Prepare v5.0.0 release

[tferr]

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]

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

[tferr]

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]

@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]

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]

I see, yeah we should definitely bring this up

[tferr]

@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]

This works for me

[tferr]

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

[elect86]

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