Merge pull request #115 from petebankhead/gradle-plugin

Use QuPath gradle plugin

build.gradle.kts

@@ -1,167 +1,32 @@
 plugins {
-    `java-library`
+    id("qupath-conventions")
     `maven-publish`
-    // Include this plugin to avoid downloading JavaCPP dependencies for all platforms
-    id("org.bytedeco.gradle-javacpp-platform")
-    id("org.openjfx.javafxplugin")
 }
 
-val moduleName = "io.github.qupath.extension.instanseg"
-
-base {
-    archivesName = rootProject.name
-    version = "0.0.1-SNAPSHOT"
-    description = "A QuPath extension for running inference with the InstanSeg deep learning model"
+qupathExtension {
+    name = "qupath-extension-instanseg"
+    version = "0.1.0-SNAPSHOT"
     group = "io.github.qupath"
+    description = "A QuPath extension for running inference with the InstanSeg deep learning model"
+    automaticModule = "qupath.extension.instanseg"
 }
 
-javafx {
-    version = libs.versions.jdk.get()
-    modules = listOf(
-        "javafx.controls",
-        "javafx.fxml",
-        "javafx.web"
-    )
-}
-
-val qupathVersion = gradle.extra["qupath.app.version"]
-
-/**
- * Define dependencies.
- * - Using 'shadow' indicates that they are already part of QuPath, so you don't need
- *   to include them in your extension. If creating a single 'shadow jar' containing your
- *   extension and all dependencies, these won't be added.
- * - Using 'implementation' indicates that you need the dependency for the extension to work,
- *   and it isn't part of QuPath already. If you are creating a single 'shadow jar', the
- *   dependency should be bundled up in the extension.
- * - Using 'testImplementation' indicates that the dependency is only needed for testing,
- *   but shouldn't be bundled up for use in the extension.
- */
 dependencies {
-    // Main QuPath user interface jar.
-    // Automatically includes other QuPath jars as subdependencies
-    implementation("io.github.qupath:qupath-gui-fx:${qupathVersion}")
-
-    // For logging - the version comes from QuPath's version catalog at
-    // https://github.com/qupath/qupath/blob/main/gradle/libs.versions.toml
-    implementation(libs.slf4j)
 
+    implementation(libs.bundles.qupath)
+    implementation(libs.bundles.logging)
     implementation(libs.qupath.fxtras)
+    implementation(libs.bundles.markdown)
+
     implementation(libs.bioimageio.spec)
     implementation(libs.deepJavaLibrary)
-    implementation(libs.commonmark)
-
     implementation("io.github.qupath:qupath-extension-djl:0.4.0-SNAPSHOT")
 
-    testImplementation("io.github.qupath:qupath-gui-fx:${qupathVersion}")
+    // For testing
     testImplementation(libs.junit)
-}
-
-/*
- * Manifest info
- */
-tasks.withType<Jar> {
-    manifest {
-        attributes(
-            mapOf("Implementation-Title" to project.name,
-                "Implementation-Version" to project.version,
-                "Automatic-Module-Name" to moduleName)
-        )
-    }
-}
-
-/*
- * Copy the LICENSE file into the jar... if we have one (we should!)
- */
-tasks.processResources {
-  from ("${projectDir}/LICENSE") {
-    into("licenses/")
-  }
-}
-
-/*
- * Define extra 'copyDependencies' task to copy dependencies into the build directory.
- */
-tasks.register<Copy>("copyDependencies") {
-    description = "Copy dependencies into the build directory for use elsewhere"
-    group = "QuPath"
-
-    from(configurations.default)
-    into("build/libs")
-}
-
-/*
- * Ensure Java compatibility, and include sources and javadocs when building
- */
-java {
-    toolchain {
-        languageVersion = JavaLanguageVersion.of(libs.versions.jdk.get())
-    }
-    withSourcesJar()
-    withJavadocJar()
-}
 
-/*
- * Create javadocs for all modules/packages in one place.
- * Use -PstrictJavadoc=true to fail on error with doclint (which is rather strict).
- */
-tasks.withType<Javadoc> {
-	options.encoding = "UTF-8"
-	val strictJavadoc = providers.gradleProperty("strictJavadoc").getOrElse("false")
-	if (!"true".equals(strictJavadoc, true)) {
-        (options as StandardJavadocDocletOptions).addStringOption("Xdoclint:none", "-quiet")
-	}
 }
 
-/*
- * Specify that the encoding should be UTF-8 for source files
- */
-tasks.withType<JavaCompile> {
-    // Include parameter names, so they are available in the script editor via reflection
-    options.compilerArgs = listOf("-parameters")
-    // Specify source should be UTF8
-    options.encoding = "UTF-8"
-}
-
-/*
- * Avoid 'Entry .gitkeep is a duplicate but no duplicate handling strategy has been set.'
- * when using withSourcesJar()
- */
-tasks.jar {
-    duplicatesStrategy = DuplicatesStrategy.INCLUDE
-}
-
-/*
- * Support tests with JUnit.
- */
-tasks.test {
-    useJUnitPlatform()
-}
-
-// Looks redundant to include this here and in settings.gradle.kts,
-// but helps overcome some gradle trouble when including this as a subproject
-// within QuPath itself (which is useful during development).
-repositories {
-
-    if ("true" == providers.gradleProperty("use-maven-local").getOrElse("false")) {
-        logger.warn("Using Maven local")
-        mavenLocal()
-    }
-
-    mavenCentral()
-
-    // Add scijava - which is where QuPath's jars are hosted
-    maven {
-        url = uri("https://maven.scijava.org/content/repositories/releases")
-    }
-
-    maven {
-        url = uri("https://maven.scijava.org/content/repositories/snapshots")
-    }
-
-}
-
-
 publishing {
     repositories {
         maven {
@@ -180,7 +45,6 @@ publishing {
     publications {
         create<MavenPublication>("mavenJava") {
             from(components["java"])
-
             pom {
                 licenses {
                     license {
@@ -191,4 +55,4 @@ publishing {
             }
         }
     }
-}
+}

settings.gradle.kts

@@ -1,34 +1,17 @@
 pluginManagement {
-    plugins {
-        id("org.bytedeco.gradle-javacpp-platform") version "1.5.10"
-        id("org.openjfx.javafxplugin") version "0.1.0"
-    }
+	repositories {
+		gradlePluginPortal()
+		maven {
+			url = uri("https://maven.scijava.org/content/repositories/releases")
+		}
+	}
 }
 
-rootProject.name = "qupath-extension-instanseg"
-var qupathVersion = "0.6.0-SNAPSHOT"
-gradle.extra["qupath.app.version"] = qupathVersion
-
-dependencyResolutionManagement {
-
-    // Access QuPath's version catalog for dependency versions
-    versionCatalogs {
-        create("libs") {
-            from("io.github.qupath:qupath-catalog:$qupathVersion")
-        }
-    }
-
-    repositories {
-        mavenCentral()
-
-        // Add scijava - which is where QuPath's jars are hosted
-        maven {
-            url = uri("https://maven.scijava.org/content/repositories/releases")
-        }
-
-        maven {
-            url = uri("https://maven.scijava.org/content/repositories/snapshots")
-        }
+qupath {
+	version = "0.6.0-SNAPSHOT"
+}
 
-    }
+// Apply QuPath Gradle settings plugin to handle configuration
+plugins {
+	id("io.github.qupath.qupath-extension-settings") version "0.2.1"
 }