X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=build.gradle;h=b2e9af101301ee97df46e743b3c2b6d154dd9945;hp=05fddc0563413be03c336b14a37ebb7bbed56933;hb=39b4859e1a1b011af5d06058461db4d075acb578;hpb=f6131ae7c9734cfcba48a29a9e34da12e54a8532

diff --git a/build.gradle b/build.gradle
index 05fddc0..b2e9af1 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1,3 +1,6 @@
+/* Convention for properties.  Read from gradle.properties, use lower_case_underlines for property names.
+ * For properties set within build.gradle, use camelCaseNoSpace.
+ */
 import org.apache.tools.ant.filters.ReplaceTokens
 import org.gradle.internal.os.OperatingSystem
 import org.gradle.plugins.ide.eclipse.model.Output
@@ -7,18 +10,21 @@ import groovy.transform.ExternalizeMethods
 import groovy.util.XmlParser
 import groovy.xml.XmlUtil
 
+
 buildscript {
-  dependencies {
-    classpath 'org.openclover:clover:4.3.1'
+  repositories {
+    mavenCentral()
+    mavenLocal()
   }
 }
 
+
 plugins {
   id 'java'
   id 'application'
   id 'eclipse'
   id 'com.github.johnrengelman.shadow' version '4.0.3'
-  id 'com.install4j.gradle' version '8.0.2'
+  id 'com.install4j.gradle' version '8.0.4'
   id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with  gradle task1 [task2 ...] taskTree
 }
 
@@ -26,12 +32,6 @@ repositories {
   jcenter()
   mavenCentral()
   mavenLocal()
-  flatDir {
-    dirs gradlePluginsDir
-  }
-}
-
-dependencies {
 }
 
 
@@ -46,11 +46,21 @@ ext {
   jalviewDirRelativePath = jalviewDir
 
   // local build environment properties
-  def localProps = "${jalviewDirAbsolutePath}/local.properties"
+  // can be "projectDir/local.properties"
+  def localProps = "${projectDir}/local.properties"
+  def propsFile = null;
   if (file(localProps).exists()) {
+    propsFile = localProps
+  }
+  // or "../projectDir_local.properties"
+  def dirLocalProps = projectDir.getParent() + "/" + projectDir.getName() + "_local.properties"
+  if (file(dirLocalProps).exists()) {
+    propsFile = dirLocalProps
+  }
+  if (propsFile != null) {
     try {
       def p = new Properties()
-      def localPropsFIS = new FileInputStream(localProps)
+      def localPropsFIS = new FileInputStream(propsFile)
       p.load(localPropsFIS)
       localPropsFIS.close()
       p.each {
@@ -58,9 +68,9 @@ ext {
           def oldval = findProperty(key)
           setProperty(key, val)
           if (oldval != null) {
-            println("Overriding property '${key}' ('${oldval}') with local.properties value '${val}'")
+            println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
           } else {
-            println("Setting unknown property '${key}' with local.properties value '${val}'")
+            println("Setting unknown property '${key}' with ${file(propsFile).getName()}s value '${val}'")
           }
       }
     } catch (Exception e) {
@@ -68,6 +78,26 @@ ext {
     }
   }
 
+  ////  
+  // Import releaseProps from the RELEASE file
+  // or a file specified via JALVIEW_RELEASE_FILE if defined
+  // Expect jalview.version and target release branch in jalview.release        
+  def releaseProps = new Properties();
+  def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
+  def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
+  try {
+    (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream { 
+     releaseProps.load(it)
+    }
+  } catch (Exception fileLoadError) {
+    throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
+  }
+  ////
+  // Set JALVIEW_VERSION if it is not already set
+  if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
+    JALVIEW_VERSION = releaseProps.get("jalview.version")
+  }
+  
   // this property set when running Eclipse headlessly
   j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
   // this property set by Eclipse
@@ -100,20 +130,25 @@ ext {
   sourceDir = string("${jalviewDir}/${bareSourceDir}")
   resourceDir = string("${jalviewDir}/${resource_dir}")
   bareTestSourceDir = string(test_source_dir)
-  testSourceDir = string("${jalviewDir}/${bareTestSourceDir}")
+  testDir = string("${jalviewDir}/${bareTestSourceDir}")
 
-  // clover
-  cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}")
   classesDir = string("${jalviewDir}/${classes_dir}")
-  if (clover.equals("true")) {
-    use_clover = true
-    classesDir = string("${buildDir}/${cloverClassesDir}")
-  } else {
-    use_clover = false
-    classesDir = string("${jalviewDir}/${classes_dir}")
-  }
 
