Formatting improvements - learning to use IntelliJ

.github/workflows/gradle.yml

@@ -23,20 +23,20 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up JDK 11
-      uses: actions/setup-java@v3
-      with:
-        java-version: '11'
-        distribution: 'temurin'
-    - name: Validate Gradle wrapper
-      uses: gradle/wrapper-validation-action@e6e38bacfdf1a337459f332974bb2327a31aaf4b
-    - name: Build with Gradle
-      uses: gradle/gradle-build-action@67421db6bd0bf253fb4bd25b31ebb98943c375e1
-      with:
-        arguments: build
-    - uses: actions/upload-artifact@v3
-      with:
-        name: jar
-        path: build/libs
-        retention-days: 7
+      - uses: actions/checkout@v3
+      - name: Set up JDK 11
+        uses: actions/setup-java@v3
+        with:
+          java-version: '11'
+          distribution: 'temurin'
+      - name: Validate Gradle wrapper
+        uses: gradle/wrapper-validation-action@e6e38bacfdf1a337459f332974bb2327a31aaf4b
+      - name: Build with Gradle
+        uses: gradle/gradle-build-action@67421db6bd0bf253fb4bd25b31ebb98943c375e1
+        with:
+          arguments: build
+      - uses: actions/upload-artifact@v3
+        with:
+          name: jar
+          path: build/libs
+          retention-days: 7

README.md

@@ -1,2 +1,3 @@
 # qp_scope
+
 Controlling a microscope through some sort of python control interface (Pycromanager) and MicroManager

build.gradle

@@ -1,12 +1,12 @@
 plugins {
-  // Main gradle plugin for building a Java library
-  //id 'java-library'
-  // Support writing the extension in Groovy (remove this if you don't want to)
-  id 'groovy'
-  // To create a shadow/fat jar that bundle up all dependencies
-  id 'com.github.johnrengelman.shadow' version '7.1.2'
-  // Include this plugin to avoid downloading JavaCPP dependencies for all platforms
-  id 'org.bytedeco.gradle-javacpp-platform'
+    // Main gradle plugin for building a Java library
+    //id 'java-library'
+    // Support writing the extension in Groovy (remove this if you don't want to)
+    id 'groovy'
+    // To create a shadow/fat jar that bundle up all dependencies
+    id 'com.github.johnrengelman.shadow' version '7.1.2'
+    // Include this plugin to avoid downloading JavaCPP dependencies for all platforms
+    id 'org.bytedeco.gradle-javacpp-platform'
 }
 
 //the module name
@@ -73,9 +73,9 @@ jar {
  * Copy the LICENSE file into the jar... if we have one (we should!)
  */
 processResources {
-  from ("${projectDir}/LICENSE") {
-    into 'licenses/'
-  }
+    from("${projectDir}/LICENSE") {
+        into 'licenses/'
+    }
 }
 
 /*
@@ -116,7 +116,7 @@ tasks.withType(Javadoc).configureEach {
  * Specify that the encoding should be UTF-8 for source files
  */
 tasks.named('compileJava') {
-	options.encoding = 'UTF-8'
+    options.encoding = 'UTF-8'
 }
 
 /*
@@ -141,7 +141,7 @@ repositories {
     // Add this if you need access to dependencies only installed locally
     mavenLocal()
 
-    flatDir{
+    flatDir {
         dirs 'C:/ImageAnalysis/QPExtensionTest/BasicStitching/build/libs'
     }
 

src/main/groovy/qupath/ext/qp_scope/QP_scope.groovy

@@ -1,92 +1,92 @@
-package qupath.ext.qp_scope;
+package qupath.ext.qp_scope
 
 import javafx.scene.control.MenuItem
-import qupath.lib.common.Version;
-import qupath.lib.gui.QuPathGUI
-import qupath.lib.gui.extensions.QuPathExtension;
-import qupath.ext.qp_scope.functions.*
 import org.slf4j.LoggerFactory
+import qupath.ext.qp_scope.functions.QP_scope_GUI
+import qupath.lib.common.Version
+import qupath.lib.gui.QuPathGUI
+import qupath.lib.gui.extensions.QuPathExtension
 
 /**
  * Built from the QuPath extension template - an extension to control a microscope through a Python interface
  */
 class QP_scope implements QuPathExtension {
 
