JAL-3521 'Debian-safe' version of minimal build.gradle and patch. Using existing...

diff --git a/utils/debian/build_gradle.patch b/utils/debian/build_gradle.patch
index 867a576..1527c79 100644 (file)
--- a/utils/debian/build_gradle.patch
+++ b/utils/debian/build_gradle.patch
@@ -1,6 +1,6 @@
---- a/build.gradle     2021-09-20 17:46:04.088152106 +0100
-+++ b/build.gradle     2021-09-20 17:46:09.180302062 +0100
-@@ -2,16 +2,6 @@
+--- a/build.gradle     2021-09-21 09:52:04.653972716 +0100
++++ b/build.gradle     2021-09-21 09:52:18.117985307 +0100
+@@ -2,56 +2,12 @@
   * For properties set within build.gradle, use camelCaseNoSpace.
   */
  import org.apache.tools.ant.filters.ReplaceTokens
@@ -14,23 +14,28 @@
 -import groovy.transform.ExternalizeMethods
 -import groovy.util.XmlParser
 -import groovy.xml.XmlUtil
- import com.vladsch.flexmark.util.ast.Node
- import com.vladsch.flexmark.html.HtmlRenderer
- import com.vladsch.flexmark.parser.Parser
-@@ -24,34 +14,17 @@
- import com.vladsch.flexmark.ext.toc.TocExtension
- 
- buildscript {
+-import com.vladsch.flexmark.util.ast.Node
+-import com.vladsch.flexmark.html.HtmlRenderer
+-import com.vladsch.flexmark.parser.Parser
+-import com.vladsch.flexmark.util.data.MutableDataSet
+-import com.vladsch.flexmark.ext.gfm.tasklist.TaskListExtension
+-import com.vladsch.flexmark.ext.tables.TablesExtension
+-import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension
+-import com.vladsch.flexmark.ext.autolink.AutolinkExtension
+-import com.vladsch.flexmark.ext.anchorlink.AnchorLinkExtension
+-import com.vladsch.flexmark.ext.toc.TocExtension
+-
+-buildscript {
 -  repositories {
 -    mavenCentral()
 -    mavenLocal()
 -  }
-   dependencies {
-     classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
-   }
- }
- 
+-  dependencies {
+-    classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
+-  }
+-}
 -
+ 
  plugins {
    id 'java'
    id 'application'
@@ -39,20 +44,25 @@
 -  id 'com.github.johnrengelman.shadow' version '4.0.3'
 -  id 'com.install4j.gradle' version '8.0.10'
 -  id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with  gradle task1 [task2 ...] taskTree
-   id 'com.palantir.git-version' version '0.12.3'
- }
- 
+-  id 'com.palantir.git-version' version '0.12.3'
+-}
+-
 -repositories {
 -  jcenter()
 -  mavenCentral()
 -  mavenLocal()
--}
--
+ }
+ 
 -
  // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
  def string(Object o) {
    return o == null ? "" : o.toString()
-@@ -96,19 +69,11 @@
+@@ -92,23 +48,15 @@
+   }
+ }
+ 
+-ext {
++project.ext {
    jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
    jalviewDirRelativePath = jalviewDir
  
@@ -74,7 +84,7 @@
    ////  
    // Import releaseProps from the RELEASE file
    // or a file specified via JALVIEW_RELEASE_FILE if defined
-@@ -128,41 +93,6 @@
+@@ -128,41 +76,6 @@
    if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
      JALVIEW_VERSION = releaseProps.get("jalview.version")
    }
@@ -116,7 +126,7 @@
  
    // essentials
    bareSourceDir = string(source_dir)
-@@ -173,214 +103,18 @@
+@@ -173,218 +86,18 @@
  
    classesDir = string("${jalviewDir}/${classes_dir}")
  
@@ -144,15 +154,7 @@
 -  getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
 -  getdownAppDistDir = getdown_app_dir_alt
 -  getdownImagesDir = string("${jalviewDir}/${getdown_images_dir}")
-+  useClover = false
-+
-+  resourceClassesDir = classesDir
-+
-+  testSourceDir = testDir
-+  testClassesDir = "${jalviewDir}/${test_output_dir}"
-+
-+  buildProperties = string("${classesDir}/${build_properties_file}")
-   getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
+-  getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
 -  reportRsyncCommand = false
 -  jvlChannelName = CHANNEL.toLowerCase()
 -  install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
@@ -179,6 +181,7 @@
 -    }
 -    install4jExtraScheme = "jalviewb"
 -    break
++  useClover = false
  
