X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=3ed6c564622fd5c61b047cc33c29db7fe7187cf7;hb=refs%2Fheads%2Fdevelop;hp=9e2b4a31a53455d9480c68f3023038c1de8566a6;hpb=8e62def6cf40cdd19e1c15ac2ed7e9f3d8b3aa54;p=jalview.git

diff --git a/build.gradle b/build.gradle
index 9e2b4a3..d057994 100644
--- a/build.gradle
+++ b/build.gradle
@@ -10,6 +10,10 @@ import org.gradle.plugins.ide.eclipse.model.Output
 import org.gradle.plugins.ide.eclipse.model.Library
 import java.security.MessageDigest
 import java.util.regex.Matcher
+import java.util.concurrent.Executors
+import java.util.concurrent.Future
+import java.util.concurrent.ScheduledExecutorService
+import java.util.concurrent.TimeUnit
 import groovy.transform.ExternalizeMethods
 import groovy.util.XmlParser
 import groovy.xml.XmlUtil
@@ -39,6 +43,7 @@ buildscript {
     classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
     classpath "org.jsoup:jsoup:1.14.3"
     classpath "com.eowise:gradle-imagemagick:0.5.1"
+    classpath 'ru.vyarus:gradle-use-python-plugin:4.0.0'
   }
 }
 
@@ -48,10 +53,11 @@ plugins {
   id 'application'
   id 'eclipse'
   id "com.diffplug.gradle.spotless" version "3.28.0"
-  id 'com.github.johnrengelman.shadow' version '4.0.3'
+  id 'com.github.johnrengelman.shadow' version '6.0.0'
   id 'com.install4j.gradle' version '10.0.3'
-  id 'com.dorongold.task-tree' version '2.1.0' // only needed to display task dependency tree with  gradle task1 [task2 ...] taskTree
+  id 'com.dorongold.task-tree' version '2.1.1' // only needed to display task dependency tree with  gradle task1 [task2 ...] taskTree
   id 'com.palantir.git-version' version '0.13.0' apply false
+  id 'ru.vyarus.use-python' version '4.0.0'
 }
 
 repositories {
@@ -229,17 +235,21 @@ ext {
   jvlChannelName = CHANNEL.toLowerCase()
   install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
   install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}"
+  install4jDMGDSStoreJSON = "${install4j_images_dir}/${install4j_dmg_ds_store_json}"
   install4jDMGBackgroundImageDir = "${install4j_images_dir}"
   install4jDMGBackgroundImageBuildDir = "build/imagemagick/install4j"
   install4jDMGBackgroundImageFile = "${install4j_dmg_background}"
-  install4jInstallerName = "${jalview_name} Non-Release Installer"
+  install4jmacOSArchiveName = "${jalview_name} Non-Release ${JALVIEW_VERSION} Installer"
   install4jExecutableName = install4j_executable_name
-  install4jExtraScheme = "jalviewx"
+  install4jExtraScheme = "jalviewextra"
   install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}")
   install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}")
   install4jPngIconFile = string("${install4j_images_dir}/${install4j_png_icon_file}")
   install4jBackground = string("${install4j_images_dir}/${install4j_background}")
   install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
+  install4jDMGFixedDSStoreX64 = "build/macos_dmg/${install4j_dmg_ds_store}-x64"
+  install4jDMGFixedDSStoreAarch64 = "build/macos_dmg/${install4j_dmg_ds_store}-aarch64"
+  install4jDMGVolumeIcon = string("${install4j_images_dir}/${install4j_dmg_volume_icon}")
   install4jCheckSums = true
 
   applicationName = "${jalview_name}"
@@ -264,7 +274,8 @@ ext {
     getdownSetAppBaseProperty = true
     reportRsyncCommand = true
     install4jSuffix = ""
-    install4jInstallerName = "${jalview_name} Installer"
+    install4jmacOSArchiveName = "Install ${jalview_name} ${JALVIEW_VERSION}"
+    install4jExtraScheme = (CHANNEL=="RELEASE")?"jalviewx":"jalviewjs"
     break
 
     case "ARCHIVE":
@@ -306,7 +317,7 @@ ext {
     JALVIEW_VERSION=JALVIEW_VERSION+"-d${suffix}-${buildDate}"
     install4jSuffix = "Develop ${suffix}"
     install4jExtraScheme = "jalviewd"
-    install4jInstallerName = "${jalview_name} Develop ${suffix} Installer"
+    install4jmacOSArchiveName = "Install ${jalview_name} Develop ${suffix} ${JALVIEW_VERSION}"
     getdownChannelName = string("develop-${suffix}")
     getdownChannelDir = string("${getdown_website_dir}/${getdownChannelName}")
     getdownAppBaseDir = string("${jalviewDir}/${getdownChannelDir}/${JAVA_VERSION}")
@@ -324,7 +335,7 @@ ext {
     
     install4jSuffix = "Develop"
     install4jExtraScheme = "jalviewd"
-    install4jInstallerName = "${jalview_name} Develop Installer"
+    install4jmacOSArchiveName = "Install ${jalview_name} Develop ${JALVIEW_VERSION}"
     backgroundImageText = true
     break
 