-  classes = classesDir
+  // clover
+  useClover = clover.equals("true")
+  cloverBuildDir = "${buildDir}/clover"
+  cloverInstrDir = file("${cloverBuildDir}/clover-instr")
+  cloverClassesDir = file("${cloverBuildDir}/clover-classes")
+  cloverReportDir = file("${buildDir}/reports/clover")
+  cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
+  cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
+  //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}/${JAVA_VERSION}")
   buildDist = true
@@ -125,7 +160,14 @@ ext {
   getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
   getdownAppDistDir = getdown_app_dir_alt
   buildProperties = string("${classesDir}/${build_properties_file}")
-  reportRsyncCmd = false
+  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"
+  install4jInstallerName = "${jalview_name} Non-Release Installer"
+  install4jExecutableName = jalview_name.replaceAll("[^\\w]+", "_").toLowerCase()
+  install4jExtraScheme = "jalviewx"
   switch (CHANNEL) {
 
     case "BUILD":
@@ -133,48 +175,79 @@ ext {
     getdown_channel_base = bamboo_channelbase
     getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}")
     getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
+    jvlChannelName += "_${getdownChannelName}"
+    // automatically add the test group Not-bamboo for exclusion 
+    if ("".equals(testng_excluded_groups)) { 
+      testng_excluded_groups = "Not-bamboo"
+    }
+    install4jExtraScheme = "jalviewb"
     break
 
     case "RELEASE":
     getdownAppDistDir = getdown_app_dir_release
     reportRsyncCommand = true
+    install4jSuffix = ""
+    install4jDSStore = "DS_Store"
+    install4jDMGBackgroundImage = "jalview_dmg_background.png"
+    install4jInstallerName = "${jalview_name} Installer"
     break
 
     case "ARCHIVE":
     getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
     getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
     getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
-    if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
+    if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
       throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
     } else {
-      packageDir = string("${ARCHIVEDIR}/${packageDir}")
+      package_dir = string("${ARCHIVEDIR}/${package_dir}")
       buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
       buildDist = false
     }
     reportRsyncCommand = true
+    install4jExtraScheme = "jalviewa"
     break
 
     case "ARCHIVELOCAL":
     getdownChannelName = string("archive/${JALVIEW_VERSION}")
     getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
     getdownAppBase = file(getdownWebsiteDir).toURI().toString()
-    if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
+    if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
       throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
     } else {
-      packageDir = string("${ARCHIVEDIR}/${packageDir}")
+      package_dir = string("${ARCHIVEDIR}/${package_dir}")
       buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
       buildDist = false
     }
     reportRsyncCommand = true
     getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+    install4jSuffix = "Archive"
+    install4jExtraScheme = "jalviewa"
     break
 
     case "DEVELOP":
     reportRsyncCommand = true
+    
+    // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
+    JALVIEW_VERSION=JALVIEW_VERSION+"-develop"
+    
+    install4jSuffix = "Develop"
+    install4jDSStore = "DS_Store-DEVELOP"
+    install4jDMGBackgroundImage = "jalview_dmg_background-DEVELOP.png"
+    install4jExtraScheme = "jalviewd"
+    install4jInstallerName = "${jalview_name} Develop Installer"
     break
 
     case "TEST-RELEASE":
     reportRsyncCommand = true
+    
+    // TEST-RELEASE is usually associated with a Jalview release series so set the version
+    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
 
     case ~/^SCRATCH(|-[-\w]*)$/:
@@ -182,6 +255,7 @@ ext {
     getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
     getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
     reportRsyncCommand = true
+    install4jSuffix = "Scratch"
     break
 
     case "TEST-LOCAL":
@@ -191,11 +265,18 @@ ext {
       getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
       getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
     }
+    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":
     getdownAppBase = file(getdownWebsiteDir).toURI().toString()
     getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+    install4jExtraScheme = "jalviewl"
     break
 
     default: // something wrong specified
@@ -208,6 +289,38 @@ ext {
     getdownAppBase = string(getProperty("getdown_appbase_override"))
     println("Overriding getdown appbase with '${getdownAppBase}'")
   }
+  // sanitise file name for jalview launcher file for this channel
+  jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_")
+  // install4j application and folder names
+  if (install4jSuffix == "") {
+    install4jApplicationName = "${jalview_name}"
+    install4jBundleId = "${install4j_bundle_id}"
+    install4jWinApplicationId = install4j_release_win_application_id
+  } else {
+    install4jApplicationName = "${jalview_name} ${install4jSuffix}"
+    install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase()
+    // add int hash of install4jSuffix to the last part of the application_id
+    def id = install4j_release_win_application_id
+    def idsplitreverse = id.split("-").reverse()
+    idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode()
+    install4jWinApplicationId = idsplitreverse.reverse().join("-")
+  }
+  // sanitise folder and id names
+  // install4jApplicationFolder = e.g. "Jalview Build"
+  install4jApplicationFolder = install4jApplicationName
+                                    .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \
+                                    .replaceAll("_+", "_") // collapse __
+  install4jInternalId = install4jApplicationName
+                                    .replaceAll(" ","_")
+                                    .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
+                                    .replaceAll("_+", "") // collapse __
+                                    //.replaceAll("_*-_*", "-") // collapse _-_
+  install4jUnixApplicationFolder = install4jApplicationName
+                                    .replaceAll(" ","_")
+                                    .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
+                                    .replaceAll("_+", "_") // collapse __
+                                    .replaceAll("_*-_*", "-") // collapse _-_
+                                    .toLowerCase()
 
   getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}")
   //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
@@ -231,6 +344,7 @@ ext {
     //libDir = j8libDir
     libDir = j11libDir
     libDistDir = j8libDir
+    digestonlyDir = j8digestonlyDir
     compile_source_compatibility = 1.8
     compile_target_compatibility = 1.8
     // these are getdown.txt properties defined dependent on the JAVA_VERSION
@@ -244,6 +358,7 @@ ext {
     JAVA_INTEGER_VERSION = string("11")
     libDir = j11libDir
     libDistDir = j11libDir
+    digestonlyDir = j11digestonlyDir
     compile_source_compatibility = 11
     compile_target_compatibility = 11
     getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
@@ -300,8 +415,8 @@ ext {
 
 
 
-  buildingHTML = string("${jalviewDir}/${docDir}/building.html")
-  helpFile = string("${classesDir}/${help_dir}/help.jhm")
+  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}")
 
@@ -344,10 +459,9 @@ sourceSets {
       srcDirs += helpParentDir
     }
 
-    jar.destinationDir = file("${jalviewDir}/${packageDir}")
+    jar.destinationDir = file("${jalviewDir}/${package_dir}")
 
     compileClasspath = files(sourceSets.main.java.outputDir)
-    //compileClasspath += files(sourceSets.main.resources.srcDirs)
     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 
     runtimeClasspath = compileClasspath
@@ -355,18 +469,19 @@ sourceSets {
 
   clover {
     java {
-      srcDirs = [ cloverInstrDir ]
-      outputDir = file("${buildDir}/${cloverClassesDir}")
+      srcDirs cloverInstrDir
+      outputDir = 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 = files( sourceSets.clover.java.outputDir )
+    //compileClasspath += files( testClassesDir )
     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+    compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
+    compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
 
     runtimeClasspath = compileClasspath
   }
@@ -374,44 +489,24 @@ sourceSets {
   test {
     java {
       srcDirs testSourceDir
-      outputDir = file("${jalviewDir}/${testOutputDir}")
+      outputDir = file(testClassesDir)
     }
 
     resources {
-      srcDirs = sourceSets.main.resources.srcDirs
+      srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
     }
 
     compileClasspath = files( sourceSets.test.java.outputDir )
-
-    if (use_clover) {
-      compileClasspath += sourceSets.clover.compileClasspath
-    } else {
-      compileClasspath += files(sourceSets.main.java.outputDir)
-    }
-
-    compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
-    compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testnglibs", include: ["**/*.jar"])
-    compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testlibs", include: ["**/*.jar"])
+    compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
+    compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
 
     runtimeClasspath = compileClasspath
   }
-}
 
-
-// clover bits
-dependencies {
-  if (use_clover) {
-    cloverCompile 'org.openclover:clover:4.3.1'
-    testCompile 'org.openclover:clover:4.3.1'
-  }
 }
 
 
-configurations {
-  cloverRuntime
-  cloverRuntime.extendsFrom cloverCompile
-}
-
+// eclipse project and settings files creation, also used by buildship
 eclipse {
   project {
     name = eclipse_project_name
@@ -546,85 +641,244 @@ eclipse {
 }
 
 
-task cloverInstr() {
-  // only instrument source, we build test classes as normal
-  inputs.files files (sourceSets.main.allJava) // , fileTree(dir: testSourceDir, include: ["**/*.java"]))
-  outputs.dir cloverInstrDir
+// clover bits
+
+
+task cleanClover {
+  doFirst {
+    delete cloverBuildDir
+    delete cloverReportDir
+  }
+}
+
+
+task cloverInstrJava(type: JavaExec) {
+  group = "Verification"
+  description = "Create clover instrumented source java files"
+
+  dependsOn cleanClover
+
+  inputs.files(sourceSets.main.allJava)
+  outputs.dir(cloverInstrDir)
+
+  //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
+  classpath = sourceSets.clover.compileClasspath
+  main = "com.atlassian.clover.CloverInstr"
+
+  def argsList = [
+    "--encoding",
+    "UTF-8",
+    "--initstring",
+    cloverDb,
+    "--destdir",
+    cloverInstrDir.getPath(),
+  ]
+  def srcFiles = sourceSets.main.allJava.files
+  argsList.addAll(
+    srcFiles.collect(
+      { file -> file.absolutePath }
+    )
+  )
+  args argsList.toArray()
 
