Unit tests for paper

.gitlab-ci.yml

@@ -0,0 +1,97 @@
+cache:
+  paths:
+    - maven.repository/
+    - models/
+    - pdb-store/
+    - .gradle-user-home/
+
+variables:
+  #  MAVEN_OPTS: "-Dmaven.repo.local=maven.repository -Dorg.slf4j.simpleLogger.log.org.apache.maven.cli.transfer.Slf4jMavenTransferListener=WARN -Xmx4g"
+  JAVA_HOME: "/usr/lib/jvm/java-8-openjdk-amd64"
+  PDB_CACHE_DIR: "./pdb-store/cache"
+  PDB_DIR: "./pdb-store"
+  MODEL_DIR: "./models"
+  GRADLE_USER_HOME: "./.gradle-user-home"
+
+# simple unit tests without requiring GPUs
+unit-tests-no-gpu:
+  image: ubuntu:bionic
+  before_script:
+    - mkdir -p ./pdb-store/cache
+    - apt-get update -qq --force-yes > /dev/null
+    - apt-get install -qq -y --allow-downgrades --allow-remove-essential --allow-change-held-packages unzip wget git openjdk-8-jdk-headless curl libgl1-mesa-glx sudo sed > /dev/null
+    - if [ ! -d "$MODEL_DIR" ]; then wget -q https://ulrik.is/scenery-demo-models.zip && unzip -q scenery-demo-models.zip; fi
+    - sudo sed -i -e '/^assistive_technologies=/s/^/#/' /etc/java-*-openjdk/accessibility.properties
+    - chmod +x gradlew
+  script:
+    - ./gradlew build -x dokkaHtml -x dokkaHtmlJar -x javadoc -x dokkaJavadocJar -PjvmTarget=1.8 -PsourceCompatibility=1.8
+
+# base job for running with GPUs
+.base-job-gpu: &base-job-gpu
+  before_script:
+    - mkdir -p ./pdb-store/cache
+    # Installs Maven, Vulkan development libraries, etc.
+    - apt-get update -qq --force-yes > /dev/null
+    - apt-get install -qq -y --allow-downgrades --allow-remove-essential --allow-change-held-packages unzip wget git openjdk-8-jdk-headless libvulkan1 libvulkan-dev vulkan-utils ocl-icd-opencl-dev clinfo curl > /dev/null
+    - curl -sL https://deb.nodesource.com/setup_14.x | bash -
+    - apt-get install -qq --force-yes nodejs
+    - npm install --save argos-cli
+    - mkdir -p /etc/OpenCL/vendors && echo "libnvidia-opencl.so.1" > /etc/OpenCL/vendors/nvidia.icd
+    # Output Vulkan driver information, but do not fail in case of non-zero
+    # return (happens e.g. if $DISPLAY is not set)
+    - vulkaninfo || true
+    - clinfo || true
+    - if [ ! -d "$MODEL_DIR" ]; then wget -q https://ulrik.is/scenery-demo-models.zip && unzip -q scenery-demo-models.zip; fi
+    - chmod +x gradlew
+    - ./gradlew --stop # stop any deamon https://stackoverflow.com/a/58397542/1047713
+  script:
+    - ./gradlew build -S -x dokkaHtml -x dokkaHtmlJar -x javadoc -x dokkaJavadocJar -PjvmTarget=1.8 -PsourceCompatibility=1.8 -Pgpu=true -i
+  artifacts:
+    when: always
+    expire_in: 48h
+    paths:
+      - results.tar.bz2
+
+scenery-nvidia:
+  image: nvidia/vulkan:1.1.121-cuda-10.1-alpha
+  <<: *base-job-gpu
+  after_script:
+    - nvidia-smi
+    - tar cvjf results.tar.bz2 screenshots/
+    - ARGOS_COMMIT=$CI_COMMIT_SHA ARGOS_BRANCH=$CI_COMMIT_REF_NAME ./node_modules/argos-cli/bin/argos upload screenshots/ --token $ARGOS_TOKEN || true
+  tags:
+    - cuda
+    - intel
+
+#scenery-amd:
+#  image: rocm/rocm-terminal
+#  <<: *base-job
+#  variables:
+#    SUDO: "sudo"
+#    GPURUN: "sudo su -m - rocm-user -c"
+#  before_script:
+#    # The rocm docker container requires the user to be in the video group which
+#    # can usually be set via docker's --group-add option. GitLab-Runner currently
+#    # has no known option for doing that. Therefore, it manually has to happen in
+#    # the job description. 
+#    - $SUDO usermod -a -G video rocm-user
+#    # Installs Maven, Vulkan development libraries, etc.
+#    - $SUDO apt-get -qq --force-yes update > /dev/null
+#    - $SUDO apt-get install -qq --force-yes unzip kmod wget git maven openjdk-8-jdk libvulkan1 libvulkan-dev vulkan-utils > /dev/null
+#    # Installs the AMD GPUopen Vulkan driver
+#    - wget https://github.com/GPUOpen-Drivers/AMDVLK/releases/download/v-2019.Q3.6/amdvlk_2019.Q3.6_amd64.deb
+#    - $SUDO dpkg -i amdvlk_2019.Q3.6_amd64.deb
+#    - $SUDO apt-get -f install
+#    - $SUDO lsmod
+#    # Output Vulkan driver information, but do not fail in case of non-zero
+#    # return (happens e.g. if $DISPLAY is not set)
+#    - vulkaninfo || true
+#    - wget -q https://ulrik.is/scenery-demo-models.zip
+#    - unzip -q scenery-demo-models.zip
+#  after_script:
+#    - rocm-smi
+#  tags:
+#    - amd
+#    - rocm
+#
+#

