work around Gradle and eclipse version issues again

addons/3dpc/build.gradle

@@ -1,8 +1,8 @@
-
 description = 'ELKI - 3D Parallel Coordinate Trees Visualization'
 dependencies {
-  compile project(':elki')
-    compile group: 'org.jogamp.jogl', name: 'jogl-all-main', version:'2.1.5-01'
-    compile group: 'org.jogamp.gluegen', name: 'gluegen-rt-main', version:'2.1.5-01'
-  compile project(':elki-batik-visualization')
+  api project(':elki')
+  api project(':elki-batik-visualization')
+  implementation group: 'org.jogamp.jogl', name: 'jogl-all-main', version:'2.1.5-01'
+  implementation group: 'org.jogamp.gluegen', name: 'gluegen-rt-main', version:'2.1.5-01'
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

addons/batikvis/build.gradle

@@ -1,11 +1,12 @@
 description = 'ELKI - Batik Visualization'
 dependencies {
-  compile group: 'org.apache.xmlgraphics', name: 'batik-swing', version:'1.11+'
-  compile group: 'org.apache.xmlgraphics', name: 'batik-rasterizer', version:'1.11+'
-  compile group: 'org.apache.xmlgraphics', name: 'batik-ext', version:'1.11+'
-  compile group: 'org.apache.xmlgraphics', name: 'batik-codec', version:'1.11+'
-  compile group: 'org.apache.xmlgraphics', name: 'xmlgraphics-commons', version:'2.3+'
-  compile group: 'xalan', name: 'xalan', version:'[2.7.2,3)'
-  compile project(':elki-gui-minigui') // For GUIUtil, otherwise elki would be enough
-  compile project(':elki-uncertain')
+  api project(':elki-gui-minigui') // For GUIUtil, otherwise elki would be enough
+  api project(':elki-uncertain')
+  implementation group: 'org.apache.xmlgraphics', name: 'batik-swing', version:'1.11+'
+  implementation group: 'org.apache.xmlgraphics', name: 'batik-rasterizer', version:'1.11+'
+  implementation group: 'org.apache.xmlgraphics', name: 'batik-ext', version:'1.11+'
+  implementation group: 'org.apache.xmlgraphics', name: 'batik-codec', version:'1.11+'
+  implementation group: 'org.apache.xmlgraphics', name: 'xmlgraphics-commons', version:'2.3+'
+  implementation group: 'xalan', name: 'xalan', version:'[2.7.2,3)'
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

addons/bundle/build.gradle

@@ -16,12 +16,14 @@ sourceSets { javadoc { java.srcDirs = ["$rootDir/elki/src/main/javadoc"] } }
 dependencies {
   // Depend on all subprojects, except those listed
   project.parent.subprojects.findAll { !bundleExclude.contains(it.path) }.each {
-    compile it
+    api it
     doc files(it.sourceSets.main.java.srcDirs)
-    testRuntime files(it.sourceSets.main.java.outputDir)
+    testRuntimeOnly files(it.sourceSets.main.java.outputDir)
   }
-  testCompile project(':elki-docutil')
-  testCompile project(path: ':elki-test-core', configuration: 'testOutput')
+  testImplementation project(':elki-docutil')
+  testImplementation project(path: ':elki-test-core', configuration: 'testOutput')
+  testRuntimeOnly project(':elki-core-dbids-int')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }
 
 jar {
@@ -32,11 +34,11 @@ jar {
     }
     attributes(
       "Main-Class" : "elki.application.ELKILauncher",
-      "Class-Path": configurations.runtime.collect { "lib/"+it.getName() }.join(' ')
+      "Class-Path": configurations.runtimeClasspath.collect { "lib/"+it.getName() }.join(' ')
     )
   }
   // Reorganize license information into a consistent folder
-  configurations.runtime.resolvedConfiguration.resolvedArtifacts.findAll
+  configurations.runtimeClasspath.resolvedConfiguration.resolvedArtifacts.findAll
   { !it.name.startsWith("elki") && !it.name.contains("xml-apis-ext") }.each { dep ->
     from(zipTree(dep.file)) {
       include("META-INF/LICENSE*")
@@ -71,7 +73,7 @@ shadowJar {
   dependsOn jar
   from jar.outputs.files // To include the bundle jar with above notices!
   configurations = [ project.configurations.runtime ]
-  destinationDir = project.parent.rootDir
+  destinationDirectory = project.parent.rootDir
   classifier = null
   manifest {
     attributes("Class-Path" : "")

