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JPMS compatibility #619

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JPMS compatibility #619

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c6a6b85
Add module-info.java
skalarproduktraum Sep 20, 2023
cc84355
Fix JPMS issues, move module-info.java to correct place (WIP)
skalarproduktraum Feb 9, 2024
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17 changes: 13 additions & 4 deletions build.gradle.kts
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Original file line number Diff line number Diff line change
Expand Up @@ -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")
Expand All @@ -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")
Expand All @@ -41,6 +43,7 @@ val lwjglArtifacts = listOf(
"lwjgl-zstd"
)


dependencies {
val scijavaParentPomVersion = project.properties["scijavaParentPOMVersion"]
val lwjglVersion = project.properties["lwjglVersion"]
Expand Down Expand Up @@ -113,6 +116,8 @@ dependencies {
api("sc.fiji:bigdataviewer-core:10.4.14")
api("sc.fiji:bigdataviewer-vistools:1.0.0-beta-28")
api("sc.fiji:bigvolumeviewer:0.3.3") {
exclude("sc.fiji", "bigdataviewer-core")
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I would suggest to add a comment explaining what it accomplishes to exclude bigdataviewer-core and bigdataviewer-vistools here, when they are included as direct dependencies immediately above.

exclude("sc.fiji", "bigdataviewer-vistools")
exclude("org.jogamp.gluegen", "gluegen-rt")
exclude("org.jogamp.jogl", "jogl-all")
}
Expand All @@ -123,9 +128,8 @@ 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")
Expand Down Expand Up @@ -154,6 +158,7 @@ dependencies {
val isRelease: Boolean
get() = System.getProperty("release") == "true"


tasks {
withType<KotlinCompile>().all {
kotlinOptions {
Expand All @@ -165,6 +170,10 @@ tasks {
withType<JavaCompile>().all {
targetCompatibility = project.properties["jvmTarget"]?.toString() ?: "21"
sourceCompatibility = project.properties["jvmTarget"]?.toString() ?: "21"
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Not a thing with this PR specifically, but maybe rather than setting -target and source, you want to configure the --release?

    options.compilerArgs.add("--release")
    options.compilerArgs.add(project.properties["jvmTarget"]?.toString() ?: "21")

Why? Because.


// Set high error limit, such that all JPMS errors are shown, it's over 9000!
options.compilerArgs.addAll("-Xmaxerrs 9001".split(" "))

}

withType<GenerateMavenPom>().configureEach {
Expand Down
5 changes: 4 additions & 1 deletion buildSrc/build.gradle.kts
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Expand Up @@ -11,9 +11,12 @@ repositories {

dependencies {
implementation("org.jetbrains.dokka:dokka-gradle-plugin:1.9.20")
// 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,
//snakeYAML, tensorFlow, junit5, jmh, misc
//snakeYAML, tensorFlow, junit5, jmh, misc
13 changes: 13 additions & 0 deletions buildSrc/src/main/kotlin/scenery/base.gradle.kts
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Expand Up @@ -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()
}
Expand Down
57 changes: 57 additions & 0 deletions src/main/java/module-info.java
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@@ -0,0 +1,57 @@
module graphics.scenery {
exports graphics.scenery;
exports graphics.scenery.atomicsimulations;
exports graphics.scenery.attribute;
exports graphics.scenery.backends;
exports graphics.scenery.compute;
exports graphics.scenery.controls;
exports graphics.scenery.effectors;
exports graphics.scenery.fonts;
exports graphics.scenery.geometry;
exports graphics.scenery.net;
exports graphics.scenery.numerics;
exports graphics.scenery.primitives;
exports graphics.scenery.proteins;
exports graphics.scenery.repl;
exports graphics.scenery.serialization;
exports graphics.scenery.textures;
exports graphics.scenery.ui;
exports graphics.scenery.utils;
exports graphics.scenery.volumes;
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If I'm reading it right, it looks like this is exporting all the graphics.scenery.* packages, but none of the graphics.scenery.*.* ones? Specifically: missing are attribute.geometry, attribute.material, attribute.renderable, attribute.spatial, backends.software, backends.vulkan, controls.behaviours, controls.eyetracking, utils.extensions. Intentional, or no?

And are you sure you want to expose so much API surface? I guess since scenery hasn't hit 1.0.0 yet, you can still break things. But this work is an opportunity to consider whether it makes sense to create any internal (non-exported) packages, no?


requires java.base;
requires java.desktop;
requires java.management;
requires java.logging;
requires jdk.unsupported;

requires kotlin.stdlib;
requires kotlin.reflect;
requires kotlinx.coroutines.core;

requires org.joml;
requires org.lwjgl;
requires org.lwjgl.vulkan;
requires org.lwjgl.tinyexr;
requires org.lwjgl.remotery;
requires org.lwjgl.openvr;
requires org.lwjgl.glfw;
requires org.lwjgl.spvc;
requires org.lwjgl.shaderc;
requires org.lwjgl.jemalloc;
requires info.picocli;
requires org.bytedeco.ffmpeg;
requires com.fasterxml.jackson.core;
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 org.slf4j;
requires bvv;
requires bdv;
// requires bdv.util;
requires net.imglib2.realtransform;
requires net.imglib2;
}
14 changes: 7 additions & 7 deletions src/test/kotlin/graphics/scenery/tests/examples/volumes/OutOfCoreRAIExample.kt
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Expand Up @@ -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
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So, scenery only uses (used) n5 in tests? Please let me know if you find a good way of dealing with test-scope dependencies with JPMS. We have found it very challenging with SciJava Ops; we were unable to make a separate module-info.java in the src/test subtree work (see scijava/scijava@ae39206 for details).

import java.nio.file.Files


Expand Down Expand Up @@ -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
Expand Down
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