From: Ben Soares <bsoares@dundee.ac.uk>
Date: Thu, 5 May 2022 16:02:39 +0000 (+0100)
Subject: JAL-4004 Now generating hugo files from help/markdown/...
X-Git-Tag: Release_2_11_2_6~64^2~8
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=729e39d052a71602d82f7808fdb3862b9d893ce8;p=jalview.git

JAL-4004 Now generating hugo files from help/markdown/...
---

diff --git a/build.gradle b/build.gradle
index d89f3ed..e6cc590 100644
--- a/build.gradle
+++ b/build.gradle
@@ -2388,87 +2388,27 @@ task dataInstallersJson {
   }
 }
 
-def hugoTemplateSubstitutions(String input) {
+def hugoTemplateSubstitutions(String input, Map extras=null) {
+  def replacements = [
+    DATE: getDate("yyyy-MM-dd"),
+    CHANNEL: propertiesChannelName,
+    APPLICATION_NAME: applicationName,
+    GIT_HASH: gitHash,
+    GIT_BRANCH: gitBranch,
+    VERSION: JALVIEW_VERSION,
+    JAVA_VERSION: JAVA_VERSION,
+    VERSION_UNDERSCORES: JALVIEW_VERSION_UNDERSCORES
+  ]
   def output = input
-  output = output.replaceAll("__DATE__", getDate("yyyy-MM-dd"))
-  output = output.replaceAll("__CHANNEL__", propertiesChannelName)
-  output = output.replaceAll("__APPLICATION_NAME__", applicationName)
-  output = output.replaceAll("__GIT_HASH__", gitHash)
-  output = output.replaceAll("__GIT_BRANCH__", gitBranch)
-  output = output.replaceAll("__VERSION__", JALVIEW_VERSION)
-  output = output.replaceAll("__JAVA_VERSION__", JAVA_VERSION)
-  output = output.replaceAll("__VERSION_UNDERSCORES__", JALVIEW_VERSION_UNDERSCORES)
-  return output
-}
-
-def ulToList(Element ul, int indent) {
-  def list = ""
-  ul.children().each { e ->
-    if (e.tagName().toLowerCase() == "ul") {
-      list = list.stripTrailing() + "\n"
-      list += ulToList(e, indent+1)
-    } else if (e.tagName().toLowerCase() == "li") {
-      def issues = []
-      def issuesText = ""
-      def mdItem = "  " * indent + "- "
-      e.childNodes().any {n ->
-        if (n.nodeName().equals("#comment")) {
-          mdItem += "{{<comment>}}${n.getData()}{{</comment>}} "
-          issuesText = n.getData().trim()
-          issues = n.getData().trim().split(/[,\s]+/).findAll { it.startsWith("JAL-") }
-          return true
-        }
-      }
-      def safeText = issuesText.replaceAll('"', '\"')
-      def joinedIssues = issues.join(",")
-      def issuesLink = (issues.size() > 0) ?
-        " {{< jal issue=\"${joinedIssues}\" alt=\"${safeText}\" >}}"
-        : ""
-      def addedIssues = false
-      e.childNodes().each { node ->
-        if (node.nodeName().toLowerCase() == "ul") {
-          // add issues link before sub list if it's last
-          if (node.nextSibling() == null) {
-            mdItem += "${issuesLink}"
-            addedIssues = true
-          }
-          mdItem = mdItem.stripTrailing() + "\n"
-          mdItem += ulToList(node, indent+1)
-        } else if (node.nodeName() == "#text") {
-          mdItem += node.text()
-        } else if (node.nodeName().toLowerCase() == "strong") {
-          mdItem += "**${node.text()}**"
-        } else if (node.nodeName().toLowerCase() == "em") {
-          // if (true || (node.text().length() > 50 && node.text().count(" ") > 10) || (!node.nextSibling().text().startsWith("\\s*\\n"))) {
-            mdItem += "*${node.text()}*"
-          // } else {