   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)
+    println("Clover: About to instrument "+srcFiles.size() +" files")
   }
 }
 
 
-task cloverReport {
+task cloverInstrTests(type: JavaExec) {
   group = "Verification"
-    description = "Createst the Clover report"
-    inputs.dir "${buildDir}/clover"
-    outputs.dir "${reportsDir}/clover"
-    onlyIf {
-      file("${buildDir}/clover/clover.db").exists()
-    }
+  description = "Create clover instrumented source test files"
+
+  dependsOn cleanClover
+
+  inputs.files(testDir)
+  outputs.dir(cloverTestInstrDir)
+
+  classpath = sourceSets.clover.compileClasspath
+  main = "com.atlassian.clover.CloverInstr"
+
+  def argsList = [
+    "--encoding",
+    "UTF-8",
+    "--initstring",
+    cloverDb,
+    "--srcdir",
+    testDir,
+    "--destdir",
+    cloverTestInstrDir.getPath(),
+  ]
+  args argsList.toArray()
+
   doFirst {
-    def argsList = ["--initstring", "${buildDir}/clover/clover.db",
-    "-o", "${reportsDir}/clover"]
-    String[] args = argsList.toArray()
-    com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
+    delete cloverTestInstrDir
+    println("Clover: About to instrument test files")
+  }
+}
+
+
+task cloverInstr {
+  group = "Verification"
+  description = "Create clover instrumented all source files"
+
+  dependsOn cloverInstrJava
+  dependsOn cloverInstrTests
+}
+
+
+cloverClasses.dependsOn cloverInstr
+
 
-    // 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)
+task cloverConsoleReport(type: JavaExec) {
+  group = "Verification"
+  description = "Creates clover console report"
+
+  onlyIf {
+    file(cloverDb).exists()
+  }
+
+  inputs.dir cloverClassesDir
+
+  classpath = sourceSets.clover.runtimeClasspath
+  main = "com.atlassian.clover.reporters.console.ConsoleReporter"
+
+  if (cloverreport_mem.length() > 0) {
+    maxHeapSize = cloverreport_mem
   }
+  if (cloverreport_jvmargs.length() > 0) {
+    jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
+  }
+
+  def argsList = [
+    "--alwaysreport",
+    "--initstring",
+    cloverDb,
+    "--unittests"
+  ]
+
+  args argsList.toArray()
 }
-// end clover bits
 
 
-compileJava {
+task cloverHtmlReport(type: JavaExec) {
+  group = "Verification"
+  description = "Creates clover HTML report"
+
+  onlyIf {
+    file(cloverDb).exists()
+  }
+
+  def cloverHtmlDir = cloverReportDir
+  inputs.dir cloverClassesDir
+  outputs.dir cloverHtmlDir
+
+  classpath = sourceSets.clover.runtimeClasspath
+  main = "com.atlassian.clover.reporters.html.HtmlReporter"
+
+  if (cloverreport_mem.length() > 0) {
+    maxHeapSize = cloverreport_mem
+  }
+  if (cloverreport_jvmargs.length() > 0) {
+    jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
+  }
+
+  def argsList = [
+    "--alwaysreport",
+    "--initstring",
+    cloverDb,
+    "--outputdir",
+    cloverHtmlDir
+  ]
+
+  if (cloverreport_html_options.length() > 0) {
+    argsList += cloverreport_html_options.split(" ")
+  }
+
+  args argsList.toArray()
+}
+
+
+task cloverXmlReport(type: JavaExec) {
+  group = "Verification"
+  description = "Creates clover XML report"
+
+  onlyIf {
+    file(cloverDb).exists()
+  }
+
+  def cloverXmlFile = "${cloverReportDir}/clover.xml"
+  inputs.dir cloverClassesDir
+  outputs.file cloverXmlFile
+
+  classpath = sourceSets.clover.runtimeClasspath
+  main = "com.atlassian.clover.reporters.xml.XMLReporter"
+
+  if (cloverreport_mem.length() > 0) {
+    maxHeapSize = cloverreport_mem
+  }
+  if (cloverreport_jvmargs.length() > 0) {
+    jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
+  }
+
+  def argsList = [
+    "--alwaysreport",
+    "--initstring",
+    cloverDb,
+    "--outfile",
+    cloverXmlFile
+  ]
+
+  if (cloverreport_xml_options.length() > 0) {
+    argsList += cloverreport_xml_options.split(" ")
+  }
+
+  args argsList.toArray()
+}
+
+
+task cloverReport {
+  group = "Verification"
+  description = "Creates clover reports"
+
+  dependsOn cloverXmlReport
+  dependsOn cloverHtmlReport
+}
+
+
+compileCloverJava {
 
