Initial commit of repo overhaul; updated test classes to JUnit 5;

.github/workflows/SonarCloud.yml

@@ -0,0 +1,41 @@
+# source: SonarCloud setup tutorial
+
+name: SonarCloud
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    types: [opened, synchronize, reopened]
+jobs:
+  build:
+    name: Build and analyze
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0  # Shallow clones should be disabled for a better relevancy of analysis
+      - name: Set up JDK 21
+        uses: actions/setup-java@v3
+        with:
+          java-version: 21
+          distribution: 'temurin' # Alternative distribution options are available, e.g. zulu
+      - name: Cache SonarCloud packages
+        uses: actions/cache@v3
+        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
+        with:
+          path: ~/.gradle/caches
+          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
+          restore-keys: ${{ runner.os }}-gradle
+      - name: Build and analyze
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+        run: ./gradlew build sonar --info

.github/workflows/gradle.yml

@@ -0,0 +1,36 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+# This workflow will build a Java project with Gradle and cache/restore any dependencies to improve the workflow execution time
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-java-with-gradle
+
+name: Java CI with Gradle
+
+on:
+  push:
+    branches: [ "main", "functional-repo" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up JDK 21
+      uses: actions/setup-java@v3
+      with:
+        java-version: '21'
+        distribution: 'temurin'
+    - name: Change wrapper permissions
+      run: chmod +x ./gradlew
+    - name: Build with Gradle
+      uses: gradle/gradle-build-action@67421db6bd0bf253fb4bd25b31ebb98943c375e1
+      with:
+        arguments: build

.github/workflows/publish-javadoc.yml

@@ -0,0 +1,25 @@
+name: Deploy Javadoc
+
+#Note: The Javadoc-publisher action only commits to javadoc branch and triggers the GitHub pages update action if there
+# are changes in the JavaDoc, i.e. it ignores the Readme.md that is used as main landing page of the GitHub pages!
+# And these need to be merged into the javadoc branch.
+
+on:
+  release:
+    types: [published] #alternatives: released, published, created
+  #push:
+    #branches:
+      #- main
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Deploy JavaDoc 🚀
+        uses: MathieuSoysal/[email protected]
+        with:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+          javadoc-branch: javadoc
+          java-version: 21
+          target-folder: javadoc/1.2
+          project: gradle

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

@@ -0,0 +1,46 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# GitHub recommends pinning actions to a commit SHA.
+# 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:
+    #branches: [ "main" ]
+  release:
+    types: [published]
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Java
+        uses: actions/setup-java@v3
+        with:
+          java-version:  '21'
+          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
+        env:
+          MAVEN_PASSWORD: ${{secrets.OSSRHPASSWORD}}
+          MAVEN_USERNAME: ${{secrets.OSSRHUSERNAME}}
+          signingKey: ${{secrets.PGP_SECRET}}
+          signingPassword: ${{secrets.PGP_PASSPHRASE}}
+        run: ./gradlew publish --no-daemon

.gitignore

@@ -7,4 +7,10 @@
 # Idea files and folders #
 .idea/
 *iml
-target/
+
+# Gradle build dir
+build/
+.gradle
+
+# EFGF evaluation test output
+ErtlFunctionalGroupsFinderEvaluationTest_Output/

CITATION.cff

@@ -1,6 +1,6 @@
 cff-version: 1.2.0
 title: ErtlFunctionalGroupsFinder
-version: 1.1.2
+version: 1.2
 message: "If you use this software, please cite it as below and also cite the accompanying scientific publication referenced below."
 type: software
 authors:
@@ -18,10 +18,8 @@ authors:
   - family-names: "Zielesny"
     given-names: "Achim"
     orcid: "https://orcid.org/0000-0003-0722-4229"
-date-released: 2022-09-22
-url: "https://github.com/zielesny/ErtlFunctionalGroupsFinder"
+url: "https://github.com/JonasSchaub/ErtlFunctionalGroupsFinder"
 license: LGPL-2.1
-doi: "10.5281/zenodo.7105728"
 references:
   - authors:
       - family-names: "Fritsch"