-          //   mdItem += "### "+node.text()
-          // }
-        } else if (node.nodeName().toLowerCase() == "br") {
-          mdItem += "<br/>\n"
-        } else if (node.nodeName().toLowerCase() == "a") {
-          mdItem += "[${node.text()}](${node.attr('href')})"
-        }
-      }
-      if (!addedIssues) {
-        mdItem += issuesLink
-      }
-      list += mdItem.stripTrailing()+"\n"
-    } else if (e.tagName().toLowerCase() == "div") {
-      e.children().each { eee ->
-        list += ulToList(eee, indent)
-      }
-    } else if (e.tagName().toLowerCase() == "strong") {
-      list += "**${e.text()}**"
-    } else if (e.tagName().toLowerCase() == "em") {
-      if (e.text().length() > 50 && e.text().count(" ") > 20) {
-        list += "*${e.text()}*"
-      } else {
-        list += "\n\n### ${e.text()}\n\n"
-      }
+  if (extras != null) {
+    extras.each{ k, v ->
+      output = output.replaceAll("__${k}__", ((v == null)?"":v))
     }
   }
-  return list
+  replacements.each{ k, v ->
+    output = output.replaceAll("__${k}__", ((v == null)?"":v))
+  }
+  return output
 }
 
 task hugoTemplates {
@@ -2478,104 +2418,94 @@ task hugoTemplates {
   def hugoTemplatesDir = file("${jalviewDir}/${hugo_templates_dir}")
   def hugoBuildDir = "${jalviewDir}/${hugo_build_dir}"
   def templateFiles = fileTree(dir: hugoTemplatesDir)
+  def releaseMdFile = file("${jalviewDir}/${releases_dir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
+  def whatsnewMdFile = file("${jalviewDir}/${whatsnew_dir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
+  def releaseTemplateFile = file("${jalviewDir}/${releases_template}")
+  def releasesTemplateFile = file("${jalviewDir}/${releases_template}")
+  def whatsnewTemplateFile = file("${jalviewDir}/${whatsnew_template}")
 
   doFirst {
     // specific release template for version archive
-    def summary = "${applicationName} ${JALVIEW_VERSION}"
     def changes = ""
-    def oldDate = null
+    def whatsnew = null
+    def givenDate = null
+    def givenChannel = null
+    def givenVersion = null
     if (CHANNEL == "RELEASE") {
       def releasesHtmlFile = file("${helpSourceDir}/${releases_html}")
-      //HTMLPARSE
-      def html = releasesHtmlFile.text
-      def doc = Jsoup.parse(html)
-      def table = doc.select("table").first()
-      def headings = table.select("tr").first().select("th").collect { it.text() }
-      def releaseRow = null
-      def trs = table.select("tr")
-      trs.any { tr ->
-        def tds = tr.select("td")
-        if (tds.size() == 0)
-          return false
-        def releaseTd = tds.first()
-        if (releaseTd.text().startsWith("${JALVIEW_VERSION} ")) {
-          releaseRow = tr
-          return true
-        }
-      }
-
-      if (releaseRow != null && headings != null && headings.size() == 3) {
-        def releaseTd = releaseRow.select("td").first()
-        def spaceIndex = releaseTd.text().indexOf(" ")
-        if (spaceIndex >= 0) {
-          oldDate = new Date().parse("dd/MM/yyyy", releaseTd.text().substring(spaceIndex+1))
-        }
-        def releaseCells = releaseRow.select("td")
-        if (releaseCells.size() == 3) {
-          def title1 = headings[1]
-          def title2 = headings[2]
-
-          def lastDotIndex = JALVIEW_VERSION.lastIndexOf(".")