build.gradle.kts

@@ -1,3 +1,4 @@
+import org.gradle.api.tasks.testing.logging.TestExceptionFormat
 import org.gradle.kotlin.dsl.implementation
 import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
 import sciview.implementation
@@ -125,6 +126,22 @@ tasks {
     }
     test {
         finalizedBy(jacocoTestReport) // report is always generated after tests run
+        testLogging {
+            // set options for log level LIFECYCLE
+//            events "failed"
+//            exceptionFormat "short"
+
+            // set options for log level DEBUG
+            debug {
+//                events "started", "skipped", "failed"
+                exceptionFormat = TestExceptionFormat.FULL
+            }
+
+            // remove standard output/error logging from --info builds
+            // by assigning only 'failed' and 'skipped' events
+//            info.events = ["failed", "skipped"]
+            showStandardStreams = true
+        }
     }
     jar {
         archiveVersion.set(rootProject.version.toString())

pom.xml

@@ -119,7 +119,7 @@
 		<imagej-mesh.version>0.8.1</imagej-mesh.version>
 		<bigdataviewer-vistools.version>1.0.0-beta-21</bigdataviewer-vistools.version>
 
-		<kotlin.version>1.4.20</kotlin.version>
+		<kotlin.version>1.4.32-release-371</kotlin.version>
 		<kotlinx-coroutines-core.version>1.3.9</kotlinx-coroutines-core.version>
 		<kotlin.compiler.jvmTarget>1.8</kotlin.compiler.jvmTarget>
 	</properties>
@@ -350,11 +350,27 @@
 			<version>${kotlin.version}</version>
 			<scope>test</scope>
 		</dependency>
+        <dependency>
+            <groupId>org.jetbrains.kotlin</groupId>
+            <artifactId>kotlin-stdlib-jdk8</artifactId>
+            <version>${kotlin.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.jetbrains.kotlin</groupId>
+            <artifactId>kotlin-test</artifactId>
+            <version>${kotlin.version}</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.jetbrains.kotlin</groupId>
+            <artifactId>kotlin-stdlib-jdk8</artifactId>
+            <version>${kotlin.version}</version>
+        </dependency>
 
