Updated Gradle to 8.5 and ran spotless apply

JonasSchaub · Dec 8, 2023 · 04c7585 · 04c7585
1 parent ba5b24b
commit 04c7585
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diff --git a/License-header/License-header.txt b/License-header/License-header.txt
@@ -2,7 +2,7 @@
  * ErtlFunctionalGroupsFinder for CDK
  * Copyright (c) $today.year Sebastian Fritsch, Stefan Neumann, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
  * 
- * Source code is available at <https://github.com/zielesny/ErtlFunctionalGroupsFinder>
+ * Source code is available at <https://github.com/JonasSchaub/ErtlFunctionalGroupsFinder>
  * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU Lesser General Public License

diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
diff --git a/...de/ibci/ertlfxgroupsfinder/performancetest/ErtlFunctionalGroupsFinderPerformanceTest.java b/...de/ibci/ertlfxgroupsfinder/performancetest/ErtlFunctionalGroupsFinderPerformanceTest.java
@@ -1,9 +1,8 @@
-/**
- * Performance test for
+/*
  * ErtlFunctionalGroupsFinder for CDK
- * Copyright (C) 2019 Jonas Schaub
+ * Copyright (c) 2023 Sebastian Fritsch, Stefan Neumann, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
  * 
- * Source code is available at <https://github.com/zielesny/ErtlFunctionalGroupsFinder>
+ * Source code is available at <https://github.com/JonasSchaub/ErtlFunctionalGroupsFinder>
  * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU Lesser General Public License
@@ -18,8 +17,27 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
+
 package de.ibci.ertlfxgroupsfinder.performancetest;
 
+import org.openscience.cdk.CDKConstants;
+import org.openscience.cdk.aromaticity.Aromaticity;
+import org.openscience.cdk.aromaticity.ElectronDonation;
+import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.graph.ConnectivityChecker;
+import org.openscience.cdk.graph.CycleFinder;
+import org.openscience.cdk.graph.Cycles;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IAtomContainerSet;
+import org.openscience.cdk.interfaces.IAtomType;
+import org.openscience.cdk.io.iterator.IteratingSDFReader;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
+import org.openscience.cdk.tools.CDKHydrogenAdder;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
+import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
+
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
@@ -39,96 +57,79 @@
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
 import java.util.concurrent.Future;
-import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.aromaticity.Aromaticity;
-import org.openscience.cdk.aromaticity.ElectronDonation;
-import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
-import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.graph.ConnectivityChecker;
-import org.openscience.cdk.graph.CycleFinder;
-import org.openscience.cdk.graph.Cycles;
-import org.openscience.cdk.interfaces.IAtom;
-import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.interfaces.IAtomContainerSet;
-import org.openscience.cdk.interfaces.IAtomType;
-import org.openscience.cdk.io.iterator.IteratingSDFReader;
-import org.openscience.cdk.silent.SilentChemObjectBuilder;
-import org.openscience.cdk.tools.CDKHydrogenAdder;
-import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
-import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
 