-          if (lastDotIndex > 0) {
-            try {
-              def patchRelease = JALVIEW_VERSION.substring(lastDotIndex+1) as Integer
-              def patchReleaseString = null
-              if (patchRelease == 0) {
-                  patchReleaseString = "first minor"
-              } else if (patchRelease == 1) {
-                  patchReleaseString = "first patch"
-              } else if (patchRelease == 2) {
-                  patchReleaseString = "second patch"
-              } else if (patchRelease == 3) {
-                  patchReleaseString = "third patch"
-              } else if (patchRelease == 4) {
-                  patchReleaseString = "fourth patch"
-              } else if (patchRelease == 5) {
-                  patchReleaseString = "fifth patch"
-              } else if (patchRelease == 6) {
-                  patchReleaseString = "sixth patch"
-              } else if (patchRelease == 7) {
-                  patchReleaseString = "seventh patch"
-              } else if (patchRelease > 13 && (patchRelease % 10 == 1)) {
-                  patchReleaseString += "st"
-              } else if (patchRelease > 13 && (patchRelease % 10 == 2)) {
-                  patchReleaseString += "nd"
-              } else if (patchRelease > 13 && (patchRelease % 10 == 3)) {
-                  patchReleaseString += "rd"
-              } else if (patchRelease != null) {
-                  patchReleaseString += "th"
-              }
-              summary += (patchReleaseString != null) ? " is the ${patchReleaseString} release in the ${JALVIEW_VERSION.substring(0,lastDotIndex)} series." : ""
-            } catch(Exception e) {
-              summary = ""
-            }
+      //MD_PARSE
+      if (releaseMdFile.exists()) {
+        def inFrontMatter = false
+        def itemComment = null
+        def firstLine = true
+        releaseMdFile.eachLine { line ->
+          if (line.matches("---")) {
+            def prev = inFrontMatter
+            inFrontMatter = firstLine
+            if (inFrontMatter != prev)
+              return
           }
-
-          [1,2].each { col ->
-            def colChanges = ""
-            if (headings[col] != null && headings[col].size() > 0) {
-              releaseCells[col].children().each { e ->
-                if (e.tagName().toLowerCase() == "ul" || e.tagName().toLowerCase() == "div") {
-                  if (colChanges != "") {
-                    colChanges = colChanges.stripTrailing() + "\n"
-                  }
-                  colChanges += ulToList(e, 0)
-                } else if (e.tagName().toLowerCase() == "em") {
-                  colChanges += "\n\n### ${e.text()}\n\n"
-                }
-              }
-            }
-            if (colChanges != "") {
-              def className = headings[col].replaceAll(" ","_").toLowerCase().replaceAll("[^_a-z]","")
-              changes += "<div class=\"${className}\">\n\n## ${headings[col]}\n\n${colChanges}\n</div>\n\n"
+          if (inFrontMatter) {
+            def m = null
+            if (m = line =~ /^date:\s*([0-9\-]+)/) {
+              givenDate = new Date().parse("yyyy-MM-dd", m[0][1])
+            } else if (m = line =~ /^channel:\s*(\S+)/) {
+              givenChannel = m[0][1]
+            } else if (m = line =~ /^version:\s*(\S+)/) {
+              givenVersion = m[0][1]
             }
+          } else {
+            changes += line+"\n"
           }
+          firstLine = false
+        }
+        if (givenVersion != null && givenVersion != JALVIEW_VERSION) {
+          throw new GradleException("'version' header (${givenVersion}) found in ${releaseMdFile} does not match JALVIEW_VERSION (${JALVIEW_VERSION})")
+        }
+        if (whatsnewMdFile.exists()) {
+          whatsnew = whatsnewMdFile.text
+        }
+        def content = releaseMdFile.text
+      }
+    }
 
-          if (changes != "") {
-            changes = "<div class=\"release_notes\">\n\n${changes}\n\n</div>"
+    def changesHugo = null
+    if (changes != null) {
+      changesHugo = '<div class="release_notes">\n\n'
+      def inSection = false
+      changes.eachLine { line ->
