cdk · johnmay · Mar 24, 2025 · Mar 22, 2025 · Mar 22, 2025 · Mar 22, 2025
diff --git a/base/core/pom.xml b/base/core/pom.xml
@@ -23,6 +23,16 @@
             <artifactId>cdk-interfaces</artifactId>
             <version>${project.parent.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-api</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-engine</artifactId>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
     <build>
@@ -47,9 +57,6 @@
         		<groupId>org.apache.maven.plugins</groupId>
         		<artifactId>maven-surefire-plugin</artifactId>
         		<version>3.2.5</version>
-        		<configuration>
-          			<skipTests>true</skipTests>
-        		</configuration>
       		</plugin>
     	</plugins>
     </build>

diff --git a/base/core/src/test/java/org/openscience/cdk/io/setting/BooleanIOSettingTest.java b/base/core/src/test/java/org/openscience/cdk/io/setting/BooleanIOSettingTest.java
@@ -0,0 +1,76 @@
+/* Copyright (C) 2025  Egon Willighagen <[email protected]>
+ *
+ * Contact: [email protected]
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.openscience.cdk.io.setting;
+
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.io.setting.IOSetting.Importance;
+
+class BooleanIOSettingTest {
+
+    @Test
+    void testConstructure() {
+        IOSetting setting = new BooleanIOSetting("Glossy", Importance.LOW, "Want glossy?", "true");
+        Assertions.assertNotNull(setting);
+        Assertions.assertEquals("Glossy", setting.getName());
+        Assertions.assertEquals(Importance.LOW, setting.getLevel());
+        Assertions.assertEquals("Want glossy?", setting.getQuestion());
+        Assertions.assertEquals("true", setting.getSetting());
+    }
+
+    @Test
+    void testIsSet() {
+        BooleanIOSetting setting = new BooleanIOSetting("Glossy", Importance.LOW, "Want glossy?", "true");
+        Assertions.assertNotNull(setting);
+        Assertions.assertTrue(setting.isSet());
+    }
+
+    @Test
+    void testSetSetting() {
+        BooleanIOSetting setting = new BooleanIOSetting("Glossy", Importance.LOW, "Want glossy?", "true");
+        Assertions.assertEquals("true", setting.getSetting());
+        try {
+			setting.setSetting("false");
+		} catch (CDKException e) {
+			Assertions.fail(e); // should not happen
+		}
+        Assertions.assertEquals("false", setting.getSetting());
+    }
+
+    @Test
+    void testSetSetting_Variants() throws CDKException {
+        BooleanIOSetting setting = new BooleanIOSetting("Glossy", Importance.LOW, "Want glossy?", "true");
+		setting.setSetting("yes"); Assertions.assertEquals("true", setting.getSetting());
+		setting.setSetting("no"); Assertions.assertEquals("false", setting.getSetting());
+		setting.setSetting("y"); Assertions.assertEquals("true", setting.getSetting());
+		setting.setSetting("n"); Assertions.assertEquals("false", setting.getSetting());
+    }
+
+    @Test
+    void testSetSetting_InvalidValue() {
+        BooleanIOSetting setting = new BooleanIOSetting("Glossy", Importance.LOW, "Want glossy?", "true");
+        try {
+			setting.setSetting("fake");
+			Assertions.fail("Expected exception was not thrown"); // should not happen
+		} catch (CDKException e) {
+			// should happen
+		}
+    }
+}
diff --git a/base/core/src/test/java/org/openscience/cdk/io/setting/IntegerIOSettingTest.java b/base/core/src/test/java/org/openscience/cdk/io/setting/IntegerIOSettingTest.java
@@ -0,0 +1,67 @@
+/* Copyright (C) 2025  Egon Willighagen <[email protected]>
+ *
+ * Contact: [email protected]
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.openscience.cdk.io.setting;
+
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.io.setting.IOSetting.Importance;
+
+class IntegerIOSettingTest {
+
+    @Test
+    void testConstructure() {
+        IOSetting setting = new IntegerIOSetting("Number of files", Importance.LOW, "How many copies do you want?", "1");
+        Assertions.assertNotNull(setting);
+        Assertions.assertEquals("Number of files", setting.getName());
+        Assertions.assertEquals(Importance.LOW, setting.getLevel());
+        Assertions.assertEquals("How many copies do you want?", setting.getQuestion());
+        Assertions.assertEquals("1", setting.getSetting());
+    }
+
+    @Test
+    void testIsSet() {
+        IntegerIOSetting setting = new IntegerIOSetting("Number of files", Importance.LOW, "How many copies do you want?", "1");
+        Assertions.assertNotNull(setting);
+        Assertions.assertEquals(1, setting.getSettingValue());
+    }
+
+    @Test
+    void testSetSetting() {
+        IOSetting setting = new IntegerIOSetting("Number of files", Importance.LOW, "How many copies do you want?", "1");
+        Assertions.assertEquals("1", setting.getSetting());
+        try {
+			setting.setSetting("2");