addons/joglvis/build.gradle

@@ -1,8 +1,8 @@
-
 description = 'ELKI - OpenGL-based Visualization'
 dependencies {
-  compile project(':elki')
-    compile group: 'org.jogamp.jogl', name: 'jogl-all-main', version:'2.1.5-01'
-    compile group: 'org.jogamp.gluegen', name: 'gluegen-rt-main', version:'2.1.5-01'
-  compile project(':elki-batik-visualization')
+  api project(':elki')
+  api project(':elki-batik-visualization')
+  implementation group: 'org.jogamp.jogl', name: 'jogl-all-main', version:'2.1.5-01'
+  implementation group: 'org.jogamp.gluegen', name: 'gluegen-rt-main', version:'2.1.5-01'
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

addons/libsvm/build.gradle

@@ -1,7 +1,9 @@
 description = 'ELKI - LibSVM based extensions'
 dependencies {
-  compile project(':elki-outlier')
-  compile group: 'tw.edu.ntu.csie', name: 'libsvm', version:'3.17'
-  testCompile project(path: ':elki-test-core', configuration: 'testOutput')
-  testCompile project(path: ':elki-outlier', configuration: 'testOutput')
+  api project(':elki-outlier')
+  implementation group: 'tw.edu.ntu.csie', name: 'libsvm', version:'3.17'
+  testImplementation project(path: ':elki-outlier', configuration: 'testOutput')
+  testImplementation project(path: ':elki-test-core', configuration: 'testOutput')
+  testRuntimeOnly project(':elki-core-dbids-int')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

addons/lucene/build.gradle

@@ -1,7 +1,7 @@
-
 description = 'ELKI - Lucene based extensions'
 dependencies {
-  compile project(':elki')
-    compile group: 'org.apache.lucene', name: 'lucene-core', version:'3.6.2'
-    compile group: 'org.apache.lucene', name: 'lucene-queries', version:'3.6.2'
+  api project(':elki')
+  implementation group: 'org.apache.lucene', name: 'lucene-core', version:'3.6.2'
+  implementation group: 'org.apache.lucene', name: 'lucene-queries', version:'3.6.2'
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

addons/tutorial/build.gradle

@@ -1,7 +1,9 @@
 description = 'ELKI - Tutorial Algorithms'
 dependencies {
-  compile project(':elki')
-  testCompile project(path: ':elki-clustering', configuration: 'testOutput')
-  testCompile project(path: ':elki-outlier', configuration: 'testOutput')
-  testCompile project(path: ':elki-test-core', configuration: 'testOutput')
+  api project(':elki')
+  testImplementation project(path: ':elki-clustering', configuration: 'testOutput')
+  testImplementation project(path: ':elki-outlier', configuration: 'testOutput')
+  testImplementation project(path: ':elki-test-core', configuration: 'testOutput')
+  testRuntimeOnly project(':elki-core-dbids-int')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

addons/uncertain/build.gradle

@@ -1,4 +1,5 @@
 description = 'ELKI - Uncertain data handling'
 dependencies {
-  compile project(':elki-clustering')
+  api project(':elki-clustering')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

addons/xtree/build.gradle

@@ -1,6 +1,8 @@
 description = 'ELKI - X-Tree'
 dependencies {
-  compile project(':elki-index-rtree')
-  compile project(':elki')
-  testCompile project(path: ':elki-test-core', configuration: 'testOutput')
+  api project(':elki')
+  api project(':elki-index-rtree')
+  testImplementation project(path: ':elki-test-core', configuration: 'testOutput')
+  testRuntimeOnly project(':elki-core-dbids-int')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

build.gradle

@@ -24,7 +24,7 @@ allprojects  {
   ext.isSnapshot = version.endsWith("-SNAPSHOT")
 
   // For tests depending on other module's tests
-  configurations { testOutput.extendsFrom testCompile }
+  configurations { testOutput.extendsFrom testImplementation }
 
   test.testLogging.showStandardStreams = true
 }

elki-classification/build.gradle

@@ -1,5 +1,7 @@
 description = 'ELKI - Classification Algorithms'
 dependencies {
-  compile project(':elki-core')
-  testCompile project(path: ':elki-test-core', configuration: 'testOutput')
+  api project(':elki-core')
+  testImplementation project(path: ':elki-test-core', configuration: 'testOutput')
+  testRuntimeOnly project(':elki-core-dbids-int')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

elki-clustering/build.gradle

@@ -1,9 +1,7 @@
 description = 'ELKI - Clustering Algorithms'
 dependencies {
-  compile project(':elki-core')
-  // compile project(':elki-precomputed') // For distance matrixes
-  // via core: compile project(':elki-index-preprocessed') // For SNN clustering
-  // compile project(':elki-index-rtree')
-  testCompile project(path: ':elki-test-core', configuration: 'testOutput')
+  api project(':elki-core')
+  testImplementation project(path: ':elki-test-core', configuration: 'testOutput')
+  testRuntimeOnly project(':elki-core-dbids-int')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }
-

elki-core-api/build.gradle

@@ -1,7 +1,7 @@
 description = 'ELKI - Core APIs'
 dependencies {
-  compile project(':elki-core-dbids')
-  testCompile group: 'junit', name: 'junit', version:'[4.8,)'
+  api project(':elki-core-dbids')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }
 