 -    case [ "RELEASE", "JALVIEWJS-RELEASE" ]:
 -    getdownAppDistDir = getdown_app_dir_release
@@ -336,12 +339,23 @@
 -  modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
 -  modules_runtimeClasspath = modules_compileClasspath
 -  */
+-  def details = versionDetails()
+-  gitHash = details.gitHash
+-  gitBranch = details.branchName
++  resourceClassesDir = classesDir
++
++  testSourceDir = testDir
++  testClassesDir = "${jalviewDir}/${test_output_dir}"
+ 
++  buildProperties = string("${classesDir}/${build_properties_file}")
++  getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
++
 +  install4jApplicationName = "${jalview_name}"
 +  
-   def details = versionDetails()
-   gitHash = details.gitHash
-   gitBranch = details.branchName
-@@ -396,71 +130,16 @@
+   println("Using a ${CHANNEL} profile.")
+ 
+   additional_compiler_args = []
+@@ -396,71 +109,16 @@
      libDistDir = j8libDir
      compile_source_compatibility = 1.8
      compile_target_compatibility = 1.8
@@ -413,7 +427,7 @@
    resourceBuildDir = string("${buildDir}/resources")
    resourcesBuildDir = string("${resourceBuildDir}/resources_build")
    helpBuildDir = string("${resourceBuildDir}/help_build")
-@@ -474,31 +153,6 @@
+@@ -474,31 +132,6 @@
    helpSourceDir = string("${helpParentDir}/${help_dir}")
    helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
  
@@ -445,7 +459,7 @@
    // ENDEXT
  }
  
-@@ -517,27 +171,12 @@
+@@ -517,27 +150,12 @@
      compileClasspath = files(sourceSets.main.java.outputDir)
      compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
  
@@ -458,11 +472,11 @@
 -      srcDirs cloverInstrDir
 -      outputDir = cloverClassesDir
 -    }
- 
+-
 -    resources {
 -      srcDirs = sourceSets.main.resources.srcDirs
 -    }
--
+ 
 -    compileClasspath = files( sourceSets.clover.java.outputDir )
 -    //compileClasspath += files( testClassesDir )
 +    compileClasspath = files(sourceSets.main.java.outputDir)
@@ -475,7 +489,7 @@
    }
  
    test {
-@@ -557,453 +196,41 @@
+@@ -557,453 +175,41 @@
      runtimeClasspath = compileClasspath
      runtimeClasspath += files(sourceSets.test.resources.srcDirs)
    }
@@ -887,11 +901,14 @@
 -  if (cloverreport_xml_options.length() > 0) {
 -    argsList += cloverreport_xml_options.split(" ")
 -  }
- 
+-
 -  args argsList.toArray()
 -}
--
--
+ 
++    compileClasspath = files( sourceSets.test.java.outputDir )
++    compileClasspath += sourceSets.main.compileClasspath
++    compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**   REMOVE_THIS_GAP  /*.jar"])
+ 
 -task cloverReport {
 -  group = "Verification"
 -  description = "Creates clover reports"
@@ -902,10 +919,7 @@
 -
 -
 -compileCloverJava {
-+    compileClasspath = files( sourceSets.test.java.outputDir )
-+    compileClasspath += sourceSets.main.compileClasspath
-+    compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**   REMOVE_THIS_GAP  /*.jar"])
- 
+-
 -  doFirst {
 -    sourceCompatibility = compile_source_compatibility
 -    targetCompatibility = compile_target_compatibility
@@ -943,7 +957,7 @@
      print ("Setting target compatibility to "+targetCompatibility+"\n")
    }
  }
-@@ -1017,7 +244,6 @@
+@@ -1017,7 +223,6 @@
  
