Prepare v4.3.0 release #212

tferr · 2023-12-21T22:09:21Z

The next release (v4.3.0) has major changes, notably: minimum Java11 requirement, several changes to auto-tracing and path refining, plus a whole slew of bug-fixes/patches/tweaks. I suspect somethings may break, and it would be useful to plan ahead. Things that we should do:

Create Fiji bundles with SNT compiled from main branch + the new launcher + OpenJDK11. We can post those here, so that folks can report issues more easily. I doubt the bulk of users is able/willing to grab the binaries themselves. I can do it for ubuntu (and maybe MacOS) (@carshadi are you able to do this for WIndows OS?)
NB: It may just be easier to just use Make Fiji Package!?
Givin up on this, since jaunch is eminient
Make sure the jupyter notebooks remain functional (and install instructions up-to-date)
Check that Junit tests haven't broken (they have been disabled in auto-builds for a while now, because of the long execution time)
Make sure javadoc generation does not fail
Test sciview functionality (sciview is scheduled to be bundled with next Fiji-Jdk 1121 release)
Make sure we are following the official contribution guidelines, since SNT is scheduled to be bundled with Fiji
Repurpose the Neuroanatomy update site to serve beta-releases of SNT

@carshadi, agree? comments?

carshadi · 2024-01-03T19:25:28Z

Sounds good to me, I'll look into the Windows bundle

tferr · 2024-01-08T10:45:39Z

Awesome! We can use SNT-v4.3.0-pre-release1 (mapped to 746b1d2) as a freeze point. It includes some minor improvements I had laying around on stalled branches, and more recent work I needed: tweaks to auto-tracing and Weka integration:

The Secondary Layer widget now lists a command to import a model from both Labkit and TWS (TWS and Labkit are now dependencies -- hopefully that won't bother you)
The PathManagerUI has a command to send Paths to TWS, and a prototype placeholder to do the same with Labkit. But I ran into a roadblock with that one.
Release notes are here: https://github.com/morphonets/SNT/releases/tag/SNT-v4.3.0-pre-release1

carshadi · 2024-01-14T01:30:52Z

@tferr when I try to open Rec. Viewer, I get this error on Windows 11

Caused by: java.lang.UnsatisfiedLinkError: Couldn't load library 'gluegen_rt'
	at com.jogamp.common.jvm.JNILibLoaderBase.loadLibraryInternal(JNILibLoaderBase.java:634)
	at com.jogamp.common.jvm.JNILibLoaderBase.access$000(JNILibLoaderBase.java:64)
	at com.jogamp.common.jvm.JNILibLoaderBase$DefaultAction.loadLibrary(JNILibLoaderBase.java:107)
	at com.jogamp.common.jvm.JNILibLoaderBase.loadLibrary(JNILibLoaderBase.java:488)
	at com.jogamp.common.os.DynamicLibraryBundle$GlueJNILibLoader.loadLibrary(DynamicLibraryBundle.java:427)
	at com.jogamp.common.os.Platform$1.run(Platform.java:321)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at com.jogamp.common.util.SecurityUtil.doPrivileged(SecurityUtil.java:82)
	at com.jogamp.common.os.Platform.<clinit>(Platform.java:290)
	at com.jogamp.opengl.GLProfile.<clinit>(GLProfile.java:154)
	at org.jzy3d.chart.Settings.detectProfile(Settings.java:28)
	at org.jzy3d.chart.Settings.<init>(Settings.java:13)
	at org.jzy3d.chart.Settings.getInstance(Settings.java:58)
	at sc.fiji.snt.viewer.Viewer3D.<init>(Viewer3D.java:351)
	at sc.fiji.snt.viewer.Viewer3D.<init>(Viewer3D.java:370)
	at sc.fiji.snt.viewer.Viewer3D.<init>(Viewer3D.java:381)
	at sc.fiji.snt.viewer.Viewer3D.<init>(Viewer3D.java:415)
	at sc.fiji.snt.SNTUI$SNTViewer3D.<init>(SNTUI.java:4258)
	at sc.fiji.snt.SNTUI$1RecWorker.doInBackground(SNTUI.java:1922)
	at sc.fiji.snt.SNTUI$1RecWorker.doInBackground(SNTUI.java:1917)
	at java.desktop/javax.swing.SwingWorker$1.call(SwingWorker.java:304)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
	at java.desktop/javax.swing.SwingWorker.run(SwingWorker.java:343)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
	at java.base/java.lang.Thread.run(Thread.java:829)

