Preparations for singularity support

.circleci/config.yml

@@ -3,7 +3,7 @@ version: 2.1
 executors:
   docker-executor:
     docker:
-      - image: cimg/openjdk:8.0.322
+      - image: cimg/openjdk:8.0.322   # Version for Gradle 5.1 should be 11.0.18?
 jobs: # a collection of steps
   build-and-test:
     environment:

README.md

@@ -89,6 +89,11 @@ To start the integration tests, please fill in host and user settings (password
 
 # Change Logs
 
+* 0.2.0
+  - major: CommandI classes to model commands and code
+  - minor: ApptainerCommmandBuilder to create a wrapping command to run code in containers
+  - patch: Library updates
+
 * 0.1.4
   - patch: Changed the conversion of EpochSeconds to ZonedDateTime for the value "0".
     * For eligibleTime it is set to null

build.gradle

@@ -16,8 +16,8 @@ apply plugin: 'maven'
 group = "com.github.theroddywms"
 
 mainClassName = 'de.dkfz.roddy.BEIntegrationTestStarter'
-sourceCompatibility = '1.8'
-targetCompatibility = '1.8'
+sourceCompatibility = JavaVersion.VERSION_1_8
+targetCompatibility = JavaVersion.VERSION_1_8
 
 /*
  * Gets the version name from the current Git tag. If the current commit is not tagged,
@@ -30,10 +30,12 @@ def getVersionName() {
 
 rootProject.version = getVersionName()
 
+compileJava.options.compilerArgs = ["-release", targetCompatibility]
+
 // Set -Pchecked on the command line to change this compiler parameter.
-if (!project.hasProperty("checked") || !project.checked) {
-    compileJava.options.compilerArgs = ["-Xlint:unchecked"]
-    compileGroovy.options.compilerArgs = ["-Xlint:unchecked"]
+if (project.hasProperty("checked") && !project.checked) {
+    compileJava.options.compilerArgs += ["-Xlint:unchecked", "-Xlint:deprecation"]
+    compileGroovy.options.compilerArgs += ["-Xlint:unchecked", "-Xlint:deprecation"]
 }
 
 repositories {
@@ -46,24 +48,27 @@ configurations.all {
 }
 
 dependencies {
-    compile 'com.fasterxml.jackson.core:jackson-core:2.9.7'
-    compile 'com.fasterxml.jackson.core:jackson-annotations:2.9.7'
-    compile 'com.fasterxml.jackson.core:jackson-databind:2.9.7'
-    compile 'org.codehaus.groovy:groovy-all:2.4.9'
-    testCompile 'junit:junit:4.12'
-    testCompile 'org.spockframework:spock-core:1.1-groovy-2.4'
-    testRuntime "net.bytebuddy:byte-buddy:1.6.5"
-    testRuntime "org.objenesis:objenesis:2.5.1"
-    testCompile 'com.google.guava:guava:23.0'
-    testCompile 'org.slf4j:slf4j-nop:1.7.25'
-    compile 'org.slf4j:slf4j-api:1.7.25'
-    compile group: 'org.apache.commons', name: 'commons-io', version: '1.3.2'
-    compile group: 'commons-codec', name: 'commons-codec', version: '1.9'
-    compile group: 'org.apache.httpcomponents', name: 'httpclient', version: '4.5.3'
-    compile group: 'commons-cli', name: 'commons-cli', version: '1.2'
-    compile group: 'org.apache.commons', name: 'commons-text', version: '1.1'
-    compile 'com.google.guava:guava:23.0'
-    compile 'com.github.theroddywms:RoddyToolLib:2.4.0'
+    implementation 'com.fasterxml.jackson.core:jackson-core:2.9.7'
+    implementation 'com.fasterxml.jackson.core:jackson-annotations:2.9.7'
+    implementation 'com.fasterxml.jackson.core:jackson-databind:2.12.7.1'
+    implementation 'org.codehaus.groovy:groovy-all:2.4.21'
+    testImplementation 'junit:junit:4.13.1'
+    testImplementation 'org.spockframework:spock-core:1.1-groovy-2.4'
+    testRuntimeOnly "net.bytebuddy:byte-buddy:1.6.5"
+    testRuntimeOnly "org.objenesis:objenesis:2.5.1"
+    testImplementation 'com.google.guava:guava:30.0-android'
+    testImplementation 'org.slf4j:slf4j-nop:1.7.25'
+    implementation 'org.slf4j:slf4j-api:1.7.25'
+    implementation group: 'org.apache.commons', name: 'commons-io', version: '1.3.2'
+    implementation group: 'commons-codec', name: 'commons-codec', version: '1.13'
+    implementation group: 'org.apache.httpcomponents', name: 'httpclient', version: '4.5.13'
+    implementation group: 'commons-cli', name: 'commons-cli', version: '1.2'
+    implementation group: 'org.apache.commons', name: 'commons-text', version: '1.1'
+    implementation 'com.google.guava:guava:30.0-android'
+    implementation 'com.github.theroddywms:RoddyToolLib:2.4.0'
+
+    // Runtime retention of @NonNull and annotations.
+    implementation 'com.github.bbottema:jetbrains-runtime-annotations:1.0.1'
 }
 
 task writePom {

src/main/groovy/de/dkfz/roddy/TestExecutionService.groovy

@@ -8,8 +8,8 @@ package de.dkfz.roddy
 
 import de.dkfz.roddy.execution.BEExecutionService
 import de.dkfz.roddy.execution.io.LocalExecutionHelper
-import de.dkfz.roddy.execution.jobs.Command
 import de.dkfz.roddy.execution.io.ExecutionResult
+import de.dkfz.roddy.execution.jobs.Command
 import de.dkfz.roddy.tools.BashUtils
 import groovy.transform.CompileStatic
 

src/main/groovy/de/dkfz/roddy/config/EmptyResourceSet.groovy

@@ -0,0 +1,25 @@
+/*
+ * Copyright (c) 2023 German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ).
+ *
+ * Distributed under the MIT License (license terms are at https://www.github.com/TheRoddyWMS/Roddy/LICENSE.txt).
+ */
+
+package de.dkfz.roddy.config
+
+
+import de.dkfz.roddy.tools.TimeUnit
+import groovy.transform.CompileStatic
+
+@CompileStatic
+class EmptyResourceSet extends ResourceSet {
+    EmptyResourceSet() {
+        super(null,
+              null,
+              null,
+              null,
+              null as TimeUnit,
+              null,
+              null,
+              null)
+    }
+}