Properly integrated endGaps option for AlignSeq.traceAlignment()

[jalview.git] / build.gradle

diff --git a/build.gradle b/build.gradle
index a917a0d..800fe42 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -53,7 +53,6 @@ plugins {
   id 'eclipse'
   id "com.diffplug.spotless" version "6.18.0" //.gradle.spotless" "3.28.0"
   id 'com.github.johnrengelman.shadow' version '8.1.1' // was 4.0.3
-  id "com.diffplug.gradle.spotless" version "3.28.0"
   id 'com.install4j.gradle' version '10.0.3'
   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
@@ -194,7 +193,7 @@ ext {
   testDir = string("${jalviewDir}/${bareTestSourceDir}")
 
   classesDir = string("${jalviewDir}/${classes_dir}")
-  outputDir = file(classesDir)
+  destinationDirectory = file(classesDir)
 
   // clover
   useClover = clover.equals("true")
@@ -592,14 +591,14 @@ sourceSets {
   main {
     java {
       srcDirs sourceDir
-      outputDir = file(classesDir)
+      destinationDirectory = file(classesDir)
     }
 
     resources {
       srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
     }
 
-    compileClasspath = files(sourceSets.main.java.outputDir)
+    compileClasspath = files(sourceSets.main.java.destinationDirectory)
     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 
     runtimeClasspath = compileClasspath
@@ -609,14 +608,14 @@ sourceSets {
   clover {
     java {
       srcDirs cloverInstrDir
-      outputDir = cloverClassesDir
+      destinationDirectory = cloverClassesDir
     }
 
     resources {
       srcDirs = sourceSets.main.resources.srcDirs
     }
 
-    compileClasspath = files( sourceSets.clover.java.outputDir )
+    compileClasspath = files( sourceSets.clover.java.destinationDirectory )
     //compileClasspath += files( testClassesDir )
     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
     compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
@@ -628,14 +627,14 @@ sourceSets {
   test {
     java {
       srcDirs testSourceDir
-      outputDir = file(testClassesDir)
+      destinationDirectory = file(testClassesDir)
     }
 
     resources {
       srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
     }
 
-    compileClasspath = files( sourceSets.test.java.outputDir )
+    compileClasspath = files( sourceSets.test.java.destinationDirectory )
     compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
     compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
 
@@ -660,7 +659,7 @@ eclipse {
   }
 
   classpath {
-    //defaultOutputDir = sourceSets.main.java.outputDir
+    //defaultOutputDir = sourceSets.main.java.destinationDirectory
     configurations.each{ c->
       if (c.isCanBeResolved()) {
         minusConfigurations += [c]
@@ -699,7 +698,7 @@ eclipse {
         HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
 
         sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
-          //don't want to add outputDir as eclipse is using its own output dir in bin/main
+          //don't want to add destinationDirectory as eclipse is using its own output dir in bin/main
           if (it.isDirectory() || ! it.exists()) {
             // don't add dirs to classpath, especially if they don't exist
             return false // groovy "continue" in .any closure
@@ -719,7 +718,7 @@ eclipse {
         }
 
         sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
-          //no longer want to add outputDir as eclipse is using its own output dir in bin/main
+          //no longer want to add destinationDirectory as eclipse is using its own output dir in bin/main
           if (it.isDirectory() || ! it.exists()) {
             // don't add dirs to classpath
             return false // groovy "continue" in .any closure
@@ -1096,7 +1095,7 @@ compileTestJava {
 
 clean {
   doFirst {
-    delete sourceSets.main.java.outputDir
+    delete sourceSets.main.java.destinationDirectory
   }
 }
 
@@ -1104,7 +1103,7 @@ clean {
 cleanTest {
   dependsOn cleanClover
   doFirst {
-    delete sourceSets.test.java.outputDir
+    delete sourceSets.test.java.destinationDirectory
   }
 }
 