-	</dependencies>
+    </dependencies>
 
 	<build>
-		<testSourceDirectory>src/test/tests</testSourceDirectory>
+		<testSourceDirectory>src/test</testSourceDirectory>
 		<plugins>
 			<plugin>
                 <groupId>org.apache.maven.plugins</groupId>
@@ -390,34 +406,34 @@
 					</execution>
 					<execution>
 						<id>compile</id>
-						<phase>validate</phase>
+						<phase>compile</phase>
 						<goals> <goal>compile</goal> </goals>
 						<configuration>
-							<sourceDirs>
-								<source>src/main/java</source>
-								<source>target/generated-sources/kapt</source>
-								<source>target/generated-sources/kaptKotlin</source>
-							</sourceDirs>
-							<jvmTarget>${kotlin.compiler.jvmTarget}</jvmTarget>
+                            <jvmTarget>${kotlin.compiler.jvmTarget}</jvmTarget>
 							<args>
 								<arg>-Werror</arg>
 								<arg>-Xopt-in=kotlin.RequiresOptIn</arg>
 							</args>
-						</configuration>
+                            <sourceDirs>
+                                <source>src/main/java</source>
+                                <source>src/main/kotlin</source>
+                            </sourceDirs>
+                        </configuration>
 					</execution>
 					<execution>
 						<id>test-compile</id>
 						<phase>test-compile</phase>
 						<goals> <goal>test-compile</goal> </goals>
-						<configuration>
-							<sourceDirs>
-								<sourceDir>${project.basedir}/src/test/tests</sourceDir>
-							</sourceDirs>
-						</configuration>
-					</execution>
+                        <configuration>
+                            <sourceDirs>
+                                <source>src/test/java</source>
+                                <source>src/test/kotlin</source>
+                            </sourceDirs>
+                        </configuration>
+                    </execution>
 				</executions>
 				<configuration>
-					<jvmTarget>${kotlin.compiler.jvmTarget}</jvmTarget>
+					<jvmTarget>1.8</jvmTarget>
 					<args>
 						<arg>-Werror</arg>
 						<arg>-Xopt-in=kotlin.RequiresOptIn</arg>
@@ -442,7 +458,15 @@
 							<goal>testCompile</goal>
 						</goals>
 					</execution>
-				</executions>
+                    <execution>
+                        <id>default-compile</id>
+                        <phase>none</phase>
+                    </execution>
+                    <execution>
+                        <id>default-testCompile</id>
+                        <phase>none</phase>
+                    </execution>
+                </executions>
 			</plugin>
 		</plugins>
 	</build>

src/main/kotlin/sc/iview/SciView.kt

@@ -480,7 +480,10 @@ class SciView : SceneryBase, CalibratedRealInterval<CalibratedAxis> {
      * Center the camera on the specified Node
      */
     fun centerOnPosition(currentPos: Vector3f?) {
-        controls.centerOnPosition(currentPos)
+        if(currentPos != null) {
+            controls.centerOnPosition(currentPos)
+        }
+        else { logger.info("The current position is null.") }
     }
 
     /**

src/test/kotlin/sc/iview/ControlPointTests.kt

@@ -0,0 +1,35 @@
+package sc.iview
+
+import graphics.scenery.Node
+import org.joml.Vector3f
+import org.junit.Test
+import sc.iview.process.ControlPoints
+import kotlin.test.assertTrue
+
+class ControlPointTests {
+
+    @Test
+    fun testAddPoint() {
+        val controlPoints = ControlPoints()
+        val node = Node("testMe")
+        controlPoints.addPoint(node)
+        assertTrue(controlPoints.getNodes().contains(node))
+    }
+
+    @Test
+    fun testSetPoints() {
+        val controlPoints = ControlPoints()
+        val nodeList = arrayOf(Vector3f(1f, 2f, 3f), Vector3f(4f, 5f, 6f))
+        controlPoints.setPoints(nodeList)
+        assertTrue { controlPoints.getNodes()[0].position == Vector3f(1f, 2f, 3f) }
+    }
+
+    @Test
+    fun testInitializeSciView() {
+        val controlPoints = ControlPoints()
+        val sv = SciView.create()
+        val numberOfNodes = sv.allSceneNodes.size
+        controlPoints.initializeSciView(sv, 0f)
+        assertTrue  { sv.allSceneNodes.size == numberOfNodes+1 }
+    }
+}

src/test/kotlin/sc/iview/Line3DTests.kt

@@ -0,0 +1,15 @@
+package sc.iview
+
+import junit.framework.Assert.assertNotNull
+import org.junit.Test
+import sc.iview.node.Line3D
+
+class Line3DTests {
+
+    //tests if a bounding box becomes null when Line does not implement HasGeometry
+    @Test
+    fun testBoundingBox() {
+        val line = Line3D()
+        assertNotNull(line.generateBoundingBox())
+    }
+}