   doFirst {
     sourceCompatibility = compile_source_compatibility
     targetCompatibility = compile_target_compatibility
-    options.compilerArgs = additional_compiler_args
+    options.compilerArgs += additional_compiler_args
     print ("Setting target compatibility to "+targetCompatibility+"\n")
   }
-
+  //classpath += configurations.cloverRuntime
 }
+// end clover bits
 
 
-compileTestJava {
-  if (use_clover) {
-    dependsOn compileCloverJava
-    classpath += configurations.cloverRuntime
-  } else {
-    classpath += sourceSets.main.runtimeClasspath
-  }
+compileJava {
+
   doFirst {
     sourceCompatibility = compile_source_compatibility
     targetCompatibility = compile_target_compatibility
     options.compilerArgs = additional_compiler_args
     print ("Setting target compatibility to "+targetCompatibility+"\n")
   }
-}
 
+}
 
-compileCloverJava {
 
+compileTestJava {
   doFirst {
     sourceCompatibility = compile_source_compatibility
     targetCompatibility = compile_target_compatibility
-    options.compilerArgs += additional_compiler_args
+    options.compilerArgs = additional_compiler_args
     print ("Setting target compatibility to "+targetCompatibility+"\n")
   }
-  classpath += configurations.cloverRuntime
 }
 
 
@@ -636,9 +890,9 @@ clean {
 
 
 cleanTest {
+  dependsOn cleanClover
   doFirst {
     delete sourceSets.test.java.outputDir
-    delete cloverInstrDir
   }
 }
 
@@ -697,8 +951,8 @@ task cleanBuildingHTML(type: Delete) {
 
 task convertBuildingMD(type: Exec) {
   dependsOn cleanBuildingHTML
-  def buildingMD = "${jalviewDir}/${docDir}/building.md"
-  def css = "${jalviewDir}/${docDir}/github.css"
+  def buildingMD = "${jalviewDir}/${doc_dir}/building.md"
+  def css = "${jalviewDir}/${doc_dir}/github.css"
 
   def pandoc = null
   pandoc_exec.split(",").each {
@@ -740,8 +994,8 @@ clean {
 
 task syncDocs(type: Sync) {
   dependsOn convertBuildingMD
-  def syncDir = "${classesDir}/${docDir}"
-  from fileTree("${jalviewDir}/${docDir}")
+  def syncDir = "${resourceClassesDir}/${doc_dir}"
+  from fileTree("${jalviewDir}/${doc_dir}")
   into syncDir
 
 }
@@ -749,7 +1003,7 @@ task syncDocs(type: Sync) {
 
 task copyHelp(type: Copy) {
   def inputDir = helpSourceDir
-  def outputDir = "${classesDir}/${help_dir}"
+  def outputDir = "${resourceClassesDir}/${help_dir}"
   from(inputDir) {
     exclude '**/*.gif'
     exclude '**/*.jpg'
@@ -777,7 +1031,7 @@ task copyHelp(type: Copy) {
 
 
 task syncLib(type: Sync) {
-  def syncDir = "${classesDir}/${libDistDir}"
+  def syncDir = "${resourceClassesDir}/${libDistDir}"
   from fileTree("${jalviewDir}/${libDistDir}")
   into syncDir
 }
@@ -786,7 +1040,7 @@ task syncLib(type: Sync) {
 task syncResources(type: Sync) {
   from resourceDir
   include "**/*.*"
-  into "${classesDir}"
+  into "${resourceClassesDir}"
   preserve {
     include "**"
   }
@@ -803,27 +1057,44 @@ task prepare {
 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
 test {
   dependsOn prepare
-  dependsOn compileJava
-  if (use_clover) {
-    dependsOn cloverInstr
-  }
+  //dependsOn compileJava ////? DELETE
 
-  if (use_clover) {
-    print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
+  if (useClover) {
+    dependsOn cloverClasses
+   } else { //?
+     dependsOn compileJava //?
   }
 
   useTestNG() {
-    includeGroups testngGroups
+    includeGroups testng_groups
+    excludeGroups testng_excluded_groups
     preserveOrder true
     useDefaultListeners=true
   }
 