@@ -1196,7 +1195,7 @@ def convertMdToHtml (FileTree mdFiles, File cssFile) {
 
 task copyDocs(type: Copy) {
   def inputDir = "${jalviewDir}/${doc_dir}"
-  def outputDir = "${docBuildDir}/${doc_dir}"
+  def destinationDirectory = "${docBuildDir}/${doc_dir}"
   from(inputDir) {
     include('**/*.txt')
     include('**/*.md')
@@ -1217,10 +1216,10 @@ task copyDocs(type: Copy) {
     exclude('**/*.html')
     exclude('**/*.xml')
   }
-  into outputDir
+  into destinationDirectory
 
   inputs.dir(inputDir)
-  outputs.dir(outputDir)
+  outputs.dir(destinationDirectory)
 }
 
 
@@ -1455,7 +1454,7 @@ def getMdSections(String content) {
 
 task copyHelp(type: Copy) {
   def inputDir = helpSourceDir
-  def outputDir = "${helpBuildDir}/${help_dir}"
+  def destinationDirectory = "${helpBuildDir}/${help_dir}"
   from(inputDir) {
     include('**/*.txt')
     include('**/*.md')
@@ -1480,11 +1479,11 @@ task copyHelp(type: Copy) {
     exclude('**/*.xml')
     exclude('**/*.jhm')
   }
-  into outputDir
+  into destinationDirectory
 
   inputs.dir(inputDir)
   outputs.files(helpFile)
-  outputs.dir(outputDir)
+  outputs.dir(destinationDirectory)
 }
 
 
@@ -1632,7 +1631,7 @@ task copyResources(type: Copy) {
   description = "Copy (and make text substitutions in) the resources dir to the build area"
 
   def inputDir = resourceDir
-  def outputDir = resourcesBuildDir
+  def destinationDirectory = resourcesBuildDir
   from(inputDir) {
     include('**/*.txt')
     include('**/*.md')
@@ -1653,10 +1652,10 @@ task copyResources(type: Copy) {
     exclude('**/*.html')
     exclude('**/*.xml')
   }
-  into outputDir
+  into destinationDirectory
 
   inputs.dir(inputDir)
-  outputs.dir(outputDir)
+  outputs.dir(destinationDirectory)
 }
 
 task copyChannelResources(type: Copy) {
@@ -1665,7 +1664,7 @@ task copyChannelResources(type: Copy) {
   description = "Copy the channel resources dir to the build resources area"
 
   def inputDir = "${channelDir}/${resource_dir}"
-  def outputDir = resourcesBuildDir
+  def destinationDirectory = resourcesBuildDir
   from(inputDir) {
     include(channel_props)
     filter(ReplaceTokens,
@@ -1679,10 +1678,10 @@ task copyChannelResources(type: Copy) {
   from(inputDir) {
     exclude(channel_props)
   }
-  into outputDir
+  into destinationDirectory
 
   inputs.dir(inputDir)
-  outputs.dir(outputDir)
+  outputs.dir(destinationDirectory)
 }
 
 task createBuildProperties(type: WriteProperties) {
@@ -2085,8 +2084,8 @@ jar {
     "Implementation-Version": JALVIEW_VERSION
   }
 
-  def outputDir = "${jalviewDir}/${package_dir}"
-  outputDir = file(outputDir)
+  def destinationDirectory = "${jalviewDir}/${package_dir}"
+  destinationDirectory = file(destinationDirectory)
   archiveFileName = rootProject.name+".jar"
   duplicatesStrategy "EXCLUDE"
 
@@ -2097,11 +2096,11 @@ jar {
   exclude "**/*.jar"
   exclude "**/*.jar.*"
 
-  inputs.dir(sourceSets.main.java.outputDir)
+  inputs.dir(sourceSets.main.java.destinationDirectory)
   sourceSets.main.resources.srcDirs.each{ dir ->
     inputs.dir(dir)
   }
-  outputs.file("${outputDir}/${archiveFileName}")
+  outputs.file("${destinationDirectory}/${archiveFileName}")
 }
 
