Fixes & Improvements

- Fixed JUnit test not running - Updated .pom - Fixed JUnit test criterion for fluxes and derivatives. Now a linear regression is built and its coefficient of determination is checked. - Improved logging. Now important notes are showed in a pop-up window prior to being written in the log. Exceptions that are written in the log also trigger a ShowMessageDialog.
kotik-coder · Jun 3, 2021 · 8ba282e · 8ba282e
1 parent 043dd78
commit 8ba282e
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Showing 12 changed files with 170 additions and 115 deletions.
diff --git a/pom.xml b/pom.xml
@@ -1,11 +1,73 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
   <modelVersion>4.0.0</modelVersion>
+
   <groupId>kotik-coder</groupId>
   <artifactId>PULsE</artifactId>
-  <version>1.91FR</version>
+  <version>1.91FM</version>
   <name>PULsE</name>
   <description>Processing Unit for Laser flash Experiments</description>
+  <developers>
+  	<developer>
+    	<id>al</id>
+        <name>Artem Lunev</name>
+        <email>alounev@list.ru</email>
+    </developer>
+  </developers>
+      <licenses>
+        <license>
+            <name>The Apache License, Version 2.0</name>
+            <url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
+        </license>
+  </licenses>
+
+    <dependencies>
+  	<dependency>
+  		<groupId>org.jfree</groupId>
+  		<artifactId>jfreechart</artifactId>
+  		<version>1.5.0</version>
+  	</dependency>
+	<dependency>
+	    <groupId>com.weblookandfeel</groupId>
+	    <artifactId>weblaf-ui</artifactId>
+	    <version>1.2.13</version>
+	</dependency>
+  	<dependency>
+  		<groupId>org.apache.commons</groupId>
+  		<artifactId>commons-math3</artifactId>
+  		<version>3.6.1</version>
+  	</dependency>
+  	<dependency>
+	    <groupId>ca.umontreal.iro.simul</groupId>
+    	<artifactId>ssj</artifactId>
+    	<version>3.3.1</version>
+  	</dependency>
+  	<dependency>
+		<groupId>commons-io</groupId>
+		<artifactId>commons-io</artifactId>
+		<version>2.6</version>
+	</dependency>
+  	<dependency>
+  	<groupId>colt</groupId>
+ 		 <artifactId>colt</artifactId>
+  		<version>1.2.0</version>
+  	</dependency>
+  	<dependency>
+	  <groupId>org.ejml</groupId>
+	  <artifactId>ejml-all</artifactId>
+	  <version>0.39</version>
+	</dependency>
+    <dependency>
+        <groupId>org.junit.jupiter</groupId>
+        <artifactId>junit-jupiter</artifactId>
+        <version>5.7.0-M1</version>
+        <scope>test</scope>
+    </dependency>
+	<!-- https://mvnrepository.com/artifact/com.numericalmethod/suanshu-20120606 -->
+  </dependencies>
+
   <build>
+     <sourceDirectory>src/main/java</sourceDirectory>
+     <testSourceDirectory>src/test</testSourceDirectory> 
     <plugins>
       <plugin>
         <artifactId>maven-compiler-plugin</artifactId>
@@ -49,75 +111,19 @@
 	      </execution>
 	    </executions>
 	  </plugin>
-	  <plugin>
-           <groupId>org.apache.maven.plugins</groupId>
-           <artifactId>maven-surefire-plugin</artifactId>
-           <version>2.22.0</version>
-           <dependencies>
-               <dependency>
-                   <groupId>org.junit.platform</groupId>
-                   <artifactId>junit-platform-surefire-provider</artifactId>
-                   <version>1.2.0</version>
-               </dependency>
-           </dependencies>
-           <configuration>
-           	<additionalClasspathElements>
-           		<additionalClasspathElement>src/test/java/</additionalClasspathElement>
-           	</additionalClasspathElements>
-           </configuration>
-       </plugin>  	  
+      <plugin>
+	      <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-surefire-plugin</artifactId>
+          <version>2.22.0</version>
+      </plugin>
+      <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-failsafe-plugin</artifactId>
+          <version>2.22.0</version>
+      </plugin>
     </plugins>
   </build>
-  <dependencies>
-  	<dependency>
-  		<groupId>org.jfree</groupId>
-  		<artifactId>jfreechart</artifactId>
-  		<version>1.5.0</version>
-  	</dependency>
-	<dependency>
-	    <groupId>com.weblookandfeel</groupId>
-	    <artifactId>weblaf-ui</artifactId>
-	    <version>1.2.13</version>
-	</dependency>
-  	<dependency>
-  		<groupId>org.apache.commons</groupId>
-  		<artifactId>commons-math3</artifactId>
-  		<version>3.6.1</version>
-  	</dependency>
-  	<dependency>
-	    <groupId>ca.umontreal.iro.simul</groupId>
-    	<artifactId>ssj</artifactId>
-    	<version>3.3.1</version>
-  	</dependency>
-  	<dependency>
-		<groupId>commons-io</groupId>
-		<artifactId>commons-io</artifactId>
-		<version>2.6</version>
-	</dependency>
-  	<dependency>
-  	<groupId>colt</groupId>
- 		 <artifactId>colt</artifactId>
-  		<version>1.2.0</version>
-  	</dependency>
-  	<dependency>
-	  <groupId>org.ejml</groupId>
-	  <artifactId>ejml-all</artifactId>
-	  <version>0.39</version>
-	</dependency>
-	<dependency>
-	<groupId>org.junit.jupiter</groupId>
-	<artifactId>junit-jupiter-engine</artifactId>
-	<version>5.2.0</version>
-	<scope>test</scope>
-	</dependency>
-	<dependency>
-		<groupId>org.junit.platform</groupId>
-		<artifactId>junit-platform-runner</artifactId>
-		<version>1.2.0</version>
-		<scope>test</scope>
-	</dependency>
-	<!-- https://mvnrepository.com/artifact/com.numericalmethod/suanshu-20120606 -->
-  </dependencies>
+
   <properties>
       <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
       <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>