 /**
- * An application for testing the performance of the ErtlFunctionalGroupsFinder.find() method under parallelization on 
- * multiple threads. 
- * 
+ * An application for testing the performance of the ErtlFunctionalGroupsFinder.find() method under parallelization on
+ * multiple threads.
+ *
  * @author Jonas Schaub
  * @version 1.0.0.1
  */
 public class ErtlFunctionalGroupsFinderPerformanceTest {
-    
+
     //<editor-fold defaultstate="collapsed" desc="Private static final constants">
     /**
      * Name of file for logging occurred exceptions
      */
     private static final String EXCEPTIONS_LOG_FILE_NAME = "Exceptions_Log.txt";
-    
+
     /**
      * Name of file for writing results
      */
     private static final String RESULTS_FILE_NAME = "Results.txt";
-    
+
     /**
      * All allowed atomic numbers to pass to the ErtlFunctionalGroupsFinder;
      * String will be split and resulting integers passed to a set
      */
     private static final String NON_METALLIC_ATOMIC_NUMBERS = "1,2,6,7,8,9,10,15,16,17,18,34,35,36,53,54,86";
     //</editor-fold>
-    
+
     //<editor-fold defaultstate="collapsed" desc="Private class variables">
     /**
      * All allowed atomic numbers to pass to the ErtlFunctionalGroupsFinder as a set of integers (will be parsed from
      * NON_METALLIC_ATOMIC_NUMBERS)
      */
     private Set<Integer> nonMetallicAtomicNumbersSet;
-    
+
     /**
      * The working directory (the jar-file's directory)
      */
     private String workingPath;
-    
+
     /**
      * The given number of different threads to use
      */
     private int numberOfThreadsToUse;
-    
+
     /**
      * All molecules loaded from the SD file
      */
     private IAtomContainer[] moleculesArray;
-    
+
     /**
      * The aromaticity model in use
      */
     private Aromaticity aromaticityModel;
     //</editor-fold>
-    
+
     //<editor-fold defaultstate="collapsed" desc="Constructor">
     /**
      * Instantiates and starts the application. It first loads all molecules from a given SD file into memory and then
-     * distributes them equally on the given number of different threads to use. It measures the time it takes for all 
-     * threads to complete the extraction of functional groups using the ErtlFunctionalGroupsFinder. It exits the system 
-     * if an unexpected exception occurs that prevents the application from working, e.g. an IllegalArgumentException 
+     * distributes them equally on the given number of different threads to use. It measures the time it takes for all
+     * threads to complete the extraction of functional groups using the ErtlFunctionalGroupsFinder. It exits the system
+     * if an unexpected exception occurs that prevents the application from working, e.g. an IllegalArgumentException
      * (will be logged to a file, not printed on the console).
      *
-     * @param anArgs the command line arguments, anArgs[0] must be the name of the SD file to load (must be located in 
+     * @param anArgs the command line arguments, anArgs[0] must be the name of the SD file to load (must be located in
      * the same directory as the application's JAR file) and anArgs[1] must be the number of different threads to use
      * @throws java.io.IOException if the constructor is unable to open a text file for logging occurred exceptions
      */
     public ErtlFunctionalGroupsFinderPerformanceTest(String[] anArgs) throws IOException {
         this.workingPath = (new File("").getAbsoluteFile().getAbsolutePath()) + File.separator;
         LocalDateTime tmpDateTime = LocalDateTime.now();
         String tmpTimeStamp = tmpDateTime.format(DateTimeFormatter.ofPattern("uuuu_MM_dd_HH_mm"));
-        File tmpExceptionsLogFile = new File(this.workingPath 
+        File tmpExceptionsLogFile = new File(this.workingPath
                 + ErtlFunctionalGroupsFinderPerformanceTest.EXCEPTIONS_LOG_FILE_NAME);
         FileWriter tmpExceptionsLogFileWriter = new FileWriter(tmpExceptionsLogFile, true);
         PrintWriter tmpExceptionsPrintWriter = new PrintWriter(tmpExceptionsLogFileWriter);
@@ -165,7 +166,7 @@ public ErtlFunctionalGroupsFinderPerformanceTest(String[] anArgs) throws IOExcep
                 tmpMetalNumbersInt[i] = Integer.parseInt(tmpMetalNumbersStrings[i]);
             }
             this.nonMetallicAtomicNumbersSet = new HashSet(Arrays.asList(tmpMetalNumbersInt));
-            File tmpResultsLogFile = new File(this.workingPath 
+            File tmpResultsLogFile = new File(this.workingPath
                     + ErtlFunctionalGroupsFinderPerformanceTest.RESULTS_FILE_NAME);
             FileWriter tmpResultsLogFileWriter = new FileWriter(tmpResultsLogFile, true);
             PrintWriter tmpResultsPrintWriter = new PrintWriter(tmpResultsLogFileWriter);
@@ -185,7 +186,7 @@ public ErtlFunctionalGroupsFinderPerformanceTest(String[] anArgs) throws IOExcep
                     tmpMolecule = this.applyFiltersAndPreprocessing(tmpMolecule);
                     tmpMoleculesList.add(tmpMolecule);
                 } catch (Exception anException) {
-                    /*If an IllegalArgumentException is thrown in applyFiltersAndPreprocessing (meaning that the molecule 
+                    /*If an IllegalArgumentException is thrown in applyFiltersAndPreprocessing (meaning that the molecule
                     should be filtered) the molecule is skipped by catching this exception*/
                 }
             }
@@ -240,7 +241,7 @@ public ErtlFunctionalGroupsFinderPerformanceTest(String[] anArgs) throws IOExcep
         }
     }
     //</editor-fold>
-    
+
     //<editor-fold defaultstate="collapsed" desc="Private methods">
     /**
      * Performs all preprocessing needed for the ErtlFunctionalGroupsFinder and throws an IllegalArgumentException
@@ -284,7 +285,7 @@ private IAtomContainer applyFiltersAndPreprocessing(IAtomContainer aMolecule) th
         this.aromaticityModel.apply(aMolecule);
         return aMolecule;
     }
-    
+
     /**
      * Appends the given exception's stack trace to a log file.
      *
@@ -296,8 +297,8 @@ private void appendToLogfile(Exception anException) {
         }
         PrintWriter tmpPrintWriter = null;
         try {
-            FileWriter tmpFileWriter = new FileWriter(this.workingPath 
-                    + ErtlFunctionalGroupsFinderPerformanceTest.EXCEPTIONS_LOG_FILE_NAME, 
+            FileWriter tmpFileWriter = new FileWriter(this.workingPath
+                    + ErtlFunctionalGroupsFinderPerformanceTest.EXCEPTIONS_LOG_FILE_NAME,
                     true);
             tmpPrintWriter = new PrintWriter(tmpFileWriter);
             StringWriter tmpStringWriter = new StringWriter();

