Merge branch 'main' into javadoc

.github/workflows/publish-javadoc.yml

@@ -5,11 +5,11 @@ name: Deploy Javadoc
 # And these need to be merged into the javadoc branch.
 
 on:
-  #release: # to trigger this only at new releases, comment this in and the next three lines out
-    #types: [created, published, released]
-  push:
-    branches:
-      - main
+  release:
+    types: [published] #alternatives: released, published, created
+  #push:
+    #branches:
+      #- main
 
 jobs:
   publish:
@@ -22,4 +22,4 @@ jobs:
           javadoc-branch: javadoc
           java-version: 17
           target-folder: javadoc
-          project: gradle
+          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:  '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
+        env:
+          MAVEN_PASSWORD: ${{secrets.OSSRHPASSWORD}}
+          MAVEN_USERNAME: ${{secrets.OSSRHUSERNAME}}
+          signingKey: ${{secrets.PGP_SECRET}}
+          signingPassword: ${{secrets.PGP_PASSPHRASE}}
+        run: ./gradlew publish --no-daemon

CITATION.cff

@@ -1,6 +1,6 @@
 cff-version: 1.2.0
 title: ART2a-Clustering-for-Java
-version: 1.0.0.0
+version: 1.0.2.1
 message: "If you use this software, please cite it as below."
 type: software
 authors:
@@ -19,7 +19,7 @@ authors:
   - family-names: "Zielesny"
     given-names: "Achim"    
     orcid: "https://orcid.org/0000-0003-0722-4229"
-date-released: 2023-06-23
+date-released: 2023-07-05
 doi: "10.5281/zenodo.8075213"
 url: "https://github.com/JonasSchaub/ART2a-Clustering-for-Java"
 license: GPL-3.0

build.gradle

@@ -20,20 +20,36 @@
 
 plugins {
     id 'application'
+    id 'org.gradle.java'
+    id 'java-library'
+    id 'java'
     id("com.diffplug.spotless") version "6.19.0"
+    id 'org.gradle.maven-publish'
+    id 'signing'
 }
 
-group 'de.unijena.cheminf.clustering.art2a'
-version '1.0.0.0'
+group = 'io.github.jonasschaub'
+archivesBaseName = 'ART2a-Clustering-for-Java'
+//see also version for publishing below!
+version = '1.0.2.1'
 
 //sourceCompatibility = 1.17
 
 //Creates javadoc and sources jars
 java {
+    toolchain {
+        languageVersion = JavaLanguageVersion.of(17)
+    }
     withJavadocJar()
     withSourcesJar()
 }
 
+javadoc {
+    if(JavaVersion.current().isJava9Compatible()) {
+        options.addBooleanOption('html5', true)
+    }
+}
+
 repositories {
     mavenCentral()
 }
@@ -43,6 +59,7 @@ dependencies {
     testImplementation(platform('org.junit:junit-bom:5.9.1'))
     testImplementation('org.junit.jupiter:junit-jupiter')
 }
+
 tasks.withType(Test).configureEach {
     useJUnitPlatform()
 