According to https://jogamp.org/wiki/index.php?title=Maven , the native libraries for all platforms are included with the following maven dependencies

 <dependencies>
    <dependency>
      <groupId>org.jogamp.gluegen</groupId>
      <artifactId>gluegen-rt-main</artifactId>
      <version>2.3.2</version>
    </dependency>
    <dependency>
      <groupId>org.jogamp.jogl</groupId>
      <artifactId>jogl-all-main</artifactId>
      <version>2.3.2</version>
    </dependency>
  </dependencies>

I tested it in 8c9d5f3 and it seems to work.

tferr · 2024-01-15T17:15:56Z

Bummer and weird. That 2.3.2 is the last official version from 2015(!). If I recall correctly, there was patched 2.4.0 version released earlier last year that was pushed to Maven by Jzy3D. I think Curtis worked on that so that our parent scijava pom would use that instead. My understanding is that the 2.4.0 version is the one currently in use by Fiji (JDK8) on all platforms. I predict downgrading it may cause conflicts elsewhere!? Shall we bring this up on Zulip?

carshadi · 2024-01-16T03:21:10Z

I see, yeah we should definitely bring this up

tferr · 2024-01-16T20:14:23Z

@carshadi , are you able to test Curtis's suggestion: https://imagesc.zulipchat.com/#narrow/stream/327238-Fiji/topic/Problems.20with.20JOGL.20dependencies.20on.20Windows.2011/near/413230673?

carshadi · 2024-01-17T00:58:10Z

This works for me

See #212 (comment)

tferr · 2024-01-18T03:00:40Z

Curtis' fix added: Let's target https://github.com/morphonets/SNT/releases/tag/SNT-v4.3.0-pre-release2 (21ea56b)

elect86 · 2024-03-12T21:35:32Z

Hello Tiago,
could you publish the 4.3.0-pre-release2?

I'd like to update the Scijava pom and get rid of the exclusions about org.jzy3d:jzy3d-emul-gl and org.jzy3d:jGL

tferr · 2024-03-14T15:28:07Z

Hi @elect86,
I don't seem to be able to do a release. I get this error weird javadoc-related error that I cannot make sense, specially since javadoc is disabled in the pom. Also mvn javadoc:javadoc | grep error detects nothing. Do you know what is causing this?

