X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=84d5f73d6e70f24c288a91242f421dbd60808e7c;hb=221d973075512e015f7c13332c77162ea6b5e7bb;hp=c6f86d64b332b3eefb643cd2d9f63e5cd02da55f;hpb=f2b2d87b1b8235ff9f8da33238e8e4d1a64efb93;p=jalview.git

diff --git a/build.gradle b/build.gradle
index c6f86d6..84d5f73 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1,16 +1,22 @@
 import org.apache.tools.ant.filters.ReplaceTokens
+//import org.apache.tools.ant.filters.ReplaceRegexp
 import org.gradle.internal.os.OperatingSystem
+import org.gradle.plugins.ide.eclipse.model.*
 
 
+import groovy.transform.ExternalizeMethods
+
 buildscript {
   dependencies {
-        classpath 'org.openclover:clover:4.3.1'
+    classpath 'org.openclover:clover:4.3.1'
+    classpath 'org.apache.commons:commons-compress:1.18'
   }
 }
 
 plugins {
   id 'java'
   id 'application'
+  id 'eclipse'
   id 'com.github.johnrengelman.shadow' version '4.0.3'
   id 'com.install4j.gradle' version '7.0.9'
 }
@@ -25,62 +31,129 @@ repositories {
 }
 
 mainClassName = launcherClass
-def cloverInstrDir = file("$buildDir/sources-instr")
+def cloverInstrDir = file("$buildDir/$cloverSourcesInstrDir")
+def classes = "$jalviewDir/$classesDir"
+
+if (clover.equals("true")) {
+  use_clover = true
+  classes = "$buildDir/$cloverClassesDir"
+} else {
+  use_clover = false
+  classes = "$jalviewDir/$classesDir"
+}
+
+// configure classpath/args for j8/j11 compilation
+
+def jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
+def libDir
+def libDistDir
+def compile_source_compatibility
+def compile_target_compatibility
+
+ext {
+  // where the getdown channel will be built.
+  // TODO: consider allowing this expression to  be overridden by -P arg
+  getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION
+  getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir
+  //getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
+  getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir
+  getdownLauncher = jalviewDir + '/' + getdown_launcher
+  getdownFilesDir = jalviewDir + '/' + getdown_files_dir + '/' + JAVA_VERSION + '/'
+  getdown_app_base = getdown_channel_base+"/"+getdown_channel_name+"/"+JAVA_VERSION+"/"
+  modules_compileClasspath = fileTree(dir: "$jalviewDir/$j11modDir", include: ["*.jar"])
+  modules_runtimeClasspath = modules_compileClasspath
+  gitHash = ""
+  gitBranch = ""
+}
+
+def JAVA_INTEGER_VERSION
+def additional_compiler_args = []
+// these are getdown.txt properties defined dependent on the JAVA_VERSION
+def getdown_alt_java_min_version
+// this property is assigned below and expanded to multiple lines in the getdown task
+def getdown_alt_multi_java_location
+// this property is for the Java library used in eclipse
+def eclipse_java_runtime_name
+if (JAVA_VERSION.equals("1.8")) {
+  JAVA_INTEGER_VERSION = "8"
+  //libDir = j8libDir
+  libDir = j11libDir
+  libDistDir = j8libDir
+  compile_source_compatibility = 1.8
+  compile_target_compatibility = 1.8
+  getdown_alt_java_min_version = getdown_alt_java8_min_version
+  getdown_alt_multi_java_location = getdown_alt_java8_txt_multi_java_location
+  eclipse_java_runtime_name = "JavaSE-1.8"
+} else if (JAVA_VERSION.equals("11")) {
+  JAVA_INTEGER_VERSION = "11"
+  libDir = j11libDir
+  libDistDir = j11libDir
+  compile_source_compatibility = 11
+  compile_target_compatibility = 11
+  getdown_alt_java_min_version = getdown_alt_java11_min_version
+  getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
+  eclipse_java_runtime_name = "JavaSE-11"
+  additional_compiler_args += [
+    '--module-path', ext.modules_compileClasspath.asPath,
+    '--add-modules', j11modules
+  ]
+} else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
+  JAVA_INTEGER_VERSION = JAVA_VERSION
+  libDir = j11libDir
+  libDistDir = j11libDir
+  compile_source_compatibility = JAVA_VERSION
+  compile_target_compatibility = JAVA_VERSION
+  getdown_alt_java_min_version = getdown_alt_java11_min_version
+  getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
+  eclipse_java_runtime_name = "JavaSE-11"
+  additional_compiler_args += [
+    '--module-path', ext.modules_compileClasspath.asPath,
+    '--add-modules', j11modules
+  ]
+} else {
+  throw new GradleException("JAVA_VERSION=$JAVA_VERSION not currently supported by Jalview")
+}
 
