Description: changing the kotlin file into a proper file for gradle
Author: Pierre Gruet <pgt@debian.org>
Forwarded: not-needed
Last-Update: 2022-07-01

--- a/build.gradle.kts
+++ b/build.gradle.kts
@@ -1,65 +1,27 @@
-import com.palantir.gradle.gitversion.VersionDetails
-import groovy.lang.Closure
 import java.net.InetAddress
 import java.util.*
 
-plugins {
-    `java-library`
-    `java-test-fixtures`
-    `maven-publish`
-    signing
-    id("io.github.gradle-nexus.publish-plugin") version "1.1.0"
-    id("com.palantir.git-version") version "0.13.0" // don't upgrade, latest version that runs on Java 8
-}
-
-val productionBuild: Boolean? by project
-
-val versionDetails: Closure<VersionDetails> by extra
-val gitDetails = versionDetails()
-
-fun boolProperty(name: String): Boolean {
-    return ((properties[name] as String?) ?: "false").toBoolean()
-}
-
-val isMiCi = boolProperty("mi-ci")
-val isRelease = boolProperty("mi-release")
-
-val longTests: String? by project
-val miCiStage = properties["mi-ci-stage"] as String?
+apply plugin: 'java'
 
 group = "com.milaboratory"
-version = if (version != "unspecified") version else ""
 description = "MiLib"
 
-java {
-    sourceCompatibility = JavaVersion.VERSION_1_8
-    withSourcesJar()
-    withJavadocJar()
-}
-
-tasks.withType<JavaCompile> {
-    options.encoding = "UTF-8"
-}
+sourceCompatibility = JavaVersion.VERSION_1_8
 
 repositories {
     mavenCentral()
-
-    // Snapshot versions of redberry-pipe distributed via this repo
-    maven {
-        url = uri("https://pub.maven.milaboratory.com")
-    }
 }
 
-val jacksonBomVersion = "2.14.0"
-val junitVersion = "4.13.2"
-val redberryPipeVersion = "1.3.0"
+def jacksonBomVersion = "2.14.0"
+def junitVersion = "4.13.2"
+def redberryPipeVersion = "1.3.0"
 
 dependencies {
-    api("org.apache.commons:commons-math3:3.6.1")
-    api("cc.redberry:pipe:$redberryPipeVersion")
+    compile("org.apache.commons:commons-math3:3.6.1")
+    compile("cc.redberry:pipe:$redberryPipeVersion")
 
-    implementation(platform("com.fasterxml.jackson:jackson-bom:$jacksonBomVersion"))
-    implementation("com.fasterxml.jackson.core:jackson-databind")
+    implementation("com.fasterxml.jackson:jackson-bom:$jacksonBomVersion")
+    implementation("com.fasterxml.jackson.core:jackson-databind:2.x")
     implementation("org.apache.commons:commons-compress:1.21")
     implementation("commons-io:commons-io:2.11.0")
     implementation("org.lz4:lz4-java:1.8.0")
@@ -67,138 +29,28 @@
     implementation("net.sf.trove4j:trove4j:3.0.3")
     implementation("com.google.guava:guava:31.1-jre")
 
-    testFixturesImplementation("junit:junit:$junitVersion")
-    testFixturesImplementation(platform("com.fasterxml.jackson:jackson-bom:$jacksonBomVersion"))
-    testFixturesImplementation("com.fasterxml.jackson.core:jackson-databind")
+    testImplementation("junit:junit:$junitVersion")
+    testImplementation("com.fasterxml.jackson:jackson-bom:$jacksonBomVersion")
+    testImplementation("com.fasterxml.jackson.core:jackson-databind:2.x")
 
     testImplementation("junit:junit:$junitVersion")
     testImplementation("org.mockito:mockito-all:1.10.19")
 }
 
-val writeBuildProperties by tasks.registering(WriteProperties::class) {
-    outputFile = file("${sourceSets.main.get().output.resourcesDir}/${project.name}-build.properties")
-    property("version", version)
-    property("name", "MiLib")
-    property("revision", gitDetails.gitHash)
-    property("branch", gitDetails.branchName ?: "")
-    property("host", InetAddress.getLocalHost().hostName)
-    property("production", productionBuild == true)
-    property("timestamp", System.currentTimeMillis())
-}
-
-tasks.processResources {
-    dependsOn(writeBuildProperties)
-}
-
-val miRepoAccessKeyId: String? by project
-val miRepoSecretAccessKey: String? by project
-
-publishing {
-    repositories {
-        if (miRepoAccessKeyId != null) {
-            maven {
-                name = "mipub"
-                url = uri("s3://milaboratory-artefacts-public-files.s3.eu-central-1.amazonaws.com/maven")
-
-                authentication {
-                    credentials(AwsCredentials::class) {
-                        accessKey = miRepoAccessKeyId!!
-                        secretKey = miRepoSecretAccessKey!!
-                    }
-                }
-            }
+sourceSets {
+    test {
+        java {
+            srcDir 'src/test/java'
+            srcDir 'src/testFixtures/java'
         }
-    }
-
-    publications.create<MavenPublication>("mavenJava") {
-        from(components["java"])
-        pom {
-            withXml {
-                asNode().apply {
-                    appendNode("name", "MiLib")
-                    appendNode(
-                        "description",
-                        "Yet another Java library for Next Generation Sequencing (NGS) data processing."
-                    )
-                    appendNode("url", "https://milaboratories.com/")
-                }
-            }
-            licenses {
-                license {
-                    name.set("The Apache License, Version 2.0")
-                    url.set("http://www.apache.org/licenses/LICENSE-2.0.txt")
-                }
-            }
-            developers {
-                developer {
-                    id.set("dbolotin")
-                    name.set("Dmitry Bolotin")
-                    email.set("bolotin.dmitriy@gmail.com")
-                }
-                developer {
-                    id.set("PoslavskySV")
-                    name.set("Stanislav Poslavsky")
-                    email.set("stvlpos@mail.ru")
-                }
-                developer {
-                    id.set("mikesh")
-                    name.set("Mikhail Shugay")
-                    email.set("mikhail.shugay@gmail.com")
-                }
-            }
-            scm {
-                url.set("scm:git:https://github.com/milaboratory/milib")
-            }
+        resources {
+            srcDir 'src/testFixtures/resources'
         }
     }
 }
 
-val signingKey: String? by project
-if (signingKey != null) {
-    signing {
-        useInMemoryPgpKeys(
-            Base64.getMimeDecoder().decode(signingKey).decodeToString(),
-            ""
-        )
-        sign(publishing.publications["mavenJava"])
-    }
-}
-
-tasks.withType<Javadoc> {
-    options {
-        this as StandardJavadocDocletOptions
-        addStringOption("Xdoclint:none", "-quiet")
-    }
-}
-
-tasks.test {
+test {
     useJUnit()
     minHeapSize = "1024m"
     maxHeapSize = "2048m"
-
-    miCiStage?.let {
-        if (it == "test") {
-            systemProperty("longTests", "true");
-        }
-    }
-    longTests?.let { systemProperty("longTests", it) }
-}
-
-nexusPublishing {
-    repositories {
-        sonatype()
-    }
-}
-
-val checkPipeNotSnapshot by tasks.registering {
-    doLast {
-        if (redberryPipeVersion.contains('-'))
-            throw GradleException("Can't publish to maven central with snapshot dependencies.")
-    }
-}
-
-afterEvaluate {
-    tasks.named("publishToSonatype") {
-        dependsOn(checkPipeNotSnapshot)
-    }
 }