 // Resources: insert version number

elki-core-data/build.gradle

@@ -1,5 +1,5 @@
 description = 'ELKI - Core Data Types'
 dependencies {
-  compile project(':elki-core-api')
-  testCompile group: 'junit', name: 'junit', version:'[4.8,)'
+  api project(':elki-core-api')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

elki-core-dbids-int/build.gradle

@@ -1,5 +1,5 @@
 description = 'ELKI - Core DBIDs Integer Implementation'
 dependencies {
-  compile project(':elki-core-dbids')
-  testCompile group: 'junit', name: 'junit', version:'[4.8,)'
+  api project(':elki-core-dbids')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

elki-core-dbids/build.gradle

@@ -1,5 +1,5 @@
 description = 'ELKI - Core DBIDs API'
 dependencies {
-  compile project(':elki-core-util')
-  testCompile group: 'junit', name: 'junit', version:'[4.8,)'
+  api project(':elki-core-util')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

elki-core-distance/build.gradle

@@ -1,6 +1,6 @@
 description = 'ELKI - Core Distance Functions'
 dependencies {
-  compile project(':elki-core-data')
-  compile project(':elki-core-math')
-  testCompile group: 'junit', name: 'junit', version:'[4.8,)'
+  api project(':elki-core-data')
+  api project(':elki-core-math')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

elki-core-math/build.gradle

@@ -1,5 +1,5 @@
 description = 'ELKI - Core Mathematics and Statistics'
 dependencies {
-  compile project(':elki-core-api')
-  testCompile group: 'junit', name: 'junit', version:'[4.8,)'
+  api project(':elki-core-api')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

elki-core-parallel/build.gradle

@@ -1,4 +1,5 @@
 description = 'ELKI - Parallel Processing Core'
 dependencies {
-  compile project(':elki-core-math')
+  api project(':elki-core-math')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

elki-core-util/build.gradle

@@ -139,8 +139,8 @@ task generateCodeHeaps(description: "Generate code from templates") {
 tasks.compileJava.dependsOn generateCodeHeaps
 
 dependencies {
-  compile project(':elki-logging')
-  compile group: 'net.jafama', name: 'jafama', version:'[2.3.0,3)'
-  compile group: 'it.unimi.dsi', name: 'fastutil', version: '[8,9)'
-  testCompile group: 'junit', name: 'junit', version:'[4.8,)'
+  api project(':elki-logging')
+  api group: 'net.jafama', name: 'jafama', version:'[2.3.0,3)'
+  api group: 'it.unimi.dsi', name: 'fastutil', version: '[8,9)'
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

elki-core/build.gradle

@@ -1,8 +1,7 @@
 description = 'ELKI - Core Miscellaneous'
 dependencies {
-  // compile project(':elki-database')
-  compile project(':elki-index-preprocessed')
-  compile project(':elki-core-parallel')
-  testRuntime project(':elki-core-dbids-int')
-  testCompile group: 'junit', name: 'junit', version:'[4.8,)'
+  api project(':elki-index-preprocessed')
+  api project(':elki-core-parallel')
+  testImplementation project(':elki-core-dbids-int')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

elki-data-generator/build.gradle

@@ -1,6 +1,8 @@
 description = 'ELKI - Data Generator'
 dependencies {
-  compile project(':elki-clustering')
-  compile project(':elki-outlier')
-  testCompile project(path: ':elki-test-core', configuration: 'testOutput')
+  api project(':elki-clustering')
+  api project(':elki-outlier')
+  testImplementation project(path: ':elki-test-core', configuration: 'testOutput')
+  testRuntimeOnly project(':elki-core-dbids-int')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

elki-database/build.gradle

@@ -1,7 +1,6 @@
 description = 'ELKI - Database'
 dependencies {
-  // compile project(':elki-core-distance') // For Euclidean distance optimizations
-  compile project(':elki-input')
-  testCompile project(':elki-core-dbids-int')
-  testCompile group: 'junit', name: 'junit', version:'[4.8,)'
+  api project(':elki-input')
+  testImplementation project(':elki-core-dbids-int')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