diff --git a/src/main/java/de/ibci/ertlfxgroupsfinder/performancetest/ExtractFunctionalGroupsTask.java b/src/main/java/de/ibci/ertlfxgroupsfinder/performancetest/ExtractFunctionalGroupsTask.java
@@ -1,9 +1,8 @@
-/**
- * Performance test for
+/*
  * ErtlFunctionalGroupsFinder for CDK
- * Copyright (C) 2019 Jonas Schaub
+ * Copyright (c) 2023 Sebastian Fritsch, Stefan Neumann, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
  * 
- * Source code is available at <https://github.com/zielesny/ErtlFunctionalGroupsFinder>
+ * Source code is available at <https://github.com/JonasSchaub/ErtlFunctionalGroupsFinder>
  * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU Lesser General Public License
@@ -18,39 +17,41 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
+
 package de.ibci.ertlfxgroupsfinder.performancetest;
 
-import java.util.concurrent.Callable;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.tools.ErtlFunctionalGroupsFinder;
 
+import java.util.concurrent.Callable;
+
 /**
- * A Callable thread that extracts functional groups from all molecules in a given array using the 
+ * A Callable thread that extracts functional groups from all molecules in a given array using the
  * ErtlFunctionalGroupsFinder class.
- * 
+ *
  * @author Jonas Schaub
  */
 public class ExtractFunctionalGroupsTask implements Callable<Integer> {
 
     private final IAtomContainer[] moleculesArray;
-    
+
     private final ErtlFunctionalGroupsFinder ertlFinder;
-    
+
     /**
      * Instantiates the thread.
-     * 
-     * @param aListOfMolecules atom containers should meet the ErtlFunctionalGroupsFinder's input specifications but 
+     *
+     * @param aListOfMolecules atom containers should meet the ErtlFunctionalGroupsFinder's input specifications but
      * any occurring exception will be caught
      */
     public ExtractFunctionalGroupsTask(IAtomContainer[] aListOfMolecules) {
         this.moleculesArray = aListOfMolecules;
         this.ertlFinder = new ErtlFunctionalGroupsFinder();
     }
-    
+
     /**
-     * Applies the ErtlFunctionalGroupsFinder.find(IAtomContainer container, boolean clone) method on all given 
+     * Applies the ErtlFunctionalGroupsFinder.find(IAtomContainer container, boolean clone) method on all given
      * molecules (parameter clone = false) and counts the occurring exceptions.
-     * 
+     *
      * @return the number of occurred exceptions
      * @throws Exception if unable to compute a result (copied from doc in Callable interface)
      */
@@ -66,5 +67,5 @@ public Integer call() throws Exception {
         }
         return tmpExceptionsCounter;
     }
-    
+
 }
diff --git a/src/main/java/de/ibci/ertlfxgroupsfinder/performancetest/Main.java b/src/main/java/de/ibci/ertlfxgroupsfinder/performancetest/Main.java
@@ -1,9 +1,8 @@
-/**
- * Performance test for
+/*
  * ErtlFunctionalGroupsFinder for CDK
- * Copyright (C) 2019 Jonas Schaub
+ * Copyright (c) 2023 Sebastian Fritsch, Stefan Neumann, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
  * 
- * Source code is available at <https://github.com/zielesny/ErtlFunctionalGroupsFinder>
+ * Source code is available at <https://github.com/JonasSchaub/ErtlFunctionalGroupsFinder>
  * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU Lesser General Public License
@@ -18,11 +17,12 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
+
 package de.ibci.ertlfxgroupsfinder.performancetest;
 
 /**
  * Main class for starting application.
- * 
+ *
  * @author Jonas Schaub
  */
 public class Main {
@@ -32,9 +32,9 @@ private Main() {
     }
 
     /**
-     * Starts the application. Command line arguments must be the name of an SD-file to read (must be located in the 
+     * Starts the application. Command line arguments must be the name of an SD-file to read (must be located in the
      * same directory as the application's .jar file) and the number of different threads to use for calculation.
-     * 
+     *
      * @param args the command line arguments
      */
     public static void main(String[] args) {
@@ -45,7 +45,5 @@ public static void main(String[] args) {
             System.exit(1);
         }
     }
-
-}
-
 
+}