@@ -339,7 +350,7 @@ ext {
     JALVIEW_VERSION = JALVIEW_VERSION+"-test"
     install4jSuffix = "Test"
     install4jExtraScheme = "jalviewt"
-    install4jInstallerName = "${jalview_name} Test Installer"
+    install4jmacOSArchiveName = "Install ${jalview_name} Test ${JALVIEW_VERSION}"
     backgroundImageText = true
     break
 
@@ -363,7 +374,7 @@ ext {
     JALVIEW_VERSION = "TEST"
     install4jSuffix = "Test-Local"
     install4jExtraScheme = "jalviewt"
-    install4jInstallerName = "${jalview_name} Test Installer"
+    install4jmacOSArchiveName = "Install ${jalview_name} Test ${JALVIEW_VERSION}"
     backgroundImageText = true
     break
 
@@ -429,6 +440,8 @@ ext {
                                     .replaceAll("_+", "_") // collapse __
                                     .replaceAll("_*-_*", "-") // collapse _-_
                                     .toLowerCase()
+  install4jmacOSArchiveX64Name = "${install4jmacOSArchiveName} (Intel)"
+  install4jmacOSArchiveAarch64Name = "${install4jmacOSArchiveName} (Apple Silicon)"
 
   getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local"
   getdownAppDir = string("${getdownAppBaseDir}/${getdownAppDistDir}")
@@ -526,6 +539,9 @@ ext {
   if (install4jHomeDir.startsWith("~/")) {
     install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
   }
+  install4jmacOSArchiveX64DMGFilename = "${install4jApplicationFolder}-${JALVIEW_VERSION}-macos-x64-java_${JAVA_INTEGER_VERSION}"
+  install4jmacOSArchiveAarch64DMGFilename = "${install4jApplicationFolder}-${JALVIEW_VERSION}-macos-aarch64-java_${JAVA_INTEGER_VERSION}"
+
 
   resourceBuildDir = string("${buildDir}/resources")
   resourcesBuildDir = string("${resourceBuildDir}/resources_build")
@@ -568,11 +584,16 @@ ext {
   jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}")
   jalviewjsJ2sProps = null
   jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
+  jalviewjsStderrLaunchFilename = "${jalviewjsSiteDir}/"+(file(jalviewjs_stderr_launch).getName())
 
   eclipseWorkspace = null
   eclipseBinary = string("")
   eclipseVersion = string("")
   eclipseDebug = false
+
+  jalviewjsChromiumUserDir = "${jalviewjsBuildDir}/${jalviewjs_chromium_user_dir}"
+  jalviewjsChromiumProfileDir = "${ext.jalviewjsChromiumUserDir}/${jalviewjs_chromium_profile_name}"
+
   // ENDEXT
 }
 
@@ -1064,7 +1085,7 @@ compileJava {
   // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
   sourceCompatibility = compile_source_compatibility
   targetCompatibility = compile_target_compatibility
-  options.compilerArgs = additional_compiler_args
+  options.compilerArgs += additional_compiler_args
   options.encoding = "UTF-8"
   doFirst {
     print ("Setting target compatibility to "+compile_target_compatibility+"\n")
@@ -1076,7 +1097,7 @@ compileJava {
 compileTestJava {
   sourceCompatibility = compile_source_compatibility
   targetCompatibility = compile_target_compatibility
-  options.compilerArgs = additional_compiler_args
+  options.compilerArgs += additional_compiler_args
   doFirst {
     print ("Setting target compatibility to "+targetCompatibility+"\n")
   }
@@ -1732,36 +1753,147 @@ task prepare {
 
 compileJava.dependsOn prepare
 run.dependsOn compileJava
-//run.dependsOn prepare
+compileTestJava.dependsOn compileJava
+
 