 sourceSets {
 
   main {
     java {
       srcDirs "$jalviewDir/$sourceDir"
-      outputDir = file("$jalviewDir/$classesDir")
+      outputDir = file("$classes")
     }
 
     resources {
       srcDirs "$jalviewDir/$resourceDir"
-      srcDirs "$jalviewDir/$libDir"
     }
 
     jar.destinationDir = file("$jalviewDir/$packageDir")
 
     compileClasspath = files(sourceSets.main.java.outputDir)
     compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
-    if (JAVA_VERSION.equals("1.8")) {
-      print("ADDING J11LIBS TO CLASSPATH")
-      compileClasspath += fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"])
-    }
-
-    runtimeClasspath = compileClasspath
-  }
-
-  modules {
-    compileClasspath = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"])
 
     runtimeClasspath = compileClasspath
   }
-  
   clover {
     java {
-        srcDirs = [ cloverInstrDir ]
-        outputDir = file("$jalviewDir/$testOutputDir")
+      srcDirs = [ cloverInstrDir ]
+      outputDir = file("${buildDir}/${cloverClassesDir}")
     }
-    
+
     resources {
       srcDirs = sourceSets.main.resources.srcDirs
     }
     compileClasspath = configurations.cloverRuntime + files( sourceSets.clover.java.outputDir )
+    compileClasspath += files(sourceSets.main.java.outputDir)
+    compileClasspath += sourceSets.main.compileClasspath
     compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
     compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
-    if (JAVA_VERSION.equals("1.8")) {
-      print("ADDING J11LIBS TO CLASSPATH")
-      compileClasspath += fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"])
-    }
 
     runtimeClasspath = compileClasspath
   }
-  
+
   test {
     java {
-      srcDirs = [ cloverInstrDir ]
+      srcDirs "$jalviewDir/$testSourceDir"
       outputDir = file("$jalviewDir/$testOutputDir")
     }
 
@@ -88,14 +161,16 @@ sourceSets {
       srcDirs = sourceSets.main.resources.srcDirs
     }
 
+    compileClasspath = files( sourceSets.test.java.outputDir )
 
-    compileClasspath += configurations.cloverRuntime + files( sourceSets.test.java.outputDir )
+    if (use_clover) {
+      compileClasspath += sourceSets.clover.compileClasspath
+    } else {
+      compileClasspath += files(sourceSets.main.java.outputDir)
+    }
+    
     compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
     compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
-    if (JAVA_VERSION.equals("1.8")) {
-      print("ADDING J11LIBS TO CLASSPATH")
-      compileClasspath += fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"])
-    }
 
     runtimeClasspath = compileClasspath
   }
@@ -103,46 +178,208 @@ sourceSets {
 
 // clover bits
 dependencies {
-  cloverCompile 'org.openclover:clover:4.3.1'
-  testCompile 'org.openclover:clover:4.3.1'
+  if (use_clover) {
+    cloverCompile 'org.openclover:clover:4.3.1'
+    testCompile 'org.openclover:clover:4.3.1'
+  }
 }
 
