X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=9161ed25e7b8c46ef5127f4dee20c14c1182a798;hb=6ed2dabde1584f0fc3bb3af66f151a14664ffaf8;hp=105612405ae00414e7003db2f8ca812f62381803;hpb=639bc5f3126d65cc1de8992b9a0fa0cfb993a9ff;p=jalview.git diff --git a/build.gradle b/build.gradle index 1056124..9161ed2 100644 --- a/build.gradle +++ b/build.gradle @@ -45,10 +45,10 @@ plugins { id 'java' id 'application' id 'eclipse' - id "com.diffplug.gradle.spotless" version "3.28.0" - id 'com.github.johnrengelman.shadow' version '4.0.3' + 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.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.dorongold.task-tree' version '2.1.0' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree id 'com.palantir.git-version' version '0.13.0' apply false } @@ -138,6 +138,7 @@ ext { if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) { JALVIEW_VERSION = releaseProps.get("jalview.version") } + println("JALVIEW_VERSION is set to '${JALVIEW_VERSION}'") // this property set when running Eclipse headlessly j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild") @@ -182,6 +183,7 @@ ext { testDir = string("${jalviewDir}/${bareTestSourceDir}") classesDir = string("${jalviewDir}/${classes_dir}") + destinationDirectory = file(classesDir) // clover useClover = clover.equals("true") @@ -546,14 +548,14 @@ sourceSets { main { java { srcDirs sourceDir - outputDir = file(classesDir) + destinationDirectory = file(classesDir) } resources { srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ] } - compileClasspath = files(sourceSets.main.java.outputDir) + compileClasspath = files(sourceSets.main.java.destinationDirectory) compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"]) runtimeClasspath = compileClasspath @@ -563,14 +565,14 @@ sourceSets { clover { java { srcDirs cloverInstrDir - outputDir = cloverClassesDir + destinationDirectory = cloverClassesDir } resources { srcDirs = sourceSets.main.resources.srcDirs } - compileClasspath = files( sourceSets.clover.java.outputDir ) + compileClasspath = files( sourceSets.clover.java.destinationDirectory ) //compileClasspath += files( testClassesDir ) compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"]) compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"]) @@ -582,14 +584,14 @@ sourceSets { test { java { srcDirs testSourceDir - outputDir = file(testClassesDir) + destinationDirectory = file(testClassesDir) } resources { srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs } - compileClasspath = files( sourceSets.test.java.outputDir ) + compileClasspath = files( sourceSets.test.java.destinationDirectory ) compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"]) @@ -614,7 +616,7 @@ eclipse { } classpath { - //defaultOutputDir = sourceSets.main.java.outputDir + //defaultOutputDir = sourceSets.main.java.destinationDirectory configurations.each{ c-> if (c.isCanBeResolved()) { minusConfigurations += [c] @@ -653,7 +655,7 @@ eclipse { HashMap alreadyAddedLibPath = new HashMap<>(); sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any { - //don't want to add outputDir as eclipse is using its own output dir in bin/main + //don't want to add destinationDirectory as eclipse is using its own output dir in bin/main if (it.isDirectory() || ! it.exists()) { // don't add dirs to classpath, especially if they don't exist return false // groovy "continue" in .any closure @@ -673,7 +675,7 @@ eclipse { } sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any { - //no longer want to add outputDir as eclipse is using its own output dir in bin/main + //no longer want to add destinationDirectory as eclipse is using its own output dir in bin/main if (it.isDirectory() || ! it.exists()) { // don't add dirs to classpath return false // groovy "continue" in .any closure @@ -1050,7 +1052,7 @@ compileTestJava { clean { doFirst { - delete sourceSets.main.java.outputDir + delete sourceSets.main.java.destinationDirectory } } @@ -1058,7 +1060,7 @@ clean { cleanTest { dependsOn cleanClover doFirst { - delete sourceSets.test.java.outputDir + delete