From: MorellThomas Date: Thu, 23 May 2024 12:53:51 +0000 (+0200) Subject: mend X-Git-Tag: Release_2_11_4_0~31^2~7 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4252cab62e3ed4c7adce7cdf01db26af603ba627;p=jalview.git mend --- diff --git a/build.diff b/build.diff deleted file mode 100644 index 313b266..0000000 --- a/build.diff +++ /dev/null @@ -1,515 +0,0 @@ ---- build.gradle.orig 2024-05-22 09:14:54.544344630 +0200 -+++ build.gradle 2024-05-22 09:45:40.809642258 +0200 -@@ -51,8 +51,8 @@ - id 'java' - id 'application' - id 'eclipse' -- id "com.diffplug.gradle.spotless" version "3.28.0" -- id 'com.github.johnrengelman.shadow' version '6.0.0' -+ id "com.diffplug.spotless" version "6.18.0" -+ id 'com.github.johnrengelman.shadow' version '8.1.1' - 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 -@@ -193,6 +193,7 @@ - testDir = string("${jalviewDir}/${bareTestSourceDir}") - - classesDir = string("${jalviewDir}/${classes_dir}") -+ destinationDirectory = file(classesDir) - - // clover - useClover = clover.equals("true") -@@ -590,14 +591,14 @@ - 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 -@@ -607,14 +608,14 @@ - 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"]) -@@ -626,14 +627,14 @@ - 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"]) - -@@ -658,7 +659,7 @@ - } - - classpath { -- //defaultOutputDir = sourceSets.main.java.outputDir -+ //defaultOutputDir = sourceSets.main.java.destinationDirectory - configurations.each{ c-> - if (c.isCanBeResolved()) { - minusConfigurations += [c] -@@ -697,7 +698,7 @@ - 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 -@@ -717,7 +718,7 @@ - } - - 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 -@@ -1094,7 +1095,7 @@ - - clean { - doFirst { -- delete sourceSets.main.java.outputDir -+ delete sourceSets.main.java.destinationDirectory - } - } - -@@ -1102,7 +1103,7 @@ - cleanTest { - dependsOn cleanClover - doFirst { -- delete sourceSets.test.java.outputDir -+ delete sourceSets.test.java.destinationDirectory - } - } - -@@ -1194,7 +1195,7 @@ - - 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') -@@ -1215,10 +1216,10 @@ - exclude('**/*.html') - exclude('**/*.xml') - } -- into outputDir -+ into destinationDirectory - - inputs.dir(inputDir) -- outputs.dir(outputDir) -+ outputs.dir(destinationDirectory) - } - - -@@ -1283,15 +1284,15 @@ - } - 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) { -@@ -1350,7 +1351,7 @@ - def inSection = false - changes.eachLine { line -> - def m = null -- if (m = line =~ /^##([^#].*)$/) { -+ if (m == line =~ /^##([^#].*)$/) { - if (inSection) { - changesHugo += "\n\n" - } -@@ -1360,7 +1361,7 @@ - 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('"', """) -@@ -1430,7 +1431,7 @@ - def sectionName = null - content.eachLine { line -> - def m = null -- if (m = line =~ /^##([^#].*)$/) { -+ if (m == line =~ /^##([^#].*)$/) { - if (sectionName != null) { - sections[sectionName] = sectionContent - sectionName = null -@@ -1453,7 +1454,7 @@ - - task copyHelp(type: Copy) { - def inputDir = helpSourceDir -- def outputDir = "${helpBuildDir}/${help_dir}" -+ def destinationDirectory = "${helpBuildDir}/${help_dir}" - from(inputDir) { - include('**/*.txt') - include('**/*.md') -@@ -1478,14 +1479,15 @@ - 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" -@@ -1562,9 +1564,9 @@ - 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" -@@ -1622,13 +1624,14 @@ - 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') -@@ -1649,10 +1652,10 @@ - exclude('**/*.html') - exclude('**/*.xml') - } -- into outputDir -+ into destinationDirectory - - inputs.dir(inputDir) -- outputs.dir(outputDir) -+ outputs.dir(destinationDirectory) - } - - task copyChannelResources(type: Copy) { -@@ -1683,6 +1686,7 @@ - - task createBuildProperties(type: WriteProperties) { - dependsOn copyResources -+ dependsOn copyChannelResources - group = "build" - description = "Create the ${buildProperties} file" - -@@ -1706,6 +1710,7 @@ - - task buildIndices(type: JavaExec) { - dependsOn copyHelp -+ //dependsOn releasesTemplates - classpath = sourceSets.main.compileClasspath - main = "com.sun.java.help.search.Indexer" - workingDir = "${helpBuildDir}/${help_dir}" -@@ -1733,7 +1738,7 @@ - dependsOn