X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;fp=build.gradle;h=46f2226196ef3e80e3120e333fc25ed7ea2b90ee;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=180d4ad0b3e5a8b28c3589af2a8cfa1c0856053b;hpb=cfb79b69d9fa44595560659bd95d1d1cd27677ad;p=jalview.git

diff --git a/build.gradle b/build.gradle
index 180d4ad..46f2226 100644
--- a/build.gradle
+++ b/build.gradle
@@ -12,6 +12,7 @@ import java.security.MessageDigest
 import groovy.transform.ExternalizeMethods
 import groovy.util.XmlParser
 import groovy.xml.XmlUtil
+
 import com.vladsch.flexmark.util.ast.Node
 import com.vladsch.flexmark.html.HtmlRenderer
 import com.vladsch.flexmark.parser.Parser
@@ -40,8 +41,9 @@ plugins {
   id 'eclipse'
   id "com.diffplug.gradle.spotless" version "3.28.0"
   id 'com.github.johnrengelman.shadow' version '4.0.3'
-  id 'com.install4j.gradle' version '8.0.4'
+  id 'com.install4j.gradle' version '8.0.10'
   id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with  gradle task1 [task2 ...] taskTree
+  id 'com.palantir.git-version' version '0.12.3'
 }
 
 repositories {
@@ -57,23 +59,13 @@ def string(Object o) {
 }
 
 
-ext {
-  jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
-  jalviewDirRelativePath = jalviewDir
-
-  // local build environment properties
-  // can be "projectDir/local.properties"
-  def localProps = "${projectDir}/local.properties"
-  def propsFile = null;
-  if (file(localProps).exists()) {
-    propsFile = localProps
+def overrideProperties(String propsFileName, boolean output = false) {
+  if (propsFileName == null) {
+    return
   }
-  // or "../projectDir_local.properties"
-  def dirLocalProps = projectDir.getParent() + "/" + projectDir.getName() + "_local.properties"
-  if (file(dirLocalProps).exists()) {
-    propsFile = dirLocalProps
-  }
-  if (propsFile != null) {
+  def propsFile = file(propsFileName)
+  if (propsFile != null && propsFile.exists()) {
+    println("Using properties from file '${propsFileName}'")
     try {
       def p = new Properties()
       def localPropsFIS = new FileInputStream(propsFile)
@@ -81,18 +73,43 @@ ext {
       localPropsFIS.close()
       p.each {
         key, val -> 
-          def oldval = findProperty(key)
-          setProperty(key, val)
-          if (oldval != null) {
-            println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
+          def oldval
+          if (project.hasProperty(key)) {
+            oldval = project.findProperty(key)
+            project.setProperty(key, val)
+            if (output) {
+              println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
+            }
           } else {
-            println("Setting unknown property '${key}' with ${file(propsFile).getName()}s value '${val}'")
+            ext.setProperty(key, val)
+            if (output) {
+              println("Setting ext property '${key}' with ${file(propsFile).getName()}s value '${val}'")
+            }
           }
       }
     } catch (Exception e) {
-      System.out.println("Exception reading local.properties")
+      println("Exception reading local.properties")
+      e.printStackTrace()
     }
   }
+}
+
+ext {
+  jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
+  jalviewDirRelativePath = jalviewDir
+
+  getdownChannelName = CHANNEL.toLowerCase()
+  // default to "default". Currently only has different cosmetics for "develop", "release", "default"
+  propertiesChannelName = ["develop", "release", "test-release", "jalviewjs", "jalviewjs-release" ].contains(getdownChannelName) ? getdownChannelName : "default"
+  // Import channel_properties
+  channelDir = string("${jalviewDir}/${channel_properties_dir}/${propertiesChannelName}")
+  channelGradleProperties = string("${channelDir}/channel_gradle.properties")
+  overrideProperties(channelGradleProperties, false)
+  // local build environment properties
+  // can be "projectDir/local.properties"
+  overrideProperties("${projectDir}/local.properties", true)
+  // or "../projectDir_local.properties"
+  overrideProperties(projectDir.getParent() + "/" + projectDir.getName() + "_local.properties", true)
 
   ////  
   // Import releaseProps from the RELEASE file
@@ -146,6 +163,8 @@ ext {
   }
   */
 
+  // datestamp
+  buildDate = new Date().format("yyyyMMdd")
   // essentials
   bareSourceDir = string(source_dir)
   sourceDir = string("${jalviewDir}/${bareSourceDir}")
@@ -166,29 +185,33 @@ ext {
   //cloverTestClassesDir = cloverClassesDir
   cloverDb = string("${cloverBuildDir}/clover.db")
 
-  resourceClassesDir = useClover ? cloverClassesDir : classesDir
 
   testSourceDir = useClover ? cloverTestInstrDir : testDir
   testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
 
   getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
   buildDist = true
+  buildProperties = null
 
   // the following values might be overridden by the CHANNEL switch
-  getdownChannelName = CHANNEL.toLowerCase()
   getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
   getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
   getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
   getdownAppDistDir = getdown_app_dir_alt
-  buildProperties = string("${resourceDir}/${build_properties_file}")
+  getdownImagesDir = string("${jalviewDir}/${getdown_images_dir}")
+  getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
   reportRsyncCommand = false
   jvlChannelName = CHANNEL.toLowerCase()
   install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
-  install4jDSStore = "DS_Store-NON-RELEASE"
-  install4jDMGBackgroundImage = "jalview_dmg_background-NON-RELEASE.png"
+  install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}"
+  install4jDMGBackgroundImage = "${install4j_images_dir}/${install4j_dmg_background}"
   install4jInstallerName = "${jalview_name} Non-Release Installer"
-  install4jExecutableName = jalview_name.replaceAll("[^\\w]+", "_").toLowerCase()
+  install4jExecutableName = install4j_executable_name
   install4jExtraScheme = "jalviewx"
+  install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}")
+  install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}")
+  install4jPngIconFile = string("${install4j_images_dir}/${install4j_png_icon_file}")
+  install4jBackground = string("${install4j_images_dir}/${install4j_background}")
   switch (CHANNEL) {
 
     case "BUILD":
@@ -204,12 +227,10 @@ ext {
     install4jExtraScheme = "jalviewb"
     break
 
-    case "RELEASE":
+    case [ "RELEASE", "JALVIEWJS-RELEASE" ]:
     getdownAppDistDir = getdown_app_dir_release
     reportRsyncCommand = true
     install4jSuffix = ""
-    install4jDSStore = "DS_Store"
-    install4jDMGBackgroundImage = "jalview_dmg_background.png"
     install4jInstallerName = "${jalview_name} Installer"
     break
 
@@ -247,13 +268,11 @@ ext {
 
     case "DEVELOP":
     reportRsyncCommand = true
-    
+    getdownSetAppBaseProperty = true
     // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
-    JALVIEW_VERSION=JALVIEW_VERSION+"-develop"
+    JALVIEW_VERSION=JALVIEW_VERSION+"-d${buildDate}"
     
     install4jSuffix = "Develop"
-    install4jDSStore = "DS_Store-DEVELOP"
-    install4jDMGBackgroundImage = "jalview_dmg_background-DEVELOP.png"
     install4jExtraScheme = "jalviewd"
     install4jInstallerName = "${jalview_name} Develop Installer"
     break
@@ -267,8 +286,6 @@ ext {
     }
     JALVIEW_VERSION = JALVIEW_VERSION+"-test"
     install4jSuffix = "Test"
-    install4jDSStore = "DS_Store-TEST-RELEASE"
-    install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
     install4jExtraScheme = "jalviewt"
     install4jInstallerName = "${jalview_name} Test Installer"
     break
@@ -292,13 +309,11 @@ ext {
     }
     JALVIEW_VERSION = "TEST"
     install4jSuffix = "Test-Local"
-    install4jDSStore = "DS_Store-TEST-RELEASE"
-    install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
     install4jExtraScheme = "jalviewt"
     install4jInstallerName = "${jalview_name} Test Installer"
     break
 
-    case "LOCAL":
+    case [ "LOCAL", "JALVIEWJS" ]:
     JALVIEW_VERSION = "TEST"
     getdownAppBase = file(getdownWebsiteDir).toURI().toString()
     getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
@@ -312,7 +327,16 @@ ext {
   }
   // override getdownAppBase if requested
   if (findProperty("getdown_appbase_override") != null) {
-    getdownAppBase = string(getProperty("getdown_appbase_override"))
+    // revert to LOCAL if empty string
+    if (string(getdown_appbase_override) == "") {
+      getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+      getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+    } else if (string(getdown_appbase_override).startsWith("file://")) {
+      getdownAppBase = string(getdown_appbase_override)
+      getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+    } else {
+      getdownAppBase = string(getdown_appbase_override)
+    }
     println("Overriding getdown appbase with '${getdownAppBase}'")
   }
   // sanitise file name for jalview launcher file for this channel
@@ -348,6 +372,7 @@ ext {
                                     .replaceAll("_*-_*", "-") // collapse _-_
                                     .toLowerCase()
 
+  getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local"
   getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}")
   //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
   getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}")
@@ -358,8 +383,9 @@ ext {
   modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
   modules_runtimeClasspath = modules_compileClasspath
   */
-  gitHash = string("")
-  gitBranch = string("")
+  def details = versionDetails()
+  gitHash = details.gitHash
+  gitBranch = details.branchName
 
   println("Using a ${CHANNEL} profile.")
 
