buildscript {
dependencies {
- //classpath files("$gradlePluginsDir/gradle-macappbundle-2.3.0-patched-2.3.0.jar")
+ classpath 'org.openclover:clover:4.3.1'
}
}
repositories {
jcenter()
mavenCentral()
+ mavenLocal()
flatDir {
dirs gradlePluginsDir
}
}
mainClassName = launcherClass
+def cloverInstrDir = file("$buildDir/$cloverSourcesInstrDir")
+def classes = "$jalviewDir/$classesDir"
+if (clover.equals("true")) {
+ use_clover = true
+ classes = "$buildDir/$cloverClassesDir"
+} else {
+ use_clover = false
+ classes = "$jalviewDir/$classesDir"
+}
sourceSets {
main {
java {
srcDirs "$jalviewDir/$sourceDir"
- outputDir = file("$jalviewDir/$classesDir")
+ outputDir = file("$classes")
}
resources {
compileClasspath = files(sourceSets.main.java.outputDir)
compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
if (JAVA_VERSION.equals("1.8")) {
- print("ADDING J11LIBS TO CLASSPATH")
+ print("ADDING J11LIBS TO CLASSPATH\n")
compileClasspath += fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"])
}
runtimeClasspath = compileClasspath
}
+ modules {
+ compileClasspath = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"])
+
+ runtimeClasspath = compileClasspath
+ }
+
+ clover {
+ java {
+ srcDirs = [ cloverInstrDir ]
+ outputDir = file("${buildDir}/${cloverClassesDir}")
+ }
+
+ resources {
+ srcDirs = sourceSets.main.resources.srcDirs
+ }
+ compileClasspath = configurations.cloverRuntime + files( sourceSets.clover.java.outputDir )
+ compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
+ compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
+ if (JAVA_VERSION.equals("1.8")) {
+ print("ADDING J11LIBS TO CLASSPATH\n")
+ compileClasspath += fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"])
+ }
+
+ runtimeClasspath = compileClasspath
+ }
+
test {
java {
srcDirs "$jalviewDir/$testSourceDir"
srcDirs = sourceSets.main.resources.srcDirs
}
- compileClasspath = sourceSets.main.compileClasspath
- compileClasspath += files( sourceSets.test.java.outputDir )
+ compileClasspath = files( sourceSets.test.java.outputDir )
+ if (use_clover) {
+ compileClasspath += sourceSets.clover.compileClasspath
+ } else {
+ compileClasspath += sourceSets.main.compileClasspath
+ compileClasspath += files(sourceSets.main.java.outputDir)
+ }
+ compileClasspath += files( sourceSets.main.resources.srcDirs)
compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
+ compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
+ if (JAVA_VERSION.equals("1.8")) {
+ print("ADDING J11LIBS TO CLASSPATH\n")
+ compileClasspath += fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"])
+ }
runtimeClasspath = compileClasspath
}
+}
- modules {
- compileClasspath = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"])
-
- runtimeClasspath = compileClasspath
+// clover bits
+dependencies {
+ if (use_clover) {
+ cloverCompile 'org.openclover:clover:4.3.1'
+ testCompile 'org.openclover:clover:4.3.1'
}
+}
+configurations {
+ cloverRuntime
+ cloverRuntime.extendsFrom cloverCompile
+}
+
+task cloverInstr() {
+ // only instrument source, we build test classes as normal
+ inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
+ outputs.dir cloverInstrDir
+
+ doFirst {
+ delete cloverInstrDir
+ def argsList = ["--initstring", "${buildDir}/clover/clover.db",
+ "-d", "${buildDir}/${cloverSourcesInstrDir}"]
+ argsList.addAll(inputs.files.files.collect({ file ->
+ file.absolutePath
+ }))
+ String[] args = argsList.toArray()
+ println("About to instrument "+args.length +" files")
+ com.atlassian.clover.CloverInstr.mainImpl(args)
+ }
+}
+
+
+task cloverReport {
+ inputs.dir "${buildDir}/clover"
+ outputs.dir "${reportsDir}/clover"
+ onlyIf {
+ file("${buildDir}/clover/clover.db").exists()
+ }
+ doFirst {
+ def argsList = ["--initstring", "${buildDir}/clover/clover.db",
+ "-o", "${reportsDir}/clover"]
+ String[] args = argsList.toArray()
+ com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
+
+ // and generate ${reportsDir}/clover/clover.xml
+ args = ["--initstring", "${buildDir}/clover/clover.db",
+ "-o", "${reportsDir}/clover/clover.xml"].toArray()
+ com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
+ }
}
+// end clover bits
+
+
compileJava {
doFirst {
}
+compileTestJava {
+
+ if (use_clover) {
+ dependsOn compileCloverJava
+ classpath += configurations.cloverRuntime
+ } else {
+ classpath += sourceSets.main.runtimeClasspath
+ }
+ doFirst {
+ if (JAVA_VERSION.equals("1.8")) {
+ sourceCompatibility = 1.8
+ targetCompatibility = 1.8
+ } else if (JAVA_VERSION.equals("11")) {
+ sourceCompatibility = 11
+ targetCompatibility = 11
+
+ options.compilerArgs = [
+ '--module-path', sourceSets.modules.compileClasspath.asPath,
+ '--add-modules', j11modules