+		} catch (CDKException e) {
+			Assertions.fail(e); // should not happen
+		}
+        Assertions.assertEquals("2", setting.getSetting());
+    }
+
+    @Test
+    void testSetSetting_InvalidValue() {
+        IOSetting setting = new IntegerIOSetting("Number of files", Importance.LOW, "How many copies do you want?", "1");
+        try {
+			setting.setSetting("false");
+			Assertions.fail("Expected exception was not thrown"); // should not happen
+		} catch (CDKException e) {
+			// should happen
+		}
+    }
+}
diff --git a/base/core/src/test/java/org/openscience/cdk/io/setting/OptionIOSettingTest.java b/base/core/src/test/java/org/openscience/cdk/io/setting/OptionIOSettingTest.java
@@ -0,0 +1,113 @@
+/* Copyright (C) 2025  Egon Willighagen <[email protected]>
+ *
+ * Contact: [email protected]
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.openscience.cdk.io.setting;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.io.setting.IOSetting.Importance;
+
+class OptionIOSettingTest {
+
+    @Test
+    void testConstructure() {
+    	List<String> options = new ArrayList<>();
+    	options.add("Option1");
+    	options.add("Option2");
+        IOSetting setting = new OptionIOSetting("Menu", Importance.LOW, "What option do you want?", options, "Option1");
+        Assertions.assertNotNull(setting);
+        Assertions.assertEquals("Menu", setting.getName());
+        Assertions.assertEquals(Importance.LOW, setting.getLevel());
+        Assertions.assertEquals("What option do you want?", setting.getQuestion());
+        Assertions.assertEquals("Option1", setting.getSetting());
+    }
+
+    @Test
+    void testSetSetting() {
+    	List<String> options = new ArrayList<>();
+    	options.add("Option1");
+    	options.add("Option2");
+        IOSetting setting = new OptionIOSetting("Menu", Importance.LOW, "What option do you want?", options, "Option1");
+        Assertions.assertEquals("Option1", setting.getSetting());
+        try {
+			setting.setSetting("Option2");
+		} catch (CDKException e) {
+			Assertions.fail(e); // should not happen
+		}
+        Assertions.assertEquals("Option2", setting.getSetting());
+    }
+
+    @Test
+    void testSetSetting_InvalidValue() {
+    	List<String> options = new ArrayList<>();
+    	options.add("Option1");
+    	options.add("Option2");
+        IOSetting setting = new OptionIOSetting("Menu", Importance.LOW, "What option do you want?", options, "Option1");
+        try {
+			setting.setSetting("Option3");
+			Assertions.fail("Expected exception was not thrown"); // should not happen
+		} catch (CDKException e) {
+			// should happen
+		}
+    }
+
+    @Test
+    void testSetSetting_Integer() {
+    	List<String> options = new ArrayList<>();
+    	options.add("Option1");
+    	options.add("Option2");
+    	OptionIOSetting setting = new OptionIOSetting("Menu", Importance.LOW, "What option do you want?", options, "Option1");
+        Assertions.assertEquals("Option1", setting.getSetting());
+        try {
+			setting.setSetting(2);
+		} catch (CDKException e) {
+			Assertions.fail(e); // should not happen
+		}
+        Assertions.assertEquals("Option2", setting.getSetting());
+    }
+
+    @Test
+    void testSetSetting_InvalidValue_Integer() {
+    	List<String> options = new ArrayList<>();
+    	options.add("Option1");
+    	options.add("Option2");
+    	OptionIOSetting setting = new OptionIOSetting("Menu", Importance.LOW, "What option do you want?", options, "Option1");
+        try {
+			setting.setSetting(3);
+			Assertions.fail("Expected exception was not thrown"); // should not happen
+		} catch (CDKException e) {
+			// should happen
+		}
+    }
+
+    @Test
+    void testGetSetting() {
+    	List<String> options = new ArrayList<>();
+    	options.add("Option1");
+    	options.add("Option2");
+    	OptionIOSetting setting = new OptionIOSetting("Menu", Importance.LOW, "What option do you want?", options, "Option1");
+    	List<String> options2 = setting.getOptions();
+        Assertions.assertEquals(2, options2.size());
+        Assertions.assertTrue(options2.contains("Option1"));
+        Assertions.assertTrue(options2.contains("Option2"));
+    }
+}
diff --git a/base/interfaces/pom.xml b/base/interfaces/pom.xml
@@ -28,16 +28,18 @@
             <artifactId>junit-jupiter-engine</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>org.hamcrest</groupId>
+            <artifactId>hamcrest</artifactId>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 	<build>
     	<plugins>
         	<plugin>
         		<groupId>org.apache.maven.plugins</groupId>
         		<artifactId>maven-surefire-plugin</artifactId>
         		<version>3.2.5</version>
-        		<configuration>
-          			<skipTests>true</skipTests>
-        		</configuration>
       		</plugin>
     	</plugins>
   	</build>