BUILD FAILURE


❯ ../scijava-scripts/release-version.sh --skip-version-check --skip-license-update 4.3.0-beta-2
From https://github.com/morphonets/SNT
 * branch              main       -> FETCH_HEAD
==========================================================================
NOTE: pom.xml.releaseBackup was committed to source control. Removing now.
==========================================================================
fatal: pathspec 'pom.xml.releaseBackup' did not match any files
openjdk 21.0.2 2024-01-16 LTS
OpenJDK Runtime Environment Zulu21.32+17-CA (build 21.0.2+13-LTS)
OpenJDK 64-Bit Server VM Zulu21.32+17-CA (build 21.0.2+13-LTS, mixed mode, sharing)
[INFO] Scanning for projects...
[INFO] 
[INFO] -------------------------< org.morphonets:SNT >-------------------------
[INFO] Building SNT 4.2.2-SNAPSHOT
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-release-plugin:3.0.1:prepare (default-cli) @ SNT ---
[INFO] starting prepare goal, composed of 17 phases: check-poms, scm-check-modifications, check-dependency-snapshots, create-backup-poms, map-release-versions, input-variables, map-development-versions, rewrite-poms-for-release, generate-release-poms, run-preparation-goals, scm-commit-release, scm-tag, rewrite-poms-for-development, remove-release-poms, run-completion-goals, scm-commit-development, end-release
[INFO] 1/17 prepare:check-poms
[INFO] 2/17 prepare:scm-check-modifications
[INFO] Verifying that there are no local modifications...
[INFO]   ignoring changes on: **/pom.xml.releaseBackup, **/pom.xml.next, **/pom.xml.tag, **/pom.xml.branch, **/release.properties, **/pom.xml.backup
[INFO] Executing: /bin/sh -c cd '/home/tferr/code/SNT' && 'git' 'rev-parse' '--show-prefix'
[INFO] Working directory: /home/tferr/code/SNT
[INFO] Executing: /bin/sh -c cd '/home/tferr/code/SNT' && 'git' 'status' '--porcelain' '.'
[INFO] Working directory: /home/tferr/code/SNT
[WARNING] Ignoring unrecognized line: ?? release.properties
[INFO] 3/17 prepare:check-dependency-snapshots
[INFO] Checking dependencies and plugins for snapshots ...
[INFO] 4/17 prepare:create-backup-poms
[INFO] Creating pom.xml backup with .releaseBackup suffix
[INFO] 5/17 prepare:map-release-versions
[INFO] 6/17 prepare:input-variables
[INFO] 7/17 prepare:map-development-versions
[INFO] 8/17 prepare:rewrite-poms-for-release
[INFO] Transforming pom.xml SNT 'SNT'...
[INFO] 9/17 prepare:generate-release-poms
[INFO] Not generating release POMs
[INFO] 10/17 prepare:run-preparation-goals
[INFO] Executing goals 'clean verify'...
[INFO] openjdk 21.0.2 2024-01-16 LTS
[INFO] OpenJDK Runtime Environment Zulu21.32+17-CA (build 21.0.2+13-LTS)
[INFO] OpenJDK 64-Bit Server VM Zulu21.32+17-CA (build 21.0.2+13-LTS, mixed mode, sharing)
[INFO] [INFO] Scanning for projects...
[INFO] [INFO] 
[INFO] [INFO] -------------------------< org.morphonets:SNT >-------------------------
[INFO] [INFO] Building SNT 4.3.0-beta-2
[INFO] [INFO] --------------------------------[ jar ]---------------------------------
[INFO] [INFO] 
[INFO] [INFO] --- maven-clean-plugin:3.3.1:clean (default-clean) @ SNT ---
[INFO] [INFO] Deleting /home/tferr/code/SNT/target
[INFO] [INFO] 
[INFO] [INFO] --- maven-enforcer-plugin:3.3.0:enforce (enforce-rules) @ SNT ---
[INFO] [INFO] Skipping Rule Enforcement.
[INFO] [INFO] 
[INFO] [INFO] --- build-helper-maven-plugin:3.4.0:regex-property (sanitize-version) @ SNT ---
[INFO] [INFO] 
[INFO] [INFO] --- build-helper-maven-plugin:3.4.0:regex-property (guess-package) @ SNT ---
[INFO] [INFO] 
[INFO] [INFO] --- buildnumber-maven-plugin:3.2.0:create (default) @ SNT ---
[INFO] [INFO] Executing: /bin/sh -c cd '/home/tferr/code/SNT' && 'git' 'rev-parse' '--verify' 'HEAD'
[INFO] [INFO] Working directory: /home/tferr/code/SNT
[INFO] [INFO] Storing buildNumber: 82d854ce4a66355f680c1a2746ce7237bd4b5bb5 at timestamp: 1710428171774
[INFO] [INFO] Executing: /bin/sh -c cd '/home/tferr/code/SNT' && 'git' 'symbolic-ref' 'HEAD'
[INFO] [INFO] Working directory: /home/tferr/code/SNT
[INFO] [INFO] Storing scmBranch: main
[INFO] [INFO] 
[INFO] [INFO] --- scijava-maven-plugin:2.2.0:set-rootdir (set-rootdir) @ SNT ---
[INFO] [INFO] Setting rootdir: /home/tferr/code/SNT
[INFO] [INFO] 
[INFO] [INFO] --- jacoco-maven-plugin:0.8.10:prepare-agent (jacoco-initialize) @ SNT ---