@@ -395,16 +421,16 @@ ext {
     '--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
+  } else if (JAVA_VERSION.equals("17")) {
+    JAVA_INTEGER_VERSION = string("17")
+    libDir = j17libDir
+    libDistDir = j17libDir
+    compile_source_compatibility = 17
+    compile_target_compatibility = 17
     getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
     getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
     getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
-    eclipseJavaRuntimeName = string("JavaSE-11")
+    eclipseJavaRuntimeName = string("JavaSE-17")
     /* compile without modules -- using classpath libraries
     additional_compiler_args += [
     '--module-path', modules_compileClasspath.asPath,
@@ -437,12 +463,19 @@ ext {
     install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
   }
 
+  resourceBuildDir = string("${buildDir}/resources")
+  resourcesBuildDir = string("${resourceBuildDir}/resources_build")
+  helpBuildDir = string("${resourceBuildDir}/help_build")
+  docBuildDir = string("${resourceBuildDir}/doc_build")
 
 
+  if (buildProperties == null) {
+    buildProperties = string("${resourcesBuildDir}/${build_properties_file}")
+  }
   buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
-  helpFile = string("${resourceClassesDir}/${help_dir}/help.jhm")
   helpParentDir = string("${jalviewDir}/${help_parent_dir}")
   helpSourceDir = string("${helpParentDir}/${help_dir}")
+  helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
 
 
   relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
@@ -457,6 +490,7 @@ ext {
   jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
   jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
   jalviewjsJalviewCoreHtmlFile = string("")
+  jalviewjsJalviewCoreName = string(jalviewjs_core_name)
   jalviewjsCoreClasslists = []
   jalviewjsJalviewTemplateName = string(jalviewjs_name)
   jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
@@ -480,16 +514,15 @@ sourceSets {
     }
 
     resources {
-      srcDirs resourceDir
-      srcDirs += helpParentDir
+      srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
     }
 
-    jar.destinationDir = file("${jalviewDir}/${package_dir}")
 
     compileClasspath = files(sourceSets.main.java.outputDir)
     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 
     runtimeClasspath = compileClasspath
+    runtimeClasspath += files(sourceSets.main.resources.srcDirs)
   }
 
   clover {
@@ -526,6 +559,7 @@ sourceSets {
     compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
 
     runtimeClasspath = compileClasspath
+    runtimeClasspath += files(sourceSets.test.resources.srcDirs)
   }
 
 }
@@ -546,14 +580,12 @@ eclipse {
 
   classpath {
     //defaultOutputDir = sourceSets.main.java.outputDir
-    def removeThese = []
-    configurations.each{
-      if (it.isCanBeResolved()) {
-        removeThese += it
+    configurations.each{ c->
+      if (c.isCanBeResolved()) {
+        minusConfigurations += [c]
       }
     }
 
-    minusConfigurations += removeThese
     plusConfigurations = [ ]
     file {
 
@@ -1003,64 +1035,6 @@ def getDate(format) {
 }
 
 
-task setGitVals {
-
-  doFirst {
-    def hashStdOut = new ByteArrayOutputStream()
-    def resultHash = exec {
-      commandLine "git", "rev-parse", "--short", "HEAD"
-      standardOutput = hashStdOut
-      ignoreExitValue true
-    }
-
-    def branchStdOut = new ByteArrayOutputStream()
-    def resultBranch = exec {
-      commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
-      standardOutput = branchStdOut
-      ignoreExitValue true
-    }
-
-    gitHash = resultHash.getExitValue() == 0 ? hashStdOut.toString().trim() : "NO_GIT_COMMITID_FOUND"
-    gitBranch = resultBranch.getExitValue() == 0 ? branchStdOut.toString().trim() : "NO_GIT_BRANCH_FOUND"
-  }
-
-  outputs.upToDateWhen { false }
-}
-
-
-task createBuildProperties(type: WriteProperties) {
-  group = "build"
-  description = "Create the ${buildProperties} file"
-  
-  dependsOn setGitVals
-  inputs.dir(sourceDir)
-  inputs.dir(resourceDir)
-  file(buildProperties).getParentFile().mkdirs()
-  outputFile (buildProperties)
-  // 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:"+gitHash+" ["+gitBranch+"]"
-  outputs.file(outputFile)
-}
-
-
-clean {
-  doFirst {
-    delete buildProperties
-  }
-}
-
-
-task cleanBuildingHTML(type: Delete) {
-  doFirst {
-    delete buildingHTML
-  }
-}
-
-
 def convertMdToHtml (FileTree mdFiles, File cssFile) {
   MutableDataSet options = new MutableDataSet()
 
@@ -1134,14 +1108,45 @@ def convertMdToHtml (FileTree mdFiles, File cssFile) {
 
     def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
     def htmlFile = file(htmlFilePath)
+    println("Creating ${htmlFilePath}")
     htmlFile.text = htmlText
   }
 }
 
