JPMS compatibility #619
+94
−12
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -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 | ||
| jacoco | ||
| id("com.github.johnrengelman.shadow") apply false | ||
| } | ||
|
|
||
|
|
||
|
|
||
| repositories { | ||
| mavenCentral() | ||
| maven("https://maven.scijava.org/content/groups/public") | ||
|
|
@@ -41,6 +43,7 @@ val lwjglArtifacts = listOf( | |
| "lwjgl-zstd" | ||
| ) | ||
|
|
||
|
|
||
| dependencies { | ||
| val scijavaParentPomVersion = project.properties["scijavaParentPOMVersion"] | ||
| val lwjglVersion = project.properties["lwjglVersion"] | ||
|
|
@@ -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") | ||
| exclude("sc.fiji", "bigdataviewer-vistools") | ||
| exclude("org.jogamp.gluegen", "gluegen-rt") | ||
| exclude("org.jogamp.jogl", "jogl-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") | ||
| listOf("core", "structure", "modfinder").forEach { | ||
| implementation("org.biojava:biojava-$it:6.0.5") { | ||
| exclude("org.slf4j", "slf4j-api") | ||
|
|
@@ -154,6 +158,7 @@ dependencies { | |
| val isRelease: Boolean | ||
| get() = System.getProperty("release") == "true" | ||
|
|
||
|
|
||
| tasks { | ||
| withType<KotlinCompile>().all { | ||
| kotlinOptions { | ||
|
|
@@ -165,6 +170,10 @@ tasks { | |
| withType<JavaCompile>().all { | ||
| targetCompatibility = project.properties["jvmTarget"]?.toString() ?: "21" | ||
| sourceCompatibility = project.properties["jvmTarget"]?.toString() ?: "21" | ||
|
There was a problem hiding this comment. Not a thing with this PR specifically, but maybe rather than setting 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 { | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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; | ||
|
There was a problem hiding this comment. If I'm reading it right, it looks like this is exporting all the 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; | ||
| } | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -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 | ||
|
There was a problem hiding this comment. 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 |
||
| 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()) | ||
|
|
||
| // load the multiresolution N5 dataset from the temporary location and wrap it | ||
| // as [net.imglib2.Volatile] dataset. | ||
| 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 | ||
|
|
||
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
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.