Fix JPMS issues, move module-info.java to correct place (WIP)

build.gradle.kts

@@ -4,6 +4,7 @@ import scenery.*
 import java.net.URL
 
 plugins {
+    `java-library`
     // kotlin and dokka versions are now managed in settings.gradle.kts and gradle.properties
     kotlin("jvm")
     kotlin("kapt")
@@ -12,11 +13,12 @@ plugins {
     scenery.base
     scenery.publish
     scenery.sign
-//    id("com.github.elect86.sciJava") version "0.0.4"
     jacoco
     id("com.github.johnrengelman.shadow") apply false
 }
 
+
+
 repositories {
     mavenCentral()
     maven("https://maven.scijava.org/content/groups/public")
@@ -39,6 +41,7 @@ val lwjglArtifacts = listOf(
         "lwjgl-jawt"
 )
 
+
 dependencies {
     val scijavaParentPomVersion = project.properties["scijavaParentPOMVersion"]
     val lwjglVersion = project.properties["lwjglVersion"]
@@ -110,6 +113,8 @@ dependencies {
     api("sc.fiji:bigdataviewer-core:10.4.13")
     api("sc.fiji:bigdataviewer-vistools:1.0.0-beta-28")
     api("sc.fiji:bigvolumeviewer:0.3.3") {
+        exclude("sc.fiji", "bigdataviewer-core")
+        exclude("sc.fiji", "bigdataviewer-vistools")
         exclude("org.jogamp.gluegen", "gluegen-rt")
         exclude("org.jogamp.jogl", "jogl-all")
     }
@@ -120,8 +125,8 @@ dependencies {
         exclude("org.lwjgl", "lwjgl-bom")
         exclude("org.lwjgl", "lwjgl")
     }
-    implementation("org.janelia.saalfeldlab:n5")
-    implementation("org.janelia.saalfeldlab:n5-imglib2")
+//    implementation("org.janelia.saalfeldlab:n5")
+//    implementation("org.janelia.saalfeldlab:n5-imglib2")
     listOf("core", "structure", "modfinder").forEach {
         implementation("org.biojava:biojava-$it:6.0.5") {
             exclude("org.slf4j", "slf4j-api")
@@ -150,6 +155,7 @@ dependencies {
 val isRelease: Boolean
     get() = System.getProperty("release") == "true"
 
+
 tasks {
     withType<KotlinCompile>().all {
         kotlinOptions {
@@ -161,6 +167,10 @@ tasks {
     withType<JavaCompile>().all {
         targetCompatibility = project.properties["jvmTarget"]?.toString() ?: "21"
         sourceCompatibility = project.properties["jvmTarget"]?.toString() ?: "21"
+
+        // Set high error limit, such that all JPMS errors are shown, it's over 9000!
+        options.compilerArgs.addAll("-Xmaxerrs 9001".split(" "))
+
     }
 
     withType<GenerateMavenPom>().configureEach {

buildSrc/build.gradle.kts

@@ -11,8 +11,11 @@ repositories {
 
 dependencies {
     implementation("org.jetbrains.dokka:dokka-gradle-plugin:1.9.10")
+//    implementation("org.gradlex:extra-java-module-info:1.8")
 }
 
+
+
 //, imagej, imgLib2, scifio, fiji, bigDataViewer, trakEM2, n5, boneJ, ome, omero,
 //groovy, apache, batik, commons, eclipseCollections, eclipseSwt, googleCloud, jackson,
 //jetty, jGraphT, jna, jogamp, kotlib, logBack, migLayout, rSyntaxTextArea, slf4j,

buildSrc/src/main/kotlin/scenery/base.gradle.kts

@@ -5,8 +5,21 @@ import org.gradle.api.tasks.testing.logging.TestLogEvent
 
 plugins {
     jacoco
+//    id("org.gradlex.extra-java-module-info")
 }
 
+//extraJavaModuleInfo {
+////    module("net.imglib2:imglib2", "net.imglib2") {
+////        mergeJar("sc.fiji:bigdataviewer-core")
+////    }
+//
+////    automaticModule("sc.fiji:bigdataviewer-core", "bdv") {
+////        mergeJar("sc.fiji:bigdataviewer-vistools")
+////    }
+//
+//    deriveAutomaticModuleNamesFromFileNames.set(true)
+//}
+
 repositories {
     mavenCentral()
 }

src/main/kotlin/module-info.java → src/main/java/module-info.java

@@ -45,13 +45,13 @@
     requires com.fasterxml.jackson.databind;
     requires com.fasterxml.jackson.dataformat.yaml;
     requires com.fasterxml.jackson.kotlin;
-    requires jinput;
-    requires trove4j;
-    requires org.scijava.ui.behaviour;
+//    requires jinput;
+//    requires trove4j;
+//    requires org.scijava.ui.behaviour;
     requires org.slf4j;
-
-//    opens java.nio;
-//    opens java.nio;
-//    opens sun.nio.ch;
-//    opens sun.
-}
+    requires bvv;
+    requires bdv;
+//    requires bdv.util;
+    requires net.imglib2.realtransform;
+    requires net.imglib2;
+}

src/test/kotlin/graphics/scenery/tests/examples/volumes/OutOfCoreRAIExample.kt

@@ -18,10 +18,10 @@ import net.imglib2.img.Img
 import net.imglib2.img.display.imagej.ImageJFunctions
 import net.imglib2.type.numeric.integer.UnsignedShortType
 import net.imglib2.type.volatiles.VolatileUnsignedShortType
-import org.janelia.saalfeldlab.n5.GzipCompression
-import org.janelia.saalfeldlab.n5.N5FSReader
-import org.janelia.saalfeldlab.n5.N5FSWriter
-import org.janelia.saalfeldlab.n5.imglib2.N5Utils
+//import org.janelia.saalfeldlab.n5.GzipCompression
+//import org.janelia.saalfeldlab.n5.N5FSReader
+//import org.janelia.saalfeldlab.n5.N5FSWriter
+//import org.janelia.saalfeldlab.n5.imglib2.N5Utils
 import java.nio.file.Files
 
 
@@ -50,12 +50,12 @@ class OutOfCoreRAIExample: SceneryBase("Out-of-core RAI Rendering example", 1280
         // and save it to a temporary location.
         val datasetName = "testDataset"
         val n5path = Files.createTempDirectory("scenery-t1-head-n5")
-        val n5 = N5FSWriter(n5path.toString())
-        N5Utils.save(img, n5, datasetName, intArrayOf(img.dimension(0).toInt(), img.dimension(1).toInt(), img.dimension(2).toInt()), GzipCompression())
+//        val n5 = N5FSWriter(n5path.toString())
+//        N5Utils.save(img, n5, datasetName, intArrayOf(img.dimension(0).toInt(), img.dimension(1).toInt(), img.dimension(2).toInt()), GzipCompression())
 
         // load the multiresolution N5 dataset from the temporary location and wrap it
         // as [net.imglib2.Volatile] dataset.
-        val ooc: RandomAccessibleInterval<UnsignedShortType> = N5Utils.openVolatile(N5FSReader(n5path.toString()), datasetName)
+        val ooc: RandomAccessibleInterval<UnsignedShortType>? = null //N5Utils.openVolatile(N5FSReader(n5path.toString()), datasetName)
         val wrapped = VolatileViews.wrapAsVolatile(ooc)
 
         // When loading datasets with multiple resolution levels, it's important to use Volatile types