 
+task copyDocs(type: Copy) {
+  def inputDir = "${jalviewDir}/${doc_dir}"
+  def outputDir = "${docBuildDir}/${doc_dir}"
+  from(inputDir) {
+    include('**/*.txt')
+    include('**/*.md')
+    include('**/*.html')
+    include('**/*.xml')
+    filter(ReplaceTokens,
+      beginToken: '$$',
+      endToken: '$$',
+      tokens: [
+        'Version-Rel': JALVIEW_VERSION,
+        'Year-Rel': getDate("yyyy")
+      ]
+    )
+  }
+  from(inputDir) {
+    exclude('**/*.txt')
+    exclude('**/*.md')
+    exclude('**/*.html')
+    exclude('**/*.xml')
+  }
+  into outputDir
+
+  inputs.dir(inputDir)
+  outputs.dir(outputDir)
+}
+
+
 task convertMdFiles {
-  dependsOn cleanBuildingHTML
-  def mdFiles = fileTree(dir: "${jalviewDir}/${doc_dir}", include: "*.md")
+  dependsOn copyDocs
+  def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
   def cssFile = file("${jalviewDir}/${flexmark_css}")
 
   doLast {
@@ -1156,25 +1161,21 @@ task convertMdFiles {
     def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
     htmlFiles.add(file(htmlFilePath))
   }
-  outputs.files(htmlFiles)
-}
-
 
-task syncDocs(type: Sync) {
-  dependsOn convertMdFiles
-  def syncDir = "${classesDir}/${doc_dir}"
-  from fileTree("${jalviewDir}/${doc_dir}")
-  into syncDir
+  outputs.files(htmlFiles)
 }
 
 
 task copyHelp(type: Copy) {
   def inputDir = helpSourceDir
-  def outputDir = "${resourceClassesDir}/${help_dir}"
+  def outputDir = "${helpBuildDir}/${help_dir}"
   from(inputDir) {
-    exclude '**/*.gif'
-    exclude '**/*.jpg'
-    exclude '**/*.png'
+    include('**/*.txt')
+    include('**/*.md')
+    include('**/*.html')
+    include('**/*.hs')
+    include('**/*.xml')
+    include('**/*.jhm')
     filter(ReplaceTokens,
       beginToken: '$$',
       endToken: '$$',
@@ -1185,9 +1186,12 @@ task copyHelp(type: Copy) {
     )
   }
   from(inputDir) {
-    include '**/*.gif'
-    include '**/*.jpg'
-    include '**/*.png'
+    exclude('**/*.txt')
+    exclude('**/*.md')
+    exclude('**/*.html')
+    exclude('**/*.hs')
+    exclude('**/*.xml')
+    exclude('**/*.jhm')
   }
   into outputDir
 
@@ -1197,40 +1201,119 @@ task copyHelp(type: Copy) {
 }
 
 
-task syncLib(type: Sync) {
-  def syncDir = "${resourceClassesDir}/${libDistDir}"
-  from fileTree("${jalviewDir}/${libDistDir}")
-  into syncDir
+task copyResources(type: Copy) {
+  group = "build"
+  description = "Copy (and make text substitutions in) the resources dir to the build area"
+
+  def inputDir = resourceDir
+  def outputDir = resourcesBuildDir
+  from(inputDir) {
+    include('**/*.txt')
+    include('**/*.md')
+    include('**/*.html')
+    include('**/*.xml')
+    filter(ReplaceTokens,
+      beginToken: '$$',
+      endToken: '$$',
+      tokens: [
+        'Version-Rel': JALVIEW_VERSION,
+        'Year-Rel': getDate("yyyy")
+      ]
+    )
+  }
+  from(inputDir) {
+    exclude('**/*.txt')
+    exclude('**/*.md')
+    exclude('**/*.html')
+    exclude('**/*.xml')
+  }
+  into outputDir
+
+  inputs.dir(inputDir)
+  outputs.dir(outputDir)
 }
 
+task copyChannelResources(type: Copy) {
+  dependsOn copyResources
+  group = "build"
+  description = "Copy the channel resources dir to the build resources area"
+
+  def inputDir = "${channelDir}/${resource_dir}"
+  def outputDir = resourcesBuildDir
+  from inputDir
+  into outputDir
 