 configurations {
-    cloverRuntime
-    cloverRuntime.extendsFrom cloverCompile
+  cloverRuntime
+  cloverRuntime.extendsFrom cloverCompile
 }
- 
-task cloverInstr() {
-    inputs.files files (sourceSets.main.allJava, fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
-    outputs.dir cloverInstrDir
-
-    doFirst {
-        delete cloverInstrDir
-        def argsList = ["--initstring", "${buildDir}/clover/clover.db",
-                        "-d", "${buildDir}/sources-instr"]
-        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)
+
+eclipse {
+  project {
+    name = "Jalview with gradle build"
+
+    natures 'org.eclipse.jdt.core.javanature',
+        'org.eclipse.jdt.groovy.core.groovyNature',
+        'org.eclipse.buildship.core.gradleprojectnature'
+
+    buildCommand 'org.eclipse.jdt.core.javabuilder'
+    buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
+  }
+
+  classpath {
+    //defaultOutputDir = sourceSets.main.java.outputDir
+    def removeThese = []
+    configurations.each{ if (it.isCanBeResolved()) {
+        removeThese += it
+      }
     }
+
+    minusConfigurations += removeThese
+    plusConfigurations = [ ]
+    file {
+
+      whenMerged { cp ->
+        def removeTheseToo = []
+        HashMap<String, Boolean> addedSrcPath = new HashMap<>();
+        cp.entries.each { entry ->
+          if (entry.kind == 'src') {
+            if (addedSrcPath.getAt(entry.path) || !(entry.path == "src" || entry.path == "test")) {
+              removeTheseToo += entry
+            } else {
+              addedSrcPath.putAt(entry.path, true)
+            }
+          }
+        }
+        cp.entries.removeAll(removeTheseToo)
+        
+        print ("CP="+cp.inspect())
+        
+        cp.entries += new Output("bin/main")
+        cp.entries += new Library(fileReference(helpParentDir))
+        cp.entries += new Library(fileReference(resourceDir))
+        
+        HashMap<String, Boolean> addedLibPath = new HashMap<>();
+        
+        // changing from sourcesets.main.classpath to specific Java version lib
+        //sourceSets.main.compileClasspath.each{
+        fileTree("$jalviewDir/$libDistDir").include("**/*.jar").include("*.jar").each {
+          //don't want to add outputDir as eclipse is using its own output dir in bin/main
+          if (it.isDirectory() || ! it.exists()) {
+            // don't add dirs to classpath
+            return
+          }
+          def itPath = it.toString()
+          if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
+            itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+          }
+          if (addedLibPath.get(itPath)) {
+            //println("Not adding duplicate entry "+itPath)
+          } else {
+            //println("Adding entry "+itPath)
+            cp.entries += new Library(fileReference(itPath))
+            addedLibPath.put(itPath, true)
+          }
+        }
+
+        // changing from sourcesets.main.classpath to specific Java version lib
+        //sourceSets.test.compileClasspath.each{
+        fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"]).each {
+          //if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) {
+          //no longer want to add outputDir as eclipse is using its own output dir in bin/main
+          if (it.isDirectory() || ! it.exists()) {
+            // don't add dirs to classpath
+            return false // groovy "break" in .each loop
+          }
+          def itPath = it.toString()
+          if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
+            itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+          }
+          if (addedLibPath.get(itPath)) {
+            // don't duplicate
+          } else {
+            def lib = new Library(fileReference(itPath))
+            // this doesn't work... yet.  Adding test=true attribute using withXml below
+            //def attrs = new Node(null, 'attributes', ["test":"true"])
+            //lib.appendNode(attrs) //
+            cp.entries += lib
+            addedLibPath.put(itPath, true)
+          }
+        }
+      }  
+
+      // withXml changes ignored by buildship, these add the "test=true" attribute
+      withXml {
+        def node = it.asNode()
+        
+        def srcTestAttributes
+        node.children().each{ cpe ->
+          def attributes = cpe.attributes()
+          if (attributes.get("kind") == "src" && attributes.get("path") == "test") {
+            srcTestAttributes = cpe.find { a -> a.name() == "attributes" }
+            return
+          }
+        }
+        def addTestAttribute = true
+        srcTestAttributes.each{a ->
+          if (a.name() == "attribute" && a.attributes().getAt("name") == "test") {
+            addTestAttribute = false
+          }
+        }
+        if (addTestAttribute) {
+          srcTestAttributes.append(new Node(null, "attribute", [name:"test", value:"true"]))
+        }
+
+        node.children().each{ cpe ->
+          def attributes = cpe.attributes()
+          if (attributes.get("kind") == "lib" && attributes.get("path").startsWith("utils/")) {
+            cpe.appendNode('attributes')
+                .appendNode('attribute', [name:"test", value:"true"])
+          }
+        }
+      } // withXML
+    } // file
+
+    containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
+  } // classpath
+
+  jdt {
+    // for the IDE, use java 11 compatibility
+    sourceCompatibility = compile_source_compatibility
+    targetCompatibility = compile_target_compatibility
+    javaRuntimeName = eclipse_java_runtime_name
+
+    file {
+      withProperties { props ->
+        def jalview_prefs = new Properties()
+        def ins = new FileInputStream(jalviewDirAbsolutePath+"/"+eclipse_extra_jdt_prefs_file)
+        jalview_prefs.load(ins)
+        ins.close()
+        jalview_prefs.forEach { t, v ->
+          if (props.getAt(t) == null) {
+            props.putAt(t, v)
+          }
+        }
+      }
+    }
+  }
+  
+  //synchronizationTasks eclipseClasspath
+  //autoBuildTasks eclipseClasspath
+} 
+
+task cloverInstr() {
+  // only instrument source, we build test classes as normal
+  inputs.files files (sourceSets.main.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
+    }))
+    String[] args = argsList.toArray()
+    println("About to instrument "+args.length +" files")
+    com.atlassian.clover.CloverInstr.mainImpl(args)
+  }
 }
+  
 
