JAL-4023 store distances as doubles

[jalview.git] / build.gradle

diff --git a/build.gradle b/build.gradle
index 7146d31..b4636bc 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -40,9 +40,9 @@ plugins {
   id 'eclipse'
   id "com.diffplug.gradle.spotless" version "3.28.0"
   id 'com.github.johnrengelman.shadow' version '4.0.3'
-  id 'com.install4j.gradle' version '8.0.10'
+  id 'com.install4j.gradle' version '9.0.6'
   id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with  gradle task1 [task2 ...] taskTree
-  id 'com.palantir.git-version' version '0.12.3'
+  id 'com.palantir.git-version' version '0.13.0' apply false
 }
 
 repositories {
@@ -52,6 +52,7 @@ repositories {
 }
 
 
+
 // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
 def string(Object o) {
   return o == null ? "" : o.toString()
@@ -102,6 +103,7 @@ ext {
   // Import channel_properties
   channelDir = string("${jalviewDir}/${channel_properties_dir}/${propertiesChannelName}")
   channelGradleProperties = string("${channelDir}/channel_gradle.properties")
+  channelPropsFile = string("${channelDir}/${resource_dir}/${channel_props}")
   overrideProperties(channelGradleProperties, false)
   // local build environment properties
   // can be "projectDir/local.properties"
@@ -113,7 +115,7 @@ ext {
   // Import releaseProps from the RELEASE file
   // or a file specified via JALVIEW_RELEASE_FILE if defined
   // Expect jalview.version and target release branch in jalview.release        
-  def releaseProps = new Properties();
+  releaseProps = new Properties();
   def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
   def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
   try {
@@ -204,7 +206,7 @@ ext {
   install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}"
   install4jDMGBackgroundImage = "${install4j_images_dir}/${install4j_dmg_background}"
   install4jInstallerName = "${jalview_name} Non-Release Installer"
-  install4jExecutableName = jalview_name.replaceAll("[^\\w]+", "_").toLowerCase()
+  install4jExecutableName = install4j_executable_name
   install4jExtraScheme = "jalviewx"
   install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}")
   install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}")
@@ -370,6 +372,7 @@ ext {
                                     .replaceAll("_*-_*", "-") // collapse _-_
                                     .toLowerCase()
 
+  getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local"
   getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}")
   //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
   getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}")
@@ -380,9 +383,21 @@ ext {
   modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
   modules_runtimeClasspath = modules_compileClasspath
   */
-  def details = versionDetails()
-  gitHash = details.gitHash
-  gitBranch = details.branchName
+
+  gitHash = "SOURCE"
+  gitBranch = "Source"
+  try {
+    apply plugin: "com.palantir.git-version"
+    def details = versionDetails()
+    gitHash = details.gitHash
+    gitBranch = details.branchName
+  } catch(org.gradle.api.internal.plugins.PluginApplicationException e) {
+    println("Not in a git repository. Using git values from RELEASE properties file.")
+    gitHash = releaseProps.getProperty("git.hash")
+    gitBranch = releaseProps.getProperty("git.branch")
+  } catch(java.lang.RuntimeException e1) {
+    throw new GradleException("Error with git-version plugin.  Directory '.git' exists but versionDetails() cannot be found.")
+  }
 
   println("Using a ${CHANNEL} profile.")
 