-task syncResources(type: Sync) {
-  dependsOn createBuildProperties
-  from resourceDir
-  include "**/*.*"
-  into "${resourceClassesDir}"
-  preserve {
-    include "**"
+  inputs.dir(inputDir)
+  outputs.dir(outputDir)
+}
+
+task createBuildProperties(type: WriteProperties) {
+  dependsOn copyResources
+  group = "build"
+  description = "Create the ${buildProperties} file"
+  
+  inputs.dir(sourceDir)
+  inputs.dir(resourcesBuildDir)
+  outputFile (buildProperties)
+  // taking time specific comment out to allow better incremental builds
+  comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
+  //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
+  property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
+  property "VERSION", JALVIEW_VERSION
+  property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
+  if (getdownSetAppBaseProperty) {
+    property "GETDOWNAPPBASE", getdownAppBase
+    property "GETDOWNAPPDISTDIR", getdownAppDistDir
   }
+  outputs.file(outputFile)
+}
+
+task buildIndices(type: JavaExec) {
+  dependsOn copyHelp
+  classpath = sourceSets.main.compileClasspath
+  main = "com.sun.java.help.search.Indexer"
+  workingDir = "${helpBuildDir}/${help_dir}"
+  def argDir = "html"
+  args = [ argDir ]
+  inputs.dir("${workingDir}/${argDir}")
+
+  outputs.dir("${classesDir}/doc")
+  outputs.dir("${classesDir}/help")
+  outputs.file("${workingDir}/JavaHelpSearch/DOCS")
+  outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
+  outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
+  outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
+  outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
+  outputs.file("${workingDir}/JavaHelpSearch/TMAP")
+}
+
+task buildResources {
+  dependsOn copyResources
+  dependsOn copyChannelResources
+  dependsOn createBuildProperties
 }
 
 
 task prepare {
-  dependsOn syncResources
-  dependsOn syncDocs
+  dependsOn buildResources
+  dependsOn copyDocs
   dependsOn copyHelp
+  dependsOn convertMdFiles
+  dependsOn buildIndices
 }
 
 
+compileJava.dependsOn prepare
+run.dependsOn compileJava
+//run.dependsOn prepare
 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
 test {
   dependsOn prepare
-  //dependsOn compileJava ////? DELETE
 
   if (useClover) {
     dependsOn cloverClasses
    } else { //?
-     dependsOn compileJava //?
+    dependsOn compileJava //?
   }
 
   useTestNG() {
@@ -1243,7 +1326,16 @@ test {
   maxHeapSize = "1024m"
 
   workingDir = jalviewDir
-  //systemProperties 'clover.jar' System.properties.clover.jar
+  def testLaf = project.findProperty("test_laf")
+  if (testLaf != null) {
+    println("Setting Test LaF to '${testLaf}'")
+    systemProperty "laf", testLaf
+  }
+  def testHiDPIScale = project.findProperty("test_HiDPIScale")
+  if (testHiDPIScale != null) {
+    println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
+    systemProperty "sun.java2d.uiScale", testHiDPIScale
+  }
   sourceCompatibility = compile_source_compatibility
   targetCompatibility = compile_target_compatibility
   jvmArgs += additional_compiler_args
@@ -1256,24 +1348,6 @@ test {
 }
 
 
-task buildIndices(type: JavaExec) {
-  dependsOn copyHelp
-  classpath = sourceSets.main.compileClasspath
-  main = "com.sun.java.help.search.Indexer"
-  workingDir = "${classesDir}/${help_dir}"
-  def argDir = "html"
-  args = [ argDir ]
-  inputs.dir("${workingDir}/${argDir}")
-
-  outputs.dir("${classesDir}/doc")
-  outputs.dir("${classesDir}/help")
-  outputs.file("${workingDir}/JavaHelpSearch/DOCS")
-  outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
-  outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
-  outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
-  outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
-  outputs.file("${workingDir}/JavaHelpSearch/TMAP")
-}
 
 
 task compileLinkCheck(type: JavaCompile) {
@@ -1290,30 +1364,30 @@ task compileLinkCheck(type: JavaCompile) {
 
 
 task linkCheck(type: JavaExec) {
-  dependsOn prepare, compileLinkCheck
+  dependsOn prepare
+  dependsOn compileLinkCheck
 
   def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
   classpath = files("${jalviewDir}/${utils_dir}")
   main = "HelpLinksChecker"
   workingDir = jalviewDir
-  args = [ "${classesDir}/${help_dir}", "-nointernet" ]
+  args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
 
   def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
-  def errFOS = outFOS
   standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
     outFOS,
-    standardOutput)
+    System.out)
   errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
     outFOS,
-    errorOutput)
+    System.err)
 
-  inputs.dir("${classesDir}/${help_dir}")
+  inputs.dir(helpBuildDir)
   outputs.file(helpLinksCheckerOutFile)
 }
 
 // import the pubhtmlhelp target
 ant.properties.basedir = "${jalviewDir}"
-ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${help_dir}"
+ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
 ant.importBuild "${utils_dir}/publishHelp.xml"
 
 
@@ -1325,19 +1399,21 @@ task cleanPackageDir(type: Delete) {
 
 
 jar {
+  dependsOn prepare
   dependsOn linkCheck
-  dependsOn buildIndices
-  dependsOn createBuildProperties
 
   manifest {
     attributes "Main-Class": main_class,
     "Permissions": "all-permissions",
-    "Application-Name": "Jalview Desktop",
-    "Codebase": application_codebase
+    "Application-Name": install4jApplicationName,
+    "Codebase": application_codebase,
+    "Implementation-Version": JALVIEW_VERSION
   }
 
