Merge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3' into releases/Release_2_...

[jalview.git] / build.gradle

diff --git a/build.gradle b/build.gradle
index 6fa6632..b2e9af1 100644 (file)
--- 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
@@ -91,7 +94,7 @@ ext {
   }
   ////
   // Set JALVIEW_VERSION if it is not already set
-  if (findProperty(JALVIEW_VERSION)==null || "".equals(JALVIEW_VERSION)) {
+  if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
     JALVIEW_VERSION = releaseProps.get("jalview.version")
   }
   
@@ -136,7 +139,7 @@ ext {
   cloverBuildDir = "${buildDir}/clover"
   cloverInstrDir = file("${cloverBuildDir}/clover-instr")
   cloverClassesDir = file("${cloverBuildDir}/clover-classes")
-  cloverReportDir = file("${cloverBuildDir}/clover-report")
+  cloverReportDir = file("${buildDir}/reports/clover")
   cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
   cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
   //cloverTestClassesDir = cloverClassesDir
@@ -193,10 +196,10 @@ ext {
     getdownChannelName = CHANNEL.toLowerCase()+"/${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}/${build_properties_file}")
       buildDist = false
     }
@@ -208,10 +211,10 @@ ext {
     getdownChannelName = string("archive/${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
     }
@@ -341,6 +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
@@ -354,6 +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"))
@@ -454,7 +459,7 @@ sourceSets {
       srcDirs += helpParentDir
     }
 
-    jar.destinationDir = file("${jalviewDir}/${packageDir}")
+    jar.destinationDir = file("${jalviewDir}/${package_dir}")
 
     compileClasspath = files(sourceSets.main.java.outputDir)
     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
@@ -642,6 +647,7 @@ eclipse {
 task cleanClover {
   doFirst {
     delete cloverBuildDir
+    delete cloverReportDir
   }
 }
 
@@ -738,6 +744,13 @@ task cloverConsoleReport(type: JavaExec) {
   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",
@@ -757,13 +770,20 @@ task cloverHtmlReport(type: JavaExec) {
     file(cloverDb).exists()
   }
 
-  def cloverHtmlDir = "${cloverReportDir}/clover"
+  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",
@@ -772,6 +792,10 @@ task cloverHtmlReport(type: JavaExec) {
     cloverHtmlDir
   ]
 
+  if (cloverreport_html_options.length() > 0) {
+    argsList += cloverreport_html_options.split(" ")
+  }
+
   args argsList.toArray()
 }
 
@@ -791,6 +815,13 @@ task cloverXmlReport(type: JavaExec) {
   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",
@@ -799,6 +830,10 @@ task cloverXmlReport(type: JavaExec) {
     cloverXmlFile
   ]
 
+  if (cloverreport_xml_options.length() > 0) {
+    argsList += cloverreport_xml_options.split(" ")
+  }
+
   args argsList.toArray()
 }
 
@@ -1057,7 +1092,7 @@ test {
 
   doFirst {
     if (useClover) {
-      print("Running tests " + (useClover?"WITH":"WITHOUT") + " clover [clover="+useClover+"]\n")
+      println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
     }
   }
 }
@@ -1126,7 +1161,7 @@ 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")
   }
 }
 
@@ -1142,7 +1177,7 @@ jar {
     "Codebase": application_codebase
   }
 
-  destinationDir = file("${jalviewDir}/${packageDir}")
+  destinationDir = file("${jalviewDir}/${package_dir}")
   archiveName = rootProject.name+".jar"
 
   exclude "cache*/**"
@@ -1152,20 +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
   }
@@ -1181,7 +1216,7 @@ task makeDist {
   dependsOn cleanPackageDir
   dependsOn syncJars
   dependsOn jar
-  outputs.dir("${jalviewDir}/${packageDir}")
+  outputs.dir("${jalviewDir}/${package_dir}")
 }
 
 
@@ -1294,7 +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
@@ -1312,6 +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")) {
@@ -1331,7 +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("${getdownWebsiteDir}/getdown.txt")
     getdown_txt.write(getdownTextString)
@@ -1358,7 +1407,7 @@ task getdownWebsite() {
       copy {
         from getdown_txt
         from getdownLauncher
-        from "${getdownWebsiteDir}/${getdown_build_properties}"
+        from "${getdownAppDir}/${getdown_build_properties}"
         if (file(getdownLauncher).getName() != getdown_launcher) {
           rename(file(getdownLauncher).getName(), getdown_launcher)
         }
@@ -1389,7 +1438,7 @@ task getdownWebsite() {
   }
 
   if (buildDist) {
-    inputs.dir("${jalviewDir}/${packageDir}")
+    inputs.dir("${jalviewDir}/${package_dir}")
   }
   outputs.dir(getdownWebsiteDir)
   outputs.dir(getdownFilesDir)