 
-//testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
 test {
-  dependsOn prepare
+  group = "Verification"
+  description = "Runs all testTaskN tasks)"
 
   if (useClover) {
     dependsOn cloverClasses
-   } else { //?
-    dependsOn compileJava //?
+  } else { //?
+    dependsOn testClasses
   }
 
+  // not running tests in this task
+  exclude "**/*"
+}
+/* testTask0 is the main test task */
+task testTask0(type: Test) {
+  group = "Verification"
+  description = "The main test task. Runs all non-testTaskN-labelled tests (unless excluded)"
   useTestNG() {
-    includeGroups testng_groups
-    excludeGroups testng_excluded_groups
+    includeGroups testng_groups.split(",")
+    excludeGroups testng_excluded_groups.split(",")
+    tasks.withType(Test).matching {it.name.startsWith("testTask") && it.name != name}.all {t -> excludeGroups t.name}
     preserveOrder true
     useDefaultListeners=true
   }
+  timeout = Duration.ofMinutes(15)
+}
 
-  maxHeapSize = "2048m"
-  jvmArgs '-Xmx2048m', '-Xms2048m'
+/* separated tests */
+task testTask1(type: Test) {
+  group = "Verification"
+  description = "Tests that need to be isolated from the main test run"
+  useTestNG() {
+    includeGroups name
+    excludeGroups testng_excluded_groups.split(",")
+    preserveOrder true
+    useDefaultListeners=true
+  }
+  timeout = Duration.ofMinutes(5)
+}
+
+task testTask2(type: Test) {
+  group = "Verification"
+  description = "Tests that need to be isolated from the main test run"
+  useTestNG() {
+    includeGroups name
+    excludeGroups testng_excluded_groups.split(",")
+    preserveOrder true
+    useDefaultListeners=true
+  }
+  timeout = Duration.ofMinutes(5)
+}
+task testTask3(type: Test) {
+  group = "Verification"
+  description = "Tests that need to be isolated from the main test run"
+  useTestNG() {
+    includeGroups name
+    excludeGroups testng_excluded_groups.split(",")
+    preserveOrder true
+    useDefaultListeners=true
+  }
+  timeout = Duration.ofMinutes(5)
+}
 
-/* delete these! 
-  maxParallelForks = 1
-  forkEvery = 1
-  failFast = true
-  jvmArgs '-Xmx2048m', '-Xms2048m'
+/* insert more testTaskNs here -- change N to next digit or other string */
+/*
+task testTaskN(type: Test) {
+  group = "Verification"
+  description = "Tests that need to be isolated from the main test run"
+  useTestNG() {
+    includeGroups name
+    excludeGroups testng_excluded_groups.split(",")
+    preserveOrder true
+    useDefaultListeners=true
+  }
+}
 */
 
+
+/*
+ * adapted from https://medium.com/@wasyl/pretty-tests-summary-in-gradle-744804dd676c
+ * to summarise test results from all Test tasks
+ */
+/* START of test tasks results summary */
+import groovy.time.TimeCategory
+import org.gradle.api.tasks.testing.logging.TestExceptionFormat
+import org.gradle.api.tasks.testing.logging.TestLogEvent
+rootProject.ext.testsResults = [] // Container for tests summaries
+
+tasks.withType(Test).matching {t -> t.getName().startsWith("testTask")}.all { testTask ->
+
+  // from original test task
+  if (useClover) {
+    dependsOn cloverClasses
+  } else { //?
+    dependsOn testClasses //?
+  }
+
+  // run main tests first
+  if (!testTask.name.equals("testTask0"))
+    testTask.mustRunAfter "testTask0"
+
+  testTask.testLogging { logging ->
+    events TestLogEvent.FAILED
+//      TestLogEvent.SKIPPED,
+//      TestLogEvent.STANDARD_OUT,
+//      TestLogEvent.STANDARD_ERROR
+
+    exceptionFormat TestExceptionFormat.FULL
+    showExceptions true
+    showCauses true
+    showStackTraces true
+    if (test_output) {
+      showStandardStreams true
+    }
+    info.events = [ TestLogEvent.FAILED ]
+  }
+
+  if (OperatingSystem.current().isMacOsX()) {
+    testTask.systemProperty "apple.awt.UIElement", "true"
+    testTask.environment "JAVA_TOOL_OPTIONS", "-Dapple.awt.UIElement=true"
+  }
+
+
+  ignoreFailures = true // Always try to run all tests for all modules
+
+  afterSuite { desc, result ->
+    if (desc.parent)
+      return // Only summarize results for whole modules
+
+    def resultsInfo = [testTask.project.name, testTask.name, result, TimeCategory.minus(new Date(result.endTime), new Date(result.startTime)), testTask.reports.html.entryPoint]
+
+    rootProject.ext.testsResults.add(resultsInfo)
+  }
+
+  // from original test task
+  maxHeapSize = "1024m"
+
   workingDir = jalviewDir
   def testLaf = project.findProperty("test_laf")
   if (testLaf != null) {
@@ -1778,12 +1910,144 @@ test {
   jvmArgs += additional_compiler_args
 