+        def m = null
+        if (m = line =~ /^##([^#].*)$/) {
+          if (inSection) {
+            changesHugo += "</div>\n\n"
+          }
+          def section = m[0][1].trim()
+          section = section.toLowerCase()
+          section = section.replaceAll(/ +/, "_")
+          section = section.replaceAll(/[^a-z0-9_\-]/, "")
+          changesHugo += "<div class=\"${section}\">\n\n"
+          inSection = true
+        } else if (m = line =~ /^(\s*-\s*)<!--([^>]+)-->(.*)/) {
+          def comment = m[0][2].trim()
+          if (comment != "") {
+            comment = comment.replaceAll('"', "&quot;")
+            def issuekeys = []
+            comment.eachMatch(/JAL-\d+/) { jal -> issuekeys += jal }
+            def newline = m[0][1]
+            if (comment.trim() != "")
+              newline += "{{<comment>}}${comment}{{</comment>}}  "
+            newline += m[0][3].trim()
+            if (issuekeys.size() > 0)
+              newline += "  {{< jal issue=\"${issuekeys.join(",")}\" alt=\"${comment}\" >}}"
+            line = newline
           }
         }
+        changesHugo += line+"\n"
+      }
+      if (inSection) {
+        changesHugo += "\n</div>\n\n"
       }
+      changesHugo += '</div>'
     }
 
     templateFiles.each{ templateFile ->
@@ -2584,7 +2514,7 @@ task hugoTemplates {
       def newRelPathName = hugoTemplateSubstitutions( relPath.toString() )
 
       def outPathName = string("${hugoBuildDir}/$newRelPathName")
-      
+
       copy {
         from templateFile
         rename(templateFile.getName(), newFileName)
@@ -2593,30 +2523,21 @@ task hugoTemplates {
 
       def newFile = file("${outPathName}/${newFileName}".toString())
       def content = newFile.text
-      // summary in version archive release pages only appears from 2.10.2b2 onwards
-      if (oldDate.format("yyyy") as Integer >= 2019 || JALVIEW_VERSION.startsWith("2.10")) {
-        def summaryFile = file("${jalviewDir}/${whatsnew_dir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
-        if (summaryFile.exists()) {
-          summary = summaryFile.text
-        } else {
-          summary = ""
-        }
-        content = content.replaceAll("__SUMMARY__", summary)
-      } else {
-        content = content.replaceAll("__SUMMARY__", "")
-      }
-      content = content.replaceAll("__CHANGES__", changes)
-      if (oldDate != null) {
-        if (oldDate[java.util.Calendar.YEAR] < 90) {
-          oldDate[java.util.Calendar.YEAR] += 2000
-        }
-        content = content.replaceAll("__DATE__", oldDate.format("yyyy-MM-dd"))
-      }
-      newFile.text = hugoTemplateSubstitutions(content)
+      newFile.text = hugoTemplateSubstitutions(content,
+        [
+          WHATSNEW: whatsnew,
+          CHANGES: changesHugo,
+          DATE: givenDate.format("yyyy-MM-dd")
+        ]
+      )
     }
+
   }
 
   inputs.dir(hugoTemplatesDir)
+  inputs.file(releaseTemplateFile)
+  inputs.file(releasesTemplateFile)
+  inputs.file(whatsnewTemplateFile)
   inputs.property("JALVIEW_VERSION", { JALVIEW_VERSION })
   inputs.property("CHANNEL", { CHANNEL })
 }
diff --git a/gradle.properties b/gradle.properties
index 239fcf6..58a5110 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -63,7 +63,7 @@ hugo_data_installers_dir = data/installers
 hugo_version_archive_dir = content/development/archive
 hugo_templates_dir = utils/hugo/templates
 releases_template = help/templates/releases.html
-whatsnew_template = help/templates/whatsnew.html
+whatsnew_template = help/templates/whatsNew.html
 releases_html = html/releases.html
 whatsnew_dir = help/markdown/whatsnew
 releases_dir = help/markdown/releases
diff --git a/help/templates/whatsNew.html b/help/templates/whatsNew.html
new file mode 100755
index 0000000..6828145
--- /dev/null
+++ b/help/templates/whatsNew.html
@@ -0,0 +1,97 @@
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>What's new ?</title>
+</head>
+<body>
+  <p>
+    <strong>Welcome to Jalview Version $$Version-Rel$$ !!</strong><br/>
+  </p>
+  <p>
+__WHATSNEW__
+  </p>
+  <p>
+    This release series provides support for two popular 3D