 
@@ -3331,10 +3330,10 @@ task jalviewjsEclipseCopyDropins(type: Copy) {
 
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
   inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
-  def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
 }
 
 
@@ -3442,13 +3441,13 @@ task jalviewjsSyncAllLibs (type: Sync) {
   dependsOn jalviewjsTransferUnzipAllLibs
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
   inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
   def outputFiles = []
   rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
+    outputFiles += "${destinationDirectory}/${filename}"
     null
   }
   preserve {
@@ -3467,13 +3466,13 @@ task jalviewjsSyncResources (type: Sync) {
   dependsOn buildResources
 
   def inputFiles = fileTree(dir: resourcesBuildDir)
-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
   def outputFiles = []
   rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
+    outputFiles += "${destinationDirectory}/${filename}"
     null
   }
   preserve {
@@ -3486,13 +3485,13 @@ task jalviewjsSyncResources (type: Sync) {
 
 task jalviewjsSyncSiteResources (type: Sync) {
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
   def outputFiles = []
   rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
+    outputFiles += "${destinationDirectory}/${filename}"
     null
   }
   preserve {
@@ -3506,13 +3505,13 @@ task jalviewjsSyncSiteResources (type: Sync) {
 task jalviewjsSyncBuildProperties (type: Sync) {
   dependsOn createBuildProperties
   def inputFiles = [file(buildProperties)]
-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
   def outputFiles = []
   rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
+    outputFiles += "${destinationDirectory}/${filename}"
     null
   }
   preserve {
@@ -3731,7 +3730,7 @@ task jalviewjsBuildAllCores {
   def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
   def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
   def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
-  def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
   def prefixFile = "${jsDir}/core/coretop2.js"
   def suffixFile = "${jsDir}/core/corebottom2.js"
 
@@ -3775,8 +3774,8 @@ task jalviewjsBuildAllCores {
     }
     def list = fileTree(dir: j2sDir, includes: filelist)
 
-    def jsfile = "${outputDir}/core${name}.js"
-    def zjsfile = "${outputDir}/core${name}.z.js"
+    def jsfile = "${destinationDirectory}/core${name}.js"
+    def zjsfile = "${destinationDirectory}/core${name}.z.js"
 
     jalviewjsCoreClasslists += [
       'jsfile': jsfile,
@@ -3794,8 +3793,8 @@ task jalviewjsBuildAllCores {
   // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
   def stevesoftClasslistName = "_stevesoft"
   def stevesoftClasslist = [
-    'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
-    'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
+    'jsfile': "${destinationDirectory}/core${stevesoftClasslistName}.js",
+    'zjsfile': "${destinationDirectory}/core${stevesoftClasslistName}.z.js",
     'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
     'name': stevesoftClasslistName
   ]
@@ -3828,8 +3827,8 @@ task jalviewjsBuildAllCores {
     ]
   )
   def allClasslist = [
-    'jsfile': "${outputDir}/core${allClasslistName}.js",
-    'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
+    'jsfile': "${destinationDirectory}/core${allClasslistName}.js",
+    'zjsfile': "${destinationDirectory}/core${allClasslistName}.z.js",
     'list': allJsFiles,
     'name': allClasslistName
   ]
@@ -3882,11 +3881,11 @@ task jalviewjsPublishCoreTemplates {
   dependsOn jalviewjsBuildAllCores
   def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
   def inputFile = file(inputFileName)
-  def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
 
   def outputFiles = []
   jalviewjsCoreClasslists.each { cl ->
-    def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
+    def outputFile = "${destinationDirectory}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
     cl['outputfile'] = outputFile
     outputFiles += outputFile
   }
@@ -3905,13 +3904,13 @@ task jalviewjsSyncCore (type: Sync) {
   dependsOn jalviewjsBuildAllCores
   dependsOn jalviewjsPublishCoreTemplates
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
   def outputFiles = []
   rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
+    outputFiles += "${destinationDirectory}/${filename}"
     null
   }
   preserve {