X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=431c67b3a7908b45ba0fbf8bdbfeb3bd8c5b6cbe;hb=ef3fcd7746645316925b66c36cd56dd68b4a38b7;hp=d611f63a2cf73cfe58575e944bcfdf63ae652c41;hpb=0bfbb0272241e40244d0e32cd7ea66108c8590b4;p=jalview.git

diff --git a/build.gradle b/build.gradle
index d611f63..431c67b 100644
--- a/build.gradle
+++ b/build.gradle
@@ -13,9 +13,6 @@ buildscript {
     mavenCentral()
     mavenLocal()
   }
-  dependencies {
-    classpath 'org.openclover:clover:4.4.1'
-  }
 }
 
 
@@ -78,6 +75,26 @@ 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 = "${jalviewDirAbsolutePath}/RELEASE";
+  try {
+    (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream { 
+     releaseProps.load(it)
+    }
+  } catch (Exception fileLoadError) {
+    throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
+  }
+  ////
+  // Set JALVIEW_VERSION if it is not already set
+  if (findProperty(JALVIEW_VERSION)==null || "".equals(JALVIEW_VERSION)) {
+    JALVIEW_VERSION = releaseProps.get("jalview.version")
+  }
+  
   // this property set when running Eclipse headlessly
   j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
   // this property set by Eclipse
@@ -112,19 +129,16 @@ ext {
   bareTestSourceDir = string(test_source_dir)
   testSourceDir = string("${jalviewDir}/${bareTestSourceDir}")
 
+  classesDir = string("${jalviewDir}/${classes_dir}")
+
   // clover
-  cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}")
+  useClover = clover.equals("true")
+  cloverInstrDir = file("${buildDir}/clover/${clover_sources_instr_dir}")
+  cloverClassesDir = file("${buildDir}/clover/${clover_classes_dir}")
+  cloverReportDir = file("${buildDir}/clover/${clover_report_dir}")
   cloverDb = string("${buildDir}/clover/clover.db")
-  classesDir = string("${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
+  resourceClassesDir = useClover ? cloverClassesDir : classesDir
 
   getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
   buildDist = true
@@ -141,8 +155,9 @@ ext {
   install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
   install4jDSStore = "DS_Store-NON-RELEASE"
   install4jDMGBackgroundImage = "jalview_dmg_background-NON-RELEASE.png"
-  install4jInstallerName = "${jalview_name} Installer"
+  install4jInstallerName = "${jalview_name} Non-Release Installer"
   install4jExecutableName = jalview_name.replaceAll("[^\\w]+", "_").toLowerCase()
+  install4jExtraScheme = "jalviewx"
   switch (CHANNEL) {
 
     case "BUILD":
@@ -152,9 +167,10 @@ ext {
     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(testngExcludedGroups)) { 
-      testngExcludedGroups = "Not-bamboo"
+    if ("".equals(testng_excluded_groups)) { 
+      testng_excluded_groups = "Not-bamboo"
     }
+    install4jExtraScheme = "jalviewb"
     break
 
     case "RELEASE":
@@ -163,6 +179,7 @@ ext {
     install4jSuffix = ""
     install4jDSStore = "DS_Store"
     install4jDMGBackgroundImage = "jalview_dmg_background.png"
+    install4jInstallerName = "${jalview_name} Installer"
     break
 
     case "ARCHIVE":
@@ -177,6 +194,7 @@ ext {
       buildDist = false
     }
     reportRsyncCommand = true
+    install4jExtraScheme = "jalviewa"
     break
 
     case "ARCHIVELOCAL":
@@ -193,16 +211,33 @@ ext {
     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"
-    JALVIEW_VERSION = "TEST"
+    install4jDSStore = "DS_Store-TEST-RELEASE"
+    install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
+    install4jExtraScheme = "jalviewt"
+    install4jInstallerName = "${jalview_name} Test Installer"
     break
 
     case ~/^SCRATCH(|-[-\w]*)$/:
@@ -220,13 +255,18 @@ ext {
       getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
       getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
     }
-    install4jSuffix = "Test-Local"
     JALVIEW_VERSION = "TEST"
+    install4jSuffix = "Test-Local"
+    install4jDSStore = "DS_Store-TEST-RELEASE"
+    install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
+    install4jExtraScheme = "jalviewt"
+    install4jInstallerName = "${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
@@ -244,19 +284,33 @@ ext {
   // install4j application and folder names
   if (install4jSuffix == "") {
     install4jApplicationName = "${jalview_name}"
+    install4jBundleId = "${install4j_bundle_id}"
+    install4jWinApplicationId = install4j_release_win_application_id
   } else {
     install4jApplicationName = "${jalview_name} ${install4jSuffix}"
-    install4jInstallerName = "${jalview_name} Non-Release Installer"
-  }
-  // sanitise folder names
+    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("[\"'~:\\\\]+", "_") // replace all awkward filename chars
-  install4jUnixApplicationFolder = install4jApplicationFolder
-                                    .toLowerCase()
+                                    .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("_+", "_")
-                                    .replaceAll("_*-_*", "-")
+                                    .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
+                                    .replaceAll("_+", "_") // collapse __
+                                    .replaceAll("_*-_*", "-") // collapse _-_
+                                    .toLowerCase()
 
   getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}")
   //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
@@ -349,8 +403,8 @@ 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}")
 
@@ -396,7 +450,6 @@ sourceSets {
     jar.destinationDir = file("${jalviewDir}/${packageDir}")
 
     compileClasspath = files(sourceSets.main.java.outputDir)
-    //compileClasspath += files(sourceSets.main.resources.srcDirs)
     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 
     runtimeClasspath = compileClasspath
@@ -404,18 +457,17 @@ 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 += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+    compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
 
     runtimeClasspath = compileClasspath
   }
@@ -423,44 +475,22 @@ sourceSets {
   test {
     java {
       srcDirs testSourceDir
-      outputDir = file("${jalviewDir}/${testOutputDir}")
+      outputDir = file("${jalviewDir}/${test_output_dir}")
     }
 
     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:4.4.1'
-    testCompile 'org.openclover:clover:4.4.1'
-  }
-}
-
-configurations {
-  cloverRuntime
-  cloverRuntime.extendsFrom cloverCompile
-}
-
-
 // eclipse project and settings files creation, also used by buildship
 eclipse {
   project {
@@ -596,27 +626,40 @@ eclipse {
 }
 
 
-task cloverInstr {
-  // only instrument source, we build test classes as normal
-  inputs.files files (sourceSets.main.allJava,sourceSets.test.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
-  outputs.dir cloverInstrDir
+// clover bits
+
+
+task cloverInstr(type: JavaExec) {
+  group = "Verification"
+  description = "Create clover instrumented source files"
+
+  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",
-      cloverDb,
-      "-d",
-      cloverInstrDir.getPath(),
-    ]
-    argsList.addAll(
-      inputs.files.files.collect(
-        { file -> file.absolutePath }
-      )
-    )
-    String[] args = argsList.toArray()
-    println("About to instrument "+args.length +" files")
-    com.atlassian.clover.CloverInstr.mainImpl(args)
+    delete cloverDb
+    println("Clover: About to instrument "+srcFiles.size() +" files")
   }
 }
 
@@ -624,33 +667,62 @@ task cloverInstr {
 cloverClasses.dependsOn cloverInstr
 
 
-task cloverReport {
+task cloverXmlReport(type: JavaExec) {
   group = "Verification"
-  description = "Creates the Clover report"
-  inputs.dir "${buildDir}/clover"
-  outputs.dir "${reportsDir}/clover"
+  description = "Creates clover XML report"
+
+  inputs.dir cloverClassesDir
+  outputs.dir cloverReportDir
   onlyIf {
     file(cloverDb).exists()
   }
-  doFirst {
-    def argsList = [
-      "--initstring",
-      cloverDb,
-      "-o",
-      "${reportsDir}/clover"
-    ]
-    String[] args = argsList.toArray()
-    com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
-
-    // and generate ${reportsDir}/clover/clover.xml
-    args = [
-      "--initstring",
-      cloverDb,
-      "-o",
-      "${reportsDir}/clover/clover.xml"
-    ].toArray()
-    com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
+
+  classpath = sourceSets.clover.runtimeClasspath
+  main = "com.atlassian.clover.reporters.xml.XMLReporter"
+
+  def argsList = [
+    "--alwaysreport",
+    "--initstring",
+    cloverDb,
+    "--outfile",
+    "${cloverReportDir}/clover.xml"
+  ]
+
+  args argsList.toArray()
+}
+
+
+task cloverHtmlReport(type: JavaExec) {
+  group = "Verification"
+  description = "Creates clover HTML report"
+
+  inputs.dir cloverClassesDir
+  outputs.dir cloverReportDir
+  onlyIf {
+    file(cloverDb).exists()
   }
+
+  classpath = sourceSets.clover.runtimeClasspath
+  main = "com.atlassian.clover.reporters.html.HtmlReporter"
+
+  def argsList = [
+    "--alwaysreport",
+    "--initstring",
+    cloverDb,
+    "--outputdir",
+    "${cloverReportDir}/clover"
+  ]
+
+  args argsList.toArray()
+}
+
+
+task cloverReport {
+  group = "Verification"
+  description = "Creates clover reports"
+
+  dependsOn cloverXmlReport
+  dependsOn cloverHtmlReport
 }
 