diff --git a/...ience/cdk/exception/CDKExceptionTest.java → ...ience/cdk/exception/CDKExceptionTest.java b/...ience/cdk/exception/CDKExceptionTest.java → ...ience/cdk/exception/CDKExceptionTest.java
@@ -1,4 +1,5 @@
 /* Copyright (C) 2004-2007  The Chemistry Development Kit (CDK) project
+ *               2025       Egon Willighagen <[email protected]>
  *
  * Contact: [email protected]
  *
@@ -21,15 +22,14 @@
 
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
-import org.openscience.cdk.test.CDKTestCase;
 
 /**
  * Checks the functionality of the CDKException class.
  *
  *
  * @see org.openscience.cdk.exception.CDKException
  */
-class CDKExceptionTest extends CDKTestCase {
+class CDKExceptionTest {
 
     @Test
     void testCDKException_String() {
@@ -43,9 +43,7 @@ void testCDKException_String() {
     void testCDKException_String_Throwable() {
         final String EXPLANATION = "No, CDK cannot compute the multidollar ligand you search for target X.";
         try {
-            int[] array = new int[0];
-            int dummy = array[50];
-            dummy = dummy + 1;
+            Integer.parseInt("multidollar ligand");
             Assertions.fail("Should not have reached this place. The test *requires* the error to occur!");
         } catch (Exception exception) {
             CDKException cdkException = new CDKException(EXPLANATION, exception);

diff --git a/...cience/cdk/exception/IntractableTest.java → ...cience/cdk/exception/IntractableTest.java b/...cience/cdk/exception/IntractableTest.java → ...cience/cdk/exception/IntractableTest.java
@@ -1,5 +1,4 @@
-/*
- * Copyright (c) 2013 European Bioinformatics Institute (EMBL-EBI)
+/* Copyright (c) 2013 European Bioinformatics Institute (EMBL-EBI)
  *                    John May <[email protected]>
  *
  * Contact: [email protected]
@@ -35,13 +34,13 @@
 class IntractableTest {
 
     @Test
-    void timeout() throws Exception {
+    void timeout() {
         Intractable e = Intractable.timeout(12);
         assertThat(e.getMessage(), is("Operation did not finish after 12 ms."));
     }
 
     @Test
-    void timeoutWithDesc() throws Exception {
+    void timeoutWithDesc() {
         Intractable e = Intractable.timeout("MCS", 200);
         assertThat(e.getMessage(), is("MCS did not finish after 200 ms."));
     }

diff --git a/...dk/exception/NoSuchAtomExceptionTest.java → ...dk/exception/NoSuchAtomExceptionTest.java b/...dk/exception/NoSuchAtomExceptionTest.java → ...dk/exception/NoSuchAtomExceptionTest.java
@@ -1,4 +1,5 @@
 /* Copyright (C) 2004-2007  The Chemistry Development Kit (CDK) project
+ *               2025       Egon Willighagen <[email protected]>
  *
  * Contact: [email protected]
  *
@@ -21,15 +22,14 @@
 
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
-import org.openscience.cdk.test.CDKTestCase;
 
 /**
  * Checks the functionality of the NoSuchAtomException class.
  *
  *
  * @see org.openscience.cdk.exception.NoSuchAtomException
  */
-class NoSuchAtomExceptionTest extends CDKTestCase {
+class NoSuchAtomExceptionTest {
 
     @Test
     void testNoSuchAtomException_String() {