@@ -69,4 +86,122 @@ spotless {
         //prettier() //needs npm installed, unsuitable...
         //clangFormat() //also needs an installation...
     }
-}
+}
+
+artifacts {
+    archives javadocJar, sourcesJar
+}
+
+publishing {
+    publications {
+        mavenJava(MavenPublication) {
+
+            groupId = 'io.github.jonasschaub'
+            artifactId = 'ART2a-Clustering-for-Java'
+            //note: this version has been published, do not try to publish it again! versions 1.0.1.0 and 1.0.1.1 were also already used for publishing!
+            version = '1.0.2.1'
+
+            from components.java
+
+            versionMapping {
+                usage('java-api') {
+                    fromResolutionOf('runtimeClasspath')
+                }
+                usage('java-runtime') {
+                    fromResolutionResult()
+                }
+            }
+
+            pom {
+
+                name = 'ART2a-Clustering-for-Java'
+                description = 'Implementation of the ART 2-A fingerprint clustering algorithm in Java.'
+                url = 'https://github.com/JonasSchaub/ART2a-Clustering-for-Java'
+
+                //this way, properties can be added:
+                //properties = [
+                        //myProp: "value",
+                        //"prop.with.dots": "anotherValue"
+                //]
+
+                licenses {
+                    license {
+                        name = 'GNU General Public License v3.0'
+                        url = 'https://www.gnu.org/licenses/lgpl-3.0.txt'
+                    }
+                }
+
+                developers {
+                    developer {
+                        id = 'B-s123'
+                        name = 'Betuel Sevindik'
+                        email = 'betuel.sevindik@studmail.w-hs.de'
+                        url = 'https://github.com/B-s123'
+                    }
+                    developer {
+                        id = 'FelixBaensch'
+                        name = 'Felix Baensch'
+                        email = 'felix.baensch@w-hs.de'
+                        url = 'https://github.com/FelixBaensch'
+                    }
+                    developer {
+                        id = 'JonasSchaub'
+                        name = 'Jonas Schaub'
+                        email = 'jonas.schaub@uni-jena.de'
+                        url = 'https://github.com/JonasSchaub'
+                    }
+                    developer {
+                        name = 'Christoph Steinbeck'
+                        email = 'christoph.steinbeck@uni-jena.de'
+                        url = 'https://cheminf.uni-jena.de/members/steinbeck/'
+                    }
+                    developer {
+                        name = 'Achim Zielesny'
+                        email = 'achim.zielesny@w-hs.de'
+                        url = 'https://www.w-hs.de/service/informationen-zur-person/person/zielesny/'
+                    }
+                }
+
+                scm {
+                    connection = 'scm:git:git://github.com/JonasSchaub/ART2a-Clustering-for-Java.git'
+                    developerConnection = 'scm:git:ssh://github.com/JonasSchaub/ART2a-Clustering-for-Java.git'
+                    url = 'https://github.com/JonasSchaub/ART2a-Clustering-for-Java/'
+                }
+            }
+        }
+    }
+    repositories {
+        maven {
+            //these two lines did not work because dir() apparently asks for a local path
+            //def releasesRepoUrl = layout.buildDirectory.dir('https://s01.oss.sonatype.org/content/repositories/releases/')
+            //def snapshotsRepoUrl = layout.buildDirectory.dir('https://s01.oss.sonatype.org/content/repositories/snapshots/')
+
+            //TODO: is this actually the way to fully automatically do it?
+            //def releasesRepoUrl = 'https://s01.oss.sonatype.org/content/repositories/releases/'
+            //def snapshotsRepoUrl = 'https://s01.oss.sonatype.org/content/repositories/snapshots/'
+            //url = version.endsWith('SNAPSHOT') ? snapshotsRepoUrl : releasesRepoUrl
+
+            //after publishing, go to https://s01.oss.sonatype.org, log in, close the staged repo, and release it if everything worked out
+            url = "https://s01.oss.sonatype.org/service/local/staging/deploy/maven2/"
+            credentials {
+                //uses keys and passwords declared in userhome/.gradle/gradle.properties
+                //username = property("ossrhUsername") as String
+                //password = property("ossrhPassword") as String
+                //uses environment variables declared in yml file which passes GitHub secrets to it
+                username = System.getenv("MAVEN_USERNAME")
+                password = System.getenv("MAVEN_PASSWORD")
+            }
+        }
+    }
+}
+
+signing {
+    //uses keys and passwords declared in userhome/.gradle/gradle.properties, works locally
+    //sign publishing.publications.mavenJava
+
+    //uses environment variables declared in yml file which passes GitHub secrets to it
+    def signingKey = System.getenv("signingKey")
+    def signingPassword = System.getenv("signingPassword")
+    useInMemoryPgpKeys(signingKey, signingPassword)
+    sign publishing.publications.mavenJava
+}

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.3-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.2-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists