FragmentFingerprints v1.2.0

.github/workflows/SonarCloud.yml → .github/workflows/SonarQube.yml

@@ -1,35 +1,36 @@
 # source: SonarCloud setup tutorial
 
-name: SonarCloud
+name: SonarQube
 on:
   push:
     branches:
       - main
+      - production
   pull_request:
     types: [opened, synchronize, reopened]
 jobs:
   build:
     name: Build and analyze
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0  # Shallow clones should be disabled for a better relevancy of analysis
       - name: Set up JDK 17
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: 17
           distribution: 'temurin' # Alternative distribution options are available, e.g. zulu
-      - name: Cache SonarCloud packages
-        uses: actions/cache@v3
+      - name: Cache SonarQube packages
+        uses: actions/cache@v4
         with:
           path: ~/.sonar/cache
           key: ${{ runner.os }}-sonar
           restore-keys: ${{ runner.os }}-sonar
       - name: Change wrapper permissions
         run: chmod +x ./gradlew
       - name: Cache Gradle packages
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.gradle/caches
           key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}

.github/workflows/gradle.yml

@@ -9,9 +9,9 @@ name: Java CI with Gradle
 
 on:
   push:
-    branches: [ "main" ]
+    branches: [ "main", "production" ]
   pull_request:
-    branches: [ "main" ]
+    branches: [ "main", "production" ]
 
 permissions:
   contents: read
@@ -20,17 +20,22 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        java: [ 17, 21, 25 ]
+    name: Java ${{ matrix.java }}
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up JDK 17
-      uses: actions/setup-java@v3
-      with:
-        java-version: '17'
-        distribution: 'temurin'
-    - name: Change wrapper permissions
-      run: chmod +x ./gradlew
-    - name: Build with Gradle
-      uses: gradle/gradle-build-action@67421db6bd0bf253fb4bd25b31ebb98943c375e1
-      with:
-        arguments: build
+      - name: Checkout sources
+        uses: actions/checkout@v4
+      - name: Set up Java
+        uses: actions/setup-java@v4
+        with:
+          java-version: ${{ matrix.java }}
+          distribution: 'temurin'
+      - name: Change wrapper permissions
+        run: chmod +x ./gradlew
+      - name: Setup Gradle
+        uses: gradle/actions/setup-gradle@v5
+      - name: Build with Gradle
+        run: ./gradlew build

.github/workflows/publish-javadoc.yml

@@ -14,12 +14,14 @@ on:
 jobs:
   publish:
     runs-on: ubuntu-latest
+    permissions:
+      contents: write  # if you have a protection rule on your repository, you'll need to give write permission to the workflow.
     steps:
       - name: Deploy JavaDoc 🚀
-        uses: MathieuSoysal/Javadoc-publisher.yml@v2.4.0
+        uses: MathieuSoysal/Javadoc-publisher.yml@v3.0.2
         with:
           GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
           javadoc-branch: javadoc
           java-version: 17
-          target-folder: javadoc/1.1
+          target-folder: javadoc/1.2.0
           project: gradle

.github/workflows/publish-to-maven-central.yml

@@ -7,8 +7,6 @@
 # To get a newer version, you will need to update the SHA.
 # You can also reference a tag or branch, but the action may change without warning.
 
-#taken from: https://docs.github.com/en/actions/publishing-packages/publishing-java-packages-with-gradle
-# and extended using https://selectfrom.dev/using-github-actions-to-automatically-publish-gradle-build-artifacts-d71c915cfa4
 name: Publish package to the Maven Central Repository
 on:
   #push:
@@ -19,28 +17,20 @@ jobs:
   publish:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Java
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version:  '17'
           distribution:  'temurin'
       - name: Change wrapper permissions
         run: chmod +x ./gradlew
       - name: Validate Gradle wrapper
         uses: gradle/wrapper-validation-action@ccb4328a959376b642e027874838f60f8e596de3
-      #- name: Publish package
-        #uses: gradle/gradle-build-action@749f47bda3e44aa060e82d7b3ef7e40d953bd629 #from the tutorial
-        ##uses: gradle/gradle-build-action@67421db6bd0bf253fb4bd25b31ebb98943c375e1 #this is the action used in the other yml file, the Gradle build
-        #with:
-          #arguments: publish
-        #env:
-          #MAVEN_USERNAME: ${{ secrets.OSSRHUSERNAME }}
-          #MAVEN_PASSWORD: ${{ secrets.OSSRHPASSWORD }}
-      - name: Publish with Gradle #from the second tutorial
+      - name: Publish with Gradle
         env:
-          MAVEN_PASSWORD: ${{secrets.OSSRHPASSWORD}}
-          MAVEN_USERNAME: ${{secrets.OSSRHUSERNAME}}
-          signingKey: ${{secrets.PGP_SECRET}}
-          signingPassword: ${{secrets.PGP_PASSPHRASE}}
-        run: ./gradlew publish --no-daemon
+          ORG_GRADLE_PROJECT_mavenCentralPassword: ${{secrets.OSSRHPASSWORD}}
+          ORG_GRADLE_PROJECT_mavenCentralUsername: ${{secrets.OSSRHUSERNAME}}
+          ORG_GRADLE_PROJECT_signingInMemoryKey: ${{secrets.PGP_SECRET}}
+          ORG_GRADLE_PROJECT_signingInMemoryKeyPassword: ${{secrets.PGP_PASSPHRASE}}
+        run: ./gradlew publishToMavenCentral

CITATION.cff

@@ -1,12 +1,15 @@
 cff-version: 1.2.0
 title: FragmentFingerprinter
-version: 1.1.0.0
+version: 1.2.0
 message: "If you use this software, please cite it as below."
 type: software
 authors:
   - family-names: "Sevindik"
     given-names: "Betuel"
     orcid: "https://orcid.org/0000-0002-9448-8603"
+  - family-names: "Rottmann"
+    given-names: "Maximilian"
+    orcid: "https://orcid.org/0009-0006-6367-9788"
   - family-names: "Baensch"
     given-names: "Felix"   
     orcid: "https://orcid.org/0000-0001-8973-8463"
@@ -20,6 +23,6 @@ authors:
     given-names: "Achim"    
     orcid: "https://orcid.org/0000-0003-0722-4229"
 doi: "10.5281/zenodo.7998215"
-date-released: 2023-10-27
+date-released: 2025-12-18
 url: "https://github.com/JonasSchaub/FragmentFingerprints"
 license: MIT

LICENSE

@@ -1,6 +1,7 @@
 MIT License
 
-Copyright (c) 2023 Betuel Sevindik, Felix Baensch, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
+Copyright (c) 2025 Betuel Sevindik, Maximilian Rottmann, Felix Baensch, Jonas
+Schaub, Christoph Steinbeck, and Achim Zielesny
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

License-header/License-header.txt

@@ -1,7 +1,8 @@
 /*
  * MIT License
  *
- * Copyright (c) $today.year Betuel Sevindik, Felix Baensch, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
+ * Copyright (c) 2025 Betuel Sevindik, Maximilian Rottmann, Felix Baensch, Jonas
+ * Schaub, Christoph Steinbeck, and Achim Zielesny
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

PerformanceTestCMDApplication/Performance_test_instruction.txt

@@ -2,7 +2,7 @@
 PERFORMANCE TEST CMD APPLICATION
 ---------------------------------
 The folder "PerformanceTestCMDApplication"
-contains the executable JAVA archive FragmentFingerprints-fat-1.1.0.0.jar.
+contains the executable JAVA archive FragmentFingerprints-fat-1.2.0.jar.
 It can be executed from the command line (command: java -jar) to do a performance snapshot of fragment fingerprinter's scaling behaviour for
 a growing number of input molecules. It requires four command line arguments: 
 
@@ -17,7 +17,7 @@ a growing number of input molecules. It requires four command line arguments:
     if only a filename or a blank path is specified, the result folder is created in the same directory as the Jar.
 * integer number (bin size). I.e. how many molecules are to be processed (in addition) per iteration.
 
