fix warnings in build.gradle, fix warnings in distro/prank

rdk · Jun 27, 2024 · efd666e · efd666e
1 parent b04799f
commit efd666e
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Showing 3 changed files with 29 additions and 42 deletions.
diff --git a/build.gradle b/build.gradle
@@ -1,6 +1,7 @@
 //file:noinspection SpellCheckingInspection
 //file:noinspection GroovyAssignabilityCheck
 
+
 buildscript {  // for "com.github.ben-manes.versions" plugin
     repositories {
         maven {
@@ -12,23 +13,27 @@ buildscript {  // for "com.github.ben-manes.versions" plugin
     }
 }
 
-apply plugin: "com.github.ben-manes.versions"   //  ./gradlew dependencyUpdates 
+plugins {
+    id 'java'
+    id 'groovy'
+}
+
+apply plugin: "com.github.ben-manes.versions"   //  ./gradlew dependencyUpdates
 
-apply plugin: 'groovy'
-apply plugin: 'java'
 
 group = 'cz.siret'
-version = '2.5-dev.6.biojava71'
+version = '2.5-dev.7'
 
 description = 'Ligand binding site prediction based on machine learning.'
 
 
-allprojects {
-    apply plugin: 'java'
-    sourceCompatibility = 17
-    targetCompatibility = 17
+java {
+    sourceCompatibility = JavaVersion.VERSION_17
+    targetCompatibility = JavaVersion.VERSION_17
 }
 
+def distroDir = "$projectDir/distro"
+
 repositories {
     mavenCentral()
     mavenLocal()
@@ -48,29 +53,29 @@ sourceSets {
     }
 }
 
+
 processResources {
     filter org.apache.tools.ant.filters.ReplaceTokens, tokens: [
             "project_version": project.version
     ]
 }
 
-task copyDependenciesToDist( type: Copy ) {
-    into "$buildDir/../distro/bin/lib"
+tasks.register('copyDependenciesToDist', Copy) {
     from configurations.runtimeClasspath
-
+    into "$distroDir/bin/lib"
 }
 
-task copyBinaryToDist( type: Copy ) {
+tasks.register('copyBinaryToDist', Copy) {
     dependsOn jar
 
-    into "$buildDir/../distro/bin"
-    from "$buildDir/bin"
+    from "$projectDir/build/bin"
+    into "$distroDir/bin"
     include "*.jar"
 }
 
-task copyDocumentation( type: Copy ) {
-    into "$buildDir/../distro/"
-    from "$buildDir/../"
+tasks.register('copyDocumentation', Copy) {
+    from "$distroDir/../"
+    into "$distroDir"
     include "README.md", "LICENSE.txt"
 }
 
@@ -91,8 +96,8 @@ jar {
 }
 
 clean {
-    delete "$buildDir/../distro/bin"
-    delete "$buildDir/../distro/test_output"
+    delete "$distroDir/bin"
+    delete "$distroDir/test_output"
 }
 
 test {
@@ -104,7 +109,7 @@ test {
     // set heap size for the test JVM(s)
     maxHeapSize = "2g"
 
-    def distroDir = "$project.projectDir/distro"
+
     inputs.dir "$distroDir/test_data"
     inputs.files("$distroDir/models", "$distroDir/config/default.groovy")
 
@@ -122,7 +127,6 @@ test {
         showStackTraces true
 
         showStandardStreams = false
-//        showStandardStreams = true
     }
 
     // listen to standard out and standard error of the test JVM(s)
@@ -149,7 +153,7 @@ static def maturityLevel(String version) {
     def qualifiersRegex = qualifiers.collect { /(?i).*[.\-]$it[.\-\d]*/ }
 
     def index = qualifiersRegex.findIndexOf { version ==~ it }
-    return (index < 0) ? qualifiers.size : index
+    return (index < 0) ? qualifiers.size() : index
 }
 
 tasks.named("dependencyUpdates").configure {
@@ -198,4 +202,5 @@ dependencies {
 
     testImplementation 'org.junit.jupiter:junit-jupiter-engine:5.10.2'
     testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.10.2'
+
 }
diff --git a/distro/prank b/distro/prank
@@ -32,13 +32,4 @@ else
 fi
 