@@ -418,16 +433,16 @@ ext {
     '--add-modules', j11modules
     ]
      */
-  } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
-    JAVA_INTEGER_VERSION = JAVA_VERSION
-    libDir = j11libDir
-    libDistDir = j11libDir
-    compile_source_compatibility = JAVA_VERSION
-    compile_target_compatibility = JAVA_VERSION
+  } else if (JAVA_VERSION.equals("17")) {
+    JAVA_INTEGER_VERSION = string("17")
+    libDir = j17libDir
+    libDistDir = j17libDir
+    compile_source_compatibility = 17
+    compile_target_compatibility = 17
     getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
     getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
     getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
-    eclipseJavaRuntimeName = string("JavaSE-11")
+    eclipseJavaRuntimeName = string("JavaSE-17")
     /* compile without modules -- using classpath libraries
     additional_compiler_args += [
     '--module-path', modules_compileClasspath.asPath,
@@ -447,11 +462,11 @@ ext {
     jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
   }
   macosJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-mac-x64/jre")
-  macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-mac-x64.tar.gz")
   windowsJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-windows-x64/jre")
-  windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-windows-x64.tar.gz")
   linuxJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-linux-x64/jre")
-  linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-linux-x64.tar.gz")
+  macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_mac_x64.tar.gz")
+  windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_windows_x64.tar.gz")
+  linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_linux_x64.tar.gz")
   install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
   install4jConfFileName = string("jalview-install4j-conf.install4j")
   install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
@@ -1408,6 +1423,8 @@ jar {
   def outputDir = "${jalviewDir}/${package_dir}"
   destinationDirectory = file(outputDir)
   archiveFileName = rootProject.name+".jar"
+  duplicatesStrategy "EXCLUDE"
+
 
   exclude "cache*/**"
   exclude "*.jar"
@@ -1473,6 +1490,9 @@ shadowJar {
     attributes "Implementation-Version": JALVIEW_VERSION,
     "Application-Name": install4jApplicationName
   }
+
+  duplicatesStrategy "INCLUDE"
+
   mainClassName = shadow_jar_main_class
   mergeServiceFiles()
   classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
@@ -1504,6 +1524,12 @@ task getdownWebsite() {
     }
     getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
 
+    copy {
+      from channelPropsFile
+      into getdownWebsiteDir
+    }
+    getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
+
     // 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) {
@@ -1571,6 +1597,18 @@ task getdownWebsite() {
         into getdownResourceDir
       }
     }
+    
+    def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
+    getdownWrapperScripts.each{ script ->
+      def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
+      if (s.exists()) {
+        copy {
+          from s
+          into "${getdownWebsiteDir}/${getdown_wrapper_script_dir}"
+        }
+        getdownTextString += "resource = ${getdown_wrapper_script_dir}/${script}\n"
+      }
+    }
 
     def codeFiles = []
     fileTree(file(package_dir)).each{ f ->
@@ -1581,7 +1619,9 @@ task getdownWebsite() {
         codeFiles += f
       }
     }
-    codeFiles.sort().each{f ->
+    def jalviewJar = jar.archiveFileName.getOrNull()
+    // put jalview.jar first for CLASSPATH and .properties files reasons
+    codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
       def name = f.getName()
       def line = "code = ${getdownAppDistDir}/${name}\n"
       getdownTextString += line
@@ -1665,6 +1705,7 @@ task getdownWebsite() {
       from launchJvl
       from getdownLauncher
       from "${getdownWebsiteDir}/${getdown_build_properties}"
+      from "${getdownWebsiteDir}/${channel_props}"
       if (file(getdownLauncher).getName() != getdown_launcher) {
         rename(file(getdownLauncher).getName(), getdown_launcher)
       }
@@ -1789,6 +1830,12 @@ task copyInstall4jTemplate {
       }
     }
 
+    // disable install screen for OSX dmg (for 2.11.2.0)
+    install4jConfigXml.'**'.macosArchive.each { macosArchive -> 
+      macosArchive.attributes().remove('executeSetupApp')
+      macosArchive.attributes().remove('setupAppId')
+    }
+
     // turn off checksum creation for LOCAL channel
     def e = install4jConfigXml.application[0]
     if (CHANNEL == "LOCAL") {
@@ -1899,6 +1946,10 @@ task installers(type: com.install4j.gradle.Install4jTask) {
     'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
     'MACOS_DMG_DS_STORE': install4jDMGDSStore,
     'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
+    'WRAPPER_LINK': getdownWrapperLink,
+    'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
+    'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
+    'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
     'INSTALLER_NAME': install4jInstallerName,
     'INSTALL4J_UTILS_DIR': install4j_utils_dir,
     'GETDOWN_WEBSITE_DIR': getdown_website_dir,
@@ -1948,7 +1999,7 @@ task installers(type: com.install4j.gradle.Install4jTask) {
     println("Using projectFile "+projectFile)
     if (!disableNotarization) { println("Will notarize OSX App DMG") }
   }
-  verbose=true
+  //verbose=true
 