-test.dependsOn cloverInstr
- 
 task cloverReport {
-    inputs.dir "${buildDir}/clover"
-    outputs.dir "${reportsDir}/clover"
-    onlyIf {
-        file("${buildDir}/clover/clover.db").exists()
-    }
-    doFirst {
-        def argsList = ["--initstring", "${buildDir}/clover/clover.db",
-                        "-o", "${reportsDir}/clover"]
-        String[] args = argsList.toArray()
-        com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
-    }
+  group = "Verification"
+  description = "Createst the Clover report"
+  inputs.dir "${buildDir}/clover"
+  outputs.dir "${reportsDir}/clover"
+  onlyIf {
+    file("${buildDir}/clover/clover.db").exists()
+  }
+  doFirst {
+    def argsList = ["--initstring", "${buildDir}/clover/clover.db",
+      "-o", "${reportsDir}/clover"]
+    String[] args = argsList.toArray()
+    com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
+
+    // and generate ${reportsDir}/clover/clover.xml
+    args = ["--initstring", "${buildDir}/clover/clover.db",
+      "-o", "${reportsDir}/clover/clover.xml"].toArray()
+    com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
+  }
 }
 
 // end clover bits
@@ -151,63 +388,40 @@ task cloverReport {
 compileJava {
 
   doFirst {
-    if (JAVA_VERSION.equals("1.8")) {
-      sourceCompatibility = 1.8
-      targetCompatibility = 1.8
-    } else if (JAVA_VERSION.equals("11")) {
-      sourceCompatibility = 11
-      targetCompatibility = 11
-
-      options.compilerArgs = [
-        '--module-path', sourceSets.modules.compileClasspath.asPath,
-        '--add-modules', j11modules
-      ]
-    }
+    sourceCompatibility = compile_source_compatibility
+    targetCompatibility = compile_target_compatibility
+    options.compilerArgs = additional_compiler_args
     print ("Setting target compatibility to "+targetCompatibility+"\n")
   }
 
 }
 
 compileTestJava {
-
+  if (use_clover) {
+    dependsOn compileCloverJava
+    classpath += configurations.cloverRuntime
+  } else {
+    classpath += sourceSets.main.runtimeClasspath
+  }
   doFirst {
-    if (JAVA_VERSION.equals("1.8")) {
-      sourceCompatibility = 1.8
-      targetCompatibility = 1.8
-    } else if (JAVA_VERSION.equals("11")) {
-      sourceCompatibility = 11
-      targetCompatibility = 11
-
-      options.compilerArgs = [
-        '--module-path', sourceSets.modules.compileClasspath.asPath,
-        '--add-modules', j11modules
-      ]
-    }
+    sourceCompatibility = compile_source_compatibility
+    targetCompatibility = compile_target_compatibility
+    options.compilerArgs = additional_compiler_args
     print ("Setting target compatibility to "+targetCompatibility+"\n")
   }
-  classpath += configurations.cloverRuntime
 }
 
 
-//compileCloverJava {
-//
-//  doFirst {
-//    if (JAVA_VERSION.equals("1.8")) {
-//      sourceCompatibility = 1.8
-//      targetCompatibility = 1.8
-//    } else if (JAVA_VERSION.equals("11")) {
-//      sourceCompatibility = 11
-//      targetCompatibility = 11
-//
-//      options.compilerArgs += [
-//        '--module-path', sourceSets.modules.compileClasspath.asPath,
-//        '--add-modules', j11modules
-//      ]
-//    }
-//    print ("Setting target compatibility to "+targetCompatibility+"\n")
-//  }
-//  classpath += configurations.cloverRuntime
-//}
+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 {
   delete sourceSets.main.java.outputDir
@@ -218,77 +432,121 @@ cleanTest {
   delete cloverInstrDir
 }
 
+// format is a string like date.format("dd MMMM yyyy")
 def getDate(format) {
   def date = new Date()
-  //return date.format("dd MMMM yyyy")
   return date.format(format)
 }
 
-def getGitHash() {
-  def stdout = new ByteArrayOutputStream()
+task setGitVals {
+  def hashStdOut = new ByteArrayOutputStream()
   exec {
     commandLine "git", "rev-parse", "--short", "HEAD"
-    standardOutput = stdout
-    workingDir = jalviewDir
+    standardOutput = hashStdOut
+    ignoreExitValue true
   }
-  return stdout.toString().trim()
-}
 
