Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

diff --git a/build.gradle b/build.gradle
index 3683195..8dcbc41 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -7,12 +7,18 @@ import groovy.transform.ExternalizeMethods
 import groovy.util.XmlParser
 import groovy.xml.XmlUtil
 
+
 buildscript {
+  repositories {
+    mavenCentral()
+    mavenLocal()
+  }
   dependencies {
     classpath 'org.openclover:clover:4.4.1'
   }
 }
 
+
 plugins {
   id 'java'
   id 'application'
@@ -26,12 +32,6 @@ repositories {
   jcenter()
   mavenCentral()
   mavenLocal()
-  flatDir {
-    dirs gradlePluginsDir
-  }
-}
-
-dependencies {
 }
 
 
@@ -104,6 +104,7 @@ ext {
 
   // clover
   cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}")
+  cloverDb = string("${buildDir}/clover/clover.db")
   classesDir = string("${jalviewDir}/${classes_dir}")
   if (clover.equals("true")) {
     use_clover = true
@@ -410,12 +411,13 @@ dependencies {
   }
 }
 
-
 configurations {
   cloverRuntime
   cloverRuntime.extendsFrom cloverCompile
 }
 
+
+// eclipse project and settings files creation, also used by buildship
 eclipse {
   project {
     name = eclipse_project_name
@@ -550,18 +552,24 @@ eclipse {
 }
 
 
-task cloverInstr() {
+task cloverInstr {
   // only instrument source, we build test classes as normal
   inputs.files files (sourceSets.main.allJava,sourceSets.test.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
   outputs.dir cloverInstrDir
 
   doFirst {
     delete cloverInstrDir
-    def argsList = ["--initstring", "${buildDir}/clover/clover.db",
-    "-d", "${buildDir}/${cloverSourcesInstrDir}"]
-    argsList.addAll(inputs.files.files.collect({ file ->
-      file.absolutePath
-    }))
+    def argsList = [
+      "--initstring",
+      cloverDb,
+      "-d",
+      cloverInstrDir.getPath(),
+    ]
+    argsList.addAll(
+      inputs.files.files.collect(
+        { file -> file.absolutePath }
+      )
+    )
     String[] args = argsList.toArray()
     println("About to instrument "+args.length +" files")
     com.atlassian.clover.CloverInstr.mainImpl(args)
@@ -569,43 +577,56 @@ task cloverInstr() {
 }
 
 
-task cloverReportHTML (type: JavaExec) {
-    inputs.dir "${buildDir}/clover"
-    outputs.dir "${reportsDir}/clover"
+cloverClasses.dependsOn cloverInstr
 
-    classpath configurations.cloverRuntime
-    maxHeapSize "${cloverReportJVMHeap}"
-    jvmArgs += "${cloverReportJVMArgs}"
-    main = "com.atlassian.clover.reporters.html.HtmlReporter"
-    args  "--initstring", "${buildDir}/clover/clover.db", "-o", "${reportsDir}/clover"
-    "${cloverReportHTMLOptions}".split(",").each {
-      args+= it.trim()
-      }
-}
 
-task cloverReportXML (type: JavaExec) {
-    inputs.dir "${buildDir}/clover"
-    outputs.dir "${reportsDir}/clover"
-    maxHeapSize "${cloverReportJVMHeap}"
-    jvmArgs "${cloverReportJVMArgs}"
-    classpath configurations.cloverRuntime
-    main = "com.atlassian.clover.reporters.xml.XMLReporter"
-    args  "--initstring", "${buildDir}/clover/clover.db", "-o", "${reportsDir}/clover/clover.xml"
-    
-    "${cloverReportXMLOptions}".split(",").each {
-      args+= it.trim()
-      }
-}
 task cloverReport {
   group = "Verification"
-    description = "Creates the Clover report"
-    inputs.dir "${buildDir}/clover"
-    outputs.dir "${reportsDir}/clover"
-    onlyIf {
-      file("${buildDir}/clover/clover.db").exists()
-    }
-    dependsOn cloverReportXML
-    dependsOn cloverReportHTML
+  description = "Creates the Clover report"
+  inputs.dir "${buildDir}/clover"
+  outputs.dir "${reportsDir}/clover"
+  onlyIf {
+    file(cloverDb).exists()
+  }
+  doFirst {
+    def argsList = [
+      "--initstring",
+      cloverDb,
+      "-o",
+      "${reportsDir}/clover"
+    ]
+    String[] args = argsList.toArray()
+    com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
+
+    // and generate ${reportsDir}/clover/clover.xml
+    args = [
+      "--initstring",
+      cloverDb,
+      "-o",
+      "${reportsDir}/clover/clover.xml"
+    ].toArray()
+    com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
+  }
+}
+
+
+compileCloverJava {
+
+  doFirst {
+    sourceCompatibility = compile_source_compatibility
+    targetCompatibility = compile_target_compatibility
+    options.compilerArgs += additional_compiler_args
+    print ("Setting target compatibility to "+targetCompatibility+"\n")
+  }
+  classpath += configurations.cloverRuntime
+}
+
+
+task cleanClover {
+  doFirst {
+    delete cloverInstrDir
+    delete cloverDb
+  }
 }
 // end clover bits
 
@@ -638,18 +659,6 @@ compileTestJava {
 }
 
 
-compileCloverJava {
-
-  doFirst {
-    sourceCompatibility = compile_source_compatibility
-    targetCompatibility = compile_target_compatibility
-    options.compilerArgs += additional_compiler_args
-    print ("Setting target compatibility to "+targetCompatibility+"\n")
-  }
-  classpath += configurations.cloverRuntime
-}
-
-
 clean {
   doFirst {
     delete sourceSets.main.java.outputDir
@@ -658,9 +667,9 @@ clean {
 
 
 cleanTest {
+  dependsOn cleanClover
   doFirst {
     delete sourceSets.test.java.outputDir
-    delete cloverInstrDir
   }
 }
 
@@ -840,6 +849,8 @@ test {
     useDefaultListeners=true
   }
 
+  maxHeapSize = "1024m"
+
   workingDir = jalviewDir
   //systemProperties 'clover.jar' System.properties.clover.jar
   sourceCompatibility = compile_source_compatibility

diff --git a/gradle.properties b/gradle.properties
index e4f0ebf..c473108 100644 (file)
--- a/gradle.properties
+++ b/gradle.properties
@@ -1,3 +1,5 @@
+org.gradle.jvmargs=-Xmx1536m -Xms512m
+
 jalviewDir = .
 
 #JAVA_VERSION = 1.8