Update PythonEnvironmentManagerUI and ApposeUtils to use Appose builders for environment configuration

* This is to reflect cellpose3, cellpose4 and stardist use pixi and trackastra uses mamba

Author: stefanhahmann

src/main/java/org/mastodon/mamut/util/appose/ApposeUtils.java

@@ -46,7 +46,7 @@
 import javax.swing.SwingUtilities;
 
 import org.apache.commons.lang3.tuple.Pair;
-import org.apposed.appose.Appose;
+import org.apposed.appose.Builder;
 import org.apposed.appose.builder.Builders;
 import org.apposed.appose.util.Environments;
 import org.mastodon.mamut.util.ByteFormatter;
@@ -71,9 +71,9 @@ private ApposeUtils()
 	 *                   to set up the environment.
 	 * @throws IOException If an I/O error occurs during the installation process.
 	 */
-	public static void installEnvironment( final String envContent ) throws IOException
+	public static void installEnvironment(final String envContent, final Builder<?> envBuilder) throws IOException
 	{
-		Appose.mamba().content( envContent ).scheme( "environment.yml" ).logDebug().rebuild();
+		envBuilder.content( envContent ).logDebug().rebuild();
 	}
 
 	/**

src/main/java/org/mastodon/mamut/util/appose/PythonEnvironmentManagerUI.java

@@ -60,6 +60,8 @@
 
 import net.miginfocom.swing.MigLayout;
 
+import org.apposed.appose.Appose;
+import org.apposed.appose.Builder;
 import org.apposed.appose.util.Environments;
 import org.mastodon.app.MastodonIcons;
 import org.mastodon.mamut.detection.cellpose.Cellpose3;
@@ -104,10 +106,10 @@ public PythonEnvironmentManagerUI( JFrame owner )
 	private void initEnvironmentPanels()
 	{
 		environmentPanels = new ArrayList<>();
-		environmentPanels.add( new EnvironmentPanel( Cellpose3.ENV_NAME, Cellpose3.ENV_FILE_CONTENT ) );
-		environmentPanels.add( new EnvironmentPanel( Cellpose4.ENV_NAME, Cellpose4.ENV_FILE_CONTENT ) );
-		environmentPanels.add( new EnvironmentPanel( StarDist.ENV_NAME, StarDist.ENV_FILE_CONTENT ) );
-		environmentPanels.add( new EnvironmentPanel( TrackastraUtils.ENV_NAME, TrackastraUtils.ENV_FILE_CONTENT ) );
+		environmentPanels.add( new EnvironmentPanel( Cellpose3.ENV_NAME, Cellpose3.ENV_FILE_CONTENT, Appose.pixi() ) );
+		environmentPanels.add( new EnvironmentPanel( Cellpose4.ENV_NAME, Cellpose4.ENV_FILE_CONTENT, Appose.pixi() ) );
+		environmentPanels.add( new EnvironmentPanel( StarDist.ENV_NAME, StarDist.ENV_FILE_CONTENT, Appose.pixi() ) );
+		environmentPanels.add( new EnvironmentPanel( TrackastraUtils.ENV_NAME, TrackastraUtils.ENV_FILE_CONTENT, Appose.mamba().scheme( "environment.yml" ) ) );
 	}
 
 	private void initLayout()
@@ -163,6 +165,8 @@ private class EnvironmentPanel extends JPanel
 
 		private final String envContent;
 
+		private final Builder< ? > envBuilder;
+
 		private final JLabel statusIcon;
 
 		private final JLabel statusLabel;
@@ -173,11 +177,12 @@ private class EnvironmentPanel extends JPanel
 
 		private final JLabel sizeValueLabel;
 
-		private EnvironmentPanel( String envName, String envContent )
+		private EnvironmentPanel( final String envName, final String envContent, final Builder< ? > envBuilder )
 		{
 			super( new MigLayout( "fill, insets 8", "[][80!][grow][]", "[]5[]5[]" ) );
 			this.envName = envName;
 			this.envContent = envContent;
+			this.envBuilder = envBuilder;
 
 			statusIcon = new JLabel();
 			statusLabel = new JLabel();
@@ -358,7 +363,7 @@ private void installEnvironmentUI()
 					() -> {
 						try
 						{
-							ApposeUtils.installEnvironment( envContent );
+							ApposeUtils.installEnvironment( envContent, envBuilder );
 						}
 						catch ( IOException e )
 						{

src/test/java/org/mastodon/mamut/util/appose/ApposeUtilsTest.java

@@ -38,6 +38,8 @@
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 
+import org.apposed.appose.Appose;
+import org.apposed.appose.Builder;
 import org.junit.jupiter.api.Test;
 
 class ApposeUtilsTest
@@ -51,8 +53,9 @@ void testInstallDeleteExistsSize() throws IOException
 				+ "  - conda-forge\n"
 				+ "dependencies:\n"
 				+ "  - python=3.10\n";
+		Builder<?> envBuilder = Appose.mamba().scheme( "environment.yml" );
 
-		ApposeUtils.installEnvironment( testEnvContent );
+		ApposeUtils.installEnvironment( testEnvContent, envBuilder );
 		assertTrue( ApposeUtils.checkEnvironmentInstalled( testEnvName ) );
 		String size = ApposeUtils.calculateEnvironmentSize( testEnvName );
 		String numberPart = size.split( " " )[ 0 ]; // "123,4"