+    structure visualisation tools, new features for discovery of 3D
+    structures, improved platform integration and a new command line
+    tool allowing Jalview to be more easily called from scripts.</p>
+
+  <p>
+    <strong>View predicted protein structures via 3D-Beacons</strong> <br>
+    Jalview 2.11.2's <a href="features/structurechooser.html">Structure
+      Chooser includes a client for the 3D-Beacons Network</a>. Launched in
+    2021, the 3D-Beacons network (<a
+      href="https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/">www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/</a>)
+    provides a central point for the retrieval of predicted and observed
+    3D structures for sequences in Uniprot, including homology models
+    from Swiss-model and deep learning based predictions from the EBI's
+    Alphafold database (Orengo et al. 2020, <a
+      href="https://doi.org/10.12688/f1000research.20559.1">doi:10.12688/f1000research.20559.1</a>).<br>
+  </p>
+
+  <p>
+    <strong>Support for viewing structures with ChimeraX and
+      Pymol</strong><br> Jalview's 3D structure viewer system has been
+    re-architected to allow easier integration of external structure
+    viewers, and takes advantage of the strucViz2 Chimera communications
+    library developed by Scooter Morris (<a
+      href="https://doi.org/10.1093/bioinformatics/btm329">doi:10.1093/bioinformatics/btm329</a>).<br /> <br />
+    The <a href="features/preferences.html#structure">Structures
+      Preferences tab</a> provides new options allowing ChimeraX and
+    Pymol to be used for visualising external 3D structures. Views
+    from all structure viewers are saved in Jalview Projects, allowing
+    them to be shared with others using Jalview 2.11.2 or later,
+    providing they have the same viewer installed and configured to be
+    used with Jalview.<br/><br/>Jalview
+    2.11.2 has been tested with <strong>Pymol 2.5.0 (community)</strong> and <strong>2.5.2
+    (incentive)</strong>. For <strong>ChimeraX, we recommend using v1.3 or later</strong>.
+  </p>
+  <p>Other highlights include:</p>
+  <ul>
+    <li>Import of annotated DNA and RNA loci via GenBank and EMBL
+      style flatfile</li>
+    <li><strong>Easier configuration of <a
+        href="features/preferences.html#startup">Jalview's memory
+          allocation</a></strong></li>
+    <li>Scripts for <a href="features/commandline.html">running
+        Jalview via the command line</a> on macOS, Linux/Unix and Windows.
+    </li>
+  </ul>
+
+
+  <p>
+      For the full details, see <a
+        href="releases.html#Jalview.2.11.2.1">the Jalview 2.11.2.1
+        release notes</a>.
+    </p>
+  <p>
+    <strong>Known Issues</strong> <br />The following known issues will
+    be addressed in a minor patch release.
+  
+  <ul>
+    <li>Display of RESNUM sequence features are not suppressed when
+      structures associated with a sequence are viewed with an external
+      viewer (Regression from 2.11.1 series)</li>
+  </ul>
+    <p></p>
+</body>
+</html>
diff --git a/utils/hugo/old_task_to_extract_markdown_from_old_releases_html.txt b/utils/hugo/old_task_to_extract_markdown_from_old_releases_html.txt
new file mode 100644
index 0000000..8f2143e
--- /dev/null
+++ b/utils/hugo/old_task_to_extract_markdown_from_old_releases_html.txt
@@ -0,0 +1,221 @@
+
+def ulToList(Element ul, int indent) {
+  def list = ""
+  ul.children().each { e ->
+    if (e.tagName().toLowerCase() == "ul") {
+      list = list.stripTrailing() + "\n"
+      list += ulToList(e, indent+1)
+    } else if (e.tagName().toLowerCase() == "li") {
+      def issues = []
+      def issuesText = ""
+      def mdItem = "  " * indent + "- "
+      e.childNodes().any {n ->
+        if (n.nodeName().equals("#comment")) {
+          mdItem += "{{<comment>}}${n.getData()}{{</comment>}} "
+          issuesText = n.getData().trim()
+          issues = n.getData().trim().split(/[,\s]+/).findAll { it.startsWith("JAL-") }
+          return true
+        }
+      }
+      def safeText = issuesText.replaceAll('"', '\"')
+      def joinedIssues = issues.join(",")
+      def issuesLink = (issues.size() > 0) ?