 
@@ -668,8 +740,7 @@ compileCloverJava {
 
 task cleanClover {
   doFirst {
-    delete cloverInstrDir
-    delete cloverDb
+    delete "${buildDir/clover}"
   }
 }
 // end clover bits
@@ -688,12 +759,6 @@ compileJava {
 
 
 compileTestJava {
-  if (use_clover) {
-    dependsOn compileCloverJava
-    classpath += configurations.cloverRuntime
-  } else {
-    classpath += sourceSets.main.runtimeClasspath
-  }
   doFirst {
     sourceCompatibility = compile_source_compatibility
     targetCompatibility = compile_target_compatibility
@@ -772,8 +837,8 @@ 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 {
@@ -815,8 +880,8 @@ 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
 
 }
@@ -824,7 +889,7 @@ 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'
@@ -852,7 +917,7 @@ task copyHelp(type: Copy) {
 
 
 task syncLib(type: Sync) {
-  def syncDir = "${classesDir}/${libDistDir}"
+  def syncDir = "${resourceClassesDir}/${libDistDir}"
   from fileTree("${jalviewDir}/${libDistDir}")
   into syncDir
 }
@@ -861,7 +926,7 @@ task syncLib(type: Sync) {
 task syncResources(type: Sync) {
   from resourceDir
   include "**/*.*"
-  into "${classesDir}"
+  into "${resourceClassesDir}"
   preserve {
     include "**"
   }
@@ -878,18 +943,16 @@ task prepare {
 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
 test {
   dependsOn prepare
-  dependsOn compileJava
-  if (use_clover) {
-    dependsOn cloverInstr
-  }
 
-  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
-    excludeGroups testngExcludedGroups
+    includeGroups testng_groups
+    excludeGroups testng_excluded_groups
     preserveOrder true
     useDefaultListeners=true
   }
@@ -898,10 +961,25 @@ test {
 
   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) {
+      print("Running tests " + (useClover?"WITH":"WITHOUT") + " clover [clover="+useClover+"]\n")
+    }
+  }
 }
 
 
@@ -927,22 +1005,22 @@ 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" ]
@@ -963,7 +1041,7 @@ 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) {
@@ -978,7 +1056,7 @@ jar {
   dependsOn createBuildProperties
 
   manifest {
-    attributes "Main-Class": mainClass,
+    attributes "Main-Class": main_class,
     "Permissions": "all-permissions",
     "Application-Name": "Jalview Desktop",
     "Codebase": application_codebase
@@ -1044,7 +1122,7 @@ shadowJar {
   manifest {
     attributes 'Implementation-Version': JALVIEW_VERSION
   }
-  mainClassName = shadowJarMainClass
+  mainClassName = shadow_jar_main_class
   mergeServiceFiles()
   classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
   minimize()
@@ -1240,8 +1318,10 @@ task getdownWebsite() {
 
 // 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"
-  description = "Digest a local dir (-P${digestDirPropertyName}=...) for getdown"
   doFirst {
     classpath = files(getdownLauncher)
     def digestDir = findProperty(digestDirPropertyName)
@@ -1318,6 +1398,7 @@ task copyInstall4jTemplate {
   def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
   inputs.file(install4jTemplateFile)
   inputs.file(install4jFileAssociationsFile)
+  inputs.property("CHANNEL", { CHANNEL })
   outputs.file(install4jConfFile)
 
   doLast {
@@ -1344,7 +1425,7 @@ 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)
@@ -1356,6 +1437,36 @@ 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)
   }
@@ -1393,7 +1504,8 @@ task installers(type: com.install4j.gradle.Install4jTask) {
   def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
 
   variables = [
-    'JALVIEW_NAME': install4jApplicationName,
+    'JALVIEW_NAME': jalview_name,
+    'JALVIEW_APPLICATION_NAME': install4jApplicationName,
     'JALVIEW_DIR': "../..",
     'OSX_KEYSTORE': OSX_KEYSTORE,
     'JSIGN_SH': JSIGN_SH,
@@ -1412,7 +1524,9 @@ 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,
+    'BUNDLE_ID': install4jBundleId,
+    'INTERNAL_ID': install4jInternalId,
+    'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
     'MACOS_DS_STORE': install4jDSStore,
     'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
     'INSTALLER_NAME': install4jInstallerName,
@@ -1425,12 +1539,16 @@ 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,
-    'UNIX_DESKTOP_ADDITIONS': install4j_unix_desktop_additions,
+    '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