   doFirst {
+    // this is not perfect yet -- we should only add the commandLineIncludePatterns to the
+    // testTasks that include the tests, and exclude all from the others.
+    // get --test argument
+    filter.commandLineIncludePatterns = test.filter.commandLineIncludePatterns
+    // do something with testTask.getCandidateClassFiles() to see if the test should silently finish because of the
+    // commandLineIncludePatterns not matching anything.  Instead we are doing setFailOnNoMatchingTests(false) below
+
+
     if (useClover) {
       println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
     }
   }
+
+
+  /* don't fail on no matching tests (so --tests will run across all testTasks) */
+  testTask.filter.setFailOnNoMatchingTests(false)
+
+  /* ensure the "test" task dependsOn all the testTasks */
+  test.dependsOn testTask
 }
 
+gradle.buildFinished {
+    def allResults = rootProject.ext.testsResults
+
+    if (!allResults.isEmpty()) {
+        printResults allResults
+        allResults.each {r ->
+          if (r[2].resultType == TestResult.ResultType.FAILURE)
+            throw new GradleException("Failed tests!")
+        }
+    }
+}
+
+private static String colString(styler, col, colour, text) {
+  return col?"${styler[colour](text)}":text
+}
+
+private static String getSummaryLine(s, pn, tn, rt, rc, rs, rf, rsk, t, col) {
+  def colour = 'black'
+  def text = rt
+  def nocol = false
+  if (rc == 0) {
+    text = "-----"
+    nocol = true
+  } else {
+    switch(rt) {
+      case TestResult.ResultType.SUCCESS:
+        colour = 'green'
+        break;
+      case TestResult.ResultType.FAILURE:
+        colour = 'red'
+        break;
+      default:
+        nocol = true
+        break;
+    }
+  }
+  StringBuilder sb = new StringBuilder()
+  sb.append("${pn}")
+  if (tn != null)
+    sb.append(":${tn}")
+  sb.append(" results: ")
+  sb.append(colString(s, col && !nocol, colour, text))
+  sb.append(" (")
+  sb.append("${rc} tests, ")
+  sb.append(colString(s, col && rs > 0, 'green', rs))
+  sb.append(" successes, ")
+  sb.append(colString(s, col && rf > 0, 'red', rf))
+  sb.append(" failures, ")
+  sb.append("${rsk} skipped) in ${t}")
+  return sb.toString()
+}
+
+private static void printResults(allResults) {
+
+    // styler from https://stackoverflow.com/a/56139852
+    def styler = 'black red green yellow blue magenta cyan white'.split().toList().withIndex(30).collectEntries { key, val -> [(key) : { "\033[${val}m${it}\033[0m" }] }
+
+    def maxLength = 0
+    def failedTests = false
+    def summaryLines = []
+    def totalcount = 0
+    def totalsuccess = 0
+    def totalfail = 0
+    def totalskip = 0
+    def totaltime = TimeCategory.getSeconds(0)
+    // sort on project name then task name
+    allResults.sort {a, b -> a[0] == b[0]? a[1]<=>b[1]:a[0] <=> b[0]}.each {
+      def projectName = it[0]
+      def taskName = it[1]
+      def result = it[2]
+      def time = it[3]
+      def report = it[4]
+      def summaryCol = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, true)
+      def summaryPlain = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, false)
+      def reportLine = "Report file: ${report}"
+      def ls = summaryPlain.length()
+      def lr = reportLine.length()
+      def m = [ls, lr].max()
+      if (m > maxLength)
+        maxLength = m
+      def info = [ls, summaryCol, reportLine]
+      summaryLines.add(info)
+      failedTests |= result.resultType == TestResult.ResultType.FAILURE
+      totalcount += result.testCount
+      totalsuccess += result.successfulTestCount
+      totalfail += result.failedTestCount
+      totalskip += result.skippedTestCount
+      totaltime += time
+    }
+    def totalSummaryCol = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, true)
+    def totalSummaryPlain = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, false)
+    def tls = totalSummaryPlain.length()
+    if (tls > maxLength)
+      maxLength = tls
+    def info = [tls, totalSummaryCol, null]
+    summaryLines.add(info)
+
+    def allSummaries = []
+    for(sInfo : summaryLines) {
+      def ls = sInfo[0]
+      def summary = sInfo[1]
+      def report = sInfo[2]
+
+      StringBuilder sb = new StringBuilder()
+      sb.append("│" + summary + " " * (maxLength - ls) + "│")
+      if (report != null) {
+        sb.append("\n│" + report + " " * (maxLength - report.length()) + "│")
+      }
+      allSummaries += sb.toString()
+    }
+
+    println "┌${"${"─" * maxLength}"}┐"
+    println allSummaries.join("\n├${"${"─" * maxLength}"}┤\n")
+    println "└${"${"─" * maxLength}"}┘"
+}
+/* END of test tasks results summary */
+
 