+        " {{< jal issue=\"${joinedIssues}\" alt=\"${safeText}\" >}}"
+        : ""
+      def addedIssues = false
+      e.childNodes().each { node ->
+        if (node.nodeName().toLowerCase() == "ul") {
+          // add issues link before sub list if it's last
+          if (node.nextSibling() == null) {
+            mdItem += "${issuesLink}"
+            addedIssues = true
+          }
+          mdItem = mdItem.stripTrailing() + "\n"
+          mdItem += ulToList(node, indent+1)
+        } else if (node.nodeName() == "#text") {
+          mdItem += node.text()
+        } else if (node.nodeName().toLowerCase() == "strong") {
+          mdItem += "**${node.text()}**"
+        } else if (node.nodeName().toLowerCase() == "em") {
+          // if (true || (node.text().length() > 50 && node.text().count(" ") > 10) || (!node.nextSibling().text().startsWith("\\s*\\n"))) {
+            mdItem += "*${node.text()}*"
+          // } else {
+          //   mdItem += "### "+node.text()
+          // }
+        } else if (node.nodeName().toLowerCase() == "br") {
+          mdItem += "<br/>\n"
+        } else if (node.nodeName().toLowerCase() == "a") {
+          mdItem += "[${node.text()}](${node.attr('href')})"
+        }
+      }
+      if (!addedIssues) {
+        mdItem += issuesLink
+      }
+      list += mdItem.stripTrailing()+"\n"
+    } else if (e.tagName().toLowerCase() == "div") {
+      e.children().each { eee ->
+        list += ulToList(eee, indent)
+      }
+    } else if (e.tagName().toLowerCase() == "strong") {
+      list += "**${e.text()}**"
+    } else if (e.tagName().toLowerCase() == "em") {
+      if (e.text().length() > 50 && e.text().count(" ") > 20) {
+        list += "*${e.text()}*"
+      } else {
+        list += "\n\n### ${e.text()}\n\n"
+      }
+    }
+  }
+  return list
+}
+
+task hugoTemplates {
+  group "website"
+  description "Create partially populated md pages for hugo website build"
+
+  def hugoTemplatesDir = file("${jalviewDir}/${hugo_templates_dir}")
+  def hugoBuildDir = "${jalviewDir}/${hugo_build_dir}"
+  def templateFiles = fileTree(dir: hugoTemplatesDir)
+
+  doFirst {
+    // specific release template for version archive
+    def summary = "${applicationName} ${JALVIEW_VERSION}"
+    def changes = ""
+    def oldDate = null
+    if (CHANNEL == "RELEASE") {
+      def releasesHtmlFile = file("${helpSourceDir}/${releases_html}")
+      //HTMLPARSE
+      def html = releasesHtmlFile.text
+      def doc = Jsoup.parse(html)
+      def table = doc.select("table").first()
+      def headings = table.select("tr").first().select("th").collect { it.text() }
+      def releaseRow = null
+      def trs = table.select("tr")
+      trs.any { tr ->
+        def tds = tr.select("td")
+        if (tds.size() == 0)
+          return false
+        def releaseTd = tds.first()
+        if (releaseTd.text().startsWith("${JALVIEW_VERSION} ")) {
+          releaseRow = tr
+          return true
+        }
+      }
+
+      if (releaseRow != null && headings != null && headings.size() == 3) {
+        def releaseTd = releaseRow.select("td").first()
+        def spaceIndex = releaseTd.text().indexOf(" ")
+        if (spaceIndex >= 0) {
+          oldDate = new Date().parse("dd/MM/yyyy", releaseTd.text().substring(spaceIndex+1))
+        }
+        def releaseCells = releaseRow.select("td")
+        if (releaseCells.size() == 3) {
+          def title1 = headings[1]
+          def title2 = headings[2]
+
+          def lastDotIndex = JALVIEW_VERSION.lastIndexOf(".")