 
-JAVA_VERSION=`"$JAVACMD" -version 2>&1 | head -1 | cut -d '"' -f 2`
-JAVA_VERSION_MAJOR=`echo $JAVA_VERSION | cut -d '.' -f 1`
-if [[ "$JAVA_VERSION_MAJOR" -ge 11 ]]; then
-    # disable Groovy warnings in Java 11
-    export JAVA_OPTS="$JAVA_OPTS  --add-opens=java.base/sun.nio.fs=ALL-UNNAMED --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.annotation=ALL-UNNAMED --add-opens=java.base/java.lang.invoke=ALL-UNNAMED --add-opens=java.base/java.lang.module=ALL-UNNAMED --add-opens=java.base/java.lang.ref=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED --add-opens=java.base/java.math=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED --add-opens=java.base/java.net.spi=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED --add-opens=java.base/java.nio.channels=ALL-UNNAMED --add-opens=java.base/java.nio.channels.spi=ALL-UNNAMED --add-opens=java.base/java.nio.charset=ALL-UNNAMED --add-opens=java.base/java.nio.charset.spi=ALL-UNNAMED --add-opens=java.base/java.nio.file=ALL-UNNAMED --add-opens=java.base/java.nio.file.attribute=ALL-UNNAMED --add-opens=java.base/java.nio.file.spi=ALL-UNNAMED --add-opens=java.base/java.security=ALL-UNNAMED --add-opens=java.base/java.security.acl=ALL-UNNAMED --add-opens=java.base/java.security.cert=ALL-UNNAMED --add-opens=java.base/java.security.interfaces=ALL-UNNAMED --add-opens=java.base/java.security.spec=ALL-UNNAMED --add-opens=java.base/java.text=ALL-UNNAMED --add-opens=java.base/java.text.spi=ALL-UNNAMED --add-opens=java.base/java.time=ALL-UNNAMED --add-opens=java.base/java.time.chrono=ALL-UNNAMED --add-opens=java.base/java.time.format=ALL-UNNAMED --add-opens=java.base/java.time.temporal=ALL-UNNAMED --add-opens=java.base/java.time.zone=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/java.util.concurrent=ALL-UNNAMED --add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED --add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED --add-opens=java.base/java.util.function=ALL-UNNAMED --add-opens=java.base/java.util.jar=ALL-UNNAMED --add-opens=java.base/java.util.regex=ALL-UNNAMED --add-opens=java.base/java.util.spi=ALL-UNNAMED --add-opens=java.base/java.util.stream=ALL-UNNAMED --add-opens=java.base/java.util.zip=ALL-UNNAMED --add-opens=java.datatransfer/java.awt.datatransfer=ALL-UNNAMED --add-opens=java.desktop/java.applet=ALL-UNNAMED --add-opens=java.desktop/java.awt=ALL-UNNAMED --add-opens=java.desktop/java.awt.color=ALL-UNNAMED --add-opens=java.desktop/java.awt.desktop=ALL-UNNAMED --add-opens=java.desktop/java.awt.dnd=ALL-UNNAMED --add-opens=java.desktop/java.awt.dnd.peer=ALL-UNNAMED --add-opens=java.desktop/java.awt.event=ALL-UNNAMED --add-opens=java.desktop/java.awt.font=ALL-UNNAMED --add-opens=java.desktop/java.awt.geom=ALL-UNNAMED --add-opens=java.desktop/java.awt.im=ALL-UNNAMED --add-opens=java.desktop/java.awt.im.spi=ALL-UNNAMED --add-opens=java.desktop/java.awt.image=ALL-UNNAMED --add-opens=java.desktop/java.awt.image.renderable=ALL-UNNAMED --add-opens=java.desktop/java.awt.peer=ALL-UNNAMED --add-opens=java.desktop/java.awt.print=ALL-UNNAMED --add-opens=java.desktop/java.beans=ALL-UNNAMED --add-opens=java.desktop/java.beans.beancontext=ALL-UNNAMED --add-opens=java.instrument/java.lang.instrument=ALL-UNNAMED --add-opens=java.logging/java.util.logging=ALL-UNNAMED --add-opens=java.management/java.lang.management=ALL-UNNAMED --add-opens=java.prefs/java.util.prefs=ALL-UNNAMED --add-opens=java.rmi/java.rmi=ALL-UNNAMED --add-opens=java.rmi/java.rmi.activation=ALL-UNNAMED --add-opens=java.rmi/java.rmi.dgc=ALL-UNNAMED --add-opens=java.rmi/java.rmi.registry=ALL-UNNAMED --add-opens=java.rmi/java.rmi.server=ALL-UNNAMED --add-opens=java.sql/java.sql=ALL-UNNAMED  --add-opens=java.desktop/javax.swing=ALL-UNNAMED --add-opens=java.desktop/javax.swing.border=ALL-UNNAMED --add-opens=java.desktop/javax.swing.text=ALL-UNNAMED --add-opens=java.desktop/javax.swing.text.html=ALL-UNNAMED --add-opens=java.desktop/sun.awt=ALL-UNNAMED --add-opens=java.desktop/sun.java2d=ALL-UNNAMED --add-opens=java.desktop/sun.font=ALL-UNNAMED"
-fi
-
-
-
 "$JAVACMD" $JAVA_OPTS -cp "${CLASSPATH}" cz.siret.prank.program.Main "$@"
diff --git a/prank.sh b/prank.sh
@@ -37,21 +37,12 @@ else
 fi
 