+  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
 
+  doFirst {
+    if (useClover) {
+      println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
+    }
+  }
 }
 
 
@@ -849,22 +1120,22 @@ task buildIndices(type: JavaExec) {
 
 task compileLinkCheck(type: JavaCompile) {
   options.fork = true
-  classpath = files("${jalviewDir}/${utilsDir}")
-  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")
+  classpath = files("${jalviewDir}/${utils_dir}")
+  destinationDir = file("${jalviewDir}/${utils_dir}")
+  source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
+
+  inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
+  inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
+  outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
+  outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
 }
 
 
 task linkCheck(type: JavaExec) {
   dependsOn prepare, compileLinkCheck
 
-  def helpLinksCheckerOutFile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.out")
-  classpath = files("${jalviewDir}/${utilsDir}")
+  def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
+  classpath = files("${jalviewDir}/${utils_dir}")
   main = "HelpLinksChecker"
   workingDir = jalviewDir
   args = [ "${classesDir}/${help_dir}", "-nointernet" ]
@@ -885,12 +1156,12 @@ task linkCheck(type: JavaExec) {
 // import the pubhtmlhelp target
 ant.properties.basedir = "${jalviewDir}"
 ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${help_dir}"
-ant.importBuild "${utilsDir}/publishHelp.xml"
+ant.importBuild "${utils_dir}/publishHelp.xml"
 
 
 task cleanPackageDir(type: Delete) {
   doFirst {
-    delete fileTree(dir: "${jalviewDir}/${packageDir}", include: "*.jar")
+    delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
   }
 }
 
@@ -900,13 +1171,13 @@ jar {
   dependsOn createBuildProperties
 
   manifest {
-    attributes "Main-Class": mainClass,
+    attributes "Main-Class": main_class,
     "Permissions": "all-permissions",
     "Application-Name": "Jalview Desktop",
     "Codebase": application_codebase
   }
 
-  destinationDir = file("${jalviewDir}/${packageDir}")
+  destinationDir = file("${jalviewDir}/${package_dir}")
   archiveName = rootProject.name+".jar"
 
   exclude "cache*/**"
@@ -916,20 +1187,20 @@ jar {
   exclude "**/*.jar.*"
 
   inputs.dir(classesDir)
-  outputs.file("${jalviewDir}/${packageDir}/${archiveName}")
+  outputs.file("${jalviewDir}/${package_dir}/${archiveName}")
 }
 
 
 task copyJars(type: Copy) {
   from fileTree(dir: classesDir, include: "**/*.jar").files
-  into "${jalviewDir}/${packageDir}"
+  into "${jalviewDir}/${package_dir}"
 }
 
 
 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
 task syncJars(type: Sync) {
   from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
-  into "${jalviewDir}/${packageDir}"
+  into "${jalviewDir}/${package_dir}"
   preserve {
     include jar.archiveName
   }
@@ -945,7 +1216,7 @@ task makeDist {
   dependsOn cleanPackageDir
   dependsOn syncJars
   dependsOn jar
-  outputs.dir("${jalviewDir}/${packageDir}")
+  outputs.dir("${jalviewDir}/${package_dir}")
 }
 
 
@@ -966,7 +1237,7 @@ shadowJar {
   manifest {
     attributes 'Implementation-Version': JALVIEW_VERSION
   }
-  mainClassName = shadowJarMainClass
+  mainClassName = shadow_jar_main_class
   mergeServiceFiles()
   classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
   minimize()
@@ -997,7 +1268,7 @@ task getdownWebsite() {
     }
     getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
 
-    // go through properties looking for getdown_txt_...
+    // set some getdown_txt_ properties then go through all properties looking for getdown_txt_...
     def props = project.properties.sort { it.key }
     if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
       props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
@@ -1009,7 +1280,11 @@ task getdownWebsite() {
       props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
     }
 
-    props.put("getdown_txt_appbase", getdownAppBase)
+    props.put("getdown_txt_title", jalview_name)
+    props.put("getdown_txt_ui.name", install4jApplicationName)
+
+    // start with appbase
+    getdownTextString += "appbase = ${getdownAppBase}\n"
     props.each{ prop, val ->
       if (prop.startsWith("getdown_txt_") && val != null) {
         if (prop.startsWith("getdown_txt_multi_")) {
@@ -1054,7 +1329,7 @@ task getdownWebsite() {
     }
 
     def codeFiles = []
-    fileTree(file(packageDir)).each{ f ->
+    fileTree(file(package_dir)).each{ f ->
       if (f.isDirectory()) {
         def files = fileTree(dir: f, include: ["*"]).getFiles()
         codeFiles += files
@@ -1072,6 +1347,16 @@ task getdownWebsite() {
       }
     }
 
