--- build.gradle 2023-07-02 09:21:09.216542293 +0200 +++ ../jalview_new/build.gradle 2023-05-15 19:20:46.892861180 +0200 @@ -45,8 +45,8 @@ 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 '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 @@ -183,6 +183,7 @@ testDir = string("${jalviewDir}/${bareTestSourceDir}") classesDir = string("${jalviewDir}/${classes_dir}") + destinationDirectory = file(classesDir) // clover useClover = clover.equals("true") @@ -547,14 +548,14 @@ 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 @@ -564,14 +565,14 @@ 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"]) @@ -583,14 +584,14 @@ 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"]) @@ -615,7 +616,7 @@ } classpath { - //defaultOutputDir = sourceSets.main.java.outputDir + //defaultOutputDir = sourceSets.main.java.destinationDirectory configurations.each{ c-> if (c.isCanBeResolved()) { minusConfigurations += [c] @@ -654,7 +655,7 @@ 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 @@ -674,7 +675,7 @@ } 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 @@ -1051,7 +1052,7 @@ clean { doFirst { - delete sourceSets.main.java.outputDir + delete sourceSets.main.java.destinationDirectory } } @@ -1059,7 +1060,7 @@ cleanTest { dependsOn cleanClover doFirst { - delete sourceSets.test.java.outputDir + delete sourceSets.test.java.destinationDirectory } } @@ -1151,7 +1152,7 @@ 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') @@ -1172,10 +1173,10 @@ exclude('**/*.html') exclude('**/*.xml') } - into outputDir + into destinationDirectory inputs.dir(inputDir) - outputs.dir(outputDir) + outputs.dir(destinationDirectory) } @@ -1240,15 +1241,15 @@ } 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) { @@ -1307,7 +1308,7 @@ def inSection = false changes.eachLine { line -> def m = null - if (m = line =~ /^##([^#].*)$/) { + if (m == line =~ /^##([^#].*)$/) { if (inSection) { changesHugo += "\n\n" } @@ -1317,7 +1318,7 @@ 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('"', """) @@ -1387,7 +1388,7 @@ def sectionName = null content.eachLine { line -> def m = null - if (m = line =~ /^##([^#].*)$/) { + if (m == line =~ /^##([^#].*)$/) { if (sectionName != null) { sections[sectionName] = sectionContent sectionName = null @@ -1410,7 +1411,7 @@ task copyHelp(type: Copy) { def inputDir = helpSourceDir - def outputDir = "${helpBuildDir}/${help_dir}" + def destinationDirectory = "${helpBuildDir}/${help_dir}" from(inputDir) { include('**/*.txt') include('**/*.md') @@ -1435,14 +1436,15 @@ exclude('**/*.xml') exclude('**/*.jhm') } - into outputDir + into destinationDirectory inputs.dir(inputDir) outputs.files(helpFile) - outputs.dir(outputDir) + outputs.dir(destinationDirectory) } +/* task releasesTemplates { group "help" description "Recreate whatsNew.html and releases.html from markdown files and templates in help" @@ -1519,9 +1521,9 @@ def lm = null def rContentProcessed = "" rContent.eachLine { line -> - if (lm = line =~ /^(\s*-)(\s*)(.*)$/) { + if (lm == line =~ /^(\s*-)(\s*)(.*)$/) { line = "${lm[0][1]}${lm[0][3]}${lm[0][2]}" - } else if (lm = line =~ /^###([^#]+.*)$/) { + } else if (lm == line =~ /^###([^#]+.*)$/) { line = "_${lm[0][1].trim()}_" } rContentProcessed += line + "\n" @@ -1579,13 +1581,14 @@ outputs.file(whatsnewHtmlFile) } +*/ 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') @@ -1606,10 +1609,10 @@ exclude('**/*.html') exclude('**/*.xml') } - into outputDir + into destinationDirectory inputs.dir(inputDir) - outputs.dir(outputDir) + outputs.dir(destinationDirectory) } task copyChannelResources(type: Copy) { @@ -1618,16 +1621,17 @@ 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 ${buildProperties} file" @@ -1651,6 +1655,7 @@ task buildIndices(type: JavaExec) { dependsOn copyHelp + //dependsOn releasesTemplates classpath = sourceSets.main.compileClasspath main = "com.sun.java.help.search.Indexer" workingDir = "${helpBuildDir}/${help_dir}" @@ -1678,15 +1683,25 @@ dependsOn buildResources dependsOn copyDocs dependsOn copyHelp - dependsOn releasesTemplates + //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 $jalviewDir @@ -1731,6 +1746,7 @@ } +/* task compileLinkCheck(type: JavaCompile) { options.fork = true classpath = files("${jalviewDir}/${utils_dir}") @@ -1765,6 +1781,7 @@ inputs.dir(helpBuildDir) outputs.file(helpLinksCheckerOutFile) } +*/ // import the pubhtmlhelp target @@ -1779,10 +1796,14 @@ } } +// block of dependencies +//compileTestJava.dependsOn compileLinkCheck // +//copyChannelResources.dependsOn compileLinkCheck // +//convertMdFiles.dependsOn compileLinkCheck // jar { dependsOn prepare - dependsOn linkCheck + dependsOn //linkCheck manifest { attributes "Main-Class": main_class, @@ -1792,8 +1813,8 @@ "Implementation-Version": JALVIEW_VERSION } - def outputDir = "${jalviewDir}/${package_dir}" - destinationDirectory = file(outputDir) + def destinationDirectory = "${jalviewDir}/${package_dir}" + destinationDirectory = file(destinationDirectory) archiveFileName = rootProject.name+".jar" duplicatesStrategy "EXCLUDE" @@ -1804,11 +1825,11 @@ exclude "**/*.jar" exclude "**/*.jar.*" - inputs.dir(sourceSets.main.java.outputDir) + inputs.dir(sourceSets.main.java.destinationDirectory) sourceSets.main.resources.srcDirs.each{ dir -> inputs.dir(dir) } - outputs.file("${outputDir}/${archiveFileName}") + outputs.file("${destinationDirectory}/${archiveFileName}") } @@ -1867,7 +1888,7 @@ mainClassName = shadow_jar_main_class mergeServiceFiles() - classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION + archiveClassifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION minimize() } @@ -2922,10 +2943,10 @@ def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar") inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}") - def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" + def destinationDirectory = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" from inputFiles - into outputDir + into destinationDirectory } @@ -3033,13 +3054,13 @@ dependsOn jalviewjsTransferUnzipAllLibs def inputFiles = fileTree(dir: "${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}/${filename}" null } preserve { @@ -3058,13 +3079,13 @@ dependsOn buildResources def inputFiles = fileTree(dir: resourcesBuildDir) - def outputDir = "${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}/${filename}" null } preserve { @@ -3077,13 +3098,13 @@ task jalviewjsSyncSiteResources (type: Sync) { def inputFiles = fileTree(dir: "${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}/${filename}" null } preserve { @@ -3097,13 +3118,13 @@ task jalviewjsSyncBuildProperties (type: Sync) { dependsOn createBuildProperties def inputFiles = [file(buildProperties)] - def outputDir = "${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}/${filename}" null } preserve { @@ -3322,7 +3343,7 @@ def swingJ2sDir = "${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" @@ -3366,8 +3387,8 @@ } 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, @@ -3385,8 +3406,8 @@ // _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 ] @@ -3419,8 +3440,8 @@ ] ) 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 ] @@ -3473,11 +3494,11 @@ 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 } @@ -3496,13 +3517,13 @@ 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 {