 
-JAVA_VERSION=`"$JAVACMD" -version 2>&1 | head -1 | cut -d '"' -f 2`
-JAVA_VERSION_MAJOR=`echo $JAVA_VERSION | cut -d '.' -f 1`
-#if [[ "$JAVA_VERSION_MAJOR" -ge 11 ]]; then
-#    # disable Groovy warnings in Java 11
-#    export JAVA_OPTS="$JAVA_OPTS  --add-opens=java.base/sun.nio.fs=ALL-UNNAMED --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.annotation=ALL-UNNAMED --add-opens=java.base/java.lang.invoke=ALL-UNNAMED --add-opens=java.base/java.lang.module=ALL-UNNAMED --add-opens=java.base/java.lang.ref=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED --add-opens=java.base/java.math=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED --add-opens=java.base/java.net.spi=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED --add-opens=java.base/java.nio.channels=ALL-UNNAMED --add-opens=java.base/java.nio.channels.spi=ALL-UNNAMED --add-opens=java.base/java.nio.charset=ALL-UNNAMED --add-opens=java.base/java.nio.charset.spi=ALL-UNNAMED --add-opens=java.base/java.nio.file=ALL-UNNAMED --add-opens=java.base/java.nio.file.attribute=ALL-UNNAMED --add-opens=java.base/java.nio.file.spi=ALL-UNNAMED --add-opens=java.base/java.security=ALL-UNNAMED --add-opens=java.base/java.security.acl=ALL-UNNAMED --add-opens=java.base/java.security.cert=ALL-UNNAMED --add-opens=java.base/java.security.interfaces=ALL-UNNAMED --add-opens=java.base/java.security.spec=ALL-UNNAMED --add-opens=java.base/java.text=ALL-UNNAMED --add-opens=java.base/java.text.spi=ALL-UNNAMED --add-opens=java.base/java.time=ALL-UNNAMED --add-opens=java.base/java.time.chrono=ALL-UNNAMED --add-opens=java.base/java.time.format=ALL-UNNAMED --add-opens=java.base/java.time.temporal=ALL-UNNAMED --add-opens=java.base/java.time.zone=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/java.util.concurrent=ALL-UNNAMED --add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED --add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED --add-opens=java.base/java.util.function=ALL-UNNAMED --add-opens=java.base/java.util.jar=ALL-UNNAMED --add-opens=java.base/java.util.regex=ALL-UNNAMED --add-opens=java.base/java.util.spi=ALL-UNNAMED --add-opens=java.base/java.util.stream=ALL-UNNAMED --add-opens=java.base/java.util.zip=ALL-UNNAMED --add-opens=java.datatransfer/java.awt.datatransfer=ALL-UNNAMED --add-opens=java.desktop/java.applet=ALL-UNNAMED --add-opens=java.desktop/java.awt=ALL-UNNAMED --add-opens=java.desktop/java.awt.color=ALL-UNNAMED --add-opens=java.desktop/java.awt.desktop=ALL-UNNAMED --add-opens=java.desktop/java.awt.dnd=ALL-UNNAMED --add-opens=java.desktop/java.awt.dnd.peer=ALL-UNNAMED --add-opens=java.desktop/java.awt.event=ALL-UNNAMED --add-opens=java.desktop/java.awt.font=ALL-UNNAMED --add-opens=java.desktop/java.awt.geom=ALL-UNNAMED --add-opens=java.desktop/java.awt.im=ALL-UNNAMED --add-opens=java.desktop/java.awt.im.spi=ALL-UNNAMED --add-opens=java.desktop/java.awt.image=ALL-UNNAMED --add-opens=java.desktop/java.awt.image.renderable=ALL-UNNAMED --add-opens=java.desktop/java.awt.peer=ALL-UNNAMED --add-opens=java.desktop/java.awt.print=ALL-UNNAMED --add-opens=java.desktop/java.beans=ALL-UNNAMED --add-opens=java.desktop/java.beans.beancontext=ALL-UNNAMED --add-opens=java.instrument/java.lang.instrument=ALL-UNNAMED --add-opens=java.logging/java.util.logging=ALL-UNNAMED --add-opens=java.management/java.lang.management=ALL-UNNAMED --add-opens=java.prefs/java.util.prefs=ALL-UNNAMED --add-opens=java.rmi/java.rmi=ALL-UNNAMED --add-opens=java.rmi/java.rmi.activation=ALL-UNNAMED --add-opens=java.rmi/java.rmi.dgc=ALL-UNNAMED --add-opens=java.rmi/java.rmi.registry=ALL-UNNAMED --add-opens=java.rmi/java.rmi.server=ALL-UNNAMED --add-opens=java.sql/java.sql=ALL-UNNAMED  --add-opens=java.desktop/javax.swing=ALL-UNNAMED --add-opens=java.desktop/javax.swing.border=ALL-UNNAMED --add-opens=java.desktop/javax.swing.text=ALL-UNNAMED --add-opens=java.desktop/javax.swing.text.html=ALL-UNNAMED --add-opens=java.desktop/sun.awt=ALL-UNNAMED --add-opens=java.desktop/sun.java2d=ALL-UNNAMED --add-opens=java.desktop/sun.font=ALL-UNNAMED"
-#fi
-
-
-
 PARAMS="$PRANK_LOCALENV_PARAMS"
 
 
-
-CMD="$JAVACMD $JAVA_OPTS -cp ${CLASSPATH} cz.siret.prank.program.Main ${PARAMS} $@"
+#CMD="$JAVACMD $JAVA_OPTS -cp ${CLASSPATH} cz.siret.prank.program.Main ${PARAMS} $@"
 #echo "+" $CMD
+
 "$JAVACMD" $JAVA_OPTS -cp "${CLASSPATH}" cz.siret.prank.program.Main ${PARAMS} "$@"