-  destinationDir = file("${jalviewDir}/${package_dir}")
-  archiveName = rootProject.name+".jar"
+  def outputDir = "${jalviewDir}/${package_dir}"
+  destinationDirectory = file(outputDir)
+  archiveFileName = rootProject.name+".jar"
+  duplicatesStrategy "EXCLUDE"
 
   exclude "cache*/**"
   exclude "*.jar"
@@ -1345,8 +1421,11 @@ jar {
   exclude "**/*.jar"
   exclude "**/*.jar.*"
 
-  inputs.dir(classesDir)
-  outputs.file("${jalviewDir}/${package_dir}/${archiveName}")
+  inputs.dir(sourceSets.main.java.outputDir)
+  sourceSets.main.resources.srcDirs.each{ dir ->
+    inputs.dir(dir)
+  }
+  outputs.file("${outputDir}/${archiveFileName}")
 }
 
 
@@ -1358,10 +1437,11 @@ task copyJars(type: Copy) {
 
 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
 task syncJars(type: Sync) {
+  dependsOn jar
   from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
   into "${jalviewDir}/${package_dir}"
   preserve {
-    include jar.archiveName
+    include jar.archiveFileName.getOrNull()
   }
 }
 
@@ -1395,8 +1475,10 @@ shadowJar {
     include("*.jar")
   }
   manifest {
-    attributes 'Implementation-Version': JALVIEW_VERSION
+    attributes "Implementation-Version": JALVIEW_VERSION,
+    "Application-Name": install4jApplicationName
   }
+  duplicatesStrategy "INCLUDE"
   mainClassName = shadow_jar_main_class
   mergeServiceFiles()
   classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
@@ -1423,7 +1505,7 @@ task getdownWebsite() {
 
     copy {
       from buildProperties
-      rename(build_properties_file, getdown_build_properties)
+      rename(file(buildProperties).getName(), getdown_build_properties)
       into getdownAppDir
     }
     getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
@@ -1439,6 +1521,14 @@ task getdownWebsite() {
     if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
       props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
     }
+    if (getdownImagesDir != null && file(getdownImagesDir).exists()) {
+      props.put("getdown_txt_ui.background_image", "${getdownImagesDir}/${getdown_background_image}")
+      props.put("getdown_txt_ui.instant_background_image", "${getdownImagesDir}/${getdown_instant_background_image}")
+      props.put("getdown_txt_ui.error_background", "${getdownImagesDir}/${getdown_error_background}")
+      props.put("getdown_txt_ui.progress_image", "${getdownImagesDir}/${getdown_progress_image}")
+      props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}")
+      props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}")
+    }
 
     props.put("getdown_txt_title", jalview_name)
     props.put("getdown_txt_ui.name", install4jApplicationName)
@@ -1487,6 +1577,18 @@ task getdownWebsite() {
         into getdownResourceDir
       }
     }
+    
+    def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
+    getdownWrapperScripts.each{ script ->
+      def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
+      if (s.exists()) {
+        copy {
+          from s
+          into "${getdownWebsiteDir}/${getdown_wrapper_script_dir}"
+        }
+        getdownTextString += "resource = ${getdown_wrapper_script_dir}/${script}\n"
+      }
+    }
 
     def codeFiles = []
     fileTree(file(package_dir)).each{ f ->
@@ -1527,6 +1629,11 @@ task getdownWebsite() {
     //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
     getdownTextString += "resource = ${getdown_launcher_new}\n"
     getdownTextString += "class = ${main_class}\n"
+    // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
+    if (getdownSetAppBaseProperty) {
+      getdownTextString += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}\n"
+      getdownTextString += "jvmarg = -Dgetdownappbase=${getdownAppBase}\n"
+    }
 
     def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
     getdown_txt.write(getdownTextString)
@@ -1535,12 +1642,14 @@ task getdownWebsite() {
     def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}")
     launchJvl.write("appbase=${getdownAppBase}")
 
+    // files going into the getdown website dir: getdown-launcher.jar
     copy {
       from getdownLauncher
       rename(file(getdownLauncher).getName(), getdown_launcher_new)
       into getdownWebsiteDir
     }
 
+    // files going into the getdown website dir: getdown-launcher(-local).jar
     copy {
       from getdownLauncher
       if (file(getdownLauncher).getName() != getdown_launcher) {
@@ -1549,23 +1658,26 @@ task getdownWebsite() {
       into getdownWebsiteDir
     }
 