diff --git a/src/main/java/pulse/input/ExperimentalData.java b/src/main/java/pulse/input/ExperimentalData.java
@@ -228,7 +228,7 @@ public double halfRiseTime() {
 				degraded.stream().map(point -> point.getY()).collect(Collectors.toList()));
 
 		if (index < 1) {
-			System.err.println(Messages.getString("ExperimentalData.HalfRiseError"));
+			System.out.println(Messages.getString("ExperimentalData.HalfRiseError"));
 			return max(getTimeSequence()) / FAIL_SAFE_FACTOR;
 		}
 

diff --git a/src/main/java/pulse/problem/statements/Problem.java b/src/main/java/pulse/problem/statements/Problem.java
@@ -1,7 +1,6 @@
 package pulse.problem.statements;
 
 import static pulse.input.listeners.CurveEventType.RESCALED;
-import static pulse.math.transforms.StandardTransformations.LOG;
 import static pulse.properties.NumericProperties.def;
 import static pulse.properties.NumericProperties.derive;
 import static pulse.properties.NumericPropertyKeyword.DIFFUSIVITY;

diff --git a/src/main/java/pulse/ui/Launcher.java b/src/main/java/pulse/ui/Launcher.java
@@ -38,6 +38,7 @@ public class Launcher {
 
 	private Launcher() {
 		arrangeErrorOutput();
+		arrangeMessages();
 	}
 
 	/**
@@ -66,7 +67,7 @@ public static void main(String[] args) {
 				JOptionPane.showMessageDialog(null, "<html>A new version of this software is available: "
 						+ newVersion.toString() + "<br>Please visit the PULsE website for more details.</html>");
 			}
-
+			
 		});
 	}
 
@@ -97,7 +98,17 @@ private void arrangeErrorOutput() {
 		try {
 			var dir = new File(decodedPath).getParent();
 			errorLog = new File(dir + File.separator + "ErrorLog_" + now() + ".log");
-			setErr(new PrintStream(errorLog));
+			setErr(new PrintStream(errorLog) {
+
+				@Override
+				public void println(String str) {
+					super.println(str);
+					JOptionPane.showMessageDialog(null, "An exception has occurred. "
+							+ "Please check the stored log!", "Exception", JOptionPane.ERROR_MESSAGE);
+				}
+
+			}
+			);
 		} catch (FileNotFoundException e) {
 			System.err.println("Unable to set up error stream");
 			e.printStackTrace();
@@ -106,6 +117,17 @@ private void arrangeErrorOutput() {
 		createShutdownHook();
 