buildResources - dependsOn copyDocs - dependsOn copyHelp -- dependsOn releasesTemplates -+ //dependsOn releasesTemplates - dependsOn convertMdFiles - dependsOn buildIndices - } -@@ -1742,6 +1747,14 @@ - compileJava.dependsOn prepare - run.dependsOn compileJava - compileTestJava.dependsOn compileJava -+compileTestJava.dependsOn buildIndices -+processResources.dependsOn copyChannelResources -+processResources.dependsOn copyResources -+processResources.dependsOn createBuildProperties -+processResources.dependsOn copyDocs -+processResources.dependsOn convertMdFiles -+processResources.dependsOn copyHelp -+processResources.dependsOn buildIndices - - - -@@ -2037,6 +2050,7 @@ - /* END of test tasks results summary */ - - -+/* - task compileLinkCheck(type: JavaCompile) { - options.fork = true - classpath = files("${jalviewDir}/${utils_dir}") -@@ -2071,6 +2085,7 @@ - inputs.dir(helpBuildDir) - outputs.file(helpLinksCheckerOutFile) - } -+*/ - - - // import the pubhtmlhelp target -@@ -2085,10 +2100,14 @@ - } - } - -+// block of dependencies -+//compileTestJava.dependsOn compileLinkCheck // -+//copyChannelResources.dependsOn compileLinkCheck // -+//convertMdFiles.dependsOn compileLinkCheck // - - jar { - dependsOn prepare -- dependsOn linkCheck -+ dependsOn //linkCheck - - manifest { - attributes "Main-Class": main_class, -@@ -2098,8 +2117,8 @@ - "Implementation-Version": JALVIEW_VERSION - } - -- def outputDir = "${jalviewDir}/${package_dir}" -- destinationDirectory = file(outputDir) -+ def destinationDirectory = "${jalviewDir}/${package_dir}" -+ destinationDirectory = file(destinationDirectory) - archiveFileName = rootProject.name+".jar" - duplicatesStrategy "EXCLUDE" - -@@ -2110,11 +2129,11 @@ - exclude "**/*.jar" - exclude "**/*.jar.*" - -- inputs.dir(sourceSets.main.java.outputDir) -+ inputs.dir(sourceSets.main.java.destinationDirectory) - sourceSets.main.resources.srcDirs.each{ dir -> - inputs.dir(dir) - } -- outputs.file("${outputDir}/${archiveFileName}") -+ outputs.file("${destinationDirectory}/${archiveFileName}") - } - - -@@ -2207,7 +2226,7 @@ - // this mainClassName is mandatory but gets ignored due to manifest created in doFirst{}. Set the Main-Class as an attribute in launcherJar instead - mainClassName = shadow_jar_main_class - mergeServiceFiles() -- classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION -+ archiveClassifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION - minimize() - } - -@@ -3388,10 +3407,10 @@ - - def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar") - inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}") -- def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" -+ def destinationDirectory = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" - - from inputFiles -- into outputDir -+ into destinationDirectory - } - - -@@ -3499,13 +3518,13 @@ - dependsOn jalviewjsTransferUnzipAllLibs - def inputFiles = fileTree(dir: "${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}/${filename}" - null - } - preserve { -@@ -3524,13 +3543,13 @@ - dependsOn buildResources - - def inputFiles = fileTree(dir: resourcesBuildDir) -- def outputDir = "${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}/${filename}" - null - } - preserve { -@@ -3543,13 +3562,13 @@ - - task jalviewjsSyncSiteResources (type: Sync) { - def inputFiles = fileTree(dir: "${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}/${filename}" - null - } - preserve { -@@ -3563,13 +3582,13 @@ - task jalviewjsSyncBuildProperties (type: Sync) { - dependsOn createBuildProperties - def inputFiles = [file(buildProperties)] -- def outputDir = "${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}/${filename}" - null - } - preserve { -@@ -3788,7 +3807,7 @@ - def swingJ2sDir = "${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" - -@@ -3832,8 +3851,8 @@ - } - 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, -@@ -3851,8 +3870,8 @@ - // _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 - ] -@@ -3885,8 +3904,8 @@ - ] - ) - 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 - ] -@@ -3939,11 +3958,11 @@ - 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 - } -@@ -3962,13 +3981,13 @@ - 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 {