Deactivate smile demos and unit tests

* The current version of smile 4.0.0 is not in sync with the latest developments of the library

src/test/java/org/mastodon/mamut/feature/dimensionalityreduction/umap/UmapSmileDemo.java

@@ -10,6 +10,7 @@
 
 public class UmapSmileDemo
 {
+	/*
 	public static void main( final String[] args )
 	{
 		int numCluster1 = 50;
@@ -19,12 +20,14 @@ public static void main( final String[] args )
 		double[][] result = Arrays.stream( umapResult ).map( row -> Arrays.stream( row ).toArray() ).toArray( double[][]::new );
 		PlotPoints.plot( sampleData, result, resultValues -> resultValues[ 0 ] > 1 );
 	}
-
+	
 	static double[][] setUpUmap( final double[][] sampleData )
 	{
 		int iterations = sampleData.length < 10_000 ? 500 : 200; // https://github.com/lmcinnes/umap/blob/a012b9d8751d98b94935ca21f278a54b3c3e1b7f/umap/umap_.py#L1073
 		double minDist = 0.1;
 		int nNeighbors = 15;
 		return UMAP.of( sampleData, MathEx::distance, nNeighbors, 2, iterations, 1, minDist, 1.0, 5, 1 );
 	}
+	
+	 */
 }

src/test/java/org/mastodon/mamut/feature/dimensionalityreduction/umap/UmapSmileDemoIris.java

@@ -26,6 +26,7 @@ public class UmapSmileDemoIris
 
 	private static final Logger logger = LoggerFactory.getLogger( MethodHandles.lookup().lookupClass() );
 
+	/*
 	public static void main( String[] args ) throws IOException, CsvValidationException
 	{
 		File file = new File( "src/test/resources/org/mastodon/mamut/feature/dimensionalityreduction/iris.tsv" );
@@ -47,18 +48,20 @@ public static void main( String[] args ) throws IOException, CsvValidationExcept
 			long t0 = System.currentTimeMillis();
 			double[][] result = setUpUmap( inputData );
 			logger.info( "UMAP took {} ms", System.currentTimeMillis() - t0 );
-
+	
 			result = Arrays.stream( result ).map( row -> Arrays.stream( row ).map( value -> value * 10d ).toArray() ) // scale up
 					.toArray( double[][]::new );
 			PlotPoints.plot( null, result, null );
 		}
 	}
-
+	
 	static double[][] setUpUmap( double[][] data )
 	{
 		int iterations = data.length < 10_000 ? 500 : 200; // https://github.com/lmcinnes/umap/blob/a012b9d8751d98b94935ca21f278a54b3c3e1b7f/umap/umap_.py#L1073
 		double minDist = 0.1;
 		int nNeighbors = 15;
 		return UMAP.of( data, MathEx::distance, nNeighbors, 2, iterations, 1, minDist, 1.0, 5, 1 );
 	}
+	
+	 */
 }

src/test/java/org/mastodon/mamut/feature/dimensionalityreduction/umap/UmapSmileDemoTgmmMini.java

@@ -26,6 +26,7 @@ public class UmapSmileDemoTgmmMini
 
 	private static final Logger logger = LoggerFactory.getLogger( MethodHandles.lookup().lookupClass() );
 
+	/*
 	public static void main( String[] args ) throws IOException, CsvValidationException
 	{
 		File file = new File( "src/test/resources/org/mastodon/mamut/feature/dimensionalityreduction/tgmm-mini-spot.csv" );
@@ -47,18 +48,20 @@ public static void main( String[] args ) throws IOException, CsvValidationExcept
 			long t0 = System.currentTimeMillis();
 			double[][] result = setUpUmap( inputData );
 			logger.info( "UMAP took {} ms", System.currentTimeMillis() - t0 );
-
+	
 			double[][] resultScaled = Arrays.stream( result ).map( row -> Arrays.stream( row ).map( value -> value * 10d ).toArray() )
 					.toArray( double[][]::new );
 			PlotPoints.plot( null, resultScaled, null );
 		}
 	}
-
+	
 	static double[][] setUpUmap( double[][] data )
 	{
 		int iterations = data.length < 10_000 ? 500 : 200; // https://github.com/lmcinnes/umap/blob/a012b9d8751d98b94935ca21f278a54b3c3e1b7f/umap/umap_.py#L1073
 		double minDist = 0.1;
 		int nNeighbors = 15;
 		return UMAP.of( data, MathEx::distance, nNeighbors, 2, iterations, 1, minDist, 1.0, 5, 1 );
 	}
+	
+	 */
 }

src/test/java/org/mastodon/mamut/feature/dimensionalityreduction/umap/UmapSmileTest.java

@@ -19,28 +19,31 @@ class UmapSmileTest
 {
 	private static final Logger logger = LoggerFactory.getLogger( MethodHandles.lookup().lookupClass() );
 
+	/*
 	@Test
 	void test()
 	{
 		int numCluster1 = 50;
 		int numCluster2 = 100;
 		// create two distinct clusters of points in 3D space, one having 50 points and the other 100 points
 		double[][] sampleData = RandomDataTools.generateSampleData( numCluster1, numCluster2 );
-
+	
 		// Recommendations for UMAP defaults: https://github.com/lmcinnes/umap/blob/a012b9d8751d98b94935ca21f278a54b3c3e1b7f/umap/umap_.py#L1073
 		int iterations = sampleData.length < 10_000 ? 500 : 200;
 		double minDist = 0.1;
 		int nNeighbors = 15;
 		long t0 = System.currentTimeMillis();
 		double[][] umapResult = UMAP.of( sampleData, MathEx::distance, nNeighbors, 2, iterations, 1, minDist, 1.0, 5, 1 );
 		logger.info( "UMAP took {} ms", System.currentTimeMillis() - t0 );
-
+	
 		assertEquals( 2, umapResult[ 0 ].length );
 		assertEquals( umapResult.length, sampleData.length ); // fails, because only the largest connected component is used inside the algorithm
-
+	
 		double[][] umapResult1 = Arrays.copyOfRange( umapResult, 0, numCluster1 );
 		double[][] umapResult2 = Arrays.copyOfRange( umapResult, numCluster1, numCluster1 + numCluster2 );
-
+	
 		DimensionalityReductionTestUtils.testNonOverlappingClusters( umapResult1, umapResult2 ); // should pass
 	}
+	
+	 */
 }