 	}
+
+	private void arrangeMessages() {
+		System.setOut( new PrintStream(System.out) {
+
+			@Override
+			public void println(String str) {
+				JOptionPane.showMessageDialog(null, Messages.getString("TextWrap.0") + str + Messages.getString("TextWrap.0"));
+			}
+
+		});
+	}
 
 	private void createShutdownHook() {
 

diff --git a/src/main/java/pulse/ui/frames/SearchOptionsFrame.java b/src/main/java/pulse/ui/frames/SearchOptionsFrame.java
@@ -82,12 +82,11 @@ public SearchOptionsFrame() {
 
 	public void update() {
 		var selected = getInstance();
-		if (selected != null) {
-			pathList.setSelectedIndex(pathSolvers.indexOf(selected));
-			pathTable.updateTable();
-		} else {
-			pathList.clearSelection();
-		}
+		if (selected == null)
+			TaskManager.getManagerInstance().selectFirstTask();
+
+		pathList.setSelectedIndex(pathSolvers.indexOf(selected));
+		pathTable.updateTable();
 	}
 
 	class PathSolversList extends JList<PathOptimiser> {

diff --git a/src/main/resources/Version.txt b/src/main/resources/Version.txt
@@ -1 +1 @@
-1.91FR
+1.91FM
diff --git a/src/main/resources/messages.properties b/src/main/resources/messages.properties
@@ -279,4 +279,6 @@ ImplicitScheme.4=<html><b>Fully Implicit Scheme</b><ul style='list-style-type:no
 MixedScheme.2=Time interval too small: 
 MixedScheme.3=Problem not supported or unknown: 
 MixedScheme.4=<html><b>Symmetric Semi-Implicit Scheme</b><ul style='list-style-type:none'><li>Order of approximation <i>O</i>(<i>h</i><sup>2</sup> + <i>&tau</i><sup>2</sup>)</li><li>Unconditionally stable</li><li>Steps are computationally more expensive but their number is fewer compared to other schemes</li><li>Finite-difference representation of boundary conditions uses a Taylor expansion with three terms</li><li>Weight is set to 0.5</li></ul></html>
-MixedScheme2.4=<html><b>Increased Accuracy Semi-implicit Scheme</b><ul style='list-style-type:none'><li>Order of approximation <i>O</i>(<i>h</i><sup>4</sup> + <i>&tau</i><sup>2</sup>)</li><li>Unconditionally stable</li><li>Steps are computationally more expensive but their number is fewer compared to other schemes</li><li>Finite-difference representation of boundary conditions uses a Taylor expansion with three terms</li><li>Auto-adjusts its weight and discrete representation of the flux derivative based on accuracy.</li></ul></html>
+MixedScheme2.4=<html><b>Increased Accuracy Semi-implicit Scheme</b><ul style='list-style-type:none'><li>Order of approximation <i>O</i>(<i>h</i><sup>4</sup> + <i>&tau</i><sup>2</sup>)</li><li>Unconditionally stable</li><li>Steps are computationally more expensive but their number is fewer compared to other schemes</li><li>Finite-difference representation of boundary conditions uses a Taylor expansion with three terms</li><li>Auto-adjusts its weight and discrete representation of the flux derivative based on accuracy.</li></ul></html>
+TextWrap.0=<html><body><p style='width: 300px;'>
+TextWrap.1=</p></body></html>
diff --git a/...ticalNonscatteringTransferValidation.java → ...test/AnalyticalNonscatteringTestCase.java b/...ticalNonscatteringTransferValidation.java → ...test/AnalyticalNonscatteringTestCase.java
@@ -1,10 +1,10 @@
-package repository;
+package test;
 
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import static pulse.properties.NumericProperties.derive;
 import static pulse.properties.NumericPropertyKeyword.OPTICAL_THICKNESS;
 import static pulse.properties.NumericPropertyKeyword.QUADRATURE_POINTS;
-import static repository.TestProfileLoader.loadTestProfileDense;
+import static test.ProfileLoader.loadTestProfileDense;
 
 import java.util.List;
 
@@ -19,10 +19,10 @@
 import pulse.problem.schemes.rte.exact.NonscatteringRadiativeTransfer;
 import pulse.problem.statements.model.ThermoOpticalProperties;
 
-class AnalyticalNonscatteringTransferValidation {
+class AnalyticalNonscatteringTestCase {
 
 	private static List<Double> testProfile;
-	private static NonscatteringTestCase testCase;
+	private static NonscatteringSetup testCase;
 
 	private NonscatteringRadiativeTransfer chand;
 	private RadiativeTransferSolver dom;
@@ -31,7 +31,7 @@ class AnalyticalNonscatteringTransferValidation {
 	@BeforeAll
 	static void setUpBeforeClass() throws Exception {
 		testProfile = loadTestProfileDense();
-		testCase = new NonscatteringTestCase(testProfile.size(), 10.0);
+		testCase = new NonscatteringSetup(testProfile.size(), 10.0);
 	}
 