-def getGitBranch() {
-  def stdout = new ByteArrayOutputStream()
+  def branchStdOut = new ByteArrayOutputStream()
   exec {
     commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
-    standardOutput = stdout
-    workingDir = jalviewDir
+    standardOutput = branchStdOut
+    ignoreExitValue true
   }
-  return stdout.toString().trim()
+
+  project.ext.gitHash = hashStdOut.toString().trim()
+  project.ext.gitBranch = branchStdOut.toString().trim()
+
+  outputs.upToDateWhen { false }
 }
 
 task createBuildProperties(type: WriteProperties) {
+  dependsOn setGitVals
   inputs.dir("$jalviewDir/$sourceDir")
+  inputs.dir("$classes")
   inputs.dir("$jalviewDir/$resourceDir")
-  outputFile "$jalviewDir/$classesDir/$buildPropertiesFile"
-  /* taking time/date specific comment out to allow better incremental builds */
-  //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
-  comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
-  property "BUILD_DATE", getDate("dd MMMM yyyy")
+  outputFile "$classes/$buildPropertiesFile"
+  // taking time specific comment out to allow better incremental builds
+  comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
+  //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
+  property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
   property "VERSION", JALVIEW_VERSION
-  property "INSTALLATION", INSTALLATION+" git-commit:"+getGitHash()+" ["+getGitBranch()+"]"
+  property "INSTALLATION", INSTALLATION+" git-commit:"+project.ext.gitHash+" ["+project.ext.gitBranch+"]"
   outputs.file(outputFile)
-  outputs.dir("$jalviewDir/$classesDir")
+}
+
+def buildingHTML = "$jalviewDir/$docDir/building.html"
+task deleteBuildingHTML(type: Delete) {
+  delete buildingHTML
+}
+
+task convertBuildingMD(type: Exec) {
+  dependsOn deleteBuildingHTML
+  def buildingMD = "$jalviewDir/$docDir/building.md"
+  def css = "$jalviewDir/$docDir/github.css"
+
+  def pandoc = null
+  pandoc_exec.split(",").each {
+    if (file(it.trim()).exists()) {
+      pandoc = it.trim()
+      return true
+    }
+  }
+
+  def hostname = "hostname".execute().text.trim()
+  if ((pandoc == null || ! file(pandoc).exists()) && hostname.equals("jv-bamboo")) {
+    pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
+  }
+
+  if (pandoc != null && file(pandoc).exists()) {
+    commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
+  } else {
+    commandLine "true"
+  }
+
+  ignoreExitValue true
+
+  inputs.file(buildingMD)
+  inputs.file(css)
+  outputs.file(buildingHTML)
+}
+clean {
+  delete buildingHTML
 }
 
 task syncDocs(type: Sync) {
-  def syncDir = "$jalviewDir/$classesDir/$docDir"
+  dependsOn convertBuildingMD
+  def syncDir = "$classes/$docDir"
   from fileTree("$jalviewDir/$docDir")
   into syncDir
 
 }
 
-def helpFile = "$jalviewDir/$classesDir/$helpDir/help.jhm"
-task syncHelp(type: Sync) {
-  inputs.files("$jalviewDir/$helpDir")
-  outputs.files(helpFile)
-
-  def syncDir = "$jalviewDir/$classesDir/$helpDir"
-  from fileTree("$jalviewDir/$helpDir")
-  into syncDir
-}
+def helpFile = "$classes/$helpDir/help.jhm"
 
 task copyHelp(type: Copy) {
-  def inputDir = "$jalviewDir/$helpDir"
-  def outputDir = "$jalviewDir/$classesDir/$helpDir"
-  from inputDir
+  def inputDir = "$jalviewDir/$helpParentDir/$helpDir"
+  def outputDir = "$classes/$helpDir"
+  from(inputDir) {
+    exclude '**/*.gif'
+    exclude '**/*.jpg'
+    exclude '**/*.png'
+    filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION])
+  }
+  from(inputDir) {
+    include '**/*.gif'
+    include '**/*.jpg'
+    include '**/*.png'
+  }
   into outputDir
-  filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': "USING_FILTER"])
+
   inputs.dir(inputDir)
   outputs.files(helpFile)
   outputs.dir(outputDir)
 }
 
 task syncLib(type: Sync) {
-  def syncDir = "$jalviewDir/$classesDir/$libDir"
-  from fileTree("$jalviewDir/$libDir")
+  def syncDir = "$classes/$libDistDir"
+  from fileTree("$jalviewDir/$libDistDir")
   into syncDir
 }
 