 task compileLinkCheck(type: JavaCompile) {
   options.fork = true
@@ -1903,22 +2167,56 @@ task cleanDist {
 }
 
 
+task launcherJar(type: Jar) {
+  manifest {
+      attributes (
+        "Main-Class": shadow_jar_main_class,
+        "Implementation-Version": JALVIEW_VERSION,
+        "Application-Name": applicationName
+      )
+  }
+}
+
 shadowJar {
   group = "distribution"
   description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
   if (buildDist) {
     dependsOn makeDist
   }
-  from ("${jalviewDir}/${libDistDir}") {
-    include("*.jar")
-  }
+
+  def jarFiles = fileTree(dir: "${jalviewDir}/${libDistDir}", include: "*.jar", exclude: "regex.jar").getFiles()
+  def groovyJars = jarFiles.findAll {it1 -> file(it1).getName().startsWith("groovy-swing")}
+  def otherJars = jarFiles.findAll {it2 -> !file(it2).getName().startsWith("groovy-swing")}
+  from groovyJars
+  from otherJars
+
   manifest {
-    attributes "Implementation-Version": JALVIEW_VERSION,
-    "Application-Name": applicationName
+    // shadowJar manifest must inheritFrom another Jar task.  Can't set attributes here.
+    inheritFrom(project.tasks.launcherJar.manifest)
+  }
+  // we need to include the groovy-swing Include-Package for it to run in the shadowJar
+  doFirst {
+    def jarFileManifests = []
+    groovyJars.each { jarFile ->
+      def mf = zipTree(jarFile).getFiles().find { it.getName().equals("MANIFEST.MF") }
+      if (mf != null) {
+        jarFileManifests += mf
+      }
+    }
+    manifest {
+      from (jarFileManifests) {
+        eachEntry { details ->
+          if (!details.key.equals("Import-Package")) {
+            details.exclude()
+          }
+        }
+      }
+    }
   }
 
   duplicatesStrategy "INCLUDE"
 
+  // this mainClassName is mandatory but gets ignored due to manifest created in doFirst{}. Set the Main-Class as an attribute in launcherJar instead
   mainClassName = shadow_jar_main_class
   mergeServiceFiles()
   classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
@@ -1972,9 +2270,9 @@ task getdownImages() {
   dependsOn getdownImagesProcess
 }
 
-task getdownWebsite() {
+task getdownWebsiteBuild() {
   group = "distribution"
-  description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
+  description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer. No digest is created."
 
   dependsOn getdownImages
   if (buildDist) {
@@ -2026,8 +2324,8 @@ task getdownWebsite() {
       props.put("getdown_txt_ui.instant_background_image", "${getdownImagesBuildDir}/${getdown_instant_background_image}")
       props.put("getdown_txt_ui.error_background", "${getdownImagesBuildDir}/${getdown_error_background}")
       props.put("getdown_txt_ui.progress_image", "${getdownImagesBuildDir}/${getdown_progress_image}")
-      props.put("getdown_txt_ui.icon", "${getdownImagesBuildDir}/${getdown_icon}")
-      props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesBuildDir}/${getdown_mac_dock_icon}")
+      props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}")
+      props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}")
     }
 
     props.put("getdown_txt_title", jalview_name)
@@ -2086,7 +2384,7 @@ task getdownWebsite() {
           from s
           into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
         }
-        getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
+        getdownTextLines += "xresource = ${getdown_wrapper_script_dir}/${script}"
       }
     }
 
@@ -2228,7 +2526,9 @@ task getdownDigestDir(type: JavaExec) {
 task getdownDigest(type: JavaExec) {
   group = "distribution"
   description = "Digest the getdown website folder"
-  dependsOn getdownWebsite
+
+  dependsOn getdownWebsiteBuild
+
   doFirst {
     classpath = files(getdownLauncher)
   }
@@ -2261,12 +2561,19 @@ task getdown() {
   }
 }
 