 	@BeforeEach
@@ -47,23 +47,23 @@ void testFluxesLowThickness() {
 		quadrature.setQuadraturePoints(derive(QUADRATURE_POINTS, 2));
 		var properties = (ThermoOpticalProperties)testCase.getTestProblem().getProperties();
 		properties.setOpticalThickness(derive(OPTICAL_THICKNESS, 0.1));
-		assertTrue(testCase.testFluxesAndDerivatives(testProfile, chand, dom, 1e-2, 3e-1));
+		assertTrue(testCase.testFluxesAndDerivatives(testProfile, chand, dom, 1e-3, 1e-1));
 	}
 
 	@Test
 	void testFluxesMediumThickness() {
 		quadrature.setQuadraturePoints(derive(QUADRATURE_POINTS, 3));
 		var properties = (ThermoOpticalProperties)testCase.getTestProblem().getProperties();
 		properties.setOpticalThickness(derive(OPTICAL_THICKNESS, 1.5));
-		assertTrue(testCase.testFluxesAndDerivatives(testProfile, chand, dom, 1e-2, 1));
+		assertTrue(testCase.testFluxesAndDerivatives(testProfile, chand, dom, 1e-3, 1e-2));
 	}
 
 	@Test
 	void testFluxesHighThickness() {
 		quadrature.setQuadraturePoints(derive(QUADRATURE_POINTS, 6));
 		var properties = (ThermoOpticalProperties)testCase.getTestProblem().getProperties();
 		properties.setOpticalThickness(derive(OPTICAL_THICKNESS, 100.0));
-		assertTrue(testCase.testFluxesAndDerivatives(testProfile, chand, dom, 1e-1, Double.POSITIVE_INFINITY));
+		assertTrue(testCase.testFluxesAndDerivatives(testProfile, chand, dom, 1e-3, 1e-2));
 	}
 
 }
diff --git a/...creteNonscatteringTransferValidation.java → ...a/test/DiscreteNonscatteringTestCase.java b/...creteNonscatteringTransferValidation.java → ...a/test/DiscreteNonscatteringTestCase.java
@@ -1,10 +1,10 @@
-package repository;
+package test;
 
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import static pulse.properties.NumericProperties.derive;
 import static pulse.properties.NumericPropertyKeyword.INTEGRATION_SEGMENTS;
 import static pulse.properties.NumericPropertyKeyword.OPTICAL_THICKNESS;
-import static repository.TestProfileLoader.loadTestProfileDense;
+import static test.ProfileLoader.loadTestProfileDense;
 
 import java.util.List;
 
@@ -19,18 +19,18 @@
 import pulse.problem.schemes.rte.exact.NonscatteringRadiativeTransfer;
 import pulse.problem.statements.model.ThermoOpticalProperties;
 
-class DiscreteNonscatteringTransferValidation {
+class DiscreteNonscatteringTestCase {
 
 	private static List<Double> testProfile;
-	private static NonscatteringTestCase testCase;
+	private static NonscatteringSetup testCase;
 
 	private NonscatteringRadiativeTransfer newton;
 	private RadiativeTransferSolver dom;
 
 	@BeforeAll
 	private static void setUpBeforeClass() {
 		testProfile = loadTestProfileDense();
-		testCase = new NonscatteringTestCase(testProfile.size(), 10.0);
+		testCase = new NonscatteringSetup(testProfile.size(), 10.0);
 	}
 
 	@BeforeEach
@@ -48,14 +48,14 @@ void setUp() throws Exception {
 	void testFluxesLowThickness() {
 		var properties = (ThermoOpticalProperties)testCase.getTestProblem().getProperties();
 		properties.setOpticalThickness(derive(OPTICAL_THICKNESS, 0.1));
-		assertTrue(testCase.testFluxesAndDerivatives(testProfile, newton, dom, 1e-2, 3e-1));
+		assertTrue(testCase.testFluxesAndDerivatives(testProfile, newton, dom, 1e-3, 1e-1));
 	}
 
 	@Test
 	void testFluxesMediumThickness() {
 		var properties = (ThermoOpticalProperties)testCase.getTestProblem().getProperties();
 		properties.setOpticalThickness(derive(OPTICAL_THICKNESS, 1.5));
-		assertTrue(testCase.testFluxesAndDerivatives(testProfile, newton, dom, 1e-2, 3e-1));
+		assertTrue(testCase.testFluxesAndDerivatives(testProfile, newton, dom, 1e-3, 1e-1));
 	}
 
 }