Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

[jalview.git] / build.gradle

diff --git a/build.gradle b/build.gradle
index 17407a9..46f2226 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -12,6 +12,7 @@ import java.security.MessageDigest
 import groovy.transform.ExternalizeMethods
 import groovy.util.XmlParser
 import groovy.xml.XmlUtil
+
 import com.vladsch.flexmark.util.ast.Node
 import com.vladsch.flexmark.html.HtmlRenderer
 import com.vladsch.flexmark.parser.Parser
@@ -52,12 +53,12 @@ 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()
 }
 
+
 def overrideProperties(String propsFileName, boolean output = false) {
   if (propsFileName == null) {
     return
@@ -164,7 +165,6 @@ ext {
 
   // datestamp
   buildDate = new Date().format("yyyyMMdd")
-
   // essentials
   bareSourceDir = string(source_dir)
   sourceDir = string("${jalviewDir}/${bareSourceDir}")
@@ -185,6 +185,7 @@ ext {
   //cloverTestClassesDir = cloverClassesDir
   cloverDb = string("${cloverBuildDir}/clover.db")
 
+
   testSourceDir = useClover ? cloverTestInstrDir : testDir
   testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
 
@@ -467,6 +468,7 @@ ext {
   helpBuildDir = string("${resourceBuildDir}/help_build")
   docBuildDir = string("${resourceBuildDir}/doc_build")
 
+
   if (buildProperties == null) {
     buildProperties = string("${resourcesBuildDir}/${build_properties_file}")
   }
@@ -515,6 +517,7 @@ sourceSets {
       srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
     }
 
+
     compileClasspath = files(sourceSets.main.java.outputDir)
     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 
@@ -1158,6 +1161,7 @@ task convertMdFiles {
     def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
     htmlFiles.add(file(htmlFilePath))
   }
+
   outputs.files(htmlFiles)
 }
 
@@ -1264,7 +1268,6 @@ task createBuildProperties(type: WriteProperties) {
   outputs.file(outputFile)
 }
 
-
 task buildIndices(type: JavaExec) {
   dependsOn copyHelp
   classpath = sourceSets.main.compileClasspath
@@ -1290,6 +1293,7 @@ task buildResources {
   dependsOn createBuildProperties
 }
 
+
 task prepare {
   dependsOn buildResources
   dependsOn copyDocs
@@ -1302,8 +1306,6 @@ task prepare {
 compileJava.dependsOn prepare
 run.dependsOn compileJava
 //run.dependsOn prepare
-
-
 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
 test {
   dependsOn prepare
@@ -1346,6 +1348,8 @@ test {
 }
 
 
+
+
 task compileLinkCheck(type: JavaCompile) {
   options.fork = true
   classpath = files("${jalviewDir}/${utils_dir}")
@@ -1381,7 +1385,6 @@ task linkCheck(type: JavaExec) {
   outputs.file(helpLinksCheckerOutFile)
 }
 
-
 // import the pubhtmlhelp target
 ant.properties.basedir = "${jalviewDir}"
 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
@@ -1412,7 +1415,6 @@ jar {
   archiveFileName = rootProject.name+".jar"
   duplicatesStrategy "EXCLUDE"
 
-
   exclude "cache*/**"
   exclude "*.jar"
   exclude "*.jar.*"
@@ -1463,7 +1465,6 @@ task cleanDist {
   dependsOn clean
 }
 
-
 shadowJar {
   group = "distribution"
   description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
@@ -1477,9 +1478,7 @@ shadowJar {
     attributes "Implementation-Version": JALVIEW_VERSION,
     "Application-Name": install4jApplicationName
   }
-
   duplicatesStrategy "INCLUDE"
-
   mainClassName = shadow_jar_main_class
   mergeServiceFiles()
   classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
@@ -1855,6 +1854,7 @@ task copyInstall4jTemplate {
       }
     }
 
+
     // write install4j file
     install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
   }
@@ -1941,7 +1941,6 @@ task installers(type: com.install4j.gradle.Install4jTask) {
     'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
     'PNG_ICON_FILE': install4jPngIconFile,
     'BACKGROUND': install4jBackground,
-
   ]
 
   //println("INSTALL4J VARIABLES:")
@@ -1995,7 +1994,6 @@ task sourceDist(type: Tar) {
 
   dependsOn createBuildProperties
   dependsOn convertMdFiles
-
   def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
   def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
   archiveFileName = outputFileName
@@ -2081,7 +2079,6 @@ task sourceDist(type: Tar) {
 //    exclude(EXCLUDE_FILES)
 //    exclude(PROCESS_FILES)
 //  }
-
   from(file(buildProperties).getParent()) {
     include(file(buildProperties).getName())
     rename(file(buildProperties).getName(), "build_properties")
@@ -2089,7 +2086,6 @@ task sourceDist(type: Tar) {
       line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
     })
   }
-
 }
 
 
@@ -2134,8 +2130,6 @@ task jalviewjsEnableAltFileProperty(type: WriteProperties) {
     property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
   }
 }
-
-
 task jalviewjsSetEclipseWorkspace {
   def propKey = "jalviewjs_eclipse_workspace"
   def propVal = null
@@ -2399,10 +2393,8 @@ task jalviewjsSyncAllLibs (type: Sync) {
   preserve {
     include "**"
   }
-
   // should this be exclude really ?
   duplicatesStrategy "INCLUDE"
-
   outputs.files outputFiles
   inputs.files inputFiles
 }