elki-docutil/build.gradle

@@ -1,4 +1,5 @@
 description = 'ELKI - Documentation Utilities'
 dependencies {
-  compile project(':elki-core-util')
+  api project(':elki-core-util')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

elki-geo/build.gradle

@@ -1,6 +1,8 @@
 description = 'ELKI - Geography Module'
 dependencies {
-  // compile project(':elki-core')
-  compile project(':elki-index') // For projected indexes
-  testCompile project(path: ':elki-test-core', configuration: 'testOutput')
+  api project(':elki-core')
+  api project(':elki-index') // For projected indexes
+  testImplementation project(path: ':elki-test-core', configuration: 'testOutput')
+  testRuntimeOnly project(':elki-core-dbids-int')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

elki-gui-minigui/build.gradle

@@ -1,4 +1,5 @@
 description = 'ELKI - MiniGUI Command Line Builder'
 dependencies {
-  compile project(':elki')
+  api project(':elki')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

elki-index-lsh/build.gradle

@@ -1,5 +1,7 @@
 description = 'ELKI - Locality Sensitive Hashing'
 dependencies {
-  compile project(':elki-index')
-  testCompile project(path: ':elki-test-core', configuration: 'testOutput')
+  api project(':elki-index')
+  testImplementation project(path: ':elki-test-core', configuration: 'testOutput')
+  testRuntimeOnly project(':elki-core-dbids-int')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

elki-index-mtree/build.gradle

@@ -1,6 +1,8 @@
 description = 'ELKI - M-Tree Variants'
 dependencies {
-  compile project(':elki-index')
-  // Currently in elki-index: compile project(':elki-index-preprocessed')
-  testCompile project(path: ':elki-test-core', configuration: 'testOutput')
+  api project(':elki-index')
+  // Currently in elki-index: api project(':elki-index-preprocessed')
+  testImplementation project(path: ':elki-test-core', configuration: 'testOutput')
+  testRuntimeOnly project(':elki-core-dbids-int')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

elki-index-preprocessed/build.gradle

@@ -1,5 +1,7 @@
 description = 'ELKI - Indexes based on preprocessing'
 dependencies {
-  compile project(':elki-database')
-  testCompile project(path: ':elki-test-core', configuration: 'testOutput')
+  api project(':elki-database')
+  testImplementation project(path: ':elki-test-core', configuration: 'testOutput')
+  testRuntimeOnly project(':elki-core-dbids-int')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

elki-index-rtree/build.gradle

@@ -1,6 +1,8 @@
 description = 'ELKI - R-Tree Variants'
 dependencies {
-  compile project(':elki-index')
-  // Currently in elki-index: compile project(':elki-index-preprocessed')
-  testCompile project(path: ':elki-test-core', configuration: 'testOutput')
+  api project(':elki-index')
+  // Currently in elki-index: api project(':elki-index-preprocessed')
+  testImplementation project(path: ':elki-test-core', configuration: 'testOutput')
+  testRuntimeOnly project(':elki-core-dbids-int')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

elki-index-various/build.gradle

@@ -1,6 +1,7 @@
 description = 'ELKI - Various indexes'
 dependencies {
-  // compile project(':elki-core')
-  compile project(':elki-index')
-  testCompile project(path: ':elki-test-core', configuration: 'testOutput')
+  api project(':elki-index')
+  testImplementation project(path: ':elki-test-core', configuration: 'testOutput')
+  testRuntimeOnly project(':elki-core-dbids-int')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

elki-index/build.gradle

@@ -1,6 +1,6 @@
 description = 'ELKI - Index Core'
 dependencies {
-  compile project(':elki-index-preprocessed') // Used by m-tree, r-tree approximations, otherwise elki-database would be enough.
-  compile project(':elki-persistent')
-  testCompile group: 'junit', name: 'junit', version:'[4.8,)'
+  api project(':elki-index-preprocessed') // Used by m-tree, r-tree approximations, otherwise elki-database would be enough.
+  api project(':elki-persistent')
+  testImplementation group: 'junit', name: 'junit', version:'[4.8,)'
 }

elki-input/build.gradle

@@ -1,7 +1,7 @@
 description = 'ELKI - Data Input'
 dependencies {
   // For length normalization and MDS:
-  compile project(':elki-core-distance')
+  api project(':elki-core-distance')
   // For testing
   testRuntimeOnly project(':elki-core-dbids-int')
   testImplementation group: 'junit', name: 'junit', version:'[4.8,)'