  
  cleanTest {
@@ -951,7 +965,163 @@
    doFirst {
      delete sourceSets.test.java.outputDir
    }
-@@ -1306,12 +532,7 @@
+@@ -1031,85 +236,6 @@
+ }
+ 
+ 
+-def convertMdToHtml (FileTree mdFiles, File cssFile) {
+-  MutableDataSet options = new MutableDataSet()
+-
+-  def extensions = new ArrayList<>()
+-  extensions.add(AnchorLinkExtension.create()) 
+-  extensions.add(AutolinkExtension.create())
+-  extensions.add(StrikethroughExtension.create())
+-  extensions.add(TaskListExtension.create())
+-  extensions.add(TablesExtension.create())
+-  extensions.add(TocExtension.create())
+-  
+-  options.set(Parser.EXTENSIONS, extensions)
+-
+-  // set GFM table parsing options
+-  options.set(TablesExtension.WITH_CAPTION, false)
+-  options.set(TablesExtension.COLUMN_SPANS, false)
+-  options.set(TablesExtension.MIN_HEADER_ROWS, 1)
+-  options.set(TablesExtension.MAX_HEADER_ROWS, 1)
+-  options.set(TablesExtension.APPEND_MISSING_COLUMNS, true)
+-  options.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true)
+-  options.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true)
+-  // GFM anchor links
+-  options.set(AnchorLinkExtension.ANCHORLINKS_SET_ID, false)
+-  options.set(AnchorLinkExtension.ANCHORLINKS_ANCHOR_CLASS, "anchor")
+-  options.set(AnchorLinkExtension.ANCHORLINKS_SET_NAME, true)
+-  options.set(AnchorLinkExtension.ANCHORLINKS_TEXT_PREFIX, "<span class=\"octicon octicon-link\"></span>")
+-
+-  Parser parser = Parser.builder(options).build()
+-  HtmlRenderer renderer = HtmlRenderer.builder(options).build()
+-
+-  mdFiles.each { mdFile ->
+-    // add table of contents
+-    def mdText = "[TOC]\n"+mdFile.text
+-
+-    // grab the first top-level title
+-    def title = null
+-    def titleRegex = /(?m)^#(\s+|([^#]))(.*)/
+-    def matcher = mdText =~ titleRegex
+-    if (matcher.size() > 0) {
+-      // matcher[0][2] is the first character of the title if there wasn't any whitespace after the #
+-      title = (matcher[0][2] != null ? matcher[0][2] : "")+matcher[0][3]
+-    }
+-    // or use the filename if none found
+-    if (title == null) {
+-      title = mdFile.getName()
+-    }
+-
+-    Node document = parser.parse(mdText)
+-    String htmlBody = renderer.render(document)
+-    def htmlText = '''<html>
+-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+-<html xmlns="http://www.w3.org/1999/xhtml">
+-  <head>
+-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+-    <meta http-equiv="Content-Style-Type" content="text/css" />
+-    <meta name="generator" content="flexmark" />
+-'''
+-    htmlText += ((title != null) ? "  <title>${title}</title>" : '' )
+-    htmlText += '''
+-    <style type="text/css">code{white-space: pre;}</style>
+-'''
+-    htmlText += ((cssFile != null) ? cssFile.text : '')
+-    htmlText += '''</head>
+-  <body>
+-'''
+-    htmlText += htmlBody
+-    htmlText += '''
+-  </body>
+-</html>
+-'''
+-
+-    def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
+-    def htmlFile = file(htmlFilePath)
+-    println("Creating ${htmlFilePath}")
+-    htmlFile.text = htmlText
+-  }
+-}
+-
+-
+ task copyDocs(type: Copy) {
+   def inputDir = "${jalviewDir}/${doc_dir}"
+   def outputDir = "${docBuildDir}/${doc_dir}"
+@@ -1140,27 +266,6 @@
+ }
+ 
+ 
+-task convertMdFiles {
+-  dependsOn copyDocs
+-  def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
+-  def cssFile = file("${jalviewDir}/${flexmark_css}")
+-
+-  doLast {
+-    convertMdToHtml(mdFiles, cssFile)
+-  }
+-
+-  inputs.files(mdFiles)
+-  inputs.file(cssFile)
+-
+-  def htmlFiles = []
+-  mdFiles.each { mdFile ->
+-    def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
+-    htmlFiles.add(file(htmlFilePath))
+-  }
+-  outputs.files(htmlFiles)
+-}
+-
+-
+ task copyHelp(type: Copy) {
+   def inputDir = helpSourceDir
+   def outputDir = "${helpBuildDir}/${help_dir}"
+@@ -1242,24 +347,15 @@
+   outputs.dir(outputDir)
+ }
+ 
+-task createBuildProperties(type: WriteProperties) {
+-  dependsOn copyResources
+-  group = "build"
+-  description = "Create the ${buildProperties} file"
+-  
+-  inputs.dir(sourceDir)
+-  inputs.dir(resourcesBuildDir)
+-  outputFile (buildProperties)
+-  // 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("HH:mm:ss dd MMMM yyyy")
+-  property "VERSION", JALVIEW_VERSION
+-  property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
+-  if (getdownSetAppBaseProperty) {
+-    property "GETDOWNAPPBASE", getdownAppBase
+-    property "GETDOWNAPPDISTDIR", getdownAppDistDir
+-  }
++task createBuildProperties(type: Copy) {
++  // using the build_properties already included in the source tarball
++  def inputFile = "build_properties"
++  def outputFile = buildProperties
++  from inputFile
++  into file(outputFile).getParent()
++  rename(file(inputFile).getName(), file(outputFile).getName())
++
++  inputs.file(inputFile)
+   outputs.file(outputFile)
+ }
+ 
+@@ -1293,7 +389,6 @@
+   dependsOn buildResources
+   dependsOn copyDocs
+   dependsOn copyHelp
+-  dependsOn convertMdFiles
+   dependsOn buildIndices
+ }
+ 
+@@ -1306,12 +401,7 @@
  //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
  test {
    dependsOn prepare
@@ -965,7 +1135,7 @@
  
