X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=build.gradle;h=3bf1649fd8d7dcb021646c91c054a2b0218a3d2e;hp=227e59ad74f18682e1681e904c8420ee5f3dca0d;hb=cb575bd620d3f32315de3ae47f7249a40e46ec89;hpb=641e9e7f1b5678250678b0fbd13c9dbfebd67eb5

diff --git a/build.gradle b/build.gradle
index 227e59a..3bf1649 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
@@ -13,9 +16,6 @@ buildscript {
     mavenCentral()
     mavenLocal()
   }
-  dependencies {
-    classpath 'org.openclover:clover:4.4.1'
-  }
 }
 
 
@@ -78,6 +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 = "${jalviewDirAbsolutePath}/RELEASE";
+  try {
+    (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream { 
+     releaseProps.load(it)
+    }
+  } catch (Exception fileLoadError) {
+    throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
+  }
+  ////
+  // Set JALVIEW_VERSION if it is not already set
+  if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
+    JALVIEW_VERSION = releaseProps.get("jalview.version")
+  }
+  
   // this property set when running Eclipse headlessly
   j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
   // this property set by Eclipse
@@ -110,21 +130,25 @@ ext {
   sourceDir = string("${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}")
-  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
+  // 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}/${JAVA_VERSION}")
   buildDist = true
@@ -153,8 +177,8 @@ ext {
     getdownAppBase = string("${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
@@ -172,10 +196,10 @@ ext {
     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
     }
@@ -187,10 +211,10 @@ ext {
     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
     }
@@ -202,15 +226,26 @@ ext {
 
     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
-    JALVIEW_VERSION = "TEST"
+    
+    // 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.png"
+    install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
     install4jExtraScheme = "jalviewt"
     install4jInstallerName = "${jalview_name} Test Installer"
     break
@@ -233,7 +268,7 @@ ext {
     JALVIEW_VERSION = "TEST"
     install4jSuffix = "Test-Local"
     install4jDSStore = "DS_Store-TEST-RELEASE"
-    install4jDMGBackgroundImage = "jalview_dmg_background.png"
+    install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
     install4jExtraScheme = "jalviewt"
     install4jInstallerName = "${jalview_name} Test Installer"
     break
@@ -280,7 +315,11 @@ ext {
                                     .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
                                     .replaceAll("_+", "") // collapse __
                                     //.replaceAll("_*-_*", "-") // collapse _-_
-  install4jUnixApplicationFolder = install4jInternalId
+  install4jUnixApplicationFolder = install4jApplicationName
+                                    .replaceAll(" ","_")
+                                    .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
+                                    .replaceAll("_+", "_") // collapse __
+                                    .replaceAll("_*-_*", "-") // collapse _-_
                                     .toLowerCase()
 
   getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}")
@@ -305,6 +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
@@ -318,6 +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"))
@@ -374,8 +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}")
 
@@ -418,10 +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
@@ -429,18 +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
   }
@@ -448,41 +489,20 @@ 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:4.4.1'
-    testCompile 'org.openclover:clover:4.4.1'
-  }
-}
 
-configurations {
-  cloverRuntime
-  cloverRuntime.extendsFrom cloverCompile
 }
 
 
@@ -621,61 +641,209 @@ 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 cleanClover {
   doFirst {
-    delete cloverInstrDir
-    def argsList = [
-      "--initstring",
-      cloverDb,
-      "-d",
-      cloverInstrDir.getPath(),
-    ]
-    argsList.addAll(
-      inputs.files.files.collect(
-        { file -> file.absolutePath }
-      )
+    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 }
     )
-    String[] args = argsList.toArray()
-    println("About to instrument "+args.length +" files")
-    com.atlassian.clover.CloverInstr.mainImpl(args)
+  )
+  args argsList.toArray()
+
+  doFirst {
+    delete cloverInstrDir
+    println("Clover: About to instrument "+srcFiles.size() +" files")
+  }
+}
+
+
+task cloverInstrTests(type: JavaExec) {
+  group = "Verification"
+  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 {
+    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
 
 
-task cloverReport {
+task cloverConsoleReport(type: JavaExec) {
   group = "Verification"
-  description = "Creates the Clover report"
-  inputs.dir "${buildDir}/clover"
-  outputs.dir "${reportsDir}/clover"
+  description = "Creates clover console report"
+
   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)
+
+  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()
+}
+
+
+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
 }
 