   inputs.dir(getdownWebsiteDir)
   inputs.file(install4jConfFile)
@@ -1965,6 +2016,22 @@ spotless {
   }
 }
 
+task createSourceReleaseProperties(type: WriteProperties) {
+  group = "distribution"
+  description = "Create the source RELEASE properties file"
+  
+  def sourceTarBuildDir = "${buildDir}/sourceTar"
+  def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
+  outputFile (sourceReleasePropertiesFile)
+
+  doFirst {
+    releaseProps.each{ key, val -> property key, val }
+    property "git.branch", gitBranch
+    property "git.hash", gitHash
+  }
+
+  outputs.file(outputFile)
+}
 
 task sourceDist(type: Tar) {
   group "distribution"
@@ -1972,6 +2039,9 @@ task sourceDist(type: Tar) {
 
   dependsOn createBuildProperties
   dependsOn convertMdFiles
+  dependsOn eclipseAllPreferences
+  dependsOn createSourceReleaseProperties
+
 
   def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
   def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
@@ -1996,6 +2066,7 @@ task sourceDist(type: Tar) {
     "*locales/**",
     "utils/InstallAnywhere",
     "**/*.log",
+    "RELEASE",
   ] 
   def PROCESS_FILES=[
     "AUTHORS",
@@ -2005,7 +2076,6 @@ task sourceDist(type: Tar) {
     "FEATURETODO",
     "LICENSE",
     "**/README",
-    "RELEASE",
     "THIRDPARTYLIBS",
     "TESTNG",
     "build.gradle",
@@ -2020,7 +2090,9 @@ task sourceDist(type: Tar) {
     "**/*.sh",
   ]
   def INCLUDE_FILES=[
-    ".settings/org.eclipse.jdt.core.jalview.prefs",
+    ".classpath",
+    ".settings/org.eclipse.buildship.core.prefs",
+    ".settings/org.eclipse.jdt.core.prefs"
   ]
 
   from(jalviewDir) {
@@ -2067,6 +2139,10 @@ task sourceDist(type: Tar) {
     })
   }
 
+  def sourceTarBuildDir = "${buildDir}/sourceTar"
+  from(sourceTarBuildDir) {
+    // this includes the appended RELEASE properties file
+  }
 }
 
 
@@ -2376,6 +2452,10 @@ task jalviewjsSyncAllLibs (type: Sync) {
   preserve {
     include "**"
   }
+
+  // should this be exclude really ?
+  duplicatesStrategy "INCLUDE"
+
   outputs.files outputFiles
   inputs.files inputFiles
 }
@@ -2623,7 +2703,7 @@ def jalviewjsCallCore(String name, FileCollection list, String prefixFile, Strin
           new org.apache.tools.ant.util.TeeOutputStream(
             logErrFOS,
             stderr),
-          errorOutput)
+          System.err)
     } else {
       standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
         logOutFOS,
@@ -2930,7 +3010,13 @@ task jalviewjsServer {
   def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
   doLast {
 
-    SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory()
+    def factory
+    try {
+      def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
+      factory = f.newInstance()
+    } catch (ClassNotFoundException e) {
+      throw new GradleException("Unable to create SimpleHttpFileServerFactory")
+    }
     def port = Integer.valueOf(jalviewjs_server_port)
     def start = port
     def running = false