@@ -296,7 +554,7 @@ task syncResources(type: Sync) {
   from "$jalviewDir/$resourceDir"
   include "**/*.*"
   exclude "install4j"
-  into "$jalviewDir/$classesDir"
+  into "$classes"
   preserve {
     include "**"
   }
@@ -312,30 +570,24 @@ task prepare {
 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
 test {
   dependsOn prepare
-  
-  
-  useTestNG()
-  options {
+  dependsOn compileJava
+  if (use_clover) {
+    dependsOn cloverInstr
+  }
+
+  print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
+
+  useTestNG() {
     includeGroups testngGroups
     preserveOrder true
+    useDefaultListeners=true
   }
-  
+
   workingDir = jalviewDir
   //systemProperties 'clover.jar' System.properties.clover.jar
-  if (JAVA_VERSION.equals("1.8")) {
-    sourceCompatibility = 1.8
-    targetCompatibility = 1.8
-  } else if (JAVA_VERSION.equals("11")) {
-    sourceCompatibility = 11
-    targetCompatibility = 11
-
-    jvmArgs += [
-      '--module-path',
-      sourceSets.modules.compileClasspath.asPath,
-      '--add-modules',
-      j11modules
-    ]
-  }
+  sourceCompatibility = compile_source_compatibility
+  targetCompatibility = compile_target_compatibility
+  jvmArgs += additional_compiler_args
   print ("Setting target compatibility to "+targetCompatibility+"\n")
 }
 
@@ -343,13 +595,13 @@ task buildIndices(type: JavaExec) {
   dependsOn copyHelp
   classpath = sourceSets.main.compileClasspath
   main = "com.sun.java.help.search.Indexer"
-  workingDir = "$jalviewDir/$classesDir/$helpDir"
+  workingDir = "$classes/$helpDir"
   def argDir = "html"
   args = [ argDir ]
   inputs.dir("$workingDir/$argDir")
 
-  outputs.dir("$jalviewDir/$classesDir/doc")
-  outputs.dir("$jalviewDir/$classesDir/help")
+  outputs.dir("$classes/doc")
+  outputs.dir("$classes/help")
   outputs.file("$workingDir/JavaHelpSearch/DOCS")
   outputs.file("$workingDir/JavaHelpSearch/DOCS.TAB")
   outputs.file("$workingDir/JavaHelpSearch/OFFSETS")
@@ -364,22 +616,27 @@ task compileLinkCheck(type: JavaCompile) {
   destinationDir = file("$jalviewDir/$utilsDir")
   source = fileTree(dir: "$jalviewDir/$utilsDir", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
 
+  inputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.java")
+  inputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.java")
   outputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.class")
   outputs.file("$jalviewDir/$utilsDir/BufferedLineReader.class")
 }
 
+def helplinkscheckeroutputfile = file("$jalviewDir/$utilsDir/HelpLinksChecker.out")
 task linkCheck(type: JavaExec) {
   dependsOn prepare, compileLinkCheck
   classpath = files("$jalviewDir/$utilsDir")
   main = "HelpLinksChecker"
-  workingDir = "$jalviewDir"
-  args = [ "$classesDir/$helpDir", "-nointernet" ]
+  workingDir = jalviewDir
+  def help = "$classes/$helpDir"
+  args = [ "$classes/$helpDir", "-nointernet" ]
 
   doFirst {
-    standardOutput new FileOutputStream("$jalviewDir/$utilsDir/HelpLinksChecker.out")
+    helplinkscheckeroutputfile.createNewFile()
+    standardOutput new FileOutputStream(helplinkscheckeroutputfile, false)
   }
 
-  outputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.out")
+  outputs.file(helplinkscheckeroutputfile)
 }
 
 task cleanPackageDir(type: Delete) {
@@ -407,18 +664,18 @@ jar {
   exclude "**/*.jar"
   exclude "**/*.jar.*"
 
-  inputs.dir("$jalviewDir/$classesDir")
+  inputs.dir("$classes")
   outputs.file("$jalviewDir/$packageDir/$archiveName")
 }
 
 task copyJars(type: Copy) {
-  from fileTree("$jalviewDir/$classesDir").include("**/*.jar").include("*.jar").files
+  from fileTree("$classes").include("**/*.jar").include("*.jar").files
   into "$jalviewDir/$packageDir"
 }
 
 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
 task syncJars(type: Sync) {
-  from fileTree("$jalviewDir/$libDir").include("**/*.jar").include("*.jar").files
+  from fileTree("$jalviewDir/$libDistDir").include("**/*.jar").include("*.jar").files
   into "$jalviewDir/$packageDir"
   preserve {
     include jar.archiveName
@@ -426,6 +683,8 @@ task syncJars(type: Sync) {
 }
 
 task makeDist {
+  group = "build"
+  description = "Put all required libraries in dist"
   // order of "cleanPackageDir", "copyJars", "jar" important!
   jar.mustRunAfter cleanPackageDir
   syncJars.mustRunAfter cleanPackageDir
@@ -442,28 +701,20 @@ task cleanDist {
 }
 
 shadowJar {
+  group = "distribution"
   dependsOn makeDist
-  if (JAVA_VERSION.equals("11")) {
-    from ("$jalviewDir/$j11libDir") {
-      include("*.jar")
-    }
+  from ("$jalviewDir/$libDistDir") {
+    include("*.jar")
   }
   mainClassName = shadowJarMainClass
   mergeServiceFiles()
-  classifier = "all"
+  classifier = "all-"+JAVA_VERSION
   minimize()
 }
 