 
@@ -687,15 +855,7 @@ compileCloverJava {
     options.compilerArgs += additional_compiler_args
     print ("Setting target compatibility to "+targetCompatibility+"\n")
   }
-  classpath += configurations.cloverRuntime
-}
-
-
-task cleanClover {
-  doFirst {
-    delete cloverInstrDir
-    delete cloverDb
-  }
+  //classpath += configurations.cloverRuntime
 }
 // end clover bits
 
@@ -713,12 +873,6 @@ compileJava {
 
 
 compileTestJava {
-  if (use_clover) {
-    dependsOn compileCloverJava
-    classpath += configurations.cloverRuntime
-  } else {
-    classpath += sourceSets.main.runtimeClasspath
-  }
   doFirst {
     sourceCompatibility = compile_source_compatibility
     targetCompatibility = compile_target_compatibility
@@ -797,8 +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 {
@@ -840,8 +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
 
 }
@@ -849,7 +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'
@@ -877,7 +1031,7 @@ task copyHelp(type: Copy) {
 
 
 task syncLib(type: Sync) {
-  def syncDir = "${classesDir}/${libDistDir}"
+  def syncDir = "${resourceClassesDir}/${libDistDir}"
   from fileTree("${jalviewDir}/${libDistDir}")
   into syncDir
 }
@@ -886,7 +1040,7 @@ task syncLib(type: Sync) {
 task syncResources(type: Sync) {
   from resourceDir
   include "**/*.*"
-  into "${classesDir}"
+  into "${resourceClassesDir}"
   preserve {
     include "**"
   }
@@ -903,18 +1057,17 @@ 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
-    excludeGroups testngExcludedGroups
+    includeGroups testng_groups
+    excludeGroups testng_excluded_groups
     preserveOrder true
     useDefaultListeners=true
   }
@@ -923,10 +1076,25 @@ 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) {
+      println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
+    }
+  }
 }
 
 
@@ -952,22 +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" ]
@@ -988,12 +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")
   }
 }
 
@@ -1003,13 +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*/**"
@@ -1019,20 +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
   }
@@ -1048,7 +1216,7 @@ task makeDist {
   dependsOn cleanPackageDir
   dependsOn syncJars
   dependsOn jar
-  outputs.dir("${jalviewDir}/${packageDir}")
+  outputs.dir("${jalviewDir}/${package_dir}")
 }
 
 
@@ -1069,7 +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()
@@ -1161,7 +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
@@ -1179,6 +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")) {
@@ -1198,7 +1376,11 @@ 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("${getdownWebsiteDir}/getdown.txt")
     getdown_txt.write(getdownTextString)
@@ -1225,7 +1407,7 @@ task getdownWebsite() {
       copy {
         from getdown_txt
         from getdownLauncher
-        from "${getdownWebsiteDir}/${getdown_build_properties}"
+        from "${getdownAppDir}/${getdown_build_properties}"
         if (file(getdownLauncher).getName() != getdown_launcher) {
           rename(file(getdownLauncher).getName(), getdown_launcher)
         }
@@ -1256,7 +1438,7 @@ task getdownWebsite() {
   }
 
   if (buildDist) {
-    inputs.dir("${jalviewDir}/${packageDir}")
+    inputs.dir("${jalviewDir}/${package_dir}")
   }
   outputs.dir(getdownWebsiteDir)
   outputs.dir(getdownFilesDir)
@@ -1265,8 +1447,10 @@ 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${digestDirPropertyName}=...) for getdown"
   doFirst {
     classpath = files(getdownLauncher)
     def digestDir = findProperty(digestDirPropertyName)
@@ -1343,6 +1527,7 @@ task copyInstall4jTemplate {
   def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
   inputs.file(install4jTemplateFile)
   inputs.file(install4jFileAssociationsFile)
+  inputs.property("CHANNEL", { CHANNEL })
   outputs.file(install4jConfFile)
 
   doLast {
@@ -1369,7 +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)
@@ -1381,6 +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)
   }
@@ -1453,15 +1668,15 @@ 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}")}
+  //println("INSTALL4J VARIABLES:")
+  //variables.each{k,v->println("${k}=${v}")}
 
   destination = "${jalviewDir}/${install4jBuildDir}"
   buildSelected = true
@@ -1489,6 +1704,7 @@ task installers(type: com.install4j.gradle.Install4jTask) {
 
 
 task sourceDist(type: Tar) {
+  dependsOn createBuildProperties
   
   def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
   def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
@@ -1580,6 +1796,15 @@ 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=SourceDist"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
+    })
+  }
+
 }