+          if (lastDotIndex > 0) {
+            try {
+              def patchRelease = JALVIEW_VERSION.substring(lastDotIndex+1) as Integer
+              def patchReleaseString = null
+              if (patchRelease == 0) {
+                  patchReleaseString = "first minor"
+              } else if (patchRelease == 1) {
+                  patchReleaseString = "first patch"
+              } else if (patchRelease == 2) {
+                  patchReleaseString = "second patch"
+              } else if (patchRelease == 3) {
+                  patchReleaseString = "third patch"
+              } else if (patchRelease == 4) {
+                  patchReleaseString = "fourth patch"
+              } else if (patchRelease == 5) {
+                  patchReleaseString = "fifth patch"
+              } else if (patchRelease == 6) {
+                  patchReleaseString = "sixth patch"
+              } else if (patchRelease == 7) {
+                  patchReleaseString = "seventh patch"
+              } else if (patchRelease > 13 && (patchRelease % 10 == 1)) {
+                  patchReleaseString += "st"
+              } else if (patchRelease > 13 && (patchRelease % 10 == 2)) {
+                  patchReleaseString += "nd"
+              } else if (patchRelease > 13 && (patchRelease % 10 == 3)) {
+                  patchReleaseString += "rd"
+              } else if (patchRelease != null) {
+                  patchReleaseString += "th"
+              }
+              summary += (patchReleaseString != null) ? " is the ${patchReleaseString} release in the ${JALVIEW_VERSION.substring(0,lastDotIndex)} series." : ""
+            } catch(Exception e) {
+              summary = ""
+            }
+          }
+
+          [1,2].each { col ->
+            def colChanges = ""
+            if (headings[col] != null && headings[col].size() > 0) {
+              releaseCells[col].children().each { e ->
+                if (e.tagName().toLowerCase() == "ul" || e.tagName().toLowerCase() == "div") {
+                  if (colChanges != "") {
+                    colChanges = colChanges.stripTrailing() + "\n"
+                  }
+                  colChanges += ulToList(e, 0)
+                } else if (e.tagName().toLowerCase() == "em") {
+                  colChanges += "\n\n### ${e.text()}\n\n"
+                }
+              }
+            }
+            if (colChanges != "") {
+              def className = headings[col].replaceAll(" ","_").toLowerCase().replaceAll("[^_a-z]","")
+              changes += "<div class=\"${className}\">\n\n## ${headings[col]}\n\n${colChanges}\n</div>\n\n"
+            }
+          }
+
+          if (changes != "") {
+            changes = "<div class=\"release_notes\">\n\n${changes}\n\n</div>"
+          }
+        }
+      }
+    }
+
+    templateFiles.each{ templateFile ->
+      def newFileName = string(hugoTemplateSubstitutions(templateFile.getName()))
+      def relPath = hugoTemplatesDir.toPath().relativize(templateFile.toPath()).getParent()
+      def newRelPathName = hugoTemplateSubstitutions( relPath.toString() )
+
+      def outPathName = string("${hugoBuildDir}/$newRelPathName")
+      
+      copy {
+        from templateFile
+        rename(templateFile.getName(), newFileName)
+        into outPathName
+      }
+
+      def newFile = file("${outPathName}/${newFileName}".toString())
+      def content = newFile.text
+      // summary in version archive release pages only appears from 2.10.2b2 onwards
+      if (oldDate.format("yyyy") as Integer >= 2019 || JALVIEW_VERSION.startsWith("2.10")) {
+        def summaryFile = file("${jalviewDir}/${whatsnew_dir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
+        if (summaryFile.exists()) {
+          summary = summaryFile.text
+        } else {
+          summary = ""
+        }
+        content = content.replaceAll("__SUMMARY__", summary)
+      } else {
+        content = content.replaceAll("__SUMMARY__", "")
+      }
+      content = content.replaceAll("__CHANGES__", changes)
+      if (oldDate != null) {
+        if (oldDate[java.util.Calendar.YEAR] < 90) {
+          oldDate[java.util.Calendar.YEAR] += 2000
+        }
+        content = content.replaceAll("__DATE__", oldDate.format("yyyy-MM-dd"))
+      }
+      newFile.text = hugoTemplateSubstitutions(content)
+    }
+  }
+
+  inputs.dir(hugoTemplatesDir)
+  inputs.property("JALVIEW_VERSION", { JALVIEW_VERSION })
+  inputs.property("CHANNEL", { CHANNEL })
+}
+
diff --git a/utils/hugo/templates/content/development/archive/Version-__VERSION_UNDERSCORES__/_index.md b/utils/hugo/templates/content/development/archive/Version-__VERSION_UNDERSCORES__/_index.md
index dc418ad..54a11dc 100644
--- a/utils/hugo/templates/content/development/archive/Version-__VERSION_UNDERSCORES__/_index.md
+++ b/utils/hugo/templates/content/development/archive/Version-__VERSION_UNDERSCORES__/_index.md
@@ -11,6 +11,6 @@ cascade:
   jalviewjslink: false
 ---
 
-__SUMMARY__
+__WHATSNEW__
 
 __CHANGES__