-ext {
-  getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir
-  getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir
-  getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
-  getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir
-  getdownLauncher = jalviewDir + '/' + getdown_launcher
-  getdownFilesDir = jalviewDir + '/' + getdown_files_dir
-}
-
 task getdownWebsite() {
+  group = "distribution"
+  description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
   dependsOn makeDist
   def getdownWebsiteResourceFilenames = []
   def getdownTextString = ""
@@ -473,11 +724,13 @@ task getdownWebsite() {
   doFirst {
     // go through properties looking for getdown_txt_...
     def props = project.properties.sort { it.key }
-    if (JAVA_VERSION.equals("11")) {
-      props.put("getdown_txt_java_min_version", getdown_alt_java11_min_version)
-    } else {
-      props.put("getdown_txt_java_min_version", getdown_alt_java8_min_version)
+    props.put("getdown_txt_java_min_version", getdown_alt_java_min_version)
+    props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location)
+
+    if (getdown_local == "true") {
+      getdown_app_base = file(getdownWebsiteDir).toURI().toString()
     }
+    props.put("getdown_txt_appbase", getdown_app_base)
     props.each{ prop, val ->
       if (prop.startsWith("getdown_txt_") && val != null) {
         if (prop.startsWith("getdown_txt_multi_")) {
@@ -537,19 +790,24 @@ task getdownWebsite() {
       }
     }
 
-    if (JAVA_VERSION.equals("11")) {
-      def j11libFiles = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"]).getFiles()
-      j11libFiles.sort().each{f ->
-        def line = "code = " + getdown_j11lib_dir + '/' + f.getName() + "\n"
-        getdownTextString += line
-        copy {
-          from f.getPath()
-          into project.ext.getdownJ11libDir
-        }
-      }
-    }
-
-    getdownTextString += "code = " + file(getdownLauncher).getName() + "\n"
+    // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
+    /*
+     if (JAVA_VERSION.equals("11")) {
+     def j11libFiles = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"]).getFiles()
+     j11libFiles.sort().each{f ->
+     def line = "code = " + getdown_j11lib_dir + '/' + f.getName() + "\n"
+     getdownTextString += line
+     copy {
+     from f.getPath()
+     into project.ext.getdownJ11libDir
+     }
+     }
+     }
+     */
+
+    // getdown-launcher.jar should not be in main application class path so the main application can move it when updated.  Listed as a resource so it gets updated.
+    //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
+    getdownTextString += "resource = " + getdown_launcher_new + "\n"
     getdownTextString += "class = " + mainClass + "\n"
 
     def getdown_txt = file(project.ext.getdownWebsiteDir + "/getdown.txt")
@@ -563,6 +821,7 @@ task getdownWebsite() {
     copy {
       from getdownLauncher
       into project.ext.getdownWebsiteDir
+      rename(file(getdownLauncher).getName(), getdown_launcher_new)
     }
 
     copy {
@@ -571,12 +830,17 @@ task getdownWebsite() {
     }
 
     copy {
+      from getdownLauncher
+      into project.ext.getdownWebsiteDir
+    }
+
+    copy {
       from jalviewDir + '/' + project.getProperty('getdown_txt_ui.background_image')
       from jalviewDir + '/' + project.getProperty('getdown_txt_ui.error_background')
       from jalviewDir + '/' + project.getProperty('getdown_txt_ui.progress_image')
       from jalviewDir + '/' + project.getProperty('getdown_txt_ui.icon')
       from jalviewDir + '/' + project.getProperty('getdown_txt_ui.mac_dock_icon')
-      into project.ext.getdownFilesDir + '/' + getdown_resource_dir 
+      into project.ext.getdownFilesDir + '/' + getdown_resource_dir
     }
   }
 
@@ -586,14 +850,19 @@ task getdownWebsite() {
 }
 
 task getdownDigest(type: JavaExec) {
+  group = "distribution"
+  description = "Digest the getdown website folder"
   dependsOn getdownWebsite
-  classpath = files(jalviewDir + '/' + getdown_core)
+  classpath = files(jalviewDir + '/' + getdown_core, jalviewDir+'/'+getdown_launcher)
   main = "com.threerings.getdown.tools.Digester"
   args project.ext.getdownWebsiteDir
+  inputs.dir(project.ext.getdownWebsiteDir)
   outputs.file(project.ext.getdownWebsiteDir + '/' + "digest2.txt")
 }
 
 task getdown() {
+  group = "distribution"
+  description = "Create the minimal and full getdown app folder for installers and website and create digest file"
   dependsOn getdownDigest
 }
 