sourceSets.test.java.destinationDirectory } } @@ -1150,7 +1152,7 @@ def convertMdToHtml (FileTree mdFiles, File cssFile) { task copyDocs(type: Copy) { def inputDir = "${jalviewDir}/${doc_dir}" - def outputDir = "${docBuildDir}/${doc_dir}" + def destinationDirectory = "${docBuildDir}/${doc_dir}" from(inputDir) { include('**/*.txt') include('**/*.md') @@ -1171,10 +1173,10 @@ task copyDocs(type: Copy) { exclude('**/*.html') exclude('**/*.xml') } - into outputDir + into destinationDirectory inputs.dir(inputDir) - outputs.dir(outputDir) + outputs.dir(destinationDirectory) } @@ -1239,15 +1241,15 @@ def mdFileComponents(File mdFile, def dateOnly=false) { } if (inFrontMatter) { def m = null - if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2})/) { + if (m == line =~ /^date:\s*(\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2})/) { map["date"] = new Date().parse("yyyy-MM-dd HH:mm:ss", m[0][1]) - } else if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2})/) { + } else if (m == line =~ /^date:\s*(\d{4}-\d{2}-\d{2})/) { map["date"] = new Date().parse("yyyy-MM-dd", m[0][1]) - } else if (m = line =~ /^channel:\s*(\S+)/) { + } else if (m == line =~ /^channel:\s*(\S+)/) { map["channel"] = m[0][1] - } else if (m = line =~ /^version:\s*(\S+)/) { + } else if (m == line =~ /^version:\s*(\S+)/) { map["version"] = m[0][1] - } else if (m = line =~ /^\s*([^:]+)\s*:\s*(\S.*)/) { + } else if (m == line =~ /^\s*([^:]+)\s*:\s*(\S.*)/) { map[ m[0][1] ] = m[0][2] } if (dateOnly && map["date"] != null) { @@ -1306,7 +1308,7 @@ task hugoTemplates { def inSection = false changes.eachLine { line -> def m = null - if (m = line =~ /^##([^#].*)$/) { + if (m == line =~ /^##([^#].*)$/) { if (inSection) { changesHugo += "\n\n" } @@ -1316,7 +1318,7 @@ task hugoTemplates { section = section.replaceAll(/[^a-z0-9_\-]/, "") changesHugo += "
\n\n" inSection = true - } else if (m = line =~ /^(\s*-\s*)(.*?)()?\s*$/) { + } else if (m == line =~ /^(\s*-\s*)(.*?)()?\s*$/) { def comment = m[0][2].trim() if (comment != "") { comment = comment.replaceAll('"', """) @@ -1386,7 +1388,7 @@ def getMdSections(String content) { def sectionName = null content.eachLine { line -> def m = null - if (m = line =~ /^##([^#].*)$/) { + if (m == line =~ /^##([^#].*)$/) { if (sectionName != null) { sections[sectionName] = sectionContent sectionName = null @@ -1406,14 +1408,53 @@ def getMdSections(String content) { return sections } + +task copyHelp(type: Copy) { + def inputDir = helpSourceDir + def destinationDirectory = "${helpBuildDir}/${help_dir}" + from(inputDir) { + include('**/*.txt') + include('**/*.md') + include('**/*.html') + include('**/*.hs') + include('**/*.xml') + include('**/*.jhm') + filter(ReplaceTokens, + beginToken: '$$', + endToken: '$$', + tokens: [ + 'Version-Rel': JALVIEW_VERSION, + 'Year-Rel': getDate("yyyy") + ] + ) + } + from(inputDir) { + exclude('**/*.txt') + exclude('**/*.md') + exclude('**/*.html') + exclude('**/*.hs') + exclude('**/*.xml') + exclude('**/*.jhm') + } + into destinationDirectory + + inputs.dir(inputDir) + outputs.files(helpFile) + outputs.dir(destinationDirectory) +} + + +/* task releasesTemplates { group "help" description "Recreate whatsNew.html and releases.html from markdown files and templates in help" + dependsOn copyHelp + def releasesTemplateFile = file("${jalviewDir}/${releases_template}") def whatsnewTemplateFile = file("${jalviewDir}/${whatsnew_template}") - def releasesHtmlFile = file("${helpSourceDir}/${releases_html}") - def whatsnewHtmlFile = file("${helpSourceDir}/${whatsnew_html}") + def releasesHtmlFile = file("${helpBuildDir}/${help_dir}/${releases_html}") + def whatsnewHtmlFile = file("${helpBuildDir}/${help_dir}/${whatsnew_html}") def releasesMdDir = "${jalviewDir}/${releases_dir}" def whatsnewMdDir = "${jalviewDir}/${whatsnew_dir}" @@ -1475,18 +1516,18 @@ task releasesTemplates { } firstPart = false } - def displayDate = releaseFilesDates[rFile].format("d MMMMM yyyy") - - def lm = null - def rContentProcessed = "" - rContent.eachLine { line -> - if (lm = line =~ /^(\s*-)(\s*)(.