[INFO] [INFO] argLine set to -javaagent:/home/tferr/.m2/repository/org/jacoco/org.jacoco.agent/0.8.10/org.jacoco.agent-0.8.10-runtime.jar=destfile=/home/tferr/code/SNT/target/jacoco.exec
[INFO] [INFO] 
[INFO] [INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ SNT ---
[INFO] [INFO] Copying 86 resources from src/main/resources to target/classes
[INFO] [INFO] 
[INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ SNT ---
[INFO] [INFO] Compiling 313 source files to /home/tferr/code/SNT/target/classes
[INFO] [INFO] /home/tferr/code/SNT/src/main/java/sc/fiji/snt/analysis/MultiTreeStatistics.java: /home/tferr/code/SNT/src/main/java/sc/fiji/snt/analysis/MultiTreeStatistics.java uses or overrides a deprecated API.
[INFO] [INFO] /home/tferr/code/SNT/src/main/java/sc/fiji/snt/analysis/MultiTreeStatistics.java: Recompile with -Xlint:deprecation for details.
[INFO] [INFO] 
[INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ SNT ---
[INFO] [INFO] Not copying test resources
[INFO] [INFO] 
[INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ SNT ---
[INFO] [INFO] Not compiling test sources
[INFO] [INFO] 
[INFO] [INFO] --- maven-surefire-plugin:3.1.2:test (default-test) @ SNT ---
[INFO] [INFO] Tests are skipped.
[INFO] [INFO] 
[INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ SNT ---
[INFO] [INFO] Building jar: /home/tferr/code/SNT/target/SNT-4.3.0-beta-2.jar
[INFO] [INFO] 
[INFO] [INFO] >>> maven-source-plugin:3.3.0:jar (attach-sources-jar) > generate-sources @ SNT >>>
[INFO] [INFO] 
[INFO] [INFO] --- maven-enforcer-plugin:3.3.0:enforce (enforce-rules) @ SNT ---
[INFO] [INFO] Skipping Rule Enforcement.
[INFO] [INFO] 
[INFO] [INFO] --- build-helper-maven-plugin:3.4.0:regex-property (sanitize-version) @ SNT ---
[INFO] [INFO] 
[INFO] [INFO] --- build-helper-maven-plugin:3.4.0:regex-property (guess-package) @ SNT ---
[INFO] [INFO] 
[INFO] [INFO] --- buildnumber-maven-plugin:3.2.0:create (default) @ SNT ---
[INFO] [INFO] 
[INFO] [INFO] --- scijava-maven-plugin:2.2.0:set-rootdir (set-rootdir) @ SNT ---
[INFO] [INFO] 
[INFO] [INFO] --- jacoco-maven-plugin:0.8.10:prepare-agent (jacoco-initialize) @ SNT ---
[INFO] [INFO] argLine set to -javaagent:/home/tferr/.m2/repository/org/jacoco/org.jacoco.agent/0.8.10/org.jacoco.agent-0.8.10-runtime.jar=destfile=/home/tferr/code/SNT/target/jacoco.exec
[INFO] [INFO] 
[INFO] [INFO] <<< maven-source-plugin:3.3.0:jar (attach-sources-jar) < generate-sources @ SNT <<<
[INFO] [INFO] 
[INFO] [INFO] 
[INFO] [INFO] --- maven-source-plugin:3.3.0:jar (attach-sources-jar) @ SNT ---
[INFO] [INFO] Building jar: /home/tferr/code/SNT/target/SNT-4.3.0-beta-2-sources.jar
[INFO] [INFO] 
[INFO] [INFO] --- jacoco-maven-plugin:0.8.10:report (jacoco-site) @ SNT ---
[INFO] [INFO] Skipping JaCoCo execution due to missing execution data file.
[INFO] [INFO] 
[INFO] [INFO] --- maven-javadoc-plugin:3.5.0:jar (attach-javadocs) @ SNT ---
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] [INFO] BUILD FAILURE
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] [INFO] Total time:  17.876 s
[INFO] [INFO] Finished at: 2024-03-14T10:56:28-04:00
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] [ERROR] Failed to execute goal org.apache.maven.plugins:maven-javadoc-plugin:3.5.0:jar (attach-javadocs) on project SNT: Execution attach-javadocs of goal org.apache.maven.plugins:maven-javadoc-plugin:3.5.0:jar failed: Unable to derive module descriptor for /home/tferr/.m2/repository/org/jzy3d/jzy3d-native-jogl-awt/2.2.1/jzy3d-native-jogl-awt-2.2.1.jar: jzy3d.native.jogl.awt: Invalid module name: 'native' is not a Java identifier -> [Help 1]
[INFO] [ERROR] 
[INFO] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[INFO] [ERROR] Re-run Maven using the -X switch to enable full debug logging.
[INFO] [ERROR] 
[INFO] [ERROR] For more information about the errors and possible solutions, please read the following articles:
[INFO] [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/PluginExecutionException
[ERROR] 
[INFO] 
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  19.899 s
[INFO] Finished at: 2024-03-14T10:56:28-04:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-release-plugin:3.0.1:prepare (default-cli) on project SNT: Maven execution failed, exit code: 1 -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
The release preparation step failed -- look above for errors and fix them.
Use "mvn javadoc:javadoc | grep error" to check for javadoc syntax errors.