@@ -616,15 +885,99 @@ install4j {
     install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
   }
   installDir = file(install4jHomeDir)
+  mediaTypes = Arrays.asList(install4jMediaTypes.split(","))
+  if (install4jFaster.equals("true")) {
+    faster = true
+  }
+}
+
+def install4jConf
+def macosJavaVMDir
+def macosJavaVMTgz
+def windowsJavaVMDir
+def windowsJavaVMTgz
+def install4jDir = "$jalviewDir/$install4jResourceDir"
+def install4jConfFile = "jalview-installers-java"+JAVA_VERSION+".install4j"
+install4jConf = "$install4jDir/$install4jConfFile"
+
+task copyInstall4jTemplate(type: Copy) {
+  macosJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/macos-jre"+JAVA_VERSION+"/jre"
+  macosJavaVMTgz = System.env.HOME+"/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre"+JAVA_VERSION+".tar.gz"
+  windowsJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/windows-jre"+JAVA_VERSION+"/jre"
+  windowsJavaVMTgz = System.env.HOME+"/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre"+JAVA_VERSION+".tar.gz"
+  from (install4jDir) {
+    include install4jTemplate
+    rename (install4jTemplate, install4jConfFile)
+    filter(ReplaceTokens, beginToken: '', endToken: '', tokens: ['9999999999': JAVA_VERSION])
+    filter(ReplaceTokens, beginToken: '$$', endToken: '$$',
+      tokens: [
+        'JAVA_VERSION': JAVA_VERSION,
+        'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
+        'VERSION': JALVIEW_VERSION,
+        'MACOS_JAVA_VM_DIR': macosJavaVMDir,
+        'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
+        'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
+        'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
+        'INSTALL4JINFOPLISTFILEASSOCIATIONS': install4jInfoPlistFileAssociations,
+        'COPYRIGHT_MESSAGE': install4jCopyrightMessage,
+        'MACOS_BUNDLE_ID': install4jMacOSBundleId
+      ]
+    )
+    if (OSX_KEYPASS=="") {
+      filter(ReplaceTokens, beginToken: 'codeSigning macEnabled="', endToken: '"', tokens: ['true':'codeSigning macEnabled="false"'])
+      filter(ReplaceTokens, beginToken: 'runPostProcessor="true" ',endToken: 'Processor', tokens: ['post':'runPostProcessor="false" postProcessor'])
+    }
+  }
+  into install4jDir
+  outputs.files(install4jConf)
+
+  doLast {
+    // include file associations in installer
+    def installerFileAssociationsXml = file("$install4jDir/$install4jInstallerFileAssociations").text
+    ant.replaceregexp(
+      byline: false,
+      flags: "s",
+      match: '<action name="EXTENSIONS_REPLACED_BY_GRADLE".*?</action>',
+      replace: installerFileAssociationsXml,
+      file: install4jConf
+    )
+    /*
+    // include uninstaller applescript app files in dmg
+    def installerDMGUninstallerXml = file("$install4jDir/$install4jDMGUninstallerAppFiles").text
+    ant.replaceregexp(
+      byline: false,
+      flags: "s",
+      match: '<file name="UNINSTALL_OLD_JALVIEW_APP_REPLACED_IN_GRADLE" file=.*?>',
+      replace: installerDMGUninstallerXml,
+      file: install4jConf
+    )
+    */
+  }
 }
 
 task installers(type: com.install4j.gradle.Install4jTask) {
+  group = "distribution"
+  description = "Create the install4j installers"
   dependsOn getdown
-  projectFile = "$jalviewDir/$install4jResourceDir/$install4jConf"
-  variables = [majorVersion: version.substring(2, 11), build: 001]
-  destination = "$jalviewDir/$install4jBuildDir"
+  dependsOn copyInstall4jTemplate
+  projectFile = file(install4jConf)
+  println("Using projectFile "+projectFile)
+  variables = [majorVersion: version.substring(2, 11), build: 001, OSX_KEYSTORE: OSX_KEYSTORE, JSIGN_SH: JSIGN_SH]
+  destination = "$jalviewDir/$install4jBuildDir/$JAVA_VERSION"
   buildSelected = true
+
+  if (OSX_KEYPASS) {
+    macKeystorePassword=OSX_KEYPASS
+    
+  }
+  
   inputs.dir(project.ext.getdownWebsiteDir)
-  outputs.dir("$jalviewDir/$install4jBuildDir")
+  inputs.file(install4jConf)
+  inputs.dir(macosJavaVMDir)
+  inputs.dir(windowsJavaVMDir)
+  outputs.dir("$jalviewDir/$install4jBuildDir/$JAVA_VERSION")
 }
 
+clean {
+  delete install4jConf
+}