    useTestNG() {
      includeGroups testng_groups
-@@ -1323,6 +544,7 @@
+@@ -1323,6 +413,7 @@
    maxHeapSize = "1024m"
  
    workingDir = jalviewDir
@@ -973,7 +1143,7 @@
    def testLaf = project.findProperty("test_laf")
    if (testLaf != null) {
      println("Setting Test LaF to '${testLaf}'")
-@@ -1338,9 +560,6 @@
+@@ -1338,9 +429,6 @@
    jvmArgs += additional_compiler_args
  
    doFirst {
@@ -983,7 +1153,7 @@
    }
  }
  
-@@ -1420,1752 +639,7 @@
+@@ -1420,1752 +508,7 @@
    sourceSets.main.resources.srcDirs.each{ dir ->
      inputs.dir(dir)
    }
@@ -2039,7 +2209,7 @@
 -      println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
 -    }
 -  }
--
+ 
 -  //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
 -  def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
 -  executable(eclipseBinary)
@@ -2059,7 +2229,7 @@
 -  }
 -}
 -
- 
+-
 -task jalviewjsTranspile(type: Exec) {
 -  dependsOn jalviewjsEclipseSetup 
 -  dependsOn jalviewjsProjectImport

diff --git a/utils/debian/debian_build.gradle b/utils/debian/debian_build.gradle
index 998645a..a0e8cd9 100644 (file)
--- a/utils/debian/debian_build.gradle
+++ b/utils/debian/debian_build.gradle
@@ -2,27 +2,10 @@
  * For properties set within build.gradle, use camelCaseNoSpace.
  */
 import org.apache.tools.ant.filters.ReplaceTokens
-import com.vladsch.flexmark.util.ast.Node
-import com.vladsch.flexmark.html.HtmlRenderer
-import com.vladsch.flexmark.parser.Parser
-import com.vladsch.flexmark.util.data.MutableDataSet
-import com.vladsch.flexmark.ext.gfm.tasklist.TaskListExtension
-import com.vladsch.flexmark.ext.tables.TablesExtension
-import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension
-import com.vladsch.flexmark.ext.autolink.AutolinkExtension
-import com.vladsch.flexmark.ext.anchorlink.AnchorLinkExtension
-import com.vladsch.flexmark.ext.toc.TocExtension
-
-buildscript {
-  dependencies {
-    classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
-  }
-}
 
 plugins {
   id 'java'
   id 'application'
-  id 'com.palantir.git-version' version '0.12.3'
 }
 
 // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
@@ -65,7 +48,7 @@ def overrideProperties(String propsFileName, boolean output = false) {
   }
 }
 
-ext {
+project.ext {
   jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
   jalviewDirRelativePath = jalviewDir
 
@@ -115,10 +98,6 @@ ext {
 
   install4jApplicationName = "${jalview_name}"
   
-  def details = versionDetails()
-  gitHash = details.gitHash
-  gitBranch = details.branchName
-
   println("Using a ${CHANNEL} profile.")
 