+    // files going into the getdown website dir: ./install dir and files
     if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
       copy {
         from getdown_txt
         from getdownLauncher
-        from "${getdownWebsiteDir}/${getdown_build_properties}"
+        from "${getdownAppDir}/${getdown_build_properties}"
         if (file(getdownLauncher).getName() != getdown_launcher) {
           rename(file(getdownLauncher).getName(), getdown_launcher)
         }
         into getdownInstallDir
       }
 
+      // and make a copy in the getdown files dir (these are not downloaded by getdown)
       copy {
         from getdownInstallDir
         into getdownFilesInstallDir
       }
     }
 
+    // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
     copy {
       from getdown_txt
       from launchJvl
@@ -1577,6 +1689,7 @@ task getdownWebsite() {
       into getdownFilesDir
     }
 
+    // and ./resources (not all downloaded by getdown)
     copy {
       from getdownResourceDir
       into "${getdownFilesDir}/${getdown_resource_dir}"
@@ -1741,11 +1854,6 @@ task copyInstall4jTemplate {
       }
     }
 
-    // remove the "Uninstall Old Jalview (optional)" symlink from DMG for non-release DS_Stores
-    if (! (CHANNEL == "RELEASE" || CHANNEL == "TEST-RELEASE" ) ) {
-      def symlink = install4jConfigXml.'**'.topLevelFiles.symlink.find { sl -> sl.'@name' == "Uninstall Old Jalview (optional).app" }
-      symlink.parent().remove(symlink)
-    }
 
     // write install4j file
     install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
@@ -1763,7 +1871,6 @@ clean {
 task installers(type: com.install4j.gradle.Install4jTask) {
   group = "distribution"
   description = "Create the install4j installers"
-  dependsOn setGitVals
   dependsOn getdown
   dependsOn copyInstall4jTemplate
 
@@ -1788,6 +1895,8 @@ task installers(type: com.install4j.gradle.Install4jTask) {
     'JALVIEW_APPLICATION_NAME': install4jApplicationName,
     'JALVIEW_DIR': "../..",
     'OSX_KEYSTORE': OSX_KEYSTORE,
+    'OSX_APPLEID': OSX_APPLEID,
+    'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
     'JSIGN_SH': JSIGN_SH,
     'JRE_DIR': getdown_app_dir_java,
     'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
@@ -1807,8 +1916,12 @@ task installers(type: com.install4j.gradle.Install4jTask) {
     'BUNDLE_ID': install4jBundleId,
     'INTERNAL_ID': install4jInternalId,
     'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
-    'MACOS_DS_STORE': install4jDSStore,
+    'MACOS_DMG_DS_STORE': install4jDMGDSStore,
     'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
+    'WRAPPER_LINK': getdownWrapperLink,
+    'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
+    'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
+    'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
     'INSTALLER_NAME': install4jInstallerName,
     'INSTALL4J_UTILS_DIR': install4j_utils_dir,
     'GETDOWN_WEBSITE_DIR': getdown_website_dir,
@@ -1824,6 +1937,10 @@ task installers(type: com.install4j.gradle.Install4jTask) {
     'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
     'EXECUTABLE_NAME': install4jExecutableName,
     'EXTRA_SCHEME': install4jExtraScheme,
+    'MAC_ICONS_FILE': install4jMacIconsFile,
+    'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
+    'PNG_ICON_FILE': install4jPngIconFile,
+    'BACKGROUND': install4jBackground,
   ]
 
   //println("INSTALL4J VARIABLES:")
@@ -1835,15 +1952,25 @@ task installers(type: com.install4j.gradle.Install4jTask) {
   if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
     faster = true
     disableSigning = true
+    disableNotarization = true
   }
 
   if (OSX_KEYPASS) {
     macKeystorePassword = OSX_KEYPASS
+  } 
+  
+  if (OSX_ALTOOLPASS) {
+    appleIdPassword = OSX_ALTOOLPASS
+    disableNotarization = false
+  } else {
+    disableNotarization = true
   }
 
   doFirst {
     println("Using projectFile "+projectFile)
+    if (!disableNotarization) { println("Will notarize OSX App DMG") }
   }
+  //verbose=true
 
   inputs.dir(getdownWebsiteDir)
   inputs.file(install4jConfFile)
@@ -1864,17 +1991,12 @@ spotless {
 task sourceDist(type: Tar) {
   group "distribution"
   description "Create a source .tar.gz file for distribution"
-  
-  dependsOn convertMdFiles
 
+  dependsOn createBuildProperties
+  dependsOn convertMdFiles
   def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
   def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
-  // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09]
-  try {
-    archiveFileName = outputFileName
-  } catch (Exception e) {
-    archiveName = outputFileName
-  }
+  archiveFileName = outputFileName
   
   compression Compression.GZIP
   
@@ -1957,6 +2079,13 @@ task sourceDist(type: Tar) {
 //    exclude(EXCLUDE_FILES)
 //    exclude(PROCESS_FILES)
 //  }
+  from(file(buildProperties).getParent()) {
+    include(file(buildProperties).getName())
+    rename(file(buildProperties).getName(), "build_properties")
+    filter({ line ->
+      line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
+    })
+  }
 }
 