*)$/) { - line = "${lm[0][1]}${lm[0][3]}${lm[0][2]}" - } else if (lm = line =~ /^###([^#]+.*)$/) { - line = "_${lm[0][1].trim()}_" - } - rContentProcessed += line + "\n" + def displayDate = releaseFilesDates[rFile].format("dd/MM/yyyy") + + def lm = null + def rContentProcessed = "" + rContent.eachLine { line -> + if (lm == line =~ /^(\s*-)(\s*)(.*)$/) { + line = "${lm[0][1]}${lm[0][3]}${lm[0][2]}" + } else if (lm == line =~ /^###([^#]+.*)$/) { + line = "_${lm[0][1].trim()}_" } + rContentProcessed += line + "\n" + } def rContentSections = getMdSections(rContentProcessed) def rVersion = versionTemplate @@ -1515,13 +1556,19 @@ task releasesTemplates { releasesHtmlFile.text = releasesTemplate if (whatsnewMdFile.exists()) { + def wnDisplayDate = releaseFilesDates[releaseMdFile] != null ? releaseFilesDates[releaseMdFile].format("dd MMMM yyyy") : "" def whatsnewMd = hugoTemplateSubstitutions(whatsnewMdFile.text) Node whatsnewNode = parser.parse(whatsnewMd) String whatsnewHtml = renderer.render(whatsnewNode) whatsnewHtml = whatsnewTemplateFile.text.replaceAll("__WHATS_NEW__", whatsnewHtml) whatsnewHtmlFile.text = hugoTemplateSubstitutions(whatsnewHtml, - [:] + [ + VERSION: JALVIEW_VERSION, + DISPLAY_DATE: wnDisplayDate + ] ) + } else if (gradle.taskGraph.hasTask(":linkCheck")) { + whatsnewHtmlFile.text = "Development build " + getDate("yyyy-MM-dd HH:mm:ss") } } @@ -1534,50 +1581,14 @@ task releasesTemplates { outputs.file(whatsnewHtmlFile) } - -task copyHelp(type: Copy) { - dependsOn releasesTemplates - - def inputDir = helpSourceDir - def outputDir = "${helpBuildDir}/${help_dir}" - from(inputDir) { - include('**/*.txt') - include('**/*.md') - include('**/*.html') - include('**/*.hs') - include('**/*.xml') - include('**/*.jhm') - filter(ReplaceTokens, - beginToken: '$$', - endToken: '$$', - tokens: [ - 'Version-Rel': JALVIEW_VERSION, - 'Year-Rel': getDate("yyyy") - ] - ) - } - from(inputDir) { - exclude('**/*.txt') - exclude('**/*.md') - exclude('**/*.html') - exclude('**/*.hs') - exclude('**/*.xml') - exclude('**/*.jhm') - } - into outputDir - - inputs.dir(inputDir) - outputs.files(helpFile) - outputs.dir(outputDir) -} - +*/ task copyResources(type: Copy) { group = "build" 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') @@ -1598,10 +1609,10 @@ 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) { @@ -1610,16 +1621,17 @@ 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 - into outputDir + into destinationDirectory inputs.dir(inputDir) - outputs.dir(outputDir) + outputs.dir(destinationDirectory) } task createBuildProperties(type: WriteProperties) { dependsOn copyResources + dependsOn copyChannelResources group = "build" description = "Create the ${buildProperties} file" @@ -1632,6 +1644,7 @@ task createBuildProperties(type: WriteProperties) { property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy") property "VERSION", JALVIEW_VERSION property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]" + property "JAVA_COMPILE_VERSION", JAVA_INTEGER_VERSION if (getdownSetAppBaseProperty) { property "GETDOWNAPPBASE", getdownAppBase property "GETDOWNAPPDISTDIR", getdownAppDistDir @@ -1642,6 +1655,7 @@ task createBuildProperties(type: WriteProperties) { task buildIndices(type: JavaExec) { dependsOn copyHelp + //dependsOn releasesTemplates classpath = sourceSets.main.compileClasspath main = "com.sun.java.help.search.Indexer" workingDir = "${helpBuildDir}/${help_dir}" @@ -1669,14 +1683,25 @@ task prepare { dependsOn buildResources dependsOn copyDocs dependsOn copyHelp + //dependsOn releasesTemplates dependsOn convertMdFiles dependsOn buildIndices } +// random block of dependencies compileJava.dependsOn prepare run.dependsOn compileJava //run.dependsOn prepare +compileTestJava.dependsOn compileJava // +compileTestJava.dependsOn buildIndices // +processResources.dependsOn copyChannelResources // +processResources.dependsOn copyResources // +processResources.dependsOn createBuildProperties // +processResources.dependsOn copyDocs // +processResources.dependsOn convertMdFiles // +processResources.dependsOn copyHelp // +processResources.dependsOn buildIndices // //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir @@ -1721,6 +1746,7 @@ test { } +/* task compileLinkCheck(type: JavaCompile) { options.fork = true classpath = files("${jalviewDir}/${utils_dir}") @@ -1741,7 +1767,7 @@ task linkCheck(type: JavaExec) { def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out") classpath = files("${jalviewDir}/${utils_dir}") main = "HelpLinksChecker" - workingDir = jalviewDir + workingDir = "${helpBuildDir}" args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ] def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append @@ -1755,6 +1781,7 @@ task linkCheck(type: JavaExec) { inputs.dir(helpBuildDir) outputs.file(helpLinksCheckerOutFile) } +*/ // import the pubhtmlhelp target @@ -1769,10 +1796,14 @@ task cleanPackageDir(type: Delete) { } } +// block of dependencies +//compileTestJava.dependsOn compileLinkCheck // +//copyChannelResources.dependsOn compileLinkCheck // +//convertMdFiles.dependsOn compileLinkCheck // jar { dependsOn prepare - dependsOn linkCheck + dependsOn //linkCheck manifest { attributes "Main-Class": main_class, @@ -1782,8 +1813,8 @@ jar { "Implementation-Version": JALVIEW_VERSION } - def outputDir = "${jalviewDir}/${package_dir}" - destinationDirectory = file(outputDir) + def destinationDirectory = "${jalviewDir}/${package_dir}" + destinationDirectory = file(destinationDirectory) archiveFileName = rootProject.name+".jar" duplicatesStrategy "EXCLUDE" @@ -1794,11 +1825,11 @@ 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}") } @@ -1857,7 +1888,7 @@ shadowJar { mainClassName = shadow_jar_main_class mergeServiceFiles() - classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION + archiveClassifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION minimize() } @@ -2912,10 +2943,10 @@ 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 } @@ -3023,13 +3054,13 @@ 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 { @@ -3048,13 +3079,13 @@ 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 { @@ -3067,13 +3098,13 @@ 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 { @@ -3087,13 +3118,13 @@ 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 { @@ -3312,7 +3343,7 @@ 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 = "${jsDir}/core/corebottom2.js" @@ -3356,8 +3387,8 @@ task jalviewjsBuildAllCores { } def list = fileTree(dir: j2sDir, includes: filelist) - def jsfile = "${outputDir}/core${name}.js" - def zjsfile = "${outputDir}/core${name}.z.js" + def jsfile = "${destinationDirectory}/core${name}.js" + def zjsfile = "${destinationDirectory}/core${name}.z.js" jalviewjsCoreClasslists += [ 'jsfile': jsfile, @@ -3375,8 +3406,8 @@ task jalviewjsBuildAllCores { // _stevesoft core. add any cores without a classlist here (and the inputs and outputs) def stevesoftClasslistName = "_stevesoft" def stevesoftClasslist = [ - 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js", - 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js", + 'jsfile': "${destinationDirectory}/core${stevesoftClasslistName}.js", + 'zjsfile': "${destinationDirectory}/core${stevesoftClasslistName}.z.js", 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"), 'name': stevesoftClasslistName ] @@ -3409,8 +3440,8 @@ task jalviewjsBuildAllCores { ] ) def allClasslist = [ - 'jsfile': "${outputDir}/core${allClasslistName}.js", - 'zjsfile': "${outputDir}/core${allClasslistName}.z.js", + 'jsfile': "${destinationDirectory}/core${allClasslistName}.js", + 'zjsfile': "${destinationDirectory}/core${allClasslistName}.z.js", 'list': allJsFiles, 'name': allClasslistName ] @@ -3463,11 +3494,11 @@ task jalviewjsPublishCoreTemplates { dependsOn jalviewjsBuildAllCores def inputFileName = "${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}_${cl.name}.html" cl['outputfile'] = outputFile outputFiles += outputFile } @@ -3486,13 +3517,13 @@ task jalviewjsSyncCore (type: Sync) { dependsOn jalviewjsBuildAllCores dependsOn jalviewjsPublishCoreTemplates def inputFiles = fileTree(dir: "${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 {