elect86 · 2024-03-14T15:37:17Z

Would you mind if I give it a try myself?

tferr · 2024-03-14T15:40:18Z

Not at all, go ahead! Do you need anything from me?

elect86 · 2024-03-14T15:43:51Z

so far no

elect86 · 2024-03-14T15:45:40Z

may I update to the latest Scijava pom 38.0.0-SNAPSHOT?

tferr · 2024-03-14T16:38:29Z

Sure!

…

On Thu, Mar 14, 2024, 11:46 Giuseppe Barbieri ***@***.***> wrote: may I update to the latest Scijava pom 38.0.0-SNAPSHOT? — Reply to this email directly, view it on GitHub <#212 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AASTWDBFTGHVDOAN2QMRGQLYYHA3VAVCNFSM6AAAAABA7ANWFKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOJXG43DIMBRHA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

elect86 · 2024-03-15T08:43:00Z

Could you add me to the repo so that I can create a new branch and work from there instead of forking?

elect86 · 2024-03-15T09:49:46Z

Which tests are supposed to pass with Maven? Because I'm getting weird errors on my machine

Otherwise what passes so far with Gradle is this

tferr · 2024-03-15T13:20:22Z

@elect86, just sent you the invite. let me know if it something else is needed.

Which tests are supposed to pass with Maven?

The tests that call SNTService fail because of those net.imagej.patcher.LegacyInjector.preinit(); errors. I can only get those to work on the IDE when I add --add-opens java.base/java.lang=ALL-UNNAMED. I will probably have to re-write those tests. I added this to the pom after looking around on SO, and I convinced myself that worked to to make the release-script happy.

elect86 · 2024-03-15T14:04:40Z

Indeed, much better now, those 3 looks ignored

tferr · 2024-03-15T14:38:00Z

Hm, not really. I had convinced myself all tests were passing with 3293439. Will need to look, but I'm in meeting all day. Won't be able to look into it immediately

elect86 · 2024-03-15T14:56:37Z

they all have @Ignore on them

elect86 · 2024-03-15T15:20:27Z

Anyway, if you want I can publish 4.3.0-pre-release3

If yes, shall I upgrade the pom-scijava to 38.0.0-SNAPSHOT, 38.0.0 or leave it to 37.0.0?

I just realized now it's a cyclic dep..

tferr · 2024-03-15T15:23:10Z

Sure go ahead. bumping it to 38.0.0-SNAPSHOT is probably a good idea.
Which dependency is cyclic? SNT itself?

elect86 · 2024-03-15T15:28:42Z

SNT and the POM

elect86 · 2024-03-15T17:22:12Z

Published, thanks for your availability Tiago!

tferr · 2024-03-15T18:29:56Z

Awesome! Did you end up pushing something here? I don't seem to notice any new commits...

elect86 · 2024-03-15T20:15:53Z

In the meanwhile I was waiting for a reply I got eager to try and start working on the fork, then I though I changed the back the remote once I got the invite, but apparently I didn't, it's all here I can push to a gradle branch here, if you want, the publishing is hardcoded, but if needed, it can be polished and made it smart

elect86 · 2024-03-16T08:06:47Z

Pushed here as well

tferr added the v4.3.0 label Dec 21, 2023

tferr added this to the v4.3.0 milestone Dec 21, 2023

tferr added v4.3.0 and removed v4.3.0 labels Dec 21, 2023

tferr pinned this issue Dec 21, 2023

tferr added a commit that referenced this issue Jan 18, 2024

Pom: fix jogamp dependencies/updates

21ea56b

See #212 (comment)

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Prepare v4.3.0 release #212

Prepare v4.3.0 release #212

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Prepare v4.3.0 release #212

Prepare v4.3.0 release #212

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