/head +sc.fiji|labkit-ui|git@github.com:juglab/labkit-ui|pull/115/head +sc.fiji|labkit-pixel-classification|git@github.com:juglab/labkit-pixel-classification|pull/12/head +sc.fiji|z_spacing|git@github.com:saalfeldlab/z-spacing|pull/28/head +sc.fiji|TrackMate|git@github.com:trackmate-sc/TrackMate|pull/289/head +sc.fiji|TrackMate-Skeleton|git@github.com:trackmate-sc/TrackMate-Skeleton|pull/2/head +sc.fiji|bigwarp_fiji|git@github.com:saalfeldlab/bigwarp|pull/170/head +net.imagej|imagej-ops|git@github.com:imagej/imagej-ops|pull/654/head ' failFile="$meltingPotDir/fail" rm -f "$failFile" From 13f63e57224139a620cd5efe90b6cfe6a0896124 Mon Sep 17 00:00:00 2001 From: tpietzsch Date: Thu, 29 Aug 2024 10:23:45 +0200 Subject: [PATCH 06/10] WIP: ImgLib2 v7: Bump version spim_data-2.3.1 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 4ce2471..1084699 100644 --- a/pom.xml +++ b/pom.xml @@ -1028,7 +1028,7 @@ ${bigdataviewer_fiji.version} - 2.2.7 + 2.3.1 ${spim_data.version} From 4cfab7ef15349d329e9b0051369ff96dc4cadc50 Mon Sep 17 00:00:00 2001 From: tpietzsch Date: Thu, 29 Aug 2024 11:40:45 +0200 Subject: [PATCH 07/10] WIP: ImgLib2 v7: add PRs https://github.com/imagej/imagej-mesh/pull/27 https://github.com/imglib/imglib2-mesh/pull/12 --- tests/run.sh | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tests/run.sh b/tests/run.sh index 7a4a7d3..ba9fa3f 100755 --- a/tests/run.sh +++ b/tests/run.sh @@ -157,6 +157,8 @@ sc.fiji|TrackMate|git@github.com:trackmate-sc/TrackMate|pull/289/head sc.fiji|TrackMate-Skeleton|git@github.com:trackmate-sc/TrackMate-Skeleton|pull/2/head sc.fiji|bigwarp_fiji|git@github.com:saalfeldlab/bigwarp|pull/170/head net.imagej|imagej-ops|git@github.com:imagej/imagej-ops|pull/654/head +net.imagej|imagej-mesh|git@github.com:imagej/imagej-mesh|pull/27/head +net.imglib2|imglib2-mesh|git@github.com:imglib/imglib2-mesh|pull/12/head ' failFile="$meltingPotDir/fail" rm -f "$failFile" From 86c3e237a426a040125fc5c413d3880433d49f18 Mon Sep 17 00:00:00 2001 From: Curtis Rueden Date: Thu, 29 Aug 2024 11:19:21 -0500 Subject: [PATCH 08/10] WIP: Update component versions for ImgLib2 v7 * imagej-mesh: 0.8.1 -> 0.8.2 * imagej-ops: 2.1.0 -> 2.2.0 * imglib2-mesh: 1.0.0 -> 1.1.0 * SPIM_Registration: 5.0.25 -> 5.0.26 * TrackMate: 7.12.1 -> 7.14.0 * TrackMate-Skeleton: 2.0.1 -> 2.0.3 * labkit-pixel-classification: 0.1.17 -> 0.1.18 * labkit-ui: 0.3.11 -> 0.4.0 --- pom.xml | 16 ++++++++-------- tests/run.sh | 8 -------- 2 files changed, 8 insertions(+), 16 deletions(-) diff --git a/pom.xml b/pom.xml index 1084699..0516221 100644 --- a/pom.xml +++ b/pom.xml @@ -502,7 +502,7 @@ ${imagej-matlab.version} - 0.8.1 + 0.8.2 ${imagej-mesh.version} @@ -526,7 +526,7 @@ ${imagej-opencv.version} - 2.1.0 + 2.2.0 ${imagej-ops.version} @@ -608,7 +608,7 @@ ${imglib2-imglyb.version} - 1.0.0 + 1.1.0 ${imglib2-mesh.version} @@ -861,7 +861,7 @@ 2.0.2 ${SPIM_Opener.version} - 5.0.25 + 5.0.26 ${SPIM_Registration.version} 2.0.3 @@ -1034,7 +1034,7 @@ - 7.12.1 + 7.14.0 ${TrackMate.version} @@ -1068,7 +1068,7 @@ ${TrackMate-Oneat.version} - 2.0.1 + 2.0.3 ${TrackMate-Skeleton.version} @@ -1207,8 +1207,8 @@ ${MaMuT.version} - 0.1.17 - 0.3.11 + 0.1.18 + 0.4.0 ${labkit-pixel-classification.version} ${labkit-ui.version} diff --git a/tests/run.sh b/tests/run.sh index ba9fa3f..ac0b71a 100755 --- a/tests/run.sh +++ b/tests/run.sh @@ -149,16 +149,8 @@ echo 'Hacking in any changed components...' # 5. Be added to the list of components to build in melt.sh (if not already present). components=' org.janelia.saalfeldlab|n5-imglib2|git@github.com:saalfeldlab/n5-imglib2|pull/54/head -sc.fiji|SPIM_Registration|git@github.com:fiji/SPIM_Registration|pull/142/head -sc.fiji|labkit-ui|git@github.com:juglab/labkit-ui|pull/115/head -sc.fiji|labkit-pixel-classification|git@github.com:juglab/labkit-pixel-classification|pull/12/head sc.fiji|z_spacing|git@github.com:saalfeldlab/z-spacing|pull/28/head -sc.fiji|TrackMate|git@github.com:trackmate-sc/TrackMate|pull/289/head -sc.fiji|TrackMate-Skeleton|git@github.com:trackmate-sc/TrackMate-Skeleton|pull/2/head sc.fiji|bigwarp_fiji|git@github.com:saalfeldlab/bigwarp|pull/170/head -net.imagej|imagej-ops|git@github.com:imagej/imagej-ops|pull/654/head -net.imagej|imagej-mesh|git@github.com:imagej/imagej-mesh|pull/27/head -net.imglib2|imglib2-mesh|git@github.com:imglib/imglib2-mesh|pull/12/head ' failFile="$meltingPotDir/fail" rm -f "$failFile" From 78b7d0fd8ce368d94bb50e7e745108ba4b21cd95 Mon Sep 17 00:00:00 2001 From: Curtis Rueden Date: Thu, 29 Aug 2024 14:53:56 -0500 Subject: [PATCH 09/10] WIP: mega-melt: add updated n5-ij into the mix --- tests/run.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/run.sh b/tests/run.sh index ac0b71a..df71786 100755 --- a/tests/run.sh +++ b/tests/run.sh @@ -149,6 +149,7 @@ echo 'Hacking in any changed components...' # 5. Be added to the list of components to build in melt.sh (if not already present). components=' org.janelia.saalfeldlab|n5-imglib2|git@github.com:saalfeldlab/n5-imglib2|pull/54/head +org.janelia.saalfeldlab|n5-ij|git@github.com:ctrueden/n5-ij|imglib2-v7 sc.fiji|z_spacing|git@github.com:saalfeldlab/z-spacing|pull/28/head sc.fiji|bigwarp_fiji|git@github.com:saalfeldlab/bigwarp|pull/170/head ' From c78698b10897bd2552770ff4de4360515151a176 Mon Sep 17 00:00:00 2001 From: tpietzsch Date: Mon, 23 Sep 2024 11:26:06 +0200 Subject: [PATCH 10/10] WIP: Update component versions for ImgLib2 imglib2-7.1.1 imglib2-algorithm-0.16.0 imglib2-ij-2.0.3 imglib2-roi-0.15.1 bigwarp-9.1.4 z_spacing-1.1.3 bigdataviewer-core-10.6.1 spim_data-2.3.2 n5-ij-4.2.2 n5-imglib2-7.0.1 --- pom.xml | 20 ++++++++++---------- tests/run.sh | 7 +------ 2 files changed, 11 insertions(+), 16 deletions(-) diff --git a/pom.xml b/pom.xml index 0516221..002520b 100644 --- a/pom.xml +++ b/pom.xml @@ -580,11 +580,11 @@ - 7.1.0 + 7.1.1 ${imglib2.version} - 0.15.3 + 0.16.0 ${imglib2-algorithm.version} @@ -600,7 +600,7 @@ ${imglib2-cache.version} - 2.0.2 + 2.0.3 ${imglib2-ij.version} @@ -616,7 +616,7 @@ ${imglib2-realtransform.version} - 0.15.0 + 0.15.1 ${imglib2-roi.version} @@ -991,7 +991,7 @@ ${jitk-tps.version} - 9.1.2 + 9.1.4 ${bigwarp.version} ${bigwarp_fiji.version} @@ -1006,13 +1006,13 @@ ${trakem2_tps.version} - 1.1.2 + 1.1.3 ${z_spacing.version} - 10.6.0 + 10.6.1 ${bigdataviewer-core.version} @@ -1028,7 +1028,7 @@ ${bigdataviewer_fiji.version} - 2.3.1 + 2.3.2 ${spim_data.version} @@ -1129,11 +1129,11 @@ ${n5-hdf5.version} - 4.2.1 + 4.2.2 ${n5-ij.version} - 7.0.0 + 7.0.1 ${n5-imglib2.version} diff --git a/tests/run.sh b/tests/run.sh index df71786..edb3e60 100755 --- a/tests/run.sh +++ b/tests/run.sh @@ -147,12 +147,7 @@ echo 'Hacking in any changed components...' # 3. Be `mvn install`ed to the local repo cache at that version; # 4. Have its version adjusted to 999 in melting pot's build.sh; # 5. Be added to the list of components to build in melt.sh (if not already present). -components=' -org.janelia.saalfeldlab|n5-imglib2|git@github.com:saalfeldlab/n5-imglib2|pull/54/head -org.janelia.saalfeldlab|n5-ij|git@github.com:ctrueden/n5-ij|imglib2-v7 -sc.fiji|z_spacing|git@github.com:saalfeldlab/z-spacing|pull/28/head -sc.fiji|bigwarp_fiji|git@github.com:saalfeldlab/bigwarp|pull/170/head -' +components='' failFile="$meltingPotDir/fail" rm -f "$failFile" echo "$components" | while read component