-	// Setting the variables here is enough for them to be available in the extension
-	String name = "Microscopy in QuPath"
-	String description = "Interact with a microscope from QuPath via Python interfaces like PycroManager or PyMMCore"
-	Version QuPathVersion = Version.parse("v0.4.4")
+    // Setting the variables here is enough for them to be available in the extension
+    String name = "Microscopy in QuPath"
+    String description = "Interact with a microscope from QuPath via Python interfaces like PycroManager or PyMMCore"
+    Version QuPathVersion = Version.parse("v0.4.4")
 
 //	@Override
 //	void installExtension(QuPathGUI qupath) {
 //		qupath.installActions(ActionTools.getAnnotatedActions(new BSCommands(qupath)))
 //		addMenuItem(qupath)
 //	}
-	@Override
-	void installExtension(QuPathGUI qupath) {
-		addMenuItem(qupath)
+    @Override
+    void installExtension(QuPathGUI qupath) {
+        addMenuItem(qupath)
+
+    }
+    /**
+     * Get the description of the extension.
+     *
+     * @return The description of the extension.
+     */
+    @Override
+    public String getDescription() {
+        return "Control a microscope!";
+    }
 
-	}
-	/**
-	 * Get the description of the extension.
-	 *
-	 * @return The description of the extension.
-	 */
-	@Override
-	public String getDescription() {
-		return "Control a microscope!";
-	}
+    /**
+     * Get the name of the extension.
+     *
+     * @return The name of the extension.
+     */
+    @Override
+    public String getName() {
+        return "qp_scope";
+    }
 
-	/**
-	 * Get the name of the extension.
-	 *
-	 * @return The name of the extension.
-	 */
-	@Override
-	public String getName() {
-		return "qp_scope";
-	}
+    private void addMenuItem(QuPathGUI qupath) {
+        def logger = LoggerFactory.getLogger(QuPathGUI.class)
+        // Check for dependencies and QuPath version
+        logger.info("QuPath Version")
+        logger.info(getQuPathVersion().toString())
+        // TODO: how to check if version is supported?
 
-	private void addMenuItem(QuPathGUI qupath) {
-		def logger = LoggerFactory.getLogger(QuPathGUI.class)
-		// Check for dependencies and QuPath version
-		logger.info("QuPath Version")
-		logger.info(getQuPathVersion().toString())
-		// TODO: how to check if version is supported?
+        // Get or create the menu
+        def menu = qupath.getMenu("Extensions>${name}", true)
 
-		// Get or create the menu
-		def menu = qupath.getMenu("Extensions>${name}", true)
+        // First menu item
+        def qpScope1 = new MenuItem("Start qp_scope")
+        // TODO: tooltip
+        qpScope1.setOnAction(e -> {
+            // TODO: check preferences for all necessary entries
+            QP_scope_GUI.createGUI1()
+        })
 
-		// First menu item
-		def qpScope1 = new MenuItem("Start qp_scope")
-		// TODO: tooltip
-		qpScope1.setOnAction(e -> {
-			// TODO: check preferences for all necessary entries
-			QP_scope_GUI.createGUI1()
-		})
+        // Second menu item
+        def qpScope2 = new MenuItem("Second scan on existing annotations")
+        // TODO: tooltip
+        qpScope2.setOnAction(e -> {
+            // TODO: check preferences for all necessary entries
+            QP_scope_GUI.createGUI2()
+        })
 
-		// Second menu item
-		def qpScope2 = new MenuItem("Second scan on existing annotations")
-		// TODO: tooltip
-		qpScope2.setOnAction(e -> {
-			// TODO: check preferences for all necessary entries
-			QP_scope_GUI.createGUI2()
-		})
+        // Third menu item - "Use current image as macro view"
+        def qpScope3 = new MenuItem("Use current image as macro view")
+        // TODO: tooltip
+        qpScope3.setOnAction(e -> {
+            QP_scope_GUI.createGUI3()
+        })
 
-		// Third menu item - "Use current image as macro view"
-		def qpScope3 = new MenuItem("Use current image as macro view")
-		// TODO: tooltip
-		qpScope3.setOnAction(e -> {
-			QP_scope_GUI.createGUI3()
-		})
+        // Add the menu items to the menu
+        menu.getItems() << qpScope1
+        menu.getItems() << qpScope2
+        menu.getItems() << qpScope3
+    }
 
-		// Add the menu items to the menu
-		menu.getItems() << qpScope1
-		menu.getItems() << qpScope2
-		menu.getItems() << qpScope3
-	}
 
-
 }
 //@ActionMenu("Extensions")
 //public class BSCommands {