+ ]
+ }
+ print ("Setting target compatibility to "+targetCompatibility+"\n")
+ }
+}
+
+
+compileCloverJava {
+
+ doFirst {
+ if (JAVA_VERSION.equals("1.8")) {
+ sourceCompatibility = 1.8
+ targetCompatibility = 1.8
+ } else if (JAVA_VERSION.equals("11")) {
+ sourceCompatibility = 11
+ targetCompatibility = 11
+
+ options.compilerArgs += [
+ '--module-path', sourceSets.modules.compileClasspath.asPath,
+ '--add-modules', j11modules
+ ]
+ }
+ print ("Setting target compatibility to "+targetCompatibility+"\n")
+ }
+ classpath += configurations.cloverRuntime
+}
+
clean {
delete sourceSets.main.java.outputDir
}
cleanTest {
delete sourceSets.test.java.outputDir
+ delete cloverInstrDir
}
def getDate(format) {
task createBuildProperties(type: WriteProperties) {
inputs.dir("$jalviewDir/$sourceDir")
inputs.dir("$jalviewDir/$resourceDir")
- outputFile "$jalviewDir/$classesDir/$buildPropertiesFile"
+ outputFile "$classes/$buildPropertiesFile"
/* taking time/date 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 "VERSION", JALVIEW_VERSION
property "INSTALLATION", INSTALLATION+" git-commit:"+getGitHash()+" ["+getGitBranch()+"]"
outputs.file(outputFile)
- outputs.dir("$jalviewDir/$classesDir")
+ outputs.dir("$classes")
}
task syncDocs(type: Sync) {
- def syncDir = "$jalviewDir/$classesDir/$docDir"
+ def syncDir = "$classes/$docDir"
from fileTree("$jalviewDir/$docDir")
into syncDir
}
-def helpFile = "$jalviewDir/$classesDir/$helpDir/help.jhm"
+def helpFile = "$classes/$helpDir/help.jhm"
task syncHelp(type: Sync) {
inputs.files("$jalviewDir/$helpDir")
outputs.files(helpFile)
- def syncDir = "$jalviewDir/$classesDir/$helpDir"
+ def syncDir = "$classes/$helpDir"
from fileTree("$jalviewDir/$helpDir")
into syncDir
}
task copyHelp(type: Copy) {
def inputDir = "$jalviewDir/$helpDir"
- def outputDir = "$jalviewDir/$classesDir/$helpDir"
+ def outputDir = "$classes/$helpDir"
from inputDir
into outputDir
filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': "USING_FILTER"])
}
task syncLib(type: Sync) {
- def syncDir = "$jalviewDir/$classesDir/$libDir"
+ def syncDir = "$classes/$libDir"
from fileTree("$jalviewDir/$libDir")
into syncDir
}
from "$jalviewDir/$resourceDir"
include "**/*.*"
exclude "install4j"
- into "$jalviewDir/$classesDir"
+ into "$classes"
preserve {
include "**"
}
dependsOn copyHelp
}
+
//testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
test {
dependsOn prepare
dependsOn compileJava
- useTestNG {
+ if (use_clover) {
+ dependsOn cloverInstr
+ }
+ print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
+
+ useTestNG() {
includeGroups testngGroups
+ preserveOrder true
+ useDefaultListeners=true
}
+
workingDir = jalviewDir
//systemProperties 'clover.jar' System.properties.clover.jar
+ if (JAVA_VERSION.equals("1.8")) {
+ sourceCompatibility = 1.8
+ targetCompatibility = 1.8
+ } else if (JAVA_VERSION.equals("11")) {
+ sourceCompatibility = 11
+ targetCompatibility = 11
+
+ jvmArgs += [
+ '--module-path',
+ sourceSets.modules.compileClasspath.asPath,
+ '--add-modules',
+ j11modules
+ ]
+ }
+ print ("Setting target compatibility to "+targetCompatibility+"\n")
}
task buildIndices(type: JavaExec) {
dependsOn copyHelp
classpath = sourceSets.main.compileClasspath
main = "com.sun.java.help.search.Indexer"
- workingDir = "$jalviewDir/$classesDir/$helpDir"
+ workingDir = "$classes/$helpDir"
def argDir = "html"
args = [ argDir ]
inputs.dir("$workingDir/$argDir")
- outputs.dir("$jalviewDir/$classesDir/doc")
- outputs.dir("$jalviewDir/$classesDir/help")
+ outputs.dir("$classes/doc")
+ outputs.dir("$classes/help")
outputs.file("$workingDir/JavaHelpSearch/DOCS")
outputs.file("$workingDir/JavaHelpSearch/DOCS.TAB")
outputs.file("$workingDir/JavaHelpSearch/OFFSETS")
dependsOn prepare, compileLinkCheck
classpath = files("$jalviewDir/$utilsDir")
main = "HelpLinksChecker"
- workingDir = "$jalviewDir"
- args = [ "$classesDir/$helpDir", "-nointernet" ]
+ workingDir = jalviewDir
+ def help = "$classes/$helpDir"
+ args = [ "$classes/$helpDir", "-nointernet" ]
+ //args = [ "$classesDir/$helpDir", "-nointernet" ]
doFirst {
standardOutput new FileOutputStream("$jalviewDir/$utilsDir/HelpLinksChecker.out")
exclude "**/*.jar"
exclude "**/*.jar.*"
- inputs.dir("$jalviewDir/$classesDir")
+ inputs.dir("$classes")
outputs.file("$jalviewDir/$packageDir/$archiveName")
}
task copyJars(type: Copy) {
- from fileTree("$jalviewDir/$classesDir").include("**/*.jar").include("*.jar").files
+ from fileTree("$classes").include("**/*.jar").include("*.jar").files
into "$jalviewDir/$packageDir"
}
inputs.dir(project.ext.getdownWebsiteDir)
outputs.dir("$jalviewDir/$install4jBuildDir")
}
+
git://source.jalview.org / jalview.git / blobdiff