+    fileTree(dir: digestonlyDir, include: ["*"]).getFiles().sort().each{f ->
+      def name = f.getName()
+      def line = "digestonly = ${getdownAppDistDir}/${name}\n"
+      getdownTextString += line
+      copy {
+        from f.getPath()
+        into getdownAppDir
+      }
+    }
+    
     // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
     /*
     if (JAVA_VERSION.equals("11")) {
@@ -1091,14 +1376,18 @@ task getdownWebsite() {
     // 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"
+    getdownTextString += "class = ${main_class}\n"
+    /* NOT setting these properties so that getdownappbase and getdowndistdir will default to release version
+     * getdownTextString += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}\n"
+     * getdownTextString += "jvmarg = -Dgetdownappbase=${getdownAppBase}\n"
+     */
 
     def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
     getdown_txt.write(getdownTextString)
 
-    def getdownLaunchJvl = ( (getdownChannelName != null && getdownChannelName.length() > 0)?"${getdownChannelName}_":"" ) + getdown_launch_jvl
-    def launch_jvl = file("${getdownWebsiteDir}/${getdown_launch_jvl}")
-    launch_jvl.write("appbase="+props.get("getdown_txt_appbase"))
+    def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
+    def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}")
+    launchJvl.write("appbase=${getdownAppBase}")
 
     copy {
       from getdownLauncher
@@ -1118,7 +1407,7 @@ task getdownWebsite() {
       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)
         }
@@ -1133,7 +1422,7 @@ task getdownWebsite() {
 
     copy {
       from getdown_txt
-      from launch_jvl
+      from launchJvl
       from getdownLauncher
       from "${getdownWebsiteDir}/${getdown_build_properties}"
       if (file(getdownLauncher).getName() != getdown_launcher) {
@@ -1149,13 +1438,31 @@ task getdownWebsite() {
   }
 
   if (buildDist) {
-    inputs.dir("${jalviewDir}/${packageDir}")
+    inputs.dir("${jalviewDir}/${package_dir}")
   }
   outputs.dir(getdownWebsiteDir)
   outputs.dir(getdownFilesDir)
 }
 
 
+// a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
+task getdownDigestDir(type: JavaExec) {
+  group "Help"
+  description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
+
+  def digestDirPropertyName = "DIGESTDIR"
+  doFirst {
+    classpath = files(getdownLauncher)
+    def digestDir = findProperty(digestDirPropertyName)
+    if (digestDir == null) {
+      throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
+    }
+    args digestDir
+  }
+  main = "com.threerings.getdown.tools.Digester"
+}
+
+
 task getdownDigest(type: JavaExec) {
   group = "distribution"
   description = "Digest the getdown website folder"
@@ -1220,6 +1527,7 @@ task copyInstall4jTemplate {
   def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
   inputs.file(install4jTemplateFile)
   inputs.file(install4jFileAssociationsFile)
+  inputs.property("CHANNEL", { CHANNEL })
   outputs.file(install4jConfFile)
 
   doLast {
@@ -1246,7 +1554,7 @@ task copyInstall4jTemplate {
     // put file association actions where placeholder action is
     def install4jFileAssociationsText = install4jFileAssociationsFile.text
     def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
-    install4jConfigXml.'**'.action.any { a ->
+    install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
       if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
         def parent = a.parent()
         parent.remove(a)
@@ -1258,6 +1566,36 @@ task copyInstall4jTemplate {
       }
     }
 
+    // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
+    // NB we're deleting the /other/ one!
+    // Also remove the examples subdir from non-release versions
+    def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
+    // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
+    if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
+      customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
+    } else {
+      // remove the examples subdir from Full File Set
+      def files = install4jConfigXml.files[0]
+      def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
+      def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
+      def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
+      def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
+      dirEntry.parent().remove(dirEntry)
+    }
+    install4jConfigXml.'**'.action.any { a ->
+      if (a.'@customizedId' == customizedIdToDelete) {
+        def parent = a.parent()
+        parent.remove(a)
+        return true
+      }
+    }
+
+    // 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)
   }
@@ -1295,7 +1633,8 @@ task installers(type: com.install4j.gradle.Install4jTask) {
   def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
 