+task getdownWebsite {
+  group = "distribution"
+  description = "A task to create the whole getdown channel website dir including digest file"
+
+  dependsOn getdownWebsiteBuild
+  dependsOn getdownDigest
+}
 
 task getdownArchiveBuild() {
   group = "distribution"
   description = "Put files in the archive dir to go on the website"
 
-  dependsOn getdownWebsite
+  dependsOn getdownWebsiteBuild
 
   def v = "v${JALVIEW_VERSION_UNDERSCORES}"
   def vDir = "${getdownArchiveDir}/${v}"
@@ -2313,6 +2620,14 @@ task getdownArchiveBuild() {
       }
     }
 
+    // the wrapper scripts dir
+    if ( file("${getdownAppBaseDir}/${getdown_wrapper_script_dir}").exists() ) {
+      copy {
+        from "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
+        into "${getdownFullArchiveDir}/${getdown_wrapper_script_dir}"
+      }
+    }
+
     getdownArchiveTxt.write(getdownArchiveTextLines.join("\n"))
 
     def vLaunchJvl = file(getdownVersionLaunchJvl)
@@ -2411,6 +2726,21 @@ task copyInstall4jTemplate {
       }
     }
 
+    // delete .VolumeIcon.icns in macos DMG if there isn't one
+    if (!file(install4jDMGVolumeIcon).exists()) {
+      println("No '.VolumeIcon.icns' file found. Removing from install4j file.")
+      install4jConfigXml.'**'.macosArchive.topLevelFiles.each { topLevelFiles ->
+        topLevelFiles.file.each() { file ->
+          if (file.attribute("name") && file.attribute("name").equals(".VolumeIcon.icns")) {
+            println("Removing "+file.toString())
+            topLevelFiles.remove(file)
+          }
+        }
+      }
+    } else {
+      println("Using '.VolumeIcon.icns' file '${install4jDMGVolumeIcon}'")
+    }
+
     // disable install screen for OSX dmg (for 2.11.2.0)
     install4jConfigXml.'**'.macosArchive.each { macosArchive -> 
       macosArchive.attributes().remove('executeSetupApp')
@@ -2525,8 +2855,66 @@ task install4jDMGBackgroundImageProcess {
   }
 }
 
-task install4jDMGBackgroundImage {
+
+python {
+  pip 'ds_store:1.3.0'
+}
+
+task install4jCustomiseDS_StoreX64(type: PythonTask) {
+  inputs.file(install4jDMGDSStore)
+  outputs.file(install4jDMGFixedDSStoreX64)
+  def command_args = [ jalview_customise_ds_store,
+    '--input', install4jDMGDSStore,
+    '--output', install4jDMGFixedDSStoreX64,
+    '--volumename', install4jmacOSArchiveX64Name,
+    '--backgroundfile', install4j_dmg_background_filename,
+    '--dmg', install4jmacOSArchiveX64DMGFilename + ".dmg",
+    '--appname', "${applicationName}.app",
+  ]
+  if (file(install4jDMGDSStoreJSON).exists()) {
+    command_args += [ '--config', install4jDMGDSStoreJSON ]
+    inputs.file(install4jDMGDSStoreJSON)
+  }
+  command = command_args
+  doFirst {
+    println("Running command '${command_args.join(' ')}'")
+  }
+}
+
+task install4jCustomiseDS_StoreAarch64(type: PythonTask) {
+  inputs.file(install4jDMGDSStore)
+  outputs.file(install4jDMGFixedDSStoreAarch64)
+  def command_args = [ jalview_customise_ds_store,
+    '--input', install4jDMGDSStore,
+    '--output', install4jDMGFixedDSStoreAarch64,
+    '--volumename', install4jmacOSArchiveAarch64Name,
+    '--backgroundfile', install4j_dmg_background_filename,
+    '--dmg', install4jmacOSArchiveAarch64DMGFilename + ".dmg",
+    '--appname', "${applicationName}.app",
+  ]
+  if (file(install4jDMGDSStoreJSON).exists()) {
+    command_args += [ '--config', install4jDMGDSStoreJSON ]
+    inputs.file(install4jDMGDSStoreJSON)
+  }
+  command = command_args
+  doFirst {
+    def print_args = []
+    for (int i = 0; i < command_args.size(); i++) {
+      def arg = command_args[i]
+      print_args += (i > 0 && !arg.startsWith("-")) ? "\"${arg}\"" : arg
+    }
+    println("Running command '${print_args.join(' ')}'")
+  }
+}
+
+task install4jCustomiseDS_Store {
+  dependsOn install4jCustomiseDS_StoreX64
+  dependsOn install4jCustomiseDS_StoreAarch64
+}
+
+task install4jDMGProcesses {
   dependsOn install4jDMGBackgroundImageProcess
+  dependsOn install4jCustomiseDS_Store
 }
 
