JAL-3295 Fixed CMD-select of sequences in alignment window

[jalview.git] / build.gradle

diff --git a/build.gradle b/build.gradle
index b07ea37..1441e7d 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -72,14 +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 @@ if (JAVA_VERSION.equals("1.8")) {
   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
@@ -298,9 +303,9 @@ eclipse {
 
   jdt {
     // for the IDE, use java 11 compatibility
-    sourceCompatibility = 11
-    targetCompatibility = 11
-    javaRuntimeName = "JavaSE-11"
+    sourceCompatibility = JAVA_VERSION
+    targetCompatibility = JAVA_VERSION
+    javaRuntimeName = eclipse_java_runtime_name
 
     file {
       withProperties { props ->
@@ -317,8 +322,8 @@ eclipse {
     }
   }
   
-  synchronizationTasks eclipseClasspath
-  autoBuildTasks eclipseClasspath
+  //synchronizationTasks eclipseClasspath
+  //autoBuildTasks eclipseClasspath
 } 
 
 task cloverInstr() {
@@ -417,32 +422,31 @@ def getDate(format) {
   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/$buildPropertiesFile"
   // taking time specific comment out to allow better incremental builds
@@ -452,10 +456,42 @@ task createBuildProperties(type: WriteProperties) {
   property "VERSION", JALVIEW_VERSION
   property "INSTALLATION", INSTALLATION+" git-commit:"+project.ext.gitHash+" ["+project.ext.gitBranch+"]"
   outputs.file(outputFile)
-  outputs.dir("$classes")
+}
+
+def buildingHTML = "$jalviewDir/$docDir/building.html"
+task deleteBuildingHTML(type: Delete) {
+  delete buildingHTML
+}
+
+task convertBuildingMD(type: Exec) {
+  dependsOn deleteBuildingHTML
+  def buildingMD = "$jalviewDir/$docDir/building.md"
+  def css = "$jalviewDir/$docDir/github.css"
+
+  def pandoc = pandoc_exec
+  def hostname = "hostname".execute().text.trim()
+  if (! file(pandoc).exists() && hostname.equals("jv-bamboo")) {
+    pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
+  }
+
+  if (file(pandoc).exists()) {
+    commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
+  } else {
+    commandLine "true"
+  }
+
+  ignoreExitValue true
+
+  inputs.file(buildingMD)
+  inputs.file(css)
+  outputs.file(buildingHTML)
+}
+clean {
+  delete buildingHTML
 }
 
 task syncDocs(type: Sync) {
+  dependsOn convertBuildingMD
   def syncDir = "$classes/$docDir"
   from fileTree("$jalviewDir/$docDir")
   into syncDir
@@ -642,6 +678,7 @@ task cleanDist {
 }
 
 shadowJar {
+  group = "distribution"
   dependsOn makeDist
   from ("$jalviewDir/$libDistDir") {
     include("*.jar")