   variables = [
-    'JALVIEW_NAME': getdown_txt_title,
+    'JALVIEW_NAME': jalview_name,
+    'JALVIEW_APPLICATION_NAME': install4jApplicationName,
     'JALVIEW_DIR': "../..",
     'OSX_KEYSTORE': OSX_KEYSTORE,
     'JSIGN_SH': JSIGN_SH,
@@ -1314,8 +1653,12 @@ task installers(type: com.install4j.gradle.Install4jTask) {
     'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
     'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz,
     'COPYRIGHT_MESSAGE': install4j_copyright_message,
-    'MACOS_BUNDLE_ID': install4j_macOS_bundle_id,
-    'INSTALLER_NAME': install4j_installer_name,
+    'BUNDLE_ID': install4jBundleId,
+    'INTERNAL_ID': install4jInternalId,
+    'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
+    'MACOS_DS_STORE': install4jDSStore,
+    'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
+    'INSTALLER_NAME': install4jInstallerName,
     'INSTALL4J_UTILS_DIR': install4j_utils_dir,
     'GETDOWN_WEBSITE_DIR': getdown_website_dir,
     'GETDOWN_FILES_DIR': getdown_files_dir,
@@ -1325,8 +1668,16 @@ task installers(type: com.install4j.gradle.Install4jTask) {
     'GETDOWN_INSTALL_DIR': getdown_install_dir,
     'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
     'BUILD_DIR': install4jBuildDir,
+    'APPLICATION_CATEGORIES': install4j_application_categories,
+    'APPLICATION_FOLDER': install4jApplicationFolder,
+    'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
+    'EXECUTABLE_NAME': install4jExecutableName,
+    'EXTRA_SCHEME': install4jExtraScheme,
   ]
 
+  //println("INSTALL4J VARIABLES:")
+  //variables.each{k,v->println("${k}=${v}")}
+
   destination = "${jalviewDir}/${install4jBuildDir}"
   buildSelected = true
 
@@ -1367,33 +1718,47 @@ task sourceDist(type: Tar) {
   
   into project.name
 
-  def EXCLUDE_FILES=["build/*","bin/*","test-output/","test-reports","tests","clover*/*"
-  ,".*"
-  ,"benchmarking/*"
-  ,"**/.*"
-  ,"*.class"
-  ,"**/*.class","${j11modDir}/**/*.jar","appletlib","**/*locales"
-  ,"*locales/**",
-  ,"utils/InstallAnywhere"] 
-  def PROCESS_FILES=[   "AUTHORS",
-  "CITATION",
-  "FEATURETODO",
-  "JAVA-11-README",
-  "FEATURETODO",
-  "LICENSE",
-  "**/README",
-  "RELEASE",
-  "THIRDPARTYLIBS","TESTNG",
-  "build.gradle",
-  "gradle.properties",
-  "**/*.java",
-  "**/*.html",
-  "**/*.xml",
-  "**/*.gradle",
-  "**/*.groovy",
-  "**/*.properties",
-  "**/*.perl",
-  "**/*.sh"]
+  def EXCLUDE_FILES=[
+    "build/*",
+    "bin/*",
+    "test-output/",
+    "test-reports",
+    "tests",
+    "clover*/*",
+    ".*",
+    "benchmarking/*",
+    "**/.*",
+    "*.class",
+    "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
+    "*locales/**",
+    "utils/InstallAnywhere",
+    "**/*.log",
+  ] 
+  def PROCESS_FILES=[
+    "AUTHORS",
+    "CITATION",
+    "FEATURETODO",
+    "JAVA-11-README",
+    "FEATURETODO",
+    "LICENSE",
+    "**/README",
+    "RELEASE",
+    "THIRDPARTYLIBS",
+    "TESTNG",
+    "build.gradle",
+    "gradle.properties",
+    "**/*.java",
+    "**/*.html",
+    "**/*.xml",
+    "**/*.gradle",
+    "**/*.groovy",
+    "**/*.properties",
+    "**/*.perl",
+    "**/*.sh",
+  ]
+  def INCLUDE_FILES=[
+    ".settings/org.eclipse.jdt.core.jalview.prefs",
+  ]
 
   from(jalviewDir) {
     exclude (EXCLUDE_FILES)
@@ -1419,14 +1784,17 @@ task sourceDist(type: Tar) {
     exclude (getdown_website_dir)
 
     // exluding these as not using jars as modules yet
-    exclude ("${j11modDir}/**/*.jar")
-  }
-  //  from (jalviewDir) {
-  //    // explicit includes for stuff that seemed to not get included
-  //    include(fileTree("test/**/*."))
-  //    exclude(EXCLUDE_FILES)
-  //    exclude(PROCESS_FILES)
-  //  }
+    exclude ("$j11modDir/**/*.jar")
+  }
+  from(jalviewDir) {
+    include(INCLUDE_FILES)
+  }
+//  from (jalviewDir) {
+//    // explicit includes for stuff that seemed to not get included
+//    include(fileTree("test/**/*."))
+//    exclude(EXCLUDE_FILES)
+//    exclude(PROCESS_FILES)
+//  }
 }