 task installerFiles(type: com.install4j.gradle.Install4jTask) {
@@ -2535,10 +2923,13 @@ task installerFiles(type: com.install4j.gradle.Install4jTask) {
   dependsOn getdown
   dependsOn copyInstall4jTemplate
   dependsOn cleanInstallersDataFiles
-  dependsOn install4jDMGBackgroundImage
+  dependsOn install4jDMGProcesses
 
   projectFile = install4jConfFile
 
+  // run install4j with 4g
+  vmParameters = ["-Xmx4294967296"]
+
   // create an md5 for the input files to use as version for install4j conf file
   def digest = MessageDigest.getInstance("MD5")
   digest.update(
@@ -2571,13 +2962,17 @@ task installerFiles(type: com.install4j.gradle.Install4jTask) {
     'BUNDLE_ID': install4jBundleId,
     'INTERNAL_ID': install4jInternalId,
     'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
-    'MACOS_DMG_DS_STORE': install4jDMGDSStore,
+    'MACOS_X64_DMG_DS_STORE': install4jDMGFixedDSStoreX64,
+    'MACOS_AARCH64_DMG_DS_STORE': install4jDMGFixedDSStoreAarch64,
     'MACOS_DMG_BG_IMAGE': "${install4jDMGBackgroundImageBuildDir}/${install4jDMGBackgroundImageFile}",
+    'MACOS_DMG_BG_FILENAME': install4j_dmg_background_filename,
     'WRAPPER_LINK': getdownWrapperLink,
     'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
     'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
+    'BATCH_WRAPPER_SCRIPT': getdown_batch_wrapper_script,
     'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
-    'INSTALLER_NAME': install4jInstallerName,
+    'MACOSARCHIVE_X64_NAME': install4jmacOSArchiveX64Name,
+    'MACOSARCHIVE_AARCH64_NAME': install4jmacOSArchiveAarch64Name,
     'INSTALL4J_UTILS_DIR': install4j_utils_dir,
     'GETDOWN_CHANNEL_DIR': getdownChannelDir,
     'GETDOWN_FILES_DIR': getdown_files_dir,
@@ -2596,6 +2991,9 @@ task installerFiles(type: com.install4j.gradle.Install4jTask) {
     'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
     'PNG_ICON_FILE': install4jPngIconFile,
     'BACKGROUND': install4jBackground,
+    'MACOSARCHIVE_X64_DMG_FILENAME': install4jmacOSArchiveX64DMGFilename,
+    'MACOSARCHIVE_AARCH64_DMG_FILENAME': install4jmacOSArchiveAarch64DMGFilename,
+    'MACOSARCHIVE_VOLUMEICON': install4jDMGVolumeIcon,
   ]
 
   def varNameMap = [
@@ -2775,6 +3173,7 @@ task sourceDist(type: Tar) {
   into project.name
 
   def EXCLUDE_FILES=[
+    "dist/*",
     "build/*",
     "bin/*",
     "test-output/",
@@ -3989,9 +4388,157 @@ task eclipseAutoBuildTask {
 }
 