-Example usage: java -jar FragmentFingerprints-fat-1.1.0.0.jar Fragments_File_PerformanceTest_13000.csv MoleculeFragments_File_PerformanceTest_13000.csv " " 1000
+Example usage: java -jar FragmentFingerprints-fat-1.2.0.jar Fragments_File_PerformanceTest_13000.csv MoleculeFragments_File_PerformanceTest_13000.csv " " 1000
 
 The CMD application will then import the data sets and create bit and count fingerprints. The application will also create output files of the
 measured runtimes and a file in which the generated fingerprints are stored line by line. So that each line 

README.md

@@ -9,18 +9,18 @@
 [![Maven Central](https://maven-badges.herokuapp.com/maven-central/io.github.jonasschaub/FragmentFingerprints/badge.svg)](https://maven-badges.herokuapp.com/maven-central/io.github.jonasschaub/FragmentFingerprints)
 [![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=JonasSchaub_FragmentFingerprints&metric=alert_status)](https://sonarcloud.io/summary/new_code?id=JonasSchaub_FragmentFingerprints)
 # FragmentFingerprints
-A library to generate fingerprints for molecular structures based on a set of fragments
+A library to generate fingerprints for molecular structures based on a set of fragments represented as SMILES strings.
 
 ## Description
 The library generates fragment fingerprints based on pre-defined fragments, 
-which can be set by the user, and can generate both bit and count fingerprints. 
+which can be set by the user. It can generate both bit and count fingerprints. 
 Fragment fingerprints are created by matching fragments or substructures of a 
-molecule with pre-defined fragments. If a match is found, the corresponding positions 
-in the fingerprint are filled. The special feature of the fragment fingerprinter is that fingerprints 
+molecule with pre-defined fragments. If a match is found, the corresponding position 
+in the fingerprint is set to true. The special feature of the fragment fingerprinter is that fingerprints 
 are generated exclusively by comparing unique SMILES (Strings). This means that both the pre-defined fragments and 
 the substructures or fragments of the molecule for which the fingerprint is 
 being generated must be represented as unique SMILES strings. The implementation of the fragment fingerprinter is based on
-the Chemistry Development Kit (CDK).
+the Chemistry Development Kit (CDK), i.e. it implements CDK interfaces for compatibility.
 
 ## Contents of this repository
 ### Sources
@@ -29,14 +29,14 @@ all source code packages including JUnit tests.
 
 ### Tests
 The test class <i>FragmentFingerprinterTest</i> tests the functionalities of fragment fingerprinter.
-Among other things, it tests whether the bit and count fingerprint of a molecule has been generated 
+Among other things, it tests whether the bit and count fingerprint of a molecule have been generated 
 correctly. Furthermore, various methods of the CountFingerprint and 
 BitSetFingerprint classes are tested.
 
 ### Test resources
 The test <a href="https://github.com/JonasSchaub/FragmentFingerprints/tree/FragmentFingerprint/src/test/resources/de/unijena/cheminf/fragment/fingerprint">"resources"</a> subfolder
 contains two text files. The text file named "FragmentList.txt" contains all key fragments. And the file 
-named "MoleculeList.txt" contains fragments/substructures of molecules. 
+named "MoleculeFragments.txt" contains fragments/substructures of molecules. 
 In total, 10 molecules with their corresponding fragments are stored in the file.
 
 ### Performance Test CMD Application
@@ -67,14 +67,14 @@ be pre-installed.
 **Needs to be pre-installed:**
 * Java Development Kit (JDK) version 17
   * [Adoptium OpenJDK](https://adoptium.net) (as one possible source of the JDK)
-* Gradle version 7.3
+* Gradle version 9.2.0
   * [Gradle Build Tool](https://gradle.org)
 
 **Managed by Gradle:**
-* Chemistry Development Kit (CDK) version 2.9
+* Chemistry Development Kit (CDK) version 2.11
   * [Chemistry Development Kit on GitHub](https://cdk.github.io/)
   * License: GNU Lesser General Public License 2.1
-* JUnit Jupiter version 5.9.1
+* JUnit Jupiter version 6.0.1
   * [JUnit ](https://junit.org/junit5/)
   * License: Eclipse Public License - v 2.0