   additional_compiler_args = []
@@ -257,85 +236,6 @@ def getDate(format) {
 }
 
 
-def convertMdToHtml (FileTree mdFiles, File cssFile) {
-  MutableDataSet options = new MutableDataSet()
-
-  def extensions = new ArrayList<>()
-  extensions.add(AnchorLinkExtension.create()) 
-  extensions.add(AutolinkExtension.create())
-  extensions.add(StrikethroughExtension.create())
-  extensions.add(TaskListExtension.create())
-  extensions.add(TablesExtension.create())
-  extensions.add(TocExtension.create())
-  
-  options.set(Parser.EXTENSIONS, extensions)
-
-  // set GFM table parsing options
-  options.set(TablesExtension.WITH_CAPTION, false)
-  options.set(TablesExtension.COLUMN_SPANS, false)
-  options.set(TablesExtension.MIN_HEADER_ROWS, 1)
-  options.set(TablesExtension.MAX_HEADER_ROWS, 1)
-  options.set(TablesExtension.APPEND_MISSING_COLUMNS, true)
-  options.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true)
-  options.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true)
-  // GFM anchor links
-  options.set(AnchorLinkExtension.ANCHORLINKS_SET_ID, false)
-  options.set(AnchorLinkExtension.ANCHORLINKS_ANCHOR_CLASS, "anchor")
-  options.set(AnchorLinkExtension.ANCHORLINKS_SET_NAME, true)
-  options.set(AnchorLinkExtension.ANCHORLINKS_TEXT_PREFIX, "<span class=\"octicon octicon-link\"></span>")
-
-  Parser parser = Parser.builder(options).build()
-  HtmlRenderer renderer = HtmlRenderer.builder(options).build()
-
-  mdFiles.each { mdFile ->
-    // add table of contents
-    def mdText = "[TOC]\n"+mdFile.text
-
-    // grab the first top-level title
-    def title = null
-    def titleRegex = /(?m)^#(\s+|([^#]))(.*)/
-    def matcher = mdText =~ titleRegex
-    if (matcher.size() > 0) {
-      // matcher[0][2] is the first character of the title if there wasn't any whitespace after the #
-      title = (matcher[0][2] != null ? matcher[0][2] : "")+matcher[0][3]
-    }
-    // or use the filename if none found
-    if (title == null) {
-      title = mdFile.getName()
-    }
-
-    Node document = parser.parse(mdText)
-    String htmlBody = renderer.render(document)
-    def htmlText = '''<html>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <meta http-equiv="Content-Style-Type" content="text/css" />
-    <meta name="generator" content="flexmark" />
-'''
-    htmlText += ((title != null) ? "  <title>${title}</title>" : '' )
-    htmlText += '''
-    <style type="text/css">code{white-space: pre;}</style>
-'''
-    htmlText += ((cssFile != null) ? cssFile.text : '')
-    htmlText += '''</head>
-  <body>
-'''
-    htmlText += htmlBody
-    htmlText += '''
-  </body>
-</html>
-'''
-
-    def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
-    def htmlFile = file(htmlFilePath)
-    println("Creating ${htmlFilePath}")
-    htmlFile.text = htmlText
-  }
-}
-
-
 task copyDocs(type: Copy) {
   def inputDir = "${jalviewDir}/${doc_dir}"
   def outputDir = "${docBuildDir}/${doc_dir}"
@@ -366,27 +266,6 @@ task copyDocs(type: Copy) {
 }
 
 
-task convertMdFiles {
-  dependsOn copyDocs
-  def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
-  def cssFile = file("${jalviewDir}/${flexmark_css}")
-
-  doLast {
-    convertMdToHtml(mdFiles, cssFile)
-  }
-
-  inputs.files(mdFiles)
-  inputs.file(cssFile)
-
-  def htmlFiles = []
-  mdFiles.each { mdFile ->
-    def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
-    htmlFiles.add(file(htmlFilePath))
-  }
-  outputs.files(htmlFiles)
-}
-
-
 task copyHelp(type: Copy) {
   def inputDir = helpSourceDir
   def outputDir = "${helpBuildDir}/${help_dir}"
@@ -468,24 +347,15 @@ task copyChannelResources(type: Copy) {
   outputs.dir(outputDir)
 }
 
-task createBuildProperties(type: WriteProperties) {
-  dependsOn copyResources
-  group = "build"
-  description = "Create the ${buildProperties} file"
-  
-  inputs.dir(sourceDir)
-  inputs.dir(resourcesBuildDir)
-  outputFile (buildProperties)
-  // 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("HH:mm:ss dd MMMM yyyy")
-  property "VERSION", JALVIEW_VERSION
-  property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
-  if (getdownSetAppBaseProperty) {
-    property "GETDOWNAPPBASE", getdownAppBase
-    property "GETDOWNAPPDISTDIR", getdownAppDistDir
-  }
+task createBuildProperties(type: Copy) {
+  // using the build_properties already included in the source tarball
+  def inputFile = "build_properties"
+  def outputFile = buildProperties
+  from inputFile
+  into file(outputFile).getParent()
+  rename(file(inputFile).getName(), file(outputFile).getName())
+
+  inputs.file(inputFile)
   outputs.file(outputFile)
 }
 
@@ -519,7 +389,6 @@ task prepare {
   dependsOn buildResources
   dependsOn copyDocs
   dependsOn copyHelp
-  dependsOn convertMdFiles
   dependsOn buildIndices
 }