From: Ben Soares Date: Tue, 18 Jun 2019 09:52:27 +0000 (+0100) Subject: Merge branch 'develop' of https://source.jalview.org/git/jalview into develop X-Git-Tag: Release_2_11_0~7^2~4 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=4131297b5166e7b66597e4e7ac7e3a0d5a10de29;hp=-c Merge branch 'develop' of https://source.jalview.org/git/jalview into develop --- 4131297b5166e7b66597e4e7ac7e3a0d5a10de29 diff --combined build.gradle index 94481e9,9f00d2b..f5149da --- a/build.gradle +++ b/build.gradle @@@ -55,7 -55,7 +55,7 @@@ ext // TODO: consider allowing this expression to be overridden by -P arg getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir - getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir + //getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir getdownLauncher = jalviewDir + '/' + getdown_launcher getdownFilesDir = jalviewDir + '/' + getdown_files_dir + '/' + JAVA_VERSION + '/' @@@ -72,14 -72,18 +72,18 @@@ def additional_compiler_args = [ def getdown_alt_java_min_version // this property is assigned below and expanded to multiple lines in the getdown task def getdown_alt_multi_java_location + // this property is for the Java library used in eclipse + def eclipse_java_runtime_name if (JAVA_VERSION.equals("1.8")) { JAVA_INTEGER_VERSION = "8" + //libDir = j8libDir libDir = j11libDir libDistDir = j8libDir compile_source_compatibility = 1.8 compile_target_compatibility = 1.8 getdown_alt_java_min_version = getdown_alt_java8_min_version getdown_alt_multi_java_location = getdown_alt_java8_txt_multi_java_location + eclipse_java_runtime_name = "JavaSE-1.8" } else if (JAVA_VERSION.equals("11")) { JAVA_INTEGER_VERSION = "11" libDir = j11libDir @@@ -88,6 -92,7 +92,7 @@@ compile_target_compatibility = 11 getdown_alt_java_min_version = getdown_alt_java11_min_version getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location + eclipse_java_runtime_name = "JavaSE-11" additional_compiler_args += [ '--module-path', ext.modules_compileClasspath.asPath, '--add-modules', j11modules @@@ -106,7 -111,6 +111,6 @@@ sourceSets resources { srcDirs "$jalviewDir/$resourceDir" - srcDirs "$jalviewDir/$libDistDir" } jar.destinationDir = file("$jalviewDir/$packageDir") @@@ -151,8 -155,7 +155,7 @@@ } else { compileClasspath += files(sourceSets.main.java.outputDir) } - //compileClasspath += sourceSets.main.compileClasspath - //compileClasspath += files( sourceSets.main.resources.srcDirs) + compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"]) compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"]) @@@ -211,15 -214,18 +214,18 @@@ eclipse } cp.entries.removeAll(removeTheseToo) + print ("CP="+cp.inspect()) + cp.entries += new Output("bin/main") cp.entries += new Library(fileReference(helpParentDir)) cp.entries += new Library(fileReference(resourceDir)) HashMap addedLibPath = new HashMap<>(); - def allPaths = sourceSets.test.compileClasspath + sourceSets.main.compileClasspath - sourceSets.main.compileClasspath.each{ - //if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) { - //no longer want to add outputDir as eclipse is using its own output dir in bin/main + + // changing from sourcesets.main.classpath to specific Java version lib + //sourceSets.main.compileClasspath.each{ + fileTree("$jalviewDir/$libDistDir").include("**/*.jar").include("*.jar").each { + //don't want to add outputDir as eclipse is using its own output dir in bin/main if (it.isDirectory() || ! it.exists()) { // don't add dirs to classpath return @@@ -237,7 -243,9 +243,9 @@@ } } - sourceSets.test.compileClasspath.each{ + // changing from sourcesets.main.classpath to specific Java version lib + //sourceSets.test.compileClasspath.each{ + fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"]).each { //if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) { //no longer want to add outputDir as eclipse is using its own output dir in bin/main if (it.isDirectory() || ! it.exists()) { @@@ -298,9 -306,9 +306,9 @@@ jdt { // for the IDE, use java 11 compatibility - sourceCompatibility = 11 - targetCompatibility = 11 - javaRuntimeName = "JavaSE-11" + sourceCompatibility = compile_source_compatibility + targetCompatibility = compile_target_compatibility + javaRuntimeName = eclipse_java_runtime_name file { withProperties { props -> @@@ -411,48 -419,46 +419,46 @@@ cleanTest delete cloverInstrDir } + // format is a string like date.format("dd MMMM yyyy") def getDate(format) { def date = new Date() return date.format(format) } - task setGitHash(type: Exec) { - workingDir = jalviewDir - commandLine "git", "rev-parse", "--short", "HEAD" - standardOutput = new ByteArrayOutputStream() - project.ext.gitHash = { - return standardOutput.toString().trim() + task setGitVals { + def hashStdOut = new ByteArrayOutputStream() + exec { + commandLine "git", "rev-parse", "--short", "HEAD" + standardOutput = hashStdOut + ignoreExitValue true } - } - task setGitBranch(type: Exec) { - workingDir = jalviewDir - commandLine "git", "rev-parse", "--abbrev-ref", "HEAD" - standardOutput = new ByteArrayOutputStream() - project.ext.gitBranch = { - return standardOutput.toString().trim() + def branchStdOut = new ByteArrayOutputStream() + exec { + commandLine "git", "rev-parse", "--abbrev-ref", "HEAD" + standardOutput = branchStdOut + ignoreExitValue true } - } - task setGitVals { - dependsOn setGitHash - dependsOn setGitBranch + project.ext.gitHash = hashStdOut.toString().trim() + project.ext.gitBranch = branchStdOut.toString().trim() + + outputs.upToDateWhen { false } } task createBuildProperties(type: WriteProperties) { dependsOn setGitVals inputs.dir("$jalviewDir/$sourceDir") + inputs.dir("$classes") inputs.dir("$jalviewDir/$resourceDir") outputFile "$classes/$buildPropertiesFile" // taking time specific comment out to allow better incremental builds - //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss") - comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd") - property "BUILD_DATE", getDate("dd MMMM yyyy") + comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss") + //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd") + property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy") property "VERSION", JALVIEW_VERSION property "INSTALLATION", INSTALLATION+" git-commit:"+project.ext.gitHash+" ["+project.ext.gitBranch+"]" outputs.file(outputFile) - outputs.dir("$classes") } def buildingHTML = "$jalviewDir/$docDir/building.html" @@@ -465,20 -471,13 +471,20 @@@ task convertBuildingMD(type: Exec) def buildingMD = "$jalviewDir/$docDir/building.md" def css = "$jalviewDir/$docDir/github.css" - def pandoc = pandoc_exec + def pandoc = null + pandoc_exec.split(",").each { + if (file(it.trim()).exists()) { + pandoc = it.trim() + return true + } + } + def hostname = "hostname".execute().text.trim() - if (! file(pandoc).exists() && hostname.equals("jv-bamboo")) { + if ((pandoc == null || ! file(pandoc).exists()) && hostname.equals("jv-bamboo")) { pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc" } - if (file(pandoc).exists()) { + if (pandoc != null && file(pandoc).exists()) { commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD } else { commandLine "true" diff --combined gradle.properties index 3d37b3f,f5c6f49..08bcbd7 --- a/gradle.properties +++ b/gradle.properties @@@ -1,5 -1,6 +1,6 @@@ jalviewDir = . + #JAVA_VERSION = 1.8 JAVA_VERSION = 11 JALVIEW_VERSION = DEVELOPMENT INSTALLATION = Source @@@ -15,9 -16,6 +16,6 @@@ jalview_keydig = SHA testngGroups = Functional - javac_source = 11 - javac_target = 11 - j8libDir = j8lib j11libDir = j11lib resourceDir = resources @@@ -50,7 -48,7 +48,7 @@@ getdown_local = fals getdown_website_dir = getdown/website getdown_resource_dir = resource getdown_app_dir = dist - getdown_j11lib_dir = j11lib + #getdown_j11lib_dir = j11lib getdown_files_dir = getdown/files getdown_launcher = getdown/lib/getdown-launcher.jar getdown_core = getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar @@@ -111,6 -109,6 +109,6 @@@ JSIGN_SH = ech eclipse_extra_jdt_prefs_file = .settings/org.eclipse.jdt.core.jalview.prefs -pandoc_exec = /usr/local/bin/pandoc +pandoc_exec = /usr/local/bin/pandoc,/usr/bin/pandoc dev = false