X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=0f4ad16bd58329358e0f3433f1a188db6a36468e;hb=refs%2Fheads%2Ffeature%2FJAL-3692enaEndpoint;hp=bd0ae207edd798ab27cf287eb36a174e5c5c705f;hpb=a02114f9eb9665810b4c1d89c9806dabcb2b4fd7;p=jalview.git

diff --git a/build.gradle b/build.gradle
index bd0ae20..0f4ad16 100644
--- a/build.gradle
+++ b/build.gradle
@@ -12,13 +12,25 @@ import java.security.MessageDigest
 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
+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"
+  }
 }
 
 
@@ -30,6 +42,7 @@ plugins {
   id 'com.github.johnrengelman.shadow' version '4.0.3'
   id 'com.install4j.gradle' version '8.0.4'
   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'
 }
 
 repositories {
@@ -148,7 +161,7 @@ ext {
   cloverBuildDir = "${buildDir}/clover"
   cloverInstrDir = file("${cloverBuildDir}/clover-instr")
   cloverClassesDir = file("${cloverBuildDir}/clover-classes")
-  cloverReportDir = file("${buildDir}/reports")
+  cloverReportDir = file("${buildDir}/reports/clover")
   cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
   cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
   //cloverTestClassesDir = cloverClassesDir
@@ -346,8 +359,9 @@ ext {
   modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
   modules_runtimeClasspath = modules_compileClasspath
   */
-  gitHash = string("")
-  gitBranch = string("")
+  def details = versionDetails()
+  gitHash = details.gitHash
+  gitBranch = details.branchName
 
   println("Using a ${CHANNEL} profile.")
 
@@ -733,6 +747,7 @@ eclipseGroovyCorePreferences.mustRunAfter eclipseJdt
 task cleanClover {
   doFirst {
     delete cloverBuildDir
+    delete cloverReportDir
   }
 }
 
@@ -855,7 +870,7 @@ task cloverHtmlReport(type: JavaExec) {
     file(cloverDb).exists()
   }
 
-  def cloverHtmlDir = "${cloverReportDir}/clover"
+  def cloverHtmlDir = cloverReportDir
   inputs.dir cloverClassesDir
   outputs.dir cloverHtmlDir
 
@@ -893,7 +908,7 @@ task cloverXmlReport(type: JavaExec) {
     file(cloverDb).exists()
   }
 
-  def cloverXmlFile = "${cloverReportDir}/clover/clover.xml"
+  def cloverXmlFile = "${cloverReportDir}/clover.xml"
   inputs.dir cloverClassesDir
   outputs.file cloverXmlFile
 
@@ -990,33 +1005,10 @@ def getDate(format) {
 }
 
 
-task setGitVals {
-  def hashStdOut = new ByteArrayOutputStream()
-  exec {
-    commandLine "git", "rev-parse", "--short", "HEAD"
-    standardOutput = hashStdOut
-    ignoreExitValue true
-  }
-
-  def branchStdOut = new ByteArrayOutputStream()
-  exec {
-    commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
-    standardOutput = branchStdOut
-    ignoreExitValue true
-  }
-
-  gitHash = hashStdOut.toString().trim()
-  gitBranch = branchStdOut.toString().trim()
-
-  outputs.upToDateWhen { false }
-}
-
-
 task createBuildProperties(type: WriteProperties) {
   group = "build"
   description = "Create the ${buildProperties} file"
   
-  dependsOn setGitVals
   inputs.dir(sourceDir)
   inputs.dir(resourceDir)
   file(buildProperties).getParentFile().mkdirs()
@@ -1045,47 +1037,110 @@ task cleanBuildingHTML(type: Delete) {
 }
 
 
-task convertBuildingMD(type: Exec) {
+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)
+    htmlFile.text = htmlText
+  }
+}
+
+
+task convertMdFiles {
   dependsOn cleanBuildingHTML
-  def buildingMD = "${jalviewDir}/${doc_dir}/building.md"
-  def css = "${jalviewDir}/${doc_dir}/github.css"
+  def mdFiles = fileTree(dir: "${jalviewDir}/${doc_dir}", include: "*.md")
+  def cssFile = file("${jalviewDir}/${flexmark_css}")
 
-  def pandoc = null
-  pandoc_exec.split(",").each {
-    if (file(it.trim()).exists()) {
-      pandoc = it.trim()
-      return true
-    }
+  doLast {
+    convertMdToHtml(mdFiles, cssFile)
   }
 
-  def buildtoolsPandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
-  if ((pandoc == null || ! file(pandoc).exists()) && file(buildtoolsPandoc).exists()) {
-    pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
-  }
+  inputs.files(mdFiles)
+  inputs.file(cssFile)
 
-  doFirst {
-    if (pandoc != null && file(pandoc).exists()) {
-        commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
-    } else {
-        println("Cannot find pandoc. Skipping convert building.md to HTML")
-        throw new StopExecutionException("Cannot find pandoc. Skipping convert building.md to HTML")
-    }
+  def htmlFiles = []
+  mdFiles.each { mdFile ->
+    def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
+    htmlFiles.add(file(htmlFilePath))
   }
-
-  ignoreExitValue true
-
-  inputs.file(buildingMD)
-  inputs.file(css)
-  outputs.file(buildingHTML)
+  outputs.files(htmlFiles)
 }
 
 
 task syncDocs(type: Sync) {
-  dependsOn convertBuildingMD
+  dependsOn convertMdFiles
   def syncDir = "${classesDir}/${doc_dir}"
   from fileTree("${jalviewDir}/${doc_dir}")
   into syncDir
-
 }
 
 
@@ -1308,6 +1363,7 @@ task cleanDist {
 
 shadowJar {
   group = "distribution"
+  description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
   if (buildDist) {
     dependsOn makeDist
   }
@@ -1683,7 +1739,6 @@ clean {
 task installers(type: com.install4j.gradle.Install4jTask) {
   group = "distribution"
   description = "Create the install4j installers"
-  dependsOn setGitVals
   dependsOn getdown
   dependsOn copyInstall4jTemplate
 
@@ -1782,7 +1837,11 @@ spotless {
 
 
 task sourceDist(type: Tar) {
+  group "distribution"
+  description "Create a source .tar.gz file for distribution"
   
+  dependsOn convertMdFiles
+
   def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
   def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
   // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09]
@@ -2858,7 +2917,7 @@ task jalviewjsIDE_PrepareSite {
   description "Sync libs and resources to site dir, but not closure cores"
 
   dependsOn jalviewjsIDE_SyncSiteAll
-  dependsOn cleanJalviewjsTransferSite
+  //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
 }