 
@@ -1964,7 +2093,7 @@ task helppages {
   dependsOn copyHelp
   dependsOn pubhtmlhelp
   
-  inputs.dir("${classesDir}/${help_dir}")
+  inputs.dir("${helpBuildDir}/${help_dir}")
   outputs.dir("${buildDir}/distributions/${help_dir}")
 }
 
@@ -2001,8 +2130,6 @@ task jalviewjsEnableAltFileProperty(type: WriteProperties) {
     property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
   }
 }
-
-
 task jalviewjsSetEclipseWorkspace {
   def propKey = "jalviewjs_eclipse_workspace"
   def propVal = null
@@ -2266,13 +2393,17 @@ task jalviewjsSyncAllLibs (type: Sync) {
   preserve {
     include "**"
   }
+  // should this be exclude really ?
+  duplicatesStrategy "INCLUDE"
   outputs.files outputFiles
   inputs.files inputFiles
 }
 
 
 task jalviewjsSyncResources (type: Sync) {
-  def inputFiles = fileTree(dir: resourceDir)
+  dependsOn buildResources
+
+  def inputFiles = fileTree(dir: resourcesBuildDir)
   def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
 
   from inputFiles
@@ -2418,12 +2549,12 @@ DEBUG: ${eclipseDebug}
         new org.apache.tools.ant.util.TeeOutputStream(
           logOutFOS,
           stdout),
-        standardOutput)
+        System.out)
       errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
         new org.apache.tools.ant.util.TeeOutputStream(
           logErrFOS,
           stderr),
-        errorOutput)
+        System.err)
     } else {
       standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
         logOutFOS,
@@ -2511,7 +2642,7 @@ def jalviewjsCallCore(String name, FileCollection list, String prefixFile, Strin
           new org.apache.tools.ant.util.TeeOutputStream(
             logErrFOS,
             stderr),
-          errorOutput)
+          System.err)
     } else {
       standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
         logOutFOS,
@@ -2555,6 +2686,10 @@ task jalviewjsBuildAllCores {
     ]
   }
 
+  // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
+  //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
+  classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
+
   jalviewjsCoreClasslists = []
 
   classlistFiles.each {
@@ -2577,8 +2712,8 @@ task jalviewjsBuildAllCores {
     }
     def list = fileTree(dir: j2sDir, includes: filelist)
 
-    def jsfile = "${outputDir}/core_${name}.js"
-    def zjsfile = "${outputDir}/core_${name}.z.js"
+    def jsfile = "${outputDir}/core${name}.js"
+    def zjsfile = "${outputDir}/core${name}.z.js"
 
     jalviewjsCoreClasslists += [
       'jsfile': jsfile,
@@ -2593,8 +2728,21 @@ task jalviewjsBuildAllCores {
     outputs.file(zjsfile)
   }
   
+  // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
+  def stevesoftClasslistName = "_stevesoft"
+  def stevesoftClasslist = [
+    'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
+    'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
+    'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
+    'name': stevesoftClasslistName
+  ]
+  jalviewjsCoreClasslists += stevesoftClasslist
+  inputs.files(stevesoftClasslist['list'])
+  outputs.file(stevesoftClasslist['jsfile'])
+  outputs.file(stevesoftClasslist['zjsfile'])
+
   // _all core
-  def allClasslistName = "all"
+  def allClasslistName = "_all"
   def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
   allJsFiles += fileTree(
     dir: libJ2sDir,
@@ -2617,8 +2765,8 @@ task jalviewjsBuildAllCores {
     ]
   )
   def allClasslist = [
-    'jsfile': "${outputDir}/core_${allClasslistName}.js",
-    'zjsfile': "${outputDir}/core_${allClasslistName}.z.js",
+    'jsfile': "${outputDir}/core${allClasslistName}.js",
+    'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
     'list': allJsFiles,
     'name': allClasslistName
   ]
@@ -2783,11 +2931,7 @@ task jalviewjsSiteTar(type: Tar) {
   description "Creates a tar.gz file for the website"
   dependsOn jalviewjsBuildSite
   def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
-  try {
-    archiveFileName = outputFilename
-  } catch (Exception e) {
-    archiveName = outputFilename
-  }
+  archiveFileName = outputFilename
 
   compression Compression.GZIP
 
@@ -2805,7 +2949,13 @@ task jalviewjsServer {
   def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
   doLast {
 
-    SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory()
+    def factory
+    try {
+      def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
+      factory = f.newInstance()
+    } catch (ClassNotFoundException e) {
+      throw new GradleException("Unable to create SimpleHttpFileServerFactory")
+    }
     def port = Integer.valueOf(jalviewjs_server_port)
     def start = port
     def running = false