 
+task jalviewjsCopyStderrLaunchFile(type: Copy) {
+  from file(jalviewjs_stderr_launch)
+  into jalviewjsSiteDir
+
+  inputs.file jalviewjs_stderr_launch
+  outputs.file jalviewjsStderrLaunchFilename
+}
+
+task cleanJalviewjsChromiumUserDir {
+  doFirst {
+    delete jalviewjsChromiumUserDir
+  }
+  outputs.dir jalviewjsChromiumUserDir
+  // always run when depended on
+  outputs.upToDateWhen { !file(jalviewjsChromiumUserDir).exists() }
+}
+
+task jalviewjsChromiumProfile {
+  dependsOn cleanJalviewjsChromiumUserDir
+  mustRunAfter cleanJalviewjsChromiumUserDir
+
+  def firstRun = file("${jalviewjsChromiumUserDir}/First Run")
+
+  doFirst {
+    mkdir jalviewjsChromiumProfileDir
+    firstRun.text = ""
+  }
+  outputs.file firstRun
+}
+
+task jalviewjsLaunchTest {
+  group "Test"
+  description "Check JalviewJS opens in a browser"
+  dependsOn jalviewjsBuildSite
+  dependsOn jalviewjsCopyStderrLaunchFile
+  dependsOn jalviewjsChromiumProfile
+
+  def macOS = OperatingSystem.current().isMacOsX()
+  def chromiumBinary = macOS ? jalviewjs_macos_chromium_binary : jalviewjs_chromium_binary
+  if (chromiumBinary.startsWith("~/")) {
+    chromiumBinary = System.getProperty("user.home") + chromiumBinary.substring(1)
+  }
+  
+  def stdout
+  def stderr
+  doFirst {
+    def timeoutms = Integer.valueOf(jalviewjs_chromium_overall_timeout) * 1000
+    
+    def binary = file(chromiumBinary)
+    if (!binary.exists()) {
+      throw new StopExecutionException("Could not find chromium binary '${chromiumBinary}'. Cannot run task ${name}.")
+    }
+    stdout = new ByteArrayOutputStream()
+    stderr = new ByteArrayOutputStream()
+    def execStdout
+    def execStderr
+    if (jalviewjs_j2s_to_console.equals("true")) {
+      execStdout = new org.apache.tools.ant.util.TeeOutputStream(
+        stdout,
+        System.out)
+      execStderr = new org.apache.tools.ant.util.TeeOutputStream(
+        stderr,
+        System.err)
+    } else {
+      execStdout = stdout
+      execStderr = stderr
+    }
+    def execArgs = [
+      "--no-sandbox", // --no-sandbox IS USED BY THE THORIUM APPIMAGE ON THE BUILDSERVER
+      "--headless=new",
+      "--disable-gpu",
+      "--timeout=${timeoutms}",
+      "--virtual-time-budget=${timeoutms}",
+      "--user-data-dir=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_chromium_user_dir}",
+      "--profile-directory=${jalviewjs_chromium_profile_name}",
+      "--allow-file-access-from-files",
+      "--enable-logging=stderr",
+      "file://${jalviewDirAbsolutePath}/${jalviewjsStderrLaunchFilename}"
+    ]
+    
+    if (true || macOS) {
+      ScheduledExecutorService executor = Executors.newScheduledThreadPool(3);
+      Future f1 = executor.submit(
+        () -> {
+          exec {
+            standardOutput = execStdout
+            errorOutput = execStderr
+            executable(chromiumBinary)
+            args(execArgs)
+            println "COMMAND: '"+commandLine.join(" ")+"'"
+          }
+          executor.shutdownNow()
+        }
+      )
+
+      def noChangeBytes = 0
+      def noChangeIterations = 0
+      executor.scheduleAtFixedRate(
+        () -> {
+          String stderrString = stderr.toString()
+          // shutdown the task if we have a success string
+          if (stderrString.contains(jalviewjs_desktop_init_string)) {
+            f1.cancel()
+            Thread.sleep(1000)
+            executor.shutdownNow()
+          }
+          // if no change in stderr for 10s then also end
+          if (noChangeIterations >= jalviewjs_chromium_idle_timeout) {
+            executor.shutdownNow()
+          }
+          if (stderrString.length() == noChangeBytes) {
+            noChangeIterations++
+          } else {
+            noChangeBytes = stderrString.length()
+            noChangeIterations = 0
+          }
+        },
+        1, 1, TimeUnit.SECONDS)
+
+      executor.schedule(new Runnable(){
+        public void run(){
+          f1.cancel()
+          executor.shutdownNow()
+        }
+      }, timeoutms, TimeUnit.MILLISECONDS)
+
+      executor.awaitTermination(timeoutms+10000, TimeUnit.MILLISECONDS)
+      executor.shutdownNow()
+    }
+
+  }
+  
+  doLast {
+    def found = false
+    stderr.toString().eachLine { line ->
+      if (line.contains(jalviewjs_desktop_init_string)) {
+        println("Found line '"+line+"'")
+        found = true
+        return
+      }
+    }
+    if (!found) {
+      throw new GradleException("Could not find evidence of Desktop launch in JalviewJS.")
+    }
+  }
+}
+  
+
 task jalviewjs {
   group "JalviewJS"
-  description "Build the site"
+  description "Build the JalviewJS site and run the launch test"
   dependsOn jalviewjsBuildSite
+  dependsOn jalviewjsLaunchTest
 }
-